#include <morphology.h>
Public Member Functions | |
| Morphology (const Morphology &) noexcept=default | |
| Morphology & | operator= (const Morphology &) noexcept=default |
| Morphology (Morphology &&) noexcept=default | |
| Morphology & | operator= (Morphology &&) noexcept=default |
Read API | |
| class | mut::Morphology |
| std::shared_ptr< Property::Properties > | properties_ |
| Morphology (const std::string &path, unsigned int options=NO_MODIFIER, std::shared_ptr< WarningHandler >=nullptr) | |
| Morphology (const HighFive::Group &group, unsigned int options=NO_MODIFIER, std::shared_ptr< WarningHandler >=nullptr) | |
| Morphology (const mut::Morphology &) | |
| Morphology (const std::string &contents, const std::string &extension, unsigned int options=NO_MODIFIER, std::shared_ptr< WarningHandler >=nullptr) | |
| Soma | soma () const |
| Mitochondria | mitochondria () const |
| EndoplasmicReticulum | endoplasmicReticulum () const |
| const std::vector< Property::Annotation > & | annotations () const |
| const std::vector< Property::Marker > & | markers () const |
| std::vector< Section > | rootSections () const |
| std::vector< Section > | sections () const |
| Section | section (uint32_t id) const |
| const Points & | points () const noexcept |
| std::vector< uint32_t > | sectionOffsets () const |
| const std::vector< morphio::floatType > & | diameters () const |
| const std::vector< morphio::floatType > & | perimeters () const |
| const std::vector< SectionType > & | sectionTypes () const |
| const std::map< int, std::vector< unsigned int > > & | connectivity () const |
| depth_iterator | depth_begin () const |
| depth_iterator | depth_end () const |
| breadth_iterator | breadth_begin () const |
| breadth_iterator | breadth_end () const |
| const SomaType & | somaType () const |
| const CellFamily & | cellFamily () const |
| const MorphologyVersion & | version () const |
| Morphology (const Property::Properties &properties, unsigned int options) | |
| template<typename Property > | |
| const std::vector< typename Property::Type > & | get () const |
Detailed Description
Class that gives read access to a Morphology file.
Following RAII, this class is ready to use after the creation and will ensure release of resources upon destruction.
Constructor & Destructor Documentation
◆ Morphology() [1/4]
|
explicit |
Open the given source to a morphology file and parse it.
- Parameters
-
source path to a source file. options is the modifier flags to be applied. All flags are defined in their corresponding morphio.enums.Option and can be composed.
Example: Morphology("neuron.asc", TWO_POINTS_SECTIONS | SOMA_SPHERE);
◆ Morphology() [2/4]
|
explicit |
Constructor from an already parsed file
◆ Morphology() [3/4]
|
explicit |
Constructor from an instance of morphio::mut::Morphology
◆ Morphology() [4/4]
|
explicit |
Load a morphology from a string
Member Function Documentation
◆ annotations()
| const std::vector<Property::Annotation>& morphio::Morphology::annotations | ( | ) | const |
Return the annotation object
◆ breadth_begin()
| breadth_iterator morphio::Morphology::breadth_begin | ( | ) | const |
Breadth first iterator
If id == -1, the iteration will be successively performed starting at each root section
◆ breadth_end()
| breadth_iterator morphio::Morphology::breadth_end | ( | ) | const |
breadth end iterator
◆ cellFamily()
| const CellFamily& morphio::Morphology::cellFamily | ( | ) | const |
Return the cell family (neuron or glia)
◆ connectivity()
| const std::map<int, std::vector<unsigned int> >& morphio::Morphology::connectivity | ( | ) | const |
Return the graph connectivity of the morphology where each section is seen as a node Note: -1 is the soma node
◆ depth_begin()
| depth_iterator morphio::Morphology::depth_begin | ( | ) | const |
Depth first iterator starting at a given section id
If id == -1, the iteration will start at each root section, successively
◆ depth_end()
| depth_iterator morphio::Morphology::depth_end | ( | ) | const |
depth end iterator
◆ diameters()
| const std::vector<morphio::floatType>& morphio::Morphology::diameters | ( | ) | const |
Return a vector with all diameters from all sections (soma points are not included)
◆ endoplasmicReticulum()
| EndoplasmicReticulum morphio::Morphology::endoplasmicReticulum | ( | ) | const |
Return the endoplasmic reticulum object
◆ markers()
| const std::vector<Property::Marker>& morphio::Morphology::markers | ( | ) | const |
Return the markers
◆ mitochondria()
| Mitochondria morphio::Morphology::mitochondria | ( | ) | const |
Return the mitochondria object
◆ perimeters()
| const std::vector<morphio::floatType>& morphio::Morphology::perimeters | ( | ) | const |
Return a vector with all perimeters from all sections
◆ points()
|
noexcept |
Return a vector with all points from all sections (soma points are not included)
◆ rootSections()
| std::vector<Section> morphio::Morphology::rootSections | ( | ) | const |
Return a vector of all root sections (sections whose parent ID are -1)
◆ section()
| Section morphio::Morphology::section | ( | uint32_t | id | ) | const |
Return the Section with the given id.
- Exceptions
-
RawDataError if the id is out of range
◆ sectionOffsets()
| std::vector<uint32_t> morphio::Morphology::sectionOffsets | ( | ) | const |
Returns a list with offsets to access data of a specific section in the points and diameters arrays.
Example: accessing diameters of n'th section will be located in the Morphology::diameters array from diameters[sectionOffsets(n)] to diameters[sectionOffsets(n+1)-1]
Note: for convenience, the last point of this array is the points() array size so that the above example works also for the last section.
◆ sections()
| std::vector<Section> morphio::Morphology::sections | ( | ) | const |
Return a vector containing all section objects
Notes: Soma is not included
◆ sectionTypes()
| const std::vector<SectionType>& morphio::Morphology::sectionTypes | ( | ) | const |
Return a vector with the section type of every section
◆ soma()
| Soma morphio::Morphology::soma | ( | ) | const |
Return the soma object
◆ somaType()
| const SomaType& morphio::Morphology::somaType | ( | ) | const |
Return the soma type
◆ version()
| const MorphologyVersion& morphio::Morphology::version | ( | ) | const |
Return the version