[Insight-users] Problem generating a 3D volume from a set of slices

Dora Szasz dora.szasz at yahoo.com
Wed May 18 13:03:16 EDT 2011 

I don't know. Maybe because the pictures have the same size?


________________________________
From: Bill Lorensen <bill.lorensen at gmail.com>
To: Dora Szasz <dora.szasz at yahoo.com>
Cc: "insight-users at itk.org" <insight-users at itk.org>
Sent: Wednesday, May 18, 2011 7:56 PM
Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices


When you remove the ->UpdateLargestPossibleRegion() I don't see why you did not get an error something like this:
$ ../bin/VolumeFromSlices.exe "/c/lorensen/Data/Dora/Dora00%02d.png" 1 5 out.mh
d
File: c:/lorensen/Data/Dora/Dora0001.png
File: c:/lorensen/Data/Dora/Dora0002.png
File: c:/lorensen/Data/Dora/Dora0003.png
File: c:/lorensen/Data/Dora/Dora0004.png
File: c:/lorensen/Data/Dora/Dora0005.png
ExceptionObject caught !

itk::ImageFileReaderException (0x146e3b0)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::Generate
OutputInformation() [with TOutputImage = itk::Image<unsigned char, 3u>, ConvertP
ixelTraits = itk::DefaultConvertPixelTraits<unsigned char>]"
File: C:/lorensen/ProjectsGIT/ITKModular/Modules/IO/Base/include/itkImageFileRea
der.txx
Line: 144
Description:  Could not create IO object for file c:/lorensen/Data/Dora/Dora0001
.png
The file doesn't exist.
Filename = c:/lorensen/Data/Dora/Dora0001.png



On Wed, May 18, 2011 at 12:54 PM, Dora Szasz <dora.szasz at yahoo.com> wrote:

Thank you, Bill....I didn't observed that the pattern is wrong. Now it is ok. I have the out.mhd file.
>Thank you a lot!
>You are a great helper and very patient!
>
>
>Dora
>
>
>
>________________________________
>From: Bill Lorensen <bill.lorensen at gmail.com>
>To: Dora Szasz <dora.szasz at yahoo.com>
>Cc: "insight-users at itk.org" <insight-users at itk.org>
>Sent: Wednesday, May 18, 2011 7:49 PM
>
>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>
>
>
>And you pattern is wrong. It should be;
>Dora00%02dd.png
>
>The first "%02d" is part of the printf format, the second "d" is part of your filenames/
>
>
>On Wed, May 18, 2011 at 12:45 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>
>I do not see the files listed in your screen dump. Are they in the same directory as the .exe file?
>>
>>
>>
>>
>>
>>On Wed, May 18, 2011 at 12:38 PM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>
>>
>>>
>>>Nothing changed. There is exactly the same exception description, without any details.
>>>
>>>________________________________
>>>From: Bill Lorensen <bill.lorensen at gmail.com>
>>>To: Dora Szasz <dora.szasz at yahoo.com>
>>>Cc: Insight-Users <insight-users at itk.org>
>>>Sent: Wednesday, May 18, 2011 7:28 PM
>>>
>>>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>>>
>>>
>>>
>>>I you remove the UpdateLargestPossibleRegion and just use writer->Update() you will probably get a more descriptive exception description.
>>>
>>>
>>>
>>>On Wed, May 18, 2011 at 12:12 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>>
>>>I suspect that it is not finding the files. Show me the exact command line you are using to run your program. Also provide a directory listing of the directory containing the files.
>>>>
>>>>The names generator generates names, it does not check to see if the names are valid files. 
>>>>
>>>>
>>>>
>>>>On Wed, May 18, 2011 at 11:54 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>>>
>>>>Dora,
>>>>>Can you send to me the 5 png files? I just built an example similar to yours and it works.
>>>>>
>>>>>Bill
>>>>>
>>>>>
>>>>>
>>>>>On Wed, May 18, 2011 at 11:10 AM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>>>>
>>>>>Ok. Thank you a lot!
>>>>>>
>>>>>>
>>>>>>
>>>>>>________________________________
>>>>>>From: Bill Lorensen <bill.lorensen at gmail.com>
>>>>>>To: Dora Szasz <dora.szasz at yahoo.com>
>>>>>>Cc: "insight-users at itk.org" <insight-users at itk.org>
>>>>>>Sent: Wednesday, May 18, 2011 5:30 PM
>>>>>>
>>>>>>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>>>>>>
>>>>>>
>>>>>>
>>>>>>I'll try to reproduce the problem. Probably not until later though.
>>>>>>
>>>>>>
>>>>>>On Wed, May 18, 2011 at 10:12 AM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>>>>>
>>>>>>Yes. Exactly the same one.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>________________________________
>>>>>>>From: Bill Lorensen <bill.lorensen at gmail.com>
>>>>>>>To: Dora Szasz <dora.szasz at yahoo.com>
>>>>>>>Cc: "insight-users at itk.org" <insight-users at itk.org>
>>>>>>>Sent: Wednesday, May 18, 2011 5:06 PM
>>>>>>>
>>>>>>>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>Do you get the same exception message?
>>>>>>>
>>>>>>>
>>>>>>>On Wed, May 18, 2011 at 9:07 AM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>>>>>>
>>>>>>>It writes me the name of the files, but no .mhd ouput file.
>>>>>>>>
>>>>>>>>
>>>>>>>>File: Dora0001.png
>>>>>>>>File: Dora0002.png
>>>>>>>>File: Dora0003.png
>>>>>>>>File: Dora0004.png
>>>>>>>>File: Dora0005.png
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>________________________________
>>>>>>>>From: Bill Lorensen <bill.lorensen at gmail.com>
>>>>>>>>To: Dora Szasz <dora.szasz at yahoo.com>
>>>>>>>>Cc: Insight-Users <insight-users at itk.org>
>>>>>>>>Sent: Wednesday, May 18, 2011 3:27 PM
>>>>>>>>
>>>>>>>>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>[please keep the mailing list involved]
>>>>>>>>Try printing out the generated filenames. Something like:
>>>>>>>>
>>>>>>>>  std::vector<std::string> names = nameGenerator->GetFileNames();
>>>>>>>>  std::vector<std::string>::iterator nit;
>>>>>>>>
>>>>>>>>  for (nit = names.begin();
>>>>>>>>       nit != names.end();
>>>>>>>>       nit++)
>>>>>>>>    {
>>>>>>>>    std::cout << "File: " << (*nit).c_str() << std::endl;
>>>>>>>>    }
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>On Wed, May 18, 2011 at 8:16 AM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>>>>>>>
>>>>>>>>I've tried all the possibilities. Even if I run BrainModel.exe 1 5 out.mhd the error appears and I don't know why.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>________________________________
>>>>>>>>>From: Bill Lorensen <bill.lorensen at gmail.com>
>>>>>>>>>To: Dora Szasz <dora.szasz at yahoo.com>
>>>>>>>>>Cc: Insight-Users <insight-users at itk.org>
>>>>>>>>>Sent: Wednesday, May 18, 2011 3:00 PM
>>>>>>>>>
>>>>>>>>>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>But the program should be run as:
>>>>>>>>>BrainModel.exe 1 5 out.mhd
>>>>>>>>>
>>>>>>>>>at least according to the source you attached.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>On Wed, May 18, 2011 at 2:00 AM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>>>>>>>>
>>>>>>>>>Hi Bill,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>Yes, the names of the files are correct, but the following  error message appears:
>>>>>>>>>>I have verified and the size of the pictures is the same. I don't know what could be the problem.
>>>>>>>>>>Thank you!
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>D:\Lib\Project\Dora\bin\Debug>BrainModel.exe Dora0001d.png Dora0005d.png out.mhd
>>>>>>>>>>ExceptionObject caught !
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>itk::ExceptionObject (00B2F4D8)
>>>>>>>>>>Location: "void __thiscall itk::ImageFileWriter<class itk::Image<unsigned char,3
>>>>>>>>>>> >::Write(void)"
>>>>>>>>>>File: d:\lib\_itk\source\code\io\itkImageFileWriter.txx
>>>>>>>>>>Line: 271
>>>>>>>>>>Description: itk::ERROR: ImageFileWriter(0012F3F8): Largest possible region does
>>>>>>>>>> not fully contain requested paste IO regionPaste IO region: ImageIORegion (00B2
>>>>>>>>>>F910)
>>>>>>>>>>  Dimension: 3
>>>>>>>>>>  Index: 0 0 0
>>>>>>>>>>  Size: 0 0 1
>>>>>>>>>>Largest possible region: ImageRegion (00B2F9C4)
>>>>>>>>>>  Dimension: 3
>>>>>>>>>>  Index: [0, 0, 0]
>>>>>>>>>>  Size: [0, 0, 1]
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>________________________________
>>>>>>>>>>From: Bill Lorensen <bill.lorensen at gmail.com>
>>>>>>>>>>To: Dora Szasz <dora.szasz at yahoo.com>
>>>>>>>>>>Cc: "insight-users at itk.org" <insight-users at itk.org>
>>>>>>>>>>Sent: Wednesday, May 18, 2011 7:03 AM
>>>>>>>>>>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>Oops...
>>>>>>>>>>Dora0001d.png
>>>>>>>>>>Dora0002d.png
>>>>>>>>>>Dora0003d.png
>>>>>>>>>>...
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>On Wed, May 18, 2011 at 12:02 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>What are the names of the file? From your code they should be something like:
>>>>>>>>>>>Dora00001d.png
>>>>>>>>>>>Dora00002d.png
>>>>>>>>>>>Dora00003d.png
>>>>>>>>>>>...
>>>>>>>>>>>
>>>>>>>>>>>Is that how your files are named?
>>>>>>>>>>>
>>>>>>>>>>>Bill
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>On Tue, May 17, 2011 at 4:19 PM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>Hello all,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>I am trying to make a 3D volume using a set of .png images. I want to obtain a 3D image (for example .mhd), but It doesn't generate any output.
>>>>>>>>>>>>My code is the following:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>#include "itkImage.h"
>>>>>>>>>>>> #include "itkImageSeriesReader.h"
>>>>>>>>>>>> #include "itkImageFileWriter.h"
>>>>>>>>>>>> #include "itkNumericSeriesFileNames.h"
>>>>>>>>>>>> #include "itkPNGImageIO.h"
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> int main( int argc, char ** argv )
>>>>>>>>>>>> {
>>>>>>>>>>>>  // Verify the number of parameters in the command line
>>>>>>>>>>>>  if( argc < 4 )
>>>>>>>>>>>>    {
>>>>>>>>>>>>    std::cerr << "Usage: " << std::endl;
>>>>>>>>>>>>    std::cerr << argv[0] << " firstSliceValue lastSliceValue outputImageFile " << std::endl;
>>>>>>>>>>>>    return EXIT_FAILURE;
>>>>>>>>>>>>    }
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  typedef unsigned char   PixelType;
>>>>>>>>>>>>  const unsigned int Dimension = 3;
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  typedef itk::Image< PixelType, Dimension >  ImageType;
>>>>>>>>>>>>  typedef itk::ImageSeriesReader< ImageType >  ReaderType;
>>>>>>>>>>>>  typedef itk::ImageFileWriter<   ImageType >  WriterType;
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  ReaderType::Pointer reader = ReaderType::New();
>>>>>>>>>>>>  WriterType::Pointer writer = WriterType::New();
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  const unsigned int first = atoi( argv[1] );
>>>>>>>>>>>>  const unsigned int last  = atoi( argv[2] );
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  const char * outputFilename = argv[3];
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  typedef itk::NumericSeriesFileNames    NameGeneratorType;
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  nameGenerator->SetSeriesFormat( "Dora00%02d.png" );
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  nameGenerator->SetStartIndex( first );
>>>>>>>>>>>>  nameGenerator->SetEndIndex( last );
>>>>>>>>>>>>  nameGenerator->SetIncrementIndex( 1 );
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  reader->SetImageIO( itk::PNGImageIO::New() );
>>>>>>>>>>>>  reader->SetFileNames( nameGenerator->GetFileNames()  );
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  writer->SetFileName( outputFilename );
>>>>>>>>>>>>  writer->SetInput( reader->GetOutput() );
>>>>>>>>>>>>  try
>>>>>>>>>>>>    {
>>>>>>>>>>>>    writer->UpdateLargestPossibleRegion();
>>>>>>>>>>>>        writer->Update();
>>>>>>>>>>>>    }
>>>>>>>>>>>>  catch( itk::ExceptionObject & err )
>>>>>>>>>>>>    {
>>>>>>>>>>>>    std::cerr << "ExceptionObject caught !" << std::endl;
>>>>>>>>>>>>    std::cerr << err << std::endl;
>>>>>>>>>>>>    return EXIT_FAILURE;
>>>>>>>>>>>>    }
>>>>>>>>>>>>  return EXIT_SUCCESS;
>>>>>>>>>>>> }
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>1. How could I modify it in order to obtain the volume?
>>>>>>>>>>>>2. How could I modify it in order to use "itkImageToVTKImageFilter.h" to display it on vtk window?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>Thank you a lot!
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>_____________________________________
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>>>>>>>>>>>>
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>>>>>>>>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>
>
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