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changeset 2082:a6d5373e471c deep-learning

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integration mainline->deep-learning
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 11 Oct 2023 17:10:45 +0200
parents fdb012c86a75 (current diff) 3ef91da06636 (diff)
children 9f7604d6b581
files Applications/Samples/WebAssembly/CMakeLists.txt Applications/StoneWebViewer/WebAssembly/CMakeLists.txt Applications/StoneWebViewer/WebAssembly/StoneModule/CMakeLists.txt OrthancStone/Resources/WebAssemblyUnitTests/CMakeLists.txt
diffstat 13 files changed, 84 insertions(+), 43 deletions(-) [+]
line wrap: on
line diff
--- a/Applications/Samples/Common/RtViewerApp.h	Wed Jul 12 21:21:11 2023 +0200
+++ b/Applications/Samples/Common/RtViewerApp.h	Wed Oct 11 17:10:45 2023 +0200
@@ -36,7 +36,6 @@
 #include "../../../OrthancStone/Sources/Volumes/DicomVolumeImage.h"
 
 #include <boost/enable_shared_from_this.hpp>
-#include <boost/thread.hpp>
 #include <boost/noncopyable.hpp>
 
 #if ORTHANC_ENABLE_SDL
--- a/Applications/Samples/Common/RtViewerView.h	Wed Jul 12 21:21:11 2023 +0200
+++ b/Applications/Samples/Common/RtViewerView.h	Wed Oct 11 17:10:45 2023 +0200
@@ -36,7 +36,6 @@
 #include "../../../OrthancStone/Sources/Volumes/VolumeSceneLayerSource.h"
 
 #include <boost/enable_shared_from_this.hpp>
-#include <boost/thread.hpp>
 #include <boost/noncopyable.hpp>
 
 namespace OrthancStone
--- a/Applications/Samples/RtViewerPlugin/CMakeLists.txt	Wed Jul 12 21:21:11 2023 +0200
+++ b/Applications/Samples/RtViewerPlugin/CMakeLists.txt	Wed Oct 11 17:10:45 2023 +0200
@@ -119,6 +119,8 @@
   ${ORTHANC_CORE_SOURCES}
   )
 
+DefineSourceBasenameForTarget(RtViewerPlugin)
+
 set_target_properties(RtViewerPlugin PROPERTIES 
   VERSION ${ORTHANC_PLUGIN_VERSION} 
   SOVERSION ${ORTHANC_PLUGIN_VERSION})
--- a/Applications/Samples/WebAssembly/CMakeLists.txt	Wed Jul 12 21:21:11 2023 +0200
+++ b/Applications/Samples/WebAssembly/CMakeLists.txt	Wed Oct 11 17:10:45 2023 +0200
@@ -46,7 +46,7 @@
 endif()
 
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ENVIRONMENT=web")
-set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s EXTRA_EXPORTED_RUNTIME_METHODS='[\"ccall\", \"cwrap\"]'")
+set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s EXPORTED_RUNTIME_METHODS='[\"ccall\", \"cwrap\"]'")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ERROR_ON_UNDEFINED_SYMBOLS=1")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ALLOW_MEMORY_GROWTH=1 -s TOTAL_MEMORY=268435456")  # 256MB + resize
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s DISABLE_DEPRECATED_FIND_EVENT_TARGET_BEHAVIOR=1")
@@ -66,6 +66,7 @@
 SET(ENABLE_DCMTK OFF)  # Not necessary
 SET(ENABLE_GOOGLE_TEST OFF)
 SET(ENABLE_LOCALE ON)  # Necessary for text rendering
+SET(ENABLE_MODULE_JOBS OFF)
 SET(ORTHANC_SANDBOXED ON)
 
 # this will set up the build system for Stone of Orthanc and will
@@ -91,6 +92,9 @@
   ${AUTOGENERATED_SOURCES}
   )
 
+DefineSourceBasenameForTarget(OrthancStone)
+
+
 ################################################################################
 
 # Define the WASM module
@@ -106,6 +110,8 @@
   ../Common/RtViewerView.h
   )
 
+DefineSourceBasenameForTarget(RtViewerWasm)
+
 set_target_properties(RtViewerWasm
   PROPERTIES
   COMPILE_FLAGS "${WASM_FLAGS}"
@@ -146,6 +152,8 @@
   SingleFrameViewer/SingleFrameViewer.cpp
   )
 
+DefineSourceBasenameForTarget(SingleFrameViewerWasm)
+
 set_target_properties(SingleFrameViewerWasm
   PROPERTIES
   COMPILE_FLAGS "${WASM_FLAGS}"
@@ -174,3 +182,10 @@
   ${CMAKE_CURRENT_BINARY_DIR}/SingleFrameViewerWasm.wasm
   DESTINATION ${ORTHANC_STONE_INSTALL_PREFIX}/SingleFrameViewer/
   )
+
+
+# Boost::Math begs for -std=c++14 since Boost 1.82.0
+set_property(TARGET OrthancStone PROPERTY CXX_STANDARD 14)
+set_property(TARGET RtViewerWasm PROPERTY CXX_STANDARD 14)
+set_property(TARGET SingleFrameViewerWasm PROPERTY CXX_STANDARD 14)
+
--- a/Applications/StoneWebViewer/NEWS	Wed Jul 12 21:21:11 2023 +0200
+++ b/Applications/StoneWebViewer/NEWS	Wed Oct 11 17:10:45 2023 +0200
@@ -7,7 +7,8 @@
 -----------
 
 * Prevent dragging series before they are ready
-* Open the first loaded series only if it is part of a selected study.
+* Open the first loaded series only if it is part of a selected study
+* Fix compatibility with Emscripten 3.1.47
 
 
 Version 2.5 (2022-12-05)
--- a/Applications/StoneWebViewer/Plugin/CMakeLists.txt	Wed Jul 12 21:21:11 2023 +0200
+++ b/Applications/StoneWebViewer/Plugin/CMakeLists.txt	Wed Oct 11 17:10:45 2023 +0200
@@ -132,6 +132,8 @@
   ${ORTHANC_CORE_SOURCES}
   )
 
+DefineSourceBasenameForTarget(StoneWebViewer)
+
 set_target_properties(StoneWebViewer PROPERTIES 
   VERSION ${STONE_WEB_VIEWER_VERSION} 
   SOVERSION ${STONE_WEB_VIEWER_VERSION})
--- a/Applications/StoneWebViewer/WebAssembly/CMakeLists.txt	Wed Jul 12 21:21:11 2023 +0200
+++ b/Applications/StoneWebViewer/WebAssembly/CMakeLists.txt	Wed Oct 11 17:10:45 2023 +0200
@@ -38,7 +38,7 @@
 endif()
 
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ENVIRONMENT=web")
-set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s EXTRA_EXPORTED_RUNTIME_METHODS='[\"ccall\", \"cwrap\"]'")
+set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s EXPORTED_RUNTIME_METHODS='[\"ccall\", \"cwrap\"]'")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ERROR_ON_UNDEFINED_SYMBOLS=1")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ALLOW_MEMORY_GROWTH=1 -s TOTAL_MEMORY=268435456")  # 256MB + resize
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s DISABLE_DEPRECATED_FIND_EVENT_TARGET_BEHAVIOR=1")
@@ -60,6 +60,7 @@
 SET(ENABLE_DCMTK_TRANSCODING OFF)
 SET(ENABLE_GOOGLE_TEST OFF)
 SET(ENABLE_LOCALE ON)  # Necessary for text rendering
+SET(ENABLE_MODULE_JOBS OFF)
 SET(ENABLE_PUGIXML ON) # Necessary for OsiriX annotations
 SET(ORTHANC_SANDBOXED ON)
 SET(ENABLE_PROTOBUF ON)           # Necessary for deep learning
@@ -99,7 +100,7 @@
 # Create the wrapper to call C++ from JavaScript
 # ---------------------------------------------------------------
 
-set(LIBCLANG "libclang-4.0.so.1" CACHE PATH "Version of clang to generate the code model")
+set(LIBCLANG "libclang.so.1" CACHE PATH "Version of clang to generate the code model")
 set(STONE_WRAPPER ${CMAKE_CURRENT_BINARY_DIR}/stone.js)
 
 include(FindPython3 OPTIONAL RESULT_VARIABLE HAS_CMAKE_PYTHON3)
@@ -153,6 +154,9 @@
   StoneWebViewer.cpp
   )
 
+# Boost::Math begs for -std=c++14 since Boost 1.82.0
+set_property(TARGET StoneWebViewer PROPERTY CXX_STANDARD 14)
+
 DefineSourceBasenameForTarget(StoneWebViewer)
 
 set_target_properties(StoneWebViewer
--- a/Applications/StoneWebViewer/WebAssembly/StoneModule/CMakeLists.txt	Wed Jul 12 21:21:11 2023 +0200
+++ b/Applications/StoneWebViewer/WebAssembly/StoneModule/CMakeLists.txt	Wed Oct 11 17:10:45 2023 +0200
@@ -47,7 +47,7 @@
 endif()
 
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ENVIRONMENT=web")
-set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s EXTRA_EXPORTED_RUNTIME_METHODS='[\"ccall\", \"cwrap\"]'")
+set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s EXPORTED_RUNTIME_METHODS='[\"ccall\", \"cwrap\"]'")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ERROR_ON_UNDEFINED_SYMBOLS=1")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ASSERTIONS=1 -s DISABLE_EXCEPTION_CATCHING=0")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ALLOW_MEMORY_GROWTH=1 -s TOTAL_MEMORY=268435456")  # 256MB + resize
@@ -124,6 +124,9 @@
   LINK_FLAGS "${WASM_LINKER_FLAGS}"
   )
 
+# Boost::Math begs for -std=c++14 since Boost 1.82.0
+set_property(TARGET StoneWebViewer PROPERTY CXX_STANDARD 14)
+
 # Make sure to have the wrapper generated
 add_dependencies(StoneWebViewer StoneWrapper)
 
--- a/CITATION.cff	Wed Jul 12 21:21:11 2023 +0200
+++ b/CITATION.cff	Wed Oct 11 17:10:45 2023 +0200
@@ -12,8 +12,8 @@
     orcid: 'https://orcid.org/0000-0001-6685-7398'
 identifiers:
   - type: url
-    value: 'http://hdl.handle.net/2078.1/257268'
-    description: Rendering Medical Images using WebAssembly
+    value: 'http://hdl.handle.net/2078.1/277125'
+    description: On the Use of WebAssembly for Rendering and Segmenting Medical Images
 repository-code: 'https://hg.orthanc-server.com/orthanc-stone/'
 url: 'https://www.orthanc-server.com/'
 license: AGPL-3.0-or-later
--- a/OrthancStone/Resources/Orthanc/CMake/DownloadOrthancFramework.cmake	Wed Jul 12 21:21:11 2023 +0200
+++ b/OrthancStone/Resources/Orthanc/CMake/DownloadOrthancFramework.cmake	Wed Oct 11 17:10:45 2023 +0200
@@ -181,6 +181,9 @@
       elseif (ORTHANC_FRAMEWORK_VERSION STREQUAL "b2e08d83e21d")
         # WSI 1.1 (framework pre-1.10.0), to remove "-std=c++11"
         set(ORTHANC_FRAMEWORK_MD5 "2eaa073cbb4b44ffba199ad93393b2b1")
+      elseif (ORTHANC_FRAMEWORK_VERSION STREQUAL "daf4807631c5")
+        # DICOMweb 1.15 (framework pre-1.12.2)
+        set(ORTHANC_FRAMEWORK_MD5 "c644aff2817306b3207c98c92e43f35f")
       endif()
     endif()
   endif()
--- a/OrthancStone/Resources/WebAssemblyUnitTests/CMakeLists.txt	Wed Jul 12 21:21:11 2023 +0200
+++ b/OrthancStone/Resources/WebAssemblyUnitTests/CMakeLists.txt	Wed Oct 11 17:10:45 2023 +0200
@@ -40,7 +40,7 @@
 endif()
 
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ENVIRONMENT=web")
-set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s EXTRA_EXPORTED_RUNTIME_METHODS='[\"ccall\", \"cwrap\"]'")
+set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s EXPORTED_RUNTIME_METHODS='[\"ccall\", \"cwrap\"]'")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ERROR_ON_UNDEFINED_SYMBOLS=1")
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s ALLOW_MEMORY_GROWTH=1 -s TOTAL_MEMORY=268435456")  # 256MB + resize
 set(WASM_LINKER_FLAGS "${WASM_LINKER_FLAGS} -s DISABLE_DEPRECATED_FIND_EVENT_TARGET_BEHAVIOR=1")
@@ -58,11 +58,12 @@
 
 include(${CMAKE_SOURCE_DIR}/../CMake/OrthancStoneWebAssemblyParameters.cmake)
 
-SET(ENABLE_DCMTK ON)  # Necessary for the tests of the Orthanc framework
-SET(ENABLE_PUGIXML ON)  # Necessary for the tests of the Orthanc framework
+SET(ENABLE_DCMTK ON)   # Necessary for the tests of the Orthanc framework
 SET(ENABLE_GOOGLE_TEST OFF)
 SET(ENABLE_LOCALE ON)  # Necessary for text rendering
-SET(ENABLE_LUA ON)  # Necessary for the tests of the Orthanc framework
+SET(ENABLE_LUA ON)     # Necessary for the tests of the Orthanc framework
+SET(ENABLE_MODULE_JOBS OFF)
+SET(ENABLE_PUGIXML ON) # Necessary for the tests of the Orthanc framework
 SET(ORTHANC_SANDBOXED ON)
 
 # this will set up the build system for Stone of Orthanc and will
@@ -121,6 +122,9 @@
   ${ORTHANC_STONE_SOURCES}
   )
 
+# Boost::Math begs for -std=c++14 since Boost 1.82.0
+set_property(TARGET UnitTests PROPERTY CXX_STANDARD 14)
+
 DefineSourceBasenameForTarget(UnitTests)
 
   
--- a/README	Wed Jul 12 21:21:11 2023 +0200
+++ b/README	Wed Oct 11 17:10:45 2023 +0200
@@ -111,6 +111,14 @@
   take place (for instance, multi-threading).
 
 
+Contributing
+------------
+
+Instructions for contributing to the Orthanc project are included in
+the Orthanc Book:
+https://book.orthanc-server.com/developers/repositories.html
+
+
 Licensing
 ---------
 
@@ -127,28 +135,28 @@
 Stone of Orthanc using the two following BibTeX entries:
 
 @Article{Jodogne2018,
-  author="Jodogne, S{\'e}bastien",
-  title="The {O}rthanc Ecosystem for Medical Imaging",
-  journal="Journal of Digital Imaging",
-  year="2018",
-  month="Jun",
-  day="01",
-  volume="31",
-  number="3",
-  pages="341--352",
-  issn="1618-727X",
-  doi="10.1007/s10278-018-0082-y",
-  url="https://doi.org/10.1007/s10278-018-0082-y"
+ title = {The Orthanc Ecosystem for Medical Imaging},
+ author = {Jodogne, S{\'e}bastien},
+ journal = {Journal of Digital Imaging},
+ volume = {31},
+ number = {3},
+ pages = {341-352},
+ issn = {1618-727X},
+ doi = {10.1007/s10278-018-0082-y},
+ publisher = {Springer Science and Business Media LLC},
+ year = {2018},
+ url = {https://doi.org/10.1007/s10278-018-0082-y}
 }
 
-@inproceedings{Jodogne2022,
-  author="Jodogne, S{\'e}bastien",
-  title="Rendering Medical Images using {WebAssembly}",
-  booktitle="Proc. of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies",
-  year="2022",
-  month="Feb",
-  volume="2",
-  pages="43--51",
-  doi="10.5220/0000156300003123",
-  url="http://hdl.handle.net/2078.1/257268"
+@Article{Jodogne2023,
+ title = {On the Use of WebAssembly for Rendering and Segmenting Medical Images},
+ author = {Jodogne, S{\'e}bastien},
+ journal = {Biomedical Engineering Systems and Technologies},
+ volume = {1814},
+ number = {1},
+ pages = {393-414},
+ issn = {1865-0937},
+ doi = {10.1007/978-3-031-38854-5_20},
+ year = {2023},
+ url = {http://hdl.handle.net/2078.1/277125}
 }
--- a/RenderingPlugin/Resources/Orthanc/Plugins/OrthancPluginCppWrapper.cpp	Wed Jul 12 21:21:11 2023 +0200
+++ b/RenderingPlugin/Resources/Orthanc/Plugins/OrthancPluginCppWrapper.cpp	Wed Oct 11 17:10:45 2023 +0200
@@ -1670,15 +1670,16 @@
       return true;
     }
 
+#ifdef _MSC_VER
+#define ORTHANC_SCANF sscanf_s
+#else
+#define ORTHANC_SCANF sscanf
+#endif
+
     // Parse the version
-    int aa, bb, cc;
-    if (
-#ifdef _MSC_VER
-      sscanf_s
-#else
-      sscanf
-#endif
-      (version, "%4d.%4d.%4d", &aa, &bb, &cc) != 3 ||
+    int aa, bb, cc = 0;
+    if ((ORTHANC_SCANF(version, "%4d.%4d.%4d", &aa, &bb, &cc) != 3 &&
+         ORTHANC_SCANF(version, "%4d.%4d", &aa, &bb) != 2) ||
       aa < 0 ||
       bb < 0 ||
       cc < 0)