[Insight-users] Problem generating a 3D volume from a set of slices
Bill Lorensen
bill.lorensen at gmail.com
Wed May 18 12:12:01 EDT 2011
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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