Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Z A A (GeneralizedPerspectiveTransformation attribute) a (LinearKernel attribute) absolute_time_overlap (Patches attribute) AbsoluteVolumeModelObjectiveMixin (class in darsia) AbstractBalancingCalibration (class in darsia) AbstractModelObjective (class in darsia) active (TranslationCorrection attribute) AdaptiveBalance (class in darsia) add() (DiffeomorphicImageRegistration method) add_grid() (OpticalImage method) add_translation_analysis() (TranslationAnalysis method) adjust() (EOTF method) AdvancedCO2MassAnalysis (class in darsia) AdvancedFlash (class in darsia) AdvancedKernelInterpolation (class in darsia) affine_balance() (in module darsia) affine_correction (CoordinateTransformation attribute) AffineBalance (class in darsia) AffineCorrection (class in darsia) AffineTransformation (class in darsia) amg_options (BeckmannAMGSolver attribute) (BeckmannCGSolver attribute) AnalysisBase (class in darsia) AndersonAcceleration (class in darsia) append() (Image method) (MultiphaseTimeSeriesData method) (SimpleMultiphaseTimeSeriesData method) apply() (DiffeomorphicImageRegistration method) (ImageRegistration method) (MultiscaleDiffeomorphicImageRegistration method) apply_balance() (AffineBalance method) (BaseBalance method) ApproximationSpace (class in darsia) assemble() (Patches method) astype() (Image method) atmospheric_pressure (CO2MassAnalysis attribute) atmospheric_pressure_gradient (CO2MassAnalysis attribute) atmospheric_temperature (CO2MassAnalysis attribute) atmospheric_temperature_gradient (CO2MassAnalysis attribute) atmospheric_temperature_map() (CO2MassAnalysis method) ax (BaseAssistant attribute) axes (CoordinateSystem attribute) axis (AxisReduction attribute) AxisReduction (class in darsia) B b (GeneralizedPerspectiveTransformation attribute) background (BaseAssistant attribute) (LabelsAssistant attribute) (LabelsMaskSelectionAssistant attribute) (LabelsMergeAssistant attribute) (LabelsPickAssistant attribute) (LabelsSegmentAssistant attribute) backward_diff() (in module darsia) balance_scaling (AdaptiveBalance attribute) (AffineBalance attribute) (ColorBalance attribute) (WhiteBalance attribute) balance_translation (AdaptiveBalance attribute) (AffineBalance attribute) balancing (ConcentrationAnalysis attribute) base (ConcentrationAnalysis attribute) (DriftCorrection attribute) (Patches attribute) base_color (ColorSpectrum attribute) base_color_image() (LabelColorPathMapRegression method) base_V_Cycle() (MG method) BaseAssistant (class in darsia) BaseBalance (class in darsia) BaseCorrection (class in darsia) BaseCriterion (class in darsia) BaseKernel (class in darsia) baseline (CO2MassAnalysis attribute) (RelativeColorCorrection attribute) BaseTransformation (class in darsia) basis() (ApproximationSpace method) (PolynomialApproximationSpace method) (RadialPolynomialApproximationSpace method) batch_analysis() (AnalysisBase method) bc_x() (TranslationAnalysis method) bc_y() (TranslationAnalysis method) BeckmannAMGSolver (class in darsia) BeckmannBregmanSolver (class in darsia) BeckmannCGSolver (class in darsia) BeckmannConvergenceCriteria (class in darsia) BeckmannConvergenceHistory (class in darsia) BeckmannDirectSolver (class in darsia) BeckmannGproxPGHDSolver (class in darsia) BeckmannKSPFieldSplitSolver (class in darsia) BeckmannKSPSolver (class in darsia) BeckmannLinearSolver (class in darsia) BeckmannLinearSolverFactory (class in darsia) BeckmannLinearSolverType (class in darsia) BeckmannNewtonSolver (class in darsia) BeckmannProblem (class in darsia) BinaryDataSelector (class in darsia) BinaryFillHoles (class in darsia) BinaryLocalConvexCover (class in darsia) BinaryRemoveSmallObjects (class in darsia) bind() (BaseCriterion method) blend_and_assemble() (Patches method) block (BaseAssistant attribute) bounding_box() (in module darsia) bounding_box_inverse() (in module darsia) box (RectangleSelectionAssistant attribute) boxes (BoxSelectionAssistant attribute) BoxSelectionAssistant (class in darsia) bregman_update (BeckmannBregmanSolver attribute) broken_darcy_with_custom_flux_block() (BeckmannProblem method) bulge_center_off (GeneralizedPerspectiveTransformation attribute) bulge_correction() (CurvatureCorrection method) bulge_factor (GeneralizedPerspectiveTransformation attribute) C c (GeneralizedPerspectiveTransformation attribute) cache_background (LabelsAssistant attribute) cached_voxel_volume (Geometry attribute) (WeightedGeometry attribute) calibrate() (DynamicThresholdModel method) (Model method) (RelativeColorCorrection method) calibrate_balancing() (AbstractBalancingCalibration method) calibrate_model() (AbstractModelObjective method) calibration_images (RelativeColorCorrection attribute) call_array() (AffineTransformation method) (BaseTransformation method) (GeneralizedPerspectiveTransformation method) call_with_output() (DiffeomorphicImageRegistration method) callbacks (BeckmannGproxPGHDSolver attribute) (BeckmannProblem attribute) cartesianToMatrixIndexing() (in module darsia) cell_to_face_average() (in module darsia) cell_weighted_flux() (BeckmannProblem method) center (ColorRange attribute) CG (class in darsia) check() (FluidFlowerConfig method) check_convergence_status() (BeckmannConvergenceCriteria method) check_equal_coordinatesystems() (in module darsia) chi_aq (MassAnalysisResults attribute) chi_g (MassAnalysisResults attribute) ClassicColorChecker (class in darsia) clean() (MultiphaseTimeSeriesAnalysis method) (MultiphaseTimeSeriesData method) (SimpleMultiphaseTimeSeriesData method) ClipModel (class in darsia) cmap (BaseAssistant attribute) co2 (ThresholdAnalysisResults attribute) co2_analysis_data (FluidFlowerCO2Meta property) co2_g (ThresholdAnalysisResults attribute) co2_g_analysis_data (FluidFlowerCO2Meta property) CO2Analysis (class in darsia) CO2MassAnalysis (class in darsia) color_aq (MultiphaseTimeSeriesAnalysis attribute) (SimpleRunAnalysis attribute) color_balance() (in module darsia) color_correction (AnalysisBase attribute) color_fractions() (SegmentationComparison method) color_g (MultiphaseTimeSeriesAnalysis attribute) (SimpleRunAnalysis attribute) color_mass (MultiphaseTimeSeriesAnalysis attribute) (SimpleRunAnalysis attribute) color_mode (ColorPathFunction attribute) (ColorRange attribute) (ColorSpectrum property) (LabelColorPathMapRegression attribute) color_path (ColorPathFunction attribute) color_range (ColorSpectrum attribute) (LabelColorPathMapRegression attribute) color_signal (SimpleMassAnalysisResults attribute) color_space (OpticalImage attribute) color_to_index() (DiscreteColorRange method) ColorBalance (class in darsia) ColorChecker (class in darsia) ColorCheckerAfter2014 (class in darsia) ColorCorrection (class in darsia) ColorMode (class in darsia) ColorPath (class in darsia) ColorPathFunction (class in darsia) ColorPathInterpolation (class in darsia) ColorRange (class in darsia) colors (ColorPath attribute) (ColorSpectrum property) (DiscreteColorRange property) ColorSpectrum (class in darsia) CombinedCriterion (class in darsia) CombinedModel (class in darsia) compare_segmentations_binary_array() (SegmentationComparison method) compute_bulge() (CurvatureCorrection method) compute_correction() (PatchwiseIlluminationCorrection method) compute_dual() (BeckmannGproxPGHDSolver method) compute_jacobian() (BeckmannNewtonSolver method) compute_kantorovich_potential() (BeckmannGproxPGHDSolver method) compute_primal() (BeckmannGproxPGHDSolver method) compute_residual() (BeckmannNewtonSolver method) compute_stretch() (CurvatureCorrection method) concentration_analysis_aq (AdvancedCO2MassAnalysis attribute) concentration_analysis_g (AdvancedCO2MassAnalysis attribute) concentration_aq (SimpleMassAnalysisResults attribute) concentration_co2_aq (MassAnalysisResults attribute) ConcentrationAnalysis (class in darsia) ConcentrationAnalysisBase (class in darsia) config (AnalysisBase attribute) (ColorCorrection attribute) (RelativeColorCorrection attribute) contains() (ImagingInterval method) (ROI method) ContinuityBasedBalancingCalibrationMixin (class in darsia) contour_length() (in module darsia) contour_smoother (ContourAnalysis attribute) ContourAnalysis (class in darsia) contours() (ContourAnalysis method) ContourSmoother (class in darsia) ContourSmootherSequence (class in darsia) convergence_criteria (BeckmannBregmanSolver attribute) (BeckmannNewtonSolver attribute) ConvergenceStatus (class in darsia) convert_dtype() (in module darsia) Coordinate (class in darsia) coordinate() (CoordinateSystem method) coordinate_vector() (CoordinateSystem method) CoordinateArray (class in darsia) coordinates (CoordinateSystem property) (SubregionAssistant attribute) CoordinateSystem (class in darsia) coordinatesystem (Image property) coordinatesystem_dst (AffineCorrection attribute) (CoordinateTransformation attribute) (TransformationCorrection attribute) coordinatesystem_src (AffineCorrection attribute) (CoordinateTransformation attribute) (TransformationCorrection attribute) CoordinateTransformation (class in darsia) copy() (ExtensiveImage method) (Image method) (OpticalImage method) (ScalarImage method) corners (CropAssistant attribute) (RectangleSelectionAssistant attribute) correct_array() (BaseCorrection method) (ColorCorrection method) (CurvatureCorrection method) (DeformationCorrection method) (DriftCorrection method) (DynamicIlluminationCorrection method) (ExperimentalColorCorrection method) (IlluminationCorrection method) (PatchwiseIlluminationCorrection method) (RelativeColorCorrection method) (ResizeCorrection method) (RotationCorrection method) (TransformationCorrection method) (TranslationCorrection method) correct_metadata() (BaseCorrection method) (CoordinateTransformation method) (CurvatureCorrection method) (GeneralizedPerspectiveCorrection method) correction (RelativeColorCorrection attribute) corrections (Rig property) create() (BeckmannLinearSolverFactory static method) CropAssistant (class in darsia) current_labels (LabelsAssistant attribute) curvature_correction (AnalysisBase attribute) CurvatureCorrection (class in darsia) CustomColorChecker (class in darsia) D data (MultiphaseTimeSeriesAnalysis attribute) (ProtocolledExperiment attribute) (RelativeColorCorrection attribute) (SimpleRunAnalysis attribute) date (Image attribute) (MassAnalysisResults attribute) (SimpleMassAnalysisResults attribute) deduct() (DiffeomorphicImageRegistration method) deduct_translation_analysis() (TranslationAnalysis method) default_parameters (GeneralizedPerspectiveTransformation attribute) define_co2_analysis() (CO2Analysis method) define_co2_gas_analysis() (CO2Analysis method) define_color_path() (in module darsia) define_correction() (RelativeColorCorrection method) define_objective_function() (AbsoluteVolumeModelObjectiveMixin method) (AbstractModelObjective method) (InjectionRateModelObjectiveMixin method) define_reference_color() (RelativeColorCorrection method) define_similar_and_reference_colors_tensorial() (RelativeColorCorrection method) define_similar_colors() (RelativeColorCorrection method) define_tracer_analysis() (TracerAnalysis method) deformation_correction (AnalysisBase attribute) DeformationCorrection (class in darsia) depth (MG attribute) detect_closest_point() (in module darsia) detect_color() (in module darsia) detect_value() (in module darsia) determine_co2() (CO2Analysis method) determine_co2_gas() (CO2Analysis method) determine_tracer() (TracerAnalysis method) df (ImagingProtocol attribute) (InjectionProtocol attribute) (PressureTemperatureProtocol attribute) DiffeomorphicImageRegistration (class in darsia) diffusion_coeff (Solver attribute) dim (AffineCorrection attribute) (AffineTransformation attribute) (BoxSelectionAssistant attribute) (CoordinateSystem attribute) (CoordinateTransformation attribute) (Grid attribute) (Solver attribute) dimensions (CoordinateSystem attribute) (Geometry attribute) (Image attribute) discrete_color_range (LabelColorPathMapRegression attribute) DiscreteColorRange (class in darsia) displacement() (DiffeomorphicImageRegistration method) distance() (ColorSpectrum method) distance_matrix() (EMD method) domain (CoordinateSystem attribute) (Image property) drift_corrected_base (AnalysisBase attribute) drift_correction (AnalysisBase attribute) DriftCorrection (class in darsia) dtype (Image property) DynamicIlluminationCorrection (class in darsia) DynamicThresholdModel (class in darsia) E eliminate_flux() (BeckmannProblem method) eliminate_lagrange_multiplier() (BeckmannProblem method) EMD (class in darsia) end (TimeWindow attribute) end_hours (TimeWindow property) EOTF (class in darsia) equalize_voxel_size() (in module darsia) equidistant_distances (ColorPath attribute) eval() (Image method) evaluate() (DiffeomorphicImageRegistration method) (ImageRegistration method) (LinearApproximation method) (MultiscaleDiffeomorphicImageRegistration method) exact_linearization() (BeckmannProblem method) exact_mass_tot (MultiphaseTimeSeriesData attribute) (SimpleMultiphaseTimeSeriesData attribute) expand_color_spectrum() (LabelColorPathMapRegression method) Experiment (class in darsia) experiment_start (ProtocolledExperiment attribute) ExperimentalColorCorrection (class in darsia) ExtensiveImage (class in darsia) extent (ColorRange attribute) extract_characteristic_data() (in module darsia) extract_color_values_patches() (PatchwiseIlluminationCorrection method) extract_features() (FeatureDetection class method) extract_quadrilateral_ROI() (in module darsia) extract_subregion() (ROI method) extrude_along_axis() (in module darsia) ExtrudedGeometry (class in darsia) ExtrudedPorousGeometry (class in darsia) F face_to_cell() (in module darsia) face_vol (Grid attribute) FeatureDetection (class in darsia) field_ises (BeckmannKSPFieldSplitSolver attribute) fig (BaseAssistant attribute) finalized (LabelsAssistant attribute) (MonochromaticAssistant attribute) finalized_prompt_input (CropAssistant attribute) find_and_warp() (PiecewisePerspectiveTransform method) find_balance() (AdaptiveBalance method) (AffineBalance method) (BaseBalance method) (ColorBalance method) (WhiteBalance method) find_cleaning_filter() (ConcentrationAnalysis method) find_color_path() (LabelColorPathMapRegression method) find_colorchecker() (in module darsia) find_effective_translation() (TranslationEstimator method) find_ideal_images_for_datetimes() (ImagingProtocol method) find_images_for_datetimes() (ImagingProtocol method) find_images_for_paths() (ImagingProtocol method) (ProtocolledExperiment method) find_images_for_time_windows() (ProtocolledExperiment method) find_images_for_times() (ProtocolledExperiment method) find_intersection() (CoordinateTransformation method) find_translation() (TranslationAnalysis method) first_call (LabelsAssistant attribute) first_restoration_then_model (ConcentrationAnalysis attribute) fit() (AffineTransformation method) (BaseTransformation method) (ColorPath method) (GeneralizedPerspectiveTransformation method) fixed_supports (AdvancedKernelInterpolation attribute) fixed_values (AdvancedKernelInterpolation attribute) flash (AdvancedCO2MassAnalysis attribute) Flash (class in darsia) flat_color_index() (DiscreteColorRange method) flat_view() (BeckmannProblem method) flatten_index() (DiscreteColorRange method) FluidFlowerCO2Meta (class in darsia) FluidFlowerConfig (class in darsia) flux_view() (BeckmannProblem method) Format (class in darsia) forward_diff() (in module darsia) from_dict() (ColorPath class method) (ColorPathInterpolation class method) (ColorSpectrum class method) (SimpleFlash class method) from_image() (CropAssistant method) from_images() (ColorRange class method) full_like() (in module darsia) FVDivergence (class in darsia) FVFullFaceReconstruction (class in darsia) FVMass (class in darsia) FVTangentialFaceReconstruction (class in darsia) G gamma (GaussianKernel attribute) GaussianKernel (class in darsia) GaussianSmoother (class in darsia) GeneralizedPerspectiveCorrection (class in darsia) GeneralizedPerspectiveTransformation (class in darsia) generate_grid() (in module darsia) Geometry (class in darsia) geometry (MultiphaseTimeSeriesAnalysis attribute) (SimpleRunAnalysis attribute) geometry() (Image method) get_base_colors() (LabelColorPathMapRegression method) get_color_map() (ColorPath method) get_color_spectrum() (LabelColorPathMapRegression method) get_combinations() (SegmentationComparison method) get_datetime() (ImagingInterval method) (ImagingProtocol method) (ProtocolledExperiment method) get_gradient() (PressureTemperatureProtocol method) get_mean_base_color() (LabelColorPathMapRegression method) get_mean_color() (in module darsia) get_state() (PressureTemperatureProtocol method) GlobalMinTwoPeakHistogrammAnalysis (class in darsia) GradientModulusCriterion (class in darsia) grid (BeckmannGproxPGHDSolver attribute) (BeckmannProblem attribute) Grid (class in darsia) group_labels() (in module darsia) H H1_regularization() (in module darsia) have_translation (TranslationAnalysis attribute) height (AnalysisBase attribute) (CropAssistant attribute) heterogeneous (MG attribute) HeterogeneousLinearModel (class in darsia) HeterogeneousModel (class in darsia) histogram (ColorSpectrum attribute) HistogrammBasedThresholding (class in darsia) hours_since_start() (Experiment method) hsv_spectrum() (in module darsia) I ignore_labels (HeterogeneousModel attribute) (LabelColorPathMapRegression attribute) ignore_spectrum (ColorPathInterpolation attribute) illumination_interpolation() (in module darsia) IlluminationCorrection (class in darsia) Image (class in darsia) ImageRegistration (class in darsia) ImagingInterval (class in darsia) ImagingProtocol (class in darsia) img (BaseAssistant attribute) (Image attribute) (MonochromaticAssistant attribute) img_as() (Image method) import_from_csv() (Rig method) imread() (in module darsia) imread_from_bytes() (in module darsia) imread_from_dicom() (in module darsia) imread_from_npz() (in module darsia) imread_from_numpy() (in module darsia) imread_from_optical() (in module darsia) imread_from_vtu() (in module darsia) in_spectrum() (ColorSpectrum method) indexing (CoordinateSystem attribute) (Image attribute) injected_mass() (InjectionProtocol method) injection_protocol (ProtocolledExperiment attribute) InjectionProtocol (class in darsia) InjectionRateModelObjectiveMixin (class in darsia) input_array_dtype (BaseTransformation attribute) input_dtype (BaseTransformation attribute) input_img (MonochromaticAssistant attribute) integral() (Image method) integrate() (Geometry method) interpolate_measurements_2d() (in module darsia) interpolate_to_image() (in module darsia) interpolate_to_image_from_csv() (in module darsia) interpolation_weights (KernelInterpolation attribute) interpret() (ColorPath method) interpret_indexing() (in module darsia) inverse() (BaseTransformation method) (PWTransformation method) inverse_approx() (EOTF method) inverse_array() (AffineTransformation method) (BaseTransformation method) (GeneralizedPerspectiveTransformation method) inverse_mass_analysis() (CO2MassAnalysis method) is_blacklisted() (ImagingProtocol method) (ProtocolledExperiment method) isometry (AffineTransformation attribute) J Jacobi (class in darsia) K kernel (KernelInterpolation attribute) KernelInterpolation (class in darsia) kwargs (AxisReduction attribute) L L (BeckmannBregmanSolver attribute) l1_dissipation() (BeckmannProblem method) L1Mode (class in darsia) label_image() (in module darsia) LabelColorMap (class in darsia) LabelColorPathMap (class in darsia) LabelColorPathMapRegression (class in darsia) LabelColorSpectrumMap (class in darsia) labels (ConcentrationAnalysis attribute) (LabelColorPathMapRegression attribute) (LabelsAssistant attribute) (LabelsMaskSelectionAssistant attribute) (LabelsMergeAssistant attribute) (LabelsPickAssistant attribute) (LabelsSegmentAssistant attribute) (Masks attribute) (PointSelectionAssistant attribute) (RectangleSelectionAssistant attribute) (VolumeAveraging attribute) LabelsAssistant (class in darsia) LabelsAssistantMenu (class in darsia) LabelsMaskSelectionAssistant (class in darsia) LabelsMergeAssistant (class in darsia) LabelsPickAssistant (class in darsia) LabelsSegmentAssistant (class in darsia) laplace() (in module darsia) length() (ContourAnalysis method) (CoordinateSystem method) leray_projection() (BeckmannGproxPGHDSolver method) linear_combination() (GaussianKernel method) (LinearKernel method) linear_solve() (BeckmannProblem method) linear_solver (BeckmannAMGSolver attribute) (BeckmannCGSolver attribute) (BeckmannDirectSolver attribute) LinearApproximation (class in darsia) LinearKernel (class in darsia) LinearModel (class in darsia) load() (AffineCorrection method) (BaseCorrection method) (ColorCorrection method) (ColorPath class method) (ColorPathInterpolation class method) (ColorRange class method) (ColorSpectrum class method) (ContourAnalysis method) (CurvatureCorrection method) (DriftCorrection method) (DynamicIlluminationCorrection method) (IlluminationCorrection method) (LabelColorMap method) (LabelColorSpectrumMap class method) (MultiphaseTimeSeriesAnalysis method) (MultiphaseTimeSeriesData method) (PatchwiseIlluminationCorrection method) (PWTransformation class method) (RelativeColorCorrection method) (Resize method) (ResizeCorrection method) (Rig class method) (SimpleFlash class method) (SimpleMultiphaseTimeSeriesData method) (TypeCorrection method) load_and_process_image() (AnalysisBase method) load_corrections() (Rig method) load_csv() (LabelColorPathMap class method) load_curvature_correction_config_from_dict() (in module darsia) load_curvature_correction_config_from_toml() (in module darsia) load_experiment() (Rig method) load_from_dict() (ColorRange class method) load_image() (TranslationAnalysis method) load_meta() (FluidFlowerCO2Meta method) local_extrema() (ContourAnalysis method) log() (CO2MassAnalysis method) (PWTransformation method) log_folder (FluidFlowerCO2Meta property) M make_consecutive() (in module darsia) make_coordinate() (in module darsia) make_extensive() (Geometry method) make_voxel() (in module darsia) make_voxel_center() (in module darsia) mask (ConcentrationAnalysis attribute) (LabelColorPathMapRegression attribute) (LabelsSegmentAssistant attribute) (VolumeAveraging attribute) mask_base (TranslationAnalysis attribute) Masks (class in darsia) masks (HeterogeneousModel attribute) mass (MassAnalysisResults attribute) (SimpleMassAnalysisResults attribute) mass() (AdvancedCO2MassAnalysis method) mass_analysis (AdvancedCO2MassAnalysis attribute) mass_analysis() (CO2MassAnalysis method) (Rig method) mass_aq (MassAnalysisResults attribute) (MultiphaseTimeSeriesData attribute) (SimpleMassAnalysisResults attribute) (SimpleMultiphaseTimeSeriesData attribute) mass_coeff (Solver attribute) mass_g (MassAnalysisResults attribute) (MultiphaseTimeSeriesData attribute) (SimpleMassAnalysisResults attribute) (SimpleMultiphaseTimeSeriesData attribute) mass_tot (MultiphaseTimeSeriesData attribute) (SimpleMultiphaseTimeSeriesData attribute) MassAnalysisResults (class in darsia) match_features() (FeatureDetection class method) match_roi() (TranslationEstimator method) matrixToCartesianIndexing() (in module darsia) max_color (ColorRange attribute) max_coordinate (CoordinateSystem attribute) max_value_aq (SimpleFlash attribute) max_value_g (SimpleFlash attribute) maxiter (Solver attribute) mean_pore_volume (VolumeAveraging attribute) Median (class in darsia) metadata() (Image method) (OpticalImage method) MG (class in darsia) min_color (ColorRange attribute) min_coordinate (CoordinateSystem attribute) min_value_aq (SimpleFlash attribute) min_value_g (SimpleFlash attribute) mobility_mode (BeckmannProblem attribute) MobilityMode (class in darsia) mode (AxisReduction attribute) (ColorPath attribute) Model (class in darsia) model (ConcentrationAnalysis attribute) model_calibration_postanalysis() (InjectionRateModelObjectiveMixin method) monochromatic_background (LabelsAssistant attribute) monochromatic_concentration_analysis() (in module darsia) MonochromaticAssistant (class in darsia) MonochromaticReduction (class in darsia) MovingAverageSmoother (class in darsia) MultiphaseTimeSeriesAnalysis (class in darsia) MultiphaseTimeSeriesData (class in darsia) MultiscaleDiffeomorphicImageRegistration (class in darsia) N N_patches (TranslationAnalysis attribute) name (BoxSelectionAssistant attribute) (ColorPath attribute) (Image attribute) (LabelsAssistant attribute) (LabelsAssistantMenu attribute) (LabelsMaskSelectionAssistant attribute) (LabelsMergeAssistant attribute) (MassAnalysisResults attribute) (MonochromaticAssistant attribute) (PointSelectionAssistant attribute) (RectangleSelectionAssistant attribute) (SimpleMassAnalysisResults attribute) (SubregionAssistant attribute) (TimeSeriesData attribute) ndofs() (AdvancedCO2MassAnalysis method) (BeckmannProblem method) next_action (LabelsAssistant attribute) norm_mode (BeckmannGproxPGHDSolver attribute) normalize() (Geometry method) normalized_signal_aq (MassAnalysisResults attribute) normalized_signal_g (MassAnalysisResults attribute) nullspace (BeckmannKSPFieldSplitSolver attribute) num_active_spatial_axes (Patches attribute) num_fixed_supports (AdvancedKernelInterpolation attribute) num_injections (InjectionProtocol attribute) num_iter (BeckmannConvergenceCriteria attribute) num_labels (Masks attribute) num_patches (Patches attribute) num_segments (ColorPath attribute) num_supports (KernelInterpolation attribute) num_voxels (Geometry attribute) (Image property) num_voxels() (CoordinateSystem method) number_peaks() (ContourAnalysis method) number_valleys() (ContourAnalysis method) O obj (HeterogeneousModel attribute) ones_like() (in module darsia) operator() (MG method) opposite_corner (Image property) OpticalImage (class in darsia) optimality_conditions() (BeckmannProblem method) optimize_balancing() (AbstractBalancingCalibration method) (ContinuityBasedBalancingCalibrationMixin method) options (BeckmannGproxPGHDSolver attribute) (BeckmannProblem attribute) origin (AnalysisBase attribute) (Image attribute) original_dtype (Image attribute) orthogonal_colors() (in module darsia) OtsuTwoPeakHistogrammAnalysis (class in darsia) output_array_dtype (BaseTransformation attribute) output_dtype (BaseTransformation attribute) P Patches (class in darsia) PatchwiseIlluminationCorrection (class in darsia) perimeter() (in module darsia) PiecewisePerspectiveTransform (class in darsia) pixel_vector() (CoordinateSystem method) plot() (ColorChecker method) (DiffeomorphicImageRegistration method) (ImageRegistration method) (MultiscaleDiffeomorphicImageRegistration method) (SegmentationComparison method) plot_contour_mass() (MultiphaseTimeSeriesAnalysis method) (SimpleRunAnalysis method) plot_contour_signal() (MultiphaseTimeSeriesAnalysis method) (SimpleRunAnalysis method) plot_grid (BaseAssistant attribute) plot_mass_over_time() (MultiphaseTimeSeriesAnalysis method) (MultiphaseTimeSeriesData method) plot_overlay_segmentation() (SegmentationComparison method) plot_peaks() (ContourAnalysis method) plot_result() (MultiphaseTimeSeriesAnalysis method) plot_translation() (TranslationAnalysis method) plot_valleys() (ContourAnalysis method) plot_volume_over_time() (MultiphaseTimeSeriesAnalysis method) (MultiphaseTimeSeriesData method) PointSelectionAssistant (class in darsia) PolyDPSmoother (class in darsia) polynomial_interpolation() (in module darsia) PolynomialApproximationSpace (class in darsia) porosity_based_averaging() (in module darsia) PorousGeometry (class in darsia) position() (Patches method) pre_bulge_correction() (CurvatureCorrection method) prepare_analysis_context() (in module darsia.presets.workflows.analysis.analysis_context) pressure_temperature_protocol (ProtocolledExperiment attribute) pressure_view() (BeckmannProblem method) PressureTemperatureProtocol (class in darsia) previous_labels (LabelsAssistant attribute) PriorPosteriorConcentrationAnalysis (class in darsia) processed_baseline_images (AnalysisBase attribute) prolongate_parameters() (MG method) prolongation() (MG method) ProtocolledExperiment (class in darsia) pts (CropAssistant attribute) (PointSelectionAssistant attribute) pw_transformation_aq_data (FluidFlowerCO2Meta property) pw_transformation_g_data (FluidFlowerCO2Meta property) PWTransformation (class in darsia) R RadialPolynomialApproximationSpace (class in darsia) random_patches() (in module darsia) range (ColorRange attribute) range_dim (Image attribute) range_num (Image attribute) read_cleaning_filter_from_file() (ConcentrationAnalysis method) read_config_from_file() (CurvatureCorrection method) read_correction() (in module darsia) read_image() (Rig method) reassign_labels() (in module darsia) RectangleSelectionAssistant (class in darsia) reduce_axis() (in module darsia) reduce_to_main_contour (ContourAnalysis attribute) reference_data (RelativeColorCorrection attribute) reference_date (Image attribute) refine() (ColorPath method) (LabelColorPathMap class method) regularization (BeckmannProblem attribute) rel_overlap (TranslationAnalysis attribute) relative (BaseAssistant attribute) relative_colors (ColorPath attribute) (ColorSpectrum property) relative_distances (ColorPath attribute) relative_space_overlap (Patches attribute) RelativeColorCorrection (class in darsia) RelativeValueCriterion (class in darsia) rescaled_flux_optimality_conditions() (BeckmannProblem method) reset() (AdaptiveBalance method) (AndersonAcceleration method) (MultiphaseTimeSeriesAnalysis method) (MultiphaseTimeSeriesData method) (SimpleMultiphaseTimeSeriesData method) reset_origin() (Image method) reset_reference_time() (Image method) residual_history (BeckmannAMGSolver attribute) Resize (class in darsia) resize() (in module darsia) resize_array() (Resize method) ResizeCorrection (class in darsia) restoration (AdvancedCO2MassAnalysis attribute) (AdvancedFlash attribute) (ConcentrationAnalysis attribute) (SimpleFlash attribute) restrict_parameters() (MG method) restriction() (MG method) return_config() (DriftCorrection method) return_coordinates (PointSelectionAssistant attribute) (RectangleSelectionAssistant attribute) return_image() (CurvatureCorrection method) return_patch_translation() (TranslationAnalysis method) REV (class in darsia) rev_size (VolumeAveraging attribute) Rig (class in darsia.presets.workflows.rig) ROI (class in darsia) roi (LabelsSegmentAssistant attribute) roi() (Image method) roi_to_mask() (in module darsia) rotation (AffineTransformation attribute) rotation_inv (AffineTransformation attribute) RotationCorrection (class in darsia) RotationCorrectionAssistant (class in darsia) rs (RectangleSelectionAssistant attribute) S s_g_cutoff (Flash attribute) s_g_max (Flash attribute) sample_absolute_color_path() (ColorPath method) saturation_aq (MassAnalysisResults attribute) saturation_g (MassAnalysisResults attribute) (SimpleMassAnalysisResults attribute) save() (AffineCorrection method) (BaseCorrection method) (ColorCorrection method) (ColorPath method) (ColorPathInterpolation method) (ColorRange method) (ColorSpectrum method) (CurvatureCorrection method) (DriftCorrection method) (DynamicIlluminationCorrection method) (IlluminationCorrection method) (Image method) (LabelColorMap method) (LabelColorSpectrumMap method) (MultiphaseTimeSeriesAnalysis method) (MultiphaseTimeSeriesData method) (PatchwiseIlluminationCorrection method) (PWTransformation method) (RelativeColorCorrection method) (Resize method) (ResizeCorrection method) (Rig method) (SimpleFlash method) (SimpleMultiphaseTimeSeriesData method) (TypeCorrection method) save_csv() (LabelColorPathMap method) SavitzkyGolaySmoother (class in darsia) scalar (Image attribute) ScalarImage (class in darsia) scaling (AffineTransformation attribute) (BaseAssistant attribute) ScalingModel (class in darsia) scatter (BaseAssistant attribute) segment() (in module darsia) SegmentationComparison (class in darsia) select_random_samples() (IlluminationCorrection method) series (Image attribute) set_center() (RadialPolynomialApproximationSpace method) set_dtype() (BaseTransformation method) set_image() (Patches method) set_parameters() (AffineTransformation method) set_parameters_as_vector() (AffineTransformation method) (BaseTransformation method) (GeneralizedPerspectiveTransformation method) set_time() (Image method) setup() (BeckmannCGSolver method) (BeckmannDirectSolver method) (BeckmannKSPSolver method) (DynamicIlluminationCorrection method) (IlluminationCorrection method) (RelativeColorCorrection method) (Rig method) setup_20_degrees_celsius() (CO2MassAnalysis method) setup_amg_options() (BeckmannGproxPGHDSolver method) setup_boolean_image_porosity() (Rig method) setup_color_corrections() (Rig method) setup_density_gaseous_co2() (CO2MassAnalysis method) setup_depth() (Rig method) setup_facies() (Rig method) setup_facies_props() (Rig method) setup_geometry() (Rig method) setup_illumination_correction() (Rig method) setup_image_porosity() (Rig method) setup_inner_labels() (Rig method) setup_kernel_problem() (KernelInterpolation method) setup_labels() (Rig method) setup_patchwise_illumination_correction() (Rig method) setup_poisson_solver() (BeckmannGproxPGHDSolver method) setup_shape_corrections() (Rig method) shape (BoxSelectionAssistant attribute) (ColorSpectrum property) (CoordinateSystem attribute) (DiscreteColorRange property) (Grid attribute) (Image property) shape_metadata() (Image method) show() (Image method) show_cmap() (ColorPath method) show_cmaps() (LabelColorPathMap method) show_image() (CurvatureCorrection method) show_matplotlib() (Image method) show_path() (ColorPath method) show_paths() (LabelColorPathMap method) show_plain() (Image method) show_plotly() (Image method) signal_aq (MassAnalysisResults attribute) signal_g (MassAnalysisResults attribute) signal_reduction (ConcentrationAnalysis attribute) SignalReduction (class in darsia) simple_curvature_correction() (CurvatureCorrection method) SimpleFlash (class in darsia) SimpleMassAnalysisResults (class in darsia) SimpleMultiphaseTimeSeriesData (class in darsia) SimpleRunAnalysis (class in darsia) single_image_analysis() (AnalysisBase method) size (ApproximationSpace property) (Masks property) (PolynomialApproximationSpace property) (RadialPolynomialApproximationSpace property) (REV attribute) slice() (Image method) smoother (MG attribute) smoother_iterations (MG attribute) solve_beckmann_problem() (BeckmannBregmanSolver method) (BeckmannGproxPGHDSolver method) (BeckmannNewtonSolver method) (BeckmannProblem method) Solver (class in darsia) solver_options (BeckmannAMGSolver attribute) (BeckmannCGSolver attribute) sort_quad() (in module darsia) space_dim (Geometry attribute) (Image attribute) space_num (Image property) spectrum (ColorSpectrum attribute) split_bregman_tvd() (in module darsia) stack() (in module darsia) StandardOtsu (class in darsia) start (TimeWindow attribute) start_date (ImagingInterval attribute) start_hours (TimeWindow property) start_id (ImagingInterval attribute) StaticThresholdModel (class in darsia) step (TimeWindow attribute) step_hours (TimeWindow property) stretch_center_off (GeneralizedPerspectiveTransformation attribute) stretch_correction() (CurvatureCorrection method) stretch_factor (GeneralizedPerspectiveTransformation attribute) subregion() (Geometry method) (Image method) (WeightedGeometry method) SubregionAssistant (class in darsia) superpose() (in module darsia) supports (KernelInterpolation attribute) T ThermodynamicState (class in darsia) threshold (BaseAssistant attribute) threshold_analysis() (Rig method) ThresholdAnalysisResults (class in darsia) ThresholdModel (class in darsia) time (Image attribute) (MassAnalysisResults attribute) (SimpleMassAnalysisResults attribute) (TimeSeriesData attribute) time_dim (Image attribute) time_interval (ImagingInterval attribute) time_interval() (Image method) time_num (Image attribute) time_since_start() (ProtocolledExperiment method) time_slice() (Image method) TimeSeriesData (class in darsia) TimeWindow (class in darsia) to_cartesian_indexing() (in module darsia) to_coordinate() (in module darsia) to_csv() (ScalarImage method) to_dict() (ColorPath method) (ColorPathInterpolation method) (ColorRange method) (ColorSpectrum method) (SimpleFlash method) to_matrix_indexing() (in module darsia) to_monochromatic() (OpticalImage method) to_trichromatic() (OpticalImage method) to_voxel() (in module darsia) to_voxel_center() (in module darsia) to_vtk() (Image method) tol (Solver attribute) tol_distance (BeckmannConvergenceCriteria attribute) tol_increment (BeckmannConvergenceCriteria attribute) tol_residual (BeckmannConvergenceCriteria attribute) TracerAnalysis (class in darsia) track() (MultiphaseTimeSeriesAnalysis method) (SimpleRunAnalysis method) transformation (TransformationCorrection attribute) TransformationCorrection (class in darsia) TransformedValueCriterion (class in darsia) translate_image() (TranslationAnalysis method) translation (AffineTransformation attribute) (TranslationAnalysis attribute) (TranslationCorrection attribute) translation_correction (AnalysisBase attribute) translation_estimator (DriftCorrection attribute) (TranslationAnalysis attribute) TranslationAnalysis (class in darsia) TranslationCorrection (class in darsia) TranslationEstimator (class in darsia) transport_density() (BeckmannProblem method) transport_density_faces() (BeckmannProblem method) TVD (class in darsia) tvd() (in module darsia) TwoPeakHistogrammAnalysis (class in darsia) TypeCorrection (class in darsia) U uncorrected_base (AnalysisBase attribute) uniform_refinement() (in module darsia) unique_labels (Masks attribute) update() (ClipModel method) (ConcentrationAnalysis method) (ExtrudedPorousGeometry method) (FluidFlowerCO2Meta method) (HeterogeneousLinearModel method) (KernelInterpolation method) (LinearModel method) (Rig method) (ScalingModel method) (SimpleFlash method) update_advanced() (AdvancedKernelInterpolation method) update_balancing_for_calibration() (AbstractBalancingCalibration method) update_base() (TranslationAnalysis method) update_base_patches() (TranslationAnalysis method) update_dst() (DiffeomorphicImageRegistration method) update_interpolation() (KernelInterpolation method) update_kernel() (KernelInterpolation method) update_metadata() (Image method) update_model_for_calibration() (AbstractModelObjective method) update_model_parameters() (ClipModel method) (ColorPathInterpolation method) (CombinedModel method) (HeterogeneousLinearModel method) (LinearModel method) (Model method) (ScalingModel method) update_parameters() (AdvancedCO2MassAnalysis method) update_params() (MG method) (Solver method) (TranslationAnalysis method) update_reference_time() (Image method) update_state() (CO2MassAnalysis method) use_coordinates (BaseAssistant attribute) V ValueCriterion (class in darsia) values (KernelInterpolation attribute) variable_supports (AdvancedKernelInterpolation attribute) variable_values (AdvancedKernelInterpolation attribute) verbose (BeckmannGproxPGHDSolver attribute) (BeckmannProblem attribute) (Solver attribute) verbosity (BaseAssistant attribute) (ConcentrationAnalysis attribute) (ContourAnalysis attribute) (LabelsAssistant attribute) (LabelsMaskSelectionAssistant attribute) (LabelsMergeAssistant attribute) (LabelsPickAssistant attribute) (LabelsSegmentAssistant attribute) volume_aq (MultiphaseTimeSeriesData attribute) volume_average() (in module darsia) volume_g (MultiphaseTimeSeriesData attribute) volume_tot (MultiphaseTimeSeriesData attribute) VolumeAveraging (class in darsia) Voxel (class in darsia) voxel() (CoordinateSystem method) voxel_size (BeckmannGproxPGHDSolver attribute) (BeckmannProblem attribute) (CoordinateSystem attribute) (Geometry attribute) (Grid attribute) (Image property) voxel_volume (Geometry attribute) (WeightedGeometry attribute) VoxelArray (class in darsia) VoxelCenter (class in darsia) VoxelCenterArray (class in darsia) voxels (CoordinateSystem property) W wasserstein_distance() (in module darsia) wasserstein_distance_to_vtk() (in module darsia) weight (BeckmannGproxPGHDSolver attribute) (BeckmannProblem attribute) (WeightedGeometry attribute) weight() (in module darsia) WeightedGeometry (class in darsia) white_balance() (in module darsia) WhiteBalance (class in darsia) width (AnalysisBase attribute) (BoxSelectionAssistant attribute) (CropAssistant attribute) write() (OpticalImage method) (ScalarImage method) write_cleaning_filter_to_file() (ConcentrationAnalysis method) write_config_to_file() (ColorCorrection method) (CurvatureCorrection method) Z zero_indices (VolumeAveraging attribute) zeros_like() (in module darsia)
