mocca package

Subpackages

• mocca.campaign package
  • Submodules
  • mocca.campaign.experiment_funcs module
    • get_sorted_compound_experiments()
    • get_unprocessed_experiments()
  • mocca.campaign.process_funcs module
    • preprocess_experiment()
    • process_compound_exp()
    • process_compound_experiments()
    • process_experiments()
    • process_gradients()
  • mocca.campaign.utils module
    • check_istd()
  • Module contents
• mocca.chromatogram package
  • Submodules
  • mocca.chromatogram.assign module
    • assign_best_match_peak()
    • assign_matched_peaks()
    • assign_peaks_compound()
    • assign_peaks_react()
    • assign_unmatched_peaks_compound()
    • assign_unmatched_peaks_react()
    • get_best_match_compound_id()
    • get_matched_peaks()
    • get_max_integral_peak()
    • get_next_unknown_id()
    • get_unknown_impurity_peaks()
    • get_unmatched_peaks()
    • reassign_impurities()
    • sort_peaks_by_best_match()
    • update_peaks_and_matches()
  • mocca.chromatogram.correct module
    • correct_istd_offset()
    • get_impure_istd_peak()
    • get_istd_offset()
    • get_istd_peak()
    • get_pure_istd_peak()
  • mocca.chromatogram.model module
    • Chromatogram
      • Chromatogram.insert_peak()
  • mocca.chromatogram.preprocessor module
    • preprocess_chromatogram()
  • mocca.chromatogram.quantify module
    • quantify_peaks()
  • mocca.chromatogram.utils module
    • check_overlap()
    • check_same_dataset()
    • get_distance_between()
  • Module contents
• mocca.components package
  • Submodules
  • mocca.components.databases module
    • BaseDatabase
      • BaseDatabase.delete_all_items()
      • BaseDatabase.insert_item()
    • QualiComponentDatabase
      • QualiComponentDatabase.insert_by_compound_id()
      • QualiComponentDatabase.update()
    • QuantComponentDatabase
      • QuantComponentDatabase.update()
  • mocca.components.models module
    • QualiComponent
      • QualiComponent.compound_id
      • QualiComponent.created_from
      • QualiComponent.left
      • QualiComponent.maximum
      • QualiComponent.offset
      • QualiComponent.right
      • QualiComponent.spectrum
      • QualiComponent.spectrum_max
    • QuantComponent
      • QuantComponent.calib_data
      • QuantComponent.calib_factors
      • QuantComponent.calib_scores
      • QuantComponent.compound_id
      • QuantComponent.created_from
      • QuantComponent.integrate_wl_idx
  • mocca.components.quali_funcs module
    • create_quali_component()
    • get_absorbance_maxima()
  • mocca.components.quant_funcs module
    • create_calibration_dict()
    • create_linear_models()
    • create_quant_component()
    • get_integrate_wl_index()
    • integrate_on_wl()
  • mocca.components.utils module
    • average_ret_times_over_peaks()
    • average_spectra_over_peaks()
    • check_peaks_compound_id()
    • filter_peaks()
    • get_filtered_peaks()
    • get_filtered_peaks_by_compound()
    • get_quant_peaks_by_compound()
    • get_valid_peaks()
    • sort_peaks_by_compound()
  • Module contents
• mocca.dad_data package
  • Subpackages
    • mocca.dad_data.apis package
      • Submodules
      • mocca.dad_data.apis.allotrope module
      • mocca.dad_data.apis.angi module
      • mocca.dad_data.apis.chemstation module
      • mocca.dad_data.apis.custom module
      • mocca.dad_data.apis.empower module
      • mocca.dad_data.apis.labsolutions module
      • Module contents
  • Submodules
  • mocca.dad_data.models module
    • CompoundData
      • CompoundData.data
      • CompoundData.experiment
      • CompoundData.hplc_system_tag
      • CompoundData.path
      • CompoundData.time
      • CompoundData.warnings
      • CompoundData.wavelength
    • DadData
      • DadData.data
      • DadData.experiment
      • DadData.hplc_system_tag
      • DadData.path
      • DadData.time
      • DadData.warnings
      • DadData.wavelength
      • DadData.wl_high_pass
      • DadData.wl_low_pass
    • GradientData
      • GradientData.original_data
    • ParafacData
      • ParafacData.boundaries
      • ParafacData.impure_peak
      • ParafacData.parafac_comp_tensor
      • ParafacData.shift
      • ParafacData.y_offset
  • mocca.dad_data.process_funcs module
    • get_peak_locs()
    • merge_peaks()
    • pick_peaks()
  • mocca.dad_data.process_gradientdata module
    • bsl_als()
    • bsl_als_alg()
  • mocca.dad_data.utils module
    • absorbance_to_array()
    • apply_filter()
    • df_to_array()
    • get_reference_signal()
    • sum_absorbance_by_time()
    • trim_data()
  • Module contents
• mocca.decomposition namespace
  • Submodules
  • mocca.decomposition.alternative_objective_funcs module
    • get_all_comp_sum()
    • get_all_non_comp_sum()
    • get_comp_sum()
    • get_impure_integral_sum()
    • get_non_comp_sum()
    • get_total_integral_sum()
  • mocca.decomposition.data_tensor module
    • create_data_tensor()
    • get_comp_peak_data_list()
    • get_comp_peaks()
    • get_offset_peak_to_comp()
    • get_parafac_tensor()
    • get_relevant_comp()
    • get_tensor_boundaries()
    • get_zero_ext_impure_peak_data()
    • get_zero_extended_peak_data()
    • get_zeros_array()
    • normalize_peak_data()
  • mocca.decomposition.iterative_parafac module
    • iterative_parafac()
  • mocca.decomposition.model module
    • DataTensor
      • DataTensor.boundaries
      • DataTensor.comp_tensor_shape
      • DataTensor.relevant_comp
      • DataTensor.tensor
      • DataTensor.y_offset
    • ParafacModel
      • ParafacModel.create_parafac_peaks()
      • ParafacModel.data_tensor
      • ParafacModel.factors
      • ParafacModel.impure_mse
      • ParafacModel.impure_peak
      • ParafacModel.iter_objective_func
      • ParafacModel.iter_offset
      • ParafacModel.n_comps
      • ParafacModel.pca_explained_variance
      • ParafacModel.peaks
      • ParafacModel.weights
  • mocca.decomposition.parafac_funcs module
    • estimate_pca_n_comps()
    • parafac()
    • print_parafac_analytics()
  • mocca.decomposition.utils module
    • check_absorbance_thresh()
    • check_any_compound_overlap()
    • check_comp_in_impure()
    • check_comp_overlap()
    • check_same_uvvis()
    • check_summed_factor_uvvis()
• mocca.peak package
  • Submodules
  • mocca.peak.check module
    • check_peak()
    • check_peak_purity()
    • check_peak_saturation()
  • mocca.peak.correct module
    • correct_offset()
  • mocca.peak.database module
    • PeakDatabase
      • PeakDatabase.increment_unknown_counter()
      • PeakDatabase.insert_peak()
      • PeakDatabase.update_unknown_counter()
  • mocca.peak.expand module
    • expand_peak()
  • mocca.peak.integrate module
    • integrate_peak()
  • mocca.peak.match module
    • get_filtered_similarity_dicts()
    • get_relative_distance()
    • get_similarity_dicts()
    • get_spectrum_correl_coef()
    • match_peak()
    • update_matches()
  • mocca.peak.models module
    • BasePeak
      • BasePeak.left
      • BasePeak.maximum
      • BasePeak.offset
      • BasePeak.right
    • CheckedPeak
      • CheckedPeak.pure
      • CheckedPeak.saturation
    • CorrectedPeak
      • CorrectedPeak.istd
    • IntegratedPeak
      • IntegratedPeak.integral
    • IstdPeak
      • IstdPeak.compound_id
      • IstdPeak.concentration
      • IstdPeak.dataset
      • IstdPeak.integral
      • IstdPeak.left
      • IstdPeak.maximum
      • IstdPeak.offset
      • IstdPeak.right
    • PickedPeak
      • PickedPeak.dataset
      • PickedPeak.idx
    • PreprocessedPeak
      • PreprocessedPeak.matches
    • ProcessedPeak
      • ProcessedPeak.compound_id
      • ProcessedPeak.concentration
      • ProcessedPeak.dataset
      • ProcessedPeak.idx
      • ProcessedPeak.integral
      • ProcessedPeak.is_compound
      • ProcessedPeak.istd
      • ProcessedPeak.left
      • ProcessedPeak.maximum
      • ProcessedPeak.offset
      • ProcessedPeak.pure
      • ProcessedPeak.right
      • ProcessedPeak.saturation
  • mocca.peak.process module
    • process_peak()
  • mocca.peak.purity_funcs module
    • get_agilent_thresholds()
    • get_correls()
    • get_max_loc()
    • get_noise_variance()
    • get_pca_explained_variance()
    • get_purity_value_agilent()
    • get_trimmed_peak_data()
    • predict_purity_unimodal()
  • mocca.peak.quantify module
    • quantify_peak()
  • mocca.peak.resolve_impure module
    • create_parafac_peak()
    • create_pure_peak()
    • get_parafac_data_shift()
  • mocca.peak.utils module
    • average_peak_spectrum()
    • get_peak_data()
    • get_retention_times()
    • is_unimodal()
  • Module contents
• mocca.report namespace
  • Submodules
  • mocca.report.bad_chromatograms module
  • mocca.report.calibration_library module
  • mocca.report.chromatograms module
  • mocca.report.compound_library module
  • mocca.report.compound_tracking module
  • mocca.report.deconvolution module
  • mocca.report.gradient module
  • mocca.report.hplc_input module
  • mocca.report.main module
  • mocca.report.peak_library module
  • mocca.report.utils module
    • settings_to_df()
• mocca.user_interaction namespace
  • Submodules
  • mocca.user_interaction.campaign module
    • HplcDadCampaign
      • HplcDadCampaign.add_hplc_input()
      • HplcDadCampaign.load_campaign()
      • HplcDadCampaign.process_all_hplc_input()
      • HplcDadCampaign.process_new_hplc_input()
      • HplcDadCampaign.save_campaign()
  • mocca.user_interaction.settings module
    • Settings
      • Settings.absorbance_threshold
      • Settings.detector_limit
      • Settings.hplc_system_tag
      • Settings.peaks_high_pass
      • Settings.peaks_low_pass
      • Settings.relative_distance_thresh
      • Settings.spectrum_correl_thresh
      • Settings.wl_high_pass
      • Settings.wl_low_pass
  • mocca.user_interaction.suggest_calibration module
    • suggest_initialization_runs()
  • mocca.user_interaction.user_objects module
    • Compound
      • Compound.conc
      • Compound.is_istd
      • Compound.is_solvent
      • Compound.key
    • CustomData
      • CustomData.data
      • CustomData.time
      • CustomData.wavelength
    • Gradient
      • Gradient.dataset
      • Gradient.path
    • HplcInput
      • HplcInput.compound
      • HplcInput.custom_data
      • HplcInput.gradient
      • HplcInput.istd
      • HplcInput.path
      • HplcInput.processed
    • InternalStandard
      • InternalStandard.conc
      • InternalStandard.key
• mocca.visualization package
  • Submodules
  • mocca.visualization.basic_plots module
    • plot_1D_data()
    • plot_1D_layer()
    • plot_1D_scatter()
    • plot_1D_scatter_layer()
  • mocca.visualization.calibration_plots module
    • plot_calibration_curves()
  • mocca.visualization.parafac_plots module
    • plot_aligned_tensor()
    • plot_impure_peak_spectra()
    • plot_normalized_integrals()
    • plot_objective_func()
    • plot_retention()
    • plot_uvvis_specs()
  • mocca.visualization.results_plot module
    • plot_chrom_with_peaks()
  • mocca.visualization.utils module
    • round_to_n()
  • Module contents

Module contents