MAINT: Clean up circular imports (mne-tools#11920)

mne/__init__.py

@@ -39,17 +39,20 @@
         "cuda",
         "datasets",
         "decoding",
+        "defaults",
         "dipole",
         "epochs",
         "event",
         "export",
         "filter",
+        "forward",
         "gui",
         "inverse_sparse",
         "io",
         "minimum_norm",
         "preprocessing",
         "report",
+        "source_space",
         "simulation",
         "stats",
         "surface",
@@ -255,7 +258,7 @@
             "spatio_temporal_tris_adjacency",
             "stc_near_sensors",
         ],
-        "source_space": [
+        "source_space._source_space": [
             "SourceSpaces",
             "add_source_space_distances",
             "get_volume_labels_from_src",

mne/_fiff/__init__.py

@@ -7,8 +7,11 @@
 # All imports should be done directly to submodules, so we don't import
 # anything here or use lazy_loader.
 
+# This warn import (made private as _warn) is just for the temporary
+# _io_dep_getattr and can be removed in 1.6 along with _dep_msg and _io_dep_getattr.
+from ..utils import warn as _warn
+
 
-# Helpers for keeping some attributes in mne/io/*.py, remove in 1.6
 _dep_msg = (
     "is deprecated will be removed in 1.6, use documented public API instead. "
     "If no appropriate public API exists, please open an issue on GitHub."
@@ -17,9 +20,8 @@
 
 def _io_dep_getattr(name, mod):
     import importlib
-    from ..utils import warn
 
     fiff_mod = importlib.import_module(f"mne._fiff.{mod}")
     obj = getattr(fiff_mod, name)
-    warn(f"mne.io.{mod}.{name} {_dep_msg}", FutureWarning)
+    _warn(f"mne.io.{mod}.{name} {_dep_msg}", FutureWarning)
     return obj

mne/_fiff/meas_info.py

@@ -64,13 +64,6 @@
     write_name_list_sanitized,
 )
 from .proc_history import _read_proc_history, _write_proc_history
-from ..transforms import (
-    invert_transform,
-    Transform,
-    _coord_frame_name,
-    _ensure_trans,
-    _frame_to_str,
-)
 from ..html_templates import _get_html_template
 from ..utils import (
     logger,
@@ -327,6 +320,7 @@ def get_montage(self):
         %(montage)s
         """
         from ..channels.montage import make_dig_montage
+        from ..transforms import _frame_to_str
 
         info = self if isinstance(self, Info) else self.info
         if info["dig"] is None:
@@ -920,6 +914,8 @@ def get_channel_types(self, picks=None, unique=False, only_data_chs=False):
 
 
 def _format_trans(obj, key):
+    from ..transforms import Transform
+
     try:
         t = obj[key]
     except KeyError:
@@ -954,6 +950,8 @@ def _check_description(description):
 
 
 def _check_dev_head_t(dev_head_t):
+    from ..transforms import Transform, _ensure_trans
+
     _validate_type(dev_head_t, (Transform, None), "info['dev_head_t']")
     if dev_head_t is not None:
         dev_head_t = _ensure_trans(dev_head_t, "meg", "head")
@@ -1581,6 +1579,7 @@ def normalize_proj(self):
     def __repr__(self):
         """Summarize info instead of printing all."""
         from ..io.kit.constants import KIT_SYSNAMES
+        from ..transforms import _coord_frame_name, Transform
 
         MAX_WIDTH = 68
         strs = ["<Info | %s non-empty values"]
@@ -2064,6 +2063,8 @@ def read_meas_info(fid, tree, clean_bads=False, verbose=None):
     meas : dict
         Node in tree that contains the info.
     """
+    from ..transforms import invert_transform, Transform
+
     #   Find the desired blocks
     meas = dir_tree_find(tree, FIFF.FIFFB_MEAS)
     if len(meas) == 0:
@@ -2511,8 +2512,6 @@ def read_meas_info(fid, tree, clean_bads=False, verbose=None):
     info["ctf_head_t"] = ctf_head_t
     info["dev_ctf_t"] = dev_ctf_t
     if dev_head_t is not None and ctf_head_t is not None and dev_ctf_t is None:
-        from ..transforms import Transform
-
         head_ctf_trans = np.linalg.inv(ctf_head_t["trans"])
         dev_ctf_trans = np.dot(head_ctf_trans, info["dev_head_t"]["trans"])
         info["dev_ctf_t"] = Transform("meg", "ctf_head", dev_ctf_trans)
@@ -3253,6 +3252,8 @@ def create_info(ch_names, sfreq, ch_types="misc", verbose=None):
 
 def _empty_info(sfreq):
     """Create an empty info dictionary."""
+    from ..transforms import Transform
+
     _none_keys = (
         "acq_pars",
         "acq_stim",

mne/_freesurfer.py

@@ -19,6 +19,7 @@
     read_ras_mni_t,
     Transform,
 )
+from .surface import read_surface, _read_mri_surface
 from .utils import (
     verbose,
     _validate_type,
@@ -356,8 +357,6 @@ def vertex_to_mni(vertices, hemis, subject, subjects_dir=None, verbose=None):
     coordinates : array, shape (n_vertices, 3)
         The MNI coordinates (in mm) of the vertices.
     """
-    from .surface import read_surface
-
     singleton = False
     if not isinstance(vertices, list) and not isinstance(vertices, np.ndarray):
         singleton = True
@@ -757,7 +756,6 @@ def _get_head_surface(surf, subject, subjects_dir, bem=None, verbose=None):
     .. versionadded: 0.24
     """
     from .bem import _bem_find_surface, read_bem_surfaces
-    from .surface import _read_mri_surface
 
     _check_option("surf", surf, ("auto", "head", "outer_skin", "head-dense", "seghead"))
     if surf in ("auto", "head", "outer_skin"):
@@ -831,7 +829,6 @@ def _get_skull_surface(surf, subject, subjects_dir, bem=None, verbose=None):
     .. versionadded: 0.24
     """
     from .bem import _bem_find_surface
-    from .surface import _read_mri_surface
 
     if bem is not None:
         try:

mne/beamformer/_compute_beamformer.py

@@ -14,7 +14,7 @@
 from ..forward.forward import is_fixed_orient, _restrict_forward_to_src_sel
 from .._fiff.proj import make_projector, Projection
 from ..minimum_norm.inverse import _get_vertno, _prepare_forward
-from ..source_space import label_src_vertno_sel
+from ..source_space._source_space import label_src_vertno_sel
 from ..utils import (
     verbose,
     check_fname,

mne/bem.py

@@ -51,6 +51,7 @@
     transform_surface_to,
 )
 from .transforms import _ensure_trans, apply_trans, Transform
+from .viz.misc import plot_bem
 from .utils import (
     verbose,
     logger,
@@ -1250,8 +1251,6 @@ def make_watershed_bem(
 
     .. versionadded:: 0.10
     """
-    from .viz.misc import plot_bem
-
     env, mri_dir, bem_dir = _prepare_env(subject, subjects_dir)
     tempdir = _TempDir()  # fsl and Freesurfer create some random junk in CWD
     run_subprocess_env = partial(run_subprocess, env=env, cwd=tempdir)
@@ -2127,8 +2126,6 @@ def make_flash_bem(
     outer skin) from a FLASH 5 MRI image synthesized from multiecho FLASH
     images acquired with spin angles of 5 and 30 degrees.
     """
-    from .viz.misc import plot_bem
-
     env, mri_dir, bem_dir = _prepare_env(subject, subjects_dir)
     tempdir = _TempDir()  # fsl and Freesurfer create some random junk in CWD
     run_subprocess_env = partial(run_subprocess, env=env, cwd=tempdir)

mne/channels/__init__.py

@@ -14,7 +14,6 @@
             "rename_channels",
             "fix_mag_coil_types",
             "read_ch_adjacency",
-            "_get_ch_type",
             "find_ch_adjacency",
             "make_1020_channel_selections",
             "combine_channels",

mne/channels/channels.py

@@ -25,6 +25,7 @@
 from scipy.spatial import Delaunay
 from scipy.stats import zscore
 
+from ..bem import _check_origin
 from ..defaults import HEAD_SIZE_DEFAULT, _handle_default
 from ..utils import (
     verbose,
@@ -55,7 +56,6 @@
     pick_types,
     _picks_by_type,
     _check_excludes_includes,
-    _contains_ch_type,
     channel_indices_by_type,
     pick_channels,
     _picks_to_idx,
@@ -107,45 +107,6 @@ def _get_meg_system(info):
     return system, have_helmet
 
 
-# TODO: Deal with name dup with mne._fiff.reference._get_ch_type
-def _get_ch_type(inst, ch_type, allow_ref_meg=False):
-    """Choose a single channel type (usually for plotting).
-
-    Usually used in plotting to plot a single datatype, e.g. look for mags,
-    then grads, then ... to plot.
-    """
-    if ch_type is None:
-        allowed_types = [
-            "mag",
-            "grad",
-            "planar1",
-            "planar2",
-            "eeg",
-            "csd",
-            "fnirs_cw_amplitude",
-            "fnirs_fd_ac_amplitude",
-            "fnirs_fd_phase",
-            "fnirs_od",
-            "hbo",
-            "hbr",
-            "ecog",
-            "seeg",
-            "dbs",
-        ]
-        allowed_types += ["ref_meg"] if allow_ref_meg else []
-        for type_ in allowed_types:
-            if isinstance(inst, Info):
-                if _contains_ch_type(inst, type_):
-                    ch_type = type_
-                    break
-            elif type_ in inst:
-                ch_type = type_
-                break
-        else:
-            raise RuntimeError("No plottable channel types found")
-    return ch_type
-
-
 @verbose
 def equalize_channels(instances, copy=True, verbose=None):
     """Equalize channel picks and ordering across multiple MNE-Python objects.
@@ -803,7 +764,6 @@ def interpolate_bads(
         -----
         .. versionadded:: 0.9.0
         """
-        from ..bem import _check_origin
         from .interpolation import (
             _interpolate_bads_eeg,
             _interpolate_bads_meeg,
@@ -1497,7 +1457,7 @@ def _compute_ch_adjacency(info, ch_type):
     ch_names : list
         The list of channel names present in adjacency matrix.
     """
-    from .. import spatial_tris_adjacency
+    from ..source_estimate import spatial_tris_adjacency
     from ..channels.layout import _find_topomap_coords, _pair_grad_sensors
 
     combine_grads = ch_type == "grad" and any(
@@ -1795,7 +1755,8 @@ def combine_channels(
         is ``True``, also containing stimulus channels).
     """
     from ..io import BaseRaw, RawArray
-    from .. import BaseEpochs, EpochsArray, Evoked, EvokedArray
+    from ..epochs import BaseEpochs, EpochsArray
+    from ..evoked import Evoked, EvokedArray
 
     ch_axis = 1 if isinstance(inst, BaseEpochs) else 0
     ch_idx = list(range(inst.info["nchan"]))

mne/channels/interpolation.py

@@ -11,7 +11,6 @@
 from .._fiff.meas_info import _simplify_info
 from .._fiff.pick import pick_types, pick_channels, pick_info
 from ..surface import _normalize_vectors
-from ..forward import _map_meg_or_eeg_channels
 from ..utils import _check_option, _validate_type
 
 
@@ -194,6 +193,8 @@ def _interpolate_bads_meeg(
     exclude=(),
     verbose=None,
 ):
+    from ..forward import _map_meg_or_eeg_channels
+
     bools = dict(meg=meg, eeg=eeg)
     info = _simplify_info(inst.info)
     for ch_type, do in bools.items():

mne/channels/layout.py

@@ -32,6 +32,7 @@
     logger,
 )
 from .channels import _get_ch_info
+from ..viz.topomap import plot_layout
 
 
 class Layout:
@@ -131,8 +132,6 @@ def plot(self, picks=None, show_axes=False, show=True):
         -----
         .. versionadded:: 0.12.0
         """
-        from ..viz.topomap import plot_layout
-
         return plot_layout(self, picks=picks, show_axes=show_axes, show=show)
 
 

mne/channels/montage.py

@@ -20,6 +20,7 @@
 import numpy as np
 
 from ..defaults import HEAD_SIZE_DEFAULT
+from .._freesurfer import get_mni_fiducials
 from ..viz import plot_montage
 from ..transforms import (
     apply_trans,
@@ -609,9 +610,6 @@ def add_estimated_fiducials(self, subject, subjects_dir=None, verbose=None):
         and then use ``mne.channels.compute_native_head_t(montage)``
         to get the head <-> MRI transform.
         """
-        # Avoid circular import
-        from .._freesurfer import get_mni_fiducials
-
         # get coordframe and fiducial coordinates
         montage_bunch = _get_data_as_dict_from_dig(self.dig)
 
@@ -654,8 +652,6 @@ def add_mni_fiducials(self, subjects_dir=None, verbose=None):
         those coordinate to be transformed to "head" space (origin
         between LPA and RPA).
         """
-        from .._freesurfer import get_mni_fiducials
-
         montage_bunch = _get_data_as_dict_from_dig(self.dig)
 
         # get the coordinate frame and check that it's MNI TAL

mne/channels/tests/test_montage.py

@@ -22,8 +22,13 @@
 )
 import matplotlib.pyplot as plt
 
-from mne import __file__ as _mne_file, create_info, read_evokeds, pick_types
-from mne.source_space import get_mni_fiducials
+from mne import (
+    __file__ as _mne_file,
+    create_info,
+    read_evokeds,
+    pick_types,
+)
+from mne.coreg import get_mni_fiducials
 from mne.utils._testing import assert_object_equal
 from mne.channels import (
     get_builtin_montages,

mne/chpi.py

@@ -30,6 +30,7 @@
 from .io import BaseRaw
 from .io.ctf.trans import _make_ctf_coord_trans_set
 from .io.kit.kit import RawKIT as _RawKIT
+from .io.kit.constants import KIT
 from .channels.channels import _get_meg_system
 from ._fiff.meas_info import _simplify_info, Info
 from ._fiff.pick import (
@@ -262,8 +263,6 @@ def extract_chpi_locs_kit(raw, stim_channel="MISC 064", *, verbose=None):
     -----
     .. versionadded:: 0.23
     """
-    from .io.kit.constants import KIT
-
     _validate_type(raw, (_RawKIT,), "raw")
     stim_chs = [
         raw.info["ch_names"][pick]