cnmodel.morphology package

cnmodel.morphology.hoc_reader

class cnmodel.morphology.hoc_reader.HocReader(hoc)

Bases: object

Provides useful methods for reading hoc structures.

Parameters:hoc – Either a hoc object that hs been already created, or a string that defines a hoc file name.

add_groups_by_section_list(names)

Add a new section groups from the hoc variables indicated in names.

Parameters:

• names (list) –

  List containing variable names as strings. Each name must refer to a list of

  Sections in hoc. If a dict is supplied instead, then it maps {hoc_list_name: section_group_name}.

• effects (modifies) (Side) –
• ----------------------- – calls add_section_group

add_section_group(name, sections, overwrite=False)

Declare a grouping of sections (or section names). Sections may be grouped by any arbitrary criteria (cell, anatomical type, etc).

Parameters:

• name (str) – name of the section group
• sections (list) – section names or hoc Section objects.

find_hoc_hname(regex)

Find hoc names matching a pattern

Parameters:regex (str) – Regular expression (Python Re module) to search for. Returns:The names of HOC objects whose hname matches regex. Return type:list

get_branch(root)

Return all sections in a branch, starting with root.

Parameters:root – The NEURON section object.

get_density(section, mechanism)

Get density mechanism that may be found the section. mechanism is a list [‘name’, ‘gbarname’]. This is needed because some mechanisms do not adhere to any convention and may have a different kind of ‘gbarname’ than ‘gbar<name>_mechname’ returns the average of the conductance density, as that may range across different values in a section (e.g., can vary by segments)

Parameters:

• section – The NEURON section object.
• mechanism (list) – mechanism is a list [‘name’, ‘gbarname’]. It is used to retrieve the mechanism density from HOC as segment.name.gbarname.

Returns:

Return type:

Mean conductance of the selected mechanism in the section, averaged across all segments of the section.

get_geometry()

modified from:neuronvisio Generate structures that describe the geometry of the sections and their segments (all segments are returned)

Returns:

• vertexes (record array containing {pos: (x,y,z), dia, sec_id}) – for each segment.
• edges (array of pairs indicating the indexes of connected) – vertexes.
• Side effects
• ———— – Modifies vertexes and edges.

get_mechanisms(section)

Get a set of all of the mechanisms inserted into a given section

Parameters:section – The NEURON section object. Returns: Return type:A list of mechanism names

get_sec_info(section)

Get the info of the given section modified from: neuronvisio

Parameters:section – The NEURON section object. Returns:containing the information, with html formatting. Return type:str

get_section(sec_name)

Get the section associated with the section name

Parameters:sec_name (str) – The name of the section object. Returns: Return type:The hoc Section object with the given name.

get_section_group(name)

Get a section group by name :param name: name of the group (dendrite, for example) :type name: str

Returns: Return type:The set of section names in the group name.

get_section_lists()

Search through all of the hoc variables to find those that are “SectionLists”

get_section_prefixes()

Go through all the sections and generate a dictionary mapping their name prefixes to the list of sections with that prefix.

For example, with sections names axon[0], axon[1], ais[0], and soma[0], we would generate the following structure:

{‘axon’: [‘axon[0]’, ‘axon[1]’],

‘ais’: [‘ais[0]’], ‘soma’: [‘soma[0]’]}

hoc_namespace()

Get a dict of the HOC namespace {‘variable_name’: hoc_object}. NOTE: this method requires NEURON >= 7.3

make_volume_data(resolution=1.0, max_size=500000000.0)

Using the current state of vertexes, edges, generates a scalar field useful for building isosurface or volumetric renderings.

Parameters:

• resolution (float, default=1.0 microns) – width (um) of a single voxel in the scalar field.
• max_size (int) – maximum allowed scalar field size (bytes).

Returns:

• * 3D scalar field indicating distance from nearest membrane,
• * 3D field indicating section IDs of nearest membrane,
• * QTransform that maps from 3D array indexes to original vertex – coordinates.

read_section_info()

Read all the information about the sections in the current hoc file Stores the result in the mechanisms class variable.

retrieve_coordinate(section)

Retrieve the coordinates of a section avoiding duplicates

Parameters:section – The NEURON section object. Returns:arrays of x, y, z, d for all the segments of the specified section. Return type:array

translate_branch(root, dx)

Move the branch beginning at root by dx.

Parameters:

• root – The NEURON section object.
• dx (array) – Which must be an array of length 3 defining the translation.

cnmodel.morphology.morphology

class cnmodel.morphology.morphology.Morphology

Bases: object

Base class for morphological structure Provides the ability to read .hoc files for NEURON simulations.

hocReader(filename=None)

Access the hoc reader

Parameters:filename (str (default: None)) – The hoc file to read and save as the morphology object

init()

swcReader(filename=None)

Access the swc reader (*NOT IMPLEMENTED*)

Parameters:filename (str (default: None)) – The swc file to read and save as the morphology object