add inscopix imaging extractor

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -60,7 +60,6 @@ body:
     attributes:
       label: Python Version
       options:
-        - "3.8"
         - "3.9"
         - "3.10"
         - "3.11"

.github/workflows/auto-publish.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.9"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/run-tests.yml

@@ -37,7 +37,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, "3.10", 3.11]
+        python-version: ["3.9", "3.10", "3.11"]
         os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
       - uses: s-weigand/setup-conda@v1

requirements-full.txt

@@ -2,3 +2,4 @@ tifffile>=2018.10.18
 scanimage-tiff-reader==1.4.1
 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 +1,52 @@
+"""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):
+        """
+        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:
+        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)])

tests/test_inscopiximagingextractor.py

@@ -0,0 +1,46 @@
+import numpy as np
+from numpy import dtype
+from numpy.testing import assert_array_equal
+
+from roiextractors import InscopixImagingExtractor
+
+from .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("float64")
+    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)
+
+
+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("int64")
+    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)
+
+
+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("int64")
+    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)