[ITK-users] LabelGeometryImageFilter: empty output of GetOrientedLabelImage and GetOrientedIntensityImage
Bill Lorensen
bill.lorensen at gmail.com
Tue Apr 7 15:01:23 EDT 2015
Great! I'll give it a look see.
Bill
On Tue, Apr 7, 2015 at 11:56 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Bill,
>
> I just have my external modules in the "ITK/Modules/External" directory. I
> manually manage the git process. Just do:
>
> cd ITK/Modules/External
> git clone https://github.com/blowekamp/itkOBBLabelMap.git
>
> When you run ccmake the "ITKOBBLabelMap" module should show up where you can
> enable it.
>
> HTH,
> Brad
>
> On Apr 7, 2015, at 2:51 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>
> 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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> _____________________________________
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>
> Visit other Kitware open-source projects at
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>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
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