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Merge pull request #366 from favreau/master
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Version 1.8.0
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favreau authored Apr 4, 2024
2 parents 3c3a346 + 370a79a commit f22a8a4
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Showing 1,187 changed files with 36,808 additions and 34,135 deletions.
4 changes: 2 additions & 2 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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(
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49 changes: 36 additions & 13 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
FROM debian:buster-20230522-slim as builder
LABEL maintainer="[email protected]"
ARG DIST_PATH=/app/dist
ARG BUILD_TYPE=Release

# Install packages
RUN apt-get update \
Expand Down Expand Up @@ -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
# --------------------------------------------------------------------------------
Expand All @@ -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 ${BRION_SRC} \
Expand All @@ -81,6 +82,7 @@ RUN wget -O cmake-linux.sh https://cmake.org/files/v3.21/cmake-3.21.1-linux-x86_
# && cd build \
# && CMAKE_PREFIX_PATH=${DIST_PATH} cmake .. -GNinja \
# -DCMAKE_INSTALL_PREFIX=${DIST_PATH} \
# -DBRION_SKIP_LIBSONATA_SUBMODULE=ON \
# && ninja install \
# && ninja clean

Expand All @@ -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
Expand All @@ -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

Expand All @@ -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 \
Expand All @@ -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 \
Expand All @@ -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 \
Expand All @@ -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

Expand All @@ -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/*
Expand Down Expand Up @@ -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"]
2 changes: 1 addition & 1 deletion bioexplorer/backend/science/fields/PointFieldBuilder.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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));
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2 changes: 1 addition & 1 deletion bioexplorer/backend/science/fields/VectorFieldBuilder.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -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));
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8 changes: 5 additions & 3 deletions bioexplorer/pythonsdk/bioexplorer/bio_explorer.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
"""
Expand All @@ -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):
"""
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2 changes: 1 addition & 1 deletion bioexplorer/pythonsdk/bioexplorer/version.py
Original file line number Diff line number Diff line change
Expand Up @@ -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"
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