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ClinicaDL cleaning #517

Merged
merged 53 commits into from
Apr 5, 2024
Merged

ClinicaDL cleaning #517

merged 53 commits into from
Apr 5, 2024

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camillebrianceau
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@pep8speaks
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pep8speaks commented Jan 19, 2024 •
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Hello @camillebrianceau! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2024-04-05 10:44:57 UTC

ncassereau
ncassereau reviewed Feb 1, 2024
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A few lines of commented-out code still remain. Other than that, looks good to me.

clinicadl/train/train_utils.py Outdated Show resolved Hide resolved
clinicadl/utils/maps_manager/maps_manager.py Outdated Show resolved Hide resolved
clinicadl/utils/maps_manager/maps_manager_utils.py Outdated Show resolved Hide resolved
@camillebrianceau camillebrianceau self-assigned this Feb 14, 2024
@camillebrianceau camillebrianceau added this to the v1.6.1 milestone Feb 15, 2024
camillebrianceau and others added 20 commits March 19, 2024 13:45
@camillebrianceau
Add option to save model for each epochs (aramis-lab#507)
ebe6256 
* add option
@dependabot @camillebrianceau
Bump pillow from 10.1.0 to 10.2.0 (aramis-lab#519)
e15f74d 
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)
a4734be 
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)
8256f7e
@camillebrianceau
Solve issue: Running predict with --overwrite delete the results on a…
d293ed8 
…ll the splits (aramis-lab#524)

* issue overwrite

* add documentation for skip leak check (last PR)
@camillebrianceau
Add option for adaptive learning rate (aramis-lab#520)
fa860da 
* first try to add an adaptive learning rate

* add documentation
@camillebrianceau
Remove clinica dependency (aramis-lab#525)
6a18a56 
* remove clinica dependency
* changes after review
@camillebrianceau
Extract tensor from BIDS (aramis-lab#521)
bce2e78 
* add prepare-data-from-bids command
@camillebrianceau
ADD modality in clinicaDL (prepare-data) (aramis-lab#518)
e46e6b3 
* add dwi-dti
@camillebrianceau
Add others callbacks (aramis-lab#497)
e276bed 
* add logger and mlflow and wandb callbacks
@camillebrianceau
hugging face (aramis-lab#468)
8d820e9 
* 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)
d2f42e5 
* Add metrics (R2 score, MCC, MK, lr-, lr+) and non parametric (bootstrap) confidence intervals
@camillebrianceau
resolve issue on predict (aramis-lab#529)
f180f04
@camillebrianceau
Update CHANGELOG for release 1.6.0 (aramis-lab#526)
dc2cc5b 
* Update CHANGELOG.md
@camillebrianceau
pyproject release (aramis-lab#530)
d40a0f8
@thibaultdvx @camillebrianceau
Use setdefault() method instead of looping over default dict
c4e058f 
Fixes aramis-lab#533
@thibaultdvx @camillebrianceau
copyright update (aramis-lab#536)
57d4f63
@thibaultdvx @camillebrianceau
Use parent or parents attributes of Pathlib Path object instead of ch…
ec48a69 
…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
@camillebrianceau
update & rebase
bd7afde
@camillebrianceau
Merge branch 'dev' into cb_clean_code
6177223
thibaultdvx
thibaultdvx reviewed Apr 4, 2024
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Some minor suggestions

clinicadl/generate/generate.py Outdated Show resolved Hide resolved
clinicadl/generate/generate.py Outdated Show resolved Hide resolved
clinicadl/generate/generate.py Outdated Show resolved Hide resolved
clinicadl/generate/generate.py
Gamma range of simulated contrast.
noise_std: List
Stadndard deviation of simulated noise.

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Contrast, gamma and motion parameters are missing.

clinicadl/generate/generate_utils.py
@@ -318,7 +318,7 @@ def generate_shepplogan_phantom(
return img


def mask_processing(mask, percentage, sigma):
def mask_processing(mask, percentage: float, sigma: float):
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mask's type?

clinicadl/utils/maps_manager/maps_manager.py Outdated Show resolved Hide resolved
clinicadl/utils/maps_manager/maps_manager.py Outdated Show resolved Hide resolved
clinicadl/utils/maps_manager/maps_manager.py Outdated Show resolved Hide resolved
clinicadl/utils/maps_manager/maps_manager.py Outdated Show resolved Hide resolved
clinicadl/utils/maps_manager/maps_manager.py Outdated Show resolved Hide resolved
thibaultdvx
thibaultdvx reviewed Apr 4, 2024
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LGTM

camillebrianceau and others added 13 commits April 5, 2024 09:47
@camillebrianceau @thibaultdvx
Update clinicadl/generate/generate.py
9f41d5b 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/generate/generate.py
ea6d130 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/generate/generate.py
5596ce3 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
3185fa9 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
7f39089 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
da60fa6 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
60687ee 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
fd55400 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
6d9b833 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
08d8f05 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
d89d13d 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
c4d26e1 
Co-authored-by: thibaultdvx <[email protected]>
@camillebrianceau @thibaultdvx
Update clinicadl/utils/maps_manager/maps_manager.py
9433381 
Co-authored-by: thibaultdvx <[email protected]>
thibaultdvx
thibaultdvx reviewed Apr 5, 2024
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LGTM

@camillebrianceau camillebrianceau merged commit bdddecf into aramis-lab:dev Apr 5, 2024
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@camillebrianceau camillebrianceau deleted the cb_clean_code branch April 5, 2024 11:04
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