celegans
def __init__(self, data_folder=None, base_dir=None, **kwargs):
docstring:
This class handles loading and parsing neuroanatomical data for the C.
elegans connectome from
https://www.biorxiv.org/content/10.1101/2020.04.30.066209v1
:param base_dir: path to directory to use for saving data (default
value None)
:param kwargs: can be used to pass path to individual data folders.
See brainrender/Utils/paths_manager.py
:param data_folder: str, path to a folder with data for the connectome
# TODO replace with downloading data
def _make_root(self, rootpath):
docstring:
Creates a root mesh by merging the mesh corresponding to each neuron,
then saves it as an obj file at rootpath
def get_neurons_by(self, getby='pair', lookup=None):
docstring:
Selects a subset of the neurons using some criteria and lookup key,
based on the neurons metadata
:param getby: str, name of the metadata key to use for selecting
neurons
:param lookup: str/int.. neurons whose attribute 'getby' matches the
lookup value will be selected
:returns: list of strings with neurons names
def get_neuron_color(self, neuron, colorby='type'):
docstring:
Get a neuron's RGB color. Colors can be assigned based on different
criteria
like the neuron's type or by individual neuron etc...
:param neuron: str, nueron name
:param colorby: str, metadata attribute to use for coloring
:returns: rgb values of color
def _get_data(self):
docstring:
Loads data and metadata for the C. elegans connectome.
def _check_neuron_argument(self, neurons):
docstring:
Checks if a list of string includes neurons name, returns only
elements of the list that are correct names
:param neurons: list of strings with neurons names
def _parse_neuron_skeleton(self, neuron):
docstring:
Parses a neuron's skeleton information from skeleton .json file
to create a vtk actor that represents the neuron
:param neuron: str, neuron name
def _get_structure_mesh(self, acronym, **kwargs):
docstring:
Get's the mesh for a brainregion, for this atlas it's just for
getting/making the root mesh
def get_neurons(self, neurons, alpha=1, as_skeleton=False,
colorby='type'):
docstring:
Renders neurons and adds returns to the scene.
:param neurons: list of names of neurons
:param alpha: float in range 0,1 - neurons transparency
:param as_skeleton: bool (Default value = False), if True neurons are
rendered as skeletons
otherwise as a full mesh showing the whole morphology
:param colorby: str, criteria to use to color the neurons. Accepts
values like type, individual etc.
def get_neurons_synapses(self, scene_store, neurons, alpha=1,
pre=False, post=False, colorby='synapse_type', draw_patches=False,
draw_arrows=True):
docstring:
THIS METHODS GETS CALLED BY SCENE, self referes to the instance of
Scene not to this class.
Renders neurons and adds them to the scene.
:param neurons: list of names of neurons
:param alpha: float in range 0,1 - neurons transparency
:param pre: bool, if True the presynaptic sites of each neuron are
rendered
:param post: bool, if True the postsynaptic sites on each neuron are
rendered
:param colorby: str, criteria to use to color the neurons.
Accepts values like synapse_type, type, individual etc.
:param draw_patches: bool, default True. If true dark patches are used
to show the location of post synapses
:param draw_arrows: bool, default True. If true arrows are used to
show the location of post synapses
def dist(p1, p2):
docstring:
no docstring
def get_point(p1, p2, d, u):
docstring:
no docstring
Last modified 2yr ago