[pre-commit.ci] auto fixes from pre-commit.com hooks

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src/pinto_lab_to_nwb/widefield/interfaces/widefield_processed_segmentationinterface.py

@@ -16,12 +16,13 @@ class WidefieldProcessedSegmentationinterface(BaseSegmentationExtractorInterface
     Extractor = WidefieldProcessedSegmentationExtractor
 
     def __init__(
-            self,
-            info_mat_file_path: FilePathType,
-            roi_from_ref_mat_file_path: FilePathType,
-            vasculature_mask_file_path: FilePathType,
-            blue_pca_mask_file_path: FilePathType,
-            verbose: bool = True):
+        self,
+        info_mat_file_path: FilePathType,
+        roi_from_ref_mat_file_path: FilePathType,
+        vasculature_mask_file_path: FilePathType,
+        blue_pca_mask_file_path: FilePathType,
+        verbose: bool = True,
+    ):
         """
 
         Parameters

src/pinto_lab_to_nwb/widefield/interfaces/widefield_segmentation_images_blue_datainterface.py

@@ -14,11 +14,11 @@ class WidefieldSegmentationImagesBlueInterface(BaseDataInterface):
     """The custom interface to add the blue channel manual and vasculature mask to the NWBFile."""
 
     def __init__(
-            self,
-            vasculature_mask_file_path: FilePathType,
-            manual_mask_file_path: FilePathType,
-            manual_mask_struct_name: str,
-            verbose: bool = True,
+        self,
+        vasculature_mask_file_path: FilePathType,
+        manual_mask_file_path: FilePathType,
+        manual_mask_struct_name: str,
+        verbose: bool = True,
     ):
         """
         The interface to add the summary images to the NWBFile.
@@ -35,7 +35,9 @@ def __init__(
         """
         super().__init__(vasculature_mask_file_path=vasculature_mask_file_path)
         self.vasculature_mask_file_path = Path(vasculature_mask_file_path)
-        assert self.vasculature_mask_file_path.exists(), f"The vasculature mask file '{vasculature_mask_file_path}' does not exist."
+        assert (
+            self.vasculature_mask_file_path.exists()
+        ), f"The vasculature mask file '{vasculature_mask_file_path}' does not exist."
 
         self.manual_mask_file_path = Path(manual_mask_file_path)
         assert self.manual_mask_file_path.exists(), f"The manual mask file '{manual_mask_file_path}' does not exist."
@@ -49,14 +51,18 @@ def __init__(
 
     def _load_vasculature_mask(self) -> np.ndarray:
         vasculature_mask_mat = read_mat(str(self.vasculature_mask_file_path))
-        assert "mask" in vasculature_mask_mat, f"The vasculature mask is missing from {self.vasculature_mask_file_path}."
+        assert (
+            "mask" in vasculature_mask_mat
+        ), f"The vasculature mask is missing from {self.vasculature_mask_file_path}."
         vasculature_mask = vasculature_mask_mat["mask"]
 
         return vasculature_mask
 
     def _load_manual_mask(self):
         manual_mask_mat = read_mat(self.manual_mask_file_path)
-        assert self.manual_mask_struct_name in manual_mask_mat, f"The manual mask is missing from {self.manual_mask_file_path}."
+        assert (
+            self.manual_mask_struct_name in manual_mask_mat
+        ), f"The manual mask is missing from {self.manual_mask_file_path}."
         manual_mask = manual_mask_mat[self.manual_mask_struct_name]
 
         return manual_mask

src/pinto_lab_to_nwb/widefield/interfaces/widefield_segmentation_images_violet_datainterface.py

@@ -25,7 +25,9 @@ def __init__(self, violet_pca_mask_file_path: FilePathType, verbose: bool = True
         """
         super().__init__(violet_pca_mask_file_path=violet_pca_mask_file_path)
         self.violet_pca_mask_file_path = Path(violet_pca_mask_file_path)
-        assert self.violet_pca_mask_file_path.exists(), f"The violet channel PCA mask file '{violet_pca_mask_file_path}' does not exist."
+        assert (
+            self.violet_pca_mask_file_path.exists()
+        ), f"The violet channel PCA mask file '{violet_pca_mask_file_path}' does not exist."
         self.verbose = verbose
 
         self._image_pca_violet = self._load_pca_mask()

src/pinto_lab_to_nwb/widefield/widefield_convert_session.py

@@ -182,7 +182,7 @@ def session_to_nwb(
     # Parameters for conversion
 
     # The folder path that contains the raw imaging data in Micro-Manager OME-TIF format (.ome.tif files).
-    #imaging_folder_path = Path("/Users/weian/data/Cherry/20230802/Cherry_20230802_20hz_1")
+    # imaging_folder_path = Path("/Users/weian/data/Cherry/20230802/Cherry_20230802_20hz_1")
     imaging_folder_path = Path("/Volumes/t7-ssd/Pinto/DrChicken_20230419_20hz")
     # The file path to the strobe sequence file.
     strobe_sequence_file_path = imaging_folder_path / "strobe_seq_1_2.mat"
@@ -196,14 +196,14 @@ def session_to_nwb(
     vasculature_mask_file_path = imaging_folder_path / "vasculature_mask_2.mat"
 
     # The file path that contains the manual mask on the full size session image (blue channel).
-    #manual_mask_file_path = imaging_folder_path / "reg_manual_mask_jlt6316_Cherry_20230802_1_1_1.mat"
+    # manual_mask_file_path = imaging_folder_path / "reg_manual_mask_jlt6316_Cherry_20230802_1_1_1.mat"
     manual_mask_file_path = imaging_folder_path / "regManualMask.mat"
     # The name of the struct in the manual mask file that contains the manual mask (e.g. "regMask" or "reg_manual_mask").
-    #manual_mask_struct_name = "reg_manual_mask"
+    # manual_mask_struct_name = "reg_manual_mask"
     manual_mask_struct_name = "regMask"
 
     # The file path that contains the Allen area label of each pixel mapped onto the reference image of the mouse and registered to the session.
-    #roi_from_ref_mat_file_path = imaging_folder_path / "ROIfromRef_1.mat"
+    # roi_from_ref_mat_file_path = imaging_folder_path / "ROIfromRef_1.mat"
     roi_from_ref_mat_file_path = imaging_folder_path / "ROIfromRef.mat"
 
     # The file path that contains the contrast based vasculature mask on the downsampled (binned) session image (blue channel).