Convert old Spectrum and TFR birthday info format on read

doc/changes/dev/13526.bugfix.rst

@@ -0,0 +1 @@
+Fix bug preventing reading of :class:`mne.time_frequency.Spectrum` and :class:`mne.time_frequency.BaseTFR` objects created in MNE<1.8 using the deprecated subject info birthday tuple format, by `Thomas Binns`_.

mne/time_frequency/spectrum.py

@@ -46,7 +46,11 @@
     check_fname,
 )
 from ..utils.misc import _pl
-from ..utils.spectrum import _get_instance_type_string, _split_psd_kwargs
+from ..utils.spectrum import (
+    _convert_old_birthday_format,
+    _get_instance_type_string,
+    _split_psd_kwargs,
+)
 from ..viz.topo import _plot_timeseries, _plot_timeseries_unified, _plot_topo
 from ..viz.topomap import _make_head_outlines, _prepare_topomap_plot, plot_psds_topomap
 from ..viz.utils import (
@@ -391,7 +395,7 @@ def __setstate__(self, state):
         self._freqs = state["freqs"]
         self._dims = state["dims"]
         self._sfreq = state["sfreq"]
-        self.info = Info(**state["info"])
+        self.info = Info(**_convert_old_birthday_format(state["info"]))
         self._data_type = state["data_type"]
         self._nave = state.get("nave")  # objs saved before #11282 won't have `nave`
         self._weights = state.get("weights")  # objs saved before #12747 won't have

mne/time_frequency/tests/test_spectrum.py

@@ -2,6 +2,7 @@
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.
 
+import datetime
 import re
 from functools import partial
 
@@ -26,7 +27,7 @@
     SpectrumArray,
     combine_spectrum,
 )
-from mne.utils import _record_warnings
+from mne.utils import _import_h5io_funcs, _record_warnings
 
 
 def test_compute_psd_errors(raw):
@@ -178,6 +179,7 @@ def _get_inst(inst, request, *, evoked=None, average_tfr=None):
 def test_spectrum_io(inst, tmp_path, request, evoked):
     """Test save/load of spectrum objects."""
     pytest.importorskip("h5io")
+    h5py = pytest.importorskip("h5py")
     fname = tmp_path / f"{inst}-spectrum.h5"
     inst = _get_inst(inst, request, evoked=evoked)
     if isinstance(inst, BaseEpochs):
@@ -190,12 +192,25 @@ def test_spectrum_io(inst, tmp_path, request, evoked):
     orig.save(fname)
     loaded = read_spectrum(fname)
     assert orig == loaded
+    # Only check following for one type
+    if not isinstance(inst, BaseEpochs):
+        return
+    # Test loading with old-style birthday format
+    fname_subject_info = tmp_path / "subject-info.h5"
+    _, write_hdf5 = _import_h5io_funcs()
+    write_hdf5(fname_subject_info, dict(birthday=(2000, 1, 1)), title="subject_info")
+    with h5py.File(fname, "r+") as f:
+        del f["mnepython/key_info/key_subject_info"]
+        f["mnepython/key_info/key_subject_info"] = h5py.ExternalLink(
+            fname_subject_info, "subject_info"
+        )
+    loaded = read_spectrum(fname)
+    assert isinstance(loaded.info["subject_info"]["birthday"], datetime.date)
     # Test Spectrum from EpochsSpectrum.average() can be read (gh-13521)
-    if isinstance(inst, BaseEpochs):
-        origavg = orig.average()
-        origavg.save(fname, overwrite=True)
-        loadedavg = read_spectrum(fname)
-        assert origavg == loadedavg
+    origavg = orig.average()
+    origavg.save(fname, overwrite=True)
+    loadedavg = read_spectrum(fname)
+    assert origavg == loadedavg
 
 
 def test_spectrum_copy(raw_spectrum):

mne/time_frequency/tests/test_tfr.py

@@ -51,7 +51,7 @@
     tfr_multitaper,
     write_tfrs,
 )
-from mne.utils import catch_logging, grand_average
+from mne.utils import _import_h5io_funcs, catch_logging, grand_average
 from mne.utils._testing import _get_suptitle
 from mne.viz.utils import (
     _channel_type_prettyprint,
@@ -620,6 +620,7 @@ def test_tfr_io(inst, average_tfr, request, tmp_path):
     """Test TFR I/O."""
     pytest.importorskip("h5io")
     pd = pytest.importorskip("pandas")
+    h5py = pytest.importorskip("h5py")
 
     tfr = _get_inst(inst, request, average_tfr=average_tfr)
     fname = tmp_path / "temp_tfr.hdf5"
@@ -679,6 +680,22 @@ def test_tfr_io(inst, average_tfr, request, tmp_path):
     tfravg.save(fname, overwrite=True)
     tfravg_loaded = read_tfrs(fname)
     assert tfravg == tfravg_loaded
+    # test loading with old-style birthday format
+    fname_multi = tmp_path / "temp_multi_tfr.hdf5"
+    write_tfrs(fname_multi, tfr)  # also check for multiple files from write_tfrs
+    fname_subject_info = tmp_path / "subject-info.hdf5"
+    _, write_hdf5 = _import_h5io_funcs()
+    write_hdf5(fname_subject_info, dict(birthday=(2000, 1, 1)), title="subject_info")
+    for this_fname in (fname, fname_multi):
+        with h5py.File(this_fname, "r+") as f:
+            if f.get("mnepython/key_info/key_subject_info"):
+                path = "mnepython/key_info/key_subject_info"
+            else:  # multi-files on linux have different path to attrs
+                path = "mnepython/idx_0/idx_1/key_info/key_subject_info"
+            del f[path]
+            f[path] = h5py.ExternalLink(fname_subject_info, "subject_info")
+        tfr_loaded = read_tfrs(this_fname)
+        assert isinstance(tfr_loaded.info["subject_info"]["birthday"], datetime.date)
     # test with taper dimension and weights
     n_tapers = 3  # anything >= 1 should do
     weights = np.ones((n_tapers, tfr.shape[2]))  # tapers x freqs

mne/time_frequency/tfr.py

@@ -59,7 +59,7 @@
     verbose,
     warn,
 )
-from ..utils.spectrum import _get_instance_type_string
+from ..utils.spectrum import _convert_old_birthday_format, _get_instance_type_string
 from ..viz.topo import _imshow_tfr, _imshow_tfr_unified, _plot_topo
 from ..viz.topomap import (
     _add_colorbar,
@@ -1433,7 +1433,7 @@ def __setstate__(self, state):
         self._dims = defaults["dims"]
         self._raw_times = np.asarray(defaults["times"], dtype=np.float64)
         self._baseline = defaults["baseline"]
-        self.info = Info(**defaults["info"])
+        self.info = Info(**_convert_old_birthday_format(defaults["info"]))
         self._data_type = defaults["data_type"]
         self._decim = defaults["decim"]
         self.preload = True
@@ -4141,7 +4141,7 @@ def _read_multiple_tfrs(tfr_data, condition=None, *, verbose=None):
             if key != condition:
                 continue
         tfr = dict(tfr)
-        tfr["info"] = Info(tfr["info"])
+        tfr["info"] = Info(_convert_old_birthday_format(tfr["info"]))
         tfr["info"]._check_consistency()
         if "metadata" in tfr:
             tfr["metadata"] = _prepare_read_metadata(tfr["metadata"])

mne/utils/spectrum.py

@@ -4,6 +4,7 @@
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.
 
+from datetime import datetime
 from inspect import currentframe, getargvalues, signature
 
 from ..utils import warn
@@ -102,3 +103,13 @@ def _split_psd_kwargs(*, plot_fun=None, kwargs=None):
     for k in plot_kwargs:
         del kwargs[k]
     return kwargs, plot_kwargs
+
+
+def _convert_old_birthday_format(info):
+    """Convert deprecated birthday tuple to datetime."""
+    subject_info = info.get("subject_info")
+    if subject_info is not None:
+        birthday = subject_info.get("birthday")
+        if isinstance(birthday, tuple):
+            info["subject_info"]["birthday"] = datetime(*birthday)
+    return info