juaml/junifer
Watch
3
0
Fork
You've already forked junifer
 0
Code Issues 14 Pull requests 2 Packages Activity Actions

[FIX]: Change all probseg_ appearances with VBM_ for consistency #320

Merged
fraimondo merged 6 commits from fix/probseg into main 2024-04-05 13:33:24 +00:00
Conversation 8 Commits 6 Files changed 17 +166 -126
fraimondo commented 2024-04-04 21:29:04 +00:00 (Migrated from github.com)
Copy link
  • fix issue with probseg_
  • description of feature: probseg_ is now replaced by VBM_
  • tests added/passed
  • add an entry for the latest changes
* [x] fix issue with `probseg_` * [x] description of feature: `probseg_` is now replaced by `VBM_` * [x] tests added/passed * [x] add an entry for the latest changes
LeSasse (Migrated from github.com) reviewed 2024-04-04 21:29:04 +00:00
codecov[bot] commented 2024-04-04 21:33:02 +00:00 (Migrated from github.com)
Copy link

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (b0a2a95) to head (1d0bf5e).

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff            @@
##              main      #320   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files            1         1           
  Lines            1         1           
=========================================
  Hits             1         1
Flag Coverage Δ
docs 100.00% <ø> (ø)

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

## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/320?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 [(`b0a2a95`)](https://app.codecov.io/gh/juaml/junifer/commit/b0a2a95f1285f8d46dce3295ab8a3723c9cfa57b?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) to head [(`1d0bf5e`)](https://app.codecov.io/gh/juaml/junifer/pull/320?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/320/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/320?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #320 +/- ## ========================================= Coverage 100.00% 100.00% ========================================= Files 1 1 Lines 1 1 ========================================= Hits 1 1 ``` | [Flag](https://app.codecov.io/gh/juaml/junifer/pull/320/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/320/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)` | | 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. </details>
github-actions[bot] commented 2024-04-04 21:48:40 +00:00 (Migrated from github.com)
Copy link
PR Preview Action v1.4.7
Preview removed because the pull request was closed.
2024-04-05 13:56 UTC
[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.4.7 :---: Preview removed because the pull request was closed. 2024-04-05 13:56 UTC <!-- Sticky Pull Request Commentpr-preview -->
synchon (Migrated from github.com) requested changes 2024-04-05 07:46:47 +00:00
docs/changes/newsfragments/320.change
@ -0,0 +1 @@
Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_
synchon (Migrated from github.com) commented 2024-04-05 07:25:57 +00:00
Copy link

Needs to be double-ticked:

``probseg_``
``VBM_``
Needs to be double-ticked: ``` ``probseg_`` ``VBM_`` ```
docs/changes/newsfragments/320.fix
@ -0,0 +1 @@
Add a validation step on the :func:`.run` function to validate the marker collection by `Fede Raimondo`_
synchon (Migrated from github.com) commented 2024-04-05 07:42:42 +00:00
Copy link

run function can be referred by:

:func:`.run`

?

``run`` function can be referred by: ``` :func:`.run` ``` ?
junifer/datagrabber/utils.py
synchon (Migrated from github.com) commented 2024-04-05 07:46:13 +00:00
Copy link

Are you sure about this that VBM is in fact probseg?

Are you sure about this that `VBM` is in fact `probseg`?
junifer/markers/parcel_aggregation.py
@ -106,3 +115,4 @@
]
def get_output_type(self, input_type: str) -> str:
"""Get output type.
synchon (Migrated from github.com) commented 2024-04-05 07:45:18 +00:00
Copy link

Worth it to include T2w?

Worth it to include ``T2w``?
junifer/markers/sphere_aggregation.py
@ -113,3 +122,4 @@
]
def get_output_type(self, input_type: str) -> str:
"""Get output type.
synchon (Migrated from github.com) commented 2024-04-05 07:45:46 +00:00
Copy link

Worth it to include T2w?

Worth it to include `T2w`?
junifer/preprocess/warping/space_warper.py
@ -102,3 +111,4 @@
]
def get_output_type(self, input_type: str) -> str:
"""Get output type.
synchon (Migrated from github.com) commented 2024-04-05 07:46:36 +00:00
Copy link

Worth it to include T2w?

Worth it to include `T2w`?
fraimondo (Migrated from github.com) reviewed 2024-04-05 09:39:12 +00:00
junifer/datagrabber/utils.py
fraimondo (Migrated from github.com) commented 2024-04-05 09:39:11 +00:00
Copy link

Yes. It is the tissue probability map.

Yes. It is the tissue probability map.
fraimondo (Migrated from github.com) reviewed 2024-04-05 09:40:17 +00:00
junifer/markers/parcel_aggregation.py
@ -106,3 +115,4 @@
]
def get_output_type(self, input_type: str) -> str:
"""Get output type.
fraimondo (Migrated from github.com) commented 2024-04-05 09:40:16 +00:00
Copy link

never header of it, but i'll do it.

never header of it, but i'll do it.
synchon (Migrated from github.com) reviewed 2024-04-05 09:58:46 +00:00
junifer/markers/parcel_aggregation.py
@ -106,3 +115,4 @@
]
def get_output_type(self, input_type: str) -> str:
"""Get output type.
synchon (Migrated from github.com) commented 2024-04-05 09:58:46 +00:00
Copy link

It's the T2 weighted image.

It's the T2 weighted image.
synchon (Migrated from github.com) approved these changes 2024-04-05 10:00:36 +00:00
Sign in to join this conversation.
Reviewers
No reviewers
LeSasse
synchon
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
0.0.4 (alpha 3)
Assignees
Clear assignees
No assignees
1 participant
Notifications
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!320
No description provided.