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modewise 0.2.0__tar.gz

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Files changed (276) hide show

modewise-0.2.0/Cargo.lock +2609 -0
modewise-0.2.0/Cargo.toml +75 -0
modewise-0.2.0/LICENSE +28 -0
modewise-0.2.0/PKG-INFO +54 -0
modewise-0.2.0/README.md +24 -0
modewise-0.2.0/THIRD_PARTY_LICENSES.md +5935 -0
modewise-0.2.0/THIRD_PARTY_NOTICES.md +287 -0
modewise-0.2.0/adapters/dataset/Cargo.toml +30 -0
modewise-0.2.0/adapters/dataset/src/channels.rs +224 -0
modewise-0.2.0/adapters/dataset/src/events_tsv.rs +62 -0
modewise-0.2.0/adapters/dataset/src/lib.rs +329 -0
modewise-0.2.0/adapters/dataset/src/participants.rs +135 -0
modewise-0.2.0/adapters/dataset/src/pattern.rs +225 -0
modewise-0.2.0/adapters/dataset/src/spec.rs +233 -0
modewise-0.2.0/adapters/dataset/tests/channels.rs +185 -0
modewise-0.2.0/adapters/dataset/tests/discover.rs +368 -0
modewise-0.2.0/adapters/dataset/tests/nifti.rs +152 -0
modewise-0.2.0/adapters/dataset/tests/participants.rs +153 -0
modewise-0.2.0/adapters/dataset/tests/properties.proptest-regressions +7 -0
modewise-0.2.0/adapters/dataset/tests/properties.rs +47 -0
modewise-0.2.0/adapters/hdf5/Cargo.toml +21 -0
modewise-0.2.0/adapters/hdf5/src/lib.rs +85 -0
modewise-0.2.0/adapters/hdf5/tests/properties.rs +35 -0
modewise-0.2.0/adapters/hdf5/tests/read.rs +93 -0
modewise-0.2.0/adapters/hdf5/tests/real_data.rs +113 -0
modewise-0.2.0/adapters/nifti/Cargo.toml +18 -0
modewise-0.2.0/adapters/nifti/src/lib.rs +148 -0
modewise-0.2.0/adapters/nifti/tests/read.rs +105 -0
modewise-0.2.0/adapters/results/Cargo.toml +30 -0
modewise-0.2.0/adapters/results/src/export.rs +524 -0
modewise-0.2.0/adapters/results/src/lib.rs +286 -0
modewise-0.2.0/adapters/results/src/tables.rs +102 -0
modewise-0.2.0/adapters/results/tests/results_dir.rs +408 -0
modewise-0.2.0/adapters/store-memory/Cargo.toml +18 -0
modewise-0.2.0/adapters/store-memory/src/lib.rs +83 -0
modewise-0.2.0/adapters/store-zarr/Cargo.toml +26 -0
modewise-0.2.0/adapters/store-zarr/src/codec.rs +572 -0
modewise-0.2.0/adapters/store-zarr/src/lib.rs +68 -0
modewise-0.2.0/adapters/store-zarr/tests/properties.rs +39 -0
modewise-0.2.0/adapters/store-zarr/tests/roundtrip.rs +449 -0
modewise-0.2.0/application/cohort/Cargo.toml +24 -0
modewise-0.2.0/application/cohort/src/designs.rs +362 -0
modewise-0.2.0/application/cohort/src/extract.rs +291 -0
modewise-0.2.0/application/cohort/src/lib.rs +90 -0
modewise-0.2.0/application/cohort/tests/designs.rs +470 -0
modewise-0.2.0/application/cohort/tests/features.rs +478 -0
modewise-0.2.0/application/operations/Cargo.toml +37 -0
modewise-0.2.0/application/operations/src/catalogue.rs +208 -0
modewise-0.2.0/application/operations/src/cwt.rs +86 -0
modewise-0.2.0/application/operations/src/emd.rs +310 -0
modewise-0.2.0/application/operations/src/epoch.rs +141 -0
modewise-0.2.0/application/operations/src/functional_connectivity.rs +92 -0
modewise-0.2.0/application/operations/src/hilbert.rs +169 -0
modewise-0.2.0/application/operations/src/lib.rs +68 -0
modewise-0.2.0/application/operations/src/mvmd.rs +246 -0
modewise-0.2.0/application/operations/src/reconstruct.rs +56 -0
modewise-0.2.0/application/operations/src/regions/mod.rs +321 -0
modewise-0.2.0/application/operations/src/regions/subset.rs +287 -0
modewise-0.2.0/application/operations/src/spectrum.rs +131 -0
modewise-0.2.0/application/operations/src/stft.rs +65 -0
modewise-0.2.0/application/operations/src/vlmd.rs +141 -0
modewise-0.2.0/application/operations/src/wavelet.rs +97 -0
modewise-0.2.0/application/operations/tests/chain.rs +154 -0
modewise-0.2.0/application/operations/tests/cwt.rs +167 -0
modewise-0.2.0/application/operations/tests/epochs.rs +297 -0
modewise-0.2.0/application/operations/tests/functional_connectivity.rs +124 -0
modewise-0.2.0/application/operations/tests/hilbert.rs +262 -0
modewise-0.2.0/application/operations/tests/operations.rs +359 -0
modewise-0.2.0/application/operations/tests/reference.rs +89 -0
modewise-0.2.0/application/operations/tests/regions.rs +434 -0
modewise-0.2.0/application/operations/tests/vlmd.rs +138 -0
modewise-0.2.0/application/pipeline/Cargo.toml +29 -0
modewise-0.2.0/application/pipeline/src/artifact.rs +154 -0
modewise-0.2.0/application/pipeline/src/batch.rs +116 -0
modewise-0.2.0/application/pipeline/src/error.rs +58 -0
modewise-0.2.0/application/pipeline/src/executor.rs +623 -0
modewise-0.2.0/application/pipeline/src/lib.rs +27 -0
modewise-0.2.0/application/pipeline/src/manifest.rs +52 -0
modewise-0.2.0/application/pipeline/src/operation.rs +77 -0
modewise-0.2.0/application/pipeline/src/plan.rs +499 -0
modewise-0.2.0/application/pipeline/src/registry.rs +41 -0
modewise-0.2.0/application/pipeline/src/spec.rs +174 -0
modewise-0.2.0/application/pipeline/src/store.rs +16 -0
modewise-0.2.0/application/pipeline/src/test_support.rs +226 -0
modewise-0.2.0/domain/brain/Cargo.toml +16 -0
modewise-0.2.0/domain/brain/src/lib.rs +10 -0
modewise-0.2.0/domain/brain/src/selection.rs +254 -0
modewise-0.2.0/domain/brain/src/table.rs +222 -0
modewise-0.2.0/domain/connectivity/Cargo.toml +14 -0
modewise-0.2.0/domain/connectivity/src/lib.rs +216 -0
modewise-0.2.0/domain/decomposition/Cargo.toml +15 -0
modewise-0.2.0/domain/decomposition/src/lib.rs +417 -0
modewise-0.2.0/domain/decomposition/src/loadings.rs +63 -0
modewise-0.2.0/domain/epochs/Cargo.toml +20 -0
modewise-0.2.0/domain/epochs/src/epochs.rs +329 -0
modewise-0.2.0/domain/epochs/src/events.rs +165 -0
modewise-0.2.0/domain/epochs/src/lib.rs +11 -0
modewise-0.2.0/domain/epochs/tests/cut.rs +433 -0
modewise-0.2.0/domain/epochs/tests/properties.rs +35 -0
modewise-0.2.0/domain/method/Cargo.toml +13 -0
modewise-0.2.0/domain/method/src/lib.rs +32 -0
modewise-0.2.0/domain/signals/Cargo.toml +17 -0
modewise-0.2.0/domain/signals/src/error.rs +17 -0
modewise-0.2.0/domain/signals/src/lib.rs +7 -0
modewise-0.2.0/domain/signals/src/sampling_rate.rs +42 -0
modewise-0.2.0/domain/signals/src/series.rs +143 -0
modewise-0.2.0/domain/signals/tests/properties.rs +36 -0
modewise-0.2.0/domain/spectral/Cargo.toml +15 -0
modewise-0.2.0/domain/spectral/src/lib.rs +302 -0
modewise-0.2.0/domain/study/Cargo.toml +14 -0
modewise-0.2.0/domain/study/src/features.rs +216 -0
modewise-0.2.0/domain/study/src/lib.rs +28 -0
modewise-0.2.0/domain/study/src/participants.rs +148 -0
modewise-0.2.0/drivers/cli/Cargo.toml +26 -0
modewise-0.2.0/drivers/cli/src/commands.rs +172 -0
modewise-0.2.0/drivers/cli/src/lib.rs +136 -0
modewise-0.2.0/drivers/cli/src/main.rs +3 -0
modewise-0.2.0/drivers/cli/tests/cli.rs +276 -0
modewise-0.2.0/drivers/python/.gitignore +4 -0
modewise-0.2.0/drivers/python/Cargo.toml +48 -0
modewise-0.2.0/drivers/python/LICENSE +28 -0
modewise-0.2.0/drivers/python/README.md +24 -0
modewise-0.2.0/drivers/python/THIRD_PARTY_LICENSES.md +5935 -0
modewise-0.2.0/drivers/python/THIRD_PARTY_NOTICES.md +287 -0
modewise-0.2.0/drivers/python/src/channels.rs +176 -0
modewise-0.2.0/drivers/python/src/cohort.rs +308 -0
modewise-0.2.0/drivers/python/src/convert.rs +30 -0
modewise-0.2.0/drivers/python/src/data.rs +98 -0
modewise-0.2.0/drivers/python/src/emd.rs +150 -0
modewise-0.2.0/drivers/python/src/events.rs +243 -0
modewise-0.2.0/drivers/python/src/functional_connectivity.rs +49 -0
modewise-0.2.0/drivers/python/src/hilbert.rs +94 -0
modewise-0.2.0/drivers/python/src/io.rs +94 -0
modewise-0.2.0/drivers/python/src/lib.rs +78 -0
modewise-0.2.0/drivers/python/src/mvmd.rs +149 -0
modewise-0.2.0/drivers/python/src/pipeline.rs +320 -0
modewise-0.2.0/drivers/python/src/results.rs +418 -0
modewise-0.2.0/drivers/python/src/saved.rs +189 -0
modewise-0.2.0/drivers/python/src/statistics.rs +274 -0
modewise-0.2.0/drivers/python/src/stft.rs +82 -0
modewise-0.2.0/drivers/python/src/vlmd.rs +55 -0
modewise-0.2.0/drivers/python/src/wavelet.rs +40 -0
modewise-0.2.0/drivers/python/tests/test_cohort.py +97 -0
modewise-0.2.0/drivers/python/tests/test_cwt.py +55 -0
modewise-0.2.0/drivers/python/tests/test_dataset.py +110 -0
modewise-0.2.0/drivers/python/tests/test_emd.py +47 -0
modewise-0.2.0/drivers/python/tests/test_epochs.py +72 -0
modewise-0.2.0/drivers/python/tests/test_functional_connectivity.py +63 -0
modewise-0.2.0/drivers/python/tests/test_hilbert.py +73 -0
modewise-0.2.0/drivers/python/tests/test_io.py +58 -0
modewise-0.2.0/drivers/python/tests/test_mvmd.py +57 -0
modewise-0.2.0/drivers/python/tests/test_nifti.py +32 -0
modewise-0.2.0/drivers/python/tests/test_pipeline.py +144 -0
modewise-0.2.0/drivers/python/tests/test_regions.py +64 -0
modewise-0.2.0/drivers/python/tests/test_spectrum.py +53 -0
modewise-0.2.0/drivers/python/tests/test_statistics.py +116 -0
modewise-0.2.0/drivers/python/tests/test_stft.py +23 -0
modewise-0.2.0/drivers/python/tests/test_stubs.py +39 -0
modewise-0.2.0/drivers/python/tests/test_vlmd.py +48 -0
modewise-0.2.0/drivers/python/tests/test_vmd.py +48 -0
modewise-0.2.0/drivers/python/tests/test_wavelet.py +23 -0
modewise-0.2.0/methods/cwt/Cargo.toml +20 -0
modewise-0.2.0/methods/cwt/src/lib.rs +120 -0
modewise-0.2.0/methods/cwt/tests/fixtures/generate.py +38 -0
modewise-0.2.0/methods/cwt/tests/fixtures/pycwt.json +1 -0
modewise-0.2.0/methods/cwt/tests/pycwt_parity.rs +153 -0
modewise-0.2.0/methods/emd/Cargo.toml +25 -0
modewise-0.2.0/methods/emd/src/boundary.rs +149 -0
modewise-0.2.0/methods/emd/src/decomposers.rs +154 -0
modewise-0.2.0/methods/emd/src/directions.rs +104 -0
modewise-0.2.0/methods/emd/src/ensemble.rs +239 -0
modewise-0.2.0/methods/emd/src/extrema.rs +78 -0
modewise-0.2.0/methods/emd/src/layout.rs +66 -0
modewise-0.2.0/methods/emd/src/lib.rs +77 -0
modewise-0.2.0/methods/emd/src/sift.rs +234 -0
modewise-0.2.0/methods/emd/src/spline.rs +90 -0
modewise-0.2.0/methods/emd/tests/ensemble_parity.rs +98 -0
modewise-0.2.0/methods/emd/tests/ensemble_synthetic.rs +171 -0
modewise-0.2.0/methods/emd/tests/fixtures/emd.json +1 -0
modewise-0.2.0/methods/emd/tests/fixtures/ensemble.json +1 -0
modewise-0.2.0/methods/emd/tests/fixtures/generate.py +86 -0
modewise-0.2.0/methods/emd/tests/fixtures/generate_ensemble.py +84 -0
modewise-0.2.0/methods/emd/tests/reference_parity.rs +173 -0
modewise-0.2.0/methods/emd/tests/synthetic.rs +208 -0
modewise-0.2.0/methods/fc/Cargo.toml +24 -0
modewise-0.2.0/methods/fc/src/lib.rs +118 -0
modewise-0.2.0/methods/fc/src/measures.rs +74 -0
modewise-0.2.0/methods/fc/tests/fixtures/generate.py +49 -0
modewise-0.2.0/methods/fc/tests/fixtures/reference.json +1 -0
modewise-0.2.0/methods/fc/tests/properties.rs +31 -0
modewise-0.2.0/methods/fc/tests/reference.rs +234 -0
modewise-0.2.0/methods/fourier/Cargo.toml +14 -0
modewise-0.2.0/methods/fourier/src/centroid.rs +48 -0
modewise-0.2.0/methods/fourier/src/lib.rs +137 -0
modewise-0.2.0/methods/hilbert/Cargo.toml +22 -0
modewise-0.2.0/methods/hilbert/src/analytic.rs +135 -0
modewise-0.2.0/methods/hilbert/src/lib.rs +9 -0
modewise-0.2.0/methods/hilbert/src/spectrum.rs +59 -0
modewise-0.2.0/methods/hilbert/tests/fixtures/generate.py +48 -0
modewise-0.2.0/methods/hilbert/tests/fixtures/reference.json +1 -0
modewise-0.2.0/methods/hilbert/tests/reference_parity.rs +133 -0
modewise-0.2.0/methods/hilbert/tests/synthetic.rs +147 -0
modewise-0.2.0/methods/mvmd/Cargo.toml +26 -0
modewise-0.2.0/methods/mvmd/src/decomposer.rs +120 -0
modewise-0.2.0/methods/mvmd/src/lib.rs +16 -0
modewise-0.2.0/methods/mvmd/src/noise_assisted.rs +122 -0
modewise-0.2.0/methods/mvmd/src/params.rs +131 -0
modewise-0.2.0/methods/mvmd/src/vmd.rs +63 -0
modewise-0.2.0/methods/mvmd/tests/fixtures/bold_like.json +1 -0
modewise-0.2.0/methods/mvmd/tests/fixtures/generate.py +49 -0
modewise-0.2.0/methods/mvmd/tests/fixtures/generate_vmd.py +40 -0
modewise-0.2.0/methods/mvmd/tests/fixtures/two_tone.json +1 -0
modewise-0.2.0/methods/mvmd/tests/fixtures/vmd.json +1 -0
modewise-0.2.0/methods/mvmd/tests/reference_parity.rs +109 -0
modewise-0.2.0/methods/mvmd/tests/synthetic.rs +93 -0
modewise-0.2.0/methods/mvmd/tests/variants.rs +165 -0
modewise-0.2.0/methods/mvmd/tests/vmd_parity.rs +81 -0
modewise-0.2.0/methods/parcellate/Cargo.toml +19 -0
modewise-0.2.0/methods/parcellate/src/lib.rs +239 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/atlas.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/atlas_qform.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/bold.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/generate.py +94 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/labels_4d.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/nilearn.json +1 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/rotated_qform.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/sform_wins.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/tr_ms.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/tr_us.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/fixtures/tr_zero.nii.gz +0 -0
modewise-0.2.0/methods/parcellate/tests/nilearn_parity.rs +110 -0
modewise-0.2.0/methods/stats/Cargo.toml +21 -0
modewise-0.2.0/methods/stats/src/dist.rs +125 -0
modewise-0.2.0/methods/stats/src/fdr.rs +48 -0
modewise-0.2.0/methods/stats/src/glm.rs +192 -0
modewise-0.2.0/methods/stats/src/lib.rs +25 -0
modewise-0.2.0/methods/stats/src/nbs.rs +111 -0
modewise-0.2.0/methods/stats/src/permutation.rs +250 -0
modewise-0.2.0/methods/stats/tests/fixtures/generate.py +114 -0
modewise-0.2.0/methods/stats/tests/fixtures/reference.json +628 -0
modewise-0.2.0/methods/stats/tests/reference.rs +484 -0
modewise-0.2.0/methods/stft/Cargo.toml +20 -0
modewise-0.2.0/methods/stft/src/lib.rs +87 -0
modewise-0.2.0/methods/stft/src/welch.rs +190 -0
modewise-0.2.0/methods/stft/tests/fixtures/generate.py +24 -0
modewise-0.2.0/methods/stft/tests/fixtures/generate_welch.py +30 -0
modewise-0.2.0/methods/stft/tests/fixtures/scipy_two_channel.json +1 -0
modewise-0.2.0/methods/stft/tests/fixtures/welch.json +1 -0
modewise-0.2.0/methods/stft/tests/scipy_parity.rs +119 -0
modewise-0.2.0/methods/stft/tests/welch_parity.rs +59 -0
modewise-0.2.0/methods/vlmd/Cargo.toml +24 -0
modewise-0.2.0/methods/vlmd/src/decomposer.rs +276 -0
modewise-0.2.0/methods/vlmd/src/lasso.rs +479 -0
modewise-0.2.0/methods/vlmd/src/lib.rs +13 -0
modewise-0.2.0/methods/vlmd/src/params.rs +179 -0
modewise-0.2.0/methods/vlmd/tests/fixtures/generate.py +84 -0
modewise-0.2.0/methods/vlmd/tests/fixtures/lasso.json +1 -0
modewise-0.2.0/methods/vlmd/tests/fixtures/reference.json +1 -0
modewise-0.2.0/methods/vlmd/tests/reference_parity.rs +125 -0
modewise-0.2.0/methods/vlmd/tests/synthetic.rs +181 -0
modewise-0.2.0/methods/wavelet/Cargo.toml +22 -0
modewise-0.2.0/methods/wavelet/filters/generate.py +37 -0
modewise-0.2.0/methods/wavelet/src/decomposer.rs +136 -0
modewise-0.2.0/methods/wavelet/src/filters.rs +37 -0
modewise-0.2.0/methods/wavelet/src/lib.rs +8 -0
modewise-0.2.0/methods/wavelet/src/modwt.rs +124 -0
modewise-0.2.0/methods/wavelet/tests/fixtures/generate.py +29 -0
modewise-0.2.0/methods/wavelet/tests/fixtures/mra.json +1 -0
modewise-0.2.0/methods/wavelet/tests/reference_parity.rs +60 -0
modewise-0.2.0/methods/wavelet/tests/synthetic.rs +140 -0
modewise-0.2.0/pyproject.toml +41 -0
modewise-0.2.0/python/modewise/__init__.py +102 -0
modewise-0.2.0/python/modewise/_cli.py +8 -0
modewise-0.2.0/python/modewise/_core.pyi +679 -0
modewise-0.2.0/python/modewise/_xarray.py +66 -0
modewise-0.2.0/python/modewise/py.typed +0 -0

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