MedRegistryCodesList Class Reference

A Class which creates registry based on readcode lists. More...

#include <MedRegistry.h>

Inheritance diagram for MedRegistryCodesList:

Public Member Functions
void	init (MedRepository &rep, int start_dur, int end_durr, int max_repo, const vector< RegistrySignal * > signal_conditions, const string &skip_pid_file="", const unordered_map< int, int > *pid_to_censor_dates=NULL)
	The init function in code API.
int	init (map< string, string > &map)
	the initializtion params.
void	clear_create_variables ()
	clears the signal_filters
void	get_registry_records (int pid, int bdate, vector< UniversalSigVec_mem > &usv, vector< MedRegistryRecord > &results)
Public Member Functions inherited from MedRegistry
void	write_text_file (const string &file_path) const
	Writes the file to text file in tab delimeted format: PID, Start_Date, End_Date, min_allowed_date, max_allowed_date, Age, RegistryValue.
void	read_text_file (const string &file_path)
	Reads the file in text format in tab delimeted.
void	create_registry (MedPidRepository &dataManager, medial::repository::fix_method method=medial::repository::fix_method::none, vector< RepProcessor * > *rep_processors=NULL)
	Creates vector of registry using already initialized MedPidRepository with signals in parallel manner for each patient.
void	get_registry_creation_codes (vector< string > &signal_codes) const
	returns the signal codes used to create the registry - to load from rep
void	get_registry_use_codes (vector< string > &signal_codes) const
	returns the signal codes used to create the registry - to use in create_registry command as input
void	get_pids (vector< int > &pids) const
	returns all patients ids from registry - unique patient ids
void	merge_records ()
	Merges registry record with same registry values (and continues in time)
void *	new_polymorphic (string dname)
	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)
	MedRegistry ()
	Default Ctor.
virtual bool	get_pid_records (PidRec &rec, int bDateCode, const vector< int > &used_sigs, vector< MedRegistryRecord > &results)
void	set_rep_for_init (MedRepository &rep)
	Sets Repository object to initialize all registry object, if not given will try to use repository path to read and initialize repository.
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
int	start_buffer_duration
	the duration buffer form start
int	end_buffer_duration
	the duration buffer from last date
int	max_repo_date
	the maximal date for the repository
bool	allow_prediciton_in_case
	If True will allow to give prediciton after\in case time range.
bool	seperate_cases
	If true will seperate each "case" time zone.
vector< RegistrySignal * >	signal_filters
	the signal filters
ADD_SERIALIZATION_FUNCS(time_unit, registry_records, start_buffer_duration, end_buffer_duration, max_repo_date, allow_prediciton_in_case, seperate_cases) private unordered_map< int, int >	pid_to_max_allowed
	< black list of patients mask
bool	init_called
	a flag to mark that init was called
Data Fields inherited from MedRegistry
vector< MedRegistryRecord >	registry_records
	the registry records vector
int	time_unit
	The time unit.

Additional Inherited Members
Static Public Member Functions inherited from MedRegistry
static MedRegistry *	make_registry (const string &registry_type, const string &init_str="")
	creates registry type and initialize it if init_str is not empty Use "binary" for MedRegistryCodesList and "categories" for MedRegistryCategories.
static MedRegistry *	make_registry (const string &registry_type, MedRepository &rep, const string &init_str="")
	creates registry type and initialize it if init_str is not empty Use "binary" for MedRegistryCodesList and "categories" for MedRegistryCategories.
static MedRegistry *	create_registry_full (const string &registry_type, const string &init_str, const string &repository_path, MedModel &model_with_rep_processor, medial::repository::fix_method method=medial::repository::fix_method::none)
	Creates vector of registry records - handles everything for you in parallel manner for each patient - uses create_registry.
Protected Attributes inherited from MedRegistry
vector< string >	signalCodes_names
	the signals codes by name
bool	need_bdate
	If true Bdate is also used in registry creation.
medial::repository::fix_method	resolve_conlicts = medial::repository::fix_method::none
	resolve conflicts in registry method
MedRepository *	rep_for_init = NULL
	repository pointer to init dicts

Detailed Description

A Class which creates registry based on readcode lists.

Important: must be initialized by init_lists first

Member Function Documentation

clear_create_variables()

void MedRegistryCodesList::clear_create_variables ( )

virtual

clears the signal_filters

Reimplemented from MedRegistry.

get_registry_records()

void MedRegistryCodesList::get_registry_records ( int  pid, int  bdate, vector< UniversalSigVec_mem > &  usv, vector< MedRegistryRecord > &  results  )

virtual

Reimplemented from MedRegistry.

init() [1/2]

int MedRegistryCodesList::init ( map< string, string > &  map )

virtual

the initializtion params.

it has also "config_signals_rules", "pid_to_censor_dates", "rep" file paths.

Parameters

rep	the repository path
pid_to_censor_dates	file path to pid censors. each line is pid TAB censor_date
config_signals_rules	file path to RegistrySignal rules. parsing is done with MedRegistryCodesList::parse_registry_rules The parsed fields from init command. if (it->first == "rep") rep_path = it->second; else if (it->first == "start_buffer_duration") start_buffer_duration = stoi(it->second); else if (it->first == "end_buffer_duration") end_buffer_duration = stoi(it->second); else if (it->first == "max_repo_date") max_repo_date = stoi(it->second); else if (it->first == "allow_prediciton_in_case") allow_prediciton_in_case = stoi(it->second) > 0; else if (it->first == "seperate_cases") seperate_cases = stoi(it->second) > 0; else if (it->first == "pid_to_censor_dates") { ifstream fr(it->second); if (!fr.good()) MTHROW_AND_ERR("Error in MedRegistryCodesList::init - unable to open %s for reading.", it->second.c_str()); string line; while (getline(fr, line)) { boost::trim(line); if (line.empty() || line.at(0) == '#') continue; vector<string> tokens; boost::split(tokens, line, boost::is_any_of("\t")); if (tokens.size() != 2) MTHROW_AND_ERR("Error in MedRegistryCodesList::init - in parsing pid_to_censor_dates file" " - %s excpeting TAB for line:\n%s\n", it->second.c_str(), line.c_str()); if (pid_to_max_allowed.find(stoi(tokens[0])) == pid_to_max_allowed.end() || pid_to_max_allowed[stoi(tokens[0])] > stoi(tokens[1])) pid_to_max_allowed[stoi(tokens[0])] = stoi(tokens[1]); } fr.close(); } else if (it->first == "config_signals_rules") registry_file_path = it->second; else MTHROW_AND_ERR("Error in MedRegistryCodesList::init - Unsupported init param \"%s\"\n", it->first.c_str());

[MedRegistryCodesList::init]

[MedRegistryCodesList::init]

Reimplemented from SerializableObject.

init() [2/2]

void MedRegistryCodesList::init	(	MedRepository &	rep,
		int	start_dur,
		int	end_durr,
		int	max_repo,
		const vector< RegistrySignal * >	signal_conditions,
		const string &	skip_pid_file = "",
		const unordered_map< int, int > *	pid_to_censor_dates = NULL
	)

The init function in code API.

Parameters

rep	initialized repository with MedDictionry for initialization
start_dur	a minimal time for patient to enter registry from first signal after birth
end_durr	a minimal time for patient to leave registry from last signal
max_repo	the last date in the repositry - censor after this date
signal_conditions	vector of rules to calc when we turn patient into case
skip_pid_file	a file with blacklist of patient ids to skip
pid_to_censor_dates	an object to map between each patient and censor date for him

Field Documentation

pid_to_max_allowed

ADD_SERIALIZATION_FUNCS (time_unit, registry_records, start_buffer_duration, end_buffer_duration, max_repo_date, allow_prediciton_in_case, seperate_cases) private unordered_map<int, int> MedRegistryCodesList::pid_to_max_allowed

< black list of patients mask

max date allowed to each pid constrain

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

• Internal/MedUtils/MedUtils/MedRegistry.h
• Internal/MedUtils/MedUtils/MedRegistry.cpp