[MAINT]: Repository maintenance #441
87 changed files with 583 additions and 1403 deletions
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@ -17,24 +17,22 @@ repos:
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- id: trailing-whitespace
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args: [--markdown-linebreak-ext=md]
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- repo: https://github.com/abravalheri/validate-pyproject
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rev: v0.23
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rev: v0.24.1
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hooks:
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- id: validate-pyproject
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 24.10.0
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hooks:
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- id: black
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exclude: ^(docs/|examples/|tools/)
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args: [--check]
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.9.3
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rev: v0.11.2
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hooks:
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- id: ruff
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types_or: [python, jupyter]
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exclude: ^(__init__.py)
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args: [--output-format, grouped, --show-fixes]
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- id: ruff-format
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types_or: [python, jupyter]
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exclude: ^(__init__.py)
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args: [--check, --diff]
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- repo: https://github.com/codespell-project/codespell
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rev: v2.4.0
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rev: v2.4.1
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hooks:
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- id: codespell
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exclude: ^(.github/|docs/)
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@ -47,10 +45,3 @@ repos:
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- id: rst-backticks
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- id: rst-directive-colons
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- id: rst-inline-touching-normal
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- repo: https://github.com/adamchainz/blacken-docs
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rev: "1.19.1"
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hooks:
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- id: blacken-docs
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additional_dependencies:
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- black==24.4.2
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args: [-l 79]
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@ -8,7 +8,6 @@
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[](https://anaconda.org/conda-forge/junifer)
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[](https://github.com/psf/black)
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[](https://github.com/charliermarsh/ruff)
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[](https://github.com/pre-commit/pre-commit)
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[](https://doi.org/10.5281/zenodo.8176570)
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@ -1,33 +1,45 @@
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name: junifer-dev
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channels:
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- conda-forge
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- defaults
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dependencies:
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- python>=3.10,<=3.11
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- click=8.1.*
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- numpy>=1.22,<1.27
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- pandas>=1.4.0,<2.2
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- nibabel>=3.2.0,<5.2
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- nilearn>=0.9.0,<=0.10.1
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- sqlalchemy>=1.4.27,<= 2.0.21
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- ruamel.yaml=0.17.*
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- h5py>=3.8,<=3.9
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- seaborn>=0.11,<=0.13
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- sphinx>=5.3,<7.3
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- sphinx-gallery>=0.11.0,<0.15.0
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- furo>=2022.9.29,<2023.10.0
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- numpydoc>=1.5.0,<1.6
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- python>=3.10,<=3.13
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- click>=8.1.3,<8.2
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- numpy>=1.26.0,<2.0.0
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- scipy>=1.10.0,<=1.15.0
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- pandas>=2.0.0,<2.3.0
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- nibabel>=5.2.0,<5.4.0
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- nilearn>=0.10.3,<=0.10.4
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- sqlalchemy>=2.0.25,<=2.1.0
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- ruamel.yaml>=0.17,<0.19
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- h5py>=3.10
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- tqdm>=4.66.1,<4.67.0
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- templateflow>=23.0.0
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- lapy>=1.0.0,<2.0.0
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- lazy_loader==0.4
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- importlib_metadata
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- looseversion==1.3.0
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- bctpy==0.6.0
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- neurokit2>=0.1.7
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- seaborn>=0.13.0,<0.14.0
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- sphinx>=7.3.0,<8.1.0
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- sphinx-gallery>=0.17.0,<0.18.0
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- furo>=2024.4.27,<2024.9.0
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- numpydoc>=1.6.0,<1.9.0
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- sphinx-copybutton>=0.5.1,<0.5.3
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- towncrier>=22.12.0,<23.7
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- towncrier>=23.10.0,<24.7.0
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- sphinxcontrib-mermaid>=0.8.1,<0.10
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- sphinxcontrib-towncrier==0.4.0a0
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- setuptools-scm>=8
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- tox
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- pre-commit
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- ruff>=0.1.0
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- ipykernel
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- pytest-cov
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- pytest
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- black
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- ruff
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- codespell
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- tomli
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- pip
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- pip:
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- datalad>=0.15.4,<0.20
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- julearn==0.3.0
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- datalad>=1.0.0,<1.2.0
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- julearn==0.3.3
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- junifer_data==1.3.0
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1
docs/changes/newsfragments/441.misc
Normal file
1
docs/changes/newsfragments/441.misc
Normal file
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@ -0,0 +1 @@
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Regular repository maintenance by updating ``.pre-commit-config.yaml``, replacing ``black`` with ``ruff-format`` and updating tool configs by `Synchon Mandal`_
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@ -5,7 +5,6 @@
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# Synchon Mandal <s.mandal@fz-juelich.de>
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# License: AGPL
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from ..pipeline import PipelineComponentRegistry
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from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
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@ -294,8 +294,7 @@ def queue(
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valid_kind = ["HTCondor", "GNUParallelLocal"]
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if kind not in valid_kind:
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raise_error(
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f"Invalid value for `kind`: {kind}, "
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f"must be one of {valid_kind}"
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f"Invalid value for `kind`: {kind}, must be one of {valid_kind}"
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)
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# Create a folder within the CWD to store the job files / config
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@ -218,8 +218,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
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# Copy executable if not local
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if hasattr(self, "_exec_path"):
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logger.info(
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f"Copying {self._executable} to "
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f"{self._exec_path.resolve()!s}"
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f"Copying {self._executable} to {self._exec_path.resolve()!s}"
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)
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shutil.copy(
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src=Path(__file__).parent.parent / "res" / self._executable,
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@ -235,15 +234,14 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
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self._elements_file_path.write_text(textwrap.dedent(self.elements()))
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# Create pre run
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logger.info(
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f"Writing {self._pre_run_path.name} to "
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f"{self._job_dir.resolve()!s}"
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f"Writing {self._pre_run_path.name} to {self._job_dir.resolve()!s}"
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)
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self._pre_run_path.touch()
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self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
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make_executable(self._pre_run_path)
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# Create run
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logger.info(
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f"Writing {self._run_path.name} to " f"{self._job_dir.resolve()!s}"
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f"Writing {self._run_path.name} to {self._job_dir.resolve()!s}"
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)
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self._run_path.touch()
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self._run_path.write_text(textwrap.dedent(self.run()))
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@ -258,8 +256,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
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make_executable(self._pre_collect_path)
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# Create collect
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logger.info(
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f"Writing {self._collect_path.name} to "
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f"{self._job_dir.resolve()!s}"
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f"Writing {self._collect_path.name} to {self._job_dir.resolve()!s}"
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)
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self._collect_path.touch()
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self._collect_path.write_text(textwrap.dedent(self.collect()))
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@ -264,9 +264,7 @@ class HTCondorAdapter(QueueContextAdapter):
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)
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junifer_collect_args = (
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"collect "
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f"{self._yaml_config_path.resolve()!s} "
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f"{verbose_args}"
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f"collect {self._yaml_config_path.resolve()!s} {verbose_args}"
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)
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log_dir_prefix = f"{self._log_dir.resolve()!s}/junifer_collect"
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fixed = (
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@ -316,7 +314,7 @@ class HTCondorAdapter(QueueContextAdapter):
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"$DAG_STATUS\n"
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)
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elif self._collect == "on_success_only":
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var += f"JOB collect {self._submit_collect_path}\n" "PARENT "
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var += f"JOB collect {self._submit_collect_path}\nPARENT "
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for idx, _ in enumerate(self._elements):
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var += f"run{idx} "
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var += "CHILD collect\n"
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@ -328,14 +326,13 @@ class HTCondorAdapter(QueueContextAdapter):
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logger.info("Creating HTCondor job")
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# Create logs
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logger.info(
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f"Creating logs directory under " f"{self._job_dir.resolve()!s}"
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f"Creating logs directory under {self._job_dir.resolve()!s}"
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)
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self._log_dir.mkdir(exist_ok=True, parents=True)
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# Copy executable if not local
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if hasattr(self, "_exec_path"):
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logger.info(
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f"Copying {self._executable} to "
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f"{self._exec_path.resolve()!s}"
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f"Copying {self._executable} to {self._exec_path.resolve()!s}"
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)
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shutil.copy(
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src=Path(__file__).parent.parent / "res" / self._executable,
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@ -344,8 +341,7 @@ class HTCondorAdapter(QueueContextAdapter):
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make_executable(self._exec_path)
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# Create pre run
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logger.info(
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f"Writing {self._pre_run_path.name} to "
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f"{self._job_dir.resolve()!s}"
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f"Writing {self._pre_run_path.name} to {self._job_dir.resolve()!s}"
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)
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self._pre_run_path.touch()
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self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
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@ -374,7 +370,7 @@ class HTCondorAdapter(QueueContextAdapter):
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self._submit_collect_path.write_text(textwrap.dedent(self.collect()))
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# Create DAG
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logger.debug(
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f"Writing {self._dag_path.name} to " f"{self._job_dir.resolve()!s}"
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f"Writing {self._dag_path.name} to {self._job_dir.resolve()!s}"
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)
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self._dag_path.touch()
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self._dag_path.write_text(textwrap.dedent(self.dag()))
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@ -18,6 +18,23 @@ def test_parse_yaml_failure() -> None:
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parse_yaml("foo.yaml")
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def test_parse_yaml_empty_elements_failure(tmp_path: Path) -> None:
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"""Test YAML parsing with empty elements failure.
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Parameters
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----------
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tmp_path : pathlib.Path
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The path to the test directory.
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"""
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# Write test file
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fname = tmp_path / "test_parse_yaml_empty_elements_failure.yaml"
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fname.write_text("elements:")
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# Check test file
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with pytest.raises(ValueError, match="elements key was defined"):
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parse_yaml(fname)
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def test_parse_yaml_success(tmp_path: Path) -> None:
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"""Test YAML parsing success.
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@ -159,6 +176,41 @@ def test_parse_yaml_absolute_path(tmp_path: Path) -> None:
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parse_yaml(yaml_fname)
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def test_parse_yaml_multi_module_deps(tmp_path: Path) -> None:
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"""Test YAML parsing with multi-module import with deps.
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Parameters
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----------
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tmp_path : pathlib.Path
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The path to the test directory.
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"""
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t_tmp_path = tmp_path / "test_with_multi_module"
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# Write .py to include
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py_path = t_tmp_path / "external"
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py_path.mkdir(exist_ok=True, parents=True)
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py_fname_1 = py_path / "first.py"
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py_fname_1.write_text(
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"import numpy as np\nfrom second import hej\n"
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"def junifer_module_deps(): return ['second.py']\n"
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)
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py_fname_2 = py_path / "second.py"
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py_fname_2.write_text("def hej(): print('hej')\n")
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# Write yaml
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yaml_path = t_tmp_path / "yamls"
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yaml_path.mkdir(exist_ok=True, parents=True)
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yaml_fname = yaml_path / "test_parse_yaml_multi_module.yaml"
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yaml_fname.write_text(
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"foo: bar\nwith:\n - ../external/first.py\n - scipy\n"
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)
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# Check test file
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parse_yaml(yaml_fname)
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def test_parse_storage_uri_relative(tmp_path: Path) -> None:
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"""Test YAML parsing with storage and relative URI.
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@ -212,3 +264,17 @@ def test_parse_storage_uri_relative(tmp_path: Path) -> None:
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assert "foo" in contents
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assert contents["foo"] == "bar"
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assert "storage" in contents
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def test_parse_yaml_queue_venv_relative(tmp_path: Path) -> None:
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"""Test YAML parsing with relative venv queue.
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Parameters
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----------
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tmp_path : pathlib.Path
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The path to the test directory.
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"""
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fname = tmp_path / "test_parse_yaml_queue_venv_relative.yaml"
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fname.write_text("queue:\n env:\n kind: venv\n name: .venv\n")
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_ = parse_yaml(fname)
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|
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@ -95,7 +95,7 @@ def get_data(
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target_data=target_data,
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extra_input=extra_input,
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)
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else:
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else: # pragma: no cover
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raise_error(f"Unknown data kind: {kind}")
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@ -125,7 +125,7 @@ def list_data(kind: str) -> list[str]:
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return ParcellationRegistry().list
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elif kind == "mask":
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return MaskRegistry().list
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else:
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else: # pragma: no cover
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raise_error(f"Unknown data kind: {kind}")
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@ -172,7 +172,7 @@ def load_data(
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return ParcellationRegistry().load(name=name, **kwargs)
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elif kind == "mask":
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return MaskRegistry().load(name=name, **kwargs)
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else:
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else: # pragma: no cover
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raise_error(f"Unknown data kind: {kind}")
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@ -217,7 +217,7 @@ def register_data(
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return MaskRegistry().register(
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name=name, space=space, overwrite=overwrite, **kwargs
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)
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else:
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else: # pragma: no cover
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raise_error(f"Unknown data kind: {kind}")
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@ -244,5 +244,5 @@ def deregister_data(kind: str, name: str) -> None:
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return ParcellationRegistry().deregister(name=name)
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elif kind == "mask":
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return MaskRegistry().deregister(name=name)
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else:
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else: # pragma: no cover
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raise_error(f"Unknown data kind: {kind}")
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|
|
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|
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@ -1,23 +0,0 @@
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-2 -53 18 PCu-PCC_LR
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-25 -26 -14 HC-PHC-AMG_L
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-47 -61 26 TPJ_L
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-3 47 -1 Medial-prefrontal-cortex_rACC(bilateral)_L
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-56 -8 -14 STS_MTG_inferior-temporal-sulcus_L
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-47 25 -5 Ventrolateral-prefrontal-cortex_temporal-pole_L
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23 -31 -12 HC-PHC_R
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-3 12 57 Middle-frontal-gyrus_LR
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49 -59 27 TPJ_R
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-45 3 45 Posterior-lateral-prefrontal-cortex_L
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-40 47 14 Frontal-pole(lateral)_L
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23 -13 -15 HC-PHC_R
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49 -5 -13 Temporal-pole_STS_MTG_R
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-37 14 -32 Temporal-pole_L
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-37 -81 30 Occ_L
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-46 24 21 Dorsolateral-prefrontal-cortex_L
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50 27 -5 Ventrolateral-prefrontal-cortex_R
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-11 55 17 Frontal_pole(medial)_L
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3 -9 5 Thalamus_R
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-5 33 22 rACC_L
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-6 -37 33 PCC_L
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-28 9 51 Superior-frontal-sulcus_L
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28 1 -19 AMG_R
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|
|
@ -1,19 +0,0 @@
|
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36.0 22.0 -4.0 RaIns
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2.0 16.0 48.0 preSMA
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48.0 12.0 30.0 rIFGp
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36.0 2.0 54.0 rdPMC
|
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48.0 30.0 24.0 rIFGa
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-38.0 -44.0 46.0 lIPS
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-24.0 -66.0 48.0 lSPL
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40.0 -46.0 46.0 rIPS
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60.0 -44.0 24.0 rIPC
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30.0 -62.0 52.0 rSPL
|
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-44.0 10.0 30.0 lIFG
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-34.0 20.0 -4.0 LaIns
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-26.0 2.0 52.0 ldPMC
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6.0 -18.0 -2.0 rThal
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-40.0 -66.0 -10.0 lIOG
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48.0 19.0 6.0 rIFG
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8.0 29.0 30.0 aMCC
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||||
-45.0 27.0 30.0 lIFG
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11.0 7.0 7.0 rNcaud
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||||
|
|
@ -1,8 +0,0 @@
|
|||
-40 -64 -12 Fusiform_L
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||||
36 22 -4 Insula_R
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||||
-44 10 32 Precentral_L
|
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60 -44 24 Temporal_Sup_R
|
||||
0 18 48 Supp_Motor_Area_L
|
||||
-36 -46 46 Parietal_Inf_L
|
||||
38 -46 44 Parietal_Inf_R
|
||||
-26 0 54 Frontal_Mid_L
|
||||
|
|
@ -1,6 +0,0 @@
|
|||
0 -53 26 PCC
|
||||
0 52 -6 MPFC
|
||||
-48 -62 36 lAG
|
||||
46 -62 32 rAG
|
||||
-24 -22 -20 lHF
|
||||
24 -22 -20 rHF
|
||||
|
|
@ -1,160 +0,0 @@
|
|||
6 64 3 vmPFC
|
||||
29 57 18 aPFC
|
||||
-29 57 10 aPFC
|
||||
0 51 32 mPFC
|
||||
-25 51 27 aPFC
|
||||
9 51 16 vmPFC
|
||||
-6 50 -1 vmPFC
|
||||
27 49 26 aPFC
|
||||
42 48 -3 vent aPFC
|
||||
-43 47 2 vent aPFC
|
||||
-11 45 17 vmPFC
|
||||
39 42 16 vlPFC
|
||||
8 42 -5 vmPFC
|
||||
9 39 20 ACC
|
||||
46 39 -15 vlPFC
|
||||
40 36 29 dlPFC
|
||||
23 33 47 sup frontal
|
||||
34 32 7 vPFC
|
||||
-2 30 27 ACC
|
||||
-16 29 54 sup frontal
|
||||
-1 28 40 ACC
|
||||
46 28 31 dlPFC
|
||||
-52 28 17 vPFC
|
||||
-44 27 33 dlPFC
|
||||
51 23 8 vFC
|
||||
38 21 -1 ant insula
|
||||
9 20 34 dACC
|
||||
-36 18 2 ant insula
|
||||
40 17 40 dFC
|
||||
-6 17 34 basal ganglia
|
||||
0 15 45 mFC
|
||||
58 11 14 frontal
|
||||
-46 10 14 vFC
|
||||
44 8 34 dFC
|
||||
60 8 34 dFC
|
||||
-42 7 36 dFC
|
||||
-55 7 23 vFC
|
||||
-20 6 7 basal ganglia
|
||||
14 6 7 basal ganglia
|
||||
-48 6 1 vFC
|
||||
10 5 51 pre-SMA
|
||||
43 1 12 vFC
|
||||
0 -1 52 SMA
|
||||
37 -2 -3 mid insula
|
||||
53 -3 32 frontal
|
||||
58 -3 17 precentral gyrus
|
||||
-12 -3 13 thalamus
|
||||
-42 -3 11 mid insula
|
||||
-44 -6 49 precentral gyrus
|
||||
-26 -8 54 parietal
|
||||
46 -8 24 precentral gyrus
|
||||
-54 -9 23 precentral gyrus
|
||||
44 -11 38 precentral gyrus
|
||||
-47 -12 36 parietal
|
||||
33 -12 16 mid insula
|
||||
-36 -12 15 mid insula
|
||||
-12 -12 6 thalamus
|
||||
11 -12 6 thalamus
|
||||
32 -12 2 mid insula
|
||||
59 -13 8 temporal
|
||||
-30 -14 1 mid insula
|
||||
-38 -15 59 parietal
|
||||
52 -15 -13 inf temporal
|
||||
-47 -18 50 parietal
|
||||
46 -20 45 parietal
|
||||
-55 -22 38 parietal
|
||||
-54 -22 22 precentral gyrus
|
||||
-54 -22 9 temporal
|
||||
41 -23 55 parietal
|
||||
42 -24 17 post insula
|
||||
11 -24 2 basal ganglia
|
||||
-59 -25 -15 inf temporal
|
||||
1 -26 31 post cingulate
|
||||
18 -27 62 parietal
|
||||
-38 -27 60 parietal
|
||||
-30 -28 9 post insula
|
||||
-24 -30 64 parietal
|
||||
51 -30 5 temporal
|
||||
-41 -31 48 post parietal
|
||||
-4 -31 -4 post cingulate
|
||||
54 -31 -18 fusiform
|
||||
-41 -37 16 temporal
|
||||
-53 -37 13 temporal
|
||||
28 -37 -15 fusiform
|
||||
-3 -38 45 precuneus
|
||||
34 -39 65 sup parietal
|
||||
8 -40 50 precuneus
|
||||
-41 -40 42 IPL
|
||||
58 -41 20 parietal
|
||||
-8 -41 3 post cingulate
|
||||
-61 -41 -2 inf temporal
|
||||
-28 -42 -11 occipital
|
||||
-5 -43 25 post cingulate
|
||||
9 -43 25 precuneus
|
||||
43 -43 8 temporal
|
||||
54 -44 43 IPL
|
||||
-55 -44 30 parietal
|
||||
-28 -44 -25 lat cerebellum
|
||||
-35 -46 48 post parietal
|
||||
42 -46 21 sup temporal
|
||||
-48 -47 49 IPL
|
||||
-41 -47 29 angular gyrus
|
||||
-59 -47 11 temporal
|
||||
-53 -50 39 IPL
|
||||
5 -50 33 precuneus
|
||||
-18 -50 1 occipital
|
||||
44 -52 47 IPL
|
||||
-5 -52 17 post cingulate
|
||||
-24 -54 -21 lat cerebellum
|
||||
-37 -54 -37 inf cerebellum
|
||||
10 -55 17 post cingulate
|
||||
-6 -56 29 precuneus
|
||||
-34 -57 -24 lat cerebellum
|
||||
-32 -58 46 IPS
|
||||
-11 -58 17 post cingulate
|
||||
32 -59 41 IPS
|
||||
51 -59 34 angular gyrus
|
||||
-34 -60 -5 occipital
|
||||
36 -60 -8 occipital
|
||||
-6 -60 -15 med cerebellum
|
||||
-25 -60 -34 inf cerebellum
|
||||
32 -61 -31 inf cerebellum
|
||||
46 -62 5 temporal
|
||||
-48 -63 35 angular gyrus
|
||||
-52 -63 15 TPJ
|
||||
-44 -63 -7 occipital
|
||||
-16 -64 -21 med cerebellum
|
||||
21 -64 -22 lat cerebellum
|
||||
19 -66 -1 occipital
|
||||
1 -66 -24 med cerebellum
|
||||
-34 -67 -29 inf cerebellum
|
||||
11 -68 42 precuneus
|
||||
17 -68 20 occipital
|
||||
-36 -69 40 IPS
|
||||
39 -71 13 occipital
|
||||
-9 -72 41 occipital
|
||||
45 -72 29 occipital
|
||||
-11 -72 -14 med cerebellum
|
||||
29 -73 29 occipital
|
||||
33 -73 -30 inf cerebellum
|
||||
-2 -75 32 occipital
|
||||
-29 -75 28 occipital
|
||||
5 -75 -11 med cerebellum
|
||||
14 -75 -21 med cerebellum
|
||||
-16 -76 33 occipital
|
||||
-42 -76 26 occipital
|
||||
9 -76 14 occipital
|
||||
15 -77 32 occipital
|
||||
20 -78 -2 occipital
|
||||
-21 -79 -33 inf cerebellum
|
||||
-6 -79 -33 inf cerebellum
|
||||
-5 -80 9 post occipital
|
||||
29 -81 14 post occipital
|
||||
33 -81 -2 post occipital
|
||||
18 -81 -33 inf cerebellum
|
||||
-37 -83 -2 post occipital
|
||||
-29 -88 8 post occipital
|
||||
13 -91 2 post occipital
|
||||
27 -91 2 post occipital
|
||||
-4 -94 12 post occipital
|
||||
|
|
@ -1,22 +0,0 @@
|
|||
2.0 56.0 18.0 dmPFC
|
||||
-8.0 54.0 34.0 dmPFC
|
||||
36.0 22.0 -8.0 raI
|
||||
-30.0 20.0 4.0 laI
|
||||
50.0 12.0 -8.0 rIFG
|
||||
54.0 16.0 20.0 rIFG/Area44
|
||||
50.0 30.0 4.0 rIFG/Area45
|
||||
-44.0 24.0 -6.0 lIFG
|
||||
-4.0 18.0 50.0 SMA
|
||||
-2.0 28.0 20.0 aMCC
|
||||
-4.0 42.0 18.0 rACC
|
||||
-2.0 -32.0 28.0 PCC
|
||||
52.0 -58.0 22.0 rTPJ
|
||||
-56.0 -58.0 22.0 lTPJ
|
||||
22.0 -2.0 -16.0 rAm
|
||||
54.0 -8.0 -16.0 rMTG
|
||||
52.0 -36.0 2.0 rpSTS
|
||||
-12.0 -4.0 12.0 laTh
|
||||
6.0 -32.0 2.0 rpTh
|
||||
26.0 -26.0 -12.0 rHippo
|
||||
2.0 -20.0 -12.0 Midbrain
|
||||
14.0 4.0 0.0 rGP
|
||||
|
|
@ -1,10 +0,0 @@
|
|||
-39.0 -21.0 54.0 lSMC*
|
||||
41.0 -16.0 57.0 rSMC*
|
||||
-3.0 -2.0 54.0 SMA
|
||||
-57.0 2.0 32.0 lPMCv
|
||||
-53.0 -24.0 21.0 lIPC
|
||||
45.0 -38.0 48.0 rIPC
|
||||
-23.0 -7.0 1.0 lBG
|
||||
25.0 -8.0 3.0 rBG
|
||||
-22.0 -52.0 26.0 lCba
|
||||
18.0 -54.0 -22.0 rCba
|
||||
|
|
@ -1,9 +0,0 @@
|
|||
-34 22 -4 leftInsula
|
||||
34 24 0 rightInsula
|
||||
-26 0 52 Frontal_Mid_L
|
||||
44 38 28 Frontal_Inf_Tri_R
|
||||
46 10 28 Frontal_Inf_Oper_R
|
||||
-6 18 50 Supp_Motor_Area_L
|
||||
-34 -52 56 Parietal_Inf_L
|
||||
32 -52 50 Parietal_Inf_R
|
||||
32 6 58 Frontal_Mid_R
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
38.0 18.0 0.0 rIns
|
||||
52.0 12.0 -4.0 rSTG
|
||||
60.0 6.0 2.0 rTP
|
||||
22.0 0.0 -4.0 rPall
|
||||
-38.0 14.0 4.0 lIns
|
||||
-58.0 0.0 6.0 lOP4
|
||||
-20.0 6.0 2.0 lPut
|
||||
4.0 6.0 46.0 rSMA
|
||||
0.0 14.0 36.0 lMCC
|
||||
-42.0 -18.0 18.0 lOP3
|
||||
-54.0 -24.0 24.0 lSMG
|
||||
-36.0 -20.0 2.0 lIns
|
||||
-14.0 -12.0 10.0 lTh
|
||||
10.0 -18.0 4.0 rTh
|
||||
56.0 -24.0 24.0 lSMG
|
||||
44.0 -14.0 16.0 rOP3
|
||||
38.0 50.0 12.0 rMFG
|
||||
-24.0 -66.0 -26.0 lCb
|
||||
|
|
@ -1,264 +0,0 @@
|
|||
-25 -98 -12 1
|
||||
27 -97 -13 2
|
||||
24 32 -18 3
|
||||
-56 -45 -24 4
|
||||
8 41 -24 5
|
||||
-21 -22 -20 6
|
||||
17 -28 -17 7
|
||||
-37 -29 -26 8
|
||||
65 -24 -19 9
|
||||
52 -34 -27 10
|
||||
55 -31 -17 11
|
||||
34 38 -12 12
|
||||
-7 -52 61 13
|
||||
-14 -18 40 14
|
||||
0 -15 47 15
|
||||
10 -2 45 16
|
||||
-7 -21 65 17
|
||||
-7 -33 72 18
|
||||
13 -33 75 19
|
||||
-54 -23 43 20
|
||||
29 -17 71 21
|
||||
10 -46 73 22
|
||||
-23 -30 72 23
|
||||
-40 -19 54 24
|
||||
29 -39 59 25
|
||||
50 -20 42 26
|
||||
-38 -27 69 27
|
||||
20 -29 60 28
|
||||
44 -8 57 29
|
||||
-29 -43 61 30
|
||||
10 -17 74 31
|
||||
22 -42 69 32
|
||||
-45 -32 47 33
|
||||
-21 -31 61 34
|
||||
-13 -17 75 35
|
||||
42 -20 55 36
|
||||
-38 -15 69 37
|
||||
-16 -46 73 38
|
||||
2 -28 60 39
|
||||
3 -17 58 40
|
||||
38 -17 45 41
|
||||
-49 -11 35 42
|
||||
36 -9 14 43
|
||||
51 -6 32 44
|
||||
-53 -10 24 45
|
||||
66 -8 25 46
|
||||
-3 2 53 47
|
||||
54 -28 34 48
|
||||
19 -8 64 49
|
||||
-16 -5 71 50
|
||||
-10 -2 42 51
|
||||
37 1 -4 52
|
||||
13 -1 70 53
|
||||
7 8 51 54
|
||||
-45 0 9 55
|
||||
49 8 -1 56
|
||||
-34 3 4 57
|
||||
-51 8 -2 58
|
||||
-5 18 34 59
|
||||
36 10 1 60
|
||||
32 -26 13 61
|
||||
65 -33 20 62
|
||||
58 -16 7 63
|
||||
-38 -33 17 64
|
||||
-60 -25 14 65
|
||||
-49 -26 5 66
|
||||
43 -23 20 67
|
||||
-50 -34 26 68
|
||||
-53 -22 23 69
|
||||
-55 -9 12 70
|
||||
56 -5 13 71
|
||||
59 -17 29 72
|
||||
-30 -27 12 73
|
||||
-41 -75 26 74
|
||||
6 67 -4 75
|
||||
8 48 -15 76
|
||||
-13 -40 1 77
|
||||
-18 63 -9 78
|
||||
-46 -61 21 79
|
||||
43 -72 28 80
|
||||
-44 12 -34 81
|
||||
46 16 -30 82
|
||||
-68 -23 -16 83
|
||||
-58 -26 -15 84
|
||||
27 16 -17 85
|
||||
-44 -65 35 86
|
||||
-39 -75 44 87
|
||||
-7 -55 27 88
|
||||
6 -59 35 89
|
||||
-11 -56 16 90
|
||||
-3 -49 13 91
|
||||
8 -48 31 92
|
||||
15 -63 26 93
|
||||
-2 -37 44 94
|
||||
11 -54 17 95
|
||||
52 -59 36 96
|
||||
23 33 48 97
|
||||
-10 39 52 98
|
||||
-16 29 53 99
|
||||
-35 20 51 100
|
||||
22 39 39 101
|
||||
13 55 38 102
|
||||
-10 55 39 103
|
||||
-20 45 39 104
|
||||
6 54 16 105
|
||||
6 64 22 106
|
||||
-7 51 -1 107
|
||||
9 54 3 108
|
||||
-3 44 -9 109
|
||||
8 42 -5 110
|
||||
-11 45 8 111
|
||||
-2 38 36 112
|
||||
-3 42 16 113
|
||||
-20 64 19 114
|
||||
-8 48 23 115
|
||||
65 -12 -19 116
|
||||
-56 -13 -10 117
|
||||
-58 -30 -4 118
|
||||
65 -31 -9 119
|
||||
-68 -41 -5 120
|
||||
13 30 59 121
|
||||
12 36 20 122
|
||||
52 -2 -16 123
|
||||
-26 -40 -8 124
|
||||
27 -37 -13 125
|
||||
-34 -38 -16 126
|
||||
28 -77 -32 127
|
||||
52 7 -30 128
|
||||
-53 3 -27 129
|
||||
47 -50 29 130
|
||||
-49 -42 1 131
|
||||
-31 19 -19 132
|
||||
-2 -35 31 133
|
||||
-7 -71 42 134
|
||||
11 -66 42 135
|
||||
4 -48 51 136
|
||||
-46 31 -13 137
|
||||
-10 11 67 138
|
||||
49 35 -12 139
|
||||
8 -91 -7 140
|
||||
17 -91 -14 141
|
||||
-12 -95 -13 142
|
||||
18 -47 -10 143
|
||||
40 -72 14 144
|
||||
8 -72 11 145
|
||||
-8 -81 7 146
|
||||
-28 -79 19 147
|
||||
20 -66 2 148
|
||||
-24 -91 19 149
|
||||
27 -59 -9 150
|
||||
-15 -72 -8 151
|
||||
-18 -68 5 152
|
||||
43 -78 -12 153
|
||||
-47 -76 -10 154
|
||||
-14 -91 31 155
|
||||
15 -87 37 156
|
||||
29 -77 25 157
|
||||
20 -86 -2 158
|
||||
15 -77 31 159
|
||||
-16 -52 -1 160
|
||||
42 -66 -8 161
|
||||
24 -87 24 162
|
||||
6 -72 24 163
|
||||
-42 -74 0 164
|
||||
26 -79 -16 165
|
||||
-16 -77 34 166
|
||||
-3 -81 21 167
|
||||
-40 -88 -6 168
|
||||
37 -84 13 169
|
||||
6 -81 6 170
|
||||
-26 -90 3 171
|
||||
-33 -79 -13 172
|
||||
37 -81 1 173
|
||||
-44 2 46 174
|
||||
48 25 27 175
|
||||
-47 11 23 176
|
||||
-53 -49 43 177
|
||||
-23 11 64 178
|
||||
58 -53 -14 179
|
||||
24 45 -15 180
|
||||
34 54 -13 181
|
||||
-21 41 -20 182
|
||||
-18 -76 -24 183
|
||||
17 -80 -34 184
|
||||
35 -67 -34 185
|
||||
47 10 33 186
|
||||
-41 6 33 187
|
||||
-42 38 21 188
|
||||
38 43 15 189
|
||||
49 -42 45 190
|
||||
-28 -58 48 191
|
||||
44 -53 47 192
|
||||
32 14 56 193
|
||||
37 -65 40 194
|
||||
-42 -55 45 195
|
||||
40 18 40 196
|
||||
-34 55 4 197
|
||||
-42 45 -2 198
|
||||
33 -53 44 199
|
||||
43 49 -2 200
|
||||
-42 25 30 201
|
||||
-3 26 44 202
|
||||
11 -39 50 203
|
||||
55 -45 37 204
|
||||
42 -0 47 205
|
||||
31 33 26 206
|
||||
48 22 10 207
|
||||
-35 20 0 208
|
||||
36 22 3 209
|
||||
37 32 -2 210
|
||||
34 16 -8 211
|
||||
-11 26 25 212
|
||||
-1 15 44 213
|
||||
-28 52 21 214
|
||||
-0 30 27 215
|
||||
5 23 37 216
|
||||
10 22 27 217
|
||||
31 56 14 218
|
||||
26 50 27 219
|
||||
-39 51 17 220
|
||||
2 -24 30 221
|
||||
6 -24 -0 222
|
||||
-2 -13 12 223
|
||||
-10 -18 7 224
|
||||
12 -17 8 225
|
||||
-5 -28 -4 226
|
||||
-22 7 -5 227
|
||||
-15 4 8 228
|
||||
31 -14 2 229
|
||||
23 10 1 230
|
||||
29 1 4 231
|
||||
-31 -11 -0 232
|
||||
15 5 7 233
|
||||
9 -4 6 234
|
||||
54 -43 22 235
|
||||
-56 -50 10 236
|
||||
-55 -40 14 237
|
||||
52 -33 8 238
|
||||
51 -29 -4 239
|
||||
56 -46 11 240
|
||||
53 33 1 241
|
||||
-49 25 -1 242
|
||||
-16 -65 -20 243
|
||||
-32 -55 -25 244
|
||||
22 -58 -23 245
|
||||
1 -62 -18 246
|
||||
33 -12 -34 247
|
||||
-31 -10 -36 248
|
||||
49 -3 -38 249
|
||||
-50 -7 -39 250
|
||||
10 -62 61 251
|
||||
-52 -63 5 252
|
||||
-47 -51 -21 253
|
||||
46 -47 -17 254
|
||||
47 -30 49 255
|
||||
22 -65 48 256
|
||||
46 -59 4 257
|
||||
25 -58 60 258
|
||||
-33 -46 47 259
|
||||
-27 -71 37 260
|
||||
-32 -1 54 261
|
||||
-42 -60 -9 262
|
||||
-17 -59 64 263
|
||||
29 -5 54 264
|
||||
|
|
@ -1,264 +0,0 @@
|
|||
22 -65 48 1
|
||||
25 -58 60 2
|
||||
-35 20 0 3
|
||||
12 36 20 4
|
||||
40 18 40 5
|
||||
54 -28 34 6
|
||||
36 22 3 7
|
||||
59 -17 29 8
|
||||
-45 0 9 9
|
||||
46 -59 4 10
|
||||
-32 -1 54 11
|
||||
32 14 56 12
|
||||
-42 -60 -9 13
|
||||
-34 3 4 14
|
||||
37 1 -4 15
|
||||
29 -5 54 16
|
||||
11 -39 50 17
|
||||
37 -65 40 18
|
||||
-34 -38 -16 19
|
||||
-52 -63 5 20
|
||||
-10 11 67 21
|
||||
-44 2 46 22
|
||||
-3 26 44 23
|
||||
49 8 -1 24
|
||||
-33 -46 47 25
|
||||
-27 -71 37 26
|
||||
55 -45 37 27
|
||||
7 8 51 28
|
||||
36 10 1 29
|
||||
-39 51 17 30
|
||||
10 -62 61 31
|
||||
-16 -5 71 32
|
||||
43 49 -2 33
|
||||
37 32 -2 34
|
||||
10 -2 45 35
|
||||
47 -30 49 36
|
||||
36 -9 14 37
|
||||
-3 2 53 38
|
||||
-51 8 -2 39
|
||||
-1 15 44 40
|
||||
31 -14 2 41
|
||||
19 -8 64 42
|
||||
-10 -2 42 43
|
||||
65 -33 20 44
|
||||
-30 -27 12 45
|
||||
6 -72 24 46
|
||||
-7 -52 61 47
|
||||
-49 -42 1 48
|
||||
-49 25 -1 49
|
||||
-5 18 34 50
|
||||
-23 11 64 51
|
||||
31 33 26 52
|
||||
-0 30 27 53
|
||||
-53 -22 23 54
|
||||
-42 -55 45 55
|
||||
-50 -34 26 56
|
||||
48 22 10 57
|
||||
31 56 14 58
|
||||
44 -8 57 59
|
||||
49 35 -12 60
|
||||
-56 -50 10 61
|
||||
2 -24 30 62
|
||||
29 -39 59 63
|
||||
-42 -74 0 64
|
||||
-34 55 4 65
|
||||
13 -1 70 66
|
||||
42 -0 47 67
|
||||
-3 42 16 68
|
||||
5 23 37 69
|
||||
51 -29 -4 70
|
||||
0 -15 47 71
|
||||
52 -33 8 72
|
||||
34 16 -8 73
|
||||
-7 -71 42 74
|
||||
-29 -43 61 75
|
||||
33 -53 44 76
|
||||
-55 -40 14 77
|
||||
-17 -59 64 78
|
||||
56 -5 13 79
|
||||
46 -47 -17 80
|
||||
-11 26 25 81
|
||||
22 -42 69 82
|
||||
-13 -40 1 83
|
||||
43 -23 20 84
|
||||
-53 -49 43 85
|
||||
-47 11 23 86
|
||||
54 -43 22 87
|
||||
53 33 1 88
|
||||
10 22 27 89
|
||||
-55 -9 12 90
|
||||
-58 -30 -4 91
|
||||
-42 45 -2 92
|
||||
56 -46 11 93
|
||||
-45 -32 47 94
|
||||
11 -66 42 95
|
||||
-28 -79 19 96
|
||||
-47 -76 -10 97
|
||||
-2 38 36 98
|
||||
-54 -23 43 99
|
||||
-28 52 21 100
|
||||
47 -50 29 101
|
||||
-2 -35 31 102
|
||||
50 -20 42 103
|
||||
-42 38 21 104
|
||||
26 50 27 105
|
||||
58 -53 -14 106
|
||||
47 10 33 107
|
||||
32 -26 13 108
|
||||
-46 31 -13 109
|
||||
10 -46 73 110
|
||||
27 -37 -13 111
|
||||
43 -72 28 112
|
||||
52 -2 -16 113
|
||||
-2 -37 44 114
|
||||
38 43 15 115
|
||||
-60 -25 14 116
|
||||
-41 6 33 117
|
||||
-2 -13 12 118
|
||||
42 -66 -8 119
|
||||
9 -4 6 120
|
||||
29 1 4 121
|
||||
15 5 7 122
|
||||
-42 25 30 123
|
||||
-26 -40 -8 124
|
||||
65 -31 -9 125
|
||||
44 -53 47 126
|
||||
-18 -76 -24 127
|
||||
-35 20 51 128
|
||||
-28 -58 48 129
|
||||
-49 -26 5 130
|
||||
-53 -10 24 131
|
||||
-47 -51 -21 132
|
||||
58 -16 7 133
|
||||
49 -42 45 134
|
||||
40 -72 14 135
|
||||
-32 -55 -25 136
|
||||
-14 -18 40 137
|
||||
-41 -75 26 138
|
||||
-16 -77 34 139
|
||||
4 -48 51 140
|
||||
-68 -41 -5 141
|
||||
35 -67 -34 142
|
||||
22 39 39 143
|
||||
-56 -13 -10 144
|
||||
15 -63 26 145
|
||||
-15 4 8 146
|
||||
29 -77 25 147
|
||||
38 -17 45 148
|
||||
23 10 1 149
|
||||
66 -8 25 150
|
||||
51 -6 32 151
|
||||
-39 -75 44 152
|
||||
-11 45 8 153
|
||||
52 7 -30 154
|
||||
-21 41 -20 155
|
||||
-12 -95 -13 156
|
||||
8 42 -5 157
|
||||
34 38 -12 158
|
||||
-16 -46 73 159
|
||||
37 -84 13 160
|
||||
18 -47 -10 161
|
||||
-11 -56 16 162
|
||||
48 25 27 163
|
||||
-53 3 -27 164
|
||||
46 16 -30 165
|
||||
-31 19 -19 166
|
||||
37 -81 1 167
|
||||
52 -59 36 168
|
||||
27 16 -17 169
|
||||
24 45 -15 170
|
||||
-44 12 -34 171
|
||||
-46 -61 21 172
|
||||
-49 -11 35 173
|
||||
-25 -98 -12 174
|
||||
-33 -79 -13 175
|
||||
11 -54 17 176
|
||||
23 33 48 177
|
||||
-3 -49 13 178
|
||||
12 -17 8 179
|
||||
-38 -33 17 180
|
||||
8 48 -15 181
|
||||
-10 39 52 182
|
||||
43 -78 -12 183
|
||||
20 -29 60 184
|
||||
-40 -19 54 185
|
||||
-20 45 39 186
|
||||
13 30 59 187
|
||||
-24 -91 19 188
|
||||
-16 29 53 189
|
||||
8 -91 -7 190
|
||||
-21 -31 61 191
|
||||
6 67 -4 192
|
||||
17 -80 -34 193
|
||||
-23 -30 72 194
|
||||
2 -28 60 195
|
||||
15 -77 31 196
|
||||
3 -17 58 197
|
||||
55 -31 -17 198
|
||||
-31 -10 -36 199
|
||||
-40 -88 -6 200
|
||||
-18 63 -9 201
|
||||
27 -59 -9 202
|
||||
49 -3 -38 203
|
||||
-31 -11 -0 204
|
||||
65 -24 -19 205
|
||||
17 -28 -17 206
|
||||
-7 51 -1 207
|
||||
24 32 -18 208
|
||||
9 54 3 209
|
||||
-7 -55 27 210
|
||||
-21 -22 -20 211
|
||||
34 54 -13 212
|
||||
-38 -15 69 213
|
||||
-38 -27 69 214
|
||||
65 -12 -19 215
|
||||
-16 -52 -1 216
|
||||
-8 48 23 217
|
||||
-3 44 -9 218
|
||||
-37 -29 -26 219
|
||||
27 -97 -13 220
|
||||
17 -91 -14 221
|
||||
6 54 16 222
|
||||
8 41 -24 223
|
||||
8 -48 31 224
|
||||
24 -87 24 225
|
||||
-58 -26 -15 226
|
||||
29 -17 71 227
|
||||
-68 -23 -16 228
|
||||
-10 -18 7 229
|
||||
-13 -17 75 230
|
||||
-7 -33 72 231
|
||||
15 -87 37 232
|
||||
-20 64 19 233
|
||||
42 -20 55 234
|
||||
26 -79 -16 235
|
||||
-10 55 39 236
|
||||
13 -33 75 237
|
||||
33 -12 -34 238
|
||||
-26 -90 3 239
|
||||
-7 -21 65 240
|
||||
10 -17 74 241
|
||||
-44 -65 35 242
|
||||
6 -59 35 243
|
||||
6 64 22 244
|
||||
-18 -68 5 245
|
||||
-16 -65 -20 246
|
||||
8 -72 11 247
|
||||
13 55 38 248
|
||||
-14 -91 31 249
|
||||
-3 -81 21 250
|
||||
20 -86 -2 251
|
||||
-50 -7 -39 252
|
||||
-56 -45 -24 253
|
||||
-8 -81 7 254
|
||||
20 -66 2 255
|
||||
6 -81 6 256
|
||||
52 -34 -27 257
|
||||
-15 -72 -8 258
|
||||
6 -24 -0 259
|
||||
28 -77 -32 260
|
||||
22 -58 -23 261
|
||||
1 -62 -18 262
|
||||
-22 7 -5 263
|
||||
-5 -28 -4 264
|
||||
|
|
|
@ -1,25 +0,0 @@
|
|||
12.0 10.0 -6.0 rNAc
|
||||
-10.0 8.0 -4.0 lPall
|
||||
36.0 20.0 -6.0 rIns
|
||||
-32.0 20.0 -4.0 lIns
|
||||
0.0 24.0 40.0 dmPFC
|
||||
0.0 54.0 -8.0 medOFC
|
||||
24.0 -2.0 -16.0 rAm
|
||||
6.0 -14.0 8.0 rTh
|
||||
-6.0 -16.0 8.0 lTh
|
||||
0.0 8.0 48.0 SMA
|
||||
8.0 -18.0 -10.0 rBrainStem
|
||||
-6.0 -18.0 -10.0 lBrainStem
|
||||
2.0 44.0 20.0 ACC
|
||||
-24.0 2.0 52.0 lMFG
|
||||
-38.0 -4.0 6.0 lIns(Id3)
|
||||
24.0 40.0 -14.0 rMidOFC(Fo3)
|
||||
-16.0 42.0 -14.0 lMidOFC(Fo3)
|
||||
40.0 32.0 32.0 raMFG
|
||||
-28.0 -56.0 48.0 lIPL(IPS)
|
||||
28.0 -58.0 50.0 rAG
|
||||
0.0 -32.0 32.0 PCC
|
||||
-36.0 50.0 10.0 lFP
|
||||
-46.0 42.0 -4.0 lLOFC
|
||||
30.0 4.0 50.0 rpMFG
|
||||
-22.0 30.0 48.0 lSFG
|
||||
|
|
@ -1,10 +0,0 @@
|
|||
-48.0 -20.0 20.0 S1_L
|
||||
-54.0 -20.0 48.0 postcentralG_S1_L
|
||||
-44.0 -26.0 58.0 postcentralG_S1_L
|
||||
-38.0 -12.0 4.0 Ins_claustrum_L
|
||||
-40.0 4.0 10.0 pars_opercularis_Ins_L
|
||||
56.0 -22.0 20.0 SMG_R
|
||||
56.0 -34.0 18.0 pSTG_R
|
||||
56.0 -38.0 28.0 IPL_SMG_R
|
||||
60.0 -20.0 32.0 postcentralG_R
|
||||
-4.0 14.0 36.0 MCC_L
|
||||
|
|
@ -1,15 +0,0 @@
|
|||
0.0 52.0 -12.0 vmPFC
|
||||
2.0 58.0 12.0 FP
|
||||
-8.0 56.0 30.0 dmPFC
|
||||
2.0 -56.0 30.0 Prc
|
||||
56.0 -50.0 18.0 rTPJ
|
||||
-48.0 -56.0 24.0 lTPJ
|
||||
54.0 -2.0 -20.0 rTP
|
||||
-54.0 -2.0 -24.0 lTP
|
||||
52.0 -18.0 -12.0 rMTG
|
||||
-54.0 -28.0 -4.0 lMTG
|
||||
50.0 -34.0 0.0 rpSTS
|
||||
-58.0 -44.0 4.0 lpSTS
|
||||
54.0 28.0 6.0 rIFG
|
||||
-48.0 30.0 -12.0 lIFG
|
||||
48.0 -72.0 8.0 rV5
|
||||
|
|
@ -1,16 +0,0 @@
|
|||
-2.0 8.0 50.0 aParacentralL
|
||||
8.0 32.0 46.0 rmpSFG
|
||||
0.0 26.0 34.0 dMCC
|
||||
50.0 8.0 32.0 rIFJ
|
||||
40.0 22.0 -4.0 raI
|
||||
46.0 36.0 20.0 rIFS
|
||||
-40.0 -12.0 60.0 lPrecentralG
|
||||
-46.0 -68.0 -6.0 lIOG
|
||||
-48.0 8.0 30.0 lIFJ
|
||||
62.0 -38.0 17.0 rTPJ
|
||||
8.0 -12.0 6.0 rTh
|
||||
32.0 -90.0 4.0 rMOG
|
||||
-42.0 12.0 -2.0 laI
|
||||
-10.0 -14.0 6.0 lTh
|
||||
6.0 -58.0 -18.0 Cb
|
||||
44.0 -44.0 46.0 rIPL
|
||||
|
|
@ -1,23 +0,0 @@
|
|||
-32.0 22.0 -2.0 aIns_l
|
||||
-48.0 10.0 26.0 IFG_l
|
||||
-46.0 26.0 24.0 lPFCc_l
|
||||
-38.0 50.0 10.0 lPFCr_l
|
||||
36.0 22.0 -6.0 aIns_r
|
||||
50.0 14.0 24.0 IFG_r
|
||||
44.0 34.0 32.0 lPFCc_r
|
||||
38.0 54.0 6.0 lPFCr_l
|
||||
2.0 18.0 48.0 pmFC
|
||||
-28.0 0.0 56.0 psFC
|
||||
30.0 2.0 56.0 psFC
|
||||
-42.0 -42.0 46.0 IPS_l
|
||||
-34.0 -52.0 48.0 SPL_l
|
||||
-24.0 -66.0 54.0 SPLp_l
|
||||
42.0 -44.0 44.0 IPSa_r
|
||||
32.0 -58.0 48.0 IPSp_r
|
||||
16.0 -66.0 56.0 SPLp_r
|
||||
-12.0 -12.0 12.0 Thal_l
|
||||
-16.0 2.0 14.0 Ncaud_l
|
||||
-16.0 0.0 2.0 GP_l
|
||||
12.0 -10.0 10.0 Thal_r
|
||||
-34.0 -66.0 -20.0 Cb_FG_l
|
||||
32.0 -64.0 -18.0 Cb_FG_r
|
||||
|
|
@ -1,17 +0,0 @@
|
|||
-46.0 6.0 30.0 IFG_l
|
||||
50.0 12.0 28.0 IFG_r
|
||||
-32.0 20.0 2.0 aIns_l
|
||||
36.0 22.0 0.0 aIns_r
|
||||
-4.0 14.0 44.0 SMA_l
|
||||
6.0 18.0 46.0 SMA_r
|
||||
-32.0 -52.0 46.0 IPS_l
|
||||
32.0 -58.0 48.0 IPS_r
|
||||
44.0 36.0 20.0 MFG_r
|
||||
-28.0 -4.0 52.0 dPMC_l
|
||||
-44.0 32.0 22.0 MFG_l
|
||||
32.0 0.0 52.0 dPMC_r
|
||||
-20.0 6.0 4.0 Put_l
|
||||
10.0 -12.0 8.0 Thal_r
|
||||
-46.0 -60.0 -10.0 ITG_l
|
||||
22.0 6.0 4.0 Put_r
|
||||
-10.0 -16.0 6.0 Thal_l
|
||||
|
|
@ -1,12 +0,0 @@
|
|||
0.0 38.0 10.0 ACC
|
||||
-24.0 -10.0 -20.0 AmyHipp_L
|
||||
24.0 -8.0 -22.0 AmyHipp_R
|
||||
-2.0 -52.0 26.0 PrC
|
||||
-2.0 32.0 -8.0 SGC
|
||||
-46.0 -66.0 18.0 TPJ_L
|
||||
50.0 -60.0 18.0 TPJ_R
|
||||
-2.0 52.0 14.0 dmPFC
|
||||
-6.0 10.0 -8.0 vBG_L
|
||||
6.0 10.0 -8.0 vBG_R
|
||||
-2.0 50.0 -10.0 vmPFC
|
||||
-54.0 -10.0 -20.0 aMTS/aMTG
|
||||
|
|
@ -1,16 +0,0 @@
|
|||
0 -53 6 PCC
|
||||
0 52 -6 MPFC
|
||||
-48 -62 36 lAG
|
||||
46 -62 32 rAG
|
||||
-24 -22 -20 lHF
|
||||
24 -22 -20 rHF
|
||||
10 -22 42 Middlecingulate
|
||||
-48 -20 38 lIPG
|
||||
0 -48 -30 cerebellum
|
||||
34 -80 -34 rCerebellum
|
||||
56 30 8 rdlPFC
|
||||
-42 -82 10 lateraloccipital
|
||||
-54 24 10 rdrPFC
|
||||
22 34 54 RSFG
|
||||
-50 14 -40 lTempP
|
||||
-38 14 54 leftmiddlefrontalgyrus(BA6)
|
||||
|
|
@ -27,7 +27,7 @@ class ANTsCoordinatesWarper:
|
|||
seeds: ArrayLike,
|
||||
target_data: dict[str, Any],
|
||||
warp_data: dict[str, Any],
|
||||
) -> ArrayLike:
|
||||
) -> ArrayLike: # pragma: no cover
|
||||
"""Warp ``seeds`` to correct space.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -339,7 +339,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
|
|||
seeds, labels, _ = self.load(name=coords)
|
||||
|
||||
# Transform coordinate if target data is native
|
||||
if target_data["space"] == "native":
|
||||
if target_data["space"] == "native": # pragma: no cover
|
||||
# Check for extra inputs
|
||||
if extra_input is None:
|
||||
raise_error(
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ class FSLCoordinatesWarper:
|
|||
seeds: ArrayLike,
|
||||
target_data: dict[str, Any],
|
||||
warp_data: dict[str, Any],
|
||||
) -> ArrayLike:
|
||||
) -> ArrayLike: # pragma: no cover
|
||||
"""Warp ``seeds`` to correct space.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -8,7 +8,13 @@ import numpy as np
|
|||
import pytest
|
||||
from numpy.testing import assert_array_equal
|
||||
|
||||
from junifer.data import CoordinatesRegistry
|
||||
from junifer.data import (
|
||||
deregister_data,
|
||||
get_data,
|
||||
list_data,
|
||||
load_data,
|
||||
register_data,
|
||||
)
|
||||
from junifer.datareader import DefaultDataReader
|
||||
from junifer.testing.datagrabbers import OasisVBMTestingDataGrabber
|
||||
|
||||
|
|
@ -16,7 +22,8 @@ from junifer.testing.datagrabbers import OasisVBMTestingDataGrabber
|
|||
def test_register_built_in_check() -> None:
|
||||
"""Test coordinates registration check for built-in coordinates."""
|
||||
with pytest.raises(ValueError, match=r"built-in"):
|
||||
CoordinatesRegistry().register(
|
||||
register_data(
|
||||
kind="coordinates",
|
||||
name="DMNBuckner",
|
||||
coordinates=np.zeros(2),
|
||||
voi_names=["1", "2"],
|
||||
|
|
@ -26,14 +33,16 @@ def test_register_built_in_check() -> None:
|
|||
|
||||
def test_register_overwrite() -> None:
|
||||
"""Test coordinates registration check for overwriting."""
|
||||
CoordinatesRegistry().register(
|
||||
register_data(
|
||||
kind="coordinates",
|
||||
name="MyList",
|
||||
coordinates=np.zeros((2, 3)),
|
||||
voi_names=["roi1", "roi2"],
|
||||
space="MNI",
|
||||
)
|
||||
with pytest.raises(ValueError, match=r"already registered"):
|
||||
CoordinatesRegistry().register(
|
||||
register_data(
|
||||
kind="coordinates",
|
||||
name="MyList",
|
||||
coordinates=np.ones((2, 3)),
|
||||
voi_names=["roi2", "roi3"],
|
||||
|
|
@ -41,7 +50,8 @@ def test_register_overwrite() -> None:
|
|||
overwrite=False,
|
||||
)
|
||||
|
||||
CoordinatesRegistry().register(
|
||||
register_data(
|
||||
kind="coordinates",
|
||||
name="MyList",
|
||||
coordinates=np.ones((2, 3)),
|
||||
voi_names=["roi2", "roi3"],
|
||||
|
|
@ -49,7 +59,7 @@ def test_register_overwrite() -> None:
|
|||
overwrite=True,
|
||||
)
|
||||
|
||||
coord, names, space = CoordinatesRegistry().load("MyList")
|
||||
coord, names, space = load_data(kind="coordinates", name="MyList")
|
||||
assert_array_equal(coord, np.ones((2, 3)))
|
||||
assert names == ["roi2", "roi3"]
|
||||
assert space == "MNI"
|
||||
|
|
@ -58,7 +68,8 @@ def test_register_overwrite() -> None:
|
|||
def test_register_valid_input() -> None:
|
||||
"""Test coordinates registration check for valid input."""
|
||||
with pytest.raises(TypeError, match=r"numpy.ndarray"):
|
||||
CoordinatesRegistry().register(
|
||||
register_data(
|
||||
kind="coordinates",
|
||||
name="MyList",
|
||||
coordinates=[1, 2],
|
||||
voi_names=["roi1", "roi2"],
|
||||
|
|
@ -66,7 +77,8 @@ def test_register_valid_input() -> None:
|
|||
overwrite=True,
|
||||
)
|
||||
with pytest.raises(ValueError, match=r"2D array"):
|
||||
CoordinatesRegistry().register(
|
||||
register_data(
|
||||
kind="coordinates",
|
||||
name="MyList",
|
||||
coordinates=np.zeros((2, 3, 4)),
|
||||
voi_names=["roi1", "roi2"],
|
||||
|
|
@ -75,7 +87,8 @@ def test_register_valid_input() -> None:
|
|||
)
|
||||
|
||||
with pytest.raises(ValueError, match=r"3 values"):
|
||||
CoordinatesRegistry().register(
|
||||
register_data(
|
||||
kind="coordinates",
|
||||
name="MyList",
|
||||
coordinates=np.zeros((2, 4)),
|
||||
voi_names=["roi1", "roi2"],
|
||||
|
|
@ -83,7 +96,8 @@ def test_register_valid_input() -> None:
|
|||
overwrite=True,
|
||||
)
|
||||
with pytest.raises(ValueError, match=r"voi_names"):
|
||||
CoordinatesRegistry().register(
|
||||
register_data(
|
||||
kind="coordinates",
|
||||
name="MyList",
|
||||
coordinates=np.zeros((2, 3)),
|
||||
voi_names=["roi1", "roi2", "roi3"],
|
||||
|
|
@ -95,13 +109,13 @@ def test_register_valid_input() -> None:
|
|||
def test_list() -> None:
|
||||
"""Test listing of available coordinates."""
|
||||
assert {"DMNBuckner", "MultiTask", "VigAtt", "WM"}.issubset(
|
||||
set(CoordinatesRegistry().list)
|
||||
set(list_data(kind="coordinates"))
|
||||
)
|
||||
|
||||
|
||||
def test_load() -> None:
|
||||
"""Test loading coordinates from file."""
|
||||
coord, names, space = CoordinatesRegistry().load("DMNBuckner")
|
||||
coord, names, space = load_data(kind="coordinates", name="DMNBuckner")
|
||||
assert coord.shape == (6, 3) # type: ignore
|
||||
assert names == ["PCC", "MPFC", "lAG", "rAG", "lHF", "rHF"]
|
||||
assert space == "MNI"
|
||||
|
|
@ -110,7 +124,7 @@ def test_load() -> None:
|
|||
def test_load_nonexisting() -> None:
|
||||
"""Test loading coordinates that not exist."""
|
||||
with pytest.raises(ValueError, match=r"not found"):
|
||||
CoordinatesRegistry().load("NonExisting")
|
||||
load_data(kind="coordinates", name="NonExisting")
|
||||
|
||||
|
||||
def test_get() -> None:
|
||||
|
|
@ -121,11 +135,19 @@ def test_get() -> None:
|
|||
element_data = reader.fit_transform(element)
|
||||
vbm_gm = element_data["VBM_GM"]
|
||||
# Get tailored coordinates
|
||||
tailored_coords, tailored_labels = CoordinatesRegistry().get(
|
||||
coords="DMNBuckner", target_data=vbm_gm
|
||||
tailored_coords, tailored_labels = get_data(
|
||||
kind="coordinates", names="DMNBuckner", target_data=vbm_gm
|
||||
)
|
||||
# Get raw coordinates
|
||||
raw_coords, raw_labels, _ = CoordinatesRegistry().load("DMNBuckner")
|
||||
raw_coords, raw_labels, _ = load_data(
|
||||
kind="coordinates", name="DMNBuckner"
|
||||
)
|
||||
# Both tailored and raw should be same for now
|
||||
assert_array_equal(tailored_coords, raw_coords)
|
||||
assert tailored_labels == raw_labels
|
||||
|
||||
|
||||
def test_deregister() -> None:
|
||||
"""Test coordinates deregistration."""
|
||||
deregister_data(kind="coordinates", name="MyList")
|
||||
assert "MyList" not in list_data(kind="coordinates")
|
||||
|
|
|
|||
|
|
@ -56,7 +56,7 @@ class ANTsMaskWarper:
|
|||
dst: str,
|
||||
target_data: dict[str, Any],
|
||||
warp_data: Optional[dict[str, Any]],
|
||||
) -> "Nifti1Image":
|
||||
) -> "Nifti1Image": # pragma: no cover
|
||||
"""Warp ``mask_img`` to correct space.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ class FSLMaskWarper:
|
|||
mask_img: "Nifti1Image",
|
||||
target_data: dict[str, Any],
|
||||
warp_data: dict[str, Any],
|
||||
) -> "Nifti1Image":
|
||||
) -> "Nifti1Image": # pragma: no cover
|
||||
"""Warp ``mask_img`` to correct space.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -20,7 +20,14 @@ from nilearn.masking import (
|
|||
)
|
||||
from numpy.testing import assert_array_almost_equal, assert_array_equal
|
||||
|
||||
from junifer.data import MaskRegistry
|
||||
from junifer.data import (
|
||||
MaskRegistry,
|
||||
deregister_data,
|
||||
get_data,
|
||||
list_data,
|
||||
load_data,
|
||||
register_data,
|
||||
)
|
||||
from junifer.data.masks import compute_brain_mask
|
||||
from junifer.data.masks._masks import (
|
||||
_load_ukb_mask,
|
||||
|
|
@ -112,7 +119,8 @@ def test_compute_brain_mask_for_native(mask_type: str) -> None:
|
|||
def test_register_built_in_check() -> None:
|
||||
"""Test mask registration check for built-in masks."""
|
||||
with pytest.raises(ValueError, match=r"built-in mask"):
|
||||
MaskRegistry().register(
|
||||
register_data(
|
||||
kind="mask",
|
||||
name="GM_prob0.2",
|
||||
mask_path="testmask.nii.gz",
|
||||
space="MNI",
|
||||
|
|
@ -122,36 +130,39 @@ def test_register_built_in_check() -> None:
|
|||
|
||||
def test_list_incorrect() -> None:
|
||||
"""Test incorrect information check for list masks."""
|
||||
assert "testmask" not in MaskRegistry().list
|
||||
assert "testmask" not in list_data(kind="mask")
|
||||
|
||||
|
||||
def test_register_already_registered() -> None:
|
||||
"""Test mask registration check for already registered."""
|
||||
# Register custom mask
|
||||
MaskRegistry().register(
|
||||
register_data(
|
||||
kind="mask",
|
||||
name="testmask",
|
||||
mask_path="testmask.nii.gz",
|
||||
space="MNI",
|
||||
)
|
||||
out = MaskRegistry().load("testmask", path_only=True)
|
||||
out = load_data(kind="mask", name="testmask", path_only=True)
|
||||
assert out[1] is not None
|
||||
assert out[1].name == "testmask.nii.gz"
|
||||
|
||||
# Try registering again
|
||||
with pytest.raises(ValueError, match=r"already registered."):
|
||||
MaskRegistry().register(
|
||||
register_data(
|
||||
kind="mask",
|
||||
name="testmask",
|
||||
mask_path="testmask.nii.gz",
|
||||
space="MNI",
|
||||
)
|
||||
MaskRegistry().register(
|
||||
register_data(
|
||||
kind="mask",
|
||||
name="testmask",
|
||||
mask_path="testmask2.nii.gz",
|
||||
space="MNI",
|
||||
overwrite=True,
|
||||
)
|
||||
|
||||
out = MaskRegistry().load("testmask", path_only=True)
|
||||
out = load_data(kind="mask", name="testmask", path_only=True)
|
||||
assert out[1] is not None
|
||||
assert out[1].name == "testmask2.nii.gz"
|
||||
|
||||
|
|
@ -185,16 +196,17 @@ def test_register(
|
|||
|
||||
"""
|
||||
# Register custom mask
|
||||
MaskRegistry().register(
|
||||
register_data(
|
||||
kind="mask",
|
||||
name=name,
|
||||
mask_path=mask_path,
|
||||
space=space,
|
||||
overwrite=overwrite,
|
||||
)
|
||||
# List available mask and check registration
|
||||
assert name in MaskRegistry().list
|
||||
assert name in list_data(kind="mask")
|
||||
# Load registered mask
|
||||
_, fname, mask_space = MaskRegistry().load(name=name, path_only=True)
|
||||
_, fname, mask_space = load_data(kind="mask", name=name, path_only=True)
|
||||
# Check values for registered mask
|
||||
assert fname is not None
|
||||
assert fname.name == f"{name}.nii.gz"
|
||||
|
|
@ -218,7 +230,7 @@ def test_list_correct(mask_name: str) -> None:
|
|||
The parametrized mask name.
|
||||
|
||||
"""
|
||||
assert mask_name in MaskRegistry().list
|
||||
assert mask_name in list_data(kind="mask")
|
||||
|
||||
|
||||
def test_load_incorrect() -> None:
|
||||
|
|
@ -270,9 +282,12 @@ def test_vickery_patil(
|
|||
The parametrized name of the mask file.
|
||||
|
||||
"""
|
||||
mask, mask_fname, space = MaskRegistry().load(name, resolution=resolution)
|
||||
mask, mask_fname, space = load_data(
|
||||
kind="mask", name=name, resolution=resolution
|
||||
)
|
||||
assert_array_almost_equal(
|
||||
mask.header["pixdim"][1:4], pixdim # type: ignore
|
||||
mask.header["pixdim"][1:4],
|
||||
pixdim, # type: ignore
|
||||
)
|
||||
assert space == "IXI549Space"
|
||||
assert mask_fname is not None
|
||||
|
|
@ -287,7 +302,9 @@ def test_vickery_patil_error() -> None:
|
|||
|
||||
def test_ukb() -> None:
|
||||
"""Test UKB mask."""
|
||||
mask, mask_fname, space = MaskRegistry().load("UKB_15K_GM", resolution=2.0)
|
||||
mask, mask_fname, space = load_data(
|
||||
kind="mask", name="UKB_15K_GM", resolution=2.0
|
||||
)
|
||||
assert_array_almost_equal(mask.header["pixdim"][1:4], 2.0) # type: ignore
|
||||
assert space == "MNI152NLin6Asym"
|
||||
assert mask_fname is not None
|
||||
|
|
@ -306,8 +323,8 @@ def test_get() -> None:
|
|||
element_data = DefaultDataReader().fit_transform(dg["sub-01"])
|
||||
vbm_gm = element_data["VBM_GM"]
|
||||
vbm_gm_img = vbm_gm["data"]
|
||||
mask = MaskRegistry().get(
|
||||
masks="compute_brain_mask", target_data=vbm_gm
|
||||
mask = get_data(
|
||||
kind="mask", names="compute_brain_mask", target_data=vbm_gm
|
||||
)
|
||||
|
||||
assert mask.shape == vbm_gm_img.shape
|
||||
|
|
@ -355,28 +372,33 @@ def test_get_errors() -> None:
|
|||
vbm_gm = element_data["VBM_GM"]
|
||||
# Test wrong masks definitions (more than one key per dict)
|
||||
with pytest.raises(ValueError, match=r"only one key"):
|
||||
MaskRegistry().get(
|
||||
masks={"GM_prob0.2": {}, "Other": {}}, target_data=vbm_gm
|
||||
get_data(
|
||||
kind="mask",
|
||||
names={"GM_prob0.2": {}, "Other": {}},
|
||||
target_data=vbm_gm,
|
||||
)
|
||||
|
||||
# Test wrong masks definitions (pass paramaeters to non-callable mask)
|
||||
with pytest.raises(ValueError, match=r"callable params"):
|
||||
MaskRegistry().get(
|
||||
masks={"GM_prob0.2": {"param": 1}}, target_data=vbm_gm
|
||||
get_data(
|
||||
kind="mask",
|
||||
names={"GM_prob0.2": {"param": 1}},
|
||||
target_data=vbm_gm,
|
||||
)
|
||||
|
||||
# Pass only parameters to the intersection function
|
||||
with pytest.raises(
|
||||
ValueError, match=r" At least one mask is required."
|
||||
):
|
||||
MaskRegistry().get(masks={"threshold": 1}, target_data=vbm_gm)
|
||||
get_data(kind="mask", names={"threshold": 1}, target_data=vbm_gm)
|
||||
|
||||
# Pass parameters to the intersection function when only one mask
|
||||
with pytest.raises(
|
||||
ValueError, match=r"parameters to the intersection"
|
||||
):
|
||||
MaskRegistry().get(
|
||||
masks=["compute_brain_mask", {"threshold": 1}],
|
||||
get_data(
|
||||
kind="mask",
|
||||
names=["compute_brain_mask", {"threshold": 1}],
|
||||
target_data=vbm_gm,
|
||||
)
|
||||
|
||||
|
|
@ -423,7 +445,7 @@ def test_nilearn_compute_masks(
|
|||
else:
|
||||
mask_spec = {mask_name: params}
|
||||
|
||||
mask = MaskRegistry().get(masks=mask_spec, target_data=bold)
|
||||
mask = get_data(kind="mask", names=mask_spec, target_data=bold)
|
||||
|
||||
assert_array_equal(mask.affine, bold_img.affine)
|
||||
|
||||
|
|
@ -449,8 +471,9 @@ def test_get_inherit() -> None:
|
|||
gm_mask = compute_brain_mask(element_data["BOLD"], threshold=0.2)
|
||||
|
||||
# Get mask using the compute_brain_mask function
|
||||
mask1 = MaskRegistry().get(
|
||||
masks={"compute_brain_mask": {"threshold": 0.2}},
|
||||
mask1 = get_data(
|
||||
kind="mask",
|
||||
names={"compute_brain_mask": {"threshold": 0.2}},
|
||||
target_data=element_data["BOLD"],
|
||||
)
|
||||
|
||||
|
|
@ -461,8 +484,9 @@ def test_get_inherit() -> None:
|
|||
"data": gm_mask,
|
||||
"space": element_data["BOLD"]["space"],
|
||||
}
|
||||
mask2 = MaskRegistry().get(
|
||||
masks="inherit",
|
||||
mask2 = get_data(
|
||||
kind="mask",
|
||||
names="inherit",
|
||||
target_data=bold_dict,
|
||||
)
|
||||
|
||||
|
|
@ -503,8 +527,8 @@ def test_get_multiple(
|
|||
target_img = element_data["BOLD"]["data"]
|
||||
resolution = np.min(target_img.header.get_zooms()[:3])
|
||||
|
||||
computed = MaskRegistry().get(
|
||||
masks=junifer_masks, target_data=element_data["BOLD"]
|
||||
computed = get_data(
|
||||
kind="mask", names=junifer_masks, target_data=element_data["BOLD"]
|
||||
)
|
||||
|
||||
masks_names = [
|
||||
|
|
@ -523,8 +547,11 @@ def test_get_multiple(
|
|||
]
|
||||
|
||||
mask_imgs = [
|
||||
MaskRegistry().load(
|
||||
t_mask, path_only=False, resolution=resolution
|
||||
load_data(
|
||||
kind="mask",
|
||||
name=t_mask,
|
||||
path_only=False,
|
||||
resolution=resolution,
|
||||
)[0]
|
||||
for t_mask in mask_files
|
||||
]
|
||||
|
|
@ -554,3 +581,9 @@ def test_get_multiple(
|
|||
|
||||
expected = intersect_masks(mask_imgs, **params)
|
||||
assert_array_equal(computed.get_fdata(), expected.get_fdata())
|
||||
|
||||
|
||||
def test_deregister() -> None:
|
||||
"""Test mask deregistration."""
|
||||
deregister_data(kind="mask", name="testmask")
|
||||
assert "testmask" not in list_data(kind="mask")
|
||||
|
|
|
|||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
|
|
@ -84,7 +84,7 @@ class ANTsParcellationWarper:
|
|||
)
|
||||
|
||||
# Native space warping
|
||||
if dst == "native":
|
||||
if dst == "native": # pragma: no cover
|
||||
# Warp data check
|
||||
if warp_data is None:
|
||||
raise_error("No `warp_data` provided")
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ class FSLParcellationWarper:
|
|||
parcellation_img: "Nifti1Image",
|
||||
target_data: dict[str, Any],
|
||||
warp_data: dict[str, Any],
|
||||
) -> "Nifti1Image":
|
||||
) -> "Nifti1Image": # pragma: no cover
|
||||
"""Warp ``parcellation_img`` to correct space.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -1035,17 +1035,17 @@ def _retrieve_shen(
|
|||
)
|
||||
if n_rois in (268, 368) and year == 2013:
|
||||
raise_error(
|
||||
f"The parameter combination `resolution = {resolution}` and "
|
||||
f"The parameter combination `n_rois = {n_rois}` and "
|
||||
"`year = 2013` is invalid"
|
||||
)
|
||||
if n_rois in (50, 100, 150) and year in (2015, 2019):
|
||||
raise_error(
|
||||
f"The parameter combination `resolution = {resolution}` and "
|
||||
f"The parameter combination `n_rois = {n_rois}` and "
|
||||
f"`year = {year}` is invalid"
|
||||
)
|
||||
if (n_rois == 268 and year == 2019) or (n_rois == 368 and year == 2015):
|
||||
raise_error(
|
||||
f"The parameter combination `resolution = {resolution}` and "
|
||||
f"The parameter combination `n_rois = {n_rois}` and "
|
||||
f"`year = {year}` is invalid"
|
||||
)
|
||||
|
||||
|
|
@ -1312,11 +1312,11 @@ def merge_parcellations(
|
|||
parcellations_names: list[str],
|
||||
labels_lists: list[list[str]],
|
||||
) -> tuple["Nifti1Image", list[str]]:
|
||||
"""Merge all parcellations from a list into one parcellation.
|
||||
"""Merge multiple parcellations.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
parcellations_list : list of niimg-like object
|
||||
parcellations_list : list of Niimg-like object
|
||||
List of parcellations to merge.
|
||||
parcellations_names: list of str
|
||||
List of names for parcellations at the corresponding indices.
|
||||
|
|
@ -1326,10 +1326,10 @@ def merge_parcellations(
|
|||
|
||||
Returns
|
||||
-------
|
||||
parcellation : niimg-like object
|
||||
Niimg-like object
|
||||
The parcellation that results from merging the list of input
|
||||
parcellations.
|
||||
labels : list of str
|
||||
list of str
|
||||
List of labels for the resultant parcellation.
|
||||
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -13,7 +13,12 @@ import pytest
|
|||
from nilearn.image import new_img_like, resample_to_img
|
||||
from numpy.testing import assert_array_almost_equal, assert_array_equal
|
||||
|
||||
from junifer.data import ParcellationRegistry
|
||||
from junifer.data import (
|
||||
get_data,
|
||||
list_data,
|
||||
load_data,
|
||||
register_data,
|
||||
)
|
||||
from junifer.data.parcellations import merge_parcellations
|
||||
from junifer.data.parcellations._parcellations import (
|
||||
_retrieve_aicha,
|
||||
|
|
@ -35,7 +40,8 @@ from junifer.testing.datagrabbers import (
|
|||
def test_register_built_in_check() -> None:
|
||||
"""Test parcellation registration check for built-in parcellations."""
|
||||
with pytest.raises(ValueError, match=r"built-in parcellation"):
|
||||
ParcellationRegistry().register(
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name="SUITxSUIT",
|
||||
parcellation_path="testparc.nii.gz",
|
||||
parcels_labels=["1", "2", "3"],
|
||||
|
|
@ -46,34 +52,40 @@ def test_register_built_in_check() -> None:
|
|||
|
||||
def test_list_incorrect() -> None:
|
||||
"""Test incorrect information check for list parcellations."""
|
||||
assert "testparc" not in ParcellationRegistry().list
|
||||
assert "testparc" not in list_data(kind="parcellation")
|
||||
|
||||
|
||||
def test_register_already_registered() -> None:
|
||||
"""Test parcellation registration check for already registered."""
|
||||
# Register custom parcellation
|
||||
ParcellationRegistry().register(
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name="testparc",
|
||||
parcellation_path="testparc.nii.gz",
|
||||
parcels_labels=["1", "2", "3"],
|
||||
space="MNI152Lin",
|
||||
)
|
||||
assert (
|
||||
ParcellationRegistry()
|
||||
.load("testparc", target_space="MNI152Lin", path_only=True)[2]
|
||||
.name
|
||||
load_data(
|
||||
kind="parcellation",
|
||||
name="testparc",
|
||||
target_space="MNI152Lin",
|
||||
path_only=True,
|
||||
)[2].name
|
||||
== "testparc.nii.gz"
|
||||
)
|
||||
|
||||
# Try registering again
|
||||
with pytest.raises(ValueError, match=r"already registered."):
|
||||
ParcellationRegistry().register(
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name="testparc",
|
||||
parcellation_path="testparc.nii.gz",
|
||||
parcels_labels=["1", "2", "3"],
|
||||
space="MNI152Lin",
|
||||
)
|
||||
ParcellationRegistry().register(
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name="testparc",
|
||||
parcellation_path="testparc2.nii.gz",
|
||||
parcels_labels=["1", "2", "3"],
|
||||
|
|
@ -82,9 +94,12 @@ def test_register_already_registered() -> None:
|
|||
)
|
||||
|
||||
assert (
|
||||
ParcellationRegistry()
|
||||
.load("testparc", target_space="MNI152Lin", path_only=True)[2]
|
||||
.name
|
||||
load_data(
|
||||
kind="parcellation",
|
||||
name="testparc",
|
||||
target_space="MNI152Lin",
|
||||
path_only=True,
|
||||
)[2].name
|
||||
== "testparc2.nii.gz"
|
||||
)
|
||||
|
||||
|
|
@ -98,27 +113,44 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
|
|||
The path to the test directory.
|
||||
|
||||
"""
|
||||
schaefer, labels, schaefer_path, _ = ParcellationRegistry().load(
|
||||
"Schaefer100x7",
|
||||
"MNI152NLin6Asym",
|
||||
schaefer, labels, schaefer_path, _ = load_data(
|
||||
kind="parcellation",
|
||||
name="Schaefer100x7",
|
||||
target_space="MNI152NLin6Asym",
|
||||
)
|
||||
assert schaefer is not None
|
||||
|
||||
# Test wrong number of labels
|
||||
ParcellationRegistry().register(
|
||||
"WrongLabels", schaefer_path, labels[:10], "MNI152Lin"
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name="WrongLabels",
|
||||
parcellation_path=schaefer_path,
|
||||
parcels_labels=labels[:10],
|
||||
space="MNI152Lin",
|
||||
)
|
||||
|
||||
with pytest.raises(ValueError, match=r"has 100 parcels but 10"):
|
||||
ParcellationRegistry().load("WrongLabels", "MNI152NLin6Asym")
|
||||
load_data(
|
||||
kind="parcellation",
|
||||
name="WrongLabels",
|
||||
target_space="MNI152NLin6Asym",
|
||||
)
|
||||
|
||||
# Test wrong number of labels
|
||||
ParcellationRegistry().register(
|
||||
"WrongLabels2", schaefer_path, [*labels, "wrong"], "MNI152Lin"
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name="WrongLabels2",
|
||||
parcellation_path=schaefer_path,
|
||||
parcels_labels=[*labels, "wrong"],
|
||||
space="MNI152Lin",
|
||||
)
|
||||
|
||||
with pytest.raises(ValueError, match=r"has 100 parcels but 101"):
|
||||
ParcellationRegistry().load("WrongLabels2", "MNI152NLin6Asym")
|
||||
load_data(
|
||||
kind="parcellation",
|
||||
name="WrongLabels2",
|
||||
target_space="MNI152NLin6Asym",
|
||||
)
|
||||
|
||||
schaefer_data = schaefer.get_fdata().copy()
|
||||
schaefer_data[schaefer_data == 50] = 0
|
||||
|
|
@ -126,11 +158,19 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
|
|||
new_schaefer_img = new_img_like(schaefer, schaefer_data)
|
||||
nib.save(new_schaefer_img, new_schaefer_path)
|
||||
|
||||
ParcellationRegistry().register(
|
||||
"WrongValues", new_schaefer_path, labels[:-1], "MNI152Lin"
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name="WrongValues",
|
||||
parcellation_path=new_schaefer_path,
|
||||
parcels_labels=labels[:-1],
|
||||
space="MNI152Lin",
|
||||
)
|
||||
with pytest.raises(ValueError, match=r"must have all the values in the"):
|
||||
ParcellationRegistry().load("WrongValues", "MNI152NLin6Asym")
|
||||
load_data(
|
||||
kind="parcellation",
|
||||
name="WrongValues",
|
||||
target_space="MNI152NLin6Asym",
|
||||
)
|
||||
|
||||
schaefer_data = schaefer.get_fdata().copy()
|
||||
schaefer_data[schaefer_data == 50] = 200
|
||||
|
|
@ -138,11 +178,19 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
|
|||
new_schaefer_img = new_img_like(schaefer, schaefer_data)
|
||||
nib.save(new_schaefer_img, new_schaefer_path)
|
||||
|
||||
ParcellationRegistry().register(
|
||||
"WrongValues2", new_schaefer_path, labels, "MNI152Lin"
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name="WrongValues2",
|
||||
parcellation_path=new_schaefer_path,
|
||||
parcels_labels=labels,
|
||||
space="MNI152Lin",
|
||||
)
|
||||
with pytest.raises(ValueError, match=r"must have all the values in the"):
|
||||
ParcellationRegistry().load("WrongValues2", "MNI152NLin6Asym")
|
||||
load_data(
|
||||
kind="parcellation",
|
||||
name="WrongValues2",
|
||||
target_space="MNI152NLin6Asym",
|
||||
)
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
|
|
@ -195,7 +243,8 @@ def test_register(
|
|||
|
||||
"""
|
||||
# Register custom parcellation
|
||||
ParcellationRegistry().register(
|
||||
register_data(
|
||||
kind="parcellation",
|
||||
name=name,
|
||||
parcellation_path=parcellation_path,
|
||||
parcels_labels=parcels_labels,
|
||||
|
|
@ -203,10 +252,13 @@ def test_register(
|
|||
overwrite=overwrite,
|
||||
)
|
||||
# List available parcellation and check registration
|
||||
assert name in ParcellationRegistry().list
|
||||
assert name in list_data(kind="parcellation")
|
||||
# Load registered parcellation
|
||||
_, lbl, fname, parcellation_space = ParcellationRegistry().load(
|
||||
name=name, target_space=space, path_only=True
|
||||
_, lbl, fname, parcellation_space = load_data(
|
||||
kind="parcellation",
|
||||
name=name,
|
||||
target_space=space,
|
||||
path_only=True,
|
||||
)
|
||||
# Check values for registered parcellation
|
||||
assert lbl == parcels_labels
|
||||
|
|
@ -237,13 +289,17 @@ def test_list_correct(parcellation_name: str) -> None:
|
|||
The parametrized parcellation name.
|
||||
|
||||
"""
|
||||
assert parcellation_name in ParcellationRegistry().list
|
||||
assert parcellation_name in list_data(kind="parcellation")
|
||||
|
||||
|
||||
def test_load_incorrect() -> None:
|
||||
"""Test loading of invalid parcellations."""
|
||||
with pytest.raises(ValueError, match=r"not found"):
|
||||
ParcellationRegistry().load("wrongparcellation", "MNI152NLin6Asym")
|
||||
load_data(
|
||||
kind="parcellation",
|
||||
name="wrongparcellation",
|
||||
target_space="MNI152NLin6Asym",
|
||||
)
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
|
|
@ -309,14 +365,15 @@ def test_schaefer(
|
|||
|
||||
"""
|
||||
parcellation_name = f"Schaefer{n_rois}x{yeo_networks}"
|
||||
assert parcellation_name in ParcellationRegistry().list
|
||||
assert parcellation_name in list_data(kind="parcellation")
|
||||
|
||||
parcellation_file = (
|
||||
f"Schaefer2018_{n_rois}Parcels_{yeo_networks}Networks_order_FSLMNI152_"
|
||||
f"{int(resolution)}mm.nii.gz"
|
||||
)
|
||||
# Load parcellation
|
||||
img, label, img_path, space = ParcellationRegistry().load(
|
||||
img, label, img_path, space = load_data(
|
||||
kind="parcellation",
|
||||
name=parcellation_name,
|
||||
target_space="MNI152NLin6Asym",
|
||||
resolution=resolution,
|
||||
|
|
@ -326,7 +383,8 @@ def test_schaefer(
|
|||
assert len(label) == n_rois
|
||||
assert space == "MNI152NLin6Asym"
|
||||
assert_array_equal(
|
||||
img.header["pixdim"][1:4], 3 * [resolution] # type: ignore
|
||||
img.header["pixdim"][1:4],
|
||||
3 * [resolution], # type: ignore
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -365,9 +423,10 @@ def test_suit(space_key: str, space: str) -> None:
|
|||
The parametrized space values.
|
||||
|
||||
"""
|
||||
assert f"SUITx{space_key}" in ParcellationRegistry().list
|
||||
assert f"SUITx{space_key}" in list_data(kind="parcellation")
|
||||
# Load parcellation
|
||||
img, label, img_path, parcellation_space = ParcellationRegistry().load(
|
||||
img, label, img_path, parcellation_space = load_data(
|
||||
kind="parcellation",
|
||||
name=f"SUITx{space_key}",
|
||||
target_space=space,
|
||||
)
|
||||
|
|
@ -398,13 +457,14 @@ def test_tian_3T_6thgeneration(scale: int, n_label: int) -> None:
|
|||
The parametrized n_label values.
|
||||
|
||||
"""
|
||||
parcellations = ParcellationRegistry().list
|
||||
parcellations = list_data(kind="parcellation")
|
||||
assert "TianxS1x3TxMNI6thgeneration" in parcellations
|
||||
assert "TianxS2x3TxMNI6thgeneration" in parcellations
|
||||
assert "TianxS3x3TxMNI6thgeneration" in parcellations
|
||||
assert "TianxS4x3TxMNI6thgeneration" in parcellations
|
||||
# Load parcellation
|
||||
img, lbl, fname, space = ParcellationRegistry().load(
|
||||
img, lbl, fname, space = load_data(
|
||||
kind="parcellation",
|
||||
name=f"TianxS{scale}x3TxMNI6thgeneration",
|
||||
target_space="MNI152NLin2009cAsym", # force highest resolution
|
||||
)
|
||||
|
|
@ -415,7 +475,8 @@ def test_tian_3T_6thgeneration(scale: int, n_label: int) -> None:
|
|||
assert len(lbl) == n_label
|
||||
assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])
|
||||
# Load parcellation
|
||||
img, lbl, fname, space = ParcellationRegistry().load(
|
||||
img, lbl, fname, space = load_data(
|
||||
kind="parcellation",
|
||||
name=f"TianxS{scale}x3TxMNI6thgeneration",
|
||||
target_space="MNI152NLin6Asym",
|
||||
resolution=2,
|
||||
|
|
@ -442,13 +503,14 @@ def test_tian_3T_nonlinear2009cAsym(scale: int, n_label: int) -> None:
|
|||
The parametrized n_label values.
|
||||
|
||||
"""
|
||||
parcellations = ParcellationRegistry().list
|
||||
parcellations = list_data(kind="parcellation")
|
||||
assert "TianxS1x3TxMNInonlinear2009cAsym" in parcellations
|
||||
assert "TianxS2x3TxMNInonlinear2009cAsym" in parcellations
|
||||
assert "TianxS3x3TxMNInonlinear2009cAsym" in parcellations
|
||||
assert "TianxS4x3TxMNInonlinear2009cAsym" in parcellations
|
||||
# Load parcellation
|
||||
img, lbl, fname, space = ParcellationRegistry().load(
|
||||
img, lbl, fname, space = load_data(
|
||||
kind="parcellation",
|
||||
name=f"TianxS{scale}x3TxMNInonlinear2009cAsym",
|
||||
target_space="MNI152NLin6Asym", # force highest resolution
|
||||
)
|
||||
|
|
@ -459,7 +521,8 @@ def test_tian_3T_nonlinear2009cAsym(scale: int, n_label: int) -> None:
|
|||
assert len(lbl) == n_label
|
||||
assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])
|
||||
# Load parcellation
|
||||
img, lbl, fname, space = ParcellationRegistry().load(
|
||||
img, lbl, fname, space = load_data(
|
||||
kind="parcellation",
|
||||
name=f"TianxS{scale}x3TxMNInonlinear2009cAsym",
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
resolution=2,
|
||||
|
|
@ -486,13 +549,14 @@ def test_tian_7T_6thgeneration(scale: int, n_label: int) -> None:
|
|||
The parametrized n_label values.
|
||||
|
||||
"""
|
||||
parcellations = ParcellationRegistry().list
|
||||
parcellations = list_data(kind="parcellation")
|
||||
assert "TianxS1x7TxMNI6thgeneration" in parcellations
|
||||
assert "TianxS2x7TxMNI6thgeneration" in parcellations
|
||||
assert "TianxS3x7TxMNI6thgeneration" in parcellations
|
||||
assert "TianxS4x7TxMNI6thgeneration" in parcellations
|
||||
# Load parcellation
|
||||
img, lbl, fname, space = ParcellationRegistry().load(
|
||||
img, lbl, fname, space = load_data(
|
||||
kind="parcellation",
|
||||
name=f"TianxS{scale}x7TxMNI6thgeneration",
|
||||
target_space="MNI152NLin6Asym",
|
||||
)
|
||||
|
|
@ -502,7 +566,8 @@ def test_tian_7T_6thgeneration(scale: int, n_label: int) -> None:
|
|||
assert space == "MNI152NLin6Asym"
|
||||
assert len(lbl) == n_label
|
||||
assert_array_almost_equal(
|
||||
img.header["pixdim"][1:4], [1.6, 1.6, 1.6] # type: ignore
|
||||
img.header["pixdim"][1:4],
|
||||
[1.6, 1.6, 1.6], # type: ignore
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -552,9 +617,10 @@ def test_aicha(version: int) -> None:
|
|||
The parametrized version values.
|
||||
|
||||
"""
|
||||
assert f"AICHA_v{version}" in ParcellationRegistry().list
|
||||
assert f"AICHA_v{version}" in list_data(kind="parcellation")
|
||||
# Load parcellation
|
||||
img, label, img_path, space = ParcellationRegistry().load(
|
||||
img, label, img_path, space = load_data(
|
||||
kind="parcellation",
|
||||
name=f"AICHA_v{version}",
|
||||
target_space="IXI549Space",
|
||||
)
|
||||
|
|
@ -610,9 +676,10 @@ def test_shen(
|
|||
The parametrized partial file names.
|
||||
|
||||
"""
|
||||
assert f"Shen_{year}_{n_rois}" in ParcellationRegistry().list
|
||||
assert f"Shen_{year}_{n_rois}" in list_data(kind="parcellation")
|
||||
# Load parcellation
|
||||
img, label, img_path, space = ParcellationRegistry().load(
|
||||
img, label, img_path, space = load_data(
|
||||
kind="parcellation",
|
||||
name=f"Shen_{year}_{n_rois}",
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
resolution=resolution,
|
||||
|
|
@ -622,7 +689,8 @@ def test_shen(
|
|||
assert space == "MNI152NLin2009cAsym"
|
||||
assert len(label) == n_labels
|
||||
assert_array_equal(
|
||||
img.header["pixdim"][1:4], 3 * [resolution] # type: ignore
|
||||
img.header["pixdim"][1:4],
|
||||
3 * [resolution], # type: ignore
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -771,7 +839,7 @@ def test_yan(
|
|||
The parametrized Kong networks values.
|
||||
|
||||
"""
|
||||
parcellations = ParcellationRegistry().list
|
||||
parcellations = list_data(kind="parcellation")
|
||||
if yeo_networks:
|
||||
parcellation_name = f"Yan{n_rois}xYeo{yeo_networks}"
|
||||
assert parcellation_name in parcellations
|
||||
|
|
@ -787,7 +855,8 @@ def test_yan(
|
|||
f"{int(resolution)}mm.nii.gz"
|
||||
)
|
||||
# Load parcellation
|
||||
img, label, img_path, space = ParcellationRegistry().load(
|
||||
img, label, img_path, space = load_data(
|
||||
kind="parcellation",
|
||||
name=parcellation_name,
|
||||
target_space="MNI152NLin6Asym",
|
||||
resolution=resolution,
|
||||
|
|
@ -797,7 +866,8 @@ def test_yan(
|
|||
assert space == "MNI152NLin6Asym"
|
||||
assert len(label) == n_rois
|
||||
assert_array_equal(
|
||||
img.header["pixdim"][1:4], 3 * [resolution] # type: ignore
|
||||
img.header["pixdim"][1:4],
|
||||
3 * [resolution], # type: ignore
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -877,7 +947,7 @@ def test_brainnetome(
|
|||
The parametrized threshold values.
|
||||
|
||||
"""
|
||||
parcellations = ParcellationRegistry().list
|
||||
parcellations = list_data(kind="parcellation")
|
||||
parcellation_name = f"Brainnetome_thr{threshold}"
|
||||
assert parcellation_name in parcellations
|
||||
|
||||
|
|
@ -887,7 +957,8 @@ def test_brainnetome(
|
|||
|
||||
parcellation_file = f"BNA-maxprob-thr{threshold}-{resolution}mm.nii.gz"
|
||||
# Load parcellation
|
||||
img, label, img_path, space = ParcellationRegistry().load(
|
||||
img, label, img_path, space = load_data(
|
||||
kind="parcellation",
|
||||
name=parcellation_name,
|
||||
target_space="MNI152NLin6Asym",
|
||||
resolution=resolution,
|
||||
|
|
@ -897,7 +968,8 @@ def test_brainnetome(
|
|||
assert space == "MNI152NLin6Asym"
|
||||
assert len(label) == 246
|
||||
assert_array_equal(
|
||||
img.header["pixdim"][1:4], 3 * [resolution] # type: ignore
|
||||
img.header["pixdim"][1:4],
|
||||
3 * [resolution], # type: ignore
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -912,11 +984,14 @@ def test_retrieve_brainnetome_incorrect_threshold() -> None:
|
|||
def test_merge_parcellations() -> None:
|
||||
"""Test merging parcellations."""
|
||||
# load some parcellations for testing
|
||||
schaefer_parcellation, schaefer_labels, _, _ = ParcellationRegistry().load(
|
||||
"Schaefer100x17", target_space="MNI152NLin2009cAsym"
|
||||
schaefer_parcellation, schaefer_labels, _, _ = load_data(
|
||||
kind="parcellation",
|
||||
name="Schaefer100x17",
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
)
|
||||
tian_parcellation, tian_labels, _, _ = ParcellationRegistry().load(
|
||||
"TianxS2x3TxMNInonlinear2009cAsym",
|
||||
tian_parcellation, tian_labels, _, _ = load_data(
|
||||
kind="parcellation",
|
||||
name="TianxS2x3TxMNInonlinear2009cAsym",
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
)
|
||||
# prepare the list of the actual parcellations
|
||||
|
|
@ -949,8 +1024,10 @@ def test_merge_parcellations_3D_multiple_non_overlapping(
|
|||
|
||||
"""
|
||||
# Get the testing parcellation
|
||||
parcellation, labels, _, _ = ParcellationRegistry().load(
|
||||
"Schaefer100x7", target_space="MNI152NLin2009cAsym"
|
||||
parcellation, labels, _, _ = load_data(
|
||||
kind="parcellation",
|
||||
name="Schaefer100x7",
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
)
|
||||
|
||||
assert parcellation is not None
|
||||
|
|
@ -986,8 +1063,10 @@ def test_merge_parcellations_3D_multiple_overlapping() -> None:
|
|||
"""Test merge_parcellations with multiple overlapping parcellations."""
|
||||
|
||||
# Get the testing parcellation
|
||||
parcellation, labels, _, _ = ParcellationRegistry().load(
|
||||
"Schaefer100x7", target_space="MNI152NLin2009cAsym"
|
||||
parcellation, labels, _, _ = load_data(
|
||||
kind="parcellation",
|
||||
name="Schaefer100x7",
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
)
|
||||
|
||||
assert parcellation is not None
|
||||
|
|
@ -1023,8 +1102,10 @@ def test_merge_parcellations_3D_multiple_duplicated_labels() -> None:
|
|||
"""Test merge_parcellations with duplicated labels."""
|
||||
|
||||
# Get the testing parcellation
|
||||
parcellation, labels, _, _ = ParcellationRegistry().load(
|
||||
"Schaefer100x7", target_space="MNI152NLin2009cAsym"
|
||||
parcellation, labels, _, _ = load_data(
|
||||
kind="parcellation",
|
||||
name="Schaefer100x7",
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
)
|
||||
|
||||
assert parcellation is not None
|
||||
|
|
@ -1064,15 +1145,17 @@ def test_get_single() -> None:
|
|||
bold = element_data["BOLD"]
|
||||
bold_img = bold["data"]
|
||||
# Get tailored parcellation
|
||||
tailored_parcellation, tailored_labels = ParcellationRegistry().get(
|
||||
parcellations=["Shen_2015_268"],
|
||||
tailored_parcellation, tailored_labels = get_data(
|
||||
kind="parcellation",
|
||||
names=["Shen_2015_268"],
|
||||
target_data=bold,
|
||||
)
|
||||
# Check shape and affine with original element data
|
||||
assert tailored_parcellation.shape == bold_img.shape[:3]
|
||||
assert_array_equal(tailored_parcellation.affine, bold_img.affine)
|
||||
# Get raw parcellation
|
||||
raw_parcellation, raw_labels, _, _ = ParcellationRegistry().load(
|
||||
raw_parcellation, raw_labels, _, _ = load_data(
|
||||
kind="parcellation",
|
||||
name="Shen_2015_268",
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
resolution=4,
|
||||
|
|
@ -1098,8 +1181,9 @@ def test_get_multi_same_space() -> None:
|
|||
bold = element_data["BOLD"]
|
||||
bold_img = bold["data"]
|
||||
# Get tailored parcellation
|
||||
tailored_parcellation, tailored_labels = ParcellationRegistry().get(
|
||||
parcellations=[
|
||||
tailored_parcellation, tailored_labels = get_data(
|
||||
kind="parcellation",
|
||||
names=[
|
||||
"Shen_2015_268",
|
||||
"TianxS1x3TxMNInonlinear2009cAsym",
|
||||
],
|
||||
|
|
@ -1116,7 +1200,8 @@ def test_get_multi_same_space() -> None:
|
|||
"TianxS1x3TxMNInonlinear2009cAsym",
|
||||
]
|
||||
for name in parcellations_names:
|
||||
img, labels, _, _ = ParcellationRegistry().load(
|
||||
img, labels, _, _ = load_data(
|
||||
kind="parcellation",
|
||||
name=name,
|
||||
target_space="MNI152NLin2009cAsym",
|
||||
resolution=4,
|
||||
|
|
@ -1152,8 +1237,9 @@ def test_get_multi_different_space() -> None:
|
|||
with OasisVBMTestingDataGrabber() as dg:
|
||||
element_data = DefaultDataReader().fit_transform(dg["sub-01"])
|
||||
# Get tailored parcellation
|
||||
ParcellationRegistry().get(
|
||||
parcellations=[
|
||||
get_data(
|
||||
kind="parcellation",
|
||||
names=[
|
||||
"Schaefer100x7",
|
||||
"TianxS1x3TxMNInonlinear2009cAsym",
|
||||
],
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
import numpy as np
|
||||
import pytest
|
||||
|
||||
|
|
|
|||
|
|
@ -76,7 +76,7 @@ def get_native_warper(
|
|||
target_data: MutableMapping,
|
||||
other_data: MutableMapping,
|
||||
inverse: bool = False,
|
||||
) -> dict:
|
||||
) -> dict: # pragma: no cover
|
||||
"""Get correct warping specification for native space.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -35,6 +35,12 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
|
|||
space : {"native", "MNI152NLin2009cAsym"}, optional
|
||||
The space to use for the data (default "MNI152NLin2009cAsym").
|
||||
|
||||
Raises
|
||||
------
|
||||
ValueError
|
||||
If invalid value is passed for:
|
||||
* ``space``
|
||||
|
||||
"""
|
||||
|
||||
def __init__(
|
||||
|
|
|
|||
|
|
@ -43,7 +43,9 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
|
|||
Raises
|
||||
------
|
||||
ValueError
|
||||
If invalid value is passed for ``tasks``.
|
||||
If invalid value is passed for:
|
||||
* ``tasks``
|
||||
* ``space``
|
||||
|
||||
"""
|
||||
|
||||
|
|
@ -79,8 +81,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
|
|||
for t in tasks:
|
||||
if t not in all_tasks:
|
||||
raise_error(
|
||||
f"{t} is not a valid task in the AOMIC PIOP1"
|
||||
" dataset!"
|
||||
f"{t} is not a valid task in the AOMIC PIOP1 dataset!"
|
||||
)
|
||||
self.tasks = tasks
|
||||
# Descriptor for space in `anat`
|
||||
|
|
|
|||
|
|
@ -43,7 +43,9 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
|
|||
Raises
|
||||
------
|
||||
ValueError
|
||||
If invalid value is passed for ``tasks``.
|
||||
If invalid value is passed for:
|
||||
* ``tasks``
|
||||
* ``space``
|
||||
|
||||
"""
|
||||
|
||||
|
|
@ -77,8 +79,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
|
|||
for t in tasks:
|
||||
if t not in all_tasks:
|
||||
raise_error(
|
||||
f"{t} is not a valid task in the AOMIC PIOP2"
|
||||
" dataset!"
|
||||
f"{t} is not a valid task in the AOMIC PIOP2 dataset!"
|
||||
)
|
||||
self.tasks = tasks
|
||||
# Descriptor for space in `anat`
|
||||
|
|
|
|||
|
|
@ -5,7 +5,6 @@
|
|||
# Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
from ..api.decorators import register_datagrabber
|
||||
from ..utils import logger
|
||||
from .datalad_base import DataladDataGrabber
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
from ..typing import DataGrabberPatterns
|
||||
from ..utils import logger, raise_error, warn_with_log
|
||||
|
||||
|
|
|
|||
|
|
@ -264,7 +264,7 @@ def test_DMCC13Benchmark_invalid_sessions():
|
|||
"""Test DMCC13Benchmark DataGrabber invalid sessions."""
|
||||
with pytest.raises(
|
||||
ValueError,
|
||||
match=("phonyses is not a valid session in " "the DMCC dataset"),
|
||||
match=("phonyses is not a valid session in the DMCC dataset"),
|
||||
):
|
||||
DMCC13Benchmark(sessions="phonyses")
|
||||
|
||||
|
|
@ -273,9 +273,7 @@ def test_DMCC13Benchmark_invalid_tasks():
|
|||
"""Test DMCC13Benchmark DataGrabber invalid tasks."""
|
||||
with pytest.raises(
|
||||
ValueError,
|
||||
match=(
|
||||
"thisisnotarealtask is not a valid task in " "the DMCC dataset"
|
||||
),
|
||||
match=("thisisnotarealtask is not a valid task in the DMCC dataset"),
|
||||
):
|
||||
DMCC13Benchmark(tasks="thisisnotarealtask")
|
||||
|
||||
|
|
@ -284,9 +282,7 @@ def test_DMCC13Benchmark_phase_encodings():
|
|||
"""Test DMCC13Benchmark DataGrabber invalid phase encodings."""
|
||||
with pytest.raises(
|
||||
ValueError,
|
||||
match=(
|
||||
"moonphase is not a valid phase encoding in " "the DMCC dataset"
|
||||
),
|
||||
match=("moonphase is not a valid phase encoding in the DMCC dataset"),
|
||||
):
|
||||
DMCC13Benchmark(phase_encodings="moonphase")
|
||||
|
||||
|
|
@ -295,6 +291,6 @@ def test_DMCC13Benchmark_runs():
|
|||
"""Test DMCC13Benchmark DataGrabber invalid runs."""
|
||||
with pytest.raises(
|
||||
ValueError,
|
||||
match=("cerebralrun is not a valid run in " "the DMCC dataset"),
|
||||
match=("cerebralrun is not a valid run in the DMCC dataset"),
|
||||
):
|
||||
DMCC13Benchmark(runs="cerebralrun")
|
||||
|
|
|
|||
|
|
@ -229,9 +229,9 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
|
|||
# feature data is not manipulated, only meta
|
||||
self.update_meta(feature_data_copy, "marker")
|
||||
# Update marker feature's metadata name
|
||||
feature_data_copy["meta"]["marker"][
|
||||
"name"
|
||||
] += f"_{feature_name}"
|
||||
feature_data_copy["meta"]["marker"]["name"] += (
|
||||
f"_{feature_name}"
|
||||
)
|
||||
|
||||
if storage is not None:
|
||||
logger.info(f"Storing in {storage}")
|
||||
|
|
|
|||
|
|
@ -116,7 +116,7 @@ class BrainPrint(BaseMarker):
|
|||
aseg_path: Path,
|
||||
norm_path: Path,
|
||||
indices: list,
|
||||
) -> Path:
|
||||
) -> Path: # pragma: no cover
|
||||
"""Generate a surface from the aseg and label files.
|
||||
|
||||
Parameters
|
||||
|
|
@ -191,7 +191,7 @@ class BrainPrint(BaseMarker):
|
|||
self,
|
||||
aseg_path: Path,
|
||||
norm_path: Path,
|
||||
) -> dict[str, Path]:
|
||||
) -> dict[str, Path]: # pragma: no cover
|
||||
"""Create surfaces from FreeSurfer aseg labels.
|
||||
|
||||
Parameters
|
||||
|
|
@ -266,7 +266,7 @@ class BrainPrint(BaseMarker):
|
|||
rh_white_path: Path,
|
||||
lh_pial_path: Path,
|
||||
rh_pial_path: Path,
|
||||
) -> dict[str, Path]:
|
||||
) -> dict[str, Path]: # pragma: no cover
|
||||
"""Create cortical surfaces from FreeSurfer labels.
|
||||
|
||||
Parameters
|
||||
|
|
@ -308,7 +308,7 @@ class BrainPrint(BaseMarker):
|
|||
def _fix_nan(
|
||||
self,
|
||||
input_data: list[Union[float, str, npt.ArrayLike]],
|
||||
) -> np.ndarray:
|
||||
) -> np.ndarray: # pragma: no cover
|
||||
"""Convert BrainPrint output with string NaN to ``numpy.nan``.
|
||||
|
||||
Parameters
|
||||
|
|
@ -330,7 +330,7 @@ class BrainPrint(BaseMarker):
|
|||
self,
|
||||
input: dict[str, Any],
|
||||
extra_input: Optional[dict] = None,
|
||||
) -> dict:
|
||||
) -> dict: # pragma: no cover
|
||||
"""Compute.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -114,9 +114,9 @@ class MultiscaleEntropyAUC(ComplexityBase):
|
|||
|
||||
assert isinstance(emb_dim, int), "Embedding dimension must be integer."
|
||||
assert isinstance(scale, int), "Scale must be integer."
|
||||
assert isinstance(
|
||||
tol, float
|
||||
), "Tolerance must be a positive float number."
|
||||
assert isinstance(tol, float), (
|
||||
"Tolerance must be a positive float number."
|
||||
)
|
||||
|
||||
_, n_roi = extracted_bold_values.shape
|
||||
MSEn_auc_roi = np.zeros((n_roi, 1))
|
||||
|
|
|
|||
|
|
@ -114,9 +114,9 @@ class RangeEntropy(ComplexityBase):
|
|||
|
||||
assert isinstance(emb_dim, int), "Embedding dimension must be integer."
|
||||
assert isinstance(delay, int), "Delay must be integer."
|
||||
assert isinstance(
|
||||
tolerance, float
|
||||
), "Tolerance must be a float number between 0 and 1."
|
||||
assert isinstance(tolerance, float), (
|
||||
"Tolerance must be a float number between 0 and 1."
|
||||
)
|
||||
|
||||
_, n_roi = extracted_bold_values.shape
|
||||
range_en_roi = np.zeros((n_roi, 1))
|
||||
|
|
|
|||
|
|
@ -115,9 +115,9 @@ class SampleEntropy(ComplexityBase):
|
|||
|
||||
assert isinstance(emb_dim, int), "Embedding dimension must be integer."
|
||||
assert isinstance(delay, int), "Delay must be integer."
|
||||
assert isinstance(
|
||||
tol, float
|
||||
), "Tolerance must be a positive float number."
|
||||
assert isinstance(tol, float), (
|
||||
"Tolerance must be a positive float number."
|
||||
)
|
||||
|
||||
_, n_roi = extracted_bold_values.shape
|
||||
samp_en_roi = np.zeros((n_roi, 1))
|
||||
|
|
|
|||
|
|
@ -151,9 +151,7 @@ class ALFFParcels(ALFFBase):
|
|||
).compute(
|
||||
input=aggregation_alff_input,
|
||||
extra_input=extra_input,
|
||||
)[
|
||||
"aggregation"
|
||||
],
|
||||
)["aggregation"],
|
||||
},
|
||||
"falff": {
|
||||
**ParcelAggregation(
|
||||
|
|
@ -165,8 +163,6 @@ class ALFFParcels(ALFFBase):
|
|||
).compute(
|
||||
input=aggregation_falff_input,
|
||||
extra_input=extra_input,
|
||||
)[
|
||||
"aggregation"
|
||||
],
|
||||
)["aggregation"],
|
||||
},
|
||||
}
|
||||
|
|
|
|||
|
|
@ -164,9 +164,7 @@ class ALFFSpheres(ALFFBase):
|
|||
).compute(
|
||||
input=aggregation_alff_input,
|
||||
extra_input=extra_input,
|
||||
)[
|
||||
"aggregation"
|
||||
],
|
||||
)["aggregation"],
|
||||
},
|
||||
"falff": {
|
||||
**SphereAggregation(
|
||||
|
|
@ -180,8 +178,6 @@ class ALFFSpheres(ALFFBase):
|
|||
).compute(
|
||||
input=aggregation_falff_input,
|
||||
extra_input=extra_input,
|
||||
)[
|
||||
"aggregation"
|
||||
],
|
||||
)["aggregation"],
|
||||
},
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
from abc import abstractmethod
|
||||
from typing import Any, ClassVar, Optional, Union
|
||||
|
||||
|
|
|
|||
|
|
@ -91,7 +91,8 @@ def test_FunctionalConnectivityParcels(
|
|||
)
|
||||
# Compute the connectivity measure
|
||||
connectivity_measure = ConnectivityMeasure(
|
||||
cov_estimator=cov_estimator, kind="correlation" # type: ignore
|
||||
cov_estimator=cov_estimator,
|
||||
kind="correlation", # type: ignore
|
||||
).fit_transform([extracted_timeseries])[0]
|
||||
|
||||
# Check that FC are almost equal
|
||||
|
|
|
|||
|
|
@ -92,7 +92,8 @@ def test_FunctionalConnectivitySpheres(
|
|||
)
|
||||
# Compute the connectivity measure
|
||||
connectivity_measure = ConnectivityMeasure(
|
||||
cov_estimator=cov_estimator, kind="correlation" # type: ignore
|
||||
cov_estimator=cov_estimator,
|
||||
kind="correlation", # type: ignore
|
||||
).fit_transform([extracted_timeseries])[0]
|
||||
|
||||
# Check that FC are almost equal
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ class AFNIReHo(metaclass=Singleton):
|
|||
},
|
||||
]
|
||||
|
||||
def __del__(self) -> None:
|
||||
def __del__(self) -> None: # pragma: no cover
|
||||
"""Terminate the class."""
|
||||
# Clear the computation cache
|
||||
logger.debug("Clearing cache for ReHo computation via AFNI")
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
from pathlib import Path
|
||||
from typing import (
|
||||
TYPE_CHECKING,
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
from typing import Any, Optional, Union
|
||||
|
||||
import numpy as np
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
from typing import Any, Optional, Union
|
||||
|
||||
import numpy as np
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Leonard Sasse <l.sasse@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
from abc import abstractmethod
|
||||
from typing import Any, ClassVar, Optional, Union
|
||||
|
||||
|
|
|
|||
|
|
@ -20,7 +20,6 @@ def test_base_marker_subclassing() -> None:
|
|||
|
||||
# Create concrete class
|
||||
class MyBaseMarker(BaseMarker):
|
||||
|
||||
_MARKER_INOUT_MAPPINGS = { # noqa: RUF012
|
||||
"BOLD": {
|
||||
"feat_1": "timeseries",
|
||||
|
|
|
|||
|
|
@ -19,7 +19,7 @@ def normalize(
|
|||
storage: StorageLike,
|
||||
features: dict[str, dict[str, Optional[str]]],
|
||||
kind: str,
|
||||
) -> pd.DataFrame:
|
||||
) -> pd.DataFrame: # pragma: no cover
|
||||
"""Read stored brainprint data and normalize either surfaces or volumes.
|
||||
|
||||
Parameters
|
||||
|
|
@ -79,7 +79,7 @@ def normalize(
|
|||
)
|
||||
else:
|
||||
raise_error(
|
||||
"Invalid value for `kind`, should be one of: " f"{valid_kind}"
|
||||
f"Invalid value for `kind`, should be one of: {valid_kind}"
|
||||
)
|
||||
|
||||
return normalized_df
|
||||
|
|
@ -89,7 +89,7 @@ def reweight(
|
|||
storage: StorageLike,
|
||||
feature_name: Optional[str] = None,
|
||||
feature_md5: Optional[str] = None,
|
||||
) -> pd.DataFrame:
|
||||
) -> pd.DataFrame: # pragma: no cover
|
||||
"""Read stored brainprint data and reweight eigenvalues.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
from typing import Optional
|
||||
|
||||
import pandas as pd
|
||||
|
|
@ -85,7 +84,7 @@ def read_transform(
|
|||
# Check bctpy import
|
||||
try:
|
||||
import bct
|
||||
except ImportError as err:
|
||||
except ImportError as err: # pragma: no cover
|
||||
raise_error(msg=str(err), klass=ImportError)
|
||||
|
||||
# Warning about function usage
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
import logging
|
||||
from pathlib import Path
|
||||
|
||||
|
|
|
|||
|
|
@ -186,7 +186,8 @@ def test_marker_collection_storage(tmp_path: Path) -> None:
|
|||
assert out is None
|
||||
|
||||
mc2 = MarkerCollection(
|
||||
markers=markers, datareader=DefaultDataReader() # type: ignore
|
||||
markers=markers,
|
||||
datareader=DefaultDataReader(), # type: ignore
|
||||
)
|
||||
mc2.validate(dg)
|
||||
assert mc2._storage is None
|
||||
|
|
|
|||
|
|
@ -197,8 +197,7 @@ class WorkDirManager(metaclass=Singleton):
|
|||
return
|
||||
if self._elementdir is not None:
|
||||
logger.debug(
|
||||
"Deleting element directory at "
|
||||
f"{self._elementdir.resolve()!s}"
|
||||
f"Deleting element directory at {self._elementdir.resolve()!s}"
|
||||
)
|
||||
shutil.rmtree(self._elementdir, ignore_errors=True)
|
||||
self._elementdir = None
|
||||
|
|
|
|||
|
|
@ -572,7 +572,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
|
|||
if bold_img.get_fdata().shape[3] != len(confound_df):
|
||||
raise_error(
|
||||
"Image time series and confounds have different length!\n"
|
||||
f"\tImage time series: { bold_img.get_fdata().shape[3]}\n"
|
||||
f"\tImage time series: {bold_img.get_fdata().shape[3]}\n"
|
||||
f"\tConfounds: {len(confound_df)}"
|
||||
)
|
||||
|
||||
|
|
|
|||
|
|
@ -5,7 +5,6 @@
|
|||
# Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
import numpy as np
|
||||
import pandas as pd
|
||||
import pytest
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
|
||||
# License: AGPL
|
||||
|
||||
|
||||
import pytest
|
||||
|
||||
from junifer.datareader import DefaultDataReader
|
||||
|
|
|
|||
|
|
@ -72,7 +72,7 @@ class ANTsWarper:
|
|||
)
|
||||
|
||||
# Native space warping
|
||||
if reference == "T1w":
|
||||
if reference == "T1w": # pragma: no cover
|
||||
logger.debug("Using ANTs for space warping")
|
||||
|
||||
# Get the min of the voxel sizes from input and use it as the
|
||||
|
|
@ -237,8 +237,7 @@ class ANTsWarper:
|
|||
if input.get("mask") is not None:
|
||||
# Create a tempfile for warped mask output
|
||||
apply_transforms_mask_out_path = element_tempdir / (
|
||||
f"warped_mask_from_{input['space']}_to_"
|
||||
f"{reference}.nii.gz"
|
||||
f"warped_mask_from_{input['space']}_to_{reference}.nii.gz"
|
||||
)
|
||||
# Set antsApplyTransforms command
|
||||
apply_transforms_mask_cmd = [
|
||||
|
|
|
|||
|
|
@ -40,7 +40,7 @@ class FSLWarper:
|
|||
self,
|
||||
input: dict[str, Any],
|
||||
extra_input: dict[str, Any],
|
||||
) -> dict[str, Any]:
|
||||
) -> dict[str, Any]: # pragma: no cover
|
||||
"""Preprocess using FSL.
|
||||
|
||||
Parameters
|
||||
|
|
|
|||
|
|
@ -77,7 +77,7 @@ class SpaceWarper(BasePreprocessor):
|
|||
self.reference = reference
|
||||
# Set required data types based on reference and
|
||||
# initialize superclass
|
||||
if self.reference == "T1w":
|
||||
if self.reference == "T1w": # pragma: no cover
|
||||
required_data_types = [self.reference, "Warp"]
|
||||
# Listify on
|
||||
if not isinstance(on, list):
|
||||
|
|
@ -170,7 +170,9 @@ class SpaceWarper(BasePreprocessor):
|
|||
"""
|
||||
logger.info(f"Warping to {self.reference} space using SpaceWarper")
|
||||
# Transform to native space
|
||||
if self.using in ["fsl", "ants", "auto"] and self.reference == "T1w":
|
||||
if (
|
||||
self.using in ["fsl", "ants", "auto"] and self.reference == "T1w"
|
||||
): # pragma: no cover
|
||||
# Check for extra inputs
|
||||
if extra_input is None:
|
||||
raise_error(
|
||||
|
|
|
|||
|
|
@ -187,7 +187,9 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
|
|||
)
|
||||
# Prepare new dataframe
|
||||
df = pd.DataFrame(
|
||||
data=data, columns=col_names, index=idx # type: ignore
|
||||
data=data,
|
||||
columns=col_names,
|
||||
index=idx, # type: ignore
|
||||
)
|
||||
# Store dataframe
|
||||
self.store_df(meta_md5=meta_md5, element=element, df=df)
|
||||
|
|
|
|||
|
|
@ -229,9 +229,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
|
|||
# Format index names for retrieved data
|
||||
meta_df.index = meta_df.index.str.replace(r"meta_", "")
|
||||
# Convert dataframe to dictionary
|
||||
out: dict[str, dict[str, str]] = meta_df.to_dict(
|
||||
orient="index"
|
||||
) # type: ignore
|
||||
out: dict[str, dict[str, str]] = meta_df.to_dict(orient="index") # type: ignore
|
||||
# Format output
|
||||
for md5, t_meta in out.items():
|
||||
for k, v in t_meta.items():
|
||||
|
|
@ -536,8 +534,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
|
|||
klass=IOError,
|
||||
)
|
||||
logger.info(
|
||||
"Collecting data from "
|
||||
f"{self.uri.parent}/*{self.uri.name}" # type: ignore
|
||||
f"Collecting data from {self.uri.parent}/*{self.uri.name}" # type: ignore
|
||||
)
|
||||
# Create new instance
|
||||
out_storage = SQLiteFeatureStorage(uri=self.uri, upsert="ignore")
|
||||
|
|
@ -596,9 +593,7 @@ def _generate_update_statements(table, index_col, rows_to_update):
|
|||
for i, (_, keys) in enumerate(pk_indb.iterrows()):
|
||||
stmt = (
|
||||
table.update()
|
||||
.where(
|
||||
and_(col == keys[j] for j, col in enumerate(pk_cols))
|
||||
) # type: ignore
|
||||
.where(and_(col == keys[j] for j, col in enumerate(pk_cols))) # type: ignore
|
||||
.values(new_records[i])
|
||||
)
|
||||
stmts.append(stmt)
|
||||
|
|
|
|||
|
|
@ -37,7 +37,8 @@ def test_element_to_index() -> None:
|
|||
assert index.levels[1].name == "idx" # type: ignore
|
||||
# Check second index level values
|
||||
assert all(
|
||||
x == i for i, x in enumerate(index.levels[1].values) # type: ignore
|
||||
x == i
|
||||
for i, x in enumerate(index.levels[1].values) # type: ignore
|
||||
)
|
||||
# Check second index level values shape
|
||||
assert index.levels[1].values.shape == (10,) # type: ignore
|
||||
|
|
@ -69,7 +70,8 @@ def test_element_to_index() -> None:
|
|||
assert index.levels[1].name == "scan" # type: ignore
|
||||
# Check second index level values
|
||||
assert all(
|
||||
x == i for i, x in enumerate(index.levels[1].values) # type: ignore
|
||||
x == i
|
||||
for i, x in enumerate(index.levels[1].values) # type: ignore
|
||||
)
|
||||
# Check second index level values shape
|
||||
assert index.levels[1].values.shape == (7,) # type: ignore
|
||||
|
|
@ -97,7 +99,8 @@ def test_element_to_index() -> None:
|
|||
assert index.levels[2].name == "idx" # type: ignore
|
||||
# Check third index level values
|
||||
assert all(
|
||||
x == i for i, x in enumerate(index.levels[2].values) # type: ignore
|
||||
x == i
|
||||
for i, x in enumerate(index.levels[2].values) # type: ignore
|
||||
)
|
||||
# Check third index level values shape
|
||||
assert index.levels[2].values.shape == (10,) # type: ignore
|
||||
|
|
|
|||
|
|
@ -13,7 +13,8 @@ def test_BaseFeatureStorage_abstractness() -> None:
|
|||
"""Test BaseFeatureStorage is abstract base class."""
|
||||
with pytest.raises(TypeError, match=r"abstract"):
|
||||
BaseFeatureStorage(
|
||||
uri="/tmp", storage_types=["matrix"] # type: ignore
|
||||
uri="/tmp",
|
||||
storage_types=["matrix"], # type: ignore
|
||||
)
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -8,15 +8,14 @@ import os
|
|||
import sys
|
||||
|
||||
|
||||
if sys.version_info < (3, 12):
|
||||
if sys.version_info < (3, 12): # pragma: no cover
|
||||
from distutils.version import LooseVersion
|
||||
else: # pragma: no cover
|
||||
else:
|
||||
from looseversion import LooseVersion
|
||||
|
||||
import logging
|
||||
import warnings
|
||||
from pathlib import Path
|
||||
from subprocess import PIPE, Popen, TimeoutExpired
|
||||
from typing import ClassVar, NoReturn, Optional, Union
|
||||
from warnings import warn
|
||||
|
||||
|
|
@ -77,7 +76,7 @@ class WrapStdOut(logging.StreamHandler):
|
|||
# just stdout) in order for this to work (tested on OSX and Linux)
|
||||
if hasattr(sys.stdout, name):
|
||||
return getattr(sys.stdout, name)
|
||||
else:
|
||||
else: # pragma: no cover
|
||||
raise AttributeError(f"'file' object has not attribute '{name}'")
|
||||
|
||||
|
||||
|
|
@ -107,11 +106,13 @@ class ColorFormatter(logging.Formatter):
|
|||
COLOR_SEQ: str = "\033[1;%dm"
|
||||
BOLD_SEQ: str = "\033[1m"
|
||||
|
||||
def __init__(self, fmt: str, datefmt: Optional[str] = None) -> None:
|
||||
def __init__(
|
||||
self, fmt: str, datefmt: Optional[str] = None
|
||||
) -> None: # pragma: no cover
|
||||
"""Initialize the ColorFormatter."""
|
||||
logging.Formatter.__init__(self, fmt, datefmt)
|
||||
|
||||
def format(self, record: logging.LogRecord) -> str:
|
||||
def format(self, record: logging.LogRecord) -> str: # pragma: no cover
|
||||
"""Format the log record.
|
||||
|
||||
Parameters
|
||||
|
|
@ -134,45 +135,6 @@ class ColorFormatter(logging.Formatter):
|
|||
return logging.Formatter.format(self, record)
|
||||
|
||||
|
||||
def _get_git_head(path: Path) -> str:
|
||||
"""Aux function to read HEAD from git.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
path : pathlib.Path
|
||||
The path to read git HEAD from.
|
||||
|
||||
Returns
|
||||
-------
|
||||
str
|
||||
Empty string if timeout expired for subprocess command execution else
|
||||
git HEAD information.
|
||||
|
||||
Raises
|
||||
------
|
||||
FileNotFoundError
|
||||
If ``path`` is invalid.
|
||||
|
||||
"""
|
||||
if not path.exists():
|
||||
raise_error(
|
||||
msg=f"This path does not exist: {path}", klass=FileNotFoundError
|
||||
)
|
||||
command = f"cd {path}; git rev-parse --verify HEAD"
|
||||
process = Popen(
|
||||
args=command,
|
||||
stdout=PIPE,
|
||||
shell=True,
|
||||
)
|
||||
try:
|
||||
stdout, _ = process.communicate(timeout=10)
|
||||
proc_stdout = stdout.strip().decode()
|
||||
except TimeoutExpired:
|
||||
process.kill()
|
||||
proc_stdout = ""
|
||||
return proc_stdout
|
||||
|
||||
|
||||
def get_versions() -> dict:
|
||||
"""Import stuff and get versions if module.
|
||||
|
||||
|
|
@ -182,52 +144,22 @@ def get_versions() -> dict:
|
|||
The module names and corresponding versions.
|
||||
|
||||
"""
|
||||
# Setup dictionary to track versions of modules
|
||||
module_versions = {}
|
||||
for name, module in sys.modules.copy().items():
|
||||
# Bypassing sub-modules of packages and
|
||||
# allowing ruamel.yaml
|
||||
if "." in name and name != "ruamel.yaml":
|
||||
continue
|
||||
if name in ["_curses"]:
|
||||
continue
|
||||
# Get version or None as string
|
||||
vstring = str(getattr(module, "__version__", None))
|
||||
module_version = LooseVersion(vstring)
|
||||
module_version = getattr(module_version, "vstring", None)
|
||||
if module_version is None:
|
||||
module_version = None
|
||||
elif "git" in module_version:
|
||||
git_path = Path(module.__file__).resolve().parent # type: ignore
|
||||
head = _get_git_head(git_path)
|
||||
module_version += f"-HEAD:{head}"
|
||||
|
||||
# Get module version
|
||||
module_version = getattr(LooseVersion(vstring), "vstring", None)
|
||||
module_versions[name] = module_version
|
||||
return module_versions
|
||||
|
||||
|
||||
# def get_ext_versions(tbox_path: Path) -> Dict:
|
||||
# """Get versions of external tools used by junifer.
|
||||
|
||||
# Parameters
|
||||
# ----------
|
||||
# tbox_path : pathlib.Path
|
||||
# The path to external toolboxes.
|
||||
|
||||
# Returns
|
||||
# -------
|
||||
# dict
|
||||
# The dependency information.
|
||||
|
||||
# """
|
||||
# versions = {}
|
||||
# # spm_path = tbox_path / 'spm12'
|
||||
# # if spm_path.exists():
|
||||
# # head = _get_git_head(spm_path)
|
||||
# # module_version = 'SPM12-HEAD:{}'.format(head)
|
||||
# # versions['spm'] = module_version
|
||||
# return versions
|
||||
|
||||
|
||||
def _close_handlers(logger: logging.Logger) -> None:
|
||||
def _close_handlers(logger: logging.Logger) -> None: # pragma: no cover
|
||||
"""Safely close relevant handlers for logger.
|
||||
|
||||
Parameters
|
||||
|
|
@ -243,55 +175,37 @@ def _close_handlers(logger: logging.Logger) -> None:
|
|||
logger.removeHandler(handler)
|
||||
|
||||
|
||||
def _safe_log(versions: dict, name: str) -> None:
|
||||
"""Log with safety.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
versions : dict
|
||||
The dictionary with keys as dependency names and values as the
|
||||
versions.
|
||||
name : str
|
||||
The dependency to look up in `versions`.
|
||||
|
||||
"""
|
||||
if name in versions:
|
||||
logger.info(f"{name}: {versions[name]}")
|
||||
|
||||
|
||||
def log_versions(tbox_path: Optional[Path] = None) -> None:
|
||||
"""Log versions of dependencies and junifer.
|
||||
|
||||
If `tbox_path` is specified, can also log versions of external toolboxes.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
tbox_path : pathlib.Path, optional
|
||||
The path to external toolboxes (default None).
|
||||
|
||||
"""
|
||||
def log_versions() -> None:
|
||||
"""Log versions of dependencies and junifer."""
|
||||
# Get versions of all found packages
|
||||
versions = get_versions()
|
||||
|
||||
# Set packages to log
|
||||
pkgs_to_log = [
|
||||
"click",
|
||||
"numpy",
|
||||
"scipy",
|
||||
"datalad",
|
||||
"pandas",
|
||||
"nibabel",
|
||||
"nilearn",
|
||||
"sqlalchemy",
|
||||
"ruamel.yaml",
|
||||
"h5py",
|
||||
"tqdm",
|
||||
"templateflow",
|
||||
"lapy",
|
||||
"junifer_data",
|
||||
"junifer",
|
||||
]
|
||||
# Log
|
||||
logger.info("===== Lib Versions =====")
|
||||
_safe_log(versions, "numpy")
|
||||
_safe_log(versions, "scipy")
|
||||
_safe_log(versions, "pandas")
|
||||
_safe_log(versions, "nipype")
|
||||
_safe_log(versions, "nitime")
|
||||
_safe_log(versions, "nilearn")
|
||||
_safe_log(versions, "nibabel")
|
||||
_safe_log(versions, "junifer")
|
||||
for pkg in pkgs_to_log:
|
||||
if pkg in versions:
|
||||
logger.info(f"{pkg}: {versions[pkg]}")
|
||||
logger.info("========================")
|
||||
|
||||
if tbox_path is not None:
|
||||
# ext_versions = get_ext_versions(tbox_path)
|
||||
# logger.info('spm: {}'.format(ext_versions['spm']))
|
||||
# logger.info('========================')
|
||||
pass
|
||||
|
||||
|
||||
def _can_use_color(handler: logging.Handler) -> bool:
|
||||
def _can_use_color(handler: logging.Handler) -> bool: # pragma: no cover
|
||||
"""Check if color can be used in the logging output.
|
||||
|
||||
Parameters
|
||||
|
|
@ -391,11 +305,7 @@ def configure_logging(
|
|||
# Set logging format
|
||||
if output_format is None:
|
||||
output_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
|
||||
# (
|
||||
# "%(asctime)s [%(levelname)s] %(message)s "
|
||||
# "(%(filename)s:%(lineno)s)"
|
||||
# )
|
||||
if _can_use_color(lh):
|
||||
if _can_use_color(lh): # pragma: no cover
|
||||
formatter = ColorFormatter(fmt=output_format)
|
||||
else:
|
||||
formatter = logging.Formatter(fmt=output_format)
|
||||
|
|
|
|||
|
|
@ -68,7 +68,9 @@ def test_log_file(tmp_path: Path) -> None:
|
|||
assert any("Warn message" in line for line in lines)
|
||||
assert any("Error message" in line for line in lines)
|
||||
|
||||
configure_logging(fname=tmp_path / "test2.log", level="INFO")
|
||||
configure_logging(
|
||||
fname=str((tmp_path / "test2.log").resolve()), level="INFO"
|
||||
)
|
||||
logger.debug("Debug message")
|
||||
logger.info("Info message")
|
||||
logger.warning("Warn message")
|
||||
|
|
@ -81,7 +83,9 @@ def test_log_file(tmp_path: Path) -> None:
|
|||
assert any("Warn message" in line for line in lines)
|
||||
assert any("Error message" in line for line in lines)
|
||||
|
||||
configure_logging(fname=tmp_path / "test3.log", level="WARNING")
|
||||
configure_logging(
|
||||
fname=tmp_path / "test3.log", level="WARNING", level_datalad="WARNING"
|
||||
)
|
||||
logger.debug("Debug message")
|
||||
logger.info("Info message")
|
||||
logger.warning("Warn message")
|
||||
|
|
@ -94,7 +98,7 @@ def test_log_file(tmp_path: Path) -> None:
|
|||
assert any("Warn message" in line for line in lines)
|
||||
assert any("Error message" in line for line in lines)
|
||||
|
||||
configure_logging(fname=tmp_path / "test4.log", level="ERROR")
|
||||
configure_logging(fname=tmp_path / "test4.log", level=logging.ERROR)
|
||||
logger.debug("Debug message")
|
||||
logger.info("Info message")
|
||||
logger.warning("Warn message")
|
||||
|
|
@ -107,7 +111,11 @@ def test_log_file(tmp_path: Path) -> None:
|
|||
assert any("Error message" in line for line in lines)
|
||||
|
||||
with pytest.warns(UserWarning, match="to avoid this message"):
|
||||
configure_logging(fname=tmp_path / "test4.log", level="WARNING")
|
||||
configure_logging(
|
||||
fname=tmp_path / "test4.log",
|
||||
level="WARNING",
|
||||
level_datalad=logging.WARNING,
|
||||
)
|
||||
logger.debug("Debug2 message")
|
||||
logger.info("Info2 message")
|
||||
logger.warning("Warn2 message")
|
||||
|
|
|
|||
|
|
@ -75,7 +75,12 @@ onthefly = [
|
|||
"bctpy==0.6.0"
|
||||
]
|
||||
neurokit2 = ["neurokit2>=0.1.7"]
|
||||
dev = ["tox", "pre-commit"]
|
||||
dev = [
|
||||
"tox",
|
||||
"pre-commit",
|
||||
"ruff",
|
||||
"towncrier",
|
||||
]
|
||||
docs = [
|
||||
"seaborn>=0.13.0,<0.14.0",
|
||||
"sphinx>=7.3.0,<8.1.0",
|
||||
|
|
@ -107,16 +112,6 @@ version_scheme = "guess-next-dev"
|
|||
local_scheme = "no-local-version"
|
||||
write_to = "junifer/_version.py"
|
||||
|
||||
[tool.black]
|
||||
line-length = 79
|
||||
target-version = ["py39", "py310", "py311", "py312", "py313"]
|
||||
extend-exclude = """
|
||||
(
|
||||
junifer/external/h5io
|
||||
| junifer/external/BrainPrint
|
||||
)
|
||||
"""
|
||||
|
||||
[tool.codespell]
|
||||
skip = "*/auto_examples/*,*.html,.git/,*.pyc,*/_build/*,*/h5io/*,*/BrainPrint/*"
|
||||
count = ""
|
||||
|
|
@ -136,6 +131,7 @@ extend-exclude = [
|
|||
"examples",
|
||||
"tools",
|
||||
]
|
||||
target-version = "py39"
|
||||
|
||||
[tool.ruff.lint]
|
||||
select = [
|
||||
|
|
@ -275,3 +271,31 @@ showcontent = true
|
|||
[tool.towncrier.fragment.change]
|
||||
name = "API Changes"
|
||||
showcontent = true
|
||||
|
||||
[tool.coverage.paths]
|
||||
source = [
|
||||
"junifer",
|
||||
"*/site-packages/junifer",
|
||||
]
|
||||
|
||||
[tool.coverage.run]
|
||||
branch = true
|
||||
omit = [
|
||||
"*/setup.py",
|
||||
"*/_version.py",
|
||||
"*/tests/*",
|
||||
"*/junifer/configs/*",
|
||||
"*/junifer/external/h5io/*",
|
||||
"*/junifer/external/BrainPrint/*",
|
||||
]
|
||||
|
||||
[tool.coverage.report]
|
||||
exclude_lines = [
|
||||
# Have to re-enable the standard pragma
|
||||
"pragma: no cover",
|
||||
# Type checking if statements should not be considered
|
||||
"if TYPE_CHECKING:",
|
||||
# Don't complain if non-runnable code isn't run:
|
||||
"if __name__ == .__main__.:",
|
||||
]
|
||||
precision = 2
|
||||
|
|
|
|||
57
tox.ini
57
tox.ini
|
|
@ -1,5 +1,13 @@
|
|||
[tox]
|
||||
envlist = ruff, black, test, coverage, codespell, py3{9,10,11,12,13}
|
||||
requires =
|
||||
tox>=4
|
||||
env_list =
|
||||
ruff,
|
||||
changelog,
|
||||
test,
|
||||
coverage,
|
||||
codespell,
|
||||
py3{9,10,11,12,13}
|
||||
isolated_build = true
|
||||
|
||||
[gh-actions]
|
||||
|
|
@ -22,20 +30,27 @@ commands =
|
|||
pytest
|
||||
|
||||
[testenv:ruff]
|
||||
description = run ruff
|
||||
skip_install = true
|
||||
deps =
|
||||
ruff>=0.1.0
|
||||
commands =
|
||||
ruff format {toxinidir}
|
||||
ruff check {toxinidir}
|
||||
|
||||
[testenv:black]
|
||||
[testenv:changelog]
|
||||
description = show changelog
|
||||
skip_install = true
|
||||
# See https://github.com/sphinx-contrib/sphinxcontrib-towncrier/issues/92
|
||||
# Pin also present in pyproject.toml
|
||||
deps =
|
||||
black
|
||||
towncrier<24.7
|
||||
lazy_loader==0.4
|
||||
commands =
|
||||
black --check --diff {toxinidir}/junifer {toxinidir}/setup.py
|
||||
towncrier build --draft
|
||||
|
||||
[testenv:test]
|
||||
description = run tests
|
||||
skip_install = false
|
||||
passenv =
|
||||
HOME
|
||||
|
|
@ -45,6 +60,7 @@ commands =
|
|||
pytest
|
||||
|
||||
[testenv:coverage]
|
||||
description = run tests with coverage
|
||||
skip_install = false
|
||||
deps =
|
||||
bctpy==0.6.0
|
||||
|
|
@ -52,42 +68,13 @@ deps =
|
|||
pytest
|
||||
pytest-cov
|
||||
commands =
|
||||
pytest --cov={envsitepackagesdir}/junifer --cov-report=xml --cov-report=term {envsitepackagesdir}/junifer
|
||||
pytest --cov={envsitepackagesdir}/junifer --cov-report=xml --cov-report=term --cov-config=pyproject.toml {envsitepackagesdir}/junifer
|
||||
|
||||
[testenv:codespell]
|
||||
description = run codespell
|
||||
skip_install = true
|
||||
deps =
|
||||
codespell
|
||||
tomli
|
||||
commands =
|
||||
codespell --toml {toxinidir}/pyproject.toml {toxinidir}/docs/ {toxinidir}/examples/ {toxinidir}/junifer/ {toxinidir}/tools/ {toxinidir}/README.md
|
||||
|
||||
################
|
||||
# Tool configs #
|
||||
################
|
||||
|
||||
[coverage:paths]
|
||||
source =
|
||||
junifer
|
||||
*/site-packages/junifer
|
||||
|
||||
[coverage:run]
|
||||
branch = true
|
||||
omit =
|
||||
*/setup.py
|
||||
*/_version.py
|
||||
*/tests/*
|
||||
*/junifer/configs/*
|
||||
*/junifer/external/h5io/*
|
||||
*/junifer/external/BrainPrint/*
|
||||
parallel = false
|
||||
|
||||
[coverage:report]
|
||||
exclude_lines =
|
||||
# Have to re-enable the standard pragma
|
||||
pragma: no cover
|
||||
# Type checking if statements should not be considered
|
||||
if TYPE_CHECKING:
|
||||
# Don't complain if non-runnable code isn't run:
|
||||
if __name__ == .__main__.:
|
||||
precision = 2
|
||||
|
|
|
|||
Loading…
Reference in a new issue