Merge pull request #257 from catalystneuro/fix_micromanagertiff_dtype

Fix `MicroManagerTiffImagingExtractor` private extractor's `dtype`

CHANGELOG.md

@@ -4,6 +4,10 @@
 
 * Updated `Suite2pSegmentationExtractor` to support multi channel and multi plane data. [PR #242](https://github.com/catalystneuro/roiextractors/pull/242)
 
+### Fixes
+
+* Fixed `MicroManagerTiffImagingExtractor` private extractor's dtype to not override the parent's dtype. [PR #257](https://github.com/catalystneuro/roiextractors/pull/257)
+
 
 
 # v0.5.4

src/roiextractors/extractors/tiffimagingextractors/micromanagertiffimagingextractor.py

@@ -100,6 +100,7 @@ def __init__(self, folder_path: PathType):
         imaging_extractors = []
         for file_path, num_frames_per_file in file_counts.items():
             extractor = _MicroManagerTiffImagingExtractor(self.folder_path / file_path)
+            extractor._dtype = self._dtype
             extractor._num_frames = num_frames_per_file
             extractor._image_size = (self._height, self._width)
             imaging_extractors.append(extractor)
@@ -207,6 +208,7 @@ def __init__(self, file_path: PathType):
         super().__init__()
 
         self.pages = self.tifffile.TiffFile(self.file_path).pages
+        self._dtype = None
         self._num_frames = None
         self._image_size = None
 
@@ -226,7 +228,7 @@ def get_channel_names(self) -> list:
         raise NotImplementedError(self.CHANNEL_NAMES_ERROR.format(self.extractor_name))
 
     def get_dtype(self):
-        raise NotImplementedError(self.DATA_TYPE_ERROR.format(self.extractor_name))
+        return self._dtype
 
     def get_video(
         self, start_frame: Optional[int] = None, end_frame: Optional[int] = None, channel: int = 0
@@ -236,7 +238,7 @@ def get_video(
 
         end_frame = end_frame or self.get_num_frames()
         start_frame = start_frame or 0
-        video = np.zeros(shape=(end_frame - start_frame, *self.get_image_size()))
+        video = np.zeros(shape=(end_frame - start_frame, *self.get_image_size()), dtype=self.get_dtype())
         for page_ind, page in enumerate(islice(self.pages, start_frame, end_frame)):
             video[page_ind] = page.asarray()
         return video

tests/test_micromanagertiffimagingextractor.py

@@ -109,7 +109,13 @@ def test_private_micromanagertiffextractor_channel_names(self):
             self.extractor._imaging_extractors[0].get_channel_names()
 
     def test_private_micromanagertiffextractor_dtype(self):
+        """Test that the dtype of the private extractor is the same as the dtype of the main extractor."""
         sub_extractor = self.extractor._imaging_extractors[0]
-        exc_msg = f"The {sub_extractor.extractor_name}Extractor does not support retrieving the data type."
-        with self.assertRaisesWith(NotImplementedError, exc_msg=exc_msg):
-            self.extractor._imaging_extractors[0].get_dtype()
+        self.assertEqual(self.extractor.get_dtype(), sub_extractor.get_dtype())
+
+    def test_private_micromanagertiffextractor_get_video(self):
+        """Test that the dtype of the video is uint16."""
+        sub_extractor = self.extractor._imaging_extractors[0]
+        expected_dtype = np.uint16
+        sub_extractor_video_dtype = sub_extractor.get_video().dtype
+        self.assertEqual(sub_extractor_video_dtype, expected_dtype)