[WIP] ENH: add connectome strength plot #2028

glemaitre · 2019-04-18T11:49:16Z

This PR adds the possibility to plot the strength of a connectome on a glass brain.
The strength is defined as the absolute sum of the edges at a node.

TODO:

add example for visualization
add tests

codecov · 2019-04-18T12:31:36Z

Codecov Report

Merging #2028 into master will increase coverage by 0.03%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #2028      +/-   ##
==========================================
+ Coverage   92.31%   92.34%   +0.03%     
==========================================
  Files         149      149              
  Lines       18781    18867      +86     
  Branches     2290     2302      +12     
==========================================
+ Hits        17337    17423      +86     
- Misses        922      924       +2     
+ Partials      522      520       -2

Impacted Files	Coverage Δ
nilearn/plotting/__init__.py	`95.65% <ø> (ø)`	⬆️
nilearn/plotting/tests/test_img_plotting.py	`99.82% <100%> (+0.01%)`	⬆️
nilearn/plotting/img_plotting.py	`89.78% <100%> (+1.51%)`	⬆️
nilearn/datasets/neurovault.py	`88.43% <0%> (-0.25%)`	⬇️
nilearn/plotting/tests/test_html_connectome.py	`100% <0%> (ø)`	⬆️
nilearn/tests/test_cache_mixin.py	`95.65% <0%> (+1.29%)`	⬆️

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codecov · 2019-04-18T12:31:36Z

Codecov Report

Merging #2028 into master will decrease coverage by 0.09%.
The diff coverage is 5.26%.

@@            Coverage Diff            @@
##           master    #2028     +/-   ##
=========================================
- Coverage   94.96%   94.86%   -0.1%     
=========================================
  Files         138      138             
  Lines       17878    17897     +19     
=========================================
+ Hits        16977    16978      +1     
- Misses        901      919     +18

Impacted Files	Coverage Δ
nilearn/plotting/__init__.py	`100% <ø> (ø)`	⬆️
nilearn/plotting/img_plotting.py	`88.59% <5.26%> (-5.5%)`	⬇️

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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GaelVaroquaux · 2019-04-18T20:01:16Z

Sorry, we've merge @illdopejake 's PR in master. There are now conflicts to address :(.

glemaitre · 2019-04-19T09:00:42Z

I'll fix that

illdopejake · 2019-04-19T09:04:19Z

Let me know if I can help

…strength

glemaitre · 2019-04-19T09:18:24Z

@illdopejake Should be good to be reviewed.

illdopejake · 2019-04-19T09:46:49Z

@glemaitre Looks great!

The one thing that we are going to explore, however, is whether the crappy connectomes that we are seeing are because the first several subjects are young children, rather than adults.

I will have a look at this and maybe we can set an argument to the fetcher to grab children or adults specifically. That way we, maybe we won't need to download 20 subjects just to run the example.

illdopejake · 2019-04-19T14:35:08Z

fyi just added the PR to a) get adults first, b) choose if you want children or adults. Find it here: #2035

kchawla-pi · 2019-08-02T11:25:37Z

nilearn/plotting/img_plotting.py

+        display.close()
+        display = None
+
+    return display


Hey @glemaitre this is a super long method, refactoring it would be helpful.

But there is no code duplication. It would not be really meaningful to cut the function into smaller functions if they are not reused.

They improve ease of understanding.

kchawla-pi · 2019-08-02T11:31:53Z

Add a whats_new entry, pull from master.

GaelVaroquaux · 2019-08-02T17:02:42Z

But there is no code duplication. It would not be really meaningful to cut the function into smaller functions if they are not reused.

+1

jeromedockes · 2019-08-02T17:28:23Z

nilearn/plotting/img_plotting.py

+
+    adjacency_matrix = np.nan_to_num(adjacency_matrix)
+
+    adjacency_matrix_shape = adjacency_matrix.shape


It looks like the 4 checks below (adjacency shape, nodes shape, both shapes, adjacency symmetry, mask symmetry) could be useful for other connectome plotting functions?

kchawla-pi · 2019-09-19T22:12:50Z

@glemaitre We are aiming for an end of September release. Think this can be included?

jeromedockes · 2019-09-30T08:58:20Z

I think this can be merged once rebased. My comment about turning the checks into functions can be ignored or left for a later PR. Hence @glemaitre do you mind rebasing?

@emdupre

…lot_connectome_strength * 'master' of https://github.com/nilearn/nilearn: (272 commits) [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888) Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162) Fixing malfunctioning allowed-failure section in Travis (nilearn#2160) Update Brainomics fetcher (nilearn#2097) Remove inplace modification in signal.clean (nilearn#2125) Iter age group prediction example (nilearn#2063) Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157) Replac conda with pip in TravisCI setup (nilearn#2141) Core devs doc and add @emdupre (nilearn#2151) Add check for vmin, vmax in plot_surf_roi (nilearn#2052) [ENH] Initial visual reports (nilearn#2019) Renamed test to deduplicate name (nilearn#2144) Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126) Update Schaefer parcelation to v0.14.3 (nilearn#2138) MAINT: Future-compatible cmap reversal (nilearn#2131) fix openmp crash (nilearn#2140) change nose to pytest on appveyor (nilearn#2130) adding fix to whatsnew fix wrong urls in nki dataset Made Flake8 happy ... # Conflicts: # examples/03_connectivity/plot_sphere_based_connectome.py

kchawla-pi · 2019-10-13T13:12:11Z

CircleCI error:

File "/home/circleci/miniconda3/envs/testenv/lib/python3.6/site-packages/sklearn/covariance/graph_lasso_.py", line 247, in graphical_lasso
    raise FloatingPointError('The system is too ill-conditioned '
FloatingPointError: The system is too ill-conditioned for this solver. The system is too ill-conditioned for this solver

kchawla-pi · 2019-10-13T13:45:24Z

Before the OSF problem I was seeing this error. We must not merge this until there is a reliable solution to this problem.

bthirion · 2019-10-13T16:20:50Z

Before the OSF problem I was seeing this error. We must not merge this until there is a reliable solution to this problem.

This is a numerical proble; hence, to move forward on this, we need to localize the problem: with which dataset does it occur ? What is the problem with this dataset.
I have tried to check, but the CircleCI failure I can see is related to download...

kchawla-pi · 2019-10-13T16:25:04Z

https://circleci.com/gh/nilearn/nilearn/4854

jeromedockes · 2019-10-13T17:30:18Z

I could reproduce it locally, I can look into it tomorrow

jeromedockes · 2019-10-13T17:38:18Z

note that the link above is from another pr:
#2035

but the error can be reproduced with either pr

jeromedockes · 2019-10-14T07:52:33Z

I open a PR on @glemaitre 's branch that fixes the issue for this one:

glemaitre#1

kchawla-pi · 2019-10-14T13:16:57Z

@jeromedockes Anything you wanna change? Or imma merge this once green.

jeromedockes · 2019-10-14T13:23:56Z

you can merge. I think we should remove the last atlas from the plot_spheres example but it can be done in a separate pr

kchawla-pi · 2019-10-14T13:40:08Z

I will remove it now, and if we decide otherwise, we can add it back in another PR.

jeromedockes · 2019-10-14T13:45:09Z

I will remove it now, and if we decide otherwise, we can add it back in another PR.

why? it's not related to this PR

kchawla-pi · 2019-10-14T13:49:34Z

Gah right. No worries.

…nt_modify_fetch_dev * 'master' of https://github.com/nilearn/nilearn: ENH: add connectome strength plot (nilearn#2028) Fix cache mixin tests (nilearn#2161) Do not fail if metadata cannot be updated for an image (nilearn#2167)

…ctome strength)

…trength) (#2174) * Fix Flake8 errors overlooked when merging PR #2028 (Plot connectome strength) * Ignore linting for W508 * Corrected linter code

* 'master' of github.com:nilearn/nilearn: Fix Flake8 errors overlooked when merging PR nilearn#2028 (Plot connectome strength) (nilearn#2174) ENH: add connectome strength plot (nilearn#2028)

…ecomposition * 'master' of https://github.com/nilearn/nilearn: Fix Flake8 errors overlooked when merging PR nilearn#2028 (Plot connectome strength) (nilearn#2174) ENH: add connectome strength plot (nilearn#2028) Fix cache mixin tests (nilearn#2161) Do not fail if metadata cannot be updated for an image (nilearn#2167) [MRG] Nans in view connectome (nilearn#2166)

…nt_modify_fetch_dev * 'master' of https://github.com/nilearn/nilearn: Removed sub-example due to unfit for lasso dataset - unstable float values (nilearn#2177) Fix Flake8 errors overlooked when merging PR nilearn#2028 (Plot connectome strength) (nilearn#2174)

@emdupre

…smooth-image * 'master' of https://github.com/nilearn/nilearn: (114 commits) [DOC] Update whats_new to reference nilearn#2013 (Merging of several examples) (nilearn#2183) Removed sub-example due to unfit for lasso dataset - unstable float values (nilearn#2177) Fix Flake8 errors overlooked when merging PR nilearn#2028 (Plot connectome strength) (nilearn#2174) ENH: add connectome strength plot (nilearn#2028) Fix cache mixin tests (nilearn#2161) Do not fail if metadata cannot be updated for an image (nilearn#2167) [MRG] Nans in view connectome (nilearn#2166) [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888) Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162) Fixing malfunctioning allowed-failure section in Travis (nilearn#2160) Update Brainomics fetcher (nilearn#2097) Remove inplace modification in signal.clean (nilearn#2125) Iter age group prediction example (nilearn#2063) Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157) Replac conda with pip in TravisCI setup (nilearn#2141) Core devs doc and add @emdupre (nilearn#2151) Add check for vmin, vmax in plot_surf_roi (nilearn#2052) [ENH] Initial visual reports (nilearn#2019) Renamed test to deduplicate name (nilearn#2144) Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126) ...

@emdupre

…te-req-dev * 'master' of https://github.com/nilearn/nilearn: (336 commits) Release Nilearn 0.6.0 alpha (nilearn#2164) Making fetch_localizer_button_task backwards compatibile (nilearn#2182) [DOC] Update whats_new to reference nilearn#2013 (Merging of several examples) (nilearn#2183) Removed sub-example due to unfit for lasso dataset - unstable float values (nilearn#2177) Fix Flake8 errors overlooked when merging PR nilearn#2028 (Plot connectome strength) (nilearn#2174) ENH: add connectome strength plot (nilearn#2028) Fix cache mixin tests (nilearn#2161) Do not fail if metadata cannot be updated for an image (nilearn#2167) [MRG] Nans in view connectome (nilearn#2166) [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888) Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162) Fixing malfunctioning allowed-failure section in Travis (nilearn#2160) Update Brainomics fetcher (nilearn#2097) Remove inplace modification in signal.clean (nilearn#2125) Iter age group prediction example (nilearn#2063) Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157) Replac conda with pip in TravisCI setup (nilearn#2141) Core devs doc and add @emdupre (nilearn#2151) Add check for vmin, vmax in plot_surf_roi (nilearn#2052) [ENH] Initial visual reports (nilearn#2019) ...

glemaitre added 2 commits April 18, 2019 12:49

EHN: add connectome strength plot

b90eeb8

DOC: add example

7dc05ff

glemaitre added 5 commits April 18, 2019 16:38

TST: add tests

cfd97b5

DOC: found the good subjects

db26e2e

PEP8

c3c283d

DOC: API and user guide

1beafbf

TST: test when passing a matplotlib colormap

ce72196

Merge remote-tracking branch 'origin/master' into is/plot_connectome_…

836c4d9

…strength

kchawla-pi reviewed Aug 2, 2019

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jeromedockes reviewed Aug 2, 2019

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kchawla-pi mentioned this pull request Oct 11, 2019

Release Nilearn 0.6.0 alpha #2164

Merged

kchawla-pi changed the title ~~EHN: add connectome strength plot~~ [WIP] EHN: add connectome strength plot Oct 13, 2019

kchawla-pi changed the title ~~[WIP] EHN: add connectome strength plot~~ [WIP] ENH: add connectome strength plot Oct 13, 2019

use subject 0

56c579b

Added whats_new entry

54edbcb

kchawla-pi merged commit b5726d6 into nilearn:master Oct 14, 2019

kchawla-pi added a commit to kchawla-pi/nilearn that referenced this pull request Oct 14, 2019

Fix Flake8 errors overlooked when merging PR nilearn#2028 (Plot conne…

2472828

…ctome strength)

kchawla-pi mentioned this pull request Oct 14, 2019

[WIP] Removed sub-example due to unfit for lasso dataset - unstable float values #2177

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[WIP] ENH: add connectome strength plot #2028

[WIP] ENH: add connectome strength plot #2028

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		adjacency_matrix = np.nan_to_num(adjacency_matrix)

		adjacency_matrix_shape = adjacency_matrix.shape

[WIP] ENH: add connectome strength plot #2028

[WIP] ENH: add connectome strength plot #2028

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