For developers¶
Contributing¶
NiFreeze is a project of the NiPreps Community, which specifies the contributing guidelines. Before delving into the code, please make sure you have read all the guidelines offered online.
Documentation¶
Documentation sources are found under the docs/ folder, and builds are archived in the gh-pages branch of the repository.
With GitHub Pages, the documentation is posted under https://www.nipreps.org/nifreeze.
We maintain versioned documentation, by storing git tags under <major>.<minor>/ folders, i.e., we do not archive every patch release, but only every minor release.
In other words, folder 0.1/ of the documentation tree contains the documents for the latest release within the 0.1.x series.
With every commit (or merge commit) to main, the development version of the documentation under the folder main/ is updated too.
The gh-pages branch is automatically maintained with a GitHub Action.
Please, do not commit manually to gh-pages.
To build the documentation locally, you first need to make sure that setuptools_scm[toml] >= 6.2 is installed in your environment and then:
cd <nifreeze-repository>/
python -m setuptools_scm # This will generate ``src/nifreeze/_version.py``
make -C docs/ html
Library API (application program interface)¶
Information on specific functions, classes, and methods.
- nifreeze.analysis package
- nifreeze.cli package
- nifreeze.data package
load()- Subpackages
- nifreeze.data.dmri package
- dMRI data representation
DWIfrom_nii()- Submodules
- nifreeze.data.dmri.base module
- nifreeze.data.dmri.io module
- nifreeze.data.dmri.utils module
DEFAULT_GRADIENT_ATOLDEFAULT_HIGHB_THRESHOLDDEFAULT_LOWB_THRESHOLDDEFAULT_MAX_S0DEFAULT_MIN_S0DEFAULT_MULTISHELL_BIN_COUNT_THRDEFAULT_NUM_BINSDTI_MIN_ORIENTATIONSGRADIENT_ABSENCE_ERROR_MSGGRADIENT_EXPECTED_COLUMNS_ERROR_MSGGRADIENT_NDIM_ERROR_MSGGRADIENT_OBJECT_ERROR_MSGGRADIENT_VOLUME_DIMENSIONALITY_MISMATCH_ERRORfind_shelling_scheme()format_gradients()transform_fsl_bvec()
- nifreeze.data.pet package
- PET data representation
PETfrom_nii()- Submodules
- nifreeze.data.pet.base module
- nifreeze.data.pet.io module
- nifreeze.data.pet.utils module
- nifreeze.data.dmri package
- Submodules
- nifreeze.data.base module
AFFINE_ABSENCE_ERROR_MSGAFFINE_NDIM_ERROR_MSGAFFINE_OBJECT_ERROR_MSGAFFINE_SHAPE_ERROR_MSGBRAINMASK_SHAPE_MISMATCH_ERROR_MSGBaseDatasetBaseDataset.__len__()BaseDataset.affineBaseDataset.brainmaskBaseDataset.datahdrBaseDataset.dataobjBaseDataset.from_filename()BaseDataset.get_filename()BaseDataset.motion_affinesBaseDataset.set_transform()BaseDataset.shape3dBaseDataset.size3dBaseDataset.to_filename()BaseDataset.to_nifti()
DATAOBJ_ABSENCE_ERROR_MSGDATAOBJ_NDIM_ERROR_MSGDATAOBJ_OBJECT_ERROR_MSGImageGridto_nifti()validate_affine()validate_dataobj()
- nifreeze.data.filtering module
- nifreeze.data.splitting module
- nifreeze.data.utils module
- nifreeze.data.base module
- nifreeze.data.dmri package
- dMRI data representation
DWIfrom_nii()- Submodules
- nifreeze.data.dmri.base module
- nifreeze.data.dmri.io module
- nifreeze.data.dmri.utils module
DEFAULT_GRADIENT_ATOLDEFAULT_HIGHB_THRESHOLDDEFAULT_LOWB_THRESHOLDDEFAULT_MAX_S0DEFAULT_MIN_S0DEFAULT_MULTISHELL_BIN_COUNT_THRDEFAULT_NUM_BINSDTI_MIN_ORIENTATIONSGRADIENT_ABSENCE_ERROR_MSGGRADIENT_EXPECTED_COLUMNS_ERROR_MSGGRADIENT_NDIM_ERROR_MSGGRADIENT_OBJECT_ERROR_MSGGRADIENT_VOLUME_DIMENSIONALITY_MISMATCH_ERRORfind_shelling_scheme()format_gradients()transform_fsl_bvec()
- nifreeze.estimator module
- nifreeze.exceptions module
- nifreeze.model package
AverageDWIModelBSplinePETModelDKIModelDTIModelExpectationModelGPModelModelFactoryTrivialModel- Submodules
- nifreeze.model.base module
- nifreeze.model.dmri module
- nifreeze.model.gpr module
- nifreeze.model.gqi module
- nifreeze.model.pet module
- nifreeze.registration package
- nifreeze.testing package
- Submodules
- nifreeze.testing.simulations module
add_b0()create_diffusion_encoding_gradient_dirs()create_random_diffusivity_eigenvalues()create_random_polar_angles()create_random_polar_coordinates()create_single_fiber_evecs()create_single_shell_gradient_table()create_three_fiber_random_volume_fractions()create_two_fiber_dominant_random_volume_fractions()create_two_fiber_nondominant_random_volume_fractions()get_query_vectors()group_values()serialize_dmri()serialize_dwi()serialize_gtab()simulate_multifiber_voxels()simulate_one_fiber_multivoxel()simulate_three_fiber_multivoxel()simulate_two_fiber_multivoxel()simulate_voxels()single_fiber_voxel()
- nifreeze.testing.simulations module
- Submodules
- nifreeze.utils package
- nifreeze.viz package