add inscopix imaging extractor (#276)

CHANGELOG.md

@@ -6,12 +6,16 @@
 
 ### Features
 
+* Add InscopixImagingExtractor [#276](https://github.com/catalystneuro/roiextractors/pull/276)
 * Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: [PR #317](https://github.com/catalystneuro/roiextractors/pull/317)
 
 ### Fixes
 
 * Remove unecessary scipy import error handling [#315](https://github.com/catalystneuro/roiextractors/pull/315)
 
+### Testing
+
+* Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: [PR #317](https://github.com/catalystneuro/roiextractors/pull/317)
 * Added daily testing workflow and fixed bug with python 3.12 by upgrading scanimage-tiff-reader version: [PR #321](https://github.com/catalystneuro/roiextractors/pull/321)
 
 # v0.5.8

requirements-full.txt

@@ -2,3 +2,4 @@ tifffile>=2018.10.18
 scanimage-tiff-reader==1.4.1.4
 neuroconv[video]>=0.4.6  # Uses the VideoCaptureContext class
 natsort>=8.3.1
+isx>=1.0.4

src/roiextractors/extractorlist.py

@@ -25,6 +25,7 @@
     MicroManagerTiffImagingExtractor,
 )
 from .extractors.sbximagingextractor import SbxImagingExtractor
+from .extractors.inscopixextractors import InscopixImagingExtractor
 from .extractors.memmapextractors import NumpyMemmapImagingExtractor
 from .extractors.memmapextractors import MemmapImagingExtractor
 from .extractors.miniscopeimagingextractor import MiniscopeImagingExtractor
@@ -50,6 +51,7 @@
     NumpyMemmapImagingExtractor,
     MemmapImagingExtractor,
     VolumetricImagingExtractor,
+    InscopixImagingExtractor,
 ]
 
 segmentation_extractor_full_list = [

src/roiextractors/extractors/inscopixextractors/__init__.py

@@ -0,0 +1,3 @@
+"""Defines extactors for Inscopix data."""
+
+from .inscopiximagingextractor import InscopixImagingExtractor

src/roiextractors/extractors/inscopixextractors/inscopiximagingextractor.py

@@ -0,0 +1,57 @@
+"""Inscopix Imaging Extractor."""
+
+import warnings
+from typing import Optional, Tuple
+
+import numpy as np
+
+from ...imagingextractor import ImagingExtractor
+from ...extraction_tools import PathType
+
+
+class InscopixImagingExtractor(ImagingExtractor):
+    """Extracts imaging data from Inscopix recordings."""
+
+    extractor_name = "InscopixImaging"
+
+    def __init__(self, file_path: PathType):
+        """
+        Create an InscopixImagingExtractor instance from a single .isx file.
+
+        Parameters
+        ----------
+        file_path : PathType
+            Path to the Inscopix file.
+        """
+        import isx
+
+        super().__init__(file_path=file_path)
+        self.movie = isx.Movie.read(str(file_path))
+
+    def get_image_size(self) -> Tuple[int, int]:
+        num_pixels = self.movie.spacing.num_pixels
+        return num_pixels
+
+    def get_num_frames(self) -> int:
+        return self.movie.timing.num_samples
+
+    def get_sampling_frequency(self) -> float:
+        return 1 / self.movie.timing.period.secs_float
+
+    def get_channel_names(self) -> list[str]:
+        warnings.warn("isx only supports single channel videos.")
+        return ["channel_0"]
+
+    def get_num_channels(self) -> int:
+        warnings.warn("isx only supports single channel videos.")
+        return 1
+
+    def get_video(
+        self, start_frame: Optional[int] = None, end_frame: Optional[int] = None, channel: int = 0
+    ) -> np.ndarray:
+        start_frame = start_frame or 0
+        end_frame = end_frame or self.get_num_frames()
+        return np.array([self.movie.get_frame_data(i) for i in range(start_frame, end_frame)])
+
+    def get_dtype(self):
+        return self.movie.data_type

tests/test_inscopiximagingextractor.py

@@ -0,0 +1,49 @@
+import numpy as np
+from numpy import dtype
+from numpy.testing import assert_array_equal
+
+from roiextractors import InscopixImagingExtractor
+
+from tests.setup_paths import OPHYS_DATA_PATH
+
+
+def test_inscopiximagingextractor_movie_128x128x100_part1():
+    file_path = OPHYS_DATA_PATH / "imaging_datasets" / "inscopix" / "movie_128x128x100_part1.isxd"
+    extractor = InscopixImagingExtractor(file_path=file_path)
+
+    assert extractor.get_num_frames() == 100
+    assert extractor.get_image_size() == (128, 128)
+    assert extractor.get_dtype() == dtype("float32")
+    assert extractor.get_sampling_frequency() == 10.0
+    assert extractor.get_channel_names() == ["channel_0"]
+    assert extractor.get_num_channels() == 1
+    assert extractor.get_video().shape == (100, 128, 128)
+    assert extractor.get_frames(frame_idxs=[0], channel=0).dtype == extractor.get_dtype()
+
+
+def test_inscopiximagingextractor_movie_longer_than_3_min():
+    file_path = OPHYS_DATA_PATH / "imaging_datasets" / "inscopix" / "movie_longer_than_3_min.isxd"
+    extractor = InscopixImagingExtractor(file_path=file_path)
+
+    assert extractor.get_num_frames() == 1248
+    assert extractor.get_image_size() == (33, 29)
+    assert extractor.get_dtype() == dtype("uint16")
+    np.testing.assert_almost_equal(extractor.get_sampling_frequency(), 5.5563890139076415)
+    assert extractor.get_channel_names() == ["channel_0"]
+    assert extractor.get_num_channels() == 1
+    assert extractor.get_video().shape == (1248, 33, 29)
+    assert extractor.get_frames(frame_idxs=[0], channel=0).dtype == extractor.get_dtype()
+
+
+def test_inscopiximagingextractor_movie_u8():
+    file_path = OPHYS_DATA_PATH / "imaging_datasets" / "inscopix" / "movie_u8.isxd"
+    extractor = InscopixImagingExtractor(file_path=file_path)
+
+    assert extractor.get_num_frames() == 5
+    assert extractor.get_image_size() == (3, 4)
+    assert extractor.get_dtype() == dtype("uint8")
+    np.testing.assert_almost_equal(extractor.get_sampling_frequency(), 20.0)
+    assert extractor.get_channel_names() == ["channel_0"]
+    assert extractor.get_num_channels() == 1
+    assert extractor.get_video().shape == (5, 3, 4)
+    assert extractor.get_frames(frame_idxs=[0], channel=0).dtype == extractor.get_dtype()