Index

A

AcquisitionConfig (class in pyfli.phasor.phasorS.phasor_locus_tools) AcquisitionMode (class in pyfli.phasor.phasorS.phasor_locus_tools) add_factor() (FactorAnalysis method) add_factor_fn() (FactorAnalysis method) add_mean_lifetime() (in module pyfli.analysis.load_results) agreed_param_table() (MonoBiClassifier method) agreement() (MonoBiClassifier method) align() (IRFAligner method) align_pixel() (IRFAligner method) all_combinations() (ConfigCombinationGenerator method) AlliGprocessedImport (class in pyfli.io.processed_data) analytical_decay_name (BaseContinuousSimulator attribute) (BaseDiscreteSimulator attribute) (ContinuousSimulator attribute) (MacroSimulator attribute) (PhotonCountSimulator attribute) (TCSPCSimulator attribute) AnalyticalHelpers (class in pyfli.analyticalWorkflow.am_utils)

analyze() (FactorAnalysis method) analyze_and_plot() (FactorAnalysis method) analyze_biexponential_and_reconstruct() (PhasorAnalyzer method) analyze_by_cluster() (FactorAnalysis method) analyze_fold_layout() (in module pyfli.io.spad_folding) anderson_darling() (TestStat method) annotate_distribution_metrics() (DLModelComparator method) annotate_stats (PlotConfig attribute) apply_binning() (FLIBinner method) apply_circular_shift() (IRFAligner method) apply_dcr() (NoiseEngine static method) apply_fold_layout() (in module pyfli.io.spad_folding) apply_fourier_shift() (IRFAligner method) apply_interpolation_mask() (StaticDataOps static method) apply_jitter() (NoiseEngine static method) apply_mask() (DataPreprocessing method) apply_poisson() (NoiseEngine static method) apply_read_noise() (NoiseEngine static method) attributes (HDF5DatasetInfo attribute)

B

BACKENDS (ParamSelector attribute), [1] BaseContinuousSimulator (class in pyfli.simulator.main_common) BaseDiscreteSimulator (class in pyfli.simulator.main_common) BaseFLIEngine (class in pyfli.simulator.sim_engine_common) BaseFLIFitter (class in pyfli.solver.base_fitter) BaseFLIImageGenerator (class in pyfli.simulator.image_generator_common) BaseReconstructor (class in pyfli.sp_analysis.base_reconstructor) BasisPatterns (class in pyfli.sp_analysis.simulator.pattern_gen) BatchSimulator (class in pyfli.simulator.sim_workflow) bayesian_evidence() (TestStat method) beta_sample() (ParameterSampler static method) BH_TCSPC() (Detector method) BHprocessedImport (class in pyfli.io.processed_data) bi_reconstruction() (in module pyfli.reconstruction.common_reconstruct)

bi_reconstruction_torch() (in module pyfli.reconstruction.common_reconstruct) BinnedFLIFitter (class in pyfli.solver.binned_fitter) bins (PlotConfig attribute) BiPipeline (class in pyfli.bayes_utils) (class in pyfli.bayes_utils.inference) bit_depth (SpadConfig attribute) (SS2BinReadResult attribute) bootstrap_ci() (TestStat method) bottom_files (SS2BinReadResult attribute) boxplot() (PlotKit static method) build() (SaveLoadDirector method) build_decay_cube() (in module pyfli.io.flim_decay_cube) build_gate_matrix() (in module pyfli.irf_deconvolution.fli_solver) build_temporal_trace() (in module pyfli.io.spad_folding)

C

calculate_uncertainties() (BaseFLIFitter method) calibrate() (PhasorAnalyzer method) calibrate_pixelwise() (PhasorAnalyzer method) calibratre_reference() (PhasorAnalyzer method) calibratre_reference_pixelwise() (PhasorAnalyzer method) candidate (SpadHDF5ReadResult attribute) capture() (MeasurementSimulator method) cdf() (PlotKit static method) CENTERS (in module pyfli.bayes_utils.posterior_pixel_plot) chunk_indices (SS2BinReadResult attribute) circular_align() (in module pyfli.io.spad_folding) circular_convolution_fft() (in module pyfli.analysis.utils) classify() (MonoBiClassifier method) classify_one() (MonoBiClassifier method) clip_crange() (ColorProcessor method) cluster_selection_mask() (FactorAnalysis method) cmap (PlotConfig attribute) CMAP_NAMES (MonoBiClassifier attribute) collapse_to_mono() (DetailedRecon method) collapse_to_xyt() (in module pyfli.io.flim_decay_cube) color() (PlotConfig method) ColorProcessor (class in pyfli.data_vnp.color_processor) colors (PlotConfig attribute) combination_table() (ConfigCombinationGenerator method) combine_ss2_10bit_subframes() (in module pyfli.io.ss2_bin) compare() (FactorAnalysis static method) compare_models() (BaseFLIFitter method) (MLEFLIFitter method) compare_selected() (FittingComparator method) compute() (CVPlot method) compute_aggregate_model_fit_result() (ParamSelector method), [1] compute_and_plot() (CVPlot method) compute_average_lifetime() (in module pyfli.solver.shared_metrics)

compute_best_model_fit_result() (ParamSelector method), [1] compute_detailed() (BiPipeline method), [1] compute_distribution_metrics() (DLModelComparator method) compute_fli_stats() (in module pyfli.solver.shared_metrics) compute_fractions() (PhasorAnalyzer method) compute_freq_axis() (in module pyfli.analysis.phasor_analysis) compute_fret_efficiency() (in module pyfli.solver.shared_metrics) compute_lifetime() (PhasorAnalyzer method) compute_modulation_lifetime() (PhasorAnalyzer method) compute_pearson_stats() (in module pyfli.solver.shared_metrics) compute_phasor() (in module pyfli.analysis.phasor_analysis) concat_sim_data() (in module pyfli.simulator.sim_workflow) confidence (SpadFoldLayout attribute) config (SaveLoadDirector attribute) ConfigCombinationGenerator (class in pyfli.data_cc.config_combinations) configure_logging() (in module pyfli.log_save.logging) CONTINUOUS (AcquisitionMode attribute) continuous_cls (BaseFLIImageGenerator attribute) (FLIImageGenerator attribute) (FLIModelImageGenerator attribute) continuous_locus() (MonoLocus method) ContinuousSimulator (class in pyfli.simulator.separate.main_factory_gen) correction (PlotConfig attribute) create_phasor_cpu() (PhasorAnalyzer method) create_phasor_gpu() (PhasorAnalyzer method) create_rois_from_threshold() (ROIMaker method) critical() (in module pyfli.log_save.logging) cross_validate() (FLICalibrator method) current_fig (Plotter attribute) CVPlot (class in pyfli.data_vnp.cv_plot) cycle_similarity (SpadFoldLayout attribute) cyclic_conv() (in module pyfli.irf_deconvolution.fli_solver) cyclic_corr() (in module pyfli.irf_deconvolution.fli_solver)

D

dark_palette() (in module pyfli.plot_style) darken_color() (in module pyfli.plot_style) data (SpadHDF5ReadResult attribute) (SpadReadResult attribute) (SS2BinReadResult attribute) data_masking() (in module pyfli.analysis.utils) DataIOUtils (class in pyfli.io.utils) DataOperations (class in pyfli.io.data_operations) DataPreprocessing (class in pyfli.data_cc.preprocessing) DataProcessor (class in pyfli.data_vnp.multi_plotter) DataSaver (class in pyfli.io.data_saving) dataset_paths (HDF5Candidate attribute) DatasetPlotter (class in pyfli.io.processed_data) DataViewer (class in pyfli.data_vnp.data_viewer) DCTBasis (class in pyfli.sp_analysis.basis) debug() (in module pyfli.log_save.logging) decay_basis() (in module pyfli.irf_deconvolution.fli_solver) decay_kernel() (in module pyfli.solver.forward_model) default_cmap() (BiPipeline static method), [1] DEFAULTS (SaveLoadDirector attribute) deinterleave_ss2_columns() (in module pyfli.io.ss2_bin)

describe() (AcquisitionConfig method) DetailedRecon (class in pyfli.reconstruction.detailed_results) detect_hot_pixels() (DataIOUtils method) detect_signal_onset() (in module pyfli.io.spad_folding) Detector (class in pyfli.io.detector) detector_frequency_mhz (SpadConfig attribute) dimension_labels (HDF5DatasetInfo attribute) discover_ss2_bin_files() (in module pyfli.io.ss2_bin) DISCRETE (AcquisitionMode attribute) discrete_cls (BaseFLIImageGenerator attribute) (FLIImageGenerator attribute) (FLIModelImageGenerator attribute) discrete_locus() (MonoLocus method) discrete_locus_circle() (in module pyfli.phasor.phasorS.phasor_locus_tools) disp_params() (MessageDisplay method) display_data() (DataViewer method) display_one() (MonoBiClassifier method) display_report() (FLICalibrator method) DLModelComparator (class in pyfli.data_vnp.multi_plotter) dmd_to_sensing_matrix() (BaseReconstructor static method) draw() (ROIMaker method) dtype (HDF5DatasetInfo attribute)

E

energy_distance() (FLIDistributionTest method) enforce_tau_ordering() (in module pyfli.solver.shared_metrics) engine_cls (BaseContinuousSimulator attribute) (BaseDiscreteSimulator attribute) (ContinuousSimulator attribute) (MacroSimulator attribute) (PhotonCountSimulator attribute) (TCSPCSimulator attribute) error() (in module pyfli.log_save.logging) estimate_irf (SolverConfig attribute)

estimate_period_bins() (in module pyfli.io.spad_folding) estimate_shift() (IRFAligner method) estimate_shift_debiased() (IRFAligner method) estimate_shift_rmse() (IRFAligner method) estimate_shift_rmse_pixel() (IRFAligner method) evaluate_all_samples() (ParamSelector method), [1] exception() (in module pyfli.log_save.logging) expdecay() (IRFGenerator static method) expected_poisson_deviance() (in module pyfli.solver.shared_metrics) export_data() (Plotter method) extract_roi_datasets() (ROIOperations method)

F

F2 (ICCDParams attribute) factor_values() (FactorAnalysis method) FactorAnalysis (class in pyfli.analysis.factor_analysis) figsize (PlotConfig attribute) filter_vars() (in module pyfli.io.data_saving) fit() (BinnedFLIFitter method) (LaguerreFLI method) fit_decay_pixel() (in module pyfli.irf_deconvolution.fli_solver) fit_image() (FLIGPUProcessor method) fit_session() (MessageDisplay method) fit_with_estimator() (BaseFLIFitter method) (MLEFLIFitter method) FittingComparator (class in pyfli.solver.comparison) FLIBinner (class in pyfli.solver.binned_fitter) FLICalibrator (class in pyfli.simulator.calibration_engine) FLICPUProcessor (class in pyfli.solver.cpu_processor) FLIDistributionTest (class in pyfli.analysis.stat_tests) FLIEngine (class in pyfli.simulator.combined.simulator_engine) FLIGPUProcessor (class in pyfli.solver.gpu_processor)

FLIImageGenerator (class in pyfli.simulator.combined.sim_image_generator) FLIModelImageGenerator (class in pyfli.simulator.separate.sim_model_image_generator) FLIModelSimulator (class in pyfli.simulator.separate.model_simulator) FLIValidator (class in pyfli.simulator.sim_calibrator) (class in pyfli.simulator.sim_stat_test) fold (SpadConfig attribute) fold_layout (SpadReadResult attribute) fold_repetitions (SpadConfig attribute) fold_smoothing_sigma (SpadConfig attribute) fold_validate (SpadConfig attribute) format_duration() (in module pyfli.log_save.logging) forward() (DCTBasis method) (HadamardBasis method) (OrthogonalBasis method) fourier_shift() (in module pyfli.irf_deconvolution.fli_solver) frechet_distance() (FLIDistributionTest method) freq_computation() (AnalyticalHelpers method) frequency_hz (AcquisitionConfig attribute) from_config() (SaveLoadDirector class method) from_value() (SpadConfig class method)

G

G0 (ICCDParams attribute) gate_count (SS2BinReadResult attribute) gate_integrated_kernel() (in module pyfli.solver.forward_model) gate_j() (in module pyfli.analysis.utils) gate_values (HDF5Candidate attribute) gate_width_frac (AcquisitionConfig attribute) GATED_N (AcquisitionMode attribute) gated_n_locus() (MonoLocus method) GATED_SINGLE (AcquisitionMode attribute) gated_single_locus() (MonoLocus method) gaussianExpIRF() (IRFGenerator static method) gaussianIRF() (IRFGenerator static method) generalized_anscombe() (in module pyfli.irf_deconvolution.detector_weights) generate_batch() (BatchSimulator method) generate_batch2D() (BatchSimulator method) generate_fourier_dct() (BasisPatterns method) generate_hadamard() (BasisPatterns method) generate_image() (BaseFLIImageGenerator method) generate_intensity_image() (PhasorAnalyzer method) generic() (Detector method)

get() (SaveLoadDirector method) get_analytical_decay() (FLIEngine method) get_assignments() (IDAssignDialog method) get_average_lifetime() (BaseFLIFitter method) get_binary_mask() (ROIMaker method) get_binned_data() (FLIBinner method) get_factor_map() (FactorAnalysis method) get_fitset_array() (FactorAnalysis method) get_format() (SpadIO static method) get_fret_efficiency() (BaseFLIFitter method) get_intensity_mask() (ROIMaker method) get_method() (PlotKit class method) get_model_analytical_decay() (FLIModelSimulator method) get_multi_cluster_mask() (ROIMaker method) get_parameters() (LaguerreFLI method) get_pixel_summary() (MessageDisplay method) get_snr() (MeasurementSimulator static method) get_threshold_binary_mask() (ROIMaker method) global_peak_norm_3d() (Normalization method) GlobalFLIFitter (class in pyfli.solver.global_fitter)

H

HadamardBasis (class in pyfli.sp_analysis.basis) harmonic (AcquisitionConfig attribute) hdf5_dataset_path (SpadConfig attribute) hdf5_folder_mode (SpadConfig attribute) hdf5_gate_group_path (SpadConfig attribute) hdf5_gate_order_attribute (SpadConfig attribute) hdf5_gate_prefix (SpadConfig attribute) hdf5_time_axis (SpadConfig attribute)

HDF5Candidate (class in pyfli.io.spad_hdf5) HDF5DatasetInfo (class in pyfli.io.spad_hdf5) height_to_time() (ToFSim method) histogram() (PlotKit static method) HistogramWidget (class in pyfli.roi_maker.roi_maker) hot_pixels() (DataIOUtils static method) hotpixel_correct() (StaticDataOps static method) huber_tv_grad() (in module pyfli.irf_deconvolution.fli_solver)

I

ICCD() (Detector method) iccd_lambda_weight() (in module pyfli.irf_deconvolution.detector_weights) iccd_to_lambda() (in module pyfli.irf_deconvolution.detector_weights) ICCDParams (class in pyfli.irf_deconvolution.detector_weights) IDAssignDialog (class in pyfli.roi_maker.roi_maker) ImageCanvas (class in pyfli.roi_maker.roi_maker) imshow_source (PlotConfig attribute) include_background_roi_in_maps (BaseFLIImageGenerator attribute) (FLIImageGenerator attribute) (FLIModelImageGenerator attribute) info() (in module pyfli.log_save.logging)

inject_phasor_result() (in module pyfli.analysis.load_results) input_format (SpadConfig attribute) inspect_spad_hdf5() (in module pyfli.io.spad_hdf5) inverse() (DCTBasis method) (HadamardBasis method) (OrthogonalBasis method) irf_inner_iters (SolverConfig attribute) irf_picker() (in module pyfli.simulator.sim_helper) irf_step (SolverConfig attribute) IRFAligner (class in pyfli.data_cc.irfAligner) IRFGenerator (class in pyfli.simulator.irf_sim.irf_generator) is_valid() (DataProcessor class method)

K

kde() (PlotKit static method) keyPressEvent() (ImageCanvas method) (ROIApp method)

kind (HDF5Candidate attribute) kolmogorov_smirnov() (TestStat method)

L

LaguerreFLI (class in pyfli.laguerre.laguerre_method) laser_frequency_mhz (SpadConfig attribute) least_squares_fit() (BaseFLIFitter method) legend_outside() (in module pyfli.plot_style) lifetime_from_locus() (in module pyfli.phasor.phasorS.phasor_locus_tools) lifetime_to_phasor() (PhasorAnalyzer method) likelihood_ratio() (TestStat method) LinearReconstructor (class in pyfli.sp_analysis.solvers) list_clusters() (FactorAnalysis method) list_factors() (FactorAnalysis method) list_fitset_keys() (FactorAnalysis method) list_fitset_targets() (FactorAnalysis method) load() (DataSaver class method) (SourceLoader method) (SpadIO static method) load_all_parallel() (DataOperations method) load_asc_file() (StaticDataOps static method) load_background() (DataOperations method) load_config() (DataSaver method) load_data() (DataOperations method) load_fitting_results() (in module pyfli.analysis.load_results) load_flim_data() (in module pyfli.io.flim_decay_cube) load_hardware_profile() (FLICalibrator static method) load_hp_image() (StaticDataOps static method)

load_irf() (DataOperations method) load_json() (DataSaver method) load_map() (FLICPUProcessor method) (LaguerreFLI method) load_mask() (DataOperations method) (ROIMaker method) load_mat_file() (StaticDataOps static method) load_model() (BiPipeline method), [1] load_npy() (DataSaver method) load_npy_file() (StaticDataOps static method) load_phasors_hdf5() (DataIOUtils method) load_ptu_file() (StaticDataOps static method) load_sdt_file() (StaticDataOps static method) load_session_arrays() (in module pyfli.analysis.load_results) load_spad() (in module pyfli.io.spad_io) load_ss2() (SpadIO static method) load_ss3() (SpadIO static method) load_tiff_file() (StaticDataOps static method) load_txt_file() (StaticDataOps static method) locus() (AcquisitionConfig method) log() (DataSaver method) (in module pyfli.log_save.logging) log_histogram() (PlotKit static method) log_to_file() (DataSaver method) lowest_zero() (ColorProcessor method)

M

MacroSimulator (class in pyfli.simulator.combined.main_factory) make_cluster_plot() (Plotter method) make_clusters() (GlobalFLIFitter method) make_dataset() (DataOperations method) make_observation() (in module pyfli.irf_deconvolution.detector_weights) make_phase_folded_trace() (in module pyfli.io.spad_folding) make_plot() (DLModelComparator method) (Plotter method) make_simulator() (in module pyfli.simulator.sim_workflow) manual_period (SpadFoldLayout attribute) manual_phase (SpadFoldLayout attribute) map() (PlotKit static method) MeasurementSimulator (class in pyfli.sp_analysis.simulator.measurement_sim) MessageDisplay (class in pyfli.data_text.msg_display) metadata (SpadReadResult attribute) METRICS (ParamSelector attribute), [1] metrics_bar() (PlotKit static method) min_fold_confidence (SpadConfig attribute) MIN_SAMPLES (DataProcessor attribute) minmax() (Normalization method) MLE_WEIGHTINGS (in module pyfli.solver.mle_fitter) MLEFLIFitter (class in pyfli.solver.mle_fitter) mmd() (FLIDistributionTest method) mode (AcquisitionConfig attribute) (SaveLoadDirector property) model_fit() (BaseFLIFitter method) MODEL_KEYS (BiPipeline attribute), [1] model_numpy() (in module pyfli.solver.forward_model) modulation_lifetime() (in module pyfli.phasor.phasorS.phasor_locus_tools) module pyfli pyfli.analysis pyfli.analysis.factor_analysis pyfli.analysis.fit_analysis pyfli.analysis.load_results pyfli.analysis.phasor_analysis pyfli.analysis.stat_tests pyfli.analysis.utils pyfli.analyticalWorkflow pyfli.analyticalWorkflow.am_utils pyfli.bayes_utils pyfli.bayes_utils.inference pyfli.bayes_utils.param_combinations pyfli.bayes_utils.posterior_pixel_plot pyfli.data_cc pyfli.data_cc.config_combinations pyfli.data_cc.irfAligner pyfli.data_cc.norm pyfli.data_cc.preprocessing pyfli.data_cc.roi pyfli.data_text pyfli.data_text.msg_display pyfli.data_vnp pyfli.data_vnp.color_processor pyfli.data_vnp.cv_plot pyfli.data_vnp.data_viewer pyfli.data_vnp.mono_bi_classifier pyfli.data_vnp.multi_plotter pyfli.img pyfli.img.logo pyfli.io pyfli.io.data_operations pyfli.io.data_ops_static pyfli.io.data_saving pyfli.io.detector pyfli.io.flim_decay_cube pyfli.io.processed_data pyfli.io.save_direction pyfli.io.spad_folding pyfli.io.spad_hdf5 pyfli.io.spad_io pyfli.io.ss2_bin pyfli.io.utils pyfli.irf_deconvolution pyfli.irf_deconvolution.detector_weights pyfli.irf_deconvolution.fli_solver pyfli.laguerre pyfli.laguerre.laguerre_method pyfli.log_save pyfli.log_save.logging pyfli.phasor pyfli.phasor.phasorS pyfli.phasor.phasorS.phasor_additional_plots pyfli.phasor.phasorS.phasor_locus pyfli.phasor.phasorS.phasor_locus_tools pyfli.phasor.phasorS.phasor_simple pyfli.phasor.phasorS.phasor_simple_plots pyfli.phasor.phasorS.phasor_simple_utils pyfli.plot_style pyfli.reconstruction pyfli.reconstruction.common_reconstruct pyfli.reconstruction.decay_reconstruction pyfli.reconstruction.detailed_results pyfli.roi_maker pyfli.roi_maker.roi_maker pyfli.roi_maker.roi_style pyfli.simulator pyfli.simulator.calibration_engine pyfli.simulator.combined pyfli.simulator.combined.main_factory pyfli.simulator.combined.sim_image_generator pyfli.simulator.combined.simulator_engine pyfli.simulator.distributions pyfli.simulator.image_generator_common pyfli.simulator.irf_sim pyfli.simulator.irf_sim.irf_generator pyfli.simulator.irf_sim.irf_offset_gen pyfli.simulator.irf_sim.tof_sim pyfli.simulator.main_common pyfli.simulator.noise_models pyfli.simulator.separate pyfli.simulator.separate.main_factory_gen pyfli.simulator.separate.model_simulator pyfli.simulator.separate.sim_model_image_generator pyfli.simulator.sim_calibrator pyfli.simulator.sim_engine_common pyfli.simulator.sim_helper pyfli.simulator.sim_stat_test pyfli.simulator.sim_workflow pyfli.solver pyfli.solver.base_fitter pyfli.solver.base_static pyfli.solver.binned_fitter pyfli.solver.comparison pyfli.solver.cpu_processor pyfli.solver.forward_model pyfli.solver.global_fitter pyfli.solver.gpu_processor pyfli.solver.mle_fitter pyfli.solver.shared_metrics pyfli.sp_analysis pyfli.sp_analysis.base_reconstructor pyfli.sp_analysis.basis pyfli.sp_analysis.main pyfli.sp_analysis.simulator pyfli.sp_analysis.simulator.measurement_sim pyfli.sp_analysis.simulator.pattern_gen pyfli.sp_analysis.simulator.reconstructor pyfli.sp_analysis.solvers pyfli.sp_analysis.spad_solvers

moment_based_guess() (in module pyfli.solver.base_static) mono_only_maps (BaseContinuousSimulator attribute) (BaseDiscreteSimulator attribute) (ContinuousSimulator attribute) (MacroSimulator attribute) (PhotonCountSimulator attribute) (TCSPCSimulator attribute) mono_reconstruction() (in module pyfli.reconstruction.common_reconstruct) mono_reconstruction_torch() (in module pyfli.reconstruction.common_reconstruct) MonoBiClassifier (class in pyfli.data_vnp.mono_bi_classifier) MonoLocus (class in pyfli.phasor.phasorS.phasor_locus) mouseDoubleClickEvent() (HistogramWidget method) mouseMoveEvent() (HistogramWidget method) (ImageCanvas method) mousePressEvent() (HistogramWidget method) (ImageCanvas method) mouseReleaseEvent() (HistogramWidget method) (ImageCanvas method) move() (ROIObject method) multidata_phasor_plot() (PhasorAdditionalPlots method) multimodal_normal() (in module pyfli.analysis.utils)

N

n_bins (AcquisitionConfig attribute) n_combinations (ConfigCombinationGenerator property) n_ex (SPADParams attribute) (TCSPCParams attribute) n_gates (AcquisitionConfig attribute) n_models (SolverConfig attribute)

negative_lag_gates() (in module pyfli.solver.forward_model) neyman_chi_square() (MLEFLIFitter method) NLSF_WEIGHTINGS (in module pyfli.solver.base_fitter) NoiseEngine (class in pyfli.simulator.noise_models) norm_scale() (Normalization method) Normalization (class in pyfli.data_cc.norm) normalize_image() (Reconstructor static method)

O

objective_function() (FLICalibrator method) OFFSET (AcquisitionMode attribute) offset_locus() (MonoLocus method) OffsetGen (class in pyfli.simulator.irf_sim.irf_offset_gen) omega_rad_per_ns (AcquisitionConfig property) onset_index (SpadFoldLayout attribute) onset_lead_bins (SpadConfig attribute) (SpadFoldLayout attribute)

onset_threshold_fraction (SpadConfig attribute) ordering_source (HDF5Candidate attribute) original_bins (SpadFoldLayout attribute) original_shape (HDF5Candidate attribute) OrthogonalBasis (class in pyfli.sp_analysis.basis) outer_iters (SolverConfig attribute)

P

paintEvent() (HistogramWidget method) (ImageCanvas method) pairwise_scatter() (ParamCorrelationMatrix method) PALETTE (MonoBiClassifier attribute) (ParamCorrelationMatrix attribute) param_keys (ParamToDecay property) PARAM_MAP_DEFAULTS (ParamToDecay attribute) PARAM_MAP_KEYS (ParamToDecay attribute) param_scatter_matrix() (MonoBiClassifier method) ParamCorrelationMatrix (class in pyfli.data_vnp.mono_bi_classifier) ParameterSampler (class in pyfli.simulator.distributions) ParamSelector (class in pyfli.bayes_utils) (class in pyfli.bayes_utils.param_combinations) ParamToDecay (class in pyfli.reconstruction.decay_reconstruction) path (HDF5DatasetInfo attribute) pca_overlap() (FLIDistributionTest method) pearson_chi_square() (in module pyfli.solver.shared_metrics) (MLEFLIFitter method) period_bins (SpadConfig attribute) (SpadFoldLayout attribute) period_ns (AcquisitionConfig property) period_score (SpadFoldLayout attribute) period_search_radius (SpadConfig attribute) phase_lifetime() (in module pyfli.phasor.phasorS.phasor_locus_tools) phase_lifetime_gated() (in module pyfli.phasor.phasorS.phasor_locus_tools) phase_origin (SpadFoldLayout attribute) phase_shift (SpadConfig attribute) (SpadFoldLayout attribute) phasor_colormap() (PhasorPlotsMixin method) phasor_kde_to_px() (PhasorAdditionalPlots method) phasor_radial_color() (PhasorPlotsMixin method) PhasorAdditionalPlots (class in pyfli.phasor.phasorS.phasor_additional_plots) PhasorAnalyzer (class in pyfli.phasor.phasorS.phasor_simple) PhasorFreqComputaion() (in module pyfli.analysis.utils) phasorlifetime_to_phasor() (PhasorAdditionalPlots method) PhasorPlotsMixin (class in pyfli.phasor.phasorS.phasor_simple_plots) photon_amplitude_guess() (in module pyfli.solver.base_static) PhotonCountSimulator (class in pyfli.simulator.separate.main_factory_gen) pile_up (SpadConfig attribute) pileup_correction() (StaticDataOps static method) pin_barycenter() (in module pyfli.irf_deconvolution.fli_solver) pin_global_shift (SolverConfig attribute) Pj_continuous_mono() (in module pyfli.analysis.utils) Pj_from_samples_mono() (in module pyfli.analysis.utils) plot() (CVPlot method) (FactorAnalysis method) (SubplotVisualizer method) plot_2d_analysis() (in module pyfli.analysis.fit_analysis) plot_2d_subplots() (in module pyfli.data_vnp.multi_plotter) plot_bin_distribution() (FactorAnalysis method) plot_by_cluster() (FactorAnalysis method) plot_decay_cube() (in module pyfli.io.flim_decay_cube) plot_derived_images() (in module pyfli.io.flim_decay_cube) plot_diagnostics() (in module pyfli.analysis.fit_analysis) plot_discrete_n_sweep() (in module pyfli.phasor.phasorS.phasor_locus_tools) plot_fitting_maps() (in module pyfli.analysis.fit_analysis) plot_fli_px() (DataViewer method) plot_map() (PhasorPlotsMixin method) plot_metrics() (DLModelComparator method) plot_noise_sensitivity() (FLICalibrator method) plot_overlay_subplots() (PhasorPlotsMixin method) plot_phasor_diagram() (PhasorPlotsMixin method) plot_phasor_figures() (in module pyfli.analysis.phasor_analysis) plot_phasor_harmonics() (PhasorPlotsMixin method) plot_phasor_overlay() (PhasorPlotsMixin method) plot_pixel_diagnostic() (in module pyfli.analysis.utils) plot_pixel_evidence() (in module pyfli.analysis.fit_analysis) plot_pixel_fit() (PhasorPlotsMixin method) plot_pixel_fit_single_exp() (PhasorPlotsMixin method) plot_pixel_posterior_fit() (in module pyfli.bayes_utils) (in module pyfli.bayes_utils.posterior_pixel_plot) plot_pure_phasor_map() (PhasorPlotsMixin method) plot_pyfli_fit_summary() (DataViewer method) plot_range_selection_grid() (FactorAnalysis method) plot_spatial_selection() (FactorAnalysis method) plot_statistical_comparison() (in module pyfli.analysis.fit_analysis) plot_traceable_analysis() (PhasorPlotsMixin method) plot_xyt() (in module pyfli.io.flim_decay_cube) PlotConfig (class in pyfli.data_vnp.multi_plotter) PlotKit (class in pyfli.data_vnp.multi_plotter) Plotter (class in pyfli.data_vnp.multi_plotter) point_type (PlotConfig attribute) poisson_deviance() (in module pyfli.solver.shared_metrics) poisson_log_likelihood() (MLEFLIFitter method) predict() (LaguerreFLI method) process() (DataProcessor static method) process_clusters() (GlobalFLIFitter method) process_differential() (MeasurementSimulator method) process_image() (FLICPUProcessor method) project_simplex() (in module pyfli.irf_deconvolution.fli_solver) pulse_positions (SpadFoldLayout attribute) pyfli module pyfli.analysis module pyfli.analysis.factor_analysis module pyfli.analysis.fit_analysis module pyfli.analysis.load_results module pyfli.analysis.phasor_analysis module pyfli.analysis.stat_tests module pyfli.analysis.utils module pyfli.analyticalWorkflow module pyfli.analyticalWorkflow.am_utils module pyfli.bayes_utils module pyfli.bayes_utils.inference module pyfli.bayes_utils.param_combinations module pyfli.bayes_utils.posterior_pixel_plot module pyfli.data_cc module pyfli.data_cc.config_combinations module pyfli.data_cc.irfAligner module pyfli.data_cc.norm module pyfli.data_cc.preprocessing module pyfli.data_cc.roi module pyfli.data_text module pyfli.data_text.msg_display module pyfli.data_vnp module pyfli.data_vnp.color_processor module pyfli.data_vnp.cv_plot module pyfli.data_vnp.data_viewer module pyfli.data_vnp.mono_bi_classifier module pyfli.data_vnp.multi_plotter module pyfli.img module pyfli.img.logo module pyfli.io module pyfli.io.data_operations module pyfli.io.data_ops_static module

pyfli.io.data_saving module pyfli.io.detector module pyfli.io.flim_decay_cube module pyfli.io.processed_data module pyfli.io.save_direction module pyfli.io.spad_folding module pyfli.io.spad_hdf5 module pyfli.io.spad_io module pyfli.io.ss2_bin module pyfli.io.utils module pyfli.irf_deconvolution module pyfli.irf_deconvolution.detector_weights module pyfli.irf_deconvolution.fli_solver module pyfli.laguerre module pyfli.laguerre.laguerre_method module pyfli.log_save module pyfli.log_save.logging module pyfli.phasor module pyfli.phasor.phasorS module pyfli.phasor.phasorS.phasor_additional_plots module pyfli.phasor.phasorS.phasor_locus module pyfli.phasor.phasorS.phasor_locus_tools module pyfli.phasor.phasorS.phasor_simple module pyfli.phasor.phasorS.phasor_simple_plots module pyfli.phasor.phasorS.phasor_simple_utils module pyfli.plot_style module pyfli.reconstruction module pyfli.reconstruction.common_reconstruct module pyfli.reconstruction.decay_reconstruction module pyfli.reconstruction.detailed_results module pyfli.roi_maker module pyfli.roi_maker.roi_maker module pyfli.roi_maker.roi_style module pyfli.simulator module pyfli.simulator.calibration_engine module pyfli.simulator.combined module pyfli.simulator.combined.main_factory module pyfli.simulator.combined.sim_image_generator module pyfli.simulator.combined.simulator_engine module pyfli.simulator.distributions module pyfli.simulator.image_generator_common module pyfli.simulator.irf_sim module pyfli.simulator.irf_sim.irf_generator module pyfli.simulator.irf_sim.irf_offset_gen module pyfli.simulator.irf_sim.tof_sim module pyfli.simulator.main_common module pyfli.simulator.noise_models module pyfli.simulator.separate module pyfli.simulator.separate.main_factory_gen module pyfli.simulator.separate.model_simulator module pyfli.simulator.separate.sim_model_image_generator module pyfli.simulator.sim_calibrator module pyfli.simulator.sim_engine_common module pyfli.simulator.sim_helper module pyfli.simulator.sim_stat_test module pyfli.simulator.sim_workflow module pyfli.solver module pyfli.solver.base_fitter module pyfli.solver.base_static module pyfli.solver.binned_fitter module pyfli.solver.comparison module pyfli.solver.cpu_processor module pyfli.solver.forward_model module pyfli.solver.global_fitter module pyfli.solver.gpu_processor module pyfli.solver.mle_fitter module pyfli.solver.shared_metrics module pyfli.sp_analysis module pyfli.sp_analysis.base_reconstructor module pyfli.sp_analysis.basis module pyfli.sp_analysis.main module pyfli.sp_analysis.simulator module pyfli.sp_analysis.simulator.measurement_sim module pyfli.sp_analysis.simulator.pattern_gen module pyfli.sp_analysis.simulator.reconstructor module pyfli.sp_analysis.solvers module pyfli.sp_analysis.spad_solvers module PyFliprocessedImport (class in pyfli.io.processed_data)

Q

qq() (PlotKit static method)

qq_reference (PlotConfig attribute)

R

raincloud() (PlotKit static method) random_true_pixel() (in module pyfli.analysis.utils) raw_frame_count (SS2BinReadResult attribute) read_derived_images() (in module pyfli.io.flim_decay_cube) read_spad_hdf5() (in module pyfli.io.spad_hdf5) read_ss2_bin_acquisition() (in module pyfli.io.ss2_bin) read_ss2_bin_file() (in module pyfli.io.ss2_bin) reconstruct() (DetailedRecon method) (ParamToDecay method) reconstruct_4d() (BaseReconstructor method) reconstruct_fourier_domain() (Reconstructor method) reconstruct_linear() (Reconstructor method) reconstruct_slice() (BaseReconstructor method) (LinearReconstructor method) (SPADPoissonReconstructor method) (TVReconstructor method) reconstruct_unit_amplitude() (ParamToDecay method) reconstruct_vectorized() (ParamToDecay method) Reconstructor (class in pyfli.sp_analysis.simulator.reconstructor) recovery_plot() (in module pyfli.analysis.utils) reduced_poisson_deviance() (in module pyfli.solver.shared_metrics) REDUCERS (ParamSelector attribute), [1] refresh_base_pixmap() (ImageCanvas method) register_fitset_target() (FactorAnalysis method) repeat_count (SpadFoldLayout attribute)

required_keys (ParamToDecay property) rescale_fit_to_measured_totals() (ParamToDecay method) reset_zoom() (ImageCanvas method) reshape_pattern() (BasisPatterns static method) resolve_params_and_bounds() (in module pyfli.solver.base_static) resolve_path() (DataSaver class method) rho1 (SolverConfig attribute) rho2 (SolverConfig attribute) rld_based_guess() (in module pyfli.solver.base_static) ROIApp (class in pyfli.roi_maker.roi_maker) ROIMaker (class in pyfli.roi_maker.roi_maker) roiNloader() (DataIOUtils method) ROIObject (class in pyfli.roi_maker.roi_maker) ROIOperations (class in pyfli.data_cc.roi) rotate() (ROIObject method) run() (BiPipeline method), [1] (SimOutput method) (SimOutputWithIRFOffset method) run_all() (FittingComparator method) (FLIDistributionTest method) run_all_tests() (TestStat method) run_calibration() (FLICalibrator method) run_comprehensive_test() (FLIValidator method), [1] run_inference() (BiPipeline method), [1] run_mono_bi_classifier() (in module pyfli.analysis.fit_analysis) run_reconstruction() (in module pyfli.sp_analysis.main)

S

sample() (ConfigCombinationGenerator method) (OffsetGen method) sample_all_params() (FLIEngine method) sample_beta() (ParameterSampler static method) sample_bi_params() (FLIModelSimulator method) sample_cube() (OffsetGen method) sample_mono_params() (FLIModelSimulator method) sample_noise_params() (ParameterSampler static method) sample_params() (FLIModelSimulator method) sample_params_name (BaseContinuousSimulator attribute) (BaseDiscreteSimulator attribute) (ContinuousSimulator attribute) (MacroSimulator attribute) (PhotonCountSimulator attribute) (TCSPCSimulator attribute) sample_picked() (OffsetGen method) sample_qe() (ParameterSampler static method) sample_shift() (ToFSim method) save_3d_array_as_tiff_sequence() (in module pyfli.analysis.utils) save_as_uint16_sequence() (in module pyfli.analysis.utils) save_config() (DataSaver method) save_detailed() (BiPipeline method), [1] save_hardware_profile() (FLICalibrator method) save_json() (DataSaver method) save_laguerre_result() (in module pyfli.analysis.load_results) save_masks() (ROIMaker method) save_npy() (DataSaver method) save_outputs() (BiPipeline method), [1] save_params() (DataSaver method) save_phasor_result() (in module pyfli.analysis.phasor_analysis) save_phasors_hdf5() (PhasorAnalyzer method) save_plot() (DataSaver method) (in module pyfli.analysis.utils) save_results() (BinnedFLIFitter method) (FittingComparator method) (FLICPUProcessor method) (FLIGPUProcessor method) (LaguerreFLI method) save_suffix (SaveLoadDirector property) save_threshold_binary_mask() (ROIMaker method) SaveLoadDirector (class in pyfli.io.save_direction) scale() (ROIObject method) scan_session_results() (in module pyfli.analysis.load_results) scatter() (PlotKit static method) scatter_matrix() (ParamCorrelationMatrix method) scatter_pair (PlotConfig attribute) score (HDF5Candidate attribute) select_best_combination() (ParamSelector method), [1] selection_mask() (FactorAnalysis method) set_display_window() (ROIMaker method) set_fit_range() (BaseFLIFitter method) shape (HDF5DatasetInfo attribute)

shared_colorbar (PlotConfig attribute) show_mean (PlotConfig attribute) show_median (PlotConfig attribute) sigma_r (ICCDParams attribute) signal_score (SpadFoldLayout attribute) sim_BI() (BatchSimulator method) SimGenerator (class in pyfli.simulator.sim_workflow) SimOutput (class in pyfli.simulator.sim_workflow) SimOutputWithIRFOffset (class in pyfli.simulator.sim_workflow) simulate_fourier_acquisition() (MeasurementSimulator method) simulate_model_tcspc() (FLIModelSimulator method) simulate_once() (SimGenerator method) (WeightedConfigSimGenerator method) simulate_tcspc() (FLIEngine method) simulate_tcspc_name (BaseDiscreteSimulator attribute) (PhotonCountSimulator attribute) (TCSPCSimulator attribute) single_ex_decay_summed_overtime() (in module pyfli.analysis.utils) sliced_wasserstein() (FLIDistributionTest method) solve_flim() (in module pyfli.irf_deconvolution.fli_solver) solve_tv() (Reconstructor method) SolverConfig (class in pyfli.irf_deconvolution.fli_solver) source_path (SpadHDF5ReadResult attribute) SourceLoader (class in pyfli.data_vnp.multi_plotter) SPAD() (Detector method) spad_hdf5_read() (StaticDataOps static method) spad_lambda_weight() (in module pyfli.irf_deconvolution.detector_weights) spad_to_lambda() (in module pyfli.irf_deconvolution.detector_weights) SpadConfig (class in pyfli.io.spad_io) SpadFoldLayout (class in pyfli.io.spad_folding) SpadHDF5ReadResult (class in pyfli.io.spad_hdf5) SpadIO (class in pyfli.io.spad_io) SPADParams (class in pyfli.irf_deconvolution.detector_weights) SPADPoissonReconstructor (class in pyfli.sp_analysis.spad_solvers) SpadReadResult (class in pyfli.io.spad_io) spatial_laplacian() (in module pyfli.irf_deconvolution.fli_solver) spatial_shape (HDF5Candidate attribute) split_mono_bi() (DetailedRecon method) SS2() (Detector method) ss2_bottom_prefix (SpadConfig attribute) ss2_expected_gate_count (SpadConfig attribute) ss2_top_prefix (SpadConfig attribute) SS2BinReadResult (class in pyfli.io.ss2_bin) SS3() (Detector method) SS3HDF5read() (StaticDataOps static method) StaticDataOps (class in pyfli.io.data_ops_static) stats() (DataProcessor static method) stats_results (Plotter attribute) stitch_results() (GlobalFLIFitter method) stretch_squeeze() (ParameterSampler static method) SubplotVisualizer (class in pyfli.data_vnp.multi_plotter) summary() (MonoBiClassifier method) super_pixel_fitting() (GlobalFLIFitter method)

T

T (SolverConfig attribute) t0_frac (AcquisitionConfig attribute) t_rec_frac (AcquisitionConfig attribute) tau_bounds (SolverConfig attribute) tau_init (SolverConfig attribute) tau_sep (SolverConfig attribute) tcspc_lambda_weight() (in module pyfli.irf_deconvolution.detector_weights) tcspc_pileup_filter() (NoiseEngine static method) tcspc_to_lambda() (in module pyfli.irf_deconvolution.detector_weights) TCSPCParams (class in pyfli.irf_deconvolution.detector_weights) TCSPCSimulator (class in pyfli.simulator.combined.main_factory) test_type (PlotConfig attribute) TestStat (class in pyfli.analysis.stat_tests) threshold_masking() (DataPreprocessing method) (in module pyfli.analysis.utils)

time_axis (HDF5Candidate attribute) to_dict() (SaveLoadDirector method) to_metadata() (HDF5Candidate method) (SpadConfig method) (SpadFoldLayout method) (SpadHDF5ReadResult method) (SS2BinReadResult method) to_pdf() (Normalization method) ToFSim (class in pyfli.simulator.irf_sim.tof_sim) top_files (SS2BinReadResult attribute) TRUNCATED (AcquisitionMode attribute) truncated_locus() (MonoLocus method) truncated_normal() (ParameterSampler static method) trust_region() (BaseFLIFitter method) TVReconstructor (class in pyfli.sp_analysis.solvers)

U

unconstrained() (BaseFLIFitter method) unweighted_sum_of_squares() (MLEFLIFitter method)

update_intensity_overlay() (ImageCanvas method) update_irf() (in module pyfli.irf_deconvolution.fli_solver)

V

VALID_MODES (SaveLoadDirector attribute) verbose (SolverConfig attribute)

violinplot() (PlotKit static method) visualize() (BiPipeline method), [1]

W

warn_once() (in module pyfli.log_save.logging) warning() (in module pyfli.log_save.logging)

WeightedConfigSimGenerator (class in pyfli.simulator.sim_workflow) wheelEvent() (ImageCanvas method) window_changed (HistogramWidget attribute)

Z

zerone() (Normalization method)