{data,vis}[GCCcore/11.3.0] ASAP v2.1, DCMTK v3.6.7 ... w/ Python 3.10.4

easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch

@@ -0,0 +1,16 @@
+# Author: Robert Jan Schlimbach (SURF)
+# ASAP/2.1 forgets a few headers, in this case cmath
+# Possibly fixed if https://github.com/computationalpathologygroup/ASAP/pull/241 gets merged
+
+diff --git a/annotation/ImageScopeRepository.cpp b/annotation/ImageScopeRepository.cpp
+index 6916a58..c135cb3 100644
+--- a/annotation/ImageScopeRepository.cpp
++++ b/annotation/ImageScopeRepository.cpp
+@@ -9,6 +9,7 @@
+ #include <stdio.h>
+ #include "pugixml.hpp"
+ #include <algorithm>
++#include <cmath>
+
+ ImageScopeRepository::ImageScopeRepository(const std::shared_ptr<AnnotationList>& list) :
+   Repository(list),

easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb

@@ -0,0 +1,72 @@
+easyblock = 'CMakeMake'
+
+name = 'ASAP'
+version = '2.1'
+
+homepage = 'https://computationalpathologygroup.github.io/ASAP/'
+description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface 
+for making annotations. It consists of two main components: an IO library for reading and writing 
+multi-resolution images and a viewer component for visualizing such images."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/computationalpathologygroup/%(name)s/archive']
+sources = [SOURCE_TAR_GZ]
+patches = [
+    'ASAP-2.1-libjpeg.patch',
+    'ASAP-2.1-pugixml.patch',
+    'ASAP-2.1-cmath.patch',
+]
+checksums = [
+    '7ba9f39d09bada808f760c5dc9ac0cda0d221fd1393a0a3f9decfd6b5e913b3c',  # ASAP-2.1.tar.gz
+    '78337d0250c567335f1a356f8761587000170b71a87b3e546b6b9330d3236b0f',  # ASAP-2.1-libjpeg.patch
+    'ab6104fb19515d0b042944bbe95fa67f55f47ef3bf18a91d337e0ca476c7385d',  # ASAP-2.1-pugixml.patch
+    '15cf6bf2ab65ce37338ea571d80ced59b4e35cf82e434b2ccec7b534778f4a33',  # ASAP-2.1-cmath.patch
+]
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+]
+dependencies = [
+    ('Boost', '1.79.0'),
+    ('Python', '3.10.4'),
+    ('OpenCV', '4.6.0', '-contrib'),
+    ('Qt5', '5.15.5'),
+    ('LibTIFF', '4.3.0'),
+    ('libjpeg-turbo', '2.1.3'),
+    ('JasPer', '2.0.33'),
+    ('DCMTK', '3.6.7'),
+    ('SWIG', '4.0.2'),
+    ('OpenSlide', '3.4.1', '-largefiles'),
+    ('pugixml', '1.12.1'),
+    ('zlib', '1.2.12'),
+]
+
+configopts = " ".join([
+    "-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide",
+    "-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include",
+    "-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK/include",
+    "-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE",
+    "-DBUILD_ASAP=TRUE",
+    "-DBUILD_EXECUTABLES=TRUE",
+    "-DBUILD_IMAGEPROCESSING=TRUE",
+    "-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE",
+    "-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig"
+])
+
+
+sanity_check_paths = {
+    'files': [
+        'bin/%(name)s',
+        'bin/multiresolutionimageinterface.py',
+        'lib/libmultiresolutionimageinterface.%s' % SHLIB_EXT],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = ['python -c "import multiresolutionimageinterface"']
+
+# ASAP installs its python interface in bin. Ugly, but we'll need to add it to PYTHONPATH
+modextrapaths = {'PYTHONPATH': ['bin']}
+
+moduleclass = 'vis'

easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch

@@ -0,0 +1,41 @@
+# Author: Robert Jan Schlimbach (SURF)
+# ASAP/2.1 uses DCMKT jpeg sources directly by manually setting a PATH
+# see https://github.com/computationalpathologygroup/ASAP/issues/32
+# we simply replace DCMTK jpeg with the default jpeglib header.
+# Need to rename jpeg_mem_src to avoid a resulting name conflic.
+
+diff --git a/multiresolutionimageinterface/VSIImage.cpp b/multiresolutionimageinterface/VSIImage.cpp
+index 509bb18..1763201 100644
+--- a/multiresolutionimageinterface/VSIImage.cpp
++++ b/multiresolutionimageinterface/VSIImage.cpp
+@@ -11,7 +11,7 @@
+ // Include DCMTK LIBJPEG for lossy and lossless JPEG compression
+ extern "C" {
+ #define boolean ijg_boolean
+-#include "dcmtk/dcmjpeg/libijg8/jpeglib8.h"
++#include "jpeglib.h"
+ #include "jpeg_mem_src.h"
+ #undef boolean
+ #undef const
+@@ -234,7 +234,7 @@ char* VSIImage::decodeTile(int no, int row, int col) const {
+       jpeg_source_mgr src_mem;
+       jpeg_create_decompress(&cinfo);
+       cinfo.err = jpeg_std_error(&jerr);      
+-      jpeg_mem_src(&cinfo, &src_mem, (void*)buf, size);
++      jpeg_mem_src_asap(&cinfo, &src_mem, (void*)buf, size);
+       jpeg_read_header(&cinfo, true);
+       if (_compressionType == 2) {
+         cinfo.jpeg_color_space = JCS_YCbCr;
+diff --git a/multiresolutionimageinterface/jpeg_mem_src.h b/multiresolutionimageinterface/jpeg_mem_src.h
+index b9b91e9..13b9040 100644
+--- a/multiresolutionimageinterface/jpeg_mem_src.h
++++ b/multiresolutionimageinterface/jpeg_mem_src.h
+@@ -47,7 +47,7 @@ static void mem_skip_input_data( j_decompress_ptr cinfo, long num_bytes )
+ 	}
+ }
+
+-static void jpeg_mem_src( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes )
++static void jpeg_mem_src_asap( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes )
+ {
+     src->init_source = mem_init_source;
+     src->fill_input_buffer = mem_fill_input_buffer;

easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch

@@ -0,0 +1,55 @@
+# Author: Robert Jan Schlimbach (SURF)
+# Patch to make ASAP/2.1 accept pugixml as non-header-only shared lib
+
+diff --git a/annotation/CMakeLists.txt b/annotation/CMakeLists.txt
+index 114babe..2156cd3 100644
+--- a/annotation/CMakeLists.txt
++++ b/annotation/CMakeLists.txt
+@@ -25,10 +25,9 @@ set(ANNOTATION_SOURCE
+ )
+
+ add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS})
+-target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY")
+ generate_export_header(annotation)
+ target_include_directories(annotation PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}> $<INSTALL_INTERFACE:include/annotation> PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR})
+-target_link_libraries(annotation PUBLIC core PRIVATE  multiresolutionimageinterface)
++target_link_libraries(annotation PUBLIC core PRIVATE  multiresolutionimageinterface ${PUGIXML_LIBRARY})
+ set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d)
+
+ IF(APPLE)
+diff --git a/cmakemodules/FindPugiXML.cmake b/cmakemodules/FindPugiXML.cmake
+index ccffcc4..9afcfb4 100644
+--- a/cmakemodules/FindPugiXML.cmake
++++ b/cmakemodules/FindPugiXML.cmake
+@@ -5,11 +5,12 @@
+ #  PugiXML_FOUND, If false, do not try to use PugiXML.
+
+ find_path(PugiXML_INCLUDE_DIR pugixml.hpp)
++find_library(PUGIXML_LIBRARY NAMES pugixml)
+
+ # handle the QUIETLY and REQUIRED arguments and set PugiXML_FOUND to TRUE if
+ # all listed variables are TRUE
+ include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
+ FIND_PACKAGE_HANDLE_STANDARD_ARGS(PugiXML
+-                                  REQUIRED_VARS PugiXML_INCLUDE_DIR)
++                                  REQUIRED_VARS PUGIXML_LIBRARY PugiXML_INCLUDE_DIR)
+
+-mark_as_advanced(PugiXML_INCLUDE_DIR)
++mark_as_advanced(PugiXML_INCLUDE_DIR PUGIXML_LIBRARY)
+diff --git a/multiresolutionimageinterface/CMakeLists.txt b/multiresolutionimageinterface/CMakeLists.txt
+index 132e6ef..8d24176 100644
+--- a/multiresolutionimageinterface/CMakeLists.txt
++++ b/multiresolutionimageinterface/CMakeLists.txt
+@@ -87,11 +87,10 @@ endif(BUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT)
+
+ add_library(multiresolutionimageinterface SHARED ${MULTIRESOLUTIONIMAGEINTERFACE_SRCS} ${MULTIRESOLUTIONIMAGEINTERFACE_HS} ${VSI_SOURCE_HS} ${VSI_SOURCE_SRCS})
+ target_include_directories(multiresolutionimageinterface PUBLIC $<BUILD_INTERFACE:${DIAGPathology_SOURCE_DIR}> $<INSTALL_INTERFACE:include> $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}> $<INSTALL_INTERFACE:include/multiresolutionimageinterface> PRIVATE ${PugiXML_INCLUDE_DIR} ${TIFF_INCLUDE_DIR})
+-target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff)
++target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff ${PUGIXML_LIBRARY})
+ IF(NOT WIN32)
+   target_link_libraries(multiresolutionimageinterface PRIVATE dl)
+ ENDIF(NOT WIN32)
+-target_compile_definitions(multiresolutionimageinterface PRIVATE PUGIXML_HEADER_ONLY)
+ generate_export_header(multiresolutionimageinterface)
+ set_target_properties(multiresolutionimageinterface PROPERTIES DEBUG_POSTFIX _d)
+

easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb

@@ -0,0 +1,49 @@
+easyblock = 'CMakeMake'
+
+name = 'DCMTK'
+version = '3.6.7'
+
+homepage = 'https://dicom.offis.de/dcmtk'
+description = """DCMTK is a collection of libraries and applications implementing large parts the DICOM standard.
+It includes software for examining, constructing and converting DICOM image files, handling offline media, sending
+and receiving images over a network connection, as well as demonstrative image storage and worklist servers."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+local_stripped_version = version.replace('.', '')
+
+source_urls = ['https://dicom.offis.de/download/%(namelower)s/dcmtk{}/'.format(local_stripped_version)]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['7c58298e3e8d60232ee6fc8408cfadd14463cc11a3c4ca4c59af5988c7e9710a']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+]
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('libjpeg-turbo', '2.1.3'),
+    ('LibTIFF', '4.3.0'),
+    ('libpng', '1.6.37'),
+    ('libxml2', '2.9.13'),
+    ('libiconv', '1.17'),
+]
+
+configopts = [
+    '-DBUILD_SHARED_LIBS=OFF',
+    '-DBUILD_SHARED_LIBS=ON'
+]
+
+
+sanity_check_paths = {
+    'files': ['bin/dcmdump', 'bin/dcmj2pnm'],
+    'dirs': ['lib'],
+}
+
+local_test_modules = ['dcmdata', 'dcmect', 'dcmfg', 'dcmiod', 'dcmnet', 'dcmrt', 'dcmseg', 'dcmsr', 'dcmtls', 'ofstd']
+sanity_check_commands = [
+    '%s_tests | grep " 0 failed"' % s for s in local_test_modules
+]
+
+moduleclass = 'data'

easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb

@@ -0,0 +1,56 @@
+easyblock = 'ConfigureMake'
+
+name = 'OpenSlide'
+version = '3.4.1'
+versionsuffix = '-largefiles'
+
+homepage = 'https://openslide.org/'
+description = """OpenSlide is a C library that provides a simple interface to
+read whole-slide images (also known as virtual slides)."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_large_file_support.patch']
+checksums = [
+    # v3.4.1.tar.gz
+    'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c',
+    # %(name)s-%(version_major_minor)s.1_large_file_support.patch
+    'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c',
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('M4', '1.4.19'),
+    ('pkg-config', '0.29.2'),
+    ('binutils', '2.38'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('libpng', '1.6.37'),
+    ('libjpeg-turbo', '2.1.3'),
+    ('LibTIFF', '4.3.0'),
+    ('OpenJPEG', '2.5.0'),
+    ('libxml2', '2.9.13'),
+    ('SQLite', '3.38.3'),
+    ('cairo', '1.17.4'),
+    ('Gdk-Pixbuf', '2.42.8'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+
+sanity_check_paths = {
+    'files': [
+        'bin/openslide-quickhash1sum',
+        'bin/openslide-show-properties',
+        'bin/openslide-write-png',
+        'lib/libopenslide.la',
+        'lib/libopenslide.%s' % SHLIB_EXT
+    ],
+    'dirs': ['include/openslide']
+}
+
+
+moduleclass = 'vis'

easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb

@@ -0,0 +1,37 @@
+easyblock = 'CMakeMake'
+
+name = 'pugixml'
+version = '1.12.1'
+
+homepage = 'https://pugixml.org/'
+description = "pugixml is a light-weight C++ XML processing library"
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/zeux/pugixml/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['1e28ab24b6e04e013d96f45d25e9f2d04c921dc68c613fd010ecaaad3892c14d']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+]
+
+configopts = " ".join([
+    "-DBUILD_SHARED_LIBS=ON",
+    "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON",
+])
+
+sanity_check_paths = {
+    'files': [
+        'include/pugiconfig.hpp',
+        'include/pugixml.hpp',
+        'lib/libpugixml.a',
+        'lib/libpugixml.%s' % SHLIB_EXT,
+        'lib/pkgconfig/pugixml.pc'
+    ],
+    'dirs': ['lib/cmake/pugixml'],
+}
+
+moduleclass = 'data'