New caps dataset #562
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New caps dataset #562
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Bumps [sqlparse](https://github.com/andialbrecht/sqlparse) from 0.4.4 to 0.5.0. - [Changelog](https://github.com/andialbrecht/sqlparse/blob/master/CHANGELOG) - [Commits](andialbrecht/sqlparse@0.4.4...0.5.0) --- updated-dependencies: - dependency-name: sqlparse dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Hello @HuguesRoy! 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 2024-05-15 09:52:28 UTC |
thibaultdvx
reviewed
Apr 22, 2024
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Thanks a lot @HuguesRoy! Could you please try to write the docstrings with the template I gave you?
clinicadl/utils/caps_dataset/caps_dataset_refactoring/caps_dataset.py
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Thanks @HuguesRoy !
I had a quick look and made some suggestions on caps_dataset.py, mainly on type hints.
Let me know if some things are not clear.
| def elem_index(self): | ||
| pass | ||
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| def label_fn(self, target: Union[str, float, int]) -> Union[float, int]: |
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It seems like the method can return None:
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| def label_fn(self, target: Union[str, float, int]) -> Union[float, int]: | |
| def label_fn(self, target: Union[str, float, int]) -> Optional[Union[float, int]]: |
| label: value of the label usable in criterion. | ||
| """ | ||
| domain_code = {"t1": 0, "flair": 1} | ||
| return domain_code[str(target)] |
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Can really target be a float, an integer, or a string ? From the dict above, it seems it can only take two values: "t1" or "flair".
| else: | ||
| return self.label_code[str(target)] | ||
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| def domain_fn(self, target: Union[str, float, int]) -> Union[float, int]: |
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Might be missing things, but it seems it can only return integers, right ?
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| def domain_fn(self, target: Union[str, float, int]) -> Union[float, int]: | |
| def domain_fn(self, target: Union[str, float, int]) -> int: |
| Args: | ||
| idx: row number of the meta-data contained in self.df | ||
| Returns: | ||
| dictionary with following items: |
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If all subclasses return dictionaries with the same structure, it might be valuable to build a custom type for this instead of relying on dictionaries.
@abc.abstractmethod
def __getitem__(self, idx: int) -> Sample:
....
@dataclass
class Sample:
image: torch.Tensor
label: int | float
participant_id: str
...WDYT?
clinicadl/utils/caps_dataset/caps_dataset_refactoring/caps_dataset.py
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| ################################## | ||
| # Transformations |
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Could be worth putting these in a separate module as this file is already pretty large. WDYT ?
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| ################################ | ||
| # TSV files loaders |
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Same kind of comment here
| ################################ | ||
| # TSV files loaders | ||
| ################################ | ||
| def load_data_test(test_path: Path, diagnoses_list, baseline=True, multi_cohort=False): |
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| def load_data_test(test_path: Path, diagnoses_list, baseline=True, multi_cohort=False): | |
| def load_data_test(test_path: Path, diagnoses_list: list[str], baseline: bool = True, multi_cohort: bool = False) -> pd.DataFrame: |
| raise ClinicaDLArgumentError( | ||
| "If multi_cohort is given, the TSV_DIRECTORY argument should be a path to a TSV file." | ||
| ) | ||
| else: |
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You don't need to have an else statement here since you raise in the if.
This would spare one level of indentation for the following code block.
| return test_df | ||
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| def load_data_test_single(test_path: Path, diagnoses_list, baseline=True): |
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| def load_data_test_single(test_path: Path, diagnoses_list, baseline=True): | |
| def load_data_test_single(test_path: Path, diagnoses_list: list[str], baseline: bool = True) -> pd.DataFrame: |
…aset.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com>
…aset.py Co-authored-by: thibaultdvx <154365476+thibaultdvx@users.noreply.github.com>
…aset.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com>
Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.66.1 to 4.66.3. - [Release notes](https://github.com/tqdm/tqdm/releases) - [Commits](tqdm/tqdm@v4.66.1...v4.66.3) --- updated-dependencies: - dependency-name: tqdm dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.0.1 to 3.0.3. - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](pallets/werkzeug@3.0.1...3.0.3) --- updated-dependencies: - dependency-name: werkzeug dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](pallets/jinja@3.1.3...3.1.4) --- updated-dependencies: - dependency-name: jinja2 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
broken path solved
Bumps [mlflow](https://github.com/mlflow/mlflow) from 2.10.1 to 2.12.1. - [Release notes](https://github.com/mlflow/mlflow/releases) - [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md) - [Commits](mlflow/mlflow@v2.10.1...v2.12.1) --- updated-dependencies: - dependency-name: mlflow dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [gunicorn](https://github.com/benoitc/gunicorn) from 21.2.0 to 22.0.0. - [Release notes](https://github.com/benoitc/gunicorn/releases) - [Commits](benoitc/gunicorn@21.2.0...22.0.0) --- updated-dependencies: - dependency-name: gunicorn dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
updated-dependencies: - dependency-name: requests dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* try a simple workflow first * try running on new ubuntu VM * fixes * bump poetry version to 1.8.3 * try removing caching.. * add workflow for testing tsv tools
* try skipping test_tsvtools when PR is in draft mode * trigger CI * add a cpu tag to avoid running cpu tests on gpu machines * run also on refactoring branch
* add test workflow on GPU for train * fix conda path * fix conflicting workdir * only run on non-draft PRs * run also on refactoring branch
* add workflow for testing interpretation task * add workflow for testing random search task * add workflow for testing resume task * add workflow for testing transfer learning task * trigger CI * trigger CI
* add cleaning step to test_tsvtools pipeline * add test_generate pipeline * add test_predict pipeline * add test_prepare_data pipeline * add test_quality_checks pipeline * add refactoring target branch, cpu tag, and draft PR filter * trigger CI
…nt in README (aramis-lab#600) * update python version used for creating conda env in README * investigate * fix
* add no-gpu and adapt-base-dir flag
* Update quality_check.py
* add FileNotFound error in tree
* run unit tests on refactoring * run linter on refactoring
* add ready_for_review event
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.18 to 1.26.19. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/1.26.19/CHANGES.rst) - [Commits](urllib3/urllib3@1.26.18...1.26.19) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [certifi](https://github.com/certifi/python-certifi) from 2024.2.2 to 2024.7.4. - [Commits](certifi/python-certifi@2024.02.02...2024.07.04) --- updated-dependencies: - dependency-name: certifi dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [zipp](https://github.com/jaraco/zipp) from 3.17.0 to 3.19.1. - [Release notes](https://github.com/jaraco/zipp/releases) - [Changelog](https://github.com/jaraco/zipp/blob/main/NEWS.rst) - [Commits](jaraco/zipp@v3.17.0...v3.19.1) --- updated-dependencies: - dependency-name: zipp dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [setuptools](https://github.com/pypa/setuptools) from 69.0.3 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.0.3...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [sentry-sdk](https://github.com/getsentry/sentry-python) from 1.40.1 to 2.8.0. - [Release notes](https://github.com/getsentry/sentry-python/releases) - [Changelog](https://github.com/getsentry/sentry-python/blob/master/CHANGELOG.md) - [Commits](getsentry/sentry-python@1.40.1...2.8.0) --- updated-dependencies: - dependency-name: sentry-sdk dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Creation of a new folder caps_dataset_refactoring containing two .py files:
caps_dataset.py: low level class caps-dataset (work only for Image datasets)concat_dataset.py: classes for concatenation, stacking and creation of dataset from control fileFor the moment, these files are not connected to the rest of
clinicadl.