Brion  2.0.0
The Blue Brain C++ I/O library
brain::neuron::Morphology Class Reference

Wrapper around brion::Morphology with higher level functions. More...

#include <morphology.h>

+ Inheritance diagram for brain::neuron::Morphology:
+ Collaboration diagram for brain::neuron::Morphology:

Public Member Functions

 Morphology (const URI &source, const Matrix4f &transform)
 Create a morphology from a URI, load all the data and transform the points. More...
 
 Morphology (const brion::Morphology &morphology, const Matrix4f &transform)
 Create a morphology from a brion::Morphology, load all the data and transform the points. More...
 
 Morphology (const URI &source)
 Create a morphology from a URI and load all the data. More...
 
 Morphology (const brion::Morphology &morphology)
 Create a morphology from a brion::Morphology and load all the data. More...
 
const Vector4fs & getPoints () const
 
const Vector2is & getSections () const
 
const SectionTypes & getSectionTypes () const
 
const Vector2is & getApicals () const
 
uint32_ts getSectionIDs (const SectionTypes &types) const
 Return the list of ids for the given section types. More...
 
Sections getSections (SectionType type) const
 Return the sections which have the given section type. More...
 
Sections getSections (const SectionTypes &types) const
 Return the sections which have any of the given section types. More...
 
Section getSection (const uint32_t &id) const
 Return the Section with the given id. More...
 
Soma getSoma () const
 Return the object with the information about the neuron soma.
 
const Matrix4f & getTransformation () const
 Returnthe transformation that was passed to the constructor or the identity matrix is no transformation was given.
 

Friends

class brain::Circuit
 

Detailed Description

Wrapper around brion::Morphology with higher level functions.

This class provides methods to facilitate some queries about morphologies in the context of circuits. Morphologies can be loaded with a transformation applied to its points, which is useful for operating in global circuit coordinates. The transformation is applied at construction so it cannot be modified or reverted.

Access to the raw data fields is still provided by getter functions.

Version
unstable

Definition at line 48 of file brain/neuron/morphology.h.

Constructor & Destructor Documentation

brain::neuron::Morphology::Morphology ( const URI &  source,
const Matrix4f &  transform 
)

Create a morphology from a URI, load all the data and transform the points.

Parameters
sourceURI of the morphology data source.
transformthe transformation matrix to apply to the points. Radii will not be affected by this transformation.
Exceptions
runtime_errorif an inconsistency is detected in the input file.
brain::neuron::Morphology::Morphology ( const brion::Morphology morphology,
const Matrix4f &  transform 
)

Create a morphology from a brion::Morphology, load all the data and transform the points.

Parameters
morphologythe brion::Morphology to load from.
transformthe transformation matrix to apply to the points. Radii will not be affected by this transformation.
Exceptions
runtime_errorif an inconsistency is detected in the input file.
brain::neuron::Morphology::Morphology ( const URI &  source)
explicit

Create a morphology from a URI and load all the data.

Parameters
sourceURI of the morphology data source.
Exceptions
runtime_errorif an inconsistency is detected in the input file.
brain::neuron::Morphology::Morphology ( const brion::Morphology morphology)
explicit

Create a morphology from a brion::Morphology and load all the data.

Parameters
morphologythe brion::Morphology to load from.
Exceptions
runtime_errorif an inconsistency is detected in the input file.

Member Function Documentation

const Vector2is& brain::neuron::Morphology::getApicals ( ) const
const Vector4fs& brain::neuron::Morphology::getPoints ( ) const
Section brain::neuron::Morphology::getSection ( const uint32_t &  id) const

Return the Section with the given id.

Exceptions
runtime_errorif the id is out of range or the given id refers to a soma section.
uint32_ts brain::neuron::Morphology::getSectionIDs ( const SectionTypes &  types) const

Return the list of ids for the given section types.

const Vector2is& brain::neuron::Morphology::getSections ( ) const
Sections brain::neuron::Morphology::getSections ( SectionType  type) const

Return the sections which have the given section type.

If type is SectionType::Soma an empty list is returned.

Sections brain::neuron::Morphology::getSections ( const SectionTypes &  types) const

Return the sections which have any of the given section types.

No sections are returned for the type SectionType::Soma.

const SectionTypes& brain::neuron::Morphology::getSectionTypes ( ) const
See also
brion::Morphology::readSectionTypes This type is not brain::SectionTypes because brion::SectionType is not convertible to brain::neuron::SectionType.

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