[ITK-users] LabelGeometryImageFilter: empty output of GetOrientedLabelImage and GetOrientedIntensityImage

[Bill Lorensen]

Thomas,

I compiled your program and ran it on one of my labeled images and it
produces the expected output.

On Sun, Apr 5, 2015 at 2:52 PM, Thomas Seidel <seidel at cvrti.utah.edu> wrote:
> Hi Bill,
>
> Thanks for your answer. Here is (part of the) source I am using.
> Do you need the image or source files?
>
>
>
>
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkLabelGeometryImageFilter.h"
>
> #include "itksys/SystemTools.hxx"
>
> #include <sstream>
>
>
> int main(int argc, char * argv[])
> {
>   // Verify command line arguments
>   if( argc < 2 )
>     {
>     std::cerr << "Usage: " << std::endl;
>     std::cerr << argv[0] << " InputImageFile [-intensity
> <IntensityImageFile>]" << std::endl;
>     return EXIT_FAILURE;
>     }
>   std::string inputFilename = argv[1];
>   std::string intensityFile;
>   bool calcIntensity = false;
>
>
>     int argcounter = 2;
>   while (argc>argcounter)
>   {
>         if (!strncmp(argv[argcounter],"-intensity",10) ) {intensityFile =
> argv[argcounter + 1]; calcIntensity = true; }
>         argcounter++;
>   }
>
>   // Setup types
>   typedef itk::Image<unsigned int, 3> IntImageType;
>   typedef itk::Image<float, 3> FloatImageType;
>   typedef itk::ImageFileReader<IntImageType>               ReaderType;
>   typedef itk::ImageFileReader<FloatImageType>
> FloatReaderType;
>
>   ReaderType::Pointer reader = ReaderType::New();
>   reader->SetFileName( inputFilename );
>   FloatReaderType::Pointer FloatReader = FloatReaderType::New();
>
>
>
>    typedef itk::LabelGeometryImageFilter< IntImageType, FloatImageType >
> LabelGeometryImageFilterType;
>    LabelGeometryImageFilterType::Pointer labelGeometryImageFilter =
> LabelGeometryImageFilterType::New();
>    labelGeometryImageFilter->SetInput( reader->GetOutput() );
>
>
>    if (calcIntensity)
>    {
>         FloatReader->SetFileName(intensityFile);
>         FloatReader->Update();
>         labelGeometryImageFilter->SetIntensityInput(FloatReader->GetOutput());
> labelGeometryImageFilter->CalculateOrientedIntensityRegionsOn();
>
>    }
>
>
>      labelGeometryImageFilter->CalculatePixelIndicesOn();
>   labelGeometryImageFilter->CalculateOrientedBoundingBoxOn();
>     labelGeometryImageFilter->CalculateOrientedLabelRegionsOn();
>
>   labelGeometryImageFilter->Update();
>
>    LabelGeometryImageFilterType::LabelsType allLabels =
> labelGeometryImageFilter->GetLabels();
>   LabelGeometryImageFilterType::LabelsType::iterator allLabelsIt;
>   std::cout << "Number of labels: " <<
> labelGeometryImageFilter->GetNumberOfLabels() << std::endl;
>   std::cout << std::endl;
>
>
>
>   for( allLabelsIt = allLabels.begin(); allLabelsIt != allLabels.end();
> allLabelsIt++ )
>     {
>
>         LabelGeometryImageFilterType::LabelPixelType labelValue = *allLabelsIt;
>
>
>         std::ostringstream stream;
>         stream << labelValue << ".vtk";
>         typedef itk::ImageFileWriter<IntImageType> WriterType;
>         WriterType::Pointer writer = WriterType::New();
>         writer->SetFileName(stream.str());
>         writer->SetInput(labelGeometryImageFilter->GetOrientedLabelImage(labelValu
> e));
>         writer->Update();
>
>         std::ostringstream stream2;
>         stream2 << labelValue << "-intensity.vtk";
>
>         if (calcIntensity) {
>                 typedef itk::ImageFileWriter<FloatImageType> FloatWriterType;
>                 FloatWriterType::Pointer Floatwriter = FloatWriterType::New();
>                 Floatwriter->SetFileName(stream2.str());
>                 Floatwriter->SetInput(labelGeometryImageFilter->GetOrientedIntensityImage
> (labelValue));
>                 Floatwriter->Update();
>         }
>     }
>
>
>
>
>
>
>   return EXIT_SUCCESS;
> }
>
>
>
>
>
>
> On 4/5/15 12:10 PM, "Bill Lorensen" <bill.lorensen at gmail.com> wrote:
>
>>Do you have a small, compilable example that illustrates the problem?
>>
>>On Sun, Apr 5, 2015 at 10:09 AM, Thomas Seidel <seidel at cvrti.utah.edu>
>>wrote:
>>> Hi all,
>>>
>>> I am using the itkLabelGeometryImageFilter to get information about the
>>> orientation of labeled objects.
>>> I provide a LabelImage and a IntensityImage.
>>> I set CalculateOrientedLabelRegionsOn() and
>>> CalculateOrientedIntensityRegionsOn().
>>>
>>> However, when I use
>>> writer->SetInput(filter->GetOrientedLabelImage());
>>> writer->Update();
>>> or
>>> writer->SetInput(filter->GetOrientedIntensityImage());
>>> writer->Update();
>>>
>>> it just generates empty images (all values 0) with the size of the
>>>oriented
>>> bounding box.
>>>
>>> Is this how the filter is supposed to work?? I was expecting the rotated
>>> labels and the rotated region of the intensity image defined by the
>>>oriented
>>> bounding box, respectively.
>>>
>>> Thanks,
>>> Thomas
>>>
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>>
>>
>>
>>--
>>Unpaid intern in BillsBasement at noware dot com
>
>
>



-- 
Unpaid intern in BillsBasement at noware dot com