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

[Bill Lorensen]

Could be a bug. Need to find a smaller test case that fails. Maybe
because of non-zero origin. I'll take a look.


On Mon, Apr 6, 2015 at 9:55 AM, Thomas Seidel <seidel at cvrti.utah.edu> wrote:
> I tried it again. I am quite sure there is nothing wrong with my input
> files because the filter apparently creates correct output measures for
> all labels (e.g. eigenvalues, bounding box, volume, etc).
> But the orientedlabelimages are all zero, except for label 0 (which is my
> background). The dimension of these images corresponds to the size
> (length, width, depth) of the oriented bounding boxes.
>
> I think the image origins are all messed up. May there something be wrong
> with the center of rotation?
>
> E.g.: label 0, which is background, has the same bounding box size as the
> input label image.
> Input LabelImage:
> dimensions: 512 1024 130 (in pixels)
> origin: [102.273, 0, 5.96985] (in physical size)
>
> oriented image of label 0:
> dimensions: 1026 515 131
> origin: [-51.2878, 50.6859, -0.132971]
>
>
> Is this a bug, or did I forget to set a parameter?
>
> Thanks,
> Thomas
>
>
>
>
>
> On 4/6/15 12:02 AM, "Bill Lorensen" <bill.lorensen at gmail.com> wrote:
>
>>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(labelVal
>>>u
>>> 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
>
>
>



-- 
Unpaid intern in BillsBasement at noware dot com