add inscopix extractor for cell_set

CHANGELOG.md

@@ -7,6 +7,7 @@
 ### Features
 
 * 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 `InscopixSegmentationExtractor` [PR #275](https://github.com/catalystneuro/roiextractors/pull/275)
 
 ### Fixes
 

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>=1.0.3

src/roiextractors/extractorlist.py

@@ -24,6 +24,7 @@
     BrukerTiffSinglePlaneImagingExtractor,
     MicroManagerTiffImagingExtractor,
 )
+from .extractors.inscopixextractors import InscopixSegmentationExtractor
 from .extractors.sbximagingextractor import SbxImagingExtractor
 from .extractors.memmapextractors import NumpyMemmapImagingExtractor
 from .extractors.memmapextractors import MemmapImagingExtractor
@@ -60,6 +61,7 @@
     ExtractSegmentationExtractor,
     SimaSegmentationExtractor,
     CaimanSegmentationExtractor,
+    InscopixSegmentationExtractor,
 ]
 
 imaging_extractor_dict = {imaging_class.extractor_name: imaging_class for imaging_class in imaging_extractor_full_list}

src/roiextractors/extractors/inscopixextractors/__init__.py

@@ -0,0 +1,3 @@
+"""Extractors for Inscopix data."""
+
+from .inscopixsegmentationextractor import InscopixSegmentationExtractor

src/roiextractors/extractors/inscopixextractors/inscopixsegmentationextractor.py

@@ -0,0 +1,68 @@
+"""Inscopix Segmentation Extractor."""
+
+import numpy as np
+
+from ...extraction_tools import PathType, ArrayType
+from ...segmentationextractor import SegmentationExtractor
+
+
+class InscopixSegmentationExtractor(SegmentationExtractor):
+    """A segmentation extractor for Inscopix."""
+
+    extractor_name = "InscopixSegmentationExtractor"
+    installed = True  # check at class level if installed or not
+    is_writable = False
+    mode = "file"
+    installation_mesg = ""  # error message when not installed
+
+    def __init__(self, file_path: PathType):
+        """Initialize a InscopixSegmentationExtractor instance.
+
+        Parameters
+        ----------
+        file_path: str
+            The location of the folder containing Inscopix *.mat output file.
+        """
+        import isx
+
+        SegmentationExtractor.__init__(self)
+        self.file_path = file_path
+        self.cell_set = isx.CellSet.read(str(file_path))
+
+    def get_num_rois(self):
+        return self.cell_set.num_cells
+
+    def get_roi_image_masks(self, roi_ids=None) -> np.ndarray:
+        if roi_ids is None:
+            roi_idx_ = range(self.get_num_rois())
+        else:
+            all_ids = self.get_roi_ids()
+            roi_idx_ = [all_ids.index(i) for i in roi_ids]
+        return np.hstack([self.cell_set.get_cell_image_data(roi_id) for roi_id in roi_idx_])
+
+    def get_roi_ids(self) -> list:
+        return [self.cell_set.get_cell_name(x) for x in range(self.get_num_rois())]
+
+    def get_image_size(self) -> ArrayType:
+        num_pixels = self.cell_set.footer["spacingInfo"]["numPixels"]
+        return num_pixels["x"], num_pixels["y"]
+
+    def get_accepted_list(self) -> list:
+        return [id for x, id in enumerate(self.get_roi_ids()) if self.cell_set.get_cell_status(x) == "accepted"]
+
+    def get_rejected_list(self) -> list:
+        return [id for x, id in enumerate(self.get_roi_ids()) if self.cell_set.get_cell_status(x) == "rejected"]
+
+    def get_traces(self, roi_ids=None, start_frame=None, end_frame=None, name="raw") -> ArrayType:
+        if roi_ids is None:
+            roi_idx_ = range(self.get_num_rois())
+        else:
+            all_ids = self.get_roi_ids()
+            roi_idx_ = [all_ids.index(i) for i in roi_ids]
+        return np.vstack([self.cell_set.get_cell_trace_data(roi_id)[start_frame:end_frame] for roi_id in roi_idx_])
+
+    def get_num_frames(self) -> int:
+        return self.cell_set.footer["timingInfo"]["numTimes"]
+
+    def get_sampling_frequency(self) -> float:
+        return 1 / self.cell_set.timing.period.secs_float

tests/test_inscopix_segmentation.py

@@ -0,0 +1,55 @@
+import numpy as np
+from numpy.testing import assert_array_equal
+
+from roiextractors import InscopixSegmentationExtractor
+
+from .setup_paths import OPHYS_DATA_PATH
+
+
+def test_inscopix_segmentation_extractor():
+    file_path = OPHYS_DATA_PATH / "segmentation_datasets" / "inscopix" / "cellset.isxd"
+    extractor = InscopixSegmentationExtractor(file_path=file_path)
+
+    assert extractor.get_num_rois() == 4
+    assert extractor.get_roi_ids() == ["C0", "C1", "C2", "C3"]
+    assert extractor.get_accepted_list() == ["C0", "C1", "C2"]
+    assert extractor.get_rejected_list() == ["C3"]
+    assert extractor.get_image_size() == (398, 366)
+    assert extractor.get_num_frames() == 5444
+    img = extractor.get_roi_image_masks(["C1"])
+    assert img.shape == (366, 398)
+    np.testing.assert_allclose(extractor.get_sampling_frequency(), 9.998700168978033)
+    assert extractor.get_traces().shape == (4, 5444)
+    assert extractor.get_traces(start_frame=10, end_frame=20).shape == (4, 10)
+    assert extractor.get_traces(start_frame=10, end_frame=20, roi_ids=["C1"]).shape == (1, 10)
+
+
+def test_inscopix_segmentation_extractor_part1():
+    file_path = OPHYS_DATA_PATH / "segmentation_datasets" / "inscopix" / "cellset_series_part1.isxd"
+    extractor = InscopixSegmentationExtractor(file_path=file_path)
+
+    assert extractor.get_num_rois() == 6
+    assert extractor.get_roi_ids() == ["C0", "C1", "C2", "C3", "C4", "C5"]
+    assert extractor.get_accepted_list() == []
+    assert extractor.get_rejected_list() == []
+    assert extractor.get_image_size() == (21, 21)
+    img = extractor.get_roi_image_masks(["C1"])
+    assert img.shape == (21, 21)
+    assert extractor.get_sampling_frequency() == 10.0
+    assert extractor.get_traces().shape == (6, 100)
+    assert extractor.get_traces(start_frame=10, end_frame=20).shape == (6, 10)
+    assert extractor.get_traces(start_frame=10, end_frame=20, roi_ids=["C1"]).shape == (1, 10)
+    assert extractor.get_num_frames() == 100
+
+
+def test_inscopix_segmentation_extractor_empty():
+    file_path = OPHYS_DATA_PATH / "segmentation_datasets" / "inscopix" / "empty_cellset.isxd"
+    extractor = InscopixSegmentationExtractor(file_path=file_path)
+
+    assert extractor.get_num_rois() == 0
+    assert extractor.get_roi_ids() == []
+    assert extractor.get_accepted_list() == []
+    assert extractor.get_rejected_list() == []
+    assert extractor.get_image_size() == (5, 4)
+    assert extractor.get_sampling_frequency() == 40.0
+    assert extractor.get_num_frames() == 7