Merge pull request #26 from AdaptiveMotorControlLab/cy/layer-inference

Inference on layer

Author: vidalmaxime

napari_cellseg3d/interface.py

@@ -335,7 +335,9 @@ def set_required(self, is_required):
         """If set to True, will be colored red if incorrectly set"""
         if is_required:
             self.text_field.textChanged.connect(self.check_ready)
-            self.check_ready()
+        else:
+            self.text_field.textChanged.disconnect(self.check_ready)
+        self.check_ready()
 
     def update_field_color(self, color: str):
         """Updates the background of the text field"""
@@ -494,10 +496,10 @@ def __init__(
         fixed: Optional[bool] = True,
     ):
         """Args:
-        min (Optional[int]): minimum value, defaults to 0
-        max (Optional[int]): maximum value, defaults to 10
-        default (Optional[int]): default value, defaults to 0
-        step (Optional[int]): step value, defaults to 1
+        min (Optional[float]): minimum value, defaults to 0
+        max (Optional[float]): maximum value, defaults to 10
+        default (Optional[float]): default value, defaults to 0
+        step (Optional[float]): step value, defaults to 1
         parent: parent widget, defaults to None
         fixed (bool): if True, sets the QSizePolicy of the spinbox to Fixed"""
 

napari_cellseg3d/model_instance_seg.py

@@ -194,15 +194,19 @@ def volume_stats(volume_image):
     """
 
     properties = regionprops(volume_image)
-    number_objects = np.amax(volume_image)
 
-    sphericity_va = []
-    sphericity_ax = [
-        sphericity_axis(
-            region.axis_major_length * 0.5, region.axis_minor_length * 0.5
-        )
-        for region in properties
-    ]
+    # sphericity_va = []
+    def sphericity(region):
+        try:
+            return sphericity_axis(
+                region.axis_major_length * 0.5, region.axis_minor_length * 0.5
+            )
+        except ValueError:
+            return (
+                np.nan
+            )  # FIXME better way ? inconsistent errors in region.axis_minor_length
+
+    sphericity_ax = [sphericity(region) for region in properties]
     # for region in properties:
     # object = (volume_image == region.label).transpose(1, 2, 0)
     # verts, faces, _, values = marching_cubes(