formatting

src/napari_segmentation_correction/_widget.py

@@ -14,7 +14,6 @@
     QFileDialog,
     QHBoxLayout,
     QLineEdit,
-    QMessageBox,
     QPushButton,
     QScrollArea,
     QTabWidget,
@@ -23,17 +22,18 @@
 )
 from skimage import measure
 
-from .copy_label_widget import CopyLabelWidget
 from .connected_components import ConnectedComponents
+from .copy_label_widget import CopyLabelWidget
 from .custom_table_widget import ColoredTableWidget
 from .erosion_dilation_widget import ErosionDilationWidget
 from .image_calculator import ImageCalculator
 from .layer_manager import LayerManager
 from .point_filter import PointFilter
+from .select_delete_widget import SelectDeleteMask
 from .size_filter_widget import SizeFilterWidget
 from .smoothing_widget import SmoothingWidget
 from .threshold_widget import ThresholdWidget
-from .select_delete_widget import SelectDeleteMask
+
 
 class AnnotateLabelsND(QWidget):
     """Widget for manual correction of label data, for example to prepare ground truth data for training a segmentation model"""

src/napari_segmentation_correction/connected_components.py

@@ -1,21 +1,24 @@
+import os
+import shutil
+
 import dask.array as da
 import napari
 import numpy as np
-from skimage.measure import label
+import tifffile
 from qtpy.QtWidgets import (
+    QFileDialog,
     QGroupBox,
     QMessageBox,
     QPushButton,
     QVBoxLayout,
     QWidget,
-    QFileDialog
 )
-import os
-import shutil
-import tifffile
 from skimage.io import imread
+from skimage.measure import label
+
 from .layer_manager import LayerManager
 
+
 class ConnectedComponents(QWidget):
     """Widget to run connected component analysis"""
 
@@ -88,7 +91,7 @@ def _conn_comp(self):
             )
             return True
         else:
-            self.label_manager.selected_layer = self.viewer.add_labels(label(self.label_manager.selected_layer.data), 
+            self.label_manager.selected_layer = self.viewer.add_labels(label(self.label_manager.selected_layer.data),
                 name=self.label_manager.selected_layer.name + "_conn_comp",
             )
             self.label_manager._update_labels(

src/napari_segmentation_correction/erosion_dilation_widget.py

@@ -6,15 +6,14 @@
 import numpy as np
 import tifffile
 from qtpy.QtWidgets import (
+    QFileDialog,
     QGroupBox,
     QHBoxLayout,
     QLabel,
-    QMessageBox,
     QPushButton,
     QSpinBox,
     QVBoxLayout,
     QWidget,
-    QFileDialog
 )
 from scipy import ndimage
 from scipy.ndimage import binary_erosion

src/napari_segmentation_correction/label_option_layer.py

@@ -43,11 +43,11 @@ def cell_copied(layer, event):
                     mask = (
                         self.data[coords[0], coords[1], :, :] == selected_label
                     )
-                elif ndims == 3: 
+                elif ndims == 3:
                     mask = (
                         self.data[coords[0], :, :] == selected_label
                     )
-                else: 
+                else:
                     print('This number of dimensions is currently not supported', ndims)
                     return
 
@@ -80,7 +80,7 @@ def cell_copied(layer, event):
                         orig_label = self.label_manager.selected_layer.data[
                             coords[-3], coords[-2], coords[-1]
                         ]
-                       
+
                         if orig_label != 0:
                             self.label_manager.selected_layer.data[coords[-3]][
                                 self.label_manager.selected_layer.data[coords[-3]] == orig_label] = 0  # set the original label to zero in current slice only
@@ -145,11 +145,11 @@ def cell_copied(layer, event):
                     mask = (
                         self.data[coords[0], :, :, :] == selected_label
                     )
-                elif ndims == 3: 
+                elif ndims == 3:
                     mask = (
                         self.data[:, :, :] == selected_label
                     )
-                else: 
+                else:
                     print('This number of dimensions is currently not supported', ndims)
                     return
 

src/napari_segmentation_correction/size_filter_widget.py

@@ -7,15 +7,14 @@
 import numpy as np
 import tifffile
 from qtpy.QtWidgets import (
+    QFileDialog,
     QGroupBox,
     QHBoxLayout,
     QLabel,
-    QMessageBox,
     QPushButton,
     QSpinBox,
     QVBoxLayout,
     QWidget,
-    QFileDialog
 )
 from skimage import measure
 from skimage.io import imread

src/napari_segmentation_correction/threshold_widget.py

@@ -1,24 +1,24 @@
+import os
+import shutil
+
 import dask.array as da
-import numpy as np
 import napari
+import numpy as np
+import tifffile
 from napari.layers import Image, Labels
 from qtpy.QtWidgets import (
+    QFileDialog,
     QGroupBox,
     QHBoxLayout,
     QLabel,
-    QMessageBox,
     QPushButton,
     QSpinBox,
     QVBoxLayout,
     QWidget,
-    QFileDialog
 )
+from skimage.io import imread
 
 from .layer_dropdown import LayerDropdown
-from skimage.io import imread 
-import os
-import tifffile
-import shutil
 
 
 class ThresholdWidget(QWidget):
@@ -82,7 +82,7 @@ def _threshold(self):
         if isinstance(self.threshold_layer.data, da.core.Array):
             if self.outputdir is None:
                 self.outputdir = QFileDialog.getExistingDirectory(self, "Select Output Folder")
-            
+
             outputdir = os.path.join(
                 self.outputdir,
                 (self.threshold_layer.name + "_threshold"),
@@ -97,7 +97,7 @@ def _threshold(self):
                 data = self.threshold_layer.data[
                     i
                 ].compute()  # Compute the current stack
-                
+
                 thresholded = (
                     data >= int(self.min_threshold.value())
                 ) & (data <= int(self.max_threshold.value()))
@@ -125,7 +125,7 @@ def _threshold(self):
                 name=self.threshold_layer.name + "_thresholded",
             )
 
-        else: 
+        else:
             thresholded = (
                 self.threshold_layer.data >= int(self.min_threshold.value())
             ) & (self.threshold_layer.data <= int(self.max_threshold.value()))