Arbor cable cell exporter and backend support in BluePyOpt #1959

lukasgd · 2022-08-24T11:13:50Z

This is functionality to support Arbor simulations with cells optimized with Neuron in BluePyOpt as implemented in BlueBrain/BluePyOpt#393 and related to #1839.

It includes exported versions and example scripts for the simplecell and l5pc examples from BluePyOpt. The format is detailed in the referenced PR. The functionality added to Arbor includes pruning a particular tag from a morphology (going through a segment tree) and calculating an approximation for the radius of the axon replacement.

Closes #1839
Closes #1221

…_hoc.py) for simplecell example (adapted from python/example/single_cell_swc.py)

…phology parsing)

thorstenhater

Nice work, a few comments

Some of the utilities seems overly specific, eg media_distal_radii
- Can we write them in terms of the public API and shuffle them to an external project?
- Or -- failing that -- generalise them?
Please add tests and documentation
Consider rebuilding prune_tags on Allow editing morphologies #1957, which does similar things.

arbor/include/arbor/morph/morphology.hpp

arbor/include/arbor/morph/segment_tree.hpp

arbor/morph/morphology.cpp

python/example/single_cell_bpo/l5pc/Readme.md

arbor/morph/segment_tree.cpp

thorstenhater · 2022-09-02T10:36:15Z

I added the two related issues to be closed

…regions

lukasgd · 2022-09-15T18:20:45Z

All requests should be addressed, prune_tag and median_distal_radii are removed (see comments for details), split_at fixed, tests and documentation added.

lukasgd · 2022-09-15T19:51:36Z

Changed the split_at implementation again to avoid redundant loops on large models. I've changed the node predicate as well to a segment id predicate - the node struct contains the parent ID in the new subtree, which seems not very useful to filter on.

thorstenhater

Only nitpicks left!

thorstenhater · 2022-09-16T12:30:12Z

python/example/single_cell_bpo/l5pc/Readme.md

@@ -0,0 +1,13 @@
+# BluePyOpt layer-5 pyramidal cell with axon-replacement
+
+This example was created in an environment with the `bluepyopt` package installed (see [installation instructions](https://github.com/BlueBrain/BluePyOpt#installation)). A cell model with parameters as published by [Markram et al., "Reconstruction and simulation of neocortical microcircuitry", Cell 163.2 (2015): 456–492](http://www.cell.com/abstract/S0092-8674%2815%2901191-5) (see [L5PC.ipynb](https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC.ipynb)) can be exported with


One last question on this: the licensing is unproblematic I hope?

I'd like to forward this to @wvangeit - is it ok to add this exported L5PC model as an example as described here to the Arbor repo?

I assume this falls under the BSD license of the entire repo? For me it's ok if you keep the reference to the original notebooks.
Are you storing any of the MOD files of the L5PC, remember that these have their own licenses.

Thank you. I didn't store any of the L5PC mechs in Arbor, but rather took the ones from the built-in BBP catalogue. This is also the ones that I used in the Arbor-Neuron validation (and actually I have even tested the K_Tst and K_Pst with Neuron to make sure the difference between the simulators we found is not due to the NMODL code).

python/example/single_cell_bpo_simple.py

python/example/single_cell_bpo_l5pc.py

arbor/morph/segment_tree.cpp

thorstenhater · 2022-09-20T09:35:54Z

@lukasgd could you

Merge master
Write a nice commit message
Squash/merge

?

brenthuisman

I checked the tutorial, looks good! Nice use of the GUI!

doc/concepts/decor.rst

doc/concepts/labels.rst

doc/tutorial/single_cell_bluepyopt.rst

thorstenhater

A few comments, nothing serious. Rest is good.

doc/tutorial/network_ring_gpu.rst

doc/tutorial/single_cell_bluepyopt.rst

lukasgd · 2022-10-18T21:22:04Z

Thanks for the feedback. @brenthuisman, I've resolved all points I've addressed in 622f204. Feel free to reopen any if you'd like further changes.

lukasgd · 2022-10-24T14:16:52Z

I've swapped the label-dict and decor arguments to the cable_cell constructor and in the returned values of read_acc. @brenthuisman, is there anything more from your review that needs to be addressed?

brenthuisman

lgtm

thorstenhater · 2022-10-25T10:15:10Z

@lukasgd would you like to write the commit message and merge the whole affair?

thorstenhater · 2022-10-25T10:15:56Z

The test failure is not critical, it's our old friend; should be gone in master

lukasgd added 10 commits April 7, 2022 19:27

Draft of simulation with BluePyOpt .json-/.acc-output (using generate…

c91b9bc

…_hoc.py) for simplecell example (adapted from python/example/single_cell_swc.py)

Added BluePyOpt simple cell example JSON/ACC output

85f1054

Added BluePyOpt l5pc example JSON/ACC output

c5787eb

Draft for BluePyOpt l5pc detailed recipe example (failing on .asc mor…

8cd53a4

…phology parsing)

Updated l5pc/simplecell BluePyOpt output

70c9c49

Axon replacement for cell optimization in BluePyOpt

ebcd963

Merge branch 'master' into bluepyopt_integration

f17938b

Merge branch 'master' into bluepyopt_integration

c5cf291

Updated BluePyOpt examples

806e25c

Formatting BluePyOpt examples

98bd501

lukasgd requested review from bcumming and thorstenhater August 24, 2022 11:13

Formatting BluePyOpt examples

fa783c3

thorstenhater requested changes Aug 24, 2022

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thorstenhater mentioned this pull request Aug 24, 2022

Translate Morphology #1777

Closed

lukasgd added 4 commits September 13, 2022 11:31

Merge branch 'master' into bluepyopt_integration

e894f7a

Tests, docs for segment_tree tag_roots and split_at fix to prune tag …

0695a75

…regions

Removing prune_tag (equivalently obtainable with tag_roots and split_at)

38ec4f7

BluePyOpt examples documentation

aa29748

lukasgd requested a review from thorstenhater September 15, 2022 18:21

Faster segment tree split/join operations

50c365e

Introducing local variables for lambda capture in split_at

c235844

lukasgd force-pushed the bluepyopt_integration branch from 0317f3b to c235844 Compare September 15, 2022 20:37

Morphology to segment_tree conversion comment

751c838

thorstenhater previously approved these changes Sep 16, 2022

View reviewed changes

Removing unneeded exceptions, capture by ref in split_at

dfaba6b

lukasgd dismissed thorstenhater’s stale review via dfaba6b September 30, 2022 09:56

BluePyOpt examples and tutorial

34cfe2c

lukasgd changed the title ~~Arbor cable cell exporter support in BluePyOpt~~ Arbor cable cell exporter and backend support in BluePyOpt Oct 14, 2022

Merge branch 'master' into bluepyopt_integration

4a3bf0c

brenthuisman suggested changes Oct 17, 2022

View reviewed changes

lukasgd added 2 commits October 17, 2022 15:37

Python formatting, BluePyOpt example and decor docs fixes

0d48fcb

Orthographic fixes on docs

df80cbc

thorstenhater previously approved these changes Oct 18, 2022

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Improved BluePyOpt tutorial

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lukasgd dismissed thorstenhater’s stale review via 622f204 October 18, 2022 15:09

BluePyOpt tutorial update

a5ce444

lukasgd added 5 commits October 19, 2022 20:12

BluePyOpt tutorial improvements

613c1c0

Merge branch 'master' into bluepyopt_integration

fb184ec

Swapping label-dict and decor in cable-cell constructors

26c2ad9

Merge branch 'master' into bluepyopt_integration

e3f4f93

Swapping label-dict and decor in BluePyOpt's read_acc

dfc25e9

brenthuisman approved these changes Oct 25, 2022

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Merge branch 'master' into bluepyopt_integration

8c72a89

lukasgd merged commit da8450e into arbor-sim:master Oct 25, 2022

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Arbor cable cell exporter and backend support in BluePyOpt #1959

Arbor cable cell exporter and backend support in BluePyOpt #1959

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thorstenhater commented Oct 25, 2022

		@@ -0,0 +1,13 @@
		# BluePyOpt layer-5 pyramidal cell with axon-replacement

		This example was created in an environment with the `bluepyopt` package installed (see [installation instructions](https://github.com/BlueBrain/BluePyOpt#installation)). A cell model with parameters as published by [Markram et al., "Reconstruction and simulation of neocortical microcircuitry", Cell 163.2 (2015): 456–492](http://www.cell.com/abstract/S0092-8674%2815%2901191-5) (see [L5PC.ipynb](https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC.ipynb)) can be exported with

Arbor cable cell exporter and backend support in BluePyOpt #1959

Arbor cable cell exporter and backend support in BluePyOpt #1959

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