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big refactoring to support sparse tiling
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 24 Nov 2016 17:48:24 +0100
parents 175d06fa292e
children 35468714a38e
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1 cmake_minimum_required(VERSION 2.8)
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2 project(OrthancWSIApplications)
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5 #####################################################################
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6 ## Parameters of the build
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7 #####################################################################
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8
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9 # Generic parameters
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10 SET(STATIC_BUILD OFF CACHE BOOL "Static build of the third-party libraries (necessary for Windows)")
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11 SET(ALLOW_DOWNLOADS OFF CACHE BOOL "Allow CMake to download packages")
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12 SET(ENABLE_PROFILING OFF CACHE BOOL "Whether to enable the generation of profiling information with gprof")
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13
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14 # Optional components
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15 SET(ENABLE_SSL OFF CACHE BOOL "Include support for SSL")
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16 SET(USE_DCMTK_361 OFF CACHE BOOL "Use forthcoming DCMTK version 3.6.1 in static builds (instead of 3.6.0)")
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17
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18 if (CMAKE_SYSTEM_NAME STREQUAL "Linux")
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19 set(TMP ON)
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20 else()
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21 set(TMP OFF)
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22 endif()
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23
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25 # Advanced parameters to fine-tune linking against system libraries
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26 SET(USE_SYSTEM_BOOST ON CACHE BOOL "Use the system version of Boost")
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27 SET(USE_SYSTEM_CURL ON CACHE BOOL "Use the system version of LibCurl")
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28 SET(USE_SYSTEM_DCMTK ON CACHE BOOL "Use the system version of DCMTK")
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29 SET(USE_SYSTEM_JSONCPP ON CACHE BOOL "Use the system version of JsonCpp")
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30 SET(USE_SYSTEM_LIBJPEG ON CACHE BOOL "Use the system version of libjpeg")
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31 SET(USE_SYSTEM_LIBPNG ON CACHE BOOL "Use the system version of libpng")
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32 SET(USE_SYSTEM_LIBTIFF ON CACHE BOOL "Use the system version of libtiff")
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33 SET(USE_SYSTEM_OPENJPEG ON CACHE BOOL "Use the system version of OpenJpeg")
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34 SET(USE_SYSTEM_OPENSSL ON CACHE BOOL "Use the system version of OpenSSL")
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35 SET(USE_SYSTEM_ZLIB ON CACHE BOOL "Use the system version of ZLib")
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36
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37 SET(DCMTK_DICTIONARY_DIR "" CACHE PATH "Directory containing the DCMTK dictionaries \"dicom.dic\" and \"private.dic\" (only when using system version of DCMTK)")
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39
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40 #####################################################################
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41 ## Configure mandatory third-party components
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42 #####################################################################
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43
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44 SET(ORTHANC_WSI_DIR ${CMAKE_CURRENT_LIST_DIR}/..)
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45 SET(ORTHANC_ROOT ${ORTHANC_WSI_DIR}/Framework/Orthanc)
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46 SET(USE_OPENJPEG_JP2 ON)
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47 SET(ENABLE_JPEG OFF) # Disable DCMTK's support for JPEG, that clashes with libtiff
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48 SET(ENABLE_JPEG_LOSSLESS OFF) # Disable DCMTK's support for JPEG-LS
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49 SET(ENABLE_DCMTK_NETWORK OFF) # Disable DCMTK's support for DICOM networking
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50 SET(STANDALONE_BUILD ON) # Embed DCMTK's dictionaries for static builds
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51 SET(USE_DCMTK_361_PRIVATE_DIC OFF) # No need for private tags
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53 include(CheckIncludeFiles)
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54 include(CheckIncludeFileCXX)
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55 include(CheckLibraryExists)
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56 include(FindPythonInterp)
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57 include(FindPkgConfig)
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58 include(CheckSymbolExists)
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59
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60 include(${ORTHANC_ROOT}/Resources/CMake/Compiler.cmake)
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61 include(${ORTHANC_ROOT}/Resources/CMake/AutoGeneratedCode.cmake)
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62 include(${ORTHANC_ROOT}/Resources/CMake/DownloadPackage.cmake)
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63 include(${ORTHANC_ROOT}/Resources/CMake/VisualStudioPrecompiledHeaders.cmake)
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64
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65 # Third-party components shipped with Orthanc
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66 include(${ORTHANC_ROOT}/Resources/CMake/DcmtkConfiguration.cmake)
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67 include(${ORTHANC_ROOT}/Resources/CMake/JsonCppConfiguration.cmake)
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68 include(${ORTHANC_ROOT}/Resources/CMake/LibCurlConfiguration.cmake)
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69 include(${ORTHANC_ROOT}/Resources/CMake/LibJpegConfiguration.cmake)
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70 include(${ORTHANC_ROOT}/Resources/CMake/LibPngConfiguration.cmake)
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71 include(${ORTHANC_ROOT}/Resources/CMake/ZlibConfiguration.cmake)
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72
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73 # Include components specific to WSI
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74 include(${ORTHANC_WSI_DIR}/Resources/CMake/Version.cmake)
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75 include(${ORTHANC_WSI_DIR}/Resources/CMake/BoostExtendedConfiguration.cmake)
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76 include(${ORTHANC_WSI_DIR}/Resources/CMake/OpenJpegConfiguration.cmake)
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77 include(${ORTHANC_WSI_DIR}/Resources/CMake/LibTiffConfiguration.cmake)
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78
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79 add_definitions(
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80 -DORTHANC_ENABLE_BASE64=1
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81 -DORTHANC_ENABLE_CURL=1
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82 -DORTHANC_ENABLE_DCMTK=1
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83 -DORTHANC_ENABLE_LOGGING=1
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84 -DORTHANC_ENABLE_MD5=0
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85 -DORTHANC_ENABLE_JPEG=0 # Disable DCMTK's support for JPEG
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86 -DORTHANC_ENABLE_PKCS11=0
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87 -DORTHANC_ENABLE_PLUGINS=1 # To enable class Orthanc::SharedLibrary
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88 -DORTHANC_ENABLE_PUGIXML=0
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89 -DORTHANC_SANDBOXED=0
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90 )
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91
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92
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93 #####################################################################
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94 ## Configure optional third-party components
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95 #####################################################################
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96
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97 if (ENABLE_SSL)
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98 set(ENABLE_PKCS11 OFF)
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99 add_definitions(-DORTHANC_ENABLE_SSL=1)
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100 include(${ORTHANC_ROOT}/Resources/CMake/OpenSslConfiguration.cmake)
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101 else()
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102 add_definitions(-DORTHANC_ENABLE_SSL=0)
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103 endif()
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104
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105
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106 #####################################################################
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107 ## Create the list of the source files that depend upon the
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108 ## precompiled headers
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109 #####################################################################
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110
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111 set(ORTHANC_WSI_SOURCES
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112 #${ORTHANC_WSI_DIR}/Framework/Messaging/PluginOrthancConnection.cpp
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113 ${ORTHANC_WSI_DIR}/Framework/Algorithms/PyramidReader.cpp
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114 ${ORTHANC_WSI_DIR}/Framework/Algorithms/ReconstructPyramidCommand.cpp
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115 ${ORTHANC_WSI_DIR}/Framework/Algorithms/TranscodeTileCommand.cpp
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116 ${ORTHANC_WSI_DIR}/Framework/DicomToolbox.cpp
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117 ${ORTHANC_WSI_DIR}/Framework/DicomizerParameters.cpp
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118 ${ORTHANC_WSI_DIR}/Framework/Enumerations.cpp
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119 ${ORTHANC_WSI_DIR}/Framework/ImageToolbox.cpp
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120 ${ORTHANC_WSI_DIR}/Framework/ImagedVolumeParameters.cpp
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121 ${ORTHANC_WSI_DIR}/Framework/Inputs/DecodedTiledPyramid.cpp
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122 ${ORTHANC_WSI_DIR}/Framework/Inputs/DicomPyramid.cpp
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123 ${ORTHANC_WSI_DIR}/Framework/Inputs/DicomPyramidInstance.cpp
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124 ${ORTHANC_WSI_DIR}/Framework/Inputs/DicomPyramidLevel.cpp
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125 ${ORTHANC_WSI_DIR}/Framework/Inputs/HierarchicalTiff.cpp
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126 ${ORTHANC_WSI_DIR}/Framework/Inputs/OpenSlideLibrary.cpp
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127 ${ORTHANC_WSI_DIR}/Framework/Inputs/OpenSlidePyramid.cpp
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128 ${ORTHANC_WSI_DIR}/Framework/Inputs/PyramidWithRawTiles.cpp
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129 ${ORTHANC_WSI_DIR}/Framework/Inputs/SingleLevelDecodedPyramid.cpp
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130 ${ORTHANC_WSI_DIR}/Framework/Inputs/TiledPyramidStatistics.cpp
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131 ${ORTHANC_WSI_DIR}/Framework/Jpeg2000Reader.cpp
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132 ${ORTHANC_WSI_DIR}/Framework/Jpeg2000Writer.cpp
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133 ${ORTHANC_WSI_DIR}/Framework/Messaging/CurlOrthancConnection.cpp
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134 ${ORTHANC_WSI_DIR}/Framework/Messaging/FolderTarget.cpp
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135 ${ORTHANC_WSI_DIR}/Framework/Messaging/IOrthancConnection.cpp
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136 ${ORTHANC_WSI_DIR}/Framework/Messaging/OrthancConnectionBase.cpp
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137 ${ORTHANC_WSI_DIR}/Framework/Messaging/OrthancTarget.cpp
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138 ${ORTHANC_WSI_DIR}/Framework/Outputs/DicomPyramidWriter.cpp
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139 ${ORTHANC_WSI_DIR}/Framework/Outputs/HierarchicalTiffWriter.cpp
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140 ${ORTHANC_WSI_DIR}/Framework/Outputs/InMemoryTiledImage.cpp
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141 ${ORTHANC_WSI_DIR}/Framework/Outputs/MultiframeDicomWriter.cpp
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142 ${ORTHANC_WSI_DIR}/Framework/Outputs/PyramidWriterBase.cpp
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143 ${ORTHANC_WSI_DIR}/Framework/Outputs/TruncatedPyramidWriter.cpp
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144 )
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145
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146 set(ORTHANC_CORE_SOURCES
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147 ${ORTHANC_ROOT}/Core/ChunkedBuffer.cpp
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148 ${ORTHANC_ROOT}/Core/DicomFormat/DicomArray.cpp
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149 ${ORTHANC_ROOT}/Core/DicomFormat/DicomMap.cpp
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150 ${ORTHANC_ROOT}/Core/DicomFormat/DicomTag.cpp
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151 ${ORTHANC_ROOT}/Core/DicomFormat/DicomValue.cpp
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152 ${ORTHANC_ROOT}/Core/Enumerations.cpp
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153 ${ORTHANC_ROOT}/Core/HttpClient.cpp
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154 ${ORTHANC_ROOT}/Core/Images/IImageWriter.cpp
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155 ${ORTHANC_ROOT}/Core/Images/Image.cpp
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156 ${ORTHANC_ROOT}/Core/Images/ImageAccessor.cpp
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157 ${ORTHANC_ROOT}/Core/Images/ImageBuffer.cpp
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158 ${ORTHANC_ROOT}/Core/Images/ImageProcessing.cpp
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159 ${ORTHANC_ROOT}/Core/Images/JpegErrorManager.cpp
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160 ${ORTHANC_ROOT}/Core/Images/JpegReader.cpp
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161 ${ORTHANC_ROOT}/Core/Images/JpegWriter.cpp
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162 ${ORTHANC_ROOT}/Core/Images/PngReader.cpp
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163 ${ORTHANC_ROOT}/Core/Images/PngWriter.cpp
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164 ${ORTHANC_ROOT}/Core/Logging.cpp
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165 ${ORTHANC_ROOT}/Core/MultiThreading/BagOfTasksProcessor.cpp
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166 ${ORTHANC_ROOT}/Core/MultiThreading/SharedMessageQueue.cpp
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167 ${ORTHANC_ROOT}/Core/SystemToolbox.cpp
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168 ${ORTHANC_ROOT}/Core/TemporaryFile.cpp
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169 ${ORTHANC_ROOT}/Core/Toolbox.cpp
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170 ${ORTHANC_ROOT}/Core/WebServiceParameters.cpp
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171 ${ORTHANC_ROOT}/OrthancServer/FromDcmtkBridge.cpp
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172 ${ORTHANC_ROOT}/OrthancServer/ServerEnumerations.cpp
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173 ${ORTHANC_ROOT}/OrthancServer/ToDcmtkBridge.cpp
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174 ${ORTHANC_ROOT}/Plugins/Engine/SharedLibrary.cpp
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175 ${ORTHANC_ROOT}/Resources/ThirdParty/base64/base64.cpp
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176 )
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177
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178 EmbedResources(
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179 ${DCMTK_DICTIONARIES}
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180 BRIGHTFIELD_OPTICAL_PATH ${ORTHANC_WSI_DIR}/Resources/BrightfieldOpticalPath.json
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181 SAMPLE_DATASET ${ORTHANC_WSI_DIR}/Resources/SampleDataset.json
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182 SRGB_ICC_PROFILE ${ORTHANC_WSI_DIR}/Resources/sRGB.icc
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183 )
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184
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185
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186 #####################################################################
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187 ## Setup precompiled headers for Microsoft Visual Studio
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188 #####################################################################
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189
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190 if (MSVC)
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191 add_definitions(-DORTHANC_USE_PRECOMPILED_HEADERS=1)
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192
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193 ADD_VISUAL_STUDIO_PRECOMPILED_HEADERS(
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194 "PrecompiledHeaders.h" "${ORTHANC_WSI_DIR}/Framework/Orthanc/Core/PrecompiledHeaders.cpp" ORTHANC_CORE_SOURCES)
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195
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196 ADD_VISUAL_STUDIO_PRECOMPILED_HEADERS(
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197 "PrecompiledHeadersWSI.h" "${ORTHANC_WSI_DIR}/Framework/PrecompiledHeadersWSI.cpp" ORTHANC_WSI_SOURCES)
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198
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199 source_group(ThirdParty\\OrthancCore FILES ${ORTHANC_CORE_SOURCES})
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200 endif()
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201
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202
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203 #####################################################################
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204 ## Create the static library containing the framework
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205 #####################################################################
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206
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207 add_library(OrthancWSIFramework STATIC
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208 ${ORTHANC_CORE_SOURCES}
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209 ${ORTHANC_WSI_SOURCES}
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210 ${AUTOGENERATED_SOURCES}
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211
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212 # Mandatory components
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213 ${BOOST_SOURCES}
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214 ${CURL_SOURCES}
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215 ${DCMTK_SOURCES}
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216 ${JSONCPP_SOURCES}
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217 ${LIBJPEG_SOURCES}
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218 ${LIBPNG_SOURCES}
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219 ${LIBTIFF_SOURCES}
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220 ${OPENJPEG_SOURCES}
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221 ${ZLIB_SOURCES}
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222
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223 # Optional components
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224 ${OPENSSL_SOURCES}
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225 )
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226
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227
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228 #####################################################################
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229 ## Build the WSI DICOM-izer
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230 #####################################################################
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231
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232 # Create the Windows resources, if need be
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233 if (${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
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234 execute_process(
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235 COMMAND
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236 ${PYTHON_EXECUTABLE} ${ORTHANC_ROOT}/Resources/WindowsResources.py
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237 ${ORTHANC_WSI_VERSION} OrthancWSIDicomizer OrthancWSIDicomizer.exe "Companion tool to Orthanc for whole-slide imaging"
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238 ERROR_VARIABLE Failure
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239 OUTPUT_FILE ${AUTOGENERATED_DIR}/OrthancWSIDicomizer.rc
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240 )
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241
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242 if (Failure)
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243 message(FATAL_ERROR "Error while computing the version information: ${Failure}")
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244 endif()
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245
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246 set(DICOMIZER_RESOURCES ${AUTOGENERATED_DIR}/OrthancWSIDicomizer.rc)
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247 endif()
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248
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249
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250 add_executable(OrthancWSIDicomizer
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251 Dicomizer.cpp
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252 ApplicationToolbox.cpp
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253 ${DICOMIZER_RESOURCES}
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254 )
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255
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256 target_link_libraries(OrthancWSIDicomizer OrthancWSIFramework ${DCMTK_LIBRARIES})
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257
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258 install(
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259 TARGETS OrthancWSIDicomizer
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260 RUNTIME DESTINATION bin
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261 )
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262
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263
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264 #####################################################################
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265 ## Build the DICOM-to-TIFF conversion tool
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266 #####################################################################
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267
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268 # Create the Windows resources, if need be
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269 if (${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
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270 execute_process(
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271 COMMAND
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272 ${PYTHON_EXECUTABLE} ${ORTHANC_ROOT}/Resources/WindowsResources.py
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273 ${ORTHANC_WSI_VERSION} OrthancWSIDicomToTiff OrthancWSIDicomToTiff.exe "Companion tool to Orthanc for whole-slide imaging"
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274 ERROR_VARIABLE Failure
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275 OUTPUT_FILE ${AUTOGENERATED_DIR}/OrthancWSIDicomToTiff.rc
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276 )
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277
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278 if (Failure)
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279 message(FATAL_ERROR "Error while computing the version information: ${Failure}")
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280 endif()
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281
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282 set(DICOM_TO_TIFF_RESOURCES ${AUTOGENERATED_DIR}/OrthancWSIDicomToTiff.rc)
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283 endif()
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284
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285
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286 add_executable(OrthancWSIDicomToTiff
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287 DicomToTiff.cpp
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288 ApplicationToolbox.cpp
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289 ${DICOM_TO_TIFF_RESOURCES}
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290 )
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291
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292 target_link_libraries(OrthancWSIDicomToTiff OrthancWSIFramework ${DCMTK_LIBRARIES})
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293
6
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294 install(
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295 TARGETS OrthancWSIDicomToTiff
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296 RUNTIME DESTINATION bin
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297 )
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298
0
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299
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300 #####################################################################
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301 ## Generate the documentation if Doxygen is present
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302 #####################################################################
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303
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304 find_package(Doxygen)
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305 if (DOXYGEN_FOUND)
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306 configure_file(
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307 ${ORTHANC_WSI_DIR}/Resources/OrthancWSI.doxygen
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308 ${CMAKE_CURRENT_BINARY_DIR}/OrthancWSI.doxygen
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309 @ONLY)
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310
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311 add_custom_target(doc
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312 ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/OrthancWSI.doxygen
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313 COMMENT "Generating documentation with Doxygen" VERBATIM
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314 )
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315 else()
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316 message("Doxygen not found. The documentation will not be built.")
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317 endif()
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318
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319
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320
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321
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322
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323
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324
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325
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326
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327
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328
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329
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330
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331
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332 add_executable(Hello
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333 Hello.cpp
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334 ApplicationToolbox.cpp
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335 )
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336
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337 target_link_libraries(Hello OrthancWSIFramework ${DCMTK_LIBRARIES})