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Fix sat #1461

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Merged
carsen-stringer merged 3 commits into from
May 26, 2026
Merged

Fix sat #1461

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e066e31
fix issues with saturation
carsen-stringer May 25, 2026
af9866c
fix two chan but weird artifact in 3rd chan
carsen-stringer May 26, 2026
ac2307e
needed to add extra channel since changing convert_images
carsen-stringer May 26, 2026
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55 changes: 35 additions & 20 deletions cellpose/gui/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -674,10 +674,10 @@ def level_change(self, r):
if self.loaded:
sval = self.sliders[r].value()
self.saturation[r][self.currentZ] = sval
if not self.autobtn.isChecked():
for r in range(3):
for i in range(len(self.saturation[r])):
self.saturation[r][i] = self.saturation[r][self.currentZ]
# if not self.autobtn.isChecked():
for r in range(3):
for i in range(len(self.saturation[r])):
self.saturation[r][i] = self.saturation[r][self.currentZ]
self.update_plot()

def keyPressEvent(self, event):
Expand Down Expand Up @@ -834,8 +834,7 @@ def enable_buttons(self):
def disable_buttons_removeROIs(self):
if len(self.model_strings) > 0:
self.ModelButtonC.setEnabled(False)
for i in range(len(self.StyleButtons)):
self.StyleButtons[i].setEnabled(False)
self.ModelButtonB.setEnabled(False)
self.newmodel.setEnabled(False)
self.loadMasks.setEnabled(False)
self.saveSet.setEnabled(False)
Expand Down Expand Up @@ -1485,14 +1484,11 @@ def update_plot(self):
if self.color == 'rgb':
self.img.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.img.setLevels(levels)
else:
self.img.setLevels(self.saturation[0][self.currentZ])
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)

elif self.color in rgb_list:
color_index = rgb_list.index(self.color)
if self.nchan > 1:
Expand All @@ -1505,6 +1501,7 @@ def update_plot(self):
elif self.color == 'gray':
if self.nchan > 1:
# exclude channels with no data:
# TODO: save this when computing saturation
ranges = np.ptp(image, tuple(range(image.ndim-1)))
range_mask = ranges > 1e-5
image = image[..., range_mask]
Expand Down Expand Up @@ -1881,12 +1878,30 @@ def compute_saturation(self, return_img=False):
else:
for n in range(self.NZ):
self.saturation[-1].append([0, 255.])
print(self.saturation[2][self.currentZ])

if img_norm.shape[-1] == 1:
self.saturation.append(self.saturation[0])
self.saturation.append(self.saturation[0])


elif len(self.saturation) == 0 or len(self.saturation[0]) != self.NZ:
self.saturation = []
for r in range(3):
self.saturation.append([])
for n in range(self.NZ):
self.saturation[-1].append([0, 255])

if img_norm.shape[-1] == 1:
if len(self.saturation) > 1:
self.saturation = [self.saturation[0]]
self.saturation.append(self.saturation[0])
self.saturation.append(self.saturation[0])
else:
self.saturation = [copy.deepcopy(self.saturation[r]) for r in range(img_norm.shape[-1])]
if len(self.saturation) == 2:
self.saturation.append([])
for n in range(self.NZ):
self.saturation[-1].append([0, 255])

self.sliders[0].setValue(self.saturation[0][self.currentZ])
self.sliders[1].setValue(self.saturation[1][self.currentZ])
self.sliders[2].setValue(self.saturation[2][self.currentZ])
# print(len(self.saturation), len(self.saturation[0]))

def get_model_path(self, custom=False):
if custom:
Expand Down
25 changes: 8 additions & 17 deletions cellpose/gui/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -179,12 +179,16 @@ def _initialize_images(parent, image, load_3D=False):

img_min = image.min()
img_max = image.max()
parent.stack = parent.stack.astype(np.float32)
parent.stack = parent.stack.astype("float32")
parent.stack -= img_min
if img_max > img_min + 1e-3:
parent.stack /= (img_max - img_min)
parent.stack *= 255

if parent.stack.shape[-1] == 2:
parent.stack = np.concatenate((parent.stack, np.zeros((*parent.stack.shape[:-1], 1), dtype="float32")), axis=-1)
print(parent.stack.shape)

if load_3D:
parent.logger.info(": converted to float and normalized values to 0.0->255.0")

Expand All @@ -194,25 +198,12 @@ def _initialize_images(parent, image, load_3D=False):
parent.imask = 0
parent.Ly, parent.Lx = parent.stack.shape[-3:-1]
parent.Ly0, parent.Lx0 = parent.stack.shape[-3:-1]
parent.nchan = parent.stack.shape[-1]
parent.layerz = 255 * np.ones((parent.Ly, parent.Lx, 4), "uint8")
if hasattr(parent, "stack_filtered"):
parent.Lyr, parent.Lxr = parent.stack_filtered.shape[-3:-1]
elif parent.restore and "upsample" in parent.restore:
parent.Lyr, parent.Lxr = int(parent.Ly * parent.ratio), int(parent.Lx *
parent.ratio)
else:
parent.Lyr, parent.Lxr = parent.Ly, parent.Lx
parent.Lyr, parent.Lxr = parent.stack.shape[-3:-1]
parent.clear_all()

if not hasattr(parent, "stack_filtered") and parent.restore:
parent.logger.info(": no 'img_restore' found, applying current settings")
parent.compute_restore()

if parent.autobtn.isChecked():
if parent.restore is None or parent.restore != "filter":
parent.logger.info(": normalization checked: computing saturation levels (and optionally filtered image)")
parent.compute_saturation()

parent.compute_saturation()
parent.compute_scale()
parent.track_changes = []

Expand Down
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