[med-svn] [Git][med-team/fast][master] Refresh and update patches to reflect changes to new upstream release
Shayan Doust
gitlab at salsa.debian.org
Tue May 26 15:09:54 BST 2020
Shayan Doust pushed to branch master at Debian Med / fast
Commits:
717d5675 by Shayan Doust at 2020-05-26T15:07:44+01:00
Refresh and update patches to reflect changes to new upstream release
Compilation not tested yet. Ideally, update to a new upstream release (3.0.0), fix licensing and do something about the big compressed test data as FTP masters suggested and then retry for a new upload
- - - - -
8 changed files:
- debian/patches/fix_source_openigtlink.patch
- debian/patches/modify_assets_location.patch
- debian/patches/modify_libs_and_output.patch
- debian/patches/opencl_header.patch
- debian/patches/prevent_cmake_downloading.patch
- debian/patches/remove_ubuntu_fonts_from_src.patch
- debian/patches/remove_unneeded_installs.patch
- debian/patches/set_cmake_options.patch
Changes:
=====================================
debian/patches/fix_source_openigtlink.patch
=====================================
@@ -4,10 +4,8 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-08-08
---
-Index: fast/source/FAST/Streamers/OpenIGTLinkStreamer.cpp
-===================================================================
---- fast.orig/source/FAST/Streamers/OpenIGTLinkStreamer.cpp 2019-08-16 00:53:40.537030532 +0100
-+++ fast/source/FAST/Streamers/OpenIGTLinkStreamer.cpp 2019-08-16 00:53:40.525030468 +0100
+--- fast.orig/source/FAST/Streamers/OpenIGTLinkStreamer.cpp
++++ fast/source/FAST/Streamers/OpenIGTLinkStreamer.cpp
@@ -1,14 +1,14 @@
#include "OpenIGTLinkStreamer.hpp"
#include "FAST/Data/Image.hpp"
@@ -31,10 +29,8 @@ Index: fast/source/FAST/Streamers/OpenIGTLinkStreamer.cpp
#include <chrono>
namespace fast {
-Index: fast/source/FAST/Streamers/Tests/DummyIGTLServer.cpp
-===================================================================
---- fast.orig/source/FAST/Streamers/Tests/DummyIGTLServer.cpp 2019-08-16 00:53:40.537030532 +0100
-+++ fast/source/FAST/Streamers/Tests/DummyIGTLServer.cpp 2019-08-16 00:53:40.525030468 +0100
+--- fast.orig/source/FAST/Streamers/Tests/DummyIGTLServer.cpp
++++ fast/source/FAST/Streamers/Tests/DummyIGTLServer.cpp
@@ -1,9 +1,9 @@
#include "DummyIGTLServer.hpp"
@@ -49,10 +45,8 @@ Index: fast/source/FAST/Streamers/Tests/DummyIGTLServer.cpp
#include "FAST/Tests/DummyObjects.hpp"
#include "FAST/Data/Image.hpp"
-Index: fast/source/FAST/Tools/OpenIGTLinkServer/GUI.cpp
-===================================================================
---- fast.orig/source/FAST/Tools/OpenIGTLinkServer/GUI.cpp 2019-08-16 00:53:40.537030532 +0100
-+++ fast/source/FAST/Tools/OpenIGTLinkServer/GUI.cpp 2019-08-16 00:53:40.529030489 +0100
+--- fast.orig/source/FAST/Tools/OpenIGTLinkServer/GUI.cpp
++++ fast/source/FAST/Tools/OpenIGTLinkServer/GUI.cpp
@@ -7,9 +7,9 @@
#include <QMessageBox>
#include <QListWidget>
@@ -73,10 +67,8 @@ Index: fast/source/FAST/Tools/OpenIGTLinkServer/GUI.cpp
-}
\ No newline at end of file
+}
-Index: fast/source/FAST/Tools/OpenIGTLinkServer/GUI.hpp
-===================================================================
---- fast.orig/source/FAST/Tools/OpenIGTLinkServer/GUI.hpp 2019-08-16 00:53:40.537030532 +0100
-+++ fast/source/FAST/Tools/OpenIGTLinkServer/GUI.hpp 2019-08-16 00:54:32.789310223 +0100
+--- fast.orig/source/FAST/Tools/OpenIGTLinkServer/GUI.hpp
++++ fast/source/FAST/Tools/OpenIGTLinkServer/GUI.hpp
@@ -1,8 +1,8 @@
#ifndef FAST_OPENIGTLINKSERVER_GUI_HPP_
#define FAST_OPENIGTLINKSERVER_GUI_HPP_
@@ -88,10 +80,8 @@ Index: fast/source/FAST/Tools/OpenIGTLinkServer/GUI.hpp
#include <thread>
-Index: fast/source/FAST/Tools/OpenIGTLinkServer/main.cpp
-===================================================================
---- fast.orig/source/FAST/Tools/OpenIGTLinkServer/main.cpp 2019-08-16 00:53:40.537030532 +0100
-+++ fast/source/FAST/Tools/OpenIGTLinkServer/main.cpp 2019-08-16 00:54:48.541394547 +0100
+--- fast.orig/source/FAST/Tools/OpenIGTLinkServer/main.cpp
++++ fast/source/FAST/Tools/OpenIGTLinkServer/main.cpp
@@ -1,5 +1,5 @@
#include <FAST/Tools/CommandLineParser.hpp>
-#include "FAST/Streamers/Tests/DummyIGTLServer.hpp"
=====================================
debian/patches/modify_assets_location.patch
=====================================
@@ -4,10 +4,8 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-09-01
---
-Index: fast/source/FAST/Config.cpp
-===================================================================
---- fast.orig/source/FAST/Config.cpp 2019-09-22 22:03:18.701184884 +0100
-+++ fast/source/FAST/Config.cpp 2019-09-22 22:03:18.701184884 +0100
+--- fast.orig/source/FAST/Config.cpp
++++ fast/source/FAST/Config.cpp
@@ -75,10 +75,10 @@
return;
@@ -32,5 +30,5 @@ Index: fast/source/FAST/Config.cpp
- mDocumentationPath = getPath() + "../doc/";
+ mDocumentationPath = getPath() + "../usr/share/fast/assets/";
mPipelinePath = getPath() + "../pipelines/";
- loadConfiguration();
- }
+ #ifdef WIN32
+ mLibraryPath = getPath() + "../bin/";
=====================================
debian/patches/modify_libs_and_output.patch
=====================================
@@ -3,20 +3,18 @@ Description: modify cmake files to use system wide "apt" packaged libs & build s
Author: Shayan Doust <hello at shayandoust.me>
---
-Index: fast/CMakeLists.txt
-===================================================================
---- fast.orig/CMakeLists.txt 2019-09-01 19:24:24.824877063 +0100
-+++ fast/CMakeLists.txt 2019-09-01 19:24:49.669024504 +0100
-@@ -34,7 +34,7 @@
- option(FAST_MODULE_WholeSlideImaging "Build whole slide imaging module" OFF)
- option(FAST_MODULE_Clarius "Build clarius ultrasound module" OFF)
+--- fast.orig/CMakeLists.txt
++++ fast/CMakeLists.txt
+@@ -36,7 +36,7 @@
+ option(FAST_MODULE_Clarius "Build clarius ultrasound module" ON)
+ option(FAST_MODULE_Dicom "Build DICOM module (DCMTK)" ON)
option(FAST_CONTINUOUS_INTEGRATION "Used for continuous integration tests" OFF)
-option(FAST_BUILD_QT5 "Download and build Qt 5.8. Turn this OFF if you want to use pre-built binaries you already have on your machine." ON)
+option(FAST_BUILD_QT5 "Download and build Qt 5.8. Turn this OFF if you want to use pre-built binaries you already have on your machine." OFF)
# Python version
set(FAST_Python_Version "" CACHE STRING "Specify which Python version to build python wrappers with. E.g. 2 or 3")
-@@ -157,10 +157,19 @@
+@@ -159,10 +159,19 @@
#### Create FAST library and executables
add_library(FAST SHARED ${FAST_SOURCE_FILES} ${HEADERS_MOC})
@@ -37,7 +35,7 @@ Index: fast/CMakeLists.txt
include(cmake/OpenMP.cmake)
## Link everything
-@@ -170,6 +179,18 @@
+@@ -173,6 +182,18 @@
qt5_use_modules(FAST Widgets OpenGL) # Add Qt 5 modules
endif()
@@ -56,7 +54,7 @@ Index: fast/CMakeLists.txt
## Build test executable
if(FAST_BUILD_TESTS)
add_executable(testFAST ${FAST_TEST_SOURCE_FILES} source/FAST/Algorithms/CoherentPointDrift/Rigid.cpp source/FAST/Algorithms/CoherentPointDrift/Rigid.hpp source/FAST/Algorithms/CoherentPointDrift/Affine.cpp source/FAST/Algorithms/CoherentPointDrift/Affine.hpp)
-@@ -243,5 +264,8 @@
+@@ -246,5 +267,8 @@
include(cmake/FASTCustomCommands.cmake)
endif(NOT FAST_BUILD_QT5 AND WIN32)
=====================================
debian/patches/opencl_header.patch
=====================================
@@ -4,10 +4,8 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-08-20
---
-Index: fast/source/FAST/Data/Access/MeshOpenCLAccess.hpp
-===================================================================
---- fast.orig/source/FAST/Data/Access/MeshOpenCLAccess.hpp 2019-08-20 01:32:31.328373455 +0100
-+++ fast/source/FAST/Data/Access/MeshOpenCLAccess.hpp 2019-08-20 01:32:31.324373422 +0100
+--- fast.orig/source/FAST/Data/Access/MeshOpenCLAccess.hpp
++++ fast/source/FAST/Data/Access/MeshOpenCLAccess.hpp
@@ -1,7 +1,7 @@
#ifndef MESH_OPENCL_ACCESS_HPP_
#define MESH_OPENCL_ACCESS_HPP_
@@ -24,10 +22,8 @@ Index: fast/source/FAST/Data/Access/MeshOpenCLAccess.hpp
-#endif
\ No newline at end of file
+#endif
-Index: fast/source/FAST/Data/Access/OpenCLBufferAccess.hpp
-===================================================================
---- fast.orig/source/FAST/Data/Access/OpenCLBufferAccess.hpp 2019-08-20 01:32:31.328373455 +0100
-+++ fast/source/FAST/Data/Access/OpenCLBufferAccess.hpp 2019-08-20 01:32:31.324373422 +0100
+--- fast.orig/source/FAST/Data/Access/OpenCLBufferAccess.hpp
++++ fast/source/FAST/Data/Access/OpenCLBufferAccess.hpp
@@ -1,7 +1,7 @@
#ifndef OPENCLBUFFERACCESS_HPP_
#define OPENCLBUFFERACCESS_HPP_
@@ -37,10 +33,8 @@ Index: fast/source/FAST/Data/Access/OpenCLBufferAccess.hpp
#include "FAST/Object.hpp"
-Index: fast/source/FAST/Data/Access/OpenCLImageAccess.hpp
-===================================================================
---- fast.orig/source/FAST/Data/Access/OpenCLImageAccess.hpp 2019-08-20 01:32:31.328373455 +0100
-+++ fast/source/FAST/Data/Access/OpenCLImageAccess.hpp 2019-08-20 01:32:31.324373422 +0100
+--- fast.orig/source/FAST/Data/Access/OpenCLImageAccess.hpp
++++ fast/source/FAST/Data/Access/OpenCLImageAccess.hpp
@@ -1,7 +1,7 @@
#ifndef OPENCLIMAGEACCESS_HPP_
#define OPENCLIMAGEACCESS_HPP_
@@ -50,10 +44,8 @@ Index: fast/source/FAST/Data/Access/OpenCLImageAccess.hpp
#include "Access.hpp"
#include "FAST/Object.hpp"
-Index: fast/source/FAST/Data/DataTypes.hpp
-===================================================================
---- fast.orig/source/FAST/Data/DataTypes.hpp 2019-08-20 01:32:31.328373455 +0100
-+++ fast/source/FAST/Data/DataTypes.hpp 2019-08-20 01:32:31.324373422 +0100
+--- fast.orig/source/FAST/Data/DataTypes.hpp
++++ fast/source/FAST/Data/DataTypes.hpp
@@ -5,7 +5,7 @@
#define _USE_MATH_DEFINES
#include <cmath>
@@ -63,10 +55,8 @@ Index: fast/source/FAST/Data/DataTypes.hpp
#include "FAST/ExecutionDevice.hpp"
#include <iostream>
#include <Eigen/Dense>
-Index: fast/source/FAST/RuntimeMeasurementManager.hpp
-===================================================================
---- fast.orig/source/FAST/RuntimeMeasurementManager.hpp 2019-08-20 01:32:31.328373455 +0100
-+++ fast/source/FAST/RuntimeMeasurementManager.hpp 2019-08-20 01:32:31.324373422 +0100
+--- fast.orig/source/FAST/RuntimeMeasurementManager.hpp
++++ fast/source/FAST/RuntimeMeasurementManager.hpp
@@ -3,7 +3,7 @@
#include <string>
=====================================
debian/patches/prevent_cmake_downloading.patch
=====================================
@@ -4,10 +4,8 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-08-08
---
-Index: fast/cmake/ExternalOpenSlide.cmake
-===================================================================
---- fast.orig/cmake/ExternalOpenSlide.cmake 2019-08-20 22:24:17.938792439 +0100
-+++ fast/cmake/ExternalOpenSlide.cmake 2019-08-20 22:24:17.926792341 +0100
+--- fast.orig/cmake/ExternalOpenSlide.cmake
++++ fast/cmake/ExternalOpenSlide.cmake
@@ -1,17 +1,17 @@
# Download and set up OpenSlide
@@ -39,10 +37,8 @@ Index: fast/cmake/ExternalOpenSlide.cmake
\ No newline at end of file
+#list(APPEND FAST_EXTERNAL_DEPENDENCIES openslide)
+#endif()
-Index: fast/cmake/ExternalZlib.cmake
-===================================================================
---- fast.orig/cmake/ExternalZlib.cmake 2019-08-20 22:24:17.938792439 +0100
-+++ fast/cmake/ExternalZlib.cmake 2019-08-20 22:24:17.926792341 +0100
+--- fast.orig/cmake/ExternalZlib.cmake
++++ fast/cmake/ExternalZlib.cmake
@@ -1,24 +1,24 @@
# Download and set up zlib
@@ -90,12 +86,10 @@ Index: fast/cmake/ExternalZlib.cmake
+#endif(WIN32)
+#list(APPEND LIBRARIES ${ZLIB_LIBRARY})
+#list(APPEND FAST_EXTERNAL_DEPENDENCIES zlib)
-Index: fast/cmake/ExternalOpenIGTLink.cmake
-===================================================================
---- fast.orig/cmake/ExternalOpenIGTLink.cmake 2019-08-20 22:24:17.938792439 +0100
-+++ fast/cmake/ExternalOpenIGTLink.cmake 2019-08-20 22:24:17.926792341 +0100
+--- fast.orig/cmake/ExternalOpenIGTLink.cmake
++++ fast/cmake/ExternalOpenIGTLink.cmake
@@ -1,30 +1,30 @@
- # Download and set up zlib
+ # Download and set up OpenIGTLink
-include(cmake/Externals.cmake)
+#include(cmake/Externals.cmake)
@@ -152,10 +146,8 @@ Index: fast/cmake/ExternalOpenIGTLink.cmake
+#endif()
+#list(APPEND LIBRARIES ${OpenIGTLink_LIBRARY})
+#list(APPEND FAST_EXTERNAL_DEPENDENCIES OpenIGTLink)
-Index: fast/cmake/ExternalFreenect2.cmake
-===================================================================
---- fast.orig/cmake/ExternalFreenect2.cmake 2019-08-20 22:24:17.938792439 +0100
-+++ fast/cmake/ExternalFreenect2.cmake 2019-08-20 22:24:17.926792341 +0100
+--- fast.orig/cmake/ExternalFreenect2.cmake
++++ fast/cmake/ExternalFreenect2.cmake
@@ -1,20 +1,20 @@
# Download and set up libfreenect2
@@ -193,10 +185,8 @@ Index: fast/cmake/ExternalFreenect2.cmake
-list(APPEND FAST_EXTERNAL_DEPENDENCIES freenect2)
+#list(APPEND LIBRARIES libfreenect2${CMAKE_SHARED_LIBRARY_SUFFIX})
+#list(APPEND FAST_EXTERNAL_DEPENDENCIES freenect2)
-Index: fast/cmake/ExternalTensorflow.cmake
-===================================================================
---- fast.orig/cmake/ExternalTensorflow.cmake 2019-08-20 22:24:17.938792439 +0100
-+++ fast/cmake/ExternalTensorflow.cmake 2019-08-20 22:24:17.934792406 +0100
+--- fast.orig/cmake/ExternalTensorflow.cmake
++++ fast/cmake/ExternalTensorflow.cmake
@@ -1,196 +1,196 @@
# Download and set up Tensorflow
@@ -234,20 +224,20 @@ Index: fast/cmake/ExternalTensorflow.cmake
- BUILD_COMMAND
- echo "Building tensorflow with bazel for CPU.." COMMAND
- cd ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/ COMMAND
-- bazel build --config=opt //tensorflow:tensorflow.dll
+- bazel build --config=opt //tensorflow:tensorflow_cc.dll
- INSTALL_COMMAND
- echo "Installing tensorflow binary" COMMAND
-- ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/tensorflow.dll.if.lib ${FAST_EXTERNAL_INSTALL_DIR}/lib/tensorflow_CPU.lib COMMAND
+- ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/tensorflow_cc.dll.if.lib ${FAST_EXTERNAL_INSTALL_DIR}/lib/tensorflow_CPU.lib COMMAND
- ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/external/protobuf_archive/protobuf.lib ${FAST_EXTERNAL_INSTALL_DIR}/lib/protobuf.lib COMMAND
-- ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/tensorflow.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/tensorflow_CPU.dll COMMAND
+- ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/tensorflow_cc.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/tensorflow_cc.dll COMMAND
- echo "Installing tensorflow headers" COMMAND
- ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/tensorflow ${FAST_EXTERNAL_INSTALL_DIR}/include/tensorflow/ COMMAND
- echo "Installing tensorflow generated headers" COMMAND
- ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-genfiles/tensorflow ${FAST_EXTERNAL_INSTALL_DIR}/include/tensorflow/ COMMAND
- echo "Installing tensorflow third party headers" COMMAND
- ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/third_party/ ${FAST_EXTERNAL_INSTALL_DIR}/include/third_party/ COMMAND
-- #echo "Installing protobuf headers" COMMAND
-- #${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-tensorflow_download/external/protobuf_archive/src/google/ ${FAST_EXTERNAL_INSTALL_DIR}/include/google/ COMMAND
+- echo "Installing protobuf headers" COMMAND
+- ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-tensorflow_download/external/protobuf_archive/src/google/ ${FAST_EXTERNAL_INSTALL_DIR}/include/google/ COMMAND
- #echo "Installing nsync headers" COMMAND
- #xcopy ${src} ${dest} /y COMMAND
- echo "Installing absl headers" COMMAND
@@ -426,20 +416,20 @@ Index: fast/cmake/ExternalTensorflow.cmake
+# BUILD_COMMAND
+# echo "Building tensorflow with bazel for CPU.." COMMAND
+# cd ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/ COMMAND
-+# bazel build --config=opt //tensorflow:tensorflow.dll
++# bazel build --config=opt //tensorflow:tensorflow_cc.dll
+# INSTALL_COMMAND
+# echo "Installing tensorflow binary" COMMAND
-+# ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/tensorflow.dll.if.lib ${FAST_EXTERNAL_INSTALL_DIR}/lib/tensorflow_CPU.lib COMMAND
++# ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/tensorflow_cc.dll.if.lib ${FAST_EXTERNAL_INSTALL_DIR}/lib/tensorflow_CPU.lib COMMAND
+# ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/external/protobuf_archive/protobuf.lib ${FAST_EXTERNAL_INSTALL_DIR}/lib/protobuf.lib COMMAND
-+# ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/tensorflow.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/tensorflow_CPU.dll COMMAND
++# ${CMAKE_COMMAND} -E copy ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/tensorflow_cc.dll ${FAST_EXTERNAL_INSTALL_DIR}/bin/tensorflow_cc.dll COMMAND
+# echo "Installing tensorflow headers" COMMAND
+# ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/tensorflow ${FAST_EXTERNAL_INSTALL_DIR}/include/tensorflow/ COMMAND
+# echo "Installing tensorflow generated headers" COMMAND
+# ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-genfiles/tensorflow ${FAST_EXTERNAL_INSTALL_DIR}/include/tensorflow/ COMMAND
+# echo "Installing tensorflow third party headers" COMMAND
+# ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/third_party/ ${FAST_EXTERNAL_INSTALL_DIR}/include/third_party/ COMMAND
-+# #echo "Installing protobuf headers" COMMAND
-+# #${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-tensorflow_download/external/protobuf_archive/src/google/ ${FAST_EXTERNAL_INSTALL_DIR}/include/google/ COMMAND
++# echo "Installing protobuf headers" COMMAND
++# ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-tensorflow_download/external/protobuf_archive/src/google/ ${FAST_EXTERNAL_INSTALL_DIR}/include/google/ COMMAND
+# #echo "Installing nsync headers" COMMAND
+# #xcopy ${src} ${dest} /y COMMAND
+# echo "Installing absl headers" COMMAND
@@ -587,83 +577,8 @@ Index: fast/cmake/ExternalTensorflow.cmake
+# )
+# endif()
+#endif(WIN32)
-Index: fast/cmake/ExternalDCMTK.cmake
-===================================================================
---- fast.orig/cmake/ExternalDCMTK.cmake 2019-08-20 22:24:17.938792439 +0100
-+++ fast/cmake/ExternalDCMTK.cmake 2019-08-20 22:24:17.934792406 +0100
-@@ -1,36 +1,36 @@
- # Download and set up DCMTK
-
--include(cmake/Externals.cmake)
-+#include(cmake/Externals.cmake)
-
--set(MODULES ofstd oflog dcmdata dcmimgle)
-+#set(MODULES ofstd oflog dcmdata dcmimgle)
-
--ExternalProject_Add(dcmtk
-- PREFIX ${FAST_EXTERNAL_BUILD_DIR}/dcmtk
-- BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/dcmtk
-- GIT_REPOSITORY "https://github.com/DCMTK/dcmtk.git"
-- GIT_TAG "DCMTK-3.6.3"
-- CMAKE_ARGS
-- -DCMAKE_MACOSX_RPATH=ON
-- -DBUILD_SHARED_LIBS=ON
-- -DBUILD_APPS=OFF
-- -DDCMTK_WITH_DOXYGEN=OFF
-- -DCMAKE_INSTALL_RPATH:STRING=$ORIGIN/../lib
-- CMAKE_CACHE_ARGS
-- -DDCMTK_MODULES:STRING=${MODULES}
-- -DCMAKE_BUILD_TYPE:STRING=Release
-- -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
-- -DCMAKE_INSTALL_MESSAGE:BOOL=LAZY
-- -DCMAKE_INSTALL_PREFIX:STRING=${FAST_EXTERNAL_INSTALL_DIR}
--)
--if(WIN32)
-- set(DCMTK_LIBRARIES ofstd.lib oflog.lib dcmdata.lib dcmimgle.lib)
--else(WIN32)
-- set(DCMTK_LIBRARIES
-- ${CMAKE_SHARED_LIBRARY_PREFIX}ofstd${CMAKE_SHARED_LIBRARY_SUFFIX}
-- ${CMAKE_SHARED_LIBRARY_PREFIX}oflog${CMAKE_SHARED_LIBRARY_SUFFIX}
-- ${CMAKE_SHARED_LIBRARY_PREFIX}dcmdata${CMAKE_SHARED_LIBRARY_SUFFIX}
-- ${CMAKE_SHARED_LIBRARY_PREFIX}dcmimgle${CMAKE_SHARED_LIBRARY_SUFFIX}
-- )
--endif(WIN32)
--list(APPEND LIBRARIES ${DCMTK_LIBRARIES})
--list(APPEND FAST_EXTERNAL_DEPENDENCIES dcmtk)
-+#ExternalProject_Add(dcmtk
-+# PREFIX ${FAST_EXTERNAL_BUILD_DIR}/dcmtk
-+# BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/dcmtk
-+# GIT_REPOSITORY "https://github.com/DCMTK/dcmtk.git"
-+# GIT_TAG "DCMTK-3.6.3"
-+# CMAKE_ARGS
-+# -DCMAKE_MACOSX_RPATH=ON
-+# -DBUILD_SHARED_LIBS=ON
-+# -DBUILD_APPS=OFF
-+# -DDCMTK_WITH_DOXYGEN=OFF
-+# -DCMAKE_INSTALL_RPATH:STRING=$ORIGIN/../lib
-+# CMAKE_CACHE_ARGS
-+# -DDCMTK_MODULES:STRING=${MODULES}
-+# -DCMAKE_BUILD_TYPE:STRING=Release
-+# -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
-+# -DCMAKE_INSTALL_MESSAGE:BOOL=LAZY
-+# -DCMAKE_INSTALL_PREFIX:STRING=${FAST_EXTERNAL_INSTALL_DIR}
-+#)
-+#if(WIN32)
-+# set(DCMTK_LIBRARIES ofstd.lib oflog.lib dcmdata.lib dcmimgle.lib)
-+#else(WIN32)
-+# set(DCMTK_LIBRARIES
-+# ${CMAKE_SHARED_LIBRARY_PREFIX}ofstd${CMAKE_SHARED_LIBRARY_SUFFIX}
-+# ${CMAKE_SHARED_LIBRARY_PREFIX}oflog${CMAKE_SHARED_LIBRARY_SUFFIX}
-+# ${CMAKE_SHARED_LIBRARY_PREFIX}dcmdata${CMAKE_SHARED_LIBRARY_SUFFIX}
-+# ${CMAKE_SHARED_LIBRARY_PREFIX}dcmimgle${CMAKE_SHARED_LIBRARY_SUFFIX}
-+# )
-+#endif(WIN32)
-+#list(APPEND LIBRARIES ${DCMTK_LIBRARIES})
-+#list(APPEND FAST_EXTERNAL_DEPENDENCIES dcmtk)
-Index: fast/cmake/ExternalEigen.cmake
-===================================================================
---- fast.orig/cmake/ExternalEigen.cmake 2019-08-20 22:24:17.938792439 +0100
-+++ fast/cmake/ExternalEigen.cmake 2019-08-20 22:24:54.467091268 +0100
+--- fast.orig/cmake/ExternalEigen.cmake
++++ fast/cmake/ExternalEigen.cmake
@@ -1,21 +1,21 @@
# Download and set up Eigen
=====================================
debian/patches/remove_ubuntu_fonts_from_src.patch
=====================================
@@ -4,11 +4,9 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-09-22
---
-Index: fast/source/FAST/Visualization/Window.cpp
-===================================================================
---- fast.orig/source/FAST/Visualization/Window.cpp 2019-09-22 23:41:42.852869766 +0100
-+++ fast/source/FAST/Visualization/Window.cpp 2019-09-22 23:41:42.848869719 +0100
-@@ -121,11 +121,11 @@
+--- fast.orig/source/FAST/Visualization/Window.cpp
++++ fast/source/FAST/Visualization/Window.cpp
+@@ -122,11 +122,11 @@
QApplication::setWindowIcon(QIcon((Config::getDocumentationPath() + "images/fast_icon.png").c_str()));
// Add all fonts in fonts folder
=====================================
debian/patches/remove_unneeded_installs.patch
=====================================
@@ -4,11 +4,9 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-08-08
---
-Index: fast/cmake/InstallFAST.cmake
-===================================================================
---- fast.orig/cmake/InstallFAST.cmake 2019-08-11 12:39:38.341225233 +0100
-+++ fast/cmake/InstallFAST.cmake 2019-08-11 12:39:38.337225198 +0100
-@@ -50,9 +50,9 @@
+--- fast.orig/cmake/InstallFAST.cmake
++++ fast/cmake/InstallFAST.cmake
+@@ -49,9 +49,9 @@
endif()
# Install Qt plugins
@@ -21,22 +19,46 @@ Index: fast/cmake/InstallFAST.cmake
# Install qt.conf
install(FILES ${PROJECT_SOURCE_DIR}/cmake/InstallFiles/qt.conf
-@@ -84,10 +84,10 @@
- DESTINATION fast/include/
- FILES_MATCHING PATTERN "*.hpp"
+@@ -65,22 +65,22 @@
)
--install(DIRECTORY ${PROJECT_BINARY_DIR}/include/
-- DESTINATION fast/include/
-- FILES_MATCHING REGEX "/[^.]+$" # Files with no extension
+
+ # Install headers
+-install(DIRECTORY ${FAST_SOURCE_DIR}
+- DESTINATION fast/include/FAST/
+- FILES_MATCHING PATTERN "*.hpp"
+-)
+-install(DIRECTORY ${FAST_SOURCE_DIR}
+- DESTINATION fast/include/FAST/
+- FILES_MATCHING PATTERN "*.h"
+-)
+-install(DIRECTORY ${PROJECT_SOURCE_DIR}/source/CL/
+- DESTINATION fast/include/CL/
+- FILES_MATCHING PATTERN "*.h"
-)
-+#install(DIRECTORY ${PROJECT_BINARY_DIR}/include/
-+# DESTINATION fast/include/
-+# FILES_MATCHING REGEX "/[^.]+$" # Files with no extension
+-install(DIRECTORY ${PROJECT_SOURCE_DIR}/source/CL/
+- DESTINATION fast/include/CL/
+- FILES_MATCHING PATTERN "*.hpp"
+-)
++#install(DIRECTORY ${FAST_SOURCE_DIR}
++# DESTINATION fast/include/FAST/
++# FILES_MATCHING PATTERN "*.hpp"
++#)
++#install(DIRECTORY ${FAST_SOURCE_DIR}
++# DESTINATION fast/include/FAST/
++# FILES_MATCHING PATTERN "*.h"
++#)
++#install(DIRECTORY ${PROJECT_SOURCE_DIR}/source/CL/
++# DESTINATION fast/include/CL/
++# FILES_MATCHING PATTERN "*.h"
++#)
++#install(DIRECTORY ${PROJECT_SOURCE_DIR}/source/CL/
++# DESTINATION fast/include/CL/
++# FILES_MATCHING PATTERN "*.hpp"
+#)
-
-
-@@ -182,36 +182,36 @@
+ # External include files needed
+ set(INCLUDE_FOLDERS
+@@ -218,59 +218,59 @@
# Install license files for depedencies
# Qt5
@@ -94,17 +116,50 @@ Index: fast/cmake/InstallFAST.cmake
+# DESTINATION fast/licenses/semaphore/
+#)
- if(FAST_MODULE_TensorFlow)
- # Tensorflow license
-@@ -220,8 +220,8 @@
- )
- endif()
-
+ # Tensorflow license
+-if(FAST_MODULE_TensorFlow)
+- install(FILES ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/LICENSE
+- DESTINATION fast/licenses/tensorflow/
+- )
+-endif()
+-if(FAST_MODULE_OpenVINO AND NOT WIN32)
+- install(FILES ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/LICENSE
+- DESTINATION fast/licenses/openvino/
+- )
+-endif()
+-
+-if(FAST_MODULE_RealSense)
+- install(FILES
+- ${FAST_EXTERNAL_BUILD_DIR}/realsense/src/realsense/LICENSE
+- ${FAST_EXTERNAL_BUILD_DIR}/realsense/src/realsense/NOTICE
+- DESTINATION fast/licenses/realsense/
+- )
+-endif()
+-
-if(FAST_BUILD_DOCS)
- install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html
- DESTINATION fast/doc
- )
-endif()
++#if(FAST_MODULE_TensorFlow)
++# install(FILES ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/LICENSE
++# DESTINATION fast/licenses/tensorflow/
++# )
++#endif()
++#if(FAST_MODULE_OpenVINO AND NOT WIN32)
++# install(FILES ${FAST_EXTERNAL_BUILD_DIR}/OpenVINO/src/OpenVINO/LICENSE
++# DESTINATION fast/licenses/openvino/
++# )
++#endif()
++
++#if(FAST_MODULE_RealSense)
++# install(FILES
++# ${FAST_EXTERNAL_BUILD_DIR}/realsense/src/realsense/LICENSE
++# ${FAST_EXTERNAL_BUILD_DIR}/realsense/src/realsense/NOTICE
++# DESTINATION fast/licenses/realsense/
++# )
++#endif()
++
+#if(FAST_BUILD_DOCS)
+# install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html
+# DESTINATION fast/doc
=====================================
debian/patches/set_cmake_options.patch
=====================================
@@ -4,11 +4,9 @@ Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-08-08
---
-Index: fast/CMakeLists.txt
-===================================================================
---- fast.orig/CMakeLists.txt 2019-08-16 02:43:32.888319227 +0100
-+++ fast/CMakeLists.txt 2019-08-16 02:43:41.820367044 +0100
-@@ -16,9 +16,9 @@
+--- fast.orig/CMakeLists.txt
++++ fast/CMakeLists.txt
+@@ -17,9 +17,9 @@
#### Options
option(FAST_BUILD_TESTS "Build FAST tests." ON)
@@ -20,13 +18,15 @@ Index: fast/CMakeLists.txt
option(FAST_DOWNLOAD_TEST_DATA "Download test data automatically (> 1 GB)" OFF)
option(FAST_MODULE_VTK "Enable interoperability with VTK" OFF)
option(FAST_MODULE_ITK "Enable interoperability with ITK" OFF)
-@@ -31,9 +31,9 @@
+@@ -31,11 +31,11 @@
+ option(FAST_MODULE_OpenVINO "Build Intel OpenVINO inference engine" OFF)
option(FAST_MODULE_Python "Build Python wrappers" OFF)
option(FAST_MODULE_Kinect "Build kinect module" OFF)
- option(FAST_MODULE_RealSense "Build real sense module" OFF)
--option(FAST_MODULE_WholeSlideImaging "Build whole slide imaging module" OFF)
-+option(FAST_MODULE_WholeSlideImaging "Build whole slide imaging module" ON)
- option(FAST_MODULE_Clarius "Build clarius ultrasound module" OFF)
+-option(FAST_MODULE_RealSense "Build real sense module" ON)
++option(FAST_MODULE_RealSense "Build real sense module" OFF)
+ option(FAST_MODULE_WholeSlideImaging "Build whole slide imaging module" ON)
+ option(FAST_MODULE_Clarius "Build clarius ultrasound module" ON)
+ option(FAST_MODULE_Dicom "Build DICOM module (DCMTK)" ON)
-option(FAST_CONTINUOUS_INTEGRATION "Used for continuous integration tests" OFF)
+option(FAST_CONTINUOUS_INTEGRATION "Used for continuous integration tests" ON)
option(FAST_BUILD_QT5 "Download and build Qt 5.8. Turn this OFF if you want to use pre-built binaries you already have on your machine." OFF)
View it on GitLab: https://salsa.debian.org/med-team/fast/-/commit/717d567508c85eb0a9c4da6246e593185f9d9ae9
--
View it on GitLab: https://salsa.debian.org/med-team/fast/-/commit/717d567508c85eb0a9c4da6246e593185f9d9ae9
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