merge origin/main

eye2bids/edf2bids.py

@@ -431,12 +431,17 @@ def edf2bids(
     # Samples to eyetrack.tsv
     samples_asc_file = _convert_edf_to_asc_samples(input_file)
     eyetrack_tsv = _samples_to_data_frame(samples_asc_file)
+    # strip blankspcace and convert empty cells to nan
+    eyetrack_tsv = eyetrack_tsv.applymap(lambda x: x.strip() if isinstance(x, str) else x)
+    eyetrack_tsv = eyetrack_tsv.replace(".", np.nan, regex=False)
 
     output_filename = generate_output_filename(
         output_dir=output_dir, input_file=input_file, suffix="_eyetrack", extension="tsv"
     )
     with open(output_filename, "w") as outfile:
-        eyetrack_tsv.to_csv(outfile, sep="\t", index=False, compression="gzip")
+        eyetrack_tsv.to_csv(
+            outfile, sep="\t", index=False, compression="gzip", na_rep="n/a"
+        )
     e2b_log.info(f"file generated: {output_filename}")
 
 

tests/test_edf2bids.py

@@ -3,6 +3,7 @@
 import json
 from pathlib import Path
 
+import pandas as pd
 import pytest
 
 from eye2bids.edf2bids import (
@@ -64,6 +65,29 @@ def test_edf_end_to_end(metadata_file, eyelink_test_data_dir):
     assert eyetrack["SamplingFrequency"] == 500
     assert eyetrack["RecordedEye"] == "Right"
 
+    expected_events_sidecar = output_dir / f"{input_file.stem}_eyetrack.tsv"
+    assert expected_events_sidecar.exists()
+
+
+@pytest.mark.skipif(not _check_edf2asc_present(), reason="edf2asc missing")
+def test_edf_nan_in_tsv(eyelink_test_data_dir):
+    """Check that dots '.' are converted to NaN in the tsv file."""
+    input_dir = eyelink_test_data_dir / "emg"
+    input_file = edf_test_files(input_dir=input_dir)[0]
+
+    output_dir = data_dir() / "output"
+    output_dir.mkdir(exist_ok=True)
+
+    edf2bids(
+        input_file=input_file,
+        output_dir=output_dir,
+    )
+
+    expected_events_sidecar = output_dir / f"{input_file.stem}_eyetrack.tsv"
+    df = pd.read_csv(expected_events_sidecar, sep="\t")
+    count = sum(i == "." for i in df["eye1_x_coordinate"])
+    assert count == 0
+
 
 @pytest.mark.parametrize(
     "folder, expected",