blowekamp/itksuperpixel

The filters from this module were integrated into ITK version 5. https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Segmentation/SuperPixel

This repository is archived.

This filters from this module have been itegrated in the main ITK repository: https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Segmentation/SuperPixel

This repository contains the materials used to generate the Insigt Journal Paper.

itkSuperPixel

Linux	macOS	Windows

This ITK module provides an implimentation of the Simple Linear Iterative Clustering (SLIC) superpixel segmentation algorithm.

Getting Started

This module should be cloned into the ITK reposiory as a subdirectory in the "Modules/External" directory.

The following is a brief list of instructions to get a external module into ITK:

cd ITK/Modules/External/ git clone https://github.com/blowekamp/itkSuperPixel.git

Then configure ITK as with cmake and set "Module_SuperPixel" to "ON" to enable this module. The external module will need to be manually updated from the git respository.

License

This software is distributed under the Apache License. Please see LICENSE for details.

Author

Bradley Lowekamp

itksuperpixel's Issues

Error on Complying the itkSuperPixel

Hi Braley,

I tried to comply this module to your ITK repo from your github account. I got the error: "'vnl_math_min' was not declared in this scope". My CMAKE's version is 3.14.0. I also tried to comply it with the latest ITK source code but there were missing files in the ITK/Modules/Core/Common/include directory. I also tried to comply it with the ITK version 4.13.1 (released on Aug 8, 2018) and still got the some other errors.

The whole errors from complying with your ITK repo is the followings:

/pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:518:103: error: ‘vnl_math_min’ was not declared in this scope /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx: In instantiation of ‘void itk::SLICImageFilter<TInputImage, TOutputImage, TDistancePixel>::ThreadedPerturbClusters(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = itk::Image<float, 2u>; TOutputImage = itk::Image<short unsigned int, 2u>; TDistancePixel = float; itk::SLICImageFilter<TInputImage, TOutputImage, TDistancePixel>::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]’: /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:689:59: required from ‘void itk::SLICImageFilter<TInputImage, TOutputImage, TDistancePixel>::ThreadedGenerateData(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = itk::Image<float, 2u>; TOutputImage = itk::Image<short unsigned int, 2u>; TDistancePixel = float; itk::SLICImageFilter<TInputImage, TOutputImage, TDistancePixel>::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]’ /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/test/itkSLICImageFilterTest.cxx:140:1: required from here /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:383:59: warning: ‘itk::ThreadIdType itk::ProcessObject::GetNumberOfThreads() const’ is deprecated (declared at /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/Core/Common/include/itkProcessObject.h:452) [-Wdeprecated-declarations] ThreadIdType numberOfThreads = this->GetNumberOfThreads(); ^ /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:388:103: warning: ‘itk::ThreadIdType itk::ProcessObject::GetNumberOfThreads() const’ is deprecated (declared at /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/Core/Common/include/itkProcessObject.h:452) [-Wdeprecated-declarations] this->GetNumberOfThreads(), ProcessObject::MultiThreaderType::GetGlobalMaximumNumberOfThreads() ); ^ /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:388:103: error: ‘vnl_math_min’ was not declared in this scope /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx: In instantiation of ‘void itk::SLICImageFilter<TInputImage, TOutputImage, TDistancePixel>::ThreadedConnectivity(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = itk::Image<float, 2u>; TOutputImage = itk::Image<short unsigned int, 2u>; TDistancePixel = float; itk::SLICImageFilter<TInputImage, TOutputImage, TDistancePixel>::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]’: /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:771:57: required from ‘void itk::SLICImageFilter<TInputImage, TOutputImage, TDistancePixel>::ThreadedGenerateData(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = itk::Image<float, 2u>; TOutputImage = itk::Image<short unsigned int, 2u>; TDistancePixel = float; itk::SLICImageFilter<TInputImage, TOutputImage, TDistancePixel>::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]’ /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/test/itkSLICImageFilterTest.cxx:140:1: required from here /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:513:59: warning: ‘itk::ThreadIdType itk::ProcessObject::GetNumberOfThreads() const’ is deprecated (declared at /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/Core/Common/include/itkProcessObject.h:452) [-Wdeprecated-declarations] ThreadIdType numberOfThreads = this->GetNumberOfThreads(); ^ /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:518:103: warning: ‘itk::ThreadIdType itk::ProcessObject::GetNumberOfThreads() const’ is deprecated (declared at /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/Core/Common/include/itkProcessObject.h:452) [-Wdeprecated-declarations] this->GetNumberOfThreads(), ProcessObject::MultiThreaderType::GetGlobalMaximumNumberOfThreads() ); ^ /pghbio/dbmi/batmanlab/chirayu/download/ITK/Modules/External/itkSuperPixel/include/itkSLICImageFilter.hxx:518:103: error: ‘vnl_math_min’ was not declared in this scope make[2]: *** [Modules/External/itkSuperPixel/test/CMakeFiles/SuperPixelTestDriver.dir/itkSLICImageFilterTest.cxx.o] Error 1 make[1]: *** [Modules/External/itkSuperPixel/test/CMakeFiles/SuperPixelTestDriver.dir/all] Error 2 [ 99%] Building CXX object Modules/Segmentation/LevelSetsv4/test/CMakeFiles/ITKLevelSetsv4TestDriver.dir/itkMultiLevelSetShiImageSubset2DTest.cxx.o [ 99%] Building CXX object Modules/Segmentation/LevelSetsv4/test/CMakeFiles/ITKLevelSetsv4TestDriver.dir/itkMultiLevelSetMalcolmImageSubset2DTest.cxx.o [ 99%] Building CXX object Modules/Segmentation/LevelSetsv4/test/CMakeFiles/ITKLevelSetsv4TestDriver.dir/itkLevelSetEvolutionNumberOfIterationsStoppingCriterionTest.cxx.o [ 99%] Building CXX object Modules/Registration/Metricsv4/test/CMakeFiles/ITKMetricsv4TestDriver.dir/itkMeanSquaresImageToImageMetricv4SpeedTest.cxx.o [ 99%] Built target ITKOptimizersv4TestDriver [ 99%] Building CXX object Modules/Registration/Metricsv4/test/CMakeFiles/ITKMetricsv4TestDriver.dir/itkMeanSquaresImageToImageMetricv4VectorRegistrationTest.cxx.o [ 99%] Linking CXX executable ../../../../bin/ITKLevelSetsv4TestDriver [ 99%] Linking CXX executable ../../../../bin/ITKMetricsv4TestDriver [ 99%] Built target ITKRegistrationMethodsv4TestDriver [ 99%] Built target ITKLevelSetsv4TestDriver [ 99%] Built target ITKMetricsv4TestDriver make: *** [all] Error 2

Thanks a lot.