Fix handling of .edf and .asc eye-tracking files

mne_bids_pipeline/_config.py

@@ -1150,6 +1150,28 @@
 Currently not implemented
 """
 
+et_has_run: bool = False
+"""
+Specify whether `run` is included in the eye-tracking data file name.
+
+???+ example "Example"
+    ``` python
+    et_has_run = False  # Case with only one run and run is omitted in the file name.
+    et_has_run = True  # Case with multiple runs. Run specification from EEG data is used.
+    ```
+"""
+
+et_has_task: bool = False
+"""
+Specify whether `task` is included in the eye-tracking data file name.
+
+???+ example "Example"
+    ``` python
+    et_has_task = False  # Case with only one task and task is omitted in the file name.
+    et_has_task = True  # Case with multiple tasks. Task specification from EEG data is used.
+    ```
+"""
+
 sync_eventtype_regex: str = ""
 """
 Regular expression which will be used to select events in the EEG file for synchronisation 

mne_bids_pipeline/steps/preprocessing/_05b_sync_eyelink.py

@@ -67,6 +67,13 @@ def get_input_fnames_sync_eyelink(
     subject: str,
     session: str | None,
 ) -> dict:
+
+    # Get from config file whether `task` is specified in the et file name
+    if cfg.et_has_task == True:
+        et_task = cfg.task
+    else:
+        et_task = None
+
     bids_basename = BIDSPath(
         subject=subject,
         session=session,
@@ -80,10 +87,10 @@ def get_input_fnames_sync_eyelink(
         extension=".fif",
     )
 
-    et_bids_basename = BIDSPath(
+    et_asc_bids_basename = BIDSPath(
         subject=subject,
         session=session,
-        task=cfg.task,
+        task=et_task,
         acquisition=cfg.acq,
         recording=cfg.rec,
         datatype="beh",
@@ -93,11 +100,10 @@ def get_input_fnames_sync_eyelink(
         extension=".asc",
     )
 
-
     et_edf_bids_basename = BIDSPath(
         subject=subject,
         session=session,
-        task=cfg.task,
+        task=et_task,
         acquisition=cfg.acq,
         recording=cfg.rec,
         datatype="beh",
@@ -115,19 +121,30 @@ def get_input_fnames_sync_eyelink(
         )
         _update_for_splits(in_files, key, single=True)
 
+        et_bids_basename_temp = et_asc_bids_basename.copy()
+
+        if cfg.et_has_run:
+            et_bids_basename_temp.update(run=run)
+
+        # _update_for_splits(in_files, key, single=True) # TODO: Find out if we need to add this or not
+
+        if not os.path.isfile(et_bids_basename_temp):
+            logger.info(**gen_log_kwargs(message=f"Couldn't find {et_bids_basename_temp} file. If edf file exists, edf2asc will be called."))
+
+            et_bids_basename_temp = et_edf_bids_basename.copy()
+
+            if cfg.et_has_run:
+                et_bids_basename_temp.update(run=run)
+
+            # _update_for_splits(in_files, key, single=True) # TODO: Find out if we need to add this or not
+
+            if not os.path.isfile(et_bids_basename_temp):
+                logger.error(**gen_log_kwargs(message=f"Also didn't find {et_bids_basename_temp} file, one of both needs to exist for ET sync."))
+                raise FileNotFoundError(f"For run {run}, could neither find .asc or .edf eye-tracking file. Please double-check the file names.")
 
         key = f"et_run-{run}"
-        in_files[key] = et_bids_basename.copy().update(
-            run=run
-        )
-        _update_for_splits(in_files, key, single=True) # TODO: Find out if we need to add this or not
+        in_files[key] = et_bids_basename_temp
 
-        key = f"et_edf_run-{run}"
-        in_files[key] = et_edf_bids_basename.copy().update(
-            run=run
-        )
-        _update_for_splits(in_files, key, single=True) # TODO: Find out if we need to add this or not
-
     return in_files
 
 
@@ -143,30 +160,35 @@ def sync_eyelink(
     session: str | None,
     in_files: dict,
 ) -> dict:
+
     """Run Sync for Eyelink."""
     import matplotlib.pyplot as plt
     from scipy.signal import correlate
 
     raw_fnames = [in_files.pop(f"raw_run-{run}") for run in cfg.runs]
     et_fnames = [in_files.pop(f"et_run-{run}") for run in cfg.runs]
-    et_edf_fnames = [in_files.pop(f"et_edf_run-{run}") for run in cfg.runs]
 
-    logger.info(**gen_log_kwargs(message=f"et_fnames {et_fnames}"))
+    logger.info(**gen_log_kwargs(message=f"Found the following eye-tracking files: {et_fnames}"))
     out_files = dict()
     bids_basename = raw_fnames[0].copy().update(processing=None, split=None, run=None)
     out_files["eyelink"] = bids_basename.copy().update(processing="eyelink", suffix="raw")
     del bids_basename
 
-    for idx, (run, raw_fname,et_fname,et_edf_fname) in enumerate(zip(cfg.runs, raw_fnames,et_fnames,et_edf_fnames)):
-        msg = f"Syncing eyelink data (fake for now) {raw_fname.basename}"
+    for idx, (run, raw_fname,et_fname) in enumerate(zip(cfg.runs, raw_fnames,et_fnames)):
+        msg = f"Syncing Eyelink ({et_fname.basename}) and EEG data ({raw_fname.basename})."
         logger.info(**gen_log_kwargs(message=msg))
         raw = mne.io.read_raw_fif(raw_fname, preload=True)
-        if not os.path.isfile(et_fname):
-            logger.info(**gen_log_kwargs(message=f"Couldn't find {et_fname} file, trying to call edf2asc."))
-            if not os.path.isfile(et_edf_fname):
-                logger.error(**gen_log_kwargs(message=f"Also didn't find {et_edf_fname} file, one of both need to exist for ET sync."))
+
+        et_format = et_fname.extension
+
+        if not et_format == '.asc':
+            assert et_format == '.edf', "ET file is neither an `.asc` nor an `.edf`. This should not have happened."
+            logger.info(**gen_log_kwargs(message=f"Converting {et_fname} file to `.asc` using edf2asc."))
             import subprocess
-            subprocess.run(["edf2asc", et_edf_fname]) # TODO: Still needs to be tested
+            subprocess.run(["edf2asc", et_fname]) # TODO: Still needs to be tested
+            print(et_fname.fpath)
+            et_fname.update(extension='.asc')
+            print(et_fname.fpath)
 
         raw_et = mne.io.read_raw_eyelink(et_fname, find_overlaps=True)
 
@@ -341,6 +363,8 @@ def get_config(
     cfg = SimpleNamespace(
         runs=get_runs(config=config, subject=subject),
         remove_blink_saccades   = config.remove_blink_saccades,
+        et_has_run = config.et_has_run,
+        et_has_task = config.et_has_task,
         sync_eventtype_regex    = config.sync_eventtype_regex,
         sync_eventtype_regex_et = config.sync_eventtype_regex_et,
         sync_heog_ch = config.sync_heog_ch,