From matimontg at gmail.com  Sat Apr  1 02:48:08 2017
From: matimontg at gmail.com (Matias)
Date: Fri, 31 Mar 2017 23:48:08 -0700 (MST)
Subject: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
In-Reply-To: <54518069-C5F9-445E-983C-FDD5A2EDA798@mail.nih.gov>
References: <1490878156334-38050.post@n7.nabble.com>
 <031C16D1-4B43-4BD8-9C80-91A2F9C72B6B@mail.nih.gov>
 <CAKKNfuLb=DnqxAnE9yY9zgo5B+Ns7DV_A7rV7yb=fenMYU0vtw@mail.gmail.com>
 <54518069-C5F9-445E-983C-FDD5A2EDA798@mail.nih.gov>
Message-ID: <CAKKNfuKEYX85a82CEkDPsLBmeW_45hL9Enipha0r5_X9mikBDQ@mail.gmail.com>

Thanks Yaniv. So how do I get this branch? I simply download the latest
version of SimpleITK?

El vie., 31 de mar. de 2017 a la(s) 19:18, Yaniv, Ziv Rafael (NIH/NLM/LHC)
[C] [via ITK - Users] <ml-node+s7n38063h22 at n7.nabble.com> escribi?:

> Hello Matias,
>
>
>
> Please take a look at the following github pull request (
> https://github.com/SimpleITK/SimpleITK/pull/134), this branch should
> provide the functionality you are looking for. See the Python example
> script included in the commit for the usage of the DICOM series writing.
>
>
>
>      hope this helps
>
>             Ziv
>
>
>
>
>
> *From: *Matias <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38063&i=0>>
>
>
> *Date: *Thursday, March 30, 2017 at 12:14 PM
>
> *To: *"[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38063&i=1>" <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38063&i=2>>
>
>
> *Subject: *Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
>
>
>
> Yes, this is what I would need to migrate to C#:
>
> It basically reads a dicom directory and performs rotation on the volume,
> then writes the resulting images back to a directory, copying the tags from
> the original images.
>
>
>
> #include "itkImage.h"
>
> #include "itkGDCMImageIO.h"
>
> #include "itkGDCMSeriesFileNames.h"
>
> #include "itkImageSeriesReader.h"
>
> #include "itkResampleImageFilter.h"
>
> #include "itkEuler3DTransform.hxx"
>
> #include "gdcmUIDGenerator.h"
>
>
>
> #include "itkImageFileWriter.h"
>
> #include "itkImageSeriesWriter.h"
>
> #include "itkNumericSeriesFileNames.h"
>
> #include "itkTranslationTransform.h"
>
> #include "string.h";
>
> #include <itkSliceIterator.h>
>
>
>
> #include <iostream>
>
> #include <string>
>
> #include <fstream>
>
>
>
>
>
>
>
> static void CopyDictionary(itk::MetaDataDictionary &fromDict,
>
> itk::MetaDataDictionary &toDict);
>
>
>
> int main(int argc, char* argv[])
>
> {
>
> if (argc < 8)
>
> {
>
> std::cerr << "Uso: " << std::endl;
>
> std::cerr << argv[0] << " Directorio_A_Rotar  DirectorioResultante Gamma
> Beta Alfa CentroRotacionX CentroRotacionY CentroRotacionZ"
>
> << std::endl;
>
> return EXIT_FAILURE;
>
> }
>
>
>
> typedef signed short    PixelType;
>
> const unsigned int      Dimension = 3;
>
> const unsigned int Dimension_Serie = 2;
>
> typedef itk::Image< PixelType, Dimension >         ImageType;
>
> typedef itk::Image<PixelType, Dimension_Serie> ImageType_Serie;
>
>
>
> typedef itk::ImageSeriesReader< ImageType >        ReaderType;
>
> ReaderType::Pointer reader = ReaderType::New();
>
>
>
> typedef itk::GDCMImageIO       ImageIOType;
>
> ImageIOType::Pointer gdcmIO = ImageIOType::New();
>
> reader->SetImageIO(gdcmIO);
>
>
>
> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
>
> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
>
> nameGenerator->SetUseSeriesDetails(true);
>
> nameGenerator->AddSeriesRestriction("0008|0021");
>
> nameGenerator->SetDirectory(argv[1]);
>
>
>
> try
>
> {
>
> std::cout << std::endl << "The directory: " << std::endl;
>
> std::cout << std::endl << argv[1] << std::endl << std::endl;
>
> std::cout << "Contains the following DICOM Series: ";
>
> std::cout << std::endl << std::endl;
>
>
>
> typedef std::vector< std::string >    SeriesIdContainer;
>
> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
>
> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
>
> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
>
> while (seriesItr != seriesEnd)
>
> {
>
> std::cout << seriesItr->c_str() << std::endl;
>
> ++seriesItr;
>
> }
>
>
>
> std::string seriesIdentifier;
>
>
>
> seriesIdentifier = seriesUID.begin()->c_str();
>
>
>
>
>
> std::cout << std::endl << std::endl;
>
> std::cout << "Now reading series: " << std::endl << std::endl;
>
> std::cout << seriesIdentifier << std::endl;
>
> std::cout << std::endl << std::endl;
>
>
>
> typedef std::vector< std::string >   FileNamesContainer;
>
> FileNamesContainer fileNames;
>
> fileNames = nameGenerator->GetFileNames(seriesIdentifier);
>
>
>
> reader->SetFileNames(fileNames);
>
>
>
> try
>
> {
>
> reader->Update();
>
> }
>
> catch (itk::ExceptionObject &ex)
>
> {
>
> std::cout << ex << std::endl;
>
> return EXIT_FAILURE;
>
> }
>
>
>
> const ImageType * inputImage = reader->GetOutput();
>
> /*int numerodedicoms = inputImage->GetLargestPossibleRegion().GetSize()[2];
>
> int dicomcentral = numerodedicoms / 2;
>
> std::cout << "Dimenion " <<  dicomcentral << std::endl;*/
>
> //itk::EncapsulateMetaData<std::string>(dictionary,
> "0020|0032","-208\\-236\\66");
>
>
>
> typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>
> FilterType::Pointer FiltroResample = FilterType::New();
>
> FiltroResample->SetInput(reader->GetOutput());
>
>
>
> typedef itk::LinearInterpolateImageFunction<ImageType, double >
> InterpolatorType;
>
> InterpolatorType::Pointer interpolator = InterpolatorType::New();
>
> FiltroResample->SetInterpolator(interpolator);
>
> FiltroResample->SetOutputDirection(inputImage->GetDirection());
>
> FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>
>
>
> ImageType::SizeType inputSize =
> inputImage->GetLargestPossibleRegion().GetSize();
>
> FiltroResample->SetSize(inputSize);
>
>
>
> const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
>
> FiltroResample->SetOutputSpacing(inputSpacing);
>
>
>
> FiltroResample->SetDefaultPixelValue(-1000); //Cambiar por un parametro
>
>
>
> typedef itk::Euler3DTransform< double > TransformType; //Transform
>
> TransformType::Pointer transform = TransformType::New();
>
> double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y,
> centro_rotacion_Z;
>
> gamma = atof(argv[3]);
>
> beta= atof(argv[4]);
>
> alfa = atof(argv[5]);
>
> centro_rotacion_X = atof(argv[6]);
>
> centro_rotacion_Y = atof(argv[7]);
>
> centro_rotacion_Z = atof(argv[8]);
>
> transform->SetRotation(gamma, beta, alfa); //Radianes en el siguiente
> orden en ITK: Gamma, Beta, Alfa | Ibarra
>
> //double centro[3] = { -14.8371, -54.9443, 175.75 }; //XmmPromedio,
> YmmPromedio, Z Central (mm): Leer directorio y tomar la del medio
>
> double centro[3] = { centro_rotacion_X, centro_rotacion_Y,
> centro_rotacion_Z }; //XmmPromedio, YmmPromedio, Z Central (mm): Leer
> directorio y tomar la del medio
>
> transform->SetCenter(centro);
>
> std::cout << "Centro: " << std::endl << std::endl;
>
> std::cout << transform->GetCenter() << std::endl;
>
>
>
> FiltroResample->SetTransform(transform);
>
> //FiltroResample->SetMetaDataDictionary(dictionary);
>
> try
>
> {
>
> FiltroResample->Update();
>
> }
>
> catch (itk::ExceptionObject &ex)
>
> {
>
> return EXIT_FAILURE;
>
> }
>
>
>
>
>
>
>
> ReaderType::DictionaryRawPointer inputDict =
> (*(reader->GetMetaDataDictionaryArray()))[0];
>
> ReaderType::DictionaryArrayType outputArray;
>
> //std::cout << "array: " << std::endl << outputArray[0] << std::endl;
>
> // To keep the new series in the same study as the original we need
>
> // to keep the same study UID. But we need new series and frame of
>
> // reference UID's.
>
> gdcm::UIDGenerator suid;
>
> //std::string seriesUID = suid.Generate();
>
> gdcm::UIDGenerator fuid;
>
> std::string frameOfReferenceUID = fuid.Generate();
>
>
>
> std::string studyUID;
>
> std::string sopClassUID;
>
> itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
>
> itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
>
> gdcmIO->KeepOriginalUIDOn();
>
>
>
> using namespace std;
>
> double myArray_Z[70]; //Cambiar esto por un argumento que especifica la
> cantidad de imagenes.
>
> double myArray_X[70]; //Cambiar esto por un argumento que especifica la
> cantidad de imagenes.
>
> double myArray_Y[70]; //Cambiar esto por un argumento que especifica la
> cantidad de imagenes.
>
>
>
> ifstream file("file.txt");
>
> if (file.is_open())
>
> {
>
> for (int i = 0; i < 70; ++i) //Recordar cambiar por el argumento que
> especifica cantidad de imagenes
>
> {
>
> file >> myArray_Z[i];
>
> }
>
> }
>
> std::cout << "valor primer Z array: " << std::endl << std::endl;
>
> std::cout << myArray_Z[0] << std::endl;
>
>
>
> for (unsigned int f = 0; f < inputSize[2]; f++)
>
> {
>
> // Create a new dictionary for this slice
>
> ReaderType::DictionaryRawPointer dict = new ReaderType::DictionaryType;
>
>
>
> // Copy the dictionary from the first slice
>
> CopyDictionary(*inputDict, *dict);
>
>
>
> // Set the UID's for the study, series, SOP  and frame of reference
>
> itk::EncapsulateMetaData<std::string>(*dict, "0020|000d", studyUID);
>
> //itk::EncapsulateMetaData<std::string>(*dict, "0020|000e", seriesUID);
>
> itk::EncapsulateMetaData<std::string>(*dict, "0020|0052",
> frameOfReferenceUID);
>
>
>
> gdcm::UIDGenerator sopuid;
>
> std::string sopInstanceUID = sopuid.Generate();
>
>
>
> itk::EncapsulateMetaData<std::string>(*dict, "0008|0018", sopInstanceUID);
>
> itk::EncapsulateMetaData<std::string>(*dict, "0002|0003", sopInstanceUID);
>
>
>
> // Change fields that are slice specific
>
> std::ostringstream value;
>
> value.str("");
>
> value << f + 1;
>
>
>
> // Image Number
>
> itk::EncapsulateMetaData<std::string>(*dict, "0020|0013", value.str());
>
>
>
> // Series Description - Append new description to current series
>
> // description
>
> std::string oldSeriesDesc;
>
> itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);
>
>
>
> value.str("");
>
> value << oldSeriesDesc
>
> << ": Resampled with pixel spacing "
>
> << inputSpacing[0] << ", "
>
> << inputSpacing[1] << ", "
>
> << inputSpacing[2];
>
> // This is an long string and there is a 64 character limit in the
>
> // standard
>
> unsigned lengthDesc = value.str().length();
>
>
>
> std::string seriesDesc(value.str(), 0,
>
> lengthDesc > 64 ? 64
>
> : lengthDesc);
>
> itk::EncapsulateMetaData<std::string>(*dict, "0008|103e", seriesDesc);
>
>
>
> // Series Number
>
> value.str("");
>
> value << 1001;
>
> itk::EncapsulateMetaData<std::string>(*dict, "0020|0011", value.str());
>
>
>
> // Derivation Description - How this image was derived
>
> value.str("");
>
> for (int i = 0; i < argc; i++)
>
> {
>
> value << argv[i] << " ";
>
> }
>
>
>
> lengthDesc = value.str().length();
>
> std::string derivationDesc(value.str(), 0,
>
> lengthDesc > 1024 ? 1024
>
> : lengthDesc);
>
> itk::EncapsulateMetaData<std::string>(*dict, "0008|2111", derivationDesc);
>
>
>
> // Image Position Patient: This is calculated by computing the
>
> // physical coordinate of the first pixel in each slice.
>
> ImageType::PointType position;
>
> ImageType::IndexType index;
>
> index[0] = 0;
>
> index[1] = 0;
>
> index[2] = myArray_Z[f];
>
> FiltroResample->GetOutput()->TransformIndexToPhysicalPoint(index,
> position);
>
>
>
> //El origen que calculamos en el proyecto no se toca. (Origen = origen -
> average)
>
>
>
> //Cambiamos el ImageOrientationPatient SOLAMENTE si el valor original en
> la imagen es: 1\0\0\0\1\0. En el caso que se cambia el signo, se debe
> cambiar el signo del origen
>
> //value.str("");
>
> //value << -1 << "\\" << 0 << "\\" << 0 << "\\" << 0 << "\\" << -1 << "\\"
> << 0; //PASAR ESTO POR ARGUMENTO!!!
>
> //itk::EncapsulateMetaData<std::string>(*dict, "0020|0037", value.str());
>
>
>
> value.str("");
>
> value << -235.1629 << "\\" << -195.0557 << "\\" << myArray_Z[f]; //PASAR
> ESTO POR ARGUMENTO!!! El origen - Centro
>
> itk::EncapsulateMetaData<std::string>(*dict, "0020|0032", value.str());
>
>
>
>
>
> // Slice Location: For now, we store the z component of the Image
>
> // Position Patient.
>
> value.str("");
>
> value << position[2];
>
> itk::EncapsulateMetaData<std::string>(*dict, "0020|1041", value.str());
>
>
>
> // Slice Thickness: For now, we store the z spacing
>
> value.str("");
>
> value << inputSpacing[2];
>
> itk::EncapsulateMetaData<std::string>(*dict, "0018|0050",
>
> value.str());
>
> // Spacing Between Slices
>
> itk::EncapsulateMetaData<std::string>(*dict, "0018|0088",
>
> value.str());
>
>
>
> // Save the dictionary
>
> outputArray.push_back(dict);
>
> }
>
>
>
>
>
> typedef itk::ImageFileWriter< ImageType > WriterType;
>
> WriterType::Pointer writer = WriterType::New();
>
>
>
> typedef itk::ImageSeriesWriter< ImageType, ImageType_Serie >
> SeriesWriterType;
>
> SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
>
> seriesWriter->SetInput(FiltroResample->GetOutput());
>
>
>
> writer->SetFileName(argv[2]);
>
> writer->SetInput(FiltroResample->GetOutput());
>
>
>
> itksys::SystemTools::MakeDirectory("Test"); //PASAR ESTO POR ARGUMENTO!!
>
> typedef itk::NumericSeriesFileNames OutputNamesGeneratorType;
>
> OutputNamesGeneratorType::Pointer outputNames =
> OutputNamesGeneratorType::New();
>
> std::string seriesFormat("Test"); //PASAR ESTO POR ARGUMENTO!!
>
> seriesFormat = seriesFormat + "/" + "IM%d.dcm";
>
> outputNames->SetSeriesFormat(seriesFormat.c_str());
>
> outputNames->SetStartIndex(1);
>
> outputNames->SetEndIndex(inputSize[2]);
>
>
>
> seriesWriter->SetImageIO(gdcmIO);
>
> seriesWriter->SetFileNames(outputNames->GetFileNames());
>
> seriesWriter->SetMetaDataDictionaryArray(&outputArray);
>
>
>
> std::cout << "Escribiendo la imagen como..." << std::endl << std::endl;
>
> std::cout << argv[2] << std::endl << std::endl;
>
>
>
> try
>
> {
>
> writer->Update();
>
> seriesWriter->Update();
>
> }
>
> catch (itk::ExceptionObject &ex)
>
> {
>
> std::cout << ex << std::endl;
>
> return EXIT_FAILURE;
>
> }
>
>
>
>
>
> }
>
> catch (itk::ExceptionObject &ex)
>
> {
>
> std::cout << ex << std::endl;
>
> return EXIT_FAILURE;
>
> }
>
>
>
> return EXIT_SUCCESS;
>
>
>
> }
>
>
>
> void CopyDictionary(itk::MetaDataDictionary &fromDict,
> itk::MetaDataDictionary &toDict)
>
> {
>
> typedef itk::MetaDataDictionary DictionaryType;
>
>
>
> DictionaryType::ConstIterator itr = fromDict.Begin();
>
> DictionaryType::ConstIterator end = fromDict.End();
>
> typedef itk::MetaDataObject< std::string > MetaDataStringType;
>
>
>
> while (itr != end)
>
> {
>
> itk::MetaDataObjectBase::Pointer  entry = itr->second;
>
>
>
> MetaDataStringType::Pointer entryvalue =
>
> dynamic_cast<MetaDataStringType *>(entry.GetPointer());
>
> if (entryvalue)
>
> {
>
> std::string tagkey = itr->first;
>
> std::string tagvalue = entryvalue->GetMetaDataObjectValue();
>
> itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
>
> }
>
> ++itr;
>
> }
>
> }
>
>
>
>
>
> El jue., 30 de mar. de 2017 a la(s) 11:25, Lowekamp, Bradley (NIH/NLM/LHC)
> [C] [via ITK - Users] <[hidden email]> escribi?:
>
> Hello,
>
> Writing correct DICOM continues to be a struggle with SimpleITK and ITK.
> It is generally recommended to directly use GDCM or DCMTK to write a proper
> DICOM series.
>
> SimpleITK tries to keep things, well, simple and straight forward. But ITK
> ties to do some smart things, which get in the way for certain uses with
> SimpleITK. We are trying to document and develop a nominal set of DICOM
> output operations that work in SimpleITK.
>
> Do you have working C++ code that works for your intended operation? Can
> you share a small section of code which does what you expect it C++?
>
> Thank,
> Brad
>
>
>
> > On Mar 30, 2017, at 8:49 AM, Matias <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=38052&i=0>> wrote:
> >
> > Hi,
> >
> > I've been dealing with ITK for years in C++ and now I would need to use
> > SimpleITK and C# as far as I can in a new proyect.
> >
> > Is the SimpleITK SeriesWriter working for Dicom Files? Last time I tried
> to
> > use it I had problems with the DicomTags, these would not copy or there
> was
> > no method to copy the tags to the resulting slices.
> >
> > Currently, I read a volume of slices, apply rotation and then I need to
> > write the resulting image as another set of slices AND keeping tag
> > information such as patient name, etc.
> >
> > Thank you,
> >
> > Matias.
> >
> >
> >
> > --
> > View this message in context:
> http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050.html
> > Sent from the ITK - Users mailing list archive at Nabble.com.
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> > _______________________________________________
> > Community mailing list
>
> > [hidden email] <http://user/SendEmail.jtp?type=node&node=38052&i=1>
> > http://public.kitware.com/mailman/listinfo/community
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> ------------------------------
>
> *If you reply to this email, your message will be added to the discussion
> below:*
>
>
> http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38052.html
>
> To unsubscribe from SimpleITK Serieswriter and DicomTags, click here.
> NAML
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>
> --
>
> Matias
>
>
> ------------------------------
>
> View this message in context: Re: [ITK-users] [ITK] SimpleITK
> Serieswriter and DicomTags
> <http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38056.html>
>
>
> Sent from the ITK - Users mailing list archive
> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> If you reply to this email, your message will be added to the discussion
> below:
>
> http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38063.html
> To unsubscribe from SimpleITK Serieswriter and DicomTags, click here
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-- 
Matias




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From dzenanz at gmail.com  Sat Apr  1 09:37:05 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 1 Apr 2017 09:37:05 -0400
Subject: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
In-Reply-To: <CAKKNfuKEYX85a82CEkDPsLBmeW_45hL9Enipha0r5_X9mikBDQ@mail.gmail.com>
References: <1490878156334-38050.post@n7.nabble.com>
 <031C16D1-4B43-4BD8-9C80-91A2F9C72B6B@mail.nih.gov>
 <CAKKNfuLb=DnqxAnE9yY9zgo5B+Ns7DV_A7rV7yb=fenMYU0vtw@mail.gmail.com>
 <54518069-C5F9-445E-983C-FDD5A2EDA798@mail.nih.gov>
 <CAKKNfuKEYX85a82CEkDPsLBmeW_45hL9Enipha0r5_X9mikBDQ@mail.gmail.com>
Message-ID: <CAPf2UMRZyV8svf3XkAOq3v=hdgsxowzt55vr7YUxWniAHLfcNA@mail.gmail.com>

Hi Matias,

you should use branch dicomWrite from Ziv's fork
<https://github.com/zivy/SimpleITK/tree/dicomWrite>.

Regards,
D?enan

On Sat, Apr 1, 2017 at 2:48 AM, Matias <matimontg at gmail.com> wrote:

> Thanks Yaniv. So how do I get this branch? I simply download the latest
> version of SimpleITK?
>
> El vie., 31 de mar. de 2017 a la(s) 19:18, Yaniv, Ziv Rafael (NIH/NLM/LHC)
> [C] [via ITK - Users] <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38064&i=0>> escribi?:
>
>> Hello Matias,
>>
>>
>>
>> Please take a look at the following github pull request (
>> https://github.com/SimpleITK/SimpleITK/pull/134), this branch should
>> provide the functionality you are looking for. See the Python example
>> script included in the commit for the usage of the DICOM series writing.
>>
>>
>>
>>      hope this helps
>>
>>             Ziv
>>
>>
>>
>>
>>
>> *From: *Matias <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=38063&i=0>>
>>
>>
>> *Date: *Thursday, March 30, 2017 at 12:14 PM
>>
>> *To: *"[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=38063&i=1>" <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=38063&i=2>>
>>
>>
>> *Subject: *Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
>>
>>
>>
>> Yes, this is what I would need to migrate to C#:
>>
>> It basically reads a dicom directory and performs rotation on the volume,
>> then writes the resulting images back to a directory, copying the tags from
>> the original images.
>>
>>
>>
>> #include "itkImage.h"
>>
>> #include "itkGDCMImageIO.h"
>>
>> #include "itkGDCMSeriesFileNames.h"
>>
>> #include "itkImageSeriesReader.h"
>>
>> #include "itkResampleImageFilter.h"
>>
>> #include "itkEuler3DTransform.hxx"
>>
>> #include "gdcmUIDGenerator.h"
>>
>>
>>
>> #include "itkImageFileWriter.h"
>>
>> #include "itkImageSeriesWriter.h"
>>
>> #include "itkNumericSeriesFileNames.h"
>>
>> #include "itkTranslationTransform.h"
>>
>> #include "string.h";
>>
>> #include <itkSliceIterator.h>
>>
>>
>>
>> #include <iostream>
>>
>> #include <string>
>>
>> #include <fstream>
>>
>>
>>
>>
>>
>>
>>
>> static void CopyDictionary(itk::MetaDataDictionary &fromDict,
>>
>> itk::MetaDataDictionary &toDict);
>>
>>
>>
>> int main(int argc, char* argv[])
>>
>> {
>>
>> if (argc < 8)
>>
>> {
>>
>> std::cerr << "Uso: " << std::endl;
>>
>> std::cerr << argv[0] << " Directorio_A_Rotar  DirectorioResultante Gamma
>> Beta Alfa CentroRotacionX CentroRotacionY CentroRotacionZ"
>>
>> << std::endl;
>>
>> return EXIT_FAILURE;
>>
>> }
>>
>>
>>
>> typedef signed short    PixelType;
>>
>> const unsigned int      Dimension = 3;
>>
>> const unsigned int Dimension_Serie = 2;
>>
>> typedef itk::Image< PixelType, Dimension >         ImageType;
>>
>> typedef itk::Image<PixelType, Dimension_Serie> ImageType_Serie;
>>
>>
>>
>> typedef itk::ImageSeriesReader< ImageType >        ReaderType;
>>
>> ReaderType::Pointer reader = ReaderType::New();
>>
>>
>>
>> typedef itk::GDCMImageIO       ImageIOType;
>>
>> ImageIOType::Pointer gdcmIO = ImageIOType::New();
>>
>> reader->SetImageIO(gdcmIO);
>>
>>
>>
>> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
>>
>> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
>>
>> nameGenerator->SetUseSeriesDetails(true);
>>
>> nameGenerator->AddSeriesRestriction("0008|0021");
>>
>> nameGenerator->SetDirectory(argv[1]);
>>
>>
>>
>> try
>>
>> {
>>
>> std::cout << std::endl << "The directory: " << std::endl;
>>
>> std::cout << std::endl << argv[1] << std::endl << std::endl;
>>
>> std::cout << "Contains the following DICOM Series: ";
>>
>> std::cout << std::endl << std::endl;
>>
>>
>>
>> typedef std::vector< std::string >    SeriesIdContainer;
>>
>> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
>>
>> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
>>
>> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
>>
>> while (seriesItr != seriesEnd)
>>
>> {
>>
>> std::cout << seriesItr->c_str() << std::endl;
>>
>> ++seriesItr;
>>
>> }
>>
>>
>>
>> std::string seriesIdentifier;
>>
>>
>>
>> seriesIdentifier = seriesUID.begin()->c_str();
>>
>>
>>
>>
>>
>> std::cout << std::endl << std::endl;
>>
>> std::cout << "Now reading series: " << std::endl << std::endl;
>>
>> std::cout << seriesIdentifier << std::endl;
>>
>> std::cout << std::endl << std::endl;
>>
>>
>>
>> typedef std::vector< std::string >   FileNamesContainer;
>>
>> FileNamesContainer fileNames;
>>
>> fileNames = nameGenerator->GetFileNames(seriesIdentifier);
>>
>>
>>
>> reader->SetFileNames(fileNames);
>>
>>
>>
>> try
>>
>> {
>>
>> reader->Update();
>>
>> }
>>
>> catch (itk::ExceptionObject &ex)
>>
>> {
>>
>> std::cout << ex << std::endl;
>>
>> return EXIT_FAILURE;
>>
>> }
>>
>>
>>
>> const ImageType * inputImage = reader->GetOutput();
>>
>> /*int numerodedicoms = inputImage->GetLargestPossibleRegion().
>> GetSize()[2];
>>
>> int dicomcentral = numerodedicoms / 2;
>>
>> std::cout << "Dimenion " <<  dicomcentral << std::endl;*/
>>
>> //itk::EncapsulateMetaData<std::string>(dictionary,
>> "0020|0032","-208\\-236\\66");
>>
>>
>>
>> typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>>
>> FilterType::Pointer FiltroResample = FilterType::New();
>>
>> FiltroResample->SetInput(reader->GetOutput());
>>
>>
>>
>> typedef itk::LinearInterpolateImageFunction<ImageType, double >
>> InterpolatorType;
>>
>> InterpolatorType::Pointer interpolator = InterpolatorType::New();
>>
>> FiltroResample->SetInterpolator(interpolator);
>>
>> FiltroResample->SetOutputDirection(inputImage->GetDirection());
>>
>> FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>>
>>
>>
>> ImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().
>> GetSize();
>>
>> FiltroResample->SetSize(inputSize);
>>
>>
>>
>> const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
>>
>> FiltroResample->SetOutputSpacing(inputSpacing);
>>
>>
>>
>> FiltroResample->SetDefaultPixelValue(-1000); //Cambiar por un parametro
>>
>>
>>
>> typedef itk::Euler3DTransform< double > TransformType; //Transform
>>
>> TransformType::Pointer transform = TransformType::New();
>>
>> double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y,
>> centro_rotacion_Z;
>>
>> gamma = atof(argv[3]);
>>
>> beta= atof(argv[4]);
>>
>> alfa = atof(argv[5]);
>>
>> centro_rotacion_X = atof(argv[6]);
>>
>> centro_rotacion_Y = atof(argv[7]);
>>
>> centro_rotacion_Z = atof(argv[8]);
>>
>> transform->SetRotation(gamma, beta, alfa); //Radianes en el siguiente
>> orden en ITK: Gamma, Beta, Alfa | Ibarra
>>
>> //double centro[3] = { -14.8371, -54.9443, 175.75 }; //XmmPromedio,
>> YmmPromedio, Z Central (mm): Leer directorio y tomar la del medio
>>
>> double centro[3] = { centro_rotacion_X, centro_rotacion_Y,
>> centro_rotacion_Z }; //XmmPromedio, YmmPromedio, Z Central (mm): Leer
>> directorio y tomar la del medio
>>
>> transform->SetCenter(centro);
>>
>> std::cout << "Centro: " << std::endl << std::endl;
>>
>> std::cout << transform->GetCenter() << std::endl;
>>
>>
>>
>> FiltroResample->SetTransform(transform);
>>
>> //FiltroResample->SetMetaDataDictionary(dictionary);
>>
>> try
>>
>> {
>>
>> FiltroResample->Update();
>>
>> }
>>
>> catch (itk::ExceptionObject &ex)
>>
>> {
>>
>> return EXIT_FAILURE;
>>
>> }
>>
>>
>>
>>
>>
>>
>>
>> ReaderType::DictionaryRawPointer inputDict = (*(reader->
>> GetMetaDataDictionaryArray()))[0];
>>
>> ReaderType::DictionaryArrayType outputArray;
>>
>> //std::cout << "array: " << std::endl << outputArray[0] << std::endl;
>>
>> // To keep the new series in the same study as the original we need
>>
>> // to keep the same study UID. But we need new series and frame of
>>
>> // reference UID's.
>>
>> gdcm::UIDGenerator suid;
>>
>> //std::string seriesUID = suid.Generate();
>>
>> gdcm::UIDGenerator fuid;
>>
>> std::string frameOfReferenceUID = fuid.Generate();
>>
>>
>>
>> std::string studyUID;
>>
>> std::string sopClassUID;
>>
>> itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
>>
>> itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
>>
>> gdcmIO->KeepOriginalUIDOn();
>>
>>
>>
>> using namespace std;
>>
>> double myArray_Z[70]; //Cambiar esto por un argumento que especifica la
>> cantidad de imagenes.
>>
>> double myArray_X[70]; //Cambiar esto por un argumento que especifica la
>> cantidad de imagenes.
>>
>> double myArray_Y[70]; //Cambiar esto por un argumento que especifica la
>> cantidad de imagenes.
>>
>>
>>
>> ifstream file("file.txt");
>>
>> if (file.is_open())
>>
>> {
>>
>> for (int i = 0; i < 70; ++i) //Recordar cambiar por el argumento que
>> especifica cantidad de imagenes
>>
>> {
>>
>> file >> myArray_Z[i];
>>
>> }
>>
>> }
>>
>> std::cout << "valor primer Z array: " << std::endl << std::endl;
>>
>> std::cout << myArray_Z[0] << std::endl;
>>
>>
>>
>> for (unsigned int f = 0; f < inputSize[2]; f++)
>>
>> {
>>
>> // Create a new dictionary for this slice
>>
>> ReaderType::DictionaryRawPointer dict = new ReaderType::DictionaryType;
>>
>>
>>
>> // Copy the dictionary from the first slice
>>
>> CopyDictionary(*inputDict, *dict);
>>
>>
>>
>> // Set the UID's for the study, series, SOP  and frame of reference
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0020|000d", studyUID);
>>
>> //itk::EncapsulateMetaData<std::string>(*dict, "0020|000e", seriesUID);
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0020|0052",
>> frameOfReferenceUID);
>>
>>
>>
>> gdcm::UIDGenerator sopuid;
>>
>> std::string sopInstanceUID = sopuid.Generate();
>>
>>
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0008|0018",
>> sopInstanceUID);
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0002|0003",
>> sopInstanceUID);
>>
>>
>>
>> // Change fields that are slice specific
>>
>> std::ostringstream value;
>>
>> value.str("");
>>
>> value << f + 1;
>>
>>
>>
>> // Image Number
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0020|0013", value.str());
>>
>>
>>
>> // Series Description - Append new description to current series
>>
>> // description
>>
>> std::string oldSeriesDesc;
>>
>> itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);
>>
>>
>>
>> value.str("");
>>
>> value << oldSeriesDesc
>>
>> << ": Resampled with pixel spacing "
>>
>> << inputSpacing[0] << ", "
>>
>> << inputSpacing[1] << ", "
>>
>> << inputSpacing[2];
>>
>> // This is an long string and there is a 64 character limit in the
>>
>> // standard
>>
>> unsigned lengthDesc = value.str().length();
>>
>>
>>
>> std::string seriesDesc(value.str(), 0,
>>
>> lengthDesc > 64 ? 64
>>
>> : lengthDesc);
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0008|103e", seriesDesc);
>>
>>
>>
>> // Series Number
>>
>> value.str("");
>>
>> value << 1001;
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0020|0011", value.str());
>>
>>
>>
>> // Derivation Description - How this image was derived
>>
>> value.str("");
>>
>> for (int i = 0; i < argc; i++)
>>
>> {
>>
>> value << argv[i] << " ";
>>
>> }
>>
>>
>>
>> lengthDesc = value.str().length();
>>
>> std::string derivationDesc(value.str(), 0,
>>
>> lengthDesc > 1024 ? 1024
>>
>> : lengthDesc);
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0008|2111",
>> derivationDesc);
>>
>>
>>
>> // Image Position Patient: This is calculated by computing the
>>
>> // physical coordinate of the first pixel in each slice.
>>
>> ImageType::PointType position;
>>
>> ImageType::IndexType index;
>>
>> index[0] = 0;
>>
>> index[1] = 0;
>>
>> index[2] = myArray_Z[f];
>>
>> FiltroResample->GetOutput()->TransformIndexToPhysicalPoint(index,
>> position);
>>
>>
>>
>> //El origen que calculamos en el proyecto no se toca. (Origen = origen -
>> average)
>>
>>
>>
>> //Cambiamos el ImageOrientationPatient SOLAMENTE si el valor original en
>> la imagen es: 1\0\0\0\1\0. En el caso que se cambia el signo, se debe
>> cambiar el signo del origen
>>
>> //value.str("");
>>
>> //value << -1 << "\\" << 0 << "\\" << 0 << "\\" << 0 << "\\" << -1 <<
>> "\\" << 0; //PASAR ESTO POR ARGUMENTO!!!
>>
>> //itk::EncapsulateMetaData<std::string>(*dict, "0020|0037", value.str());
>>
>>
>>
>> value.str("");
>>
>> value << -235.1629 << "\\" << -195.0557 << "\\" << myArray_Z[f]; //PASAR
>> ESTO POR ARGUMENTO!!! El origen - Centro
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0020|0032", value.str());
>>
>>
>>
>>
>>
>> // Slice Location: For now, we store the z component of the Image
>>
>> // Position Patient.
>>
>> value.str("");
>>
>> value << position[2];
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0020|1041", value.str());
>>
>>
>>
>> // Slice Thickness: For now, we store the z spacing
>>
>> value.str("");
>>
>> value << inputSpacing[2];
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0018|0050",
>>
>> value.str());
>>
>> // Spacing Between Slices
>>
>> itk::EncapsulateMetaData<std::string>(*dict, "0018|0088",
>>
>> value.str());
>>
>>
>>
>> // Save the dictionary
>>
>> outputArray.push_back(dict);
>>
>> }
>>
>>
>>
>>
>>
>> typedef itk::ImageFileWriter< ImageType > WriterType;
>>
>> WriterType::Pointer writer = WriterType::New();
>>
>>
>>
>> typedef itk::ImageSeriesWriter< ImageType, ImageType_Serie >
>> SeriesWriterType;
>>
>> SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
>>
>> seriesWriter->SetInput(FiltroResample->GetOutput());
>>
>>
>>
>> writer->SetFileName(argv[2]);
>>
>> writer->SetInput(FiltroResample->GetOutput());
>>
>>
>>
>> itksys::SystemTools::MakeDirectory("Test"); //PASAR ESTO POR ARGUMENTO!!
>>
>> typedef itk::NumericSeriesFileNames OutputNamesGeneratorType;
>>
>> OutputNamesGeneratorType::Pointer outputNames =
>> OutputNamesGeneratorType::New();
>>
>> std::string seriesFormat("Test"); //PASAR ESTO POR ARGUMENTO!!
>>
>> seriesFormat = seriesFormat + "/" + "IM%d.dcm";
>>
>> outputNames->SetSeriesFormat(seriesFormat.c_str());
>>
>> outputNames->SetStartIndex(1);
>>
>> outputNames->SetEndIndex(inputSize[2]);
>>
>>
>>
>> seriesWriter->SetImageIO(gdcmIO);
>>
>> seriesWriter->SetFileNames(outputNames->GetFileNames());
>>
>> seriesWriter->SetMetaDataDictionaryArray(&outputArray);
>>
>>
>>
>> std::cout << "Escribiendo la imagen como..." << std::endl << std::endl;
>>
>> std::cout << argv[2] << std::endl << std::endl;
>>
>>
>>
>> try
>>
>> {
>>
>> writer->Update();
>>
>> seriesWriter->Update();
>>
>> }
>>
>> catch (itk::ExceptionObject &ex)
>>
>> {
>>
>> std::cout << ex << std::endl;
>>
>> return EXIT_FAILURE;
>>
>> }
>>
>>
>>
>>
>>
>> }
>>
>> catch (itk::ExceptionObject &ex)
>>
>> {
>>
>> std::cout << ex << std::endl;
>>
>> return EXIT_FAILURE;
>>
>> }
>>
>>
>>
>> return EXIT_SUCCESS;
>>
>>
>>
>> }
>>
>>
>>
>> void CopyDictionary(itk::MetaDataDictionary &fromDict,
>> itk::MetaDataDictionary &toDict)
>>
>> {
>>
>> typedef itk::MetaDataDictionary DictionaryType;
>>
>>
>>
>> DictionaryType::ConstIterator itr = fromDict.Begin();
>>
>> DictionaryType::ConstIterator end = fromDict.End();
>>
>> typedef itk::MetaDataObject< std::string > MetaDataStringType;
>>
>>
>>
>> while (itr != end)
>>
>> {
>>
>> itk::MetaDataObjectBase::Pointer  entry = itr->second;
>>
>>
>>
>> MetaDataStringType::Pointer entryvalue =
>>
>> dynamic_cast<MetaDataStringType *>(entry.GetPointer());
>>
>> if (entryvalue)
>>
>> {
>>
>> std::string tagkey = itr->first;
>>
>> std::string tagvalue = entryvalue->GetMetaDataObjectValue();
>>
>> itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
>>
>> }
>>
>> ++itr;
>>
>> }
>>
>> }
>>
>>
>>
>>
>>
>> El jue., 30 de mar. de 2017 a la(s) 11:25, Lowekamp, Bradley
>> (NIH/NLM/LHC) [C] [via ITK - Users] <[hidden email]> escribi?:
>>
>> Hello,
>>
>> Writing correct DICOM continues to be a struggle with SimpleITK and ITK.
>> It is generally recommended to directly use GDCM or DCMTK to write a proper
>> DICOM series.
>>
>> SimpleITK tries to keep things, well, simple and straight forward. But
>> ITK ties to do some smart things, which get in the way for certain uses
>> with SimpleITK. We are trying to document and develop a nominal set of
>> DICOM output operations that work in SimpleITK.
>>
>> Do you have working C++ code that works for your intended operation? Can
>> you share a small section of code which does what you expect it C++?
>>
>> Thank,
>> Brad
>>
>>
>>
>> > On Mar 30, 2017, at 8:49 AM, Matias <[hidden email]
>> <http://user/SendEmail.jtp?type=node&node=38052&i=0>> wrote:
>> >
>> > Hi,
>> >
>> > I've been dealing with ITK for years in C++ and now I would need to use
>> > SimpleITK and C# as far as I can in a new proyect.
>> >
>> > Is the SimpleITK SeriesWriter working for Dicom Files? Last time I
>> tried to
>> > use it I had problems with the DicomTags, these would not copy or there
>> was
>> > no method to copy the tags to the resulting slices.
>> >
>> > Currently, I read a volume of slices, apply rotation and then I need to
>> > write the resulting image as another set of slices AND keeping tag
>> > information such as patient name, etc.
>> >
>> > Thank you,
>> >
>> > Matias.
>> >
>> >
>> >
>> > --
>> > View this message in context: http://itk-users.7.n7.nabble.
>> com/SimpleITK-Serieswriter-and-DicomTags-tp38050.html
>> > Sent from the ITK - Users mailing list archive at Nabble.com.
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>> > _______________________________________________
>> > Community mailing list
>>
>> > [hidden email] <http://user/SendEmail.jtp?type=node&node=38052&i=1>
>> > http://public.kitware.com/mailman/listinfo/community
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
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>>
>> ------------------------------
>>
>> *If you reply to this email, your message will be added to the discussion
>> below:*
>>
>> http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-
>> and-DicomTags-tp38050p38052.html
>>
>> To unsubscribe from SimpleITK Serieswriter and DicomTags, click here.
>> NAML
>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
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>> --
>>
>> Matias
>>
>>
>> ------------------------------
>>
>> View this message in context: Re: [ITK-users] [ITK] SimpleITK
>> Serieswriter and DicomTags
>> <http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38056.html>
>>
>>
>> Sent from the ITK - Users mailing list archive
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>>
>>
>> _____________________________________
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>> http://www.kitware.com/products/protraining.php
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> --
> Matias
>
> ------------------------------
> View this message in context: Re: [ITK-users] [ITK] SimpleITK
> Serieswriter and DicomTags
> <http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38064.html>
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From zivrafael.yaniv at nih.gov  Sun Apr  2 09:58:47 2017
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Sun, 2 Apr 2017 13:58:47 +0000
Subject: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
In-Reply-To: <CAPf2UMRZyV8svf3XkAOq3v=hdgsxowzt55vr7YUxWniAHLfcNA@mail.gmail.com>
References: <1490878156334-38050.post@n7.nabble.com>
 <031C16D1-4B43-4BD8-9C80-91A2F9C72B6B@mail.nih.gov>
 <CAKKNfuLb=DnqxAnE9yY9zgo5B+Ns7DV_A7rV7yb=fenMYU0vtw@mail.gmail.com>
 <54518069-C5F9-445E-983C-FDD5A2EDA798@mail.nih.gov>
 <CAKKNfuKEYX85a82CEkDPsLBmeW_45hL9Enipha0r5_X9mikBDQ@mail.gmail.com>
 <CAPf2UMRZyV8svf3XkAOq3v=hdgsxowzt55vr7YUxWniAHLfcNA@mail.gmail.com>
Message-ID: <89767550-AE53-4FCB-81F0-66A709E3253F@mail.nih.gov>

Hi Matias,

We should get it into the main SimpleITK repository shortly (after testing etc..). For now please follow D?enan?s recommendation (clone my forked repository, checkout the dicomWrite branch and build SimpleITK from that branch).

     regards
        Ziv

From: D?enan Zuki? <dzenanz at gmail.com>
Date: Saturday, April 1, 2017 at 9:37 AM
To: Matias <matimontg at gmail.com>
Cc: Insight-users <insight-users at itk.org>
Subject: Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags

Hi Matias,

you should use branch dicomWrite from Ziv's fork<https://github.com/zivy/SimpleITK/tree/dicomWrite>.

Regards,
D?enan

On Sat, Apr 1, 2017 at 2:48 AM, Matias <matimontg at gmail.com<mailto:matimontg at gmail.com>> wrote:
Thanks Yaniv. So how do I get this branch? I simply download the latest version of SimpleITK?
El vie., 31 de mar. de 2017 a la(s) 19:18, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] [via ITK - Users] <[hidden email]<http://user/SendEmail.jtp?type=node&node=38064&i=0>> escribi?:
Hello Matias,

Please take a look at the following github pull request (https://github.com/SimpleITK/SimpleITK/pull/134), this branch should provide the functionality you are looking for. See the Python example script included in the commit for the usage of the DICOM series writing.

     hope this helps
            Ziv


From: Matias <[hidden email]<http://user/SendEmail.jtp?type=node&node=38063&i=0>>

Date: Thursday, March 30, 2017 at 12:14 PM
To: "[hidden email]<http://user/SendEmail.jtp?type=node&node=38063&i=1>" <[hidden email]<http://user/SendEmail.jtp?type=node&node=38063&i=2>>

Subject: Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags

Yes, this is what I would need to migrate to C#:
It basically reads a dicom directory and performs rotation on the volume, then writes the resulting images back to a directory, copying the tags from the original images.

#include "itkImage.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkResampleImageFilter.h"
#include "itkEuler3DTransform.hxx"
#include "gdcmUIDGenerator.h"

#include "itkImageFileWriter.h"
#include "itkImageSeriesWriter.h"
#include "itkNumericSeriesFileNames.h"
#include "itkTranslationTransform.h"
#include "string.h";
#include <itkSliceIterator.h>

#include <iostream>
#include <string>
#include <fstream>



static void CopyDictionary(itk::MetaDataDictionary &fromDict,
itk::MetaDataDictionary &toDict);

int main(int argc, char* argv[])
{
if (argc < 8)
{
std::cerr << "Uso: " << std::endl;
std::cerr << argv[0] << " Directorio_A_Rotar  DirectorioResultante Gamma Beta Alfa CentroRotacionX CentroRotacionY CentroRotacionZ"
<< std::endl;
return EXIT_FAILURE;
}

typedef signed short    PixelType;
const unsigned int      Dimension = 3;
const unsigned int Dimension_Serie = 2;
typedef itk::Image< PixelType, Dimension >         ImageType;
typedef itk::Image<PixelType, Dimension_Serie> ImageType_Serie;

typedef itk::ImageSeriesReader< ImageType >        ReaderType;
ReaderType::Pointer reader = ReaderType::New();

typedef itk::GDCMImageIO       ImageIOType;
ImageIOType::Pointer gdcmIO = ImageIOType::New();
reader->SetImageIO(gdcmIO);

typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->AddSeriesRestriction("0008|0021");
nameGenerator->SetDirectory(argv[1]);

try
{
std::cout << std::endl << "The directory: " << std::endl;
std::cout << std::endl << argv[1] << std::endl << std::endl;
std::cout << "Contains the following DICOM Series: ";
std::cout << std::endl << std::endl;

typedef std::vector< std::string >    SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
while (seriesItr != seriesEnd)
{
std::cout << seriesItr->c_str() << std::endl;
++seriesItr;
}

std::string seriesIdentifier;

seriesIdentifier = seriesUID.begin()->c_str();


std::cout << std::endl << std::endl;
std::cout << "Now reading series: " << std::endl << std::endl;
std::cout << seriesIdentifier << std::endl;
std::cout << std::endl << std::endl;

typedef std::vector< std::string >   FileNamesContainer;
FileNamesContainer fileNames;
fileNames = nameGenerator->GetFileNames(seriesIdentifier);

reader->SetFileNames(fileNames);

try
{
reader->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}

const ImageType * inputImage = reader->GetOutput();
/*int numerodedicoms = inputImage->GetLargestPossibleRegion().GetSize()[2];
int dicomcentral = numerodedicoms / 2;
std::cout << "Dimenion " <<  dicomcentral << std::endl;*/
//itk::EncapsulateMetaData<std::string>(dictionary, "0020|0032","-208\\-236\\66");

typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
FilterType::Pointer FiltroResample = FilterType::New();
FiltroResample->SetInput(reader->GetOutput());

typedef itk::LinearInterpolateImageFunction<ImageType, double > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
FiltroResample->SetInterpolator(interpolator);
FiltroResample->SetOutputDirection(inputImage->GetDirection());
FiltroResample->SetOutputOrigin(inputImage->GetOrigin());

ImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().GetSize();
FiltroResample->SetSize(inputSize);

const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
FiltroResample->SetOutputSpacing(inputSpacing);

FiltroResample->SetDefaultPixelValue(-1000); //Cambiar por un parametro

typedef itk::Euler3DTransform< double > TransformType; //Transform
TransformType::Pointer transform = TransformType::New();
double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z;
gamma = atof(argv[3]);
beta= atof(argv[4]);
alfa = atof(argv[5]);
centro_rotacion_X = atof(argv[6]);
centro_rotacion_Y = atof(argv[7]);
centro_rotacion_Z = atof(argv[8]);
transform->SetRotation(gamma, beta, alfa); //Radianes en el siguiente orden en ITK: Gamma, Beta, Alfa | Ibarra
//double centro[3] = { -14.8371, -54.9443, 175.75 }; //XmmPromedio, YmmPromedio, Z Central (mm): Leer directorio y tomar la del medio
double centro[3] = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z }; //XmmPromedio, YmmPromedio, Z Central (mm): Leer directorio y tomar la del medio
transform->SetCenter(centro);
std::cout << "Centro: " << std::endl << std::endl;
std::cout << transform->GetCenter() << std::endl;

FiltroResample->SetTransform(transform);
//FiltroResample->SetMetaDataDictionary(dictionary);
try
{
FiltroResample->Update();
}
catch (itk::ExceptionObject &ex)
{
return EXIT_FAILURE;
}



ReaderType::DictionaryRawPointer inputDict = (*(reader->GetMetaDataDictionaryArray()))[0];
ReaderType::DictionaryArrayType outputArray;
//std::cout << "array: " << std::endl << outputArray[0] << std::endl;
// To keep the new series in the same study as the original we need
// to keep the same study UID. But we need new series and frame of
// reference UID's.
gdcm::UIDGenerator suid;
//std::string seriesUID = suid.Generate();
gdcm::UIDGenerator fuid;
std::string frameOfReferenceUID = fuid.Generate();

std::string studyUID;
std::string sopClassUID;
itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
gdcmIO->KeepOriginalUIDOn();

using namespace std;
double myArray_Z[70]; //Cambiar esto por un argumento que especifica la cantidad de imagenes.
double myArray_X[70]; //Cambiar esto por un argumento que especifica la cantidad de imagenes.
double myArray_Y[70]; //Cambiar esto por un argumento que especifica la cantidad de imagenes.

ifstream file("file.txt");
if (file.is_open())
{
for (int i = 0; i < 70; ++i) //Recordar cambiar por el argumento que especifica cantidad de imagenes
{
file >> myArray_Z[i];
}
}
std::cout << "valor primer Z array: " << std::endl << std::endl;
std::cout << myArray_Z[0] << std::endl;

for (unsigned int f = 0; f < inputSize[2]; f++)
{
// Create a new dictionary for this slice
ReaderType::DictionaryRawPointer dict = new ReaderType::DictionaryType;

// Copy the dictionary from the first slice
CopyDictionary(*inputDict, *dict);

// Set the UID's for the study, series, SOP  and frame of reference
itk::EncapsulateMetaData<std::string>(*dict, "0020|000d", studyUID);
//itk::EncapsulateMetaData<std::string>(*dict, "0020|000e", seriesUID);
itk::EncapsulateMetaData<std::string>(*dict, "0020|0052", frameOfReferenceUID);

gdcm::UIDGenerator sopuid;
std::string sopInstanceUID = sopuid.Generate();

itk::EncapsulateMetaData<std::string>(*dict, "0008|0018", sopInstanceUID);
itk::EncapsulateMetaData<std::string>(*dict, "0002|0003", sopInstanceUID);

// Change fields that are slice specific
std::ostringstream value;
value.str("");
value << f + 1;

// Image Number
itk::EncapsulateMetaData<std::string>(*dict, "0020|0013", value.str());

// Series Description - Append new description to current series
// description
std::string oldSeriesDesc;
itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);

value.str("");
value << oldSeriesDesc
<< ": Resampled with pixel spacing "
<< inputSpacing[0] << ", "
<< inputSpacing[1] << ", "
<< inputSpacing[2];
// This is an long string and there is a 64 character limit in the
// standard
unsigned lengthDesc = value.str().length();

std::string seriesDesc(value.str(), 0,
lengthDesc > 64 ? 64
: lengthDesc);
itk::EncapsulateMetaData<std::string>(*dict, "0008|103e", seriesDesc);

// Series Number
value.str("");
value << 1001;
itk::EncapsulateMetaData<std::string>(*dict, "0020|0011", value.str());

// Derivation Description - How this image was derived
value.str("");
for (int i = 0; i < argc; i++)
{
value << argv[i] << " ";
}

lengthDesc = value.str().length();
std::string derivationDesc(value.str(), 0,
lengthDesc > 1024 ? 1024
: lengthDesc);
itk::EncapsulateMetaData<std::string>(*dict, "0008|2111", derivationDesc);

// Image Position Patient: This is calculated by computing the
// physical coordinate of the first pixel in each slice.
ImageType::PointType position;
ImageType::IndexType index;
index[0] = 0;
index[1] = 0;
index[2] = myArray_Z[f];
FiltroResample->GetOutput()->TransformIndexToPhysicalPoint(index, position);

//El origen que calculamos en el proyecto no se toca. (Origen = origen - average)

//Cambiamos el ImageOrientationPatient SOLAMENTE si el valor original en la imagen es: 1\0\0\0\1\0. En el caso que se cambia el signo, se debe cambiar el signo del origen
//value.str("");
//value << -1 << "\\" << 0 << "\\" << 0 << "\\" << 0 << "\\" << -1 << "\\" << 0; //PASAR ESTO POR ARGUMENTO!!!
//itk::EncapsulateMetaData<std::string>(*dict, "0020|0037", value.str());

value.str("");
value << -235.1629 << "\\" << -195.0557 << "\\" << myArray_Z[f]; //PASAR ESTO POR ARGUMENTO!!! El origen - Centro
itk::EncapsulateMetaData<std::string>(*dict, "0020|0032", value.str());


// Slice Location: For now, we store the z component of the Image
// Position Patient.
value.str("");
value << position[2];
itk::EncapsulateMetaData<std::string>(*dict, "0020|1041", value.str());

// Slice Thickness: For now, we store the z spacing
value.str("");
value << inputSpacing[2];
itk::EncapsulateMetaData<std::string>(*dict, "0018|0050",
value.str());
// Spacing Between Slices
itk::EncapsulateMetaData<std::string>(*dict, "0018|0088",
value.str());

// Save the dictionary
outputArray.push_back(dict);
}


typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();

typedef itk::ImageSeriesWriter< ImageType, ImageType_Serie > SeriesWriterType;
SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
seriesWriter->SetInput(FiltroResample->GetOutput());

writer->SetFileName(argv[2]);
writer->SetInput(FiltroResample->GetOutput());

itksys::SystemTools::MakeDirectory("Test"); //PASAR ESTO POR ARGUMENTO!!
typedef itk::NumericSeriesFileNames OutputNamesGeneratorType;
OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New();
std::string seriesFormat("Test"); //PASAR ESTO POR ARGUMENTO!!
seriesFormat = seriesFormat + "/" + "IM%d.dcm";
outputNames->SetSeriesFormat(seriesFormat.c_str());
outputNames->SetStartIndex(1);
outputNames->SetEndIndex(inputSize[2]);

seriesWriter->SetImageIO(gdcmIO);
seriesWriter->SetFileNames(outputNames->GetFileNames());
seriesWriter->SetMetaDataDictionaryArray(&outputArray);

std::cout << "Escribiendo la imagen como..." << std::endl << std::endl;
std::cout << argv[2] << std::endl << std::endl;

try
{
writer->Update();
seriesWriter->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}


}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}

return EXIT_SUCCESS;

}

void CopyDictionary(itk::MetaDataDictionary &fromDict, itk::MetaDataDictionary &toDict)
{
typedef itk::MetaDataDictionary DictionaryType;

DictionaryType::ConstIterator itr = fromDict.Begin();
DictionaryType::ConstIterator end = fromDict.End();
typedef itk::MetaDataObject< std::string > MetaDataStringType;

while (itr != end)
{
itk::MetaDataObjectBase::Pointer  entry = itr->second;

MetaDataStringType::Pointer entryvalue =
dynamic_cast<MetaDataStringType *>(entry.GetPointer());
if (entryvalue)
{
std::string tagkey = itr->first;
std::string tagvalue = entryvalue->GetMetaDataObjectValue();
itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
}
++itr;
}
}


El jue., 30 de mar. de 2017 a la(s) 11:25, Lowekamp, Bradley (NIH/NLM/LHC) [C] [via ITK - Users] <[hidden email]> escribi?:
Hello,

Writing correct DICOM continues to be a struggle with SimpleITK and ITK. It is generally recommended to directly use GDCM or DCMTK to write a proper DICOM series.

SimpleITK tries to keep things, well, simple and straight forward. But ITK ties to do some smart things, which get in the way for certain uses with SimpleITK. We are trying to document and develop a nominal set of DICOM output operations that work in SimpleITK.

Do you have working C++ code that works for your intended operation? Can you share a small section of code which does what you expect it C++?

Thank,
Brad


> On Mar 30, 2017, at 8:49 AM, Matias <[hidden email]<http://user/SendEmail.jtp?type=node&node=38052&i=0>> wrote:
>
> Hi,
>
> I've been dealing with ITK for years in C++ and now I would need to use
> SimpleITK and C# as far as I can in a new proyect.
>
> Is the SimpleITK SeriesWriter working for Dicom Files? Last time I tried to
> use it I had problems with the DicomTags, these would not copy or there was
> no method to copy the tags to the resulting slices.
>
> Currently, I read a volume of slices, apply rotation and then I need to
> write the resulting image as another set of slices AND keeping tag
> information such as patient name, etc.
>
> Thank you,
>
> Matias.
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com<http://www.kitware.com>
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
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--
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________________________________
View this message in context: Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags<http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38056.html>

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--
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http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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Please keep messages on-topic and check the ITK FAQ at:
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From fisidoro at ethz.ch  Sun Apr  2 17:17:50 2017
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Sun, 2 Apr 2017 21:17:50 +0000
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
Message-ID: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>

Hallo,

I use ITK with Python Wrap. I need to interface my Python code with a Cython-wrapped C++ code that takes only numpy array as input and returns numpy array as output.

Hence, I need to convert the Python itk images into numpy array to be given as input to the wrapped C++ code, and then convert the numpy array in output from the wrapped C++ code back into python itk images.

Question 1) How can I do that in an efficient way? I found some posts on itk.PyBuffer but I could not find anywhere any reference on how to install it on my itk wrap build.

Question 2) The purpose of writing a part of my algorithm in C++ is to speed up the code. If the conversion between python itk images and numpy arrays is slow, I would lose all the speed gain obtained with the C++ implementation. Are there better ways to deal with that?

Thank you,

Fabio.

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From matt.mccormick at kitware.com  Mon Apr  3 14:40:50 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 3 Apr 2017 14:40:50 -0400
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
Message-ID: <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>

Hallo Fabio,


> I use ITK with Python Wrap. I need to interface my Python code with a
> Cython-wrapped C++ code that takes only numpy array as input and returns
> numpy array as output.

Cool. By the way, you may be interested in scikit-build [1], which is
a good way to build Cython-wrapped C++ code. We are using it for the
ITK and SimpleITK Python packages, and it has good Cython and CMake
support.


> Hence, I need to convert the Python itk images into numpy array to be given
> as input to the wrapped C++ code, and then convert the numpy array in output
> from the wrapped C++ code back into python itk images.
>
>
>
> Question 1) How can I do that in an efficient way? I found some posts on
> itk.PyBuffer but I could not find anywhere any reference on how to install
> it on my itk wrap build.

Yes, itk.PyBuffer works great for that. Please review a PR for some
additional documentation:

  https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18

This has been available in ITK for a few releases as a Remote module,
which can be enabled by setting

  Module_BridgeNumPy=ON

in ITK's CMake configuration.


Since ITK 4.11.0, it is easier to build since it does not require the
NumPy headers.


In current ITK Git master (to be 4.12.0) the module is enabled by default.


Nightly ITK Python packages for ITK Git master are now being built:

  https://github.com/InsightSoftwareConsortium/ITKPythonPackage

macOS and Linux are available. Windows packages will be available over
the coming weeks.



> Question 2) The purpose of writing a part of my algorithm in C++ is to speed
> up the code. If the conversion between python itk images and numpy arrays is
> slow, I would lose all the speed gain obtained with the C++ implementation.
> Are there better ways to deal with that?

The newer versions ITKBridgeNumPy use a NumPy array view, which does
not do any copies during the conversion, and it is very fast.


HTH,
Matt


[1] http://scikit-build.org/

From matt.mccormick at kitware.com  Mon Apr  3 15:18:03 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 3 Apr 2017 15:18:03 -0400
Subject: [ITK-users] Patch for ApproximateSignedDistanceMapImageFilter
In-Reply-To: <c99adb7c-9b4b-847f-3bac-3f497126c437@neuro.ma.uni-heidelberg.de>
References: <ffaf9bf3-b2f9-7d6f-bd94-6e0ae84d2c68@neuro.ma.uni-heidelberg.de>
 <CAHwLD2WZpHuRywU7DY8H9Xp6XMgw+OLEfrbzXKc9sC8BHvRQ0A@mail.gmail.com>
 <874f690f-ff74-bb01-6d1e-bc479abeb547@neuro.ma.uni-heidelberg.de>
 <CAHwLD2XZvEX+LgWhifVc=iZZs0ZeUBTsaChVEu4Sp_LGFftmJA@mail.gmail.com>
 <f84deabd-fd59-32b0-14b6-413822581cda@neuro.ma.uni-heidelberg.de>
 <CAHwLD2V_SJ6toyNvCOpbMiFeW-gJ0AVr2Pt9xfCvA4ydqtV6qg@mail.gmail.com>
 <c99adb7c-9b4b-847f-3bac-3f497126c437@neuro.ma.uni-heidelberg.de>
Message-ID: <CALzTN-ShzDHSdCo-AmU2G_1jaHZgRFFeJ0-MXVNOHi963gDvfg@mail.gmail.com>

Hi Christina,

> 2nd attempt using approach 1)  (see below). What about typos in comments I
> removed during bug fixing? Include into this patch as well or keep them
> separate?

Thanks! This patch has been uploaded:

  http://review.source.kitware.com/#/c/22149/3


The typos could go in a different patch (ideally), but it is OK, if
they are included.

Thanks,
Matt



> Additionally you find a small application creating an image with a bright
> square on dark background which displays the image together with the result
> of ApproximateSignedDistanceMapImageFilter. The pixel value of the square is
> 1 by default but can be changed via command line.
>
> Regards,
> Christina
>
>
> On 29.03.2017 15:12, Francois Budin wrote:
>
> Hello Christina,
>
> I see different paths to try to solve this issue and I am not sure which one
> is the best one:
> 1) You could modify the itkIsoContourDistanceImageFilter class so that
> m_LevelSetValue is of some real type. When looking in the implementation of
> this filter,  you can see that sometimes, m_LevelSetValue is casted to a
> real type [1], so maybe it makes sense to do that.
> 2) Casting is one solution, but you have to be careful if you want to cast
> to float or double. If you cast to float, and the input is of type double,
> you will loose precision. If you always cast to double, you might use a lot
> of memory. Sadly, in the itkNumericTraits, there is no way of asking for
> "the smallest floating type that contains my current type". You can call
> "RealType" which will be "double", or "FloatType" which will be float. One
> strength of casting, is that if you perform it in place, it can actually not
> do anything if it doesn't need to [2].
> 3) To avoid casting when you don't need to (your type is float or double),
> you could use the SFINAE concept like it is used here [3]. This is more
> complex and may not be worth it.
>
> Beware that images may contain pixels that are not only scalar values, but
> also RGB, RGBA, vectors. I am not sure if the ApproximateDistance filter
> supports these types, but it is good to be careful, when modifying the code,
> to not restrict the usage of a filter to scalar if not required. To avoid
> that kind of issues, and to answer your original question, you can use the
> Rebind structure [4].
>
> I hope this helps.
> I will be out of town for a week, and most likely will have limited to no
> access to the internet, so don't be surprised if I do not answer your next
> message within the next week.
>
> Thanks for helping!
> Francois
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/DistanceMap/include/itkIsoContourDistanceImageFilter.hxx#L314
> [2]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.hxx#L42
> [3]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/ImageBase/include/itkConvertPixelBuffer.h#L153-L161
> [4]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/Smoothing/include/itkSmoothingRecursiveGaussianImageFilter.h#L84-L85
>
> On Wed, Mar 29, 2017 at 7:10 AM, Chr. Rossmanith
> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>
>> Hi Francois,
>>
>> I'm getting back to this issue. I'll introduce an intermediate image in
>> the mini pipeline used in ApproximateSignedDistanceMapImageFilter which has
>> a floating type for pixel values. Given
>>
>>   /** Type for input image. */
>>   typedef TInputImage InputImageType;
>>
>> how can I define a corresponding image type FloatImageType replacing the
>> unknown pixel type by float? I can't write itk::Image< float, xxx > because
>> I don't know xxx.
>>
>> Is there a way to query the pixel type to avoid applying the
>> CastImageFilter in case we already get floating valued pixels?
>>
>> Christina
>>
>>
>>
>> On 03.03.2017 14:58, Francois Budin wrote:
>>
>> Hi Christina,
>>
>> Maybe your idea was good but needs more work (e.g. cast the input image to
>> the output type? at least if input is not a float, or maybe something else).
>> I am glad you found a solution that works for you. If you need your software
>> to be faster, you can also replace the SignedDanielssonDistanceMap with the
>> SignedMauerDistanceMap [1].
>>
>> Hope this helps, and thanks for your contribution. Do not hesitate to
>> submit a new patch to solve your original problem if you find a solution.
>>
>> Francois
>> [1]
>> https://itk.org/Doxygen/html/classitk_1_1SignedMaurerDistanceMapImageFilter.html
>>
>> On Fri, Mar 3, 2017 at 8:23 AM, Chr. Rossmanith
>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>
>>> Hi Francois,
>>>
>>> really strange, on Wednesday changing the data type made my application
>>> work as expected (but obviously there must have been an additional change
>>> which really made the application work...). When trying to build a small
>>> example for you, I failed. I still think that feeding a 0/1 image into
>>> ApproximateSignedDistanceMapImageFilter makes sense.
>>>
>>> Originally I'm interested in ContourExtractor2D, which operates on a
>>> distance map using 0 as contour level. Unlike in the  ContourExtractor2D
>>> example I've decided to use SignedDanielssonDistanceMap which works fine
>>> without any patches.
>>>
>>> So send the patch to /dev/null for the moment...
>>>
>>> Christina
>>>
>>>
>>>  On 02.03.2017 16:17, Francois Budin wrote:
>>>
>>> Hello Christina,
>>>
>>> I just reviewed you patch. You are changing the type of the variable
>>> levelSetValue to OutputPixelType which is suppose to be a floating point
>>> value.
>>> However, the computation is done with InputPixelType variables
>>> (m_InsideValue and m_OutsideValue) and divided by an integer. Additionally,
>>> the resulting value is used in:
>>>   m_IsoContourFilter->SetLevelSetValue(levelSetValue);
>>>
>>> which accepts values of InputPixelType [1] since IsoContourType is
>>> defined as:
>>>   typedef IsoContourDistanceImageFilter< InputImageType, OutputImageType
>>> >   IsoContourType;
>>>
>>> I am not sure if your patch solves the problem that you mentioned. Do you
>>> have a test that would verify that the new behavior corresponds to your
>>> expectations? Based on the code review I have done, I would not expect the
>>> behavior of the filter to change.
>>>
>>> Let me know if I missed a detail. Thank you for your contribution!
>>> Francois
>>>
>>> [1]
>>> https://itk.org/Doxygen/html/classitk_1_1IsoContourDistanceImageFilter.html
>>>
>>> On Wed, Mar 1, 2017 at 8:12 AM, Chr. Rossmanith
>>> <cr at neuro.ma.uni-heidelberg.de> wrote:
>>>>
>>>> For binary images with 0 for background and 1 for objects with an
>>>> integer input pixel type there is a problem representing the average of 0
>>>> and 1 = 0.5 with the input pixel type. The output pixel type is required to
>>>> be a floating pixel type (filter documentation), so it should be safe to
>>>> change the type of levelSetValue to OutputPixelType.
>>>>
>>>> Regards,
>>>> Christina
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>
>>>
>>
>>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Mon Apr  3 15:19:07 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 3 Apr 2017 15:19:07 -0400
Subject: [ITK-users] Otsu Filter in Statistic and Review/statistics
In-Reply-To: <CADiSopPMsSgdjAq50+147tYvn7PgAhemFqrBfhrTx7RoXWfUxA@mail.gmail.com>
References: <CADiSopPMsSgdjAq50+147tYvn7PgAhemFqrBfhrTx7RoXWfUxA@mail.gmail.com>
Message-ID: <CALzTN-R2pEDcXt+Bri=Oxz4JbG0BGDPHiLTAWW3e0EW_-59bzQ@mail.gmail.com>

Hi Zein,

It sounds like this is ITKv3.  A number of Otsu fixes have been made
in ITKv4 - upgrading will likely fix the issue.

HTH,
Matt

On Fri, Mar 31, 2017 at 4:42 AM, Zein Salah <zeinsalah at gmail.com> wrote:
> Hi,
>
> I had a strange behavior regarding otsu filter. My code is as simple as
> this:
>
>
>     typedef itk::Statistics::ScalarImageToHistogramGenerator<ImageType>
> ScalarImageToHistogramGeneratorType;
>     typedef ScalarImageToHistogramGeneratorType::HistogramType
> HistogramType;
>     typedef itk::OtsuMultipleThresholdsCalculator<HistogramType>
> OtsuCalculatorType;
>
>     ScalarImageToHistogramGeneratorType::Pointer
> scalarImageToHistogramGenerator =
> ScalarImageToHistogramGeneratorType::New();
>     scalarImageToHistogramGenerator->SetNumberOfBins(128);
>     scalarImageToHistogramGenerator->SetInput(itkImage);
>     scalarImageToHistogramGenerator->Compute();
>
>
>     OtsuCalculatorType::Pointer otsuCalculator = OtsuCalculatorType::New();
>     otsuCalculator->SetNumberOfThresholds(numberOfThresholds);
>
> otsuCalculator->SetInputHistogram(scalarImageToHistogramGenerator->GetOutput());
>     otsuCalculator->Update();
>
>     const OtsuCalculatorType::OutputType& thresholdVector =
> otsuCalculator->GetOutput();
>     HistogramType::MeasurementType threshold =
> thresholdVector[usedThreshold];
>
>
> I tested this with itk configured with ITK_USE_REVIEW_STATISTICS set to ON
> and once to OFF.
> With some images, the results is not the same.
>
> Is this a known issue?
>
> thanks,
> Zein
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Mon Apr  3 15:19:07 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 3 Apr 2017 15:19:07 -0400
Subject: [ITK-users] Otsu Filter in Statistic and Review/statistics
In-Reply-To: <CADiSopPMsSgdjAq50+147tYvn7PgAhemFqrBfhrTx7RoXWfUxA@mail.gmail.com>
References: <CADiSopPMsSgdjAq50+147tYvn7PgAhemFqrBfhrTx7RoXWfUxA@mail.gmail.com>
Message-ID: <CALzTN-R2pEDcXt+Bri=Oxz4JbG0BGDPHiLTAWW3e0EW_-59bzQ@mail.gmail.com>

Hi Zein,

It sounds like this is ITKv3.  A number of Otsu fixes have been made
in ITKv4 - upgrading will likely fix the issue.

HTH,
Matt

On Fri, Mar 31, 2017 at 4:42 AM, Zein Salah <zeinsalah at gmail.com> wrote:
> Hi,
>
> I had a strange behavior regarding otsu filter. My code is as simple as
> this:
>
>
>     typedef itk::Statistics::ScalarImageToHistogramGenerator<ImageType>
> ScalarImageToHistogramGeneratorType;
>     typedef ScalarImageToHistogramGeneratorType::HistogramType
> HistogramType;
>     typedef itk::OtsuMultipleThresholdsCalculator<HistogramType>
> OtsuCalculatorType;
>
>     ScalarImageToHistogramGeneratorType::Pointer
> scalarImageToHistogramGenerator =
> ScalarImageToHistogramGeneratorType::New();
>     scalarImageToHistogramGenerator->SetNumberOfBins(128);
>     scalarImageToHistogramGenerator->SetInput(itkImage);
>     scalarImageToHistogramGenerator->Compute();
>
>
>     OtsuCalculatorType::Pointer otsuCalculator = OtsuCalculatorType::New();
>     otsuCalculator->SetNumberOfThresholds(numberOfThresholds);
>
> otsuCalculator->SetInputHistogram(scalarImageToHistogramGenerator->GetOutput());
>     otsuCalculator->Update();
>
>     const OtsuCalculatorType::OutputType& thresholdVector =
> otsuCalculator->GetOutput();
>     HistogramType::MeasurementType threshold =
> thresholdVector[usedThreshold];
>
>
> I tested this with itk configured with ITK_USE_REVIEW_STATISTICS set to ON
> and once to OFF.
> With some images, the results is not the same.
>
> Is this a known issue?
>
> thanks,
> Zein
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Mon Apr  3 18:52:02 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 3 Apr 2017 18:52:02 -0400
Subject: [ITK-users] Maintenance of the Insight Toolkit
Message-ID: <CALzTN-TLxrO3zk35iyK1E_8c4Eib-SrZe5eTJgKbZSfADTwutA@mail.gmail.com>

Hi folks,

As United States government is re-examines the value of its funding
initiatives, we have an opportunity to explain the value of the
Insight Toolkit (ITK) project, and its associated open science
community.

The National Library of Medicine (NLM) has driven open science and
reproducible research long before the recent surge in popularity of
the movement. Not only did the NLM start the Insight Toolkit project
in 1999, but it has continuously enabled it to thrive by supporting
community development, maintenance, and algorithmic and technological
advances to this day.

Open science needs active communities, supported communities,
standards, open-source tools, strong ties will commercial / clinical
efforts, high-quality practices, transparency, and more - and those
are exactly the strengths of our community's toolkits, applications,
and projects. We should to encourage the NLM (NIH, DHHS, US
Government) to continue to prioritize these efforts via their funding.


To emphasize the impact of this community, please share your story. We
would like to describe outstanding projects and efforts that use the
Insight Toolkit. If you have stories, descriptions, or statistics of
the impact of ITK or projects that leverage it, they justify future
investments in this area.

If you can help, please send a description of your project or your
relationship with the Insight Toolkit for research, industry, or
education to <matt.mccormick at kitware.com> by Tuesday, April 11th.


For example,

Dear US National Library of Medicine,

Thanks you for funding the Insight Toolkit project and supporting its
maintenance and community. For the past two years, the documentation,
software, and community have been a valuable resource for my research
on neurocognitive imaging.

Sincerely,
Alice Insight, PhD
Reproducible University


Thank you,
Matt

From blowekamp at mail.nih.gov  Wed Apr  5 08:57:15 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Wed, 5 Apr 2017 12:57:15 +0000
Subject: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
In-Reply-To: <89767550-AE53-4FCB-81F0-66A709E3253F@mail.nih.gov>
References: <1490878156334-38050.post@n7.nabble.com>
 <031C16D1-4B43-4BD8-9C80-91A2F9C72B6B@mail.nih.gov>
 <CAKKNfuLb=DnqxAnE9yY9zgo5B+Ns7DV_A7rV7yb=fenMYU0vtw@mail.gmail.com>
 <54518069-C5F9-445E-983C-FDD5A2EDA798@mail.nih.gov>
 <CAKKNfuKEYX85a82CEkDPsLBmeW_45hL9Enipha0r5_X9mikBDQ@mail.gmail.com>
 <CAPf2UMRZyV8svf3XkAOq3v=hdgsxowzt55vr7YUxWniAHLfcNA@mail.gmail.com>
 <89767550-AE53-4FCB-81F0-66A709E3253F@mail.nih.gov>
Message-ID: <E23A02F4-FEB0-4802-828D-586CCE790883@mail.nih.gov>

Hello Matias,

Ziv's patch was merged into SimpleITK?s master branch yesterday. The CDash builds[1] compiled the update and created binaries which are linked in the golden boxes. I believe you want CSharp for window 64[2].

Enjoy!
Brad

[1] https://open.cdash.org/index.php?project=SimpleITK
[2] https://open.cdash.org/viewFiles.php?buildid=4839224

On Apr 2, 2017, at 9:58 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov<mailto:zivrafael.yaniv at nih.gov>> wrote:

Hi Matias,

We should get it into the main SimpleITK repository shortly (after testing etc..). For now please follow D?enan?s recommendation (clone my forked repository, checkout the dicomWrite branch and build SimpleITK from that branch).

     regards
        Ziv

From: D?enan Zuki? <dzenanz at gmail.com<mailto:dzenanz at gmail.com>>
Date: Saturday, April 1, 2017 at 9:37 AM
To: Matias <matimontg at gmail.com<mailto:matimontg at gmail.com>>
Cc: Insight-users <insight-users at itk.org<mailto:insight-users at itk.org>>
Subject: Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags

Hi Matias,

you should use branch dicomWrite from Ziv's fork<https://github.com/zivy/SimpleITK/tree/dicomWrite>.

Regards,
D?enan

On Sat, Apr 1, 2017 at 2:48 AM, Matias <matimontg at gmail.com<mailto:matimontg at gmail.com>> wrote:
Thanks Yaniv. So how do I get this branch? I simply download the latest version of SimpleITK?
El vie., 31 de mar. de 2017 a la(s) 19:18, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] [via ITK - Users] <[hidden email]<http://user/SendEmail.jtp?type=node&node=38064&i=0>> escribi?:
Hello Matias,

Please take a look at the following github pull request (https://github.com/SimpleITK/SimpleITK/pull/134), this branch should provide the functionality you are looking for. See the Python example script included in the commit for the usage of the DICOM series writing.

     hope this helps
            Ziv


From: Matias <[hidden email]<http://user/SendEmail.jtp?type=node&node=38063&i=0>>

Date: Thursday, March 30, 2017 at 12:14 PM
To: "[hidden email]<http://user/SendEmail.jtp?type=node&node=38063&i=1>" <[hidden email]<http://user/SendEmail.jtp?type=node&node=38063&i=2>>

Subject: Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags

Yes, this is what I would need to migrate to C#:
It basically reads a dicom directory and performs rotation on the volume, then writes the resulting images back to a directory, copying the tags from the original images.

#include "itkImage.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkResampleImageFilter.h"
#include "itkEuler3DTransform.hxx"
#include "gdcmUIDGenerator.h"

#include "itkImageFileWriter.h"
#include "itkImageSeriesWriter.h"
#include "itkNumericSeriesFileNames.h"
#include "itkTranslationTransform.h"
#include "string.h";
#include <itkSliceIterator.h>

#include <iostream>
#include <string>
#include <fstream>



static void CopyDictionary(itk::MetaDataDictionary &fromDict,
itk::MetaDataDictionary &toDict);

int main(int argc, char* argv[])
{
if (argc < 8)
{
std::cerr << "Uso: " << std::endl;
std::cerr << argv[0] << " Directorio_A_Rotar  DirectorioResultante Gamma Beta Alfa CentroRotacionX CentroRotacionY CentroRotacionZ"
<< std::endl;
return EXIT_FAILURE;
}

typedef signed short    PixelType;
const unsigned int      Dimension = 3;
const unsigned int Dimension_Serie = 2;
typedef itk::Image< PixelType, Dimension >         ImageType;
typedef itk::Image<PixelType, Dimension_Serie> ImageType_Serie;

typedef itk::ImageSeriesReader< ImageType >        ReaderType;
ReaderType::Pointer reader = ReaderType::New();

typedef itk::GDCMImageIO       ImageIOType;
ImageIOType::Pointer gdcmIO = ImageIOType::New();
reader->SetImageIO(gdcmIO);

typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->AddSeriesRestriction("0008|0021");
nameGenerator->SetDirectory(argv[1]);

try
{
std::cout << std::endl << "The directory: " << std::endl;
std::cout << std::endl << argv[1] << std::endl << std::endl;
std::cout << "Contains the following DICOM Series: ";
std::cout << std::endl << std::endl;

typedef std::vector< std::string >    SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
while (seriesItr != seriesEnd)
{
std::cout << seriesItr->c_str() << std::endl;
++seriesItr;
}

std::string seriesIdentifier;

seriesIdentifier = seriesUID.begin()->c_str();


std::cout << std::endl << std::endl;
std::cout << "Now reading series: " << std::endl << std::endl;
std::cout << seriesIdentifier << std::endl;
std::cout << std::endl << std::endl;

typedef std::vector< std::string >   FileNamesContainer;
FileNamesContainer fileNames;
fileNames = nameGenerator->GetFileNames(seriesIdentifier);

reader->SetFileNames(fileNames);

try
{
reader->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}

const ImageType * inputImage = reader->GetOutput();
/*int numerodedicoms = inputImage->GetLargestPossibleRegion().GetSize()[2];
int dicomcentral = numerodedicoms / 2;
std::cout << "Dimenion " <<  dicomcentral << std::endl;*/
//itk::EncapsulateMetaData<std::string>(dictionary, "0020|0032","-208\\-236\\66");

typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
FilterType::Pointer FiltroResample = FilterType::New();
FiltroResample->SetInput(reader->GetOutput());

typedef itk::LinearInterpolateImageFunction<ImageType, double > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
FiltroResample->SetInterpolator(interpolator);
FiltroResample->SetOutputDirection(inputImage->GetDirection());
FiltroResample->SetOutputOrigin(inputImage->GetOrigin());

ImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().GetSize();
FiltroResample->SetSize(inputSize);

const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
FiltroResample->SetOutputSpacing(inputSpacing);

FiltroResample->SetDefaultPixelValue(-1000); //Cambiar por un parametro

typedef itk::Euler3DTransform< double > TransformType; //Transform
TransformType::Pointer transform = TransformType::New();
double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z;
gamma = atof(argv[3]);
beta= atof(argv[4]);
alfa = atof(argv[5]);
centro_rotacion_X = atof(argv[6]);
centro_rotacion_Y = atof(argv[7]);
centro_rotacion_Z = atof(argv[8]);
transform->SetRotation(gamma, beta, alfa); //Radianes en el siguiente orden en ITK: Gamma, Beta, Alfa | Ibarra
//double centro[3] = { -14.8371, -54.9443, 175.75 }; //XmmPromedio, YmmPromedio, Z Central (mm): Leer directorio y tomar la del medio
double centro[3] = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z }; //XmmPromedio, YmmPromedio, Z Central (mm): Leer directorio y tomar la del medio
transform->SetCenter(centro);
std::cout << "Centro: " << std::endl << std::endl;
std::cout << transform->GetCenter() << std::endl;

FiltroResample->SetTransform(transform);
//FiltroResample->SetMetaDataDictionary(dictionary);
try
{
FiltroResample->Update();
}
catch (itk::ExceptionObject &ex)
{
return EXIT_FAILURE;
}



ReaderType::DictionaryRawPointer inputDict = (*(reader->GetMetaDataDictionaryArray()))[0];
ReaderType::DictionaryArrayType outputArray;
//std::cout << "array: " << std::endl << outputArray[0] << std::endl;
// To keep the new series in the same study as the original we need
// to keep the same study UID. But we need new series and frame of
// reference UID's.
gdcm::UIDGenerator suid;
//std::string seriesUID = suid.Generate();
gdcm::UIDGenerator fuid;
std::string frameOfReferenceUID = fuid.Generate();

std::string studyUID;
std::string sopClassUID;
itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
gdcmIO->KeepOriginalUIDOn();

using namespace std;
double myArray_Z[70]; //Cambiar esto por un argumento que especifica la cantidad de imagenes.
double myArray_X[70]; //Cambiar esto por un argumento que especifica la cantidad de imagenes.
double myArray_Y[70]; //Cambiar esto por un argumento que especifica la cantidad de imagenes.

ifstream file("file.txt");
if (file.is<http://file.is>_open())
{
for (int i = 0; i < 70; ++i) //Recordar cambiar por el argumento que especifica cantidad de imagenes
{
file >> myArray_Z[i];
}
}
std::cout << "valor primer Z array: " << std::endl << std::endl;
std::cout << myArray_Z[0] << std::endl;

for (unsigned int f = 0; f < inputSize[2]; f++)
{
// Create a new dictionary for this slice
ReaderType::DictionaryRawPointer dict = new ReaderType::DictionaryType;

// Copy the dictionary from the first slice
CopyDictionary(*inputDict, *dict);

// Set the UID's for the study, series, SOP  and frame of reference
itk::EncapsulateMetaData<std::string>(*dict, "0020|000d", studyUID);
//itk::EncapsulateMetaData<std::string>(*dict, "0020|000e", seriesUID);
itk::EncapsulateMetaData<std::string>(*dict, "0020|0052", frameOfReferenceUID);

gdcm::UIDGenerator sopuid;
std::string sopInstanceUID = sopuid.Generate();

itk::EncapsulateMetaData<std::string>(*dict, "0008|0018", sopInstanceUID);
itk::EncapsulateMetaData<std::string>(*dict, "0002|0003", sopInstanceUID);

// Change fields that are slice specific
std::ostringstream value;
value.str("");
value << f + 1;

// Image Number
itk::EncapsulateMetaData<std::string>(*dict, "0020|0013", value.str());

// Series Description - Append new description to current series
// description
std::string oldSeriesDesc;
itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);

value.str("");
value << oldSeriesDesc
<< ": Resampled with pixel spacing "
<< inputSpacing[0] << ", "
<< inputSpacing[1] << ", "
<< inputSpacing[2];
// This is an long string and there is a 64 character limit in the
// standard
unsigned lengthDesc = value.str().length();

std::string seriesDesc(value.str(), 0,
lengthDesc > 64 ? 64
: lengthDesc);
itk::EncapsulateMetaData<std::string>(*dict, "0008|103e", seriesDesc);

// Series Number
value.str("");
value << 1001;
itk::EncapsulateMetaData<std::string>(*dict, "0020|0011", value.str());

// Derivation Description - How this image was derived
value.str("");
for (int i = 0; i < argc; i++)
{
value << argv[i] << " ";
}

lengthDesc = value.str().length();
std::string derivationDesc(value.str(), 0,
lengthDesc > 1024 ? 1024
: lengthDesc);
itk::EncapsulateMetaData<std::string>(*dict, "0008|2111", derivationDesc);

// Image Position Patient: This is calculated by computing the
// physical coordinate of the first pixel in each slice.
ImageType::PointType position;
ImageType::IndexType index;
index[0] = 0;
index[1] = 0;
index[2] = myArray_Z[f];
FiltroResample->GetOutput()->TransformIndexToPhysicalPoint(index, position);

//El origen que calculamos en el proyecto no se toca. (Origen = origen - average)

//Cambiamos el ImageOrientationPatient SOLAMENTE si el valor original en la imagen es: 1\0\0\0\1\0. En el caso que se cambia el signo, se debe cambiar el signo del origen
//value.str("");
//value << -1 << "\\" << 0 << "\\" << 0 << "\\" << 0 << "\\" << -1 << "\\" << 0; //PASAR ESTO POR ARGUMENTO!!!
//itk::EncapsulateMetaData<std::string>(*dict, "0020|0037", value.str());

value.str("");
value << -235.1629 << "\\" << -195.0557 << "\\" << myArray_Z[f]; //PASAR ESTO POR ARGUMENTO!!! El origen - Centro
itk::EncapsulateMetaData<std::string>(*dict, "0020|0032", value.str());


// Slice Location: For now, we store the z component of the Image
// Position Patient.
value.str("");
value << position[2];
itk::EncapsulateMetaData<std::string>(*dict, "0020|1041", value.str());

// Slice Thickness: For now, we store the z spacing
value.str("");
value << inputSpacing[2];
itk::EncapsulateMetaData<std::string>(*dict, "0018|0050",
value.str());
// Spacing Between Slices
itk::EncapsulateMetaData<std::string>(*dict, "0018|0088",
value.str());

// Save the dictionary
outputArray.push_back(dict);
}


typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();

typedef itk::ImageSeriesWriter< ImageType, ImageType_Serie > SeriesWriterType;
SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
seriesWriter->SetInput(FiltroResample->GetOutput());

writer->SetFileName(argv[2]);
writer->SetInput(FiltroResample->GetOutput());

itksys::SystemTools::MakeDirectory("Test"); //PASAR ESTO POR ARGUMENTO!!
typedef itk::NumericSeriesFileNames OutputNamesGeneratorType;
OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New();
std::string seriesFormat("Test"); //PASAR ESTO POR ARGUMENTO!!
seriesFormat = seriesFormat + "/" + "IM%d.dcm";
outputNames->SetSeriesFormat(seriesFormat.c_str());
outputNames->SetStartIndex(1);
outputNames->SetEndIndex(inputSize[2]);

seriesWriter->SetImageIO(gdcmIO);
seriesWriter->SetFileNames(outputNames->GetFileNames());
seriesWriter->SetMetaDataDictionaryArray(&outputArray);

std::cout << "Escribiendo la imagen como..." << std::endl << std::endl;
std::cout << argv[2] << std::endl << std::endl;

try
{
writer->Update();
seriesWriter->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}


}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}

return EXIT_SUCCESS;

}

void CopyDictionary(itk::MetaDataDictionary &fromDict, itk::MetaDataDictionary &toDict)
{
typedef itk::MetaDataDictionary DictionaryType;

DictionaryType::ConstIterator itr = fromDict.Begin();
DictionaryType::ConstIterator end = fromDict.End();
typedef itk::MetaDataObject< std::string > MetaDataStringType;

while (itr != end)
{
itk::MetaDataObjectBase::Pointer  entry = itr->second;

MetaDataStringType::Pointer entryvalue =
dynamic_cast<MetaDataStringType *>(entry.GetPointer());
if (entryvalue)
{
std::string tagkey = itr->first;
std::string tagvalue = entryvalue->GetMetaDataObjectValue();
itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
}
++itr;
}
}


El jue., 30 de mar. de 2017 a la(s) 11:25, Lowekamp, Bradley (NIH/NLM/LHC) [C] [via ITK - Users] <[hidden email]> escribi?:
Hello,

Writing correct DICOM continues to be a struggle with SimpleITK and ITK. It is generally recommended to directly use GDCM or DCMTK to write a proper DICOM series.

SimpleITK tries to keep things, well, simple and straight forward. But ITK ties to do some smart things, which get in the way for certain uses with SimpleITK. We are trying to document and develop a nominal set of DICOM output operations that work in SimpleITK.

Do you have working C++ code that works for your intended operation? Can you share a small section of code which does what you expect it C++?

Thank,
Brad


> On Mar 30, 2017, at 8:49 AM, Matias <[hidden email]<http://user/SendEmail.jtp?type=node&node=38052&i=0>> wrote:
>
> Hi,
>
> I've been dealing with ITK for years in C++ and now I would need to use
> SimpleITK and C# as far as I can in a new proyect.
>
> Is the SimpleITK SeriesWriter working for Dicom Files? Last time I tried to
> use it I had problems with the DicomTags, these would not copy or there was
> no method to copy the tags to the resulting slices.
>
> Currently, I read a volume of slices, apply rotation and then I need to
> write the resulting image as another set of slices AND keeping tag
> information such as patient name, etc.
>
> Thank you,
>
> Matias.
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050.html
> Sent from the ITK - Users mailing list archive at Nabble.com<http://nabble.com>.
> _____________________________________
> Powered by www.kitware.com<http://www.kitware.com/>
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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> _______________________________________________
> Community mailing list
> [hidden email]<http://user/SendEmail.jtp?type=node&node=38052&i=1>
> http://public.kitware.com/mailman/listinfo/community

_____________________________________
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________________________________
If you reply to this email, your message will be added to the discussion below:
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To unsubscribe from SimpleITK Serieswriter and DicomTags, click here.
NAML<http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
--
Matias

________________________________
View this message in context: Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags<http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38056.html>

Sent from the ITK - Users mailing list archive<http://itk-users.7.n7.nabble.com/> at Nabble.com<http://nabble.com>.

_____________________________________
Powered by www.kitware.com<http://www.kitware.com/>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
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--
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________________________________
View this message in context: Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags<http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38064.html>
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From matimontg at gmail.com  Wed Apr  5 09:22:09 2017
From: matimontg at gmail.com (Matias)
Date: Wed, 5 Apr 2017 06:22:09 -0700 (MST)
Subject: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
In-Reply-To: <E23A02F4-FEB0-4802-828D-586CCE790883@mail.nih.gov>
References: <1490878156334-38050.post@n7.nabble.com>
 <031C16D1-4B43-4BD8-9C80-91A2F9C72B6B@mail.nih.gov>
 <CAKKNfuLb=DnqxAnE9yY9zgo5B+Ns7DV_A7rV7yb=fenMYU0vtw@mail.gmail.com>
 <54518069-C5F9-445E-983C-FDD5A2EDA798@mail.nih.gov>
 <CAKKNfuKEYX85a82CEkDPsLBmeW_45hL9Enipha0r5_X9mikBDQ@mail.gmail.com>
 <CAPf2UMRZyV8svf3XkAOq3v=hdgsxowzt55vr7YUxWniAHLfcNA@mail.gmail.com>
 <89767550-AE53-4FCB-81F0-66A709E3253F@mail.nih.gov>
 <E23A02F4-FEB0-4802-828D-586CCE790883@mail.nih.gov>
Message-ID: <CAKKNfu+q2q5id109TQ1KQwm05pHwjZhHZSuXPy88DJi-FXZCMg@mail.gmail.com>

Awesome, thanks!

El mi?., 5 de abr. de 2017 a la(s) 09:57, Lowekamp, Bradley (NIH/NLM/LHC)
[C] [via ITK - Users] <ml-node+s7n38072h1 at n7.nabble.com> escribi?:

> Hello Matias,
>
> Ziv's patch was merged into SimpleITK?s master branch yesterday. The CDash
> builds[1] compiled the update and created binaries which are linked in the
> golden boxes. I believe you want CSharp for window 64[2].
>
> Enjoy!
> Brad
>
> [1] https://open.cdash.org/index.php?project=SimpleITK
> [2] https://open.cdash.org/viewFiles.php?buildid=4839224
>
> On Apr 2, 2017, at 9:58 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <[hidden
> email] <http:///user/SendEmail.jtp?type=node&node=38072&i=0>> wrote:
>
> Hi Matias,
>
> We should get it into the main SimpleITK repository shortly (after testing
> etc..). For now please follow D?enan?s recommendation (clone my forked
> repository, checkout the dicomWrite branch and build SimpleITK from that
> branch).
>
>      regards
>         Ziv
>
>
> *From: *D?enan Zuki? <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38072&i=1>>
> *Date: *Saturday, April 1, 2017 at 9:37 AM
> *To: *Matias <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38072&i=2>>
> *Cc: *Insight-users <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38072&i=3>>
>
>
> *Subject: *Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
>
> Hi Matias,
>
> you should use branch dicomWrite from Ziv's fork
> <https://github.com/zivy/SimpleITK/tree/dicomWrite>.
>
> Regards,
> D?enan
>
>
> On Sat, Apr 1, 2017 at 2:48 AM, Matias <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38072&i=4>> wrote:
>
> Thanks Yaniv. So how do I get this branch? I simply download the latest
> version of SimpleITK?
> El vie., 31 de mar. de 2017 a la(s) 19:18, Yaniv, Ziv Rafael (NIH/NLM/LHC)
> [C] [via ITK - Users] <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=38064&i=0>> escribi?:
>
> Hello Matias,
>
> Please take a look at the following github pull request (
> https://github.com/SimpleITK/SimpleITK/pull/134), this branch should
> provide the functionality you are looking for. See the Python example
> script included in the commit for the usage of the DICOM series writing.
>
>      hope this helps
>             Ziv
>
>
> *From: *Matias <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=38063&i=0>>
>
> *Date: *Thursday, March 30, 2017 at 12:14 PM
> *To: *"[hidden email] <http://user/SendEmail.jtp?type=node&node=38063&i=1>"
> <[hidden email] <http://user/SendEmail.jtp?type=node&node=38063&i=2>>
>
> *Subject: *Re: [ITK-users] [ITK] SimpleITK Serieswriter and DicomTags
>
> Yes, this is what I would need to migrate to C#:
> It basically reads a dicom directory and performs rotation on the volume,
> then writes the resulting images back to a directory, copying the tags from
> the original images.
>
> #include "itkImage.h"
> #include "itkGDCMImageIO.h"
> #include "itkGDCMSeriesFileNames.h"
> #include "itkImageSeriesReader.h"
> #include "itkResampleImageFilter.h"
> #include "itkEuler3DTransform.hxx"
> #include "gdcmUIDGenerator.h"
>
> #include "itkImageFileWriter.h"
> #include "itkImageSeriesWriter.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkTranslationTransform.h"
> #include "string.h";
> #include <itkSliceIterator.h>
>
> #include <iostream>
> #include <string>
> #include <fstream>
>
>
>
> static void CopyDictionary(itk::MetaDataDictionary &fromDict,
> itk::MetaDataDictionary &toDict);
>
> int main(int argc, char* argv[])
> {
> if (argc < 8)
> {
> std::cerr << "Uso: " << std::endl;
> std::cerr << argv[0] << " Directorio_A_Rotar  DirectorioResultante Gamma
> Beta Alfa CentroRotacionX CentroRotacionY CentroRotacionZ"
> << std::endl;
> return EXIT_FAILURE;
> }
>
> typedef signed short    PixelType;
> const unsigned int      Dimension = 3;
> const unsigned int Dimension_Serie = 2;
> typedef itk::Image< PixelType, Dimension >         ImageType;
> typedef itk::Image<PixelType, Dimension_Serie> ImageType_Serie;
>
> typedef itk::ImageSeriesReader< ImageType >        ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
>
> typedef itk::GDCMImageIO       ImageIOType;
> ImageIOType::Pointer gdcmIO = ImageIOType::New();
> reader->SetImageIO(gdcmIO);
>
> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
> nameGenerator->SetUseSeriesDetails(true);
> nameGenerator->AddSeriesRestriction("0008|0021");
> nameGenerator->SetDirectory(argv[1]);
>
> try
> {
> std::cout << std::endl << "The directory: " << std::endl;
> std::cout << std::endl << argv[1] << std::endl << std::endl;
> std::cout << "Contains the following DICOM Series: ";
> std::cout << std::endl << std::endl;
>
> typedef std::vector< std::string >    SeriesIdContainer;
> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
> while (seriesItr != seriesEnd)
> {
> std::cout << seriesItr->c_str() << std::endl;
> ++seriesItr;
> }
>
> std::string seriesIdentifier;
>
> seriesIdentifier = seriesUID.begin()->c_str();
>
>
> std::cout << std::endl << std::endl;
> std::cout << "Now reading series: " << std::endl << std::endl;
> std::cout << seriesIdentifier << std::endl;
> std::cout << std::endl << std::endl;
>
> typedef std::vector< std::string >   FileNamesContainer;
> FileNamesContainer fileNames;
> fileNames = nameGenerator->GetFileNames(seriesIdentifier);
>
> reader->SetFileNames(fileNames);
>
> try
> {
> reader->Update();
> }
> catch (itk::ExceptionObject &ex)
> {
> std::cout << ex << std::endl;
> return EXIT_FAILURE;
> }
>
> const ImageType * inputImage = reader->GetOutput();
> /*int numerodedicoms = inputImage->GetLargestPossibleRegion().GetSize()[2];
> int dicomcentral = numerodedicoms / 2;
> std::cout << "Dimenion " <<  dicomcentral << std::endl;*/
> //itk::EncapsulateMetaData<std::string>(dictionary,
> "0020|0032","-208\\-236\\66");
>
> typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
> FilterType::Pointer FiltroResample = FilterType::New();
> FiltroResample->SetInput(reader->GetOutput());
>
> typedef itk::LinearInterpolateImageFunction<ImageType, double >
> InterpolatorType;
> InterpolatorType::Pointer interpolator = InterpolatorType::New();
> FiltroResample->SetInterpolator(interpolator);
> FiltroResample->SetOutputDirection(inputImage->GetDirection());
> FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>
> ImageType::SizeType inputSize =
> inputImage->GetLargestPossibleRegion().GetSize();
> FiltroResample->SetSize(inputSize);
>
> const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
> FiltroResample->SetOutputSpacing(inputSpacing);
>
> FiltroResample->SetDefaultPixelValue(-1000); //Cambiar por un parametro
>
> typedef itk::Euler3DTransform< double > TransformType; //Transform
> TransformType::Pointer transform = TransformType::New();
> double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y,
> centro_rotacion_Z;
> gamma = atof(argv[3]);
> beta= atof(argv[4]);
> alfa = atof(argv[5]);
> centro_rotacion_X = atof(argv[6]);
> centro_rotacion_Y = atof(argv[7]);
> centro_rotacion_Z = atof(argv[8]);
> transform->SetRotation(gamma, beta, alfa); //Radianes en el siguiente
> orden en ITK: Gamma, Beta, Alfa | Ibarra
> //double centro[3] = { -14.8371, -54.9443, 175.75 }; //XmmPromedio,
> YmmPromedio, Z Central (mm): Leer directorio y tomar la del medio
> double centro[3] = { centro_rotacion_X, centro_rotacion_Y,
> centro_rotacion_Z }; //XmmPromedio, YmmPromedio, Z Central (mm): Leer
> directorio y tomar la del medio
> transform->SetCenter(centro);
> std::cout << "Centro: " << std::endl << std::endl;
> std::cout << transform->GetCenter() << std::endl;
>
> FiltroResample->SetTransform(transform);
> //FiltroResample->SetMetaDataDictionary(dictionary);
> try
> {
> FiltroResample->Update();
> }
> catch (itk::ExceptionObject &ex)
> {
> return EXIT_FAILURE;
> }
>
>
>
> ReaderType::DictionaryRawPointer inputDict =
> (*(reader->GetMetaDataDictionaryArray()))[0];
> ReaderType::DictionaryArrayType outputArray;
> //std::cout << "array: " << std::endl << outputArray[0] << std::endl;
> // To keep the new series in the same study as the original we need
> // to keep the same study UID. But we need new series and frame of
> // reference UID's.
> gdcm::UIDGenerator suid;
> //std::string seriesUID = suid.Generate();
> gdcm::UIDGenerator fuid;
> std::string frameOfReferenceUID = fuid.Generate();
>
> std::string studyUID;
> std::string sopClassUID;
> itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
> itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
> gdcmIO->KeepOriginalUIDOn();
>
> using namespace std;
> double myArray_Z[70]; //Cambiar esto por un argumento que especifica la
> cantidad de imagenes.
> double myArray_X[70]; //Cambiar esto por un argumento que especifica la
> cantidad de imagenes.
> double myArray_Y[70]; //Cambiar esto por un argumento que especifica la
> cantidad de imagenes.
>
> ifstream file("file.txt");
> if (file.is_open())
> {
> for (int i = 0; i < 70; ++i) //Recordar cambiar por el argumento que
> especifica cantidad de imagenes
> {
> file >> myArray_Z[i];
> }
> }
> std::cout << "valor primer Z array: " << std::endl << std::endl;
> std::cout << myArray_Z[0] << std::endl;
>
> for (unsigned int f = 0; f < inputSize[2]; f++)
> {
> // Create a new dictionary for this slice
> ReaderType::DictionaryRawPointer dict = new ReaderType::DictionaryType;
>
> // Copy the dictionary from the first slice
> CopyDictionary(*inputDict, *dict);
>
> // Set the UID's for the study, series, SOP  and frame of reference
> itk::EncapsulateMetaData<std::string>(*dict, "0020|000d", studyUID);
> //itk::EncapsulateMetaData<std::string>(*dict, "0020|000e", seriesUID);
> itk::EncapsulateMetaData<std::string>(*dict, "0020|0052",
> frameOfReferenceUID);
>
> gdcm::UIDGenerator sopuid;
> std::string sopInstanceUID = sopuid.Generate();
>
> itk::EncapsulateMetaData<std::string>(*dict, "0008|0018", sopInstanceUID);
> itk::EncapsulateMetaData<std::string>(*dict, "0002|0003", sopInstanceUID);
>
> // Change fields that are slice specific
> std::ostringstream value;
> value.str("");
> value << f + 1;
>
> // Image Number
> itk::EncapsulateMetaData<std::string>(*dict, "0020|0013", value.str());
>
> // Series Description - Append new description to current series
> // description
> std::string oldSeriesDesc;
> itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);
>
> value.str("");
> value << oldSeriesDesc
> << ": Resampled with pixel spacing "
> << inputSpacing[0] << ", "
> << inputSpacing[1] << ", "
> << inputSpacing[2];
> // This is an long string and there is a 64 character limit in the
> // standard
> unsigned lengthDesc = value.str().length();
>
> std::string seriesDesc(value.str(), 0,
> lengthDesc > 64 ? 64
> : lengthDesc);
> itk::EncapsulateMetaData<std::string>(*dict, "0008|103e", seriesDesc);
>
> // Series Number
> value.str("");
> value << 1001;
> itk::EncapsulateMetaData<std::string>(*dict, "0020|0011", value.str());
>
> // Derivation Description - How this image was derived
> value.str("");
> for (int i = 0; i < argc; i++)
> {
> value << argv[i] << " ";
> }
>
> lengthDesc = value.str().length();
> std::string derivationDesc(value.str(), 0,
> lengthDesc > 1024 ? 1024
> : lengthDesc);
> itk::EncapsulateMetaData<std::string>(*dict, "0008|2111", derivationDesc);
>
> // Image Position Patient: This is calculated by computing the
> // physical coordinate of the first pixel in each slice.
> ImageType::PointType position;
> ImageType::IndexType index;
> index[0] = 0;
> index[1] = 0;
> index[2] = myArray_Z[f];
> FiltroResample->GetOutput()->TransformIndexToPhysicalPoint(index,
> position);
>
> //El origen que calculamos en el proyecto no se toca. (Origen = origen -
> average)
>
> //Cambiamos el ImageOrientationPatient SOLAMENTE si el valor original en
> la imagen es: 1\0\0\0\1\0. En el caso que se cambia el signo, se debe
> cambiar el signo del origen
> //value.str("");
> //value << -1 << "\\" << 0 << "\\" << 0 << "\\" << 0 << "\\" << -1 << "\\"
> << 0; //PASAR ESTO POR ARGUMENTO!!!
> //itk::EncapsulateMetaData<std::string>(*dict, "0020|0037", value.str());
>
> value.str("");
> value << -235.1629 << "\\" << -195.0557 << "\\" << myArray_Z[f]; //PASAR
> ESTO POR ARGUMENTO!!! El origen - Centro
> itk::EncapsulateMetaData<std::string>(*dict, "0020|0032", value.str());
>
>
> // Slice Location: For now, we store the z component of the Image
> // Position Patient.
> value.str("");
> value << position[2];
> itk::EncapsulateMetaData<std::string>(*dict, "0020|1041", value.str());
>
> // Slice Thickness: For now, we store the z spacing
> value.str("");
> value << inputSpacing[2];
> itk::EncapsulateMetaData<std::string>(*dict, "0018|0050",
> value.str());
> // Spacing Between Slices
> itk::EncapsulateMetaData<std::string>(*dict, "0018|0088",
> value.str());
>
> // Save the dictionary
> outputArray.push_back(dict);
> }
>
>
> typedef itk::ImageFileWriter< ImageType > WriterType;
> WriterType::Pointer writer = WriterType::New();
>
> typedef itk::ImageSeriesWriter< ImageType, ImageType_Serie >
> SeriesWriterType;
> SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
> seriesWriter->SetInput(FiltroResample->GetOutput());
>
> writer->SetFileName(argv[2]);
> writer->SetInput(FiltroResample->GetOutput());
>
> itksys::SystemTools::MakeDirectory("Test"); //PASAR ESTO POR ARGUMENTO!!
> typedef itk::NumericSeriesFileNames OutputNamesGeneratorType;
> OutputNamesGeneratorType::Pointer outputNames =
> OutputNamesGeneratorType::New();
> std::string seriesFormat("Test"); //PASAR ESTO POR ARGUMENTO!!
> seriesFormat = seriesFormat + "/" + "IM%d.dcm";
> outputNames->SetSeriesFormat(seriesFormat.c_str());
> outputNames->SetStartIndex(1);
> outputNames->SetEndIndex(inputSize[2]);
>
> seriesWriter->SetImageIO(gdcmIO);
> seriesWriter->SetFileNames(outputNames->GetFileNames());
> seriesWriter->SetMetaDataDictionaryArray(&outputArray);
>
> std::cout << "Escribiendo la imagen como..." << std::endl << std::endl;
> std::cout << argv[2] << std::endl << std::endl;
>
> try
> {
> writer->Update();
> seriesWriter->Update();
> }
> catch (itk::ExceptionObject &ex)
> {
> std::cout << ex << std::endl;
> return EXIT_FAILURE;
> }
>
>
> }
> catch (itk::ExceptionObject &ex)
> {
> std::cout << ex << std::endl;
> return EXIT_FAILURE;
> }
>
> return EXIT_SUCCESS;
>
> }
>
> void CopyDictionary(itk::MetaDataDictionary &fromDict,
> itk::MetaDataDictionary &toDict)
> {
> typedef itk::MetaDataDictionary DictionaryType;
>
> DictionaryType::ConstIterator itr = fromDict.Begin();
> DictionaryType::ConstIterator end = fromDict.End();
> typedef itk::MetaDataObject< std::string > MetaDataStringType;
>
> while (itr != end)
> {
> itk::MetaDataObjectBase::Pointer  entry = itr->second;
>
> MetaDataStringType::Pointer entryvalue =
> dynamic_cast<MetaDataStringType *>(entry.GetPointer());
> if (entryvalue)
> {
> std::string tagkey = itr->first;
> std::string tagvalue = entryvalue->GetMetaDataObjectValue();
> itk::EncapsulateMetaData<std::string>(toDict, tagkey, tagvalue);
> }
> ++itr;
> }
> }
>
>
> El jue., 30 de mar. de 2017 a la(s) 11:25, Lowekamp, Bradley (NIH/NLM/LHC)
> [C] [via ITK - Users] <[hidden email]> escribi?:
>
> Hello,
>
> Writing correct DICOM continues to be a struggle with SimpleITK and ITK.
> It is generally recommended to directly use GDCM or DCMTK to write a proper
> DICOM series.
>
> SimpleITK tries to keep things, well, simple and straight forward. But ITK
> ties to do some smart things, which get in the way for certain uses with
> SimpleITK. We are trying to document and develop a nominal set of DICOM
> output operations that work in SimpleITK.
>
> Do you have working C++ code that works for your intended operation? Can
> you share a small section of code which does what you expect it C++?
>
> Thank,
> Brad
>
>
> > On Mar 30, 2017, at 8:49 AM, Matias <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=38052&i=0>> wrote:
> >
> > Hi,
> >
> > I've been dealing with ITK for years in C++ and now I would need to use
> > SimpleITK and C# as far as I can in a new proyect.
> >
> > Is the SimpleITK SeriesWriter working for Dicom Files? Last time I tried
> to
> > use it I had problems with the DicomTags, these would not copy or there
> was
> > no method to copy the tags to the resulting slices.
> >
> > Currently, I read a volume of slices, apply rotation and then I need to
> > write the resulting image as another set of slices AND keeping tag
> > information such as patient name, etc.
> >
> > Thank you,
> >
> > Matias.
> >
> >
> >
> > --
> > View this message in context:
> http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050.html
> > Sent from the ITK - Users mailing list archive at Nabble.com
> <http://nabble.com>.
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> > _______________________________________________
> > Community mailing list
> > [hidden email] <http://user/SendEmail.jtp?type=node&node=38052&i=1>
> > http://public.kitware.com/mailman/listinfo/community
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> ------------------------------
> *If you reply to this email, your message will be added to the discussion
> below:*
>
> http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38052.html
> To unsubscribe from SimpleITK Serieswriter and DicomTags, click here.
> NAML
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>
> --
> Matias
>
> ------------------------------
> View this message in context: Re: [ITK-users] [ITK] SimpleITK
> Serieswriter and DicomTags
> <http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38056.html>
>
>
> Sent from the ITK - Users mailing list archive
> <http://itk-users.7.n7.nabble.com/> at Nabble.com <http://nabble.com>.
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
> *If you reply to this email, your message will be added to the discussion
> below:*
>
> http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38063.html
> To unsubscribe from SimpleITK Serieswriter and DicomTags, click here.
> NAML
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>
> --
> Matias
>
> ------------------------------
> View this message in context: Re: [ITK-users] [ITK] SimpleITK
> Serieswriter and DicomTags
> <http://itk-users.7.n7.nabble.com/SimpleITK-Serieswriter-and-DicomTags-tp38050p38064.html>
> Sent from the ITK - Users mailing list archive
> <http://itk-users.7.n7.nabble.com/> at
>
> --
Matias




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From sidharta.gupta93 at gmail.com  Thu Apr  6 08:34:14 2017
From: sidharta.gupta93 at gmail.com (sidharta)
Date: Thu, 6 Apr 2017 05:34:14 -0700 (MST)
Subject: [ITK-users] Extract slice from ResampleFilter
Message-ID: <1491482054290-38074.post@n7.nabble.com>

Dear all, 

I am trying to extract density profile along a trajectory in CT. Using some
adjustments to contour-based segmentation and getting a mesh from the binary
mask, I computed certain trajectories tangential to certain faces/vertices
of the mesh. 

Now, I have the coordinates of the target point and a tangent to the target.
So, depending on the spacing, I extract all the points along the tangent
which are 5mm away from the target. I am using following code to generate
densities after I have got the physical coordinates along this line. 

void generateDensities(std::vector<Vector3d> points,
InternalImageType::Pointer image){

	InternalImageType::IndexType pixelIndex;
	PointType point;
	itk::ContinuousIndex<double, Dimension> pixel;	
	linearInterpolationContinuousIndexType::Pointer interpolate =
linearInterpolationContinuousIndexType::New();

	interpolate->SetInputImage(image);

	std::vector<int> HU_values;
	std::vector<double> HU_values_interpolate;
	std::vector<InternalImageType::IndexType> Pixel_indices;
	std::vector<itk::ContinuousIndex&lt;double, Dimension>>
Pixel_indices_interpolated;
	// std::cout << "Generating with interpolation" << std::endl;
	for (int i = 0; i < points.size(); i++)
	{
		Vector3d temp_point = points.at(i);
		point[0] = temp_point[0];
		point[1] = temp_point[1];
		point[2] = temp_point[2];
		// std::cout << "Getting continuous index " << std::endl;
		bool isInside = image->TransformPhysicalPointToContinuousIndex(point,
pixel);
		if (isInside)
		{
			InternalImageType::PixelType pixelValue =
interpolate->EvaluateAtContinuousIndex(pixel);
			HU_values_interpolate.push_back(pixelValue);
			Pixel_indices_interpolated.push_back(pixel);
		}
		else
			std::cout << "Point " << point << " with index " << pixel << "is outside"
<< std::endl;
	}
	All_HU_values_interpolated.push_back(HU_values_interpolate);
	All_pixel_indices_interpolated.push_back(Pixel_indices_interpolated);
	HU_values_interpolate.clear();
	HU_values.clear();
}

Now, for verification that I am actually getting in fact the correct values,
I would like to extract the oblique slice along this trajectory and I figure
I have to use the Resample filter to "transform" the CT so that rotation
puts the resampled CT coordinate system parallel to the trajectory and the
origin translated to the start of the trajectory. Now, along the trajectory,
with the set of collinear points (along the trajectory), I can get a lot of
planes (oblique slices essentially) which have the trajectory in them. So to
get around this, I figure if I give another point which is non-collinear to
these points, I can specify the exact oblique slice I want. However, this is
something I have to figure out for a lot of trajectories for the same CT and
then correspondingly for others. Can someone tell me how can I achieve this
"automatically" for all trajectories/CTs? 
PS. All CTs have the same spacing and origin. 
Kindly also mention if you think the function for generating the densities
is correct or not? Eitherways I would like to validate. 

Thank you,
Sidharta




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From francois.budin at kitware.com  Thu Apr  6 09:27:58 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Thu, 6 Apr 2017 09:27:58 -0400
Subject: [ITK-users] Patch for ApproximateSignedDistanceMapImageFilter
In-Reply-To: <CALzTN-ShzDHSdCo-AmU2G_1jaHZgRFFeJ0-MXVNOHi963gDvfg@mail.gmail.com>
References: <ffaf9bf3-b2f9-7d6f-bd94-6e0ae84d2c68@neuro.ma.uni-heidelberg.de>
 <CAHwLD2WZpHuRywU7DY8H9Xp6XMgw+OLEfrbzXKc9sC8BHvRQ0A@mail.gmail.com>
 <874f690f-ff74-bb01-6d1e-bc479abeb547@neuro.ma.uni-heidelberg.de>
 <CAHwLD2XZvEX+LgWhifVc=iZZs0ZeUBTsaChVEu4Sp_LGFftmJA@mail.gmail.com>
 <f84deabd-fd59-32b0-14b6-413822581cda@neuro.ma.uni-heidelberg.de>
 <CAHwLD2V_SJ6toyNvCOpbMiFeW-gJ0AVr2Pt9xfCvA4ydqtV6qg@mail.gmail.com>
 <c99adb7c-9b4b-847f-3bac-3f497126c437@neuro.ma.uni-heidelberg.de>
 <CALzTN-ShzDHSdCo-AmU2G_1jaHZgRFFeJ0-MXVNOHi963gDvfg@mail.gmail.com>
Message-ID: <CAHwLD2WXLwZ-S+bpxmX_D=TeaV7UX3goHqOU6vMorYcH0qbAeg@mail.gmail.com>

Thanks Christina for taking care of this problem! The patch you submitted
looks good to me. It would be perfect if you could create a test using the
images your generate to ensure that the problem does not appear again in
the future.

Francois

On Mon, Apr 3, 2017 at 3:18 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Christina,
>
> > 2nd attempt using approach 1)  (see below). What about typos in comments
> I
> > removed during bug fixing? Include into this patch as well or keep them
> > separate?
>
> Thanks! This patch has been uploaded:
>
>   http://review.source.kitware.com/#/c/22149/3
>
>
> The typos could go in a different patch (ideally), but it is OK, if
> they are included.
>
> Thanks,
> Matt
>
>
>
> > Additionally you find a small application creating an image with a bright
> > square on dark background which displays the image together with the
> result
> > of ApproximateSignedDistanceMapImageFilter. The pixel value of the
> square is
> > 1 by default but can be changed via command line.
> >
> > Regards,
> > Christina
> >
> >
> > On 29.03.2017 15:12, Francois Budin wrote:
> >
> > Hello Christina,
> >
> > I see different paths to try to solve this issue and I am not sure which
> one
> > is the best one:
> > 1) You could modify the itkIsoContourDistanceImageFilter class so that
> > m_LevelSetValue is of some real type. When looking in the implementation
> of
> > this filter,  you can see that sometimes, m_LevelSetValue is casted to a
> > real type [1], so maybe it makes sense to do that.
> > 2) Casting is one solution, but you have to be careful if you want to
> cast
> > to float or double. If you cast to float, and the input is of type
> double,
> > you will loose precision. If you always cast to double, you might use a
> lot
> > of memory. Sadly, in the itkNumericTraits, there is no way of asking for
> > "the smallest floating type that contains my current type". You can call
> > "RealType" which will be "double", or "FloatType" which will be float.
> One
> > strength of casting, is that if you perform it in place, it can actually
> not
> > do anything if it doesn't need to [2].
> > 3) To avoid casting when you don't need to (your type is float or
> double),
> > you could use the SFINAE concept like it is used here [3]. This is more
> > complex and may not be worth it.
> >
> > Beware that images may contain pixels that are not only scalar values,
> but
> > also RGB, RGBA, vectors. I am not sure if the ApproximateDistance filter
> > supports these types, but it is good to be careful, when modifying the
> code,
> > to not restrict the usage of a filter to scalar if not required. To avoid
> > that kind of issues, and to answer your original question, you can use
> the
> > Rebind structure [4].
> >
> > I hope this helps.
> > I will be out of town for a week, and most likely will have limited to no
> > access to the internet, so don't be surprised if I do not answer your
> next
> > message within the next week.
> >
> > Thanks for helping!
> > Francois
> >
> > [1]
> > https://github.com/InsightSoftwareConsortium/ITK/
> blob/master/Modules/Filtering/DistanceMap/include/
> itkIsoContourDistanceImageFilter.hxx#L314
> > [2]
> > https://github.com/InsightSoftwareConsortium/ITK/
> blob/master/Modules/Filtering/ImageFilterBase/include/
> itkCastImageFilter.hxx#L42
> > [3]
> > https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/
> ImageBase/include/itkConvertPixelBuffer.h#L153-L161
> > [4]
> > https://github.com/InsightSoftwareConsortium/ITK/
> blob/master/Modules/Filtering/Smoothing/include/
> itkSmoothingRecursiveGaussianImageFilter.h#L84-L85
> >
> > On Wed, Mar 29, 2017 at 7:10 AM, Chr. Rossmanith
> > <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>
> >> Hi Francois,
> >>
> >> I'm getting back to this issue. I'll introduce an intermediate image in
> >> the mini pipeline used in ApproximateSignedDistanceMapImageFilter
> which has
> >> a floating type for pixel values. Given
> >>
> >>   /** Type for input image. */
> >>   typedef TInputImage InputImageType;
> >>
> >> how can I define a corresponding image type FloatImageType replacing the
> >> unknown pixel type by float? I can't write itk::Image< float, xxx >
> because
> >> I don't know xxx.
> >>
> >> Is there a way to query the pixel type to avoid applying the
> >> CastImageFilter in case we already get floating valued pixels?
> >>
> >> Christina
> >>
> >>
> >>
> >> On 03.03.2017 14:58, Francois Budin wrote:
> >>
> >> Hi Christina,
> >>
> >> Maybe your idea was good but needs more work (e.g. cast the input image
> to
> >> the output type? at least if input is not a float, or maybe something
> else).
> >> I am glad you found a solution that works for you. If you need your
> software
> >> to be faster, you can also replace the SignedDanielssonDistanceMap with
> the
> >> SignedMauerDistanceMap [1].
> >>
> >> Hope this helps, and thanks for your contribution. Do not hesitate to
> >> submit a new patch to solve your original problem if you find a
> solution.
> >>
> >> Francois
> >> [1]
> >> https://itk.org/Doxygen/html/classitk_1_1SignedMaurerDistanceMapImageF
> ilter.html
> >>
> >> On Fri, Mar 3, 2017 at 8:23 AM, Chr. Rossmanith
> >> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>>
> >>> Hi Francois,
> >>>
> >>> really strange, on Wednesday changing the data type made my application
> >>> work as expected (but obviously there must have been an additional
> change
> >>> which really made the application work...). When trying to build a
> small
> >>> example for you, I failed. I still think that feeding a 0/1 image into
> >>> ApproximateSignedDistanceMapImageFilter makes sense.
> >>>
> >>> Originally I'm interested in ContourExtractor2D, which operates on a
> >>> distance map using 0 as contour level. Unlike in the
> ContourExtractor2D
> >>> example I've decided to use SignedDanielssonDistanceMap which works
> fine
> >>> without any patches.
> >>>
> >>> So send the patch to /dev/null for the moment...
> >>>
> >>> Christina
> >>>
> >>>
> >>>  On 02.03.2017 16:17, Francois Budin wrote:
> >>>
> >>> Hello Christina,
> >>>
> >>> I just reviewed you patch. You are changing the type of the variable
> >>> levelSetValue to OutputPixelType which is suppose to be a floating
> point
> >>> value.
> >>> However, the computation is done with InputPixelType variables
> >>> (m_InsideValue and m_OutsideValue) and divided by an integer.
> Additionally,
> >>> the resulting value is used in:
> >>>   m_IsoContourFilter->SetLevelSetValue(levelSetValue);
> >>>
> >>> which accepts values of InputPixelType [1] since IsoContourType is
> >>> defined as:
> >>>   typedef IsoContourDistanceImageFilter< InputImageType,
> OutputImageType
> >>> >   IsoContourType;
> >>>
> >>> I am not sure if your patch solves the problem that you mentioned. Do
> you
> >>> have a test that would verify that the new behavior corresponds to your
> >>> expectations? Based on the code review I have done, I would not expect
> the
> >>> behavior of the filter to change.
> >>>
> >>> Let me know if I missed a detail. Thank you for your contribution!
> >>> Francois
> >>>
> >>> [1]
> >>> https://itk.org/Doxygen/html/classitk_1_1IsoContourDistanceImageFilter
> .html
> >>>
> >>> On Wed, Mar 1, 2017 at 8:12 AM, Chr. Rossmanith
> >>> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>>>
> >>>> For binary images with 0 for background and 1 for objects with an
> >>>> integer input pixel type there is a problem representing the average
> of 0
> >>>> and 1 = 0.5 with the input pixel type. The output pixel type is
> required to
> >>>> be a floating pixel type (filter documentation), so it should be safe
> to
> >>>> change the type of levelSetValue to OutputPixelType.
> >>>>
> >>>> Regards,
> >>>> Christina
> >>>>
> >>>>
> >>>> _____________________________________
> >>>> Powered by www.kitware.com
> >>>>
> >>>> Visit other Kitware open-source projects at
> >>>> http://www.kitware.com/opensource/opensource.html
> >>>>
> >>>> Kitware offers ITK Training Courses, for more information visit:
> >>>> http://www.kitware.com/products/protraining.php
> >>>>
> >>>> Please keep messages on-topic and check the ITK FAQ at:
> >>>> http://www.itk.org/Wiki/ITK_FAQ
> >>>>
> >>>> Follow this link to subscribe/unsubscribe:
> >>>> http://public.kitware.com/mailman/listinfo/insight-users
> >>>>
> >>>
> >>>
> >>
> >>
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
> >
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From yxp233 at postech.ac.kr  Fri Apr  7 19:27:51 2017
From: yxp233 at postech.ac.kr (=?ks_c_5601-1987?B?WGlhb3BlbmcgWWFuZyi76r73sOa/tbD4x9Cw+ik=?=)
Date: Fri, 7 Apr 2017 23:27:51 +0000
Subject: [ITK-users] Speed Issue
Message-ID: <TY1PR04MB0895A147CFE652E8D77FAC37D40C0@TY1PR04MB0895.apcprd04.prod.outlook.com>

Hi,

I found that ITK (such as fast-marching level-set, threshold-based level-set, and region growing) does not use all CPU cores during computation. 

My questions include:
1. Does ITK support full CPU cores computation?
2. Did anyone try to speed up ITK? If so, What is the best and fast way to speed up ITK? And how much faster than before can I achieve?

I appreciate any help in advance. Thank you.

Best regards,
Xiaopeng

From syed.nauman at ge.com  Fri Apr  7 17:29:58 2017
From: syed.nauman at ge.com (Nauman, Syed (GE Healthcare, consultant))
Date: Fri, 7 Apr 2017 21:29:58 +0000
Subject: [ITK-users] Private Tags with itk 4.7 and gdcm
Message-ID: <3890D9E960F85D4FA055392AAA00D285C36A5B@ALPURAPA25.e2k.ad.ge.com>

Hello,
I read some posts about private tags not working properly but couldn't find a way to load private tags.

I'm using DicomSeriesReadPrintTags_8cxx

And I used
dicomIO->LoadPrivateTagsOn()

and
nameGenerator->SetLoadPrivateTags ( true );

But I get values for all private tags as

(0043|10a8)  = MlwtNVwyNSA=

I can view using any tool to see  the value as
(0043|10b2) Private tag data                   LO: ['9548', '162.6', '338.391', '-2.870712']

I wonder shall I need to add this tag in dictionary as well?
I tried playing around with the gdcm dictionary like;
const gdcm::Global &g = gdcm::Global::GetInstance();
const gdcm::Dicts &dicts = g.GetDicts();
const gdcm::Dict & pubdict=dicts.GetPublicDict();

but it doesn't provide any example or any source about how to use private dictionaries or add any tag values in that?
Can some one please help here with some source code about how to resolve this issue with itk 4.7 and gdcm 2.2

Thanks,






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From dzenanz at gmail.com  Fri Apr  7 21:43:09 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 7 Apr 2017 21:43:09 -0400
Subject: [ITK-users] Private Tags with itk 4.7 and gdcm
In-Reply-To: <3890D9E960F85D4FA055392AAA00D285C36A5B@ALPURAPA25.e2k.ad.ge.com>
References: <3890D9E960F85D4FA055392AAA00D285C36A5B@ALPURAPA25.e2k.ad.ge.com>
Message-ID: <CAPf2UMTVfHm4bB0q5C3+EMxZp4YEL7-6X8QyYPUr7=2VL8751Q@mail.gmail.com>

Hi Syed,

I think that you need to do base64-decoding. E.g. MlwtNVwyNSA= yields
2\-5\25

Regards,
D?enan

On Fri, Apr 7, 2017 at 5:29 PM, Nauman, Syed (GE Healthcare, consultant) <
syed.nauman at ge.com> wrote:

> Hello,
>
> I read some posts about private tags not working properly but couldn?t
> find a way to load private tags.
>
>
>
> I?m using DicomSeriesReadPrintTags_8cxx
>
>
>
> And I used
>
> dicomIO->LoadPrivateTagsOn()
>
>
>
> and
>
> nameGenerator->SetLoadPrivateTags ( true );
>
>
>
> But I get values for all private tags as
>
>
>
> (0043|10a8)  = MlwtNVwyNSA=
>
>
>
> I can view using any tool to see  the value as
>
> (0043|10b2) Private tag data                   LO: ['9548', '162.6',
> '338.391', '-2.870712']
>
>
>
> I wonder shall I need to add this tag in dictionary as well?
>
> I tried playing around with the gdcm dictionary like;
>
> const gdcm::Global &g = gdcm::Global::GetInstance();
>
> const gdcm::Dicts &dicts = g.GetDicts();
>
> const gdcm::Dict & pubdict=dicts.GetPublicDict();
>
>
>
> but it doesn?t provide any example or any source about how to use private
> dictionaries or add any tag values in that?
>
> Can some one please help here with some source code about how to resolve
> this issue with itk 4.7 and gdcm 2.2
>
>
>
> Thanks,
>
>
>
>
>
>
>
>
>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From matimontg at gmail.com  Sat Apr  8 11:33:10 2017
From: matimontg at gmail.com (Matias)
Date: Sat, 8 Apr 2017 08:33:10 -0700 (MST)
Subject: [ITK-users] Correct this stereotactic error in a Volume
Message-ID: <1491665590917-38079.post@n7.nabble.com>

Hi,I'm dealing with an image which was captured somewhat incorrectly and I'm
trying to solve or correct the stereotactic frame snake figure so that it
gets as a line.Here's the Volume I'm trying to rectify: Look at the "snake"
figure in the stereotactic oblique stick.
<http://itk-users.7.n7.nabble.com/file/n38079/screenshot.jpg> Is there any
method in ITK to solve this? we did apply a resample (every 1mm) but did not
work. We also rotated the volume using Euler3D and some precalculated angles
(Gamma, Beta,Alfa) and still remained the same.I think is a matter of
rotating every 10 slides or so which is where we see the stereotactic frame
movement in the slides but not sure how to perform this. We thought of
rotating each slide but that doesn't work since it has to rotate the volume.



--
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From dzenanz at gmail.com  Sat Apr  8 16:51:00 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 8 Apr 2017 16:51:00 -0400
Subject: [ITK-users] Extract slice from ResampleFilter
In-Reply-To: <1491482054290-38074.post@n7.nabble.com>
References: <1491482054290-38074.post@n7.nabble.com>
Message-ID: <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>

Hi Sidharta,

your function to calculate interpolated Hounsfield values seems correct.

Your problem of selecting oblique slice to resample can be reduced to
finding a plane which passed through your first and last point, and as an
arbitrary constraint passes through point [0,0,0]. If this point is
collinear with your line then pick point [1,0,0], [0,1,0] or [0,0,1]. One
of them will not be collinear.

In order to resample your oblique slice, you need to figure out a transform
matrix which transforms your first point to coordinates [0,0,0], your last
point to coordinates e.g. [1000,0,0] and transforms the normal of your
plane to be parallel with vector [0,0,1].

Then use resample filter, set your transform matrix and set as target
image's region index [0,0,0] and size [1001,1,1]. Alternatively index
[0,-10,0] and size [1001,21,1] if you want to have a real 2D slice to look
at.

Hope this helps,
D?enan

On Thu, Apr 6, 2017 at 8:34 AM, sidharta <sidharta.gupta93 at gmail.com> wrote:

> Dear all,
>
> I am trying to extract density profile along a trajectory in CT. Using some
> adjustments to contour-based segmentation and getting a mesh from the
> binary
> mask, I computed certain trajectories tangential to certain faces/vertices
> of the mesh.
>
> Now, I have the coordinates of the target point and a tangent to the
> target.
> So, depending on the spacing, I extract all the points along the tangent
> which are 5mm away from the target. I am using following code to generate
> densities after I have got the physical coordinates along this line.
>
> void generateDensities(std::vector<Vector3d> points,
> InternalImageType::Pointer image){
>
>         InternalImageType::IndexType pixelIndex;
>         PointType point;
>         itk::ContinuousIndex<double, Dimension> pixel;
>         linearInterpolationContinuousIndexType::Pointer interpolate =
> linearInterpolationContinuousIndexType::New();
>
>         interpolate->SetInputImage(image);
>
>         std::vector<int> HU_values;
>         std::vector<double> HU_values_interpolate;
>         std::vector<InternalImageType::IndexType> Pixel_indices;
>         std::vector<itk::ContinuousIndex&lt;double, Dimension>>
> Pixel_indices_interpolated;
>         // std::cout << "Generating with interpolation" << std::endl;
>         for (int i = 0; i < points.size(); i++)
>         {
>                 Vector3d temp_point = points.at(i);
>                 point[0] = temp_point[0];
>                 point[1] = temp_point[1];
>                 point[2] = temp_point[2];
>                 // std::cout << "Getting continuous index " << std::endl;
>                 bool isInside = image->TransformPhysicalPointToContin
> uousIndex(point,
> pixel);
>                 if (isInside)
>                 {
>                         InternalImageType::PixelType pixelValue =
> interpolate->EvaluateAtContinuousIndex(pixel);
>                         HU_values_interpolate.push_back(pixelValue);
>                         Pixel_indices_interpolated.push_back(pixel);
>                 }
>                 else
>                         std::cout << "Point " << point << " with index "
> << pixel << "is outside"
> << std::endl;
>         }
>         All_HU_values_interpolated.push_back(HU_values_interpolate);
>         All_pixel_indices_interpolated.push_back(Pixel_
> indices_interpolated);
>         HU_values_interpolate.clear();
>         HU_values.clear();
> }
>
> Now, for verification that I am actually getting in fact the correct
> values,
> I would like to extract the oblique slice along this trajectory and I
> figure
> I have to use the Resample filter to "transform" the CT so that rotation
> puts the resampled CT coordinate system parallel to the trajectory and the
> origin translated to the start of the trajectory. Now, along the
> trajectory,
> with the set of collinear points (along the trajectory), I can get a lot of
> planes (oblique slices essentially) which have the trajectory in them. So
> to
> get around this, I figure if I give another point which is non-collinear to
> these points, I can specify the exact oblique slice I want. However, this
> is
> something I have to figure out for a lot of trajectories for the same CT
> and
> then correspondingly for others. Can someone tell me how can I achieve this
> "automatically" for all trajectories/CTs?
> PS. All CTs have the same spacing and origin.
> Kindly also mention if you think the function for generating the densities
> is correct or not? Eitherways I would like to validate.
>
> Thank you,
> Sidharta
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From matimontg at gmail.com  Sat Apr  8 18:08:22 2017
From: matimontg at gmail.com (Matias)
Date: Sat, 8 Apr 2017 15:08:22 -0700 (MST)
Subject: [ITK-users] Rotating image results in last slices being half empty
Message-ID: <1491689302258-38081.post@n7.nabble.com>

Hi,I'm rotating a volume (Using the Euler3DTransform) and the final set of
slices are half black or empty.here's an example when rotating a volume of
10 slices:Am I missing something such as changing the origin or maybe
computing the center incorrectly? (The center is passed as parameter from
another program) <http://itk-users.7.n7.nabble.com/file/n38081/capture.jpg>
And here's the code I'm using:	typedef itk::ResampleImageFilter<ImageType,
ImageType> FilterType;		FilterType::Pointer FiltroResample =
FilterType::New();		FiltroResample->SetInput(reader->GetOutput());		typedef
itk::LinearInterpolateImageFunction<ImageType, double > InterpolatorType;	
InterpolatorType::Pointer interpolator = InterpolatorType::New();	
FiltroResample->SetInterpolator(interpolator);	
FiltroResample->SetOutputDirection(inputImage->GetDirection());	
FiltroResample->SetOutputOrigin(inputImage->GetOrigin());	
ImageType::SizeType inputSize =
inputImage->GetLargestPossibleRegion().GetSize();	
FiltroResample->SetSize(inputSize);		const ImageType::SpacingType&
inputSpacing = inputImage->GetSpacing();	
FiltroResample->SetOutputSpacing(inputSpacing);	
FiltroResample->SetDefaultPixelValue(-1000);		typedef itk::Euler3DTransform<
double > TransformType; //Transform		TransformType::Pointer transform =
TransformType::New();		double alfa, beta, gamma, centro_rotacion_X,
centro_rotacion_Y, centro_rotacion_Z, origenX,origenY;		gamma =
atof(argv[2]);		beta = atof(argv[3]);		alfa = atof(argv[4]);	
centro_rotacion_X = atof(argv[5]);		centro_rotacion_Y = atof(argv[6]);	
centro_rotacion_Z = atof(argv[7]);		origenX = atof(argv[8]);		origenY =
atof(argv[9]);		transform->SetRotation(gamma, beta, alfa);		double centro[3]
= { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z };	
transform->SetCenter(centro);               
FiltroResample->SetTransform(transform);         	FiltroResample->Update();



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From bakkari.abdelkhalek at hotmail.fr  Sun Apr  9 16:00:06 2017
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sun, 9 Apr 2017 20:00:06 +0000
Subject: [ITK-users] Maximum distance between points - Point Set -
Message-ID: <AM2PR09MB05629FDD72A2BD20B8B26BE8830E0@AM2PR09MB0562.eurprd09.prod.outlook.com>

Dear insight-users,


I would like to ask, if I could specify the Maximum distance between points after extracting the points using BinaryMaskToNarrowBandPointSetFilter.


Thank you in advance.


Kind regards,


Abdelkhalek Bakkari
Ph.D candidate in Computer Science
Institute of Applied Computer Science
Lodz University of Technology, Poland


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From matt.mccormick at kitware.com  Sun Apr  9 18:19:37 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 9 Apr 2017 18:19:37 -0400
Subject: [ITK-users] Speed Issue
In-Reply-To: <TY1PR04MB0895A147CFE652E8D77FAC37D40C0@TY1PR04MB0895.apcprd04.prod.outlook.com>
References: <TY1PR04MB0895A147CFE652E8D77FAC37D40C0@TY1PR04MB0895.apcprd04.prod.outlook.com>
Message-ID: <CALzTN-T49Qc=PPutK7fUYJUCFxDLvo0c3LFESw5d0ZqtdoLu=w@mail.gmail.com>

Hi Xiaopeng,

> I found that ITK (such as fast-marching level-set, threshold-based level-set, and region growing) does not use all CPU cores during computation.
>
> My questions include:
> 1. Does ITK support full CPU cores computation?

In general, most algorithm implementations are multi-threaded and
intended to use all CPU cores. There may be some implementations that
should be multi-threaded or there may be some implementations that
could be improved in their thread utilization.


> 2. Did anyone try to speed up ITK? If so, What is the best and fast way to speed up ITK? And how much faster than before can I achieve?

There are ongoing efforts to improve performance - your participation
is welcome.  See:

  http://public.kitware.com/pipermail/insight-developers/2017-April/025151.html


Thanks,
Matt

From sidharta.gupta93 at gmail.com  Mon Apr 10 05:29:55 2017
From: sidharta.gupta93 at gmail.com (sidharta)
Date: Mon, 10 Apr 2017 02:29:55 -0700 (MST)
Subject: [ITK-users] Extract slice from ResampleFilter
In-Reply-To: <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
Message-ID: <1491816595489-38084.post@n7.nabble.com>

Dear D?enan,

Thank you for your reply. Actually, I found a third point which gives me the
exact (informative) slice I am looking for. Should I resample the image
twice, first rotate the image to the direction of the trajectory and move
the origin to the start of the trajectory and second rotate the image to the
angle between the trajectory and the third point? I will try what you said
and get back to you. I am asking because I don't think resampling twice
makes sense. 

Thank you for your time.
Sidharta



--
View this message in context: http://itk-users.7.n7.nabble.com/Extract-slice-from-ResampleFilter-tp38074p38084.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Mon Apr 10 08:36:47 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 10 Apr 2017 12:36:47 +0000
Subject: [ITK-users] Speed Issue
In-Reply-To: <TY1PR04MB0895A147CFE652E8D77FAC37D40C0@TY1PR04MB0895.apcprd04.prod.outlook.com>
References: <TY1PR04MB0895A147CFE652E8D77FAC37D40C0@TY1PR04MB0895.apcprd04.prod.outlook.com>
Message-ID: <65848276-41CC-46D4-BAF3-F529A51C1FC9@mail.nih.gov>

Hello,

Regarding single threaded region growing, the nature of regions growing with a breadth first algorithm is inherently single threaded. However, the equivalent results can be obtained by doing a global threshold, followed by connect components analysis. Both of those algorithms are efficiently multi-threaded. Depending on the size of the image, shape of region, and other factors, one approach may be more efficient than the other.

HTH,
Brad


> On Apr 7, 2017, at 7:27 PM, Xiaopeng Yang(???????) <yxp233 at postech.ac.kr> wrote:
> 
> Hi,
> 
> I found that ITK (such as fast-marching level-set, threshold-based level-set, and region growing) does not use all CPU cores during computation. 
> 
> My questions include:
> 1. Does ITK support full CPU cores computation?
> 2. Did anyone try to speed up ITK? If so, What is the best and fast way to speed up ITK? And how much faster than before can I achieve?
> 
> I appreciate any help in advance. Thank you.
> 
> Best regards,
> Xiaopeng
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From dzenanz at gmail.com  Mon Apr 10 09:24:50 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 10 Apr 2017 09:24:50 -0400
Subject: [ITK-users] [ITK]  Extract slice from ResampleFilter
In-Reply-To: <1491816595489-38084.post@n7.nabble.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
Message-ID: <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>

?Hi Sidharta,

you definitely should not resample twice. All you need is to compound the
two transforms (multiply their matrices)?. And apply a single resampling.
But for debugging purposes, you could also display the resampled output
after only the first transform.

Regards,
D?enan

On Mon, Apr 10, 2017 at 5:29 AM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> Dear D?enan,
>
> Thank you for your reply. Actually, I found a third point which gives me
> the
> exact (informative) slice I am looking for. Should I resample the image
> twice, first rotate the image to the direction of the trajectory and move
> the origin to the start of the trajectory and second rotate the image to
> the
> angle between the trajectory and the third point? I will try what you said
> and get back to you. I am asking because I don't think resampling twice
> makes sense.
>
> Thank you for your time.
> Sidharta
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074p38084.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
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From zilu at libero.it  Mon Apr 10 14:19:33 2017
From: zilu at libero.it (zilu)
Date: Mon, 10 Apr 2017 11:19:33 -0700 (MST)
Subject: [ITK-users] beautiful stuff
Message-ID: <1916655864.20170410211908@libero.it>

Yo! 

Look at  that  beautiful stuff, isn't  it amazing?  Take  a look here http://vossignoria.net/enemy.php?4547

Take care, Valentina Scubla





--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/beautiful-stuff-tp7589797.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From aharr8 at uwo.ca  Tue Apr 11 08:36:13 2017
From: aharr8 at uwo.ca (Andrew Harris)
Date: Tue, 11 Apr 2017 08:36:13 -0400
Subject: [ITK-users] [ITK] Normalized Cross Correlation returns perfect
 alignment with images not even overlapping
In-Reply-To: <CAPf2UMToH7Qxg3s-gpfJKK=QgL-6dJj7xHdZU4-=dfzQAe1dQw@mail.gmail.com>
References: <CAJ0LxQKHaRJCUodREJg0wDTrZExKhfjx259NiVkzQ+mE=av_+w@mail.gmail.com>
 <CAPf2UMToH7Qxg3s-gpfJKK=QgL-6dJj7xHdZU4-=dfzQAe1dQw@mail.gmail.com>
Message-ID: <CAJ0LxQK9qh7XX0+sryhoigJB4kPNUrC9kj_osi4h3zm_SRRkQQ@mail.gmail.com>

In the image mask, the parts we want to include in the calculation are
bright and the parts that we want to exclude are dark, is that the opposite
of what it should be?

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Thu, Mar 30, 2017 at 7:25 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Andrew,
>
> your masks might be inverted. If NCC gets all black pixels in both images,
> the correlation will be perfect.
>
> Regards,
> D?enan
>
> On Thu, Mar 30, 2017 at 2:13 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
>> Hi, I'm hoping someone can guide me toward an explanation of this.  I run
>> my pipeline on various ultrasound image sets and get an NCC between 0.65
>> and 0.8 for good alignments, but on some sets the NCC returns 1.0 when the
>> images aren't even overlapping.  I have the black areas of the image masked
>> out, and have even tried cranking up the threshold to be sure the darker
>> areas aren't being included to no avail.  Any thoughts?
>>
>> --
>>
>> AH
>>
>>
>> ------------------------------------------------------------
>> -----------------------------------
>>
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From francois.budin at kitware.com  Tue Apr 11 09:00:16 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Tue, 11 Apr 2017 09:00:16 -0400
Subject: [ITK-users] [ITK] Normalized Cross Correlation returns perfect
 alignment with images not even overlapping
In-Reply-To: <CAJ0LxQK9qh7XX0+sryhoigJB4kPNUrC9kj_osi4h3zm_SRRkQQ@mail.gmail.com>
References: <CAJ0LxQKHaRJCUodREJg0wDTrZExKhfjx259NiVkzQ+mE=av_+w@mail.gmail.com>
 <CAPf2UMToH7Qxg3s-gpfJKK=QgL-6dJj7xHdZU4-=dfzQAe1dQw@mail.gmail.com>
 <CAJ0LxQK9qh7XX0+sryhoigJB4kPNUrC9kj_osi4h3zm_SRRkQQ@mail.gmail.com>
Message-ID: <CAHwLD2WD2wYE4GWX-sxFt8UippfJ6A4OEUz5P+r1NgJEOA1mNw@mail.gmail.com>

Hello Andrew,

Did you try to initialize the registration with [1] for example?
If the images do not overlap at all at the beginning of the registration,
the algorithm might only do what D?enan said, match black pixels.
Initializing the transform should help.

Hope this helps,
Francois

[1]
https://itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.html

On Tue, Apr 11, 2017 at 8:36 AM, Andrew Harris <aharr8 at uwo.ca> wrote:

> In the image mask, the parts we want to include in the calculation are
> bright and the parts that we want to exclude are dark, is that the opposite
> of what it should be?
>
> --
>
> AH
>
>
> ------------------------------------------------------------
> -----------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Thu, Mar 30, 2017 at 7:25 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Andrew,
>>
>> your masks might be inverted. If NCC gets all black pixels in both
>> images, the correlation will be perfect.
>>
>> Regards,
>> D?enan
>>
>> On Thu, Mar 30, 2017 at 2:13 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>
>>> Hi, I'm hoping someone can guide me toward an explanation of this.  I
>>> run my pipeline on various ultrasound image sets and get an NCC between
>>> 0.65 and 0.8 for good alignments, but on some sets the NCC returns 1.0 when
>>> the images aren't even overlapping.  I have the black areas of the image
>>> masked out, and have even tried cranking up the threshold to be sure the
>>> darker areas aren't being included to no avail.  Any thoughts?
>>>
>>> --
>>>
>>> AH
>>>
>>>
>>> ------------------------------------------------------------
>>> -----------------------------------
>>>
>>> *This email and any attachments thereto may contain private,
>>> confidential, and privileged materials for the sole use of the intended
>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>> attachments thereto) by other than the intended recipient is strictly
>>> prohibited. If you are not the intended recipient, please contact the
>>> sender immediately and permanently destroy this email and any attachments
>>> thereto.*
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From matt.mccormick at kitware.com  Tue Apr 11 10:29:23 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 11 Apr 2017 10:29:23 -0400
Subject: [ITK-users] beautiful stuff
In-Reply-To: <1916655864.20170410211908@libero.it>
References: <1916655864.20170410211908@libero.it>
Message-ID: <CALzTN-S0Aujtpg_PA+uG6x4MNqFQPLHgwMoEUp+Va7vL6SXE3g@mail.gmail.com>

This message has been identified as spam and the account suspended.

On Mon, Apr 10, 2017 at 2:19 PM, zilu via Insight-users
<insight-users at itk.org> wrote:
> Yo!
>
> Look at  that  beautiful stuff, isn't  it amazing?  Take  a look here http://vossignoria.net/enemy.php?4547
>
> Take care, Valentina Scubla
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/beautiful-stuff-tp7589797.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From sidharta.gupta93 at gmail.com  Tue Apr 11 12:00:13 2017
From: sidharta.gupta93 at gmail.com (sidharta)
Date: Tue, 11 Apr 2017 09:00:13 -0700 (MST)
Subject: [ITK-users] [ITK]  Extract slice from ResampleFilter
In-Reply-To: <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
Message-ID: <1491926413097-38091.post@n7.nabble.com>

Hey D?enan,

So, I kind of got the equation of the plane and the normal to the plane
where all the three non-collinear points lie. Then, I got the angle between
this normal and the z-axis of the image. I resample the image by rotating in
3D about the z-axis. How do I extract the exact slice from the resampled
image? Is it actually required to resample the 3D Dicom, can I not resample
a 2D image (just for optimization purposes)? I read the documentation
(ITKSoftwareGuide) which shows one example for 3D resampling, however not
how to save a particular slice. Kindly correct me if I am wrong. 


Thank you for your time.
Best Regards,
Sidharta



--
View this message in context: http://itk-users.7.n7.nabble.com/Extract-slice-from-ResampleFilter-tp38074p38091.html
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From aharr8 at uwo.ca  Tue Apr 11 14:02:49 2017
From: aharr8 at uwo.ca (Andrew Harris)
Date: Tue, 11 Apr 2017 14:02:49 -0400
Subject: [ITK-users] [ITK] Normalized Cross Correlation returns perfect
 alignment with images not even overlapping
In-Reply-To: <CAHwLD2WD2wYE4GWX-sxFt8UippfJ6A4OEUz5P+r1NgJEOA1mNw@mail.gmail.com>
References: <CAJ0LxQKHaRJCUodREJg0wDTrZExKhfjx259NiVkzQ+mE=av_+w@mail.gmail.com>
 <CAPf2UMToH7Qxg3s-gpfJKK=QgL-6dJj7xHdZU4-=dfzQAe1dQw@mail.gmail.com>
 <CAJ0LxQK9qh7XX0+sryhoigJB4kPNUrC9kj_osi4h3zm_SRRkQQ@mail.gmail.com>
 <CAHwLD2WD2wYE4GWX-sxFt8UippfJ6A4OEUz5P+r1NgJEOA1mNw@mail.gmail.com>
Message-ID: <CAJ0LxQK+-LYPCjpJQ0pGKL5XNV8HXu1wXbfUHx1RusgBgOw11Q@mail.gmail.com>

Hello Francois and D?enan,

Because of the way the images were captured, there is a known common point
of overlap, so we set the centre to that point in the expectation that the
transform would rotate and translate about that point when the registration
is run.  Have I misunderstood the design or is that what should be
happening?

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*

On Tue, Apr 11, 2017 at 9:00 AM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Andrew,
>
> Did you try to initialize the registration with [1] for example?
> If the images do not overlap at all at the beginning of the registration,
> the algorithm might only do what D?enan said, match black pixels.
> Initializing the transform should help.
>
> Hope this helps,
> Francois
>
> [1] https://itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.
> html
>
> On Tue, Apr 11, 2017 at 8:36 AM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
>> In the image mask, the parts we want to include in the calculation are
>> bright and the parts that we want to exclude are dark, is that the opposite
>> of what it should be?
>>
>> --
>>
>> AH
>>
>>
>> ------------------------------------------------------------
>> -----------------------------------
>>
>> *This email and any attachments thereto may contain private,
>> confidential, and privileged materials for the sole use of the intended
>> recipient. Any reviewing, copying, or distribution of this email (or any
>> attachments thereto) by other than the intended recipient is strictly
>> prohibited. If you are not the intended recipient, please contact the
>> sender immediately and permanently destroy this email and any attachments
>> thereto.*
>>
>> On Thu, Mar 30, 2017 at 7:25 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>>> Hi Andrew,
>>>
>>> your masks might be inverted. If NCC gets all black pixels in both
>>> images, the correlation will be perfect.
>>>
>>> Regards,
>>> D?enan
>>>
>>> On Thu, Mar 30, 2017 at 2:13 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>
>>>> Hi, I'm hoping someone can guide me toward an explanation of this.  I
>>>> run my pipeline on various ultrasound image sets and get an NCC between
>>>> 0.65 and 0.8 for good alignments, but on some sets the NCC returns 1.0 when
>>>> the images aren't even overlapping.  I have the black areas of the image
>>>> masked out, and have even tried cranking up the threshold to be sure the
>>>> darker areas aren't being included to no avail.  Any thoughts?
>>>>
>>>> --
>>>>
>>>> AH
>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> -----------------------------------
>>>>
>>>> *This email and any attachments thereto may contain private,
>>>> confidential, and privileged materials for the sole use of the intended
>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>> attachments thereto) by other than the intended recipient is strictly
>>>> prohibited. If you are not the intended recipient, please contact the
>>>> sender immediately and permanently destroy this email and any attachments
>>>> thereto.*
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From dzenanz at gmail.com  Tue Apr 11 14:03:19 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 11 Apr 2017 14:03:19 -0400
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <1491926413097-38091.post@n7.nabble.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
Message-ID: <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>

Hi Sidartha,

you can use extract filter
<https://itk.org/Doxygen/html/classitk_1_1ExtractImageFilter.html> to
extract a single slice from a 3D image. Take a look at the examples liked
from the documentation page.

Regards,
D?enan

On Tue, Apr 11, 2017 at 12:00 PM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> Hey D?enan,
>
> So, I kind of got the equation of the plane and the normal to the plane
> where all the three non-collinear points lie. Then, I got the angle between
> this normal and the z-axis of the image. I resample the image by rotating
> in
> 3D about the z-axis. How do I extract the exact slice from the resampled
> image? Is it actually required to resample the 3D Dicom, can I not resample
> a 2D image (just for optimization purposes)? I read the documentation
> (ITKSoftwareGuide) which shows one example for 3D resampling, however not
> how to save a particular slice. Kindly correct me if I am wrong.
>
>
> Thank you for your time.
> Best Regards,
> Sidharta
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074p38091.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From dzenanz at gmail.com  Tue Apr 11 14:07:26 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 11 Apr 2017 14:07:26 -0400
Subject: [ITK-users] [ITK] Normalized Cross Correlation returns perfect
 alignment with images not even overlapping
In-Reply-To: <CAJ0LxQK+-LYPCjpJQ0pGKL5XNV8HXu1wXbfUHx1RusgBgOw11Q@mail.gmail.com>
References: <CAJ0LxQKHaRJCUodREJg0wDTrZExKhfjx259NiVkzQ+mE=av_+w@mail.gmail.com>
 <CAPf2UMToH7Qxg3s-gpfJKK=QgL-6dJj7xHdZU4-=dfzQAe1dQw@mail.gmail.com>
 <CAJ0LxQK9qh7XX0+sryhoigJB4kPNUrC9kj_osi4h3zm_SRRkQQ@mail.gmail.com>
 <CAHwLD2WD2wYE4GWX-sxFt8UippfJ6A4OEUz5P+r1NgJEOA1mNw@mail.gmail.com>
 <CAJ0LxQK+-LYPCjpJQ0pGKL5XNV8HXu1wXbfUHx1RusgBgOw11Q@mail.gmail.com>
Message-ID: <CAPf2UMTxtuKXA1zAiFZixUakT9eNNHLL1U+F=8-Mx9Tz9Q5DUg@mail.gmail.com>

Hi Andrew,

it is good to use such additional constraints when possible. But you also
have to initialize the transform somehow, otherwise it might get
auto-initialized to all modifiable parameters being equal to zero. That is
usually a bad initial transform - hence Francois' suggestion.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Tue, Apr 11, 2017 at 2:02 PM, Andrew Harris <aharr8 at uwo.ca> wrote:

> Hello Francois and D?enan,
>
> Because of the way the images were captured, there is a known common point
> of overlap, so we set the centre to that point in the expectation that the
> transform would rotate and translate about that point when the registration
> is run.  Have I misunderstood the design or is that what should be
> happening?
>
> --
>
> AH
>
>
> ------------------------------------------------------------
> -----------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Tue, Apr 11, 2017 at 9:00 AM, Francois Budin <
> francois.budin at kitware.com> wrote:
>
>> Hello Andrew,
>>
>> Did you try to initialize the registration with [1] for example?
>> If the images do not overlap at all at the beginning of the registration,
>> the algorithm might only do what D?enan said, match black pixels.
>> Initializing the transform should help.
>>
>> Hope this helps,
>> Francois
>>
>> [1] https://itk.org/Doxygen/html/classitk_1_1CenteredTransformIn
>> itializer.html
>>
>> On Tue, Apr 11, 2017 at 8:36 AM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>
>>> In the image mask, the parts we want to include in the calculation are
>>> bright and the parts that we want to exclude are dark, is that the opposite
>>> of what it should be?
>>>
>>> --
>>>
>>> AH
>>>
>>>
>>> ------------------------------------------------------------
>>> -----------------------------------
>>>
>>> *This email and any attachments thereto may contain private,
>>> confidential, and privileged materials for the sole use of the intended
>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>> attachments thereto) by other than the intended recipient is strictly
>>> prohibited. If you are not the intended recipient, please contact the
>>> sender immediately and permanently destroy this email and any attachments
>>> thereto.*
>>>
>>> On Thu, Mar 30, 2017 at 7:25 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>>
>>>> Hi Andrew,
>>>>
>>>> your masks might be inverted. If NCC gets all black pixels in both
>>>> images, the correlation will be perfect.
>>>>
>>>> Regards,
>>>> D?enan
>>>>
>>>> On Thu, Mar 30, 2017 at 2:13 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>>>>
>>>>> Hi, I'm hoping someone can guide me toward an explanation of this.  I
>>>>> run my pipeline on various ultrasound image sets and get an NCC between
>>>>> 0.65 and 0.8 for good alignments, but on some sets the NCC returns 1.0 when
>>>>> the images aren't even overlapping.  I have the black areas of the image
>>>>> masked out, and have even tried cranking up the threshold to be sure the
>>>>> darker areas aren't being included to no avail.  Any thoughts?
>>>>>
>>>>> --
>>>>>
>>>>> AH
>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> -----------------------------------
>>>>>
>>>>> *This email and any attachments thereto may contain private,
>>>>> confidential, and privileged materials for the sole use of the intended
>>>>> recipient. Any reviewing, copying, or distribution of this email (or any
>>>>> attachments thereto) by other than the intended recipient is strictly
>>>>> prohibited. If you are not the intended recipient, please contact the
>>>>> sender immediately and permanently destroy this email and any attachments
>>>>> thereto.*
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>
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From francois.budin at kitware.com  Tue Apr 11 14:14:01 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Tue, 11 Apr 2017 18:14:01 +0000
Subject: [ITK-users] [ITK] Normalized Cross Correlation returns perfect
 alignment with images not even overlapping
In-Reply-To: <CAPf2UMTxtuKXA1zAiFZixUakT9eNNHLL1U+F=8-Mx9Tz9Q5DUg@mail.gmail.com>
References: <CAJ0LxQKHaRJCUodREJg0wDTrZExKhfjx259NiVkzQ+mE=av_+w@mail.gmail.com>
 <CAPf2UMToH7Qxg3s-gpfJKK=QgL-6dJj7xHdZU4-=dfzQAe1dQw@mail.gmail.com>
 <CAJ0LxQK9qh7XX0+sryhoigJB4kPNUrC9kj_osi4h3zm_SRRkQQ@mail.gmail.com>
 <CAHwLD2WD2wYE4GWX-sxFt8UippfJ6A4OEUz5P+r1NgJEOA1mNw@mail.gmail.com>
 <CAJ0LxQK+-LYPCjpJQ0pGKL5XNV8HXu1wXbfUHx1RusgBgOw11Q@mail.gmail.com>
 <CAPf2UMTxtuKXA1zAiFZixUakT9eNNHLL1U+F=8-Mx9Tz9Q5DUg@mail.gmail.com>
Message-ID: <CAHwLD2Ws03nyKGp3vaCT9TmTePWeSOOwR3vu=sbFrwExabEHuQ@mail.gmail.com>

Hello Andrew,

Another thing you can look at is if your transform parameters ratios are
set to reasonable values. You typically have a ratio you can set between
rotation, translation, scaling. If these are not set to appropriate values,
the final transform could be wrong.
In your case, it sounds like you are already performing the translation as
an initialization. Maybe you can modify your parameters so that it performs
mostly a rotation.

Hope this helps,
Fran?ois

On Tue, Apr 11, 2017, 14:07 D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Andrew,
>
> it is good to use such additional constraints when possible. But you also
> have to initialize the transform somehow, otherwise it might get
> auto-initialized to all modifiable parameters being equal to zero. That is
> usually a bad initial transform - hence Francois' suggestion.
>
> Regards,
> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Tue, Apr 11, 2017 at 2:02 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
> Hello Francois and D?enan,
>
> Because of the way the images were captured, there is a known common point
> of overlap, so we set the centre to that point in the expectation that the
> transform would rotate and translate about that point when the registration
> is run.  Have I misunderstood the design or is that what should be
> happening?
>
> --
>
> AH
>
>
>
> -----------------------------------------------------------------------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Tue, Apr 11, 2017 at 9:00 AM, Francois Budin <
> francois.budin at kitware.com> wrote:
>
> Hello Andrew,
>
> Did you try to initialize the registration with [1] for example?
> If the images do not overlap at all at the beginning of the registration,
> the algorithm might only do what D?enan said, match black pixels.
> Initializing the transform should help.
>
> Hope this helps,
> Francois
>
> [1]
> https://itk.org/Doxygen/html/classitk_1_1CenteredTransformInitializer.html
>
> On Tue, Apr 11, 2017 at 8:36 AM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
> In the image mask, the parts we want to include in the calculation are
> bright and the parts that we want to exclude are dark, is that the opposite
> of what it should be?
>
> --
>
> AH
>
>
>
> -----------------------------------------------------------------------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> On Thu, Mar 30, 2017 at 7:25 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
> Hi Andrew,
>
> your masks might be inverted. If NCC gets all black pixels in both images,
> the correlation will be perfect.
>
> Regards,
> D?enan
>
> On Thu, Mar 30, 2017 at 2:13 PM, Andrew Harris <aharr8 at uwo.ca> wrote:
>
> Hi, I'm hoping someone can guide me toward an explanation of this.  I run
> my pipeline on various ultrasound image sets and get an NCC between 0.65
> and 0.8 for good alignments, but on some sets the NCC returns 1.0 when the
> images aren't even overlapping.  I have the black areas of the image masked
> out, and have even tried cranking up the threshold to be sure the darker
> areas aren't being included to no avail.  Any thoughts?
>
> --
>
> AH
>
>
>
> -----------------------------------------------------------------------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
>
>
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From swetha.bsharma at gmail.com  Wed Apr 12 04:11:35 2017
From: swetha.bsharma at gmail.com (Swetha Sharma)
Date: Wed, 12 Apr 2017 13:41:35 +0530
Subject: [ITK-users] Transforming a point
Message-ID: <CACDHZEQUAsT-oqbcVqDCnEP2Nqz2ttY5_-KbJur80P_x=B_bcA@mail.gmail.com>

Hi,

  I have a affine transformation matrix with a set of points as fixed
landmarks and moving landmarks. I was trying to verify the transformation
by using the transform point method in the transformation class,ideally i
should get back the fixed points when i give the moving points as input ,
but I am not getting it as the output.  The code which i used is as below:

typedef itk::AffineTransform<double,3> AffineTransformType;
AffineTransformType::Pointer transf;

transf = dynamic_cast<AffineTransformType*>( transfm.GetPointer() );
typedef itk::Similarity3DTransform<double> SimilarityTransformType;
SimilarityTransformType::Pointer transform = SimilarityTransformType::New();

typedef itk::LandmarkBasedTransformInitializer< SimilarityTransformType,
InputImageType, InputImageType >
LandmarkBasedTransformInitializerType;
   LandmarkBasedTransformInitializerType::Pointer
landmarkBasedTransformInitializer =
   LandmarkBasedTransformInitializerType::New();

   typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer
  LandmarkContainerType;
   typedef LandmarkBasedTransformInitializerType::LandmarkPointType
 LandmarkPointType;

   LandmarkContainerType movingLandmarks;

   LandmarkPointType movingPoint;

   double *ptrf_moving_point = ptf_moving_landmark_pointslist;
   for(int
iPointIndex=0;iPointIndex<iNumberofLandMarkPoints_moving;iPointIndex++){
   movingPoint[0] = (*( ptrf_moving_point )) ;
movingPoint[1] = (*( ptrf_moving_point + 1));
movingPoint[2] = (*( ptrf_moving_point + 2));
movingLandmarks.push_back( movingPoint );
ptrf_moving_point = ptrf_moving_point + 3;
   }

   typedef itk::PointSet< double, 3 >   PointSetType;
   PointSetType::Pointer registeredPointSet = PointSetType::New();
   typedef PointSetType::PointType     PointType;
   PointType registeredPoint;
   typedef PointSetType::PointsContainer  PointsContainer;
   PointsContainer::Pointer registeredPointContainer =
PointsContainer::New();

   for(int i=0;i<movingLandmarks.size();i++){
  registeredPoint =   transf->TransformPoint( movingLandmarks[i] );
       registeredPointContainer->InsertElement( i, registeredPoint );
   }

   registeredPointSet->SetPoints(registeredPointContainer);

//Write the registered pointset into file
std::ofstream   registeredFile;
registeredFile.open( "registered_points.txt");
if( registeredFile.fail() )
{
  return -1;
}
for( int i = 0; i<registeredPointSet->GetNumberOfPoints(); i++)
{
  registeredPointSet->GetPoint( i, & registeredPoint );
  for(int j = 0; j<3; j++)
  {
   registeredFile<<registeredPoint[j]<<"\t";
  }
  registeredFile<<"\n";
}

 Is there a mistake in the code ?How do I transform the points?
-swetha
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From sidharta.gupta93 at gmail.com  Wed Apr 12 07:44:55 2017
From: sidharta.gupta93 at gmail.com (sidharta)
Date: Wed, 12 Apr 2017 04:44:55 -0700 (MST)
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
Message-ID: <1491997495031-38097.post@n7.nabble.com>

Hi D?enan,

Of course I would use that (sorry for not mentioning it that I know this
already), but how do I get this particular plane (2D slice)? I don't want to
hard code anything.

Hope you understand 
Thank you for your time
Sidharta



--
View this message in context: http://itk-users.7.n7.nabble.com/Extract-slice-from-ResampleFilter-tp38074p38097.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From francois.budin at kitware.com  Wed Apr 12 08:46:12 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 12 Apr 2017 08:46:12 -0400
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <1491997495031-38097.post@n7.nabble.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
Message-ID: <CAHwLD2U4R9dzPn9EvWFao3=J=4+wzCmo+_RaoFLkQACJmH_9XA@mail.gmail.com>

Hello Sidharta,

You can use the filter called ExtractImageFilter [1]. You should be able to
achieve your goal with that.
Hope this helps,

Francois

[1] https://itk.org/Doxygen/html/classitk_1_1ExtractImageFilter.html

On Wed, Apr 12, 2017 at 7:44 AM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> Hi D?enan,
>
> Of course I would use that (sorry for not mentioning it that I know this
> already), but how do I get this particular plane (2D slice)? I don't want
> to
> hard code anything.
>
> Hope you understand
> Thank you for your time
> Sidharta
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074p38097.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From dzenanz at gmail.com  Wed Apr 12 09:03:52 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 12 Apr 2017 09:03:52 -0400
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <1491997495031-38097.post@n7.nabble.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
Message-ID: <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>

Hi Sidharta,

to get the particular plane you want, set up the transform in such a way
that that slice gets transformed to some know spatial position (e.g. your
first point to coordinates [0,0,0] and your last point to coordinates
[1000,0,0]). Then you only need to resample your volume to a 3D image of
thickness 1 slice which passes through points [0,0,0] and [1000,0,0]. You
don't even need extract filter with this approach.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Wed, Apr 12, 2017 at 7:44 AM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> Hi D?enan,
>
> Of course I would use that (sorry for not mentioning it that I know this
> already), but how do I get this particular plane (2D slice)? I don't want
> to
> hard code anything.
>
> Hope you understand
> Thank you for your time
> Sidharta
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074p38097.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From zivrafael.yaniv at nih.gov  Wed Apr 12 09:41:13 2017
From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C])
Date: Wed, 12 Apr 2017 13:41:13 +0000
Subject: [ITK-users] [ITK]  Transforming a point
In-Reply-To: <CACDHZEQUAsT-oqbcVqDCnEP2Nqz2ttY5_-KbJur80P_x=B_bcA@mail.gmail.com>
References: <CACDHZEQUAsT-oqbcVqDCnEP2Nqz2ttY5_-KbJur80P_x=B_bcA@mail.gmail.com>
Message-ID: <A63EEEAE-70FD-41FC-A5E7-9E9B7C7EFD77@mail.nih.gov>

Hello Swetha,

In general, the transformations computed using the ITK registration framework are from the fixed coordinate system to the moving coordinate system. Thus, the transformation should be applied as T(point_fixed) = point_moving.

I did not read your code so I may be missing something specific to your work, but this mapping is something that many newcomers to ITK seem to get confused with.

     hope this helps
             Ziv


From: Swetha Sharma <swetha.bsharma at gmail.com>
Date: Wednesday, April 12, 2017 at 4:11 AM
To: Insight-users <insight-users at itk.org>
Subject: [ITK] [ITK-users] Transforming a point

Hi,

  I have a affine transformation matrix with a set of points as fixed landmarks and moving landmarks. I was trying to verify the transformation by using the transform point method in the transformation class,ideally i should get back the fixed points when i give the moving points as input , but I am not getting it as the output.  The code which i used is as below:

typedef itk::AffineTransform<double,3> AffineTransformType;
AffineTransformType::Pointer transf;

transf = dynamic_cast<AffineTransformType*>( transfm.GetPointer() );
typedef itk::Similarity3DTransform<double> SimilarityTransformType;
SimilarityTransformType::Pointer transform = SimilarityTransformType::New();

typedef itk::LandmarkBasedTransformInitializer< SimilarityTransformType, InputImageType, InputImageType >
LandmarkBasedTransformInitializerType;
   LandmarkBasedTransformInitializerType::Pointer landmarkBasedTransformInitializer =
   LandmarkBasedTransformInitializerType::New();

   typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer     LandmarkContainerType;
   typedef LandmarkBasedTransformInitializerType::LandmarkPointType          LandmarkPointType;

   LandmarkContainerType movingLandmarks;

   LandmarkPointType movingPoint;

   double *ptrf_moving_point = ptf_moving_landmark_pointslist;
   for(int iPointIndex=0;iPointIndex<iNumberofLandMarkPoints_moving;iPointIndex++){
   movingPoint[0] = (*( ptrf_moving_point )) ;
movingPoint[1] = (*( ptrf_moving_point + 1));
movingPoint[2] = (*( ptrf_moving_point + 2));
movingLandmarks.push_back( movingPoint );
ptrf_moving_point = ptrf_moving_point + 3;
   }

   typedef itk::PointSet< double, 3 >   PointSetType;
   PointSetType::Pointer registeredPointSet = PointSetType::New();
   typedef PointSetType::PointType     PointType;
   PointType registeredPoint;
   typedef PointSetType::PointsContainer  PointsContainer;
   PointsContainer::Pointer registeredPointContainer = PointsContainer::New();

   for(int i=0;i<movingLandmarks.size();i++){
  registeredPoint =   transf->TransformPoint( movingLandmarks[i] );
       registeredPointContainer->InsertElement( i, registeredPoint );
   }

   registeredPointSet->SetPoints(registeredPointContainer);

//Write the registered pointset into file
std::ofstream   registeredFile;
registeredFile.open( "registered_points.txt");
if( registeredFile.fail() )
{
  return -1;
}
for( int i = 0; i<registeredPointSet->GetNumberOfPoints(); i++)
{
  registeredPointSet->GetPoint( i, & registeredPoint );
  for(int j = 0; j<3; j++)
  {
   registeredFile<<registeredPoint[j]<<"\t";
  }
  registeredFile<<"\n";
}

 Is there a mistake in the code ?How do I transform the points?
-swetha
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From fisidoro at ethz.ch  Wed Apr 12 14:16:10 2017
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Wed, 12 Apr 2017 18:16:10 +0000
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
Message-ID: <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>

Thank you. I am trying to build ITK Wrap Python with Module_BridgeNumPy=ON with Visual Studio 2017.

I get the following type of errors:

12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\xstring(1905,26): error G3F63BFAE: constexpr variable '_Memcpy_move_offset' must be initialized by a constant expression
12>        static constexpr size_t _Memcpy_move_offset = offsetof(_Mydata_t, _Bx);
12>                                ^                     ~~~~~~~~~~~~~~~~~~~~~~~~
12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\stdexcept:23:21: note: in instantiation of template class 'std::basic_string<char, std::char_traits<char>, std::allocator<char> >' requested here
12>                : _Mybase(_Message.c_str())
12>                                  ^
12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\xstring:1905:48: note: cast that performs the conversions of a reinterpret_cast is not allowed in a constant expression
12>        static constexpr size_t _Memcpy_move_offset = offsetof(_Mydata_t, _Bx);
12>                                                      ^
12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32: note: expanded from macro 'offsetof'
12>        #define offsetof(s,m) ((size_t)&reinterpret_cast<char const volatile&>((((s*)0)->m)))


The build worked with Visual Studio 2015 instead.

Can I fix this issue with Visual Studio 2017 somehow?

Thank you.

----------------------------------------------------------------------
Fabio D?Isidoro - PhD Student
Institute of Biomechanics
HPP O 14
H?nggerbergring 64
8093 Z?rich, Switzerland

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com] 
Sent: Montag, 3. April 2017 20:41
To: D'Isidoro Fabio <fisidoro at ethz.ch>
Cc: insight-users at itk.org
Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)

Hallo Fabio,


> I use ITK with Python Wrap. I need to interface my Python code with a 
> Cython-wrapped C++ code that takes only numpy array as input and 
> returns numpy array as output.

Cool. By the way, you may be interested in scikit-build [1], which is a good way to build Cython-wrapped C++ code. We are using it for the ITK and SimpleITK Python packages, and it has good Cython and CMake support.


> Hence, I need to convert the Python itk images into numpy array to be 
> given as input to the wrapped C++ code, and then convert the numpy 
> array in output from the wrapped C++ code back into python itk images.
>
>
>
> Question 1) How can I do that in an efficient way? I found some posts 
> on itk.PyBuffer but I could not find anywhere any reference on how to 
> install it on my itk wrap build.

Yes, itk.PyBuffer works great for that. Please review a PR for some additional documentation:

  https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18

This has been available in ITK for a few releases as a Remote module, which can be enabled by setting

  Module_BridgeNumPy=ON

in ITK's CMake configuration.


Since ITK 4.11.0, it is easier to build since it does not require the NumPy headers.


In current ITK Git master (to be 4.12.0) the module is enabled by default.


Nightly ITK Python packages for ITK Git master are now being built:

  https://github.com/InsightSoftwareConsortium/ITKPythonPackage

macOS and Linux are available. Windows packages will be available over the coming weeks.



> Question 2) The purpose of writing a part of my algorithm in C++ is to 
> speed up the code. If the conversion between python itk images and 
> numpy arrays is slow, I would lose all the speed gain obtained with the C++ implementation.
> Are there better ways to deal with that?

The newer versions ITKBridgeNumPy use a NumPy array view, which does not do any copies during the conversion, and it is very fast.


HTH,
Matt


[1] http://scikit-build.org/

From dzenanz at gmail.com  Wed Apr 12 15:54:09 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 12 Apr 2017 15:54:09 -0400
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>
Message-ID: <CAPf2UMTzTTRTQpFKJj_vnx88XN+PoZmiiQvJg3k1huk=zqv1Dg@mail.gmail.com>

Hi Fabio,

let me give it a try with VS2017 and Wrapping+NumPy. I will report back
when I have an update.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Wed, Apr 12, 2017 at 2:16 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:

> Thank you. I am trying to build ITK Wrap Python with Module_BridgeNumPy=ON
> with Visual Studio 2017.
>
> I get the following type of errors:
>
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
> ols/MSVC/14.10.25017/include\xstring(1905,26): error G3F63BFAE: constexpr
> variable '_Memcpy_move_offset' must be initialized by a constant expression
> 12>        static constexpr size_t _Memcpy_move_offset =
> offsetof(_Mydata_t, _Bx);
> 12>                                ^
>  ~~~~~~~~~~~~~~~~~~~~~~~~
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
> ols/MSVC/14.10.25017/include\stdexcept:23:21: note: in instantiation of
> template class 'std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >' requested here
> 12>                : _Mybase(_Message.c_str())
> 12>                                  ^
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
> ols/MSVC/14.10.25017/include\xstring:1905:48: note: cast that performs
> the conversions of a reinterpret_cast is not allowed in a constant
> expression
> 12>        static constexpr size_t _Memcpy_move_offset =
> offsetof(_Mydata_t, _Bx);
> 12>                                                      ^
> 12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32:
> note: expanded from macro 'offsetof'
> 12>        #define offsetof(s,m) ((size_t)&reinterpret_cast<char const
> volatile&>((((s*)0)->m)))
>
>
> The build worked with Visual Studio 2015 instead.
>
> Can I fix this issue with Visual Studio 2017 somehow?
>
> Thank you.
>
> ----------------------------------------------------------------------
> Fabio D?Isidoro - PhD Student
> Institute of Biomechanics
> HPP O 14
> H?nggerbergring 64
> 8093 Z?rich, Switzerland
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 3. April 2017 20:41
> To: D'Isidoro Fabio <fisidoro at ethz.ch>
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>
> Hallo Fabio,
>
>
> > I use ITK with Python Wrap. I need to interface my Python code with a
> > Cython-wrapped C++ code that takes only numpy array as input and
> > returns numpy array as output.
>
> Cool. By the way, you may be interested in scikit-build [1], which is a
> good way to build Cython-wrapped C++ code. We are using it for the ITK and
> SimpleITK Python packages, and it has good Cython and CMake support.
>
>
> > Hence, I need to convert the Python itk images into numpy array to be
> > given as input to the wrapped C++ code, and then convert the numpy
> > array in output from the wrapped C++ code back into python itk images.
> >
> >
> >
> > Question 1) How can I do that in an efficient way? I found some posts
> > on itk.PyBuffer but I could not find anywhere any reference on how to
> > install it on my itk wrap build.
>
> Yes, itk.PyBuffer works great for that. Please review a PR for some
> additional documentation:
>
>   https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18
>
> This has been available in ITK for a few releases as a Remote module,
> which can be enabled by setting
>
>   Module_BridgeNumPy=ON
>
> in ITK's CMake configuration.
>
>
> Since ITK 4.11.0, it is easier to build since it does not require the
> NumPy headers.
>
>
> In current ITK Git master (to be 4.12.0) the module is enabled by default.
>
>
> Nightly ITK Python packages for ITK Git master are now being built:
>
>   https://github.com/InsightSoftwareConsortium/ITKPythonPackage
>
> macOS and Linux are available. Windows packages will be available over the
> coming weeks.
>
>
>
> > Question 2) The purpose of writing a part of my algorithm in C++ is to
> > speed up the code. If the conversion between python itk images and
> > numpy arrays is slow, I would lose all the speed gain obtained with the
> C++ implementation.
> > Are there better ways to deal with that?
>
> The newer versions ITKBridgeNumPy use a NumPy array view, which does not
> do any copies during the conversion, and it is very fast.
>
>
> HTH,
> Matt
>
>
> [1] http://scikit-build.org/
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From fisidoro at ethz.ch  Wed Apr 12 16:02:58 2017
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Wed, 12 Apr 2017 20:02:58 +0000
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <CAPf2UMTzTTRTQpFKJj_vnx88XN+PoZmiiQvJg3k1huk=zqv1Dg@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>
 <CAPf2UMTzTTRTQpFKJj_vnx88XN+PoZmiiQvJg3k1huk=zqv1Dg@mail.gmail.com>
Message-ID: <50B858FB5F53124F9E32314E5C1B409445968862@MBX212.d.ethz.ch>

Ok, thanks. Moe specifically I am using now Visual Studio 2017 Preview.

Fabio.
From: D?enan Zuki? [mailto:dzenanz at gmail.com]
Sent: Mittwoch, 12. April 2017 21:54
To: D'Isidoro Fabio <fisidoro at ethz.ch>
Cc: Matt McCormick <matt.mccormick at kitware.com>; insight-users at itk.org
Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)

Hi Fabio,

let me give it a try with VS2017 and Wrapping+NumPy. I will report back when I have an update.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Wed, Apr 12, 2017 at 2:16 PM, D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>> wrote:
Thank you. I am trying to build ITK Wrap Python with Module_BridgeNumPy=ON with Visual Studio 2017.

I get the following type of errors:

12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\xstring(1905,26): error G3F63BFAE: constexpr variable '_Memcpy_move_offset' must be initialized by a constant expression
12>        static constexpr size_t _Memcpy_move_offset = offsetof(_Mydata_t, _Bx);
12>                                ^                     ~~~~~~~~~~~~~~~~~~~~~~~~
12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\stdexcept:23:21: note: in instantiation of template class 'std::basic_string<char, std::char_traits<char>, std::allocator<char> >' requested here
12>                : _Mybase(_Message.c_str())
12>                                  ^
12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\xstring:1905:48: note: cast that performs the conversions of a reinterpret_cast is not allowed in a constant expression
12>        static constexpr size_t _Memcpy_move_offset = offsetof(_Mydata_t, _Bx);
12>                                                      ^
12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32: note: expanded from macro 'offsetof'
12>        #define offsetof(s,m) ((size_t)&reinterpret_cast<char const volatile&>((((s*)0)->m)))


The build worked with Visual Studio 2015 instead.

Can I fix this issue with Visual Studio 2017 somehow?

Thank you.

----------------------------------------------------------------------
Fabio D?Isidoro - PhD Student
Institute of Biomechanics
HPP O 14
H?nggerbergring 64
8093 Z?rich, Switzerland

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>]
Sent: Montag, 3. April 2017 20:41
To: D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>>
Cc: insight-users at itk.org<mailto:insight-users at itk.org>
Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)

Hallo Fabio,


> I use ITK with Python Wrap. I need to interface my Python code with a
> Cython-wrapped C++ code that takes only numpy array as input and
> returns numpy array as output.

Cool. By the way, you may be interested in scikit-build [1], which is a good way to build Cython-wrapped C++ code. We are using it for the ITK and SimpleITK Python packages, and it has good Cython and CMake support.


> Hence, I need to convert the Python itk images into numpy array to be
> given as input to the wrapped C++ code, and then convert the numpy
> array in output from the wrapped C++ code back into python itk images.
>
>
>
> Question 1) How can I do that in an efficient way? I found some posts
> on itk.PyBuffer but I could not find anywhere any reference on how to
> install it on my itk wrap build.

Yes, itk.PyBuffer works great for that. Please review a PR for some additional documentation:

  https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18

This has been available in ITK for a few releases as a Remote module, which can be enabled by setting

  Module_BridgeNumPy=ON

in ITK's CMake configuration.


Since ITK 4.11.0, it is easier to build since it does not require the NumPy headers.


In current ITK Git master (to be 4.12.0) the module is enabled by default.


Nightly ITK Python packages for ITK Git master are now being built:

  https://github.com/InsightSoftwareConsortium/ITKPythonPackage

macOS and Linux are available. Windows packages will be available over the coming weeks.



> Question 2) The purpose of writing a part of my algorithm in C++ is to
> speed up the code. If the conversion between python itk images and
> numpy arrays is slow, I would lose all the speed gain obtained with the C++ implementation.
> Are there better ways to deal with that?

The newer versions ITKBridgeNumPy use a NumPy array view, which does not do any copies during the conversion, and it is very fast.


HTH,
Matt


[1] http://scikit-build.org/
_____________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

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From dzenanz at gmail.com  Wed Apr 12 16:26:06 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 12 Apr 2017 16:26:06 -0400
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409445968862@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>
 <CAPf2UMTzTTRTQpFKJj_vnx88XN+PoZmiiQvJg3k1huk=zqv1Dg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968862@MBX212.d.ethz.ch>
Message-ID: <CAPf2UMTnBFm_egB_cKFsVhzH5tDMn7_uA=8y76j1diCbnAK73Q@mail.gmail.com>

I reproduced the error. I am looking into fixing it.

On Wed, Apr 12, 2017 at 4:02 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:

> Ok, thanks. Moe specifically I am using now *Visual Studio 2017 Preview*.
>
>
>
> Fabio.
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Mittwoch, 12. April 2017 21:54
> *To:* D'Isidoro Fabio <fisidoro at ethz.ch>
> *Cc:* Matt McCormick <matt.mccormick at kitware.com>; insight-users at itk.org
>
> *Subject:* Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>
>
>
> Hi Fabio,
>
>
>
> let me give it a try with VS2017 and Wrapping+NumPy. I will report back
> when I have an update.
>
>
>
> Regards,
>
> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
>
>
> On Wed, Apr 12, 2017 at 2:16 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
>
> Thank you. I am trying to build ITK Wrap Python with Module_BridgeNumPy=ON
> with Visual Studio 2017.
>
> I get the following type of errors:
>
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/
> Tools/MSVC/14.10.25017/include\xstring(1905,26): error G3F63BFAE:
> constexpr variable '_Memcpy_move_offset' must be initialized by a constant
> expression
> 12>        static constexpr size_t _Memcpy_move_offset =
> offsetof(_Mydata_t, _Bx);
> 12>                                ^
>  ~~~~~~~~~~~~~~~~~~~~~~~~
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/
> Tools/MSVC/14.10.25017/include\stdexcept:23:21: note: in instantiation of
> template class 'std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >' requested here
> 12>                : _Mybase(_Message.c_str())
> 12>                                  ^
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/
> Tools/MSVC/14.10.25017/include\xstring:1905:48: note: cast that performs
> the conversions of a reinterpret_cast is not allowed in a constant
> expression
> 12>        static constexpr size_t _Memcpy_move_offset =
> offsetof(_Mydata_t, _Bx);
> 12>                                                      ^
> 12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32:
> note: expanded from macro 'offsetof'
> 12>        #define offsetof(s,m) ((size_t)&reinterpret_cast<char const
> volatile&>((((s*)0)->m)))
>
>
> The build worked with Visual Studio 2015 instead.
>
> Can I fix this issue with Visual Studio 2017 somehow?
>
> Thank you.
>
> ----------------------------------------------------------------------
> Fabio D?Isidoro - PhD Student
> Institute of Biomechanics
> HPP O 14
> H?nggerbergring 64
> 8093 Z?rich, Switzerland
>
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 3. April 2017 20:41
> To: D'Isidoro Fabio <fisidoro at ethz.ch>
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>
> Hallo Fabio,
>
>
> > I use ITK with Python Wrap. I need to interface my Python code with a
> > Cython-wrapped C++ code that takes only numpy array as input and
> > returns numpy array as output.
>
> Cool. By the way, you may be interested in scikit-build [1], which is a
> good way to build Cython-wrapped C++ code. We are using it for the ITK and
> SimpleITK Python packages, and it has good Cython and CMake support.
>
>
> > Hence, I need to convert the Python itk images into numpy array to be
> > given as input to the wrapped C++ code, and then convert the numpy
> > array in output from the wrapped C++ code back into python itk images.
> >
> >
> >
> > Question 1) How can I do that in an efficient way? I found some posts
> > on itk.PyBuffer but I could not find anywhere any reference on how to
> > install it on my itk wrap build.
>
> Yes, itk.PyBuffer works great for that. Please review a PR for some
> additional documentation:
>
>   https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18
>
> This has been available in ITK for a few releases as a Remote module,
> which can be enabled by setting
>
>   Module_BridgeNumPy=ON
>
> in ITK's CMake configuration.
>
>
> Since ITK 4.11.0, it is easier to build since it does not require the
> NumPy headers.
>
>
> In current ITK Git master (to be 4.12.0) the module is enabled by default.
>
>
> Nightly ITK Python packages for ITK Git master are now being built:
>
>   https://github.com/InsightSoftwareConsortium/ITKPythonPackage
>
> macOS and Linux are available. Windows packages will be available over the
> coming weeks.
>
>
>
> > Question 2) The purpose of writing a part of my algorithm in C++ is to
> > speed up the code. If the conversion between python itk images and
> > numpy arrays is slow, I would lose all the speed gain obtained with the
> C++ implementation.
> > Are there better ways to deal with that?
>
> The newer versions ITKBridgeNumPy use a NumPy array view, which does not
> do any copies during the conversion, and it is very fast.
>
>
> HTH,
> Matt
>
>
> [1] http://scikit-build.org/
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
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From francois.budin at kitware.com  Wed Apr 12 16:26:34 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 12 Apr 2017 16:26:34 -0400
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409445968862@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>
 <CAPf2UMTzTTRTQpFKJj_vnx88XN+PoZmiiQvJg3k1huk=zqv1Dg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968862@MBX212.d.ethz.ch>
Message-ID: <CAHwLD2UN1-ULXN4oT2FCJa0UCzF7XmaXB3LJqwVOC9R4p8GGBw@mail.gmail.com>

Fabio,

To add a little bit of extra information about using BridgeNumpy:

>From NumPy to ITK, the memory is never copied, and always shared between
the NumPy array and the ITK image.
>From ITK to NumPy, the memory is not copied at first, if the data is not
changed from the NumPy side (e.g. if the ITK image is changed, the NumPy
array will be modified too), but if you modify the NumPy array directly,
NumPy will create a copy of the data. This also means that if you were to
modify the NumPy array, the modifications would not be visible in the ITK
image.

A limited workaround to this is:

# Get NumPy array from image
arr_image = itk.GetArrayFromImage(image)
# Create copy of array that can be modified in-place
arr = arr_image.copy()
# Modify array
?
# Update image in-place with new array
arr_image.setfield(arr,arr_image.dtype)

The advantage of this method is that the image will be updated. However,
there is an explicit copy of your data.
If the copy step is skipped and the original NumPy array is modified, a
copy of the data will be performed by NumPy and you may not be aware of it
until you see that the data in the NumPy array and the image do not match
anymore.

Hope this helps,
Francois

On Wed, Apr 12, 2017 at 4:02 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:

> Ok, thanks. Moe specifically I am using now *Visual Studio 2017 Preview*.
>
>
>
> Fabio.
>
> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
> *Sent:* Mittwoch, 12. April 2017 21:54
> *To:* D'Isidoro Fabio <fisidoro at ethz.ch>
> *Cc:* Matt McCormick <matt.mccormick at kitware.com>; insight-users at itk.org
>
> *Subject:* Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>
>
>
> Hi Fabio,
>
>
>
> let me give it a try with VS2017 and Wrapping+NumPy. I will report back
> when I have an update.
>
>
>
> Regards,
>
> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
>
>
> On Wed, Apr 12, 2017 at 2:16 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
>
> Thank you. I am trying to build ITK Wrap Python with Module_BridgeNumPy=ON
> with Visual Studio 2017.
>
> I get the following type of errors:
>
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/
> Tools/MSVC/14.10.25017/include\xstring(1905,26): error G3F63BFAE:
> constexpr variable '_Memcpy_move_offset' must be initialized by a constant
> expression
> 12>        static constexpr size_t _Memcpy_move_offset =
> offsetof(_Mydata_t, _Bx);
> 12>                                ^
>  ~~~~~~~~~~~~~~~~~~~~~~~~
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/
> Tools/MSVC/14.10.25017/include\stdexcept:23:21: note: in instantiation of
> template class 'std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >' requested here
> 12>                : _Mybase(_Message.c_str())
> 12>                                  ^
> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/
> Tools/MSVC/14.10.25017/include\xstring:1905:48: note: cast that performs
> the conversions of a reinterpret_cast is not allowed in a constant
> expression
> 12>        static constexpr size_t _Memcpy_move_offset =
> offsetof(_Mydata_t, _Bx);
> 12>                                                      ^
> 12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32:
> note: expanded from macro 'offsetof'
> 12>        #define offsetof(s,m) ((size_t)&reinterpret_cast<char const
> volatile&>((((s*)0)->m)))
>
>
> The build worked with Visual Studio 2015 instead.
>
> Can I fix this issue with Visual Studio 2017 somehow?
>
> Thank you.
>
> ----------------------------------------------------------------------
> Fabio D?Isidoro - PhD Student
> Institute of Biomechanics
> HPP O 14
> H?nggerbergring 64
> 8093 Z?rich, Switzerland
>
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 3. April 2017 20:41
> To: D'Isidoro Fabio <fisidoro at ethz.ch>
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>
> Hallo Fabio,
>
>
> > I use ITK with Python Wrap. I need to interface my Python code with a
> > Cython-wrapped C++ code that takes only numpy array as input and
> > returns numpy array as output.
>
> Cool. By the way, you may be interested in scikit-build [1], which is a
> good way to build Cython-wrapped C++ code. We are using it for the ITK and
> SimpleITK Python packages, and it has good Cython and CMake support.
>
>
> > Hence, I need to convert the Python itk images into numpy array to be
> > given as input to the wrapped C++ code, and then convert the numpy
> > array in output from the wrapped C++ code back into python itk images.
> >
> >
> >
> > Question 1) How can I do that in an efficient way? I found some posts
> > on itk.PyBuffer but I could not find anywhere any reference on how to
> > install it on my itk wrap build.
>
> Yes, itk.PyBuffer works great for that. Please review a PR for some
> additional documentation:
>
>   https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18
>
> This has been available in ITK for a few releases as a Remote module,
> which can be enabled by setting
>
>   Module_BridgeNumPy=ON
>
> in ITK's CMake configuration.
>
>
> Since ITK 4.11.0, it is easier to build since it does not require the
> NumPy headers.
>
>
> In current ITK Git master (to be 4.12.0) the module is enabled by default.
>
>
> Nightly ITK Python packages for ITK Git master are now being built:
>
>   https://github.com/InsightSoftwareConsortium/ITKPythonPackage
>
> macOS and Linux are available. Windows packages will be available over the
> coming weeks.
>
>
>
> > Question 2) The purpose of writing a part of my algorithm in C++ is to
> > speed up the code. If the conversion between python itk images and
> > numpy arrays is slow, I would lose all the speed gain obtained with the
> C++ implementation.
> > Are there better ways to deal with that?
>
> The newer versions ITKBridgeNumPy use a NumPy array view, which does not
> do any copies during the conversion, and it is very fast.
>
>
> HTH,
> Matt
>
>
> [1] http://scikit-build.org/
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Wed Apr 12 16:50:08 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 12 Apr 2017 16:50:08 -0400
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <CAHwLD2UN1-ULXN4oT2FCJa0UCzF7XmaXB3LJqwVOC9R4p8GGBw@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>
 <CAPf2UMTzTTRTQpFKJj_vnx88XN+PoZmiiQvJg3k1huk=zqv1Dg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968862@MBX212.d.ethz.ch>
 <CAHwLD2UN1-ULXN4oT2FCJa0UCzF7XmaXB3LJqwVOC9R4p8GGBw@mail.gmail.com>
Message-ID: <CAPf2UMSiCv7BTcu7kuq-ZaX2gTVwcoUxk3S4MgTfdtPY7khBLw@mail.gmail.com>

Hi Fabio,

it looks like we will have to wait somewhat until VS writers get around to
implement __builtin_offsetof
<https://developercommunity.visualstudio.com/content/problem/22196/static-assert-cannot-compile-constexprs-method-tha.html>

I don't know why it doesn't trigger when Python wrapping is OFF. I will
look into it more.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Wed, Apr 12, 2017 at 4:26 PM, Francois Budin <francois.budin at kitware.com>
wrote:

> Fabio,
>
> To add a little bit of extra information about using BridgeNumpy:
>
> From NumPy to ITK, the memory is never copied, and always shared between
> the NumPy array and the ITK image.
> From ITK to NumPy, the memory is not copied at first, if the data is not
> changed from the NumPy side (e.g. if the ITK image is changed, the NumPy
> array will be modified too), but if you modify the NumPy array directly,
> NumPy will create a copy of the data. This also means that if you were to
> modify the NumPy array, the modifications would not be visible in the ITK
> image.
>
> A limited workaround to this is:
>
> # Get NumPy array from image
> arr_image = itk.GetArrayFromImage(image)
> # Create copy of array that can be modified in-place
> arr = arr_image.copy()
> # Modify array
> ?
> # Update image in-place with new array
> arr_image.setfield(arr,arr_image.dtype)
>
> The advantage of this method is that the image will be updated. However,
> there is an explicit copy of your data.
> If the copy step is skipped and the original NumPy array is modified, a
> copy of the data will be performed by NumPy and you may not be aware of it
> until you see that the data in the NumPy array and the image do not match
> anymore.
>
> Hope this helps,
> Francois
>
> On Wed, Apr 12, 2017 at 4:02 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
>
>> Ok, thanks. Moe specifically I am using now *Visual Studio 2017 Preview*.
>>
>>
>>
>> Fabio.
>>
>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>> *Sent:* Mittwoch, 12. April 2017 21:54
>> *To:* D'Isidoro Fabio <fisidoro at ethz.ch>
>> *Cc:* Matt McCormick <matt.mccormick at kitware.com>; insight-users at itk.org
>>
>> *Subject:* Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>>
>>
>>
>> Hi Fabio,
>>
>>
>>
>> let me give it a try with VS2017 and Wrapping+NumPy. I will report back
>> when I have an update.
>>
>>
>>
>> Regards,
>>
>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>
>>
>>
>> On Wed, Apr 12, 2017 at 2:16 PM, D'Isidoro Fabio <fisidoro at ethz.ch>
>> wrote:
>>
>> Thank you. I am trying to build ITK Wrap Python with
>> Module_BridgeNumPy=ON with Visual Studio 2017.
>>
>> I get the following type of errors:
>>
>> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
>> ols/MSVC/14.10.25017/include\xstring(1905,26): error G3F63BFAE:
>> constexpr variable '_Memcpy_move_offset' must be initialized by a constant
>> expression
>> 12>        static constexpr size_t _Memcpy_move_offset =
>> offsetof(_Mydata_t, _Bx);
>> 12>                                ^
>>  ~~~~~~~~~~~~~~~~~~~~~~~~
>> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
>> ols/MSVC/14.10.25017/include\stdexcept:23:21: note: in instantiation of
>> template class 'std::basic_string<char, std::char_traits<char>,
>> std::allocator<char> >' requested here
>> 12>                : _Mybase(_Message.c_str())
>> 12>                                  ^
>> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
>> ols/MSVC/14.10.25017/include\xstring:1905:48: note: cast that performs
>> the conversions of a reinterpret_cast is not allowed in a constant
>> expression
>> 12>        static constexpr size_t _Memcpy_move_offset =
>> offsetof(_Mydata_t, _Bx);
>> 12>                                                      ^
>> 12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32:
>> note: expanded from macro 'offsetof'
>> 12>        #define offsetof(s,m) ((size_t)&reinterpret_cast<char const
>> volatile&>((((s*)0)->m)))
>>
>>
>> The build worked with Visual Studio 2015 instead.
>>
>> Can I fix this issue with Visual Studio 2017 somehow?
>>
>> Thank you.
>>
>> ----------------------------------------------------------------------
>> Fabio D?Isidoro - PhD Student
>> Institute of Biomechanics
>> HPP O 14
>> H?nggerbergring 64
>> 8093 Z?rich, Switzerland
>>
>>
>> -----Original Message-----
>> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
>> Sent: Montag, 3. April 2017 20:41
>> To: D'Isidoro Fabio <fisidoro at ethz.ch>
>> Cc: insight-users at itk.org
>> Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>>
>> Hallo Fabio,
>>
>>
>> > I use ITK with Python Wrap. I need to interface my Python code with a
>> > Cython-wrapped C++ code that takes only numpy array as input and
>> > returns numpy array as output.
>>
>> Cool. By the way, you may be interested in scikit-build [1], which is a
>> good way to build Cython-wrapped C++ code. We are using it for the ITK and
>> SimpleITK Python packages, and it has good Cython and CMake support.
>>
>>
>> > Hence, I need to convert the Python itk images into numpy array to be
>> > given as input to the wrapped C++ code, and then convert the numpy
>> > array in output from the wrapped C++ code back into python itk images.
>> >
>> >
>> >
>> > Question 1) How can I do that in an efficient way? I found some posts
>> > on itk.PyBuffer but I could not find anywhere any reference on how to
>> > install it on my itk wrap build.
>>
>> Yes, itk.PyBuffer works great for that. Please review a PR for some
>> additional documentation:
>>
>>   https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18
>>
>> This has been available in ITK for a few releases as a Remote module,
>> which can be enabled by setting
>>
>>   Module_BridgeNumPy=ON
>>
>> in ITK's CMake configuration.
>>
>>
>> Since ITK 4.11.0, it is easier to build since it does not require the
>> NumPy headers.
>>
>>
>> In current ITK Git master (to be 4.12.0) the module is enabled by default.
>>
>>
>> Nightly ITK Python packages for ITK Git master are now being built:
>>
>>   https://github.com/InsightSoftwareConsortium/ITKPythonPackage
>>
>> macOS and Linux are available. Windows packages will be available over
>> the coming weeks.
>>
>>
>>
>> > Question 2) The purpose of writing a part of my algorithm in C++ is to
>> > speed up the code. If the conversion between python itk images and
>> > numpy arrays is slow, I would lose all the speed gain obtained with the
>> C++ implementation.
>> > Are there better ways to deal with that?
>>
>> The newer versions ITKBridgeNumPy use a NumPy array view, which does not
>> do any copies during the conversion, and it is very fast.
>>
>>
>> HTH,
>> Matt
>>
>>
>> [1] http://scikit-build.org/
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From swetha.bsharma at gmail.com  Thu Apr 13 01:12:20 2017
From: swetha.bsharma at gmail.com (Swetha Sharma)
Date: Thu, 13 Apr 2017 05:12:20 +0000
Subject: [ITK-users] [ITK]  Transforming a point
In-Reply-To: <A63EEEAE-70FD-41FC-A5E7-9E9B7C7EFD77@mail.nih.gov>
References: <CACDHZEQUAsT-oqbcVqDCnEP2Nqz2ttY5_-KbJur80P_x=B_bcA@mail.gmail.com>
 <A63EEEAE-70FD-41FC-A5E7-9E9B7C7EFD77@mail.nih.gov>
Message-ID: <CACDHZESbftJCrCQn-zHubmjpAaugntuTkr3jQwHOW7gze38Hdw@mail.gmail.com>

It was helpful thanks ziv
Swetha

On Wed, 12 Apr 2017, 19:11 Yaniv, Ziv Rafael (NIH/NLM/LHC) [C], <
zivrafael.yaniv at nih.gov> wrote:

> Hello Swetha,
>
>
>
> In general, the transformations computed using the ITK registration
> framework are from the fixed coordinate system to the moving coordinate
> system. Thus, the transformation should be applied as T(point_fixed) =
> point_moving.
>
>
>
> I did not read your code so I may be missing something specific to your
> work, but this mapping is something that many newcomers to ITK seem to get
> confused with.
>
>
>
>      hope this helps
>
>              Ziv
>
>
>
>
>
> *From: *Swetha Sharma <swetha.bsharma at gmail.com>
> *Date: *Wednesday, April 12, 2017 at 4:11 AM
> *To: *Insight-users <insight-users at itk.org>
> *Subject: *[ITK] [ITK-users] Transforming a point
>
>
>
> Hi,
>
>
>
>   I have a affine transformation matrix with a set of points as fixed
> landmarks and moving landmarks. I was trying to verify the transformation
> by using the transform point method in the transformation class,ideally i
> should get back the fixed points when i give the moving points as input ,
> but I am not getting it as the output.  The code which i used is as below:
>
>
>
> typedef itk::AffineTransform<double,3> AffineTransformType;
>
> AffineTransformType::Pointer transf;
>
>
>
> transf = dynamic_cast<AffineTransformType*>( transfm.GetPointer() );
>
> typedef itk::Similarity3DTransform<double> SimilarityTransformType;
>
> SimilarityTransformType::Pointer transform =
> SimilarityTransformType::New();
>
>
>
> typedef itk::LandmarkBasedTransformInitializer< SimilarityTransformType,
> InputImageType, InputImageType >
>
> LandmarkBasedTransformInitializerType;
>
>    LandmarkBasedTransformInitializerType::Pointer
> landmarkBasedTransformInitializer =
>
>    LandmarkBasedTransformInitializerType::New();
>
>
>
>    typedef LandmarkBasedTransformInitializerType::LandmarkPointContainer
>   LandmarkContainerType;
>
>    typedef LandmarkBasedTransformInitializerType::LandmarkPointType
>    LandmarkPointType;
>
>
>
>    LandmarkContainerType movingLandmarks;
>
>
>
>    LandmarkPointType movingPoint;
>
>
>
>    double *ptrf_moving_point = ptf_moving_landmark_pointslist;
>
>    for(int
> iPointIndex=0;iPointIndex<iNumberofLandMarkPoints_moving;iPointIndex++){
>
>    movingPoint[0] = (*( ptrf_moving_point )) ;
>
> movingPoint[1] = (*( ptrf_moving_point + 1));
>
> movingPoint[2] = (*( ptrf_moving_point + 2));
>
> movingLandmarks.push_back( movingPoint );
>
> ptrf_moving_point = ptrf_moving_point + 3;
>
>    }
>
>
>
>    typedef itk::PointSet< double, 3 >   PointSetType;
>
>    PointSetType::Pointer registeredPointSet = PointSetType::New();
>
>    typedef PointSetType::PointType     PointType;
>
>    PointType registeredPoint;
>
>    typedef PointSetType::PointsContainer  PointsContainer;
>
>    PointsContainer::Pointer registeredPointContainer =
> PointsContainer::New();
>
>
>
>    for(int i=0;i<movingLandmarks.size();i++){
>
>   registeredPoint =   transf->TransformPoint( movingLandmarks[i] );
>
>        registeredPointContainer->InsertElement( i, registeredPoint );
>
>    }
>
>
>
>    registeredPointSet->SetPoints(registeredPointContainer);
>
>
>
> //Write the registered pointset into file
>
> std::ofstream   registeredFile;
>
> registeredFile.open( "registered_points.txt");
>
> if( registeredFile.fail() )
>
> {
>
>   return -1;
>
> }
>
> for( int i = 0; i<registeredPointSet->GetNumberOfPoints(); i++)
>
> {
>
>   registeredPointSet->GetPoint( i, & registeredPoint );
>
>   for(int j = 0; j<3; j++)
>
>   {
>
>    registeredFile<<registeredPoint[j]<<"\t";
>
>   }
>
>   registeredFile<<"\n";
>
> }
>
>
>
>  Is there a mistake in the code ?How do I transform the points?
>
> -swetha
>
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From wangtao_ at sjtu.edu.cn  Thu Apr 13 08:25:37 2017
From: wangtao_ at sjtu.edu.cn (wangtaoiz)
Date: Thu, 13 Apr 2017 05:25:37 -0700 (MST)
Subject: [ITK-users] HistogramEqualization in ITK
Message-ID: <1492086337666-38108.post@n7.nabble.com>

Dear all
  I want to use itk::AdaptiveHistogramEqualizationImageFilter to do a
HistogramEqualization filter on a image as follow:
<http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_200959.png> 
So I set the parameters SetAlpha(0.5), SetBeta(0.5), the result is as
follow:
<http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_201446.png> 
but actually the result I want is showed as follow (which is generated by
opencv cvEqualizeHist() function):
<http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_201132.png> 
So I want to ask you if I can get that HistogramEqualization result by ITK?

Thanks a lot
Wang



--
View this message in context: http://itk-users.7.n7.nabble.com/HistogramEqualization-in-ITK-tp38108.html
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From blowekamp at mail.nih.gov  Thu Apr 13 09:00:28 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 13 Apr 2017 13:00:28 +0000
Subject: [ITK-users] [ITK]  HistogramEqualization in ITK
In-Reply-To: <1492086337666-38108.post@n7.nabble.com>
References: <1492086337666-38108.post@n7.nabble.com>
Message-ID: <88D11A0A-4B06-4DF1-9BE5-F13D5B9A7550@mail.nih.gov>

Hello,

You need to read and study the two algorithms closer. There is a referenced paper in the ITK documentation[1].

You should also look into the HistogramMatchingImageFilter [2].

HTH,
Brad

[1] https://itk.org/Doxygen/html/classitk_1_1AdaptiveHistogramEqualizationImageFilter.html
[2] https://itk.org/Doxygen/html/classitk_1_1HistogramMatchingImageFilter.html


> On Apr 13, 2017, at 8:25 AM, wangtaoiz <wangtao_ at sjtu.edu.cn> wrote:
> 
> Dear all
>  I want to use itk::AdaptiveHistogramEqualizationImageFilter to do a
> HistogramEqualization filter on a image as follow:
> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_200959.png> 
> So I set the parameters SetAlpha(0.5), SetBeta(0.5), the result is as
> follow:
> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_201446.png> 
> but actually the result I want is showed as follow (which is generated by
> opencv cvEqualizeHist() function):
> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_201132.png> 
> So I want to ask you if I can get that HistogramEqualization result by ITK?
> 
> Thanks a lot
> Wang
> 
> 
> 
> --
> View this message in context: http://itk-users.7.n7.nabble.com/HistogramEqualization-in-ITK-tp38108.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community


From sidharta.gupta93 at gmail.com  Thu Apr 13 09:04:04 2017
From: sidharta.gupta93 at gmail.com (sidharta)
Date: Thu, 13 Apr 2017 06:04:04 -0700 (MST)
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
 <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
Message-ID: <1492088644485-38110.post@n7.nabble.com>

Hi D?enan,

So I am doing something as follows: 

// Vectors for calculating normal_to_plane - The plane/slice I want to
extract

Vector3d ST, SP, normal_to_plane; // This is a custom 3D Vector library
ST = traj_start - traj_end; // start and end of the trajectory - vector 1
SP = traj_start - third_point; // start and third point gives another vector
- vector 2
// Now with two vectors I can get the direction of the normal to the plane
normal_to_plane = ST.cross(SP); // cross product essentially

// Getting angles between normal to the plane and the coordinate axes
double angle_plane_z = std::acos((normal_to_plane[2] * 1) /
norm(normal_to_plane)); // angle between plane and z axis
double angle_plane_y = std::acos((normal_to_plane[1] * 1) /
norm(normal_to_plane)); // angle between plane and y axis
double angle_plane_x = std::acos((normal_to_plane[0] * 1) /
norm(normal_to_plane)); // angle between plane and x axis

// Instantiate an Euler Transform
typedef itk::Euler3DTransform<double> ETransformType;
ETransformType::Pointer eulerTransform = ETransformType::New();

// This because - Quote from ITKSoftwareGuide "Rotations are performed
around the origin of physical coordinates?not the image origin nor the image
center"
ETransformType::OutputVectorType translation1;
translation1[0] = -origin_dcm[0]; // origin_dcm is the origin of the dicom
translation1[1] = -origin_dcm[1]; 
translation1[2] = -origin_dcm[2];
eulerTransform->Translate(translation1);
eulerTransform->SetRotation(angle_plane_x, angle_plane_y, angle_plane_z);

// Get back to the origin of the dicom
ETransformType::OutputVectorType translation2;
translation2[0] = origin_dcm[0];
translation2[1] = origin_dcm[1];
translation2[2] = origin_dcm[2];

// Instantiate the ResampleFilter
// typedef double InternalPixelType;
// typedef itk::Image< InternalPixelType, Dimension > InternalImageType; //
For clarity
typedef itk::ResampleImageFilter<InternalImageType, InternalImageType>
ResampleFilterType;

ResampleFilterType::Pointer filter = ResampleFilterType::New();

typedef itk::NearestNeighborInterpolateImageFunction<
		InternalImageType, double> InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
filter->SetInterpolator(interpolator);

filter->SetDefaultPixelValue(0);
filter->SetOutputSpacing(image->GetSpacing());
filter->SetOutputOrigin(image->GetOrigin()); // If I change this to
traj_start, the dicom looks completely off, as in not intended.
filter->SetOutputDirection(image->GetDirection()); // I have my doubts about
this too
filter->SetSize(image->GetSize()); // Of course, as you suggested, I would
set the thickness here as 1, but I was doing this for testing purposes.
filter->SetInput(image);

So, what do you think about this code? Am I doing it correctly? I feel
really dumb asking you to check my code but unfortunately I can't find any
relevant example for 3D resampling. Additionally, (no offense) but I don't
get what you mean by "target region index" with respect to the resampling
filter? Do you mean the SetOrigin()? As you also see, I am essentially not
applying any translation to the origin. Just a rotation for testing
purposes.

Thank you for your time.
Best Regards,
Sidharta





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View this message in context: http://itk-users.7.n7.nabble.com/Extract-slice-from-ResampleFilter-tp38074p38110.html
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From francois.budin at kitware.com  Thu Apr 13 09:06:39 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Thu, 13 Apr 2017 09:06:39 -0400
Subject: [ITK-users] HistogramEqualization in ITK
In-Reply-To: <1492086337666-38108.post@n7.nabble.com>
References: <1492086337666-38108.post@n7.nabble.com>
Message-ID: <CAHwLD2VhjhAmCj-yV5y9qui3dOrmVWxgNDCqAiM8OUABBv2MVQ@mail.gmail.com>

Hello Wang,

One good way to explore the parameters to figure out which set gives you
the result you want would be to write a short Python script:
reader=itk.ImageFileReader[itk.Image[itk.UC,2]].New(FileName="/home/fbudin/Downloads/chest.png")
myFilter=itk.AdaptiveHistogramEqualizationImageFilter.New(reader)
for alpha in range(0,11):
  for beta in range(0,11):
    myFilter.SetAlpha(alpha*.1)
    myFilter.SetBeta(beta*.1)
    filename="/tmp/myFilter"+str(alpha)+"_"+str(beta)+".png"
    itk.ImageFileWriter.New(hm,FileName=filename).Update()

I was not able to generate an image that looked exactly like the "opencv"
image you sent, but that may be due to:
-The implementation of this algorithm in OpenCV is different
-The difference of the output is only due to different visualization
parameters (Window/Level settings that are different for the different
images).

Hope this helps,
Francois

On Thu, Apr 13, 2017 at 8:25 AM, wangtaoiz <wangtao_ at sjtu.edu.cn> wrote:

> Dear all
>   I want to use itk::AdaptiveHistogramEqualizationImageFilter to do a
> HistogramEqualization filter on a image as follow:
> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_200959.png>
> So I set the parameters SetAlpha(0.5), SetBeta(0.5), the result is as
> follow:
> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_201446.png>
> but actually the result I want is showed as follow (which is generated by
> opencv cvEqualizeHist() function):
> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_201132.png>
> So I want to ask you if I can get that HistogramEqualization result by ITK?
>
> Thanks a lot
> Wang
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/HistogramEqualization-in-ITK-tp38108.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From francois.budin at kitware.com  Thu Apr 13 09:12:23 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Thu, 13 Apr 2017 09:12:23 -0400
Subject: [ITK-users] HistogramEqualization in ITK
In-Reply-To: <CAHwLD2VhjhAmCj-yV5y9qui3dOrmVWxgNDCqAiM8OUABBv2MVQ@mail.gmail.com>
References: <1492086337666-38108.post@n7.nabble.com>
 <CAHwLD2VhjhAmCj-yV5y9qui3dOrmVWxgNDCqAiM8OUABBv2MVQ@mail.gmail.com>
Message-ID: <CAHwLD2U=Sx3z6__nOdM6aR7s2o0WD1QaHj+ETK48io3OYMwbMw@mail.gmail.com>

Correction on the last line of what I sent:
    itk.ImageFileWriter.New(myFilter,FileName=filename).Update()

On Thu, Apr 13, 2017 at 9:06 AM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Wang,
>
> One good way to explore the parameters to figure out which set gives you
> the result you want would be to write a short Python script:
> reader=itk.ImageFileReader[itk.Image[itk.UC,2]].New(
> FileName="/home/fbudin/Downloads/chest.png")
> myFilter=itk.AdaptiveHistogramEqualizationImageFilter.New(reader)
> for alpha in range(0,11):
>   for beta in range(0,11):
>     myFilter.SetAlpha(alpha*.1)
>     myFilter.SetBeta(beta*.1)
>     filename="/tmp/myFilter"+str(alpha)+"_"+str(beta)+".png"
>     itk.ImageFileWriter.New(hm,FileName=filename).Update()
>
> I was not able to generate an image that looked exactly like the "opencv"
> image you sent, but that may be due to:
> -The implementation of this algorithm in OpenCV is different
> -The difference of the output is only due to different visualization
> parameters (Window/Level settings that are different for the different
> images).
>
> Hope this helps,
> Francois
>
> On Thu, Apr 13, 2017 at 8:25 AM, wangtaoiz <wangtao_ at sjtu.edu.cn> wrote:
>
>> Dear all
>>   I want to use itk::AdaptiveHistogramEqualizationImageFilter to do a
>> HistogramEqualization filter on a image as follow:
>> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_200959.png
>> >
>> So I set the parameters SetAlpha(0.5), SetBeta(0.5), the result is as
>> follow:
>> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_201446.png
>> >
>> but actually the result I want is showed as follow (which is generated by
>> opencv cvEqualizeHist() function):
>> <http://itk-users.7.n7.nabble.com/file/n38108/snipaste20170413_201132.png
>> >
>> So I want to ask you if I can get that HistogramEqualization result by
>> ITK?
>>
>> Thanks a lot
>> Wang
>>
>>
>>
>> --
>> View this message in context: http://itk-users.7.n7.nabble.c
>> om/HistogramEqualization-in-ITK-tp38108.html
>> Sent from the ITK - Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
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From dzenanz at gmail.com  Thu Apr 13 10:37:12 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Apr 2017 10:37:12 -0400
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <1492088644485-38110.post@n7.nabble.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
 <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
 <1492088644485-38110.post@n7.nabble.com>
Message-ID: <CAPf2UMR-XDnwXmjE3aHfekZ4geEe2oXN0ge4F8xJtduBmooQ3Q@mail.gmail.com>

Hi Sidartha,

the code looks OK. The index is [0,0,0] by default, so just setting size is
enough. My idea was not to apply translation2, then you would not have to
set origin on the resample filter (it would start from [0,0,0]).

I think you are forgetting to apply second translation, and you are not
applying any transformation to the resample filter. Something like this is
needed:
filter->SetTransform(eulerTransform);

What results are you getting?

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Thu, Apr 13, 2017 at 9:04 AM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> Hi D?enan,
>
> So I am doing something as follows:
>
> // Vectors for calculating normal_to_plane - The plane/slice I want to
> extract
>
> Vector3d ST, SP, normal_to_plane; // This is a custom 3D Vector library
> ST = traj_start - traj_end; // start and end of the trajectory - vector 1
> SP = traj_start - third_point; // start and third point gives another
> vector
> - vector 2
> // Now with two vectors I can get the direction of the normal to the plane
> normal_to_plane = ST.cross(SP); // cross product essentially
>
> // Getting angles between normal to the plane and the coordinate axes
> double angle_plane_z = std::acos((normal_to_plane[2] * 1) /
> norm(normal_to_plane)); // angle between plane and z axis
> double angle_plane_y = std::acos((normal_to_plane[1] * 1) /
> norm(normal_to_plane)); // angle between plane and y axis
> double angle_plane_x = std::acos((normal_to_plane[0] * 1) /
> norm(normal_to_plane)); // angle between plane and x axis
>
> // Instantiate an Euler Transform
> typedef itk::Euler3DTransform<double> ETransformType;
> ETransformType::Pointer eulerTransform = ETransformType::New();
>
> // This because - Quote from ITKSoftwareGuide "Rotations are performed
> around the origin of physical coordinates?not the image origin nor the
> image
> center"
> ETransformType::OutputVectorType translation1;
> translation1[0] = -origin_dcm[0]; // origin_dcm is the origin of the dicom
> translation1[1] = -origin_dcm[1];
> translation1[2] = -origin_dcm[2];
> eulerTransform->Translate(translation1);
> eulerTransform->SetRotation(angle_plane_x, angle_plane_y, angle_plane_z);
>
> // Get back to the origin of the dicom
> ETransformType::OutputVectorType translation2;
> translation2[0] = origin_dcm[0];
> translation2[1] = origin_dcm[1];
> translation2[2] = origin_dcm[2];
>
> // Instantiate the ResampleFilter
> // typedef double InternalPixelType;
> // typedef itk::Image< InternalPixelType, Dimension > InternalImageType; //
> For clarity
> typedef itk::ResampleImageFilter<InternalImageType, InternalImageType>
> ResampleFilterType;
>
> ResampleFilterType::Pointer filter = ResampleFilterType::New();
>
> typedef itk::NearestNeighborInterpolateImageFunction<
>                 InternalImageType, double> InterpolatorType;
> InterpolatorType::Pointer interpolator = InterpolatorType::New();
> filter->SetInterpolator(interpolator);
>
> filter->SetDefaultPixelValue(0);
> filter->SetOutputSpacing(image->GetSpacing());
> filter->SetOutputOrigin(image->GetOrigin()); // If I change this to
> traj_start, the dicom looks completely off, as in not intended.
> filter->SetOutputDirection(image->GetDirection()); // I have my doubts
> about
> this too
> filter->SetSize(image->GetSize()); // Of course, as you suggested, I would
> set the thickness here as 1, but I was doing this for testing purposes.
> filter->SetInput(image);
>
> So, what do you think about this code? Am I doing it correctly? I feel
> really dumb asking you to check my code but unfortunately I can't find any
> relevant example for 3D resampling. Additionally, (no offense) but I don't
> get what you mean by "target region index" with respect to the resampling
> filter? Do you mean the SetOrigin()? As you also see, I am essentially not
> applying any translation to the origin. Just a rotation for testing
> purposes.
>
> Thank you for your time.
> Best Regards,
> Sidharta
>
>
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074p38110.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From dzenanz at gmail.com  Thu Apr 13 10:48:40 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Apr 2017 10:48:40 -0400
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <CAPf2UMSiCv7BTcu7kuq-ZaX2gTVwcoUxk3S4MgTfdtPY7khBLw@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>
 <CAPf2UMTzTTRTQpFKJj_vnx88XN+PoZmiiQvJg3k1huk=zqv1Dg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968862@MBX212.d.ethz.ch>
 <CAHwLD2UN1-ULXN4oT2FCJa0UCzF7XmaXB3LJqwVOC9R4p8GGBw@mail.gmail.com>
 <CAPf2UMSiCv7BTcu7kuq-ZaX2gTVwcoUxk3S4MgTfdtPY7khBLw@mail.gmail.com>
Message-ID: <CAPf2UMRgovC=UE-CHmmSyxsY=QowKz8TXGhjk+O5DeW-gy3Vpw@mail.gmail.com>

Hi Fabio,

the first error is coming from ITKCommonCastXML project, and the other
first 1000 errors are also coming from*CastXML and *Swig projects. This
means that the wrapping infrastructure is somehow triggering that bug in
VS2017.

The easiest thing to try is update CastXML, which Matt said would take care
of. Let's see if that helps.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Wed, Apr 12, 2017 at 4:50 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Fabio,
>
> it looks like we will have to wait somewhat until VS writers get around to
> implement __builtin_offsetof
> <https://developercommunity.visualstudio.com/content/problem/22196/static-assert-cannot-compile-constexprs-method-tha.html>
>
> I don't know why it doesn't trigger when Python wrapping is OFF. I will
> look into it more.
>
> Regards,
> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Wed, Apr 12, 2017 at 4:26 PM, Francois Budin <
> francois.budin at kitware.com> wrote:
>
>> Fabio,
>>
>> To add a little bit of extra information about using BridgeNumpy:
>>
>> From NumPy to ITK, the memory is never copied, and always shared between
>> the NumPy array and the ITK image.
>> From ITK to NumPy, the memory is not copied at first, if the data is not
>> changed from the NumPy side (e.g. if the ITK image is changed, the NumPy
>> array will be modified too), but if you modify the NumPy array directly,
>> NumPy will create a copy of the data. This also means that if you were to
>> modify the NumPy array, the modifications would not be visible in the ITK
>> image.
>>
>> A limited workaround to this is:
>>
>> # Get NumPy array from image
>> arr_image = itk.GetArrayFromImage(image)
>> # Create copy of array that can be modified in-place
>> arr = arr_image.copy()
>> # Modify array
>> ?
>> # Update image in-place with new array
>> arr_image.setfield(arr,arr_image.dtype)
>>
>> The advantage of this method is that the image will be updated. However,
>> there is an explicit copy of your data.
>> If the copy step is skipped and the original NumPy array is modified, a
>> copy of the data will be performed by NumPy and you may not be aware of it
>> until you see that the data in the NumPy array and the image do not match
>> anymore.
>>
>> Hope this helps,
>> Francois
>>
>> On Wed, Apr 12, 2017 at 4:02 PM, D'Isidoro Fabio <fisidoro at ethz.ch>
>> wrote:
>>
>>> Ok, thanks. Moe specifically I am using now *Visual Studio 2017 Preview*
>>> .
>>>
>>>
>>>
>>> Fabio.
>>>
>>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>>> *Sent:* Mittwoch, 12. April 2017 21:54
>>> *To:* D'Isidoro Fabio <fisidoro at ethz.ch>
>>> *Cc:* Matt McCormick <matt.mccormick at kitware.com>; insight-users at itk.org
>>>
>>> *Subject:* Re: [ITK-users] ITK Python: numpy to itk image (and
>>> viceversa)
>>>
>>>
>>>
>>> Hi Fabio,
>>>
>>>
>>>
>>> let me give it a try with VS2017 and Wrapping+NumPy. I will report back
>>> when I have an update.
>>>
>>>
>>>
>>> Regards,
>>>
>>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>>
>>>
>>>
>>> On Wed, Apr 12, 2017 at 2:16 PM, D'Isidoro Fabio <fisidoro at ethz.ch>
>>> wrote:
>>>
>>> Thank you. I am trying to build ITK Wrap Python with
>>> Module_BridgeNumPy=ON with Visual Studio 2017.
>>>
>>> I get the following type of errors:
>>>
>>> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
>>> ols/MSVC/14.10.25017/include\xstring(1905,26): error G3F63BFAE:
>>> constexpr variable '_Memcpy_move_offset' must be initialized by a constant
>>> expression
>>> 12>        static constexpr size_t _Memcpy_move_offset =
>>> offsetof(_Mydata_t, _Bx);
>>> 12>                                ^
>>>  ~~~~~~~~~~~~~~~~~~~~~~~~
>>> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
>>> ols/MSVC/14.10.25017/include\stdexcept:23:21: note: in instantiation of
>>> template class 'std::basic_string<char, std::char_traits<char>,
>>> std::allocator<char> >' requested here
>>> 12>                : _Mybase(_Message.c_str())
>>> 12>                                  ^
>>> 12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/To
>>> ols/MSVC/14.10.25017/include\xstring:1905:48: note: cast that performs
>>> the conversions of a reinterpret_cast is not allowed in a constant
>>> expression
>>> 12>        static constexpr size_t _Memcpy_move_offset =
>>> offsetof(_Mydata_t, _Bx);
>>> 12>                                                      ^
>>> 12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32:
>>> note: expanded from macro 'offsetof'
>>> 12>        #define offsetof(s,m) ((size_t)&reinterpret_cast<char const
>>> volatile&>((((s*)0)->m)))
>>>
>>>
>>> The build worked with Visual Studio 2015 instead.
>>>
>>> Can I fix this issue with Visual Studio 2017 somehow?
>>>
>>> Thank you.
>>>
>>> ----------------------------------------------------------------------
>>> Fabio D?Isidoro - PhD Student
>>> Institute of Biomechanics
>>> HPP O 14
>>> H?nggerbergring 64
>>> 8093 Z?rich, Switzerland
>>>
>>>
>>> -----Original Message-----
>>> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
>>> Sent: Montag, 3. April 2017 20:41
>>> To: D'Isidoro Fabio <fisidoro at ethz.ch>
>>> Cc: insight-users at itk.org
>>> Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>>>
>>> Hallo Fabio,
>>>
>>>
>>> > I use ITK with Python Wrap. I need to interface my Python code with a
>>> > Cython-wrapped C++ code that takes only numpy array as input and
>>> > returns numpy array as output.
>>>
>>> Cool. By the way, you may be interested in scikit-build [1], which is a
>>> good way to build Cython-wrapped C++ code. We are using it for the ITK and
>>> SimpleITK Python packages, and it has good Cython and CMake support.
>>>
>>>
>>> > Hence, I need to convert the Python itk images into numpy array to be
>>> > given as input to the wrapped C++ code, and then convert the numpy
>>> > array in output from the wrapped C++ code back into python itk images.
>>> >
>>> >
>>> >
>>> > Question 1) How can I do that in an efficient way? I found some posts
>>> > on itk.PyBuffer but I could not find anywhere any reference on how to
>>> > install it on my itk wrap build.
>>>
>>> Yes, itk.PyBuffer works great for that. Please review a PR for some
>>> additional documentation:
>>>
>>>   https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18
>>>
>>> This has been available in ITK for a few releases as a Remote module,
>>> which can be enabled by setting
>>>
>>>   Module_BridgeNumPy=ON
>>>
>>> in ITK's CMake configuration.
>>>
>>>
>>> Since ITK 4.11.0, it is easier to build since it does not require the
>>> NumPy headers.
>>>
>>>
>>> In current ITK Git master (to be 4.12.0) the module is enabled by
>>> default.
>>>
>>>
>>> Nightly ITK Python packages for ITK Git master are now being built:
>>>
>>>   https://github.com/InsightSoftwareConsortium/ITKPythonPackage
>>>
>>> macOS and Linux are available. Windows packages will be available over
>>> the coming weeks.
>>>
>>>
>>>
>>> > Question 2) The purpose of writing a part of my algorithm in C++ is to
>>> > speed up the code. If the conversion between python itk images and
>>> > numpy arrays is slow, I would lose all the speed gain obtained with
>>> the C++ implementation.
>>> > Are there better ways to deal with that?
>>>
>>> The newer versions ITKBridgeNumPy use a NumPy array view, which does not
>>> do any copies during the conversion, and it is very fast.
>>>
>>>
>>> HTH,
>>> Matt
>>>
>>>
>>> [1] http://scikit-build.org/
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>
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From sidharta.gupta93 at gmail.com  Thu Apr 13 11:01:24 2017
From: sidharta.gupta93 at gmail.com (sidharta)
Date: Thu, 13 Apr 2017 08:01:24 -0700 (MST)
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <CAPf2UMR-XDnwXmjE3aHfekZ4geEe2oXN0ge4F8xJtduBmooQ3Q@mail.gmail.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
 <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
 <1492088644485-38110.post@n7.nabble.com>
 <CAPf2UMR-XDnwXmjE3aHfekZ4geEe2oXN0ge4F8xJtduBmooQ3Q@mail.gmail.com>
Message-ID: <1492095684045-38115.post@n7.nabble.com>

Hi  D?enan,

Sorry about that, I missed the line in the post. I am, in fact, adding that
line filter->SetTransform(). 

Apologies, but I don't know how I can share .dcm/.mhd image. I am just going
to add the desirable which I did using Amira, which is where I got the idea
of using EulerTransform. 
<http://itk-users.7.n7.nabble.com/file/n38115/snapshot.jpg> . The big sphere
is the third point and the two small ones are the start and end of the
trajectory. The slices on the bounding box are essentially on the origin.
So, with vector math I could get the equation of the plane and so forth. If
you want to see the output .dcm, kindly let me know how I can share it with
you ( from a cloud probably but I don't know what you prefer).

Thank you for your swift reply and patience.

Regards,
Sidharta



--
View this message in context: http://itk-users.7.n7.nabble.com/Extract-slice-from-ResampleFilter-tp38074p38115.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From dzenanz at gmail.com  Thu Apr 13 11:13:32 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Apr 2017 11:13:32 -0400
Subject: [ITK-users] Rotating image results in last slices being half
	empty
In-Reply-To: <1491689302258-38081.post@n7.nabble.com>
References: <1491689302258-38081.post@n7.nabble.com>
Message-ID: <CAPf2UMTPg3Ntp=W7y-5ONO43DnVcGB+RXZ0aacqP2gaE_bBC1w@mail.gmail.com>

Hi Matias,

you are not using origenX or origenY after they are defined. But your
program (with modifications to make it compile) works for me:
[image: Inline image 1]

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Sat, Apr 8, 2017 at 6:08 PM, Matias <matimontg at gmail.com> wrote:

> Hi, I'm rotating a volume (Using the Euler3DTransform) and the final set
> of slices are half black or empty. here's an example when rotating a volume
> of 10 slices: Am I missing something such as changing the origin or maybe
> computing the center incorrectly? (The center is passed as parameter from
> another program) And here's the code I'm using: typedef
> itk::ResampleImageFilter<ImageType, ImageType> FilterType;
> FilterType::Pointer FiltroResample = FilterType::New();
> FiltroResample->SetInput(reader->GetOutput()); typedef itk::
> LinearInterpolateImageFunction<ImageType, double > InterpolatorType;
> InterpolatorType::Pointer interpolator = InterpolatorType::New();
> FiltroResample->SetInterpolator(interpolator); FiltroResample->
> SetOutputDirection(inputImage->GetDirection()); FiltroResample->
> SetOutputOrigin(inputImage->GetOrigin()); ImageType::SizeType inputSize =
> inputImage->GetLargestPossibleRegion().GetSize(); FiltroResample->SetSize(inputSize);
> const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
> FiltroResample->SetOutputSpacing(inputSpacing); FiltroResample->SetDefaultPixelValue(-1000);
> typedef itk::Euler3DTransform< double > TransformType; //Transform
> TransformType::Pointer transform = TransformType::New(); double alfa, beta,
> gamma, centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z,
> origenX,origenY; gamma = atof(argv[2]); beta = atof(argv[3]); alfa =
> atof(argv[4]); centro_rotacion_X = atof(argv[5]); centro_rotacion_Y =
> atof(argv[6]); centro_rotacion_Z = atof(argv[7]); origenX = atof(argv[8]);
> origenY = atof(argv[9]); transform->SetRotation(gamma, beta, alfa); double
> centro[3] = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z };
> transform->SetCenter(centro); FiltroResample->SetTransform(transform);
> FiltroResample->Update();
> ------------------------------
> View this message in context: Rotating image results in last slices being
> half empty
> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081.html>
> Sent from the ITK - Users mailing list archive
> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Thu Apr 13 11:16:23 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Apr 2017 11:16:23 -0400
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <1492095684045-38115.post@n7.nabble.com>
References: <1491482054290-38074.post@n7.nabble.com>
 <CAPf2UMSnuk2Y78rjJ6NMT30N9J2=db9DDc0RSYaiT6mbMBKdtQ@mail.gmail.com>
 <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
 <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
 <1492088644485-38110.post@n7.nabble.com>
 <CAPf2UMR-XDnwXmjE3aHfekZ4geEe2oXN0ge4F8xJtduBmooQ3Q@mail.gmail.com>
 <1492095684045-38115.post@n7.nabble.com>
Message-ID: <CAPf2UMTwVyFK-=wj8=3n0BL+e4fW8OPjZNYvM=Em87-NygT0MA@mail.gmail.com>

?Hi Siddartha,

you can share using cloud tools, e.g. Dropbox or Google Drive.

But I think you forgot to ask the question: I don't know what you are
asking.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)?

On Thu, Apr 13, 2017 at 11:01 AM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> Hi  D?enan,
>
> Sorry about that, I missed the line in the post. I am, in fact, adding that
> line filter->SetTransform().
>
> Apologies, but I don't know how I can share .dcm/.mhd image. I am just
> going
> to add the desirable which I did using Amira, which is where I got the idea
> of using EulerTransform.
> <http://itk-users.7.n7.nabble.com/file/n38115/snapshot.jpg> . The big
> sphere
> is the third point and the two small ones are the start and end of the
> trajectory. The slices on the bounding box are essentially on the origin.
> So, with vector math I could get the equation of the plane and so forth. If
> you want to see the output .dcm, kindly let me know how I can share it with
> you ( from a cloud probably but I don't know what you prefer).
>
> Thank you for your swift reply and patience.
>
> Regards,
> Sidharta
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074p38115.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From sidharta.gupta93 at gmail.com  Thu Apr 13 11:33:52 2017
From: sidharta.gupta93 at gmail.com (sidharta)
Date: Thu, 13 Apr 2017 08:33:52 -0700 (MST)
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <CAPf2UMTwVyFK-=wj8=3n0BL+e4fW8OPjZNYvM=Em87-NygT0MA@mail.gmail.com>
References: <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
 <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
 <1492088644485-38110.post@n7.nabble.com>
 <CAPf2UMR-XDnwXmjE3aHfekZ4geEe2oXN0ge4F8xJtduBmooQ3Q@mail.gmail.com>
 <1492095684045-38115.post@n7.nabble.com>
 <CAPf2UMTwVyFK-=wj8=3n0BL+e4fW8OPjZNYvM=Em87-NygT0MA@mail.gmail.com>
Message-ID: <1492097632375-38118.post@n7.nabble.com>

So if you think the code is correct and is doing what you suggested (or what
I think it should do using the eulerTransform), you mentioned setting
targetRegionIndex in ResampleFilter to get one single slice. I don't see
this targetRegionIndex or do you mean set origin. I am going to send you the
link to the dropbox folder in a private mail.



--
View this message in context: http://itk-users.7.n7.nabble.com/Extract-slice-from-ResampleFilter-tp38074p38118.html
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From dzenanz at gmail.com  Thu Apr 13 13:44:58 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 13 Apr 2017 13:44:58 -0400
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <1492097632375-38118.post@n7.nabble.com>
References: <1491816595489-38084.post@n7.nabble.com>
 <CAPf2UMSTW=6Ym69o=mc07T3N6Wu9nZEw3w0-AcXQkV6H3ZfHng@mail.gmail.com>
 <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
 <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
 <1492088644485-38110.post@n7.nabble.com>
 <CAPf2UMR-XDnwXmjE3aHfekZ4geEe2oXN0ge4F8xJtduBmooQ3Q@mail.gmail.com>
 <1492095684045-38115.post@n7.nabble.com>
 <CAPf2UMTwVyFK-=wj8=3n0BL+e4fW8OPjZNYvM=Em87-NygT0MA@mail.gmail.com>
 <1492097632375-38118.post@n7.nabble.com>
Message-ID: <CAPf2UMQrJGSxRZZKMgVdBz=1wGjmfZc_HL=aA_sPC1P9xrxhzw@mail.gmail.com>

The target region is the region (index and size) you set in the resample
filter. It is just a difference in terminology between you and me.

I took a look at the images you supplied. Because of transformations, this
is hard to debug.

I realized it would be easier to construct the output image to be in the
same physical space as the input image, and have identity transform applied
to resample filter (used by default). Pseudo-code:

ImageType::DirectionType dir;
ST.normalize();
dir[0]=ST; //vector from first point to second
vec3 second=normal.cross(ST); //make the second vector orthogonal to first
and the normal
second.normalize();
dir[1]=second;
normal.normalize();
dir[2]=normal;
filter->SetOutputDirection(dir);
filter->SetOrigin(traj_start);
//it will be more math to compute proper size (so that resampled image ends
at traj_end), and proper spacing (project original spacing onto coordinate
system established by new dir matrix or use isotropic spacing equal to
cubic root of sp[0]*sp[1]*sp[2]).

With this approach you can use e.g. Slicer <https://www.slicer.org/> to
look at both the original and resampled images, and also define fiducial
points for your 3 points of interest.

P.S. If you share any more images, please save them with compression
applied (writer->SetUseCompression(true);).

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Thu, Apr 13, 2017 at 11:33 AM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> So if you think the code is correct and is doing what you suggested (or
> what
> I think it should do using the eulerTransform), you mentioned setting
> targetRegionIndex in ResampleFilter to get one single slice. I don't see
> this targetRegionIndex or do you mean set origin. I am going to send you
> the
> link to the dropbox folder in a private mail.
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074p38118.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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From blowekamp at mail.nih.gov  Fri Apr 14 11:55:40 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Fri, 14 Apr 2017 15:55:40 +0000
Subject: [ITK-users] [ANN] SimpleITK 1.0.0 Release
Message-ID: <3A9B6734-7719-4069-8E7B-E0F1B35A0A5F@mail.nih.gov>

The SimpleITK Development Team and the Insight Software Consortium are proud to announce the first major release of SimpleITK.

SimpleITK is a simplified multi-language interface to the National Library of Medicine?s Insight Segmentation and Registration Toolkit (ITK). Providing an easy to use interface to ITK.

SimpleITK is intended to broaden the use of ITK to researchers and domain scientist who are novice software developers, enabling them to benefit from the image-analysis power of ITK. For experienced software developers, the toolkit enables rapid prototyping of image segmentation and registration frameworks and facilitates evaluation of the effects algorithmic parameter settings have on results with minimal programming effort. In the educational setting SimpleITK's concise interface allows students to experiment with well known algorithms, enhancing their understanding of algorithm performance without the need for advanced software engineering skills.

The toolkit development process follows best software engineering practices including code reviews and continuous integration testing, with results displayed online allowing everyone to gauge the status of the current code and any code that is under consideration for incorporation into the toolkit. User support is available through a dedicated mailing list and the project?s Wiki.
SimpleITK is available for the following programing languages: Python, R, Java, C#, C++, Lua, Ruby, and TCL. Binary versions of the toolkit are available for the GNU Linux, Apple OS X, and Microsoft Windows operating systems. All of the source code is freely available on github under an Apache-2.0 license.


Downloading SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK Wiki (https://itk.org/Wiki/SimpleITK/GettingStarted).

- Python Binary Downloads

  - Python binary wheels are available for download. It is important to have the latest version of pip to ensure correct wheel compatibility and installation. To install the latest SimpleITK package form PyPI:
  ```
  pip install --upgrade pip
  pip install SimpleITK
  ```

  - Many Conda package have been upload to Anaconda Cloud on the `SimpleITK`. These can be installed with:
  ```
  conda install -c simpleitk simpleitk
  ```

- A complete available set of compiled binaries, including select CSharp and Java distributions, along with source and data tar-balls are available on Source Forge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/).


Release Notes

- Key Improvements:
  - Improved Python data bridge
    - New Python method `GetArrayViewFromImage` provides copy free read-only access
    - Updated Python data structures to use `memory view` objects
  - New language specific building SimpleITK front-ends
    - R devtools based installer (https://github.com/SimpleITK/SimpleITKRInstaller).
    - Python: scripts for building wheels (https://github.com/SimpleITK/SimpleITKPythonPackage) and a Conda recipe (https://github.com/SimpleITK/SimpleITKCondaRecipe).
  - Improved writing DICOM tags when writing a slice, and disabled writing a DICOM series with the ImageSeriesWriter
  - Support use of virtual image domain in the `ImageRegistrationMethod`
  - OnePlusOneOptimizer added to registration framework
  - Improved support for R: propogating C++ exceptions into R, additional R tests
  - Additional tests for Java
  - Python and R notebooks repository illustrating the basics and more advanced functionality of SimpleITK (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks)
  - Added continous integration via CircleCI
  - Updated version and improved integration of Google Test
  - Updated ITK version to 4.11.0+
  - Updated minimal required CMake version to 3.0, and numerous CMake changes to support various build configurations
  - Fix, "pip install" works for Apple Mac OS X.
  - Updated to usage of SWIG 3.0.11 ( using the latest SIWG is strongly recommended for R )
  - Reorganized examples directory into example based sub-directories with multiple languages
  - Improvements to documentation transmogrification scripts
  - Many bug fixes and improvement to the build system!

- Additional Improvements:
  - Added multi-hash ExternalData support for sha512
  - Added R Documentation files
  - Update Python and Java documentation strings files
  - Fix allowing undefined symbols when building standalone language wrapping
  - Reorganized examples directory
  - Reorganized filter libraries to match ITK modules
  - Improved compilation with more specific ITK module usage
  - Now using modern CMake 3 style properties for exported libraries

- API Changes
  - Replaced return Self with void for wrapped languages, to address memory and segmentation fault issue.
  - Depricated CMake variables with "SITK" prefix, now consistenly using the "SimpleITK" prefix for configurable CMake variables
  - Removed `ImageSeriesReader::GetGDCMSeriesFileNames` parameter `loadPrivateTags` parameter. This removes an overloaded version of the class method.
  - Added `sitkWallClock` enum for a sentinel value for random number seed to indicate initialization from the clock
  - New method `Image::GetNumberOfPixels`
  - New method `LabelMapContourOverlayImageFilter::SetColormap`
  - New method `LabelMapToRGBImageFilter::SetColormap`
  - New method `ImageRegistrationMethod::SetVirtualDomain`
  - New method `ImageRegistrationMethod::SetVirtualDomainFromImage`
  - New seed parameter to `ImageRegistrationMethod::AddMetricSamplingSeed` method
  - `CastImageFilter::SetOutputPixelType` method no longer accepts the pixel ID by value, uses only enumerated type


Enjoy!

Bradley Lowekamp

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From matimontg at gmail.com  Fri Apr 14 12:26:37 2017
From: matimontg at gmail.com (Matias)
Date: Fri, 14 Apr 2017 09:26:37 -0700 (MST)
Subject: [ITK-users] Rotating image results in last slices being half
 empty
In-Reply-To: <CAPf2UMTPg3Ntp=W7y-5ONO43DnVcGB+RXZ0aacqP2gaE_bBC1w@mail.gmail.com>
References: <1491689302258-38081.post@n7.nabble.com>
 <CAPf2UMTPg3Ntp=W7y-5ONO43DnVcGB+RXZ0aacqP2gaE_bBC1w@mail.gmail.com>
Message-ID: <CAKKNfuJgURGNVtmX15ZpF4=Ca=__VkAX6-2E3=MDnhW=7WHcoA@mail.gmail.com>

Thanks Dzenan. I actually use OrigenX and OrigenY to assign it to the DCM
tags. Just curious, how did you compile to use with Slicer?

El jue., 13 de abr. de 2017 a la(s) 12:14, D?enan Zuki? [via ITK - Users] <
ml-node+s7n38116h65 at n7.nabble.com> escribi?:

> Hi Matias,
>
> you are not using origenX or origenY after they are defined. But your
> program (with modifications to make it compile) works for me:
> [image: Inline image 1]
>
> Regards,
> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Sat, Apr 8, 2017 at 6:08 PM, Matias <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38116&i=0>> wrote:
>
>> Hi, I'm rotating a volume (Using the Euler3DTransform) and the final set
>> of slices are half black or empty. here's an example when rotating a volume
>> of 10 slices: Am I missing something such as changing the origin or maybe
>> computing the center incorrectly? (The center is passed as parameter from
>> another program) And here's the code I'm using: typedef
>> itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>> FilterType::Pointer FiltroResample = FilterType::New();
>> FiltroResample->SetInput(reader->GetOutput()); typedef
>> itk::LinearInterpolateImageFunction<ImageType, double > InterpolatorType;
>> InterpolatorType::Pointer interpolator = InterpolatorType::New();
>> FiltroResample->SetInterpolator(interpolator);
>> FiltroResample->SetOutputDirection(inputImage->GetDirection());
>> FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>> ImageType::SizeType inputSize =
>> inputImage->GetLargestPossibleRegion().GetSize();
>> FiltroResample->SetSize(inputSize); const ImageType::SpacingType&
>> inputSpacing = inputImage->GetSpacing();
>> FiltroResample->SetOutputSpacing(inputSpacing);
>> FiltroResample->SetDefaultPixelValue(-1000); typedef itk::Euler3DTransform<
>> double > TransformType; //Transform TransformType::Pointer transform =
>> TransformType::New(); double alfa, beta, gamma, centro_rotacion_X,
>> centro_rotacion_Y, centro_rotacion_Z, origenX,origenY; gamma =
>> atof(argv[2]); beta = atof(argv[3]); alfa = atof(argv[4]);
>> centro_rotacion_X = atof(argv[5]); centro_rotacion_Y = atof(argv[6]);
>> centro_rotacion_Z = atof(argv[7]); origenX = atof(argv[8]); origenY =
>> atof(argv[9]); transform->SetRotation(gamma, beta, alfa); double centro[3]
>> = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z };
>> transform->SetCenter(centro); FiltroResample->SetTransform(transform);
>> FiltroResample->Update();
>> ------------------------------
>> View this message in context: Rotating image results in last slices
>> being half empty
>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081.html>
>> Sent from the ITK - Users mailing list archive
>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
>
> http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081p38116.html
> To unsubscribe from Rotating image results in last slices being half
> empty, click here
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=38081&code=bWF0aW1vbnRnQGdtYWlsLmNvbXwzODA4MXwtMTk0NzIxNTA4Mw==>
> .
> NAML
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>
-- 
Matias




--
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From dzenanz at gmail.com  Fri Apr 14 13:15:49 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 14 Apr 2017 13:15:49 -0400
Subject: [ITK-users] Rotating image results in last slices being half
	empty
In-Reply-To: <CAKKNfuJgURGNVtmX15ZpF4=Ca=__VkAX6-2E3=MDnhW=7WHcoA@mail.gmail.com>
References: <1491689302258-38081.post@n7.nabble.com>
 <CAPf2UMTPg3Ntp=W7y-5ONO43DnVcGB+RXZ0aacqP2gaE_bBC1w@mail.gmail.com>
 <CAKKNfuJgURGNVtmX15ZpF4=Ca=__VkAX6-2E3=MDnhW=7WHcoA@mail.gmail.com>
Message-ID: <CAPf2UMTjW_QxdXGUUprRZnkPXAYe4GXpw2XQ4wBivF2L5AbhKg@mail.gmail.com>

Hi Matias,

I didn't compile to use with Slicer. I only open the input and output image
in Slicer to visualize them.

But making a Slicer CLI module is fairly easy. You can take a look at one
<https://github.com/Slicer/Slicer/tree/master/Modules/CLI/AddScalarVolumes/>
of the existing modules, docs
<https://www.slicer.org/wiki/Documentation/Nightly/Developers/Modules>
including
extension wizard
<https://www.slicer.org/wiki/Documentation/Nightly/Developers/ExtensionWizard>
.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Fri, Apr 14, 2017 at 12:26 PM, Matias <matimontg at gmail.com> wrote:

> Thanks Dzenan. I actually use OrigenX and OrigenY to assign it to the DCM
> tags. Just curious, how did you compile to use with Slicer?
>
> El jue., 13 de abr. de 2017 a la(s) 12:14, D?enan Zuki? [via ITK - Users] <[hidden
> email] <http:///user/SendEmail.jtp?type=node&node=38121&i=0>> escribi?:
>
>> Hi Matias,
>>
>> you are not using origenX or origenY after they are defined. But your
>> program (with modifications to make it compile) works for me:
>> [image: Inline image 1]
>>
>> Regards,
>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>
>> On Sat, Apr 8, 2017 at 6:08 PM, Matias <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=38116&i=0>> wrote:
>> Hi, I'm rotating a volume (Using the Euler3DTransform) and the final set
>> of slices are half black or empty. here's an example when rotating a volume
>> of 10 slices: Am I missing something such as changing the origin or maybe
>> computing the center incorrectly? (The center is passed as parameter from
>> another program) And here's the code I'm using: typedef
>> itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>> FilterType::Pointer FiltroResample = FilterType::New();
>> FiltroResample->SetInput(reader->GetOutput()); typedef itk::
>> LinearInterpolateImageFunction<ImageType, double > InterpolatorType;
>> InterpolatorType::Pointer interpolator = InterpolatorType::New();
>> FiltroResample->SetInterpolator(interpolator); FiltroResample->
>> SetOutputDirection(inputImage->GetDirection()); FiltroResample->
>> SetOutputOrigin(inputImage->GetOrigin()); ImageType::SizeType inputSize
>> = inputImage->GetLargestPossibleRegion().GetSize();
>> FiltroResample->SetSize(inputSize); const ImageType::SpacingType&
>> inputSpacing = inputImage->GetSpacing(); FiltroResample->
>> SetOutputSpacing(inputSpacing); FiltroResample->SetDefaultPixelValue(-1000);
>> typedef itk::Euler3DTransform< double > TransformType; //Transform
>> TransformType::Pointer transform = TransformType::New(); double alfa, beta,
>> gamma, centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z,
>> origenX,origenY; gamma = atof(argv[2]); beta = atof(argv[3]); alfa =
>> atof(argv[4]); centro_rotacion_X = atof(argv[5]); centro_rotacion_Y =
>> atof(argv[6]); centro_rotacion_Z = atof(argv[7]); origenX = atof(argv[8]);
>> origenY = atof(argv[9]); transform->SetRotation(gamma, beta, alfa); double
>> centro[3] = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z };
>> transform->SetCenter(centro); FiltroResample->SetTransform(transform);
>> FiltroResample->Update();
>> ------------------------------
>> View this message in context: Rotating image results in last slices
>> being half empty
>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081.html>
>> Sent from the ITK - Users mailing list archive
>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
> http://itk-users.7.n7.nabble.com/Rotating-image-results-in-
> last-slices-being-half-empty-tp38081p38116.html
> To unsubscribe from Rotating image results in last slices being half
> empty, click here.
> NAML
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
> --
> Matias
>
> ------------------------------
> View this message in context: Re: [ITK-users] Rotating image results in
> last slices being half empty
> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081p38121.html>
>
> Sent from the ITK - Users mailing list archive
> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Fri Apr 14 13:16:53 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 14 Apr 2017 13:16:53 -0400
Subject: [ITK-users] Rotating image results in last slices being half
	empty
In-Reply-To: <CAPf2UMTjW_QxdXGUUprRZnkPXAYe4GXpw2XQ4wBivF2L5AbhKg@mail.gmail.com>
References: <1491689302258-38081.post@n7.nabble.com>
 <CAPf2UMTPg3Ntp=W7y-5ONO43DnVcGB+RXZ0aacqP2gaE_bBC1w@mail.gmail.com>
 <CAKKNfuJgURGNVtmX15ZpF4=Ca=__VkAX6-2E3=MDnhW=7WHcoA@mail.gmail.com>
 <CAPf2UMTjW_QxdXGUUprRZnkPXAYe4GXpw2XQ4wBivF2L5AbhKg@mail.gmail.com>
Message-ID: <CAPf2UMTgGvgj06Seb7MjvicBxZ0cr30MddD7P=syzHCHp6nE4Q@mail.gmail.com>

Here is the code I used:

#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
#include <itkResampleImageFilter.h>
#include <itkEuler3DTransform.h>

template< typename TImage >
itk::SmartPointer<TImage> ReadImage(const char *filename)
{
    typedef itk::ImageFileReader<TImage> ReaderType;
    typename ReaderType::Pointer r = ReaderType::New();
    r->SetFileName(filename);
    r->Update();
    return r->GetOutput();
}

template< typename TImage >
void WriteImage(itk::SmartPointer<TImage> out, const char *filename)
{
    typedef itk::ImageFileWriter<TImage> WriterType;
    typename WriterType::Pointer w = WriterType::New();
    w->SetInput(out);
    w->SetFileName(filename);
    //w->SetUseCompression(true);
    w->Update();
}

int main(int argc, char *argv[])
{
    const unsigned int dimension = 3;
    typedef itk::Image<short, dimension> ImageType;
    ImageType::Pointer inputImage = ReadImage<ImageType>("C:/CBCT.nrrd");

    typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
    FilterType::Pointer FiltroResample = FilterType::New();
    FiltroResample->SetInput(inputImage);
    typedef itk::LinearInterpolateImageFunction<ImageType, double>
InterpolatorType;
    InterpolatorType::Pointer interpolator = InterpolatorType::New();
    FiltroResample->SetInterpolator(interpolator);
    FiltroResample->SetOutputDirection(inputImage->GetDirection());
    FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
    ImageType::SizeType inputSize =
inputImage->GetLargestPossibleRegion().GetSize();
    FiltroResample->SetSize(inputSize);
    const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
    FiltroResample->SetOutputSpacing(inputSpacing);
    FiltroResample->SetDefaultPixelValue(-1000);
    typedef itk::Euler3DTransform<double> TransformType;
    TransformType::Pointer transform = TransformType::New();
    transform->SetRotation(0.2, 0.3, 0.5);
    double centro[3] = { 10,20,30 };
    transform->SetCenter(centro);
    FiltroResample->SetTransform(transform);
    FiltroResample->Update();
    WriteImage<ImageType>(FiltroResample->GetOutput(),
"C:/cbctResampled.nrrd");
}

On Fri, Apr 14, 2017 at 1:15 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Matias,
>
> I didn't compile to use with Slicer. I only open the input and output
> image in Slicer to visualize them.
>
> But making a Slicer CLI module is fairly easy. You can take a look at one
> <https://github.com/Slicer/Slicer/tree/master/Modules/CLI/AddScalarVolumes/>
> of the existing modules, docs
> <https://www.slicer.org/wiki/Documentation/Nightly/Developers/Modules> including
> extension wizard
> <https://www.slicer.org/wiki/Documentation/Nightly/Developers/ExtensionWizard>
> .
>
> Regards,
> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Fri, Apr 14, 2017 at 12:26 PM, Matias <matimontg at gmail.com> wrote:
>
>> Thanks Dzenan. I actually use OrigenX and OrigenY to assign it to the DCM
>> tags. Just curious, how did you compile to use with Slicer?
>>
>> El jue., 13 de abr. de 2017 a la(s) 12:14, D?enan Zuki? [via ITK - Users]
>> <[hidden email] <http:///user/SendEmail.jtp?type=node&node=38121&i=0>>
>> escribi?:
>>
>>> Hi Matias,
>>>
>>> you are not using origenX or origenY after they are defined. But your
>>> program (with modifications to make it compile) works for me:
>>> [image: Inline image 1]
>>>
>>> Regards,
>>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>>
>>> On Sat, Apr 8, 2017 at 6:08 PM, Matias <[hidden email]
>>> <http:///user/SendEmail.jtp?type=node&node=38116&i=0>> wrote:
>>> Hi, I'm rotating a volume (Using the Euler3DTransform) and the final set
>>> of slices are half black or empty. here's an example when rotating a volume
>>> of 10 slices: Am I missing something such as changing the origin or maybe
>>> computing the center incorrectly? (The center is passed as parameter from
>>> another program) And here's the code I'm using: typedef
>>> itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>>> FilterType::Pointer FiltroResample = FilterType::New();
>>> FiltroResample->SetInput(reader->GetOutput()); typedef
>>> itk::LinearInterpolateImageFunction<ImageType, double >
>>> InterpolatorType; InterpolatorType::Pointer interpolator =
>>> InterpolatorType::New(); FiltroResample->SetInterpolator(interpolator);
>>> FiltroResample->SetOutputDirection(inputImage->GetDirection());
>>> FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>>> ImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().GetSize();
>>> FiltroResample->SetSize(inputSize); const ImageType::SpacingType&
>>> inputSpacing = inputImage->GetSpacing(); FiltroResample->SetOutputSpacing(inputSpacing);
>>> FiltroResample->SetDefaultPixelValue(-1000); typedef
>>> itk::Euler3DTransform< double > TransformType; //Transform
>>> TransformType::Pointer transform = TransformType::New(); double alfa, beta,
>>> gamma, centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z,
>>> origenX,origenY; gamma = atof(argv[2]); beta = atof(argv[3]); alfa =
>>> atof(argv[4]); centro_rotacion_X = atof(argv[5]); centro_rotacion_Y =
>>> atof(argv[6]); centro_rotacion_Z = atof(argv[7]); origenX = atof(argv[8]);
>>> origenY = atof(argv[9]); transform->SetRotation(gamma, beta, alfa); double
>>> centro[3] = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z };
>>> transform->SetCenter(centro); FiltroResample->SetTransform(transform);
>>> FiltroResample->Update();
>>> ------------------------------
>>> View this message in context: Rotating image results in last slices
>>> being half empty
>>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081.html>
>>> Sent from the ITK - Users mailing list archive
>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>> ------------------------------
>> If you reply to this email, your message will be added to the discussion
>> below:
>> http://itk-users.7.n7.nabble.com/Rotating-image-results-in-l
>> ast-slices-being-half-empty-tp38081p38116.html
>> To unsubscribe from Rotating image results in last slices being half
>> empty, click here.
>> NAML
>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>> --
>> Matias
>>
>> ------------------------------
>> View this message in context: Re: [ITK-users] Rotating image results in
>> last slices being half empty
>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081p38121.html>
>>
>> Sent from the ITK - Users mailing list archive
>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From matimontg at gmail.com  Sat Apr 15 10:27:45 2017
From: matimontg at gmail.com (Matias Montroull)
Date: Sat, 15 Apr 2017 11:27:45 -0300
Subject: [ITK-users] Rotating image results in last slices being half
	empty
In-Reply-To: <CAPf2UMTgGvgj06Seb7MjvicBxZ0cr30MddD7P=syzHCHp6nE4Q@mail.gmail.com>
References: <1491689302258-38081.post@n7.nabble.com>
 <CAPf2UMTPg3Ntp=W7y-5ONO43DnVcGB+RXZ0aacqP2gaE_bBC1w@mail.gmail.com>
 <CAKKNfuJgURGNVtmX15ZpF4=Ca=__VkAX6-2E3=MDnhW=7WHcoA@mail.gmail.com>
 <CAPf2UMTjW_QxdXGUUprRZnkPXAYe4GXpw2XQ4wBivF2L5AbhKg@mail.gmail.com>
 <CAPf2UMTgGvgj06Seb7MjvicBxZ0cr30MddD7P=syzHCHp6nE4Q@mail.gmail.com>
Message-ID: <CAKKNfuLws0kK9TxR3MuNwho_386U7GauiZRmxPcQ4TkBy8km0Q@mail.gmail.com>

Dzenan,
The center of rotation is set to use milimeters or image coordinates?
Thanks

Matias

On Apr 14, 2017 2:17 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:

> Here is the code I used:
>
> #include <itkImageFileReader.h>
> #include <itkImageFileWriter.h>
> #include <itkResampleImageFilter.h>
> #include <itkEuler3DTransform.h>
>
> template< typename TImage >
> itk::SmartPointer<TImage> ReadImage(const char *filename)
> {
>     typedef itk::ImageFileReader<TImage> ReaderType;
>     typename ReaderType::Pointer r = ReaderType::New();
>     r->SetFileName(filename);
>     r->Update();
>     return r->GetOutput();
> }
>
> template< typename TImage >
> void WriteImage(itk::SmartPointer<TImage> out, const char *filename)
> {
>     typedef itk::ImageFileWriter<TImage> WriterType;
>     typename WriterType::Pointer w = WriterType::New();
>     w->SetInput(out);
>     w->SetFileName(filename);
>     //w->SetUseCompression(true);
>     w->Update();
> }
>
> int main(int argc, char *argv[])
> {
>     const unsigned int dimension = 3;
>     typedef itk::Image<short, dimension> ImageType;
>     ImageType::Pointer inputImage = ReadImage<ImageType>("C:/CBCT.nrrd");
>
>     typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>     FilterType::Pointer FiltroResample = FilterType::New();
>     FiltroResample->SetInput(inputImage);
>     typedef itk::LinearInterpolateImageFunction<ImageType, double>
> InterpolatorType;
>     InterpolatorType::Pointer interpolator = InterpolatorType::New();
>     FiltroResample->SetInterpolator(interpolator);
>     FiltroResample->SetOutputDirection(inputImage->GetDirection());
>     FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>     ImageType::SizeType inputSize = inputImage->
> GetLargestPossibleRegion().GetSize();
>     FiltroResample->SetSize(inputSize);
>     const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
>     FiltroResample->SetOutputSpacing(inputSpacing);
>     FiltroResample->SetDefaultPixelValue(-1000);
>     typedef itk::Euler3DTransform<double> TransformType;
>     TransformType::Pointer transform = TransformType::New();
>     transform->SetRotation(0.2, 0.3, 0.5);
>     double centro[3] = { 10,20,30 };
>     transform->SetCenter(centro);
>     FiltroResample->SetTransform(transform);
>     FiltroResample->Update();
>     WriteImage<ImageType>(FiltroResample->GetOutput(),
> "C:/cbctResampled.nrrd");
> }
>
> On Fri, Apr 14, 2017 at 1:15 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Matias,
>>
>> I didn't compile to use with Slicer. I only open the input and output
>> image in Slicer to visualize them.
>>
>> But making a Slicer CLI module is fairly easy. You can take a look at one
>> <https://github.com/Slicer/Slicer/tree/master/Modules/CLI/AddScalarVolumes/>
>> of the existing modules, docs
>> <https://www.slicer.org/wiki/Documentation/Nightly/Developers/Modules> including
>> extension wizard
>> <https://www.slicer.org/wiki/Documentation/Nightly/Developers/ExtensionWizard>
>> .
>>
>> Regards,
>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>
>> On Fri, Apr 14, 2017 at 12:26 PM, Matias <matimontg at gmail.com> wrote:
>>
>>> Thanks Dzenan. I actually use OrigenX and OrigenY to assign it to the
>>> DCM tags. Just curious, how did you compile to use with Slicer?
>>>
>>> El jue., 13 de abr. de 2017 a la(s) 12:14, D?enan Zuki? [via ITK -
>>> Users] <[hidden email]
>>> <http:///user/SendEmail.jtp?type=node&node=38121&i=0>> escribi?:
>>>
>>>> Hi Matias,
>>>>
>>>> you are not using origenX or origenY after they are defined. But your
>>>> program (with modifications to make it compile) works for me:
>>>> [image: Inline image 1]
>>>>
>>>> Regards,
>>>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>>>
>>>> On Sat, Apr 8, 2017 at 6:08 PM, Matias <[hidden email]
>>>> <http:///user/SendEmail.jtp?type=node&node=38116&i=0>> wrote:
>>>> Hi, I'm rotating a volume (Using the Euler3DTransform) and the final
>>>> set of slices are half black or empty. here's an example when rotating a
>>>> volume of 10 slices: Am I missing something such as changing the origin or
>>>> maybe computing the center incorrectly? (The center is passed as parameter
>>>> from another program) And here's the code I'm using: typedef
>>>> itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>>>> FilterType::Pointer FiltroResample = FilterType::New();
>>>> FiltroResample->SetInput(reader->GetOutput()); typedef
>>>> itk::LinearInterpolateImageFunction<ImageType, double >
>>>> InterpolatorType; InterpolatorType::Pointer interpolator =
>>>> InterpolatorType::New(); FiltroResample->SetInterpolator(interpolator);
>>>> FiltroResample->SetOutputDirection(inputImage->GetDirection());
>>>> FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>>>> ImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().GetSize();
>>>> FiltroResample->SetSize(inputSize); const ImageType::SpacingType&
>>>> inputSpacing = inputImage->GetSpacing(); FiltroResample->SetOutputSpacing(inputSpacing);
>>>> FiltroResample->SetDefaultPixelValue(-1000); typedef
>>>> itk::Euler3DTransform< double > TransformType; //Transform
>>>> TransformType::Pointer transform = TransformType::New(); double alfa, beta,
>>>> gamma, centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z,
>>>> origenX,origenY; gamma = atof(argv[2]); beta = atof(argv[3]); alfa =
>>>> atof(argv[4]); centro_rotacion_X = atof(argv[5]); centro_rotacion_Y =
>>>> atof(argv[6]); centro_rotacion_Z = atof(argv[7]); origenX = atof(argv[8]);
>>>> origenY = atof(argv[9]); transform->SetRotation(gamma, beta, alfa); double
>>>> centro[3] = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z };
>>>> transform->SetCenter(centro); FiltroResample->SetTransform(transform);
>>>> FiltroResample->Update();
>>>> ------------------------------
>>>> View this message in context: Rotating image results in last slices
>>>> being half empty
>>>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081.html>
>>>> Sent from the ITK - Users mailing list archive
>>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>> ------------------------------
>>> If you reply to this email, your message will be added to the discussion
>>> below:
>>> http://itk-users.7.n7.nabble.com/Rotating-image-results-in-l
>>> ast-slices-being-half-empty-tp38081p38116.html
>>> To unsubscribe from Rotating image results in last slices being half
>>> empty, click here.
>>> NAML
>>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>> --
>>> Matias
>>>
>>> ------------------------------
>>> View this message in context: Re: [ITK-users] Rotating image results in
>>> last slices being half empty
>>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081p38121.html>
>>>
>>> Sent from the ITK - Users mailing list archive
>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>
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From dzenanz at gmail.com  Sat Apr 15 10:33:57 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 15 Apr 2017 10:33:57 -0400
Subject: [ITK-users] Rotating image results in last slices being half
	empty
In-Reply-To: <CAKKNfuLws0kK9TxR3MuNwho_386U7GauiZRmxPcQ4TkBy8km0Q@mail.gmail.com>
References: <1491689302258-38081.post@n7.nabble.com>
 <CAPf2UMTPg3Ntp=W7y-5ONO43DnVcGB+RXZ0aacqP2gaE_bBC1w@mail.gmail.com>
 <CAKKNfuJgURGNVtmX15ZpF4=Ca=__VkAX6-2E3=MDnhW=7WHcoA@mail.gmail.com>
 <CAPf2UMTjW_QxdXGUUprRZnkPXAYe4GXpw2XQ4wBivF2L5AbhKg@mail.gmail.com>
 <CAPf2UMTgGvgj06Seb7MjvicBxZ0cr30MddD7P=syzHCHp6nE4Q@mail.gmail.com>
 <CAKKNfuLws0kK9TxR3MuNwho_386U7GauiZRmxPcQ4TkBy8km0Q@mail.gmail.com>
Message-ID: <CAPf2UMQoL4yqgRfVcidMYHoijtMW+Vn=2iB705517F9wRs=_Wg@mail.gmail.com>

Hi Matias,

center of rotation should use physical units (millimeters).

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Sat, Apr 15, 2017 at 10:27 AM, Matias Montroull <matimontg at gmail.com>
wrote:

> Dzenan,
> The center of rotation is set to use milimeters or image coordinates?
> Thanks
>
> Matias
>
> On Apr 14, 2017 2:17 PM, "D?enan Zuki?" <dzenanz at gmail.com> wrote:
>
>> Here is the code I used:
>>
>> #include <itkImageFileReader.h>
>> #include <itkImageFileWriter.h>
>> #include <itkResampleImageFilter.h>
>> #include <itkEuler3DTransform.h>
>>
>> template< typename TImage >
>> itk::SmartPointer<TImage> ReadImage(const char *filename)
>> {
>>     typedef itk::ImageFileReader<TImage> ReaderType;
>>     typename ReaderType::Pointer r = ReaderType::New();
>>     r->SetFileName(filename);
>>     r->Update();
>>     return r->GetOutput();
>> }
>>
>> template< typename TImage >
>> void WriteImage(itk::SmartPointer<TImage> out, const char *filename)
>> {
>>     typedef itk::ImageFileWriter<TImage> WriterType;
>>     typename WriterType::Pointer w = WriterType::New();
>>     w->SetInput(out);
>>     w->SetFileName(filename);
>>     //w->SetUseCompression(true);
>>     w->Update();
>> }
>>
>> int main(int argc, char *argv[])
>> {
>>     const unsigned int dimension = 3;
>>     typedef itk::Image<short, dimension> ImageType;
>>     ImageType::Pointer inputImage = ReadImage<ImageType>("C:/CBCT.nrrd");
>>
>>     typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>>     FilterType::Pointer FiltroResample = FilterType::New();
>>     FiltroResample->SetInput(inputImage);
>>     typedef itk::LinearInterpolateImageFunction<ImageType, double>
>> InterpolatorType;
>>     InterpolatorType::Pointer interpolator = InterpolatorType::New();
>>     FiltroResample->SetInterpolator(interpolator);
>>     FiltroResample->SetOutputDirection(inputImage->GetDirection());
>>     FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>>     ImageType::SizeType inputSize = inputImage->GetLargestPossible
>> Region().GetSize();
>>     FiltroResample->SetSize(inputSize);
>>     const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
>>     FiltroResample->SetOutputSpacing(inputSpacing);
>>     FiltroResample->SetDefaultPixelValue(-1000);
>>     typedef itk::Euler3DTransform<double> TransformType;
>>     TransformType::Pointer transform = TransformType::New();
>>     transform->SetRotation(0.2, 0.3, 0.5);
>>     double centro[3] = { 10,20,30 };
>>     transform->SetCenter(centro);
>>     FiltroResample->SetTransform(transform);
>>     FiltroResample->Update();
>>     WriteImage<ImageType>(FiltroResample->GetOutput(),
>> "C:/cbctResampled.nrrd");
>> }
>>
>> On Fri, Apr 14, 2017 at 1:15 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>>> Hi Matias,
>>>
>>> I didn't compile to use with Slicer. I only open the input and output
>>> image in Slicer to visualize them.
>>>
>>> But making a Slicer CLI module is fairly easy. You can take a look at
>>> one
>>> <https://github.com/Slicer/Slicer/tree/master/Modules/CLI/AddScalarVolumes/>
>>> of the existing modules, docs
>>> <https://www.slicer.org/wiki/Documentation/Nightly/Developers/Modules> including
>>> extension wizard
>>> <https://www.slicer.org/wiki/Documentation/Nightly/Developers/ExtensionWizard>
>>> .
>>>
>>> Regards,
>>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>>
>>> On Fri, Apr 14, 2017 at 12:26 PM, Matias <matimontg at gmail.com> wrote:
>>>
>>>> Thanks Dzenan. I actually use OrigenX and OrigenY to assign it to the
>>>> DCM tags. Just curious, how did you compile to use with Slicer?
>>>>
>>>> El jue., 13 de abr. de 2017 a la(s) 12:14, D?enan Zuki? [via ITK -
>>>> Users] <[hidden email]
>>>> <http:///user/SendEmail.jtp?type=node&node=38121&i=0>> escribi?:
>>>>
>>>>> Hi Matias,
>>>>>
>>>>> you are not using origenX or origenY after they are defined. But your
>>>>> program (with modifications to make it compile) works for me:
>>>>> [image: Inline image 1]
>>>>>
>>>>> Regards,
>>>>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>>>>
>>>>> On Sat, Apr 8, 2017 at 6:08 PM, Matias <[hidden email]
>>>>> <http:///user/SendEmail.jtp?type=node&node=38116&i=0>> wrote:
>>>>> Hi, I'm rotating a volume (Using the Euler3DTransform) and the final
>>>>> set of slices are half black or empty. here's an example when rotating a
>>>>> volume of 10 slices: Am I missing something such as changing the origin or
>>>>> maybe computing the center incorrectly? (The center is passed as parameter
>>>>> from another program) And here's the code I'm using: typedef
>>>>> itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>>>>> FilterType::Pointer FiltroResample = FilterType::New();
>>>>> FiltroResample->SetInput(reader->GetOutput()); typedef
>>>>> itk::LinearInterpolateImageFunction<ImageType, double >
>>>>> InterpolatorType; InterpolatorType::Pointer interpolator =
>>>>> InterpolatorType::New(); FiltroResample->SetInterpolator(interpolator);
>>>>> FiltroResample->SetOutputDirection(inputImage->GetDirection());
>>>>> FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>>>>> ImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().GetSize();
>>>>> FiltroResample->SetSize(inputSize); const ImageType::SpacingType&
>>>>> inputSpacing = inputImage->GetSpacing(); FiltroResample->SetOutputSpacing(inputSpacing);
>>>>> FiltroResample->SetDefaultPixelValue(-1000); typedef
>>>>> itk::Euler3DTransform< double > TransformType; //Transform
>>>>> TransformType::Pointer transform = TransformType::New(); double alfa, beta,
>>>>> gamma, centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z,
>>>>> origenX,origenY; gamma = atof(argv[2]); beta = atof(argv[3]); alfa =
>>>>> atof(argv[4]); centro_rotacion_X = atof(argv[5]); centro_rotacion_Y =
>>>>> atof(argv[6]); centro_rotacion_Z = atof(argv[7]); origenX = atof(argv[8]);
>>>>> origenY = atof(argv[9]); transform->SetRotation(gamma, beta, alfa); double
>>>>> centro[3] = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z };
>>>>> transform->SetCenter(centro); FiltroResample->SetTransform(transform);
>>>>> FiltroResample->Update();
>>>>> ------------------------------
>>>>> View this message in context: Rotating image results in last slices
>>>>> being half empty
>>>>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081.html>
>>>>> Sent from the ITK - Users mailing list archive
>>>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>> ------------------------------
>>>> If you reply to this email, your message will be added to the
>>>> discussion below:
>>>> http://itk-users.7.n7.nabble.com/Rotating-image-results-in-l
>>>> ast-slices-being-half-empty-tp38081p38116.html
>>>> To unsubscribe from Rotating image results in last slices being half
>>>> empty, click here.
>>>> NAML
>>>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>>> --
>>>> Matias
>>>>
>>>> ------------------------------
>>>> View this message in context: Re: [ITK-users] Rotating image results
>>>> in last slices being half empty
>>>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081p38121.html>
>>>>
>>>> Sent from the ITK - Users mailing list archive
>>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>
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From matimontg at gmail.com  Mon Apr 17 19:11:54 2017
From: matimontg at gmail.com (Matias)
Date: Mon, 17 Apr 2017 16:11:54 -0700 (MST)
Subject: [ITK-users] Euler3DTransform not taking user defined Center of
	Rotation?
Message-ID: <1492470714966-38126.post@n7.nabble.com>

Hi,I'm trying to rotate a volume and use an user defined center but no matter
what value I set, it seems the rotation is always performed using the same
center (not sure which, maybe a default center)?Here's the code I'm using..
am I missing something?	typedef itk::Euler3DTransform< double >
TransformType; //Transform		TransformType::Pointer transform =
TransformType::New();		double alfa, beta, gamma, centro_rotacion_X,
centro_rotacion_Y, centro_rotacion_Z, origenX,origenY;		gamma =
atof(argv[2]);		beta = atof(argv[3]);		alfa = atof(argv[4]);	
centro_rotacion_X = atof(argv[5]);		centro_rotacion_Y = atof(argv[6]);	
centro_rotacion_Z = atof(argv[7]);		double centro[3] = { centro_rotacion_X,
centro_rotacion_Y, centro_rotacion_Z }; 		transform->SetCenter(centro);			
transform->SetRotation(gamma, beta, alfa);



--
View this message in context: http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126.html
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From francois.budin at kitware.com  Tue Apr 18 13:46:59 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Tue, 18 Apr 2017 13:46:59 -0400
Subject: [ITK-users] Euler3DTransform not taking user defined Center of
	Rotation?
In-Reply-To: <1492470714966-38126.post@n7.nabble.com>
References: <1492470714966-38126.post@n7.nabble.com>
Message-ID: <CAHwLD2XWwQ_E2HoNQE6nbDMzRJOhqDtmSwbrHDPdX+x6pUAr3A@mail.gmail.com>

Hello Matias,

I used the Euler3DTransform in a python terminal to see if I had problems
setting the center and the angle, and everything seems to work as expected:

trans=itk.Euler3DTransform.D.New()
trans.SetCenter([0,0,0])
trans.SetRotation(10,0,0)
trans.TransformPoint([0,0,0])
Out[46]: itkPointD3 ([0, 0, 0])  <-expected as the transform center is
[0,0,0]

trans.SetCenter([10,0,0])
trans.TransformPoint([0,0,0])
Out[48]: itkPointD3 ([5.16482, -7.96596, 3.62828]) <-rotation not around
[0,0,0] but around [10,0,0]

To try to understand you problem, I would advise you to print the content
of your transform to see if it is set as you expect. In my case, I get:

Euler3DTransform (0x18da8a0)
  RTTI typeinfo:   itk::Euler3DTransform<double>
  Reference Count: 1
  Modified Time: 377
  Debug: Off
  Object Name:
  Observers:
    none
  Matrix:
    0.483518 -0.362828 0.796596
    0.796596 0.559609 -0.228631
    -0.362828 0.745113 0.559609
  Offset: [5.16482, -7.96596, 3.62828]
  Center: [10, 0, 0]
  Translation: [0, 0, 0]
  Inverse:
    0.483518 0.796596 -0.362828
    -0.362828 0.559609 0.745113
    0.796596 -0.228631 0.559609
  Singular: 0
  Euler's angles: AngleX=40 AngleY=10 AngleZ=10
  m_ComputeZYX = 0

Hope this helps,
Francois



On Mon, Apr 17, 2017 at 7:11 PM, Matias <matimontg at gmail.com> wrote:

> Hi, I'm trying to rotate a volume and use an user defined center but no
> matter what value I set, it seems the rotation is always performed using
> the same center (not sure which, maybe a default center)? Here's the code
> I'm using.. am I missing something? typedef itk::Euler3DTransform< double >
> TransformType; //Transform TransformType::Pointer transform =
> TransformType::New(); double alfa, beta, gamma, centro_rotacion_X,
> centro_rotacion_Y, centro_rotacion_Z, origenX,origenY; gamma =
> atof(argv[2]); beta = atof(argv[3]); alfa = atof(argv[4]);
> centro_rotacion_X = atof(argv[5]); centro_rotacion_Y = atof(argv[6]);
> centro_rotacion_Z = atof(argv[7]); double centro[3] = { centro_rotacion_X,
> centro_rotacion_Y, centro_rotacion_Z }; transform->SetCenter(centro);
> transform->SetRotation(gamma, beta, alfa);
> ------------------------------
> View this message in context: Euler3DTransform not taking user defined
> Center of Rotation?
> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126.html>
> Sent from the ITK - Users mailing list archive
> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From yxp233 at postech.ac.kr  Wed Apr 19 07:53:49 2017
From: yxp233 at postech.ac.kr (=?utf-8?B?WGlhb3BlbmcgWWFuZyjsgrDsl4Xqsr3smIHqs7XtlZnqs7wp?=)
Date: Wed, 19 Apr 2017 11:53:49 +0000
Subject: [ITK-users] Multithreading
Message-ID: <TY1PR04MB0895E50FEA1054F7BA83666CD4180@TY1PR04MB0895.apcprd04.prod.outlook.com>

Dear Users,

Have anyone tried to convert ITKFastMarchingImageFilter from single thread to multithread?

What is the best way to implement multithreading to that filter? Thank you.

Best regards,
Xiaopeng

From sidharta.gupta93 at gmail.com  Wed Apr 19 09:40:38 2017
From: sidharta.gupta93 at gmail.com (sidharta)
Date: Wed, 19 Apr 2017 06:40:38 -0700 (MST)
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <CAPf2UMQrJGSxRZZKMgVdBz=1wGjmfZc_HL=aA_sPC1P9xrxhzw@mail.gmail.com>
References: <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
 <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
 <1492088644485-38110.post@n7.nabble.com>
 <CAPf2UMR-XDnwXmjE3aHfekZ4geEe2oXN0ge4F8xJtduBmooQ3Q@mail.gmail.com>
 <1492095684045-38115.post@n7.nabble.com>
 <CAPf2UMTwVyFK-=wj8=3n0BL+e4fW8OPjZNYvM=Em87-NygT0MA@mail.gmail.com>
 <1492097632375-38118.post@n7.nabble.com>
 <CAPf2UMQrJGSxRZZKMgVdBz=1wGjmfZc_HL=aA_sPC1P9xrxhzw@mail.gmail.com>
Message-ID: <1492609238543-38129.post@n7.nabble.com>

Hi D?enan,

Thank you for your reply. I implemented this, and learned some cool stuff in
3DSlicer (in order to compare the two images) but as you said, the size is
difficult to compute. When I set the origin explicitly, to the start of the
trajectory, the resampled image looks good in the direction I want it to be
in, however, lot of information is lost. After putting my head into it for
the past two weeks, I realized there are other ways to achieve I want this
too. Does it make sense to you that I construct another 2D image (or 3D with
thickness 1) by essentially copying the voxel values at the trajectory
points and around it (probably the size equal to the dimensions of the
original image in the x,y direction)? The aim ultimately is in fact to get
one slice which best represents the HU values. I apologize for asking such
silly questions.

Just putting the code of what I did, let me know if it is in fact what you
suggested me to do:

Vector3d ST, SP, normal_to_plane;
	ST = traj_end - traj_start;
	SP = third_point - traj_start;
	normal_to_plane = ST.cross(SP);
	std::cout << "Vector ST : " << ST << " Vector SP : " << SP << " Direction
of normal : " << normal_to_plane << std::endl;

	InternalImageType::DirectionType dir;
	// vector from start to the end of the trajectory 
	Vector3d normalized_ST = ST.normalized();
	dir[0][0] = normalized_ST[0];
	dir[0][1] = normalized_ST[1];
	dir[0][2] = normalized_ST[2];

	Vector3d second = normal_to_plane.cross(ST);
	Vector3d normalized_second = second.normalized();
	dir[1][0] = normalized_second[0];
	dir[1][1] = normalized_second[1];
	dir[1][2] = normalized_second[2];

	Vector3d normalized_normal = normal_to_plane.normalized();
	dir[2][0] = normalized_normal[0];
	dir[2][1] = normalized_normal[1];
	dir[2][2] = normalized_normal[2];

	// traj_start += normalized_second * 10;
	double mpr_start[3] = { traj_start[0]  , traj_start[1] , traj_start[2]};

	std::cout << "Previous image direction " << image->GetDirection() <<
std::endl;
	std::cout << "New Image Direction " << dir << std::endl;

	getSliceMPR(image, mpr_start, dir);

void getSliceMPR(InternalImageType::Pointer &image, double
output_origin[Dimension], InternalImageType::DirectionType dir)
{

	// Instantiate Resample Filter here
	ResampleFilterType::Pointer filter = ResampleFilterType::New();
	// Instantiate Transform for resampling
	// Changing the Output direction instead of setting the transform
	// filter->SetTransform(transform);

	typedef itk::NearestNeighborInterpolateImageFunction<
		InternalImageType, double> InterpolatorType;

	// Instantiate the interpolator
	InterpolatorType::Pointer interpolator = InterpolatorType::New();
	filter->SetInterpolator(interpolator);

	// Set pixels of the output image that end up being mapped outside the
extent of the input image to -1500
	filter->SetDefaultPixelValue(-1500);

	// Sampling grid of the output space - pixel spacing in mm
	// Hard coded here
	filter->SetOutputSpacing(image->GetSpacing());


    // filter->SetOutputOrigin(image->GetOrigin());
	
	filter->SetOutputOrigin(output_origin);
	filter->SetOutputDirection(dir);
	InternalImageType::SizeType size;
	filter->SetSize(image->GetLargestPossibleRegion().GetSize());

	filter->SetInput(image);

	typedef itk::ImageFileWriter<InternalImageType> WriterType;
	
	WriterType::Pointer writer = WriterType::New();
	writer->SetFileName("C:/Users/api/Desktop/Resampled/resampled_2.mhd");
	writer->SetUseCompression(true);
	writer->SetInput(filter->GetOutput());
	try{
		writer->Update();

	}
	catch (itk::ExceptionObject & excep){

		std::cerr << "Exception catched!.." << std::endl;
		std::cerr << excep << std::endl;
	}

}



--
View this message in context: http://itk-users.7.n7.nabble.com/Extract-slice-from-ResampleFilter-tp38074p38129.html
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From dzenanz at gmail.com  Wed Apr 19 11:29:53 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 19 Apr 2017 11:29:53 -0400
Subject: [ITK-users] [ITK] Extract slice from ResampleFilter
In-Reply-To: <1492609238543-38129.post@n7.nabble.com>
References: <1491926413097-38091.post@n7.nabble.com>
 <CAPf2UMTF5SodUKkw0TWx_YmY8kx+oiKuohW66AgMi-hG0Me1vQ@mail.gmail.com>
 <1491997495031-38097.post@n7.nabble.com>
 <CAPf2UMRe_CSNYXEtiFjPqjw_fjZJ8QQThG3d7dmMFwO0D+_SHw@mail.gmail.com>
 <1492088644485-38110.post@n7.nabble.com>
 <CAPf2UMR-XDnwXmjE3aHfekZ4geEe2oXN0ge4F8xJtduBmooQ3Q@mail.gmail.com>
 <1492095684045-38115.post@n7.nabble.com>
 <CAPf2UMTwVyFK-=wj8=3n0BL+e4fW8OPjZNYvM=Em87-NygT0MA@mail.gmail.com>
 <1492097632375-38118.post@n7.nabble.com>
 <CAPf2UMQrJGSxRZZKMgVdBz=1wGjmfZc_HL=aA_sPC1P9xrxhzw@mail.gmail.com>
 <1492609238543-38129.post@n7.nabble.com>
Message-ID: <CAPf2UMRbKM9qEuMRJLSAUrh4hKv3M8D3Z624CAYVodgnauSoGA@mail.gmail.com>

Hi Sidharta,

you seem to have implemented what I suggested.

"essentially copying the voxel values at the trajectory points and around
it" can be achieved by using nearest neighbor interpolator instead of
linear interpolator. But it looks like you are already using nearest
neighbor, so you should try using linear interpolator, or even windowed sinc
<https://itk.org/Doxygen/html/classitk_1_1WindowedSincInterpolateImageFunction.html>
interpolator to get higher quality.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Wed, Apr 19, 2017 at 9:40 AM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> Hi D?enan,
>
> Thank you for your reply. I implemented this, and learned some cool stuff
> in
> 3DSlicer (in order to compare the two images) but as you said, the size is
> difficult to compute. When I set the origin explicitly, to the start of the
> trajectory, the resampled image looks good in the direction I want it to be
> in, however, lot of information is lost. After putting my head into it for
> the past two weeks, I realized there are other ways to achieve I want this
> too. Does it make sense to you that I construct another 2D image (or 3D
> with
> thickness 1) by essentially copying the voxel values at the trajectory
> points and around it (probably the size equal to the dimensions of the
> original image in the x,y direction)? The aim ultimately is in fact to get
> one slice which best represents the HU values. I apologize for asking such
> silly questions.
>
> Just putting the code of what I did, let me know if it is in fact what you
> suggested me to do:
>
> Vector3d ST, SP, normal_to_plane;
>         ST = traj_end - traj_start;
>         SP = third_point - traj_start;
>         normal_to_plane = ST.cross(SP);
>         std::cout << "Vector ST : " << ST << " Vector SP : " << SP << "
> Direction
> of normal : " << normal_to_plane << std::endl;
>
>         InternalImageType::DirectionType dir;
>         // vector from start to the end of the trajectory
>         Vector3d normalized_ST = ST.normalized();
>         dir[0][0] = normalized_ST[0];
>         dir[0][1] = normalized_ST[1];
>         dir[0][2] = normalized_ST[2];
>
>         Vector3d second = normal_to_plane.cross(ST);
>         Vector3d normalized_second = second.normalized();
>         dir[1][0] = normalized_second[0];
>         dir[1][1] = normalized_second[1];
>         dir[1][2] = normalized_second[2];
>
>         Vector3d normalized_normal = normal_to_plane.normalized();
>         dir[2][0] = normalized_normal[0];
>         dir[2][1] = normalized_normal[1];
>         dir[2][2] = normalized_normal[2];
>
>         // traj_start += normalized_second * 10;
>         double mpr_start[3] = { traj_start[0]  , traj_start[1] ,
> traj_start[2]};
>
>         std::cout << "Previous image direction " << image->GetDirection()
> <<
> std::endl;
>         std::cout << "New Image Direction " << dir << std::endl;
>
>         getSliceMPR(image, mpr_start, dir);
>
> void getSliceMPR(InternalImageType::Pointer &image, double
> output_origin[Dimension], InternalImageType::DirectionType dir)
> {
>
>         // Instantiate Resample Filter here
>         ResampleFilterType::Pointer filter = ResampleFilterType::New();
>         // Instantiate Transform for resampling
>         // Changing the Output direction instead of setting the transform
>         // filter->SetTransform(transform);
>
>         typedef itk::NearestNeighborInterpolateImageFunction<
>                 InternalImageType, double> InterpolatorType;
>
>         // Instantiate the interpolator
>         InterpolatorType::Pointer interpolator = InterpolatorType::New();
>         filter->SetInterpolator(interpolator);
>
>         // Set pixels of the output image that end up being mapped outside
> the
> extent of the input image to -1500
>         filter->SetDefaultPixelValue(-1500);
>
>         // Sampling grid of the output space - pixel spacing in mm
>         // Hard coded here
>         filter->SetOutputSpacing(image->GetSpacing());
>
>
>     // filter->SetOutputOrigin(image->GetOrigin());
>
>         filter->SetOutputOrigin(output_origin);
>         filter->SetOutputDirection(dir);
>         InternalImageType::SizeType size;
>         filter->SetSize(image->GetLargestPossibleRegion().GetSize());
>
>         filter->SetInput(image);
>
>         typedef itk::ImageFileWriter<InternalImageType> WriterType;
>
>         WriterType::Pointer writer = WriterType::New();
>         writer->SetFileName("C:/Users/api/Desktop/Resampled/
> resampled_2.mhd");
>         writer->SetUseCompression(true);
>         writer->SetInput(filter->GetOutput());
>         try{
>                 writer->Update();
>
>         }
>         catch (itk::ExceptionObject & excep){
>
>                 std::cerr << "Exception catched!.." << std::endl;
>                 std::cerr << excep << std::endl;
>         }
>
> }
>
>
>
> --
> View this message in context: http://itk-users.7.n7.nabble.
> com/Extract-slice-from-ResampleFilter-tp38074p38129.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
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From matimontg at gmail.com  Wed Apr 19 11:56:09 2017
From: matimontg at gmail.com (Matias)
Date: Wed, 19 Apr 2017 08:56:09 -0700 (MST)
Subject: [ITK-users] Euler3DTransform not taking user defined Center of
 Rotation?
In-Reply-To: <CAHwLD2XWwQ_E2HoNQE6nbDMzRJOhqDtmSwbrHDPdX+x6pUAr3A@mail.gmail.com>
References: <1492470714966-38126.post@n7.nabble.com>
 <CAHwLD2XWwQ_E2HoNQE6nbDMzRJOhqDtmSwbrHDPdX+x6pUAr3A@mail.gmail.com>
Message-ID: <CAKKNfuKstHTTM3e0FvHBgEDdnHeoPB7dKSM_ZJ99e=ndm=zj_w@mail.gmail.com>

Thanks Francois,

There's something strange in the matrix and Offset, this is what I get:

Center:

[-246.422, -149.871, 20]

Matrix:
1 0 0
0 1 0
0 0 1

Offset:
[0, 0, 0]

El mar., 18 de abr. de 2017 a la(s) 14:47, Francois Budin-3 [via ITK -
Users] <ml-node+s7n38127h6 at n7.nabble.com> escribi?:

> Hello Matias,
>
> I used the Euler3DTransform in a python terminal to see if I had problems
> setting the center and the angle, and everything seems to work as expected:
>
> trans=itk.Euler3DTransform.D.New()
> trans.SetCenter([0,0,0])
> trans.SetRotation(10,0,0)
> trans.TransformPoint([0,0,0])
> Out[46]: itkPointD3 ([0, 0, 0])  <-expected as the transform center is
> [0,0,0]
>
> trans.SetCenter([10,0,0])
> trans.TransformPoint([0,0,0])
> Out[48]: itkPointD3 ([5.16482, -7.96596, 3.62828]) <-rotation not around
> [0,0,0] but around [10,0,0]
>
> To try to understand you problem, I would advise you to print the content
> of your transform to see if it is set as you expect. In my case, I get:
>
> Euler3DTransform (0x18da8a0)
>   RTTI typeinfo:   itk::Euler3DTransform<double>
>   Reference Count: 1
>   Modified Time: 377
>   Debug: Off
>   Object Name:
>   Observers:
>     none
>   Matrix:
>     0.483518 -0.362828 0.796596
>     0.796596 0.559609 -0.228631
>     -0.362828 0.745113 0.559609
>   Offset: [5.16482, -7.96596, 3.62828]
>   Center: [10, 0, 0]
>   Translation: [0, 0, 0]
>   Inverse:
>     0.483518 0.796596 -0.362828
>     -0.362828 0.559609 0.745113
>     0.796596 -0.228631 0.559609
>   Singular: 0
>   Euler's angles: AngleX=40 AngleY=10 AngleZ=10
>   m_ComputeZYX = 0
>
> Hope this helps,
> Francois
>
>
>
> On Mon, Apr 17, 2017 at 7:11 PM, Matias <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38127&i=0>> wrote:
>
>> Hi, I'm trying to rotate a volume and use an user defined center but no
>> matter what value I set, it seems the rotation is always performed using
>> the same center (not sure which, maybe a default center)? Here's the code
>> I'm using.. am I missing something? typedef itk::Euler3DTransform< double >
>> TransformType; //Transform TransformType::Pointer transform =
>> TransformType::New(); double alfa, beta, gamma, centro_rotacion_X,
>> centro_rotacion_Y, centro_rotacion_Z, origenX,origenY; gamma =
>> atof(argv[2]); beta = atof(argv[3]); alfa = atof(argv[4]);
>> centro_rotacion_X = atof(argv[5]); centro_rotacion_Y = atof(argv[6]);
>> centro_rotacion_Z = atof(argv[7]); double centro[3] = { centro_rotacion_X,
>> centro_rotacion_Y, centro_rotacion_Z }; transform->SetCenter(centro);
>> transform->SetRotation(gamma, beta, alfa);
>> ------------------------------
>> View this message in context: Euler3DTransform not taking user defined
>> Center of Rotation?
>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126.html>
>> Sent from the ITK - Users mailing list archive
>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
>
> http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126p38127.html
> To unsubscribe from Euler3DTransform not taking user defined Center of
> Rotation?, click here
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=38126&code=bWF0aW1vbnRnQGdtYWlsLmNvbXwzODEyNnwtMTk0NzIxNTA4Mw==>
> .
> NAML
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>
-- 
Matias




--
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From francois.budin at kitware.com  Wed Apr 19 13:30:14 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 19 Apr 2017 13:30:14 -0400
Subject: [ITK-users] Euler3DTransform not taking user defined Center of
	Rotation?
In-Reply-To: <CAKKNfuKstHTTM3e0FvHBgEDdnHeoPB7dKSM_ZJ99e=ndm=zj_w@mail.gmail.com>
References: <1492470714966-38126.post@n7.nabble.com>
 <CAHwLD2XWwQ_E2HoNQE6nbDMzRJOhqDtmSwbrHDPdX+x6pUAr3A@mail.gmail.com>
 <CAKKNfuKstHTTM3e0FvHBgEDdnHeoPB7dKSM_ZJ99e=ndm=zj_w@mail.gmail.com>
Message-ID: <CAHwLD2WD4YODpUkmTk_MsAHwYjO6aUq=JjvuK_SXsta1sMT_dQ@mail.gmail.com>

Hello Matias,

I created a small executable based on the code you sent me:

#include <itkEuler3DTransform.h>

int main(int argc, char* argv[])
{
  typedef itk::Euler3DTransform< double > TransformType;
//Transform
  TransformType::Pointer transform = TransformType::New();
double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y,
centro_rotacion_Z, origenX,origenY;
gamma = atof(argv[2]);
beta = atof(argv[3]);
alfa = atof(argv[4]);
centro_rotacion_X = atof(argv[5]);
centro_rotacion_Y = atof(argv[6]);
centro_rotacion_Z = atof(argv[7]);
double centro[3] = { centro_rotacion_X, centro_rotacion_Y,
centro_rotacion_Z };
transform->SetCenter(centro);
transform->SetRotation(gamma, beta, alfa);
std::cout<<transform->GetCenter()<<std::endl;
std::cout<<transform->GetMatrix()<<std::endl;
std::cout<<transform<<std::endl;
  return 0;
}

And the results are correct:
./Euler 10 20 30 40 50 60 70
[50, 60, 70]
0.56923 -0.304067 0.763885
0.716525 -0.272165 -0.642275
0.403198 0.912945 0.0629472

Euler3DTransform (0x1126e80)
  RTTI typeinfo:   itk::Euler3DTransform<double>
  Reference Count: 2
  Modified Time: 3
  Debug: Off
  Object Name:
  Observers:
    none
  Matrix:
    0.56923 -0.304067 0.763885
    0.716525 -0.272165 -0.642275
    0.403198 0.912945 0.0629472
  Offset: [-13.6894, 85.4629, -9.34292]
  Center: [50, 60, 70]
  Translation: [0, 0, 0]
  Inverse:
    0.56923 0.716525 0.403198
    -0.304067 -0.272165 0.912945
    0.763885 -0.642275 0.0629472
  Singular: 0
  Euler's angles: AngleX=20 AngleY=30 AngleZ=40
  m_ComputeZYX = 0


On Wed, Apr 19, 2017 at 11:56 AM, Matias <matimontg at gmail.com> wrote:

> Thanks Francois,
>
> There's something strange in the matrix and Offset, this is what I get:
>
> Center:
>
> [-246.422, -149.871, 20]
>
> Matrix:
> 1 0 0
> 0 1 0
> 0 0 1
>
> Offset:
> [0, 0, 0]
>
> El mar., 18 de abr. de 2017 a la(s) 14:47, Francois Budin-3 [via ITK -
> Users] <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=38131&i=0>> escribi?:
>
>> Hello Matias,
>>
>> I used the Euler3DTransform in a python terminal to see if I had problems
>> setting the center and the angle, and everything seems to work as expected:
>>
>> trans=itk.Euler3DTransform.D.New()
>> trans.SetCenter([0,0,0])
>> trans.SetRotation(10,0,0)
>> trans.TransformPoint([0,0,0])
>> Out[46]: itkPointD3 ([0, 0, 0])  <-expected as the transform center is
>> [0,0,0]
>>
>> trans.SetCenter([10,0,0])
>> trans.TransformPoint([0,0,0])
>> Out[48]: itkPointD3 ([5.16482, -7.96596, 3.62828]) <-rotation not around
>> [0,0,0] but around [10,0,0]
>>
>> To try to understand you problem, I would advise you to print the content
>> of your transform to see if it is set as you expect. In my case, I get:
>>
>> Euler3DTransform (0x18da8a0)
>>   RTTI typeinfo:   itk::Euler3DTransform<double>
>>   Reference Count: 1
>>   Modified Time: 377
>>   Debug: Off
>>   Object Name:
>>   Observers:
>>     none
>>   Matrix:
>>     0.483518 -0.362828 0.796596
>>     0.796596 0.559609 -0.228631
>>     -0.362828 0.745113 0.559609
>>   Offset: [5.16482, -7.96596, 3.62828]
>>   Center: [10, 0, 0]
>>   Translation: [0, 0, 0]
>>   Inverse:
>>     0.483518 0.796596 -0.362828
>>     -0.362828 0.559609 0.745113
>>     0.796596 -0.228631 0.559609
>>   Singular: 0
>>   Euler's angles: AngleX=40 AngleY=10 AngleZ=10
>>   m_ComputeZYX = 0
>>
>> Hope this helps,
>> Francois
>>
>>
>>
>> On Mon, Apr 17, 2017 at 7:11 PM, Matias <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=38127&i=0>> wrote:
>> Hi, I'm trying to rotate a volume and use an user defined center but no
>> matter what value I set, it seems the rotation is always performed using
>> the same center (not sure which, maybe a default center)? Here's the code
>> I'm using.. am I missing something? typedef itk::Euler3DTransform< double >
>> TransformType; //Transform TransformType::Pointer transform =
>> TransformType::New(); double alfa, beta, gamma, centro_rotacion_X,
>> centro_rotacion_Y, centro_rotacion_Z, origenX,origenY; gamma =
>> atof(argv[2]); beta = atof(argv[3]); alfa = atof(argv[4]);
>> centro_rotacion_X = atof(argv[5]); centro_rotacion_Y = atof(argv[6]);
>> centro_rotacion_Z = atof(argv[7]); double centro[3] = { centro_rotacion_X,
>> centro_rotacion_Y, centro_rotacion_Z }; transform->SetCenter(centro);
>> transform->SetRotation(gamma, beta, alfa);
>> ------------------------------
>> View this message in context: Euler3DTransform not taking user defined
>> Center of Rotation?
>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126.html>
>> Sent from the ITK - Users mailing list archive
>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
> http://itk-users.7.n7.nabble.com/Euler3DTransform-not-
> taking-user-defined-Center-of-Rotation-tp38126p38127.html
> To unsubscribe from Euler3DTransform not taking user defined Center of
> Rotation?, click here.
> NAML
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
> --
> Matias
>
> ------------------------------
> View this message in context: Re: [ITK-users] Euler3DTransform not taking
> user defined Center of Rotation?
> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126p38131.html>
>
> Sent from the ITK - Users mailing list archive
> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Wed Apr 19 14:36:50 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 19 Apr 2017 14:36:50 -0400
Subject: [ITK-users] Euler3DTransform not taking user defined Center of
	Rotation?
In-Reply-To: <CAHwLD2WD4YODpUkmTk_MsAHwYjO6aUq=JjvuK_SXsta1sMT_dQ@mail.gmail.com>
References: <1492470714966-38126.post@n7.nabble.com>
 <CAHwLD2XWwQ_E2HoNQE6nbDMzRJOhqDtmSwbrHDPdX+x6pUAr3A@mail.gmail.com>
 <CAKKNfuKstHTTM3e0FvHBgEDdnHeoPB7dKSM_ZJ99e=ndm=zj_w@mail.gmail.com>
 <CAHwLD2WD4YODpUkmTk_MsAHwYjO6aUq=JjvuK_SXsta1sMT_dQ@mail.gmail.com>
Message-ID: <CAPf2UMSnoYw6GHQp6VfYqVJJMWx2Cvsu1DjxLF1qwyeXtnewfw@mail.gmail.com>

Hi Matias,

translation (called offset in some of the classes) and center of rotation
are different things, and taken care of differently.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Wed, Apr 19, 2017 at 1:30 PM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Matias,
>
> I created a small executable based on the code you sent me:
>
> #include <itkEuler3DTransform.h>
>
> int main(int argc, char* argv[])
> {
>   typedef itk::Euler3DTransform< double > TransformType;
> //Transform
>   TransformType::Pointer transform = TransformType::New();
> double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y,
> centro_rotacion_Z, origenX,origenY;
> gamma = atof(argv[2]);
> beta = atof(argv[3]);
> alfa = atof(argv[4]);
> centro_rotacion_X = atof(argv[5]);
> centro_rotacion_Y = atof(argv[6]);
> centro_rotacion_Z = atof(argv[7]);
> double centro[3] = { centro_rotacion_X, centro_rotacion_Y,
> centro_rotacion_Z };
> transform->SetCenter(centro);
> transform->SetRotation(gamma, beta, alfa);
> std::cout<<transform->GetCenter()<<std::endl;
> std::cout<<transform->GetMatrix()<<std::endl;
> std::cout<<transform<<std::endl;
>   return 0;
> }
>
> And the results are correct:
> ./Euler 10 20 30 40 50 60 70
> [50, 60, 70]
> 0.56923 -0.304067 0.763885
> 0.716525 -0.272165 -0.642275
> 0.403198 0.912945 0.0629472
>
> Euler3DTransform (0x1126e80)
>   RTTI typeinfo:   itk::Euler3DTransform<double>
>   Reference Count: 2
>   Modified Time: 3
>   Debug: Off
>   Object Name:
>   Observers:
>     none
>   Matrix:
>     0.56923 -0.304067 0.763885
>     0.716525 -0.272165 -0.642275
>     0.403198 0.912945 0.0629472
>   Offset: [-13.6894, 85.4629, -9.34292]
>   Center: [50, 60, 70]
>   Translation: [0, 0, 0]
>   Inverse:
>     0.56923 0.716525 0.403198
>     -0.304067 -0.272165 0.912945
>     0.763885 -0.642275 0.0629472
>   Singular: 0
>   Euler's angles: AngleX=20 AngleY=30 AngleZ=40
>   m_ComputeZYX = 0
>
>
> On Wed, Apr 19, 2017 at 11:56 AM, Matias <matimontg at gmail.com> wrote:
>
>> Thanks Francois,
>>
>> There's something strange in the matrix and Offset, this is what I get:
>>
>> Center:
>>
>> [-246.422, -149.871, 20]
>>
>> Matrix:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>>
>> Offset:
>> [0, 0, 0]
>>
>> El mar., 18 de abr. de 2017 a la(s) 14:47, Francois Budin-3 [via ITK -
>> Users] <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=38131&i=0>> escribi?:
>>
>>> Hello Matias,
>>>
>>> I used the Euler3DTransform in a python terminal to see if I had
>>> problems setting the center and the angle, and everything seems to work as
>>> expected:
>>>
>>> trans=itk.Euler3DTransform.D.New()
>>> trans.SetCenter([0,0,0])
>>> trans.SetRotation(10,0,0)
>>> trans.TransformPoint([0,0,0])
>>> Out[46]: itkPointD3 ([0, 0, 0])  <-expected as the transform center is
>>> [0,0,0]
>>>
>>> trans.SetCenter([10,0,0])
>>> trans.TransformPoint([0,0,0])
>>> Out[48]: itkPointD3 ([5.16482, -7.96596, 3.62828]) <-rotation not around
>>> [0,0,0] but around [10,0,0]
>>>
>>> To try to understand you problem, I would advise you to print the
>>> content of your transform to see if it is set as you expect. In my case, I
>>> get:
>>>
>>> Euler3DTransform (0x18da8a0)
>>>   RTTI typeinfo:   itk::Euler3DTransform<double>
>>>   Reference Count: 1
>>>   Modified Time: 377
>>>   Debug: Off
>>>   Object Name:
>>>   Observers:
>>>     none
>>>   Matrix:
>>>     0.483518 -0.362828 0.796596
>>>     0.796596 0.559609 -0.228631
>>>     -0.362828 0.745113 0.559609
>>>   Offset: [5.16482, -7.96596, 3.62828]
>>>   Center: [10, 0, 0]
>>>   Translation: [0, 0, 0]
>>>   Inverse:
>>>     0.483518 0.796596 -0.362828
>>>     -0.362828 0.559609 0.745113
>>>     0.796596 -0.228631 0.559609
>>>   Singular: 0
>>>   Euler's angles: AngleX=40 AngleY=10 AngleZ=10
>>>   m_ComputeZYX = 0
>>>
>>> Hope this helps,
>>> Francois
>>>
>>>
>>>
>>> On Mon, Apr 17, 2017 at 7:11 PM, Matias <[hidden email]
>>> <http:///user/SendEmail.jtp?type=node&node=38127&i=0>> wrote:
>>> Hi, I'm trying to rotate a volume and use an user defined center but no
>>> matter what value I set, it seems the rotation is always performed using
>>> the same center (not sure which, maybe a default center)? Here's the code
>>> I'm using.. am I missing something? typedef itk::Euler3DTransform< double >
>>> TransformType; //Transform TransformType::Pointer transform =
>>> TransformType::New(); double alfa, beta, gamma, centro_rotacion_X,
>>> centro_rotacion_Y, centro_rotacion_Z, origenX,origenY; gamma =
>>> atof(argv[2]); beta = atof(argv[3]); alfa = atof(argv[4]);
>>> centro_rotacion_X = atof(argv[5]); centro_rotacion_Y = atof(argv[6]);
>>> centro_rotacion_Z = atof(argv[7]); double centro[3] = { centro_rotacion_X,
>>> centro_rotacion_Y, centro_rotacion_Z }; transform->SetCenter(centro);
>>> transform->SetRotation(gamma, beta, alfa);
>>> ------------------------------
>>> View this message in context: Euler3DTransform not taking user defined
>>> Center of Rotation?
>>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126.html>
>>> Sent from the ITK - Users mailing list archive
>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>> ------------------------------
>> If you reply to this email, your message will be added to the discussion
>> below:
>> http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking
>> -user-defined-Center-of-Rotation-tp38126p38127.html
>> To unsubscribe from Euler3DTransform not taking user defined Center of
>> Rotation?, click here.
>> NAML
>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>> --
>> Matias
>>
>> ------------------------------
>> View this message in context: Re: [ITK-users] Euler3DTransform not
>> taking user defined Center of Rotation?
>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126p38131.html>
>>
>> Sent from the ITK - Users mailing list archive
>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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>
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From dzenanz at gmail.com  Wed Apr 19 15:57:09 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 19 Apr 2017 15:57:09 -0400
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <CAPf2UMRgovC=UE-CHmmSyxsY=QowKz8TXGhjk+O5DeW-gy3Vpw@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968817@MBX212.d.ethz.ch>
 <CAPf2UMTzTTRTQpFKJj_vnx88XN+PoZmiiQvJg3k1huk=zqv1Dg@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B409445968862@MBX212.d.ethz.ch>
 <CAHwLD2UN1-ULXN4oT2FCJa0UCzF7XmaXB3LJqwVOC9R4p8GGBw@mail.gmail.com>
 <CAPf2UMSiCv7BTcu7kuq-ZaX2gTVwcoUxk3S4MgTfdtPY7khBLw@mail.gmail.com>
 <CAPf2UMRgovC=UE-CHmmSyxsY=QowKz8TXGhjk+O5DeW-gy3Vpw@mail.gmail.com>
Message-ID: <CAPf2UMRCfpD=UdY=vjE=cf7NVHg6y6qr=FHY56eUQf16epDeDA@mail.gmail.com>

Hi Fabio,

I just tested the master branch after CastXML was updated. Unfortunately,
it didn't help. The compile errors are still present in VS2017 with
wrapping.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Thu, Apr 13, 2017 at 10:48 AM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Fabio,
>
> the first error is coming from ITKCommonCastXML project, and the other
> first 1000 errors are also coming from*CastXML and *Swig projects. This
> means that the wrapping infrastructure is somehow triggering that bug in
> VS2017.
>
> The easiest thing to try is update CastXML, which Matt said would take
> care of. Let's see if that helps.
>
> Regards,
> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Wed, Apr 12, 2017 at 4:50 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Fabio,
>>
>> it looks like we will have to wait somewhat until VS writers get around
>> to implement __builtin_offsetof
>> <https://developercommunity.visualstudio.com/content/problem/22196/static-assert-cannot-compile-constexprs-method-tha.html>
>>
>> I don't know why it doesn't trigger when Python wrapping is OFF. I will
>> look into it more.
>>
>> Regards,
>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>
>> On Wed, Apr 12, 2017 at 4:26 PM, Francois Budin <
>> francois.budin at kitware.com> wrote:
>>
>>> Fabio,
>>>
>>> To add a little bit of extra information about using BridgeNumpy:
>>>
>>> From NumPy to ITK, the memory is never copied, and always shared between
>>> the NumPy array and the ITK image.
>>> From ITK to NumPy, the memory is not copied at first, if the data is not
>>> changed from the NumPy side (e.g. if the ITK image is changed, the NumPy
>>> array will be modified too), but if you modify the NumPy array directly,
>>> NumPy will create a copy of the data. This also means that if you were to
>>> modify the NumPy array, the modifications would not be visible in the ITK
>>> image.
>>>
>>> A limited workaround to this is:
>>>
>>> # Get NumPy array from image
>>> arr_image = itk.GetArrayFromImage(image)
>>> # Create copy of array that can be modified in-place
>>> arr = arr_image.copy()
>>> # Modify array
>>> ?
>>> # Update image in-place with new array
>>> arr_image.setfield(arr,arr_image.dtype)
>>>
>>> The advantage of this method is that the image will be updated. However,
>>> there is an explicit copy of your data.
>>> If the copy step is skipped and the original NumPy array is modified, a
>>> copy of the data will be performed by NumPy and you may not be aware of it
>>> until you see that the data in the NumPy array and the image do not match
>>> anymore.
>>>
>>> Hope this helps,
>>> Francois
>>>
>>> On Wed, Apr 12, 2017 at 4:02 PM, D'Isidoro Fabio <fisidoro at ethz.ch>
>>> wrote:
>>>
>>>> Ok, thanks. Moe specifically I am using now *Visual Studio 2017
>>>> Preview*.
>>>>
>>>>
>>>>
>>>> Fabio.
>>>>
>>>> *From:* D?enan Zuki? [mailto:dzenanz at gmail.com]
>>>> *Sent:* Mittwoch, 12. April 2017 21:54
>>>> *To:* D'Isidoro Fabio <fisidoro at ethz.ch>
>>>> *Cc:* Matt McCormick <matt.mccormick at kitware.com>;
>>>> insight-users at itk.org
>>>>
>>>> *Subject:* Re: [ITK-users] ITK Python: numpy to itk image (and
>>>> viceversa)
>>>>
>>>>
>>>>
>>>> Hi Fabio,
>>>>
>>>>
>>>>
>>>> let me give it a try with VS2017 and Wrapping+NumPy. I will report back
>>>> when I have an update.
>>>>
>>>>
>>>>
>>>> Regards,
>>>>
>>>> D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>>>
>>>>
>>>>
>>>> On Wed, Apr 12, 2017 at 2:16 PM, D'Isidoro Fabio <fisidoro at ethz.ch>
>>>> wrote:
>>>>
>>>> Thank you. I am trying to build ITK Wrap Python with
>>>> Module_BridgeNumPy=ON with Visual Studio 2017.
>>>>
>>>> I get the following type of errors:
>>>>
>>>> 12>C:/Program Files (x86)/Microsoft Visual
>>>> Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\xstring(1905,26):
>>>> error G3F63BFAE: constexpr variable '_Memcpy_move_offset' must be
>>>> initialized by a constant expression
>>>> 12>        static constexpr size_t _Memcpy_move_offset =
>>>> offsetof(_Mydata_t, _Bx);
>>>> 12>                                ^
>>>>  ~~~~~~~~~~~~~~~~~~~~~~~~
>>>> 12>C:/Program Files (x86)/Microsoft Visual
>>>> Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\stdexcept:23:21:
>>>> note: in instantiation of template class 'std::basic_string<char,
>>>> std::char_traits<char>, std::allocator<char> >' requested here
>>>> 12>                : _Mybase(_Message.c_str())
>>>> 12>                                  ^
>>>> 12>C:/Program Files (x86)/Microsoft Visual
>>>> Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\xstring:1905:48:
>>>> note: cast that performs the conversions of a reinterpret_cast is not
>>>> allowed in a constant expression
>>>> 12>        static constexpr size_t _Memcpy_move_offset =
>>>> offsetof(_Mydata_t, _Bx);
>>>> 12>                                                      ^
>>>> 12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32:
>>>> note: expanded from macro 'offsetof'
>>>> 12>        #define offsetof(s,m) ((size_t)&reinterpret_cast<char const
>>>> volatile&>((((s*)0)->m)))
>>>>
>>>>
>>>> The build worked with Visual Studio 2015 instead.
>>>>
>>>> Can I fix this issue with Visual Studio 2017 somehow?
>>>>
>>>> Thank you.
>>>>
>>>> ----------------------------------------------------------------------
>>>> Fabio D?Isidoro - PhD Student
>>>> Institute of Biomechanics
>>>> HPP O 14
>>>> H?nggerbergring 64
>>>> 8093 Z?rich, Switzerland
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
>>>> Sent: Montag, 3. April 2017 20:41
>>>> To: D'Isidoro Fabio <fisidoro at ethz.ch>
>>>> Cc: insight-users at itk.org
>>>> Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>>>>
>>>> Hallo Fabio,
>>>>
>>>>
>>>> > I use ITK with Python Wrap. I need to interface my Python code with a
>>>> > Cython-wrapped C++ code that takes only numpy array as input and
>>>> > returns numpy array as output.
>>>>
>>>> Cool. By the way, you may be interested in scikit-build [1], which is a
>>>> good way to build Cython-wrapped C++ code. We are using it for the ITK and
>>>> SimpleITK Python packages, and it has good Cython and CMake support.
>>>>
>>>>
>>>> > Hence, I need to convert the Python itk images into numpy array to be
>>>> > given as input to the wrapped C++ code, and then convert the numpy
>>>> > array in output from the wrapped C++ code back into python itk images.
>>>> >
>>>> >
>>>> >
>>>> > Question 1) How can I do that in an efficient way? I found some posts
>>>> > on itk.PyBuffer but I could not find anywhere any reference on how to
>>>> > install it on my itk wrap build.
>>>>
>>>> Yes, itk.PyBuffer works great for that. Please review a PR for some
>>>> additional documentation:
>>>>
>>>>   https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18
>>>>
>>>> This has been available in ITK for a few releases as a Remote module,
>>>> which can be enabled by setting
>>>>
>>>>   Module_BridgeNumPy=ON
>>>>
>>>> in ITK's CMake configuration.
>>>>
>>>>
>>>> Since ITK 4.11.0, it is easier to build since it does not require the
>>>> NumPy headers.
>>>>
>>>>
>>>> In current ITK Git master (to be 4.12.0) the module is enabled by
>>>> default.
>>>>
>>>>
>>>> Nightly ITK Python packages for ITK Git master are now being built:
>>>>
>>>>   https://github.com/InsightSoftwareConsortium/ITKPythonPackage
>>>>
>>>> macOS and Linux are available. Windows packages will be available over
>>>> the coming weeks.
>>>>
>>>>
>>>>
>>>> > Question 2) The purpose of writing a part of my algorithm in C++ is to
>>>> > speed up the code. If the conversion between python itk images and
>>>> > numpy arrays is slow, I would lose all the speed gain obtained with
>>>> the C++ implementation.
>>>> > Are there better ways to deal with that?
>>>>
>>>> The newer versions ITKBridgeNumPy use a NumPy array view, which does
>>>> not do any copies during the conversion, and it is very fast.
>>>>
>>>>
>>>> HTH,
>>>> Matt
>>>>
>>>>
>>>> [1] http://scikit-build.org/
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>
>
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From matimontg at gmail.com  Wed Apr 19 16:18:38 2017
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 19 Apr 2017 17:18:38 -0300
Subject: [ITK-users] Euler3DTransform not taking user defined Center of
	Rotation?
In-Reply-To: <CAHwLD2WD4YODpUkmTk_MsAHwYjO6aUq=JjvuK_SXsta1sMT_dQ@mail.gmail.com>
References: <1492470714966-38126.post@n7.nabble.com>
 <CAHwLD2XWwQ_E2HoNQE6nbDMzRJOhqDtmSwbrHDPdX+x6pUAr3A@mail.gmail.com>
 <CAKKNfuKstHTTM3e0FvHBgEDdnHeoPB7dKSM_ZJ99e=ndm=zj_w@mail.gmail.com>
 <CAHwLD2WD4YODpUkmTk_MsAHwYjO6aUq=JjvuK_SXsta1sMT_dQ@mail.gmail.com>
Message-ID: <CAKKNfu+BTibdFWnzP1O-Dn_S=oMfwHcUjr+b_oNz5DVTnxGUcg@mail.gmail.com>

Would it be because I'm compiling in Debug mode?

Matias

On Apr 19, 2017 2:30 PM, "Francois Budin" <francois.budin at kitware.com>
wrote:

> Hello Matias,
>
> I created a small executable based on the code you sent me:
>
> #include <itkEuler3DTransform.h>
>
> int main(int argc, char* argv[])
> {
>   typedef itk::Euler3DTransform< double > TransformType;
> //Transform
>   TransformType::Pointer transform = TransformType::New();
> double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y,
> centro_rotacion_Z, origenX,origenY;
> gamma = atof(argv[2]);
> beta = atof(argv[3]);
> alfa = atof(argv[4]);
> centro_rotacion_X = atof(argv[5]);
> centro_rotacion_Y = atof(argv[6]);
> centro_rotacion_Z = atof(argv[7]);
> double centro[3] = { centro_rotacion_X, centro_rotacion_Y,
> centro_rotacion_Z };
> transform->SetCenter(centro);
> transform->SetRotation(gamma, beta, alfa);
> std::cout<<transform->GetCenter()<<std::endl;
> std::cout<<transform->GetMatrix()<<std::endl;
> std::cout<<transform<<std::endl;
>   return 0;
> }
>
> And the results are correct:
> ./Euler 10 20 30 40 50 60 70
> [50, 60, 70]
> 0.56923 -0.304067 0.763885
> 0.716525 -0.272165 -0.642275
> 0.403198 0.912945 0.0629472
>
> Euler3DTransform (0x1126e80)
>   RTTI typeinfo:   itk::Euler3DTransform<double>
>   Reference Count: 2
>   Modified Time: 3
>   Debug: Off
>   Object Name:
>   Observers:
>     none
>   Matrix:
>     0.56923 -0.304067 0.763885
>     0.716525 -0.272165 -0.642275
>     0.403198 0.912945 0.0629472
>   Offset: [-13.6894, 85.4629, -9.34292]
>   Center: [50, 60, 70]
>   Translation: [0, 0, 0]
>   Inverse:
>     0.56923 0.716525 0.403198
>     -0.304067 -0.272165 0.912945
>     0.763885 -0.642275 0.0629472
>   Singular: 0
>   Euler's angles: AngleX=20 AngleY=30 AngleZ=40
>   m_ComputeZYX = 0
>
>
> On Wed, Apr 19, 2017 at 11:56 AM, Matias <matimontg at gmail.com> wrote:
>
>> Thanks Francois,
>>
>> There's something strange in the matrix and Offset, this is what I get:
>>
>> Center:
>>
>> [-246.422, -149.871, 20]
>>
>> Matrix:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>>
>> Offset:
>> [0, 0, 0]
>>
>> El mar., 18 de abr. de 2017 a la(s) 14:47, Francois Budin-3 [via ITK -
>> Users] <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=38131&i=0>> escribi?:
>>
>>> Hello Matias,
>>>
>>> I used the Euler3DTransform in a python terminal to see if I had
>>> problems setting the center and the angle, and everything seems to work as
>>> expected:
>>>
>>> trans=itk.Euler3DTransform.D.New()
>>> trans.SetCenter([0,0,0])
>>> trans.SetRotation(10,0,0)
>>> trans.TransformPoint([0,0,0])
>>> Out[46]: itkPointD3 ([0, 0, 0])  <-expected as the transform center is
>>> [0,0,0]
>>>
>>> trans.SetCenter([10,0,0])
>>> trans.TransformPoint([0,0,0])
>>> Out[48]: itkPointD3 ([5.16482, -7.96596, 3.62828]) <-rotation not around
>>> [0,0,0] but around [10,0,0]
>>>
>>> To try to understand you problem, I would advise you to print the
>>> content of your transform to see if it is set as you expect. In my case, I
>>> get:
>>>
>>> Euler3DTransform (0x18da8a0)
>>>   RTTI typeinfo:   itk::Euler3DTransform<double>
>>>   Reference Count: 1
>>>   Modified Time: 377
>>>   Debug: Off
>>>   Object Name:
>>>   Observers:
>>>     none
>>>   Matrix:
>>>     0.483518 -0.362828 0.796596
>>>     0.796596 0.559609 -0.228631
>>>     -0.362828 0.745113 0.559609
>>>   Offset: [5.16482, -7.96596, 3.62828]
>>>   Center: [10, 0, 0]
>>>   Translation: [0, 0, 0]
>>>   Inverse:
>>>     0.483518 0.796596 -0.362828
>>>     -0.362828 0.559609 0.745113
>>>     0.796596 -0.228631 0.559609
>>>   Singular: 0
>>>   Euler's angles: AngleX=40 AngleY=10 AngleZ=10
>>>   m_ComputeZYX = 0
>>>
>>> Hope this helps,
>>> Francois
>>>
>>>
>>>
>>> On Mon, Apr 17, 2017 at 7:11 PM, Matias <[hidden email]
>>> <http:///user/SendEmail.jtp?type=node&node=38127&i=0>> wrote:
>>> Hi, I'm trying to rotate a volume and use an user defined center but no
>>> matter what value I set, it seems the rotation is always performed using
>>> the same center (not sure which, maybe a default center)? Here's the code
>>> I'm using.. am I missing something? typedef itk::Euler3DTransform< double >
>>> TransformType; //Transform TransformType::Pointer transform =
>>> TransformType::New(); double alfa, beta, gamma, centro_rotacion_X,
>>> centro_rotacion_Y, centro_rotacion_Z, origenX,origenY; gamma =
>>> atof(argv[2]); beta = atof(argv[3]); alfa = atof(argv[4]);
>>> centro_rotacion_X = atof(argv[5]); centro_rotacion_Y = atof(argv[6]);
>>> centro_rotacion_Z = atof(argv[7]); double centro[3] = { centro_rotacion_X,
>>> centro_rotacion_Y, centro_rotacion_Z }; transform->SetCenter(centro);
>>> transform->SetRotation(gamma, beta, alfa);
>>> ------------------------------
>>> View this message in context: Euler3DTransform not taking user defined
>>> Center of Rotation?
>>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126.html>
>>> Sent from the ITK - Users mailing list archive
>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>> ------------------------------
>> If you reply to this email, your message will be added to the discussion
>> below:
>> http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking
>> -user-defined-Center-of-Rotation-tp38126p38127.html
>> To unsubscribe from Euler3DTransform not taking user defined Center of
>> Rotation?, click here.
>> NAML
>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>> --
>> Matias
>>
>> ------------------------------
>> View this message in context: Re: [ITK-users] Euler3DTransform not
>> taking user defined Center of Rotation?
>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126p38131.html>
>>
>> Sent from the ITK - Users mailing list archive
>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From matimontg at gmail.com  Wed Apr 19 16:31:00 2017
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 19 Apr 2017 20:31:00 +0000
Subject: [ITK-users] Euler3DTransform not taking user defined Center of
	Rotation?
In-Reply-To: <CAKKNfu+BTibdFWnzP1O-Dn_S=oMfwHcUjr+b_oNz5DVTnxGUcg@mail.gmail.com>
References: <1492470714966-38126.post@n7.nabble.com>
 <CAHwLD2XWwQ_E2HoNQE6nbDMzRJOhqDtmSwbrHDPdX+x6pUAr3A@mail.gmail.com>
 <CAKKNfuKstHTTM3e0FvHBgEDdnHeoPB7dKSM_ZJ99e=ndm=zj_w@mail.gmail.com>
 <CAHwLD2WD4YODpUkmTk_MsAHwYjO6aUq=JjvuK_SXsta1sMT_dQ@mail.gmail.com>
 <CAKKNfu+BTibdFWnzP1O-Dn_S=oMfwHcUjr+b_oNz5DVTnxGUcg@mail.gmail.com>
Message-ID: <CAKKNfuLr3_O0w+zuz+Q90=9EnD30tqP54He-cFCPP8_Ac8qaXA@mail.gmail.com>

Ok, I figured I was calling getmatrix and getoffset before the SetRotation
function.. Now it works well:
Centro:

[-246.422, -149.871, 20]

0.999686 0.0131081 0.0213481
-0.0131859 0.999907 0.00350517
-0.0213002 -0.00378556 0.999766

[1.46023, -3.33334, -5.8115]

I will check with different centers to see if the matrix changes

El mi?., 19 de abr. de 2017 a la(s) 17:18, Matias Montroull <
matimontg at gmail.com> escribi?:

> Would it be because I'm compiling in Debug mode?
>
>
> Matias
>
> On Apr 19, 2017 2:30 PM, "Francois Budin" <francois.budin at kitware.com>
> wrote:
>
>> Hello Matias,
>>
>> I created a small executable based on the code you sent me:
>>
>> #include <itkEuler3DTransform.h>
>>
>> int main(int argc, char* argv[])
>> {
>>   typedef itk::Euler3DTransform< double > TransformType;
>> //Transform
>>   TransformType::Pointer transform = TransformType::New();
>> double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y,
>> centro_rotacion_Z, origenX,origenY;
>> gamma = atof(argv[2]);
>> beta = atof(argv[3]);
>> alfa = atof(argv[4]);
>> centro_rotacion_X = atof(argv[5]);
>> centro_rotacion_Y = atof(argv[6]);
>> centro_rotacion_Z = atof(argv[7]);
>> double centro[3] = { centro_rotacion_X, centro_rotacion_Y,
>> centro_rotacion_Z };
>> transform->SetCenter(centro);
>> transform->SetRotation(gamma, beta, alfa);
>> std::cout<<transform->GetCenter()<<std::endl;
>> std::cout<<transform->GetMatrix()<<std::endl;
>> std::cout<<transform<<std::endl;
>>   return 0;
>> }
>>
>> And the results are correct:
>> ./Euler 10 20 30 40 50 60 70
>> [50, 60, 70]
>> 0.56923 -0.304067 0.763885
>> 0.716525 -0.272165 -0.642275
>> 0.403198 0.912945 0.0629472
>>
>> Euler3DTransform (0x1126e80)
>>   RTTI typeinfo:   itk::Euler3DTransform<double>
>>   Reference Count: 2
>>   Modified Time: 3
>>   Debug: Off
>>   Object Name:
>>   Observers:
>>     none
>>   Matrix:
>>     0.56923 -0.304067 0.763885
>>     0.716525 -0.272165 -0.642275
>>     0.403198 0.912945 0.0629472
>>   Offset: [-13.6894, 85.4629, -9.34292]
>>   Center: [50, 60, 70]
>>   Translation: [0, 0, 0]
>>   Inverse:
>>     0.56923 0.716525 0.403198
>>     -0.304067 -0.272165 0.912945
>>     0.763885 -0.642275 0.0629472
>>   Singular: 0
>>   Euler's angles: AngleX=20 AngleY=30 AngleZ=40
>>   m_ComputeZYX = 0
>>
>>
>> On Wed, Apr 19, 2017 at 11:56 AM, Matias <matimontg at gmail.com> wrote:
>>
>>> Thanks Francois,
>>>
>>> There's something strange in the matrix and Offset, this is what I get:
>>>
>>> Center:
>>>
>>> [-246.422, -149.871, 20]
>>>
>>> Matrix:
>>> 1 0 0
>>> 0 1 0
>>> 0 0 1
>>>
>>> Offset:
>>> [0, 0, 0]
>>>
>>> El mar., 18 de abr. de 2017 a la(s) 14:47, Francois Budin-3 [via ITK -
>>> Users] <[hidden email]
>>> <http:///user/SendEmail.jtp?type=node&node=38131&i=0>> escribi?:
>>>
>>>> Hello Matias,
>>>>
>>>> I used the Euler3DTransform in a python terminal to see if I had
>>>> problems setting the center and the angle, and everything seems to work as
>>>> expected:
>>>>
>>>> trans=itk.Euler3DTransform.D.New()
>>>> trans.SetCenter([0,0,0])
>>>> trans.SetRotation(10,0,0)
>>>> trans.TransformPoint([0,0,0])
>>>> Out[46]: itkPointD3 ([0, 0, 0])  <-expected as the transform center is
>>>> [0,0,0]
>>>>
>>>> trans.SetCenter([10,0,0])
>>>> trans.TransformPoint([0,0,0])
>>>> Out[48]: itkPointD3 ([5.16482, -7.96596, 3.62828]) <-rotation not
>>>> around [0,0,0] but around [10,0,0]
>>>>
>>>> To try to understand you problem, I would advise you to print the
>>>> content of your transform to see if it is set as you expect. In my case, I
>>>> get:
>>>>
>>>> Euler3DTransform (0x18da8a0)
>>>>   RTTI typeinfo:   itk::Euler3DTransform<double>
>>>>   Reference Count: 1
>>>>   Modified Time: 377
>>>>   Debug: Off
>>>>   Object Name:
>>>>   Observers:
>>>>     none
>>>>   Matrix:
>>>>     0.483518 -0.362828 0.796596
>>>>     0.796596 0.559609 -0.228631
>>>>     -0.362828 0.745113 0.559609
>>>>   Offset: [5.16482, -7.96596, 3.62828]
>>>>   Center: [10, 0, 0]
>>>>   Translation: [0, 0, 0]
>>>>   Inverse:
>>>>     0.483518 0.796596 -0.362828
>>>>     -0.362828 0.559609 0.745113
>>>>     0.796596 -0.228631 0.559609
>>>>   Singular: 0
>>>>   Euler's angles: AngleX=40 AngleY=10 AngleZ=10
>>>>   m_ComputeZYX = 0
>>>>
>>>> Hope this helps,
>>>> Francois
>>>>
>>>>
>>>>
>>>> On Mon, Apr 17, 2017 at 7:11 PM, Matias <[hidden email]
>>>> <http:///user/SendEmail.jtp?type=node&node=38127&i=0>> wrote:
>>>> Hi, I'm trying to rotate a volume and use an user defined center but no
>>>> matter what value I set, it seems the rotation is always performed using
>>>> the same center (not sure which, maybe a default center)? Here's the code
>>>> I'm using.. am I missing something? typedef itk::Euler3DTransform< double >
>>>> TransformType; //Transform TransformType::Pointer transform =
>>>> TransformType::New(); double alfa, beta, gamma, centro_rotacion_X,
>>>> centro_rotacion_Y, centro_rotacion_Z, origenX,origenY; gamma =
>>>> atof(argv[2]); beta = atof(argv[3]); alfa = atof(argv[4]);
>>>> centro_rotacion_X = atof(argv[5]); centro_rotacion_Y = atof(argv[6]);
>>>> centro_rotacion_Z = atof(argv[7]); double centro[3] = { centro_rotacion_X,
>>>> centro_rotacion_Y, centro_rotacion_Z }; transform->SetCenter(centro);
>>>> transform->SetRotation(gamma, beta, alfa);
>>>> ------------------------------
>>>> View this message in context: Euler3DTransform not taking user defined
>>>> Center of Rotation?
>>>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126.html>
>>>> Sent from the ITK - Users mailing list archive
>>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>> ------------------------------
>>> If you reply to this email, your message will be added to the discussion
>>> below:
>>>
>>> http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126p38127.html
>>> To unsubscribe from Euler3DTransform not taking user defined Center of
>>> Rotation?, click here.
>>> NAML
>>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>> --
>>> Matias
>>>
>>> ------------------------------
>>> View this message in context: Re: [ITK-users] Euler3DTransform not
>>> taking user defined Center of Rotation?
>>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126p38131.html>
>>>
>>> Sent from the ITK - Users mailing list archive
>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>> --
Matias
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From francois.budin at kitware.com  Wed Apr 19 17:35:57 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 19 Apr 2017 17:35:57 -0400
Subject: [ITK-users] Euler3DTransform not taking user defined Center of
	Rotation?
In-Reply-To: <CAKKNfuLr3_O0w+zuz+Q90=9EnD30tqP54He-cFCPP8_Ac8qaXA@mail.gmail.com>
References: <1492470714966-38126.post@n7.nabble.com>
 <CAHwLD2XWwQ_E2HoNQE6nbDMzRJOhqDtmSwbrHDPdX+x6pUAr3A@mail.gmail.com>
 <CAKKNfuKstHTTM3e0FvHBgEDdnHeoPB7dKSM_ZJ99e=ndm=zj_w@mail.gmail.com>
 <CAHwLD2WD4YODpUkmTk_MsAHwYjO6aUq=JjvuK_SXsta1sMT_dQ@mail.gmail.com>
 <CAKKNfu+BTibdFWnzP1O-Dn_S=oMfwHcUjr+b_oNz5DVTnxGUcg@mail.gmail.com>
 <CAKKNfuLr3_O0w+zuz+Q90=9EnD30tqP54He-cFCPP8_Ac8qaXA@mail.gmail.com>
Message-ID: <CAHwLD2XfK=Q8iYsirm00gZVC0QBke=7nXD1c0t9VsY94MD5geg@mail.gmail.com>

Thank you for the update. The matrix should change when you update the
center as setting the center calls the function to recompute the matrix.

On Wed, Apr 19, 2017 at 4:31 PM, Matias Montroull <matimontg at gmail.com>
wrote:

> Ok, I figured I was calling getmatrix and getoffset before the SetRotation
> function.. Now it works well:
> Centro:
>
> [-246.422, -149.871, 20]
>
> 0.999686 0.0131081 0.0213481
> -0.0131859 0.999907 0.00350517
> -0.0213002 -0.00378556 0.999766
>
> [1.46023, -3.33334, -5.8115]
>
> I will check with different centers to see if the matrix changes
>
> El mi?., 19 de abr. de 2017 a la(s) 17:18, Matias Montroull <
> matimontg at gmail.com> escribi?:
>
>> Would it be because I'm compiling in Debug mode?
>>
>>
>> Matias
>>
>> On Apr 19, 2017 2:30 PM, "Francois Budin" <francois.budin at kitware.com>
>> wrote:
>>
>>> Hello Matias,
>>>
>>> I created a small executable based on the code you sent me:
>>>
>>> #include <itkEuler3DTransform.h>
>>>
>>> int main(int argc, char* argv[])
>>> {
>>>   typedef itk::Euler3DTransform< double > TransformType;
>>> //Transform
>>>   TransformType::Pointer transform = TransformType::New();
>>> double alfa, beta, gamma, centro_rotacion_X, centro_rotacion_Y,
>>> centro_rotacion_Z, origenX,origenY;
>>> gamma = atof(argv[2]);
>>> beta = atof(argv[3]);
>>> alfa = atof(argv[4]);
>>> centro_rotacion_X = atof(argv[5]);
>>> centro_rotacion_Y = atof(argv[6]);
>>> centro_rotacion_Z = atof(argv[7]);
>>> double centro[3] = { centro_rotacion_X, centro_rotacion_Y,
>>> centro_rotacion_Z };
>>> transform->SetCenter(centro);
>>> transform->SetRotation(gamma, beta, alfa);
>>> std::cout<<transform->GetCenter()<<std::endl;
>>> std::cout<<transform->GetMatrix()<<std::endl;
>>> std::cout<<transform<<std::endl;
>>>   return 0;
>>> }
>>>
>>> And the results are correct:
>>> ./Euler 10 20 30 40 50 60 70
>>> [50, 60, 70]
>>> 0.56923 -0.304067 0.763885
>>> 0.716525 -0.272165 -0.642275
>>> 0.403198 0.912945 0.0629472
>>>
>>> Euler3DTransform (0x1126e80)
>>>   RTTI typeinfo:   itk::Euler3DTransform<double>
>>>   Reference Count: 2
>>>   Modified Time: 3
>>>   Debug: Off
>>>   Object Name:
>>>   Observers:
>>>     none
>>>   Matrix:
>>>     0.56923 -0.304067 0.763885
>>>     0.716525 -0.272165 -0.642275
>>>     0.403198 0.912945 0.0629472
>>>   Offset: [-13.6894, 85.4629, -9.34292]
>>>   Center: [50, 60, 70]
>>>   Translation: [0, 0, 0]
>>>   Inverse:
>>>     0.56923 0.716525 0.403198
>>>     -0.304067 -0.272165 0.912945
>>>     0.763885 -0.642275 0.0629472
>>>   Singular: 0
>>>   Euler's angles: AngleX=20 AngleY=30 AngleZ=40
>>>   m_ComputeZYX = 0
>>>
>>>
>>> On Wed, Apr 19, 2017 at 11:56 AM, Matias <matimontg at gmail.com> wrote:
>>>
>>>> Thanks Francois,
>>>>
>>>> There's something strange in the matrix and Offset, this is what I get:
>>>>
>>>> Center:
>>>>
>>>> [-246.422, -149.871, 20]
>>>>
>>>> Matrix:
>>>> 1 0 0
>>>> 0 1 0
>>>> 0 0 1
>>>>
>>>> Offset:
>>>> [0, 0, 0]
>>>>
>>>> El mar., 18 de abr. de 2017 a la(s) 14:47, Francois Budin-3 [via ITK -
>>>> Users] <[hidden email]
>>>> <http:///user/SendEmail.jtp?type=node&node=38131&i=0>> escribi?:
>>>>
>>>>> Hello Matias,
>>>>>
>>>>> I used the Euler3DTransform in a python terminal to see if I had
>>>>> problems setting the center and the angle, and everything seems to work as
>>>>> expected:
>>>>>
>>>>> trans=itk.Euler3DTransform.D.New()
>>>>> trans.SetCenter([0,0,0])
>>>>> trans.SetRotation(10,0,0)
>>>>> trans.TransformPoint([0,0,0])
>>>>> Out[46]: itkPointD3 ([0, 0, 0])  <-expected as the transform center is
>>>>> [0,0,0]
>>>>>
>>>>> trans.SetCenter([10,0,0])
>>>>> trans.TransformPoint([0,0,0])
>>>>> Out[48]: itkPointD3 ([5.16482, -7.96596, 3.62828]) <-rotation not
>>>>> around [0,0,0] but around [10,0,0]
>>>>>
>>>>> To try to understand you problem, I would advise you to print the
>>>>> content of your transform to see if it is set as you expect. In my case, I
>>>>> get:
>>>>>
>>>>> Euler3DTransform (0x18da8a0)
>>>>>   RTTI typeinfo:   itk::Euler3DTransform<double>
>>>>>   Reference Count: 1
>>>>>   Modified Time: 377
>>>>>   Debug: Off
>>>>>   Object Name:
>>>>>   Observers:
>>>>>     none
>>>>>   Matrix:
>>>>>     0.483518 -0.362828 0.796596
>>>>>     0.796596 0.559609 -0.228631
>>>>>     -0.362828 0.745113 0.559609
>>>>>   Offset: [5.16482, -7.96596, 3.62828]
>>>>>   Center: [10, 0, 0]
>>>>>   Translation: [0, 0, 0]
>>>>>   Inverse:
>>>>>     0.483518 0.796596 -0.362828
>>>>>     -0.362828 0.559609 0.745113
>>>>>     0.796596 -0.228631 0.559609
>>>>>   Singular: 0
>>>>>   Euler's angles: AngleX=40 AngleY=10 AngleZ=10
>>>>>   m_ComputeZYX = 0
>>>>>
>>>>> Hope this helps,
>>>>> Francois
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Apr 17, 2017 at 7:11 PM, Matias <[hidden email]
>>>>> <http:///user/SendEmail.jtp?type=node&node=38127&i=0>> wrote:
>>>>> Hi, I'm trying to rotate a volume and use an user defined center but
>>>>> no matter what value I set, it seems the rotation is always performed using
>>>>> the same center (not sure which, maybe a default center)? Here's the code
>>>>> I'm using.. am I missing something? typedef itk::Euler3DTransform< double >
>>>>> TransformType; //Transform TransformType::Pointer transform =
>>>>> TransformType::New(); double alfa, beta, gamma, centro_rotacion_X,
>>>>> centro_rotacion_Y, centro_rotacion_Z, origenX,origenY; gamma =
>>>>> atof(argv[2]); beta = atof(argv[3]); alfa = atof(argv[4]);
>>>>> centro_rotacion_X = atof(argv[5]); centro_rotacion_Y = atof(argv[6]);
>>>>> centro_rotacion_Z = atof(argv[7]); double centro[3] = { centro_rotacion_X,
>>>>> centro_rotacion_Y, centro_rotacion_Z }; transform->SetCenter(centro);
>>>>> transform->SetRotation(gamma, beta, alfa);
>>>>> ------------------------------
>>>>> View this message in context: Euler3DTransform not taking user
>>>>> defined Center of Rotation?
>>>>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126.html>
>>>>> Sent from the ITK - Users mailing list archive
>>>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>> ------------------------------
>>>> If you reply to this email, your message will be added to the
>>>> discussion below:
>>>> http://itk-users.7.n7.nabble.com/Euler3DTransform-not-
>>>> taking-user-defined-Center-of-Rotation-tp38126p38127.html
>>>> To unsubscribe from Euler3DTransform not taking user defined Center of
>>>> Rotation?, click here.
>>>> NAML
>>>> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>>> --
>>>> Matias
>>>>
>>>> ------------------------------
>>>> View this message in context: Re: [ITK-users] Euler3DTransform not
>>>> taking user defined Center of Rotation?
>>>> <http://itk-users.7.n7.nabble.com/Euler3DTransform-not-taking-user-defined-Center-of-Rotation-tp38126p38131.html>
>>>>
>>>> Sent from the ITK - Users mailing list archive
>>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>> --
> Matias
>
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From matt.mccormick at kitware.com  Thu Apr 20 18:26:32 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 20 Apr 2017 18:26:32 -0400
Subject: [ITK-users] Beta ITK Python packages are now available for testing!
Message-ID: <CALzTN-Sjc0BDQn_291i+V67BJsz5RGN4v5rk7F8aQ+R72uoVMg@mail.gmail.com>

Hi folks,

We now have binary ITK Python packages available for testing! To install,
run

  python -m pip install --upgrade pip
  python -m pip install itk -f
https://github.com/InsightSoftwareConsortium/ITKPythonPackage/releases/tag/latest

These are beta packages that are created on a daily basis. We have packages
for Linux, macOSX, and Windows for Python 2.7, 3.5, and 3.6, along with
source distributions (sdist's). Please share your experiences with these
packages. Initial testing suggests that these packages work both with
system Python distributions, Python distributions downloaded from python.org,
and Anaconda Python distributions.

Thanks,
Matt
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From francois.budin at kitware.com  Fri Apr 21 08:51:54 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Fri, 21 Apr 2017 08:51:54 -0400
Subject: [ITK-users] Beta ITK Python packages are now available for
	testing!
In-Reply-To: <CALzTN-Sjc0BDQn_291i+V67BJsz5RGN4v5rk7F8aQ+R72uoVMg@mail.gmail.com>
References: <CALzTN-Sjc0BDQn_291i+V67BJsz5RGN4v5rk7F8aQ+R72uoVMg@mail.gmail.com>
Message-ID: <CAHwLD2WjrCoasUPTMcGTsKiYZpDBnx=-=cP+pCbbcSs81ZfgxQ@mail.gmail.com>

This is great news!

On Thu, Apr 20, 2017 at 6:26 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi folks,
>
> We now have binary ITK Python packages available for testing! To install,
> run
>
>   python -m pip install --upgrade pip
>   python -m pip install itk -f https://github.com/
> InsightSoftwareConsortium/ITKPythonPackage/releases/tag/latest
>
> These are beta packages that are created on a daily basis. We have
> packages for Linux, macOSX, and Windows for Python 2.7, 3.5, and 3.6, along
> with source distributions (sdist's). Please share your experiences with
> these packages. Initial testing suggests that these packages work both with
> system Python distributions, Python distributions downloaded from
> python.org, and Anaconda Python distributions.
>
> Thanks,
> Matt
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From fisidoro at ethz.ch  Sat Apr 22 11:48:44 2017
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Sat, 22 Apr 2017 15:48:44 +0000
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
Message-ID: <50B858FB5F53124F9E32314E5C1B40944597AC46@MBX212.d.ethz.ch>

Thank you Matt,

I am looking now at scikit-build. 

Do you think I can use it to build C++/CUDA accelerated codes that use ITK too?

Is there a link to a simple example of how to setup a scikit-build for an ITK-based C++ code?

Thank you,
Fabio.

-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com] 
Sent: Montag, 3. April 2017 20:41
To: D'Isidoro Fabio <fisidoro at ethz.ch>
Cc: insight-users at itk.org
Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)

Hallo Fabio,


> I use ITK with Python Wrap. I need to interface my Python code with a 
> Cython-wrapped C++ code that takes only numpy array as input and 
> returns numpy array as output.

Cool. By the way, you may be interested in scikit-build [1], which is a good way to build Cython-wrapped C++ code. We are using it for the ITK and SimpleITK Python packages, and it has good Cython and CMake support.


> Hence, I need to convert the Python itk images into numpy array to be 
> given as input to the wrapped C++ code, and then convert the numpy 
> array in output from the wrapped C++ code back into python itk images.
>
>
>
> Question 1) How can I do that in an efficient way? I found some posts 
> on itk.PyBuffer but I could not find anywhere any reference on how to 
> install it on my itk wrap build.

Yes, itk.PyBuffer works great for that. Please review a PR for some additional documentation:

  https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18

This has been available in ITK for a few releases as a Remote module, which can be enabled by setting

  Module_BridgeNumPy=ON

in ITK's CMake configuration.


Since ITK 4.11.0, it is easier to build since it does not require the NumPy headers.


In current ITK Git master (to be 4.12.0) the module is enabled by default.


Nightly ITK Python packages for ITK Git master are now being built:

  https://github.com/InsightSoftwareConsortium/ITKPythonPackage

macOS and Linux are available. Windows packages will be available over the coming weeks.



> Question 2) The purpose of writing a part of my algorithm in C++ is to 
> speed up the code. If the conversion between python itk images and 
> numpy arrays is slow, I would lose all the speed gain obtained with the C++ implementation.
> Are there better ways to deal with that?

The newer versions ITKBridgeNumPy use a NumPy array view, which does not do any copies during the conversion, and it is very fast.


HTH,
Matt


[1] http://scikit-build.org/

From asertyuio at yahoo.fr  Sat Apr 22 12:46:09 2017
From: asertyuio at yahoo.fr (asertyuio)
Date: Sat, 22 Apr 2017 18:46:09 +0200
Subject: [ITK-users] releaseData flag, partial update in a complex pipeline
In-Reply-To: <50B858FB5F53124F9E32314E5C1B40944597AC46@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B40944597AC46@MBX212.d.ethz.ch>
Message-ID: <6b521a71-d7b7-8361-76cf-0cd3dba9a1d7@yahoo.fr>

Dear Users,

I have trouble applying the concepts behind the release data flag, and
memory management  of itk to a particular problem.

I?m developing a filter with, for part of it, it a rather complex mini
pipeline.
H, R, RS, W, WS and M are itk filters.
The filter will be updated frequently, and I?m trying to make the update
only update necessary parts, while keeping memory imprinting as low as
possible.

Here is a schematic, simplified graph representing my filter :

|H | \ v \ R \ -> take as input a parameter P1 that do not change often |
\ / \ /\ v v v | RS W | | | | | v | \ WS | \ | / v v v M -> takes
parameters P2 that are often updated |

I would like to be able to release the output data of the filter R and
of the filter W, updating them only if the parameter P1 change (which
would trigger update for the whole pipeline), while still being able to
change P2 without having to recalculate R, W and RS.

I think it may be possible with the releaseData flag, don?t really
understand where it should be putted, and if this will do what I need.

Thanks a lot for you help !
Yann

?
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From zhuangming.shen at sphic.org.cn  Mon Apr 24 03:54:40 2017
From: zhuangming.shen at sphic.org.cn (=?utf-8?B?5rKI5bqE5piO?=)
Date: Mon, 24 Apr 2017 07:54:40 +0000
Subject: [ITK-users] Reconstruct non-transverse scanned MR images
Message-ID: <1493020478635.58701@sphic.org.cn>

?Hi all,


I have a set of DICOM MR images which is scanned in Coronal, not Transverse. As a result, when I reconstructed them to a 3D volume using ITK, its orientation seems to be not the same as the that of the Transverse scanned 3D volume, whose orientation is standard LPS. My questions are


(1) Should I reorientation the Coronal scanned 3D volume to standard LPS orientation?

(2) If need, should I use itk.OrientImageFilter to do that? Or use any other methods?

(3) If need use itk.OrientImageFilter, how to write "orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_LPS)" using Python?


Thanks in advance.



Regards,


Zhuangming Shen

?
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From blowekamp at mail.nih.gov  Mon Apr 24 11:35:59 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Mon, 24 Apr 2017 15:35:59 +0000
Subject: [ITK-users] releaseData flag,
 partial update in a complex pipeline
In-Reply-To: <6b521a71-d7b7-8361-76cf-0cd3dba9a1d7@yahoo.fr>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B40944597AC46@MBX212.d.ethz.ch>
 <6b521a71-d7b7-8361-76cf-0cd3dba9a1d7@yahoo.fr>
Message-ID: <41F1BDD4-8A68-4998-A1C7-5A3B2DF9D544@mail.nih.gov>

Hello,

To the best of my knowledge and experience with the ITK pipeline, when the output of a filter ( H or R ) is used as multiple inputs with the ReleaseData, the data from the output ( H or R ) will be release after _each_ filter which use that output data. So the result is that the minimal amount of memory is consumed! But in a complex pipeline like yours filters will be executed multiple times for a single update.

Based on your comments you likely want to set only R and W to ReleaseData automatically. This ensures that all the inputs to M are cached and available. The trade off is that R will get execute twice. Alternatively, you could just manually release the output of R after execution.

HTH,
Brad

On Apr 22, 2017, at 12:46 PM, asertyuio via Insight-users <insight-users at itk.org<mailto:insight-users at itk.org>> wrote:


Dear Users,

I have trouble applying the concepts behind the release data flag, and memory management  of itk to a particular problem.

I?m developing a filter with, for part of it, it a rather complex mini pipeline.
H, R, RS, W, WS and M are itk filters.
The filter will be updated frequently, and I?m trying to make the update only update necessary parts, while keeping memory imprinting as low as possible.

Here is a schematic, simplified graph representing my filter :

    H
    | \
    v  \
    R   \    -> take as input a parameter P1 that do not change often
    |    \
   / \   /\
  v   v v  |
 RS    W   |
  |    |   |
  |    v   |
   \  WS   |
    \  |  /
     v v v
       M     -> takes parameters P2 that are often updated


I would like to be able to release the output data of the filter R and of the filter W, updating them only if the parameter P1 change (which would trigger update for the whole pipeline), while still being able to change P2 without having to recalculate R, W and RS.

I think it may be possible with the releaseData flag, don?t really understand where it should be putted, and if this will do what I need.

Thanks a lot for you help !
Yann

?
_____________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users

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From matt.mccormick at kitware.com  Mon Apr 24 13:39:51 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 24 Apr 2017 13:39:51 -0400
Subject: [ITK-users] ITK Python: numpy to itk image (and viceversa)
In-Reply-To: <50B858FB5F53124F9E32314E5C1B40944597AC46@MBX212.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B40944597AC46@MBX212.d.ethz.ch>
Message-ID: <CALzTN-SGBjtbBy8NY2K2r1GKZ0hDYhseyXAgOd=gYPGSFCc-cA@mail.gmail.com>

Hi Fabio,

Yes, building Python extensions that depend on libraries like Cuda is muich
easier with CMake build system support in scikit-build.

I will follow up with an example of how to set up scikit-build for
ITK-based C++ code.

Thanks,
Matt

On Sat, Apr 22, 2017 at 11:48 AM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:

> Thank you Matt,
>
> I am looking now at scikit-build.
>
> Do you think I can use it to build C++/CUDA accelerated codes that use ITK
> too?
>
> Is there a link to a simple example of how to setup a scikit-build for an
> ITK-based C++ code?
>
> Thank you,
> Fabio.
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 3. April 2017 20:41
> To: D'Isidoro Fabio <fisidoro at ethz.ch>
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)
>
> Hallo Fabio,
>
>
> > I use ITK with Python Wrap. I need to interface my Python code with a
> > Cython-wrapped C++ code that takes only numpy array as input and
> > returns numpy array as output.
>
> Cool. By the way, you may be interested in scikit-build [1], which is a
> good way to build Cython-wrapped C++ code. We are using it for the ITK and
> SimpleITK Python packages, and it has good Cython and CMake support.
>
>
> > Hence, I need to convert the Python itk images into numpy array to be
> > given as input to the wrapped C++ code, and then convert the numpy
> > array in output from the wrapped C++ code back into python itk images.
> >
> >
> >
> > Question 1) How can I do that in an efficient way? I found some posts
> > on itk.PyBuffer but I could not find anywhere any reference on how to
> > install it on my itk wrap build.
>
> Yes, itk.PyBuffer works great for that. Please review a PR for some
> additional documentation:
>
>   https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18
>
> This has been available in ITK for a few releases as a Remote module,
> which can be enabled by setting
>
>   Module_BridgeNumPy=ON
>
> in ITK's CMake configuration.
>
>
> Since ITK 4.11.0, it is easier to build since it does not require the
> NumPy headers.
>
>
> In current ITK Git master (to be 4.12.0) the module is enabled by default.
>
>
> Nightly ITK Python packages for ITK Git master are now being built:
>
>   https://github.com/InsightSoftwareConsortium/ITKPythonPackage
>
> macOS and Linux are available. Windows packages will be available over the
> coming weeks.
>
>
>
> > Question 2) The purpose of writing a part of my algorithm in C++ is to
> > speed up the code. If the conversion between python itk images and
> > numpy arrays is slow, I would lose all the speed gain obtained with the
> C++ implementation.
> > Are there better ways to deal with that?
>
> The newer versions ITKBridgeNumPy use a NumPy array view, which does not
> do any copies during the conversion, and it is very fast.
>
>
> HTH,
> Matt
>
>
> [1] http://scikit-build.org/
>
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From asertyuio at yahoo.fr  Tue Apr 25 11:55:39 2017
From: asertyuio at yahoo.fr (asertyuio)
Date: Tue, 25 Apr 2017 17:55:39 +0200
Subject: [ITK-users] releaseData flag,
 partial update in a complex pipeline
In-Reply-To: <41F1BDD4-8A68-4998-A1C7-5A3B2DF9D544@mail.nih.gov>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B40944597AC46@MBX212.d.ethz.ch>
 <6b521a71-d7b7-8361-76cf-0cd3dba9a1d7@yahoo.fr>
 <41F1BDD4-8A68-4998-A1C7-5A3B2DF9D544@mail.nih.gov>
Message-ID: <c00f1842-2011-d00c-86f8-039fc9b9fa3b@yahoo.fr>

Thanks for your answer Brad !

Just to confirm that I understood well:

To unsure that only the needed parts are actualized I call the global
update, I need to:

  *

    use the H, R, RS, W, WS, M filters as members

  *

    set up their relationships in the filter constructor

  *

    do the update at the M filter

Then I can call manually releaseData on the R and W filter after the
call to M update().

And that should do the trick, and release data should not make the
downstream filters RS and WS to update, right ?

Ok, after rereading what the software guide tells about that:

    Filter execution occurs
    when a) the filter is modified as a result of modifying an instance
    variable; b) the input to the filter
    changes; c) the input data has been released
    ? ITK Software guide p. 200

So it seems like if I release the data of W or R, updating M will force
WS and RS to update? Am I wrong ?

If I want the filter to have the expected behavior, Is it possible to
trigger the update manually ?
I?m thinking of disconnecting RS and WS by using new smart pointers for
R and W output, checking manually the modified state to conditionally
call update when relevant.

Yann

Le 24/04/2017 ? 17:35, Lowekamp, Bradley (NIH/NLM/LHC) [C] a ?crit :

> Hello,
>
> To the best of my knowledge and experience with the ITK pipeline, when
> the output of a filter ( H or R ) is used as multiple inputs with the
> ReleaseData, the data from the output ( H or R ) will be release after
> _each_ filter which use that output data. So the result is that the
> minimal amount of memory is consumed! But in a complex pipeline like
> yours filters will be executed multiple times for a single update.
>
> Based on your comments you likely want to set only R and W to
> ReleaseData automatically. This ensures that all the inputs to M are
> cached and available. The trade off is that R will get execute twice.
> Alternatively, you could just manually release the output of R after
> execution.
>
> HTH,
> Brad
>
>> On Apr 22, 2017, at 12:46 PM, asertyuio via Insight-users
>> <insight-users at itk.org <mailto:insight-users at itk.org>> wrote:
>>
>> Dear Users,
>>
>> I have trouble applying the concepts behind the release data flag,
>> and memory management  of itk to a particular problem.
>>
>> I?m developing a filter with, for part of it, it a rather complex
>> mini pipeline.
>> H, R, RS, W, WS and M are itk filters.
>> The filter will be updated frequently, and I?m trying to make the
>> update only update necessary parts, while keeping memory imprinting
>> as low as possible.
>>
>> Here is a schematic, simplified graph representing my filter :
>>
>> |H | \ v \ R \ -> take as input a parameter P1 that do not change
>> often | \ / \ /\ v v v | RS W | | | | | v | \ WS | \ | / v v v M ->
>> takes parameters P2 that are often updated |
>>
>> I would like to be able to release the output data of the filter R
>> and of the filter W, updating them only if the parameter P1 change
>> (which would trigger update for the whole pipeline), while still
>> being able to change P2 without having to recalculate R, W and RS.
>>
>> I think it may be possible with the releaseData flag, don?t really
>> understand where it should be putted, and if this will do what I need.
>>
>> Thanks a lot for you help !
>> Yann
>>
>> ?
>> _____________________________________
>> Powered by www.kitware.com <http://www.kitware.com>
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>
?
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From blowekamp at mail.nih.gov  Tue Apr 25 13:19:14 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 25 Apr 2017 17:19:14 +0000
Subject: [ITK-users] releaseData flag,
 partial update in a complex pipeline
In-Reply-To: <c00f1842-2011-d00c-86f8-039fc9b9fa3b@yahoo.fr>
References: <50B858FB5F53124F9E32314E5C1B409445967065@MBX212.d.ethz.ch>
 <CALzTN-SxZgnF-Zc1NCbJNR0y-TO8Y6PNjozmOUJTxzhP5USW+w@mail.gmail.com>
 <50B858FB5F53124F9E32314E5C1B40944597AC46@MBX212.d.ethz.ch>
 <6b521a71-d7b7-8361-76cf-0cd3dba9a1d7@yahoo.fr>
 <41F1BDD4-8A68-4998-A1C7-5A3B2DF9D544@mail.nih.gov>
 <c00f1842-2011-d00c-86f8-039fc9b9fa3b@yahoo.fr>
Message-ID: <04F6A8B8-8E44-4728-85F9-EB96958EC0B9@mail.nih.gov>

Hello,

You also need to graft the input and output so that updates and propagation of the mini-pipeline does not propagate beyond the mini-pipeline[1] [2].

Your approach sounds about right. But there are a lot of stumbling block with this approach and just a couple ways to do everything ?proper?. Also this goal of ?caching? the internal data, is not what is generally done in ITK. Most filters in ITK, prefer to release the data and keep memory usage to a minimum. It frequently turns out, that keeping a pipeline?s memory foot print small is important to fast execution and allows the processing to scale to larger data sets too.

The ?ReleaseData? flag does not cause the pipeline to be re-executed. You will have to examine the pipeline code and the time stamps of the relevant objects to determine the effect of ?manual? releasing the data, and how to best do it for your situation.

HTH,
Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageFeature/include/itkUnsharpMaskImageFilter.hxx#L78-L79
[2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageFeature/include/itkUnsharpMaskImageFilter.hxx#L100-L102

On Apr 25, 2017, at 11:55 AM, asertyuio via Insight-users <insight-users at itk.org<mailto:insight-users at itk.org>> wrote:


Thanks for your answer Brad !

Just to confirm that I understood well:

To unsure that only the needed parts are actualized I call the global update, I need to:

  *
use the H, R, RS, W, WS, M filters as members
  *
set up their relationships in the filter constructor
  *
do the update at the M filter

Then I can call manually releaseData on the R and W filter after the call to M update().

And that should do the trick, and release data should not make the downstream filters RS and WS to update, right ?

Ok, after rereading what the software guide tells about that:

Filter execution occurs
when a) the filter is modified as a result of modifying an instance variable; b) the input to the filter
changes; c) the input data has been released
? ITK Software guide p. 200

So it seems like if I release the data of W or R, updating M will force WS and RS to update? Am I wrong ?

If I want the filter to have the expected behavior, Is it possible to trigger the update manually ?
I?m thinking of disconnecting RS and WS by using new smart pointers for R and W output, checking manually the modified state to conditionally call update when relevant.

Yann

Le 24/04/2017 ? 17:35, Lowekamp, Bradley (NIH/NLM/LHC) [C] a ?crit :


Hello,

To the best of my knowledge and experience with the ITK pipeline, when the output of a filter ( H or R ) is used as multiple inputs with the ReleaseData, the data from the output ( H or R ) will be release after _each_ filter which use that output data. So the result is that the minimal amount of memory is consumed! But in a complex pipeline like yours filters will be executed multiple times for a single update.

Based on your comments you likely want to set only R and W to ReleaseData automatically. This ensures that all the inputs to M are cached and available. The trade off is that R will get execute twice. Alternatively, you could just manually release the output of R after execution.

HTH,
Brad

On Apr 22, 2017, at 12:46 PM, asertyuio via Insight-users <insight-users at itk.org<mailto:insight-users at itk.org>> wrote:


Dear Users,

I have trouble applying the concepts behind the release data flag, and memory management  of itk to a particular problem.

I?m developing a filter with, for part of it, it a rather complex mini pipeline.
H, R, RS, W, WS and M are itk filters.
The filter will be updated frequently, and I?m trying to make the update only update necessary parts, while keeping memory imprinting as low as possible.

Here is a schematic, simplified graph representing my filter :

    H
    | \
    v  \
    R   \    -> take as input a parameter P1 that do not change often
    |    \
   / \   /\
  v   v v  |
 RS    W   |
  |    |   |
  |    v   |
   \  WS   |
    \  |  /
     v v v
       M     -> takes parameters P2 that are often updated


I would like to be able to release the output data of the filter R and of the filter W, updating them only if the parameter P1 change (which would trigger update for the whole pipeline), while still being able to change P2 without having to recalculate R, W and RS.

I think it may be possible with the releaseData flag, don?t really understand where it should be putted, and if this will do what I need.

Thanks a lot for you help !
Yann

?
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?
_____________________________________
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From ninarock at list.ru  Wed Apr 26 04:07:53 2017
From: ninarock at list.ru (Butterfly)
Date: Wed, 26 Apr 2017 01:07:53 -0700 (MST)
Subject: [ITK-users] Understanding ITK_COMPUTER_MEMORY_SIZE parameter in
	CMake
Message-ID: <1493194073402-7589858.post@n2.nabble.com>

Hello everyone,

I cannot understand the purpose of the ITK_COMPUTER_MEMORY_SIZE parameter in
CMake. I build ITK on a computer that has 8GB RAM, so I set this parameter
to 8.

1) Will the program fail on computers with < 8GB RAM ?
2) Will the program fail on computers with >= 8GB RAM, but on 32Bit OS (so
with RAM usage limited to 4) ?
3) Will the program use ONLY 8GB of available RAM on computers with >> 8GB
RAM ? 

Thank you very much in advance!






--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Understanding-ITK-COMPUTER-MEMORY-SIZE-parameter-in-CMake-tp7589858.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From francois.budin at kitware.com  Wed Apr 26 08:13:18 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Wed, 26 Apr 2017 08:13:18 -0400
Subject: [ITK-users] Understanding ITK_COMPUTER_MEMORY_SIZE parameter in
	CMake
In-Reply-To: <1493194073402-7589858.post@n2.nabble.com>
References: <1493194073402-7589858.post@n2.nabble.com>
Message-ID: <CAHwLD2VmTx9zCBbarJOvBizVUKExG29eseP0bqDEmfGpvBC9=Q@mail.gmail.com>

Hello,

This parameter is used to assess if certain tests are run. If the value is
too low (I think under 8GB), a few tests will not be run. It will not have
any inpact on the ITK library and how it is compiled.
Hope this helps,

Francois

On Wed, Apr 26, 2017 at 4:07 AM, Butterfly via Insight-users <
insight-users at itk.org> wrote:

> Hello everyone,
>
> I cannot understand the purpose of the ITK_COMPUTER_MEMORY_SIZE parameter
> in
> CMake. I build ITK on a computer that has 8GB RAM, so I set this parameter
> to 8.
>
> 1) Will the program fail on computers with < 8GB RAM ?
> 2) Will the program fail on computers with >= 8GB RAM, but on 32Bit OS (so
> with RAM usage limited to 4) ?
> 3) Will the program use ONLY 8GB of available RAM on computers with >> 8GB
> RAM ?
>
> Thank you very much in advance!
>
>
>
>
>
>
> --
> View this message in context: http://itk-insight-users.
> 2283740.n2.nabble.com/Understanding-ITK-COMPUTER-MEMORY-SIZE-parameter-in-
> CMake-tp7589858.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From ninarock at list.ru  Thu Apr 27 03:57:24 2017
From: ninarock at list.ru (Butterfly)
Date: Thu, 27 Apr 2017 00:57:24 -0700 (MST)
Subject: [ITK-users] Understanding ITK_COMPUTER_MEMORY_SIZE parameter in
 CMake
In-Reply-To: <CAHwLD2VmTx9zCBbarJOvBizVUKExG29eseP0bqDEmfGpvBC9=Q@mail.gmail.com>
References: <1493194073402-7589858.post@n2.nabble.com>
 <CAHwLD2VmTx9zCBbarJOvBizVUKExG29eseP0bqDEmfGpvBC9=Q@mail.gmail.com>
Message-ID: <1493279844766-7589860.post@n2.nabble.com>

Great, many many thanks!!!



--
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Sent from the ITK Insight Users mailing list archive at Nabble.com.

From mrguilfoyle at gmail.com  Thu Apr 27 07:28:19 2017
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Thu, 27 Apr 2017 12:28:19 +0100
Subject: [ITK-users] SimpleITK SyN and BSpline SyN Deformable Registration
Message-ID: <6F7BFBD1-E001-45D4-AF06-82016879CCA0@gmail.com>

Hello

Is there any prospect of the itk::SyNImageRegistrationMethod and its::BSplineSyNImageRegistrationMethod deformable registration algorithms being made available via SimpleITK?

Thanks

From blowekamp at mail.nih.gov  Thu Apr 27 08:57:51 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 27 Apr 2017 12:57:51 +0000
Subject: [ITK-users] SimpleITK SyN and BSpline SyN Deformable
 Registration
In-Reply-To: <6F7BFBD1-E001-45D4-AF06-82016879CCA0@gmail.com>
References: <6F7BFBD1-E001-45D4-AF06-82016879CCA0@gmail.com>
Message-ID: <D2B19824-5ADE-46E2-AEF8-24635B40E785@mail.nih.gov>

Hello Mathew,


It has not come up as a priority yet. Can you please add two feature requests to SimpleITK?s Github Issue tracker [1].

In general though ANTs is the go to interface for using the SyN algorithms [2] for most common applications.


[1] https://github.com/SimpleITK/SimpleITK/issues
[2] http://stnava.github.io/ANTs/

> On Apr 27, 2017, at 7:28 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> 
> Hello
> 
> Is there any prospect of the itk::SyNImageRegistrationMethod and its::BSplineSyNImageRegistrationMethod deformable registration algorithms being made available via SimpleITK?
> 
> Thanks
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From fisidoro at ethz.ch  Thu Apr 27 16:58:07 2017
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Thu, 27 Apr 2017 20:58:07 +0000
Subject: [ITK-users] ITK PyBuffer get physical point coordinates
Message-ID: <50B858FB5F53124F9E32314E5C1B409445984B2A@MBX112.d.ethz.ch>

Hallo,

I know it's possible to get a numpy array of an itk image with:

itk.PyBuffer[ImageType].GetArrayFromImage(Image)

Is it by any chance also possible to obtain a (flattended) numpy array of the physical coordinates of the image pixels too?

Thank you!

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From blowekamp at mail.nih.gov  Thu Apr 27 17:16:17 2017
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Thu, 27 Apr 2017 21:16:17 +0000
Subject: [ITK-users] [ITK]  ITK PyBuffer get physical point coordinates
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409445984B2A@MBX112.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409445984B2A@MBX112.d.ethz.ch>
Message-ID: <AFE79C09-C98A-48D2-A4BA-EB5873E7D8D9@mail.nih.gov>

Hi!

You can generate an image of the physical locations of each pixel with the PhysicalPointImageSource filter:
https://itk.org/Doxygen/html/classitk_1_1PhysicalPointImageSource.html

Very recently added is the SetReferenceImage, which can be use to copy the meta data from one image to the parameters of this filter. If your version is not super recent then you can manually set the Size, Spacing, Origin, Direction and StartIndex.

After you generate the point image you should be able to convert to with the same method.

HTH,
Brad


On Apr 27, 2017, at 4:58 PM, D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>> wrote:

Hallo,

I know it?s possible to get a numpy array of an itk image with:

itk.PyBuffer[ImageType].GetArrayFromImage(Image)

Is it by any chance also possible to obtain a (flattended) numpy array of the physical coordinates of the image pixels too?

Thank you!

_____________________________________
Powered by www.kitware.com<http://www.kitware.com/>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users
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From shindinobot at gmail.com  Thu Apr 27 22:45:02 2017
From: shindinobot at gmail.com (Shaw-Peng Yang)
Date: Fri, 28 Apr 2017 10:45:02 +0800
Subject: [ITK-users] Remove me from this mailing list
Message-ID: <CACQN_55yRwMEWg+Df_1JSokbF=SgZqB-GYe3=FpttE-iC1whAg@mail.gmail.com>

To Whom it may concern,
Please remove me from this mailing list.
Thanks,
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From indianzeppelin at gmail.com  Fri Apr 28 03:20:46 2017
From: indianzeppelin at gmail.com (Girish Mallya)
Date: Fri, 28 Apr 2017 08:20:46 +0100
Subject: [ITK-users] Remove me from this mailing list
In-Reply-To: <CACQN_55yRwMEWg+Df_1JSokbF=SgZqB-GYe3=FpttE-iC1whAg@mail.gmail.com>
References: <CACQN_55yRwMEWg+Df_1JSokbF=SgZqB-GYe3=FpttE-iC1whAg@mail.gmail.com>
Message-ID: <CAA+VR6iz3b_9Y2pxL6Qgmsd85Zp97DSYYSSyYR_egCMRpcNrFg@mail.gmail.com>

Hi Shaw-Peng,

You can do that yourself using the subscribe/unsubscribe link. Here it is -
http://public.kitware.com/mailman/listinfo/insight-users.

On 28 Apr 2017 3:45 am, "Shaw-Peng Yang" <shindinobot at gmail.com> wrote:

To Whom it may concern,
Please remove me from this mailing list.
Thanks,


_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
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From fisidoro at ethz.ch  Fri Apr 28 12:05:03 2017
From: fisidoro at ethz.ch (D'Isidoro  Fabio)
Date: Fri, 28 Apr 2017 16:05:03 +0000
Subject: [ITK-users] [ITK]  ITK PyBuffer get physical point coordinates
In-Reply-To: <AFE79C09-C98A-48D2-A4BA-EB5873E7D8D9@mail.nih.gov>
References: <50B858FB5F53124F9E32314E5C1B409445984B2A@MBX112.d.ethz.ch>
 <AFE79C09-C98A-48D2-A4BA-EB5873E7D8D9@mail.nih.gov>
Message-ID: <50B858FB5F53124F9E32314E5C1B409445984BBC@MBX112.d.ethz.ch>

Thank you for your reply.


1)     I have tried as a first step the following:

DRRPhy = itk.PhysicalPointImageSource[itk.Image[itk.Point[itk.F, Dimension], Dimension]].New()

But I get the error:

KeyError: "itkTemplate : No template (<class 'itkPointPython.itkPointF3'>, 3) for the itk::Image class"

So I guess I can?t generate an image with itk.Points as PixelType. Therefore I chose to use a VectorImage as ImageType in Input to the PhysicalPointImageSource.

sourceImage = itk.PhysicalPointImageSource[itk.VectorImage[itk.F, Dimension]].New()
sourceImage.SetSize(size)
sourceImage.SetSpacing(spacing)
sourceImage.SetOrigin(origin)
#DRRPhy.SetIndex(start) it does not work, how to set the start index?
DRRPhy.SetDirection(direction)


2)     However, using PyBuffer to get a numpy array form that does not work:

sourceImageArray = itk.PyBuffer[ImageType].GetArrayFromImage(sourceImage)

I get the error:

AttributeError: 'itkPhysicalPointImageSourceVIF3' object has no attribute 'GetLargestPossibleRegion'


Am I doing the right thing in point 1) ?
How could I solve point 2) ?

Thank you !

Fabio.

From: Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp at mail.nih.gov]
Sent: Donnerstag, 27. April 2017 23:16
To: D'Isidoro Fabio <fisidoro at ethz.ch>
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] ITK PyBuffer get physical point coordinates

Hi!

You can generate an image of the physical locations of each pixel with the PhysicalPointImageSource filter:
https://itk.org/Doxygen/html/classitk_1_1PhysicalPointImageSource.html

Very recently added is the SetReferenceImage, which can be use to copy the meta data from one image to the parameters of this filter. If your version is not super recent then you can manually set the Size, Spacing, Origin, Direction and StartIndex.

After you generate the point image you should be able to convert to with the same method.

HTH,
Brad


On Apr 27, 2017, at 4:58 PM, D'Isidoro Fabio <fisidoro at ethz.ch<mailto:fisidoro at ethz.ch>> wrote:

Hallo,

I know it?s possible to get a numpy array of an itk image with:

itk.PyBuffer[ImageType].GetArrayFromImage(Image)

Is it by any chance also possible to obtain a (flattended) numpy array of the physical coordinates of the image pixels too?

Thank you!

_____________________________________
Powered by www.kitware.com<http://www.kitware.com/>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users
_______________________________________________
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From KevinSeanLee at live.com  Fri Apr 28 13:25:57 2017
From: KevinSeanLee at live.com (Sean Lee)
Date: Fri, 28 Apr 2017 17:25:57 +0000
Subject: [ITK-users] multiple itk filters in vtk pipeline issue
Message-ID: <MWHPR18MB0944D2F4B33C41E81C3B1967A9130@MWHPR18MB0944.namprd18.prod.outlook.com>

I am trying to apply image processing with itk through vtk pipeline. It seems no problems with single itk filter, but did not work well with multiple itk filters. The pseudo code is as following:


in constructor:


m_ItkImage = ItkImageType::New();

m_ItkImageFilter = ItkImageFilterType::New();


in image processing function:


m_ItkImage gets an image from vtk pipeline


m_ItkImageFilter->SetInput(m_ItkImage);

m_ItkImageFilter->Update();


m_ItkImageFilter->GetOutput() was sent back to the vtk pipeline


I debugged the m_ItkImage and m_ItkImageFilter->GetOutput(), and saw that m_ItkImage was updated but m_ItkImageFilter was not through the vtk pipeline.


How can I make m_ItkImageFilter->GetOutput() updated too through the vtk pipeline?


Thank you for your time.



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From aharr8 at uwo.ca  Fri Apr 28 16:10:59 2017
From: aharr8 at uwo.ca (Andrew Harris)
Date: Fri, 28 Apr 2017 16:10:59 -0400
Subject: [ITK-users] [ITK] CommandIterationUpdate optimizer position
	reporting
Message-ID: <CAJ0LxQ+LqyCHg41Xbwn4D=zaUtwWkdd-eEn1WCPvba-yTB1mtA@mail.gmail.com>

Hello,
I'm attempting to track the movement of images under registration using
various optimizers.  I have a CommandIterationUpdate observer set up to
write the optimizer positions to file, and when I use a Gradient Descent or
Powell optimizer I get a vector for the translation applied using
optimizer->GetCurrentPosition(), however if I use the LBFGSB optimizer I
get zero vectors all the way down (it returns the correct result though).
Is the functionality of GetCurrentPosition() different in the LBFGSB
optimizer than the others?

--

AH


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From francois.budin at kitware.com  Fri Apr 28 17:11:55 2017
From: francois.budin at kitware.com (Francois Budin)
Date: Fri, 28 Apr 2017 17:11:55 -0400
Subject: [ITK-users] [ITK] ITK PyBuffer get physical point coordinates
In-Reply-To: <50B858FB5F53124F9E32314E5C1B409445984BBC@MBX112.d.ethz.ch>
References: <50B858FB5F53124F9E32314E5C1B409445984B2A@MBX112.d.ethz.ch>
 <AFE79C09-C98A-48D2-A4BA-EB5873E7D8D9@mail.nih.gov>
 <50B858FB5F53124F9E32314E5C1B409445984BBC@MBX112.d.ethz.ch>
Message-ID: <CAHwLD2VbLoYfmC6zEv8uxN84dcv=tb0bDqPMdFaGrQbeegPmqQ@mail.gmail.com>

Hello Fabio,

I was able to use this filter in Python. Here is the commands I typed:
In [14]: ImageType=itk.Image[itk.Vector[itk.F,2],2]

In [15]: source=itk.PhysicalPointImageSource[ImageType].New()

In [16]: source.SetSize([5,5])

In [17]: source.SetOrigin([0,0])

In [18]: source.SetSpacing([.5,.5])

In [19]: source.Update()

In [20]: itk.GetArrayFromImage(source)
Out[20]:
itkndarray([[[ 0. ,  0. ],
        [ 0.5,  0. ],
        [ 1. ,  0. ],
        [ 1.5,  0. ],
        [ 2. ,  0. ]],

       [[ 0. ,  0.5],
        [ 0.5,  0.5],
        [ 1. ,  0.5],
        [ 1.5,  0.5],
        [ 2. ,  0.5]],

       [[ 0. ,  1. ],
        [ 0.5,  1. ],
        [ 1. ,  1. ],
        [ 1.5,  1. ],
        [ 2. ,  1. ]],

       [[ 0. ,  1.5],
        [ 0.5,  1.5],
        [ 1. ,  1.5],
        [ 1.5,  1.5],
        [ 2. ,  1.5]],

       [[ 0. ,  2. ],
        [ 0.5,  2. ],
        [ 1. ,  2. ],
        [ 1.5,  2. ],
        [ 2. ,  2. ]]], dtype=float32)

It also worked with VectorImages:

In [22]: ImageType=itk.VectorImage[itk.F,2]

In [23]: source=itk.PhysicalPointImageSource[ImageType].New()

In [24]: source.SetOrigin([0,0])

In [25]: source.SetSize([5,5])

In [26]: source.SetSpacing([.5,.5])

In [27]: source.Update()

In [28]: itk.GetArrayFromImage(source)


To answer your questions:
1) This filter is only wrapped over image of vectors and vector images. You
can have the list of types that are available in Python with
itk.PhysicalPointImageSource.GetTypes()
2) You may have a version of ITK Python for which VectorImage is not
wrapped for PyBuffer. You can try to update your ITK Python [1]

Hope this helps,
Francois

[1] https://github.com/InsightSoftwareConsortium/ITKPythonPackage

On Fri, Apr 28, 2017 at 12:05 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:

> Thank you for your reply.
>
>
>
> 1)     I have tried as a first step the following:
>
>
>
> DRRPhy = itk.PhysicalPointImageSource[itk.Image[itk.Point[itk.F,
> Dimension], Dimension]].New()
>
>
>
> But I get the error:
>
>
>
> KeyError: "itkTemplate : No template (<class 'itkPointPython.itkPointF3'>,
> 3) for the itk::Image class"
>
>
>
> So I guess I can?t generate an image with itk.Points as PixelType.
> Therefore I chose to use a VectorImage as ImageType in Input to the
> PhysicalPointImageSource.
>
>
>
> sourceImage = itk.PhysicalPointImageSource[itk.VectorImage[itk.F,
> Dimension]].New()
>
> sourceImage.SetSize(size)
>
> sourceImage.SetSpacing(spacing)
>
> sourceImage.SetOrigin(origin)
>
> #DRRPhy.SetIndex(start) it does not work, how to set the start index?
>
> DRRPhy.SetDirection(direction)
>
>
>
> 2)     However, using PyBuffer to get a numpy array form that does not
> work:
>
>
>
> sourceImageArray = itk.PyBuffer[ImageType].GetArrayFromImage(sourceImage)
>
>
>
> I get the error:
>
>
>
> AttributeError: 'itkPhysicalPointImageSourceVIF3' object has no attribute
> 'GetLargestPossibleRegion'
>
>
>
>
>
> Am I doing the right thing in point 1) ?
>
> How could I solve point 2) ?
>
>
>
> Thank you !
>
>
>
> Fabio.
>
>
>
> *From:* Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp at mail.nih.gov]
>
> *Sent:* Donnerstag, 27. April 2017 23:16
> *To:* D'Isidoro Fabio <fisidoro at ethz.ch>
> *Cc:* insight-users at itk.org
> *Subject:* Re: [ITK] [ITK-users] ITK PyBuffer get physical point
> coordinates
>
>
>
> Hi!
>
>
>
> You can generate an image of the physical locations of each pixel with the
> PhysicalPointImageSource filter:
>
> https://itk.org/Doxygen/html/classitk_1_1PhysicalPointImageSource.html
>
>
>
> Very recently added is the SetReferenceImage, which can be use to copy the
> meta data from one image to the parameters of this filter. If your version
> is not super recent then you can manually set the Size, Spacing, Origin,
> Direction and StartIndex.
>
>
>
> After you generate the point image you should be able to convert to with
> the same method.
>
>
>
> HTH,
>
> Brad
>
>
>
>
>
> On Apr 27, 2017, at 4:58 PM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:
>
>
>
> Hallo,
>
>
>
> I know it?s possible to get a numpy array of an itk image with:
>
>
>
> itk.PyBuffer[ImageType].GetArrayFromImage(Image)
>
>
>
> Is it by any chance also possible to obtain a (flattended) numpy array of
> the physical coordinates of the image pixels too?
>
>
>
> Thank you!
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
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>
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From matt.mccormick at kitware.com  Fri Apr 28 18:59:56 2017
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 28 Apr 2017 18:59:56 -0400
Subject: [ITK-users] multiple itk filters in vtk pipeline issue
In-Reply-To: <MWHPR18MB0944D2F4B33C41E81C3B1967A9130@MWHPR18MB0944.namprd18.prod.outlook.com>
References: <MWHPR18MB0944D2F4B33C41E81C3B1967A9130@MWHPR18MB0944.namprd18.prod.outlook.com>
Message-ID: <CALzTN-QsZmUbvNVq_6EQgtMV-nCMUpNqNZh86cDLuNMS96zrbw@mail.gmail.com>

Hi Sean,

There are two filters in the ITKVTKGlue module (it has to be enabled
explicitly in your ITK build with the Module_ITKVTKGlue option) that are
used to glue together ITK and VTK pipelines. See these examples:


https://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.html


https://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Documentation.html

Hope this helps,
Matt

On Fri, Apr 28, 2017 at 1:25 PM, Sean Lee <KevinSeanLee at live.com> wrote:

> I am trying to apply image processing with itk through vtk pipeline. It
> seems no problems with single itk filter, but did not work well with
> multiple itk filters. The pseudo code is as following:
>
>
> in constructor:
>
>
> m_ItkImage = ItkImageType::New();
>
> m_ItkImageFilter = ItkImageFilterType::New();
>
>
> in image processing function:
>
>
> m_ItkImage gets an image from vtk pipeline
>
>
> m_ItkImageFilter->SetInput(m_ItkImage);
>
> m_ItkImageFilter->Update();
>
>
> m_ItkImageFilter->GetOutput() was sent back to the vtk pipeline
>
>
> I debugged the m_ItkImage and m_ItkImageFilter->GetOutput(), and saw that
> m_ItkImage was updated but m_ItkImageFilter was not through the vtk
> pipeline.
>
>
> How can I make m_ItkImageFilter->GetOutput() updated too through the vtk
> pipeline?
>
>
> Thank you for your time.
>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Sat Apr 29 13:54:09 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 29 Apr 2017 13:54:09 -0400
Subject: [ITK-users] [ITK] CommandIterationUpdate optimizer position
	reporting
In-Reply-To: <CAJ0LxQ+LqyCHg41Xbwn4D=zaUtwWkdd-eEn1WCPvba-yTB1mtA@mail.gmail.com>
References: <CAJ0LxQ+LqyCHg41Xbwn4D=zaUtwWkdd-eEn1WCPvba-yTB1mtA@mail.gmail.com>
Message-ID: <CAPf2UMRVavkFLjjEKqzJ4wC4SJZJhGTxjxxOqKoUCHEY+=xNpQ@mail.gmail.com>

Hi Andrew,

different optimizers have different behavior (e.g. small steps vs big
steps), but even the programming interface is not uniform. Some functions
are called differently e.g. maximumSteps vs iterationCount etc. You should
look at the respective examples for each optimizer which you plan to use to
see how iteration tracking is set up.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Fri, Apr 28, 2017 at 4:10 PM, Andrew Harris <aharr8 at uwo.ca> wrote:

> Hello,
> I'm attempting to track the movement of images under registration using
> various optimizers.  I have a CommandIterationUpdate observer set up to
> write the optimizer positions to file, and when I use a Gradient Descent or
> Powell optimizer I get a vector for the translation applied using
> optimizer->GetCurrentPosition(), however if I use the LBFGSB optimizer I
> get zero vectors all the way down (it returns the correct result though).
> Is the functionality of GetCurrentPosition() different in the LBFGSB
> optimizer than the others?
>
> --
>
> AH
>
>
> ------------------------------------------------------------
> -----------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From aharr8 at uwo.ca  Sat Apr 29 14:15:01 2017
From: aharr8 at uwo.ca (Andrew Harris)
Date: Sat, 29 Apr 2017 14:15:01 -0400
Subject: [ITK-users] [itk] Unhandled exception when using Mean Squares and
	Powell Optimizer
Message-ID: <CAJ0LxQLokh8-7bGsDtM3zgPAEbnUnHAO7X1VBxDXGHucnWRoKQ@mail.gmail.com>

Hello,
I'm getting an exception saying too many samples are outside the moving
image buffer when I use the MeanSquaresImageToImageMetric with the
PowellOptimizer that doesn't occur when I
use NormalizedCorrelationImageToImageMetric
or MattesMutualInformationImageToImageMetric.  I thought it might be
because the optimizer is seeking to maximize the metric so I tried calling
MaximizeOff on it but got the same exception.  Any ideas would be
appreciated.

--

AH


-----------------------------------------------------------------------------------------------

*This email and any attachments thereto may contain private,
confidential, and privileged materials for the sole use of the intended
recipient. Any reviewing, copying, or distribution of this email (or any
attachments thereto) by other than the intended recipient is strictly
prohibited. If you are not the intended recipient, please contact the
sender immediately and permanently destroy this email and any attachments
thereto.*
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From dzenanz at gmail.com  Sat Apr 29 15:46:06 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 29 Apr 2017 15:46:06 -0400
Subject: [ITK-users] [itk] Unhandled exception when using Mean Squares
 and Powell Optimizer
In-Reply-To: <CAJ0LxQLokh8-7bGsDtM3zgPAEbnUnHAO7X1VBxDXGHucnWRoKQ@mail.gmail.com>
References: <CAJ0LxQLokh8-7bGsDtM3zgPAEbnUnHAO7X1VBxDXGHucnWRoKQ@mail.gmail.com>
Message-ID: <CAPf2UMRvbHxw4aEY0pLgjt=jPU1-cY=_xtO9aJuKOJeQTAs-BA@mail.gmail.com>

Hi Andrew,

if this is happening on the first iteration, your initial parameters do not
overlap your images well. If this is happening in some later iteration, the
other optimizer might be veering of course during optimization, pushing
your images apart and ultimately causing the error. From experience, the
initial parameters are almost always to blame.

Regards,
D?enan

On Sat, Apr 29, 2017 at 2:15 PM, Andrew Harris <aharr8 at uwo.ca> wrote:

> Hello,
> I'm getting an exception saying too many samples are outside the moving
> image buffer when I use the MeanSquaresImageToImageMetric with the
> PowellOptimizer that doesn't occur when I use
> NormalizedCorrelationImageToImageMetric or MattesMutualInformationImageToImageMetric.
> I thought it might be because the optimizer is seeking to maximize the
> metric so I tried calling MaximizeOff on it but got the same exception.
> Any ideas would be appreciated.
>
> --
>
> AH
>
>
> ------------------------------------------------------------
> -----------------------------------
>
> *This email and any attachments thereto may contain private,
> confidential, and privileged materials for the sole use of the intended
> recipient. Any reviewing, copying, or distribution of this email (or any
> attachments thereto) by other than the intended recipient is strictly
> prohibited. If you are not the intended recipient, please contact the
> sender immediately and permanently destroy this email and any attachments
> thereto.*
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
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>
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From swetha.bsharma at gmail.com  Sat Apr 29 22:40:58 2017
From: swetha.bsharma at gmail.com (Swetha Sharma)
Date: Sun, 30 Apr 2017 08:10:58 +0530
Subject: [ITK-users] function to find if image has foreground pixels in
	binaryvolume
Message-ID: <CACDHZEQD2Z1ORgD4-s=N+__u2fGunbxJoExkimv_Dutc2u9J+Q@mail.gmail.com>

Hi All,

I am looking for a function which checks existence of foreground pixel in
binary volume.
-swetha
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From dzenanz at gmail.com  Sun Apr 30 10:36:29 2017
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sun, 30 Apr 2017 10:36:29 -0400
Subject: [ITK-users] function to find if image has foreground pixels in
	binaryvolume
In-Reply-To: <CACDHZEQD2Z1ORgD4-s=N+__u2fGunbxJoExkimv_Dutc2u9J+Q@mail.gmail.com>
References: <CACDHZEQD2Z1ORgD4-s=N+__u2fGunbxJoExkimv_Dutc2u9J+Q@mail.gmail.com>
Message-ID: <CAPf2UMT6Du7qOU9d4mrmXGxsC0MfxRKxgGR_FmZL4u7K8D1Wcw@mail.gmail.com>

Hi Swetha,

combine image->TransformPhysicalPointToIndex()
<https://itk.org/Doxygen/html/classitk_1_1ImageBase.html#af4a7c9c3787e9fdafbaaade2e02efa25>
to
see if the point is in the image and image->GetPixel()
<https://itk.org/Doxygen/html/classitk_1_1Image.html#ad424c945604f339130b4ffe81b99738e>
to
check whether the value is greater than zero.

Regards,
D?enan Zuki?, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Sat, Apr 29, 2017 at 10:40 PM, Swetha Sharma <swetha.bsharma at gmail.com>
wrote:

> Hi All,
>
> I am looking for a function which checks existence of foreground pixel in
> binary volume.
> -swetha
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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