Move NeuroM morphology specs to MorphIO #313

asanin-epfl · 2021-05-12T09:38:33Z

~~Not finished. Still need to make two svg images.~~

Move specs about Point, Segment, Section, Neurite from NeuroM to MorphIO.

Solution to #312

arnaudon · 2021-05-18T06:10:27Z

doc/source/specification.rst

+-------
+
+A section is a series of one or more segments. Each section has a type associated with it. The type shows what part of
+the neuron a section represents. The type can be the axon, the soma, and so on.


could we put here the real list of sectiontypes?

arnaudon · 2021-05-18T06:11:50Z

doc/source/specification.rst

+3. forking point, forking point
+4. starting point, end point
+
+Starting point is the first point of a section without parent. Forking point is the last point of a section that has


I would move this paragraph before the bullet point, so we know what the different points represent before we read it.

Definitions go immediately after their usage. Putting them before, breaks the narration.

arnaudon · 2021-05-18T06:12:16Z

doc/source/specification.rst

+Neurite
+-------
+
+A neurite is essentially a tree of sections(`Section`_). The tree structure implies the following:


Suggested change

A neurite is essentially a tree of sections(`Section`_). The tree structure implies the following:

A neurite is a tree of sections(`Section`_). The tree structure implies the following:

Done. It is funny that I took the phrase from NeuroM docs.

arnaudon · 2021-05-18T06:14:13Z

doc/source/specification.rst

+the file. In the NRN simulator, the soma which is considered as a section (contrary to MorphIO)
+is placed first and then neurites are sorted according to their type.
+
+The final order is the following:


final in what sense? In neuron ordering?

arnaudon · 2021-05-18T06:15:44Z

doc/source/specification.rst

+In MorphIO each section is identified by an ID. By default, the section IDs will correspond to
+the order of section appearance while performing a depth-first traversal on every neurites. The
+neurite order is the order of appearance in the file. Alternatively, the NRN simulator way of
+ordering section can be used by specifying the flag ``morphio::Option::NRN_ID`` when opening


I use this: options=morphio.Option.nrn_order, is it the same as NRN_ID?

NRN_ID is a typo. Fixing this. Thank you.

arnaudon · 2021-05-18T06:17:28Z

doc/source/specification.rst

+***********************************
+Prior to version 3.0.0, when a section had a single child section (aka unifurcation), the child section would be merged
+with its parent when reading or writing the file. Since version 3.0.0, merging does not happen when reading. Yet
+writing of such sections is not allowed.


could you point to remove_unifurcation method? If you try to save, what happens, this is called? I'm not sure I tried to save with unifurcations, but I find this weird that we cannot save these as they are.

asanin-epfl · 2021-05-26T08:40:46Z

I would still need @tomdele or @mgeplf approval here for merging.

tomdele · 2021-05-26T09:00:49Z

I am checking now

doc/source/specification.rst

tomdele · 2021-05-26T09:58:41Z

doc/source/specification.rst

+Section ordering
+****************
+In MorphIO each section is identified by an ID. By default, the section IDs will correspond to
+the order of section appearance while performing a depth-first traversal on every neurites. The


I am not sure we a have a stability guaranty with DFS. Isn't the DFS a consequence of the file formats (specially for swc or ascii) ?

What is DFS? Depth-first-...? I agree that this statement is wrong. I bluntly copied it from NeuroM. I need to edit it.

Depth-first-search sorry

Because it depends on the ordering of the neighbors and so it depends on the graph / tree underlying implementation and/or the nodes / edges insertion.
Most extreme case: if you are using something like a adjacency sets (with unordered set) you cannot guaranty a stable iterator on the tree/graph.

Can you please help me with clarification on this. I'm lost in the sources of MorphIO.

Should I just delete this paragraph on section ordering?

So this is tricky ...
The section ids are format dependent.

For the swc this is indeed a DFS and the sections ids are ordered using the placement of the sample inside the file. So the first neighbor is the first sample found in the file (no matter the sample id).

For the ascii same DFS and ordered via the placement inside the file of each sections.

For the h5 it depends on the section ordering inside the file. The sections exist already we just read them.

so, I'm putting this into docs? Would it be ok for you?

lol actually after thinking about it and having a better understanding, I think the doc is correct...

XD, should I put something like "verified by Tom" among the lines?

"TomDele seal of approval".

Co-authored-by: tomdele <[email protected]>

tomdele

ok after checking I think this is quite ok !

Thanks for this @asanin-epfl

asanin-epfl · 2021-05-26T13:50:52Z

Thank you for the thorough review!

tomdele · 2021-05-26T13:56:48Z

Thank you for the thorough review!

That was harder than expected for me :D

Move in NeuroM specs

95eca0a

asanin-epfl added the WIP Work in Progress label May 12, 2021

asanin-epfl self-assigned this May 12, 2021

asanin-epfl mentioned this pull request May 12, 2021

revise documentation BlueBrain/NeuroM#917

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asanin-epfl added 3 commits May 13, 2021 20:53

delete redundant svg artifacts

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add section images

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better text explanation

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asanin-epfl changed the title ~~Move in NeuroM specs~~ Move NeuroM specs May 14, 2021

asanin-epfl removed the WIP Work in Progress label May 14, 2021

asanin-epfl requested review from mgeplf, tomdele, arnaudon and adrien-berchet May 14, 2021 12:06

asanin-epfl added 2 commits May 14, 2021 19:48

clean NeuroM artifacts

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fix soma description

c780bbe

asanin-epfl removed the request for review from mgeplf May 17, 2021 08:38

arnaudon reviewed May 18, 2021

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Alexis comments

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asanin-epfl requested a review from arnaudon May 21, 2021 09:18

arnaudon approved these changes May 26, 2021

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asanin-epfl mentioned this pull request May 26, 2021

Use MorphIO specification for definitions doc page BlueBrain/NeuroM#925

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asanin-epfl changed the title ~~Move NeuroM specs~~ Move NeuroM morphology specs to MorphIO May 26, 2021

asanin-epfl merged commit 8879b80 into master May 26, 2021

asanin-epfl deleted the specs-from-neurom branch May 26, 2021 13:54

mgeplf pushed a commit that referenced this pull request Aug 10, 2021

Move NeuroM morphology specs to MorphIO (#313)

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Move NeuroM morphology specs to MorphIO #313

Move NeuroM morphology specs to MorphIO #313

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tomdele commented May 26, 2021

	A neurite is essentially a tree of sections(`Section`_). The tree structure implies the following:
	A neurite is a tree of sections(`Section`_). The tree structure implies the following:

Move NeuroM morphology specs to MorphIO #313

Move NeuroM morphology specs to MorphIO #313

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