Merge branch 'main' of https://www.github.com/mouseland/cellpose

cellpose/gui/gui.py

@@ -1375,7 +1375,8 @@ def remove_stroke(self, delete_points=True, stroke_ind=-1):
             if self.outlinesOn:
                 self.layerz[stroke[outpix,1],stroke[outpix,2]] = np.array(self.outcolor)
             if delete_points:
-                self.current_point_set = self.current_point_set[:-1*(stroke[:,-1]==1).sum()]
+               # self.current_point_set = self.current_point_set[:-1*(stroke[:,-1]==1).sum()]
+               del self.current_point_set[stroke_ind]
             self.update_layer()
 
         del self.strokes[stroke_ind]
@@ -1590,10 +1591,9 @@ def update_crosshairs(self):
 
     def add_set(self):
         if len(self.current_point_set) > 0:
-            self.current_point_set = np.array(self.current_point_set)
             while len(self.strokes) > 0:
                 self.remove_stroke(delete_points=False)
-            if len(self.current_point_set) > 8:
+            if len(self.current_point_set[0]) > 8:
                 color = self.colormap[self.ncells,:3]
                 median = self.add_mask(points=self.current_point_set, color=color)
                 if median is not None:
@@ -1610,51 +1610,61 @@ def add_set(self):
             self.current_point_set = []
             self.update_layer()
 
-    def add_mask(self, points=None, color=(100,200,50)):
+    def add_mask(self, points=None, color=(100,200,50), dense=True):
+        # points is list of strokes
+
+        points_all = np.concatenate(points, axis=0)
+
         # loop over z values
         median = []
-        if points.shape[1] < 3:
-            points = np.concatenate((np.zeros((points.shape[0],1), "int32"), points), axis=1)
-        zdraw = np.unique(points[:,0])
+        zdraw = np.unique(points_all[:,0])
         zrange = np.arange(zdraw.min(), zdraw.max()+1, 1, int)
         zmin = zdraw.min()
         pix = np.zeros((2,0), "uint16")
         mall = np.zeros((len(zrange), self.Ly, self.Lx), "bool")
         k=0
         for z in zdraw:
-            iz = points[:,0] == z
-            vr = points[iz,1]
-            vc = points[iz,2]
-            # get points inside drawn points
-            mask = np.zeros((np.ptp(vr)+4, np.ptp(vc)+4), np.uint8)
-            pts = np.stack((vc-vc.min()+2,vr-vr.min()+2), axis=-1)[:,np.newaxis,:]
-            mask = cv2.fillPoly(mask, [pts], (255,0,0))
-            ar, ac = np.nonzero(mask)
-            ar, ac = ar+vr.min()-2, ac+vc.min()-2
-            # get dense outline
-            contours = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
-            pvc, pvr = contours[-2][0].squeeze().T            
-            vr, vc = pvr + vr.min() - 2, pvc + vc.min() - 2
-            # concatenate all points
-            ar, ac = np.hstack((np.vstack((vr, vc)), np.vstack((ar, ac))))
-            # if these pixels are overlapping with another cell, reassign them
-            ioverlap = self.cellpix[z][ar, ac] > 0
-            if (~ioverlap).sum() < 8:
-                print('ERROR: cell too small without overlaps, not drawn')
-                return None
-            elif ioverlap.sum() > 0:
-                ar, ac = ar[~ioverlap], ac[~ioverlap]
-                # compute outline of new mask
-                mask = np.zeros((np.ptp(ar)+4, np.ptp(ac)+4), np.uint8)
-                mask[ar-ar.min()+2, ac-ac.min()+2] = 1
-                contours = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
-                pvc, pvr = contours[-2][0].squeeze().T            
-                vr, vc = pvr + ar.min() - 2, pvc + ac.min() - 2
-            self.draw_mask(z, ar, ac, vr, vc, color)
-
-            median.append(np.array([np.median(ar), np.median(ac)]))
+            ars, acs, vrs, vcs = np.zeros(0, "int"), np.zeros(0, "int"), np.zeros(0, "int"), np.zeros(0, "int")
+            for stroke in points:
+                stroke = np.concatenate(stroke, axis=0).reshape(-1, 4)
+                iz = stroke[:,0] == z
+                vr = stroke[iz,1]
+                vc = stroke[iz,2]
+                if iz.sum() > 0:
+                    # get points inside drawn points
+                    mask = np.zeros((np.ptp(vr)+4, np.ptp(vc)+4), np.uint8)
+                    pts = np.stack((vc-vc.min()+2,vr-vr.min()+2), axis=-1)[:,np.newaxis,:]
+                    mask = cv2.fillPoly(mask, [pts], (255,0,0))
+                    ar, ac = np.nonzero(mask)
+                    ar, ac = ar+vr.min()-2, ac+vc.min()-2
+                    # get dense outline
+                    contours = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
+                    pvc, pvr = contours[-2][0].squeeze().T            
+                    vr, vc = pvr + vr.min() - 2, pvc + vc.min() - 2
+                    # concatenate all points
+                    ar, ac = np.hstack((np.vstack((vr, vc)), np.vstack((ar, ac))))
+                    # if these pixels are overlapping with another cell, reassign them
+                    ioverlap = self.cellpix[z][ar, ac] > 0
+                    if (~ioverlap).sum() < 8:
+                        print('ERROR: cell too small without overlaps, not drawn')
+                        return None
+                    elif ioverlap.sum() > 0:
+                        ar, ac = ar[~ioverlap], ac[~ioverlap]
+                        # compute outline of new mask
+                        mask = np.zeros((np.ptp(ar)+4, np.ptp(ac)+4), np.uint8)
+                        mask[ar-ar.min()+2, ac-ac.min()+2] = 1
+                        contours = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
+                        pvc, pvr = contours[-2][0].squeeze().T            
+                        vr, vc = pvr + ar.min() - 2, pvc + ac.min() - 2
+                    ars = np.concatenate((ars, ar), axis=0)
+                    acs = np.concatenate((acs, ac), axis=0)
+                    vrs = np.concatenate((vrs, vr), axis=0)
+                    vcs = np.concatenate((vcs, vc), axis=0)
+            self.draw_mask(z, ars, acs, vrs, vcs, color)
+
+            median.append(np.array([np.median(ars), np.median(acs)]))
             mall[z-zmin, ar, ac] = True
-            pix = np.append(pix, np.vstack((ar, ac)), axis=-1)
+            pix = np.append(pix, np.vstack((ars, acs)), axis=-1)
 
         mall = mall[:, pix[0].min():pix[0].max()+1, pix[1].min():pix[1].max()+1].astype(np.float32)
         ymin, xmin = pix[0].min(), pix[1].min()
@@ -1688,12 +1698,12 @@ def draw_mask(self, z, ar, ac, vr, vc, color, idx=None):
         self.cellpix[z, vr, vc] = idx
         self.cellpix[z, ar, ac] = idx
         self.outpix[z, vr, vc] = idx
-        self.layerz[ar, ac, :3] = color
-        if self.masksOn:
-            self.layerz[ar, ac, -1] = self.opacity
-        if self.outlinesOn:
-            self.layerz[vr, vc] = np.array(self.outcolor)
-
+        if z==self.currentZ:
+            self.layerz[ar, ac, :3] = color
+            if self.masksOn:
+                self.layerz[ar, ac, -1] = self.opacity
+            if self.outlinesOn:
+                self.layerz[vr, vc] = np.array(self.outcolor)
 
     def compute_scale(self):
         self.diameter = float(self.Diameter.text())

cellpose/gui/guiparts.py

@@ -463,7 +463,6 @@ def hoverEvent(self, ev):
                 self.drawAt(ev.pos())
                 if self.is_at_start(ev.pos()):
                     self.end_stroke()
-
         else:
             ev.acceptClicks(QtCore.Qt.RightButton)
             #ev.acceptClicks(QtCore.Qt.LeftButton)
@@ -501,11 +500,11 @@ def end_stroke(self):
             self.parent.stroke_appended = True
             self.parent.current_stroke = np.array(self.parent.current_stroke)
             ioutline = self.parent.current_stroke[:,3]==1
-            self.parent.current_point_set.extend(list(self.parent.current_stroke[ioutline]))
+            self.parent.current_point_set.append(list(self.parent.current_stroke[ioutline]))
             self.parent.current_stroke = []
             if self.parent.autosave:
                 self.parent.add_set()
-        if len(self.parent.current_point_set) > 0 and self.parent.autosave:
+        if len(self.parent.current_point_set) and len(self.parent.current_point_set[0]) > 0 and self.parent.autosave:
             self.parent.add_set()
         self.parent.in_stroke = False
 
@@ -517,7 +516,6 @@ def tabletEvent(self, ev):
 
     def drawAt(self, pos, ev=None):
         mask = self.strokemask
-        set = self.parent.current_point_set
         stroke = self.parent.current_stroke
         pos = [int(pos.y()), int(pos.x())]
         dk = self.drawKernel

docs/gui.rst

@@ -28,6 +28,9 @@ For multi-channel, multi-Z tiff's, the expected format is Z x channels x Ly x Lx
     image with ``_seg.npy`` appended, make sure you have WRITE access 
     in the folder, otherwise the file will not save.
 
+.. image:: https://www.cellpose.org/static/images/cellpose_gui.png
+    :width: 600
+
 Using the GUI 
 ~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -48,20 +51,32 @@ Main GUI mouse controls (works in all views):
 -  Start draw mask = right-click
 -  End draw mask = right-click, or return to circle at beginning
 
+Drawing masks 
+~~~~~~~~~~~~~~~~~~~~~~
+
+Masks are started with right-click, then hover your mouse (do not hold it down), 
+and return it to the red circle to complete the mask. The mask should now be completed.
+
 Overlaps in masks are NOT allowed. If you draw a mask on top of another
 mask, it is cropped so that it doesn't overlap with the old mask. Masks
 in 2D should be single strokes (if *single_stroke* is checked).
 
 If you want to draw masks in 3D, then you can turn *single_stroke*
 option off and draw a stroke on each plane with the cell and then press
-ENTER.
-
-.. image:: https://www.cellpose.org/static/images/cellpose_gui.png
-    :width: 600
+ENTER. You can also draw multiple strokes on the same plane for 
+complex cell shapes, but do not do this in 2D if you plan to train a cellpose model 
+(the cell flows will not work correctly).
 
 .. note::
     3D labelling will fill in unlabelled z-planes so that you do not
-    have to densely label, for example you can skip some planes.
+    have to densely label, for example you can skip some planes, and the 
+    cell will be interpolated between planes.
+
+After each mask is drawn in 2D, it is saved to the ``_seg.npy``. If this is slow (for 
+large images), this "autosave" option can be turned off in the "File" menu 
+("Disable autosave _seg.npy file"). In 3D, 
+the mask is never auto-saved, instead save masks by clicking CTRL+S, or "Save" in the 
+"File" menu.
 
 Bulk Mask Deletion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~