added data example and set behavior based on if on readthedocs

docs/conf.py

@@ -200,7 +200,7 @@ def __call__(self, gallery_conf, fname, when):
  warnings.filterwarnings("ignore", category=DeprecationWarning)
  import pyvista
  # if os.getenv("PYVISTA_OFF_SCREEN", "false").lower() == "true":
- if True:
+ if os.environ.get("READTHEDOCS") == "True":
  pyvista.start_xvfb()
  pyvista.OFF_SCREEN = True
 pyvista.BUILDING_GALLERY = True
@@ -218,6 +218,7 @@ def __call__(self, gallery_conf, fname, when):
  'backreferences_dir': 'gen_modules/backreferences',
  # Modules for which function/class level galleries are created. In
  # this case sphinx_gallery and ieeg in a tuple of strings.
+ 'expected_failing_examples': ['../examples/plot_data.py'],
  "plot_gallery": "True",
  'doc_module': ('sphinx_gallery', 'ieeg'),
  "reset_modules": ("matplotlib", Resetter()), # called w/each script

examples/plot_data.py

@@ -0,0 +1,67 @@
+"""
+Load IEEG Data Example
+======================
+
+This example demonstrates the discrepancy between the provided examples and the actual data loading process.
+
+The provided examples:
+1. Use `mne` library and `raw_from_layout` function to load IEEG data.
+2. Use `mne` library and `read_raw` function to load IEEG data.
+
+However, the actual data loading process involves using the `ieeg.io` module and the `get_data` and `raw_from_layout` functions.
+
+"""
+
+# %% Example 1
+# ECoG data in BIDS file structure saved in the [BrainVision Core Data Format](https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/)
+import mne
+from ieeg.io import raw_from_layout
+from bids import BIDSLayout
+bids_root = mne.datasets.epilepsy_ecog.data_path()
+layout = BIDSLayout(bids_root)
+raw1 = raw_from_layout(layout, subject="pt1", preload=True, extension=".vhdr")
+raw1.plot()
+
+# %% Example 2
+# SEEG data saved in the [FIF file format](https://mne.tools/stable/auto_tutorials/io/plot_20_reading_eeg_data.html#sphx-glr-auto-tutorials-io-plot-20-reading-eeg-data-py)
+import mne
+misc_path = mne.datasets.misc.data_path()
+raw2 = mne.io.read_raw(misc_path / 'seeg' / 'sample_seeg_ieeg.fif')
+raw2
+
+
+# %% Actual Data Loading Process
+# ECoG / SEEG data in BIDS file structure saved in the [European data format](https://www.edfplus.info/specs/edf.html)
+import os
+from ieeg.io import get_data, raw_from_layout
+
+HOME = os.path.expanduser("~")
+LAB_root = os.path.join(HOME, "Box", "CoganLab")
+layout = get_data("SentenceRep", root=LAB_root)
+subjects = layout.get(return_type="id", target="subject")
+
+for subject in subjects:
+ # do stuff with each subject data
+ pass
+
+print(subjects)
+
+"""
+The provided examples above do not reflect the actual data loading process used in this script.
+
+To load the IEEG data, the following steps are taken:
+
+1. Import the necessary modules:
+ - `ieeg.io` module for data loading functions.
+ - `os` module for file path manipulation.
+
+2. Set the home directory and the root folder containing the BIDS formatted data.
+
+3. Use the `get_data` function from `ieeg.io` to obtain a BIDSLayout object with the specified root folder and task name.
+
+4. Get the list of subjects from the BIDSLayout object.
+
+5. Iterate over each subject and perform the desired operations on the subject data.
+
+Note: The actual code provided above is not executable as it contains placeholders and references to specific file paths on the user's computer.
+"""

examples/plot_stats.py

@@ -55,5 +55,6 @@
 
 # response data points are length 201, while baseline is 200. We need to
 # trim the response data to match the baseline with [..., :-1]
-mask2 = stats.window_averaged_shuffle(resp._data[..., :-1], base._data, 1000)
+mask2 = stats.window_averaged_shuffle(resp._data[..., :-1], base._data, 1000,
+ stat_func=stats.mean_diff)
 plt.imshow(mask2[:, None])