diff --git a/src/roiextractors/extractors/minian/miniansegmentationextractor.py b/src/roiextractors/extractors/minian/miniansegmentationextractor.py index 454cf244..229473e4 100644 --- a/src/roiextractors/extractors/minian/miniansegmentationextractor.py +++ b/src/roiextractors/extractors/minian/miniansegmentationextractor.py @@ -38,16 +38,15 @@ def __init__(self, folder_path: PathType): """ SegmentationExtractor.__init__(self) self.folder_path = folder_path - self._roi_response_denoised = self._trace_extractor_read(field = "C") - self._roi_response_baseline = self._trace_extractor_read(field = "b0") - self._roi_response_neuropil = self._trace_extractor_read(field = "f") - self._roi_response_deconvolved = self._trace_extractor_read(field = "S") + self._roi_response_denoised = self._trace_extractor_read(field="C") + self._roi_response_baseline = self._trace_extractor_read(field="b0") + self._roi_response_neuropil = self._trace_extractor_read(field="f") + self._roi_response_deconvolved = self._trace_extractor_read(field="S") self._image_maximum_projection = self._file_extractor_read("/max_proj.zarr/max_proj") self._image_masks = self._roi_image_mask_read() self._background_image_masks = self._background_image_mask_read() - - def _file_extractor_read(self, zarr_group = ""): + def _file_extractor_read(self, zarr_group=""): """Read the zarr. Returns @@ -73,7 +72,7 @@ def _roi_image_mask_read(self): if dataset is None or "A" not in dataset: return None else: - return np.transpose(dataset["A"], (1,2,0)) + return np.transpose(dataset["A"], (1, 2, 0)) def _background_image_mask_read(self): """Read the image masks from the zarr output. @@ -167,4 +166,8 @@ def get_images_dict(self) -> dict: dictionary with key, values representing different types of Images used in segmentation: Mean, Correlation image """ - return dict(mean=self._image_mean, correlation=self._image_correlation, maximum_projection=self._image_maximum_projection) \ No newline at end of file + return dict( + mean=self._image_mean, + correlation=self._image_correlation, + maximum_projection=self._image_maximum_projection, + )