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[ENH]: Add support for on-the-fly template space transformation #299

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synchon merged 47 commits from feat/multi-mni-support into main 2024-04-03 16:02:20 +00:00
Conversation 11 Commits 47 Files changed 34 +2052 -1485
synchon commented 2024-02-02 09:30:16 +00:00 (Migrated from github.com)
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  • description of feature/fix
  • tests added/passed
  • add an entry for the latest changes

This PR adds support for on-the-fly template space transformation in junifer.data.get_parcellation() and junifer.data.get_mask() enabling merging of multi-space parcellation and mask. The target space is set as per the datagrabber's specification and all of the other assets are transformed to it and then applied.

* [x] description of feature/fix * [x] tests added/passed * [x] add an entry for the latest changes This PR adds support for on-the-fly template space transformation in `junifer.data.get_parcellation()` and `junifer.data.get_mask()` enabling merging of multi-space parcellation and mask. The target space is set as per the datagrabber's specification and all of the other assets are transformed to it and then applied.
codecov[bot] commented 2024-02-02 09:31:08 +00:00 (Migrated from github.com)
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (e82603f) to head (78d63d6).

Additional details and impacted files

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@@             Coverage Diff              @@
##             main      #299       +/-   ##
============================================
+ Coverage   88.15%   100.00%   +11.84%     
============================================
  Files         111         1      -110     
  Lines        4820         1     -4819     
  Branches      957         0      -957     
============================================
- Hits         4249         1     -4248     
+ Misses        417         0      -417     
+ Partials      154         0      -154
Flag Coverage Δ
docs 100.00% <ø> (ø)
junifer ?

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see 110 files with indirect coverage changes

## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/299?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report All modified and coverable lines are covered by tests :white_check_mark: > Project coverage is 100.00%. Comparing base [(`e82603f`)](https://app.codecov.io/gh/juaml/junifer/commit/e82603f36f09fcd392a187496cf0c3f5e0e05c06?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) to head [(`78d63d6`)](https://app.codecov.io/gh/juaml/junifer/pull/299?dropdown=coverage&src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml). <details><summary>Additional details and impacted files</summary> [![Impacted file tree graph](https://app.codecov.io/gh/juaml/junifer/pull/299/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://app.codecov.io/gh/juaml/junifer/pull/299?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #299 +/- ## ============================================ + Coverage 88.15% 100.00% +11.84% ============================================ Files 111 1 -110 Lines 4820 1 -4819 Branches 957 0 -957 ============================================ - Hits 4249 1 -4248 + Misses 417 0 -417 + Partials 154 0 -154 ``` | [Flag](https://app.codecov.io/gh/juaml/junifer/pull/299/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/299/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/299/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `?` | | 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. [see 110 files with indirect coverage changes](https://app.codecov.io/gh/juaml/junifer/pull/299/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) </details>
synchon commented 2024-02-06 13:43:15 +00:00 (Migrated from github.com)
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Needs to go after #298

Needs to go after #298
fraimondo (Migrated from github.com) reviewed 2024-02-14 15:06:01 +00:00
github-actions[bot] commented 2024-02-14 15:30:50 +00:00 (Migrated from github.com)
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PR Preview Action v1.4.7
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synchon commented 2024-03-27 10:06:48 +00:00 (Migrated from github.com)
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@fraimondo Can we merge this?

@fraimondo Can we merge this?
fraimondo (Migrated from github.com) reviewed 2024-03-27 15:03:27 +00:00
junifer/data/template_spaces.py
@ -121,15 +124,19 @@ def get_template(
Raises
fraimondo (Migrated from github.com) commented 2024-03-27 15:00:50 +00:00
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What do you mean with "whole". Does it come from any toolbox? I know that usually it is named "brain" mask to reference the GM, WM and CSF masks.

What do you mean with `"whole"`. Does it come from any toolbox? I know that usually it is named "brain" mask to reference the GM, WM and CSF masks.
fraimondo commented 2024-03-27 15:03:40 +00:00 (Migrated from github.com)
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@synchon Just that one question.

@synchon Just that one question.
synchon (Migrated from github.com) reviewed 2024-03-27 15:15:25 +00:00
junifer/data/template_spaces.py
@ -121,15 +124,19 @@ def get_template(
Raises
synchon (Migrated from github.com) commented 2024-03-27 15:15:25 +00:00
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It means "whole brain", but since I couldn't find an alternative for it, I used "whole".

It means "whole brain", but since I couldn't find an alternative for it, I used "whole".
fraimondo (Migrated from github.com) reviewed 2024-03-28 09:24:21 +00:00
junifer/data/template_spaces.py
@ -121,15 +124,19 @@ def get_template(
Raises
fraimondo (Migrated from github.com) commented 2024-03-28 09:24:21 +00:00
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it should be "brain" then. That's the brain mask.

it should be "brain" then. That's the brain mask.
synchon (Migrated from github.com) reviewed 2024-03-28 09:38:13 +00:00
junifer/data/template_spaces.py
@ -121,15 +124,19 @@ def get_template(
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synchon (Migrated from github.com) commented 2024-03-28 09:38:13 +00:00
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Addressed.

Addressed.
fraimondo (Migrated from github.com) approved these changes 2024-04-01 15:36:18 +00:00
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