commit: d23b080b9afe74c6590a9827d505e9234c00deb0
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 01:48:55 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 01:48:55 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d23b080b
sci-libs/itk: add 5.3.0
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch | 550 +++++++++++++++++++++
sci-libs/itk/itk-5.3.0.ebuild | 251 ++++++++++
2 files changed, 801 insertions(+)
diff --git a/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch
b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch
new file mode 100644
index 000000000..27f139553
--- /dev/null
+++ b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch
@@ -0,0 +1,550 @@
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -1,16 +1,32 @@
+ project(ITKOpenJPEG)
+ set(ITKOpenJPEG_THIRD_PARTY 1)
+
+-set(ITKOpenJPEG_INCLUDE_DIRS
+- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+- )
+-set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg"
${ITK_USE_SYSTEM_LIBRARIES})
++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG)
++
++if(ITK_USE_SYSTEM_OPENJPEG)
++ find_package(OpenJPEG REQUIRED)
++ set(ITKOpenJPEG_INCLUDE_DIRS
++ ${ITKOpenJPEG_BINARY_DIR}/src
++ )
++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS
++ ${OPENJPEG_INCLUDE_DIRS}
++ )
++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}")
++ set(ITKOpenJPEG_NO_SRC 1)
++else()
++ set(ITKOpenJPEG_INCLUDE_DIRS
++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++ )
++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++endif()
++
++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h)
+ set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
+-
+ itk_module_impl()
+
+-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h
++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h
+ DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR}
+ COMPONENT Development
+ )
+diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
+rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h
++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in
+@@ -25,6 +25,12 @@
+ #ifndef itk_openjpeg_h
+ #define itk_openjpeg_h
+
+-#include <itkopenjpeg/openjpeg.h>
++/* Use the openjpeg library configured for ITK. */
++#cmakedefine ITK_USE_SYSTEM_OPENJPEG
++#ifdef ITK_USE_SYSTEM_OPENJPEG
++# include <openjpeg.h>
++#else
++# include <itkopenjpeg/openjpeg.h>
++#endif
+
+ #endif
+--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+@@ -27,8 +27,6 @@
+ extern "C"
+ {
+ #include "openjpeg.h"
+-#include "j2k.h"
+-#include "jp2.h"
+ }
+
+
+@@ -139,11 +137,11 @@
+ {
+ itkDebugMacro(<< "ReadImageInformation()");
+
+- FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+- /* decompression parameters */
++ /* set decoding parameters to default values */
++
opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+
+- if (!l_file)
++ opj_stream_t * cio =
opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
++ if (!cio)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " <<
this->GetFileName() << std::endl
+ <<
"Reason: "
+@@ -151,10 +149,5 @@
+ }
+
+- /* set decoding parameters to default values */
+-
opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+-
+- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true);
+-
+ this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */
+
+ opj_image_t * l_image = nullptr;
+@@ -188,9 +181,8 @@
+
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -202,10 +194,9 @@
+ {
+ /* JPEG 2000 compressed image data */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -217,10 +208,9 @@
+ {
+ /* JPEG 2000, JPIP */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+@@ -230,7 +220,6 @@
+ }
+ default:
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -248,26 +237,8 @@
+ }
+
+- // Image parameters - first tile
+- OPJ_INT32 l_tile_x0;
+- OPJ_INT32 l_tile_y0;
+-
+- // Image parameters - tile width, height and number of tiles
+- OPJ_UINT32 l_tile_width;
+- OPJ_UINT32 l_tile_height;
+- OPJ_UINT32 l_nb_tiles_x;
+- OPJ_UINT32 l_nb_tiles_y;
+-
+ itkDebugMacro(<< "Trying to read header now...");
+
+- bResult = opj_read_header(this->m_Internal->m_Dinfo,
+- &l_image,
+- &l_tile_x0,
+- &l_tile_y0,
+- &l_tile_width,
+- &l_tile_height,
+- &l_nb_tiles_x,
+- &l_nb_tiles_y,
+- cio);
++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image);
+
+ if (!bResult)
+ {
+@@ -284,13 +255,21 @@
+ }
+
+- this->m_Internal->m_TileStartX = l_tile_x0;
+- this->m_Internal->m_TileStartY = l_tile_y0;
++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo);
++ if (!cp)
++ {
++ opj_stream_destroy(cio);
++ opj_image_destroy(l_image);
++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
++ << "Reason:
Error while reading image header");
++ }
++ this->m_Internal->m_TileStartX = cp->tx0;
++ this->m_Internal->m_TileStartY = cp->ty0;
+
+- this->m_Internal->m_TileWidth = l_tile_width;
+- this->m_Internal->m_TileHeight = l_tile_height;
++ this->m_Internal->m_TileWidth = cp->tdx;
++ this->m_Internal->m_TileHeight = cp->tdy;
+
+- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x;
+- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y;
++ this->m_Internal->m_NumberOfTilesInX = cp->tw;
++ this->m_Internal->m_NumberOfTilesInY = cp->th;
+
+
+ itkDebugMacro(<< "Number of Components = " << l_image->numcomps);
+@@ -307,6 +286,7 @@
+ else
+ {
+ opj_stream_destroy(cio);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+ << "Reason: "
+ << "Unknown
precision in file: "
+@@ -320,6 +300,6 @@
+ break;
+ case 3:
+- if (l_image->color_space != CLRSPC_SRGB)
++ if (l_image->color_space != OPJ_CLRSPC_SRGB)
+ {
+ itkWarningMacro(<< "file does not specify color space, assuming
sRGB");
+ }
+@@ -349,7 +329,6 @@
+
+ /* close the byte stream */
+ opj_stream_destroy(cio);
+- fclose(l_file);
+
+ if (this->m_Internal->m_Dinfo)
+ {
+@@ -368,16 +347,7 @@
+ {
+ itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin");
+
+- FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+- if (!l_file)
+- {
+- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " <<
this->GetFileName() << std::endl
+- <<
"Reason: "
+- <<
itksys::SystemTools::GetLastSystemError());
+- }
+-
+- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file,
true);
++ opj_stream_t * l_stream =
opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
+ if (!l_stream)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+@@ -397,9 +367,10 @@
+ {
+ /* JPEG-2000 codestream */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_J2K)
returns nullptr");
+@@ -410,9 +381,10 @@
+ {
+ /* JPEG 2000 compressed image data */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_JP2)
returns nullptr");
+@@ -423,9 +395,10 @@
+ {
+ /* JPEG 2000, JPIP */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_decompress(CODEC_JPT)
returns nullptr");
+@@ -433,7 +406,7 @@
+ break;
+ }
+ default:
+- fclose(l_file);
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -445,32 +418,17 @@
+ if (!opj_setup_decoder(this->m_Internal->m_Dinfo,
&(this->m_Internal->m_DecompressionParameters)))
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+ << "Reason:
opj_setup_decoder returns false");
+ }
+
+- OPJ_INT32 l_tile_x0, l_tile_y0;
+-
+- OPJ_UINT32 l_tile_width;
+- OPJ_UINT32 l_tile_height;
+- OPJ_UINT32 l_nb_tiles_x;
+- OPJ_UINT32 l_nb_tiles_y;
+-
+- bool bResult = opj_read_header(this->m_Internal->m_Dinfo,
+- &l_image,
+- &l_tile_x0,
+- &l_tile_y0,
+- &l_tile_width,
+- &l_tile_height,
+- &l_nb_tiles_x,
+- &l_nb_tiles_y,
+- l_stream);
++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo,
&l_image);
+
+ if (!bResult)
+ {
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+ << "Reason:
opj_read_header returns false");
+ }
+@@ -499,7 +457,7 @@
+ itkDebugMacro(<< "p_end_x = " << p_end_x);
+ itkDebugMacro(<< "p_end_y = " << p_end_y);
+
+- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x,
p_start_y, p_end_x, p_end_y);
++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image,
p_start_x, p_start_y, p_end_x, p_end_y);
+
+ itkDebugMacro(<< "opj_set_decode_area() after");
+
+@@ -509,6 +467,5 @@
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+ << "Reason:
opj_set_decode_area returns false");
+ }
+@@ -525,13 +482,14 @@
+
+ OPJ_UINT32 l_max_data_size = 1000;
+
+- bool l_go_on = true;
++ OPJ_BOOL l_go_on = true;
+
+ auto * l_data = (OPJ_BYTE *)malloc(1000);
+
+ while (l_go_on)
+ {
+ bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo,
++ l_stream,
+ &l_tile_index,
+ &l_data_size,
+ &l_current_tile_x0,
+@@ -540,13 +498,11 @@
+ &l_current_tile_y1,
+ &l_nb_comps,
+- &l_go_on,
+- l_stream);
++ &l_go_on);
+
+ if (!tileHeaderRead)
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+@@ -571,7 +527,6 @@
+ if (!l_data)
+ {
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+@@ -590,7 +545,6 @@
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+@@ -654,7 +608,6 @@
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+@@ -667,13 +620,11 @@
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " <<
this->GetFileName() << std::endl
+ << "Reason:
error whle reading image");
+ }
+
+ /* close the byte stream */
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+
+ if (this->m_Internal->m_Dinfo)
+ {
+@@ -840,13 +791,13 @@
+
+ parameters.numresolution = numberOfResolutions;
+
+- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY;
++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY;
+ opj_image_cmptparm_t cmptparms[3];
+
+ if (this->GetNumberOfComponents() == 3)
+ {
+
+- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB :
CLRSPC_UNSPECIFIED;
++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ?
OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED;
+
+ /* initialize image components */
+ memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t));
+@@ -864,7 +815,7 @@
+
+ if (this->GetNumberOfComponents() == 1)
+ {
+- color_space = CLRSPC_GRAY;
++ color_space = OPJ_CLRSPC_GRAY;
+
+ /* initialize image components */
+ memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t));
+@@ -941,8 +892,9 @@
+ if (extension == ".j2k")
+ {
+- cinfo = opj_create_compress(CODEC_J2K);
++ cinfo = opj_create_compress(OPJ_CODEC_J2K);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_J2K) returns
nullptr");
+@@ -950,9 +902,10 @@
+ }
+ else if (extension == ".jp2")
+ {
+- cinfo = opj_create_compress(CODEC_JP2);
++ cinfo = opj_create_compress(OPJ_CODEC_JP2);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_JP2) returns
nullptr");
+@@ -960,9 +913,10 @@
+ }
+ else if (extension == ".jpt")
+ {
+- cinfo = opj_create_compress(CODEC_JPT);
++ cinfo = opj_create_compress(OPJ_CODEC_JPT);
+ if (!cinfo)
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: opj_create_compress(CODEC_JPT) returns
nullptr");
+@@ -970,6 +924,7 @@
+ }
+ else
+ {
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " <<
this->GetFileName() << std::endl
+ << "Reason:
unknown encode format: " << extension);
+ }
+@@ -985,23 +940,19 @@
+
+ if (!opj_setup_encoder(cinfo, ¶meters, l_image))
+ {
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " <<
this->GetFileName() << std::endl
+ << "Reason:
opj_setup_encoder returns false");
+ }
+
+- FILE * l_file = fopen(parameters.outfile, "wb");
+- if (!l_file)
+- {
+- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " <<
this->GetFileName() << std::endl
+- <<
"Reason: "
+- <<
itksys::SystemTools::GetLastSystemError());
+- }
+-
+ /* open a byte stream for writing */
+ /* allocate memory for all tiles */
+- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false);
++ opj_stream_t * cio =
opj_stream_create_default_file_stream(parameters.outfile, false);
+ if (!cio)
+ {
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -1017,7 +968,8 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " <<
this->GetFileName() << std::endl
+ << "Reason:
opj_start_compress returns false");
+ }
+@@ -1026,7 +978,8 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " <<
this->GetFileName() << std::endl
+ << "Reason:
opj_encode returns false");
+ }
+@@ -1035,14 +988,14 @@
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ opj_destroy_codec(cinfo);
++ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " <<
this->GetFileName() << std::endl
+ << "Reason:
opj_end_compress returns false");
+ }
+
+ /* close and free the byte stream */
+ opj_stream_destroy(cio);
+- fclose(l_file);
+
+ /* free remaining compression structures */
+ opj_destroy_codec(cinfo);
+--- a/Modules/Nonunit/Review/src/CMakeLists.txt
++++ b/Modules/Nonunit/Review/src/CMakeLists.txt
+@@ -5,7 +5,7 @@
+
+ add_library(ITKReview ${ITKReview_SRC})
+ itk_module_link_dependencies()
+-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES}
${ITKIOLSM_LIBRARIES} itkopenjpeg)
++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES}
${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES})
+ itk_module_target(ITKReview)
+
+
diff --git a/sci-libs/itk/itk-5.3.0.ebuild b/sci-libs/itk/itk-5.3.0.ebuild
new file mode 100644
index 000000000..54b7c89b3
--- /dev/null
+++ b/sci-libs/itk/itk-5.3.0.ebuild
@@ -0,0 +1,251 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} )
+VIRTUALX_REQUIRED="manual"
+
+inherit cmake python-single-r1 virtualx
+
+# rsync: [sender] link_stat
"/distfiles/1c/itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
(in gentoo) failed: No such file or directory (2)
+
+MY_PN="InsightToolkit"
+MY_P="${MY_PN}-${PV}"
+GLI_V="1.2.0"
+IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c"
+TEST_HASH="bb6d3b9a932333901465c75417fe8859124f5fed"
+declare -a GLI_TEST_HASHES=(
+
"a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a"
+
"bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f"
+)
+
+GLI_TEST_SRC=""
+for i in "${GLI_TEST_HASHES[@]}"; do
+
GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download
-> ${PN}-test-${i} "
+done
+
+DESCRIPTION="NLM Insight Segmentation and Registration Toolkit"
+HOMEPAGE="https://itk.org";
+SRC_URI="
+
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz
+
https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/refs/tags/v${GLI_V}.tar.gz
-> ITKGenericLabelInterpolator-${GLI_V}
+
https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz ->
ITKAdaptiveDenoising-${PV}.tar.gz
+ test? (
+
https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz
+
https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz
-> ${P}-testingdata.tar.gz
+ ${GLI_TEST_SRC}
+ )
+ "
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="debug doc examples fftw itkv4-compat python review test vtkglue"
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-cpp/eigen:3
+ dev-libs/double-conversion:0=
+ dev-libs/expat:0=
+ media-libs/openjpeg:2
+ media-libs/libpng:0=
+ media-libs/tiff:0=[jpeg]
+ sci-libs/dcmtk:0=
+ sci-libs/hdf5:0=[cxx]
+ sci-libs/gdcm:0=
+ sys-libs/zlib:0=
+ media-libs/libjpeg-turbo:0=
+ fftw? ( sci-libs/fftw:3.0= )
+ vtkglue? (
+ sci-libs/vtk:0=[rendering]
+ python? (
+ sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}]
+ )
+ )
+ python? ( ${PYTHON_DEPS} )
+"
+DEPEND="${RDEPEND}
+ sys-apps/coreutils
+ python? (
+ >=dev-lang/swig-2.0:0
+ dev-libs/castxml
+ )
+ doc? ( app-doc/doxygen )
+"
+BDEPEND="
+ test? (
+ vtkglue? ( ${VIRTUALX_DEPEND} )
+ python? (
+ $(python_gen_cond_dep
'dev-python/numpy[${PYTHON_USEDEP}]')
+ )
+ )
+"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-5.2.1-system-tiff-has-64.patch"
+ "${FILESDIR}/${PN}-5.3.0-system-openjpeg.patch"
+)
+
+pkg_pretend() {
+ if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then
+ elog "To tune ITK to make the best use of working memory you
can set"
+ elog " ITK_COMPUTER_MEMORY_SIZE=XX"
+ elog "in make.conf, default is 1 (unit is GB)"
+ fi
+ if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then
+ elog "For Python language bindings, you can define the
dimensions"
+ elog "you want to create bindings for by setting"
+ elog " ITK_WRAP_DIMS=X;Y;Z..."
+ elog "in make.conf, default is 2;3 for 2D and 3D data"
+ fi
+}
+
+src_prepare() {
+ # drop bundled libs
+ local -a DROPS=(
+ DoubleConversion/src/double-conversion
+ Eigen3/src/itkeigen
+ Expat/src/expat
+ GDCM/src/gdcm
+ JPEG/src/itkjpeg
+ HDF5/src/itkhdf5
+ OpenJPEG/src/openjpeg
+ PNG/src/itkpng
+ TIFF/src/itktiff
+ )
+ local x
+ for x in "${DROPS[@]}"; do
+ ebegin "Dropping bundled ${x%%/*}"
+ rm -r "Modules/ThirdParty/${x}" || die
+ eend $?
+ done
+ {
+ find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name
src -printf '%P\n'
+ printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,'
+ } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die
+
+ # Remote modules
+ ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}"
Modules/External/ITKGenericLabelInterpolator || die
+ ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}"
Modules/External/ITKAdaptiveDenoising || die
+
+ cmake_src_prepare
+
+ if use test; then
+ cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" ||
die
+ mv "../ITKTestingData-${TEST_HASH}"
"${BUILD_DIR}/.ExternalData" || die
+ for i in "${GLI_TEST_HASHES[@]}"; do
+ cp "${DISTDIR}/${PN}-test-${i}"
".ExternalData/SHA512/${i}" || die
+ cp "${DISTDIR}/${PN}-test-${i}"
"${BUILD_DIR}/.ExternalData/SHA512/${i}" || die
+ done
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)"
+ -DITK_INSTALL_DOC_DIR="share/doc/${P}"
+ -DBUILD_EXAMPLES="$(usex examples ON OFF)"
+ -DBUILD_SHARED_LIBS=ON
+ -DBUILD_TESTING="$(usex test ON OFF)"
+
-Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion"
+
-DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData"
+ -DGDCM_USE_SYSTEM_OPENJPEG=ON
+ -DITK_FORBID_DOWNLOADS:BOOL=ON
+ -DITK_INSTALL_LIBRARY_DIR=$(get_libdir)
+ -DITK_USE_REVIEW="$(usex review ON OFF)"
+ -DITK_USE_SYSTEM_DCMTK=ON
+ -DITK_USE_SYSTEM_DOUBLECONVERSION=ON
+ -DITK_USE_SYSTEM_CASTXML=ON
+ -DITK_USE_SYSTEM_EIGEN=ON
+ -DITK_USE_SYSTEM_EXPAT=ON
+ -DITK_USE_SYSTEM_GDCM=ON
+ -DITK_USE_SYSTEM_HDF5=ON
+ -DITK_USE_SYSTEM_JPEG=ON
+ -DITK_USE_SYSTEM_OPENJPEG=ON
+ -DITK_USE_SYSTEM_PNG=ON
+ -DITK_USE_SYSTEM_SWIG=ON
+ -DITK_USE_SYSTEM_TIFF=ON
+ -DITK_USE_SYSTEM_ZLIB=ON
+ -DITK_USE_KWSTYLE=OFF
+ -DITK_BUILD_DEFAULT_MODULES=ON
+ -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}"
+ -DModule_AdaptiveDenoising:BOOL=ON
+ -DModule_GenericLabelInterpolator:BOOL=ON
+ -DModule_ITKReview:BOOL=ON
+ -DWRAP_ITK_JAVA=OFF
+ -DWRAP_ITK_TCL=OFF
+ -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat)
+ )
+ if use fftw; then
+ mycmakeargs+=(
+ -DUSE_FFTWD=ON
+ -DUSE_FFTWF=ON
+ -DUSE_SYSTEM_FFTW=ON
+ -DITK_WRAP_double=ON
+ -DITK_WRAP_vector_double=ON
+ -DITK_WRAP_covariant_vector_double=ON
+ -DITK_WRAP_complex_double=ON
+ )
+ fi
+ if use vtkglue; then
+ mycmakeargs+=(
+ -DModule_ITKVtkGlue=ON
+ )
+ fi
+ if use python; then
+ mycmakeargs+=(
+ -DITK_WRAP_PYTHON=ON
+ -DPython3_EXECUTABLE="${PYTHON}"
+ -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}"
+ )
+ else
+ mycmakeargs+=(
+ -DITK_WRAP_PYTHON=OFF
+ )
+ fi
+ cmake_src_configure
+}
+
+src_install() {
+ cmake_src_install
+
+ if use examples; then
+ docinto examples
+ docompress -x /usr/share/doc/${PF}/examples
+ dodoc -r "${S}"/Examples/*
+ fi
+
+ echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} ||
die
+ local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit"
+ if use python; then
+ echo
"PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >>
"${T}"/40${PN} || die
+
ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib"
+ fi
+ echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die
+ doenvd "${T}"/40${PN}
+
+ if use doc; then
+ cd "${WORKDIR}"/html || die
+ rm *.md5 || die "Failed to remove superfluous hashes"
+ einfo "Installing API docs. This may take some time."
+ docinto api-docs
+ dodoc -r *
+ fi
+
+ use python && python_optimize
+}
+
+src_test() {
+ # Failing tests reported upstream:
+ # https://github.com/ntustison/ITKAdaptiveDenoising/issues/13
+ if use vtkglue; then
+ virtx cmake_src_test -E
"(AdaptiveNonLocalMeansDenoisingImageFilterTest1|AdaptiveNonLocalMeansDenoisingImageFilterTest2)"
+ else
+ cmake_src_test -E
"(AdaptiveNonLocalMeansDenoisingImageFilterTest1|AdaptiveNonLocalMeansDenoisingImageFilterTest2)"
+ fi
+}
