Proj id and proj name access (mne-tools#13261)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 2 people

doc/changes/devel/13261.newfeature.rst

@@ -0,0 +1 @@
+User can set values for fields ``proj_id`` and ``proj_name`` in ``Info`` dict, by :newcontrib:`Laurent Le Mentec`.

doc/changes/names.inc

@@ -166,6 +166,7 @@
 .. _Larry Eisenman:  https://github.com/lneisenman
 .. _Lau Møller Andersen: https://github.com/ualsbombe
 .. _Laura Gwilliams: https://lauragwilliams.github.io
+.. _Laurent Le Mentec: https://github.com/LaurentLM
 .. _Leonardo Barbosa: https://github.com/noreun
 .. _Leonardo Rochael Almeida: https://github.com/leorochael
 .. _Liberty Hamilton: https://github.com/libertyh

mne/_fiff/meas_info.py

@@ -1173,10 +1173,10 @@ class Info(ValidatedDict, SetChannelsMixin, MontageMixin, ContainsMixin):
 
     .. warning::
         The only entries that should be manually changed by the user are:
-        ``info['bads']``, ``info['description']``, ``info['device_info']``
-        ``info['dev_head_t']``, ``info['experimenter']``,
-        ``info['helium_info']``, ``info['line_freq']``, ``info['temp']``,
-        and ``info['subject_info']``.
+        ``info['bads']``, ``info['description']``, ``info['device_info']``,
+        ``info['proj_id']``, ``info['proj_name']``, ``info['dev_head_t']``,
+        ``info['experimenter']``, ``info['helium_info']``,
+        ``info['line_freq']``, ``info['temp']``, and ``info['subject_info']``.
 
         All other entries should be considered read-only, though they can be
         modified by various MNE-Python functions or methods (which have
@@ -1634,8 +1634,8 @@ class Info(ValidatedDict, SetChannelsMixin, MontageMixin, ContainsMixin):
         "Please use methods inst.add_channels(), "
         "inst.drop_channels(), and inst.pick() instead.",
         "proc_history": "proc_history cannot be set directly.",
-        "proj_id": "proj_id cannot be set directly.",
-        "proj_name": "proj_name cannot be set directly.",
+        "proj_id": partial(_check_types, name="proj_id", types=(int, None), cast=int),
+        "proj_name": partial(_check_types, name="proj_name", types=(str, None)),
         "projs": "projs cannot be set directly. "
         "Please use methods inst.add_proj() and inst.del_proj() "
         "instead.",
@@ -2206,7 +2206,7 @@ def read_meas_info(fid, tree, clean_bads=False, verbose=None):
             description = tag.data
         elif kind == FIFF.FIFF_PROJ_ID:
             tag = read_tag(fid, pos)
-            proj_id = tag.data
+            proj_id = int(tag.data.item())
         elif kind == FIFF.FIFF_PROJ_NAME:
             tag = read_tag(fid, pos)
             proj_name = tag.data
@@ -3009,6 +3009,21 @@ def _where_isinstance(values, kind):
             return values[int(idx)]
         elif len(idx) > 1:
             raise RuntimeError(msg)
+    # proj_id
+    elif _check_isinstance(values, (int, type(None)), all) and key == "proj_id":
+        unique_values = set(values)
+        if len(unique_values) != 1:
+            logger.info("Found multiple proj_ids, using the first one.")
+        return list(unique_values)[0]
+
+    elif key == "experimenter" or key == "proj_name":
+        if _check_isinstance(values, (str, type(None)), all):
+            unique_values = set(values)
+            unique_values.discard(None)
+            if len(unique_values) == 1:
+                return list(unique_values)[0]
+            else:
+                return None
     # other
     else:
         unique_values = set(values)
@@ -3018,7 +3033,7 @@ def _where_isinstance(values, kind):
             logger.info("Found multiple StringIO instances. Setting value to `None`")
             return None
         elif isinstance(list(unique_values)[0], str):
-            logger.info("Found multiple filenames. Setting value to `None`")
+            logger.info(f"Found multiple {key}. Setting value to `None`")
             return None
         else:
             raise RuntimeError(msg)
@@ -3498,7 +3513,7 @@ def anonymize_info(info, daysback=None, keep_his=False, verbose=None):
     info["description"] = default_desc
     with info._unlock():
         if info["proj_id"] is not None:
-            info["proj_id"] = np.zeros_like(info["proj_id"])
+            info["proj_id"] = 0
         if info["proj_name"] is not None:
             info["proj_name"] = default_str
         if info["utc_offset"] is not None:

mne/_fiff/tests/test_meas_info.py

@@ -637,7 +637,7 @@ def _test_anonymize_info(base_info, tmp_path):
         for lev in tp[:-1]:
             this = this[lev]
         this[tp[-1]] = default_str
-    exp_info["proj_id"] = np.array([0])
+    exp_info["proj_id"] = 0
     for key in ("sex", "id", "height", "weight"):
         exp_info["subject_info"][key] = 0
     exp_info["subject_info"]["his_id"] = str(default_subject_id)
@@ -798,7 +798,7 @@ def _complete_info(info):
     info["experimenter"] = "f"
     info["description"] = "g"
     with info._unlock():
-        info["proj_id"] = np.ones(1, int)
+        info["proj_id"] = 1
         info["proj_name"] = "h"
         info["utc_offset"] = "i"
         d = (1717707794, 2)
@@ -1217,6 +1217,7 @@ def test_info_bad():
     info["line_freq"] = 50.0
     info["bads"] = info["ch_names"][:1]
     info["temp"] = ("whatever", 1.0)
+
     with pytest.raises(RuntimeError, match=r"info\['temp'\]"):
         info["bad_key"] = 1.0
     for key, match in [("sfreq", r"inst\.resample"), ("chs", r"inst\.add_channels")]:
@@ -1277,3 +1278,15 @@ def test_tag_consistency():
     assert call_set == call_names, "Mismatch between _call_dict and _call_dict_names"
     # TODO: This was inspired by FIFF_DIG_STRING gh-13083, we should ideally add a test
     # that those dig points can actually be read in correctly at some point.
+
+
+def test_proj_id_entries():
+    """Test that proj_id entries are the right type."""
+    info = create_info(5, 1000.0, "eeg")
+    info["proj_id"] = 123
+    # Boolean should be cast into an int
+    info["proj_id"] = True
+    with pytest.raises(TypeError, match="must be an instance"):
+        info["proj_id"] = "bad"
+    with pytest.raises(TypeError, match="must be an instance"):
+        info["proj_id"] = np.array([123])

mne/conftest.py

@@ -195,6 +195,7 @@ def pytest_configure(config: pytest.Config):
     ignore:process .* is multi-threaded, use of fork/exec.*:DeprecationWarning
     # sklearn
     ignore:Python binding for RankQuantileOptions.*:RuntimeWarning
+    ignore:.*The `disp` and `iprint` options of the L-BFGS-B solver.*:DeprecationWarning
     """  # noqa: E501
     for warning_line in warning_lines.split("\n"):
         warning_line = warning_line.strip()

mne/forward/tests/test_make_forward.py

@@ -719,10 +719,10 @@ def test_make_forward_dipole(tmp_path):
     # Make sure each coordinate is close to reference
     # NB tolerance should be set relative to snr of simulated evoked!
     assert_allclose(
-        dip_fit.pos, dip_test.pos, rtol=0, atol=1.3e-2, err_msg="position mismatch"
+        dip_fit.pos, dip_test.pos, rtol=0, atol=1.5e-2, err_msg="position mismatch"
     )
     assert dist < 1e-2  # within 1 cm
-    assert corr > 0.985
+    assert corr > 0.98
     assert gc_dist < 20  # less than 20 degrees
     assert amp_err < 10e-9  # within 10 nAm
 

mne/preprocessing/tests/test_fine_cal.py

@@ -77,7 +77,7 @@ def test_compute_fine_cal(kind):
         angle_limit = 5
         gwoma = [66, 68]
         ggoma = [55, 150]
-        ggwma = [60, 86]
+        ggwma = [52, 86]
         sfs = [26, 27, 61, 63, 61, 63, 68, 70]
         cl3 = [0.6, 0.7]
     else:
@@ -243,7 +243,7 @@ def test_fine_cal_systems(system, tmp_path):
         int_order = 5
         corrs = (0.13, 0.0, 0.12)
         sfs = [4, 5, 125, 155]
-        corr_tol = 0.34
+        corr_tol = 0.38
     else:
         assert system == "triux", f"Unknown system {system}"
         raw = read_raw_fif(tri_fname)

mne/utils/tests/test_config.py

@@ -13,6 +13,7 @@
 from urllib.error import URLError
 
 import pytest
+from flaky import flaky
 
 import mne
 import mne.utils.config
@@ -173,6 +174,7 @@ def test_get_subjects_dir(tmp_path, monkeypatch):
         get_subjects_dir(raise_error=True)
 
 
+@flaky(max_runs=3)
 @pytest.mark.slowtest
 @requires_good_network
 def test_sys_info_check_outdated(monkeypatch):