Commit 16777848 authored by Sebastien Jodogne's avatar Sebastien Jodogne
Browse files

New upstream version 0.5

parent 963c233f

.hg_archival.txt

+4 −4
Original line number Diff line number Diff line 
repo: 4a7a53257c7df5a97aea39377b8c9a6e815c9763

node: 84b3128ba48f6f333b4b949794ceac16c3afc820

branch: OrthancWSI-0.4

node: 38d12348a1534ecb5f7c428aa5dd5235b76df338

branch: OrthancWSI-0.5

latesttag: null

latesttagdistance: 102

changessincelatesttag: 103
 
latesttagdistance: 146

changessincelatesttag: 148

AUTHORS

+1 −1
Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ Authors 
  4000 Liege

  Belgium



* Osimis <info@osimis.io>

* Osimis S.A. <info@osimis.io>

  Rue des Chasseurs Ardennais 3

  4031 Liege 

  Belgium

Applications/ApplicationToolbox.cpp

+89 −7
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ 
 * Orthanc - A Lightweight, RESTful DICOM Store

 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics

 * Department, University Hospital of Liege, Belgium

 * Copyright (C) 2017 Osimis, Belgium

 * Copyright (C) 2017-2018 Osimis S.A., Belgium

 *

 * This program is free software: you can redistribute it and/or

 * modify it under the terms of the GNU Affero General Public License
@@ -22,11 +22,13 @@ 
#include "ApplicationToolbox.h"



#include "../Framework/Inputs/OpenSlideLibrary.h"

#include "../Resources/Orthanc/Core/HttpClient.h"

#include "../Resources/Orthanc/Core/Logging.h"

#include "../Resources/Orthanc/Core/MultiThreading/BagOfTasksProcessor.h"

#include "../Resources/Orthanc/Core/SystemToolbox.h"

#include "../Resources/Orthanc/OrthancServer/FromDcmtkBridge.h"



#include <Core/DicomParsing/FromDcmtkBridge.h>

#include <Core/HttpClient.h>

#include <Core/Logging.h>

#include <Core/MultiThreading/BagOfTasksProcessor.h>

#include <Core/OrthancException.h>

#include <Core/SystemToolbox.h>



#include <boost/filesystem.hpp>

#include <boost/lexical_cast.hpp>
@@ -35,6 +37,16 @@ 
#include <cassert>





static const char* OPTION_CA_CERTIFICATES = "ca-certificates";

static const char* OPTION_PASSWORD = "password";

static const char* OPTION_PROXY = "proxy";

static const char* OPTION_TIMEOUT = "timeout";

static const char* OPTION_URL = "orthanc";

static const char* OPTION_USERNAME = "username";

static const char* OPTION_VERIFY_PEERS = "verify-peers";

      





static bool DisplayPerformanceWarning()

{

  (void) DisplayPerformanceWarning;   // Disable warning about unused function
@@ -163,6 +175,11 @@ namespace OrthancWSI 
      bool ok = false;

      boost::cmatch what;



      // Set white as the default color to avoid compiler warnings

      red = 255;

      green = 255;

      blue = 255;



      try

      {

        if (regex_match(color.c_str(), what, pattern))
@@ -200,7 +217,7 @@ namespace OrthancWSI 
        << path << " " << ORTHANC_WSI_VERSION << std::endl

        << "Copyright (C) 2012-2016 Sebastien Jodogne, "

        << "Medical Physics Department, University Hospital of Liege (Belgium)" << std::endl

        << "Copyright (C) 2017 Osimis S.A. (Belgium)" << std::endl

        << "Copyright (C) 2017-2018 Osimis S.A. (Belgium)" << std::endl

        << "Licensing AGPL: GNU AGPL version 3 or later <http://gnu.org/licenses/agpl.html>." << std::endl

        << "This is free software: you are free to change and redistribute it." << std::endl

        << "There is NO WARRANTY, to the extent permitted by law." << std::endl
@@ -229,5 +246,70 @@ namespace OrthancWSI 


      LOG(WARNING) << "Orthanc WSI version: " << version;

    }





  

    void AddRestApiOptions(boost::program_options::options_description& section)

    {

      section.add_options()

        (OPTION_USERNAME, boost::program_options::value<std::string>(),

         "Username for the target Orthanc server")

        (OPTION_PASSWORD, boost::program_options::value<std::string>(),

         "Password for the target Orthanc server")

        (OPTION_PROXY, boost::program_options::value<std::string>(),

         "HTTP proxy to be used")

        (OPTION_TIMEOUT, boost::program_options::value<int>()->default_value(0),

         "HTTP timeout (in seconds, 0 means no timeout)")

        (OPTION_VERIFY_PEERS, boost::program_options::value<bool>()->default_value(true),

         "Enable the verification of the peers during HTTPS requests")

        (OPTION_CA_CERTIFICATES, boost::program_options::value<std::string>()->default_value(""),

         "Path to the CA (certification authority) certificates to validate peers in HTTPS requests")

        ;

    }





    void SetupRestApi(Orthanc::WebServiceParameters& parameters,

                      const boost::program_options::variables_map& options)

    {

      if (options.count(OPTION_URL))

      {

        parameters.SetUrl(options[OPTION_URL].as<std::string>());

      }



      if (options.count(OPTION_USERNAME) &&

          options.count(OPTION_PASSWORD))

      {

        parameters.SetUsername(options[OPTION_USERNAME].as<std::string>());

        parameters.SetPassword(options[OPTION_PASSWORD].as<std::string>());

      }



      if (options.count(OPTION_TIMEOUT))

      {

        int timeout = options[OPTION_TIMEOUT].as<int>();

        if (timeout < 0)

        {

          LOG(ERROR) << "Timeouts cannot be negative: " << timeout;

          throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);

        }

        else

        {

          Orthanc::HttpClient::SetDefaultTimeout(timeout);

        }



        if (options.count(OPTION_PROXY))

        {

          Orthanc::HttpClient::SetDefaultProxy(options[OPTION_PROXY].as<std::string>());

        }

      }



#if ORTHANC_ENABLE_SSL == 1

      if (options.count(OPTION_VERIFY_PEERS) ||

          options.count(OPTION_CA_CERTIFICATES))

      {

        Orthanc::HttpClient::ConfigureSsl(options[OPTION_VERIFY_PEERS].as<bool>(),

                                          options[OPTION_CA_CERTIFICATES].as<std::string>());

      }

#endif

    }

  }

}

Applications/ApplicationToolbox.h

+9 −2
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ 
 * Orthanc - A Lightweight, RESTful DICOM Store

 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics

 * Department, University Hospital of Liege, Belgium

 * Copyright (C) 2017 Osimis, Belgium

 * Copyright (C) 2017-2018 Osimis S.A., Belgium

 *

 * This program is free software: you can redistribute it and/or

 * modify it under the terms of the GNU Affero General Public License
@@ -21,10 +21,12 @@ 


#pragma once



#include "../Resources/Orthanc/Core/MultiThreading/BagOfTasks.h"

#include <Core/MultiThreading/BagOfTasks.h>

#include <Core/WebServiceParameters.h>



#include <string>

#include <stdint.h>

#include <boost/program_options.hpp>



namespace OrthancWSI

{
@@ -45,5 +47,10 @@ namespace OrthancWSI 
    void PrintVersion(const char* path);



    void ShowVersionInLog(const char* path);



    void AddRestApiOptions(boost::program_options::options_description& section);



    void SetupRestApi(Orthanc::WebServiceParameters& parameters,

                      const boost::program_options::variables_map& options);

  }

}

Applications/CMakeLists.txt

+56 −130
Original line number Diff line number Diff line 
cmake_minimum_required(VERSION 2.8)

project(OrthancWSIApplications)



include(${CMAKE_SOURCE_DIR}/../Resources/CMake/Version.cmake)





#####################################################################

## Parameters of the build
@@ -11,31 +13,11 @@ SET(STATIC_BUILD OFF CACHE BOOL "Static build of the third-party libraries (nece 
SET(ALLOW_DOWNLOADS OFF CACHE BOOL "Allow CMake to download packages")

SET(ENABLE_PROFILING OFF CACHE BOOL "Whether to enable the generation of profiling information with gprof")



# Optional components

SET(ENABLE_SSL OFF CACHE BOOL "Include support for SSL")

SET(USE_DCMTK_361 OFF CACHE BOOL "Use forthcoming DCMTK version 3.6.1 in static builds (instead of 3.6.0)")



if (CMAKE_SYSTEM_NAME STREQUAL "Linux")

  set(TMP ON)

else()

  set(TMP OFF)

endif()





# Advanced parameters to fine-tune linking against system libraries

SET(USE_SYSTEM_BOOST ON CACHE BOOL "Use the system version of Boost")

SET(USE_SYSTEM_CURL ON CACHE BOOL "Use the system version of LibCurl")

SET(USE_SYSTEM_DCMTK ON CACHE BOOL "Use the system version of DCMTK")

SET(USE_SYSTEM_JSONCPP ON CACHE BOOL "Use the system version of JsonCpp")

SET(USE_SYSTEM_LIBJPEG ON CACHE BOOL "Use the system version of libjpeg")

SET(USE_SYSTEM_LIBPNG ON CACHE BOOL "Use the system version of libpng")

SET(USE_SYSTEM_LIBTIFF ON CACHE BOOL "Use the system version of libtiff")

SET(USE_SYSTEM_OPENJPEG ON CACHE BOOL "Use the system version of OpenJpeg")

SET(USE_SYSTEM_OPENSSL ON CACHE BOOL "Use the system version of OpenSSL")

SET(USE_SYSTEM_ZLIB ON CACHE BOOL "Use the system version of ZLib")

SET(USE_SYSTEM_ORTHANC_SDK ON CACHE BOOL "Use the system version of the Orthanc plugin SDK")



SET(DCMTK_DICTIONARY_DIR "" CACHE PATH "Directory containing the DCMTK dictionaries \"dicom.dic\" and \"private.dic\" (only when using system version of DCMTK)") 





#####################################################################
@@ -43,56 +25,39 @@ SET(DCMTK_DICTIONARY_DIR "" CACHE PATH "Directory containing the DCMTK dictionar 
#####################################################################



SET(ORTHANC_WSI_DIR ${CMAKE_CURRENT_LIST_DIR}/..)

SET(ORTHANC_ROOT ${ORTHANC_WSI_DIR}/Resources/Orthanc)

SET(USE_OPENJPEG_JP2 ON)

SET(ENABLE_JPEG OFF)           # Disable DCMTK's support for JPEG, that clashes with libtiff

SET(ENABLE_JPEG_LOSSLESS OFF)  # Disable DCMTK's support for JPEG-LS

SET(ENABLE_DCMTK_NETWORK OFF)  # Disable DCMTK's support for DICOM networking



include(${CMAKE_SOURCE_DIR}/../Resources/Orthanc/DownloadOrthancFramework.cmake)



UNSET(STANDALONE_BUILD CACHE)

SET(STANDALONE_BUILD ON)       # Embed DCMTK's dictionaries for static builds

SET(USE_DCMTK_361_PRIVATE_DIC OFF)  # No need for private tags



include(CheckIncludeFiles)

include(CheckIncludeFileCXX)

include(CheckLibraryExists)

include(FindPythonInterp)

include(FindPkgConfig)

include(CheckSymbolExists)



include(${ORTHANC_ROOT}/Resources/CMake/Compiler.cmake)

include(${ORTHANC_ROOT}/Resources/CMake/AutoGeneratedCode.cmake)

include(${ORTHANC_ROOT}/Resources/CMake/DownloadPackage.cmake)



set(ORTHANC_FRAMEWORK_PLUGIN OFF)

include(${ORTHANC_ROOT}/Resources/CMake/OrthancFrameworkParameters.cmake)



SET(ENABLE_CRYPTO_OPTIONS ON)

SET(ENABLE_DCMTK ON)

SET(ENABLE_DCMTK_JPEG OFF)          # Disable DCMTK's support for JPEG, that clashes with libtiff

SET(ENABLE_DCMTK_JPEG_LOSSLESS OFF) # Disable DCMTK's support for JPEG-LS

SET(ENABLE_DCMTK_NETWORKING OFF)    # Disable DCMTK's support for DICOM networking

SET(ENABLE_JPEG ON)

SET(ENABLE_LOCALE ON)               # Enable support for locales (notably in Boost)

SET(ENABLE_PNG ON)

SET(ENABLE_SSL ON)

SET(ENABLE_WEB_CLIENT ON)

SET(ENABLE_ZLIB ON)

SET(HAS_EMBEDDED_RESOURCES ON)



include(${ORTHANC_ROOT}/Resources/CMake/VisualStudioPrecompiledHeaders.cmake)

include(${ORTHANC_ROOT}/Resources/CMake/OrthancFrameworkConfiguration.cmake)

include_directories(${ORTHANC_ROOT})



# Third-party components shipped with Orthanc

include(${ORTHANC_ROOT}/Resources/CMake/DcmtkConfiguration.cmake)

include(${ORTHANC_ROOT}/Resources/CMake/JsonCppConfiguration.cmake)

include(${ORTHANC_ROOT}/Resources/CMake/LibCurlConfiguration.cmake)

include(${ORTHANC_ROOT}/Resources/CMake/LibJpegConfiguration.cmake)

include(${ORTHANC_ROOT}/Resources/CMake/LibPngConfiguration.cmake)

include(${ORTHANC_ROOT}/Resources/CMake/ZlibConfiguration.cmake)



# Include components specific to WSI

include(${ORTHANC_WSI_DIR}/Resources/CMake/Version.cmake)

include(${ORTHANC_WSI_DIR}/Resources/CMake/BoostExtendedConfiguration.cmake)

include(${ORTHANC_WSI_DIR}/Resources/CMake/OpenJpegConfiguration.cmake)

include(${ORTHANC_WSI_DIR}/Resources/CMake/LibTiffConfiguration.cmake)



add_definitions(

  -DORTHANC_BUILD_UNIT_TESTS=0  # For FromDcmtkBridge

  -DORTHANC_ENABLE_BASE64=1

  -DORTHANC_ENABLE_CURL=1

  -DORTHANC_ENABLE_DCMTK=1

  -DORTHANC_ENABLE_JPEG=0       # Disable DCMTK's support for JPEG

  -DORTHANC_ENABLE_LOGGING=1

  -DORTHANC_ENABLE_LOGGING_PLUGIN=0

  -DORTHANC_ENABLE_LUA=0        # For FromDcmtkBridge

  -DORTHANC_ENABLE_MD5=0

  -DORTHANC_ENABLE_PKCS11=0

  -DORTHANC_ENABLE_PLUGINS=1    # To enable class Orthanc::SharedLibrary

  -DORTHANC_ENABLE_PUGIXML=0

  -DORTHANC_SANDBOXED=0

  -DHAS_ORTHANC_EXCEPTION=1

  )





#####################################################################
@@ -100,7 +65,7 @@ add_definitions( 
#####################################################################



if (STATIC_BUILD OR NOT USE_SYSTEM_ORTHANC_SDK)

  include_directories(${ORTHANC_ROOT}/Sdk-1.0.0)

  include_directories(${CMAKE_SOURCE_DIR}/../Resources/Orthanc/Sdk-1.0.0)

else ()

  CHECK_INCLUDE_FILE_CXX(orthanc/OrthancCPlugin.h HAVE_ORTHANC_H)

  if (NOT HAVE_ORTHANC_H)
@@ -109,19 +74,6 @@ else () 
endif()





#####################################################################

## Configure optional third-party components

#####################################################################



if (ENABLE_SSL)

  set(ENABLE_PKCS11 OFF)

  add_definitions(-DORTHANC_ENABLE_SSL=1)

  include(${ORTHANC_ROOT}/Resources/CMake/OpenSslConfiguration.cmake)

else()

  add_definitions(-DORTHANC_ENABLE_SSL=0)

endif()





#####################################################################

## Create the list of the source files that depend upon the

## precompiled headers
@@ -158,49 +110,6 @@ set(ORTHANC_WSI_SOURCES 
  ${ORTHANC_WSI_DIR}/Framework/Outputs/TruncatedPyramidWriter.cpp

  )



set(ORTHANC_CORE_SOURCES

  ${ORTHANC_ROOT}/Core/ChunkedBuffer.cpp

  ${ORTHANC_ROOT}/Core/DicomFormat/DicomArray.cpp

  ${ORTHANC_ROOT}/Core/DicomFormat/DicomMap.cpp

  ${ORTHANC_ROOT}/Core/DicomFormat/DicomTag.cpp

  ${ORTHANC_ROOT}/Core/DicomFormat/DicomValue.cpp

  ${ORTHANC_ROOT}/Core/Enumerations.cpp

  ${ORTHANC_ROOT}/Core/HttpClient.cpp

  ${ORTHANC_ROOT}/Core/Images/IImageWriter.cpp

  ${ORTHANC_ROOT}/Core/Images/Image.cpp

  ${ORTHANC_ROOT}/Core/Images/ImageAccessor.cpp

  ${ORTHANC_ROOT}/Core/Images/ImageBuffer.cpp

  ${ORTHANC_ROOT}/Core/Images/ImageProcessing.cpp

  ${ORTHANC_ROOT}/Core/Images/JpegErrorManager.cpp

  ${ORTHANC_ROOT}/Core/Images/JpegReader.cpp

  ${ORTHANC_ROOT}/Core/Images/JpegWriter.cpp

  ${ORTHANC_ROOT}/Core/Images/PngReader.cpp

  ${ORTHANC_ROOT}/Core/Images/PngWriter.cpp

  ${ORTHANC_ROOT}/Core/Logging.cpp

  ${ORTHANC_ROOT}/Core/MultiThreading/BagOfTasksProcessor.cpp

  ${ORTHANC_ROOT}/Core/MultiThreading/SharedMessageQueue.cpp

  ${ORTHANC_ROOT}/Core/SystemToolbox.cpp

  ${ORTHANC_ROOT}/Core/TemporaryFile.cpp

  ${ORTHANC_ROOT}/Core/Toolbox.cpp

  ${ORTHANC_ROOT}/Core/WebServiceParameters.cpp

  ${ORTHANC_ROOT}/OrthancServer/FromDcmtkBridge.cpp

  ${ORTHANC_ROOT}/OrthancServer/ServerEnumerations.cpp

  ${ORTHANC_ROOT}/OrthancServer/ToDcmtkBridge.cpp



  ${ORTHANC_ROOT}/Plugins/Engine/SharedLibrary.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/OrthancPluginCppWrapper.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/DicomDatasetReader.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/DicomPath.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/DicomTag.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/FullOrthancDataset.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/IOrthancConnection.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/OrthancHttpConnection.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/OrthancPluginConnection.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/SimplifiedOrthancDataset.cpp



  ${ORTHANC_ROOT}/Resources/ThirdParty/base64/base64.cpp

  )



EmbedResources(

  ${DCMTK_DICTIONARIES}

  BRIGHTFIELD_OPTICAL_PATH  ${ORTHANC_WSI_DIR}/Resources/BrightfieldOpticalPath.json
@@ -208,6 +117,10 @@ EmbedResources( 
  SRGB_ICC_PROFILE          ${ORTHANC_WSI_DIR}/Resources/sRGB.icc

  )



add_definitions(

  -DHAS_ORTHANC_EXCEPTION=1

  )





#####################################################################

## Setup precompiled headers for Microsoft Visual Studio
@@ -216,11 +129,18 @@ EmbedResources( 
if (MSVC)

  add_definitions(-DORTHANC_USE_PRECOMPILED_HEADERS=1)



  set(TMP

    ${ORTHANC_CORE_SOURCES_INTERNAL}

    ${ORTHANC_DICOM_SOURCES_INTERNAL}

    )

  

  ADD_VISUAL_STUDIO_PRECOMPILED_HEADERS(

    "PrecompiledHeaders.h" "${ORTHANC_WSI_DIR}/Resources/Orthanc/Core/PrecompiledHeaders.cpp" ORTHANC_CORE_SOURCES)

    "PrecompiledHeaders.h" "${ORTHANC_ROOT}/Core/PrecompiledHeaders.cpp"

    TMP ORTHANC_CORE_PCH)



  ADD_VISUAL_STUDIO_PRECOMPILED_HEADERS(

    "PrecompiledHeadersWSI.h" "${ORTHANC_WSI_DIR}/Framework/PrecompiledHeadersWSI.cpp" ORTHANC_WSI_SOURCES)

    "PrecompiledHeadersWSI.h" "${ORTHANC_WSI_DIR}/Framework/PrecompiledHeadersWSI.cpp"

    ORTHANC_WSI_SOURCES ORTHANC_WSI_PCH)



  source_group(ThirdParty\\OrthancCore FILES ${ORTHANC_CORE_SOURCES})

endif()
@@ -231,23 +151,29 @@ endif() 
#####################################################################



add_library(OrthancWSIFramework STATIC

  ${ORTHANC_CORE_SOURCES}

  ${ORTHANC_CORE_PCH}

  ${ORTHANC_CORE_SOURCES_INTERNAL}

  ${ORTHANC_CORE_SOURCES_DEPENDENCIES}

  ${ORTHANC_DICOM_SOURCES_INTERNAL}

  ${ORTHANC_DICOM_SOURCES_DEPENDENCIES}

  ${ORTHANC_WSI_PCH}

  ${ORTHANC_WSI_SOURCES}

  ${AUTOGENERATED_SOURCES}

  ${BOOST_EXTENDED_SOURCES}



  ${ORTHANC_ROOT}/Plugins/Samples/Common/OrthancPluginCppWrapper.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/DicomDatasetReader.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/DicomPath.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/DicomTag.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/FullOrthancDataset.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/IOrthancConnection.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/OrthancHttpConnection.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/OrthancPluginConnection.cpp

  ${ORTHANC_ROOT}/Plugins/Samples/Common/SimplifiedOrthancDataset.cpp



  # Mandatory components

  ${BOOST_SOURCES}

  ${CURL_SOURCES}

  ${DCMTK_SOURCES}

  ${JSONCPP_SOURCES}

  ${LIBJPEG_SOURCES}

  ${LIBPNG_SOURCES}

  ${LIBTIFF_SOURCES}

  ${OPENJPEG_SOURCES}

  ${ZLIB_SOURCES}



  # Optional components

  ${OPENSSL_SOURCES}

  )