Merge branch 'main' into dev-devel

Author: cbrnr

doc/changes/devel/13112.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with :func:`mne.io.read_raw_egi` where ``info["dev_head_t"]`` was an identity matrix instead of ``None``, by `Eric Larson`_.

mne/_fiff/meas_info.py

@@ -3326,13 +3326,12 @@ 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",
         "ctf_head_t",
         "description",
+        "dev_head_t",
         "dev_ctf_t",
         "dig",
         "experimenter",
@@ -3373,7 +3372,6 @@ def _empty_info(sfreq):
     info["highpass"] = 0.0
     info["sfreq"] = float(sfreq)
     info["lowpass"] = info["sfreq"] / 2.0
-    info["dev_head_t"] = Transform("meg", "head")
     info._update_redundant()
     info._check_consistency()
     return info

mne/chpi.py

@@ -55,6 +55,7 @@
     _sss_basis,
 )
 from .transforms import (
+    Transform,
     _angle_between_quats,
     _fit_matched_points,
     _quat_to_affine,
@@ -1274,6 +1275,7 @@ def compute_chpi_locs(
     t_step_max=1.0,
     too_close="raise",
     adjust_dig=False,
+    *,
     verbose=None,
 ):
     """Compute locations of each cHPI coils over time.
@@ -1323,6 +1325,7 @@ def compute_chpi_locs(
     _check_option("too_close", too_close, ["raise", "warning", "info"])
     _check_chpi_param(chpi_amplitudes, "chpi_amplitudes")
     _validate_type(info, Info, "info")
+    _validate_type(info["dev_head_t"], Transform, "info['dev_head_t']")
     sin_fits = chpi_amplitudes  # use the old name below
     del chpi_amplitudes
     proj = sin_fits["proj"]

mne/forward/_make_forward.py

@@ -485,7 +485,8 @@ def _prepare_for_forward(
     info = Info(
         chs=info["chs"],
         comps=info["comps"],
-        dev_head_t=info["dev_head_t"],
+        # The forward-writing code always wants a dev_head_t, so give an identity one
+        dev_head_t=info["dev_head_t"] or Transform("meg", "head"),
         mri_file=info_trans,
         mri_id=mri_id,
         meas_file=info_extra,

mne/forward/forward.py

@@ -318,7 +318,6 @@ def _get_tag_int(fid, node, name, id_):
     """Check we have an appropriate tag."""
     tag = find_tag(fid, node, id_)
     if tag is None:
-        fid.close()
         raise ValueError(name + " tag not found")
     return int(tag.data.item())
 
@@ -649,7 +648,6 @@ def read_forward_solution(fname, include=(), exclude=(), *, ordered=True, verbos
                 mri_head_t["from"] != FIFF.FIFFV_COORD_MRI
                 or mri_head_t["to"] != FIFF.FIFFV_COORD_HEAD
             ):
-                fid.close()
                 raise ValueError("MRI/head coordinate transformation not found")
         fwd["mri_head_t"] = mri_head_t
 
@@ -1124,7 +1122,6 @@ def write_forward_meas_info(fid, info):
     # get transformation from CTF and DEVICE to HEAD coordinate frame
     meg_head_t = info.get("dev_head_t", info.get("ctf_head_t"))
     if meg_head_t is None:
-        fid.close()
         raise ValueError("Head<-->sensor transform not found")
     write_coord_trans(fid, meg_head_t)
 

mne/forward/tests/test_make_forward.py

@@ -791,6 +791,7 @@ def test_use_coil_def(tmp_path):
     info = create_info(1, 1000.0, "mag")
     info["chs"][0]["coil_type"] = 9999
     info["chs"][0]["loc"][:] = [0, 0, 0.02, 1, 0, 0, 0, 1, 0, 0, 0, 1]
+    info["dev_head_t"] = Transform("meg", "head")
     sphere = make_sphere_model((0.0, 0.0, 0.0), 0.01)
     src = setup_volume_source_space(pos=5, sphere=sphere)
     trans = Transform("head", "mri", None)

mne/io/artemis123/artemis123.py

@@ -398,6 +398,8 @@ def __init__(
                     self, tmin=0, tmax=0.25, t_window=0.25, t_step_min=0.25
                 )
                 assert len(coil_amplitudes["times"]) == 1
+                # Need an ititial dev_head_t to compute coil locations
+                self.info["dev_head_t"] = Transform("meg", "head")
                 coil_locs = compute_chpi_locs(self.info, coil_amplitudes)
                 with info._unlock():
                     info["hpi_results"] = None

mne/io/artemis123/tests/test_artemis123.py

@@ -59,6 +59,7 @@ def test_dev_head_t():
     """Test dev_head_t computation for Artemis123."""
     # test a random selected point
     raw = read_raw_artemis123(short_hpi_1kz_fname, preload=True, add_head_trans=False)
+    assert raw.info["dev_head_t"] is None
     meg_picks = pick_types(raw.info, meg=True, eeg=False)
 
     # checked against matlab reader.

mne/io/egi/tests/test_egi.py

@@ -83,6 +83,7 @@ def test_egi_mff_pause(fname, skip_times, event_times):
                 events_as_annotations=False,
             )
     assert raw.info["sfreq"] == 250.0  # true for all of these files
+    assert raw.info["dev_head_t"] is None  # no MEG data
     assert len(raw.annotations) == len(skip_times)
 
     # assert event onsets match expected times

mne/io/fiff/tests/test_raw_fiff.py

@@ -37,6 +37,7 @@
 from mne.filter import filter_data
 from mne.io import RawArray, base, concatenate_raws, match_channel_orders, read_raw_fif
 from mne.io.tests.test_raw import _test_concat, _test_raw_reader
+from mne.transforms import Transform
 from mne.utils import (
     _dt_to_stamp,
     _record_warnings,
@@ -1642,7 +1643,8 @@ def test_add_channels():
 
     # Testing force updates
     raw_arr_info = create_info(["1", "2"], raw_meg.info["sfreq"], "eeg")
-    orig_head_t = raw_arr_info["dev_head_t"]
+    assert raw_arr_info["dev_head_t"] is None
+    orig_head_t = Transform("meg", "head")
     raw_arr = rng.randn(2, raw_eeg.n_times)
     raw_arr = RawArray(raw_arr, raw_arr_info)
     # This should error because of conflicts in Info