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Add option to use longitudinal data for validation #483

Merged
merged 54 commits into from
Apr 3, 2024
Merged

Add option to use longitudinal data for validation #483

merged 54 commits into from
Apr 3, 2024

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camillebrianceau
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@camillebrianceau camillebrianceau commented Sep 28, 2023 •
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PR to solve the issue mentioned in the Google group (https://groups.google.com/g/clinica-user/c/YA685EhIPIM).

I added an option valid_longitudinal to allow clinicadl to validate longitudinal data and not only on baseline data.

CI data: https://github.com/aramis-lab/clinicadl_data_ci/pull/37

@camillebrianceau camillebrianceau marked this pull request as draft September 28, 2023 20:51
@camillebrianceau camillebrianceau marked this pull request as ready for review October 25, 2023 08:54
@camillebrianceau camillebrianceau added this to the v1.6.1 milestone Feb 15, 2024
@camillebrianceau camillebrianceau self-assigned this Mar 13, 2024
camillebrianceau and others added 24 commits March 21, 2024 11:37
@camillebrianceau
default to false
beb6354
@dependabot @camillebrianceau
Bump urllib3 from 2.0.5 to 2.0.6 (aramis-lab#486)
55e2128 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.5 to 2.0.6.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](urllib3/urllib3@v2.0.5...2.0.6)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@sophieloiz @camillebrianceau
Sl dart ssda (aramis-lab#485)
759baf2 
* Add proposed SSDA method for MICCAI
@camillebrianceau
Prepare next release (1.5.1) (aramis-lab#484)
dd5a9ba 
* prepare next release (1.5.1)
@dependabot @camillebrianceau
MNT: Bump gitpython from 3.1.36 to 3.1.37 (aramis-lab#490)
459ea1b 
Bumps [gitpython](https://github.com/gitpython-developers/GitPython) from 3.1.36 to 3.1.37.
- [Release notes](https://github.com/gitpython-developers/GitPython/releases)
- [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES)
- [Commits](gitpython-developers/GitPython@3.1.36...3.1.37)

---
updated-dependencies:
- dependency-name: gitpython
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot @camillebrianceau
Bump urllib3 from 2.0.6 to 2.0.7 (aramis-lab#495)
442aad2 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.6 to 2.0.7.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](urllib3/urllib3@2.0.6...2.0.7)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@camillebrianceau
solve issue aramis-lab#491 (aramis-lab#492)
564a601
@dependabot @camillebrianceau
Bump werkzeug from 2.3.7 to 3.0.1 (aramis-lab#496)
454c0cc 
Bumps [werkzeug](https://github.com/pallets/werkzeug) from 2.3.7 to 3.0.1.
- [Release notes](https://github.com/pallets/werkzeug/releases)
- [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst)
- [Commits](pallets/werkzeug@2.3.7...3.0.1)

---
updated-dependencies:
- dependency-name: werkzeug
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@camillebrianceau
fix adapt bug (aramis-lab#498)
1445ef0
@camillebrianceau
Update index.md
9c95d4c
@dependabot @camillebrianceau
Bump mlflow from 2.7.1 to 2.8.1 (aramis-lab#500)
ea8bdfb 
Bumps [mlflow](https://github.com/mlflow/mlflow) from 2.7.1 to 2.8.1.
- [Release notes](https://github.com/mlflow/mlflow/releases)
- [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md)
- [Commits](mlflow/mlflow@v2.7.1...v2.8.1)

---
updated-dependencies:
- dependency-name: mlflow
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot @camillebrianceau
Bump pyarrow from 13.0.0 to 14.0.1 (aramis-lab#501)
2e26afa 
Bumps [pyarrow](https://github.com/apache/arrow) from 13.0.0 to 14.0.1.
- [Commits](apache/arrow@go/v13.0.0...go/v14.0.1)

---
updated-dependencies:
- dependency-name: pyarrow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@NicolasGensollen @camillebrianceau
fix typos (aramis-lab#503)
52eba51
@camillebrianceau
Update Generate.md
b37775f
@dependabot @camillebrianceau
Bump actions/setup-python from 4 to 5
669a7a8 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
@camillebrianceau
try to update to python 3.11.x (aramis-lab#504)
166cc68 
* update to python 3.11.x and torch 2.1
@dependabot @camillebrianceau
Bump mlflow from 2.8.1 to 2.9.2 (aramis-lab#511)
4681c20 
Bumps [mlflow](https://github.com/mlflow/mlflow) from 2.8.1 to 2.9.2.
- [Release notes](https://github.com/mlflow/mlflow/releases)
- [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md)
- [Commits](mlflow/mlflow@v2.8.1...v2.9.2)

---
updated-dependencies:
- dependency-name: mlflow
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: camillebrianceau <[email protected]>
@camillebrianceau
Add missing model methods (aramis-lab#499)
60b5ee7 
* add models methods
@camillebrianceau
minor changes (aramis-lab#505)
30e8e1b 
* bug generate trivial

* print only one time logger
@camillebrianceau
Add option to save model for each epochs (aramis-lab#507)
6c77ca1 
* add option
@dependabot @camillebrianceau
Bump pillow from 10.1.0 to 10.2.0 (aramis-lab#519)
6078670 
Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.1.0 to 10.2.0.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@10.1.0...10.2.0)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@dependabot @camillebrianceau
Bump jinja2 from 3.1.2 to 3.1.3 (aramis-lab#514)
ab9c44f 
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.2 to 3.1.3.
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@3.1.2...3.1.3)

---
updated-dependencies:
- dependency-name: jinja2
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
@camillebrianceau
add option to skip data leakage check (aramis-lab#523)
1a9bf59
@camillebrianceau
Solve issue: Running predict with --overwrite delete the results on a…
cd7c4e2 
…ll the splits (aramis-lab#524)

* issue overwrite

* add documentation for skip leak check (last PR)
camillebrianceau and others added 21 commits March 21, 2024 11:43
@camillebrianceau
ADD modality in clinicaDL (prepare-data) (aramis-lab#518)
d2732ff 
* add dwi-dti
@camillebrianceau
Add others callbacks (aramis-lab#497)
36c3512 
* add logger and mlflow and wandb callbacks
@camillebrianceau
hugging face (aramis-lab#468)
e5e380f 
* adapt to clinicadl hugging face organization

* finish skip leak check to use clinicadl with downloaded masp
@camillebrianceau
test sofiene ci pull request copy (aramis-lab#528)
08e521f 
* Add metrics (R2 score, MCC, MK, lr-, lr+) and non parametric (bootstrap) confidence intervals
@camillebrianceau
resolve issue on predict (aramis-lab#529)
93f10b6
@camillebrianceau
Update CHANGELOG for release 1.6.0 (aramis-lab#526)
af9ee60 
* Update CHANGELOG.md
@camillebrianceau
pyproject release (aramis-lab#530)
674333b
@thibaultdvx @camillebrianceau
Use setdefault() method instead of looping over default dict
89a7150 
Fixes aramis-lab#533
@thibaultdvx @camillebrianceau
copyright update (aramis-lab#536)
4e8daa3
@thibaultdvx @camillebrianceau
Use parent or parents attributes of Pathlib Path object instead of ch…
c455f62 
…aining ".." strings (aramis-lab#535)

* Use parent or parents attributes of Pathlib Path object instead of chaining ".." strings

* Use parent or parents attributes of Pathlib Path object instead of chaining ".." strings

* remove redundant cast
@NicolasGensollen @camillebrianceau
[INFRA] Use python 3.11 in the readthedocs workflow (aramis-lab#541)
b082139 
* use python 3.11 in readthedocs workflow
* try adding poetry back but version 1.7
@camillebrianceau
Solve CI pb in random search tests (aramis-lab#540)
0da4106 
* solve ci pb in random search
@NicolasGensollen @camillebrianceau
update isort (aramis-lab#542)
3bbd719
@thibaultdvx @camillebrianceau
fix typeerror issue and improve type hints
063f060
@thibaultdvx @camillebrianceau
update type hint
29b1d8b
@thibaultdvx @NicolasGensollen @camillebrianceau
replace with f-string
1be247d 
Co-authored-by: Gensollen <[email protected]>
@NicolasGensollen @camillebrianceau
[INFRA] Use ruff instead of black and use codespell (aramis-lab#546)
91f68f7 
* configure pre-commit hook

* update pyproject.toml

* update ci lint pipeline

* fix typos

* fix more typos

* fix remaining typos

* skip codespell on toml clinicadl config as there is a typo in the file format specifications

* fix formatting issues

* format again
@camillebrianceau
rebase poetry
c58a02b
@camillebrianceau
Merge branch 'dev' into cb_add_validation_option
a12bcfb
@camillebrianceau
merge options
2dfa57d
@camillebrianceau
Merge branch 'dev' into cb_add_validation_option
a101189
thibaultdvx
thibaultdvx reviewed Apr 3, 2024
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@camillebrianceau, LGTM regarding the code (aside from two minor typos). I trust you on the functional content!

clinicadl/utils/cli_param/option.py Outdated Show resolved Hide resolved
clinicadl/utils/cli_param/train_option.py Outdated Show resolved Hide resolved
@camillebrianceau camillebrianceau merged commit 6bfaccd into aramis-lab:dev Apr 3, 2024
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@camillebrianceau camillebrianceau deleted the cb_add_validation_option branch April 3, 2024 15:19
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