Merge pull request #366 from favreau/master

Version 1.8.0

CMakeLists.txt

@@ -22,8 +22,8 @@ set(NAME BIOEXPLORER)
 
 set(PACKAGE_VERSION_ABI 1)
 set(PACKAGE_VERSION_MAJOR 1)
-set(PACKAGE_VERSION_MINOR 7)
-set(PACKAGE_VERSION_PATCH 1)
+set(PACKAGE_VERSION_MINOR 8)
+set(PACKAGE_VERSION_PATCH 0)
 
 # Get the Git revision using the git command
 execute_process(

Dockerfile

@@ -20,6 +20,7 @@
 FROM debian:buster-20230522-slim as builder
 LABEL maintainer="cyrille.favreau@epfl.ch"
 ARG DIST_PATH=/app/dist
+ARG BUILD_TYPE=Release
 
 # Install packages
 RUN apt-get update \
@@ -50,14 +51,14 @@ RUN apt-get update \
    libglm-dev \
    libtiff-dev \
    libmpfr-dev \
+   libdcmtk-dev \
    pkg-config \
    wget \
    ca-certificates \
    exiv2 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-
 # --------------------------------------------------------------------------------
 # Get CMake 3.21.1
 # --------------------------------------------------------------------------------
@@ -69,7 +70,7 @@ RUN wget -O cmake-linux.sh https://cmake.org/files/v3.21/cmake-3.21.1-linux-x86_
 # Install Brion
 # https://github.com/BlueBrain/Brion
 # --------------------------------------------------------------------------------
-# ARG BRION_TAG=3.3.9
+# ARG BRION_TAG=3.3.14
 # ARG BRION_SRC=/app/brion
 
 # RUN mkdir -p ${BRION_SRC} \
@@ -81,6 +82,7 @@ RUN wget -O cmake-linux.sh https://cmake.org/files/v3.21/cmake-3.21.1-linux-x86_
 #    && cd build \
 #    && CMAKE_PREFIX_PATH=${DIST_PATH} cmake .. -GNinja \
 #    -DCMAKE_INSTALL_PREFIX=${DIST_PATH} \
+#    -DBRION_SKIP_LIBSONATA_SUBMODULE=ON \
 #    && ninja install \
 #    && ninja clean
 
@@ -104,12 +106,24 @@ ENV PATH $PATH:${ISPC_PATH}/bin
 # Install embree
 # https://github.com/embree/embree/releases
 # --------------------------------------------------------------------------------
-ARG EMBREE_VERSION=3.5.2
-ARG EMBREE_FILE=embree-${EMBREE_VERSION}.x86_64.linux.tar.gz
-RUN mkdir -p ${DIST_PATH} \
-   && wget --no-verbose https://github.com/embree/embree/releases/download/v${EMBREE_VERSION}/${EMBREE_FILE} \
-   && tar zxvf ${EMBREE_FILE} -C ${DIST_PATH} --strip-components=1 \
-   && rm -rf ${DIST_PATH}/bin ${DIST_PATH}/doc
+ARG EMBREE_TAG=v3.8.0
+ARG EMBREE_SRC=/app/embree
+
+RUN mkdir -p ${EMBREE_SRC} \
+   && git clone https://github.com/embree/embree.git ${EMBREE_SRC} \
+   && cd ${EMBREE_SRC} \
+   && git checkout ${EMBREE_TAG} \
+   && mkdir -p build \
+   && cd build \
+   && CMAKE_PREFIX_PATH=${DIST_PATH} cmake .. -GNinja \
+   -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
+   -DEMBREE_ISPC_EXECUTABLE=${ISPC_PATH}/bin/ispc \
+   -DEMBREE_TUTORIALS=OFF \
+   -DEMBREE_IGNORE_INVALID_RAYS=ON \
+   -DEMBREE_ISA_AVX512SKX=ON \
+   -DCMAKE_INSTALL_PREFIX=${DIST_PATH} \
+   && ninja install \
+   && ninja clean
 
 # --------------------------------------------------------------------------------
 # Install OSPRay
@@ -125,9 +139,15 @@ RUN mkdir -p ${OSPRAY_SRC} \
    && mkdir -p build \
    && cd build \
    && CMAKE_PREFIX_PATH=${DIST_PATH} cmake .. -GNinja \
+   -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
    -DOSPRAY_ENABLE_TUTORIALS=OFF \
    -DOSPRAY_ENABLE_APPS=OFF \
    -DCMAKE_INSTALL_PREFIX=${DIST_PATH} \
+   -DOSPRAY_APPS_BENCHMARK=OFF \
+   -DOSPRAY_APPS_EXAMPLEVIEWER=OFF \
+   -DOSPRAY_APPS_UTILITIES=OFF \
+   -DOSPRAY_AUTO_DOWNLOAD_TEST_IMAGES=OFF \
+   -DOSPRAY_ENABLE_TUTORIALS=OFF \
    && ninja install \
    && ninja clean
 
@@ -146,7 +166,7 @@ RUN mkdir -p ${LWS_SRC} \
    && mkdir -p build \
    && cd build \
    && cmake .. -GNinja \
-   -DCMAKE_BUILD_TYPE=Release \
+   -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
    -DLWS_STATIC_PIC=ON \
    -DLWS_WITH_SSL=ON \
    -DLWS_WITH_ZLIB=OFF \
@@ -173,21 +193,20 @@ RUN mkdir -p ${ROCKETS_SRC} \
    && mkdir -p build \
    && cd build \
    && CMAKE_PREFIX_PATH=${DIST_PATH} cmake .. -GNinja \
+   -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
    -DCMAKE_INSTALL_PREFIX=${DIST_PATH} \
    && ninja install \
    && ninja clean
 
 # --------------------------------------------------------------------------------
 # Install BioExplorer
-# https://github.com/BlueBrain/BioExplorer
 # --------------------------------------------------------------------------------
 ARG BIOEXPLORER_SRC=/app
 ADD . ${BIOEXPLORER_SRC}
 
 WORKDIR /app
 
 RUN cd ${BIOEXPLORER_SRC} \
-   && git clone --recursive https://github.com/BlueBrain/BioExplorer.git \
    && rm -rf build \
    && mkdir build \
    && cd build \
@@ -197,9 +216,10 @@ RUN cd ${BIOEXPLORER_SRC} \
    CMAKE_PREFIX_PATH=${DIST_PATH} \
    LDFLAGS="-lCGAL" \
    cmake .. -GNinja \
+   -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
    -DCMAKE_INSTALL_PREFIX=${DIST_PATH} \
-   -DCMAKE_BUILD_TYPE=Release \
    -DCGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE=ON \
+   -DPLATFORM_UNIT_TESTING_ENABLED=OFF \
    -DPLATFORM_USE_CGAL=ON \
    -DPLATFORM_OPTIX6_ENABLED=OFF \
    -DPLATFORM_NETWORKING_ENABLED=ON \
@@ -212,6 +232,7 @@ RUN cd ${BIOEXPLORER_SRC} \
    -DBIOEXPLORER_SONATA_ENABLED=OFF \
    -DBIOEXPLORER_METABOLISM_ENABLED=OFF \
    -DBIOEXPLORER_MEDIAMAKER_ENABLED=ON \
+   -DMEDICALIMAGING_BUILD_ENABLED=ON \
    && ninja install \
    && ninja clean
 
@@ -238,6 +259,8 @@ RUN apt-get update \
    libpqxx-6.2 \
    libtiff5 \
    libmpfr6 \
+   libtbb-dev \
+   dcmtk \
    exiv2 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
@@ -266,4 +289,4 @@ EXPOSE 8200
 # See https://docs.docker.com/engine/reference/run/#entrypoint-default-command-to-execute-at-runtime
 # for more docs
 ENTRYPOINT ["service"]
-CMD ["--http-server", ":8200", "--plugin", "MediaMaker", "--plugin", "BioExplorer"]
+CMD ["--http-server", ":8200", "--plugin", "MediaMaker", "--plugin", "DICOM", "--plugin", "BioExplorer"]

bioexplorer/backend/science/fields/PointFieldBuilder.cpp

@@ -140,7 +140,7 @@ void PointFieldBuilder::buildOctree(core::Engine& engine, core::Model& model, co
 
     const auto& params = engine.getParametersManager().getApplicationParameters();
     const auto& engineName = params.getEngine();
-    auto field = model.createField(dimensions, spacing, offset, indices, data, OctreeDataType::point);
+    auto field = model.createField(dimensions, spacing, offset, indices, data, OctreeDataType::odt_points);
     const size_t materialId = FIELD_MATERIAL_ID;
     model.addField(materialId, field);
     model.createMaterial(materialId, std::to_string(materialId));

bioexplorer/backend/science/fields/VectorFieldBuilder.cpp

@@ -144,7 +144,7 @@ void VectorFieldBuilder::buildOctree(core::Engine& engine, core::Model& model, c
 
     const auto& params = engine.getParametersManager().getApplicationParameters();
     const auto& engineName = params.getEngine();
-    auto field = model.createField(dimensions, spacing, offset, indices, data, OctreeDataType::vector);
+    auto field = model.createField(dimensions, spacing, offset, indices, data, OctreeDataType::odt_vectors);
     const size_t materialId = FIELD_MATERIAL_ID;
     model.addField(materialId, field);
     model.createMaterial(materialId, std::to_string(materialId));

bioexplorer/pythonsdk/bioexplorer/bio_explorer.py

@@ -393,8 +393,10 @@ def __init__(
         Parameters used to define how cells should be represented using the SDF technique
 
         :report_id: (int, optional): Report id
-        :value_range: (Vector2, optional): Range of values for the mapped data. Defaults are [-80.0, -10.0]
-        :scaling_range: (Vector2, optional): Minimum and maximum scaling factors. Defaults are [-1.0, 1.0] (no scaling)
+        :value_range: (Vector2, optional): Range of values for the mapped data. Defaults are
+        [-80.0, -10.0]
+        :scaling_range: (Vector2, optional): Minimum and maximum scaling factors. Defaults are
+        [-1.0, 1.0] (no scaling)
         :initial_simulation_frame: (int, optional): Initial simulation frame. Default is 0
         :load_non_simulated_nodes: Defines if non-simulated should be loaded
         """
@@ -408,7 +410,7 @@ def __init__(
         self.value_range = value_range
         self.scaling_range = scaling_range
         self.initial_simulation_frame = initial_simulation_frame
-        self.load_non_simulated_nodes=load_non_simulated_nodes
+        self.load_non_simulated_nodes = load_non_simulated_nodes
 
     def to_list(self):
         """

bioexplorer/pythonsdk/bioexplorer/version.py

@@ -21,4 +21,4 @@
 # You should have received a copy of the GNU General Public License along with
 # this program.  If not, see <https://www.gnu.org/licenses/>.
 
-VERSION = "1.7.1"
+VERSION = "1.8.0"