[Insight-users] Problem generating a 3D volume from a set of slices
Dora Szasz
dora.szasz at yahoo.com
Wed May 18 12:54:16 EDT 2011
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?
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>On Wed, May 18, 2011 at 12:38 PM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>
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>>
>>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!
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>_____________________________________
>>>>>>>>>>>Powered by www.kitware.com
>>>>>>>>>>>
>>>>>>>>>>>Visit other Kitware open-source projects at
>>>>>>>>>>>http://www.kitware.com/opensource/opensource.html
>>>>>>>>>>>
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>>>>>>>>>>>
>>>>>>>>>>>Please keep messages on-topic and check the ITK FAQ at:
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>>>>>>>>>>>
>>>>>>>>>>>Follow this link to subscribe/unsubscribe:
>>>>>>>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
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