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 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