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Improve NodeList support for different region types #1280

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adamjhn opened this issue May 15, 2021 · 0 comments · Fixed by #2780
Closed

Improve NodeList support for different region types #1280

adamjhn opened this issue May 15, 2021 · 0 comments · Fixed by #2780
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@ramcdougal @rgourdine
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bug improvement Improvement over existing implementation rxd reaction-diffusion

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@adamjhn
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adamjhn commented May 15, 2021

Context

NodeList calls should only raise an error if all of the nodes can not test the condition. Currently it raises an error if any of the nodes can not test the condition.

Overview of the issue

For example, this gives an error, because NodeExtracellular doesn't support _in_sec method;

from neuron import h, rxd
sec = h.Section(name='sec')
cyt = rxd.Region(h.allsec())
ecs = rxd.Extracellular(-10, -10, -10, 10, 10, 10, dx=10)
k = rxd.Species([ecs,cyt],name='k', charge=1)
nd = k.nodes(sec)
print(nd.x)

Expected result/behavior

I'd expect calls to NodeList to only give an error when all of the node give an error, so the above would return an list containing one node for k in sec(0.5), so would print;

[0.5]

NEURON setup

  • Version: master branch
  • Installation method cmake build
  • OS + Version: Ubuntu 18.04.5
  • Compiler + Version: gcc 8.4.0

Minimal working example - MWE

from neuron import h, rxd
sec = h.Section(name='sec')
cyt = rxd.Region(h.allsec())
ecs = rxd.Extracellular(-10, -10, -10, 10, 10, 10, dx=10)
k = rxd.Species([ecs,cyt],name='k', charge=1)
nd = k.nodes(sec)
  • CMake build commands:
git clone git@github.com:neuronsimulator/nrn.git
mkdir -p build/install && cd build
cmake -DNRN_ENABLE_CORENEURON=OFF -DNRN_ENABLE_PYTHON=ON -DPYTHON_EXECUTABLE=`which python3` -DNRN_ENABLE_TESTS=ON -DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_RX3D=ON -DNRN_ENABLE_INTERVIEWS=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_INSTALL_PREFIX=`pwd`/install ..
cmake --build . --
>>> from neuron import h, rxd
>>> sec = h.Section(name='sec')
>>> cyt = rxd.Region(h.allsec())
>>> ecs = rxd.Extracellular(-10, -10, -10, 10, 10, 10, dx=10)
>>> k = rxd.Species([ecs,cyt],name='k', charge=1)
>>> nd = k.nodes(sec)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/adam/neuron/nrn.ns/build/install/lib/python/neuron/rxd/nodelist.py", line 9, in __call__
    return NodeList([i for i in self if i.satisfies(restriction)])
  File "/home/adam/neuron/nrn.ns/build/install/lib/python/neuron/rxd/nodelist.py", line 9, in <listcomp>
    return NodeList([i for i in self if i.satisfies(restriction)])
  File "/home/adam/neuron/nrn.ns/build/install/lib/python/neuron/rxd/node.py", line 801, in satisfies
    raise RxDException("unrecognized node condition: %r" % condition)
neuron.rxd.rxdException.RxDException: unrecognized node condition: sec
@adamjhn adamjhn added bug improvement Improvement over existing implementation rxd reaction-diffusion labels May 15, 2021
@ramcdougal ramcdougal self-assigned this May 27, 2023
rgourdine added a commit that referenced this issue Mar 15, 2024
@rgourdine
resolve #1280
122c1e2
@rgourdine rgourdine mentioned this issue Mar 15, 2024
Merged
pramodk pushed a commit that referenced this issue May 8, 2024
@rgourdine
Nodelist support different regions (#2780)
2b040b7 
resolve #1280
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@ramcdougal ramcdougal

@rgourdine rgourdine

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bug improvement Improvement over existing implementation rxd reaction-diffusion
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Nodelist support different regions neuronsimulator/nrn
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@ramcdougal @adamjhn @rgourdine