[Insight-users] Problem generating a 3D volume from a set of slices
Dora Szasz
dora.szasz at yahoo.com
Wed May 18 12:38:24 EDT 2011
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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>>>>>>>>>
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>>>>>>>>>
>>>>>>>>>Please keep messages on-topic and check the ITK FAQ at:
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>>>>>>>>>
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>>>>>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>
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