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neuromorphovis.sh
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neuromorphovis.sh
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#!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2016 - 2023, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <[email protected]>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is free software: you can redistribute it and/or modify it under the terms of the
# GNU General Public License as published by the Free Software Foundation, version 3 of the License.
#
# This Blender-based tool is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with this program.
# If not, see <http://www.gnu.org/licenses/>.
####################################################################################################
# If no configuration file is provided, then report it and exit
if [ $# -eq 0 ]
then echo "No configuration file is provided, EXITING!"; exit
fi
# Source the input configuration file to use the parameters
echo "Using the configuration file [$1]"
source $1
#####################################################################################################
BOOL_ARGS=''
#####################################################################################################
# Ignoring Branches
if [ "$IGNORE_AXON" == "yes" ];
then BOOL_ARGS+=' --ignore-axons '; fi
if [ "$IGNORE_BASAL_DENDRITES" == "yes" ];
then BOOL_ARGS+=' --ignore-basal-dendrites '; fi
if [ "$IGNORE_APICAL_DENDRITES" == "yes" ];
then BOOL_ARGS+=' --ignore-apical-dendrites '; fi
if [ "$CONNECT_SOMA_MESH_TO_ARBORS" == "yes" ];
then BOOL_ARGS+=' --connect-soma-arbors'; fi
####################################################################################################
# Rendering parameters
if [ "$RENDER_SOMA_IMAGE" == "yes" ];
then BOOL_ARGS+=' --render-soma-mesh '; fi
if [ "$RENDER_SOMA_PROGRESSIVE_SEQUENCE" == "yes" ];
then BOOL_ARGS+=' --render-soma-mesh-progressive '; fi
if [ "$RENDER_SOMA_360_SEQUENCE" == "yes" ];
then BOOL_ARGS+=' --render-soma-mesh-360 '; fi
if [ "$RENDER_NEURON_MORPHOLOGY_IMAGE" == "yes" ];
then BOOL_ARGS+=' --render-neuron-morphology '; fi
if [ "$RENDER_NEURON_MORPHOLOGY_360_SEQUENCE" == "yes" ];
then BOOL_ARGS+=' --render-neuron-morphology-360 '; fi
if [ "$RENDER_NEURON_MORPHOLOGY_PROGRESSIVE_SEQUENCE" == "yes" ];
then BOOL_ARGS+=' --render-neuron-morphology-progressive '; fi
if [ "$RENDER_NEURON_MESH_IMAGE" == "yes" ];
then BOOL_ARGS+=' --render-neuron-mesh '; fi
if [ "$RENDER_NEURON_MESH_360_SEQUENCE" == "yes" ];
then BOOL_ARGS+=' --render-neuron-mesh-360 '; fi
if [ "$RENDER_IMAGES_TO_SCALE" == "yes" ];
then BOOL_ARGS+=' --render-to-scale '; fi
if [ "$RENDER_SCALE_BAR" == "yes" ];
then BOOL_ARGS+=' --render-scale-bar '; fi
####################################################################################################
# Morphology positioning parameters
if [ "$GLOBAL_COORDINATES" == "yes" ];
then BOOL_ARGS+=' --global-coordinates '; fi
if [ "$ADD_NUCLEUS" == "yes" ];
then BOOL_ARGS+=' --add-nucleus '; fi
####################################################################################################
# Export morphology
if [ "$EXPORT_NEURON_MORPHOLOGY_SWC" == "yes" ];
then BOOL_ARGS+=' --export-morphology-swc'; fi
if [ "$EXPORT_NEURON_MORPHOLOGY_BLEND" == "yes" ];
then BOOL_ARGS+=' --export-morphology-blend '; fi
if [ "#EXPORT_NEURON_MORPHOLOGY_SEGMENTS" == "yes" ];
then BOOL_ARGS+=' --export-morphology-segments'; fi
####################################################################################################
# Export soma mesh
if [ "$EXPORT_SOMA_MESH_PLY" == "yes" ];
then BOOL_ARGS+=' --export-soma-mesh-ply '; fi
if [ "$EXPORT_SOMA_MESH_OBJ" == "yes" ];
then BOOL_ARGS+=' --export-soma-mesh-obj '; fi
if [ "$EXPORT_SOMA_MESH_STL" == "yes" ];
then BOOL_ARGS+=' --export-soma-mesh-stl '; fi
if [ "$EXPORT_SOMA_MESH_BLEND" == "yes" ];
then BOOL_ARGS+=' --export-soma-mesh-blend '; fi
####################################################################################################
# Export neuron mesh
if [ "$EXPORT_NEURON_MESH_PLY" == "yes" ];
then BOOL_ARGS+=' --export-neuron-mesh-ply '; fi
if [ "$EXPORT_NEURON_MESH_OBJ" == "yes" ];
then BOOL_ARGS+=' --export-neuron-mesh-obj '; fi
if [ "$EXPORT_NEURON_MESH_STL" == "yes" ];
then BOOL_ARGS+=' --export-neuron-mesh-stl '; fi
if [ "$EXPORT_NEURON_MESH_BLEND" == "yes" ];
then BOOL_ARGS+=' --export-neuron-mesh-blend '; fi
if [ "$EXPORT_INDIVIDUALS" == "yes" ];
then BOOL_ARGS+=' --export-individuals '; fi
####################################################################################################
# Morphology analysis
if [ "$ANALYZE_MORPHOLOGY_SKELETON" == "yes" ];
then BOOL_ARGS+=' --analyze-morphology '; fi
####################################################################################################
# echo 'FLAGS:' $BOOL_ARGS
echo -e "\nRUNNING ... NeuroMorphoVis \n"
../../../python/bin/python3.10 neuromorphovis.py \
--blender=$BLENDER_EXECUTABLE \
--input=$INPUT \
--blue-config=$BLUE_CONFIG \
--gid=$GID \
--target=$TARGET \
--morphology-file=$MORPHOLOGY_FILE \
--morphology-directory=$MORPHOLOGY_DIRECTORY \
--output-directory=$OUTPUT_DIRECTORY \
--morphology-reconstruction-algorithm=$MORPHOLOGY_RECONSTRUCTION_ALGORITHM \
--morphology-skeleton-style=$SKELETON_STYLE \
--morphology-color-coding=$MORPHOLOGY_COLOR_CODING_SCHEME \
--morphology-colormap=$MORPHOLOGY_COLORMAP \
--meshing-algorithm=$MESHING_TECHNIQUE \
--axon-branching-order=$MAX_AXON_BRANCHING_ORDER \
--basal-dendrites-branching-order=$MAX_BASAL_DENDRITES_BRANCHING_ORDER \
--apical-dendrites-branching-order=$MAX_APICAL_DENDRITES_BRANCHING_ORDER \
--soma-representation=$SOMA_REPRESENTATION \
--soma-stiffness=$SOMA_STIFFNESS \
--soma-subdivision-level=$SOMA_SUBDIVISION_LEVEL \
--edges=$EDGES \
--surface=$SURFACE \
--spines=$SPINES \
--spines-quality=SPINES_QUALITY \
--number-spines-per-micron=$NUMBER_SPINES_PER_MICRON \
--soma-color=$SOMA_COLOR \
--axons-color=$AXON_COLOR \
--apical-dendrites-color=$APICAL_DENDRITE_COLOR \
--basal-dendrites-color=$BASAL_DENDRITES_COLOR \
--spines-color=$SPINES_COLOR \
--nucleus-color=$NUCLEUS_COLOR \
--samples-radii=$SAMPLES_RADII \
--radii-scale-factor=$RADII_SCALE_FACTOR \
--unified-morphology-radius=$UNIFIED_SAMPLES_RADIUS \
--axon-radius=$AXON_RADIUS \
--apical-dendrites-radius=$APICAL_DENDRITES_RADIUS \
--basal-dendrites-radius=$BASAL_DENDRITES_RADIUS \
--bevel-sides=$SECTION_BEVEL_SIDES \
--camera-view=$CAMERA_VIEW \
--rendering-view=$RENDERING_VIEW \
--frame-resolution=$FRAME_RESOLUTION \
--resolution-scale-factor=$RESOLUTION_SCALE_FACTOR \
--close-up-dimensions=$CLOSEUP_VIEW_DIMENSIONS \
--image-file-format=$IMAGE_FILE_FORMAT \
--shader=$SHADER \
--execution-node=$EXECUTION_NODE \
--tessellation-level=$TESSELLATION_LEVEL \
$BOOL_ARGS
echo -e "\nDONE ... NeuroMorphoVis \n"
####################################################################################################