junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__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/_version.py +9 -19
- junifer/api/__init__.pyi +17 -2
- junifer/api/functions.py +222 -39
- junifer/api/queue_context/__init__.pyi +11 -3
- junifer/api/queue_context/gnu_parallel_local_adapter.py +81 -120
- junifer/api/queue_context/htcondor_adapter.py +118 -181
- junifer/api/queue_context/queue_context_adapter.py +51 -7
- junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py +10 -35
- junifer/api/queue_context/tests/test_htcondor_adapter.py +13 -50
- junifer/api/res/fsl/run_fsl_docker.sh +4 -0
- junifer/api/tests/test_functions.py +863 -36
- junifer/cli/__init__.py +1 -7
- junifer/cli/cli.py +41 -22
- junifer/cli/parser.py +23 -147
- junifer/cli/tests/data/gmd_mean.yaml +6 -6
- junifer/cli/tests/data/gmd_mean_htcondor.yaml +6 -5
- junifer/cli/tests/data/partly_cloudy_agg_mean_tian.yml +1 -0
- junifer/cli/tests/test_cli.py +120 -4
- junifer/cli/tests/test_cli_utils.py +23 -6
- junifer/cli/utils.py +14 -9
- junifer/configs/__init__.py +5 -0
- junifer/configs/__init__.pyi +0 -0
- junifer/configs/juseless/datagrabbers/__init__.pyi +4 -2
- junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +18 -24
- junifer/configs/juseless/datagrabbers/camcan_vbm.py +20 -27
- junifer/configs/juseless/datagrabbers/ixi_vbm.py +44 -52
- junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py +0 -7
- junifer/configs/juseless/datagrabbers/tests/test_ucla.py +2 -19
- junifer/configs/juseless/datagrabbers/ucla.py +111 -104
- junifer/configs/juseless/datagrabbers/ukb_vbm.py +19 -25
- junifer/configs/py.typed +0 -0
- junifer/conftest.py +63 -24
- junifer/data/_dispatch.py +9 -19
- junifer/data/coordinates/_ants_coordinates_warper.py +4 -1
- junifer/data/coordinates/_coordinates.py +51 -6
- junifer/data/coordinates/_fsl_coordinates_warper.py +4 -1
- junifer/data/coordinates/tests/test_coordinates.py +15 -3
- junifer/data/coordinates/tests/test_coordinates_names.py +37 -0
- junifer/data/maps/_ants_maps_warper.py +18 -12
- junifer/data/maps/_fsl_maps_warper.py +7 -3
- junifer/data/maps/_maps.py +12 -8
- junifer/data/maps/tests/test_maps.py +13 -21
- junifer/data/masks/_ants_mask_warper.py +18 -12
- junifer/data/masks/_fsl_mask_warper.py +7 -3
- junifer/data/masks/_masks.py +15 -12
- junifer/data/masks/tests/test_masks.py +20 -17
- junifer/data/parcellations/_ants_parcellation_warper.py +18 -12
- junifer/data/parcellations/_fsl_parcellation_warper.py +7 -5
- junifer/data/parcellations/_parcellations.py +125 -91
- junifer/data/parcellations/tests/test_parcellations.py +122 -1
- junifer/data/template_spaces.py +117 -50
- junifer/data/tests/test_template_spaces.py +10 -7
- junifer/data/utils.py +10 -8
- junifer/datagrabber/__init__.pyi +38 -5
- junifer/datagrabber/aomic/__init__.pyi +8 -1
- junifer/datagrabber/aomic/_types.py +22 -0
- junifer/datagrabber/aomic/id1000.py +193 -183
- junifer/datagrabber/aomic/piop1.py +215 -259
- junifer/datagrabber/aomic/piop2.py +211 -244
- junifer/datagrabber/aomic/tests/test_id1000.py +70 -53
- junifer/datagrabber/aomic/tests/test_piop1.py +98 -102
- junifer/datagrabber/aomic/tests/test_piop2.py +88 -85
- junifer/datagrabber/base.py +253 -79
- junifer/datagrabber/datalad_base.py +127 -76
- junifer/datagrabber/dmcc13_benchmark.py +204 -289
- junifer/datagrabber/hcp1200/__init__.pyi +7 -2
- junifer/datagrabber/hcp1200/datalad_hcp1200.py +61 -40
- junifer/datagrabber/hcp1200/hcp1200.py +151 -164
- junifer/datagrabber/hcp1200/tests/test_hcp1200.py +116 -128
- junifer/datagrabber/multiple.py +183 -63
- junifer/datagrabber/pattern.py +358 -227
- junifer/datagrabber/pattern_datalad.py +84 -124
- junifer/datagrabber/pattern_validation_mixin.py +22 -50
- junifer/datagrabber/tests/test_base.py +17 -4
- junifer/datagrabber/tests/test_datalad_base.py +20 -27
- junifer/datagrabber/tests/test_dmcc13_benchmark.py +110 -122
- junifer/datagrabber/tests/test_multiple.py +293 -31
- junifer/datagrabber/tests/test_pattern.py +577 -18
- junifer/datagrabber/tests/test_pattern_datalad.py +177 -107
- junifer/datagrabber/tests/test_pattern_validation_mixin.py +9 -51
- junifer/datareader/default.py +8 -5
- junifer/datareader/tests/test_default_reader.py +1 -1
- junifer/external/BrainPrint/.codecov.yml +2 -0
- junifer/external/BrainPrint/.codespellignore +2 -0
- junifer/external/BrainPrint/.github/ISSUE_TEMPLATE/bug-report.md +45 -0
- junifer/external/BrainPrint/.github/ISSUE_TEMPLATE/documentation.md +12 -0
- junifer/external/BrainPrint/.github/ISSUE_TEMPLATE/feature-request.md +24 -0
- junifer/external/BrainPrint/.github/ISSUE_TEMPLATE/questions-help-support.md +28 -0
- junifer/external/BrainPrint/.github/dependabot.yml +6 -0
- junifer/external/BrainPrint/.github/workflows/build.yml +53 -0
- junifer/external/BrainPrint/.github/workflows/code-style.yml +44 -0
- junifer/external/BrainPrint/.github/workflows/doc.yml +65 -0
- junifer/external/BrainPrint/.github/workflows/publish.yml +31 -0
- junifer/external/BrainPrint/.github/workflows/pytest.yml +54 -0
- junifer/external/BrainPrint/.gitignore +123 -0
- junifer/external/BrainPrint/LICENSE +21 -0
- junifer/external/BrainPrint/README.md +108 -0
- junifer/external/BrainPrint/brainprint/cli/__init__.py +11 -0
- junifer/external/BrainPrint/brainprint/cli/help_text.py +169 -0
- junifer/external/BrainPrint/brainprint/cli/parser.py +150 -0
- junifer/external/BrainPrint/brainprint/cli/utils.py +14 -0
- junifer/external/BrainPrint/brainprint/commands/__init__.py +0 -0
- junifer/external/BrainPrint/brainprint/commands/sys_info.py +18 -0
- junifer/external/BrainPrint/brainprint/utils/tests/__init__.py +0 -0
- junifer/external/BrainPrint/brainprint/utils/tests/test_config.py +33 -0
- junifer/external/BrainPrint/doc/Makefile +20 -0
- junifer/external/BrainPrint/doc/_static/.gitkeep +0 -0
- junifer/external/BrainPrint/doc/_templates/autosummary/class.rst +10 -0
- junifer/external/BrainPrint/doc/_templates/autosummary/function.rst +8 -0
- junifer/external/BrainPrint/doc/_templates/autosummary/module.rst +6 -0
- junifer/external/BrainPrint/doc/api/index.rst +11 -0
- junifer/external/BrainPrint/doc/conf.py +272 -0
- junifer/external/BrainPrint/doc/index.rst +140 -0
- junifer/external/BrainPrint/doc/links.inc +36 -0
- junifer/external/BrainPrint/doc/make.bat +35 -0
- junifer/external/BrainPrint/doc/references.bib +23 -0
- junifer/external/BrainPrint/pyproject.toml +170 -0
- junifer/external/BrainPrint/setup.py +3 -0
- junifer/external/__init__.py +5 -0
- junifer/external/__init__.pyi +0 -0
- junifer/external/nilearn/junifer_connectivity_measure.py +95 -39
- junifer/external/nilearn/junifer_nifti_spheres_masker.py +226 -67
- junifer/external/nilearn/tests/test_junifer_connectivity_measure.py +39 -27
- junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py +231 -21
- junifer/external/py.typed +0 -0
- junifer/markers/__init__.pyi +6 -3
- junifer/markers/base.py +126 -76
- junifer/markers/brainprint.py +30 -39
- junifer/markers/complexity/__init__.py +20 -3
- junifer/markers/complexity/complexity_base.py +40 -41
- junifer/markers/complexity/hurst_exponent.py +22 -35
- junifer/markers/complexity/multiscale_entropy_auc.py +53 -41
- junifer/markers/complexity/perm_entropy.py +22 -36
- junifer/markers/complexity/range_entropy.py +22 -35
- junifer/markers/complexity/range_entropy_auc.py +27 -36
- junifer/markers/complexity/sample_entropy.py +22 -36
- junifer/markers/complexity/tests/test_complexity_registry.py +48 -0
- junifer/markers/complexity/tests/test_hurst_exponent.py +47 -36
- junifer/markers/complexity/tests/test_multiscale_entropy_auc.py +50 -36
- junifer/markers/complexity/tests/test_perm_entropy.py +48 -36
- junifer/markers/complexity/tests/test_range_entropy.py +47 -36
- junifer/markers/complexity/tests/test_range_entropy_auc.py +47 -36
- junifer/markers/complexity/tests/test_sample_entropy.py +48 -36
- junifer/markers/complexity/tests/test_weighted_perm_entropy.py +50 -36
- junifer/markers/complexity/weighted_perm_entropy.py +22 -36
- junifer/markers/ets_rss.py +35 -31
- junifer/markers/falff/__init__.pyi +7 -1
- junifer/markers/falff/_afni_falff.py +22 -9
- junifer/markers/falff/_junifer_falff.py +47 -31
- junifer/markers/falff/falff_base.py +80 -60
- junifer/markers/falff/falff_maps.py +17 -41
- junifer/markers/falff/falff_parcels.py +26 -51
- junifer/markers/falff/falff_spheres.py +34 -61
- junifer/markers/falff/tests/test_falff_maps.py +20 -23
- junifer/markers/falff/tests/test_falff_mask.py +99 -0
- junifer/markers/falff/tests/test_falff_parcels.py +14 -10
- junifer/markers/falff/tests/test_falff_spheres.py +14 -10
- junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py +32 -34
- junifer/markers/functional_connectivity/edge_functional_connectivity_maps.py +12 -25
- junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py +19 -34
- junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py +24 -44
- junifer/markers/functional_connectivity/functional_connectivity_base.py +50 -40
- junifer/markers/functional_connectivity/functional_connectivity_maps.py +12 -25
- junifer/markers/functional_connectivity/functional_connectivity_parcels.py +19 -34
- junifer/markers/functional_connectivity/functional_connectivity_spheres.py +24 -45
- junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py +21 -22
- junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_maps.py +8 -7
- junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py +8 -4
- junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py +8 -4
- junifer/markers/functional_connectivity/tests/test_functional_connectivity_maps.py +8 -7
- junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py +9 -5
- junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py +8 -12
- junifer/markers/maps_aggregation.py +77 -55
- junifer/markers/parcel_aggregation.py +91 -70
- junifer/markers/reho/__init__.pyi +7 -1
- junifer/markers/reho/_afni_reho.py +23 -14
- junifer/markers/reho/_junifer_reho.py +112 -123
- junifer/markers/reho/reho_base.py +115 -37
- junifer/markers/reho/reho_maps.py +18 -32
- junifer/markers/reho/reho_parcels.py +26 -41
- junifer/markers/reho/reho_spheres.py +33 -54
- junifer/markers/reho/tests/test_junifer_reho.py +178 -0
- junifer/markers/reho/tests/test_reho_maps.py +27 -25
- junifer/markers/reho/tests/test_reho_parcels.py +28 -22
- junifer/markers/reho/tests/test_reho_spheres.py +16 -12
- junifer/markers/sphere_aggregation.py +88 -72
- junifer/markers/temporal_snr/temporal_snr_base.py +32 -30
- junifer/markers/temporal_snr/temporal_snr_maps.py +9 -18
- junifer/markers/temporal_snr/temporal_snr_parcels.py +19 -27
- junifer/markers/temporal_snr/temporal_snr_spheres.py +27 -41
- junifer/markers/temporal_snr/tests/test_temporal_snr_base.py +2 -2
- junifer/markers/temporal_snr/tests/test_temporal_snr_maps.py +17 -22
- junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py +11 -3
- junifer/markers/temporal_snr/tests/test_temporal_snr_spheres.py +9 -9
- junifer/markers/tests/test_brainprint.py +10 -9
- junifer/markers/tests/test_ets_rss.py +7 -3
- junifer/markers/tests/test_lost_regions.py +279 -0
- junifer/markers/tests/test_maps_aggregation.py +67 -114
- junifer/markers/tests/test_marker_utils.py +40 -1
- junifer/markers/tests/test_markers_base.py +275 -6
- junifer/markers/tests/test_parcel_aggregation.py +91 -53
- junifer/markers/tests/test_sphere_aggregation.py +53 -47
- junifer/markers/utils.py +267 -5
- junifer/onthefly/__init__.py +2 -3
- junifer/onthefly/__init__.pyi +4 -0
- junifer/onthefly/_brainprint.py +3 -5
- junifer/onthefly/py.typed +0 -0
- junifer/onthefly/read_transform.py +11 -9
- junifer/onthefly/tests/test_read_transform.py +7 -7
- junifer/pipeline/__init__.pyi +4 -2
- junifer/pipeline/marker_collection.py +14 -10
- junifer/pipeline/pipeline_component_registry.py +25 -6
- junifer/pipeline/pipeline_step_mixin.py +5 -12
- junifer/pipeline/tests/test_data_object_dumper.py +10 -10
- junifer/pipeline/tests/test_marker_collection.py +145 -168
- junifer/pipeline/tests/test_pipeline_component_registry.py +52 -8
- junifer/pipeline/tests/test_pipeline_step_mixin.py +12 -26
- junifer/pipeline/tests/test_update_meta_mixin.py +4 -5
- junifer/pipeline/tests/test_workdir_manager.py +39 -0
- junifer/pipeline/update_meta_mixin.py +13 -10
- junifer/pipeline/utils.py +22 -17
- junifer/pipeline/workdir_manager.py +41 -32
- junifer/preprocess/__init__.pyi +9 -4
- junifer/preprocess/_temporal_filter.py +34 -33
- junifer/preprocess/_temporal_slicer.py +17 -30
- junifer/preprocess/base.py +99 -55
- junifer/preprocess/confounds/__init__.pyi +10 -2
- junifer/preprocess/confounds/fmriprep_confound_remover.py +87 -109
- junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +64 -45
- junifer/preprocess/smoothing/__init__.pyi +2 -2
- junifer/preprocess/smoothing/_afni_smoothing.py +8 -7
- junifer/preprocess/smoothing/_fsl_smoothing.py +6 -4
- junifer/preprocess/smoothing/_nilearn_smoothing.py +7 -5
- junifer/preprocess/smoothing/smoothing.py +59 -40
- junifer/preprocess/smoothing/tests/test_smoothing.py +28 -8
- junifer/preprocess/tests/test_preprocess_base.py +17 -9
- junifer/preprocess/tests/test_temporal_filter.py +37 -16
- junifer/preprocess/tests/test_temporal_slicer.py +12 -12
- junifer/preprocess/warping/__init__.pyi +2 -2
- junifer/preprocess/warping/_ants_warper.py +56 -40
- junifer/preprocess/warping/_fsl_warper.py +49 -36
- junifer/preprocess/warping/_utils.py +106 -0
- junifer/preprocess/warping/space_warper.py +99 -98
- junifer/preprocess/warping/tests/test_space_warper.py +46 -41
- junifer/preprocess/warping/tests/test_warping_utils.py +163 -0
- junifer/stats.py +46 -34
- junifer/storage/__init__.pyi +8 -4
- junifer/storage/base.py +129 -64
- junifer/storage/hdf5.py +307 -199
- junifer/storage/pandas_base.py +46 -24
- junifer/storage/sqlite.py +99 -62
- junifer/storage/tests/data/collected_h5io_fork.hdf5 +0 -0
- junifer/storage/tests/test_hdf5.py +147 -12
- junifer/storage/tests/test_repeated_storage.py +293 -0
- junifer/storage/tests/test_sqlite.py +9 -20
- junifer/storage/tests/test_storage_base.py +18 -21
- junifer/storage/tests/test_utils.py +83 -22
- junifer/storage/utils.py +58 -38
- junifer/testing/__init__.pyi +2 -2
- junifer/testing/datagrabbers.py +480 -44
- junifer/testing/registry.py +12 -0
- junifer/testing/tests/test_adhdtesting_datagrabber.py +24 -0
- junifer/testing/tests/test_oasisvmbtesting_datagrabber.py +5 -0
- junifer/testing/tests/test_partlycloudytesting_datagrabber.py +52 -0
- junifer/testing/tests/test_spmauditory_datagrabber.py +16 -0
- junifer/testing/tests/test_testing_registry.py +31 -0
- junifer/testing/tests/test_testing_utils.py +35 -0
- junifer/testing/tests/test_uclacnpvbmtesting_datagrabber.py +81 -0
- junifer/testing/utils.py +33 -1
- junifer/tests/test_stats.py +1 -5
- junifer/typing/__init__.pyi +2 -0
- junifer/typing/_typing.py +34 -19
- junifer/typing/py.typed +0 -0
- junifer/utils/__init__.pyi +10 -1
- junifer/utils/_config.py +1 -2
- junifer/utils/helpers.py +68 -2
- junifer/utils/logging.py +31 -7
- junifer/utils/tests/test_helpers.py +36 -1
- {junifer-0.0.7.dev332.dist-info → junifer-0.0.8.dist-info}/METADATA +43 -35
- junifer-0.0.8.dist-info/RECORD +402 -0
- {junifer-0.0.7.dev332.dist-info → junifer-0.0.8.dist-info}/WHEEL +1 -1
- junifer/cli/tests/test_parser.py +0 -280
- junifer/external/h5io/h5io/__init__.py +0 -15
- junifer/external/h5io/h5io/_h5io.py +0 -767
- junifer/external/h5io/h5io/_version.py +0 -1
- junifer/external/h5io/h5io/chunked_array.py +0 -94
- junifer/external/h5io/h5io/chunked_list.py +0 -65
- junifer/markers/complexity/__init__.pyi +0 -17
- junifer-0.0.7.dev332.dist-info/RECORD +0 -353
- {junifer-0.0.7.dev332.dist-info → junifer-0.0.8.dist-info}/entry_points.txt +0 -0
- {junifer-0.0.7.dev332.dist-info → junifer-0.0.8.dist-info}/licenses/AUTHORS.rst +0 -0
- {junifer-0.0.7.dev332.dist-info → junifer-0.0.8.dist-info}/licenses/LICENSE.md +0 -0
- {junifer-0.0.7.dev332.dist-info → junifer-0.0.8.dist-info}/top_level.txt +0 -0
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Summary: JUelich NeuroImaging FEature extractoR
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