junifer 0.0.5.dev242__py3-none-any.whl → 0.0.6__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- junifer/__init__.py +2 -31
- junifer/__init__.pyi +37 -0
- junifer/_version.py +9 -4
- junifer/api/__init__.py +3 -5
- junifer/api/__init__.pyi +4 -0
- junifer/api/decorators.py +14 -19
- junifer/api/functions.py +165 -109
- junifer/api/py.typed +0 -0
- junifer/api/queue_context/__init__.py +2 -4
- junifer/api/queue_context/__init__.pyi +5 -0
- junifer/api/queue_context/gnu_parallel_local_adapter.py +22 -6
- junifer/api/queue_context/htcondor_adapter.py +23 -6
- junifer/api/queue_context/py.typed +0 -0
- junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py +3 -3
- junifer/api/queue_context/tests/test_htcondor_adapter.py +3 -3
- junifer/api/tests/test_functions.py +168 -74
- junifer/cli/__init__.py +24 -0
- junifer/cli/__init__.pyi +3 -0
- junifer/{api → cli}/cli.py +141 -125
- junifer/cli/parser.py +235 -0
- junifer/cli/py.typed +0 -0
- junifer/{api → cli}/tests/test_cli.py +8 -8
- junifer/{api/tests/test_api_utils.py → cli/tests/test_cli_utils.py} +5 -4
- junifer/{api → cli}/tests/test_parser.py +2 -2
- junifer/{api → cli}/utils.py +6 -16
- junifer/configs/juseless/__init__.py +2 -2
- junifer/configs/juseless/__init__.pyi +3 -0
- junifer/configs/juseless/datagrabbers/__init__.py +2 -12
- junifer/configs/juseless/datagrabbers/__init__.pyi +13 -0
- junifer/configs/juseless/datagrabbers/ixi_vbm.py +2 -2
- junifer/configs/juseless/datagrabbers/py.typed +0 -0
- junifer/configs/juseless/datagrabbers/tests/test_ucla.py +2 -2
- junifer/configs/juseless/datagrabbers/ucla.py +4 -4
- junifer/configs/juseless/py.typed +0 -0
- junifer/conftest.py +25 -0
- junifer/data/__init__.py +2 -42
- junifer/data/__init__.pyi +29 -0
- junifer/data/_dispatch.py +248 -0
- junifer/data/coordinates/__init__.py +9 -0
- junifer/data/coordinates/__init__.pyi +5 -0
- junifer/data/coordinates/_ants_coordinates_warper.py +104 -0
- junifer/data/coordinates/_coordinates.py +385 -0
- junifer/data/coordinates/_fsl_coordinates_warper.py +81 -0
- junifer/data/{tests → coordinates/tests}/test_coordinates.py +26 -33
- junifer/data/masks/__init__.py +9 -0
- junifer/data/masks/__init__.pyi +6 -0
- junifer/data/masks/_ants_mask_warper.py +177 -0
- junifer/data/masks/_fsl_mask_warper.py +106 -0
- junifer/data/masks/_masks.py +802 -0
- junifer/data/{tests → masks/tests}/test_masks.py +67 -63
- junifer/data/parcellations/__init__.py +9 -0
- junifer/data/parcellations/__init__.pyi +6 -0
- junifer/data/parcellations/_ants_parcellation_warper.py +166 -0
- junifer/data/parcellations/_fsl_parcellation_warper.py +89 -0
- junifer/data/parcellations/_parcellations.py +1388 -0
- junifer/data/{tests → parcellations/tests}/test_parcellations.py +165 -295
- junifer/data/pipeline_data_registry_base.py +76 -0
- junifer/data/py.typed +0 -0
- junifer/data/template_spaces.py +44 -79
- junifer/data/tests/test_data_utils.py +1 -2
- junifer/data/tests/test_template_spaces.py +8 -4
- junifer/data/utils.py +109 -4
- junifer/datagrabber/__init__.py +2 -26
- junifer/datagrabber/__init__.pyi +27 -0
- junifer/datagrabber/aomic/__init__.py +2 -4
- junifer/datagrabber/aomic/__init__.pyi +5 -0
- junifer/datagrabber/aomic/id1000.py +81 -52
- junifer/datagrabber/aomic/piop1.py +83 -55
- junifer/datagrabber/aomic/piop2.py +85 -56
- junifer/datagrabber/aomic/py.typed +0 -0
- junifer/datagrabber/aomic/tests/test_id1000.py +19 -12
- junifer/datagrabber/aomic/tests/test_piop1.py +52 -18
- junifer/datagrabber/aomic/tests/test_piop2.py +50 -17
- junifer/datagrabber/base.py +22 -18
- junifer/datagrabber/datalad_base.py +71 -34
- junifer/datagrabber/dmcc13_benchmark.py +31 -18
- junifer/datagrabber/hcp1200/__init__.py +2 -3
- junifer/datagrabber/hcp1200/__init__.pyi +4 -0
- junifer/datagrabber/hcp1200/datalad_hcp1200.py +3 -3
- junifer/datagrabber/hcp1200/hcp1200.py +26 -15
- junifer/datagrabber/hcp1200/py.typed +0 -0
- junifer/datagrabber/hcp1200/tests/test_hcp1200.py +8 -2
- junifer/datagrabber/multiple.py +14 -9
- junifer/datagrabber/pattern.py +132 -96
- junifer/datagrabber/pattern_validation_mixin.py +206 -94
- junifer/datagrabber/py.typed +0 -0
- junifer/datagrabber/tests/test_datalad_base.py +27 -12
- junifer/datagrabber/tests/test_dmcc13_benchmark.py +28 -11
- junifer/datagrabber/tests/test_multiple.py +48 -2
- junifer/datagrabber/tests/test_pattern_datalad.py +1 -1
- junifer/datagrabber/tests/test_pattern_validation_mixin.py +6 -6
- junifer/datareader/__init__.py +2 -2
- junifer/datareader/__init__.pyi +3 -0
- junifer/datareader/default.py +6 -6
- junifer/datareader/py.typed +0 -0
- junifer/external/nilearn/__init__.py +2 -3
- junifer/external/nilearn/__init__.pyi +4 -0
- junifer/external/nilearn/junifer_connectivity_measure.py +25 -17
- junifer/external/nilearn/junifer_nifti_spheres_masker.py +4 -4
- junifer/external/nilearn/py.typed +0 -0
- junifer/external/nilearn/tests/test_junifer_connectivity_measure.py +17 -16
- junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py +2 -3
- junifer/markers/__init__.py +2 -38
- junifer/markers/__init__.pyi +37 -0
- junifer/markers/base.py +11 -14
- junifer/markers/brainprint.py +12 -14
- junifer/markers/complexity/__init__.py +2 -18
- junifer/markers/complexity/__init__.pyi +17 -0
- junifer/markers/complexity/complexity_base.py +9 -11
- junifer/markers/complexity/hurst_exponent.py +7 -7
- junifer/markers/complexity/multiscale_entropy_auc.py +7 -7
- junifer/markers/complexity/perm_entropy.py +7 -7
- junifer/markers/complexity/py.typed +0 -0
- junifer/markers/complexity/range_entropy.py +7 -7
- junifer/markers/complexity/range_entropy_auc.py +7 -7
- junifer/markers/complexity/sample_entropy.py +7 -7
- junifer/markers/complexity/tests/test_complexity_base.py +1 -1
- junifer/markers/complexity/tests/test_hurst_exponent.py +5 -5
- junifer/markers/complexity/tests/test_multiscale_entropy_auc.py +5 -5
- junifer/markers/complexity/tests/test_perm_entropy.py +5 -5
- junifer/markers/complexity/tests/test_range_entropy.py +5 -5
- junifer/markers/complexity/tests/test_range_entropy_auc.py +5 -5
- junifer/markers/complexity/tests/test_sample_entropy.py +5 -5
- junifer/markers/complexity/tests/test_weighted_perm_entropy.py +5 -5
- junifer/markers/complexity/weighted_perm_entropy.py +7 -7
- junifer/markers/ets_rss.py +12 -11
- junifer/markers/falff/__init__.py +2 -3
- junifer/markers/falff/__init__.pyi +4 -0
- junifer/markers/falff/_afni_falff.py +38 -45
- junifer/markers/falff/_junifer_falff.py +16 -19
- junifer/markers/falff/falff_base.py +7 -11
- junifer/markers/falff/falff_parcels.py +9 -9
- junifer/markers/falff/falff_spheres.py +8 -8
- junifer/markers/falff/py.typed +0 -0
- junifer/markers/falff/tests/test_falff_spheres.py +3 -1
- junifer/markers/functional_connectivity/__init__.py +2 -12
- junifer/markers/functional_connectivity/__init__.pyi +13 -0
- junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py +9 -8
- junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py +8 -8
- junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py +7 -7
- junifer/markers/functional_connectivity/functional_connectivity_base.py +13 -12
- junifer/markers/functional_connectivity/functional_connectivity_parcels.py +8 -8
- junifer/markers/functional_connectivity/functional_connectivity_spheres.py +7 -7
- junifer/markers/functional_connectivity/py.typed +0 -0
- junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py +1 -2
- junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py +1 -2
- junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py +6 -6
- junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py +5 -5
- junifer/markers/parcel_aggregation.py +22 -17
- junifer/markers/py.typed +0 -0
- junifer/markers/reho/__init__.py +2 -3
- junifer/markers/reho/__init__.pyi +4 -0
- junifer/markers/reho/_afni_reho.py +29 -35
- junifer/markers/reho/_junifer_reho.py +13 -14
- junifer/markers/reho/py.typed +0 -0
- junifer/markers/reho/reho_base.py +7 -11
- junifer/markers/reho/reho_parcels.py +10 -10
- junifer/markers/reho/reho_spheres.py +9 -9
- junifer/markers/sphere_aggregation.py +22 -17
- junifer/markers/temporal_snr/__init__.py +2 -3
- junifer/markers/temporal_snr/__init__.pyi +4 -0
- junifer/markers/temporal_snr/py.typed +0 -0
- junifer/markers/temporal_snr/temporal_snr_base.py +11 -10
- junifer/markers/temporal_snr/temporal_snr_parcels.py +8 -8
- junifer/markers/temporal_snr/temporal_snr_spheres.py +7 -7
- junifer/markers/tests/test_ets_rss.py +3 -3
- junifer/markers/tests/test_parcel_aggregation.py +24 -24
- junifer/markers/tests/test_sphere_aggregation.py +6 -6
- junifer/markers/utils.py +3 -3
- junifer/onthefly/__init__.py +2 -1
- junifer/onthefly/_brainprint.py +138 -0
- junifer/onthefly/read_transform.py +5 -8
- junifer/pipeline/__init__.py +2 -10
- junifer/pipeline/__init__.pyi +13 -0
- junifer/{markers/collection.py → pipeline/marker_collection.py} +8 -14
- junifer/pipeline/pipeline_component_registry.py +294 -0
- junifer/pipeline/pipeline_step_mixin.py +15 -11
- junifer/pipeline/py.typed +0 -0
- junifer/{markers/tests/test_collection.py → pipeline/tests/test_marker_collection.py} +2 -3
- junifer/pipeline/tests/test_pipeline_component_registry.py +200 -0
- junifer/pipeline/tests/test_pipeline_step_mixin.py +36 -37
- junifer/pipeline/tests/test_update_meta_mixin.py +4 -4
- junifer/pipeline/tests/test_workdir_manager.py +43 -0
- junifer/pipeline/update_meta_mixin.py +21 -17
- junifer/pipeline/utils.py +6 -6
- junifer/pipeline/workdir_manager.py +19 -5
- junifer/preprocess/__init__.py +2 -10
- junifer/preprocess/__init__.pyi +11 -0
- junifer/preprocess/base.py +10 -10
- junifer/preprocess/confounds/__init__.py +2 -2
- junifer/preprocess/confounds/__init__.pyi +3 -0
- junifer/preprocess/confounds/fmriprep_confound_remover.py +243 -64
- junifer/preprocess/confounds/py.typed +0 -0
- junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +121 -14
- junifer/preprocess/py.typed +0 -0
- junifer/preprocess/smoothing/__init__.py +2 -2
- junifer/preprocess/smoothing/__init__.pyi +3 -0
- junifer/preprocess/smoothing/_afni_smoothing.py +40 -40
- junifer/preprocess/smoothing/_fsl_smoothing.py +22 -32
- junifer/preprocess/smoothing/_nilearn_smoothing.py +35 -14
- junifer/preprocess/smoothing/py.typed +0 -0
- junifer/preprocess/smoothing/smoothing.py +11 -13
- junifer/preprocess/warping/__init__.py +2 -2
- junifer/preprocess/warping/__init__.pyi +3 -0
- junifer/preprocess/warping/_ants_warper.py +136 -32
- junifer/preprocess/warping/_fsl_warper.py +73 -22
- junifer/preprocess/warping/py.typed +0 -0
- junifer/preprocess/warping/space_warper.py +39 -11
- junifer/preprocess/warping/tests/test_space_warper.py +5 -9
- junifer/py.typed +0 -0
- junifer/stats.py +5 -5
- junifer/storage/__init__.py +2 -10
- junifer/storage/__init__.pyi +11 -0
- junifer/storage/base.py +47 -13
- junifer/storage/hdf5.py +95 -33
- junifer/storage/pandas_base.py +12 -11
- junifer/storage/py.typed +0 -0
- junifer/storage/sqlite.py +11 -11
- junifer/storage/tests/test_hdf5.py +86 -4
- junifer/storage/tests/test_sqlite.py +2 -2
- junifer/storage/tests/test_storage_base.py +5 -2
- junifer/storage/tests/test_utils.py +33 -7
- junifer/storage/utils.py +95 -9
- junifer/testing/__init__.py +2 -3
- junifer/testing/__init__.pyi +4 -0
- junifer/testing/datagrabbers.py +10 -11
- junifer/testing/py.typed +0 -0
- junifer/testing/registry.py +4 -7
- junifer/testing/tests/test_testing_registry.py +9 -17
- junifer/tests/test_stats.py +2 -2
- junifer/typing/__init__.py +9 -0
- junifer/typing/__init__.pyi +31 -0
- junifer/typing/_typing.py +68 -0
- junifer/utils/__init__.py +2 -12
- junifer/utils/__init__.pyi +18 -0
- junifer/utils/_config.py +110 -0
- junifer/utils/_yaml.py +16 -0
- junifer/utils/helpers.py +6 -6
- junifer/utils/logging.py +117 -8
- junifer/utils/py.typed +0 -0
- junifer/{pipeline → utils}/singleton.py +19 -14
- junifer/utils/tests/test_config.py +59 -0
- {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info}/METADATA +43 -38
- junifer-0.0.6.dist-info/RECORD +350 -0
- {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info}/WHEEL +1 -1
- junifer-0.0.6.dist-info/entry_points.txt +2 -0
- junifer/api/parser.py +0 -118
- junifer/data/coordinates.py +0 -408
- junifer/data/masks.py +0 -670
- junifer/data/parcellations.py +0 -1828
- junifer/pipeline/registry.py +0 -177
- junifer/pipeline/tests/test_registry.py +0 -150
- junifer-0.0.5.dev242.dist-info/RECORD +0 -275
- junifer-0.0.5.dev242.dist-info/entry_points.txt +0 -2
- /junifer/{api → cli}/tests/data/gmd_mean.yaml +0 -0
- /junifer/{api → cli}/tests/data/gmd_mean_htcondor.yaml +0 -0
- /junifer/{api → cli}/tests/data/partly_cloudy_agg_mean_tian.yml +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/AutobiographicalMemory_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/CogAC_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/CogAR_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/DMNBuckner_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/Dosenbach2010_MNI_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/Empathy_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/Motor_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/MultiTask_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/PhysioStress_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/Power2011_MNI_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/Power2013_MNI_VOIs.tsv +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/Rew_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/Somatosensory_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/ToM_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/VigAtt_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/WM_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/eMDN_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/eSAD_VOIs.txt +0 -0
- /junifer/data/{VOIs → coordinates/VOIs}/meta/extDMN_VOIs.txt +0 -0
- {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info/licenses}/AUTHORS.rst +0 -0
- {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info/licenses}/LICENSE.md +0 -0
- {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info}/top_level.txt +0 -0
junifer/pipeline/registry.py
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"""Provide functions for registry."""
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# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
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# Leonard Sasse <l.sasse@fz-juelich.de>
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# Synchon Mandal <s.mandal@fz-juelich.de>
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# License: AGPL
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from typing import TYPE_CHECKING, Dict, List, Optional, Union
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if TYPE_CHECKING:
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from ..datagrabber import BaseDataGrabber
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from ..storage import BaseFeatureStorage
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from .pipeline_step_mixin import PipelineStepMixin
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__all__ = ["register", "get_step_names", "get_class", "build"]
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# Define valid steps for operation
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_VALID_STEPS: List[str] = [
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# Define registry for valid steps
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Registered function class.
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------
|
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ValueError
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def build(
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|
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) -> Union["BaseDataGrabber", "PipelineStepMixin", "BaseFeatureStorage"]:
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"""Ensure that the given object is an instance of the given class.
|
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|
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----------
|
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|
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|
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|
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Name of the function.
|
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|
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Class to be checked against.
|
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|
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Parameters to pass to the base class constructor (default None).
|
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|
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|
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-------
|
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|
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object
|
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An instance of the given base class.
|
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|
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|
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|
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Raises
|
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|
-
------
|
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|
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RuntimeError
|
145
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If there is a problem creating the instance.
|
146
|
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ValueError
|
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-
If the created object with the given name is not an instance of the
|
148
|
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base class.
|
149
|
-
|
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|
-
"""
|
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# Set default init parameters
|
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if init_params is None:
|
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|
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init_params = {}
|
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|
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# Get class of the registered function
|
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|
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logger.debug(f"Building {step}/{name}")
|
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|
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klass = get_class(step=step, name=name)
|
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|
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logger.debug(f"\tClass: {klass.__name__}")
|
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|
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logger.debug(f"\tInit params: {init_params}")
|
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|
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try:
|
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|
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# Create instance of the class
|
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|
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object_ = klass(**init_params)
|
162
|
-
except (ValueError, TypeError) as e:
|
163
|
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raise_error(
|
164
|
-
msg=f"Failed to create {step} ({name}). Error: {e}",
|
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|
-
klass=RuntimeError,
|
166
|
-
exception=e,
|
167
|
-
)
|
168
|
-
# Verify created instance belongs to the base class
|
169
|
-
if not isinstance(object_, baseclass):
|
170
|
-
raise_error(
|
171
|
-
msg=(
|
172
|
-
f"Invalid {step} ({object_.__class__.__name__}). "
|
173
|
-
f"Must inherit from {baseclass.__name__}"
|
174
|
-
),
|
175
|
-
klass=ValueError,
|
176
|
-
)
|
177
|
-
return object_
|
@@ -1,150 +0,0 @@
|
|
1
|
-
"""Provide tests for registry."""
|
2
|
-
|
3
|
-
# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
|
4
|
-
# Leonard Sasse <l.sasse@fz-juelich.de>
|
5
|
-
# Synchon Mandal <s.mandal@fz-juelich.de>
|
6
|
-
# License: AGPL
|
7
|
-
import logging
|
8
|
-
from abc import ABC
|
9
|
-
from typing import Type
|
10
|
-
|
11
|
-
import pytest
|
12
|
-
|
13
|
-
from junifer.datagrabber import PatternDataGrabber
|
14
|
-
from junifer.pipeline.registry import (
|
15
|
-
build,
|
16
|
-
get_class,
|
17
|
-
get_step_names,
|
18
|
-
register,
|
19
|
-
)
|
20
|
-
from junifer.storage import SQLiteFeatureStorage
|
21
|
-
|
22
|
-
|
23
|
-
def test_register_invalid_step():
|
24
|
-
"""Test register invalid step name."""
|
25
|
-
with pytest.raises(ValueError, match="Invalid step:"):
|
26
|
-
register(step="foo", name="bar", klass=str)
|
27
|
-
|
28
|
-
|
29
|
-
# TODO: improve parametrization
|
30
|
-
@pytest.mark.parametrize(
|
31
|
-
"step, name, klass",
|
32
|
-
[
|
33
|
-
("datagrabber", "pattern-dg", PatternDataGrabber),
|
34
|
-
("storage", "sqlite-storage", SQLiteFeatureStorage),
|
35
|
-
],
|
36
|
-
)
|
37
|
-
def test_register(
|
38
|
-
caplog: pytest.LogCaptureFixture, step: str, name: str, klass: Type
|
39
|
-
) -> None:
|
40
|
-
"""Test register.
|
41
|
-
|
42
|
-
Parameters
|
43
|
-
----------
|
44
|
-
caplog : pytest.LogCaptureFixture
|
45
|
-
The pytest.LogCaptureFixture object.
|
46
|
-
step : str
|
47
|
-
The parametrized name of the step.
|
48
|
-
name : str
|
49
|
-
The parametrized name of the function.
|
50
|
-
klass : str
|
51
|
-
The parametrized name of the base class.
|
52
|
-
|
53
|
-
"""
|
54
|
-
with caplog.at_level(logging.INFO):
|
55
|
-
# Register
|
56
|
-
register(step=step, name=name, klass=klass)
|
57
|
-
# Check logging message
|
58
|
-
assert "Registering" in caplog.text
|
59
|
-
|
60
|
-
|
61
|
-
def test_get_step_names_invalid_step() -> None:
|
62
|
-
"""Test get step name invalid step name."""
|
63
|
-
with pytest.raises(ValueError, match="Invalid step:"):
|
64
|
-
get_step_names(step="foo")
|
65
|
-
|
66
|
-
|
67
|
-
def test_get_step_names_absent() -> None:
|
68
|
-
"""Test get step names for absent name."""
|
69
|
-
# Get step names for datagrabber
|
70
|
-
datagrabbers = get_step_names(step="datagrabber")
|
71
|
-
# Check for datagrabber step name
|
72
|
-
assert "bar" not in datagrabbers
|
73
|
-
|
74
|
-
|
75
|
-
def test_get_step_names() -> None:
|
76
|
-
"""Test get step names."""
|
77
|
-
# Register datagrabber
|
78
|
-
register(step="datagrabber", name="bar", klass=str)
|
79
|
-
# Get step names for datagrabber
|
80
|
-
datagrabbers = get_step_names(step="datagrabber")
|
81
|
-
# Check for datagrabber step name
|
82
|
-
assert "bar" in datagrabbers
|
83
|
-
|
84
|
-
|
85
|
-
def test_get_class_invalid_step() -> None:
|
86
|
-
"""Test get class invalid step name."""
|
87
|
-
with pytest.raises(ValueError, match="Invalid step:"):
|
88
|
-
get_class(step="foo", name="bar")
|
89
|
-
|
90
|
-
|
91
|
-
def test_get_class_invalid_name() -> None:
|
92
|
-
"""Test get class invalid function name."""
|
93
|
-
with pytest.raises(ValueError, match="Invalid name:"):
|
94
|
-
get_class(step="datagrabber", name="foo")
|
95
|
-
|
96
|
-
|
97
|
-
# TODO: enable parametrization
|
98
|
-
def test_get_class():
|
99
|
-
"""Test get class."""
|
100
|
-
# Register datagrabber
|
101
|
-
register(step="datagrabber", name="bar", klass=str)
|
102
|
-
# Get class
|
103
|
-
obj = get_class(step="datagrabber", name="bar")
|
104
|
-
assert isinstance(obj, type(str))
|
105
|
-
|
106
|
-
|
107
|
-
# TODO: possible parametrization?
|
108
|
-
def test_build():
|
109
|
-
"""Test building objects from names."""
|
110
|
-
import numpy as np
|
111
|
-
|
112
|
-
# Define abstract base class
|
113
|
-
class SuperClass(ABC):
|
114
|
-
pass
|
115
|
-
|
116
|
-
# Define concrete class
|
117
|
-
class ConcreteClass(SuperClass):
|
118
|
-
def __init__(self, value=1):
|
119
|
-
self.value = value
|
120
|
-
|
121
|
-
# Register
|
122
|
-
register(step="datagrabber", name="concrete", klass=ConcreteClass)
|
123
|
-
|
124
|
-
# Build
|
125
|
-
obj = build(step="datagrabber", name="concrete", baseclass=SuperClass)
|
126
|
-
assert isinstance(obj, ConcreteClass)
|
127
|
-
assert obj.value == 1
|
128
|
-
|
129
|
-
# Build
|
130
|
-
obj = build(
|
131
|
-
step="datagrabber",
|
132
|
-
name="concrete",
|
133
|
-
baseclass=SuperClass,
|
134
|
-
init_params={"value": 2},
|
135
|
-
)
|
136
|
-
assert isinstance(obj, ConcreteClass)
|
137
|
-
assert obj.value == 2
|
138
|
-
|
139
|
-
# Check error
|
140
|
-
with pytest.raises(ValueError, match="Must inherit"):
|
141
|
-
build(step="datagrabber", name="concrete", baseclass=np.ndarray)
|
142
|
-
|
143
|
-
# Check error
|
144
|
-
with pytest.raises(RuntimeError, match="Failed to create"):
|
145
|
-
build(
|
146
|
-
step="datagrabber",
|
147
|
-
name="concrete",
|
148
|
-
baseclass=SuperClass,
|
149
|
-
init_params={"wrong": 2},
|
150
|
-
)
|
@@ -1,275 +0,0 @@
|
|
1
|
-
junifer/__init__.py,sha256=-T9XmiCCL0j3YLx-0Pph15sPfL5FlcBDscajjJ-V4sU,604
|
2
|
-
junifer/_version.py,sha256=5ar8KTPD2riEkS9RKe7tYuw4gZesZ5Gonw6vdJ43Z_8,428
|
3
|
-
junifer/stats.py,sha256=BjQb2lfTGDP9l4UuQYmJFcJJNRfbJDGlNvC06SJaDDE,6237
|
4
|
-
junifer/api/__init__.py,sha256=lwyIF0hPc7fICuSoddJfay0LPqlTRxHJ_xbtizgFYZA,312
|
5
|
-
junifer/api/cli.py,sha256=53pews3mXkJ7DUDSkV51PbitYnuVAdQRkWG-gjO08Uw,16142
|
6
|
-
junifer/api/decorators.py,sha256=DCctYgmBf8QTZGtjKXLCYYeBapt00IwskH2_0NoIDT4,2727
|
7
|
-
junifer/api/functions.py,sha256=dnQvLDHE3bSLP9yBj3MkNLYdy8jhvjTF5vI4IDGwpbE,13105
|
8
|
-
junifer/api/parser.py,sha256=f7xZbn3MW1GEEJnb1SlCGkAj9n6gvquzjDB5knmBDcA,4443
|
9
|
-
junifer/api/utils.py,sha256=dyjTdPMwX9qeCrn8SQT2Pjshfnu-y1FEyujV7lCzvm0,3333
|
10
|
-
junifer/api/queue_context/__init__.py,sha256=1ZO7e0rlfCvgXeVsfqZhHTqqIEbE_lOExCLro5jYaFA,353
|
11
|
-
junifer/api/queue_context/gnu_parallel_local_adapter.py,sha256=x2eQRVkhwJKd-Kx8AYia4F8nYnOLJrFzMGMjcwUygEc,9561
|
12
|
-
junifer/api/queue_context/htcondor_adapter.py,sha256=92pt4M_r52inBVlQ2M8Di6quEKW4Xcq3qVNRXaV4rGY,13233
|
13
|
-
junifer/api/queue_context/queue_context_adapter.py,sha256=a6UE8xavDfuaZbkWYsayVs6l-rwIrbpFSpqSyHsEeYY,1577
|
14
|
-
junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py,sha256=BPoewP50mfFPubRfcMYvEydIpW8k4p4T7NzRy8tAe1A,6604
|
15
|
-
junifer/api/queue_context/tests/test_htcondor_adapter.py,sha256=1vDAyIYQj_sFEhSC76duK7u6sd7K3kGFC-pfpjJNLYg,8619
|
16
|
-
junifer/api/res/run_conda.bash,sha256=Axm0xTsP6doUV0X0k6nUP_UJr_2GzA8CPvulQZ01Uno,517
|
17
|
-
junifer/api/res/run_conda.zsh,sha256=32Sm1VNjsrpdH_Wi46jGhPbrJjrmNlPIHtkQ6cHVUkU,515
|
18
|
-
junifer/api/res/run_venv.bash,sha256=aynMRwBgFzYc4CAWbnne_A0UPD5ZFd81w62u22IXzPo,507
|
19
|
-
junifer/api/res/run_venv.zsh,sha256=PaZJ5444TBdM3XntUETyxyngQ9xtjiq7I6hhHQev2Hc,506
|
20
|
-
junifer/api/res/afni/3dAFNItoNIFTI,sha256=Fsy5S5rwIBb1MepLfl_5FQhE7gv6NDwNyAR_k036NmM,51
|
21
|
-
junifer/api/res/afni/3dRSFC,sha256=MkPtS_nKEoJOHDAT3ZP9IA-SvMdhyzZDiyxObV_XI3g,44
|
22
|
-
junifer/api/res/afni/3dReHo,sha256=Jb5B97iPPPQ14zAz7tK5BVG4jPZyOe9c6kgM6ixKaY8,44
|
23
|
-
junifer/api/res/afni/afni,sha256=idLvNWHwd6P4jWXfk6hMXQckdpcTJYbvnLC3uNP6sBg,42
|
24
|
-
junifer/api/res/afni/run_afni_docker.sh,sha256=aXUBL7RaTDpXJFmLXTUH3lkr7K3SRm78sOzh32M_wew,1130
|
25
|
-
junifer/api/res/ants/ResampleImage,sha256=oJKZ31rBAW20ETozB8Ub5SbXMuhmZfrerpJTnRu-hOY,51
|
26
|
-
junifer/api/res/ants/antsApplyTransforms,sha256=SqlQEJ2RMMw_qGyDaNTXKzQqO7Bvrm6y5SEPmyqHiYc,57
|
27
|
-
junifer/api/res/ants/antsApplyTransformsToPoints,sha256=lqyvQGo8oI-RNpNlRqz-BvLHh7Th5HQgsDZjHF6nEeI,65
|
28
|
-
junifer/api/res/ants/run_ants_docker.sh,sha256=IZN1o2ppW7roe83t1Hi7bzAM4qQ26l-5PW36YA5IQEg,1120
|
29
|
-
junifer/api/res/freesurfer/mri_binarize,sha256=d6tjwyOTvLxaMcmUMaeYdR6gE0aI0Bj7ITnDLO3eNdk,56
|
30
|
-
junifer/api/res/freesurfer/mri_mc,sha256=sTVbj27M_rjs1RIj6dyp_OTSN4ZB3Q_7f2A5z-ri1QA,50
|
31
|
-
junifer/api/res/freesurfer/mri_pretess,sha256=BxhyeD8M3jxIpA_1i6sMAHcsaBQQtvfPu2i1u_nGFBg,55
|
32
|
-
junifer/api/res/freesurfer/mris_convert,sha256=7r6L2nQlBNUMJwtsRiIicU_LvKi5GQ9pQUkbDP__p_Q,56
|
33
|
-
junifer/api/res/freesurfer/run_freesurfer_docker.sh,sha256=zn6fa0lNAMx3KNZqLcjUYhabpCmcqSETBtqqiqiRQAY,1848
|
34
|
-
junifer/api/res/fsl/applywarp,sha256=DBgHfsn1yXWq0t-P7J0YvrjjJNgiblwDsh9L1hF9v_w,46
|
35
|
-
junifer/api/res/fsl/flirt,sha256=tSjiUco8ui8AbHD7mTzChEwbR0Rf_4iJTgzYTPF_WuQ,42
|
36
|
-
junifer/api/res/fsl/img2imgcoord,sha256=Zmaw3oJYrEltcXiPyEubXry9ppAq3SND52tdDWGgeZk,49
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37
|
-
junifer/api/res/fsl/run_fsl_docker.sh,sha256=pq-fcNdLuvHzVIQePN4GebZGlcE2UF-xj5rBIqAMz4g,1122
|
38
|
-
junifer/api/res/fsl/std2imgcoord,sha256=-X5wRH6XMl0yqnTACJX6MFhO8DFOEWg42MHRxGvimXg,49
|
39
|
-
junifer/api/tests/test_api_utils.py,sha256=aM4cCMf3orGURlXTcjBk0TVV0TF9yuFr4biH7eDG0F8,2696
|
40
|
-
junifer/api/tests/test_cli.py,sha256=kyDu-51lBmIBlQ2MnmmecC3nENrQuZRpk0bCkAPqmWM,10969
|
41
|
-
junifer/api/tests/test_functions.py,sha256=unLxIMwB3f7HF3ESq0JCfRaQhNB9Xj0JEi1OMkWsgtQ,17753
|
42
|
-
junifer/api/tests/test_parser.py,sha256=eUz2JPVb0_cxvoeI1O_C5PMNs5v_lDzGsN6fV1VW5Eg,6109
|
43
|
-
junifer/api/tests/data/gmd_mean.yaml,sha256=Ohb_C5cfQMK-59U9O1ZhejXyBtzLc5Y4cv8QyYq2azg,330
|
44
|
-
junifer/api/tests/data/gmd_mean_htcondor.yaml,sha256=f7NLv_KIJXTiPNFmOWl2Vw8EfwojhfkGtwbh5prbd6w,417
|
45
|
-
junifer/api/tests/data/partly_cloudy_agg_mean_tian.yml,sha256=nS8K_R1hEuV71Vv-i9SYjnDGAK2FClQqBiE4kOuQ_ys,313
|
46
|
-
junifer/configs/__init__.py,sha256=mE70B1Sc7Tn4uts1vMVF7Ie6hdj7PuDvmDmie3soA9I,121
|
47
|
-
junifer/configs/juseless/__init__.py,sha256=kQ8b7wIYfpUqQXlWzZQkGzSUfAOi_VLyLq4brRz6-Dg,188
|
48
|
-
junifer/configs/juseless/datagrabbers/__init__.py,sha256=vDg8wL5fs3mpsA4modWXpXqYkRy6neP-RiMlGdfTe58,623
|
49
|
-
junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py,sha256=dhOeIQg-IVDatJu2Y1ObuAANdMoYDgACtMOu-9SHzh8,1474
|
50
|
-
junifer/configs/juseless/datagrabbers/camcan_vbm.py,sha256=_d_nMmKQbGEK644wCMmVfHaI2ioTmDmg5ypr_Ik3hDI,1538
|
51
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