Fix override of channel_name in Suite2pSegmentationExtractor

CHANGELOG.md

@@ -7,7 +7,7 @@
 ### Fixes
 
 * Fixed `MicroManagerTiffImagingExtractor` private extractor's dtype to not override the parent's dtype. [PR #257](https://github.com/catalystneuro/roiextractors/pull/257)
-
+* Fixed override of `channel_name` in `Suite2pSegmentationExtractor`. [PR #263](https://github.com/catalystneuro/roiextractors/pull/263)
 
 
 # v0.5.4

src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py

@@ -168,8 +168,9 @@ def __init__(
 
         self.iscell = self._load_npy("iscell.npy", mmap_mode="r")
 
-        channel_name = "OpticalChannel" if len(channel_names) == 1 else channel_name.capitalize()
-        self._channel_names = [channel_name]
+        # The name of the OpticalChannel object is "OpticalChannel" if there is only one channel, otherwise it is
+        # "Chan1" or "Chan2".
+        self._channel_names = ["OpticalChannel" if len(channel_names) == 1 else channel_name.capitalize()]
 
         self._image_correlation = self._correlation_image_read()
         image_mean_name = "meanImg" if channel_name == "chan1" else f"meanImg_chan2"

tests/test_suite2psegmentationextractor.py

@@ -28,6 +28,10 @@ def setUpClass(cls):
         cls.first_channel_raw_traces = np.load(cls.folder_path / "plane0" / "F.npy").T
         cls.second_channel_raw_traces = np.load(cls.folder_path / "plane0" / "F_chan2.npy").T
 
+        options = np.load(cls.folder_path / "plane0" / "ops.npy", allow_pickle=True).item()
+        cls.first_channel_mean_image = options["meanImg"]
+        cls.second_channel_mean_image = options["meanImg_chan2"]
+
         cls.image_size = (128, 128)
         cls.num_rois = 15
 
@@ -43,7 +47,7 @@ def tearDownClass(cls):
         # remove the temporary directory and its contents
         shutil.rmtree(cls.test_dir)
 
-    def test_channel_names(self):
+    def test_available_channel_names(self):
         self.assertEqual(
             Suite2pSegmentationExtractor.get_available_channels(folder_path=self.folder_path), self.channel_names
         )
@@ -98,7 +102,7 @@ def test_num_frames(self):
     def test_sampling_frequency(self):
         self.assertEqual(self.extractor.get_sampling_frequency(), 10.0)
 
-    def test_channel_names(self):
+    def test_optical_channel_names(self):
         self.assertEqual(self.extractor.get_channel_names(), ["Chan1"])
 
     def test_num_channels(self):
@@ -125,3 +129,14 @@ def test_extractor_image_masks_selected_rois(self):
         """Test that the image masks are correctly extracted for a subset of ROIs."""
         roi_indices = list(range(5))
         assert_array_equal(self.extractor.get_roi_image_masks(roi_ids=roi_indices), self.image_masks[..., roi_indices])
+
+    def test_first_channel_mean_image(self):
+        """Test that the mean image is correctly loaded from the extractor."""
+        images_dict = self.extractor.get_images_dict()
+        assert_array_equal(images_dict["mean"], self.first_channel_mean_image)
+
+    def test_second_channel_mean_image(self):
+        """Test that the mean image for the second channel is correctly loaded from the extractor."""
+        extractor = Suite2pSegmentationExtractor(folder_path=self.folder_path, channel_name="chan2")
+        images_dict = extractor.get_images_dict()
+        assert_array_equal(images_dict["mean"], self.second_channel_mean_image)