[Insight-users] Problem generating a 3D volume from a set of slices
Bill Lorensen
bill.lorensen at gmail.com
Wed May 18 12:56:38 EDT 2011
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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