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Remove .views state, fix gradZ 3D GUI display #1432

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100 changes: 80 additions & 20 deletions cellpose/gui/gui.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -328,7 +328,7 @@ def make_buttons(self):
self.l0.addWidget(self.satBox, b, 0, 1, 9)

widget_row = 0
self.view = 0 # 0=image, 1=flowsXY, 2=flowsZ, 3=cellprob
# self.view = 0 # 0=image, 1=flowsXY, 2=flowsZ, 3=cellprob
self.color = 0 # 0=RGB, 1=gray, 2=R, 3=G, 4=B
self.RGBDropDown = QComboBox()
self.RGBDropDown.addItems(
Expand All @@ -350,6 +350,7 @@ def make_buttons(self):
self.ViewDropDown.setFont(self.medfont)
self.ViewDropDown.model().item(3).setEnabled(False)
self.ViewDropDown.currentIndexChanged.connect(self.update_plot)
self.view = 0 # must reference the property after the dropdown is created
self.satBoxG.addWidget(self.ViewDropDown, widget_row, 0, 2, 3)

label = QLabel("[pageup / pagedown]")
Expand Down Expand Up @@ -686,11 +687,9 @@ def keyPressEvent(self, event):
) == QtCore.Qt.Key_D:
self.get_next_image()
elif event.key() == QtCore.Qt.Key_PageDown:
self.view = (self.view + 1) % (nviews)
self.ViewDropDown.setCurrentIndex(self.view)
self.go_next_previous_view()
elif event.key() == QtCore.Qt.Key_PageUp:
self.view = (self.view - 1) % (nviews)
self.ViewDropDown.setCurrentIndex(self.view)
self.go_next_previous_view(-1)

# can change background or stroke size if cell not finished
if event.key() == QtCore.Qt.Key_Up or event.key() == QtCore.Qt.Key_W:
Expand Down Expand Up @@ -982,7 +981,6 @@ def reset(self):
# -- set menus to default -- #
self.color = 0
self.RGBDropDown.setCurrentIndex(self.color)
self.view = 0
self.ViewDropDown.setCurrentIndex(0)
self.ViewDropDown.model().item(self.ViewDropDown.count() - 1).setEnabled(False)
self.delete_restore()
Expand All @@ -998,6 +996,36 @@ def reset(self):
self.removing_region = False
self.remove_roi_obj = None

@property
def view(self):
"""Current view mode as a string (e.g. 'image', 'gradXY', 'cellprob', 'restored')."""
return self.ViewDropDown.currentText()

@view.setter
def view(self, value: int|str):
"""Set the active view in the ViewDropDown.

Parameters
----------
value : int or str
If int, sets the dropdown to that index. If str, matches against
available items ('image', 'gradXY', 'cellprob', 'restored') and
selects the matching entry.

Raises
------
ValueError
If value is neither an int nor a str.
"""
if isinstance(value, int):
self.ViewDropDown.setCurrentIndex(value)
elif isinstance(value, str):
items = [self.ViewDropDown.itemText(i) for i in range(self.ViewDropDown.count())]
if value in items:
self.ViewDropDown.setCurrentIndex(items.index(value))
else:
raise ValueError('Incompatible view drop down setting')

def delete_restore(self):
""" delete restored imgs but don't reset settings """
if hasattr(self, "stack_filtered"):
Expand Down Expand Up @@ -1342,17 +1370,27 @@ def mouse_moved(self, pos):

def color_choose(self):
self.color = self.RGBDropDown.currentIndex()
self.view = 0
self.ViewDropDown.setCurrentIndex(self.view)
self.view = 'image'
self.update_plot()

def update_plot(self):
self.view = self.ViewDropDown.currentIndex()
self.Ly, self.Lx, _ = self.stack[self.currentZ].shape

if self.view == 0 or self.view == self.ViewDropDown.count() - 1:
image = self.stack[
self.currentZ] if self.view == 0 else self.stack_filtered[self.currentZ]
is_image_view = self.view == 'image'
is_restored_view = self.view == 'restored'

flowp_map = {
'gradXY' : 0,
'cellprob' : 1,
'gradZ' : 4,
}

if is_image_view or is_restored_view:
if is_image_view:
image = self.stack[self.currentZ]
else:
self.stack_filtered[self.currentZ]
if self.color == 0:
self.img.setImage(image, autoLevels=False, lut=None)
if self.nchan > 1:
Expand Down Expand Up @@ -1388,12 +1426,9 @@ def update_plot(self):
self.img.setLevels(self.saturation[0][self.currentZ])
else:
image = np.zeros((self.Ly, self.Lx), np.uint8)
if len(self.flows) >= self.view - 1 and len(self.flows[self.view - 1]) > 0:
image = self.flows[self.view - 1][self.currentZ]
if self.view > 1:
self.img.setImage(image, autoLevels=False, lut=self.bwr)
else:
self.img.setImage(image, autoLevels=False, lut=None)
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])

for r in range(3):
Expand Down Expand Up @@ -1946,10 +1981,11 @@ def compute_segmentation(self, custom=False, model_name=None, load_model=True):
flows_new.append(flows[0].copy()) # RGB flow
flows_new.append((np.clip(normalize99(flows[2].copy()), 0, 1) *
255).astype("uint8")) # cellprob
flows_new.append(flows[1].copy()) # XY flows
flows_new.append(flows[1].copy()) # XY(Z) flows
flows_new.append(flows[2].copy()) # original cellprob

if self.load_3D:
# append Z flows (or zeros in stitching case): Z flows are flows[4]
if stitch_threshold == 0.:
flows_new.append((flows[1][0] / 10 * 127 + 127).astype("uint8"))
else:
Expand All @@ -1972,8 +2008,7 @@ def compute_segmentation(self, custom=False, model_name=None, load_model=True):
Lz, Ly, Lx = self.NZ, self.Ly, self.Lx
Lz0, Ly0, Lx0 = flows_new[0].shape[:3]
print("GUI_INFO: resizing flows to original image size")
for j in range(len(flows_new)):
flow0 = flows_new[j]
for flows0 in flows_new:
if Ly0 != Ly:
flow0 = resize_image(flow0, Ly=Ly, Lx=Lx,
no_channels=flow0.ndim==3,
Expand Down Expand Up @@ -2009,3 +2044,28 @@ def compute_segmentation(self, custom=False, model_name=None, load_model=True):
self.recompute_masks = False
except Exception as e:
print("ERROR: %s" % e)


def go_next_previous_view(self, increment=1):
""" Go to the next view using `increment` """

# skip disabled views
num_items = self.ViewDropDown.count()
enabled = []
for i in range(num_items):
enabled.append(self.ViewDropDown.model().item(i).isEnabled())

if not any(enabled):
self.logger.error('No available views are enabled. Cannot adjust view.')
return

idx = self.ViewDropDown.currentIndex() + increment

for _ in range(num_items):
idx %= num_items
if enabled[idx]:
self.ViewDropDown.setCurrentIndex(idx)
return
idx += increment

self.logger.error('Could not find an emabled view.')
16 changes: 9 additions & 7 deletions cellpose/gui/gui3d.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -445,18 +445,22 @@ def update_ortho(self):
zmin, zmax = z - self.dz, z + self.dz
self.zc = z - zmin
self.update_crosshairs()
if self.view == 0 or self.view == 4:

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

if is_image_view or is_restored_view:
for j in range(2):
if j == 0:
if self.view == 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:
image = self.stack[
zmin:zmax,
y, :].copy() if self.view == 0 else self.stack_filtered[zmin:zmax,
y, :].copy() if is_image_view else self.stack_filtered[zmin:zmax,
y, :].copy()
if self.nchan == 1:
# show single channel
Expand Down Expand Up @@ -613,11 +617,9 @@ def keyPressEvent(self, event):
self.scroll.setValue(self.currentZ)
updated = True
elif event.key() == QtCore.Qt.Key_PageDown:
self.view = (self.view + 1) % (nviews)
self.ViewDropDown.setCurrentIndex(self.view)
self.go_next_previous_view()
elif event.key() == QtCore.Qt.Key_PageUp:
self.view = (self.view - 1) % (nviews)
self.ViewDropDown.setCurrentIndex(self.view)
self.go_next_previous_view(-1)

# can change background or stroke size if cell not finished
if event.key() == QtCore.Qt.Key_Up or event.key() == QtCore.Qt.Key_W:
Expand Down
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