.comp and .loc addresses #285 #288
Conversation
There was a problem hiding this comment.
Thanks a lot, I really like how this is done now!
If I understand correctly, currently, the following will not do the same:
nseg = 8
branch1.loc(0.0).set("radius", 1.0)
branch2.comp(0).set("radius", 1.0)Instead, the following two would do the same thing:
branch1.loc(0.0).set("radius", 1.0)
branch2.comp(nseg-1).set("radius", 1.0)Your tests work because index_of_loc takes care of this here.
This weird behavior is because of #30, but I think it will be confusing for users. I think that an easy fix should be to compute self.pointer.nseg-index in the adjust_view of CompartmentView and add the nseg-index_of_loc(...) in your tests.
| view["global_cell_index"] = view["cell_index"] | ||
| return CompartmentView(self, view) | ||
| elif key in self.group_nodes: | ||
| # if key == "comp": |
There was a problem hiding this comment.
Thanks for cleaning this up! (please remove the comments)
| if index == "all": | ||
| pass | ||
| else: | ||
| # support for legacy code |
There was a problem hiding this comment.
Since it is only 5 people hacking on Jaxley right now I do not think that we have to support legacy code. Please remove this.
| """Return a compartment of the discretized branch. | ||
|
|
||
| Args: | ||
| index: integer or float between 0 to 1 for |
There was a problem hiding this comment.
Since it is only 5 people hacking on Jaxley right now I do not think that we have to support legacy code. Please remove the legacy option.
|
Did not see this PR. Also addressed this in #277, since I needed the functionality to get all my tests to pass. Can revert what I did then. @lappalainenj I think one only needs to change jaxley/jaxley/modules/branch.py Line 71 in 4429745 jaxley/jaxley/modules/branch.py Line 142 in 4429745 to and replace jaxley/jaxley/modules/branch.py Line 76 in 4429745 by if key == "loc": return CompartmentView(self, view).loc
else: return CompartmentView(self, view).locAlso don't forget to change all prev |
This introduces comp(index: int) and loc(loc: float). To keep legacy code intact, this will trigger a warning if comp(loc: float) is used but still work. I added a unit test, showing that both methods yield equivalent simulations. This defines _compartment_view, comp, and loc in both Branch and BranchView -- I do not know if having both is desirable?