nirs4all.synthesis package
Submodules
- nirs4all.synthesis.accelerated module
AcceleratedArraysAcceleratedArrays.arangeAcceleratedArrays.arrayAcceleratedArrays.backendAcceleratedArrays.cosAcceleratedArrays.dotAcceleratedArrays.expAcceleratedArrays.linspaceAcceleratedArrays.logAcceleratedArrays.matmulAcceleratedArrays.onesAcceleratedArrays.random_normalAcceleratedArrays.random_uniformAcceleratedArrays.sinAcceleratedArrays.sqrtAcceleratedArrays.sumAcceleratedArrays.to_numpyAcceleratedArrays.zeros
AcceleratedGeneratorAcceleratorBackendbenchmark_backends()create_accelerated_arrays()detect_best_backend()generate_spectra_batch_accelerated()generate_voigt_profiles_accelerated()get_acceleration_speedup_estimate()get_backend_info()is_gpu_available()
- nirs4all.synthesis.benchmarks module
BenchmarkDatasetInfoBenchmarkDatasetInfo.domainBenchmarkDatasetInfo.full_nameBenchmarkDatasetInfo.licenseBenchmarkDatasetInfo.measurement_modeBenchmarkDatasetInfo.n_samplesBenchmarkDatasetInfo.n_wavelengthsBenchmarkDatasetInfo.nameBenchmarkDatasetInfo.notesBenchmarkDatasetInfo.referenceBenchmarkDatasetInfo.sample_typeBenchmarkDatasetInfo.source_urlBenchmarkDatasetInfo.summary()BenchmarkDatasetInfo.targetsBenchmarkDatasetInfo.typical_peak_densityBenchmarkDatasetInfo.typical_snrBenchmarkDatasetInfo.wavelength_range
BenchmarkDomainLoadedBenchmarkDatasetcreate_synthetic_matching_benchmark()get_benchmark_info()get_benchmark_spectral_properties()get_datasets_by_domain()list_benchmark_datasets()load_benchmark_dataset()
- nirs4all.synthesis.builder module
BuilderStateBuilderState.aggregate_nameBuilderState.aggregate_variabilityBuilderState.as_datasetBuilderState.batch_effects_enabledBuilderState.batch_gain_stdBuilderState.batch_offset_stdBuilderState.class_separationBuilderState.class_separation_methodBuilderState.class_weightsBuilderState.complexityBuilderState.component_libraryBuilderState.component_namesBuilderState.concentration_methodBuilderState.custom_paramsBuilderState.custom_wavelengthsBuilderState.edge_artifacts_configBuilderState.environmental_configBuilderState.generate_sample_idsBuilderState.group_namesBuilderState.hidden_factorsBuilderState.include_metadataBuilderState.instrumentBuilderState.instrument_wavelength_gridBuilderState.interaction_strengthBuilderState.measurement_modeBuilderState.n_batchesBuilderState.n_classesBuilderState.n_confoundersBuilderState.n_groupsBuilderState.n_regimesBuilderState.n_repetitionsBuilderState.n_samplesBuilderState.nameBuilderState.noise_heteroscedasticityBuilderState.nonlinear_interactionsBuilderState.polynomial_degreeBuilderState.random_stateBuilderState.regime_methodBuilderState.regime_overlapBuilderState.sample_id_prefixBuilderState.scattering_effects_configBuilderState.shuffleBuilderState.signal_to_confound_ratioBuilderState.sourcesBuilderState.spectral_maskingBuilderState.stratifyBuilderState.target_componentBuilderState.target_rangeBuilderState.target_transformBuilderState.temporal_driftBuilderState.train_ratioBuilderState.wavelength_endBuilderState.wavelength_startBuilderState.wavelength_step
- nirs4all.synthesis.components module
NIRBandSpectralComponentSpectralComponent.bandsSpectralComponent.cas_numberSpectralComponent.categorySpectralComponent.compute()SpectralComponent.correlation_groupSpectralComponent.formulaSpectralComponent.has_bands_in_range()SpectralComponent.info()SpectralComponent.is_normalized()SpectralComponent.nameSpectralComponent.normalized()SpectralComponent.referencesSpectralComponent.subcategorySpectralComponent.synonymsSpectralComponent.tagsSpectralComponent.validate()
available_components()component_info()get_component()list_categories()normalize_component_amplitudes()search_components()validate_component_coverage()validate_predefined_components()
- nirs4all.synthesis.config module
- nirs4all.synthesis.detectors module
DetectorConfigDetectorSimulatorDetectorSpectralResponseDetectorSpectralResponse.cutoff_wavelengthDetectorSpectralResponse.detector_typeDetectorSpectralResponse.get_response_at()DetectorSpectralResponse.peak_qeDetectorSpectralResponse.peak_wavelengthDetectorSpectralResponse.responseDetectorSpectralResponse.short_cutoffDetectorSpectralResponse.wavelengths
NoiseModelConfigNoiseModelConfig.adc_bitsNoiseModelConfig.flicker_corner_freqNoiseModelConfig.flicker_noise_enabledNoiseModelConfig.full_scaleNoiseModelConfig.quantization_noise_enabledNoiseModelConfig.read_noise_electronsNoiseModelConfig.read_noise_enabledNoiseModelConfig.shot_noise_enabledNoiseModelConfig.shot_noise_factorNoiseModelConfig.thermal_noise_enabledNoiseModelConfig.thermal_noise_factor
get_default_noise_config()get_detector_response()get_detector_wavelength_range()list_detector_types()simulate_detector_effects()
- nirs4all.synthesis.domains module
ConcentrationPriorDomainCategoryDomainConfigDomainConfig.additional_paramsDomainConfig.categoryDomainConfig.complexityDomainConfig.component_weightsDomainConfig.concentration_priorsDomainConfig.descriptionDomainConfig.get_component_weights()DomainConfig.measurement_modeDomainConfig.n_components_rangeDomainConfig.nameDomainConfig.noise_levelDomainConfig.sample_components()DomainConfig.sample_concentrations()DomainConfig.typical_componentsDomainConfig.typical_sample_typesDomainConfig.wavelength_range
create_domain_aware_library()get_domain_components()get_domain_config()get_domains_for_component()list_domains()
- nirs4all.synthesis.environmental module
EnvironmentalEffectsConfigMoistureConfigSpectralRegionTemperatureConfigTemperatureConfig.custom_regionsTemperatureConfig.delta_temperatureTemperatureConfig.enable_broadeningTemperatureConfig.enable_intensityTemperatureConfig.enable_shiftTemperatureConfig.reference_temperatureTemperatureConfig.region_specificTemperatureConfig.sample_temperatureTemperatureConfig.temperature_variation
TemperatureEffectParamsget_temperature_effect_regions()
- nirs4all.synthesis.exporter module
CSVVariationGeneratorCSVVariationGenerator.as_fragmented()CSVVariationGenerator.as_single_file()CSVVariationGenerator.generate_all_variations()CSVVariationGenerator.with_comma_delimiter()CSVVariationGenerator.with_precision()CSVVariationGenerator.with_row_index()CSVVariationGenerator.with_semicolon_delimiter()CSVVariationGenerator.with_tab_delimiter()CSVVariationGenerator.without_headers()
DatasetExporterExportConfigexport_to_csv()export_to_folder()
- nirs4all.synthesis.fitter module
ComponentFitResultComponentFitResult.baseline_coefficientsComponentFitResult.component_namesComponentFitResult.concentrationsComponentFitResult.fitted_spectrumComponentFitResult.r_squaredComponentFitResult.residualsComponentFitResult.rmseComponentFitResult.summary()ComponentFitResult.to_dict()ComponentFitResult.top_components()ComponentFitResult.wavelengths
ComponentFitterDerivativeAwareForwardModelFitterDerivativeAwareForwardModelFitter.__post_init__()DerivativeAwareForwardModelFitter.baseline_orderDerivativeAwareForwardModelFitter.canonical_gridDerivativeAwareForwardModelFitter.componentsDerivativeAwareForwardModelFitter.derivative_orderDerivativeAwareForwardModelFitter.fit()DerivativeAwareForwardModelFitter.ils_sigma_boundsDerivativeAwareForwardModelFitter.path_length_boundsDerivativeAwareForwardModelFitter.sg_polyorderDerivativeAwareForwardModelFitter.sg_windowDerivativeAwareForwardModelFitter.target_gridDerivativeAwareForwardModelFitter.wl_shift_bounds
DomainInferenceEdgeArtifactInferenceEdgeArtifactInference.boundary_peak_amplitudesEdgeArtifactInference.curvature_typeEdgeArtifactInference.detector_modelEdgeArtifactInference.edge_noise_ratioEdgeArtifactInference.has_detector_rolloffEdgeArtifactInference.has_edge_artifactsEdgeArtifactInference.has_edge_curvatureEdgeArtifactInference.has_stray_lightEdgeArtifactInference.has_truncated_peaksEdgeArtifactInference.left_edge_intensityEdgeArtifactInference.right_edge_intensityEdgeArtifactInference.stray_light_fraction
EnvironmentalInferenceFittedParametersFittedParameters.baseline_amplitudeFittedParameters.boundary_components_configFittedParameters.complexityFittedParameters.detected_componentsFittedParameters.domain_inferenceFittedParameters.edge_artifact_inferenceFittedParameters.edge_artifacts_configFittedParameters.emsc_configFittedParameters.environmental_inferenceFittedParameters.from_dict()FittedParameters.global_slope_meanFittedParameters.global_slope_stdFittedParameters.inferred_domainFittedParameters.inferred_instrumentFittedParameters.instrument_inferenceFittedParameters.is_preprocessedFittedParameters.load()FittedParameters.measurement_modeFittedParameters.measurement_mode_confidenceFittedParameters.moisture_configFittedParameters.noise_baseFittedParameters.noise_signal_depFittedParameters.particle_size_configFittedParameters.path_length_stdFittedParameters.preprocessing_inferenceFittedParameters.preprocessing_typeFittedParameters.save()FittedParameters.scatter_alpha_stdFittedParameters.scatter_beta_stdFittedParameters.scattering_inferenceFittedParameters.source_nameFittedParameters.source_propertiesFittedParameters.suggested_n_componentsFittedParameters.summary()FittedParameters.temperature_configFittedParameters.tilt_stdFittedParameters.to_dict()FittedParameters.to_full_config()FittedParameters.to_generator_kwargs()FittedParameters.wavelength_endFittedParameters.wavelength_startFittedParameters.wavelength_step
ForwardModelFitterInstrumentChainInstrumentInferenceMeasurementModeInferenceOperatorVarianceParamsOptimizedComponentFitterOptimizedFitResultOptimizedFitResult.baseline_coefficientsOptimizedFitResult.baseline_r_squaredOptimizedFitResult.component_namesOptimizedFitResult.concentrationsOptimizedFitResult.fitted_spectrumOptimizedFitResult.n_componentsOptimizedFitResult.n_priority_componentsOptimizedFitResult.r_squaredOptimizedFitResult.residualsOptimizedFitResult.rmseOptimizedFitResult.summary()OptimizedFitResult.top_components()OptimizedFitResult.wavelengths
PCAVarianceParamsPreprocessingInferencePreprocessingInference.confidencePreprocessingInference.global_meanPreprocessingInference.global_rangePreprocessingInference.is_preprocessedPreprocessingInference.oscillation_frequencyPreprocessingInference.per_sample_std_variationPreprocessingInference.preprocessing_typePreprocessingInference.suggested_inversePreprocessingInference.zero_crossing_ratio
PreprocessingTypeRealBandFitResultRealBandFitResult.amplitudesRealBandFitResult.band_assignmentsRealBandFitResult.band_centersRealBandFitResult.band_namesRealBandFitResult.baseline_coefficientsRealBandFitResult.fitted_spectrumRealBandFitResult.n_bandsRealBandFitResult.r_squaredRealBandFitResult.residualsRealBandFitResult.rmseRealBandFitResult.sigmasRealBandFitResult.summary()RealBandFitResult.top_bands()RealBandFitResult.wavelengths
RealBandFitterRealDataFitterScatteringInferenceSpectralPropertiesSpectralProperties.baseline_convexitySpectralProperties.baseline_offsetSpectralProperties.carbohydrate_band_intensitySpectralProperties.center_noise_stdSpectralProperties.curvature_stdSpectralProperties.edge_curvature_asymmetrySpectralProperties.edge_curvature_intensitySpectralProperties.effective_resolutionSpectralProperties.global_meanSpectralProperties.global_rangeSpectralProperties.global_stdSpectralProperties.has_boundary_rise_leftSpectralProperties.has_boundary_rise_rightSpectralProperties.kubelka_munk_linearitySpectralProperties.kurtosisSpectralProperties.left_edge_noise_stdSpectralProperties.left_edge_slopeSpectralProperties.lipid_band_intensitySpectralProperties.mean_curvatureSpectralProperties.mean_slopeSpectralProperties.mean_spectrumSpectralProperties.n_peaks_meanSpectralProperties.n_samplesSpectralProperties.n_wavelengthsSpectralProperties.nameSpectralProperties.noise_correlation_lengthSpectralProperties.noise_estimateSpectralProperties.oh_band_positionsSpectralProperties.pca_explained_varianceSpectralProperties.pca_n_components_95SpectralProperties.peak_positionsSpectralProperties.peak_wavenumbersSpectralProperties.protein_band_intensitySpectralProperties.right_edge_noise_stdSpectralProperties.right_edge_slopeSpectralProperties.sample_to_sample_offset_stdSpectralProperties.sample_to_sample_slope_stdSpectralProperties.scatter_baseline_curvatureSpectralProperties.scatter_baseline_slopeSpectralProperties.skewnessSpectralProperties.slope_stdSpectralProperties.slopesSpectralProperties.snr_estimateSpectralProperties.std_spectrumSpectralProperties.temperature_sensitivity_scoreSpectralProperties.water_band_intensitySpectralProperties.water_band_variationSpectralProperties.wavelength_rangeSpectralProperties.wavelengths
VarianceFitResultVarianceFittercompare_datasets()compute_spectral_properties()fit_components()fit_components_optimized()fit_real_bands()fit_to_real_data()fit_variance()multiscale_derivative_fit()multiscale_fit()
- nirs4all.synthesis.generator module
- nirs4all.synthesis.instruments module
- nirs4all.synthesis.measurement_modes module
- nirs4all.synthesis.metadata module
- nirs4all.synthesis.prior module
MatrixTypeNIRSPriorConfigNIRSPriorConfig.domain_weightsNIRSPriorConfig.get_domain_weight()NIRSPriorConfig.instrument_given_domainNIRSPriorConfig.matrix_given_domainNIRSPriorConfig.mode_given_categoryNIRSPriorConfig.n_classes_rangeNIRSPriorConfig.n_samples_rangeNIRSPriorConfig.n_targets_rangeNIRSPriorConfig.noise_level_rangeNIRSPriorConfig.normalize_weights()NIRSPriorConfig.particle_size_rangeNIRSPriorConfig.target_type_weightsNIRSPriorConfig.temperature_range
PriorSamplerPriorSampler.sample()PriorSampler.sample_batch()PriorSampler.sample_components()PriorSampler.sample_domain()PriorSampler.sample_for_domain()PriorSampler.sample_for_instrument()PriorSampler.sample_instrument()PriorSampler.sample_instrument_category()PriorSampler.sample_matrix_type()PriorSampler.sample_measurement_mode()PriorSampler.sample_n_samples()PriorSampler.sample_noise_level()PriorSampler.sample_particle_size()PriorSampler.sample_target_config()PriorSampler.sample_temperature()
get_domain_compatible_instruments()get_instrument_typical_modes()sample_prior()sample_prior_batch()
- nirs4all.synthesis.procedural module
FunctionalGroupTypeProceduralComponentConfigProceduralComponentConfig.amplitude_variabilityProceduralComponentConfig.anharmonicityProceduralComponentConfig.anharmonicity_variabilityProceduralComponentConfig.bandwidth_variabilityProceduralComponentConfig.combination_amplitude_factorProceduralComponentConfig.functional_groupsProceduralComponentConfig.h_bond_strengthProceduralComponentConfig.h_bond_variabilityProceduralComponentConfig.include_combinationsProceduralComponentConfig.include_overtonesProceduralComponentConfig.max_combinationsProceduralComponentConfig.max_overtone_orderProceduralComponentConfig.n_fundamental_bandsProceduralComponentConfig.wavelength_range
ProceduralComponentGenerator
- nirs4all.synthesis.products module
CategoryGeneratorComponentVariationComponentVariation.__post_init__()ComponentVariation.componentComponentVariation.compute_asComponentVariation.correlated_withComponentVariation.correlationComponentVariation.max_valueComponentVariation.meanComponentVariation.min_valueComponentVariation.stdComponentVariation.valueComponentVariation.variation_type
ProductGeneratorProductTemplateVariationTypegenerate_product_samples()get_product_template()list_product_categories()list_product_domains()list_product_templates()product_template_info()
- nirs4all.synthesis.scattering module
- nirs4all.synthesis.sources module
- nirs4all.synthesis.targets module
- nirs4all.synthesis.validation module
DatasetComparisonResultMetricResultRealismMetricSpectralRealismScoreSpectralRealismScore.adversarial_aucSpectralRealismScore.baseline_curvature_overlapSpectralRealismScore.correlation_length_overlapSpectralRealismScore.derivative_ks_pvalueSpectralRealismScore.metric_resultsSpectralRealismScore.overall_passSpectralRealismScore.peak_density_ratioSpectralRealismScore.snr_magnitude_matchSpectralRealismScore.summary()SpectralRealismScore.to_dict()SpectralRealismScore.warnings
ValidationErrorcompute_adversarial_validation_auc()compute_baseline_curvature()compute_correlation_length()compute_derivative_statistics()compute_distribution_overlap()compute_peak_density()compute_snr()compute_spectral_realism_scorecard()quick_realism_check()validate_against_benchmark()validate_concentrations()validate_spectra()validate_synthetic_output()validate_wavelengths()
- nirs4all.synthesis.wavenumber module
CombinationBandResultOvertoneResultapply_hydrogen_bonding_shift()calculate_combination_band()calculate_overtone_position()classify_wavelength_extended()classify_wavelength_zone()convert_bandwidth_to_wavelength()convert_bandwidth_to_wavenumber()estimate_bandwidth_broadening()get_all_zones_extended()get_all_zones_wavelength()get_nir_overtones_for_fundamental()get_zone_wavelength_range()is_nir_region()is_visible_region()wavelength_to_wavenumber()wavenumber_to_wavelength()