Index A | B | C | E | F | I | M | N | P | R | S | T | V | W | Y | Z A apply_inverse (waveorder.cli.settings.BirefringenceSettings attribute) (waveorder.cli.settings.FluorescenceSettings attribute) (waveorder.cli.settings.PhaseSettings attribute) apply_orientation_offset() (in module waveorder.stokes) B background_path (waveorder.cli.settings.BirefringenceApplyInverseSettings attribute) birefringence (waveorder.cli.settings.ReconstructionSettings attribute) BirefringenceApplyInverseSettings (class in waveorder.cli.settings) BirefringenceSettings (class in waveorder.cli.settings) BirefringenceTransferFunctionSettings (class in waveorder.cli.settings) C calculate_intensity_to_stokes_matrix() (in module waveorder.stokes) calculate_stokes_to_intensity_matrix() (in module waveorder.stokes) check_background_path() (waveorder.cli.settings.BirefringenceApplyInverseSettings class method) E estimate_adr_from_stokes() (in module waveorder.stokes) estimate_ar_from_stokes012() (in module waveorder.stokes) F flip_orientation (waveorder.cli.settings.BirefringenceApplyInverseSettings attribute) fluorescence (waveorder.cli.settings.ReconstructionSettings attribute) FluorescenceSettings (class in waveorder.cli.settings) FluorescenceTransferFunctionSettings (class in waveorder.cli.settings) FourierApplyInverseSettings (class in waveorder.cli.settings) FourierTransferFunctionSettings (class in waveorder.cli.settings) I index_of_refraction_media (waveorder.cli.settings.FourierTransferFunctionSettings attribute) input_channel_names (waveorder.cli.settings.ReconstructionSettings attribute) invert_phase_contrast (waveorder.cli.settings.PhaseTransferFunctionSettings attribute) M mmul() (in module waveorder.stokes) module waveorder.cli.settings waveorder.stokes mueller_from_stokes() (in module waveorder.stokes) MyBaseModel (class in waveorder.cli.settings) N na_det() (waveorder.cli.settings.FourierTransferFunctionSettings class method) na_ill() (waveorder.cli.settings.PhaseTransferFunctionSettings class method) numerical_aperture_detection (waveorder.cli.settings.FourierTransferFunctionSettings attribute) numerical_aperture_illumination (waveorder.cli.settings.PhaseTransferFunctionSettings attribute) P phase (waveorder.cli.settings.ReconstructionSettings attribute) PhaseSettings (class in waveorder.cli.settings) PhaseTransferFunctionSettings (class in waveorder.cli.settings) R reconstruction_algorithm (waveorder.cli.settings.FourierApplyInverseSettings attribute) reconstruction_dimension (waveorder.cli.settings.ReconstructionSettings attribute) ReconstructionSettings (class in waveorder.cli.settings) regularization_strength (waveorder.cli.settings.FourierApplyInverseSettings attribute) remove_estimated_background (waveorder.cli.settings.BirefringenceApplyInverseSettings attribute) rotate_orientation (waveorder.cli.settings.BirefringenceApplyInverseSettings attribute) S stokes012_after_ar() (in module waveorder.stokes) stokes_after_adr() (in module waveorder.stokes) swing (waveorder.cli.settings.BirefringenceTransferFunctionSettings attribute) swing_range() (waveorder.cli.settings.BirefringenceTransferFunctionSettings class method) T time_indices (waveorder.cli.settings.ReconstructionSettings attribute) transfer_function (waveorder.cli.settings.BirefringenceSettings attribute) (waveorder.cli.settings.FluorescenceSettings attribute) (waveorder.cli.settings.PhaseSettings attribute) TV_iterations (waveorder.cli.settings.FourierApplyInverseSettings attribute) TV_rho_strength (waveorder.cli.settings.FourierApplyInverseSettings attribute) V validate_reconstruction_types() (waveorder.cli.settings.ReconstructionSettings class method) W warn_unit_consistency() (waveorder.cli.settings.FluorescenceTransferFunctionSettings class method) (waveorder.cli.settings.FourierTransferFunctionSettings class method) wavelength_emission (waveorder.cli.settings.FluorescenceTransferFunctionSettings attribute) wavelength_illumination (waveorder.cli.settings.WavelengthIllumination attribute) WavelengthIllumination (class in waveorder.cli.settings) waveorder.cli.settings module waveorder.stokes module Y yx_pixel_size (waveorder.cli.settings.FourierTransferFunctionSettings attribute) Z z_focus_offset (waveorder.cli.settings.FourierTransferFunctionSettings attribute) z_padding (waveorder.cli.settings.FourierTransferFunctionSettings attribute) z_pixel_size (waveorder.cli.settings.FourierTransferFunctionSettings attribute)