sonataexplorer::neuroscience::common::MorphologyLoader Class Reference

#include <MorphologyLoader.h>

Inheritance diagram for sonataexplorer::neuroscience::common::MorphologyLoader:

Collaboration diagram for sonataexplorer::neuroscience::common::MorphologyLoader:

Public Member Functions
	MorphologyLoader (core::Scene &scene, core::PropertyMap &&loaderParams, const core::Transformation &transformation=core::Transformation())
std::string	getName () const final
strings	getSupportedStorage () const final
bool	isSupported (const std::string &storage, const std::string &extension) const final
core::PropertyMap	getProperties () const final
core::ModelDescriptorPtr	importFromBlob (core::Blob &&blob, const core::LoaderProgress &callback, const core::PropertyMap &properties) const final
core::ModelDescriptorPtr	importFromStorage (const std::string &storage, const core::LoaderProgress &callback, const core::PropertyMap &properties) const final
ParallelModelContainer	importMorphology (const Gid &gid, const core::PropertyMap &properties, const std::string &source, const uint64_t index, const SynapsesInfo &synapsesInfo, const core::Matrix4f &transformation=core::Matrix4f(), CompartmentReportPtr compartmentReport=nullptr, const float mitochondriaDensity=0.f, const float voltageScaling=1.f, const floats &voltages=floats()) const
	importMorphology imports a single morphology from a specified URI More...
void	setBaseMaterialId (const size_t materialId)
	setBaseMaterialId Set the base material ID for the morphology More...
Public Member Functions inherited from core::Loader
	Loader (Scene &scene)
virtual	~Loader ()=default

Static Public Member Functions
static core::PropertyMap	getCLIProperties ()
static void	createMissingMaterials (core::Model &model, const bool castUserData=false)
	createMissingMaterials Checks that all materials exist for existing geometry in the model. Missing materials are created with the default parameters More...
static const brain::neuron::SectionTypes	getSectionTypesFromProperties (const core::PropertyMap &properties)

Additional Inherited Members
Protected Attributes inherited from core::Loader
Scene &	_scene

Detailed Description

Loads morphologies from SWC and H5, and Circuit Config files

Definition at line 49 of file MorphologyLoader.h.

Constructor & Destructor Documentation

MorphologyLoader()

sonataexplorer::neuroscience::common::MorphologyLoader::MorphologyLoader	(	core::Scene &	scene,
		core::PropertyMap &&	loaderParams,
		const core::Transformation &	transformation = core::Transformation()
	)

Definition at line 73 of file MorphologyLoader.cpp.

Member Function Documentation

createMissingMaterials()

void sonataexplorer::neuroscience::common::MorphologyLoader::createMissingMaterials ( core::Model &  model, const bool  castUserData = false  )

static

createMissingMaterials Checks that all materials exist for existing geometry in the model. Missing materials are created with the default parameters

Definition at line 1227 of file MorphologyLoader.cpp.

getCLIProperties()

PropertyMap sonataexplorer::neuroscience::common::MorphologyLoader::getCLIProperties ( )

static

Definition at line 1187 of file MorphologyLoader.cpp.

getName()

std::string sonataexplorer::neuroscience::common::MorphologyLoader::getName ( ) const

finalvirtual

Returns

The loader name

Implements core::Loader.

Definition at line 80 of file MorphologyLoader.cpp.

getProperties()

PropertyMap sonataexplorer::neuroscience::common::MorphologyLoader::getProperties ( ) const

finalvirtual

Returns

The loader properties

Reimplemented from core::Loader.

Definition at line 1182 of file MorphologyLoader.cpp.

getSectionTypesFromProperties()

const brain::neuron::SectionTypes sonataexplorer::neuroscience::common::MorphologyLoader::getSectionTypesFromProperties ( const core::PropertyMap &  properties )

static

Definition at line 1213 of file MorphologyLoader.cpp.

getSupportedStorage()

std::vector< std::string > sonataexplorer::neuroscience::common::MorphologyLoader::getSupportedStorage ( ) const

finalvirtual

Returns

The loaders supported file extensions

Implements core::Loader.

Definition at line 85 of file MorphologyLoader.cpp.

importFromBlob()

ModelDescriptorPtr sonataexplorer::neuroscience::common::MorphologyLoader::importFromBlob ( core::Blob &&  blob, const core::LoaderProgress &  callback, const core::PropertyMap &  properties  ) const

finalvirtual

Import the data from the blob and return the created model.

Parameters

blob	the blob containing the data to import
callback	Callback for loader progress
properties	Properties used for loading

Returns

the model that has been created by the loader

Implements core::Loader.

Definition at line 1157 of file MorphologyLoader.cpp.

importFromStorage()

ModelDescriptorPtr sonataexplorer::neuroscience::common::MorphologyLoader::importFromStorage ( const std::string &  storage, const core::LoaderProgress &  callback, const core::PropertyMap &  properties  ) const

finalvirtual

Implements core::Loader.

Definition at line 1163 of file MorphologyLoader.cpp.

importMorphology()

ParallelModelContainer sonataexplorer::neuroscience::common::MorphologyLoader::importMorphology	(	const Gid &	gid,
		const core::PropertyMap &	properties,
		const std::string &	source,
		const uint64_t	index,
		const SynapsesInfo &	synapsesInfo,
		const core::Matrix4f &	transformation = core::Matrix4f(),
		CompartmentReportPtr	compartmentReport = nullptr,
		const float	mitochondriaDensity = 0.f,
		const float	voltageScaling = 1.f,
		const floats &	voltages = floats()
	)		const

importMorphology imports a single morphology from a specified URI

Parameters

uri	URI of the morphology
index	Index of the morphology
defaultMaterialId	Material to use
compartmentReport	Compartment report to map to the morphology

Returns

Model container

Definition at line 96 of file MorphologyLoader.cpp.

isSupported()

bool sonataexplorer::neuroscience::common::MorphologyLoader::isSupported ( const std::string &  storage, const std::string &  extension  ) const

finalvirtual

Query the loader if it can load the given file

Implements core::Loader.

Definition at line 90 of file MorphologyLoader.cpp.

setBaseMaterialId()

void sonataexplorer::neuroscience::common::MorphologyLoader::setBaseMaterialId ( const size_t  materialId )

inline

setBaseMaterialId Set the base material ID for the morphology

Parameters

materialId

Id of the base material ID for the morphology

Definition at line 98 of file MorphologyLoader.h.

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The documentation for this class was generated from the following files:

• bioexplorer/backend/plugins/Sonata/plugin/neuroscience/common/MorphologyLoader.h
• bioexplorer/backend/plugins/Sonata/plugin/neuroscience/common/MorphologyLoader.cpp