adding imagecodecs dependency and reactivating 3D drawing and adding …

…other gui features (MouseLand#493)

cellpose/gui/gui.py

@@ -180,7 +180,7 @@ def __init__(self, image=None):
 
  self.setStyleSheet("QMainWindow {background: 'black';}")
  self.stylePressed = ("QPushButton {Text-align: left; "
- "background-color: rgb(100,50,100); "
+ "background-color: rgb(150,50,150); "
  "border-color: white;"
  "color:white;}")
  self.styleUnpressed = ("QPushButton {Text-align: left; "
@@ -411,7 +411,7 @@ def make_buttons(self):
  self.scale_on = True
  self.ScaleOn = QCheckBox('scale disk on')
  self.ScaleOn.setFont(self.medfont)
- self.ScaleOn.setStyleSheet('color: red;')
+ self.ScaleOn.setStyleSheet('color: rgb(150,50,150);')
  self.ScaleOn.setChecked(True)
  self.ScaleOn.setToolTip('see current diameter as red disk at bottom')
  self.ScaleOn.toggled.connect(self.toggle_scale)
@@ -468,7 +468,7 @@ def make_buttons(self):
  self.flow_threshold = QLineEdit()
  self.flow_threshold.setText('0.4')
  self.flow_threshold.returnPressed.connect(self.compute_cprob)
- self.flow_threshold.setFixedWidth(60)
+ self.flow_threshold.setFixedWidth(70)
  self.l0.addWidget(self.flow_threshold, b,5,1,4)
 
  b+=1
@@ -480,9 +480,22 @@ def make_buttons(self):
  self.cellprob_threshold = QLineEdit()
  self.cellprob_threshold.setText('0.0')
  self.cellprob_threshold.returnPressed.connect(self.compute_cprob)
- self.cellprob_threshold.setFixedWidth(60)
+ self.cellprob_threshold.setFixedWidth(70)
  self.l0.addWidget(self.cellprob_threshold, b,5,1,4)
 
+ b+=1
+ label = QLabel('stitch_threshold:')
+ label.setToolTip('for 3D volumes, turn on stitch_threshold to stitch masks across planes instead of running cellpose in 3D (see docs for details)')
+ label.setStyleSheet(label_style)
+ label.setFont(self.medfont)
+ self.l0.addWidget(label, b, 0,1,5)
+ self.stitch_threshold = QLineEdit()
+ self.stitch_threshold.setText('0.0')
+ #self.cellprob_threshold.returnPressed.connect(self.compute_cprob)
+ self.stitch_threshold.setFixedWidth(70)
+ self.l0.addWidget(self.stitch_threshold, b,5,1,4)
+
+
  b+=1
  self.GB = QGroupBox('model zoo')
  self.GB.setStyleSheet("QGroupBox { border: 1px solid white; color:white; padding: 10px 0px;}")
@@ -559,6 +572,13 @@ def make_buttons(self):
  self.progress.setStyleSheet('color: gray;')
  self.l0.addWidget(self.progress, b,0,1,9)
 
+ b+=1
+ self.roi_count = QLabel('0 ROIs')
+ self.roi_count.setStyleSheet('color: white;')
+ self.roi_count.setFont(self.boldfont)
+ self.roi_count.setAlignment(QtCore.Qt.AlignRight)
+ self.l0.addWidget(self.roi_count, b,0,1,9)
+
  b+=1
  line = QHLine()
  line.setStyleSheet('color: white;')
@@ -674,10 +694,12 @@ def keyPressEvent(self, event):
  if self.NZ>1:
  if event.key() == QtCore.Qt.Key_Left:
  self.currentZ = max(0,self.currentZ-1)
- self.zpos.setText(str(self.currentZ))
+ self.scroll.setValue(self.currentZ)
+ updated = True
  elif event.key() == QtCore.Qt.Key_Right:
  self.currentZ = min(self.NZ-1, self.currentZ+1)
- self.zpos.setText(str(self.currentZ))
+ self.scroll.setValue(self.currentZ)
+ updated = True
  else:
  if event.key() == QtCore.Qt.Key_X:
  self.MCheckBox.toggle()
@@ -894,6 +916,7 @@ def move_in_Z(self):
  self.currentZ = min(self.NZ, max(0, int(self.scroll.value())))
  self.zpos.setText(str(self.currentZ))
  self.update_plot()
+ self.draw_layer()
  self.update_layer()
 
 
@@ -1037,7 +1060,6 @@ def reset(self):
  self.flows = [[],[],[],[],[[]]]
  self.stack = np.zeros((1,self.Ly,self.Lx,3))
  # masks matrix
- self.layers = 0*np.ones((1,self.Ly,self.Lx,4), np.uint8)
  self.layerz = 0*np.ones((self.Ly,self.Lx,4), np.uint8)
  # image matrix with a scale disk
  self.radii = 0*np.ones((self.Ly,self.Lx,4), np.uint8)
@@ -1066,8 +1088,6 @@ def autosave_on(self):
  def clear_all(self):
  self.prev_selected = 0
  self.selected = 0
- #self.layers_undo, self.cellpix_undo, self.outpix_undo = [],[],[]
- self.layers = 0*np.ones((self.NZ,self.Ly,self.Lx,4), np.uint8)
  self.layerz = 0*np.ones((self.Ly,self.Lx,4), np.uint8)
  self.cellpix = np.zeros((self.NZ,self.Ly,self.Lx), np.uint32)
  self.outpix = np.zeros((self.NZ,self.Ly,self.Lx), np.uint32)
@@ -1082,8 +1102,6 @@ def select_cell(self, idx):
  if self.selected > 0:
  z = self.currentZ
  self.layerz[self.cellpix[z]==idx] = np.array([255,255,255,self.opacity])
- #if self.outlinesOn:
- # self.layers[self.outpix==idx] = np.array(self.outcolor)
  self.update_layer()
 
  def unselect_cell(self):
@@ -1191,13 +1209,13 @@ def undo_remove_cell(self):
  self.redo.setEnabled(False)
 
 
- def remove_stroke(self, delete_points=True):
+ def remove_stroke(self, delete_points=True, stroke_ind=-1):
  #self.current_stroke = get_unique_points(self.current_stroke)
- stroke = np.array(self.strokes[-1])
- inZ = stroke[0,0]==self.currentZ
+ stroke = np.array(self.strokes[stroke_ind])
  cZ = self.currentZ
+ inZ = stroke[0,0]==cZ
  if inZ:
- outpix = self.outpix[self.currentZ, stroke[:,1],stroke[:,2]]>0
+ outpix = self.outpix[cZ, stroke[:,1],stroke[:,2]]>0
  self.layerz[stroke[~outpix,1],stroke[~outpix,2]] = np.array([0,0,0,0])
  cellpix = self.cellpix[cZ, stroke[:,1], stroke[:,2]]
  ccol = self.cellcolors.copy()
@@ -1213,8 +1231,9 @@ def remove_stroke(self, delete_points=True):
  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()]
- del self.strokes[-1]
  self.update_layer()
+
+ del self.strokes[stroke_ind]
 
  def plot_clicked(self, event):
  if event.button()==QtCore.Qt.LeftButton and (event.modifiers() != QtCore.Qt.ShiftModifier and
@@ -1312,11 +1331,15 @@ def update_plot(self):
 
  def update_layer(self):
  if self.masksOn or self.outlinesOn:
- self.draw_layer()
+ #self.draw_layer()
  self.layer.setImage(self.layerz, autoLevels=False)
+ self.update_roi_count()
  self.win.show()
  self.show()
 
+ def update_roi_count(self):
+ self.roi_count.setText(f'{self.ncells} ROIs')
+
  def update_ortho(self):
  if self.NZ>1 and self.orthobtn.isChecked():
  dzcurrent = self.dz
@@ -1486,14 +1509,17 @@ def draw_mask(self, z, ar, ac, vr, vc, color, idx=None):
  def compute_scale(self):
  self.diameter = float(self.Diameter.text())
  self.pr = int(float(self.Diameter.text()))
- radii = np.zeros((self.Ly+self.pr,self.Lx), np.uint8)
- self.radii = np.zeros((self.Ly+self.pr,self.Lx,4), np.uint8)
- yy,xx = disk([self.Ly+self.pr/2-1, self.pr/2+1],
- self.pr/2, self.Ly+self.pr, self.Lx)
- self.radii[yy,xx,0] = 255
- self.radii[yy,xx,-1] = 255#self.opacity * (radii>0)
+ self.radii_padding = int(self.pr*1.25)
+ self.radii = np.zeros((self.Ly+self.radii_padding,self.Lx,4), np.uint8)
+ yy,xx = disk([self.Ly+self.radii_padding/2-1, self.pr/2+1],
+ self.pr/2, self.Ly+self.radii_padding, self.Lx)
+ # rgb(150,50,150)
+ self.radii[yy,xx,0] = 150
+ self.radii[yy,xx,1] = 50
+ self.radii[yy,xx,2] = 150
+ self.radii[yy,xx,3] = 255
  self.update_plot()
- self.p0.setYRange(0,self.Ly+self.pr)
+ self.p0.setYRange(0,self.Ly+self.radii_padding)
  self.p0.setXRange(0,self.Lx)
  self.win.show()
  self.show()
@@ -1506,10 +1532,18 @@ def draw_masks(self):
 
  def draw_layer(self):
  if self.masksOn:
+ self.layerz = np.zeros((self.Ly,self.Lx,4), np.uint8)
  self.layerz[...,:3] = self.cellcolors[self.cellpix[self.currentZ],:]
  self.layerz[...,3] = self.opacity * (self.cellpix[self.currentZ]>0).astype(np.uint8)
  if self.selected>0:
  self.layerz[self.cellpix[self.currentZ]==self.selected] = np.array([255,255,255,self.opacity])
+ cZ = self.currentZ
+ stroke_z = np.array([s[0][0] for s in self.strokes])
+ inZ = np.nonzero(stroke_z == cZ)[0]
+ if len(inZ) > 0:
+ for i in inZ:
+ stroke = np.array(self.strokes[i])
+ self.layerz[stroke[:,1], stroke[:,2]] = np.array([255,0,255,100])
  else:
  self.layerz[...,3] = 0
 
@@ -1563,11 +1597,6 @@ def initialize_model(self, model_name=None):
 
  def add_model(self):
  io._add_model(self)
- #a_list = ["abc", "def", "ghi"]
- #textfile = open("a_file.txt", "w")
- #for element in a_list:
- # textfile.write(element + "\n")
- #textfile.close()
  return
 
  def remove_model(self):
@@ -1685,8 +1714,11 @@ def compute_model(self, model_name=None):
  self.initialize_model(model_name)
  self.progress.setValue(10)
  do_3D = False
+ stitch_threshold = False
  if self.NZ > 1:
- do_3D = True
+ stitch_threshold = float(self.stitch_threshold.text())
+ stitch_threshold = 0 if stitch_threshold <= 0 or stitch_threshold > 1 else stitch_threshold
+ do_3D = True if stitch_threshold==0 else False
  data = self.stack.copy()
  else:
  data = self.stack[0].copy()
@@ -1699,7 +1731,8 @@ def compute_model(self, model_name=None):
  diameter=self.diameter,
  cellprob_threshold=cellprob_threshold,
  flow_threshold=flow_threshold,
- do_3D=do_3D, 
+ do_3D=do_3D,
+ stitch_threshold=stitch_threshold, 
  progress=self.progress)[:2]
  except Exception as e:
  print('NET ERROR: %s'%e)
@@ -1712,12 +1745,12 @@ def compute_model(self, model_name=None):
  # flows = flows[0]
  self.flows[0] = flows[0].copy() #RGB flow
  self.flows[1] = (np.clip(normalize99(flows[2].copy()), 0, 1) * 255).astype(np.uint8) #dist/prob
- if not do_3D:
+ if not do_3D and not stitch_threshold > 0:
  masks = masks[np.newaxis,...]
  self.flows[0] = resize_image(self.flows[0], masks.shape[-2], masks.shape[-1],
  interpolation=cv2.INTER_NEAREST)
  self.flows[1] = resize_image(self.flows[1], masks.shape[-2], masks.shape[-1])
- if not do_3D:
+ if not do_3D and not stitch_threshold > 0:
  self.flows[2] = np.zeros(masks.shape[1:], dtype=np.uint8)
  self.flows = [self.flows[n][np.newaxis,...] for n in range(len(self.flows))]
  else:
@@ -1737,8 +1770,10 @@ def compute_model(self, model_name=None):
  io._masks_to_gui(self, masks, outlines=None)
  self.progress.setValue(100)
 
- if not do_3D:
+ if not do_3D and not stitch_threshold > 0:
  self.recompute_masks = True
+ else:
+ self.recompute_masks = False
  except Exception as e:
  print('ERROR: %s'%e)
 
@@ -1750,6 +1785,7 @@ def enable_buttons(self):
  self.StyleButtons[i].setEnabled(True)
  self.StyleButtons[i].setStyleSheet(self.styleUnpressed)
  self.SizeButton.setEnabled(True)
+ self.SCheckBox.setEnabled(True)
  self.SizeButton.setStyleSheet(self.styleUnpressed)
  self.newmodel.setEnabled(True)
  self.loadMasks.setEnabled(True)

cellpose/gui/guiparts.py

@@ -36,6 +36,9 @@ def __init__(self, parent, model_name, text):
  self.model_name = model_name
 
  def press(self, parent):
+ for i in range(len(parent.StyleButtons)):
+ parent.StyleButtons[i].setStyleSheet(parent.styleUnpressed)
+ self.setStyleSheet(parent.stylePressed)
  parent.compute_model(self.model_name)
 
 class TrainWindow(QDialog):
@@ -636,7 +639,7 @@ def tabletEvent(self, ev):
  #print(ev.pressure())
 
  def drawAt(self, pos, ev=None):
- mask = self.greenmask
+ mask = self.strokemask
  set = self.parent.current_point_set
  stroke = self.parent.current_stroke
  pos = [int(pos.y()), int(pos.x())]
@@ -691,7 +694,7 @@ def setDrawKernel(self, kernel_size=3):
  offmask = np.zeros((bs,bs,1))
  opamask = 100 * kernel[:,:,np.newaxis]
  self.redmask = np.concatenate((onmask,offmask,offmask,onmask), axis=-1)
- self.greenmask = np.concatenate((onmask,offmask,onmask,opamask), axis=-1)
+ self.strokemask = np.concatenate((onmask,offmask,onmask,opamask), axis=-1)
 
 
 class RangeSlider(QSlider):

docs/gui.rst

@@ -53,9 +53,11 @@ 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 (cellpose 1.0 only currently). 
-3D labelling will fill in unlabelled z-planes so that you do not
-have to as densely label.
+ENTER. 
+
+.. 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.
 
 
 Segmentation options

setup.py

@@ -2,10 +2,13 @@
 from setuptools import setup
 
 install_deps = ['numpy>=1.20.0', 'scipy', 'natsort',
- 'tifffile', 'tqdm', 'numba', 
+ 'tifffile', 'tqdm', 
+ 'numba>=0.53.0', 
+ 'llvmlite',
  'torch>=1.6',
  'opencv-python-headless',
- 'fastremap'
+ 'fastremap',
+ 'imagecodecs'
  ]
 
 gui_deps = [