def compute_cprob(self):
rerun = False
if self.cellprob != self.probslider.value():
rerun = True
self.cellprob = self.probslider.value()
if self.threshold != self.threshslider.value() / 10.:
rerun = True
self.threshold = self.threshslider.value() / 10.
if not rerun:
return
if self.threshold == 3.0 or self.NZ > 1:
thresh = None
print(
'computing masks with cell prob=%0.3f, no flow error threshold'
% (self.cellprob))
else:
thresh = self.threshold
print(
'computing masks with cell prob=%0.3f, flow error threshold=%0.3f'
% (self.cellprob, thresh))
maski = dynamics.get_masks(self.flows[3].copy(),
iscell=(self.flows[4][-1] > self.cellprob),
flows=self.flows[4][:-1],
threshold=thresh)
if self.NZ == 1:
maski = dynamics.fill_holes(maski)
self.masksOn = True
self.outlinesOn = True
self.MCheckBox.setChecked(True)
self.OCheckBox.setChecked(True)
if maski.ndim < 3:
maski = maski[np.newaxis, ...]
print('%d cells found' % (len(np.unique(maski)[1:])))
io._masks_to_gui(self, maski, outlines=None)
self.show()
def compute_model(self):
self.progress.setValue(0)
if 1:
self.clear_all()
self.flows = [[], [], []]
self.initialize_model()
print('using model %s' % self.current_model)
self.progress.setValue(10)
do_3D = False
if self.NZ > 1:
do_3D = True
data = self.stack.copy()
else:
data = [self.stack[0].copy()]
channels = self.get_channels()
self.diameter = float(self.Diameter.text())
try:
masks, flows, _, _ = self.model.eval(
data,
channels=channels,
diameter=self.diameter,
invert=self.invert.isChecked(),
do_3D=do_3D,
progress=self.progress)
except Exception as e:
print('NET ERROR: %s' % e)
self.progress.setValue(0)
return
self.progress.setValue(75)
if not do_3D:
masks = masks[0][np.newaxis, :, :]
flows = flows[0]
self.flows[0] = flows[0]
self.flows[1] = (np.clip(utils.normalize99(flows[2]), 0, 1) *
255).astype(np.uint8)
if not do_3D:
self.flows[2] = np.zeros(flows[1][0].shape, dtype=np.uint8)
self.flows = [
self.flows[n][np.newaxis, ...]
for n in range(len(self.flows))
]
else:
self.flows[2] = (flows[1][0] / 10 * 127 + 127).astype(np.uint8)
print('%d cells found with unet' % (len(np.unique(masks)[1:])))
self.progress.setValue(80)
z = 0
self.masksOn = True
self.outlinesOn = True
self.MCheckBox.setChecked(True)
self.OCheckBox.setChecked(True)
io._masks_to_gui(self, masks, outlines=None)
self.progress.setValue(100)
self.toggle_server(off=True)
else: #except Exception as e:
print('ERROR: %s' % e)