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✨ Correlation heatmaps #1

Merged
merged 84 commits into from
May 26, 2020
Merged

✨ Correlation heatmaps #1

merged 84 commits into from
May 26, 2020

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shnizzedy
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  • heatmaps.py includes functions to generate, annotate, save, and display heatmaps from correlation matrices
  • correlation_matrix.py to create correlation matrices, filepath matrices, and to run heatmap generation given 2 output directories
  • configs
    • defaults.py lists the defined feature keys and maps them to how they're named in C-PAC and fmriprep
    • subjects.py includes helper functions to generate appropriate subject lists for different steps in the process for different software
  • set up Circle CI
  • updated a few lines from Python 2 syntax to Python 3
  • added two --help outputs to README

anibalsolon and others added 30 commits April 16, 2019 14:51
@anibalsolon
move stuff around
aa44ae2
@sgiavasis
Updated the CircleCI pipeline config.
4406132
@XinhuiLi
Update pipe-test_ci.yml
d3bcd55
@XinhuiLi
Update pipe-test_ci.yml
7f93261
@HechengJin0
template based segmentation fix typo
e09cfed
@HechengJin0
fix typo segmentation
fd4054e
@sgiavasis
Changed "ndmg_mode" to "output_tree" key in configs.
e11c03e
@HechengJin0
Merge branch 'master' of github.com:FCP-INDI/C-PAC into feature/erosi…
1ad26c1 
…on_mm
@sgiavasis
Merge branch 'develop' into feature/preconfigs
be5036a
@XinhuiLi
update configs
f91c7af
@shnizzedy @XinhuiLi @HechengJin0
📰 start w/ regressors
3d7efcc 
Co-authored-by: Xinhui Li <sucyli1017@gmail.com>
Co-authored-by: Hecheng Jin <47699110+HechengJin0@users.noreply.github.com>
@shnizzedy
🚧 💛 🔬 📰 ≟ on Circle CI
0bddf1b
@shnizzedy
🚜 Port function definitions from notebook to script
c53d76e
@shnizzedy
🚜 Port function definitions from notebook to script
39e74ef
@shnizzedy
🚧 💛 persist_to_workspace
b61b9c8
@shnizzedy
🚜 Port remaining functions from notebook
42b4fa3
@shnizzedy
💚 🐍 PEP 263
6c18f13 
Declare encoding to pass in Python2 until #1114 is resolved
@shnizzedy
🚜 Finish abstracting from notebook
ad6e5d0
@shnizzedy
💚 Fix imports
32a8b56
@shnizzedy
🧙 Add autoreload magics
07509ee
@shnizzedy
✨ Handle lists of strings and no session specifications
d194862
@shnizzedy
✨ generate_heatmaps function + heatmaps CLI
cc5ded5 
Ref #1211
@shnizzedy
🚧 Begin CPAC config
95a636f
@shnizzedy
🚧
7a983a8
@shnizzedy
🚧
b2a3868
@shnizzedy
📰 Benchmarks index
1465618
@shnizzedy
🚧 Prep to run current branch if not already run
0f5f66f
@shnizzedy
🤝 Merge branch 'feature/auto-heatmaps' of github.com:FCP-INDI/C-PAC i…
3f27032 
…nto feature/auto-heatmaps
@shnizzedy
🚧 WIP automatic correlation heatmaps
e54c8fa
@shnizzedy
🚧
b20b65f
shnizzedy and others added 12 commits March 31, 2020 16:19
@shnizzedy
🔇
08ed714
@shnizzedy
💄 Print filepaths without given directories
88d25e2 
Resolves https://github.com/shnizzedy/CPAC_regtest_pack/blob/3d484bd1e270013266a2aceb5f0a31fb043146d7/correlation_matrix.py#L144
@shnizzedy
🚑 Check path for Nonetype
c9671a0
@shnizzedy
🎨 '/' inside "run_path"
d5bb536
@shnizzedy
💄 Wrap long paths
f7d9c70
@shnizzedy
🔈 "Not found"
5448b63
@shnizzedy
🚑 Handle a variety of subject ID formats (#2)
0719989
@shnizzedy
⏩ Merge remote-tracking branch 'steve/master' into feat/heatmaps
88d1598 
* steve/master:
  Updated the CURRENT-BRANCH run scripts.
  Fixed output directory name in fmriprep-options preconfig runner script.
  Updated the run scripts to use the new regression test data config, and added scripts for ndmg and fmriprep-options preconfigs.
  Add new regression test data configuration.
@shnizzedy
⚡ Logs aren't subjects
13d0c46
@shnizzedy
🚑 Handle splitting sessions & users separately for separate softwares
be37011 
Ref #3
@shnizzedy
💄 Don't format/wrap if not plaintext
0124b49
@shnizzedy
⚡ Logs aren't subjects
6c2f33b
shnizzedy and others added 4 commits April 13, 2020 11:24
@shnizzedy
⏪ Revert 3cf1caf
41e6e4f
@shnizzedy
🔨 path → paths
3c88f63 
+ trim from head for off-by-n
@shnizzedy
💄 bbox_inches="tight"
cae19f0
@shnizzedy
👷 Debug heatmaps (#8)
479739c 
* Allow `path` property of `Subject_Session_Feature` instances to hold list of path strings instead of restricting to a single path per run
* Match lengths of mismatched-length vectors by trimming head of longer vector
* Trim whitespace around saved heatmap figures
@sgiavasis
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Once again, great stuff! Pulling this in, for preparation of the next phase of the testing infrastructure.

@sgiavasis sgiavasis merged commit b979fa7 into sgiavasis:master May 26, 2020
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5 participants
@shnizzedy @sgiavasis @anibalsolon @XinhuiLi @HechengJin0