"""Atlas data fetching and loading functions."""
from neuromaps_mouse.datasets.utils import (
MOUSEMAPS_ATLASES,
fetch_files,
get_data_dir
)
[docs]
def get_atlas_dir(data_dir=None):
"""Return path to the atlas data directory.
Parameters
----------
data_dir : str or Path, optional
Base data directory. If None, uses the default. Default is None.
Returns
-------
Path
Path to the atlases subdirectory.
"""
data_dir = get_data_dir(data_dir=data_dir)
return data_dir / "atlases"
[docs]
def fetch_allenccfv3(which=None, return_single=True, data_dir=None, verbose=1):
"""Fetch Allen CCFv3 atlas files.
Parameters
----------
which : str or list of str, optional
Which atlas file(s) to fetch. Use 'all' or None to fetch all.
Default is None.
return_single : bool, optional
If True and only one file is fetched, return a single path instead
of a list. Default is True.
data_dir : str or Path, optional
Base data directory. If None, uses the default. Default is None.
verbose : int, optional
Verbosity level. Default is 1.
Returns
-------
Path or list of Path
Path(s) to the fetched atlas file(s).
"""
data_dir = get_data_dir(data_dir=data_dir)
atlas = MOUSEMAPS_ATLASES["allen-ccfv3"]
available_files = list(atlas["files"].keys())
if which is None or which == "all":
which = list(available_files)
if not isinstance(which, list):
which = [which]
atlas_files = []
for w in which:
if w is None or w not in available_files:
raise ValueError(
f"Invalid 'which' value: {w}. " f"Should be one of {available_files}"
)
atlas_files.append(atlas["files"][w])
targ_fname_list = fetch_files(
atlas_files, file_type="atlases", data_dir=data_dir, verbose=verbose
)
if len(targ_fname_list) == 1 and return_single:
return targ_fname_list[0]
else:
return targ_fname_list
[docs]
def fetch_all_atlases():
"""Fetch all available atlases."""
pass