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annotate Applications/CMakeLists.txt @ 289:5f783bf882fe

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add warning about anisotropic pixel spacing
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 13 Jul 2023 12:49:50 +0200
parents cf20f8417eaa
children 053af6d76f2a
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1 # Orthanc - A Lightweight, RESTful DICOM Store
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2 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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3 # Department, University Hospital of Liege, Belgium
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4 # Copyright (C) 2017-2023 Osimis S.A., Belgium
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5 # Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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6 #
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7 # This program is free software: you can redistribute it and/or
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8 # modify it under the terms of the GNU Affero General Public License
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9 # as published by the Free Software Foundation, either version 3 of
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10 # the License, or (at your option) any later version.
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11 #
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12 # This program is distributed in the hope that it will be useful, but
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13 # WITHOUT ANY WARRANTY; without even the implied warranty of
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14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 # Affero General Public License for more details.
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16 #
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17 # You should have received a copy of the GNU Affero General Public License
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18 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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19
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20
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21 cmake_minimum_required(VERSION 2.8)
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22 project(OrthancWSIApplications)
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23
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24 include(${CMAKE_SOURCE_DIR}/../Resources/CMake/Version.cmake)
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25
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26
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27 #####################################################################
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28 ## Parameters of the build
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29 #####################################################################
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30
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31 # Generic parameters
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32 SET(STATIC_BUILD OFF CACHE BOOL "Static build of the third-party libraries (necessary for Windows)")
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33 SET(ALLOW_DOWNLOADS OFF CACHE BOOL "Allow CMake to download packages")
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34 SET(ENABLE_PROFILING OFF CACHE BOOL "Whether to enable the generation of profiling information with gprof")
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35
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36 # Advanced parameters to fine-tune linking against system libraries
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37 SET(USE_SYSTEM_LIBTIFF ON CACHE BOOL "Use the system version of libtiff")
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38 SET(USE_SYSTEM_OPENJPEG ON CACHE BOOL "Use the system version of OpenJpeg")
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39
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40
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41
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42 #####################################################################
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43 ## Configure mandatory third-party components
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44 #####################################################################
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45
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46 SET(ORTHANC_WSI_DIR ${CMAKE_CURRENT_LIST_DIR}/..)
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47 SET(USE_OPENJPEG_JP2 ON)
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48
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49 include(${CMAKE_SOURCE_DIR}/../Resources/Orthanc/CMake/DownloadOrthancFramework.cmake)
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50
197
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51 if (ORTHANC_FRAMEWORK_SOURCE STREQUAL "system")
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52 if (ORTHANC_FRAMEWORK_USE_SHARED)
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53 include(FindBoost)
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54 find_package(Boost COMPONENTS filesystem program_options regex system thread)
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55
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56 if (NOT Boost_FOUND)
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57 message(FATAL_ERROR "Unable to locate Boost on this system")
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58 endif()
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59
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60 include(FindDCMTK)
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61 link_libraries(${Boost_LIBRARIES} ${DCMTK_LIBRARIES} jsoncpp)
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62 endif()
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63
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64 link_libraries(${ORTHANC_FRAMEWORK_LIBRARIES})
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65
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66 else()
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67 include_directories(${ORTHANC_FRAMEWORK_ROOT})
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69 UNSET(STANDALONE_BUILD CACHE)
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70 SET(STANDALONE_BUILD ON) # Embed DCMTK's dictionaries for static builds
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71
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72 include(${ORTHANC_FRAMEWORK_ROOT}/../Resources/CMake/OrthancFrameworkParameters.cmake)
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74 SET(ENABLE_CRYPTO_OPTIONS ON)
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75 SET(ENABLE_DCMTK ON)
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76 SET(ENABLE_DCMTK_JPEG OFF) # Disable DCMTK's support for JPEG, that clashes with libtiff
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77 SET(ENABLE_DCMTK_JPEG_LOSSLESS OFF) # Disable DCMTK's support for JPEG-LS
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78 SET(ENABLE_DCMTK_NETWORKING OFF) # Disable DCMTK's support for DICOM networking
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79 SET(ENABLE_JPEG ON)
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80 SET(ENABLE_LOCALE ON) # Enable support for locales (notably in Boost)
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81 SET(ENABLE_OPENSSL_ENGINES ON)
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82 SET(ENABLE_PNG ON)
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83 SET(ENABLE_SSL ON)
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84 SET(ENABLE_WEB_CLIENT ON)
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85 SET(ENABLE_ZLIB ON)
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86
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87 include(${ORTHANC_FRAMEWORK_ROOT}/../Resources/CMake/VisualStudioPrecompiledHeaders.cmake)
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88 include(${ORTHANC_FRAMEWORK_ROOT}/../Resources/CMake/OrthancFrameworkConfiguration.cmake)
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89
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90 include(${ORTHANC_WSI_DIR}/Resources/CMake/BoostExtendedConfiguration.cmake)
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91 endif()
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93
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94 # Include components specific to WSI
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95 include(${ORTHANC_WSI_DIR}/Resources/CMake/OpenJpegConfiguration.cmake)
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96 include(${ORTHANC_WSI_DIR}/Resources/CMake/LibTiffConfiguration.cmake)
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97
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99
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100 #####################################################################
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101 ## Create the list of the source files that depend upon the
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102 ## precompiled headers
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103 #####################################################################
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104
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105 set(ORTHANC_WSI_SOURCES
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106 ${ORTHANC_WSI_DIR}/Framework/Algorithms/PyramidReader.cpp
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107 ${ORTHANC_WSI_DIR}/Framework/Algorithms/ReconstructPyramidCommand.cpp
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108 ${ORTHANC_WSI_DIR}/Framework/Algorithms/TranscodeTileCommand.cpp
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109 ${ORTHANC_WSI_DIR}/Framework/DicomToolbox.cpp
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110 ${ORTHANC_WSI_DIR}/Framework/DicomizerParameters.cpp
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111 ${ORTHANC_WSI_DIR}/Framework/Enumerations.cpp
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112 ${ORTHANC_WSI_DIR}/Framework/ImageToolbox.cpp
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113 ${ORTHANC_WSI_DIR}/Framework/ImagedVolumeParameters.cpp
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114 ${ORTHANC_WSI_DIR}/Framework/Inputs/CytomineImage.cpp
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115 ${ORTHANC_WSI_DIR}/Framework/Inputs/DecodedTiledPyramid.cpp
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116 ${ORTHANC_WSI_DIR}/Framework/Inputs/DicomPyramid.cpp
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117 ${ORTHANC_WSI_DIR}/Framework/Inputs/DicomPyramidInstance.cpp
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118 ${ORTHANC_WSI_DIR}/Framework/Inputs/DicomPyramidLevel.cpp
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119 ${ORTHANC_WSI_DIR}/Framework/Inputs/HierarchicalTiff.cpp
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120 ${ORTHANC_WSI_DIR}/Framework/Inputs/OpenSlideLibrary.cpp
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121 ${ORTHANC_WSI_DIR}/Framework/Inputs/OpenSlidePyramid.cpp
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122 ${ORTHANC_WSI_DIR}/Framework/Inputs/PyramidWithRawTiles.cpp
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123 ${ORTHANC_WSI_DIR}/Framework/Inputs/SingleLevelDecodedPyramid.cpp
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124 ${ORTHANC_WSI_DIR}/Framework/Inputs/TiledPyramidStatistics.cpp
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125 ${ORTHANC_WSI_DIR}/Framework/Jpeg2000Reader.cpp
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126 ${ORTHANC_WSI_DIR}/Framework/Jpeg2000Writer.cpp
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127 ${ORTHANC_WSI_DIR}/Framework/MultiThreading/BagOfTasksProcessor.cpp
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128 ${ORTHANC_WSI_DIR}/Framework/Outputs/DicomPyramidWriter.cpp
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129 ${ORTHANC_WSI_DIR}/Framework/Outputs/HierarchicalTiffWriter.cpp
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130 ${ORTHANC_WSI_DIR}/Framework/Outputs/InMemoryTiledImage.cpp
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131 ${ORTHANC_WSI_DIR}/Framework/Outputs/MultiframeDicomWriter.cpp
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132 ${ORTHANC_WSI_DIR}/Framework/Outputs/PyramidWriterBase.cpp
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133 ${ORTHANC_WSI_DIR}/Framework/Outputs/TruncatedPyramidWriter.cpp
151
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134 ${ORTHANC_WSI_DIR}/Framework/Targets/FolderTarget.cpp
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135 ${ORTHANC_WSI_DIR}/Framework/Targets/OrthancTarget.cpp
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136 )
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137
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138 EmbedResources(
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139 ${DCMTK_DICTIONARIES}
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140 BRIGHTFIELD_OPTICAL_PATH ${ORTHANC_WSI_DIR}/Resources/BrightfieldOpticalPath.json
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141 SAMPLE_DATASET ${ORTHANC_WSI_DIR}/Resources/SampleDataset.json
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142 SRGB_ICC_PROFILE ${ORTHANC_WSI_DIR}/Resources/sRGB.icc
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143 )
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144
141
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145 add_definitions(
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146 -DORTHANC_ENABLE_LOGGING_PLUGIN=0
141
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147 )
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148
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149
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150 #####################################################################
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151 ## Setup precompiled headers for Microsoft Visual Studio
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152 #####################################################################
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153
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154 if (MSVC)
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155 add_definitions(-DORTHANC_USE_PRECOMPILED_HEADERS=1)
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156
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157 set(TMP
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158 ${ORTHANC_CORE_SOURCES_INTERNAL}
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159 ${ORTHANC_DICOM_SOURCES_INTERNAL}
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160 )
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161
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162 ADD_VISUAL_STUDIO_PRECOMPILED_HEADERS(
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163 "PrecompiledHeaders.h" "${ORTHANC_FRAMEWORK_ROOT}/PrecompiledHeaders.cpp"
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164 TMP ORTHANC_CORE_PCH)
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165
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166 ADD_VISUAL_STUDIO_PRECOMPILED_HEADERS(
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167 "PrecompiledHeadersWSI.h" "${ORTHANC_WSI_DIR}/Framework/PrecompiledHeadersWSI.cpp"
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168 ORTHANC_WSI_SOURCES ORTHANC_WSI_PCH)
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169
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170 source_group(ThirdParty\\OrthancCore FILES ${ORTHANC_CORE_SOURCES})
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171 endif()
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172
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173
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174 #####################################################################
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175 ## Create the static library containing the framework
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176 #####################################################################
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177
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178 add_library(OrthancWSIFramework STATIC
192
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179 ${ORTHANC_WSI_PCH}
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180 ${ORTHANC_WSI_SOURCES}
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181
118
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182 ${ORTHANC_CORE_PCH}
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183 ${ORTHANC_CORE_SOURCES_INTERNAL}
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184 ${ORTHANC_CORE_SOURCES_DEPENDENCIES}
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185 ${ORTHANC_DICOM_SOURCES_INTERNAL}
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186 ${ORTHANC_DICOM_SOURCES_DEPENDENCIES}
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187 ${AUTOGENERATED_SOURCES}
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188 ${BOOST_EXTENDED_SOURCES}
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189
196
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190 ${ORTHANC_WSI_DIR}/Resources/Orthanc/Stone/DicomDatasetReader.cpp
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191 ${ORTHANC_WSI_DIR}/Resources/Orthanc/Stone/FullOrthancDataset.cpp
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192 ${ORTHANC_WSI_DIR}/Resources/Orthanc/Stone/IOrthancConnection.cpp
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193 ${ORTHANC_WSI_DIR}/Resources/Orthanc/Stone/OrthancHttpConnection.cpp
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194
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195 # Mandatory components
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196 ${LIBTIFF_SOURCES}
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197 ${OPENJPEG_SOURCES}
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198 )
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199
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200 DefineSourceBasenameForTarget(OrthancWSIFramework)
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201
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202
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203 #####################################################################
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204 ## Build the WSI DICOM-izer
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205 #####################################################################
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206
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207 # Create the Windows resources, if need be
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208 if (${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
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209 execute_process(
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210 COMMAND
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211 ${PYTHON_EXECUTABLE} ${ORTHANC_FRAMEWORK_ROOT}/../Resources/WindowsResources.py
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212 ${ORTHANC_WSI_VERSION} OrthancWSIDicomizer OrthancWSIDicomizer.exe "Companion tool to Orthanc for whole-slide imaging"
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213 ERROR_VARIABLE Failure
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214 OUTPUT_FILE ${AUTOGENERATED_DIR}/OrthancWSIDicomizer.rc
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215 )
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216
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217 if (Failure)
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218 message(FATAL_ERROR "Error while computing the version information: ${Failure}")
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219 endif()
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220
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221 set(DICOMIZER_RESOURCES ${AUTOGENERATED_DIR}/OrthancWSIDicomizer.rc)
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222 endif()
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223
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224
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225 add_executable(OrthancWSIDicomizer
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226 Dicomizer.cpp
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227 ApplicationToolbox.cpp
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228 ${DICOMIZER_RESOURCES}
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229 )
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230
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231 DefineSourceBasenameForTarget(OrthancWSIDicomizer)
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232
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233 target_link_libraries(OrthancWSIDicomizer OrthancWSIFramework ${DCMTK_LIBRARIES})
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234
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235 install(
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236 TARGETS OrthancWSIDicomizer
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237 RUNTIME DESTINATION bin
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238 )
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239
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240
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241 #####################################################################
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242 ## Build the DICOM-to-TIFF conversion tool
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243 #####################################################################
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244
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245 # Create the Windows resources, if need be
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246 if (${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
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247 execute_process(
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248 COMMAND
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249 ${PYTHON_EXECUTABLE} ${ORTHANC_FRAMEWORK_ROOT}/../Resources/WindowsResources.py
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250 ${ORTHANC_WSI_VERSION} OrthancWSIDicomToTiff OrthancWSIDicomToTiff.exe "Companion tool to Orthanc for whole-slide imaging"
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251 ERROR_VARIABLE Failure
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252 OUTPUT_FILE ${AUTOGENERATED_DIR}/OrthancWSIDicomToTiff.rc
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253 )
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254
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255 if (Failure)
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256 message(FATAL_ERROR "Error while computing the version information: ${Failure}")
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257 endif()
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258
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259 set(DICOM_TO_TIFF_RESOURCES ${AUTOGENERATED_DIR}/OrthancWSIDicomToTiff.rc)
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260 endif()
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261
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262
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263 add_executable(OrthancWSIDicomToTiff
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264 DicomToTiff.cpp
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265 ApplicationToolbox.cpp
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266 ${DICOM_TO_TIFF_RESOURCES}
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267 )
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268
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269 DefineSourceBasenameForTarget(OrthancWSIDicomToTiff)
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270
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271 target_link_libraries(OrthancWSIDicomToTiff OrthancWSIFramework ${DCMTK_LIBRARIES})
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272
6
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273 install(
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274 TARGETS OrthancWSIDicomToTiff
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275 RUNTIME DESTINATION bin
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276 )
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277
0
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278
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279 #####################################################################
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280 ## Generate the documentation if Doxygen is present
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281 #####################################################################
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282
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283 find_package(Doxygen)
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284 if (DOXYGEN_FOUND)
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285 configure_file(
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286 ${ORTHANC_WSI_DIR}/Resources/OrthancWSI.doxygen
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287 ${CMAKE_CURRENT_BINARY_DIR}/OrthancWSI.doxygen
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288 @ONLY)
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289
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290 add_custom_target(doc
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291 ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/OrthancWSI.doxygen
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292 COMMENT "Generating documentation with Doxygen" VERBATIM
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293 )
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294 else()
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295 message("Doxygen not found. The documentation will not be built.")
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296 endif()