From 672bdf4357f815c63dfab91d9c8e257266bceb21 Mon Sep 17 00:00:00 2001
From: "Lumberbot (aka Jack)"
 <39504233+meeseeksmachine@users.noreply.github.com>
Date: Thu, 16 Jan 2025 12:15:42 -0800
Subject: [PATCH] Backport PR #13062 on branch maint/1.9 (BUG: Fix bug with
 interval calculation) (#13064)

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
---
 .pre-commit-config.yaml                  |  2 +-
 README.rst                               |  2 +-
 azure-pipelines.yml                      |  2 +-
 doc/changes/devel/13062.bugfix.rst       |  1 +
 mne/preprocessing/_fine_cal.py           | 15 +++++++++------
 mne/preprocessing/tests/test_fine_cal.py | 14 +++++++++++++-
 6 files changed, 26 insertions(+), 10 deletions(-)
 create mode 100644 doc/changes/devel/13062.bugfix.rst

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e7a931b5713..06918b99de1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -78,7 +78,7 @@ repos:
         language: python
         entry: ./tools/hooks/sync_dependencies.py
         files: pyproject.toml
-        additional_dependencies: ["mne"]
+        additional_dependencies: ["mne==1.9.0"]
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
diff --git a/README.rst b/README.rst
index 50e0daaa52c..cfa7488324f 100644
--- a/README.rst
+++ b/README.rst
@@ -72,7 +72,7 @@ The minimum required dependencies to run MNE-Python are:
 
 .. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↓↓↓
 
-- `Python <https://www.python.org>`__ ≥ 3.9
+- `Python <https://www.python.org>`__ ≥ 3.10
 - `NumPy <https://numpy.org>`__ ≥ 1.23
 - `SciPy <https://scipy.org>`__ ≥ 1.9
 - `Matplotlib <https://matplotlib.org>`__ ≥ 3.6
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 3ca4177174f..2bf2cd07bd3 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -244,7 +244,7 @@ stages:
           PYTHONIOENCODING: 'utf-8'
           AZURE_CI_WINDOWS: 'true'
           PYTHON_ARCH: 'x64'
-        timeoutInMinutes: 75
+        timeoutInMinutes: 80
         strategy:
           maxParallel: 4
           matrix:
diff --git a/doc/changes/devel/13062.bugfix.rst b/doc/changes/devel/13062.bugfix.rst
new file mode 100644
index 00000000000..9e01fc4c835
--- /dev/null
+++ b/doc/changes/devel/13062.bugfix.rst
@@ -0,0 +1 @@
+Fix computation of time intervals in :func:`mne.preprocessing.compute_fine_calibration` by `Eric Larson`_.
diff --git a/mne/preprocessing/_fine_cal.py b/mne/preprocessing/_fine_cal.py
index 41d20539ce0..b43983a87eb 100644
--- a/mne/preprocessing/_fine_cal.py
+++ b/mne/preprocessing/_fine_cal.py
@@ -156,11 +156,12 @@ def compute_fine_calibration(
     # 1. Rotate surface normals using magnetometer information (if present)
     #
     cals = np.ones(len(info["ch_names"]))
-    time_idxs = raw.time_as_index(np.arange(0.0, raw.times[-1], t_window))
-    if len(time_idxs) <= 1:
-        time_idxs = np.array([0, len(raw.times)], int)
-    else:
-        time_idxs[-1] = len(raw.times)
+    end = len(raw.times) + 1
+    time_idxs = np.arange(0, end, int(round(t_window * raw.info["sfreq"])))
+    if len(time_idxs) == 1:
+        time_idxs = np.concatenate([time_idxs, [end]])
+    if time_idxs[-1] != end:
+        time_idxs[-1] = end
     count = 0
     locs = np.array([ch["loc"] for ch in info["chs"]])
     zs = locs[mag_picks, -3:].copy()
@@ -388,9 +389,11 @@ def _adjust_mag_normals(info, data, origin, ext_order, *, angle_limit, err_limit
     each_err = _data_err(data, S_tot, cals, axis=-1)[picks_mag]
     n_bad = (each_err > err_limit).sum()
     if n_bad:
+        bad_max = np.argmax(each_err)
         reason.append(
             f"{n_bad} residual{_pl(n_bad)} > {err_limit:0.1f}% "
-            f"(max: {each_err.max():0.2f}%)"
+            f"(max: {each_err[bad_max]:0.2f}% @ "
+            f"{info['ch_names'][picks_mag[bad_max]]})"
         )
     reason = ", ".join(reason)
     if reason:
diff --git a/mne/preprocessing/tests/test_fine_cal.py b/mne/preprocessing/tests/test_fine_cal.py
index 02c596bf4bc..45971620db5 100644
--- a/mne/preprocessing/tests/test_fine_cal.py
+++ b/mne/preprocessing/tests/test_fine_cal.py
@@ -20,7 +20,7 @@
 )
 from mne.preprocessing.tests.test_maxwell import _assert_shielding
 from mne.transforms import _angle_dist_between_rigid
-from mne.utils import object_diff
+from mne.utils import catch_logging, object_diff
 
 # Define fine calibration filepaths
 data_path = testing.data_path(download=False)
@@ -289,3 +289,15 @@ def test_fine_cal_systems(system, tmp_path):
     got_corrs = np.corrcoef([raw_data, raw_sss_data, raw_sss_cal_data])
     got_corrs = got_corrs[np.triu_indices(3, 1)]
     assert_allclose(got_corrs, corrs, atol=corr_tol)
+    if system == "fil":
+        with catch_logging(verbose=True) as log:
+            compute_fine_calibration(
+                raw.copy().crop(0, 0.12).pick(raw.ch_names[:12]),
+                t_window=0.06,  # 2 segments
+                angle_limit=angle_limit,
+                err_limit=err_limit,
+                ext_order=2,
+                verbose=True,
+            )
+        log = log.getvalue()
+        assert "(averaging over 2 time intervals)" in log, log