refactored init to manually accept args rather than automatically par…

…sing from metadata to support old testing file

src/roiextractors/extractors/tiffimagingextractors/scanimagetiffimagingextractor.py

@@ -38,14 +38,46 @@ def extract_extra_metadata(
     return extra_metadata
 
 
+def parse_metadata(metadata):
+    """Parse metadata dictionary to extract relevant information.
+
+    Notes
+    -----
+    SI.hChannels.channelsActive = '[1;2;...;N]' where N is the number of active channels.
+    SI.hChannels.channelName = "{'channel_name_1' 'channel_name_2' ... 'channel_name_M'}"
+        where M is the number of channels (active or not).
+    """
+    sampling_frequency = float(metadata["SI.hRoiManager.scanVolumeRate"])
+    num_channels = len(metadata["SI.hChannels.channelsActive"].split(";"))
+    num_planes = int(metadata["SI.hStackManager.numSlices"])
+    frames_per_slice = int(metadata["SI.hStackManager.framesPerSlice"])
+    channel_names = metadata["SI.hChannels.channelName"].split("'")[1::2][:num_channels]
+    metadata_parsed = dict(
+        sampling_frequency=sampling_frequency,
+        num_channels=num_channels,
+        num_planes=num_planes,
+        frames_per_slice=frames_per_slice,
+        channel_names=channel_names,
+    )
+    return metadata_parsed
+
+
 class ScanImageTiffImagingExtractor(ImagingExtractor):
     """Specialized extractor for reading TIFF files produced via ScanImage."""
 
     extractor_name = "ScanImageTiffImaging"
     is_writable = True
     mode = "file"
 
-    def __init__(self, file_path: PathType) -> None:
+    def __init__(
+        self,
+        file_path: PathType,
+        sampling_frequency: float,
+        num_channels: Optional[int] = 1,
+        num_planes: Optional[int] = 1,
+        frames_per_slice: Optional[int] = 1,
+        channel_names: Optional[list] = None,
+    ) -> None:
         """Create a ScanImageTiffImagingExtractor instance from a TIFF file produced by ScanImage.
 
         The underlying data is stored in a round-robin format collapsed into 3 dimensions (frames, rows, columns).
@@ -62,24 +94,29 @@ def __init__(self, file_path: PathType) -> None:
         ----------
         file_path : PathType
             Path to the TIFF file.
+        sampling_frequency : float
+            Sampling frequency of each plane (scanVolumeRate) in Hz.
+        num_channels : int, optional
+            Number of active channels that were acquired (default=1).
+        num_planes : int, optional
+            Number of depth planes that were acquired (default=1).
+        frames_per_slice : int, optional
+            Number of frames per depth plane that were acquired (default=1).
+        channel_names : list, optional
+            Names of the channels that were acquired (default=None).
         """
         super().__init__()
         self.file_path = Path(file_path)
-        ScanImageTiffReader = _get_scanimage_reader()
-        extra_metadata = extract_extra_metadata(file_path)
-        # SI.hChannels.channelsActive = '[1;2;...;N]' where N is the number of active channels
-        self._num_channels = len(extra_metadata["SI.hChannels.channelsActive"].split(";"))
-        self._num_planes = int(extra_metadata["SI.hStackManager.numSlices"])
-        frames_per_slice = int(extra_metadata["SI.hStackManager.framesPerSlice"])
+        self._sampling_frequency = sampling_frequency
+        self.metadata = extract_extra_metadata(file_path)
+        self._num_channels = num_channels
+        self._num_planes = num_planes
         if frames_per_slice != 1:
             raise NotImplementedError(
                 "Extractor cannot handle multiple frames per slice. Please raise an issue to request this feature: "
                 "https://github.com/catalystneuro/roiextractors/issues "
             )
-        self._sampling_frequency = float(extra_metadata["SI.hRoiManager.scanVolumeRate"])
-        # SI.hChannels.channelName = "{'channel_name_1' 'channel_name_2' ... 'channel_name_N'}"
-        #   where N is the number of channels (active or not)
-        self._channel_names = extra_metadata["SI.hChannels.channelName"].split("'")[1::2][: self._num_channels]
+        self._channel_names = channel_names
 
         valid_suffixes = [".tiff", ".tif", ".TIFF", ".TIF"]
         if self.file_path.suffix not in valid_suffixes:
@@ -88,6 +125,7 @@ def __init__(self, file_path: PathType) -> None:
                 f"Suffix ({self.file_path.suffix}) is not of type {suffix_string}! "
                 f"The {self.extractor_name}Extractor may not be appropriate for the file."
             )
+        ScanImageTiffReader = _get_scanimage_reader()
         with ScanImageTiffReader(str(self.file_path)) as io:
             shape = io.shape()  # [frames, rows, columns]
         if len(shape) == 3:

tests/temp_test_scanimage.py

@@ -1,20 +1,42 @@
 # scratch file to test scanimage tiff extractor
 from roiextractors import ScanImageTiffImagingExtractor
+from roiextractors.extractors.tiffimagingextractors.scanimagetiffimagingextractor import (
+    extract_extra_metadata,
+    parse_metadata,
+)
 
 
 def main():
+    example_test = "/Users/pauladkisson/Documents/CatalystNeuro/ROIExtractors/ophys_testing_data/imaging_datasets/ScanImage/sample_scanimage_version_3_8.tiff"
     example_holo = "/Volumes/T7/CatalystNeuro/NWB/MouseV1/raw-tiffs/2ret/20230119_w57_1_2ret_00001.tif"
     example_single = "/Users/pauladkisson/Documents/CatalystNeuro/ROIExtractors/ophys_testing_data/imaging_datasets/ScanImage/scanimage_20220801_single.tif"
     example_volume = "/Users/pauladkisson/Documents/CatalystNeuro/ROIExtractors/ophys_testing_data/imaging_datasets/ScanImage/scanimage_20220801_volume.tif"
     example_multivolume = "/Users/pauladkisson/Documents/CatalystNeuro/ROIExtractors/ophys_testing_data/imaging_datasets/ScanImage/scanimage_20220801_multivolume.tif"
 
-    extractor = ScanImageTiffImagingExtractor(file_path=example_holo)
+    extractor = ScanImageTiffImagingExtractor(file_path=example_test, sampling_frequency=30.0)
+    print("Example test file loads!")
+
+    metadata = extract_extra_metadata(example_holo)
+    metadata_parsed = parse_metadata(metadata)
+    extractor = ScanImageTiffImagingExtractor(file_path=example_holo, **metadata_parsed)
     print("Example holographic file loads!")
-    extractor = ScanImageTiffImagingExtractor(file_path=example_single)
+
+    metadata = extract_extra_metadata(example_single)
+    metadata_parsed = parse_metadata(metadata)
+    metadata_parsed["frames_per_slice"] = 1  # Multiple frames per slice is not supported yet
+    extractor = ScanImageTiffImagingExtractor(file_path=example_single, **metadata_parsed)
     print("Example single-plane file loads!")
-    extractor = ScanImageTiffImagingExtractor(file_path=example_volume)
+
+    metadata = extract_extra_metadata(example_volume)
+    metadata_parsed = parse_metadata(metadata)
+    metadata_parsed["frames_per_slice"] = 1  # Multiple frames per slice is not supported yet
+    extractor = ScanImageTiffImagingExtractor(file_path=example_volume, **metadata_parsed)
     print("Example volume file loads!")
-    extractor = ScanImageTiffImagingExtractor(file_path=example_multivolume)
+
+    metadata = extract_extra_metadata(example_multivolume)
+    metadata_parsed = parse_metadata(metadata)
+    metadata_parsed["frames_per_slice"] = 1  # Multiple frames per slice is not supported yet
+    extractor = ScanImageTiffImagingExtractor(file_path=example_multivolume, **metadata_parsed)
     print("Example multivolume file loads!")
 
 

tests/test_scan_image_tiff.py

@@ -17,7 +17,7 @@ class TestScanImageTiffExtractor(TestCase):
     def setUpClass(cls):
         cls.file_path = OPHYS_DATA_PATH / "imaging_datasets" / "Tif" / "sample_scanimage.tiff"
         cls.tmpdir = Path(mkdtemp())
-        cls.imaging_extractor = ScanImageTiffImagingExtractor(file_path=cls.file_path)
+        cls.imaging_extractor = ScanImageTiffImagingExtractor(file_path=cls.file_path, sampling_frequency=30.0)
         with ScanImageTiffReader(filename=str(cls.imaging_extractor.file_path)) as io:
             cls.data = io.data()