MedSamples Class Reference

MedSamples represent a collection of samples per different id
The data is conatined in a vector of MedIdSamples. More...

#include <MedSamples.h>

Inheritance diagram for MedSamples:

Public Member Functions
	MedSamples ()
	Constructor. init time_unit according to default.
void	clear ()
	Clear data and init time_unit according to default.
int	insert_preds (MedFeatures &featuresData)
	Extract predictions from MedFeatures and insert to corresponding samples Samples in MedFeatures are assumed to be of the same size and order as in MedSamples.
int	copy_attributes (const vector< MedSample > &samples)
	Copy attributes from MedSample vector.
void	get_ids (vector< int > &ids) const
	Get all patient ids.
void	append (MedSamples &newSamples)
	Append new MedIdSamples at the end of current ones.
int	read_from_bin_file (const string &file_name)
	Read from bin file.
int	write_to_bin_file (const string &file_name)
	Write to bin file.
int	read_from_file (const string &file_name, bool sort_rows=true)
	Read from text file.
int	write_to_file (const string &fname, int pred_precision=-1, bool print_attributes=true)
	Write to text file in new format.
void	write_to_file (ofstream &of, int pred_precision, bool print_attributes, bool print_header)
void	get_preds (vector< float > &preds) const
	Extract a single vector of concatanated predictions.
void	get_preds_channel (vector< float > &preds, int channel)
void	get_y (vector< float > &y) const
	Extract a vector of all outcomes.
void	get_categs (vector< float > &categs) const
	Get a list of all categories (different values) appearing in the outcome.
void	get_attr_values (const string &attr_name, vector< float > &values) const
	get a vector corresponding to given attr (name should include attr_)
void	export_to_sample_vec (vector< MedSample > &vec_samples) const
	Get all MedSamples as a single vector.
void	import_from_sample_vec (const vector< MedSample > &vec_samples, bool allow_split_inconsistency=false)
	Set MedSamples from a single vector.
void	sort_by_id_date ()
	Sort by id and then date.
void	normalize ()
	Make sure that : (1) every pid has one idSample at most and (2) everything is sorted.
bool	same_as (MedSamples &other, int mode)
	Comparison function : mode 0 requires equal id/time, mode 1 requires equal outcome info, mode 2 also compares split and prediction.
int	nSamples () const
	Return number of samples.
int	nSplits ()
	Return number of splits, also check mismatches between idSample and internal MedSamples and set idSamples.split if missing.
int	get_predictions_size (int &nPreds)
	Get predictions vector size. Return -1 if not-consistent.
int	get_all_attributes (vector< string > &attributes, vector< string > &str_attributes) const
	Get all attributes. Return -1 if not-consistent.
void	dilute (float prob)
	given a probability dilution prob, dilute current samples
void	binary_dilute (float p0, float p1)
	will dilute 0 labeled samples (traditionally controls) with p0, and all the rest with p1
void	subtract (MedSamples &_dont_include)
	removing all ids that appear in _dont_include from the current samples
void	split_train_test (MedSamples &train, MedSamples &test, float p_test)
	gets p_test and splits by id , p_test of the ids into test, and the rest into train
void	split_by_split (MedSamples &in_split, MedSamples &off_split, int split)
	gets a split number and splits samples to lists in/off the split
void	add_splits_from_file (string f_splits)
	adding splits to the samples given in an external file
void	init_all_jrecs ()
	initializing all jrecs to contain pid and time
void	flatten (vector< MedSample > &flat) const
void	insertRec (int pid, int time, float outcome, int outcomeTime)
	API's for online insertions : main use case is a single time point for prediction per pid.
void	insertRec (int pid, int time, float outcome, int outcomeTime, float pred)
void	insertRec (int pid, int time)
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	time_unit = MedTime::Date
	The time unit in which the samples are given. Default: Date.
vector< MedIdSamples >	idSamples
	The vector of MedIdSamples.
int	raw_format = 0

Detailed Description

MedSamples represent a collection of samples per different id
The data is conatined in a vector of MedIdSamples.

Member Function Documentation

copy_attributes()

int MedSamples::copy_attributes

(

const vector< MedSample > &

samples

)

Copy attributes from MedSample vector.

This function is mainly used to
Extract post processors results from MedFeatures and insert to corresponding samples
Samples in MedFeatures are assumed to be of the same size and order as in MedSamples

Returns

-1 if samples and features do not match in length, 0 upon success

insert_preds()

int MedSamples::insert_preds

(

MedFeatures &

featuresData

)

Extract predictions from MedFeatures and insert to corresponding samples
Samples in MedFeatures are assumed to be of the same size and order as in MedSamples.

Returns

-1 if samples and features do not match in length, 0 upon success

read_from_bin_file()

int MedSamples::read_from_bin_file ( const string &  file_name )

inline

Read from bin file.

Returns

-1 upon failure to open file, 0 upon success

read_from_file()

int MedSamples::read_from_file	(	const string &	file_name,
		bool	sort_rows = true
	)

Read from text file.

If a line starting with EVENT_FIELDS (followed by tabe-delimeted field names : id,date,outcome,outcome_date,split,pred) appears before the data lines, it is used to determine fields positions, otherwise - old or new formats are used.

Returns

-1 upon failure to open file, 0 upon success

same_as()

bool MedSamples::same_as	(	MedSamples &	other,
		int	mode
	)

Comparison function : mode 0 requires equal id/time, mode 1 requires equal outcome info, mode 2 also compares split and prediction.

Returns

true if equal , false otherwise

write_to_bin_file()

int MedSamples::write_to_bin_file ( const string &  file_name )

inline

Write to bin file.

Returns

-1 upon failure to open file, 0 upon success

write_to_file()

int MedSamples::write_to_file	(	const string &	fname,
		int	pred_precision = -1,
		bool	print_attributes = true
	)

Write to text file in new format.

Returns

-1 upon failure to open file, 0 upon success

---

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

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