needed to add extra channel since changing convert_images

Author: carsen-stringer

cellpose/gui/gui.py

@@ -1885,24 +1885,23 @@ def compute_saturation(self, return_img=False):
                 self.saturation.append([])
                 for n in range(self.NZ):
                     self.saturation[-1].append([0, 255])
-                self.sliders[r].setValue([0, 255])
 
         if img_norm.shape[-1] == 1:
             if len(self.saturation) > 1:
                 self.saturation = [self.saturation[0]]
             self.saturation.append(self.saturation[0])
             self.saturation.append(self.saturation[0])
-            self.sliders[1].setValue(self.saturation[1][self.currentZ])
-            self.sliders[2].setValue(self.saturation[2][self.currentZ])
         else:
             self.saturation = [copy.deepcopy(self.saturation[r]) for r in range(img_norm.shape[-1])]
             if len(self.saturation) == 2:
                 self.saturation.append([])
                 for n in range(self.NZ):
                     self.saturation[-1].append([0, 255])
-                self.sliders[2].setValue(self.saturation[2][self.currentZ])
-        print(len(self.saturation))
-        print(len(self.saturation[0]))
+        
+        self.sliders[0].setValue(self.saturation[0][self.currentZ])
+        self.sliders[1].setValue(self.saturation[1][self.currentZ])
+        self.sliders[2].setValue(self.saturation[2][self.currentZ])
+        # print(len(self.saturation), len(self.saturation[0]))
 
     def get_model_path(self, custom=False):
         if custom:

cellpose/gui/io.py

@@ -179,12 +179,16 @@ def _initialize_images(parent, image, load_3D=False):
 
     img_min = image.min()
     img_max = image.max()
-    parent.stack = parent.stack.astype(np.float32)
+    parent.stack = parent.stack.astype("float32")
     parent.stack -= img_min
     if img_max > img_min + 1e-3:
         parent.stack /= (img_max - img_min)
     parent.stack *= 255
 
+    if parent.stack.shape[-1] == 2:
+        parent.stack = np.concatenate((parent.stack, np.zeros((*parent.stack.shape[:-1], 1), dtype="float32")), axis=-1)
+    print(parent.stack.shape)
+
     if load_3D:
         parent.logger.info(": converted to float and normalized values to 0.0->255.0")
 
@@ -196,19 +200,9 @@ def _initialize_images(parent, image, load_3D=False):
     parent.Ly0, parent.Lx0 = parent.stack.shape[-3:-1]
     parent.nchan = parent.stack.shape[-1]
     parent.layerz = 255 * np.ones((parent.Ly, parent.Lx, 4), "uint8")
-    if hasattr(parent, "stack_filtered"):
-        parent.Lyr, parent.Lxr = parent.stack_filtered.shape[-3:-1]
-    elif parent.restore and "upsample" in parent.restore:
-        parent.Lyr, parent.Lxr = int(parent.Ly * parent.ratio), int(parent.Lx *
-                                                                    parent.ratio)
-    else:
-        parent.Lyr, parent.Lxr = parent.Ly, parent.Lx
+    parent.Lyr, parent.Lxr = parent.stack.shape[-3:-1]
     parent.clear_all()
 
-    if not hasattr(parent, "stack_filtered") and parent.restore:
-        parent.logger.info(": no 'img_restore' found, applying current settings")
-        parent.compute_restore()
-
     parent.compute_saturation()    
     parent.compute_scale()
     parent.track_changes = []