Commit efe0c750 authored by Shayan Doust's avatar Shayan Doust
Browse files

New upstream version 3.0.0~rc3+ds

parent fa7ddbe1

CMakeLists.txt

+1 −1
Original line number Diff line number Diff line
@@ -234,7 +234,7 @@ configure_file( 
# Setup inference engines

foreach(ENGINE ${FAST_INFERENCE_ENGINES})

    message("---- Adding inference engnine ${ENGINE}")

    add_dependencies(testFAST ${ENGINE})

    #add_dependencies(testFAST ${ENGINE})

endforeach()



if(NOT FAST_BUILD_QT5 AND WIN32)

README.md

+4 −2
Original line number Diff line number Diff line
@@ -23,7 +23,7 @@ If you use FAST for research, please cite this article. 


### Download



If you are only interested in using/testing FAST, and not developing FAST, please download a [stable binary release](https://github.com/smistad/FAST/releases).

If you are only interested in using/testing FAST, and not developing FAST, please download a [stable binary release](https://github.com/smistad/FAST/releases). Make sure you have the [requirements](https://github.com/smistad/FAST/wiki/Requirements) installed before using the releases.



### Build
@@ -36,4 +36,6 @@ To setup and build the framework, see the instructions for your operating system 


To start using the framework, see the [Getting started with FAST](https://github.com/smistad/FAST/wiki/Getting-started-with-FAST) guide or the [examples page](https://github.com/smistad/FAST/wiki/Examples).



![Surface mesh extracted from a large abdominal CT scan in about 100 ms using FAST and a modern GPU.](https://github.com/smistad/FAST/wiki/images/surface_extraction.png) ![Ultrasound image segmented using binary thresholding.](https://github.com/smistad/FAST/wiki/images/binary_thresholding.png)
 
![Surface mesh extracted from a large abdominal CT scan.](https://github.com/smistad/FAST/wiki/images/surface_extraction.png) ![Alpha blending ray casting rendering of a thorax CT image.](https://github.com/smistad/FAST/wiki/images/volume_renderer.jpg) 



![Ultrasound image segmentation using neural netwoks.](https://github.com/smistad/FAST/wiki/images/ultrasound_segmentation.jpg)  ![Whole slide microscopy image.](https://github.com/smistad/FAST/wiki/images/wsi.jpg)

cmake/ExternalEigen.cmake

+2 −2
Original line number Diff line number Diff line
@@ -7,7 +7,7 @@ ExternalProject_Add(eigen 
        BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/eigen

        #GIT_REPOSITORY "https://github.com/RLovelett/eigen.git"

        #GIT_TAG "a46d2e7337c4656f00abe54a8115f6d76153a048"

        URL "https://bitbucket.org/eigen/eigen/get/f3a22f35b044.tar.gz"

        URL "https://bitbucket.org/eigen/eigen/get/b4890dc.tar.gz"

        INSTALL_DIR ${FAST_EXTERNAL_INSTALL_DIR}

        CMAKE_CACHE_ARGS

            -DCMAKE_BUILD_TYPE:STRING=Release

cmake/ExternalTensorflow.cmake

+57 −38
Original line number Diff line number Diff line
@@ -5,34 +5,54 @@ include(${PROJECT_SOURCE_DIR}/cmake/Externals.cmake) 
if(WIN32)

    set(GIT_EXECUTABLE "git.exe")

    # Use CMake to build tensorflow on windows

    ExternalProject_Add(tensorflow

    if(FAST_BUILD_TensorFlow_CPU OR FAST_BUILD_TensorFlow_CUDA)

        ExternalProject_Add(tensorflow_download

            PREFIX ${FAST_EXTERNAL_BUILD_DIR}/tensorflow

            BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/tensorflow

            GIT_REPOSITORY "https://github.com/smistad/tensorflow.git"

            GIT_TAG "fast"

            # Need to override this because tensorflow creates a file in the source dir

            # and cmake files to stash these files

            UPDATE_COMMAND

                ${GIT_EXECUTABLE} pull origin fast

            # Must use CONFIGURE_COMMAND because CMakeLists.txt is not in the src root of tensorflow

            GIT_TAG "fast-updated"

            UPDATE_COMMAND ""

            CONFIGURE_COMMAND ""

            BUILD_COMMAND ""

            INSTALL_COMMAND ""

        )

    endif()

    if(FAST_BUILD_TensorFlow_CPU)



    ExternalProject_Add(tensorflow_CPU

            DEPENDS tensorflow_download

            PREFIX ${FAST_EXTERNAL_BUILD_DIR}/tensorflow

            BINARY_DIR ${FAST_EXTERNAL_BUILD_DIR}/tensorflow

            DOWNLOAD_COMMAND ""

            UPDATE_COMMAND ""

            CONFIGURE_COMMAND

                ${CMAKE_COMMAND}

                ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/tensorflow/contrib/cmake/

                -G${CMAKE_GENERATOR}

		-Thost=x64

                -DCMAKE_BUILD_TYPE:STRING=Release

                -Dtensorflow_BUILD_PYTHON_BINDINGS=OFF

                -Dtensorflow_ENABLE_SNAPPY_SUPPORT=ON

                -Dtensorflow_BUILD_CC_EXAMPLE=OFF

                -Dtensorflow_BUILD_SHARED_LIB=ON

                -Dtensorflow_BUILD_CONTRIB_KERNELS=OFF

                -Dtensorflow_ENABLE_GRPC_SUPPORT=OFF

                -Dtensorflow_WIN_CPU_SIMD_OPTIONS=/arch:AVX

                #-Dtensorflow_ENABLE_GPU=ON

                -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF

                -DCMAKE_INSTALL_MESSAGE:BOOL=LAZY

                -DCMAKE_INSTALL_PREFIX:STRING=${FAST_EXTERNAL_INSTALL_DIR}

                echo "Configuring TensorFlow..." COMMAND

                cd ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/ COMMAND

                ${PROJECT_SOURCE_DIR}/cmake/TensorflowConfigureCPU.bat COMMAND

                echo "Done TF configure"

            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

            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/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

                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 nsync headers"  COMMAND

                #xcopy ${src} ${dest} /y COMMAND

                echo "Installing absl headers"  COMMAND

                ${CMAKE_COMMAND} -E copy_directory ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-tensorflow_download/external/com_google_absl/absl/ ${FAST_EXTERNAL_INSTALL_DIR}/include/absl/

    )

    endif()

else(WIN32)

    # Use bazel to build tensorflow on linux

    set(GIT_EXECUTABLE "git")
@@ -90,8 +110,8 @@ else(WIN32) 
                cp -rf ${FAST_EXTERNAL_BUILD_DIR}/tensorflow_rocm/src/tensorflow_download_rocm/third_party/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ &&

                echo "Installing protobuf headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow_rocm/src/tensorflow_download_rocm/bazel-out/)/../../../external/protobuf_archive/src/google/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                echo "Installing nsync headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow_rocm/src/tensorflow_download_rocm/bazel-out/)/../../../external/nsync/public/*.h ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                #echo "Installing nsync headers" &&

                #bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow_rocm/src/tensorflow_download_rocm/bazel-out/)/../../../external/nsync/public/*.h ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                echo "Installing absl headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow_rocm/src/tensorflow_download_rocm/bazel-out/)/../../../external/com_google_absl/absl/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf"

    )
@@ -112,13 +132,13 @@ else(WIN32) 
                cd ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/ && bazel build -c opt --config=cuda --copt=-mfpmath=both --copt=-march=core-avx2 //tensorflow:libtensorflow_cc.so

            INSTALL_COMMAND

                echo "Installing tensorflow binary" &&

                cp -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/libtensorflow_cc.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CUDA.so &&

                cp -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/libtensorflow_framework.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_framework_CUDA.so &&

                cp -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/libtensorflow_cc.so.1.14.0 ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CUDA.so &&

                cp -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/libtensorflow_framework.so.1.14.0 ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_framework_CUDA.so &&

                chmod a+w ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CUDA.so &&

                chmod a+w ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_framework_CUDA.so &&

                patchelf --set-soname libtensorflow_cc_CUDA.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CUDA.so &&

                patchelf --set-soname libtensorflow_framework_CUDA.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_framework_CUDA.so &&

                patchelf --replace-needed libtensorflow_framework.so libtensorflow_framework_CUDA.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CUDA.so &&

                patchelf --replace-needed libtensorflow_framework.so.1 libtensorflow_framework_CUDA.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CUDA.so &&

                #echo "Installing mkl binaries" &&

                #bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/mkl/lib/libmklml_intel.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/ -Rf" &&

                #bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/mkl/lib/libiomp5.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/ -Rf" &&
@@ -130,8 +150,8 @@ else(WIN32) 
                cp -rf ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/third_party/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ &&

                echo "Installing protobuf headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/protobuf_archive/src/google/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                echo "Installing nsync headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/nsync/public/*.h ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                #echo "Installing nsync headers" &&

                #bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/nsync/public/*.h ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                echo "Installing absl headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/com_google_absl/absl/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf"

    )
@@ -152,13 +172,13 @@ else(WIN32) 
                cd ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/ && bazel build --config=opt --copt=-mfpmath=both --copt=-march=core-avx2 //tensorflow:libtensorflow_cc.so

            INSTALL_COMMAND

                echo "Installing tensorflow binary" &&

                cp -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/libtensorflow_cc.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CPU.so &&

                cp -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/libtensorflow_framework.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_framework_CPU.so &&

                cp -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/libtensorflow_cc.so.1.14.0 ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CPU.so &&

                cp -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-bin/tensorflow/libtensorflow_framework.so.1.14.0 ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_framework_CPU.so &&

                chmod a+w ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CPU.so &&

                chmod a+w ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_framework_CPU.so &&

                patchelf --set-soname libtensorflow_cc_CPU.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CPU.so &&

                patchelf --set-soname libtensorflow_framework_CPU.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_framework_CPU.so &&

                patchelf --replace-needed libtensorflow_framework.so libtensorflow_framework_CPU.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CPU.so &&

                patchelf --replace-needed libtensorflow_framework.so.1 libtensorflow_framework_CPU.so ${FAST_EXTERNAL_INSTALL_DIR}/lib/libtensorflow_cc_CPU.so &&

                echo "Installing tensorflow headers" &&

                cp -rf ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/tensorflow/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ &&

                echo "Installing tensorflow generated headers" &&
@@ -167,11 +187,10 @@ else(WIN32) 
                cp -rf ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/third_party/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ &&

                echo "Installing protobuf headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/protobuf_archive/src/google/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                echo "Installing nsync headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/nsync/public/*.h ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                #echo "Installing nsync headers" &&

                #bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/nsync/public/*.h ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf" &&

                echo "Installing absl headers" &&

                bash -c "cp $(readlink -f ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/bazel-out/)/../../../external/com_google_absl/absl/ ${FAST_EXTERNAL_INSTALL_DIR}/include/ -Rf"

    )

    endif()

endif(WIN32)

cmake/InstallFAST.cmake

+7 −4
Original line number Diff line number Diff line
@@ -41,6 +41,9 @@ elseif(APPLE) 
    )

else()

	file(GLOB SOs ${PROJECT_BINARY_DIR}/lib/*.so*)

	foreach(SO ${SOs})

		execute_process(COMMAND echo "Setting runtime path of ${SO}" COMMAND patchelf --set-rpath "$ORIGIN/../lib" ${SO})

    endforeach()

    install(FILES ${SOs}

        DESTINATION fast/lib

    )
@@ -212,7 +215,7 @@ install(FILES ${PROJECT_SOURCE_DIR}/cmake/InstallFiles/Semaphore_LICENSE.txt 


if(FAST_MODULE_TensorFlow)

    # Tensorflow license

	install(FILES ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow/LICENSE

	install(FILES ${FAST_EXTERNAL_BUILD_DIR}/tensorflow/src/tensorflow_download/LICENSE

        DESTINATION fast/licenses/tensorflow/

    )

endif()