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Merge pull request #7 from daspk04/format-style
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[STYLE] Format via Alejandra
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@daspk04
daspk04 authored Jul 29, 2024
2 parents fc40483 + 1fa79bc commit f0d570d
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25 changes: 11 additions & 14 deletions flake.nix
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Original file line number Diff line number Diff line change
Expand Up @@ -7,22 +7,19 @@
flake-utils.url = "github:numtide/flake-utils";
};

outputs =
{ self
, nixpkgs
, nixpkgs-unstable
, flake-utils
,
}:
outputs = {
self,
nixpkgs,
nixpkgs-unstable,
flake-utils,
}:
flake-utils.lib.eachDefaultSystem (
system:
let
pkgs = import nixpkgs { inherit system; };
system: let
pkgs = import nixpkgs {inherit system;};
python = pkgs.python312; # we fix python version to 3.12 here for the OTB
in
rec {
packages.shark = pkgs.callPackage ./pkgs/shark/. { inherit system; };
packages.itk_4_13 = pkgs.callPackage ./pkgs/itk_4_13_3/. { inherit system; };
in rec {
packages.shark = pkgs.callPackage ./pkgs/shark/. {inherit system;};
packages.itk_4_13 = pkgs.callPackage ./pkgs/itk_4_13_3/. {inherit system;};
packages.otb = pkgs.callPackage ./pkgs/otb/. {
inherit system;
shark = packages.shark;
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318 changes: 159 additions & 159 deletions pkgs/itk_4_13_3/default.nix
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Original file line number Diff line number Diff line change
@@ -1,166 +1,166 @@
{ lib
, stdenv
, fetchgit
, cmake
, expat
, fftw
, fftwFloat
, gdcm
, hdf5-cpp
, libjpeg
, libminc
, libtiff
, libpng
, libuuid
, xz
, vtk
, zlib
, ...
}:
let
{
lib,
stdenv,
fetchgit,
cmake,
expat,
fftw,
fftwFloat,
gdcm,
hdf5-cpp,
libjpeg,
libminc,
libtiff,
libpng,
libuuid,
xz,
vtk,
zlib,
...
}: let
versionMeta = builtins.fromJSON (builtins.readFile ./version.json);
in
stdenv.mkDerivation rec {
pname = "itk";
version = versionMeta.version;
stdenv.mkDerivation rec {
pname = "itk";
version = versionMeta.version;

src = builtins.fetchGit {
name = pname;
url = "https://github.com/InsightSoftwareConsortium/ITK";
# version is same as OTB Superbuild
# https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/-/blob/develop/SuperBuild/CMake/External_itk.cmake?ref_type=heads#L149
ref = "refs/tags/v${version}";
rev = versionMeta.rev;
};
src = builtins.fetchGit {
name = pname;
url = "https://github.com/InsightSoftwareConsortium/ITK";
# version is same as OTB Superbuild
# https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/-/blob/develop/SuperBuild/CMake/External_itk.cmake?ref_type=heads#L149
ref = "refs/tags/v${version}";
rev = versionMeta.rev;
};

# https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/-/tree/develop/SuperBuild/patches/ITK?ref_type=heads
# todo: check if all the patches are required for nix
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/-/tree/develop/SuperBuild/patches/ITK?ref_type=heads
# todo: check if all the patches are required for nix
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
# "-DITK_USE_KWSTYLE=OFF"
# todo: check if this needs to be enabled as nixpkgs for ITK 5.2.X has this disabled
"-DITK_USE_SYSTEM_EIGEN=OFF"
# "-DITK_USE_SYSTEM_EXPAT=ON"
# "-DITK_USE_SYSTEM_ZLIB=ON"
# "-DITK_USE_SYSTEM_TIFF=ON"
# "-DITK_USE_SYSTEM_PNG=ON"
"-DModule_ITKCommon=ON"
#"-DModule_ITKTestKernel=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_ITKDiffusionTensorImage=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_ITKFEM=ON"
"-DModule_ITKNarrowBand=ON"
"-DModule_ITKNeuralNetworks=ON"
"-DModule_ITKOptimizers=ON"
"-DModule_ITKOptimizersv4=ON"
"-DModule_ITKPolynomials=ON"
"-DModule_ITKStatistics=ON"
"-DModule_ITKRegistrationCommon=ON"
#"-DModule_ITKFEMRegistration=ON"
"-DModule_ITKGPURegistrationCommon=ON"
"-DModule_ITKGPUPDEDeformableRegistration=ON"
"-DModule_ITKMetricsv4=ON"
"-DModule_ITKPDEDeformableRegistration=ON"
"-DModule_ITKRegistrationMethodsv4=ON"
#"-DModule_ITKBioCell=ON"
"-DModule_ITKClassifiers=ON"
"-DModule_ITKConnectedComponents=ON"
"-DModule_ITKDeformableMesh=ON"
"-DModule_ITKKLMRegionGrowing=ON"
"-DModule_ITKLabelVoting=ON"
"-DModule_ITKLevelSets=ON"
"-DModule_ITKLevelSetsv4=ON"
#"-DModule_ITKLevelSetsv4Visualization=ON"
"-DModule_ITKMarkovRandomFieldsClassifiers=ON"
"-DModule_ITKRegionGrowing=ON"
"-DModule_ITKSignedDistanceFunction=ON"
"-DModule_ITKVoronoi=ON"
"-DModule_ITKWatersheds=ON"
];
# 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
# "-DITK_USE_KWSTYLE=OFF"
# todo: check if this needs to be enabled as nixpkgs for ITK 5.2.X has this disabled
"-DITK_USE_SYSTEM_EIGEN=OFF"
# "-DITK_USE_SYSTEM_EXPAT=ON"
# "-DITK_USE_SYSTEM_ZLIB=ON"
# "-DITK_USE_SYSTEM_TIFF=ON"
# "-DITK_USE_SYSTEM_PNG=ON"
"-DModule_ITKCommon=ON"
#"-DModule_ITKTestKernel=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_ITKDiffusionTensorImage=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_ITKFEM=ON"
"-DModule_ITKNarrowBand=ON"
"-DModule_ITKNeuralNetworks=ON"
"-DModule_ITKOptimizers=ON"
"-DModule_ITKOptimizersv4=ON"
"-DModule_ITKPolynomials=ON"
"-DModule_ITKStatistics=ON"
"-DModule_ITKRegistrationCommon=ON"
#"-DModule_ITKFEMRegistration=ON"
"-DModule_ITKGPURegistrationCommon=ON"
"-DModule_ITKGPUPDEDeformableRegistration=ON"
"-DModule_ITKMetricsv4=ON"
"-DModule_ITKPDEDeformableRegistration=ON"
"-DModule_ITKRegistrationMethodsv4=ON"
#"-DModule_ITKBioCell=ON"
"-DModule_ITKClassifiers=ON"
"-DModule_ITKConnectedComponents=ON"
"-DModule_ITKDeformableMesh=ON"
"-DModule_ITKKLMRegionGrowing=ON"
"-DModule_ITKLabelVoting=ON"
"-DModule_ITKLevelSets=ON"
"-DModule_ITKLevelSetsv4=ON"
#"-DModule_ITKLevelSetsv4Visualization=ON"
"-DModule_ITKMarkovRandomFieldsClassifiers=ON"
"-DModule_ITKRegionGrowing=ON"
"-DModule_ITKSignedDistanceFunction=ON"
"-DModule_ITKVoronoi=ON"
"-DModule_ITKWatersheds=ON"
];

nativeBuildInputs = [ cmake xz ];
buildInputs = [
libuuid
];
propagatedBuildInputs = [
# The dependencies we've un-vendored from ITK, must be propagated,
# otherwise other software built against ITK fails to configure since ITK headers
# refer to these previously vendored libraries:
expat
fftw
fftwFloat
hdf5-cpp
libjpeg
libpng
libtiff
zlib
];
nativeBuildInputs = [cmake xz];
buildInputs = [
libuuid
];
propagatedBuildInputs = [
# The dependencies we've un-vendored from ITK, must be propagated,
# otherwise other software built against ITK fails to configure since ITK headers
# refer to these previously vendored libraries:
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; [ daskpk04 ];
};
}
meta = {
description = "Insight Segmentation and Registration Toolkit";
homepage = "https://www.itk.org";
license = lib.licenses.asl20;
maintainers = with lib.maintainers; [daskpk04];
};
}
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