def params(self, parent):
# have a named tuple for all parameters
nmin, nmax = parent.norm.span()
return PrimaryMask.params(
(
PrimaryMask.AdaptiveThreshold,
self.medianRadius.value(),
self.windowSize.value(),
self.minContrast.value(),
parent.removeBorderObjects.isChecked(),
parent.fillHoles.isChecked(),
nmin,
nmax,
parent.sizeMin.value(),
parent.sizeMax.value(),
parent.intensityMin.value(),
parent.intensityMax.value(),
parent.galSize.value(),
self.watershed.isChecked(),
self.seedingSize.value(),
parent.zsliceMethod.currentIndex(),
parent.zslice.value(),
parent.outlineSmoothing.value(),
)
)
def threshold(self, image, params):
image = self.normalize(image, params.norm_min, params.norm_max)
smoothed = gaussianFilter(image, params. median_radius)
label_image = PrimaryMask(params.mask)(smoothed, **params._asdict())
# imsave("/home/hoefler/images/%s" %self.fff.replace(".lsm", ".png"),
# label_image)
image = ccore.numpy_to_image(image, copy=True)
label_image = ccore.numpy_to_image(
label_image.astype(np.int16), copy=True)
cnt = ccore.ImageMaskContainer(image, label_image, False, True, True)
# need watershed_mask for other color channels
return cnt
def _setupPrimaryMasks(self):
for name, cls in PrimaryMask.itermasks():
self.pmask.addItem(name)
self.stack.addWidget(cls.widget(self))
# hide combobox
if not AtConfig().enable_plugins:
self.pmask.hide()
self.pmask.setCurrentIndex(
self.pmask.findText(PrimaryMask.AdaptiveThreshold))
def primarySettings(self):
primary = self.root.attrib[self.PRIMARY]
settings = dict()
# segmentation
segm = self.root.xpath("%s/%s" %(primary, self.SEGMENTATION))[0]
# XXX - stay compatible with old settings files, use adapitve threshold
# as default
if not segm.attrib.has_key('mask'):
values = [PM.AdaptiveThreshold]
values.extend(attrib2values(segm.attrib))
else:
values = attrib2values(segm.attrib)
settings[segm.tag] = PM.params(values)
# feature groups
fgrp = self.root.xpath("%s/%s" %(primary, self.FEATUREGROUPS))[0]
settings[fgrp.tag] = self._attrib2dict(fgrp.attrib)
return validate_tagname(primary, reverse=True), settings
