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cuisto.config

config module, part of cuisto.

Contains the Config class.

Config(config_file) #

The configuration class.

Reads input configuration file and provides its constant.

Parameters:

Name Type Description Default
config_file str

Full path to the configuration file to load.

 required

Returns:

Name Type Description
cfg Config object.

Constructor.

Source code in cuisto/config.py 
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def __init__(self, config_file):
    """Constructor."""
    with open(config_file, "rb") as fid:
        cfg = tomllib.load(fid)

        for key in cfg:
            setattr(self, key, cfg[key])

    self.config_file = config_file
    self.bg_atlas = BrainGlobeAtlas(self.atlas["name"], check_latest=False)
    self.get_blacklist()
    self.get_leaves_list()

get_blacklist() #

Wraps cuisto.utils.get_blacklist.

Source code in cuisto/config.py 
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def get_blacklist(self):
    """Wraps cuisto.utils.get_blacklist."""

    self.atlas["blacklist"] = utils.get_blacklist(
        self.files["blacklist"], self.bg_atlas
    )

get_hue_palette(mode) #

Get color palette given hue.

Maps hue to colors in channels or hemispheres.

Parameters:

Name Type Description Default
mode (hemisphere, channel)
"hemisphere"

Returns:

Name Type Description
palette dict

Maps a hue level to a color, usable in seaborn.
Source code in cuisto/config.py 
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def get_hue_palette(self, mode: str) -> dict:
    """
    Get color palette given hue.

    Maps hue to colors in channels or hemispheres.

    Parameters
    ----------
    mode : {"hemisphere", "channel"}

    Returns
    -------
    palette : dict
        Maps a hue level to a color, usable in seaborn.

    """
    params = getattr(self, mode)

    if params["hue"] == "channel":
        # replace channels by their new names
        palette = {
            self.channels["names"][k]: v for k, v in self.channels["colors"].items()
        }
    elif params["hue"] == "hemisphere":
        # replace hemispheres by their new names
        palette = {
            self.hemispheres["names"][k]: v
            for k, v in self.hemispheres["colors"].items()
        }
    else:
        palette = None
        warnings.warn(f"hue={self.regions["display"]["hue"]} not supported.")

    return palette

get_injection_sites(animals) #

Get list of injection sites coordinates for each animals, for each channels.

Parameters:

Name Type Description Default
animals list of str

List of animals.

 required

Returns:

Name Type Description
injection_sites dict

{"x": {channel0: [x]}, "y": {channel1: [y]}}
Source code in cuisto/config.py 
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def get_injection_sites(self, animals: list[str]) -> dict:
    """
    Get list of injection sites coordinates for each animals, for each channels.

    Parameters
    ----------
    animals : list of str
        List of animals.

    Returns
    -------
    injection_sites : dict
        {"x": {channel0: [x]}, "y": {channel1: [y]}}

    """
    injection_sites = {
        axis: {channel: [] for channel in self.channels["names"].keys()}
        for axis in ["x", "y", "z"]
    }

    for animal in animals:
        for channel in self.channels["names"].keys():
            injx, injy, injz = utils.get_injection_site(
                animal,
                self.files["infos"],
                channel,
                stereo=self.distributions["stereo"],
            )
            if injx is not None:
                injection_sites["x"][channel].append(injx)
            if injy is not None:
                injection_sites["y"][channel].append(injy)
            if injz is not None:
                injection_sites["z"][channel].append(injz)

    return injection_sites

get_leaves_list() #

Wraps utils.get_leaves_list.

Source code in cuisto/config.py 
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def get_leaves_list(self):
    """Wraps utils.get_leaves_list."""

    self.atlas["leaveslist"] = utils.get_leaves_list(self.bg_atlas)