Added tests for scanimage utils

src/roiextractors/extractors/tiffimagingextractors/scanimagetiff_utils.py

@@ -27,7 +27,7 @@ def extract_extra_metadata(
 
     Notes
     -----
-    Known to work on SI versions v3.8.0, v2019bR0, and v2022.0.0.
+    Known to work on SI versions v3.8.0, v2019bR0, v2022.0.0, and v2023.0.0
     """
     ScanImageTiffReader = _get_scanimage_reader()
     io = ScanImageTiffReader(str(file_path))
@@ -102,7 +102,7 @@ def parse_metadata(metadata: dict) -> dict:
 
     Notes
     -----
-    Known to work on SI versions v2019bR0 and v2022.0.0.
+    Known to work on SI versions v2019bR0, v2022.0.0, and v2023.0.0. Fails on v3.8.0.
     SI.hChannels.channelsActive = string of MATLAB-style vector with channel integers (see parse_matlab_vector).
     SI.hChannels.channelName = "{'channel_name_1' 'channel_name_2' ... 'channel_name_M'}"
         where M is the number of channels (active or not).
@@ -167,9 +167,19 @@ def extract_timestamps_from_file(file_path: PathType) -> np.ndarray:
     -------
     timestamps : numpy.ndarray
         Array of frame timestamps in seconds.
+
+    Raises
+    ------
+    AssertionError
+        If the frame timestamps are not found in the TIFF file.
+
+    Notes
+    -----
+    Known to work on SI versions v2019bR0, v2022.0.0, and v2023.0.0. Fails on v3.8.0.
     """
     ScanImageTiffReader = _get_scanimage_reader()
     io = ScanImageTiffReader(str(file_path))
+    assert "frameTimestamps_sec" in io.description(iframe=0), "frameTimestamps_sec not found in TIFF file"
     num_frames = io.shape()[0]
     timestamps = np.zeros(num_frames)
     for iframe in range(num_frames):
@@ -179,4 +189,5 @@ def extract_timestamps_from_file(file_path: PathType) -> np.ndarray:
             if "frameTimestamps_sec" in line:
                 timestamps[iframe] = float(line.split("=")[1].strip())
                 break
+
     return timestamps

tests/test_scanimage_utils.py

@@ -0,0 +1,128 @@
+import pytest
+from numpy.testing import assert_array_equal
+from ScanImageTiffReader import ScanImageTiffReader
+from roiextractors.extractors.tiffimagingextractors.scanimagetiff_utils import (
+    _get_scanimage_reader,
+    extract_extra_metadata,
+    parse_matlab_vector,
+    parse_metadata,
+    parse_metadata_v3_8,
+    extract_timestamps_from_file,
+)
+
+from .setup_paths import OPHYS_DATA_PATH
+
+
+def test_get_scanimage_reader():
+    ScanImageTiffReader = _get_scanimage_reader()
+    assert ScanImageTiffReader is not None
+
+
+@pytest.mark.parametrize(
+    "filename, expected_key, expected_value",
+    [
+        ("sample_scanimage_version_3_8.tiff", "state.software.version", "3.8"),
+        ("scanimage_20220801_single.tif", "SI.VERSION_MAJOR", "2022"),
+        ("scanimage_20220923_roi.tif", "SI.VERSION_MAJOR", "2023"),
+    ],
+)
+def test_extract_extra_metadata(filename, expected_key, expected_value):
+    file_path = OPHYS_DATA_PATH / "imaging_datasets" / "ScanImage" / filename
+    metadata = extract_extra_metadata(file_path)
+    assert metadata[expected_key] == expected_value
+
+
+@pytest.mark.parametrize(
+    "matlab_vector, expected_vector",
+    [
+        ("[1 2 3]", [1, 2, 3]),
+        ("[1,2,3]", [1, 2, 3]),
+        ("[1, 2, 3]", [1, 2, 3]),
+        ("[1;2;3]", [1, 2, 3]),
+        ("[1; 2; 3]", [1, 2, 3]),
+    ],
+)
+def test_parse_matlab_vector(matlab_vector, expected_vector):
+    vector = parse_matlab_vector(matlab_vector)
+    assert vector == expected_vector
+
+
+@pytest.mark.parametrize(
+    "filename, expected_metadata",
+    [
+        (
+            "scanimage_20220801_single.tif",
+            {
+                "sampling_frequency": 15.2379,
+                "num_channels": 1,
+                "num_planes": 20,
+                "frames_per_slice": 24,
+                "channel_names": ["Channel 1"],
+            },
+        ),
+        (
+            "scanimage_20220923_roi.tif",
+            {
+                "sampling_frequency": 29.1248,
+                "num_channels": 2,
+                "num_planes": 2,
+                "frames_per_slice": 2,
+                "channel_names": ["Channel 1", "Channel 4"],
+            },
+        ),
+    ],
+)
+def test_parse_metadata(filename, expected_metadata):
+    file_path = OPHYS_DATA_PATH / "imaging_datasets" / "ScanImage" / filename
+    metadata = extract_extra_metadata(file_path)
+    metadata = parse_metadata(metadata)
+    assert metadata == expected_metadata
+
+
+def test_parse_metadata_v3_8():
+    file_path = OPHYS_DATA_PATH / "imaging_datasets" / "ScanImage" / "sample_scanimage_version_3_8.tiff"
+    metadata = extract_extra_metadata(file_path)
+    metadata = parse_metadata_v3_8(metadata)
+    expected_metadata = {"sampling_frequency": 3.90625, "num_channels": 1, "num_planes": 1}
+    assert metadata == expected_metadata
+
+
+@pytest.mark.parametrize(
+    "filename, expected_timestamps",
+    [
+        ("scanimage_20220801_single.tif", [0.45951611, 0.98468446, 1.50985974]),
+        (
+            "scanimage_20220923_roi.tif",
+            [
+                0.0,
+                0.0,
+                0.03433645,
+                0.03433645,
+                1.04890375,
+                1.04890375,
+                1.08324025,
+                1.08324025,
+                2.12027815,
+                2.12027815,
+                2.15461465,
+                2.15461465,
+                2.7413649,
+                2.7413649,
+                2.7757014,
+                2.7757014,
+                3.23987545,
+                3.23987545,
+                3.27421195,
+                3.27421195,
+                3.844804,
+                3.844804,
+                3.87914055,
+                3.87914055,
+            ],
+        ),
+    ],
+)
+def test_extract_timestamps_from_file(filename, expected_timestamps):
+    file_path = OPHYS_DATA_PATH / "imaging_datasets" / "ScanImage" / filename
+    timestamps = extract_timestamps_from_file(file_path)
+    assert_array_equal(timestamps, expected_timestamps)