A Repository panel completer for a complete panel of signals that are dependent and given on same time. More...

#include <RepProcess.h>

Inheritance diagram for RepPanelCompleter:

Public Member Functions
int	init (map< string, string > &mapper)

void	init_defaults ()
	initialize to default values : Should be implemented for inheriting classes that have parameters

int	update_signal_names (string panel, string &names)

int	update_panels (string &panels)

void	set_signal_ids (MedSignals &sigs)
	set signal-ids : Should be implemented for inheriting classes that have signalId

void	fit_for_repository (MedPidRepository &rep)
	make changes to RepProcessor according to available signals in Repository

void	init_tables (MedDictionarySections &dict, MedSignals &sigs)
	Init required tables : Should be implemented for inheriting classes that have such tables.

void	init_lists ()
	Fill req- and aff-signals vectors.

void	read_metadata ()

int	_learn (MedPidRepository &rep, MedSamples &samples, vector< RepProcessor * > &prev_processors)
	In this class there's never learning - we init tables and return 0 immediately.

int	_apply (PidDynamicRec &rec, vector< int > &time_points, vector< vector< float > > &attributes_mat)
	apply processing on a single PidDynamicRec at a set of time-points : Should be implemented for all inheriting classes

int	apply_red_line_completer (PidDynamicRec &rec, vector< int > &time_points)

int	apply_white_line_completer (PidDynamicRec &rec, vector< int > &time_points)

int	apply_platelets_completer (PidDynamicRec &rec, vector< int > &time_points)

int	apply_lipids_completer (PidDynamicRec &rec, vector< int > &time_points)

int	apply_eGFR_completer (PidDynamicRec &rec, vector< int > &time_points)

int	apply_BMI_completer (PidDynamicRec &rec, vector< int > &time_points)

int	apply_GCS_completer (PidDynamicRec &rec, vector< int > &time_points)

int	perpare_for_age_and_gender (PidDynamicRec &rec, int &age, int &bYear, int &gender)

float	completer_round (float value, float orig_res, float final_res, float factor)

float	set_resolution (float value, float res)

void	get_panels (vector< UniversalSigVec > &usvs, vector< int > &panel_times, vector< vector< float > > &panels, int time_limit, int panel_size)

int	triplet_complete (vector< float > &panel, float factor, int x_idx, int y_idx, int z_idx, vector< float > &orig_res, vector< float > &final_res, vector< float > &conv, vector< int > &changed)

int	sum_complete (vector< float > &panel, int sum, vector< int > &summands, vector< float > &orig_res, vector< float > &final_res, vector< float > &conv, vector< int > &changed)

int	reciprocal_complete (vector< float > &panel, float factor, int x_idx, int y_idx, vector< float > &orig_res, vector< float > &final_res, vector< float > &conv, vector< int > &changed)

int	egfr_complete (vector< float > &panel, float age, int gender, vector< float > &orig_res, vector< float > &final_res, vector< float > &conv, vector< int > &changed)

int	update_signals (PidDynamicRec &rec, int iver, vector< vector< float > > &panels, vector< int > &panel_times, vector< int > &sigs_ids, vector< int > &changed)

void	print ()
	optional printing of processor

Public Member Functions inherited from RepProcessor
virtual void	clear ()

virtual int	init (void *params)
	initialize from a params object : Should be implemented for inheriting classes that have parameters

virtual void	set_signal (const string &_signalName)
	set signal-name : Should be implemented for inheriting classes that have signalName

virtual void	get_required_signal_names (unordered_set< string > &signalNames)
	Append required signal names to set : parent function just uses req_signals.

virtual void	get_required_signal_names (unordered_set< string > &signalNames, unordered_set< string > preReqSignals)
	Append required signal names to set only if processor is actually required to produce any of preReqSignals : parent function just uses req_signals.

virtual void	set_required_signal_ids (MedDictionarySections &dict)
	Fill req_signal_ids : parent function just fills from req_signals.

virtual void	add_virtual_signals (map< string, int > &_virtual_signals, map< string, string > &_virtual_signals_generic) const
	rep processors CREATING virtual signals need to implement this: adding their signals to the pile

virtual void	get_required_signal_ids (unordered_set< int > &signalIds)
	Append required signal names to set : parent function just uses req_signals.

virtual void	get_required_signal_ids (unordered_set< int > &signalIds, unordered_set< int > preReqSignals)
	Append required signal names to set only if processor is actually required to produce any of preReqSignals : parent function just uses req_signals.

virtual void	set_affected_signal_ids (MedDictionarySections &dict)
	Fill aff_signal_ids : parent function just fills from aff_signals.

bool	is_signal_affected (int signalId)
	Check if a signal is affected by processor </summray> Returns true if affected, false if not

bool	is_signal_affected (string &signalName)

virtual void	register_virtual_section_name_id (MedDictionarySections &dict)
	Register section id to section name of new virtual signals.

virtual bool	filter (unordered_set< string > &reqSignals)
	Check if processor (and 'sub'-processors within) should be applied according to set of required signals </summray> Returns true if processor is not required and can be filtered, false otherwise

virtual void	init_attributes ()
	Init attributes information : Should be implemented for inheriting classes that have attributes.

virtual int	_conditional_learn (MedPidRepository &rep, MedSamples &samples, vector< RepProcessor * > &prev_processors, unordered_set< int > &neededSignalIds)
	learn processing model on a subset of samples only if required. Apply set of preceeding processors on DynamicPidRec before learning :

int	learn (MedPidRepository &rep, MedSamples &samples, vector< RepProcessor * > &prev_processors)
	learn processing model on a subset of ids. Apply set of preceeding processors on DynamicPidRec before learning

int	learn (MedPidRepository &rep)
	learn on all pids in repository, using fake samples - works only for repProcessors that ignore sample dates

int	learn (MedPidRepository &rep, MedSamples &samples)
	learn on subset of samples without preceesing processors

virtual int	conditional_learn (MedPidRepository &rep, MedSamples &samples, vector< RepProcessor * > &prev_processors, unordered_set< int > &neededSignalIds)
	learn processing model on a subset of samples only if required. Apply set of preceeding processors on DynamicPidRec before learning :

int	conditional_learn (MedPidRepository &rep, MedSamples &samples, unordered_set< int > &neededSignalIds)
	learn processing model on a subset of ids only if required without preceesing processors

virtual int	_conditional_apply (PidDynamicRec &rec, vector< int > &time_points, unordered_set< int > &neededSignalIds, vector< vector< float > > &attributes_vals)
	apply processing on a single PidDynamicRec at a set of time-points only if required : May be implemented for inheriting classes

virtual int	_apply_simple (PidDynamicRec &rec, vector< int > &time_points)

int	apply (PidDynamicRec &rec, vector< int > &time_points, vector< vector< float > > &attributes_vals)
	apply processing on a single PidDynamicRec at a set of time-points

int	conditional_apply (PidDynamicRec &rec, vector< int > &time_points, unordered_set< int > &neededSignalIds, vector< vector< float > > &attributes_vals)
	apply processing on a single PidDynamicRec at a set of time-points only if required : if any of the signals in neededSignalIds is actually affected by processor

int	apply (PidDynamicRec &rec, MedIdSamples &samples)
	apply processing on a single PidDynamicRec at a set of time-points given by samples

int	conditional_apply (PidDynamicRec &rec, MedIdSamples &samples, unordered_set< int > &neededSignalIds)
	apply processing on a single PidDynamicRec at a set of time-points given by samples only if required

int	conditional_apply_without_attributes (PidDynamicRec &rec, const MedIdSamples &samples, unordered_set< int > &neededSignalIds)
	apply processing on a single PidDynamicRec at a set of time-points given by samples only if required, not affecting attributes

virtual void	dprint (const string &pref, int rp_flag)
	used for debug prints, each inheriting class can overload this one to get a more precise debug print.

virtual void	make_summary ()

virtual void	get_required_signal_categories (unordered_map< string, vector< string > > &signal_categories_in_use) const
	returns for each used signal it's used categories

void *	new_polymorphic (string derived_class_name)
	for polymorphic classes that want to be able to serialize/deserialize a pointer * to the derived class given its type one needs to implement this function to return a new to the derived class given its type (as in my_type)

size_t	get_processor_size ()
	get size of processor + processor_type

size_t	processor_serialize (unsigned char *blob)
	seialize processor + processor_type

Public Member Functions inherited from SerializableObject
virtual int	version () const
	Relevant for serializations.

virtual string	my_class_name () const
	For better handling of serializations it is highly recommended that each SerializableObject inheriting class will implement the next method.

virtual void	serialized_fields_name (vector< string > &field_names) const
	The names of the serialized fields.

virtual void	pre_serialization ()

virtual void	post_deserialization ()

virtual size_t	get_size ()
	Gets bytes sizes for serializations.

virtual size_t	serialize (unsigned char *blob)
	Serialiazing object to blob memory. return number ob bytes wrote to memory.

virtual size_t	deserialize (unsigned char *blob)
	Deserialiazing blob to object. returns number of bytes read.

size_t	serialize_vec (vector< unsigned char > &blob)

size_t	deserialize_vec (vector< unsigned char > &blob)

virtual size_t	serialize (vector< unsigned char > &blob)

virtual size_t	deserialize (vector< unsigned char > &blob)

virtual int	read_from_file (const string &fname)
	read and deserialize model

virtual int	write_to_file (const string &fname)
	serialize model and write to file

virtual int	read_from_file_unsafe (const string &fname)
	read and deserialize model without checking version number - unsafe read

int	init_from_string (string init_string)
	Init from string.

int	init_params_from_file (string init_file)

int	init_param_from_file (string file_str, string &param)

int	update_from_string (const string &init_string)

virtual int	update (map< string, string > &map)
	Virtual to update object from parsed fields.

virtual string	object_json () const

Data Fields
vector< vector< string > >	panel_signal_names

vector< vector< int > >	panel_signal_ids

int	bdateId

int	genderId

string	genderSignalName

float	missing_val = MED_MAT_MISSING_VALUE

SimValHandleTypes	sim_val_handler = SIM_VAL_LAST_VAL

string	metadata_file

vector< vector< float > >	original_sig_res

vector< vector< float > >	final_sig_res

vector< vector< float > >	sig_conversion_factors

Data Fields inherited from RepProcessor
RepProcessorTypes	processor_type = REP_PROCESS_LAST
	type of repository processor

unordered_set< string >	req_signals
	names of signals required for processsing

unordered_set< int >	req_signal_ids
	ids of signals required for processing

unordered_set< string >	aff_signals
	names of signals affected by processing

unordered_set< int >	aff_signal_ids
	ids of signals affected by processing

bool	unconditional = false
	indicated that processor should ALWAYS be applied

vector< string >	attributes
	attributes generated by the processor (optional)

vector< pair< string, int > >	virtual_signals
	virtual signals are created only in rep processors but can be used by any rep processor that comes after or any feture generator as a regular signal.

vector< pair< string, string > >	virtual_signals_generic

Additional Inherited Members
Static Public Member Functions inherited from RepProcessor
static RepProcessor *	make_processor (string name)
	create a new repository processor from name

static RepProcessor *	make_processor (string type, string params)
	create a new repository processor from name and a parameters string

static RepProcessor *	make_processor (RepProcessorTypes type)
	create a new repository processor from type

static RepProcessor *	make_processor (RepProcessorTypes type, string params)
	create a new repository processor from type and a parameters string

static RepProcessor *	create_processor (string &params)
	create a new repository processor from parameters string which contains rp_type

Detailed Description

A Repository panel completer for a complete panel of signals that are dependent and given on same time.

TODO: add support for look in the past threshold

Member Function Documentation

◆ _apply()

int RepPanelCompleter::_apply	(	PidDynamicRec &	rec,
		vector< int > &	time_points,
		vector< vector< float > > &	attributes_mat
	)

virtual

apply processing on a single PidDynamicRec at a set of time-points : Should be implemented for all inheriting classes

Reimplemented from RepProcessor.

◆ _learn()

int RepPanelCompleter::_learn	(	MedPidRepository &	rep,
		MedSamples &	samples,
		vector< RepProcessor * > &	prev_processors
	)

inlinevirtual

In this class there's never learning - we init tables and return 0 immediately.

Reimplemented from RepProcessor.

◆ fit_for_repository()

void RepPanelCompleter::fit_for_repository ( MedPidRepository & rep )

virtual

make changes to RepProcessor according to available signals in Repository

Reimplemented from RepProcessor.

◆ init()

int RepPanelCompleter::init ( map< string, string > & mapper )

virtual

        if (panel2type.find(field) != panel2type.end()) {
            if (update_signal_names(field, entry.second) != 0) return -1;
        }
        else if (field == "missing") missing_val = stof(entry.second);
        else if (field == "config" || field == "metadata") metadata_file = entry.second;
        else if (field == "unconditional") unconditional = stoi(entry.second) > 0;
        else if (field == "sim_val" || field == "sim_val_handler") sim_val_handler = RepSimValHandler::get_sim_val_handle_type(entry.second);
        else if (field == "panels") {
            if (update_panels(entry.second) != 0) return -1;
        }

[RepPanelCompleter::init]

Reimplemented from RepProcessor.

◆ init_defaults()

void RepPanelCompleter::init_defaults ( )

virtual

initialize to default values : Should be implemented for inheriting classes that have parameters

Reimplemented from RepProcessor.

◆ init_tables()

void RepPanelCompleter::init_tables	(	MedDictionarySections &	dict,
		MedSignals &	sigs
	)

virtual

Init required tables : Should be implemented for inheriting classes that have such tables.

Reimplemented from RepProcessor.

◆ print()

void RepPanelCompleter::print ( )

virtual

optional printing of processor

Reimplemented from RepProcessor.

◆ set_signal_ids()

void RepPanelCompleter::set_signal_ids ( MedSignals & sigs )

virtual

set signal-ids : Should be implemented for inheriting classes that have signalId

Reimplemented from RepProcessor.

The documentation for this class was generated from the following files:

Internal/MedProcessTools/MedProcessTools/RepProcess.h
Internal/MedProcessTools/MedProcessTools/PanelCompleter.cpp

Public Member Functions

Data Fields

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ _apply()

◆ _learn()

◆ fit_for_repository()

◆ init()

◆ init_defaults()

◆ init_tables()

◆ print()

◆ set_signal_ids()