Mixed subtree processing #981

mgeplf · 2022-02-16T07:46:41Z

No description provided.

neurom/features/__init__.py

neurom/features/morphology.py

tests/features/test_get_features.py

neurom/features/morphology.py

Calculate the distance of the morphology points to the soma, instead to (0,0,0)

The feature throws a warning if path distances deeper than the first section are used and handles all special cases wrt the combinations of min/max filters.

Make sholl_frequency return an empty list for a neurite_type that is not present in the morphology.

codecov-commenter · 2022-03-03T23:21:37Z

Codecov Report

Merging #981 (d427225) into master (c6d187a) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##            master      #981   +/-   ##
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  Coverage   100.00%   100.00%           
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  Files           36        36           
  Lines         2421      2505   +84     
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+ Hits          2421      2505   +84

* Use the standard pyproject.toml build-system * Update publish-sdist with python3.9 * Set min python version to 3.7

Thanks!

…ves (#1001)

…#1002) The NeuroM deprecation warning configuration was hijacking the warnings setup in order to enable visibility of the DeprecationWarning. This change doesn't enforce a warning filter configuration, but increases the stack level of the warn function to 3. Setting it to 3 brings the warning stacl level to the __main__ (e.g. user's interactive shell) where the visibility of the DeprecationWarning is by default enabled.

- Refactor features to utilize the iterators and mappers as much as possible. - Reduce the number of nested functions/closures by moving them to section features. - neurom.features.segment_taper_rates were fixed to return signed taper rates.

Allow passing downstream iterator_type in partition asymmetry functions

Fixes principal_direction_extent to calculate correctly the extent of the projections along the principal directions.

doc/source/heterogeneous.rst

mgeplf

I think one decision we should make is whether to throw a warning (w/ a way of turning it off) if it's a mixed subtree, but ppl haven't specified it.

mgeplf · 2022-04-21T11:32:35Z

neurom/core/morphology.py

+
+    A sub-neurite can be either the entire tree or a homogeneous downstream
+    sub-tree.
+    """


do we want to check/error/differenciate/document what happens if there is a dendrite - axon - dendrite - axon situation?

Added a warning if the neurite is not an AcD

Also, I changed the way that identifies the subtrees so that it creates a subtree for each different type it encounters downstream, regardless if it has been added to the list. This allows to have a dendrite-axon-dendrite-axon situation, which was not possible before due to the set I was using.

neurom/core/morphology.py

neurom/features/__init__.py

neurom/features/bifurcation.py

neurom/features/morphology.py

mgeplf · 2022-04-21T11:56:25Z

neurom/features/morphology.py

+        sections = filter(is_type(neurite_type), morph)
+    else:
+        if use_subtrees:
+            sections = iter_sections(morph, section_filter=is_type(neurite_type))


if we drop that, do any of the tests fail? I'd consider removing it if not?

eleftherioszisis

rebase yo

* A heterogeneous morphology consists of zero or more homogeneous and at least one heterogeneous neurite trees extending from the soma; * 'heterogeneous neurite trees ' is called a 'mixed subtree' for brevity * this is a breaking change with how NeuroM<=3.x works * this will fix #975

* Mixed subtree processing (#981) * Refactor tests for test_mixed.py (#1027) * Remove deprecated modules and functions/classes & warnings (#1026, #1032) * Use readonly morphio Morphology by default (#979) * Morphology level radial distance features use the soma as reference point (#1030) * Expose subtree processing from the morph_stats api (#1034) * Remove pyXX prefix for lint, docs, and coverage (#1038) * Fix tutorials and add tutorial testenv (#1039) * Add isort for formatting/linting (#1040) * Add testing of example scripts (#1041) * Make documentation/docstrings testable (#1035) * Add black to neurom, format everything, and add to lint (#1042) * Fix load_morpholgies to always resolve paths (#1047) * allow Morphology objects to be either mut or immut (#1049) * Replace iter_* methods by properties in core objects and improve iter_segments (#1054) * Decouple Morphology constructor from io (#1120) * Move soma methods to functions (#1118)

mgeplf commented Feb 16, 2022

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mgeplf commented Feb 16, 2022

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eleftherioszisis mentioned this pull request Feb 24, 2022

Fix the trunk_origin_radii feature #986

Merged

eleftherioszisis changed the title ~~Subtree processing example~~ [WIP] Mixed subtree processing Feb 24, 2022

Use soma center in sholl_frequency distance calculation (#989)

b6c3beb

Calculate the distance of the morphology points to the soma, instead to (0,0,0)

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from 835ac4e to 96ff8af Compare February 25, 2022 09:58

Fix the trunk_origin_radii feature (#986)

d120263

The feature throws a warning if path distances deeper than the first section are used and handles all special cases wrt the combinations of min/max filters.

eleftherioszisis added the version 4.0 label Feb 28, 2022

Fix sholl_frequency for NA neurite_type (#990)

d896651

Make sholl_frequency return an empty list for a neurite_type that is not present in the morphology.

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from 6acd5a5 to 15782a9 Compare February 28, 2022 13:06

Add py39 and py310 for tests (#984)

e071ba5

eleftherioszisis self-assigned this Mar 3, 2022

eleftherioszisis and others added 5 commits March 4, 2022 09:22

Make output file in morph_check required (#992)

0b7b5ea

Minor housekeeping (#993)

8c3efc8

* Use the standard pyproject.toml build-system * Update publish-sdist with python3.9 * Set min python version to 3.7

Fix doc of neurom.core.morphology.Neurite.iter_sections method (#994)

c570a2f

Thanks!

Add volume density at the morphology level (#996)

cfc7012

Remove duplicate points in principal_direction_extents (#999)

127d6fd

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from 0dd71a2 to f2c87d0 Compare March 10, 2022 12:31

Fix parition_asymmetry Uylings to not throw for bifurcations with lea…

f57feb2

…ves (#1001)

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from ce410ce to f6db8be Compare March 14, 2022 12:02

eleftherioszisis changed the title ~~[WIP] Mixed subtree processing~~ Mixed subtree processing Mar 15, 2022

introduce flatten (#1003)

a9e3020

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from 1ba9840 to 5a2d799 Compare March 16, 2022 11:09

Refactor features (#1005)

1b64091

- Refactor features to utilize the iterators and mappers as much as possible. - Reduce the number of nested functions/closures by moving them to section features. - neurom.features.segment_taper_rates were fixed to return signed taper rates.

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from 5a2d799 to 9957c7e Compare March 18, 2022 14:12

Generalize partition asymmetry (#1006)

fdf9f78

Allow passing downstream iterator_type in partition asymmetry functions

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from 9957c7e to 2d054bb Compare March 18, 2022 17:07

Fix principal direction extent (#1008)

ba29611

Fixes principal_direction_extent to calculate correctly the extent of the projections along the principal directions.

eleftherioszisis added 7 commits April 14, 2022 20:56

Fix year and pylint spacing

607d572

Move extract_subneurites where it is used

dff7540

Factor out signature checking using inspect

f3df2c3

Use **kwargs in _get_neurite_feature_value

5bf8076

Add morphology heterogeneous tests

8732868

Cleanup neurite features

2357027

Add new feature, refactor, and more tests

8bba54f

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from 800f82e to 8bba54f Compare April 16, 2022 22:13

eleftherioszisis and others added 4 commits April 18, 2022 15:52

Refactor morphology.py

a3791b2

Add documentation

44938b5

Generalize iupstream to also stop at node

c3b1ddc

some doc reflow

cbe287a

mgeplf commented Apr 21, 2022

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doc/source/heterogeneous.rst Show resolved Hide resolved

eleftherioszisis added 2 commits April 21, 2022 10:27

Simplify iupstream

94a6a8c

Add brief description for total_volume for default mode

1848f1d

mgeplf commented Apr 21, 2022

View reviewed changes

eleftherioszisis added 5 commits April 21, 2022 20:10

Make neurites iterable readable

baded71

Drop extra line

15aecdb

Use full path of section features

cd21427

Add warning for non AcD neurites

cd70e90

Do not use a set for subtrees to allow finding many of same type.

d427225

eleftherioszisis force-pushed the zisis/heterogeneous-neurites branch from 8ebcbec to d427225 Compare April 25, 2022 08:30

eleftherioszisis approved these changes Apr 25, 2022

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eleftherioszisis suggested changes Apr 25, 2022

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mgeplf changed the base branch from master to v4 April 25, 2022 13:16

eleftherioszisis approved these changes Apr 25, 2022

View reviewed changes

mgeplf merged commit 57b634d into v4 Apr 25, 2022

mgeplf deleted the zisis/heterogeneous-neurites branch April 25, 2022 13:32

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Mixed subtree processing #981

Mixed subtree processing #981

mgeplf commented Feb 16, 2022

codecov-commenter commented Mar 3, 2022 •

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Mixed subtree processing #981

Mixed subtree processing #981

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mgeplf commented Feb 16, 2022

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