Performance tests improvements

.github/workflows/test.yml

@@ -43,21 +43,21 @@ jobs:
           sudo apt install libgdcm-dev
 
       # install from source, because apt has old version
-      - name: Install GoogleTest and GoogleMock
+      - name: Install xsimd
+        if: ${{ endsWith(matrix.gamma-version, 'SIMD') }}
         run: |
-          git clone https://github.com/google/googletest.git -b v1.13.0
-          cd googletest
+          git clone https://github.com/xtensor-stack/xsimd.git -b 11.1.0
+          cd xsimd
           mkdir build && cd build
           cmake ..
           make
           sudo make install
 
       # install from source, because apt has old version
-      - name: Install xsimd
-        if: ${{ endsWith(matrix.gamma-version, 'SIMD') }}
+      - name: Install GoogleTest and GoogleMock
         run: |
-          git clone https://github.com/xtensor-stack/xsimd.git -b 11.1.0
-          cd xsimd
+          git clone https://github.com/google/googletest.git -b v1.13.0
+          cd googletest
           mkdir build && cd build
           cmake ..
           make
@@ -86,6 +86,28 @@ jobs:
         run: |
           cmake --install build --prefix ./yagit_install_dir
 
+  run-setup-linux:
+    if: >
+      github.repository == 'DataMedSci/yagit' &&
+      !contains(github.event.head_commit.message, '[ci skip]') &&
+      !contains(github.event.head_commit.message, '[skip ci]')
+    name: Run setup.sh on Linux
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Check versions
+        run: |
+          gcc --version
+          g++ --version
+          cmake --version
+
+      - name: Run setup.sh script
+        run: |
+          ./setup.sh
+
   build-windows:
     if: >
       github.repository == 'DataMedSci/yagit' &&

.gitignore

@@ -107,3 +107,8 @@ docs/build
 # tests data files
 !tests/unit/data/*.dcm
 !tests/unit/data/*.mha
+
+# plot output files
+*plot*.png
+*plot*.svg
+*plot*.pdf

conanfile.txt

@@ -1,7 +1,7 @@
 [requires]
 gdcm/3.0.20
-gtest/1.13.0
 xsimd/11.1.0
+gtest/1.13.0
 
 [generators]
 CMakeDeps

examples/gamma3D.cpp

@@ -39,7 +39,7 @@
 std::string floatToString(float d){
     std::ostringstream oss;
     oss << d;
-    return oss.str(); 
+    return oss.str();
 }
 
 std::string gammaParametersToString(const yagit::GammaParameters& gammaParams){

setup.bat

@@ -18,8 +18,8 @@ set BUILD_EXAMPLES=ON
 set BUILD_TESTING=OFF
 set BUILD_PERFORMANCE_TESTING=OFF
 
-set REF_IMG=original_dose_beam_4.dcm
-set EVAL_IMG=logfile_dose_beam_4.dcm
+set REF_IMG=img_reference.dcm
+set EVAL_IMG=img_evaluated.dcm
 
 set INSTALL=OFF
 set INSTALL_DIR=./yagit
@@ -30,7 +30,7 @@ if not exist build\CMakeCache.txt (
     echo CONFIGURING CMAKE FIRST TIME...
     mkdir build
     cd build
-    conan install ..
+    conan install .. --output-folder . --build missing
     cmake .. -DCMAKE_TOOLCHAIN_FILE=conan_toolchain.cmake
     cd ..
 )
@@ -95,10 +95,10 @@ if %INSTALL% == ON (
     echo:
     echo INSTALLING...
     IF "%INSTALL_DIR%" NEQ "" (
-        echo INSTALLING TO %INSTALL_DIR%
+        echo INSTALLING IN %INSTALL_DIR%
         cmake --install build --prefix %INSTALL_DIR%
     ) else (
-        echo INSTALLING TO SYSTEM DIRECTORY
+        echo INSTALLING IN SYSTEM DIRECTORY
         echo MAKE SURE YOU RUN THIS AS ADMINISTRATOR
         cmake --install build
     )

setup.sh

@@ -0,0 +1,160 @@
+#!/bin/bash
+
+BUILD_TYPE=Release
+BUILD_SHARED_LIBS=OFF
+
+# INSTALL_DEPENDENCIES=OFF
+INSTALL_DEPENDENCIES=LOCAL
+# INSTALL_DEPENDENCIES=GLOBAL  # requires root privileges
+# INSTALL_DEPENDENCIES=CONAN
+
+# GAMMA_VERSION=SEQUENTIAL
+GAMMA_VERSION=THREADS
+# GAMMA_VERSION=SIMD
+# GAMMA_VERSION=THREADS_SIMD
+
+SIMD_EXTENSION=DEFAULT
+# SIMD_EXTENSION=AVX2
+
+ENABLE_FMA=OFF
+
+BUILD_EXAMPLES=ON
+BUILD_TESTING=OFF
+BUILD_PERFORMANCE_TESTING=OFF
+
+REF_IMG=img_reference.dcm
+EVAL_IMG=img_evaluated.dcm
+
+INSTALL=OFF
+INSTALL_DIR=./yagit
+
+
+# ============================================================
+mkdir -p build
+cd build
+
+# ============================================================
+
+install () {
+    # $1 - path to library to install
+
+    cd $1
+    mkdir -p build && cd build
+    cmake .. -DCMAKE_BUILD_TYPE=Release
+    cmake --build . --config Release -j
+
+    if [ $INSTALL_DEPENDENCIES == LOCAL ]; then
+        cmake --install . --prefix ./installed
+    elif [ $INSTALL_DEPENDENCIES == GLOBAL ]; then
+        sudo cmake --install .
+    fi
+
+    cd ../..
+}
+
+DEPENDENCIES_PATHS=""
+TOOLCHAIN_FILE=""
+
+if [[ $INSTALL_DEPENDENCIES == LOCAL || $INSTALL_DEPENDENCIES == GLOBAL ]]; then
+    echo "INSTALLING DEPENDENCIES..."
+    mkdir -p deps && cd deps
+
+    # GDCM
+    if [ ! -d GDCM ]; then
+        git clone https://github.com/malaterre/GDCM.git -b v3.0.22
+        install GDCM
+    fi
+
+    # xsimd
+    if [ ! -d xsimd ]; then
+        git clone https://github.com/xtensor-stack/xsimd.git -b 11.1.0
+        install xsimd
+    fi
+
+    # GoogleTest
+    if [ ! -d googletest ]; then
+        git clone https://github.com/google/googletest.git -b v1.13.0
+        install googletest
+    fi
+
+    if [ $INSTALL_DEPENDENCIES == LOCAL ]; then
+        GDCM_PATH="$(pwd)/GDCM/build/installed"
+        XSIMD_PATH="$(pwd)/xsimd/build/installed"
+        GTEST_PATH="$(pwd)/googletest/build/installed"
+        DEPENDENCIES_PATHS="$GDCM_PATH;$XSIMD_PATH;$GTEST_PATH"
+    fi
+
+    cd ..
+elif [ $INSTALL_DEPENDENCIES == CONAN ]; then
+    conan install .. --output-folder . --build missing
+    TOOLCHAIN_FILE=conan_toolchain.cmake
+fi
+
+
+# ============================================================
+echo ""
+echo "CONFIGURING CMAKE..."
+cmake .. -DCMAKE_BUILD_TYPE=$BUILD_TYPE \
+         -DBUILD_SHARED_LIBS=$BUILD_SHARED_LIBS \
+         -DGAMMA_VERSION=$GAMMA_VERSION \
+         -DSIMD_EXTENSION=$SIMD_EXTENSION \
+         -DENABLE_FMA=$ENABLE_FMA \
+         -DBUILD_EXAMPLES=$BUILD_EXAMPLES \
+         -DBUILD_TESTING=$BUILD_TESTING \
+         -DBUILD_PERFORMANCE_TESTING=$BUILD_PERFORMANCE_TESTING \
+         -DCMAKE_PREFIX_PATH="$DEPENDENCIES_PATHS" \
+         -DCMAKE_TOOLCHAIN_FILE="$TOOLCHAIN_FILE"
+
+
+# ============================================================
+echo ""
+echo "COMPILING..."
+cmake --build . --config $BUILD_TYPE -j
+COMPILE_RESULT=$?
+cd ..
+
+if [ $COMPILE_RESULT -ne 0 ]; then
+    exit $COMPILE_RESULT
+fi
+
+
+# ============================================================
+if [ $BUILD_EXAMPLES == ON ]; then
+    echo ""
+    echo "RUNNING EXAMPLES..."
+    ./build/examples/gamma2DInterp "$REF_IMG" "$EVAL_IMG"
+    echo ""
+    ./build/examples/gamma25D "$REF_IMG" "$EVAL_IMG"
+    echo ""
+    ./build/examples/gamma3D "$REF_IMG" "$EVAL_IMG"
+    echo ""
+    ./build/examples/gammaImage
+fi
+
+if [ $BUILD_TESTING == ON ]; then
+    echo ""
+    echo "RUNNING UNIT TESTS..."
+    ctest -C $BUILD_TYPE --test-dir build --output-on-failure
+fi
+
+if [ $BUILD_PERFORMANCE_TESTING == ON ]; then
+    echo ""
+    echo "RUNNING PERFORMANCE TEST..."
+    ./build/tests/performance/gammaPerf "$REF_IMG" "$EVAL_IMG" gammaTimes.csv
+    echo ""
+    ./build/tests/performance/interpPerf "$EVAL_IMG"
+fi
+
+
+# ============================================================
+if [ $INSTALL == ON ]; then
+    echo ""
+    echo "INSTALLING..."
+    if [ -n "$INSTALL_DIR" ]; then
+        echo "INSTALLING IN $INSTALL_DIR"
+        cmake --install build --prefix "$INSTALL_DIR"
+    else
+        echo "INSTALLING IN SYSTEM DIRECTORY"
+        sudo cmake --install build
+    fi
+fi

src/GammaResult.cpp

@@ -25,7 +25,7 @@
 namespace yagit{
 
 double GammaResult::passingRate() const{
-    return static_cast<value_type>(std::count_if(m_data.begin(), m_data.end(), [](value_type el) {
+    return static_cast<double>(std::count_if(m_data.begin(), m_data.end(), [](value_type el) {
         return !std::isnan(el) && el <= 1;
     })) / nansize();
 }

src/Interpolation.cpp

@@ -27,13 +27,13 @@ namespace yagit::Interpolation{
 namespace{
 // absolute tolerance that is useful for floating-point computations
 // currently it is absolute tolerance, but it can be changed to relative tolerance if it turns out to work better
-constexpr double Tolerance{5e-6};
+constexpr double Tolerance{5e-7};
 
 float calcNewOffset(float oldOffset, float gridOffset, float spacing){
     // calculate closest point to oldOffset that is greater than or equal to oldOffset and also lies on grid.
     // Tolerance here is useful in cases where value passed to ceil function is e.g. 12.0000001 due to computer 
     // floating-point errors and will be evaluated as 13 which is actually an incorrect result (correct is 12)
-    int n = std::ceil((oldOffset - gridOffset) / static_cast<double>(spacing) - Tolerance);
+    int n = std::ceil((oldOffset - gridOffset - Tolerance) / static_cast<double>(spacing));
     float newOffset = gridOffset + n * spacing;
     return newOffset;
 }
@@ -43,7 +43,7 @@ constexpr uint32_t calcNewSize(uint32_t oldSize, float oldSpacing, float offsetR
     // Tolerance here is useful in cases where value passed to truncation function (cast to integer)
     // is e.g. 15.9999999 due to computer floating-point errors and will be evaluated as 15 which is actually
     // an incorrect result (correct is 16)
-    return static_cast<uint32_t>((oldSpacing * (oldSize - 1) - offsetRel) / newSpacing + 1 + Tolerance);
+    return static_cast<uint32_t>((oldSpacing * (oldSize - 1) - offsetRel + Tolerance) / newSpacing + 1);
 }
 }
 

src/gamma/Gamma.cpp

@@ -129,8 +129,8 @@ GammaResult gammaIndex2DClassic(const ImageData& refImg2D, const ImageData& eval
 
 GammaResult gammaIndex2_5DClassic(const ImageData& refImg3D, const ImageData& evalImg3D,
                                   const GammaParameters& gammaParams){
-    if(refImg3D.getSize().frames != evalImg3D.getSize().frames){
-        throw std::invalid_argument("reference image and evaluated image don't have the same number of frames");
+    if(evalImg3D.getSize().frames < refImg3D.getSize().frames){
+        throw std::invalid_argument("evaluated image must have at least the same number of frames as the reference image");
     }
     validateGammaParameters(gammaParams);
 

src/gamma/GammaSimd.cpp

@@ -163,8 +163,8 @@ GammaResult gammaIndex2DClassic(const ImageData& refImg2D, const ImageData& eval
 
 GammaResult gammaIndex2_5DClassic(const ImageData& refImg3D, const ImageData& evalImg3D,
                                   const GammaParameters& gammaParams){
-    if(refImg3D.getSize().frames != evalImg3D.getSize().frames){
-        throw std::invalid_argument("reference image and evaluated image don't have the same number of frames");
+    if(evalImg3D.getSize().frames < refImg3D.getSize().frames){
+        throw std::invalid_argument("evaluated image must have at least the same number of frames as the reference image");
     }
     validateGammaParameters(gammaParams);
 

src/gamma/GammaThreads.cpp

@@ -254,8 +254,8 @@ GammaResult gammaIndex2DClassic(const ImageData& refImg2D, const ImageData& eval
 
 GammaResult gammaIndex2_5DClassic(const ImageData& refImg3D, const ImageData& evalImg3D,
                                   const GammaParameters& gammaParams){
-    if(refImg3D.getSize().frames != evalImg3D.getSize().frames){
-        throw std::invalid_argument("reference image and evaluated image don't have the same number of frames");
+    if(evalImg3D.getSize().frames < refImg3D.getSize().frames){
+        throw std::invalid_argument("evaluated image must have at least the same number of frames as the reference image");
     }
     validateGammaParameters(gammaParams);
 

src/gamma/GammaThreadsSimd.cpp

@@ -353,8 +353,8 @@ GammaResult gammaIndex2DClassic(const ImageData& refImg2D, const ImageData& eval
 
 GammaResult gammaIndex2_5DClassic(const ImageData& refImg3D, const ImageData& evalImg3D,
                                   const GammaParameters& gammaParams){
-    if(refImg3D.getSize().frames != evalImg3D.getSize().frames){
-        throw std::invalid_argument("reference image and evaluated image don't have the same number of frames");
+    if(evalImg3D.getSize().frames < refImg3D.getSize().frames){
+        throw std::invalid_argument("evaluated image must have at least the same number of frames as the reference image");
     }
     validateGammaParameters(gammaParams);