Python API¶
- class morphio.AccessMode¶
Members:
MODE_READ
MODE_WRITE
MODE_OVERWRITE
MODE_READWRITE
MODE_READOVERWRITE
- property name¶
handle) -> str
- Type
(self
- class morphio.Annotation¶
Container class for information about anomalies detected while parsing the file (no soma, section with a single child…)
- property details¶
Returns the details
- property diameters¶
Returns the list of diameters of annotated points
- property line_number¶
Returns the lineNumber
- property perimeters¶
Returns the list of perimeters of annotated points
- property points¶
Returns the list of coordinates of annotated points
- property section_id¶
Returns the sectionId
- property type¶
Returns the type
- class morphio.AnnotationType¶
Members:
single_child : Indicates that a section has only one child
- property name¶
handle) -> str
- Type
(self
- class morphio.CellLevel¶
Container class for information available at the cell level (cell type, file version, soma type)
- property cell_family¶
Returns the cell family (neuron or glia)
- property soma_type¶
Returns the soma type
- property version¶
Returns the version
- class morphio.EndoplasmicReticulum¶
The entry-point class to access endoplasmic reticulum data Spec https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
- property filament_counts¶
Returns the number of filaments for each neuronal section
- property section_indices¶
Returns the list of neuronal section indices
- property surface_areas¶
Returns the surface areas for each neuronal section
- property volumes¶
Returns the list of neuronal section indices
- exception morphio.IDSequenceError¶
- class morphio.IterType¶
Members:
depth_first
breadth_first
upstream
- property name¶
handle) -> str
- Type
(self
- exception morphio.MissingParentError¶
- class morphio.Mitochondria¶
The entry-point class to access mitochondrial data By design, it is the equivalent of the Morphology class but at the mitochondrial level As the Morphology class, it implements a section accessor and a root section accessor returning views on the Properties object for the queried mitochondrial section
- property root_sections¶
Returns a list of all root sections (section whose parent ID is -1)
- section(section_id: int) morphio::MitoSection ¶
Returns the mithochondrial section with the given ID
- property sections¶
Returns a list of all mitochondrial sections
- class morphio.MitochondriaPointLevel¶
Container class for the information available at the mitochondrial point level (enclosing neuronal section, relative distance to start of neuronal section, diameter)
- exception morphio.MorphioError¶
- exception morphio.MultipleTrees¶
- class morphio.Option¶
Members:
no_modifier
two_points_sections
soma_sphere
no_duplicates
nrn_order
- property name¶
handle) -> str
- Type
(self
- class morphio.PointLevel¶
Container class for information available at the point level (point coordinate, diameter, perimeter)
- property diameters¶
Returns the list of diameters
- property perimeters¶
Returns the list of perimeters
- property points¶
Returns the list of point coordinates
- class morphio.Properties¶
The higher level container structure is Property::Properties
- property cell_level¶
Returns the structure that stores information at the cell level
- property point_level¶
Returns the structure that stores information at the point level
- property section_level¶
Returns the structure that stores information at the section level
- exception morphio.RawDataError¶
- exception morphio.SectionBuilderError¶
- class morphio.SectionLevel¶
Container class for information available at the section level (section type, parent section)
- property children¶
Returns a dictionary where key is a section ID and value is the list of children section IDs
- property section_types¶
Returns the list of section types
- property sections¶
Returns a list of [offset, parent section ID]
- class morphio.SectionType¶
Members:
undefined
soma
axon
basal_dendrite
apical_dendrite
- property name¶
handle) -> str
- Type
(self
- exception morphio.SomaError¶
- class morphio.SomaType¶
Members:
SOMA_UNDEFINED
SOMA_SINGLE_POINT
SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS
SOMA_CYLINDERS
SOMA_SIMPLE_CONTOUR
- property name¶
handle) -> str
- Type
(self
- exception morphio.UnknownFileType¶
- class morphio.VasculatureSectionType¶
Members:
undefined
vein
artery
venule
arteriole
venous_capillary
arterial_capillary
transitional
- property name¶
handle) -> str
- Type
(self
- class morphio.Warning¶
Members:
undefined
mitochondria_write_not_supported
write_no_soma
write_empty_morphology
soma_non_conform
no_soma_found
disconnected_neurite
wrong_duplicate
appending_empty_section
wrong_root_point
only_child
- property name¶
handle) -> str
- Type
(self
- exception morphio.WriterError¶
- morphio.set_ignored_warning(*args, **kwargs)¶
Overloaded function.
set_ignored_warning
(warning: morphio::enums::Warning, ignore: bool = True) → NoneIgnore/Unignore a specific warning message
set_ignored_warning
(warning: List[morphio::enums::Warning], ignore: bool = True) → NoneIgnore/Unignore a list of warnings
- morphio.set_maximum_warnings(arg0: int) None ¶
Set the maximum number of warnings to be printed on screen 0 will print no warning -1 will print them all