Skip to content

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 
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
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
    if self.atlas["name"]:
        self.bg_atlas = BrainGlobeAtlas(self.atlas["name"], check_latest=False)
    else:
        self.bg_atlas = None

    # name axes to handle ABBA/Brainglobe atlases differences
    if self.atlas["type"] in ("abba", "brain"):
        self.Xname = "Atlas_X"  # antero-posterior (rostro-caudal)
        self.Yname = "Atlas_Y"  # infero-superior (dorso-ventral)
        self.Zname = "Atlas_Z"  # left-right (medio-lateral)
    elif self.atlas["type"] in ("brainglobe", "cord"):
        self.Xname = "Atlas_Z"  # antero-posterior (rostro-caudal)
        self.Yname = "Atlas_Y"  # infero-superior (dorso-ventral)
        self.Zname = "Atlas_X"  # left-right (medio-lateral)
    else:
        raise ValueError(
            f"{self.atlas['type']} not supported, choose either 'abba' or 'brainglobe'."
        )

    self.get_blacklist()
    self.get_leaves_list()

get_blacklist() #

Wraps cuisto.utils.get_blacklist.

Source code in cuisto/config.py 
63
64
65
66
67
68
69
def get_blacklist(self):
    """Wraps cuisto.utils.get_blacklist."""

    if os.path.isfile(self.files["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 
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
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 
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
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 
71
72
73
74
def get_leaves_list(self):
    """Wraps utils.get_leaves_list."""

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