Merge pull request #1423 from MouseLand/saturation_fix

Gray saturation fix: drop blank channels from mean

Author: carsen-stringer

cellpose/gui/gui.py

@@ -1374,6 +1374,10 @@ def update_plot(self):
                     self.img.setLevels(self.saturation[0][self.currentZ])
             elif self.color == 4:
                 if self.nchan > 1:
+                    # exclude channels with no data:
+                    ranges = np.ptp(image, tuple(range(image.ndim-1)))
+                    range_mask = ranges > 1e-5
+                    image = image[..., range_mask]
                     image = image.mean(axis=-1)
                 self.img.setImage(image, autoLevels=False, lut=None)
                 self.img.setLevels(self.saturation[0][self.currentZ])

cellpose/gui/gui3d.py

@@ -486,6 +486,10 @@ def update_ortho(self):
                                 self.saturation[0][self.currentZ])
                     elif self.color == 4:
                         if image.ndim > 2:
+                            # exclude blank channels: 
+                            ranges = np.ptp(image, tuple(range(image.ndim-1)))
+                            range_mask = ranges > 1e-5
+                            image = image[..., range_mask]
                             image = image.astype("float32").mean(axis=2).astype("uint8")
                         self.imgOrtho[j].setImage(image, autoLevels=False, lut=None)
                         self.imgOrtho[j].setLevels(self.saturation[0][self.currentZ])