Setting the class of pathobjects changes the hierarchy

[ap--]

As reported here:

https://forum.image.sc/t/paquo-detection-path-class-updates-causing-changes-in-hierarchy/101806/5

Solution is likely to be:

from @petebankhead
Yes, the object hierarchy doesn’t usually know when the properties of an object change – which is a good thing, because hierarchy updates are expensive.

You do generally need to remove/add an object if its ROI changes, but not if its classification changes.

The relevant code paths are:

update_path_class

paquo/paquo/pathobjects.py

Lines 221 to 229 in 18ae97a

	def update_path_class(self: PathROIObjectType, pc: Optional[QuPathPathClass], probability: float = math.nan) -> None:
	"""updating the class or probability has to be done via this method"""
	if not (pc is None or isinstance(pc, QuPathPathClass)):
	raise TypeError("requires QuPathPathClass")
	else:
	pc = pc if pc is None else pc.java_object
	self.java_object.setPathClass(pc, probability)
	if self._update_callback:
	self._update_callback(self) # type: ignore[arg-type]

on an existing hierarchy this will call the _update_callback. This is set here

PathObjectProxy.add

paquo/paquo/hierarchy.py

Lines 132 to 146 in 18ae97a

	def add(self, x: PathROIObjectType) -> None:
	"""adds a new path object to the proxy"""
	if self._mask:
	raise OSError("cannot modify view")
	if self._readonly:
	raise OSError("project in readonly mode")
	if not isinstance(x, self._paquo_cls):
	raise TypeError(f"requires {self._paquo_cls.__name__} instance got {x.__class__.__name__}")
	try:
	if self._hierarchy.autoflush:
	self._java_hierarchy.addObject(x.java_object, True)
	else:
	self._java_hierarchy.addObject(x.java_object, False)
	finally:
	self._list_invalidate_cache()

get's called then and is probably the cause for loosing the hierarchy. we could just disable it for modifications that are not related to the ROI of the pathobject.

Easiest way would be to add a update_hierarchy kwarg to the PathObjectProxy.add which defaults to True and pass update_hierarchy=False to the callback when updating the class.

We should first add a test that reproduces the current issue though.