aba_utils

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parse_neurons_colors [#28]

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def parse_neurons_colors(neurons, color):
  docstring:
Prepares the color info to render neurons
:param neurons: str, list, dict. File(s) with neurons data or list of
rendered neurons.
:param color: default None. Can be:
- None: each neuron is given a random color
- color: rbg, hex etc. If a single color is passed all neurons will
have that color
- cmap: str with name of a colormap: neurons are colored based on
their sequential order and cmap
- dict: a dictionary specifying a color for soma, dendrites and axon
actors, will be the same for all neurons
- list: a list of length = number of neurons with either a single
color for each neuron
or a dictionary of colors for each neuron

parse_tractography_colors [#147]

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def parse_tractography_colors(tractography, include_all_inj_regions,
color=None, color_by='manual', VIP_regions=[], VIP_color=None,
others_color='salmon'):
  docstring:
parses color arguments to render tracrography data
:param tractography: list of dictionaries with tractography data
:param color: color of rendered tractography data
:param color_by: str, specifies which criteria to use to color the
tractography (Default value = "manual")
Options:
- manual: the user needs to provide a color or list of colors
- target_region: tracts are colored according to the region where the
injection was done.
if VIP_regions is passed, then only tracts for the VIP regions are
colored
:param VIP_regions: list of brain regions with VIP treatement (Default
value = [])
:param VIP_color: str, color to use for VIP data (Default value =
None)
:param include_all_inj_regions: bool (Default value = False)
:param others_color: str, color for not VIP data (Default value =
"white")

experiments_source_search [#243]

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def experiments_source_search(mca, SOI, *args, source=True, **kwargs):
  docstring:
Returns data about experiments whose injection was in the SOI,
structure of interest
:param SOI: str, structure of interest. Acronym of structure to use as
seed for teh search
:param *args:
:param source: (Default value = True)
:param **kwargs:

parse_streamline [#301]

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def parse_streamline(*args, filepath=None, data=None,
show_injection_site=True, color='ivory', alpha=0.8, radius=10,
**kwargs):
  docstring:
Given a path to a .json file with streamline data (or the data
themselves), render the streamline as tubes actors.
Either filepath or data should be passed
:param filepath: str, optional. Path to .json file with streamline
data (Default value = None)
:param data: panadas.DataFrame, optional. DataFrame with streamline
data. (Default value = None)
:param color: str color of the streamlines (Default value = 'ivory')
:param alpha: float transparency of the streamlines (Default value =
.8)
:param radius: int radius of the streamlines actor (Default value =
10)
:param show_injection_site: bool, if True spheres are used to render
the injection volume (Default value = True)
:param *args:
:param **kwargs:

make_url_given_id [#378]

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def make_url_given_id(expid):
  docstring:
Get url of JSON file for an experiment, give it's ID number
:param expid: int with experiment ID number

download_streamlines [#390]

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def download_streamlines(eids, streamlines_folder=None):
  docstring:
Given a list of expeirmental IDs, it downloads the streamline data
from the https://neuroinformatics.nl cache and saves them as
json files.
:param eids: list of integers with experiments IDs
:param streamlines_folder: str path to the folder where the JSON files
should be saved, if None the default is used (Default value = None)

extract_ids_from_csv [#430]

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def extract_ids_from_csv(csv_file, download=False, **kwargs):
  docstring:
Parse CSV file to extract experiments IDs and link to downloadable
streamline data
Given a CSV file with info about experiments downloaded from:
http://connectivity.brain-map.org
extract experiments ID and get links to download (compressed)
streamline data from https://neuroinformatics.nl.
Also return the experiments IDs to download data from:
https://neuroinformatics.nl/HBP/allen-connectivity-viewer/streamline-
downloader.html
:param csv_file: str with path to csv file
:param download: if True the data are downloaded automatically
(Default value = False)
:param **kwargs:
Last modified 2yr ago