intensity_normalization package¶
Subpackages¶
- intensity_normalization.cli package
- Submodules
- intensity_normalization.cli.coregister module
- intensity_normalization.cli.fcm module
- intensity_normalization.cli.histogram module
- intensity_normalization.cli.kde module
- intensity_normalization.cli.lsq module
- intensity_normalization.cli.nyul module
- intensity_normalization.cli.preprocess module
- intensity_normalization.cli.ravel module
- intensity_normalization.cli.tissue_membership module
- intensity_normalization.cli.whitestripe module
- intensity_normalization.cli.zscore module
- Module contents
- intensity_normalization.normalize package
- Submodules
- intensity_normalization.normalize.base module
- intensity_normalization.normalize.fcm module
FCMNormalize
FCMNormalize.add_method_specific_arguments()
FCMNormalize.calculate_location()
FCMNormalize.calculate_scale()
FCMNormalize.call_from_argparse_args()
FCMNormalize.description()
FCMNormalize.from_argparse_args()
FCMNormalize.fullname()
FCMNormalize.get_parent_parser()
FCMNormalize.is_fit
FCMNormalize.name()
FCMNormalize.save_additional_info()
- intensity_normalization.normalize.kde module
- intensity_normalization.normalize.lsq module
LeastSquaresNormalize
LeastSquaresNormalize.add_method_specific_arguments()
LeastSquaresNormalize.calculate_location()
LeastSquaresNormalize.calculate_scale()
LeastSquaresNormalize.call_from_argparse_args()
LeastSquaresNormalize.description()
LeastSquaresNormalize.from_argparse_args()
LeastSquaresNormalize.fullname()
LeastSquaresNormalize.get_parent_parser()
LeastSquaresNormalize.load_standard_tissue_means()
LeastSquaresNormalize.name()
LeastSquaresNormalize.save_additional_info()
LeastSquaresNormalize.save_standard_tissue_means()
LeastSquaresNormalize.scaling_factor()
LeastSquaresNormalize.tissue_means()
- intensity_normalization.normalize.nyul module
NyulNormalize
NyulNormalize.add_method_specific_arguments()
NyulNormalize.call_from_argparse_args()
NyulNormalize.description()
NyulNormalize.from_argparse_args()
NyulNormalize.fullname()
NyulNormalize.get_landmarks()
NyulNormalize.load_standard_histogram()
NyulNormalize.name()
NyulNormalize.normalize_image()
NyulNormalize.percentiles
NyulNormalize.save_additional_info()
NyulNormalize.save_standard_histogram()
- intensity_normalization.normalize.ravel module
RavelNormalize
RavelNormalize.add_method_specific_arguments()
RavelNormalize.create_image_matrix_and_control_voxels()
RavelNormalize.description()
RavelNormalize.estimate_unwanted_factors()
RavelNormalize.from_argparse_args()
RavelNormalize.fullname()
RavelNormalize.name()
RavelNormalize.normalize_image()
RavelNormalize.process_directories()
RavelNormalize.save_additional_info()
RavelNormalize.set_template()
RavelNormalize.set_template_mask()
RavelNormalize.teardown()
RavelNormalize.template
RavelNormalize.template_mask
RavelNormalize.use_mni_as_template()
- intensity_normalization.normalize.whitestripe module
WhiteStripeNormalize
WhiteStripeNormalize.add_method_specific_arguments()
WhiteStripeNormalize.calculate_location()
WhiteStripeNormalize.calculate_scale()
WhiteStripeNormalize.description()
WhiteStripeNormalize.from_argparse_args()
WhiteStripeNormalize.fullname()
WhiteStripeNormalize.name()
WhiteStripeNormalize.plot_histogram_from_args()
WhiteStripeNormalize.setup()
WhiteStripeNormalize.teardown()
- intensity_normalization.normalize.zscore module
- Module contents
- intensity_normalization.plot package
- intensity_normalization.util package
Submodules¶
intensity_normalization.base_cli module¶
CLI base class for normalization/preprocessing methods Author: Jacob Reinhold <jcreinhold@gmail.com> Created on: 06 Jun 2021
- class intensity_normalization.base_cli.CLIMixin[source]¶
Bases:
object
- append_name_to_file(filepath: intnormt.PathLike, alternate_path: intnormt.PathLike | None = None) pathlib.Path [source]¶
intensity_normalization.errors module¶
Project-specific errors Author: Jacob Reinhold <jcreinhold@gmail.com> Created on: 24 Apr 2018
intensity_normalization.typing module¶
Project-specific types Author: Jacob Reinhold <jcreinhold@gmail.com> Created on: 01 Jun 2021
- class intensity_normalization.typing.ImageLike(*args, **kwargs)[source]¶
Bases:
Protocol
[S_co
,T_co
,U_co
]support anything that implements the methods here
- property ndim: integer[NBit] | int¶
- property shape: tuple[int, ...]¶
- class intensity_normalization.typing.Modality(value)[source]¶
Bases:
Enum
An enumeration.
- FLAIR: str = 'flair'¶
- MD: str = 'md'¶
- OTHER: str = 'other'¶
- PD: str = 'pd'¶
- T1: str = 't1'¶
- T2: str = 't2'¶
- class intensity_normalization.typing.SplitFilename(path, base, ext)[source]¶
Bases:
NamedTuple
- base: str¶
Alias for field number 1
- ext: str¶
Alias for field number 2
- path: Path¶
Alias for field number 0
- class intensity_normalization.typing.TissueType(value)[source]¶
Bases:
Enum
An enumeration.
- CSF: str = 'csf'¶
- GM: str = 'gm'¶
- WM: str = 'wm'¶
- classmethod from_string(string: str) TissueType [source]¶
Module contents¶
Top-level package for intensity-normalization.