refactor and fix

eye2bids/edf2bids.py

@@ -115,7 +115,6 @@ def _convert_edf_to_asc_samples(input_file: str | Path) -> Path:
 
 
 def _calibrations(df: pd.DataFrame) -> pd.DataFrame:
-    print(df)
     return df[df[3] == "CALIBRATION"]
 
 
@@ -350,7 +349,6 @@ def edf2bids(
 
     # CONVERSION events
     events_asc_file = _convert_edf_to_asc_events(input_file)
-    samples_asc_file = _convert_edf_to_asc_samples(input_file)
 
     events = _load_asc_file(events_asc_file)
     df_ms = _load_asc_file_as_df(events_asc_file)
@@ -362,12 +360,7 @@ def edf2bids(
         with open(metadata_file) as f:
             metadata = yaml.load(f, Loader=SafeLoader)
 
-    # file naming check
-
-    filename = Path(input_file).stem
-    substring_eyetrack = "_eyetrack"
-    substring_events = "_events"
-
+    # events.json Metadata
     eyetrack_json = {
         "Manufacturer": "SR-Research",
         "EnvironmentCoordinates": metadata.get("EnvironmentCoordinates"),
@@ -396,13 +389,14 @@ def edf2bids(
         "StopTime": _extract_StopTime(events),
     }
 
-    suffix = "_eyetrack" if substring_eyetrack not in filename else ""
-    output_filename = output_dir / f"{filename}{suffix}.json"
+    output_filename = generate_output_filename(
+        output_dir=output_dir, input_file=input_file, suffix="_eyetrack", extension="json"
+    )
     with open(output_filename, "w") as outfile:
         json.dump(eyetrack_json, outfile, indent=4)
     e2b_log.info(f"file generated: {output_filename}")
 
-    # Events.json Metadata
+    # events.json Metadata
     events_json = {
         "InstitutionAddress": metadata.get("InstitutionAddress"),
         "InstitutionName": metadata.get("InstitutionName"),
@@ -415,26 +409,33 @@ def edf2bids(
         "TaskName": _extract_TaskName(events),
     }
 
-    if substring_events not in filename:
-        with open(output_dir / (filename + "_events.json"), "w") as outfile:
-            json.dump(events_json, outfile, indent=4)
-        e2b_log.info(f"file generated: {output_dir / (filename + '_events.json')}")
-    else:
-        with open(output_dir / (filename + ".json"), "w") as outfile:
-            json.dump(events_json, outfile, indent=4)
-        e2b_log.info(f"file generated: {output_dir / (filename + '.json')}")
+    output_filename = generate_output_filename(
+        output_dir=output_dir, input_file=input_file, suffix="_events", extension="json"
+    )
+    with open(output_filename, "w") as outfile:
+        json.dump(events_json, outfile, indent=4)
+    e2b_log.info(f"file generated: {output_filename}")
 
     # Samples to eyetrack.tsv
+    samples_asc_file = _convert_edf_to_asc_samples(input_file)
     eyetrack_tsv = _samples_to_data_frame(samples_asc_file)
 
-    if substring_eyetrack not in filename:
-        with open(output_dir / (filename + "_eyetrack.tsv"), "w") as outfile:
-            eyetrack_tsv.to_csv(outfile, sep="\t", index=False, compression="gzip")
-        e2b_log.info(f"file generated: {output_dir / (filename + '_eyetrack.tsv')}")
-    else:
-        with open(output_dir / (filename + ".tsv"), "w") as outfile:
-            eyetrack_tsv.to_csv(outfile, sep="\t", index=False, compression="gzip")
-        e2b_log.info(f"file generated: {output_dir / (filename + '.tsv')}")
+    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")
+    e2b_log.info(f"file generated: {output_filename}")
+
+
+def generate_output_filename(
+    output_dir: Path, input_file: Path, suffix: str, extension: str
+) -> Path:
+    """Generate output filename."""
+    filename = Path(input_file).stem
+    if filename.endswith(suffix):
+        suffix = ""
+    return output_dir / f"{filename}{suffix}.{extension}"
 
 
 if __name__ == "__main__":

tests/test_cli.py

@@ -40,3 +40,18 @@ def test_edf_cli(use_relative_path, metadata_file, output_dir, eyelink_test_data
         command.extend(["--output_dir", output_dir])
 
     cli(command)
+
+
+@pytest.mark.skipif(not _check_edf2asc_present(), reason="edf2asc missing")
+@pytest.mark.parametrize(
+    "input_file", edf_test_files(input_dir=data_dir() / "osf" / "eyelink")
+)
+def test_all_edf_files(input_file):
+    command = [
+        "eye2bids",
+        "--input_file",
+        str(input_file),
+        "--output_dir",
+        str(data_dir() / "output"),
+    ]
+    cli(command)

tests/test_edf2bids.py

@@ -39,7 +39,7 @@ def test_convert_edf_to_asc_events(input_file):
 @pytest.mark.skipif(not _check_edf2asc_present(), reason="edf2asc missing")
 @pytest.mark.parametrize("metadata_file", [data_dir() / "metadata.yml", None])
 def test_edf_end_to_end(metadata_file, eyelink_test_data_dir):
-    input_dir = eyelink_test_data_dir / "decisions"
+    input_dir = eyelink_test_data_dir / "satf"
     input_file = edf_test_files(input_dir=input_dir)[0]
 
     output_dir = data_dir() / "output"
@@ -61,7 +61,7 @@ def test_edf_end_to_end(metadata_file, eyelink_test_data_dir):
     assert expected_data_sidecar.exists()
     with open(expected_data_sidecar) as f:
         eyetrack = json.load(f)
-    assert eyetrack["SamplingFrequency"] == 1000
+    assert eyetrack["SamplingFrequency"] == 500
     assert eyetrack["RecordedEye"] == "Right"
 
 
@@ -99,9 +99,6 @@ def test_extract_CalibrationType(folder, expected, eyelink_test_data_dir):
 def test_extract_ScreenResolution(folder, expected, eyelink_test_data_dir):
     input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
-    print(asc_test_files(input_dir=input_dir))
-    print(asc_file)
-    print(str(asc_file).endswith("samples.asc"))
     df_ms_reduced = _load_asc_file_as_reduced_df(asc_file)
     assert _extract_ScreenResolution(df_ms_reduced) == expected