Neurons.h

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/*
 *
 * The Blue Brain BioExplorer is a tool for scientists to extract and analyse
 * scientific data from visualization
 *
 * This file is part of Blue Brain BioExplorer <https://github.com/BlueBrain/BioExplorer>
 *
 * Copyright 2020-2024 Blue BrainProject / EPFL
 *
 * 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, either version 3 of the License, or (at your option) any later
 * version.
 *
 * This program 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 <https://www.gnu.org/licenses/>.
 */
 
#pragma once
 
#include "Morphologies.h"
 
#include <science/api/Params.h>
#include <science/common/Types.h>
 
namespace bioexplorer
{
namespace morphology
{
using Varicosities = std::map<uint64_t, Vector3ds>;
 
class Neurons : public Morphologies
{
public:
    Neurons(core::Scene& scene, const details::NeuronsDetails& details, const core::Vector3d& assemblyPosition,
            const core::Quaterniond& assemblyRotation, const core::LoaderProgress& callback = core::LoaderProgress());
 
    Vector4ds getNeuronSectionPoints(const uint64_t neuronId, const uint64_t sectionId);
 
    Vector3ds getNeuronVaricosities(const uint64_t neuronId);
 
private:
    double _getDisplacementValue(const DisplacementElement& element) final;
 
    void _logRealismParams();
 
    void _buildModel(const core::LoaderProgress& callback);
 
    void _buildContours(common::ThreadSafeContainer& container, const NeuronSomaMap& somas);
 
    void _buildSurface(const NeuronSomaMap& somas);
 
    void _buildSomasOnly(core::Model& model, common::ThreadSafeContainer& container, const NeuronSomaMap& somas);
 
    void _buildOrientations(common::ThreadSafeContainer& container, const NeuronSomaMap& somas);
 
    void _buildMorphology(common::ThreadSafeContainer& container, const uint64_t neuronId, const NeuronSoma& soma,
                          const uint64_t neuronIndex, const float* voltages = nullptr);
 
    SectionSynapseMap _buildDebugSynapses(const uint64_t neuronId, const SectionMap& sections);
 
    void _addArrow(common::ThreadSafeContainer& container, const uint64_t neuronId, const core::Vector3d& somaPosition,
                   const core::Quaterniond& somaRotation, const core::Vector4d& srcNode, const core::Vector4d& dstNode,
                   const details::NeuronSectionType sectionType, const size_t baseMaterialId,
                   const double distanceToSoma);
 
    void _addSection(common::ThreadSafeContainer& container, const uint64_t neuronId, const uint64_t morphologyId,
                     const uint64_t sectionId, const Section& section, const core::Vector3d& somaPosition,
                     const core::Quaterniond& somaRotation, const double somaRadius, const size_t baseMaterialId,
                     const double mitochondriaDensity, const uint64_t somaUserData, const SectionSynapseMap& synapses,
                     const double distanceToSoma, const common::Neighbours& somaNeighbours,
                     const float voltageScaling = 1.f);
 
    void _addSpine(common::ThreadSafeContainer& container, const uint64_t neuronId, const uint64_t morphologyId,
                   const uint64_t sectionId, const Synapse& synapse, const size_t baseMaterialId,
                   const core::Vector3d& surfacePosition, const double radiusAtSurfacePosition);
 
    void _addSectionInternals(common::ThreadSafeContainer& container, const uint64_t neuronId,
                              const core::Vector3d& somaPosition, const core::Quaterniond& somaRotation,
                              const double sectionLength, const double sectionVolume, const core::Vector4fs& points,
                              const double mitochondriaDensity, const size_t baseMaterialId);
 
    void _addAxonMyelinSheath(common::ThreadSafeContainer& container, const uint64_t neuronId,
                              const core::Vector3d& somaPosition, const core::Quaterniond& somaRotation,
                              const double sectionLength, const core::Vector4fs& points,
                              const double mitochondriaDensity, const size_t materialId);
 
    void _addVaricosity(core::Vector4fs& points);
 
    void _attachSimulationReport(core::Model& model);
 
    const details::NeuronsDetails _details;
    core::Scene& _scene;
    Varicosities _varicosities;
    uint64_t _nbSpines{0};
    double _maxDistanceToSoma{0.0};
    core::Vector2d _minMaxSomaRadius{1e6, -1e6};
    common::SimulationReport _simulationReport;
    details::NeuronsReportParameters _neuronsReportParameters;
};
} // namespace morphology
} // namespace bioexplorer