Changing cluster id of a cell.

Quite often when working with mitosis you may want to reassign cell’s cluster id i.e. to make a given cell belong to a different cluster than it currently does. You might think that statement like:


is a good way of accomplishing it. This could have worked with CC3D versions prior to 3.4.2 . However, this is not the case anymore and in fact this is an easy recipe for hard to find bugs that will crash your simulation with very enigmatic messages. So what is wrong here? First of all you need to realize that all the cells (strictly speaking pointers to CellG objects) in the CompuCell3D are stored in a sorted container called inventory. The ordering of the cells in the inventory is based on cluster id and cell id. Thus when a cell is created it is inserted to inventory and positioned according to cluster id and cell id. When you iterate inventory cells with lowest cluster id will be listed first. Within cells of the same cluster id cells with lowest cell id will be listed first. In any case if the cell is in the inventory and you do brute force cluster id reassignment the position of the cell in the inventory will not be changed. Why should it be? However when this cell is deleted CompuCell3D will first try to remove the cell from inventory based on cell id and cluster id and it will not find the cell because you have altered cluster id so it will ignore the request however it will delete underlying cell object so the net outcome is that you will end up with an entry in the inventory which has pointer to a cell that has been deleted. Next time you iterate through inventory and try go perform any operation on the cell the CC3D will crash because it will try to perform something with a cell that has been deleted. To avoid such situations always use the following construct to change clusterId of the cell:

reassignIdFlag = self.inventory.reassignClusterId(cell,550)

When you attempt to use former syntax CC3D will throw an exception and inform you that you need to chang the syntax.