[ITK] [ITK-users] LabelGeometryImageFilter: empty output of GetOrientedLabelImage and GetOrientedIntensityImage
Bill Lorensen
bill.lorensen at gmail.com
Mon Apr 6 13:13:33 EDT 2015
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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