MedSample Class Reference

MedSample represents a signle sample: id + time (date)
Additional (optinal) entries: outcome, outcome_date, split and prediction
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#include <MedSamples.h>

Inheritance diagram for MedSample:

Public Member Functions
	MedSample ()
	Constructor.
	MedSample (int _id, int _time, int _outcome, int _outcomeTime)
	~MedSample ()
	Destructor.
void	print (const string prefix)
	printing the sample (with a prefix)
void	print ()
	printing the sample
int	parse_from_string (string &s, int time_unit)
	Get sample from tab-delimited string, in old or new format (<split> and <prediction> optional, <predictions> can be several numbers (tab delimited)) old format: EVENT <id> <time> <outcome> <outcomeLen(dummy here)> <outcomeTime> <split> <predictions> new format: SAMPLE <id> <time> <outcome> <outcomeTime> <split> <predictions>
int	parse_from_string (string &s, const map< string, int > &pos, const vector< int > &pred_pos, const map< string, int > &attr_pos, const map< string, int > &str_attr_pos, int time_unit, int raw_format, const string &delimeter="\t")
	Get sample from tab-delimited string, where pos indicate the position of each field (fields are id,date,outcome,outcome_date,split,pred or pred_,attr_NAME) if pos is empty, check old and new formats.
int	parse_from_string (const vector< string > &fields, const map< string, int > &pos, const vector< int > &pred_pos, const map< string, int > &attr_pos, const map< string, int > &str_attr_pos, int time_unit, int raw_format, const string &delimeter)
void	write_to_string (string &s, int time_unit, bool write_attrib=true, const string &delimeter="\t", int pred_precision=-1) const
	Write to string in new format.
int	get_all_attributes (vector< string > &attributes, vector< string > &str_attributes) const
	Get sample attributes.
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 *	new_polymorphic (string derived_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)
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)
virtual int	init (map< string, string > &map)
	Virtual to init object from parsed fields.
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	id = -1
	Patient id.
int	split = -1
	Cross-validation split. -1 if not given. Proper use is to set the same split for all samples of a given id (MedIdSamples), but this is not enforced.
int	time = 0
	Time (Date)
float	outcome = 0
	Outcome.
int	outcomeTime = 0
	Outcome time (date)
vector< float >	prediction
	Prediction(s) - empty if non given.
map< string, float >	attributes
	Attribute(s) - empty if non given.
map< string, string >	str_attributes
	Attribute(s) - empty if non given.
json	jrec
	a json record that can be built along side the sample to contain any information in a nice json format

Detailed Description

MedSample represents a signle sample: id + time (date)
Additional (optinal) entries: outcome, outcome_date, split and prediction

Member Function Documentation

parse_from_string() [1/2]

int MedSample::parse_from_string	(	string &	s,
		const map< string, int > &	pos,
		const vector< int > &	pred_pos,
		const map< string, int > &	attr_pos,
		const map< string, int > &	str_attr_pos,
		int	time_unit,
		int	raw_format,
		const string &	delimeter = "\t"
	)

Get sample from tab-delimited string, where pos indicate the position of each field (fields are id,date,outcome,outcome_date,split,pred or pred_,attr_NAME) if pos is empty, check old and new formats.

Returns

0 upon success, -1 upon failure to parse

parse_from_string() [2/2]

int MedSample::parse_from_string	(	string &	s,
		int	time_unit
	)

Get sample from tab-delimited string, in old or new format (<split> and <prediction> optional, <predictions> can be several numbers (tab delimited))
old format: EVENT <id> <time> <outcome> <outcomeLen(dummy here)> <outcomeTime> <split> <predictions>
new format: SAMPLE <id> <time> <outcome> <outcomeTime> <split> <predictions>

Returns

0 upon success, -1 if string does not fit any of the formats

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

• Internal/MedProcessTools/MedProcessTools/MedSamples.h
• Internal/MedProcessTools/MedProcessTools/MedSamples.cpp