Bug fixes (#20)

* fix #19

* fix #18

* fix test

.gitignore

@@ -4,6 +4,8 @@ tests/data/**/*.json
 **/*.edf
 **/*.EDF
 eye2bids/_version.py
+events.json
+eyetrack.json
 
 # General
 .DS_Store

eye2bids/_cli.py

@@ -40,14 +40,13 @@ def cli(argv: Sequence[str] = sys.argv) -> None:
 
     args, _ = parser.parse_known_args(argv[1:])
 
-    input_file = args.input_file
-    input_file = Path(input_file).resolve()
+    input_file = Path(args.input_file).resolve()
 
     metadata_file = args.metadata_file
-    if metadata_file is not None:
-        metadata_file = metadata_file[0]
+    if metadata_file not in [None, ""]:
+        metadata_file = Path(metadata_file).resolve()
 
-    output_dir = args.output_dir
+    output_dir = Path(args.output_dir).resolve()
 
     set_verbosity(args.verbosity)
 

eye2bids/_parser.py

@@ -68,6 +68,6 @@ def global_parser() -> ArgumentParser:
         choices=[0, 1, 2, 3],
         default=2,
         type=int,
-        nargs=1,
+        nargs=2,
     )
     return parser

eye2bids/edf2bids.py

@@ -23,43 +23,64 @@ def _check_inputs(
     output_dir: str | Path | None = None,
     interactive: bool = False,
 ) -> tuple[Path, Path | None, Path]:
+    """Check if inputs are valid."""
     if input_file is None:
         if interactive:
             input_file = Prompt.ask("Enter the edf file path")
         else:
             raise FileNotFoundError("No input file specified")
+
     if isinstance(input_file, str):
-        input_file = Path(input_file)
-    if input_file.exists():
-        e2b_log.info(f"file found: {input_file}")
+        cheked_input_file = Path(input_file)
+    elif isinstance(input_file, Path):
+        cheked_input_file = input_file
+
+    if cheked_input_file.exists():
+        e2b_log.info(f"input file found: {cheked_input_file}")
     else:
-        raise FileNotFoundError(f"No such file: {input_file}")
+        raise FileNotFoundError(f"No such input file: {cheked_input_file}")
 
-    if metadata_file is None and interactive:
+    if metadata_file in [None, ""] and interactive:
         e2b_log.info(
             """Load the metadata.yml file with the additional metadata.\n
             This file must contain at least the additional REQUIRED metadata
             in the format specified in the BIDS specification.\n"""
         )
         metadata_file = Prompt.ask("Enter the file path to the metadata.yml file")
-    if isinstance(metadata_file, str):
-        metadata_file = Path(metadata_file)
-    if isinstance(metadata_file, str):
-        metadata_file = Path(metadata_file)
-    if isinstance(metadata_file, Path):
-        if metadata_file.exists():
-            e2b_log.info(f"file found: {metadata_file}")
-        else:
-            raise FileNotFoundError(f"No such file: {metadata_file}")
 
+    if metadata_file in ["", None]:
+        checked_metadata_file = None
+    elif isinstance(metadata_file, str):
+        checked_metadata_file = Path(metadata_file)
+    elif isinstance(metadata_file, Path):
+        checked_metadata_file = metadata_file
+
+    if isinstance(checked_metadata_file, Path):
+        if not checked_metadata_file.exists():
+            raise FileNotFoundError(f"No such metadata file: {checked_metadata_file}")
+        if checked_metadata_file.is_file():
+            e2b_log.info(f"metadata file found: {checked_metadata_file}")
+        elif checked_metadata_file.is_dir():
+            raise IsADirectoryError(
+                f"metadata file is a directory: {checked_metadata_file}"
+            )
+
+    return cheked_input_file, checked_metadata_file, _check_output_dir(output_dir)
+
+
+def _check_output_dir(output_dir: str | Path | None = None) -> Path:
+    """Check if output directory is valid."""
     if output_dir is None:
         output_dir = input("Enter the output directory: ")
     if isinstance(output_dir, str):
-        output_dir = Path(output_dir)
-    if not output_dir.exists():
-        output_dir.mkdir(parents=True, exist_ok=True)
+        checked_output_dir = Path(output_dir)
+    elif isinstance(output_dir, Path):
+        checked_output_dir = output_dir
 
-    return input_file, metadata_file, output_dir
+    if not checked_output_dir.exists():
+        checked_output_dir.mkdir(parents=True, exist_ok=True)
+
+    return checked_output_dir
 
 
 def _check_edf2asc_present() -> bool:
@@ -159,7 +180,7 @@ def _extract_MaximalCalibrationError(df: pd.DataFrame) -> list[float]:
 
 
 def _extract_AverageCalibrationError(df: pd.DataFrame) -> list[float]:
-    if _has_validation(df):
+    if not _has_validation(df):
         return []
     return np.array(_validations(df)[[9]]).astype(float).tolist()
 

tests/conftest.py

@@ -0,0 +1,25 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import pytest
+
+
+def data_dir() -> Path:
+    return Path(__file__).parent / "data"
+
+
+def asc_test_files(input_dir: Path = data_dir()) -> list[Path]:
+    return list(input_dir.glob("**/*.asc"))
+
+
+def edf_test_files(input_dir: Path = data_dir()) -> list[Path]:
+    files = list(input_dir.glob("**/*.edf"))
+    EDF_files = list(input_dir.glob("**/*.EDF"))
+    files.extend(EDF_files)
+    return files
+
+
+@pytest.fixture
+def eyelink_test_data_dir() -> Path:
+    return data_dir() / "osf" / "eyelink"

tests/test_cli.py

@@ -0,0 +1,44 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import pytest
+
+from eye2bids._cli import cli
+from eye2bids.edf2bids import _check_edf2asc_present
+
+from .conftest import data_dir, edf_test_files
+
+
+def root_dir() -> Path:
+    """Return the root directory of the project."""
+    return Path(__file__).parent.parent
+
+
+@pytest.mark.parametrize("metadata_file", [data_dir() / "metadata.yml", None])
+@pytest.mark.parametrize("output_dir", [data_dir() / "output", None])
+@pytest.mark.parametrize("use_relative_path", [False, True])
+def test_edf_cli(use_relative_path, metadata_file, output_dir, eyelink_test_data_dir):
+    if not _check_edf2asc_present():
+        pytest.skip("edf2asc missing")
+
+    input_dir = eyelink_test_data_dir / "decisions"
+    input_file = edf_test_files(input_dir=input_dir)[0]
+
+    if use_relative_path:
+        input_file = input_file.relative_to(root_dir())
+
+    command = ["eye2bids", "--input_file", str(input_file)]
+    if metadata_file is not None:
+        if use_relative_path:
+            metadata_file = metadata_file.relative_to(root_dir())
+        metadata_file = str(metadata_file)
+        command.extend(["--metadata_file", metadata_file])
+
+    if output_dir is not None:
+        if use_relative_path:
+            output_dir = output_dir.relative_to(root_dir())
+        output_dir = str(output_dir)
+        command.extend(["--output_dir", output_dir])
+
+    cli(command)

tests/test_edf2bids.py

@@ -26,20 +26,7 @@
     edf2bids,
 )
 
-
-def data_dir() -> Path:
-    return Path(__file__).parent / "data"
-
-
-def asc_test_files(input_dir: Path = data_dir()) -> list[Path]:
-    return list(input_dir.glob("**/*.asc"))
-
-
-def edf_test_files(input_dir: Path = data_dir()) -> list[Path]:
-    files = list(input_dir.glob("**/*.edf"))
-    EDF_files = list(input_dir.glob("**/*.EDF"))
-    files.extend(EDF_files)
-    return files
+from .conftest import asc_test_files, data_dir, edf_test_files
 
 
 @pytest.mark.parametrize("input_file", edf_test_files())
@@ -51,11 +38,11 @@ def test_convert_edf_to_asc(input_file):
 
 
 @pytest.mark.parametrize("metadata_file", [data_dir() / "metadata.yml", None])
-def test_edf_end_to_end(metadata_file):
+def test_edf_end_to_end(metadata_file, eyelink_test_data_dir):
     if not _check_edf2asc_present():
         pytest.skip("edf2asc missing")
 
-    input_dir = data_dir() / "osf" / "eyelink" / "decisions"
+    input_dir = eyelink_test_data_dir / "decisions"
     input_file = edf_test_files(input_dir=input_dir)[0]
 
     output_dir = data_dir() / "output"
@@ -91,8 +78,8 @@ def test_edf_end_to_end(metadata_file):
         ("vergence", "HV9"),
     ],
 )
-def test_extract_CalibrationType(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_CalibrationType(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     df_ms_reduced = _load_asc_file_as_reduced_df(asc_file)
     assert _extract_CalibrationType(df_ms_reduced) == expected
@@ -110,8 +97,8 @@ def test_extract_CalibrationType(folder, expected):
         ("vergence", [1919, 1079]),
     ],
 )
-def test_extract_ScreenResolution(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+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]
     df_ms_reduced = _load_asc_file_as_reduced_df(asc_file)
     assert _extract_ScreenResolution(df_ms_reduced) == expected
@@ -129,8 +116,8 @@ def test_extract_ScreenResolution(folder, expected):
         ("vergence", ""),
     ],
 )
-def test_extract_CalibrationUnit(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_CalibrationUnit(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     df_ms_reduced = _load_asc_file_as_reduced_df(asc_file)
     assert _extract_CalibrationUnit(df_ms_reduced) == expected
@@ -193,8 +180,8 @@ def test_extract_CalibrationUnit(folder, expected):
         ("vergence", []),
     ],
 )
-def test_extract_CalibrationPosition(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_CalibrationPosition(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     df_ms_reduced = _load_asc_file_as_reduced_df(asc_file)
     assert _extract_CalibrationPosition(df_ms_reduced) == expected
@@ -212,8 +199,8 @@ def test_extract_CalibrationPosition(folder, expected):
         ("vergence", "P-CR"),
     ],
 )
-def test_extract_EyeTrackingMethod(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_EyeTrackingMethod(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     events = _load_asc_file(asc_file)
     assert _extract_EyeTrackingMethod(events) == expected
@@ -231,8 +218,8 @@ def test_extract_EyeTrackingMethod(folder, expected):
         ("vergence", 1000),
     ],
 )
-def test_extract_SamplingFrequency(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_SamplingFrequency(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     df_ms_reduced = _load_asc_file_as_reduced_df(asc_file)
     assert _extract_SamplingFrequency(df_ms_reduced) == expected
@@ -250,8 +237,8 @@ def test_extract_SamplingFrequency(folder, expected):
         ("vergence", "CENTROID"),
     ],
 )
-def test_extract_PupilFitMethod(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_PupilFitMethod(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     df_ms_reduced = _load_asc_file_as_reduced_df(asc_file)
     assert _extract_PupilFitMethod(df_ms_reduced) == expected
@@ -269,8 +256,8 @@ def test_extract_PupilFitMethod(folder, expected):
         ("vergence", "CL1-72N02"),
     ],
 )
-def test_extract_DeviceSerialNumber(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_DeviceSerialNumber(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     events = _load_asc_file(asc_file)
     assert _extract_DeviceSerialNumber(events) == expected
@@ -288,8 +275,8 @@ def test_extract_DeviceSerialNumber(folder, expected):
         ("vergence", "Both"),
     ],
 )
-def test_extract_RecordedEye(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_RecordedEye(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     df_ms_reduced = _load_asc_file_as_reduced_df(asc_file)
     assert _extract_RecordedEye(df_ms_reduced) == expected
@@ -307,8 +294,8 @@ def test_extract_RecordedEye(folder, expected):
         ("vergence", "EYELINK II CL v4.56 Aug 18 2010"),
     ],
 )
-def test_extract_ManufacturersModelName(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_ManufacturersModelName(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     events = _load_asc_file(asc_file)
     assert _extract_ManufacturersModelName(events) == expected
@@ -326,8 +313,8 @@ def test_extract_ManufacturersModelName(folder, expected):
         ("vergence", []),
     ],
 )
-def test_extract_MaximalCalibrationError(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_MaximalCalibrationError(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     df_ms = _load_asc_file_as_df(asc_file)
     assert _extract_MaximalCalibrationError(df_ms) == expected
@@ -338,15 +325,15 @@ def test_extract_MaximalCalibrationError(folder, expected):
     [
         ("decisions", []),
         ("emg", []),
-        ("lt", []),
+        ("lt", [[0.16], [0.18]]),
         ("pitracker", []),
-        ("rest", []),
+        ("rest", [[0.65]]),
         ("satf", []),
         ("vergence", []),
     ],
 )
-def test_extract_AverageCalibrationError(folder, expected):
-    input_dir = data_dir() / "osf" / "eyelink" / folder
+def test_extract_AverageCalibrationError(folder, expected, eyelink_test_data_dir):
+    input_dir = eyelink_test_data_dir / folder
     asc_file = asc_test_files(input_dir=input_dir)[0]
     df_ms = _load_asc_file_as_df(asc_file)
     assert _extract_AverageCalibrationError(df_ms) == expected