[ITK-users] LabelGeometryImageFilter: empty output of GetOrientedLabelImage and GetOrientedIntensityImage
Bill Lorensen
bill.lorensen at gmail.com
Tue Apr 7 14:51:14 EDT 2015
Brad,
I don't see a remote.cmake file for your external module.
Bill
On Tue, Apr 7, 2015 at 5:37 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
>
> I have a much improved version of the algorithm to compute oriented bounding boxes here:
>
> https://github.com/blowekamp/itkOBBLabelMap
>
> It is correctly accounts for the image's physical spacing, origin, and direction cosines, significantly faster, and more memory efficient. Here would be a close to turn-key test/example for this task:
>
> https://github.com/blowekamp/itkOBBLabelMap/blob/master/test/itkOrientedBoundingBoxImageLabelMapFilterTest2.cxx
>
> HTH,
> Brad
>
> On Apr 7, 2015, at 1:38 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>
>> 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
>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
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>>
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>>
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