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

[Bill Lorensen]

I have a 2D example that fails when the origin is not 0.0. Now I'll
try to find the bug.


On Mon, Apr 6, 2015 at 10:13 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> 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



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