Blue Brain BioExplorer
Namespaces | Classes | Enumerations | Functions | Variables
bioexplorer Namespace Reference

Namespaces

 atlas
 
 common
 
 connectomics
 
 details
 
 fields
 
 io
 
 mediamaker
 
 meshing
 
 metabolism
 
 molecularsystems
 
 morphology
 
 rendering
 
 vasculature
 

Classes

class  BioExplorerPlugin
 This class implements the BioExplorer plugin. More...
 

Enumerations

enum class  DisplacementElement {
  vasculature_segment_strength = 0 , vasculature_segment_frequency = 1 , morphology_soma_strength = 2 , morphology_soma_frequency = 3 ,
  morphology_section_strength = 4 , morphology_section_frequency = 5 , morphology_nucleus_strength = 6 , morphology_nucleus_frequency = 7 ,
  morphology_mitochondrion_strength = 8 , morphology_mitochondrion_frequency = 9 , morphology_myelin_steath_strength = 10 , morphology_myelin_steath_frequency = 11 ,
  morphology_spine_strength = 12 , morphology_spine_frequency = 13
}
 

Functions

Boxd vector_to_bounds (const doubles &lowBounds, const doubles &highBounds)
 
void _addBioExplorerVoxelRenderer (Engine &engine)
 
void _addBioExplorerDensityRenderer (Engine &engine)
 
void _addBioExplorerPathTracingRenderer (Engine &engine)
 
void _addBioExplorerGolgiStyleRenderer (Engine &engine)
 
ExtensionPlugin * core_plugin_create (int argc, char **argv)
 

Variables

const std::string PLUGIN_API_PREFIX = "be-"
 
const double DEFAULT_VASCULATURE_SEGMENT_STRENGTH = 0.3
 
const double DEFAULT_VASCULATURE_SEGMENT_FREQUENCY = 0.5
 
const double DEFAULT_MORPHOLOGY_SOMA_STRENGTH = 0.1
 
const double DEFAULT_MORPHOLOGY_SOMA_FREQUENCY = 3.0
 
const double DEFAULT_MORPHOLOGY_SECTION_STRENGTH = 0.15
 
const double DEFAULT_MORPHOLOGY_SECTION_FREQUENCY = 2.0
 
const double DEFAULT_MORPHOLOGY_NUCLEUS_STRENGTH = 0.01
 
const double DEFAULT_MORPHOLOGY_NUCLEUS_FREQUENCY = 2.0
 
const double DEFAULT_MORPHOLOGY_MITOCHONDRION_STRENGTH = 0.2
 
const double DEFAULT_MORPHOLOGY_MITOCHONDRION_FREQUENCY = 100.0
 
const double DEFAULT_MORPHOLOGY_MYELIN_STEATH_STRENGTH = 0.1
 
const double DEFAULT_MORPHOLOGY_MYELIN_STEATH_FREQUENCY = 2.5
 
const double DEFAULT_MORPHOLOGY_SPINE_STRENGTH = 0.01
 
const double DEFAULT_MORPHOLOGY_SPINE_FREQUENCY = 25.0
 
const std::string CONTENTS_DELIMITER = "||||"
 
const std::string METADATA_ASSEMBLY = "Assembly"
 
const std::string METADATA_PDB_ID = "PDBId"
 
const std::string METADATA_HEADER = "Header"
 
const std::string METADATA_ATOMS = "Atoms"
 
const std::string METADATA_BONDS = "Bonds"
 
const std::string METADATA_SIZE = "Size"
 
const std::string METADATA_BRICK_ID = "BrickId"
 
const std::string ARG_DB_HOST = "--db-host"
 
const std::string ARG_DB_PORT = "--db-port"
 
const std::string ARG_DB_NAME = "--db-name"
 
const std::string ARG_DB_USER = "--db-user"
 
const std::string ARG_DB_PASSWORD = "--db-password"
 
const std::string ARG_DB_NB_CONNECTIONS = "--db-nb-connections"
 
const std::string ARG_DB_BATCH_SIZE = "--db-batch-size"
 
const size_t DEFAULT_DB_NB_CONNECTIONS = 8
 
const size_t DEFAULT_BATCH_SIZE = 1000
 
const std::string ARG_OOC_ENABLED = "--ooc-enabled"
 
const std::string ARG_OOC_VISIBLE_BRICKS = "--ooc-visible-bricks"
 
const std::string ARG_OOC_UPDATE_FREQUENCY = "--ooc-update-frequency"
 
const std::string ARG_OOC_UNLOAD_BRICKS = "--ooc-unload-bricks"
 
const std::string ARG_OOC_SHOW_GRID = "--ooc-show-grid"
 
const std::string ARG_OOC_NB_BRICKS_PER_CYCLE = "--ooc-nb-bricks-per-cycle"
 
const std::string ENV_ROCKETS_DISABLE_SCENE_BROADCASTING = "ROCKETS_DISABLE_SCENE_BROADCASTING"
 
const size_t DEFAULT_BEZIER_STEP = 4
 
const double NO_GRID_ALIGNMENT = 0.0
 

Enumeration Type Documentation

◆ DisplacementElement

enum bioexplorer::DisplacementElement
strong
Enumerator
vasculature_segment_strength 
vasculature_segment_frequency 
morphology_soma_strength 
morphology_soma_frequency 
morphology_section_strength 
morphology_section_frequency 
morphology_nucleus_strength 
morphology_nucleus_frequency 
morphology_mitochondrion_strength 
morphology_mitochondrion_frequency 
morphology_myelin_steath_strength 
morphology_myelin_steath_frequency 
morphology_spine_strength 
morphology_spine_frequency 

Definition at line 28 of file Displacement.h.

Function Documentation

◆ _addBioExplorerDensityRenderer()

void bioexplorer::_addBioExplorerDensityRenderer ( Engine &  engine)

Definition at line 157 of file BioExplorerPlugin.cpp.

◆ _addBioExplorerGolgiStyleRenderer()

void bioexplorer::_addBioExplorerGolgiStyleRenderer ( Engine &  engine)

Definition at line 191 of file BioExplorerPlugin.cpp.

◆ _addBioExplorerPathTracingRenderer()

void bioexplorer::_addBioExplorerPathTracingRenderer ( Engine &  engine)

Definition at line 173 of file BioExplorerPlugin.cpp.

◆ _addBioExplorerVoxelRenderer()

void bioexplorer::_addBioExplorerVoxelRenderer ( Engine &  engine)

Definition at line 145 of file BioExplorerPlugin.cpp.

◆ core_plugin_create()

ExtensionPlugin* bioexplorer::core_plugin_create ( int  argc,
char **  argv 
)

Definition at line 2205 of file BioExplorerPlugin.cpp.

◆ vector_to_bounds()

Boxd bioexplorer::vector_to_bounds ( const doubles &  lowBounds,
const doubles &  highBounds 
)

Definition at line 130 of file BioExplorerPlugin.cpp.

Variable Documentation

◆ ARG_DB_BATCH_SIZE

const std::string bioexplorer::ARG_DB_BATCH_SIZE = "--db-batch-size"

Definition at line 57 of file Types.h.

◆ ARG_DB_HOST

const std::string bioexplorer::ARG_DB_HOST = "--db-host"

Definition at line 51 of file Types.h.

◆ ARG_DB_NAME

const std::string bioexplorer::ARG_DB_NAME = "--db-name"

Definition at line 53 of file Types.h.

◆ ARG_DB_NB_CONNECTIONS

const std::string bioexplorer::ARG_DB_NB_CONNECTIONS = "--db-nb-connections"

Definition at line 56 of file Types.h.

◆ ARG_DB_PASSWORD

const std::string bioexplorer::ARG_DB_PASSWORD = "--db-password"

Definition at line 55 of file Types.h.

◆ ARG_DB_PORT

const std::string bioexplorer::ARG_DB_PORT = "--db-port"

Definition at line 52 of file Types.h.

◆ ARG_DB_USER

const std::string bioexplorer::ARG_DB_USER = "--db-user"

Definition at line 54 of file Types.h.

◆ ARG_OOC_ENABLED

const std::string bioexplorer::ARG_OOC_ENABLED = "--ooc-enabled"

Definition at line 62 of file Types.h.

◆ ARG_OOC_NB_BRICKS_PER_CYCLE

const std::string bioexplorer::ARG_OOC_NB_BRICKS_PER_CYCLE = "--ooc-nb-bricks-per-cycle"

Definition at line 67 of file Types.h.

◆ ARG_OOC_SHOW_GRID

const std::string bioexplorer::ARG_OOC_SHOW_GRID = "--ooc-show-grid"

Definition at line 66 of file Types.h.

◆ ARG_OOC_UNLOAD_BRICKS

const std::string bioexplorer::ARG_OOC_UNLOAD_BRICKS = "--ooc-unload-bricks"

Definition at line 65 of file Types.h.

◆ ARG_OOC_UPDATE_FREQUENCY

const std::string bioexplorer::ARG_OOC_UPDATE_FREQUENCY = "--ooc-update-frequency"

Definition at line 64 of file Types.h.

◆ ARG_OOC_VISIBLE_BRICKS

const std::string bioexplorer::ARG_OOC_VISIBLE_BRICKS = "--ooc-visible-bricks"

Definition at line 63 of file Types.h.

◆ CONTENTS_DELIMITER

const std::string bioexplorer::CONTENTS_DELIMITER = "||||"

Definition at line 38 of file Types.h.

◆ DEFAULT_BATCH_SIZE

const size_t bioexplorer::DEFAULT_BATCH_SIZE = 1000

Definition at line 59 of file Types.h.

◆ DEFAULT_BEZIER_STEP

const size_t bioexplorer::DEFAULT_BEZIER_STEP = 4

Definition at line 73 of file Types.h.

◆ DEFAULT_DB_NB_CONNECTIONS

const size_t bioexplorer::DEFAULT_DB_NB_CONNECTIONS = 8

Definition at line 58 of file Types.h.

◆ DEFAULT_MORPHOLOGY_MITOCHONDRION_FREQUENCY

const double bioexplorer::DEFAULT_MORPHOLOGY_MITOCHONDRION_FREQUENCY = 100.0

Definition at line 56 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_MITOCHONDRION_STRENGTH

const double bioexplorer::DEFAULT_MORPHOLOGY_MITOCHONDRION_STRENGTH = 0.2

Definition at line 55 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_MYELIN_STEATH_FREQUENCY

const double bioexplorer::DEFAULT_MORPHOLOGY_MYELIN_STEATH_FREQUENCY = 2.5

Definition at line 58 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_MYELIN_STEATH_STRENGTH

const double bioexplorer::DEFAULT_MORPHOLOGY_MYELIN_STEATH_STRENGTH = 0.1

Definition at line 57 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_NUCLEUS_FREQUENCY

const double bioexplorer::DEFAULT_MORPHOLOGY_NUCLEUS_FREQUENCY = 2.0

Definition at line 54 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_NUCLEUS_STRENGTH

const double bioexplorer::DEFAULT_MORPHOLOGY_NUCLEUS_STRENGTH = 0.01

Definition at line 53 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_SECTION_FREQUENCY

const double bioexplorer::DEFAULT_MORPHOLOGY_SECTION_FREQUENCY = 2.0

Definition at line 52 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_SECTION_STRENGTH

const double bioexplorer::DEFAULT_MORPHOLOGY_SECTION_STRENGTH = 0.15

Definition at line 51 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_SOMA_FREQUENCY

const double bioexplorer::DEFAULT_MORPHOLOGY_SOMA_FREQUENCY = 3.0

Definition at line 50 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_SOMA_STRENGTH

const double bioexplorer::DEFAULT_MORPHOLOGY_SOMA_STRENGTH = 0.1

Definition at line 49 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_SPINE_FREQUENCY

const double bioexplorer::DEFAULT_MORPHOLOGY_SPINE_FREQUENCY = 25.0

Definition at line 60 of file Displacement.h.

◆ DEFAULT_MORPHOLOGY_SPINE_STRENGTH

const double bioexplorer::DEFAULT_MORPHOLOGY_SPINE_STRENGTH = 0.01

Definition at line 59 of file Displacement.h.

◆ DEFAULT_VASCULATURE_SEGMENT_FREQUENCY

const double bioexplorer::DEFAULT_VASCULATURE_SEGMENT_FREQUENCY = 0.5

Definition at line 47 of file Displacement.h.

◆ DEFAULT_VASCULATURE_SEGMENT_STRENGTH

const double bioexplorer::DEFAULT_VASCULATURE_SEGMENT_STRENGTH = 0.3

Definition at line 46 of file Displacement.h.

◆ ENV_ROCKETS_DISABLE_SCENE_BROADCASTING

const std::string bioexplorer::ENV_ROCKETS_DISABLE_SCENE_BROADCASTING = "ROCKETS_DISABLE_SCENE_BROADCASTING"

Definition at line 70 of file Types.h.

◆ METADATA_ASSEMBLY

const std::string bioexplorer::METADATA_ASSEMBLY = "Assembly"

Definition at line 41 of file Types.h.

◆ METADATA_ATOMS

const std::string bioexplorer::METADATA_ATOMS = "Atoms"

Definition at line 44 of file Types.h.

◆ METADATA_BONDS

const std::string bioexplorer::METADATA_BONDS = "Bonds"

Definition at line 45 of file Types.h.

◆ METADATA_BRICK_ID

const std::string bioexplorer::METADATA_BRICK_ID = "BrickId"

Definition at line 47 of file Types.h.

◆ METADATA_HEADER

const std::string bioexplorer::METADATA_HEADER = "Header"

Definition at line 43 of file Types.h.

◆ METADATA_PDB_ID

const std::string bioexplorer::METADATA_PDB_ID = "PDBId"

Definition at line 42 of file Types.h.

◆ METADATA_SIZE

const std::string bioexplorer::METADATA_SIZE = "Size"

Definition at line 46 of file Types.h.

◆ NO_GRID_ALIGNMENT

const double bioexplorer::NO_GRID_ALIGNMENT = 0.0

Definition at line 76 of file Types.h.

◆ PLUGIN_API_PREFIX

const std::string bioexplorer::PLUGIN_API_PREFIX = "be-"

Definition at line 79 of file BioExplorerPlugin.cpp.