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Add aomic masks #179

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LeSasse merged 4 commits from add_aomic_masks into main 2023-02-27 11:03:38 +00:00
Conversation 10 Commits 4 Files changed 10 +190 -64
LeSasse commented 2023-01-27 11:22:46 +00:00 (Migrated from github.com)
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  • fix #177
  • description of feature/fix
  • tests added/passed
  • add an entry to the latest changes

This pull request adds the fMRIprep masks for BOLD images in MNI space as well as T1w images in MNI space to the AOMIC datagrabbers.

* [x] fix #177 * [x] description of feature/fix * [x] tests added/passed * [x] add an entry to the [latest changes](../docs/changes/latest.inc) This pull request adds the fMRIprep masks for BOLD images in MNI space as well as T1w images in MNI space to the AOMIC datagrabbers.
fraimondo (Migrated from github.com) reviewed 2023-01-27 11:22:46 +00:00
codecov[bot] commented 2023-01-27 11:23:00 +00:00 (Migrated from github.com)
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Codecov Report

Merging #179 (5352093) into main (38a3fd4) will increase coverage by 0.02%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #179      +/-   ##
==========================================
+ Coverage   93.51%   93.53%   +0.02%     
==========================================
  Files          75       75              
  Lines        2866     2878      +12     
  Branches      515      515              
==========================================
+ Hits         2680     2692      +12     
  Misses        126      126              
  Partials       60       60
Flag Coverage Δ
docs 100.00% <ø> (ø)
junifer 93.52% <100.00%> (+0.02%) ⬆️

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

Impacted Files Coverage Δ
junifer/datagrabber/aomic/id1000.py 100.00% <100.00%> (ø)
junifer/datagrabber/aomic/piop1.py 100.00% <100.00%> (ø)
junifer/datagrabber/aomic/piop2.py 100.00% <100.00%> (ø)
# [Codecov](https://codecov.io/gh/juaml/junifer/pull/179?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report > Merging [#179](https://codecov.io/gh/juaml/junifer/pull/179?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (5352093) into [main](https://codecov.io/gh/juaml/junifer/commit/38a3fd49a5ebba8581b5df0b059d084974b7a6f4?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (38a3fd4) will **increase** coverage by `0.02%`. > The diff coverage is `100.00%`. [![Impacted file tree graph](https://codecov.io/gh/juaml/junifer/pull/179/graphs/tree.svg?width=650&height=150&src=pr&token=5H21JuZXMw&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml)](https://codecov.io/gh/juaml/junifer/pull/179?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #179 +/- ## ========================================== + Coverage 93.51% 93.53% +0.02% ========================================== Files 75 75 Lines 2866 2878 +12 Branches 515 515 ========================================== + Hits 2680 2692 +12 Misses 126 126 Partials 60 60 ``` | Flag | Coverage Δ | | |---|---|---| | docs | `100.00% <ø> (ø)` | | | junifer | `93.52% <100.00%> (+0.02%)` | :arrow_up: | 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. | [Impacted Files](https://codecov.io/gh/juaml/junifer/pull/179?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [junifer/datagrabber/aomic/id1000.py](https://codecov.io/gh/juaml/junifer/pull/179?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhZ3JhYmJlci9hb21pYy9pZDEwMDAucHk=) | `100.00% <100.00%> (ø)` | | | [junifer/datagrabber/aomic/piop1.py](https://codecov.io/gh/juaml/junifer/pull/179?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhZ3JhYmJlci9hb21pYy9waW9wMS5weQ==) | `100.00% <100.00%> (ø)` | | | [junifer/datagrabber/aomic/piop2.py](https://codecov.io/gh/juaml/junifer/pull/179?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhZ3JhYmJlci9hb21pYy9waW9wMi5weQ==) | `100.00% <100.00%> (ø)` | |
LeSasse commented 2023-01-27 13:30:36 +00:00 (Migrated from github.com)
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@synchon any idea why tox tests are failing for some of these?

@synchon any idea why tox tests are failing for some of these?
synchon commented 2023-01-27 13:33:29 +00:00 (Migrated from github.com)
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@synchon any idea why tox tests are failing for some of these?

HCP data fetching issues with datalad. You might wanna rebase on main just to be sure you have the latest HCP test changes.

> @synchon any idea why tox tests are failing for some of these? HCP data fetching issues with datalad. You might wanna rebase on `main` just to be sure you have the latest HCP test changes.
LeSasse commented 2023-01-27 13:36:39 +00:00 (Migrated from github.com)
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@synchon any idea why tox tests are failing for some of these?

HCP data fetching issues with datalad. You might wanna rebase on main just to be sure you have the latest HCP test changes.

thanks, you should make yourself a little Github bot that always replies for people to rebase on main.

> > @synchon any idea why tox tests are failing for some of these? > > HCP data fetching issues with datalad. You might wanna rebase on `main` just to be sure you have the latest HCP test changes. thanks, you should make yourself a little Github bot that always replies for people to rebase on main.
github-actions[bot] commented 2023-01-27 13:41:24 +00:00 (Migrated from github.com)
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PR Preview Action v1.3.0
Preview removed because the pull request was closed.
2023-02-27 11:07 UTC
[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.3.0 :---: Preview removed because the pull request was closed. 2023-02-27 11:07 UTC <!-- Sticky Pull Request Commentpr-preview -->
synchon commented 2023-01-27 13:41:45 +00:00 (Migrated from github.com)
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@synchon any idea why tox tests are failing for some of these?

HCP data fetching issues with datalad. You might wanna rebase on main just to be sure you have the latest HCP test changes.

thanks, you should make yourself a little Github bot that always replies for people to rebase on main.

lol, yes totally, weekend to-do.

> > > @synchon any idea why tox tests are failing for some of these? > > > > > > HCP data fetching issues with datalad. You might wanna rebase on `main` just to be sure you have the latest HCP test changes. > > thanks, you should make yourself a little Github bot that always replies for people to rebase on main. lol, yes totally, weekend to-do.
synchon (Migrated from github.com) requested changes 2023-01-30 10:45:23 +00:00
docs/changes/latest.inc
@ -40,6 +40,9 @@ Enhancements
- Add support for nilearn computed masks (``compute_epi_mask``, ``compute_brain_mask``, ``compute_background_mask``,
synchon (Migrated from github.com) commented 2023-01-30 10:43:28 +00:00
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Just to follow the naming convention: Add fMRIPrep ...

Just to follow the naming convention: Add fMRIPrep ...
synchon (Migrated from github.com) commented 2023-01-30 10:43:30 +00:00
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. at the end.

`.` at the end.
LeSasse (Migrated from github.com) reviewed 2023-01-30 10:48:56 +00:00
docs/changes/latest.inc
@ -40,6 +40,9 @@ Enhancements
- Add support for nilearn computed masks (``compute_epi_mask``, ``compute_brain_mask``, ``compute_background_mask``,
LeSasse (Migrated from github.com) commented 2023-01-30 10:48:55 +00:00
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oops yeah always get that wrong

oops yeah always get that wrong
synchon (Migrated from github.com) approved these changes 2023-01-30 12:19:28 +00:00
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