Settings

class waveorder.cli.settings.BirefringenceApplyInverseSettings(*, wavelength_illumination: PositiveFloat = 0.532, background_path: str | Path = '', remove_estimated_background: bool = False, flip_orientation: bool = False, rotate_orientation: bool = False)

background_path: str | Path

classmethod check_background_path(v)

flip_orientation: bool

remove_estimated_background: bool

rotate_orientation: bool

class waveorder.cli.settings.BirefringenceSettings(*, transfer_function: BirefringenceTransferFunctionSettings = BirefringenceTransferFunctionSettings(swing=0.1), apply_inverse: BirefringenceApplyInverseSettings = BirefringenceApplyInverseSettings(wavelength_illumination=0.532, background_path='', remove_estimated_background=False, flip_orientation=False, rotate_orientation=False))

apply_inverse: BirefringenceApplyInverseSettings

transfer_function: BirefringenceTransferFunctionSettings

class waveorder.cli.settings.BirefringenceTransferFunctionSettings(*, swing: float = 0.1)

swing: float

classmethod swing_range(v)

class waveorder.cli.settings.FluorescenceSettings(*, transfer_function: FluorescenceTransferFunctionSettings = FluorescenceTransferFunctionSettings(yx_pixel_size=0.325, z_pixel_size=2.0, z_padding=0, z_focus_offset=0, index_of_refraction_media=1.3, numerical_aperture_detection=1.2, wavelength_emission=0.507), apply_inverse: FourierApplyInverseSettings = FourierApplyInverseSettings(reconstruction_algorithm='Tikhonov', regularization_strength=0.001, TV_rho_strength=0.001, TV_iterations=1))

apply_inverse: FourierApplyInverseSettings

transfer_function: FluorescenceTransferFunctionSettings

class waveorder.cli.settings.FluorescenceTransferFunctionSettings(*, yx_pixel_size: PositiveFloat = 0.325, z_pixel_size: PositiveFloat = 2.0, z_padding: NonNegativeInt = 0, z_focus_offset: int | Literal['auto'] = 0, index_of_refraction_media: PositiveFloat = 1.3, numerical_aperture_detection: PositiveFloat = 1.2, wavelength_emission: PositiveFloat = 0.507)

classmethod warn_unit_consistency(v, values)

wavelength_emission: PositiveFloat

class waveorder.cli.settings.FourierApplyInverseSettings(*, reconstruction_algorithm: Literal['Tikhonov', 'TV'] = 'Tikhonov', regularization_strength: NonNegativeFloat = 0.001, TV_rho_strength: PositiveFloat = 0.001, TV_iterations: NonNegativeInt = 1)

TV_iterations: NonNegativeInt

TV_rho_strength: PositiveFloat

reconstruction_algorithm: Literal['Tikhonov', 'TV']

regularization_strength: NonNegativeFloat

class waveorder.cli.settings.FourierTransferFunctionSettings(*, yx_pixel_size: PositiveFloat = 0.325, z_pixel_size: PositiveFloat = 2.0, z_padding: NonNegativeInt = 0, z_focus_offset: int | Literal['auto'] = 0, index_of_refraction_media: PositiveFloat = 1.3, numerical_aperture_detection: PositiveFloat = 1.2)

index_of_refraction_media: PositiveFloat

classmethod na_det(v, values)

numerical_aperture_detection: PositiveFloat

classmethod warn_unit_consistency(v, values)

yx_pixel_size: PositiveFloat

z_focus_offset: int | Literal['auto']

z_padding: NonNegativeInt

z_pixel_size: PositiveFloat

class waveorder.cli.settings.MyBaseModel

class waveorder.cli.settings.PhaseSettings(*, transfer_function: PhaseTransferFunctionSettings = PhaseTransferFunctionSettings(wavelength_illumination=0.532, yx_pixel_size=0.325, z_pixel_size=2.0, z_padding=0, z_focus_offset=0, index_of_refraction_media=1.3, numerical_aperture_detection=1.2, numerical_aperture_illumination=0.5, invert_phase_contrast=False), apply_inverse: FourierApplyInverseSettings = FourierApplyInverseSettings(reconstruction_algorithm='Tikhonov', regularization_strength=0.001, TV_rho_strength=0.001, TV_iterations=1))

apply_inverse: FourierApplyInverseSettings

transfer_function: PhaseTransferFunctionSettings

class waveorder.cli.settings.PhaseTransferFunctionSettings(*, wavelength_illumination: PositiveFloat = 0.532, yx_pixel_size: PositiveFloat = 0.325, z_pixel_size: PositiveFloat = 2.0, z_padding: NonNegativeInt = 0, z_focus_offset: int | Literal['auto'] = 0, index_of_refraction_media: PositiveFloat = 1.3, numerical_aperture_detection: PositiveFloat = 1.2, numerical_aperture_illumination: NonNegativeFloat = 0.5, invert_phase_contrast: bool = False)

invert_phase_contrast: bool

classmethod na_ill(v, values)

numerical_aperture_illumination: NonNegativeFloat

class waveorder.cli.settings.ReconstructionSettings(*, input_channel_names: List[str] = ['State0', 'State1', 'State2', 'State3'], time_indices: NonNegativeInt | List[NonNegativeInt] | Literal['all'] = 'all', reconstruction_dimension: Literal[2, 3] = 3, birefringence: BirefringenceSettings | None = None, phase: PhaseSettings | None = None, fluorescence: FluorescenceSettings | None = None)

birefringence: BirefringenceSettings | None

fluorescence: FluorescenceSettings | None

input_channel_names: List[str]

phase: PhaseSettings | None

reconstruction_dimension: Literal[2, 3]

time_indices: NonNegativeInt | List[NonNegativeInt] | Literal['all']

classmethod validate_reconstruction_types(values)

class waveorder.cli.settings.WavelengthIllumination(*, wavelength_illumination: PositiveFloat = 0.532)

wavelength_illumination: PositiveFloat