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Enable to distinguish manual and automatic masks in GUI #1130

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48 changes: 42 additions & 6 deletions cellpose/gui/gui.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -268,6 +268,7 @@ def __init__(self, image=None, logger=None):
for i in range(3):
self.cmap.append(
make_cmap(i).getLookupTable(start=0.0, stop=255.0, alpha=False))
self.manualPatternSide = 6

if MATPLOTLIB:
self.colormap = (plt.get_cmap("gist_ncar")(np.linspace(0.0, .9, 1000000)) *
Expand Down Expand Up @@ -431,6 +432,15 @@ def make_buttons(self):
self.MCheckBox.toggled.connect(self.toggle_masks)
self.drawBoxG.addWidget(self.MCheckBox, b0, 0, 1, 5)

b0 += 1
# don't distinguish masks of manually labelled cells
self.markManualMasksOn = True
self.MMCheckBox = QCheckBox("DISTINGUISH MANUAL [M]")
self.MMCheckBox.setFont(self.medfont)
self.MMCheckBox.setChecked(True)
self.MMCheckBox.toggled.connect(self.toggle_masks)
self.drawBoxG.addWidget(self.MMCheckBox, b0, 0, 1, 5)

b0 += 1
# turn off outlines
self.outlinesOn = False # turn off by default
Expand Down Expand Up @@ -883,6 +893,8 @@ def keyPressEvent(self, event):
1).isEnabled())
if event.key() == QtCore.Qt.Key_X:
self.MCheckBox.toggle()
if event.key() == QtCore.Qt.Key_M:
self.MMCheckBox.toggle()
if event.key() == QtCore.Qt.Key_Z:
self.OCheckBox.toggle()
if event.key() == QtCore.Qt.Key_Left or event.key(
Expand Down Expand Up @@ -1150,6 +1162,10 @@ def toggle_masks(self):
self.masksOn = True
else:
self.masksOn = False
if self.MMCheckBox.isChecked():
self.markManualMasksOn = True
else:
self.markManualMasksOn = False
if self.OCheckBox.isChecked():
self.outlinesOn = True
else:
Expand Down Expand Up @@ -1808,7 +1824,17 @@ def draw_mask(self, z, ar, ac, vr, vc, color, idx=None):
if z == self.currentZ:
self.layerz[ar, ac, :3] = color
if self.masksOn:
self.layerz[ar, ac, -1] = self.opacity
if self.markManualMasksOn:
c = np.tile(np.array([[True, False], [False, True]]),
(self.cellpix.shape[1:] +
np.array((self.manualPatternSide - 1,) * 2))
// (2 * self.manualPatternSide)
).repeat(self.manualPatternSide, axis=1) \
.repeat(self.manualPatternSide, axis=0)
self.layerz[ar, ac, -1] = self.opacity * np.logical_not(
c[ar, ac]).astype(np.uint8)
else:
self.layerz[ar, ac, -1] = self.opacity
if self.outlinesOn:
self.layerz[vr, vc] = np.array(self.outcolor)

Expand Down Expand Up @@ -1858,13 +1884,23 @@ def draw_layer(self):
#print(self.cellpix.shape, self.outpix.shape, self.cellpix.max(), self.outpix.max())
self.layerz = np.zeros((self.Ly, self.Lx, 4), np.uint8)
if self.masksOn:
self.layerz[..., :3] = self.cellcolors[self.cellpix[self.currentZ], :]
self.layerz[..., 3] = self.opacity * (self.cellpix[self.currentZ]
> 0).astype(np.uint8)
cZ = self.currentZ
self.layerz[..., :3] = self.cellcolors[self.cellpix[cZ], :]
self.layerz[..., 3] = self.opacity * (self.cellpix[cZ] > 0).astype(np.uint8)
if self.markManualMasksOn and self.ismanual.sum() > 0:
c = np.tile(np.array([[True, False], [False, True]]),
(self.cellpix.shape[1:] +
np.array((self.manualPatternSide - 1,) * 2))
// (2 * self.manualPatternSide)
).repeat(self.manualPatternSide, axis=1) \
.repeat(self.manualPatternSide, axis=0)
self.layerz[..., 3] -= self.opacity * (
self.ismanual[np.maximum(self.cellpix[cZ], 1) - 1] &
c[:self.cellpix.shape[1], :self.cellpix.shape[2]] & \
(self.cellpix[cZ] > 0)).astype(np.uint8)
if self.selected > 0:
self.layerz[self.cellpix[self.currentZ] == self.selected] = np.array(
self.layerz[self.cellpix[cZ] == 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:
Expand Down
4 changes: 4 additions & 0 deletions cellpose/gui/guihelpwindowtext.html
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,10 @@
<td>X</td>
<td>turn masks ON or OFF</td>
</tr>
<tr>
<td>M</td>
<td>distinguish masks of manually labelled cells ON or OFF</td>
</tr>
<tr>
<td>Z</td>
<td>toggle outlines ON or OFF</td>
Expand Down
3 changes: 3 additions & 0 deletions cellpose/gui/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -386,6 +386,9 @@ def _load_seg(parent, filename=None, image=None, image_file=None, load_3D=False)

_masks_to_gui(parent, dat["masks"], outlines=dat["outlines"], colors=colors)

if "ismanual" in dat and len(dat["ismanual"]) == parent.ncells:
parent.ismanual = dat["ismanual"]

parent.draw_layer()
if "est_diam" in dat:
parent.Diameter.setText("%0.1f" % dat["est_diam"])
Expand Down