disconnect between Studio and C++ for custom cell functions, etc.

[rheiland]

I'd welcome a discussion about this issue. In the C++ custom.cpp, create_cell_types(), we define cell types' functions. But this assumes those cell types (beyond cell_defaults) have been defined, e.g. via initialize_cell_definitions_from_pugixml. The Studio allows dynamic creation of cell types, but this only defines them in the XML. When a Copy of a cell type is created in the Studio, we somehow want it to also inherent the functions of the original cell type (or at least have that option). Actually, the issue goes beyond just wanting to copy custom cell functions.

I noticed this as a "problem" when I was playing with a potential reference model for the POSE grant where I had defined a horizontal motility vector for cell_defaults and I wanted copies of this (in the Studio) to inherent the same motility vector. More recently, I've been experimenting with a new custom_division_function which gets invoked in the divide() function. Once again, it works fine for the cell_defaults, but not for any copied cell type.

[drbergman]

Isn't this the purpose of the parent attribute for cell types? That's what I assume these lines were written for:

PhysiCell/core/PhysiCell_cell.cpp

Lines 1920 to 1940 in 3d7051f

	Cell_Definition* pParent = NULL;
	if( cd_node.attribute( "parent_type" ) )
	{ pParent = find_cell_definition( cd_node.attribute( "parent_type" ).value() ); }
	// if it's not the default and no parent stated, inherit from default
	bool use_default_as_parent_without_specifying = false;
	if( pParent == NULL && pCD != &cell_defaults )
	{
	pParent = &cell_defaults;
	use_default_as_parent_without_specifying = true;
	}
	// if we found something to inherit from, then do it!
	if( pParent != NULL )
	{
	std::cout << "\tCopying from type " << pParent->name << " ... " << std::endl;
	*pCD = *pParent;
	// but recover the name and ID (type)
	pCD->name = cd_node.attribute("name").value();
	pCD->type = cd_node.attribute("ID").as_int();
	}

Could we just add a way to set the parent type in studio and be good on this?