set_ncomp for single section model

[kirkw-1]

set_ncomp works fine where my cell model has both soma and axon, but when I try to import morphology with only soma or only axon to test that section, then set_ncomp raises this error (morphology attached).

Number of branches: 1
Traceback (most recent call last):

File ~/venv_jaxley/lib/python3.10/site-packages/spyder_kernels/customize/utils.py:209 in exec_encapsulate_locals
exec_fun(compile(code_ast, filename, "exec"), globals, None)

File ~/venv_jaxley/lib/python3.10/site-packages/spyder_kernels/customize/spyderpdb.py:856 in run
super(SpyderPdb, self).run(cmd, globals, locals)

File /usr/lib/python3.10/bdb.py:598 in run
exec(cmd, globals, locals)

File ~/
branch.set_ncomp(1 + 2*int(np.sum(branch.nodes["length"])/40), initialize=False)

File ~/venv_jaxley/lib/python3.10/site-packages/jaxley/modules/base.py:1175 in set_ncomp
and len(self._branches_in_view) == len(self.base._branches_in_view)

AssertionError: This is not allowed for cells.

cell1_axon (copy).txt

[michaeldeistler]

Thanks for reporting! The issue happens because your SWC creates just a single branch. In that case, you can simply do:

cell = jx.read_swc("file.swc", ncomp=4)  # Instead of `set_ncomp(4)`

Does this work?

Either way, the fact that set_ncomp is not working is a bug, and I will fix it asap. Thank you!
Michael

[kirkw-1]

Thanks, yes setting ncomp directly as a scalar during the import works for now, will revert when I update jaxley.

[michaeldeistler]

Update: I have just released Jaxley version 0.11.1 which should fix the issue.