PAData Class Reference

The PAData 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 PAData:

Public Member Functions
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	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 ()

Public Attributes
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 PAData 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 PAData::PAData	(	in	fullFilenameOrPath,
		in	pStruct
	)

Constructor for PAData 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 PAData.

Member Function Documentation

static function PAData::appendStruct ( in  ltStruct, in  rtStruct  )

static

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.

Parameters

ltStruct	A structure whose fields are to be appended by the other.
rtStruct	A structure whose fields are will be appened to the other.

Return values

ltStruct

The resultof append rtStruct to ltStruct.

Note

For example:

ltStruct =

ydata: [1 1]

accel: [1x1 struct]

[x]: 0.5000

[y]: 1

rtStruct =

xdata: [1 100]

PAData.structEval(ltStruct,rtStruct)

ans =

ydata: [1 1]

xdata: [1 100]

accel: [1x1 struct]

[xdata]: [1 100]

[x]: [10.5000 10.5000 2.5000]

[y]: [2 3 4]

function PAData::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.

function PAData::classifyUsageForAllAxes

(

in

obj

)

Classifies the usage state for each axis using count data from each axis.

Parameters

obj	Instance of PAData.

Return values

didClassify

True/False depending on success.

function PAData::classifyUsageState	(	in	obj,
		in	countActivity
	)

Categorizes the study's usage state.

Parameters

obj	Instance of PAData.
vector	of count activity to apply classification rules too. If not provided, then the vector magnitude is used by default.

Return values

usageVec	A vector of length obj.dateTimeNum whose values represent the usage category at each sample instance specified by dateTimeNum. c usageVec(activeVec) = 30 c usageVec(inactiveVec) = 25 c usageVec(~awakeVsAsleepVec) = 20 c usageVec(sleepVec) = 15 sleep period (could be a nap) c usageVec(remSleepVec) = 10 REM sleep c usageVec(nonwearVec) = 5 Non-wear c usageVec(studyOverVec) = 0 Non-wear, study over.
usageState	A three column matrix identifying usage state and duration. Column 1 is the usage state, column 2 and column 3 are the states start and stop times (datenums).

Note

Usage states are categorized as follows:

• c -1 Nonwear
• c 0 Sleep - 0.25 rem, 0.75 nonrem
• c 1 Wake - inactive
• c 1 Wake - wake

Return values

startStopDatenums

Start and stop datenums for each usage state row entry of usageState.

function PAData::datenum2window	(	in	obj,
		in	datenumSample,
		in	structType
	)

Returns the display window for the given datenum.

Parameters

obj	Instance of PAData.
datenumSample	A date number (datenum) that should be in the range of instance variable dateTimeNum
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

window

The window.

function PAData::describeActivity	(	in	obj,
		in	categoryStr
	)

Describes an activity.

Note

This is not yet implemented.

Parameters

obj	Instance of PAData.
categoryStr	The type of activity to describe. This is a string. Values include: c sleep c wake c inactivity

Return values

activityStruct

A struct describing the activity. Fields include: c empty

function PAData::durationSamples

(

in

obj

)

Returns the number of samples contained in the time series data.

Parameters

obj	Instance of PAData

Return values

durationSamp

Number of elements contained in durSamples instance var (initialized by number of elements in accelRaw.x

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

Extracts features from the identified signal.

Parameters

obj	Instance of PAData.
signalTagLine	Tag identifying the signal to extract features from. Default is 'accel.count.vecMag'
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 PAData::getActivityTags ( )

static

function PAData::getAggregateDurationInMinutes

(

in

obj

)

Returns the current aggregate duration in minutes.

Parameters

obj	Instance of PAData

Return values

aggregateDuration

The current window;

function PAData::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.

Parameters

obj	Instance of PAData
featureFcn	Function name or handle to use to obtain features.
signalTagLine	String name of the field to obtain data from.
elapsedStartHour	Elapsed hour (starting from 00:00 for new day) to begin aligning feature vectors.
intervalDurationHours	number of hours between consecutively aligned feature vectors.

Note

For example if elapsedStartHour is 1 and intervalDurationHours is 24, then alignedFeatureVecs will start at 01:00 of each day (and last for 24 hours a piece).

Return values

alignedFeatureVecs	Matrix of row vectors, each of which is a feature calculated according to featureFcn and aligned according to elapsed start time and interval duration in hours. Consecutive rows are vector values in order of the section they are calculated from.
alignedStartDateVecs	Nx6 matrix of datevec values whose rows correspond to the start datevec of the corresponding row of alignedFeatureVecs.

function PAData::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.

Parameters

obj	Instance of PAData

Return values

binCount

The total number of frames contained in the data.

Note

In the case of data size is not broken perfectly into frames, but has an incomplete frame, the window count is rounded down. For example, if the frame duration 1 min, and the study is 1.5 minutes long, then the frame count is 1.

function PAData::getBinRate

(

in

obj

)

Returns the aggregate bin rate in units of aggregate bins/second.

Parameters

obj	Instance of PAData

Return values

fs	Aggregate bins per second.

function PAData::getColor	(	in	obj,
		in	structType
	)

Returns the color instance variable.

Parameters

obj	Instance of PAData
structType	String specifying the structure type of label to retrieve. Possible values include (all are included if this is not) timeSeries (default) features bins

Return values

colorStruct

A struct of color values correspodning to the time series fields of obj.color.

function PAData::getCurUncorrectedWindowRange	(	in	obj,
		in	structType
	)

Returns the current windows range.

Parameters

obj	Instance of PAData.
structType	Optional string identifying the type of data to obtain the offset from. Can be timeSeries (default) features bins

Return values

A	2x1 vector with start, stop range of the current window returned as samples beginning with 1 for the first sample.

Note

This uses instance variables windowDurSec, curWindow, and sampleRate to determine the sample range for the current window. The first value is floored and the second is ceil'ed.

function PAData::getCurWindow

(

in

obj

)

Returns the current window.

Parameters

obj	Instance of PAData

Return values

curWindow

The current window;

function PAData::getCurWindowRange	(	in	obj,
		in	structType
	)

Returns a structure of PAData's time series data.

Parameters

obj	Instance of PAData.
structType	Optional string identifying the type of data to obtain the offset from. Can be timeSeries (default) features bins

Return values

A	2x1 vector with start, stop range of the current window returned as samples beginning with 1 for the first sample. The second value (i.e. the stop sample) is capped at the current value of durationSamples().

Note

This uses instance variables windowDurSec, curWindow, and sampleRate to determine the sample range for the current window.

static function PAData::getDefaultParameters ( )

static

Returns a structure of PAData'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 PAData::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 PAData::getDisplayMinMax

(

in

obj

)

Returns the minimum and maximum amplitudes that can be displayed uner the current configuration.

Parameters

obj	Instance of PAData.

Return values

yLim	1x2 vector containing ymin and ymax.

static function PAData::getDummyDisplayStruct ( in  structType )

static

Returns a struct with subfields that hold the line properties for graphic display of the time series instance variables.

Parameters

structType

(Optional) String 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 PAData's time series instance variables, which include: accel.(accelType).x.(xdata, ydata, color) accel.(accelType).y.(xdata, ydata, color) accel.(accelType).z.(xdata, ydata, color) accel.(accelType).vecMag.(xdata, ydata, color) inclinometer.(xdata, ydata, color) lux.(xdata, ydata, color)

static function PAData::getDummyStruct ( in  structType )

static

Returns an empty struct with fields that mirror PAData's time series instance variables that contain.

Parameters

structType

(Optional) String 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 PAData's time series, feature, or aggregate bin instance variables. Time series include: accel.(accelType).x accel.(accelType).y accel.(accelType).z accel.(accelType).vecMag steps lux inclinometer

static function PAData::getExtractorDescriptions ( )

static

Returns a cell listing of available feature extraction methods as strings.

Return values

extractorDescriptions

Cell listing with description of feature extraction methods. none No feature extraction rms Root mean square hash sum median mean

Note

These methods can be passed as the argument to PAData's prefilter() method.

static function PAData::getFeatureDescriptionStruct ( )

static

Returns a struct of feature extraction methods and string descriptions as the corresponding values.

Return values

featureStruct

A struct of feature extraction methods and string descriptions as the corresponding values.

static function PAData::getFeatureDescriptionStructWithPSDBands ( )

static

function PAData::getFilename

(

in

obj

)

Returns the filename, pathname, and full filename (pathname + filename) of the file that the accelerometer data was loaded from.

Parameters

obj	Instance of PAData

Return values

filename	The short filename of the accelerometer data.
pathname	The pathname of the accelerometer data.
fullFilename	The full filename of the accelerometer data.

function PAData::getFrameableSampleCount

(

in

obj

)

function PAData::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.

Parameters

obj	Instance of PAData

Return values

frameCount

The total number of frames contained in the data.

Note

In the case of data size is not broken perfectly into frames, but has an incomplete frame, the window count is rounded down (floor). For example, if the frame duration 1 min, and the study is 1.5 minutes long, then the frame count is 1.

function PAData::getFrameDuration

(

in

obj

)

Returns the frame duration (in hours and minutes)

Parameters

obj	Instance of PAData

Return values

curFrameDurationMin	The current frame duration minutes field;
curFramDurationHour	The current frame duration hours field;

function PAData::getFrameDurationInMinutes

(

in

obj

)

function PAData::getFrameRate

(

in

obj

)

Returns the frame rate in units of frames/second.

Parameters

obj	Instance of PAData

Return values

fs	Frames rate in Hz.

function PAData::getFullFilename

(

in

obj

)

Returns the full filename (pathname + filename) of the accelerometer data.

Parameters

obj	Instance of PAData

Return values

fullFilename

The full filenmae of the accelerometer data.

Note

See also getFilename()

function PAData::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 PAData.

  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 PAData::getLabel	(	in	obj,
		in	structType
	)

Returns the label instance variable.

Parameters

obj	Instance of PAData
structType	String specifying the structure type of label to retrieve. Possible values include: timeSeries (default) features bins

Return values

labelStruct

A struct of string values which serve to label the correspodning to the time series fields of obj.label.

function PAData::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.

Parameters

obj

Instance of PAData.

fieldType

String value identifying the time series data to perform the minmax operation on. Can be one of the following: struct Returns a structure of minmax values with organization correspoding to that found by getStruct() instance method. all Returns a 1x2 vector of the global minimum and maximum value found for any of the time series data stored in obj. accel.count Returns a struct of minmax values for x,y, and z - accel.raw Returns a struct of minmax values for x,y, and z - lux Returns a 1x2 minmax vector for lux values. inclinometer Returns a struct of minmax values for lux fields. steps Returns a struct of minmax values for step fields.

Return values

minMax

Minimum maximum values for each time series field contained in obj.getStruct() or a single 2x1 vector of min max values for the field name specified.

function PAData::getOffAccelType	(	in	obj,
		in	accelTypeStr
	)

Retuns the accelType that is not set. This is useful in later removing unwanted accel fields.

Parameters

obj	Instance of PAData.
accelTypeStr	(optional) String that can be used in place of obj.accelType for determining the current accel type to find the opposing accel type of (i.e. the offAccelType).

Return values

offAccelType

Enumerated type which is either count When accelType is raw raw When accelType is count [] All other cases.

function PAData::getOffset	(	in	obj,
		in	structType
	)

Returns the offset instance variable.

Parameters

obj	Instance of PAData
structType	String specifying the structure type of label to retrieve. Possible values include (all are included if this not): timeSeries (default) features bins

Return values

offsetStruct

A struct of scalar values correspodning to the struct type fields of obj.offset.

static function PAData::getPrefilterMethods ( )

static

Returns a cell listing of available prefilter methods as strings.

Return values

prefilterMethods

Cell listing of prefilter methods. none No prefiltering rms Root mean square hash sum median mean

Note

These methods can be passed as the argument to PAData's prefilter() method.

function PAData::getPropertyStruct	(	in	obj,
		in	propertyName,
		in	structType
	)

Returns the visible instance variable.

Parameters

obj	Instance of PAData
propertyName	Name of instance variable being requested.
structType	String specifying the structure type of label to retrieve. Possible values include (all are included if this is not) timeSeries (default) features bins

Return values

visibileStruct

A struct of obj's visible field values

function PAData::getPSD

(

in

obj

)

static function PAData::getPSDBandNames ( )

static

function PAData::getPSDBands	(	in	obj,
		in	numBands
	)

static function PAData::getPSDExtractorDescriptions ( )

static

static function PAData::getPSDFeatureDescriptionStruct ( )

static

function PAData::getPSDSettings

(

in

obj

)

static function PAData::getRecurseMinmax ( in  dataStruct )

static

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.

Parameters

dataStruct

A structure whose fields are either structures or vectors.

Return values

minmaxVec

Nx2 vector of minmax values for the given dataStruct.

function PAData::getSampleRate

(

in

obj

)

Returns the samplerate of the x-axis accelerometer.

Parameters

obj	Instance of PAData

Return values

fs	Sample rate of the x-axis accelerometer.

function PAData::getSamplesPerWindow	(	in	obj,
		in	structType
	)

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

Parameters

obj	Instance of PAData.
structType	Optional string 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

Number

of samples, frames, or bins per window display;

Note

Calcuation based on instance variables windowDurSec and sampleRate

function PAData::getSaveParameters

(

in

obj

)

Returns a structure of PAData's saveable parameters as a struct.

Parameters

obj	Instance of PAData.

Return values

pStruct

A structure of save parameters which include the following fields curWindow pathname filename windowDurSec aggregateDurMin frameDurMin frameDurHour

function PAData::getScale	(	in	obj,
		in	structType
	)

Returns the scale instance variable.

Parameters

obj	Instance of PAData
structType	String specifying the structure type of label to retrieve. Possible values include (all are included if this not): timeSeries (default) features bins

Return values

scaleStruct

A struct of scalar values correspodning to the time series fields of obj.scale.

function PAData::getStartStopDatenum

(

in

obj

)

Returns the start and stop datenums for the study.

Parameters

obj	Instance of PAData

Return values

startstopnum

A 1x2 vector. startstopnum(1) The datenum of the study's start startstopnum(2) The datenum of the study's end.

function PAData::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.

Parameters

obj	Instance of PAData.
choice	(optional) String indicating the type of structure to be returned; optional. Can be dummy Empty data. dummydisplay Holds generic line properties for the time series structure. current Time series data with offset and scaling values applied. currentdisplay Time series data with offset and scaling values applied and stored as 'ydata' child fields. displayoffset [x,y,z] offsets of the current time series data being displayed. Values are stored in .position child field all All (default) All available sensor fields
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 PAData's time series, aggregate bins, or features instance data. The fields for time series data include: accel.(obj.accelType).x accel.(obj.accelType).y accel.(obj.accelType).z accel.(obj.accelType).vecMag steps inclinometer lux

static function PAData::getStructNameFromDescription ( in  description )

static

Returns the fieldname of PAData's struct types (see getStructTypes()) that matches the string argument.

Parameters

description

String description that can be timeSeries = 'time series'; bins = 'aggregate bins'; features = 'features';

Return values

structName

Name of the field that matches the description.

Note

For example:

structName = PAData.getStructNameFromDescription('time series');

results in structName = 'timeSeries'

static function PAData::getStructTypes ( )

static

Returns a struct representing the internal architecture used by PAData to hold and process acceleration data.

• timeSeries = 'time series';
• bins = 'aggregate bins';
• features = 'features';

  Return values

  structType

  Struct with the following fields and corresponding string values.

  Note

  This is helpful in identifying different offset, scale, label, color, and miscellaneous graphic and data choices.

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

Returns studyID instance variable.

Parameters

Instance	of PAData
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 PAData::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 PAData::getUsageClassificationRules

(

in

this

)

function PAData::getVisible	(	in	obj,
		in	structType
	)

Returns the visible instance variable.

Parameters

obj	Instance of PAData
structType	String specifying the structure type of label to retrieve. Possible values include (all are included if this is not) timeSeries (default) features bins

Return values

visibileStruct

A struct of obj's visible field values

function PAData::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.

Parameters

obj	Instance of PAData

Return values

windowCount

The maximum/last window allowed

Note

In the case of data size is not broken perfectly into windows, but has an incomplete window, the window count is rounded up. For example, if the time series data is 10 s in duration and the window size is defined as 30 seconds, then the windowCount is 1.

function PAData::getWindowDurSec

(

in

obj

)

Returns the private intance variable windowDurSec.

Parameters

obj	Instance of PAData

Return values

windowDurationSec

The value of windowDurSec

function PAData::getWindowSamplerate	(	in	obj,
		in	structType
	)

Returns the sampling rate for the current window display selection.

Parameters

obj	Instance of PAData
structType	Optional string identifying the type of data to obtain the offset from. Can be timeSeries (default) - sample units are sample points features - sample units are frames bins - sample units are bins

Return values

Sample

rate of the data being viewed in Hz.

function PAData::loadCountFile	(	in	obj,
		in	fullCountFilename
	)

Loads an accelerometer "count" data file.

Parameters

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

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

Loads an accelerometer data file.

Parameters

obj	Instance of PAData.
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 PAData::loadFileHeader	(	in	obj,
		in	fullFilename
	)

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

Parameters

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

function PAData::loadGT3XFile	(	in	obj,
		in	fullFilename
	)

Loads an accelerometer's raw data from binary files stored in the path name given.

Parameters

obj	Instance of PAData.
pathWithRawBinaryFiles	Name of the path (a string) that contains raw acceleromater data stored in one or more binary files.

Note

Currently, only two firmware versions are supported:

• 2.5.0
• 3.1.0

function PAData::loadPathOfRawBinary	(	in	obj,
		in	pathWithRawBinaryFiles
	)

Loads an accelerometer's raw data from binary files stored in the path name given.

Parameters

obj	Instance of PAData.
pathWithRawBinaryFiles	Name of the path (a string) that contains raw acceleromater data stored in one or more binary files.

Note

Currently, only two firmware versions are supported:

• 2.5.0
• 3.1.0

function PAData::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).

Parameters

obj	Instance of PAData.
fullRawCSVFilename	The full (i.e. with path) filename for raw data to load.

static function PAData::merge_nearby_events ( in  event_mat_in, in  min_samples  )

static

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.

Parameters

event_mat_in	is a two column matrix
min_samples	is a scalar value

Return values

merged_events	The output of merging event_mat's events that are separated by less than min_samples.
merged_indices	is a logical vector of the row indices that were merged from event_mat_in. - these are the indices of the in event_mat_in that are removed/replaced

Note

Lifted from SEV's CLASS_events.m - authored by Hyatt Moore IV

static function PAData::mergedCell ( in  startDateNum, in  stopDateNum, in  dateNumDelta, in  sampledDateVec, in  tmpDataCell, in  missingValue  )

static

Helper function for loading raw and count file formats to ensure proper ordering and I/O error handling.

Parameters

startDateNum	The start date number that the ordered data cell should begin at. (should be generated using datenum())
stopDateNum	The date number (generated using datenum()) that the ordered data cell ends at.
dateNumDelta	The difference between two successive date number samples.
sampledDateVec	Vector of date number values taken between startDateNum and stopDateNum (inclusive) and are in the order and size as the individual cell components of tmpDataCell
tmpDataCell	A cell of vectors whose individual values correspond to the order of sampledDateVec
missingValue	(Optional) Value to be used in the ordered output data cell where the tmpDataCell does not have corresponding values. The default is 'nan'.

Return values

orderedDataCell	A cell of vectors that are taken from tmpDataCell but initially filled with the missing value parameter and ordered according to synthDateNum.
synthDateVec	Matrix of date vectors ([Y, Mon,Day, Hr, Mn, Sec]) generated by startDateNum:dateNumDelta:stopDateNum which correponds to the row order of orderedDataCell cell values/vectors
synthDateNum	Vector of date numbers corresponding to the date vector matrix return argument.

Note

This is a helper function for loading raw and count file formats to ensure proper ordering and I/O error handling.

static function PAData::mergeStruct ( in  ltStruct, in  rtStruct  )

static

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.

Parameters

ltStruct	A structure whose fields are to be appended by the other.
rtStruct	A structure whose fields are will be appened to the other.

Return values

ltStruct

The result of merging rtStruct with ltStruct.

Note

For example:

ltStruct =

accel: [1x1 struct]

[x]: 0.5000

[y]: 1

lux: [1x1 struct]

[z]: 0.5000

rtStruct =

accel: [1x1 struct]

[pos]: [0.5000, 1, 0]

PAData.structEval(rtStruct,ltStruct)

ans =

accel: [1x1 struct]

[x]: 0.5000

[y]: 1

[pos]: [0.5000, 1, 0]

lux: [1x1 struct]

[z]: 0.5000

[pos]: [0.5000, 1, 0]

static function PAData::minmax ( in  dataStruct )

static

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.

Parameters

dataStruct

A structure whose fields are either structures or vectors.

Return values

structMinMax

a struct whose fields correspond to those of the input struct and whose values are [min, max] vectors that correspond to the minimum and maximum values found in the input structure for that field.

Note

Consider the example

dataStruct.accel.x = [-1 20 5 13];

dataStruct.accel.y = [1 70 9 3];

dataStruct.accel.z = [-10 2 5 1];

dataStruct.lux = [0 0 0 9];

structRange.accel is [-10 70]

structRange.lux is [0 9]

static function PAData::movingSummer ( in  signal, in  filterOrder  )

static

Moving summer finite impulse response filter.

Parameters

signal	Vector of sample data to filter.
filterOrder	filter order; number of taps in the filter

Return values

summedSignal

The filtered signal.

Note

The filter delay is taken into account such that the return signal is offset by half the delay.

static function PAData::overwriteEmptyStruct ( in  ltStruct, in  rtStruct  )

static

Inserts the second argument into any empty fields of the first struct argument.

Parameters

ltStruct	A structure whose empty fields will be set to the second argument.
rtStruct	A structure

Return values

ltStruct

The structure that results from inserting rtStruct into ltStruct.

Note

For example:

ltStruct =

accel: [1x1 struct]

[x]: []

[y]: []

lux: []

rtStruct =

color: 'k'

data: [1x1 struct]

[pos]: [0.5000, 1, 0]

PAData.structEval(rtStruct,ltStruct)

ans =

accel: [1x1 struct]

[x]: [1x1 struct]

color: 'k'

data: [1x1 struct]

[pos]: [0.5000, 1, 0]

[y]: [1x1 struct]

color: 'k'

data: [1x1 struct]

[pos]: [0.5000, 1, 0]

lux: [1x1 struct]

color: 'k'

data: [1x1 struct]

[pos]: [0.5000, 1, 0]

static function PAData::parseInfoTxt ( in  infoTxtFullFilename )

static

Parses the information found in input file name and returns the result as a struct of field-value pairs.

Parameters

obj	Instance of PAData.
infoTxtFullFilename	Name of the info.txt that contains sensor meta data.

Return values

infoStruct	A struct of the field value pairings parsed from info.txt
firmware	String value of Firmware field as found in the info.txt file. It is set to the empty string when not found.

Note

Currently, only two firmware versions are supported:

• 2.5.0
• 3.1.0

function PAData::prefilter	(	in	obj,
		in	method
	)

Prefilters accelerometer data.

Note

Not currently implemented.

Parameters

obj	Instance of PAData.
method	String name of the prefilter method.

function PAData::pruneStruct	(	in	obj,
		in	accelStruct
	)

static function PAData::reprocessEventVector ( in  logicalVec, in  min_duration_samples, in  merge_distance_samples  )

static

Removes periods of activity that are too short and groups nearby activity groups together.

Parameters

logicalVec	Initial vector which has 1's where an event or activity is occurring at that sample.
min_duration_samples	The minimum number of consecutive samples required for a run of on (1) samples to be kept.
merge_distance_samples	The maximum number of samples considered when looking for adjacent runs to merge together. Adjacent runs that are within this distance are merged into a single run beginning at the start of the first and stopping at the end of the last run.

Return values

processVec

A vector of size (logicalVec) that has removed runs (of 1) that are too short and merged runs that are close enough together.

function PAData::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 PAData. %

Note

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

function PAData::sample2window	(	in	obj,
		in	sample,
		in	windowDurSec,
		in	samplerate
	)

Calculates, and returns, the window for the given sample index of a signal.

Parameters

obj	Instance of PAData.
sample	Sample point to discover the containing window of.
windowDurSec	Window duration in seconds (scalar) (optional)
samplerate	Sample rate of the data (optional)

Return values

window

The window.

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

Saves data to an ascii file.

Note

This is not yet implemented.

Parameters

obj	Instance of PAData.
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 PAData::setAggregateDurationMinutes	(	in	obj,
		in	aggregateDurationMin
	)

Set the aggregate duration (in minutes) instance variable.

Parameters

obj	Instance of PAData
aggregateDurationMin	The aggregate duration to set aggregateDurMin to.

Return values

aggregateDurationMin

The current value of instance variable aggregateDurMin.

Note

If the input argument for aggregateDurationMin is negative or exceeds the current frame duration value (in minutes), then it is not used and the current frame duration is retained (and also returned).

function PAData::setColor	(	in	obj,
		in	fieldName,
		in	newColor
	)

Sets the color instance variable for a particular sub field.

Parameters

obj	Instance of PAData
fieldName	Dynamic field name to set in the 'color' struct.

Note

For example if fieldName = 'timeSeries.accel.vecMag' then obj.color.timeSerie.accel.vecMag = newColor; is evaluated.

Parameters

newColor

1x3 vector to set obj.color.(fieldName) to.

function PAData::setCurWindow	(	in	obj,
		in	window
	)

Set the current window for the instance variable accelObj (PAData)

Parameters

obj	Instance of PAData
window	The window to set curWindow to.

Return values

curWindow

The current value of instance variable curWindow.

Note

If the input argument for window is negative or exceeds the maximum window value for the time series data, then it is not used and the curWindow value is retained, and also returned.

function PAData::setFrameDurationHours	(	in	obj,
		in	frameDurationHours
	)

Set the frame duration (hours) instance variable.

Parameters

obj	Instance of PAData
frameDurationHours	The frame duration to set frameDurHours instance variable to.

Return values

frameDurationHours

The current value of instance variable frameDurHour.

Note

If the input argument for frameDurationHours is negative or exceeds the maximum duration of data, then it is not used and the current frame duration is retained (and also returned).

function PAData::setFrameDurationMinutes	(	in	obj,
		in	frameDurationMin
	)

Set the frame duration (in minutes) instance variable.

Parameters

obj	Instance of PAData
frameDurationMin	The frame duration to set frameDurMin to.

Return values

frameDurationMin

The current value of instance variable frameDurMin.

Note

If the input argument for frameDurationMin is negative or exceeds the maximum duration of data, then it is not used and the current frame duration is retained (and also returned).

function PAData::setFullFilename	(	in	obj,
		in	fullfilename
	)

Sets the pathname and filename instance variables using the input full filename.

Parameters

obj	Instance of PAData
fullfilename	The full filenmae of the accelerometer data that will be set

Return values

success

(T/F) -true: if fullfilename exists and is instance variables are set false: otherwise

Note

See also getFilename()

function PAData::setOffset	(	in	obj,
		in	fieldName,
		in	newOffset
	)

Sets the offset instance variable for a particular sub field.

Parameters

obj	Instance of PAData
fieldName	Dynamic field name to set in the 'offset' struct.

Note

For example if fieldName = 'timeSeries.vecMag' then obj.offset.timeSeries.vecMag = newOffset; is evaluated.

Parameters

newOffset

y-axis offset to set obj.offset.(fieldName) to.

function PAData::setProperty	(	in	obj,
		in	propertyName,
		in	fieldName,
		in	propertyValueStr
	)

Sets the specified instance variable for a particular sub field.

Parameters

obj	Instance of PAData
propertyName	instance variable to set the property of.
fieldName	Dynamic field name to set in the propertyName struct.
propertyValueStr	String value of property to set fieldName to.

function PAData::setScale	(	in	obj,
		in	fieldName,
		in	newScale
	)

Sets the scale instance variable for a particular sub field.

Parameters

obj	Instance of PAData
fieldName	Dynamic field name to set in the 'scale' struct.

Note

For example if fieldName = 'timeSeries.vecMag' then obj.scale.timeSeries.vecMag = newScale; is evaluated.

Parameters

newScale

Scalar value to set obj.scale.(fieldName) to.

function PAData::setUsageClassificationRules	(	in	this,
		in	ruleStruct
	)

Updates the usage state rules with an input struct.

Parameters

function PAData::setVisible	(	in	obj,
		in	fieldName,
		in	newVisibilityStr
	)

Sets the visible instance variable for a particular sub field.

Parameters

obj	Instance of PAData
fieldName	Dynamic field name to set in the 'visible' struct.
newVisibilityStr	Visibility property value.

Note

Valid values include

• on
• off

function PAData::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.

Parameters

obj	Instance of PAData
durSec	Duration in seconds. Must be positive. Value is first rounded to ensure it is an integer.

Return values

durSec

Window duration in seconds of obj.

Note

Instance variable curWindow is recalculated based on new window duration.

static function PAData::struct2vec ( in  structure, in  vector  )

static

flattens a structure to a single dimensional array (i.e. a vector)

Parameters

structure

A struct with any number of fields.

Return values

vector

A vector with values that are taken from the structure.

static function PAData::structEval ( in  operand, in  ltStruct, in  rtStruct, in  optionalDestFieldOrValue  )

static

Evaluates the two structures, field for field, using the function name provided.

Parameters

operand	A string name of the operation (via 'eval') to conduct at the lowest level. Additional operands include: passthrough Requires Optional field name to be set. calculateposition (requires rtStruct to have .xdata and .ydata fields.
ltStruct	A structure whose fields are either structures or vectors.
rtStruct	A structure whose fields are either structures or vectors.
optionalDestField	Optional field name to subset the resulting output structure to (see last example). This can be useful if the output structure will be passed as input that expects a specific sub field name for the values (e.g. line properties). See last example below.

Return values

resultStruct

A structure with same fields as ltStruct and rtStruct whose values are the result of applying operand to corresponding fields.

Note

In the special case that operand is set to 'passthrough' only ltStruct is used (enter ltStruct as the rtStruct value) and the optionalDestField must be set (i.e. cannot be empty). The purpose of the 'passthrough' operation is to insert a field named optionalDestField between any field/non-struct value pairs.

For example:

ltStruct =

x: 2

accel: [1x1 struct]

[x]: 0.5000

[y]: 1

rtStruct =

x: [10 10 2]

accel: [1x1 struct]

[x]: [10 10 2]

[y]: [1 2 3]

PAData.structEval('plus',rtStruct,ltStruct)

ans =

x: [12 12 4]

accel: [1x1 struct]

[x]: [10.5000 10.5000 2.5000]

[y]: [2 3 4]

PAData.structEval('plus',rtStruct,ltStruct,'ydata')

ans =

x.ydata: [12 12 4]

accel: [1x1 struct]

[x].ydata: [10.5000 10.5000 2.5000]

[y].ydata: [2 3 4]

PAData.structEval('passthrough',ltStruct,ltStruct,'string')

ans =

x.string: 2

accel: [1x1 struct]

[x].string: 0.5000

[y].string: 1

PAData.structEval('overwrite',ltStruct,ltStruct,value)

ans =

x: value

accel: [1x1 struct]

[x]: value

[y]: value

static function PAData::structScalarEval ( in  operand, in  ltStruct, in  A, in  optionalDestField  )

static

Evaluates the two structures, field for field, using the function name provided.

Parameters

operand	A string name of the operation (via 'eval') to conduct at the lowest level.
ltStruct	A structure whose fields are either structures or vectors.
A	Matrix value of the same dimension as the first structure's (ltStruct) non-struct field values.
optionalDestField	Optional field name to subset the resulting output structure to (see last example). This can be useful if the output structure will be passed as input that expects a specific sub field name for the values (e.g. line properties). See last example below.

Return values

resultStruct

A structure with same fields as ltStruct and optionally the optionalDestField whose values are the result of applying operand to corresponding fields and the input matrix.

Note

For example:

ltStruct =

x.position: [10 10 2]

accel: [1x1 struct]

[x.position]: [10 10 2]

[y.position]: [1 2 3]

A =

[1 1 0]

PAData.structEval('plus',ltStruct,A)

ans =

x.position: [11 11 2]

accel: [1x1 struct]

[x.position]: [11 11 2]

[y.position]: [2 3 3]

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

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

Parameters

obj	Instance of PAData
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 PAData'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 PAData::subsref	(	in	obj,
		in	s
	)

static function PAData::subsStruct ( in  structIn, in  indices  )

static

Returns structure whose values are taken from the struct and indices provided.

Parameters

structIn	Struct of indicable data.
indices	Vector (logical or ordinal) of indices to select time series data by.

Return values

structOut

Struct with matching fields as input struct, with values taken at indices.

static function PAData::thresholdcrossings ( in  line_in, in  threshold_line  )

static

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.

Return values

static function PAData::unrollEvents ( in  eventsStartStop, in  vectorSize  )

static

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.

Parameters

eventStartStop
vectorSize	The length or size of the sample data to unroll the start stop events back to.

Note

eventStartStop = thresholdCrossings(vector,0);

Return values

vector

static function PAData::updateStructWithStruct ( in  structToUpdate, in  structToUpdateWith  )

static

function PAData::window2datenum	(	in	obj,
		in	windowSample
	)

Returns the starting datenum for the window given.

Parameters

obj	Instance of PAData.
windowSample	Index of the window to check. %

Return values

dateNum

the datenum value at the start of windowSample.

Note

The starting point is adjusted based on obj startDatenum value and its windowDurSec instance variable.

Member Data Documentation

Property PAData::accel

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

• raw Structure of raw x,y,z accelerations. Fields are:
  • x x-axis
  • y y-axis
  • z z-axis
• count Structure of actigraph derived counts for x,y,z acceleration readings. Fields are:
  • x x-axis
  • y y-axis
  • z z-axis
  • vecMag vectorMagnitude

Property PAData::accelType

Type of acceleration stored; can be.

• raw This is not processed
• count This is preprocessed
• all - This is both raw and count accel fields.

Property PAData::color

Property PAData::dateTimeNum

The numeric value for each date time sample provided by.

Property PAData::durationSec

Durtion of the sampled data in seconds.

Property PAData::inclinometer

Structure of inclinometer values. Fields include:

• off
• standing
• sitting
• lying

Property PAData::label

Property PAData::lineproperty

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

Property PAData::lux

Luminance levels.

Constant Property PAData::NUM_PSD_BANDS = 5

Property PAData::offset

Property PAData::psd

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

• frames PSD of the data currently in the frames member variable.
• count Structure of actigraph derived counts for x,y,z acceleration readings. Fields are:
  • x x-axis
  • y y-axis
  • z z-axis
  • vecMag vectorMagnitude
• raw Structure of raw x,y,z accelerations. Fields are:
  • x x-axis
  • y y-axis
  • z z-axis

Property PAData::scale

Property PAData::startDate

Start Date.

Property PAData::startDatenums

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

Property PAData::startTime

Start Time.

Property PAData::steps

Steps - unknown? Maybe pedometer type reading?

Property PAData::stopDatenums

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

Property PAData::studyID

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

Note

See getStudyIDFromBasename()

Property PAData::timeStamp

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

Property PAData::usage

Structure of usage states determined from the following axes counts:

• x x-axis
• y y-axis
• z z-axis
• vecMag vectorMagnitude

Property PAData::visible

Property PAData::yDelta

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

• c_version_comments/PAData.cpp