pt3dstyle logical connection should be at center of soma section (instead of center of contour). - Githubissues

neuronsimulator / nrn

NEURON Simulator

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pt3dstyle logical connection should be at center of soma section (instead of center of contour). #2981

Open nrnhines opened 1 month ago

nrnhines commented 1 month ago

Closes #2973

The logical connection after import3d neurolucida3 file should be invariant on h.define_shape(). That is, the location of the rest of the tree should not change relative to the soma.

This is accomplished by updating the logical connection point of dendrites at instantiation when the actual 3-d soma section points are known (after processing the contour).

The two (related) substantive changes in this PR are noted in the comments.

Test added

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nrnhines commented 1 month ago

The many CI failures are perplexing. On my machine I have similar errors for ninja testfor this pr but also for the master. ie. Ubuntu 24.04, gcc version 13.2.0 (Ubuntu 13.2.0-23ubuntu4), Python 3.12.3 (via pyenv)

The following tests FAILED:
      3 - unit_tests::benchmarks (Failed)
     86 - parallel::subworld (Failed)
     88 - parallel::netpar (Failed)
     89 - parallel::bas (Failed)
     90 - parallel::nrntest_fast (Failed)
     92 - nmodl_tests::test_disc (Failed)
     93 - nmodl_tests::test_function_table (Failed)
     94 - nmodl_tests::test_kinetic (Failed)
    123 - pyinit::nrniv_py3.12_python_check_sys_path (Failed)
    125 - pyinit::nrniv_py3.12_nrnpython_check_sys_path (Failed)
    127 - pyinit::nrniv_py3.12_python_check_sys_prefix (Failed)
    129 - pyinit::nrniv_py3.12_nrnpython_check_sys_prefix (Failed)
    131 - pyinit::nrniv_py3.12_python_check_sys_exec_prefix (Failed)
    133 - pyinit::nrniv_py3.12_nrnpython_check_sys_exec_prefix (Failed)
    159 - pyinit::nrniv_pydef_python_check_sys_path (Failed)
    161 - pyinit::nrniv_pydef_nrnpython_check_sys_path (Failed)
    163 - pyinit::nrniv_pydef_python_check_sys_prefix (Failed)
    165 - pyinit::nrniv_pydef_nrnpython_check_sys_prefix (Failed)
    167 - pyinit::nrniv_pydef_python_check_sys_exec_prefix (Failed)
    169 - pyinit::nrniv_pydef_nrnpython_check_sys_exec_prefix (Failed)
    194 - external_nrntest (Failed)
    207 - testcorenrn_vecevent::compare_results (Failed)

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sonarcloud[bot] commented 6 days ago

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

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