celegans

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celegans
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​Celegans​
​__init__ [#62]​
​_make_root [#84]​
​get_neurons_by [#119]​
​get_neuron_color [#151]​
​_get_data [#186]​
​_check_neuron_argument [#249]​
​_parse_neuron_skeleton [#272]​
​_get_structure_mesh [#308]​
​get_neurons [#329]​
​get_neurons_synapses [#371]​
​dist [#518]​
​get_point [#525]​
Celegans
__init__ [#62]
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def __init__(self, data_folder=None, base_dir=None, **kwargs):
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docstring:
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This class handles loading and parsing neuroanatomical data for the C.
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    elegans connectome from
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​
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https://www.biorxiv.org/content/10.1101/2020.04.30.066209v1
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​
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:param base_dir: path to directory to use for saving data (default
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    value None)
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​
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:param kwargs: can be used to pass path to individual data folders.
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    See brainrender/Utils/paths_manager.py
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​
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:param data_folder: str, path to a folder with data for the connectome
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    # TODO replace with downloading data
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_make_root [#84]
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def _make_root(self, rootpath):
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Creates a root mesh by merging the mesh corresponding to each neuron,
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​
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then saves it as an obj file at rootpath
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get_neurons_by [#119]
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def get_neurons_by(self, getby='pair', lookup=None):
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Selects a subset of the neurons using some criteria and lookup key,
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​
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based on the neurons metadata
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​
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:param getby: str, name of the metadata key to use for selecting
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    neurons
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​
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:param lookup: str/int.. neurons whose attribute 'getby' matches the
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    lookup value will be selected
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​
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:returns: list of strings with neurons names
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get_neuron_color [#151]
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def get_neuron_color(self, neuron, colorby='type'):
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Get a neuron's RGB color. Colors can be assigned based on different
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    criteria
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​
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like the neuron's type or by individual neuron etc...
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​
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:param neuron: str, nueron name
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​
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:param colorby: str, metadata attribute to use for coloring
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​
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:returns: rgb values of color
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_get_data [#186]
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def _get_data(self):
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Loads data and metadata for the C. elegans connectome.
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_check_neuron_argument [#249]
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def _check_neuron_argument(self, neurons):
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Checks if a list of string includes neurons name, returns only
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​
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elements of the list that are correct names
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​
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:param neurons: list of strings with neurons names
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_parse_neuron_skeleton [#272]
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def _parse_neuron_skeleton(self, neuron):
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Parses a neuron's skeleton information from skeleton .json file
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​
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to create a vtk actor that represents the neuron
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​
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:param neuron: str, neuron name
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_get_structure_mesh [#308]
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def _get_structure_mesh(self, acronym, **kwargs):
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Get's the mesh for a brainregion, for this atlas it's just for
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​
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getting/making the root mesh
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get_neurons [#329]
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def get_neurons(self, neurons, alpha=1, as_skeleton=False,
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    colorby='type'):
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Renders neurons and adds returns to the scene.
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​
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:param neurons: list of names of neurons
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​
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:param alpha: float in range 0,1 -  neurons transparency
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​
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:param as_skeleton: bool (Default value = False), if True neurons are
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    rendered as skeletons
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otherwise as a full mesh showing the whole morphology
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:param colorby: str, criteria to use to color the neurons. Accepts
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    values like type, individual etc.
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get_neurons_synapses [#371]
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def get_neurons_synapses(self, scene_store, neurons, alpha=1,
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    pre=False, post=False, colorby='synapse_type', draw_patches=False,
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    draw_arrows=True):
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THIS METHODS GETS CALLED BY SCENE, self referes to the instance of
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    Scene not to this class.
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​
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Renders neurons and adds them to the scene.
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​
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:param neurons: list of names of neurons
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​
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:param alpha: float in range 0,1 -  neurons transparency
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​
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:param pre: bool, if True the presynaptic sites of each neuron are
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    rendered
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​
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:param post: bool, if True the postsynaptic sites on each neuron are
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    rendered
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​
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:param colorby: str, criteria to use to color the neurons.
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​
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 Accepts values like synapse_type, type, individual etc.
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:param draw_patches: bool, default True. If true dark patches are used
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    to show the location of post synapses
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​
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:param draw_arrows: bool, default True. If true arrows are used to
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    show the location of post synapses
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dist [#518]
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def dist(p1, p2):
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get_point [#525]
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def get_point(p1, p2, d, u):
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atlas
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Contents
Celegans
__init__ [#62]
_make_root [#84]
get_neurons_by [#119]
get_neuron_color [#151]
_get_data [#186]
_check_neuron_argument [#249]
_parse_neuron_skeleton [#272]
_get_structure_mesh [#308]
get_neurons [#329]
get_neurons_synapses [#371]
dist [#518]
get_point [#525]