[ITK] [ITK-users] itkImageFileWriter + ExtractSliceImageFilter: largest region exception

Marcos fotosentido at gmail.com
Wed Sep 9 11:36:23 EDT 2015 

Hi,

GetBufferedRegion gives me the same numbers as GetLargestPossibleRegion:
index: 0, 0, 0
size: 512, 512, 12

I also tried, just after reading the image, using ImageDuplicator:

reader = ReaderType::New();

    reader->SetFileName(fileName);


    dicomIO = itk::GDCMImageIO::New();


    typedef itk::ImageDuplicator< ImageType > DuplicatorType;

    DuplicatorType::Pointer duplicator = DuplicatorType::New();



    reader->SetImageIO(dicomIO);

    try

    {

        reader->Update();

        image = reader->GetOutput();


        // duplicar imagen

        duplicator->SetInputImage(image);

        duplicator->Update();

        imageToSave = duplicator->GetOutput();

     }

     catch

     ...



None worked.

I saw the ExtractImageFilter example, so I changed to
extracter->SetDirectionCollapseToSubmatrix() instead of
SetDirectionCollapseToIdentity().

The filename is "C:/Users/M/r.png", in Windows.
Nothing. Same error.

bmp: itkbmpimageio.cxx:727
jpg: itkjpegimageio.cxx:454
png: itkpngimageio.cxx:521

By the way, it would be better if the exception messages were captured
in my writer's try catch. I have to dive into these sources.


2015-09-08 22:05 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> Hello,
>
> You can use the Image::GetBufferedRegion method and print the resulting
> ImageRegion.
>
> This looks like there is a pipelining issue to me. I'd recommend trying to
> simplify by not reusing the Image data object. Yes you will need to
> recompute, but it may help to narrow down the problem.
>
> Brad
>
>
>
> On Sep 8, 2015, at 3:06 PM, Marcos <fotosentido at gmail.com> wrote:
>
> Hi,
>
> I know the input and desired regions, not sure how to look for the
> buffered region.
>
> 1. Reviewing my code I saw I didn't set the input image for the extracter,
> so I added:
> extracter->SetInput(image);
>
> Good, right? But no. Still the same error.
>
> 2. Then I tried switching to itkExtractImageFilter, and I got:
> Exception at 0x7633c42d, code: 0xe06d7363: C++ exception, flags=0x1
> (execution cannot be continued) (first chance) at
> c:\itk-4.8.0-installed\include\itk-4.8\itkextractimagefilter.hxx:242
>
> So I had to look inside this code (why don't throw me more info in the try
> catch?) to see what's happening, and I read this:
> itkExceptionMacro( << "It is required that the strategy for collapsing
> the direction matrix be explicitly specified. " << "Set with either
> myfilter->SetDirectionCollapseToIdentity() or
> myfilter->SetDirectionCollapseToSubmatrix() " << typeid( ImageBase<
> InputImageDimension > * ).name() );
> 3. I also tried to insert a:
> image->Update();
> or
> image->UpdateOutputData();
> with same results.
>
> I was thinking about passing the reader, but I'd like to apply changes to
> my image, so this method would receive a modified copy (no DeepCopy method
> like in vtk?)
>
>
> Yes, the input image is connected to a pipeline:
> itk::Image -> itk::ImageToVTKImageFilter -> vtk::vtkImageFlip ->
> vtkImageData -> vtkImageViewer2
>
>
> Thanks again for your interest.
>
>
> 2015-09-08 16:16 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:
>
>> Hello,
>>
>> What is the buffered region for the input image? Is the input image
>> connected to a pipeline?
>>
>> Perhaps you just forgot to update the input image before running this
>> function?
>>
>> Brad
>>
>> On Sep 7, 2015, at 5:21 PM, Marcos <fotosentido at gmail.com> wrote:
>>
>> Hi,
>>
>> I have a method that was exporting fine one frame from my itk::Image.
>>
>> My method:
>>
>> void Exporter::exportOriginal(QString fileName, ImageType::Pointer image, int frame)
>>
>> {
>>
>>     typedef itk::ImageFileWriter<FrameImageType> WriterType;
>>
>>     WriterType::Pointer writer = WriterType::New();
>>
>>
>>     writer->SetFileName(fileName.toStdString().c_str());
>>
>>
>>     ImageType::RegionType inputRegion = image->GetLargestPossibleRegion();
>>
>>
>>     ImageType::IndexType index = inputRegion.GetIndex();
>>
>>     ImageType::SizeType size = inputRegion.GetSize();
>>
>>
>>     index[0] = 0;
>>
>>     index[1] = 0;
>>
>>     index[2] = frame;
>>
>>
>>     // 3D to 2D
>>
>>     size[2] = 0;
>>
>>
>>     ImageType::RegionType outputRegion;
>>
>>     outputRegion.SetIndex(index);
>>
>>     outputRegion.SetSize(size);
>>
>>
>>     typedef itk::Testing::ExtractSliceImageFilter<ImageType, FrameImageType> ExtractType;
>>
>>     ExtractType::Pointer extracter = ExtractType::New();
>>
>>     extracter->SetExtractionRegion(outputRegion);
>>
>>
>>     writer->SetInput(extracter->GetOutput());
>>
>>     try
>>
>>     {
>>
>>         writer->Update();
>>
>>     }
>>
>>     catch (itk::ExceptionObject &ex)
>>
>>     {
>>
>>         std:cerr << ex << std::endl;
>>
>>     }
>>
>> }
>>
>>
>> as inputRegion, I have:
>> index: [0, 0, 0]
>> size: [512, 512, 12]
>>
>> as outputRegion, I have:
>> index: [0, 0, 1]                   # first frame
>> size: [512, 512, 0]
>>
>>
>>
>> But I'm not sure what happened, now with every image I got an exception:
>> itkimagefilewriter.hxx:287: "Largest possible region does not fully
>> contain requested paste IO region"
>>
>> By the way, my try catch is not getting the exception message, I had to
>> look inside the writer class.
>> Any ideas? Thank you.
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