otb: init at 9.0.0 (#325630)

    githubId = 7589338;

    name = "Daniel Șerbănescu";

  };

  daspk04 = {

    email = "dpratyush.k@gmail.com";

    github = "daspk04";

    githubId = 28738918;

    name = "Pratyush Das";

  };

  datafoo = {

    github = "datafoo";

    githubId = 34766150;

diff -burN InsightToolkit-4.10.0.orig/CMake/FindFFTW.cmake InsightToolkit-4.10.0/CMake/FindFFTW.cmake

--- InsightToolkit-4.10.0.orig/CMake/FindFFTW.cmake	2016-06-16 14:21:15.226203872 +0200

+++ InsightToolkit-4.10.0/CMake/FindFFTW.cmake	2016-06-16 14:23:48.966202670 +0200

@@ -35,14 +35,12 @@

   set(FFTW_LIB_SEARCHPATH

     ${FFTW_INSTALL_BASE_PATH}/lib

     ${FFTW_INSTALL_BASE_PATH}/lib64

-    /usr/lib/fftw

-    /usr/local/lib/fftw

   )

   if(ITK_USE_FFTWD)

     mark_as_advanced(FFTWD_LIB)

-    find_library(FFTWD_LIB fftw3 ${FFTW_LIB_SEARCHPATH}) #Double Precision Lib

-    find_library(FFTWD_THREADS_LIB fftw3_threads ${FFTW_LIB_SEARCHPATH}) #Double Precision Lib only if compiled with threads support

+    find_library(FFTWD_LIB fftw3 ${FFTW_LIB_SEARCHPATH} NO_DEFAULT_PATH) #Double Precision Lib

+    find_library(FFTWD_THREADS_LIB fftw3_threads ${FFTW_LIB_SEARCHPATH} NO_DEFAULT_PATH) #Double Precision Lib only if compiled with threads support

     if(FFTWD_LIB)

       set(FFTWD_FOUND 1)

@@ -55,8 +53,8 @@

   if(ITK_USE_FFTWF)

     mark_as_advanced(FFTWF_LIB)

-    find_library(FFTWF_LIB fftw3f ${FFTW_LIB_SEARCHPATH}) #Single Precision Lib

-    find_library(FFTWF_THREADS_LIB fftw3f_threads ${FFTW_LIB_SEARCHPATH}) #Single Precision Lib only if compiled with threads support

+    find_library(FFTWF_LIB fftw3f ${FFTW_LIB_SEARCHPATH} NO_DEFAULT_PATH) #Single Precision Lib

+    find_library(FFTWF_THREADS_LIB fftw3f_threads ${FFTW_LIB_SEARCHPATH} NO_DEFAULT_PATH) #Single Precision Lib only if compiled with threads support

     if(FFTWF_LIB)

       set(FFTWF_FOUND 1)

diff -burN InsightToolkit-4.12.0.orig/Modules/ThirdParty/VNL/src/CMakeLists.txt InsightToolkit-4.12.0/Modules/ThirdParty/VNL/src/CMakeLists.txt

--- InsightToolkit-4.12.0.orig/Modules/ThirdParty/VNL/src/CMakeLists.txt	2017-08-22 11:53:55.960938649 +0200

+++ InsightToolkit-4.12.0/Modules/ThirdParty/VNL/src/CMakeLists.txt	2017-08-22 11:56:07.289820954 +0200

@@ -18,10 +18,14 @@

 # Retrive the variable type to CACHE.

 set(BUILD_EXAMPLES ${BUILD_EXAMPLES} CACHE BOOL "Build the examples from the ITK Software Guide." FORCE)

-foreach(lib itkvcl itkv3p_netlib itktestlib itkvnl itkvnl_algo itknetlib)

+foreach(lib itkvcl itkv3p_netlib itkvnl itkvnl_algo itknetlib)

   itk_module_target(${lib} NO_INSTALL)

 endforeach()

+if(BUILD_TESTING)

+  itk_module_target(itktestlib NO_INSTALL)

+endif()

+

 foreach(exe

     netlib_integral_test

     netlib_lbfgs_example

diff -burN InsightToolkit-4.12.0.orig/Modules/ThirdParty/VNL/src/vxl/core/CMakeLists.txt InsightToolkit-4.12.0/Modules/ThirdParty/VNL/src/vxl/core/CMakeLists.txt

--- InsightToolkit-4.12.0.orig/Modules/ThirdParty/VNL/src/vxl/core/CMakeLists.txt	2017-08-22 11:53:55.960938649 +0200

+++ InsightToolkit-4.12.0/Modules/ThirdParty/VNL/src/vxl/core/CMakeLists.txt	2017-08-22 11:56:56.410150930 +0200

@@ -131,8 +131,10 @@

   set(CORE_VIDEO_FOUND OFF CACHE INTERNAL "VXL core video libraries built")

 endif ()

-# common test executable

-add_subdirectory(testlib)

+# common test executable if testing enabled

+if(BUILD_TESTING)

+  add_subdirectory(testlib)

+endif()

 # Tests that check and output the vxl configuration

 # NOTE: some external projects remove the tests directory (aka ITK)

--- a/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h

+++ b/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h

@@ -43,85 +43,7 @@

 #endif

 #if defined(__GNUC__) && !defined(__ICC) // icc 8.0 defines __GNUC__

-# define VCL_GCC

-# if (__GNUC__ < 4)

-#  error "forget it."

-# elif (__GNUC__==4)

-#  define VCL_GCC_4

-#  if (__GNUC_MINOR__ > 0 )

-#   define VCL_GCC_41

-#  else

-#   define VCL_GCC_40

-#  endif

-# elif (__GNUC__==5)

-#  define VCL_GCC_5

-#  if (__GNUC_MINOR__ > 2 )

-#   define VCL_GCC_53

-#  elif (__GNUC_MINOR__ > 1 )

-#   define VCL_GCC_52

-#  elif (__GNUC_MINOR__ > 0 )

-#   define VCL_GCC_51

-#  else

-#   define VCL_GCC_50

-#  endif

-# elif (__GNUC__==6)

-#  define VCL_GCC_6

-#  if (__GNUC_MINOR__ > 2 )

-#   define VCL_GCC_63

-#  elif (__GNUC_MINOR__ > 1 )

-#   define VCL_GCC_62

-#  elif (__GNUC_MINOR__ > 0 )

-#   define VCL_GCC_61

-#  else

-#   define VCL_GCC_60

-#  endif

-# elif (__GNUC__==7)

-#  define VCL_GCC_7

-#  if (__GNUC_MINOR__ > 2 )

-#   define VCL_GCC_73

-#  elif (__GNUC_MINOR__ > 1 )

-#   define VCL_GCC_72

-#  elif (__GNUC_MINOR__ > 0 )

-#   define VCL_GCC_71

-#  else

-#   define VCL_GCC_70

-#  endif

-# elif (__GNUC__==8)

-#  define VCL_GCC_8

-#  if (__GNUC_MINOR__ > 2 )

-#   define VCL_GCC_83

-#  elif (__GNUC_MINOR__ > 1 )

-#   define VCL_GCC_82

-#  elif (__GNUC_MINOR__ > 0 )

-#   define VCL_GCC_81

-#  else

-#   define VCL_GCC_80

-#  endif

-# elif (__GNUC__==9)

-#  define VCL_GCC_9

-#  if (__GNUC_MINOR__ > 2 )

-#   define VCL_GCC_93

-#  elif (__GNUC_MINOR__ > 1 )

-#   define VCL_GCC_92

-#  elif (__GNUC_MINOR__ > 0 )

-#   define VCL_GCC_91

-#  else

-#   define VCL_GCC_90

-#  endif

-# elif (__GNUC__==10)

-#  define VCL_GCC_10

-#  if (__GNUC_MINOR__ > 2 )

-#   define VCL_GCC_103

-#  elif (__GNUC_MINOR__ > 1 )

-#   define VCL_GCC_102

-#  elif (__GNUC_MINOR__ > 0 )

-#   define VCL_GCC_101

-#  else

-#   define VCL_GCC_100

-#  endif

-# else

-#  error "Dunno about this gcc"

-# endif

+# define VCL_GCC_73

 #endif

 #if defined(_WIN32) || defined(WIN32)

--- a/Modules/ThirdParty/VNL/src/vxl/vcl/tests/test_preprocessor.cxx

+++ b/Modules/ThirdParty/VNL/src/vxl/vcl/tests/test_preprocessor.cxx

@@ -64,6 +64,12 @@

   ++minor_count;

 #endif

+#ifdef VCL_GCC_73

+  ++compiler_count;

+  ++major_count;

+  ++minor_count;

+#endif

+

 #ifdef VCL_VC

   ++compiler_count;

 #endif

{

  lib,

  stdenv,

  fetchFromGitHub,

  cmake,

  expat,

  fftw,

  fftwFloat,

  hdf5-cpp,

  libjpeg,

  libtiff,

  libpng,

  libuuid,

  xz,

  vtk,

  zlib,

}:

# this ITK version is old and is only required for OTB package

# https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/-/blob/develop/SuperBuild/CMake/External_itk.cmake?ref_type=heads#L149

stdenv.mkDerivation (finalAttrs: {

  pname = "itk";

  version = "4.13.3";

  src = fetchFromGitHub {

    owner = "InsightSoftwareConsortium";

    repo = "ITK";

    rev = "v${finalAttrs.version}";

    hash = "sha256-lcoJ+H+nVlvleBqbmupu+yg+4iZQ4mTs9pt1mQac+xg=";

  };

  # https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/-/tree/develop/SuperBuild/patches/ITK?ref_type=heads

  patches = [

    ./itk-1-fftw-all.diff

    ./itk-2-itktestlib-all.diff

    ./itk-3-remove-gcc-version-debian-medteam-all.diff

  ];

  # https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/-/blob/develop/SuperBuild/CMake/External_itk.cmake?ref_type=heads

  cmakeFlags = [

    "-DBUILD_TESTING=OFF"

    "-DBUILD_EXAMPLES=OFF"

    "-DBUILD_SHARED_LIBS=ON"

    "-DITK_BUILD_DEFAULT_MODULES=OFF"

    "-DITKGroup_Core=OFF"

    "-DITK_FORBID_DOWNLOADS=ON"

    "-DITK_USE_SYSTEM_LIBRARIES=ON" # finds common libraries e.g. hdf5, libpng, libtiff, libjpeg, zlib etc

    "-DModule_ITKCommon=ON"

    "-DModule_ITKFiniteDifference=ON"

    "-DModule_ITKGPUCommon=ON"

    "-DModule_ITKGPUFiniteDifference=ON"

    "-DModule_ITKImageAdaptors=ON"

    "-DModule_ITKImageFunction=ON"

    "-DModule_ITKMesh=ON"

    "-DModule_ITKQuadEdgeMesh=ON"

    "-DModule_ITKSpatialObjects=ON"

    "-DModule_ITKTransform=ON"

    "-DModule_ITKTransformFactory=ON"

    "-DModule_ITKIOTransformBase=ON"

    "-DModule_ITKIOTransformInsightLegacy=ON"

    "-DModule_ITKIOTransformMatlab=ON"

    "-DModule_ITKAnisotropicSmoothing=ON"

    "-DModule_ITKAntiAlias=ON"

    "-DModule_ITKBiasCorrection=ON"

    "-DModule_ITKBinaryMathematicalMorphology=ON"

    "-DModule_ITKColormap=ON"

    "-DModule_ITKConvolution=ON"

    "-DModule_ITKCurvatureFlow=ON"

    "-DModule_ITKDeconvolution=ON"

    "-DModule_ITKDenoising=ON"

    "-DModule_ITKDisplacementField=ON"

    "-DModule_ITKDistanceMap=ON"

    "-DModule_ITKFastMarching=ON"

    "-DModule_ITKFFT=ON"

    "-DModule_ITKGPUAnisotropicSmoothing=ON"

    "-DModule_ITKGPUImageFilterBase=ON"

    "-DModule_ITKGPUSmoothing=ON"

    "-DModule_ITKGPUThresholding=ON"

    "-DModule_ITKImageCompare=ON"

    "-DModule_ITKImageCompose=ON"

    "-DModule_ITKImageFeature=ON"

    "-DModule_ITKImageFilterBase=ON"

    "-DModule_ITKImageFusion=ON"

    "-DModule_ITKImageGradient=ON"

    "-DModule_ITKImageGrid=ON"

    "-DModule_ITKImageIntensity=ON"

    "-DModule_ITKImageLabel=ON"

    "-DModule_ITKImageSources=ON"

    "-DModule_ITKImageStatistics=ON"

    "-DModule_ITKLabelMap=ON"

    "-DModule_ITKMathematicalMorphology=ON"

    "-DModule_ITKPath=ON"

    "-DModule_ITKQuadEdgeMeshFiltering=ON"

    "-DModule_ITKSmoothing=ON"

    "-DModule_ITKSpatialFunction=ON"

    "-DModule_ITKThresholding=ON"

    "-DModule_ITKEigen=ON"

    "-DModule_ITKNarrowBand=ON"

    "-DModule_ITKNeuralNetworks=ON"

    "-DModule_ITKOptimizers=ON"

    "-DModule_ITKOptimizersv4=ON"

    "-DModule_ITKPolynomials=ON"

    "-DModule_ITKStatistics=ON"

    "-DModule_ITKRegistrationCommon=ON"

    "-DModule_ITKGPURegistrationCommon=ON"

    "-DModule_ITKGPUPDEDeformableRegistration=ON"

    "-DModule_ITKMetricsv4=ON"

    "-DModule_ITKPDEDeformableRegistration=ON"

    "-DModule_ITKRegistrationMethodsv4=ON"

    "-DModule_ITKClassifiers=ON"

    "-DModule_ITKConnectedComponents=ON"

    "-DModule_ITKDeformableMesh=ON"

    "-DModule_ITKKLMRegionGrowing=ON"

    "-DModule_ITKLabelVoting=ON"

    "-DModule_ITKLevelSets=ON"

    "-DModule_ITKLevelSetsv4=ON"

    "-DModule_ITKMarkovRandomFieldsClassifiers=ON"

    "-DModule_ITKRegionGrowing=ON"

    "-DModule_ITKSignedDistanceFunction=ON"

    "-DModule_ITKVoronoi=ON"

    "-DModule_ITKWatersheds=ON"

  ];

  nativeBuildInputs = [

    cmake

    xz

  ];

  buildInputs = [ libuuid ];

  propagatedBuildInputs = [

    # similar to 5.2.x, we progagate these inputs for OTB

    expat

    fftw

    fftwFloat

    hdf5-cpp

    libjpeg

    libpng

    libtiff

    zlib

  ];

  meta = {

    description = "Insight Segmentation and Registration Toolkit";

    homepage = "https://www.itk.org";

    license = lib.licenses.asl20;

    maintainers = with lib.maintainers; [ daspk04 ];

    platforms = with lib.platforms; linux;

  };

})