"""Class to handle no temporal but spatial data."""
from __future__ import annotations # c.f. PEP 563, PEP 649
from copy import copy, deepcopy
from typing import TYPE_CHECKING
import numpy as np
from mne import Info, pick_info
from mne.utils import check_version
if check_version("mne", "1.6"):
from mne._fiff.pick import _picks_to_idx
else:
from mne.io.pick import _picks_to_idx
from ..utils._checks import _check_type
from ..utils._docs import fill_doc
from ..utils.mixin import ChannelsMixin, ContainsMixin, MontageMixin
if TYPE_CHECKING:
from typing import Any, Union
from .._typing import ScalarFloatArray
from . import ChInfo
[docs]
class ChData(ChannelsMixin, ContainsMixin, MontageMixin):
"""ChData stores atemporal data with its spatial information.
`~pycrostates.io.ChData` is similar to a raw instance where temporality has been
removed. Only the spatial information, stored as a `~pycrostates.io.ChInfo` is
retained.
Parameters
----------
data : array
Data array of shape ``(n_channels, n_samples)``.
info : mne.Info | ChInfo
Atemporal measurement information. If a `mne.Info` is provided, it is converted
to a `~pycrostates.io.ChInfo`.
"""
def __init__(self, data: ScalarFloatArray, info: Union[Info, ChInfo]):
from . import ChInfo
_check_type(data, (np.ndarray,), "data")
_check_type(info, (Info, ChInfo), "info")
if data.ndim != 2:
raise ValueError(
"Argument 'data' should be a 2D array (n_channels, n_samples). The "
f"provided array shape is {data.shape} which has {data.ndim} "
"dimensions."
)
if not len(info["ch_names"]) == data.shape[0]:
raise ValueError(
"Argument 'data' and 'info' do not have the same number of channels."
)
self._data = data
self._info = info if isinstance(info, ChInfo) else ChInfo(info)
def __repr__(self) -> str: # noqa: D401
"""String representation."""
name = self.__class__.__name__
s = f"< {name} | {self._data.shape[-1]} samples >"
return s
def _repr_html_(self, caption=None):
"""HTML representation."""
from ..html_templates import repr_templates_env
template = repr_templates_env.get_template("ChData.html.jinja")
info_repr = self._info._repr_html_() # pylint: disable=protected-access
return template.render(n_samples=self._data.shape[-1], info_repr=info_repr)
def __eq__(self, other: Any) -> bool:
"""Equality == method."""
if (
isinstance(other, ChData)
and other.info == self.info
and other._data.shape == self._data.shape
and np.allclose(other._data, self._data)
):
return True
else:
return False
def __ne__(self, other: Any) -> bool:
"""Different != method."""
return not self.__eq__(other)
[docs]
def copy(
self,
deep: bool = True,
):
"""Return a copy of the instance.
Parameters
----------
deep : bool
If True, `~copy.deepcopy` is used instead of `~copy.copy`.
"""
if deep:
return deepcopy(self)
return copy(self)
[docs]
@fill_doc
def get_data(self, picks=None) -> ScalarFloatArray:
"""Retrieve the data array.
Parameters
----------
%(picks_all)s
Returns
-------
data : array
Data array of shape ``(n_channels, n_samples)``.
"""
picks = _picks_to_idx(self._info, picks, none="all", exclude="bads")
data = self._data.copy()
return data[picks, :]
[docs]
@fill_doc
def pick(self, picks, exclude="bads"):
"""Pick a subset of channels.
Parameters
----------
%(picks_all)s
exclude : list | str
Set of channels to exclude, only used when picking based on types (e.g.,
``exclude="bads"`` when ``picks="meg"``).
Returns
-------
inst : ChData
The instance modified in-place.
"""
picks = _picks_to_idx(self._info, picks, exclude=exclude)
info = pick_info(self._info, picks, copy=False)
data = self._data[picks, :]
self._info = info
self._data = data
return self
def _get_channel_positions(self, picks=None):
"""Get channel locations from info.
Parameters
----------
picks : str | list | slice | None
None selects the good data channels.
Returns
-------
pos : array of shape (n_channels, 3)
Channel X/Y/Z locations.
"""
picks = _picks_to_idx(self.info, picks)
chs = self.info["chs"]
pos = np.array([chs[k]["loc"][:3] for k in picks])
n_zero = np.sum(np.sum(np.abs(pos), axis=1) == 0)
if n_zero > 1: # XXX some systems have origin (0, 0, 0)
raise ValueError(
f"Could not extract channel positions for {n_zero} channels."
)
return pos
# --------------------------------------------------------------------
@property
def info(self) -> ChInfo:
"""Atemporal measurement information.
:type: ChInfo
"""
return self._info
@property
def ch_names(self):
"""Channel names."""
return self.info["ch_names"]
@property
def preload(self):
"""Preload required by some MNE functions."""
return True
