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Fix PyQtGraph shape mismatch exception by passing levels synchronously #1477

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Fix PyQtGraph shape mismatch exception by passing levels synchronously #1477

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18 changes: 7 additions & 11 deletions cellpose/gui/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1482,22 +1482,21 @@ def update_plot(self):
else:
image = self.stack_filtered[self.currentZ]
if self.color == 'rgb':
self.img.setImage(image, autoLevels=False, lut=None)
if self.nchan > 1:
levels = np.array([self.saturation[r][self.currentZ] for r in range(image.shape[-1])])
else:
levels = self.saturation[0][self.currentZ]
self.img.setLevels(levels)
self.img.setImage(image, autoLevels=False, lut=None, levels=levels)

elif self.color in rgb_list:
color_index = rgb_list.index(self.color)
if self.nchan > 1:
image = image[:, :, color_index]
self.img.setImage(image, autoLevels=False, lut=self.cmap[color_index+1])
if self.nchan > 1:
self.img.setLevels(self.saturation[color_index][self.currentZ])
levels = self.saturation[color_index][self.currentZ]
else:
self.img.setLevels(self.saturation[0][self.currentZ])
levels = self.saturation[0][self.currentZ]
self.img.setImage(image, autoLevels=False, lut=self.cmap[color_index+1], levels=levels)
elif self.color == 'gray':
if self.nchan > 1:
# exclude channels with no data:
Expand All @@ -1506,19 +1505,16 @@ def update_plot(self):
range_mask = ranges > 1e-5
image = image[..., range_mask]
image = image.mean(axis=-1)
self.img.setImage(image, autoLevels=False, lut=None)
self.img.setLevels(self.saturation[0][self.currentZ])
self.img.setImage(image, autoLevels=False, lut=None, levels=self.saturation[0][self.currentZ])
elif self.color == 'spectral':
if self.nchan > 1:
image = image.mean(axis=-1)
self.img.setImage(image, autoLevels=False, lut=self.cmap[0])
self.img.setLevels(self.saturation[0][self.currentZ])
self.img.setImage(image, autoLevels=False, lut=self.cmap[0], levels=self.saturation[0][self.currentZ])
else:
image = np.zeros((self.Ly, self.Lx), np.uint8)
if len(self.flows[flowp_map[self.view]]) > 0:
image = self.flows[flowp_map[self.view]][self.currentZ]
self.img.setImage(image, autoLevels=False, lut=self.bwr)
self.img.setLevels([0.0, 255.0])
self.img.setImage(image, autoLevels=False, lut=self.bwr, levels=[0.0, 255.0])

for r in range(3):
# setValue on the slider triggers update_plot() so it needs to be suppressed
Expand Down