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Fix: Exit early from update_orthos() when orthos are off #1458

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Fix: Exit early from update_orthos() when orthos are off #1458

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186 changes: 94 additions & 92 deletions cellpose/gui/gui3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -426,102 +426,104 @@ def update_crosshairs(self):
self.hLineOrtho[0].setPos(self.yortho)

def update_ortho(self):
if self.NZ > 1 and self.orthobtn.isChecked():
dzcurrent = self.dz
self.dz = min(100, max(3, int(self.dzedit.text())))
self.zaspect = max(0.01, min(100., float(self.zaspectedit.text())))
self.dzedit.setText(str(self.dz))
self.zaspectedit.setText(str(self.zaspect))
if self.dz != dzcurrent:
self.pOrtho[0].setXRange(-self.dz / 3, self.dz * 2 + self.dz / 3)
self.pOrtho[1].setYRange(-self.dz / 3, self.dz * 2 + self.dz / 3)
dztot = min(self.NZ, self.dz * 2)
y = self.yortho
x = self.xortho
z = self.currentZ
if dztot == self.NZ:
zmin, zmax = 0, self.NZ
if not (self.NZ > 1 and self.orthobtn.isChecked()):
return

dzcurrent = self.dz
self.dz = min(100, max(3, int(self.dzedit.text())))
self.zaspect = max(0.01, min(100., float(self.zaspectedit.text())))
self.dzedit.setText(str(self.dz))
self.zaspectedit.setText(str(self.zaspect))
if self.dz != dzcurrent:
self.pOrtho[0].setXRange(-self.dz / 3, self.dz * 2 + self.dz / 3)
self.pOrtho[1].setYRange(-self.dz / 3, self.dz * 2 + self.dz / 3)
dztot = min(self.NZ, self.dz * 2)
y = self.yortho
x = self.xortho
z = self.currentZ
if dztot == self.NZ:
zmin, zmax = 0, self.NZ
else:
if z - self.dz < 0:
zmin = 0
zmax = zmin + self.dz * 2
elif z + self.dz >= self.NZ:
zmax = self.NZ
zmin = zmax - self.dz * 2
else:
if z - self.dz < 0:
zmin = 0
zmax = zmin + self.dz * 2
elif z + self.dz >= self.NZ:
zmax = self.NZ
zmin = zmax - self.dz * 2
zmin, zmax = z - self.dz, z + self.dz
self.zc = z - zmin
self.update_crosshairs()

is_image_view = self.view == 'image'
is_restored_view = self.view == 'restored'

rgb_list = ['red', 'green', 'blue']

if is_image_view or is_restored_view:
for j in range(2):
if j == 0:
if is_image_view:
image = self.stack[zmin:zmax, :, x].transpose(1, 0, 2).copy()
else:
image = self.stack_filtered[zmin:zmax, :,
x].transpose(1, 0, 2).copy()
else:
zmin, zmax = z - self.dz, z + self.dz
self.zc = z - zmin
self.update_crosshairs()

is_image_view = self.view == 'image'
is_restored_view = self.view == 'restored'

rgb_list = ['red', 'green', 'blue']

if is_image_view or is_restored_view:
for j in range(2):
if j == 0:
if is_image_view:
image = self.stack[zmin:zmax, :, x].transpose(1, 0, 2).copy()
else:
image = self.stack_filtered[zmin:zmax, :,
x].transpose(1, 0, 2).copy()
image = self.stack[
zmin:zmax,
y, :].copy() if is_image_view else self.stack_filtered[zmin:zmax,
y, :].copy()
if self.nchan == 1:
# show single channel
image = image[..., 0]
if self.color == 'rgb':
self.imgOrtho[j].setImage(image, autoLevels=False, lut=None)
if self.nchan > 1:
levels = np.array([
self.saturation[0][self.currentZ],
self.saturation[1][self.currentZ],
self.saturation[2][self.currentZ]
])
self.imgOrtho[j].setLevels(levels)
else:
image = self.stack[
zmin:zmax,
y, :].copy() if is_image_view else self.stack_filtered[zmin:zmax,
y, :].copy()
if self.nchan == 1:
# show single channel
image = image[..., 0]
if self.color == 'rgb':
self.imgOrtho[j].setImage(image, autoLevels=False, lut=None)
if self.nchan > 1:
levels = np.array([
self.saturation[0][self.currentZ],
self.saturation[1][self.currentZ],
self.saturation[2][self.currentZ]
])
self.imgOrtho[j].setLevels(levels)
else:
self.imgOrtho[j].setLevels(
self.saturation[0][self.currentZ])
elif self.color in rgb_list:
color_index = rgb_list.index(self.color)
if self.nchan > 1:
image = image[..., color_index]
self.imgOrtho[j].setImage(image, autoLevels=False,
lut=self.cmap[color_index + 1])
if self.nchan > 1:
self.imgOrtho[j].setLevels(
self.saturation[color_index][self.currentZ])
else:
self.imgOrtho[j].setLevels(
self.saturation[0][self.currentZ])
elif self.color == 'gray':
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])
elif self.color == 'spectral':
if image.ndim > 2:
image = image.astype("float32").mean(axis=2).astype("uint8")
self.imgOrtho[j].setImage(image, autoLevels=False,
lut=self.cmap[0])
self.imgOrtho[j].setLevels(self.saturation[0][self.currentZ])
self.pOrtho[0].setAspectLocked(lock=True, ratio=self.zaspect)
self.pOrtho[1].setAspectLocked(lock=True, ratio=1. / self.zaspect)
self.imgOrtho[j].setLevels(
self.saturation[0][self.currentZ])
elif self.color in rgb_list:
color_index = rgb_list.index(self.color)
if self.nchan > 1:
image = image[..., color_index]
self.imgOrtho[j].setImage(image, autoLevels=False,
lut=self.cmap[color_index + 1])
if self.nchan > 1:
self.imgOrtho[j].setLevels(
self.saturation[color_index][self.currentZ])
else:
self.imgOrtho[j].setLevels(
self.saturation[0][self.currentZ])
elif self.color == 'gray':
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])
elif self.color == 'spectral':
if image.ndim > 2:
image = image.astype("float32").mean(axis=2).astype("uint8")
self.imgOrtho[j].setImage(image, autoLevels=False,
lut=self.cmap[0])
self.imgOrtho[j].setLevels(self.saturation[0][self.currentZ])
self.pOrtho[0].setAspectLocked(lock=True, ratio=self.zaspect)
self.pOrtho[1].setAspectLocked(lock=True, ratio=1. / self.zaspect)

else:
image = np.zeros((10, 10), "uint8")
self.imgOrtho[0].setImage(image, autoLevels=False, lut=None)
self.imgOrtho[0].setLevels([0.0, 255.0])
self.imgOrtho[1].setImage(image, autoLevels=False, lut=None)
self.imgOrtho[1].setLevels([0.0, 255.0])
else:
image = np.zeros((10, 10), "uint8")
self.imgOrtho[0].setImage(image, autoLevels=False, lut=None)
self.imgOrtho[0].setLevels([0.0, 255.0])
self.imgOrtho[1].setImage(image, autoLevels=False, lut=None)
self.imgOrtho[1].setLevels([0.0, 255.0])

zrange = zmax - zmin
self.layer_ortho = [
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