The PAFitBit class helps loads and stores accelerometer data used in the physical activity monitoring project. The project is aimed at reducing obesity and improving health in children. More...

Inheritance diagram for PAFitBit:

Public Member Functions
function	PAFitBit (in fullFilenameOrPath, in pStruct)
	Constructor for PAFitBit class. More...

function	getStudyID (in obj, in outputType)
	Returns studyID instance variable. More...

function	loadFileHeader (in obj, in fullFilename)
	Load CSV header values (start time, start date, and window period). More...

function	getHeaderAsString (in obj)
	Returns header values as a single, printable string. Results include. More...

function	loadFile (in obj, in fullfilename)
	Loads an accelerometer data file. More...

function	loadFitBitFile (in obj, in fullCountFilename)
	Loads an accelerometer "count" data file. More...

function	resampleCountData (in obj)
	Resamples previously loaded 'count' data to match sample rate of raw accelerometer data that has been loaded in a following step (see loadFile()). More...

function	extractFeature (in obj, in signalTagLine, in method)
	Extracts features from the identified signal. More...

function	saveToFile (in obj, in activityType, in saveFilename)
	Saves data to an ascii file. More...

function	subsindex (in obj, in indices, in structType)
	overloaded subsindex method returns structure of time series data at indices provided. More...

function	subsref (in obj, in s)

Public Member Functions inherited from PAData
function	PAData (in fullFilenameOrPath, in pStruct)
	Constructor for PAData class. More...

function	getCurWindowRange (in obj, in structType)
	Returns a structure of PAData's time series data. More...

function	getCurUncorrectedWindowRange (in obj, in structType)
	Returns the current windows range. More...

function	getSamplesPerWindow (in obj, in structType)
	Returns the number of sample units (samples, bins, frames) for the for the current window resolution (duration in seconds). More...

function	getWindowSamplerate (in obj, in structType)
	Returns the sampling rate for the current window display selection. More...

function	getSampleRate (in obj)
	Returns the samplerate of the x-axis accelerometer. More...

function	getUsageClassificationRules (in this)

function	setUsageClassificationRules (in this, in ruleStruct)
	Updates the usage state rules with an input struct. More...

function	getFrameRate (in obj)
	Returns the frame rate in units of frames/second. More...

function	getBinRate (in obj)
	Returns the aggregate bin rate in units of aggregate bins/second. More...

function	setCurWindow (in obj, in window)
	Set the current window for the instance variable accelObj (PAData) More...

function	getCurWindow (in obj)
	Returns the current window. More...

function	setAggregateDurationMinutes (in obj, in aggregateDurationMin)
	Set the aggregate duration (in minutes) instance variable. More...

function	getAggregateDurationInMinutes (in obj)
	Returns the current aggregate duration in minutes. More...

function	getBinCount (in obj)
	Returns the total number of aggregated bins the data can be divided into based on frame rate and the duration of the time series data. More...

function	getStudyID (in obj, in outputType)
	Returns studyID instance variable. More...

function	setFrameDurationMinutes (in obj, in frameDurationMin)
	Set the frame duration (in minutes) instance variable. More...

function	setFrameDurationHours (in obj, in frameDurationHours)
	Set the frame duration (hours) instance variable. More...

function	getFrameDuration (in obj)
	Returns the frame duration (in hours and minutes) More...

function	getFrameDurationInMinutes (in obj)

function	getFrameCount (in obj)
	Returns the total number of frames the data can be divided into evenly based on frame rate and the duration of the time series data. More...

function	durationSamples (in obj)
	Returns the number of samples contained in the time series data. More...

function	setWindowDurSec (in obj, in durSec)
	Set the window duration value in seconds. This is the displays window size (i.e. one window shown at a time), in seconds. More...

function	getVisible (in obj, in structType)
	Returns the visible instance variable. More...

function	getColor (in obj, in structType)
	Returns the color instance variable. More...

function	getScale (in obj, in structType)
	Returns the scale instance variable. More...

function	getOffset (in obj, in structType)
	Returns the offset instance variable. More...

function	getLabel (in obj, in structType)
	Returns the label instance variable. More...

function	getOffAccelType (in obj, in accelTypeStr)
	Retuns the accelType that is not set. This is useful in later removing unwanted accel fields. More...

function	getPropertyStruct (in obj, in propertyName, in structType)
	Returns the visible instance variable. More...

function	pruneStruct (in obj, in accelStruct)

function	setOffset (in obj, in fieldName, in newOffset)
	Sets the offset instance variable for a particular sub field. More...

function	setScale (in obj, in fieldName, in newScale)
	Sets the scale instance variable for a particular sub field. More...

function	setColor (in obj, in fieldName, in newColor)
	Sets the color instance variable for a particular sub field. More...

function	setVisible (in obj, in fieldName, in newVisibilityStr)
	Sets the visible instance variable for a particular sub field. More...

function	setProperty (in obj, in propertyName, in fieldName, in propertyValueStr)
	Sets the specified instance variable for a particular sub field. More...

function	getWindowCount (in obj)
	Returns the total number of windows the data can be divided into based on sampling rate, window resolution (i.e. duration), and the size of the time series data. More...

function	getStartStopDatenum (in obj)
	Returns the start and stop datenums for the study. More...

function	getDisplayMinMax (in obj)
	Returns the minimum and maximum amplitudes that can be displayed uner the current configuration. More...

function	getMinmax (in obj, in fieldType)
	Returns the minmax value(s) for the object's (obj) time series data Returns either a structure or 1x2 vector of [min, max] values for the field specified. More...

function	getFilename (in obj)
	Returns the filename, pathname, and full filename (pathname + filename) of the file that the accelerometer data was loaded from. More...

function	setFullFilename (in obj, in fullfilename)
	Sets the pathname and filename instance variables using the input full filename. More...

function	getFullFilename (in obj)
	Returns the full filename (pathname + filename) of the accelerometer data. More...

function	getWindowDurSec (in obj)
	Returns the private intance variable windowDurSec. More...

function	loadFileHeader (in obj, in fullFilename)
	Load CSV header values (start time, start date, and window period). More...

function	getHeaderAsString (in obj)
	Returns header values as a single, printable string. Results include. More...

function	loadFile (in obj, in fullfilename)
	Loads an accelerometer data file. More...

function	loadCountFile (in obj, in fullCountFilename)
	Loads an accelerometer "count" data file. More...

function	loadRawCSVFile (in obj, in fullRawCSVFilename)
	Loads an accelerometer raw data file. This function is intended to be called from loadFile() to ensure that loadCountFile is called in advance to guarantee that the auxialiary sensor measurements are loaded into the object (obj). The auxialiary measures (e.g. lux, steps) are upsampled to the sampling rate of the raw data (typically 40 Hz). More...

function	loadGT3XFile (in obj, in fullFilename)
	Loads an accelerometer's raw data from binary files stored in the path name given. More...

function	loadPathOfRawBinary (in obj, in pathWithRawBinaryFiles)
	Loads an accelerometer's raw data from binary files stored in the path name given. More...

function	resampleCountData (in obj)
	Resamples previously loaded 'count' data to match sample rate of raw accelerometer data that has been loaded in a following step (see loadFile()). More...

function	sample2window (in obj, in sample, in windowDurSec, in samplerate)
	Calculates, and returns, the window for the given sample index of a signal. More...

function	datenum2window (in obj, in datenumSample, in structType)
	Returns the display window for the given datenum. More...

function	window2datenum (in obj, in windowSample)
	Returns the starting datenum for the window given. More...

function	prefilter (in obj, in method)
	Prefilters accelerometer data. More...

function	getFrameableSampleCount (in obj)

function	extractFeature (in obj, in signalTagLine, in method)
	Extracts features from the identified signal. More...

function	calculatePSD (in obj, in signalTagLine)
	Calculates the PSD for the current frames and assigns the result to obj.psd.frames. Will also assign obj.frames_signalTagLine to the signalTagLine argument when provided, otherwise the current value for obj.frames_signalTagLine is assumed to be correct and specific for the source of the frame data. PSD bands are assigned to their named fields (e.g. psd_band_1) in the obj.features.(bandName) field. More...

function	getPSD (in obj)

function	getPSDBands (in obj, in numBands)

function	getPSDSettings (in obj)

function	getAlignedFeatureVecs (in obj, in featureFcn, in signalTagLine, in elapsedStartHour, in intervalDurationHours)
	Calculates a desired feature for a particular acceleration object's field value. and returns it as a matrix of elapsed time aligned vectors. More...

function	classifyUsageForAllAxes (in obj)
	Classifies the usage state for each axis using count data from each axis. More...

function	classifyUsageState (in obj, in countActivity)
	Categorizes the study's usage state. More...

function	describeActivity (in obj, in categoryStr)
	Describes an activity. More...

function	saveToFile (in obj, in activityType, in saveFilename)
	Saves data to an ascii file. More...

function	subsindex (in obj, in indices, in structType)
	overloaded subsindex method returns structure of time series data at indices provided. More...

function	subsref (in obj, in s)

function	getStruct (in obj, in choice, in structType)
	Returns a structure of PAData's time series fields and values, depending on the user's input selection. More...

function	getSaveParameters (in obj)
	Returns a structure of PAData's saveable parameters as a struct. More...

Static Public Member Functions
static function	getDefaultTagLineLabels ()
	returns a cell of tag lines and the associated label describing the tag line. More...

static function	getDefaultParameters ()
	Returns a structure of PAFitBit's default parameters as a struct. More...

static function	getStudyIDFromBasename (in baseName)
	Parses the input file's basename (i.e. sans folder and extension) for the study id. This will vary according from site to site as there is little standardization for file naming. More...

Static Public Member Functions inherited from PAData
static function	parseInfoTxt (in infoTxtFullFilename)
	Parses the information found in input file name and returns the result as a struct of field-value pairs. More...

static function	reprocessEventVector (in logicalVec, in min_duration_samples, in merge_distance_samples)
	Removes periods of activity that are too short and groups nearby activity groups together. More...

static function	movingSummer (in signal, in filterOrder)
	Moving summer finite impulse response filter. More...

static function	unrollEvents (in eventsStartStop, in vectorSize)
	Helper function to convert an Nx2 matrix of start stop events into a single logical vector with 1's located at the locations corresponding to the samples inclusively between eventStartStops row entries. More...

static function	getDefaultTagLineLabels ()
	returns a cell of tag lines and the associated label describing the tag line. More...

static function	getDefaultParameters ()
	Returns a structure of PAData's default parameters as a struct. More...

static function	subsStruct (in structIn, in indices)
	Returns structure whose values are taken from the struct and indices provided. More...

static function	mergedCell (in startDateNum, in stopDateNum, in dateNumDelta, in sampledDateVec, in tmpDataCell, in missingValue)
	Helper function for loading raw and count file formats to ensure proper ordering and I/O error handling. More...

static function	structEval (in operand, in ltStruct, in rtStruct, in optionalDestFieldOrValue)
	Evaluates the two structures, field for field, using the function name provided. More...

static function	structScalarEval (in operand, in ltStruct, in A, in optionalDestField)
	Evaluates the two structures, field for field, using the function name provided. More...

static function	appendStruct (in ltStruct, in rtStruct)
	Appends the fields of one to another. Values for fields of the same name are taken from the right struct (rtStruct) and built into the output struct. If the left struct does not have a matching field, then it will be created with the right structs value. More...

static function	mergeStruct (in ltStruct, in rtStruct)
	Merge the fields of one struct with another. Copies over matching field values. Similar to appendStruct, but now the second argument is itself a struct with similar organization as the first argument. More...

static function	overwriteEmptyStruct (in ltStruct, in rtStruct)
	Inserts the second argument into any empty fields of the first struct argument. More...

static function	struct2vec (in structure, in vector)
	flattens a structure to a single dimensional array (i.e. a vector) More...

static function	minmax (in dataStruct)
	Evaluates the range (min, max) of components found in the input struct argument and returns the range as struct values with matching fieldnames/organization as the input struct's highest level. More...

static function	updateStructWithStruct (in structToUpdate, in structToUpdateWith)

static function	getRecurseMinmax (in dataStruct)
	Recursive helper function for minmax() input struct argument and returns the range as struct values with matching fieldnames/organization as the input struct's highest level. More...

static function	getDummyStruct (in structType)
	Returns an empty struct with fields that mirror PAData's time series instance variables that contain. More...

static function	getDummyDisplayStruct (in structType)
	Returns a struct with subfields that hold the line properties for graphic display of the time series instance variables. More...

static function	getPrefilterMethods ()
	Returns a cell listing of available prefilter methods as strings. More...

static function	getExtractorDescriptions ()
	Returns a cell listing of available feature extraction methods as strings. More...

static function	getFeatureDescriptionStruct ()
	Returns a struct of feature extraction methods and string descriptions as the corresponding values. More...

static function	getFeatureDescriptionStructWithPSDBands ()

static function	getPSDFeatureDescriptionStruct ()

static function	getPSDExtractorDescriptions ()

static function	getStructTypes ()
	Returns a struct representing the internal architecture used by PAData to hold and process acceleration data. More...

static function	getStructNameFromDescription (in description)
	Returns the fieldname of PAData's struct types (see getStructTypes()) that matches the string argument. More...

static function	thresholdcrossings (in line_in, in threshold_line)
	Returns start and stop pairs of the sample points where where line_in is greater (i.e. crosses) than threshold_line threshold_line and line_in must be of the same length if threshold_line is not a scalar value. More...

static function	merge_nearby_events (in event_mat_in, in min_samples)
	Merges events, that are separated by less than some minimum number of samples, into a single event that stretches from the start of the first event and spans until the last event of each minimally separated event pairings. Events that are not minimally separated by another event are retained with the output. More...

static function	getStudyIDFromBasename (in baseName)
	Parses the input file's basename (i.e. sans folder and extension) for the study id. This will vary according from site to site as there is little standardization for file naming. More...

static function	getActivityTags ()

static function	getPSDBandNames ()

Additional Inherited Members
Public Attributes inherited from PAData
Constant Property	NUM_PSD_BANDS = 5

Property	accelType
	Type of acceleration stored; can be. More...

Property	accel
	Structure of count and raw accelerations structs (x,y,z). Fields are: More...

Property	usage
	Structure of usage states determined from the following axes counts: More...

Property	psd
	Structure of power spectral densities for count and raw accelerations structs (x,y,z). Fields are: More...

Property	inclinometer
	Structure of inclinometer values. Fields include: More...

Property	steps
	Steps - unknown? Maybe pedometer type reading? More...

Property	timeStamp
	Time of day (HH:MM:SS) of sample reading. More...

Property	lux
	Luminance levels. More...

Property	startTime
	Start Time. More...

Property	startDate
	Start Date. More...

Property	durationSec
	Durtion of the sampled data in seconds. More...

Property	dateTimeNum
	The numeric value for each date time sample provided by. More...

Property	startDatenums
	Numeric values for date time sample for the start of extracted features. More...

Property	stopDatenums
	Numeric values for date time sample for when the extracted features stop/end. More...

Property	lineproperty
	Struct of line handle properties corresponding to the fields of linehandle. These are derived from the input files loaded by the PAData class. More...

Property	label

Property	color

Property	offset

Property	scale

Property	visible

Property	yDelta

Property	studyID
	Identifier (string) for the file data that was loaded. More...

Detailed Description

The PAFitBit class helps loads and stores accelerometer data used in the physical activity monitoring project. The project is aimed at reducing obesity and improving health in children.

Constructor & Destructor Documentation

function PAFitBit::PAFitBit	(	in	fullFilenameOrPath,
		in	pStruct
	)

Constructor for PAFitBit class.

Parameters

fullFilenameOrPath	Either (1) the full filename (i.e. with pathname) of accelerometer data to load. or (2) the path that contains raw accelerometer data stored in binary file(s) - Firmware versions 2.5 or 3.1 only.
pStruct	Optional struct of parameters to use. If it is not included then parameters from getDefaultParameters method are used.

Return values

Instance of PAFitBit.

Member Function Documentation

function PAFitBit::extractFeature	(	in	obj,
		in	signalTagLine,
		in	method
	)

Extracts features from the identified signal.

Parameters

obj	Instance of PAFitBit.
signalTagLine	Tag identifying the signal to extract features from. Default is 'accel.fitbit.steps'
method	String name of the extraction method. Possible values include: c none c all c rms c median c mean c sum c var c std c mode c usagestate c psd

static function PAFitBit::getDefaultParameters ( )

static

Returns a structure of PAFitBit's default parameters as a struct.

Return values

pStruct

A structure of default parameters which include the following fields

curWindow
pathname
filename
windowDurSec
aggregateDurMin
frameDurMin
frameDurHour
windowDurSec
scale
label
offset
color
visible
usageState Struct defining usage state classification thresholds and parameters.

Note: This is useful with the PASettings companion class.; When adding default parameters, be sure to match saveable parameters in getSaveParameters()

static function PAFitBit::getDefaultTagLineLabels ( )

static

returns a cell of tag lines and the associated label describing the tag line.

Return values

tagLines	Cell of tag lines
labels	Cell of string descriptions that correspond to tag lines in the tagLines cell.

Note: Tag lines are useful for dynamic struct indexing into structs returned by getStruct.

function PAFitBit::getHeaderAsString ( in obj )

Returns header values as a single, printable string. Results include.

Filename
Duration ([dd] Days, [hh] hr [mm] min [ss] sec]
Window count
Start Date
Start Time
Parameters

obj Instance of PAFitBit.

Return values

headerStr Character array listing header fields and corresponding values. Field and values are separated by colon (:), while field:values are separated from each other with newlines (
).

function PAFitBit::getStudyID	(	in	obj,
		in	outputType
	)

Returns studyID instance variable.

Parameters

Instance	of PAFitBit
Optional	output format for the study id. Can be 'string' 'numeric'

Return values

Study ID that identifies the data (i.e. what or who it is attributed to).

static function PAFitBit::getStudyIDFromBasename ( in baseName )

static

Parses the input file's basename (i.e. sans folder and extension) for the study id. This will vary according from site to site as there is little standardization for file naming.

Parameters

File	basename (i.e. sans path and file extension).

Return values

Study ID

function PAFitBit::loadFile	(	in	obj,
		in	fullfilename
	)

Loads an accelerometer data file.

Parameters

obj	Instance of PAFitBit.
fullfilename	(optional) Full filename to load. If this is not included, or does not exist, then the instance variables pathname and filename are used to identify the file to load.

function PAFitBit::loadFileHeader	(	in	obj,
		in	fullFilename
	)

Load CSV header values (start time, start date, and window period).

Parameters

obj	Instance of PAFitBit.
fullFilename	The full filename to open and examine.

function PAFitBit::loadFitBitFile	(	in	obj,
		in	fullCountFilename
	)

Loads an accelerometer "count" data file.

Parameters

obj	Instance of PAFitBit.
fullCountFilename	The full (i.e. with path) filename to load.

function PAFitBit::resampleCountData ( in obj )

Resamples previously loaded 'count' data to match sample rate of raw accelerometer data that has been loaded in a following step (see loadFile()).

Parameters

obj	Instance of PAFitBit. %

Note: countPeriodSec, sampleRate, steps, lux, and accel values must be set in advance of this call.

function PAFitBit::saveToFile	(	in	obj,
		in	activityType,
		in	saveFilename
	)

Saves data to an ascii file.

Note: This is not yet implemented.

Parameters

obj	Instance of PAFitBit.
activityType	The type of activity to save. This is a string. Values include: c usageState c activitiy c inactivity c sleep
saveFilename	Name of the file to save data to.

Note: This method is under construction and does not actually save any data at the moment.

function PAFitBit::subsindex	(	in	obj,
		in	indices,
		in	structType
	)

overloaded subsindex method returns structure of time series data at indices provided.

Parameters

obj	Instance of PAFitBit
indices	Vector (logical or ordinal) of indices to select time series data by.
structType	String (optional) identifying the type of data to obtain the offset from. Can be `timeSeries` (default) - units are sample points `features` - units are frames `bins` - units are bins

Return values

dat	A struct of PAFitBit's time series instance data for the indices provided. The fields include: accel.(accelType).x accel.(accelType).y accel.(accelType).z accel.(accelType).vecMag steps lux inclinometer

function PAFitBit::subsref	(	in	obj,
		in	s
	)

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

c_version_comments/PAFitBit.cpp

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation