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Medial Code Documentation
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RepProcessor is the parent class for processing a MedRepository or PidDynamicRec
Basic functionalities:
learn : learn the processoring parameters from a given list of ids and a rpository
apply : process a dynamic PidDynamicRec
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More...
#include "InfraMed/InfraMed/InfraMed.h"#include "InfraMed/InfraMed/MedPidRepository.h"#include "MedProcessTools/MedProcessTools/MedSamples.h"#include "MedProcessTools/MedProcessTools/MedProcessUtils.h"#include <SerializableObject/SerializableObject/SerializableObject.h>#include "MedProcessTools/MedProcessTools/MedValueCleaner.h"#include <MedMat/MedMat/MedMat.h>#include <omp.h>Go to the source code of this file.
Data Structures | |
| class | RepProcessor |
| class | RepMultiProcessor |
| RepMultiProcessor is a repository processor which contains a vector of simpler processors that can be learned/applied in parallel. More... | |
| class | remove_stats |
| class | RepBasicOutlierCleaner |
| A simple cleaner considering each value of a certain signal separatley. More... | |
| class | confRecord |
| Parameters for configured outliers cleaner. More... | |
| class | RepConfiguredOutlierCleaner |
| RepConfiguredOutlierCleaner is a simple cleaner considering each value of a certain signal separatley, but this time use configuration file that holds for each signal the logical values, statistically confirmed values and distribution for relearning statistical values. More... | |
| class | RepRuleBasedOutlierCleaner |
| A cleaner that is based on rules that describe relations of signal values to each other. More... | |
| class | RepNbrsOutlierCleaner |
| RepNbrsOutlierCleaner is cleaner that looks at the neighbourhood of a certain signal value. More... | |
| class | RepSimValHandler |
| class | RepPanelCompleter |
| A Repository panel completer for a complete panel of signals that are dependent and given on same time. More... | |
| class | SimpleCalculator |
| RepCalcSimpleSignals is a rep processor containing several calculators to calculate new signals. More... | |
| class | EmptyCalculator |
| Dummy top create empty virtual signal. More... | |
| class | RatioCalculator |
| Calcs ratio between 2 inputs signals. More... | |
| class | KfreCalculator |
| KFRE calculator based on Age, Gender and eGFR (in that order) More... | |
| class | eGFRCalculator |
| eGFR calculator based on Creatinine, Gender and Age. More... | |
| class | logCalculator |
| does log operation More... | |
| class | SumCalculator |
| does linear sum with factors on vector of input signals, has b0 as constant res := b0 + sum_sigma(i=1..N){ factor[i] * input[i]} More... | |
| class | RangeCalculator |
| A simple Range check that return in_range_val if within range and returns out_range_val if outside range. More... | |
| class | MultiplyCalculator |
| A multiply operation with power on both arguments. More... | |
| class | SetCalculator |
| A is in set operation which return binary output res := in_range_val if is in set otherwise out_range_val. More... | |
| class | ExistsCalculator |
| A is in as exists operation which return binary output res := in_range_val if signal exists otherwise out_range_val. More... | |
| class | ConstantValueCalculator |
| class | RepCalcSimpleSignals |
| A simple class for calculating virtual signals. More... | |
| class | RepCombineSignals |
| RepCreateReigsty creates registries (e.g. More... | |
| class | RepSplitSignal |
| split signal based on set of values. More... | |
| class | RepAggregationPeriod |
| creates a signal of time ranges in which the input signal (usually medication) was active ranges are combined based on the period parameter the signal value is not transfered to the output signal More... | |
| class | RepBasicRangeCleaner |
| class | RepSignalRate |
| Normalize Signal Values by time - divide by time to calculate rate. More... | |
| class | RepAggregateSignal |
| An Aggregator for signal in sliding time window. More... | |
| struct | category_time_interval |
| struct | category_event_state |
| struct | combination_state |
| class | RepCreateBitSignal |
| class | RepCheckReq |
| RepCheckReq does not actually process the repository but rather check each sample for compliance with some requirment, and adjust the sample's corresponding attribute. More... | |
| class | RepHistoryLimit |
| class | RepNumericNoiser |
| class | RepReoderChannels |
Enumerations | |
| enum | RepProcessorTypes { REP_PROCESS_MULTI , REP_PROCESS_BASIC_OUTLIER_CLEANER , REP_PROCESS_NBRS_OUTLIER_CLEANER , REP_PROCESS_CONFIGURED_OUTLIER_CLEANER , REP_PROCESS_RULEBASED_OUTLIER_CLEANER , REP_PROCESS_CALC_SIGNALS , REP_PROCESS_COMPLETE , REP_PROCESS_CHECK_REQ , REP_PROCESS_SIM_VAL , REP_PROCESS_SIGNAL_RATE , REP_PROCESS_COMBINE , REP_PROCESS_SPLIT , REP_PROCESS_AGGREGATION_PERIOD , REP_PROCESS_BASIC_RANGE_CLEANER , REP_PROCESS_AGGREGATE , REP_PROCESS_HISTORY_LIMIT , REP_PROCESS_CREATE_REGISTRY , REP_PROCESS_CREATE_BIT_SIGNAL , REP_PROCESS_CATEGORY_DESCENDERS , REP_PROCESS_REODER_CHANNELS , REP_PROCESS_FILTER_BY_CHANNELS , REP_PROCESS_NUMERIC_NOISER , REP_PROCESS_FILTER_BY_DIAG , REP_PROCESS_LAST } |
| Define types of repository processors. More... | |
| enum | SimValHandleTypes { SIM_VAL_FIRST_VAL , SIM_VAL_LAST_VAL , SIM_VAL_MEAN , SIM_VAL_REM , SIM_VAL_REM_DIFF , SIM_VAL_MIN , SIM_VAL_MAX , MULT_VAL_LAST } |
| SimValHandler handles multiple values at the same time. | |
| enum | PanelCompleterTypes { REP_CMPLT_RED_LINE_PANEL , REP_CMPLT_WHITE_LINE_PANEL , REP_CMPLT_PLATELETS_PANEL , REP_CMPLT_LIPIDS_PANEL , REP_CMPLT_EGFR_PANEL , REP_CMPLT_BMI_PANEL , REP_CMPLT_GCS , REP_CMPLT_LAST } |
| RepPanelCompleter fills-in calculatable signal values. More... | |
| enum | RedPanelSignals { RED_PNL_MCV , RED_PNL_HCT , RED_PNL_RBC , RED_PNL_MCH , RED_PNL_MCHC , RED_PNL_HGB , RED_PNL_LAST } |
| enum | WhitePanelSignals { WHITE_PNL_WBC , WHITE_PNL_EOS_N , WHITE_PNL_EOS_P , WHITE_PNL_NEU_N , WHITE_PNL_NEU_P , WHITE_PNL_LYM_N , WHITE_PNL_LYM_P , WHITE_PNL_MON_N , WHITE_PNL_MON_P , WHITE_PNL_BAS_N , WHITE_PNL_BAS_P , WHITE_PNL_LAST } |
| enum | PltsPanelSignals { PLT_PNL_PLTS , PLT_PNL_PLT_HCT , PLT_PNL_MPV , PLT_PNL_LAST } |
| enum | LipidsPanelSignals { LIPIDS_PNL_CHOL , LIPIDS_PNL_LDL , LIPIDS_PNL_HDL , LIPIDS_PNL_HDL_OVER_CHOL , LIPIDS_PNL_CHOL_OVER_HDL , LIPIDS_PNL_HDL_OVER_LDL , LIPIDS_PNL_LDL_OVER_HDL , LIPIDS_PNL_NON_HDL_CHOL , LIPIDS_PNL_HDL_OVER_NON_HDL , LIPIDS_PNL_TRGS , LIPIDS_PNL_VLDL , LIPIDS_PNL_LAST } |
| enum | eGFRPanelSignals { EGFR_PNL_CRT , EGFR_PNL_CKD_EPI , EGFR_PNL_MDRD , EGFR_PNL_LAST } |
| enum | BMIPanelSignals { BMI_PNL_BMI , BMI_PNL_WGT , BMI_PNL_HGT , BMI_PNL_HGT_SQR , BMI_PNL_LAST } |
| enum | GCSPanelSignals { GCS_PNL , GCS_PNL_EYE , GCS_PNL_MOTOR , GCS_PNL_VERBAL , GCS_PNL_LAST } |
| enum | range_op_type { all = 0 , first = 1 , last = 2 } |
| A filter on signal events using other range signal with time periods. | |
Functions | |
| RepProcessorTypes | rep_processor_name_to_type (const string &procesor_name) |
| get RepProcessorTypes from name | |
| void | learnDistributionBorders (float &borderHi, float &borderLo, vector< float > filteredValues) |
| int | get_values (MedRepository &rep, MedSamples &samples, int signalId, int time_channel, int val_channel, float range_min, float range_max, vector< float > &values, vector< RepProcessor * > &prev_cleaners) |
| Get values of a signal from a set of samples applying a set of preceeding cleaners. | |
| int | get_values (MedRepository &rep, MedSamples &samples, int signalId, int time_channel, int val_channel, float range_min, float range_max, vector< float > &values) |
| Get values of a signal from a set of samples. | |
RepProcessor is the parent class for processing a MedRepository or PidDynamicRec
Basic functionalities:
learn : learn the processoring parameters from a given list of ids and a rpository
apply : process a dynamic PidDynamicRec
.
| enum PanelCompleterTypes |
RepPanelCompleter fills-in calculatable signal values.
Enriching existing signals
The available completions are currently -
Signals above are the default values. They can be changed, keeping the order, or set to NULL, in which case the completion is not-performed
| enum RepProcessorTypes |
Define types of repository processors.
Define types of repository processors
| Enumerator | |
|---|---|
| REP_PROCESS_MULTI | "multi_processor" or "multi" to activate RepMultiProcessor |
| REP_PROCESS_BASIC_OUTLIER_CLEANER | "basic_outlier_cleaner" or "basic_cln" to activate RepBasicOutlierCleaner |
| REP_PROCESS_NBRS_OUTLIER_CLEANER | "nbrs_outlier_cleaner" or "nbrs_cln" to activate RepNbrsOutlierCleaner |
| REP_PROCESS_CONFIGURED_OUTLIER_CLEANER | "configured_outlier_cleaner" or "conf_cln" to activate RepConfiguredOutlierCleaner |
| REP_PROCESS_RULEBASED_OUTLIER_CLEANER | "rulebased_outlier_cleaner" or "rule_cln" to activate RepRuleBasedOutlierCleaner |
| REP_PROCESS_CALC_SIGNALS | "calc_signals" or "calculator" to activate RepCalcSimpleSignals |
| REP_PROCESS_COMPLETE | "complete" to activate RepPanelCompleter |
| REP_PROCESS_CHECK_REQ | "req" or "requirements" check compliance with minimal requirement to activate RepCheckReq |
| REP_PROCESS_SIM_VAL | "sim_val" or "sim_val_handler" handle multiple simultanous values to activate RepSimValHandler |
| REP_PROCESS_SIGNAL_RATE | "signal_rate" combine complition for Drug rate based on Drug amount to activate RepSignalRate |
| REP_PROCESS_COMBINE | "combine" flatten signals to 1 signal by dates. if conflict chooses based on order given. to activate RepCombineSignals |
| REP_PROCESS_SPLIT | "split" split signal to two signals based on set of values - usefull for example to give diffrent rule\factor to diffrent drug units. to actiate RepSplitSignal |
| REP_PROCESS_AGGREGATION_PERIOD | "aggregation_period" - creates RepAggregationPeriod |
| REP_PROCESS_BASIC_RANGE_CLEANER | "basic_range_cleaner" or "range_cln" to activate RepBasicRangeCleaner |
| REP_PROCESS_AGGREGATE | "aggregate" - aggregate signal in sliding time window to calc some aggregation function. to activate RepAggregateSignal |
| REP_PROCESS_HISTORY_LIMIT | "history_limit" chomps the history for a signal to be at a certain given time window relative to the prediction point. creates RepHistoryLimit |
| REP_PROCESS_CREATE_REGISTRY | "create_registry" creates a registry signal (TimeRange to values). creates RepCreateRegistry |
| REP_PROCESS_CREATE_BIT_SIGNAL | "bit_signal" creates a state of categories (typically drugs) encoded in bits. creates RepCreateBitSignal |
| REP_PROCESS_CATEGORY_DESCENDERS | "category_descenders" creates all descenders values for each category value. Creates RepCategoryDescenders |
| REP_PROCESS_REODER_CHANNELS | "reoder_channels" reorder signal channels. Creates RepReoderChannels |
| REP_PROCESS_FILTER_BY_CHANNELS | "filter_channels" reorder signal channels. Creates RepFilterByChannel |
| REP_PROCESS_NUMERIC_NOISER | "numeric_noiser" adds gaussian noise to value and uniform noise to time for numeric signal. Creates RepNumericNoiser |
| REP_PROCESS_FILTER_BY_DIAG | "filter_by_diag". Creates RepClearSignalByDiag |
1.9.8