[ENH]: Refactor Preprocessors to sync data and their paths #408

Merged

synchon merged 5 commits from refactor/preprocessor into main 2024-12-03 10:26:06 +00:00

Conversation 3 Commits 5 Files changed 9 +290 -118

synchon commented 2024-12-02 12:24:40 +00:00 (Migrated from github.com)

Copy link

• description of feature/fix
• tests added/passed
• add an entry for the latest changes

This PR refactors Preprocessors to sync data and their paths so that the results are idempotent. This also adds support for warping masks, if present, in SpaceWarper.

* [x] description of feature/fix * [x] tests added/passed * [x] add an entry for the latest changes This PR refactors Preprocessors to sync data and their paths so that the results are idempotent. This also adds support for warping masks, if present, in `SpaceWarper`.

codecov[bot] commented 2024-12-02 12:31:50 +00:00 (Migrated from github.com)

Copy link

Codecov Report

Attention: Patch coverage is 0% with 62 lines in your changes missing coverage. Please review.

Project coverage is 0.01%. Comparing base (c776b39) to head (3ef304d).
Report is 6 commits behind head on main.

Files with missing lines	Patch %	Lines
junifer/preprocess/warping/_ants_warper.py	0.00%	18 Missing ⚠️
junifer/preprocess/smoothing/_afni_smoothing.py	0.00%	11 Missing ⚠️
.../preprocess/confounds/fmriprep_confound_remover.py	0.00%	10 Missing ⚠️
junifer/preprocess/smoothing/_nilearn_smoothing.py	0.00%	9 Missing ⚠️
junifer/preprocess/warping/_fsl_warper.py	0.00%	9 Missing ⚠️
junifer/preprocess/smoothing/_fsl_smoothing.py	0.00%	4 Missing ⚠️
junifer/preprocess/smoothing/smoothing.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##            main    #408      +/-   ##
========================================
- Coverage   0.01%   0.01%   -0.01%     
========================================
  Files        133     133              
  Lines       5583    5609      +26     
========================================
  Hits           1       1              
- Misses      5582    5608      +26     

Flag	Coverage Δ
docs	100.00% <ø> (ø)
junifer	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
junifer/preprocess/smoothing/smoothing.py	0.00% <0.00%> (ø)
junifer/preprocess/smoothing/_fsl_smoothing.py	0.00% <0.00%> (ø)
junifer/preprocess/smoothing/_nilearn_smoothing.py	0.00% <0.00%> (ø)
junifer/preprocess/warping/_fsl_warper.py	0.00% <0.00%> (ø)
.../preprocess/confounds/fmriprep_confound_remover.py	0.00% <0.00%> (ø)
junifer/preprocess/smoothing/_afni_smoothing.py	0.00% <0.00%> (ø)
junifer/preprocess/warping/_ants_warper.py	0.00% <0.00%> (ø)

## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/408?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report Attention: Patch coverage is `0%` with `62 lines` in your changes missing coverage. Please review. > Project coverage is 0.01%. Comparing base [(`c776b39`)](https://app.codecov.io/gh/juaml/junifer/commit/c776b394c792c96bd4ca5434925c895d7802750a?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) to head [(`3ef304d`)](https://app.codecov.io/gh/juaml/junifer/commit/3ef304d99ae26048efce60bbc1bf278c2d67647c?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml). > Report is 6 commits behind head on main. | [Files with missing lines](https://app.codecov.io/gh/juaml/junifer/pull/408?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Patch % | Lines | |---|---|---| | [junifer/preprocess/warping/\_ants\_warper.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fwarping%2F_ants_warper.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3dhcnBpbmcvX2FudHNfd2FycGVyLnB5) | 0.00% | [18 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [junifer/preprocess/smoothing/\_afni\_smoothing.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fsmoothing%2F_afni_smoothing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3Ntb290aGluZy9fYWZuaV9zbW9vdGhpbmcucHk=) | 0.00% | [11 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [.../preprocess/confounds/fmriprep\_confound\_remover.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fconfounds%2Ffmriprep_confound_remover.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL2NvbmZvdW5kcy9mbXJpcHJlcF9jb25mb3VuZF9yZW1vdmVyLnB5) | 0.00% | [10 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [junifer/preprocess/smoothing/\_nilearn\_smoothing.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fsmoothing%2F_nilearn_smoothing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3Ntb290aGluZy9fbmlsZWFybl9zbW9vdGhpbmcucHk=) | 0.00% | [9 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [junifer/preprocess/warping/\_fsl\_warper.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fwarping%2F_fsl_warper.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3dhcnBpbmcvX2ZzbF93YXJwZXIucHk=) | 0.00% | [9 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [junifer/preprocess/smoothing/\_fsl\_smoothing.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fsmoothing%2F_fsl_smoothing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3Ntb290aGluZy9fZnNsX3Ntb290aGluZy5weQ==) | 0.00% | [4 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [junifer/preprocess/smoothing/smoothing.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fsmoothing%2Fsmoothing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3Ntb290aGluZy9zbW9vdGhpbmcucHk=) | 0.00% | [1 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | <details><summary>Additional details and impacted files</summary> [](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #408 +/- ## ======================================== - Coverage 0.01% 0.01% -0.01% ======================================== Files 133 133 Lines 5583 5609 +26 ======================================== Hits 1 1 - Misses 5582 5608 +26 ``` | [Flag](https://app.codecov.io/gh/juaml/junifer/pull/408/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [docs](https://app.codecov.io/gh/juaml/junifer/pull/408/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `100.00% <ø> (ø)` | | | [junifer](https://app.codecov.io/gh/juaml/junifer/pull/408/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `0.00% <0.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files with missing lines](https://app.codecov.io/gh/juaml/junifer/pull/408?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [junifer/preprocess/smoothing/smoothing.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fsmoothing%2Fsmoothing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3Ntb290aGluZy9zbW9vdGhpbmcucHk=) | `0.00% <0.00%> (ø)` | | | [junifer/preprocess/smoothing/\_fsl\_smoothing.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fsmoothing%2F_fsl_smoothing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3Ntb290aGluZy9fZnNsX3Ntb290aGluZy5weQ==) | `0.00% <0.00%> (ø)` | | | [junifer/preprocess/smoothing/\_nilearn\_smoothing.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fsmoothing%2F_nilearn_smoothing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3Ntb290aGluZy9fbmlsZWFybl9zbW9vdGhpbmcucHk=) | `0.00% <0.00%> (ø)` | | | [junifer/preprocess/warping/\_fsl\_warper.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fwarping%2F_fsl_warper.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3dhcnBpbmcvX2ZzbF93YXJwZXIucHk=) | `0.00% <0.00%> (ø)` | | | [.../preprocess/confounds/fmriprep\_confound\_remover.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fconfounds%2Ffmriprep_confound_remover.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL2NvbmZvdW5kcy9mbXJpcHJlcF9jb25mb3VuZF9yZW1vdmVyLnB5) | `0.00% <0.00%> (ø)` | | | [junifer/preprocess/smoothing/\_afni\_smoothing.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fsmoothing%2F_afni_smoothing.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3Ntb290aGluZy9fYWZuaV9zbW9vdGhpbmcucHk=) | `0.00% <0.00%> (ø)` | | | [junifer/preprocess/warping/\_ants\_warper.py](https://app.codecov.io/gh/juaml/junifer/pull/408?src=pr&el=tree&filepath=junifer%2Fpreprocess%2Fwarping%2F_ants_warper.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9wcmVwcm9jZXNzL3dhcnBpbmcvX2FudHNfd2FycGVyLnB5) | `0.00% <0.00%> (ø)` | | </details>

github-actions[bot] commented 2024-12-02 12:40:56 +00:00 (Migrated from github.com)

Copy link

PR Preview Action v1.4.8
Preview removed because the pull request was closed.
2024-12-03 10:39 UTC

[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.4.8 :---: Preview removed because the pull request was closed. 2024-12-03 10:39 UTC <!-- Sticky Pull Request Commentpr-preview -->

fraimondo (Migrated from github.com) approved these changes 2024-12-03 10:22:01 +00:00

Sign in to join this conversation.

Reviewers

No reviewers

fraimondo

Labels

Clear labels   

CRITICAL

High Priority Issue

  

Stale

  

WIP

Work in progress

  

bug

Something isn't working

  

concept

Design/Implementation concepts

  

coordinate

Issues or pull requests related to coordinates (ROIs)

  

dataset

Issues or pull requests related to datagrabbers or datasets

  

dependencies

Pull requests that update a dependency file

  

documentation

Improvements or additions to documentation

  

duplicate

This issue or pull request already exists

  

enhancement

New feature or request

  

github_actions

Pull requests that update GitHub Actions code

  

good first issue

Good for newcomers

  

help wanted

Extra attention is needed

  

invalid

This doesn't seem right

  

maintenance

Issues or pull requests related to maintenance

  

maps

Issues or pull requests related to maps (probabilistic atlases)

  

marker

Issues or pull requests related to markers

  

mask

Issues or pull requests related to masks

  

on hold

Issue waiting on other issue(s)

  

parcellation

Issues or pull requests related to parcellations (deterministic atlases)

  

preprocess

Issues or pull requests related to preprocessors

  

question

Further information is requested

  

ready

Pull request is ready for review and merge

  

storage

Issues or pull requests related to marker storage or retrieval

  

template-space

Issues or pull requests related to template spaces

  

triage

New issues waiting to be reviewed

  

wontfix

This will not be worked on

No labels

CRITICAL

Stale

WIP

bug

concept

coordinate

dataset

dependencies

documentation

duplicate

enhancement

github_actions

good first issue

help wanted

invalid

maintenance

maps

marker

mask

on hold

parcellation

preprocess

question

ready

storage

template-space

triage

wontfix

Milestone

Clear milestone

No items

No milestone

0.0.6 (alpha 5)

Assignees

Clear assignees

No assignees

1 participant

Notifications

Subscribe

Due date

The due date is invalid or out of range. Please use the format "yyyy-mm-dd".

No due date set.

Dependencies

No dependencies set

Reference

juaml/junifer!408

No description provided.