[Insight-users] Problem generating a 3D volume from a set of slices
Bill Lorensen
bill.lorensen at gmail.com
Wed May 18 12:49:27 EDT 2011
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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