Complete Function Reference
This generated reference documents Fyron public functions, classes, methods, signatures, parameters, defaults, and return notes directly from the source tree. It complements the curated module pages, which explain workflows, interpretation, and common pitfalls.
The generator is AST-based, so optional extras are not imported during documentation builds.
Use this page for exact call signatures. Use the linked module guides for input shapes, required columns, saved artifacts, failure modes, and clinical interpretation.
Reference Groups
- FHIR Reference: 78 top-level public APIs.
- DICOM And Imaging Reference: 29 top-level public APIs.
- BOA Reference: 17 top-level public APIs.
- Cohort And Analysis Reference: 72 top-level public APIs.
- Survival Reference: 17 top-level public APIs.
- ML, Validation, And Explainability Reference: 94 top-level public APIs.
- Core, Publication, And Utility Reference: 78 top-level public APIs.
Public API Index
FHIR Reference
fyron.fhir.auth.Authfyron.fhir.auth.Auth.token_envfyron.fhir.auth.Auth.closefyron.fhir.auth.TokenAuthfyron.fhir.auth.TokenAuth.is_refresh_requiredfyron.fhir.auth.now_utcfyron.fhir.builder.attachmentfyron.fhir.builder.build_bundlefyron.fhir.builder.build_conditionfyron.fhir.builder.build_diagnostic_reportfyron.fhir.builder.build_document_referencefyron.fhir.builder.build_encounterfyron.fhir.builder.build_endpointfyron.fhir.builder.build_imaging_measurement_bundlefyron.fhir.builder.build_imaging_study_referencefyron.fhir.builder.build_llm_extraction_bundlefyron.fhir.builder.build_medication_statementfyron.fhir.builder.build_model_devicefyron.fhir.builder.build_observationfyron.fhir.builder.build_observation_componentfyron.fhir.builder.build_procedurefyron.fhir.builder.build_provenancefyron.fhir.builder.build_service_requestfyron.fhir.builder.build_specimenfyron.fhir.builder.codeable_conceptfyron.fhir.builder.codingfyron.fhir.builder.dicom_codefyron.fhir.builder.icd10fyron.fhir.builder.identifierfyron.fhir.builder.loincfyron.fhir.builder.quantityfyron.fhir.builder.read_fhir_jsonfyron.fhir.builder.referencefyron.fhir.builder.snomedfyron.fhir.builder.summarize_fhir_bundlefyron.fhir.builder.summarize_fhir_resourcefyron.fhir.builder.ucum_quantityfyron.fhir.builder.validate_fhir_bundlefyron.fhir.builder.validate_fhir_referencesfyron.fhir.builder.validate_fhir_resourcefyron.fhir.builder.write_fhir_jsonfyron.fhir.mapping.build_bundle_from_dataframefyron.fhir.mapping.build_conditions_from_dataframefyron.fhir.mapping.build_document_references_from_dataframefyron.fhir.mapping.build_imaging_measurements_from_dataframefyron.fhir.mapping.build_observations_from_dataframefyron.fhir.mapping.extract_coding_summaryfyron.fhir.mapping.fhir_validation_reportfyron.fhir.mapping.read_fhir_mappingfyron.fhir.mapping.validate_coding_systemsfyron.fhir.mapping.validate_fhir_mappingfyron.fhir.mapping.validate_fhir_mapping_resultfyron.fhir.mapping.validate_fhir_payloadfyron.fhir.mapping.write_fhir_mappingfyron.fhir.path_presets.get_fhir_path_presetfyron.fhir.rest.FHIRRestClientfyron.fhir.rest.FHIRRestClient.closefyron.fhir.rest.FHIRRestClient.fetch_bundlesfyron.fhir.rest.FHIRRestClient.fetch_bundles_parallelfyron.fhir.rest.FHIRRestClient.fetch_bundles_partitionedfyron.fhir.rest.FHIRRestClient.bundles_to_dataframefyron.fhir.rest.FHIRRestClient.query_to_dataframe_partitionedfyron.fhir.rest.FHIRRestClient.query_to_dataframefyron.fhir.rest.FHIRRestClient.query_from_dataframefyron.fhir.rest.FHIRRestClient.query_dffyron.fhir.rest.FHIRRestClient.search_dffyron.fhir.rest.FHIRRestClient.query_df_partitionedfyron.fhir.rest.FHIRRestClient.search_df_partitionedfyron.fhir.rest.FHIRRestClient.query_df_fromfyron.fhir.rest.FHIRRestClient.search_df_fromfyron.fhir.rest.FHIRRestClient.bundles_to_dffyron.fhir.rest.FHIRRestClient.create_resourcefyron.fhir.rest.FHIRRestClient.update_resourcefyron.fhir.rest.FHIRRestClient.submit_bundlefyron.fhir.rest.FHIRWriteResultfyron.fhir.rest.QueryJobfyron.fhir.rest.RepeatedParamfyron.fhir.rest.ResponseCachefyron.fhir.rest.ResponseCache.getfyron.fhir.rest.ResponseCache.setfyron.fhir.rest.build_partition_paramsfyron.fhir.rest.flatten_datafyron.fhir.rest.parse_fhir_pathfyron.fhir.sql.FHIRSQLClientfyron.fhir.sql.FHIRSQLClient.closefyron.fhir.sql.FHIRSQLClient.queryfyron.fhir.sql.FHIRSQLClient.query_to_dataframefyron.fhir.sql.FHIRSQLClient.query_dffyron.fhir.sql.FHIRSQLClient.query_df_streamfyron.fhir.sql.FHIRSQLClient.query_df_parallelfyron.fhir.sql.FHIRSQLClient.query_from_dataframefyron.fhir.sql.FHIRSQLClient.query_df_fromfyron.fhir.sql.SQLConfigfyron.fhir.types.FHIRObjfyron.fhir.types.FHIRObj.to_jsonfyron.fhir.types.FHIRObj.to_dictfyron.fhir.utils.extract_conditionfyron.fhir.utils.extract_diagnostic_reportfyron.fhir.utils.extract_encounterfyron.fhir.utils.extract_imaging_studyfyron.fhir.utils.extract_observationfyron.fhir.utils.extract_patientfyron.fhir.utils.extract_procedurefyron.fhir.utils.process_condition_bundlefyron.fhir.utils.process_diagnostic_report_bundlefyron.fhir.utils.process_encounter_bundlefyron.fhir.utils.process_imaging_study_bundlefyron.fhir.utils.process_observation_bundlefyron.fhir.utils.process_patient_bundlefyron.fhir.utils.process_procedure_bundlefyron.fhir.utils.safe_get
DICOM And Imaging Reference
fyron.dicom.client.DICOMDownloaderfyron.dicom.client.DICOMDownloader.closefyron.dicom.client.DICOMDownloader.download_idfyron.dicom.client.DICOMDownloader.download_seriesfyron.dicom.client.DICOMDownloader.download_studyfyron.dicom.client.DICOMDownloader.download_from_dataframefyron.dicom.client.DICOMDownloader.download_from_dffyron.dicom.client.DicomResultfyron.dicom.seg.label_map_to_segmentsfyron.dicom.seg.load_source_dicom_seriesfyron.dicom.seg.read_segment_descriptionsfyron.dicom.seg.summarize_dicom_segfyron.dicom.seg.validate_dicom_segfyron.dicom.seg.validate_segment_descriptionsfyron.dicom.seg.write_dicom_segfyron.dicom.synthetic.write_synthetic_dicom_seriesfyron.dicom.synthetic.write_synthetic_niftifyron.imaging.dicom_io.get_dicom_series_idsfyron.imaging.dicom_io.read_dicom_headerfyron.imaging.dicom_io.read_dicom_seriesfyron.imaging.nifti_io.read_niftifyron.imaging.nifti_io.write_niftifyron.imaging.normalize.normalize_ctfyron.imaging.normalize.normalize_mrfyron.imaging.qc.check_image_mask_alignmentfyron.imaging.qc.summarize_dicom_series_geometryfyron.imaging.qc.summarize_intensity_rangefyron.imaging.qc.summarize_mask_volumefyron.imaging.qc.summarize_nifti_geometryfyron.imaging.segmentation.dice_scorefyron.imaging.segmentation.hausdorff_distancefyron.imaging.segmentation.label_overlap_tablefyron.imaging.segmentation.segmentation_metric_tablefyron.imaging.segmentation.surface_dicefyron.imaging.segmentation.volume_difference
BOA Reference
fyron.boa_extraction.experimental_aortic_calcification.extract_experimental_aortic_calcification_featuresfyron.boa_extraction.experimental_aortic_calcification.extract_experimental_cohort_aortic_calcification_featuresfyron.boa_extraction.features.discover_boa_casesfyron.boa_extraction.features.extract_boa_featuresfyron.boa_extraction.features.extract_body_region_featuresfyron.boa_extraction.features.extract_cohort_body_region_featuresfyron.boa_extraction.features.extract_cohort_total_featuresfyron.boa_extraction.features.extract_total_segmentation_featuresfyron.boa_extraction.features.read_json_filefyron.boa_radiomics.features.discover_boa_radiomics_casesfyron.boa_radiomics.features.extract_boa_radiomics_featuresfyron.boa_radiomics.features.extract_case_radiomics_featuresfyron.visualization.boa.create_boa_segmentation_collagefyron.visualization.curate_previews.PreviewSourcefyron.visualization.curate_previews.discover_preview_sourcesfyron.visualization.curate_previews.prepare_curate_image_previewsfyron.visualization.volume_difference.plot_volume_difference_heatmap
Cohort And Analysis Reference
fyron.cohort.tables.build_survival_columnsfyron.cohort.tables.build_time_to_event_endpointfyron.cohort.tables.cohort_profilefyron.cohort.tables.join_cohort_tablesfyron.cohort.tables.validate_cohort_tablefyron.dataframe.add_code_indicatorsfyron.dataframe.add_date_differencefyron.dataframe.add_icd10_disease_groupsfyron.dataframe.add_ops_categoriesfyron.dataframe.add_time_window_flagfyron.dataframe.age_at_datefyron.dataframe.classify_icd10fyron.dataframe.classify_icd10_stringfyron.dataframe.classify_opsfyron.dataframe.classify_ops_stringfyron.dataframe.date_differencefyron.dataframe.explode_code_columnfyron.dataframe.icd10_group_prevalencefyron.dataframe.normalize_codefyron.dataframe.ops_category_prevalencefyron.dataframe.split_code_stringfyron.descriptive.analysis.compare_descriptive_groupsfyron.descriptive.analysis.create_table_onefyron.descriptive.analysis.describe_categoricalfyron.descriptive.analysis.describe_numericfyron.descriptive.analysis.summarize_endpointfyron.phenotyping.rules.combine_phenotypesfyron.phenotyping.rules.define_code_phenotypefyron.phenotyping.rules.define_lab_threshold_phenotypefyron.phenotyping.rules.define_medication_exposurefyron.phenotyping.rules.phenotype_summaryfyron.preprocessing.encoding.apply_categorical_encoderfyron.preprocessing.encoding.encode_categoricalfyron.preprocessing.encoding.fit_categorical_encoderfyron.preprocessing.encoding.summarize_encoding_planfyron.preprocessing.imputation.apply_imputerfyron.preprocessing.imputation.fit_imputerfyron.preprocessing.imputation.impute_dataframefyron.preprocessing.imputation.summarize_imputation_planfyron.preprocessing.qc.compare_train_test_balancefyron.preprocessing.qc.detect_potential_leakagefyron.preprocessing.qc.feature_matrix_reportfyron.preprocessing.qc.find_duplicate_idsfyron.preprocessing.qc.summarize_categorical_levelsfyron.preprocessing.qc.summarize_missingnessfyron.statistics.bootstrap.BootstrapResultfyron.statistics.bootstrap.BootstrapResult.to_dictfyron.statistics.bootstrap.bootstrap_binary_classification_metricsfyron.statistics.bootstrap.bootstrap_metricfyron.statistics.bootstrap.bootstrap_summaryfyron.statistics.comparison.bootstrap_auc_differencefyron.statistics.comparison.mcnemar_testfyron.statistics.correction.adjust_p_valuesfyron.statistics.correction.p_value_correction_tablefyron.statistics.effects.cliffs_deltafyron.statistics.effects.cohens_dfyron.statistics.effects.cramers_vfyron.statistics.effects.odds_ratio_cifyron.statistics.effects.risk_ratio_cifyron.statistics.effects.standardized_mean_differencefyron.statistics.qc.correlation_pvalue_tablefyron.statistics.qc.missingness_by_group_tablefyron.statistics.qc.normality_tablefyron.statistics.qc.outlier_tablefyron.statistics.regression.fit_linear_regression_tablefyron.statistics.regression.fit_logistic_regression_tablefyron.statistics.regression.vif_tablefyron.statistics.tests.StatisticalTestResultfyron.statistics.tests.StatisticalTestResult.to_dictfyron.statistics.tests.categorical_testfyron.statistics.tests.compare_multiple_groupsfyron.statistics.tests.compare_two_groupsfyron.statistics.tests.correlation_testfyron.statistics.tests.normality_test
Survival Reference
fyron.survival.boosting.train_gradient_survival_boostingfyron.survival.cox.fit_multivariate_coxfyron.survival.cox.fit_univariate_coxfyron.survival.groups.create_survival_groupsfyron.survival.groups.default_tau_from_observed_timesfyron.survival.kaplan_meier.KaplanMeierPlotResultfyron.survival.kaplan_meier.plot_kaplan_meierfyron.survival.outputs.cox_forest_tablefyron.survival.outputs.survival_prediction_tablefyron.survival.ph_diagnostics.check_ph_assumptionsfyron.survival.ph_diagnostics.plot_schoenfeld_residualsfyron.survival.ph_diagnostics.schoenfeld_residuals_tablefyron.survival.ph_diagnostics.schoenfeld_test_tablefyron.survival.rmst.calculate_rmstfyron.survival.rmst.compare_rmstfyron.survival.weibull_aft.fit_weibull_aftfyron.survival.weibull_aft.plot_aft_survival_curves
ML, Validation, And Explainability Reference
fyron.explainability.inspection.explain_model_summaryfyron.explainability.inspection.explain_patient_predictionfyron.explainability.inspection.partial_dependence_tablefyron.explainability.inspection.permutation_importance_tablefyron.explainability.inspection.shap_summary_tablefyron.explainability.inspection.shap_values_tablefyron.feature_selection.selection.boruta_feature_selectionfyron.feature_selection.selection.combine_feature_selection_resultsfyron.feature_selection.selection.correlation_filterfyron.feature_selection.selection.model_importance_selectionfyron.feature_selection.selection.permutation_importance_selectionfyron.feature_selection.selection.stability_selectionfyron.feature_selection.selection.univariate_feature_screeningfyron.feature_selection.selection.variance_filterfyron.flow.tracking.FlowStepfyron.flow.tracking.FlowTrackerfyron.flow.tracking.FlowTracker.add_stepfyron.flow.tracking.FlowTracker.to_dataframefyron.flow.tracking.FlowTracker.to_markdownfyron.flow.tracking.FlowTracker.to_text_flowchartfyron.flow.tracking.FlowTracker.printfyron.flow.tracking.track_filterfyron.ml.boruta_selection.run_boruta_feature_selectionfyron.ml.class_weights.compute_class_weightsfyron.ml.class_weights.compute_scale_pos_weightfyron.ml.class_weights.sample_weights_for_sklearnfyron.ml.cv.cross_validate_modelfyron.ml.defaults.get_default_param_gridfyron.ml.evaluation.apply_probability_calibratorfyron.ml.evaluation.evaluate_external_validationfyron.ml.evaluation.evaluate_locked_thresholdfyron.ml.evaluation.fit_probability_calibratorfyron.ml.evaluation.model_card_summaryfyron.ml.evaluation.nested_cross_validate_modelfyron.ml.importance.get_feature_importancefyron.ml.importance.plot_feature_importancefyron.ml.metrics.calculate_classification_metricsfyron.ml.persistence.load_estimatorfyron.ml.persistence.save_estimatorfyron.ml.pipeline.run_classification_pipelinefyron.ml.plots.add_stat_annotationsfyron.ml.plots.format_p_value_annotationfyron.ml.plots.plot_alluvial_flowfyron.ml.plots.plot_binned_marker_heatmapfyron.ml.plots.plot_bland_altmanfyron.ml.plots.plot_calibration_curvefyron.ml.plots.plot_cohort_flowfyron.ml.plots.plot_confusion_matrixfyron.ml.plots.plot_correlation_heatmapfyron.ml.plots.plot_cross_validated_rocfyron.ml.plots.plot_decision_curvefyron.ml.plots.plot_densityfyron.ml.plots.plot_dice_by_labelfyron.ml.plots.plot_directional_ratio_rowsfyron.ml.plots.plot_external_validation_metricsfyron.ml.plots.plot_feature_importancefyron.ml.plots.plot_feature_selection_summaryfyron.ml.plots.plot_forest_estimatesfyron.ml.plots.plot_grouped_bar_with_significancefyron.ml.plots.plot_grouped_boxplotfyron.ml.plots.plot_grouped_correlation_heatmapsfyron.ml.plots.plot_hazard_ratiosfyron.ml.plots.plot_histogramfyron.ml.plots.plot_kaplan_meierfyron.ml.plots.plot_likert_scalefyron.ml.plots.plot_metric_barsfyron.ml.plots.plot_missingness_barfyron.ml.plots.plot_patterned_barfyron.ml.plots.plot_precision_recall_curvefyron.ml.plots.plot_raincloudfyron.ml.plots.plot_risk_score_distributionfyron.ml.plots.plot_roc_curvefyron.ml.plots.plot_segmentation_overlay_gridfyron.ml.plots.plot_signed_feature_weightsfyron.ml.plots.plot_significance_barsfyron.ml.plots.plot_stability_selectionfyron.ml.plots.plot_survival_calibrationfyron.ml.plots.plot_swarmplotfyron.ml.plots.plot_swimmerfyron.ml.plots.plot_table_one_summaryfyron.ml.plots.plot_time_dependent_aucfyron.ml.plots.plot_volcanofyron.ml.plots.plot_wafflefyron.ml.plots.plot_waterfallfyron.ml.plots.stat_test_pairsfyron.ml.search.grid_search_modelfyron.ml.splitting.train_test_split_datafyron.ml.training.train_random_forestfyron.ml.training.train_xgboostfyron.validation.classification.bootstrap_classification_metricsfyron.validation.classification.calibration_summaryfyron.validation.classification.decision_curve_tablefyron.validation.classification.find_best_thresholdfyron.validation.classification.subgroup_metric_tablefyron.validation.survival.bootstrap_concordance_indexfyron.validation.survival.brier_score_at_timefyron.validation.survival.external_survival_validationfyron.validation.survival.survival_calibration_at_timefyron.validation.survival.time_dependent_auc_table
Core, Publication, And Utility Reference
fyron.audit.manifest.analysis_run_manifestfyron.audit.manifest.create_provenance_manifestfyron.audit.manifest.hash_filefyron.audit.manifest.write_manifestfyron.banner.get_bannerfyron.banner.get_run_footerfyron.banner.get_run_headerfyron.banner.print_bannerfyron.console.configure_loggingfyron.console.console_messagefyron.console.errorfyron.console.format_countfyron.console.format_durationfyron.console.format_pathfyron.console.get_loggerfyron.console.get_timerfyron.console.infofyron.console.successfyron.console.supports_colorfyron.console.warningfyron.core.env.load_envfyron.core.io.DataIOfyron.core.io.DataIO.read_csvfyron.core.io.DataIO.write_csvfyron.core.io.DataIO.read_excelfyron.core.io.DataIO.write_excelfyron.core.io.DataIO.read_jsonfyron.core.io.DataIO.write_jsonfyron.core.io.DataIO.read_tablefyron.core.io.DataIO.write_tablefyron.core.io.DataIO.summarize_tablefyron.core.io.DataIO.describe_filefyron.core.io.TeableClientfyron.core.io.TeableClient.list_recordsfyron.core.io.TeableClient.list_spacesfyron.core.io.TeableClient.list_basesfyron.core.io.TeableClient.create_basefyron.core.io.TeableClient.get_or_create_basefyron.core.io.TeableClient.list_tablesfyron.core.io.TeableClient.create_tablefyron.core.io.TeableClient.get_or_create_tablefyron.core.io.TeableClient.read_tablefyron.core.io.TeableClient.create_recordsfyron.core.io.TeableClient.delete_recordsfyron.core.io.TeableClient.clear_tablefyron.core.io.TeableClient.write_dataframefyron.core.io.TeableClient.overwrite_tablefyron.core.io.TeableClient.read_cohortfyron.core.io.TeableClient.write_research_cohortfyron.core.io.TeableClient.create_research_cohort_tablefyron.core.io.TeableClient.summarize_teable_tablefyron.core.io.TeableConfigfyron.core.io.describe_filefyron.core.io.ensure_parent_dirfyron.core.io.read_csvfyron.core.io.read_excelfyron.core.io.read_jsonfyron.core.io.read_tablefyron.core.io.summarize_tablefyron.core.io.write_csvfyron.core.io.write_excelfyron.core.io.write_jsonfyron.core.io.write_tablefyron.core.s3.S3Storagefyron.core.s3.S3Storage.keyfyron.core.s3.S3Storage.existsfyron.core.s3.S3Storage.listfyron.core.s3.S3Storage.read_bytesfyron.core.s3.S3Storage.write_bytesfyron.core.s3.S3Storage.read_jsonfyron.core.s3.S3Storage.write_jsonfyron.core.s3.S3Storage.read_tablefyron.core.s3.S3Storage.write_tablefyron.core.s3.S3Storage.download_filefyron.core.s3.S3Storage.upload_filefyron.core.s3.parse_s3_urifyron.core.s3.read_s3_tablefyron.core.s3.write_s3_tablefyron.curate.build_compose_commandfyron.curate.default_app_dirfyron.curate.start_curatorfyron.datasets.make_boa_like_folderfyron.datasets.make_classification_cohortfyron.datasets.make_clinical_cohortfyron.datasets.make_dicom_seriesfyron.datasets.make_nifti_pairfyron.datasets.make_survival_cohortfyron.datasets.preparation.prepare_nnunetv2_datasetfyron.datasets.preparation.prepare_yolo_classification_datasetfyron.datasets.preparation.prepare_yolo_detection_datasetfyron.datasets.preparation.validate_nnunetv2_datasetfyron.datasets.preparation.validate_yolo_datasetfyron.datasets.preparation.write_dataset_manifestfyron.documents.client.DocumentDownloaderfyron.documents.client.DocumentDownloader.closefyron.documents.client.DocumentDownloader.download_idfyron.documents.client.DocumentDownloader.download_urlfyron.documents.client.DocumentDownloader.download_urlsfyron.documents.client.DocumentDownloader.download_from_dataframefyron.documents.client.DocumentDownloader.download_from_dffyron.documents.client.DocumentResultfyron.get_bannerfyron.get_run_footerfyron.get_run_headerfyron.llm.agent.LLMAgentfyron.llm.agent.LLMAgent.promptfyron.llm.agent.LLMAgent.chatfyron.llm.agent.LLMAgent.run_on_dataframefyron.llm.agent.LLMAgent.run_on_documentsfyron.llm.agent.LLMAgent.prompt_documentsfyron.llm.agent.LLMAgent.prompt_dataframefyron.llm.agent.LLMAgent.prompt_dffyron.llm.agent.LLMAgent.run_prompt_on_dataframefyron.llm.agent.LLMAgent.describe_python_filefyron.llm.agent.LLMAgent.run_on_directoryfyron.llm.agent.LLMAgent.prompt_directoryfyron.llm.agent.LLMConfigfyron.plotting_palettes.PaletteSpecfyron.plotting_palettes.get_colormapfyron.plotting_palettes.get_palettefyron.plotting_palettes.list_palettesfyron.plotting_palettes.palette_grayscale_contrastfyron.plotting_palettes.palette_luminance_tablefyron.plotting_palettes.preview_palettefyron.plotting_palettes.resolve_colormapfyron.plotting_palettes.resolve_palettefyron.plotting_palettes.set_plot_stylefyron.print_bannerfyron.reporting.tables.cohort_flow_tablefyron.reporting.tables.compare_models_tablefyron.reporting.tables.dataframe_to_markdownfyron.reporting.tables.format_estimate_cifyron.reporting.tables.metrics_tablefyron.reporting.tables.summarize_baseline_table