Support Aperio SVS with CPU LZW and jpeg2k decoder

- Update Jpeg decoder to consider colorspace of the JPEG image
  - We need to set a proper color space from TIFF metadata to the decoder
  - Update tjDecompress2() method call with jpeg_decode_buffer() that modified
    tjDecompress2() implementation
  - Add `jpeg_color_space_` to IFD Class.
- Move additional includes to their own cmake files
- Add Jpeg2k decoder with OpenJpeg
  - Added fast color conversion logic with pre-calculated table
- Add LZW decoder with libtiff's implementation
  - Take part of the code to provide only LZW decoder part
- Add `rows_per_strip_` and `predictor_` attributers to IFD class, to support
  LZW
- Refactor TIFF:resolve_vendor_format() to support Aperio SVS metadata
- Support LZW compressed image (with multi strips) for associated image.

Addresses #17

LICENSE-3rdparty.md

@@ -30,6 +30,8 @@ libtiff
 - Copyright:
  - Sam Leffler
  - Silicon Graphics, Inc.
+- Files:
+ - cpp/plugins/cucim.kit.cuslide/src/cuslide/lzw/lzw_libtiff.cpp : Implementation of lzw decoder.
 
 fmt
 - License: MIT License
@@ -106,6 +108,9 @@ OpenJPEG
  - David Janssens
  - Centre National d'Etudes Spatiales (CNES), France
  - CS Systemes d'Information, France
+- Files:
+ - cpp/plugins/cucim.kit.cuslide/src/cuslide/jpeg2k/libopenjpeg.cpp : Implementation of jpeg2k decoder.
+ - cpp/plugins/cucim.kit.cuslide/src/cuslide/jpeg2k/color_conversion.cpp : Implementation of color conversion methods.
 
 NVIDIA nvJPEG
 - License: NVIDIA License

cpp/plugins/cucim.kit.cuslide/CMakeLists.txt

@@ -28,7 +28,7 @@ file(STRINGS ${CMAKE_CURRENT_LIST_DIR}/VERSION VERSION)
 # Append local cmake module path
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake/modules")
 
-project(cuslide VERSION ${VERSION} DESCRIPTION "cuslide" LANGUAGES CXX CUDA)
+project(cuslide VERSION ${VERSION} DESCRIPTION "cuslide" LANGUAGES C CXX CUDA)
 set(CUCIM_PLUGIN_NAME "cucim.kit.cuslide")
 
 ################################################################################
@@ -126,6 +126,7 @@ add_definitions(-D_GLIBCXX_USE_CXX11_ABI=0) # TODO: create two library, one with
 #superbuild_depend(cucim)
 superbuild_depend(fmt)
 superbuild_depend(libjpeg-turbo) # libjpeg-turbo should be located before libtiff as libtiff depends on libjpeg-turbo
+superbuild_depend(libopenjpeg)
 superbuild_depend(libtiff)
 superbuild_depend(catch2)
 superbuild_depend(openslide)
@@ -172,6 +173,16 @@ add_library(${CUCIM_PLUGIN_NAME}
  src/cuslide/deflate/deflate.h
  src/cuslide/jpeg/libjpeg_turbo.cpp
  src/cuslide/jpeg/libjpeg_turbo.h
+ src/cuslide/jpeg2k/color_conversion.cpp
+ src/cuslide/jpeg2k/color_conversion.h
+ src/cuslide/jpeg2k/color_table.h
+ src/cuslide/jpeg2k/libopenjpeg.cpp
+ src/cuslide/jpeg2k/libopenjpeg.h
+ ${deps-libopenjpeg_SOURCE_DIR}/src/bin/common/color.c # for color_sycc_to_rgb() and color_apply_icc_profile()
+ src/cuslide/lzw/lzw.cpp
+ src/cuslide/lzw/lzw.h
+ src/cuslide/lzw/lzw_libtiff.cpp
+ src/cuslide/lzw/lzw_libtiff.h
  src/cuslide/raw/raw.cpp
  src/cuslide/raw/raw.h
  src/cuslide/tiff/ifd.cpp
@@ -185,6 +196,14 @@ add_library(${CUCIM_PLUGIN_NAME}
 # Note: Since cuslide.cpp is using nlohmann/json.hpp which nvcc cannot parse properly, set other files for cudart.
 set_source_files_properties(src/cuslide/jpeg/libjpeg_turbo.cpp PROPERTIES LANGUAGE CUDA)
 
+# compile color.c for libopenjpeg with c++
+set_source_files_properties(${deps-libopenjpeg_SOURCE_DIR}/src/bin/common/color.c
+ PROPERTIES
+ LANGUAGE C
+ CMAKE_CXX_VISIBILITY_PRESET default
+ CMAKE_C_VISIBILITY_PRESET default
+ CMAKE_VISIBILITY_INLINES_HIDDEN OFF)
+
 # Compile options
 set_target_properties(${CUCIM_PLUGIN_NAME}
  PROPERTIES
@@ -211,6 +230,8 @@ target_link_libraries(${CUCIM_PLUGIN_NAME}
  cucim::cucim
  deps::libtiff
  deps::libjpeg-turbo
+ deps::libopenjpeg
+ deps::libopenjpeg-lcms2
  deps::pugixml
  deps::json
  deps::libdeflate
@@ -222,8 +243,6 @@ target_include_directories(${CUCIM_PLUGIN_NAME}
  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
  PRIVATE
  ${CMAKE_CURRENT_LIST_DIR}/src
- # turbojpeg.h is not included in 'turbojpeg-static' so manually include
- ${deps-libjpeg-turbo_SOURCE_DIR}
  )
 
 # Do not generate SONAME as this would be used as plugin

cpp/plugins/cucim.kit.cuslide/cmake/deps/libjpeg-turbo.cmake

@@ -64,8 +64,13 @@ if (NOT TARGET deps::libjpeg-turbo)
  cucim_restore_build_shared_libs()
 
  add_library(deps::libjpeg-turbo INTERFACE IMPORTED GLOBAL)
-
  target_link_libraries(deps::libjpeg-turbo INTERFACE turbojpeg-static)
+ target_include_directories(deps::libjpeg-turbo
+ INTERFACE
+ # turbojpeg.h is not included in 'turbojpeg-static' so manually include
+ ${deps-libjpeg-turbo_SOURCE_DIR}
+ )
+
  set(deps-libjpeg-turbo_SOURCE_DIR ${deps-libjpeg-turbo_SOURCE_DIR} CACHE INTERNAL "" FORCE)
  mark_as_advanced(deps-libjpeg-turbo_SOURCE_DIR)
  set(deps-libjpeg-turbo_BINARY_DIR ${deps-libjpeg-turbo_BINARY_DIR} CACHE INTERNAL "" FORCE)

cpp/plugins/cucim.kit.cuslide/cmake/deps/libopenjpeg.cmake

@@ -0,0 +1,112 @@
+# Apache License, Version 2.0
+# Copyright 2020-2021 NVIDIA Corporation
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+if (NOT TARGET deps::libopenjpeg)
+
+ FetchContent_Declare(
+ deps-libopenjpeg
+ GIT_REPOSITORY https://github.com/uclouvain/openjpeg.git
+ GIT_TAG v2.4.0
+ GIT_SHALLOW TRUE
+ )
+ FetchContent_GetProperties(deps-libopenjpeg)
+ if (NOT deps-libopenjpeg_POPULATED)
+ message(STATUS "Fetching libopenjpeg sources")
+ FetchContent_Populate(deps-libopenjpeg)
+ message(STATUS "Fetching libopenjpeg sources - done")
+ endif ()
+
+ # Create static library
+ # It build a static library when both BUILD_SHARED_LIBS and BUILD_STATIC_LIBS are ON
+ # (build-debug/_deps/deps-libopenjpeg-src/src/lib/openjp2/CMakeLists.txt:94)
+ #
+ # if(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+ cucim_set_build_shared_libs(ON)
+
+ ###########################################################################
+ # Build liblcms2 with the source in libopenjpeg
+ ###########################################################################
+ message(" ##GG ${deps-libopenjpeg_SOURCE_DIR}")
+
+ add_subdirectory(${deps-libopenjpeg_SOURCE_DIR}/thirdparty/liblcms2 ${deps-libopenjpeg_BINARY_DIR}/thirdparty/liblcms2)
+
+ # Override the output library folder path
+ set_target_properties(lcms2
+ PROPERTIES
+ OUTPUT_NAME "lcms2"
+ ARCHIVE_OUTPUT_DIRECTORY ${deps-libopenjpeg_BINARY_DIR}/thirdparty/lib)
+
+ # Override definition of OPJ_HAVE_LIBLCMS2 to build color_apply_icc_profile() method
+ target_compile_definitions(lcms2
+ PUBLIC
+ OPJ_HAVE_LIBLCMS2=1
+ )
+
+ # Set PIC to prevent the following error message
+ # : /usr/bin/ld: _deps/deps-libopenjpeg-build/thirdparty/lib/liblcms2.a(cmserr.c.o): relocation R_X86_64_PC32 against symbol `_cmsMemPluginChunk' can not be used when making a shared object; recompile with -fPIC
+ # /usr/bin/ld: final link failed: bad value
+ set_target_properties(lcms2 PROPERTIES POSITION_INDEPENDENT_CODE ON)
+
+ add_library(deps::libopenjpeg-lcms2 INTERFACE IMPORTED GLOBAL)
+ target_link_libraries(deps::libopenjpeg-lcms2 INTERFACE lcms2)
+ target_include_directories(deps::libopenjpeg-lcms2
+ INTERFACE
+ # lcms2.h is not included in 'lcms2' so manually include
+ ${deps-libopenjpeg_SOURCE_DIR}/thirdparty/liblcms2/include
+ )
+
+ set(deps-libopenjpeg-lcms2_SOURCE_DIR ${deps-libopenjpeg_SOURCE_DIR}/thirdparty/liblcms2 CACHE INTERNAL "" FORCE)
+ mark_as_advanced(deps-libopenjpeg-lcms2_SOURCE_DIR)
+ set(deps-libopenjpeg-lcms2_BINARY_DIR ${deps-libopenjpeg_BINARY_DIR}/thirdparty/liblcms2 CACHE INTERNAL "" FORCE)
+ mark_as_advanced(deps-libopenjpeg-lcms2_BINARY_DIR)
+
+ ###########################################################################
+
+ add_subdirectory(${deps-libopenjpeg_SOURCE_DIR} ${deps-libopenjpeg_BINARY_DIR} EXCLUDE_FROM_ALL)
+
+ # Disable visibility to not expose unnecessary symbols
+ set_target_properties(openjp2_static
+ PROPERTIES
+ C_VISIBILITY_PRESET hidden
+ CXX_VISIBILITY_PRESET hidden
+ VISIBILITY_INLINES_HIDDEN YES
+ )
+ # target_compile_options(openjp2_static PRIVATE $<$<CXX_COMPILER_ID:GNU>:-march=core-avx2>)
+
+ # Set PIC to prevent the following error message
+ # : /usr/bin/ld: lib/libopenjp2.a(cio.c.o): relocation R_X86_64_PC32 against symbol `opj_stream_read_skip' can not be used when making a shared object; recompile with -fPIC
+ # /usr/bin/ld: final link failed: bad value
+ set_target_properties(openjp2_static PROPERTIES POSITION_INDEPENDENT_CODE ON)
+ cucim_restore_build_shared_libs()
+
+ add_library(deps::libopenjpeg INTERFACE IMPORTED GLOBAL)
+ target_link_libraries(deps::libopenjpeg INTERFACE openjp2_static)
+ target_include_directories(deps::libopenjpeg
+ INTERFACE
+ # openjpeg.h is not included in 'openjp2_static' so manually include
+ ${deps-libopenjpeg_SOURCE_DIR}/src/lib/openjp2
+ # opj_config.h is not included in openjp2_static so manually include
+ ${deps-libopenjpeg_BINARY_DIR}/src/lib/openjp2
+ # color.h is not included in 'openjp2_static' so manually include
+ ${deps-libopenjpeg_SOURCE_DIR}/src/bin/common
+ # opj_apps_config.h is not included in 'openjp2_static' so manually include
+ ${deps-libopenjpeg_BINARY_DIR}/src/bin/common
+ )
+
+ set(deps-libopenjpeg_SOURCE_DIR ${deps-libopenjpeg_SOURCE_DIR} CACHE INTERNAL "" FORCE)
+ mark_as_advanced(deps-libopenjpeg_SOURCE_DIR)
+ set(deps-libopenjpeg_BINARY_DIR ${deps-libopenjpeg_BINARY_DIR} CACHE INTERNAL "" FORCE)
+ mark_as_advanced(deps-libopenjpeg_BINARY_DIR)
+endif ()

cpp/plugins/cucim.kit.cuslide/src/cuslide/cuslide.cpp

@@ -75,7 +75,7 @@ static bool CUCIM_ABI checker_is_valid(const char* file_name, const char* buf, s
  (void)size;
  auto file = std::filesystem::path(file_name);
  auto extension = file.extension().string();
- if (extension.compare(".tif") == 0 || extension.compare(".tiff") == 0)
+ if (extension.compare(".tif") == 0 || extension.compare(".tiff") == 0 || extension.compare(".svs") == 0)
  {
  return true;
  }
@@ -100,42 +100,29 @@ static bool CUCIM_ABI parser_parse(CuCIMFileHandle* handle, cucim::io::format::I
 
  auto tif = static_cast<cuslide::tiff::TIFF*>(handle->client_data);
 
- std::vector<size_t> main_ifd_list;
-
  size_t ifd_count = tif->ifd_count();
  size_t level_count = tif->level_count();
- for (size_t i = 0; i < ifd_count; i++)
+
+ // If not Aperio SVS format (== Ordinary Pyramid TIFF image)
+ if (tif->ifd(0)->image_description().rfind("Aperio", 0) != 0)
  {
- const std::shared_ptr<cuslide::tiff::IFD>& ifd = tif->ifd(i);
-
- // const char* char_ptr = ifd->model().c_str();
- // uint32_t width = ifd->width();
- // uint32_t height = ifd->height();
- // uint32_t bits_per_sample = ifd->bits_per_sample();
- // uint32_t samples_per_pixel = ifd->samples_per_pixel();
- uint64_t subfile_type = ifd->subfile_type();
- // printf("image_description:\n%s\n", ifd->image_description().c_str());
- // printf("model=%s, width=%u, height=%u, model=%p bits_per_sample:%u, samples_per_pixel=%u, %lu \n",
- // char_ptr,
- // width, height, char_ptr, bits_per_sample, samples_per_pixel, subfile_type);
- if (subfile_type == 0)
+ std::vector<size_t> main_ifd_list;
+ for (size_t i = 0; i < ifd_count; i++)
  {
- main_ifd_list.push_back(i);
+ const std::shared_ptr<cuslide::tiff::IFD>& ifd = tif->ifd(i);
+ uint64_t subfile_type = ifd->subfile_type();
+ if (subfile_type == 0)
+ {
+ main_ifd_list.push_back(i);
+ }
  }
- }
 
- // Assume that the image has only one main (high resolution) image.
- if (main_ifd_list.size() != 1)
- {
- throw std::runtime_error(
- fmt::format("This format has more than one image with Subfile Type 0 so cannot be loaded!"));
- }
-
- // Explicitly forbid loading SVS format (#17)
- if (tif->ifd(0)->image_description().rfind("Aperio", 0) == 0)
- {
- throw std::runtime_error(
- fmt::format("cuCIM doesn't support Aperio SVS for now (https://github.com/rapidsai/cucim/issues/17)."));
+ // Assume that the image has only one main (high resolution) image.
+ if (main_ifd_list.size() != 1)
+ {
+ throw std::runtime_error(
+ fmt::format("This format has more than one image with Subfile Type 0 so cannot be loaded!"));
+ }
  }
 
  //