intensity_normalization package

Subpackages

• intensity_normalization.cli package
  • Submodules
  • intensity_normalization.cli.coregister module
    • coregister_main()
  • intensity_normalization.cli.fcm module
    • fcm_main()
  • intensity_normalization.cli.histogram module
    • histogram_main()
  • intensity_normalization.cli.kde module
    • kde_main()
  • intensity_normalization.cli.lsq module
    • lsq_main()
  • intensity_normalization.cli.nyul module
    • nyul_main()
  • intensity_normalization.cli.preprocess module
    • preprocess_main()
  • intensity_normalization.cli.ravel module
    • ravel_main()
  • intensity_normalization.cli.tissue_membership module
    • tissue_membership_main()
  • intensity_normalization.cli.whitestripe module
    • whitestripe_main()
  • intensity_normalization.cli.zscore module
    • zscore_main()
  • Module contents
• intensity_normalization.normalize package
  • Submodules
  • intensity_normalization.normalize.base module
    • DirectoryNormalizeCLI
      • DirectoryNormalizeCLI.before_fit()
      • DirectoryNormalizeCLI.fit()
      • DirectoryNormalizeCLI.fit_from_directories()
    • LocationScaleCLIMixin
      • LocationScaleCLIMixin.from_argparse_args()
      • LocationScaleCLIMixin.get_parent_parser()
    • SingleImageNormalizeCLI
      • SingleImageNormalizeCLI.call_from_argparse_args()
      • SingleImageNormalizeCLI.plot_histogram_from_args()
  • 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
    • KDENormalize
      • KDENormalize.calculate_location()
      • KDENormalize.calculate_scale()
      • KDENormalize.description()
      • KDENormalize.fullname()
      • KDENormalize.name()
  • 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
    • ZScoreNormalize
      • ZScoreNormalize.calculate_location()
      • ZScoreNormalize.calculate_scale()
      • ZScoreNormalize.description()
      • ZScoreNormalize.fullname()
      • ZScoreNormalize.name()
      • ZScoreNormalize.plot_histogram_from_args()
      • ZScoreNormalize.setup()
      • ZScoreNormalize.teardown()
  • Module contents
• intensity_normalization.plot package
  • Submodules
  • intensity_normalization.plot.histogram module
    • HistogramPlotter
      • HistogramPlotter.call_from_argparse_args()
      • HistogramPlotter.description()
      • HistogramPlotter.from_argparse_args()
      • HistogramPlotter.from_directories()
      • HistogramPlotter.fullname()
      • HistogramPlotter.get_parent_parser()
      • HistogramPlotter.name()
      • HistogramPlotter.plot_all_histograms()
    • plot_histogram()
  • Module contents
• intensity_normalization.util package
  • Submodules
  • intensity_normalization.util.coregister module
    • Registrator
      • Registrator.description()
      • Registrator.from_argparse_args()
      • Registrator.fullname()
      • Registrator.get_parent_parser()
      • Registrator.load_image()
      • Registrator.name()
      • Registrator.register_images()
      • Registrator.register_images_to_templates()
    • register()
  • intensity_normalization.util.histogram_tools module
    • get_first_tissue_mode()
    • get_largest_tissue_mode()
    • get_last_tissue_mode()
    • get_tissue_mode()
    • smooth_histogram()
  • intensity_normalization.util.io module
    • gather_images()
    • gather_images_and_masks()
    • glob_ext()
    • split_filename()
    • zip_with_nones()
  • intensity_normalization.util.preprocess module
    • Preprocessor
      • Preprocessor.description()
      • Preprocessor.from_argparse_args()
      • Preprocessor.fullname()
      • Preprocessor.get_parent_parser()
      • Preprocessor.load_image()
      • Preprocessor.name()
    • preprocess()
  • intensity_normalization.util.tissue_membership module
    • TissueMembershipFinder
      • TissueMembershipFinder.description()
      • TissueMembershipFinder.from_argparse_args()
      • TissueMembershipFinder.fullname()
      • TissueMembershipFinder.get_parent_parser()
      • TissueMembershipFinder.name()
    • find_tissue_memberships()
  • Module contents

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

Bases: object

static add_method_specific_arguments(parent_parser: ArgumentParser) → ArgumentParser

append_name_to_file(filepath: intnormt.PathLike, alternate_path: intnormt.PathLike | None = None) → pathlib.Path

abstract call_from_argparse_args(args: Namespace, /, **kwargs: Any) → None

abstract static description() → str

abstract classmethod from_argparse_args(args: Namespace) → T

abstract static fullname() → str

abstract classmethod get_parent_parser(desc: str, valid_modalities: frozenset[str] = frozenset({'flair', 'md', 'other', 'pd', 't1', 't2'}), **kwargs: Any) → ArgumentParser

static load_image(image_path: str | PathLike) → pymedio.image.Image

classmethod main(parser: ArgumentParser) → Callable[[Namespace | list[str] | None], int]

abstract static name() → str

classmethod parser() → ArgumentParser

class intensity_normalization.base_cli.DirectoryCLI

Bases: CLIMixin

abstract call_from_argparse_args(args: Namespace, /, **kwargs: Any) → None

classmethod get_parent_parser(desc: str, valid_modalities: frozenset[str] = frozenset({'flair', 'md', 'other', 'pd', 't1', 't2'}), **kwargs: Any) → ArgumentParser

class intensity_normalization.base_cli.SingleImageCLI

Bases: CLIMixin

call_from_argparse_args(args: Namespace, /, **kwargs: Any) → None

classmethod get_parent_parser(desc: str, valid_modalities: frozenset[str] = frozenset({'flair', 'md', 'other', 'pd', 't1', 't2'}), **kwargs: Any) → ArgumentParser

intensity_normalization.base_cli.setup_log(verbosity: int) → None

set logger with verbosity logging level and message

intensity_normalization.errors module

Project-specific errors Author: Jacob Reinhold <jcreinhold@gmail.com> Created on: 24 Apr 2018

exception intensity_normalization.errors.NormalizationError

Bases: RuntimeError

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)

Bases: Protocol[S_co, T_co, U_co]

support anything that implements the methods here

any(axis: int | tuple[int, ...] | None = None) → Any

flatten() → T_co

mean() → float

min() → float

property ndim: integer[NBit] | int

nonzero() → Any

reshape(*shape: SupportsIndex, order: Literal['A', 'C', 'F'] | None = Ellipsis) → T_co

property shape: tuple[int, ...]

squeeze() → Any

std() → float

sum() → Float | Int

transpose(*axes: int) → T_co

class intensity_normalization.typing.Modality(value)

Bases: Enum

An enumeration.

FLAIR: str = 'flair'

MD: str = 'md'

OTHER: str = 'other'

PD: str = 'pd'

T1: str = 't1'

T2: str = 't2'

classmethod from_string(string: str | Modality) → Modality

class intensity_normalization.typing.SplitFilename(path, base, ext)

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)

Bases: Enum

An enumeration.

CSF: str = 'csf'

GM: str = 'gm'

WM: str = 'wm'

classmethod from_string(string: str) → TissueType

to_fullname() → str

to_int() → int

class intensity_normalization.typing.dir_path

Bases: _ParseType

class intensity_normalization.typing.file_path

Bases: _ParseType

intensity_normalization.typing.new_parse_type(func: Callable[[Any], Any], name: str) → NewParseType

class intensity_normalization.typing.nonnegative_float

Bases: _ParseType

class intensity_normalization.typing.nonnegative_int

Bases: _ParseType

class intensity_normalization.typing.positive_float

Bases: _ParseType

class intensity_normalization.typing.positive_int

Bases: _ParseType

class intensity_normalization.typing.positive_int_or_none

Bases: _ParseType

class intensity_normalization.typing.positive_odd_int_or_none

Bases: _ParseType

class intensity_normalization.typing.probability_float

Bases: _ParseType

class intensity_normalization.typing.probability_float_or_none

Bases: _ParseType

class intensity_normalization.typing.save_file_path

Bases: _ParseType

Module contents

Top-level package for intensity-normalization.