Main VivoScript object to access other modules and perform generic actions. More...

#include <ScriptMaster.h>

Public Member Functions
void	setVersion (string version)
	Set a string representing the script version that will be used in audit log messages.

string	getVersion ()
	Get the string representing the script version.

void	askForCancelReason (bool ask)
	Set whether a prompt asks for a reason if the user cancels the script, which can be written to the audit trail.

bool	isAskingForCancelReason ()
	Whether a prompt will asks for a reason if the user cancels the script, which can be written to the audit trail.

void	debug (string text)
	Prints output to debugger and/or logfile.

Object	mainWin ()
	Returns MainWin object.

Object	bedRemovalTool ()
	Returns advanced bedremoval object.

Object	matrixManipulationTool ()
	Returns MatrixManipulation object.

Object	dataManager ()
	Returns Data Manager object.

Object	dataList ()
	Returns dataList object.

Object	sliceViewer ()
	Returns SliceView object.

Object	multiViewer ()
	Returns MultiView object.

Object	controller ()
	Returns SliceView Controller object.

Object	mipController ()
	Returns mipController object.

Object	vtkController ()
	Returns VTK Controller object.

Object	vtkViewer ()
	Returns vtkViewer object.

Object	workList ()
	Returns Worklist object.

Object	visibilityManager ()
	Returns Visibility Manager object.

Object	BrainAtlasTool (bool visible=true, bool quiet=false)
	Opens the Brain Atlas Tool.

Object	MASTool (string libraryPath=string(""))
	Opens Multi-Atlas Segmentation Tool, formerly known as Whole Body Atlas)

void	quit ()
	Quits VivoQuant after confirmation (in interactive session) or automatically (in –script session)

Index	index (int i)
	Get a script image index object used to reference data in the Data Manager The index should be passed directly to function, ie: var t = op.testFunc(VQ.index(1));.

Index	index (int i, int j)
	Get a script image index object used to reference data in the Data Manager The index should be passed directly to function, ie: var t = op.testFunc(VQ.index(0,1));.

Index	flatIndex (int i)
	Get a script flat image index object used to reference data in the Data Manager The index should be passed directly to function, ie: var t = op.testFunc(VQ.flatIndex(1));.

Object	getIndexContainer (int i)
	Get a script image index container used to reference data in the Data Manager. Use .get() function of the container to access the internal index.

Object	getIndexContainer (int i, int j)
	Get a script image index container used to reference data in the Data Manager. Use .get() function of the container to access the internal index.

string	counter (int c, int s)
	Convenience function to return a 0-padded counter.

void	showMessage (string msg, bool modal=true)
	Displays dialog box with user-defined message.

bool	askYesNoQuestion (string msg, bool modal=true)
	Displays dialog box with "Yes" or "No" option.

Object	progressDialog (string label, string cancelButtonText, int minimum, int maximum)
	Returns a progress dialog object, which can be used to show the current state of a longer process.

VariantMap	getValues (string title, VariantMap &map, bool modal=true)
	Displays a dialog requesting multiple user inputs in a single form.

Object	getLocalPath (string caption="Select directory:", string startDir=string("."))
	Returns path of directory selected by user in file dialog.

Object	getSavePath (string caption=string("Select output file:"), string startDir=string("."), string filter=string())
	Returns path to file selected by user in file dialog.

Array< string >	getLocalFiles (string caption="Select files:", string startDir=string("."))
	Returns array of paths to files selected by user in file dialog.

string	getVivoScriptDir ()
	Returns VivoScript directory.

void	mkdir (string path, string subdir)
	Creates sub-directory at specified path.

bool	fileExists (string path)
	Checks whether file at specified path exists.

bool	folderExists (string path)
	Checks whether file at specified path exists.

bool	openFileExternally (string path)
	Opens a local file in an external application.

Object	minMaxTool ()
	Returns MinMax Tool object.

bool	isInteractive ()
	Checks whether current VivoQuant session is interactive.

void	setInteractive (bool b)
	Sets VivoQuant to interactive (or not)

void	updateProcessingParameters ()
	Update the ITK and VTK thread settings based on the config.

bool	isTestMode ()
	Checks whether current VivoQuant session is in test mode.

void	setTestMode (bool b=true)
	Sets VivoQuant to test mode (or not)

string	lumiQuantMaster ()
	Returns LumiQuant master settings file from VivoQuant directory.

Object	dicomBrowser (AbstractDicomRepository *rep)
	Returns VivoQuant's Data Browser object for a given DICOM repository.

Object	dcmRep (string text)
	Creates and returns a DICOM repository object.

Object	currentDcmRep ()
	Returns the DICOM repository object corresponding to the repository that is currently active in the DICOM Browser.

Object	loadRepository (string name)
	Returns DICOM repository object from DICOM repository saved in VivoQuant.

Object	getListOfRepositories (string type=string())
	Returns array of repositories stored in VivoQuant.

void	abort ()
	Aborts current script.

Object	queryStudies (AbstractDicomRepository *rep, string patientName, string patientID=string(), string dateRange=string(), string studyDesc=string())
	Performs query of DICOM repository for studies matching argument criteria.

Object	querySeries (AbstractDicomRepository *rep, string studyInstanceUID)
	Performs query of DICOM repository for series within a given study, and returns series matching criteria.

Object	queryImages (AbstractDicomRepository *rep, string studyInstanceUID, string seriesInstanceUID)
	Performs query of DICOM repository for images within a series, and returns images matching criteria.

Object	query (AbstractDicomRepository *rep, string query, Array< string > arguments=Array< string >(), Object &fields=Object(), bool isPost=false)
	Performs custom query of DICOM repository using the iPACS API.

string	getDcmString (AbstractDicomRepository *rep, string tag, string studyInstanceUID, string seriesInstanceUID, string sopInstanceUID)
	Looks up the value of the specified tag in the DICOM header of an image in the repository.

Object	downloadImages (AbstractDicomRepository *rep, string studyInstanceUID, string seriesInstanceUID, string sopInstanceUID=string())
	Downloads image to cache.

Object	downloadImages (string targetDir, AbstractDicomRepository *rep, string studyInstanceUID, string seriesInstanceUID, string sopInstanceUID=string())
	Downloads image to a location on disk.

Object	downloadImages (string targetDir, bool forceRedownload, AbstractDicomRepository *rep, string studyInstanceUID, string seriesInstanceUID, string sopInstanceUID=string())
	Downloads image to a location on disk.

Object	queryDataPoints (AbstractDicomRepository *rep, string type, string uid, string form)
	Perform query of DICOM repository for datapoints at project, study, series, or image level, and returns datapoints matching criteria.

Object	submitDataPoint (AbstractDicomRepository *rep, string uid, Object &data, string type=string())
	Submits datapoint to DICOM repository.

Object	logMessage (Index dataIndex, string msg, string noipacsTitle=string("Get iPACS from data"), string type=string())
	Creates a log message on the given's data iPACS repository.

Object	logMessage (AbstractDicomRepository *rep, string msg, string type=string())
	Creates a log message on the given DICOM repository.

void	auditTrailMessage (string msg, string project="/", string type=string())
	Creates an audit trail message on the current repository.

void	auditTrailGenerateNewUID ()
	Generates a new session ID for audit trail messages.

void	dicomBrowserLoad (AbstractDicomRepository *rep, string studyInstanceUID, string seriesInstanceUID, bool append=false, bool isPlanar=false, bool force4Dto3D=false)
	Downloads image(s) from DICOM repository and loads them into the Data Manager.

void	dicomBrowserLoad (DicomBrowser *dcmBrowser, string studyInstanceUID, string seriesInstanceUID, string sopInstanceUID=string())
	Downloads image(s) from DICOM repository and loads them into Data Manager.

Object	queryStudyPlan (AbstractDicomRepository *rep, string plan, string cohort, string group, string animal, string modality, string date, string event="$0")

Object	getWidget (string name)
	Returns an object containing functions/properties of specified widget. Widgets are UI elements (e.g. buttons, checkboxes, combo boxes, etc.) in VivoQuant.

Object	currentOp ()
	Returns an object containing functions for the currently loaded operator.

Object	currentView ()
	Returns an object containing functions for the currently loaded view mode.

Array< string >	availableItems (string name)
	Returns available items from widget with multiple options.

Array< string >	availableItemsObj (Object obj)
	Returns available items from widget with multiple options.

Array< string >	availableOperators ()
	Returns list of available operators.

void	setOption (string cbname, string opt)
	Set widget to given option; for use with widgets with multiple options (e.g. comboboxes)

void	setOptionObj (Object obj, string opt)
	Set widget to given option; for use with widgets with multiple options (e.g. comboboxes)

string	stripCredentials (string url_string)
	Returns URL of DICOM repository with credentials (username and password) removed.

void	setConfig (string entry, Variant &val, bool force=false)
	Sets option in VivoQuant configuration to given value.

string	getConfig (string entry, string defaultValue=string())
	Returns current value of option in VivoQuant configuration.

void	forceUpdateTheme ()
	Force the UI theme to update.

string	getHome ()
	Returns VivoQuant installation directory.

string	getCache ()
	Returns VivoQuant cache directory.

string	getCurrentDir ()
	Returns current path.

string	getScriptPath ()
	Returns the location of the script being executed.

string	getTempFolder ()
	Returns Temp folder for current user.

bool	deletePath (string path)
	Deletes folder and all its contents at given path.

bool	deleteFile (string filepath)
	Deletes file at given path.

bool	copyFile (string filepath, string newpath)
	Copies file from one path to another.

bool	renameFile (string filepath, string newname)
	Renames file at given path.

bool	rmDir (string dirpath)
	Removes directory at given path.

string	preProcess (string protocol, bool showDialog=false)
	Runs Pre-Processing Tool tool with the given protocol.

Object	PreProcessingTool (bool showDialog=true)
	Opens the Pre-Processing Tool.

int	storeData (AbstractDicomRepository *rep, Index idx, DICOMImageFormat format, bool compress=false)
	Stores DICOM data to a DICOM repository.

int	storeDataByTimepoint (AbstractDicomRepository *rep, int idx, DICOMImageFormat format, bool compress=false, TimePointsSettings timepointOption=TimePointsSettings::AllTimePoints, TimepointFilesSettings timepointPerFileOption=TimepointFilesSettings::SingleFileForAllTimepoints)
	Stores DICOM data to a DICOM repository, with the option to save by timepoint.

bool	storeAsRaw (string filepath, Index idx)
	Stores data to disk in MHD/RAW (or MHD/ZRAW) file format.

int	storeAsDICOM (string filepath, Index idx, DICOMImageFormat format, bool compress=false, bool quiet=true)
	Stores data to disk in DICOM file format.

int	storeAsDICOMByTimepoint (string filepath, int idx, DICOMImageFormat format, bool compress=false, TimePointsSettings timepointOption=TimePointsSettings::AllTimePoints, TimepointFilesSettings timepointPerFileOption=TimepointFilesSettings::SingleFileForAllTimepoints)
	Stores data to disk in DICOM file format, with the option to save by timepoint.

void	saveDataViaITK4D (string filepath)
	Stores all data in Data Manager to disk as a single ITK 4D dataset in MHD/RAW or MHD/ZRAW file format.

void	saveDataViaITK (string filepath, Index idx)
	Stores data to disk in ITK MHD/RAW or MHD/ZRAW file format.

bool	writeFile (string filepath, string text)
	Writes file to disk with given text.

bool	appendFile (string filepath, string text)
	Appends text to file on disk.

Array< string >	readFile (string filepath)
	Reads file into array of strings.

Object	brukerImporter ()
	Returns Bruker Importer object.

Object	analyzeImporter ()
	Returns Analyze Importer object.

Object	imgInfImporter ()
	Returns Img/Inf Importer object.

Object	gelImporter ()
	Returns Gel Importer object.

Object	rawImporter ()
	Returns Raw Importer object.

Object	imgHdrImporter ()
	Returns Img/Hdr Importer object.

Object	vevoImporter (string filename)
	Returns Vevo object.

void	centerCursor ()
	Moves cursor to center of image in each viewport (i.e. moves each viewport to center slice)

Object	webDisk (string rep)
	Return IPACS WebDisk object for project in given iPACS repository.

bool	saveScreenshot (string fileName)
	Saves screenshot of VivoQuant.

string	applicationName ()
	Returns name + version of current instance of VivoQuant.

Object	zipTool ()
	Returns Zip Tool object.

double	sin (double f)
	Returns sin of angle.

double	cos (double f)
	Returns cosine of angle.

void	evalDialog (string text=string())
	Opens VivoScript evaluation window with given text.

void	splitROI2DICOM (Index idx)
	For each ROI in the 3D ROI Tool, creates a masked image of a given image in the Data Manager, where voxels outside the ROI are mapped to the given image's minimum.

Array< string >	lsDir (string dir, string nameFilter=string(), int filter=QDir::AllEntries\|QDir::NoDotAndDotDot, QDir::SortFlags sort=QDir::Name)
	Returns array of files in given directory on local disk.

int	rand ()
	Returns a random integer.

int	rand (int max)
	Returns random positive integer less than given maximum.

float	frand ()
	Returns a random float.

void	suspend (string message=string())
	Suspends script and opens a modeless "Resume" dialog.

string	getHash (string key, string def=string())
	Returns current value of key in hash.

double	getHashNum (string key, double def=0.0f)
	Returns current numerical value of key in hash.

Array< string >	getHashKeys ()
	Returns array of all keys in hash.

void	setHash (string key, string val)
	Sets value of key in hash.

void	clearHash ()
	Clears all keys and values stored in hash.

bool	storeHash (string fileName)
	Stores all keys and values in hash to local file.

bool	loadHash (string fileName)
	Loads local file, containing hash keys and values, to VivoQuant's persistent hash.

string	getEnv (string key, string defaultValue=string())
	Get the system's environment variables.

string	startTool (string tool, string baseDir=".", Array< string > args=Array< string >())
	Start an external tool.

void	bedRemoval (string bedName=string())
	Invokes CT bed removal tool. If bedName is provided, this bed will automatically be selected.

Object	getROIStats (Index idx, int roiID, int layerID=-1)
	Returns object with ROI quantification table information for given dataset and ROI.

Object	getROIStats (Index idx)
	Returns array of ROI quantification table information for given dataset and ALL ROIs.

string	atlasPath ()
	Returns path where atlases are stored.

Object	getMPRWidget ()
	Returns MPR widget.

void	loadRGB (Index idx, Array< string > imgFiles, float voxX, float voxY, float voxZ, int rgbRep=4, bool forcePlanar=true)

Object	getMModeSegmentationTool ()
	Returns Ultrasound M-Mode Segmentation tool object.

Object	getDicomAnonymizer ()
	Returns DICOM Anonymizer Tool object.

Object	getDicomRelabeler ()
	Returns DICOM Relabeler Tool object.

Object	getCorticalThicknessTool ()
	Returns cortical thickness tool object.

Object	getBedRemovalWidget (string name)
	Return Widget name in Bedremoval Dialog.

double	getHalfLife (string name)
	Get an isotope's half life.

Object	readCSVFile (string name)
	Parse a CSV file into arrays of values.

string	getDefaultPal (string modality, int i)
	get default palette from modality

string	getOS ()
	get current Operating System name

Detailed Description

Main VivoScript object to access other modules and perform generic actions.

Member Function Documentation

◆ appendFile()

bool appendFile	(	string	filepath,
		string	text
	)

Appends text to file on disk.

Parameters

filepath	Path of output file
text	Text to write to output file

◆ askForCancelReason()

void askForCancelReason ( bool ask )

Set whether a prompt asks for a reason if the user cancels the script, which can be written to the audit trail.

Parameters

ask	If true, a prompt will ask the user to enter a reason if they do something that cancels the script while it is running

◆ askYesNoQuestion()

bool askYesNoQuestion	(	string	msg,
		bool	modal = `true`
	)

Displays dialog box with "Yes" or "No" option.

Parameters

msg	Message displayed in dialog box
modal	Determines whether VivoQuant is inaccesible while dialog box is open (true) or accesible (false)

Returns: bool true (if "Yes") or false (if "No")

◆ auditTrailMessage()

void auditTrailMessage	(	string	msg,
		string	project = `"/"`,
		string	type = `string()`
	)

Creates an audit trail message on the current repository.

Parameters

msg	The message to be logged
project	The project to log the message to
type	Message type

◆ availableItems()

Array< string > availableItems ( string name )

Returns available items from widget with multiple options.

Parameters

name	Name of widget

◆ availableItemsObj()

Array< string > availableItemsObj ( Object obj )

Returns available items from widget with multiple options.

Note: Takes widget object as input (can be accessed by VQ.getWidget('widgetName')

Parameters

obj	Widget object, which can be accessed by ScriptMaster::getWidget

◆ BrainAtlasTool()

Object BrainAtlasTool	(	bool	visible = `true`,
		bool	quiet = `false`
	)

Opens the Brain Atlas Tool.

Parameters

visible	Whether or not the tool dialog is shown upon being created
quiet	Whether or not the tool is in quiet mode. In quiet mode no warnings or popups will be displayed.

◆ copyFile()

bool copyFile	(	string	filepath,
		string	newpath
	)

Copies file from one path to another.

Parameters

Current	path to file
New	path to file

Returns: bool True if file copied successfully, false otherwise

◆ cos()

double cos ( double f )

inline

Returns cosine of angle.

Parameters

f	Angle (in radians)

◆ counter()

string counter	(	int	c,
		int	s
	)

inline

Convenience function to return a 0-padded counter.

Parameters

c	Number to pad
s	Number of digits in padded output

◆ dcmRep()

Object dcmRep ( string text )

Creates and returns a DICOM repository object.

Parameters

text	Location of DICOM repository. Can be URL, local directory, or other path to a DICOM repository. Local folders should start with "folder://" followed by the path. iPACS (R) repositories should start with "ipacss://".

◆ debug()

void debug ( string text )

Prints output to debugger and/or logfile.

Parameters

text	String to be printed

◆ deleteFile()

bool deleteFile ( string filepath )

Deletes file at given path.

Parameters

filepath Path to file

Returns: bool True if file deleted successfully, false otherwise

◆ deletePath()

bool deletePath ( string path )

Deletes folder and all its contents at given path.

Parameters

path	to be deleted

Returns: bool True if path deleted successfully, false otherwise

◆ dicomBrowser()

Object dicomBrowser ( AbstractDicomRepository * rep )

Returns VivoQuant's Data Browser object for a given DICOM repository.

Parameters

rep	DICOM repository to use with Data Browser object

◆ dicomBrowserLoad() [1/2]

void dicomBrowserLoad	(	AbstractDicomRepository *	rep,
		string	studyInstanceUID,
		string	seriesInstanceUID,
		bool	append = `false`,
		bool	isPlanar = `false`,
		bool	force4Dto3D = `false`
	)

Downloads image(s) from DICOM repository and loads them into the Data Manager.

Parameters

rep	DICOM repository
studyInstanceUID	StudyInstanceUID of study in which image(s) are found
seriesInstanceUID	SeriesInstanceUID of series in which image(s) are found
append	Determines whether incoming data is appended (1) or opened to replace data currently loaded in Data Manager (0)
isPlanar	(optional) determines whether VivoQuant loads incoming data as planar (1) or not (0)
force4Dto3D	(optional) determines whether VivoQuant loads incoming 4D data as 4D (1) or 3

◆ dicomBrowserLoad() [2/2]

void dicomBrowserLoad	(	DicomBrowser *	dcmBrowser,
		string	studyInstanceUID,
		string	seriesInstanceUID,
		string	sopInstanceUID = `string()`
	)

Downloads image(s) from DICOM repository and loads them into Data Manager.

Parameters

dcmBrowser	DICOM browser object
studyInstanceUID	StudyInstanceUID of study in which image(s) are found
seriesInstanceUID	SeriesInstanceUID of series in which image(s) are found
sopInstanceUID	SOPInstanceUID of image(s)

◆ downloadImages() [1/3]

Object downloadImages	(	AbstractDicomRepository *	rep,
		string	studyInstanceUID,
		string	seriesInstanceUID,
		string	sopInstanceUID = `string()`
	)

Downloads image to cache.

Parameters

rep	DICOM repository
studyInstanceUID	StudyInstanceUID of study
seriesInstanceUID	SeriesInstanceUID of series
sopInstanceUID	SOPInstanceUID of image

◆ downloadImages() [2/3]

Object downloadImages	(	string	targetDir,
		AbstractDicomRepository *	rep,
		string	studyInstanceUID,
		string	seriesInstanceUID,
		string	sopInstanceUID = `string()`
	)

Downloads image to a location on disk.

Parameters

targetDir	Desired location on disk
rep	DICOM repository
studyInstanceUID	StudyInstanceUID of study
seriesInstanceUID	SeriesInstanceUID of series
sopInstanceUID	SOPInstanceUID of image

◆ downloadImages() [3/3]

Object downloadImages	(	string	targetDir,
		bool	forceRedownload,
		AbstractDicomRepository *	rep,
		string	studyInstanceUID,
		string	seriesInstanceUID,
		string	sopInstanceUID = `string()`
	)

Downloads image to a location on disk.

Parameters

targetDir	Desired location on disk
rep	DICOM repository
studyInstanceUID	StudyInstanceUID of study
seriesInstanceUID	SeriesInstanceUID of series
sopInstanceUID	SOPInstanceUID of image
forceRedownload	whether to re-download if the image is already in the cache

◆ evalDialog()

void evalDialog ( string text = string() )

Opens VivoScript evaluation window with given text.

Parameters

text	Text to write in VivoScript evaluation window

◆ fileExists()

bool fileExists ( string path )

Checks whether file at specified path exists.

Parameters

path	Full path to file

◆ flatIndex()

Index flatIndex ( int i )

Get a script flat image index object used to reference data in the Data Manager The index should be passed directly to function, ie: var t = op.testFunc(VQ.flatIndex(1));.

Parameters

i	The first level position

Note: A flat index is the position relative to all children element in the Data Manager For example, if the Data Manager contains two dynamic data set: 0.(T0,T1) and 1.(T0,T1,T2), to access Data 1.T2, the index 4 can be used.

◆ folderExists()

bool folderExists ( string path )

Checks whether file at specified path exists.

Parameters

path	Full path to folder

◆ frand()

float frand ( )

Returns a random float.

Returns: a random float value

◆ getConfig()

string getConfig	(	string	entry,
		string	defaultValue = `string()`
	)

Returns current value of option in VivoQuant configuration.

Parameters

entry Option in VivoQuant configuration

◆ getDcmString()

string getDcmString	(	AbstractDicomRepository *	rep,
		string	tag,
		string	studyInstanceUID,
		string	seriesInstanceUID,
		string	sopInstanceUID
	)

Looks up the value of the specified tag in the DICOM header of an image in the repository.

Parameters

rep	DICOM repository
tag	DICOM tag
studyInstanceUID	StudyInstanceUID of study
seriesInstanceUID	SeriesInstanceUID of series
sopInstanceUID	SOPInstanceUID of image

◆ getDefaultPal()

string getDefaultPal	(	string	modality,
		int	i
	)

get default palette from modality

Parameters

image	modality
index	in datamanager

Returns: palette name

◆ getEnv()

string getEnv	(	string	key,
		string	defaultValue = `string()`
	)

Get the system's environment variables.

Parameters

key	Name of system environment variable
defaultValue	The default value if they key does not exists

Returns: The variable's value

◆ getHalfLife()

double getHalfLife ( string name )

Get an isotope's half life.

Parameters

name	The isotope's name

◆ getHash()

string getHash	(	string	key,
		string	def = `string()`
	)

inline

Returns current value of key in hash.

Parameters

key	Key in hash

Returns: Value of key in hash as string

◆ getHashNum()

double getHashNum	(	string	key,
		double	def = `0.0f`
	)

inline

Returns current numerical value of key in hash.

Parameters

Key in hash

Returns: Value of key in hash as double

◆ getIndexContainer() [1/2]

Object getIndexContainer ( int i )

Get a script image index container used to reference data in the Data Manager. Use .get() function of the container to access the internal index.

Parameters

i	The first level position

◆ getIndexContainer() [2/2]

Object getIndexContainer	(	int	i,
		int	j
	)

Get a script image index container used to reference data in the Data Manager. Use .get() function of the container to access the internal index.

Parameters

i	The first level position (parent)
j	The second level position (child)

◆ getLocalFiles()

Array< string > getLocalFiles	(	string	caption = `"Select files:"`,
		string	startDir = `string(".")`
	)

Returns array of paths to files selected by user in file dialog.

Parameters

caption	Text in title of dialog
startDir	Default path at which the file dialog starts

◆ getLocalPath()

Object getLocalPath	(	string	caption = `"Select directory:"`,
		string	startDir = `string(".")`
	)

Returns path of directory selected by user in file dialog.

Parameters

caption	Text in title of dialog
startDir	Default path at which file dialog starts

◆ getOS()

string getOS ( )

get current Operating System name

Returns: current OS name. Possible outputs are: Linux, MacOS, Windows and Other.

◆ getROIStats() [1/2]

Object getROIStats ( Index idx )

Returns array of ROI quantification table information for given dataset and ALL ROIs.

Parameters

idx	Index of timestamp dataset from which to calculate stats (see flatIndex())

◆ getROIStats() [2/2]

Object getROIStats	(	Index	idx,
		int	roiID,
		int	layerID = `-1`
	)

Returns object with ROI quantification table information for given dataset and ROI.

Parameters

idx	Index of timestamp dataset from which to calculate stats (see flatIndex())
roiID	Index of ROI for which to calculate stats

◆ getSavePath()

Object getSavePath	(	string	caption = `string("Select output file:")`,
		string	startDir = `string(".")`,
		string	filter = `string()`
	)

Returns path to file selected by user in file dialog.

Parameters

caption	Text in title of dialog
startDir	Default path at which file dialog starts
filter	File type filter for file dialog

◆ getValues()

VariantMap getValues	(	string	title,
		VariantMap &	map,
		bool	modal = `true`
	)

Displays a dialog requesting multiple user inputs in a single form.

Minimal example:

var values = VQ.getValues("Enter ID", { "ID": ["text", ""] });

Creates a modal or non-modal dialog containing one input widget per entry in map. Each map entry produces a labeled row in the form, where the key is used as the label and the value describes the input type and its parameters.

Parameters

title	Window title of the dialog.
map	A map from label text to an input specification. The specification may be either a string or a VariantList:

If the value is a string, it is interpreted as the input type or default value (see implicit behavior below).
If the value is a VariantList, the first element specifies the input type (case-insensitive), and the remaining elements provide type-specific parameters.

Supported explicit input types:

['text',   string default]
['int',    int default, int min, int max, int step]
['double', double default, double min, double max,
            int decimals, double step]
['item',   Array<string> items]

All parameters are optional unless otherwise noted.

Implicit behavior:

If the first element does not match a supported type:
- A single value results in a text input initialized with that value.
- Multiple values result in a combo box containing all values.

For item inputs, the list of items must be provided.

Parameters

modal If true, the dialog is modal and blocks interaction with the rest of the application while open.

Returns: A map from label text to the value entered by the user. The value type depends on the input widget (string, int, double). If the dialog is cancelled, script execution is aborted.

Examples: (see detailed examples below)

◆ getVersion()

string getVersion ( )

Get the string representing the script version.

Parameters

version The version string

◆ getWidget()

Object getWidget ( string name )

Returns an object containing functions/properties of specified widget. Widgets are UI elements (e.g. buttons, checkboxes, combo boxes, etc.) in VivoQuant.

Parameters

name	Name of widget. Names of widgets can be revealed by clicking the Lookup button on the VivoScript toolbar, and clicking the widget.

◆ index() [1/2]

Index index ( int i )

Get a script image index object used to reference data in the Data Manager The index should be passed directly to function, ie: var t = op.testFunc(VQ.index(1));.

Parameters

i	The first level position

Note: Children element cannot be accessed with this function (see flatIndex())

◆ index() [2/2]

Index index	(	int	i,
		int	j
	)

Get a script image index object used to reference data in the Data Manager The index should be passed directly to function, ie: var t = op.testFunc(VQ.index(0,1));.

Parameters

i	The first level position (parent)
j	The second level position (child)

◆ loadHash()

bool loadHash ( string fileName )

Loads local file, containing hash keys and values, to VivoQuant's persistent hash.

Note: Definitions in file should be formatted as "key1 = val1", with each definition separated by a newline. To check whether file was loaded successfully, try VQ.suspend(VQ.getHash(key1)) for a given key in your file. The dialog box that appears should display the value of the given key.

Parameters

fileName Path to file

◆ loadRepository()

Object loadRepository ( string name )

Returns DICOM repository object from DICOM repository saved in VivoQuant.

Parameters

name	Name of DICOM repository saved in VivoQuant

◆ loadRGB()

void loadRGB	(	Index	idx,
		Array< string >	imgFiles,
		float	voxX,
		float	voxY,
		float	voxZ,
		int	rgbRep = `4`,
		bool	forcePlanar = `true`
	)

Load RGB data without the voxel size prompt.

Parameters

idx	Index where opened data should be positioned in the DataManager (see index())
imgFiles	Index List of RGB image to load as a volume
voxX	Expected X voxel size
voxY	Expected Y voxel size
voxZ	Expected Z voxel size
rgbRep	Representation of RGB values (0=Red, 1=Green, 2=Blue, 3=AVG, 4=SUM, 5=MAX, 6=MIN)
forcePlanar	Force volume to load as planar

◆ logMessage() [1/2]

Object logMessage	(	AbstractDicomRepository *	rep,
		string	msg,
		string	type = `string()`
	)

Creates a log message on the given DICOM repository.

Parameters

rep	The DicomRepository object
msg	The message to be logged
type	Message type

◆ logMessage() [2/2]

Object logMessage	(	Index	dataIndex,
		string	msg,
		string	noipacsTitle = `string("Get iPACS from data")`,
		string	type = `string()`
	)

Creates a log message on the given's data iPACS repository.

Parameters

dataIndex	The data index (see index())
msg	The message to be logged
noipacsTitle	Default no iPACS title for warning
type	Message type

◆ lsDir()

Array< string > lsDir	(	string	dir,
		string	nameFilter = `string()`,
		int	filter = `QDir::AllEntries\|QDir::NoDotAndDotDot`,
		QDir::SortFlags	sort = `QDir::Name`
	)

Returns array of files in given directory on local disk.

Parameters

dir	Directory on local disk
nameFilter	Expression to use to filter files. Wildcard (*) is acceptable.

◆ MASTool()

Object MASTool ( string libraryPath = string("") )

Opens Multi-Atlas Segmentation Tool, formerly known as Whole Body Atlas)

Parameters

libraryPath The path of the library to be used

◆ mkdir()

void mkdir	(	string	path,
		string	subdir
	)

Creates sub-directory at specified path.

Parameters

path	Path in which to create new subdirectory
subdir	Name of new subdirectory

◆ openFileExternally()

bool openFileExternally ( string path )

Opens a local file in an external application.

Parameters

path	Full path to file

Returns: True if the request to the operating system to open the file was successfully made, false if the request failed or the file does not exist

◆ preProcess()

string preProcess	(	string	protocol,
		bool	showDialog = `false`
	)

Runs Pre-Processing Tool tool with the given protocol.

Parameters

protocol	String with protocol
showDialog	Whether or not the tool dialog is shown upon being created

◆ PreProcessingTool()

Object PreProcessingTool ( bool showDialog = true )

Opens the Pre-Processing Tool.

Parameters

showDialog Whether or not the tool dialog is shown upon being created

◆ progressDialog()

Object progressDialog	(	string	label,
		string	cancelButtonText,
		int	minimum,
		int	maximum
	)

Returns a progress dialog object, which can be used to show the current state of a longer process.

Note: Use method setValue(x) to set the current value of the progress dialog.; Use method hide() to hide the progress dialog

Parameters

label	Text in title of dialog box
cancelButtonText	Text in button that cancels process
minimum	Minimum value progress dialog object can take
maxmimum	Maximum value progress dialog object can take

◆ query()

Object query	(	AbstractDicomRepository *	rep,
		string	query,
		Array< string >	arguments = `Array< string >()`,
		Object &	fields = `Object()`,
		bool	isPost = `false`
	)

Performs custom query of DICOM repository using the iPACS API.

Parameters

rep	DICOM repository
base	endpoint for the query
arguments	(optional) additional arguments to supply to the query
fields	(optional) fields to submit along with query
isPost	(optional) use POST method for the query

Returns: JSON that is the result of the query or undefined if the request was invalid or the repository doesn't support the iPACS API Example: var output = query(...); if(!output) { // query failed } else { // query was successful and output is an object containing the json result of the query }

◆ queryDataPoints()

Object queryDataPoints	(	AbstractDicomRepository *	rep,
		string	type,
		string	uid,
		string	form
	)

Perform query of DICOM repository for datapoints at project, study, series, or image level, and returns datapoints matching criteria.

Note: Example: VQ.queryDataPoints(rep,'study','1.2.3.4.5','annotation') queries study-level annotation datapoints on study with StudyInstanceUID 1.2.3.4.5

Parameters

rep	DICOM repository
type	Level at which to query datapoints (e.g. project, studies, series, or images)
uid	UID of study, series, or image for which to query datapoints. If querying project-level datapoints, leave this field blank.
form	Form name of datapoint to query

◆ queryImages()

Object queryImages	(	AbstractDicomRepository *	rep,
		string	studyInstanceUID,
		string	seriesInstanceUID
	)

Performs query of DICOM repository for images within a series, and returns images matching criteria.

Parameters

rep	DICOM repository
studyInstanceUID	StudyInstanceUID of study
seriesInstanceUID	SeriesInstanceUID of series

◆ querySeries()

Object querySeries	(	AbstractDicomRepository *	rep,
		string	studyInstanceUID
	)

Performs query of DICOM repository for series within a given study, and returns series matching criteria.

Parameters

rep	DICOM repository
studyInstanceUID	StudyInstanceUID of study

◆ queryStudies()

Object queryStudies	(	AbstractDicomRepository *	rep,
		string	patientName,
		string	patientID = `string()`,
		string	dateRange = `string()`,
		string	studyDesc = `string()`
	)

Performs query of DICOM repository for studies matching argument criteria.

Parameters

rep	DICOM repository
patientName	PatientsName filter
patientID	PatientID filter
dateRange	Date filter
studyDesc	StudyDescription filter

◆ queryStudyPlan()

Object queryStudyPlan	(	AbstractDicomRepository *	rep,
		string	plan,
		string	cohort,
		string	group,
		string	animal,
		string	modality,
		string	date,
		string	event = `"$0"`
	)

If

Parameters

event is omitted, the first event of the day is returned

◆ rand() [1/2]

int rand ( )

Returns a random integer.

Returns

◆ rand() [2/2]

int rand ( int max )

Returns random positive integer less than given maximum.

Parameters

max	Maximum value of random positive integer

◆ readCSVFile()

Object readCSVFile ( string name )

Parse a CSV file into arrays of values.

Parameters

name	The CSV file to read

Returns: A 2D arrays containing the values in the file

◆ readFile()

Array< string > readFile ( string filepath )

Reads file into array of strings.

Parameters

filepath Path to file

◆ renameFile()

bool renameFile	(	string	filepath,
		string	newname
	)

Renames file at given path.

Parameters

Current	path to file
New	path to file

Returns: bool True if file renamed successfully, false otherwise

◆ rmDir()

bool rmDir ( string dirpath )

Removes directory at given path.

Parameters

dirpath Path to directory

Returns: bool True if directory removed successfully, false otherwise

◆ saveDataViaITK()

void saveDataViaITK	(	string	filepath,
		Index	idx
	)

Stores data to disk in ITK MHD/RAW or MHD/ZRAW file format.

Parameters

filepath	Path of output file. Note: should end in .RAW or .ZRAW to output MHD/RAW or MHD/ZRAW pair, respectively.
idx	Index of data to save in Data Manager (see index())

◆ saveDataViaITK4D()

void saveDataViaITK4D ( string filepath )

Stores all data in Data Manager to disk as a single ITK 4D dataset in MHD/RAW or MHD/ZRAW file format.

Parameters

filepath Path of output file. Note: should end in .RAW or .ZRAW to output MHD/RAW or MHD/ZRAW pair, respectively.

◆ saveScreenshot()

bool saveScreenshot ( string fileName )

Saves screenshot of VivoQuant.

Parameters

fileName Output path of screenshot

◆ setConfig()

void setConfig	(	string	entry,
		Variant &	val,
		bool	force = `false`
	)

Sets option in VivoQuant configuration to given value.

Parameters

entry	Option in VivoQuant configuration
val	Desired value
force	(optional) If val is not a recognized value for the entry, determines whether the entry will be forced to take on the value (1) or not (0)

◆ setHash()

void setHash	(	string	key,
		string	val
	)

inline

Sets value of key in hash.

Parameters

key	Key in hash
val	Value for key

◆ setInteractive()

void setInteractive ( bool b )

inline

Sets VivoQuant to interactive (or not)

Parameters

b	Determines whether VivoQuant is interactive (1) or not (0)

◆ setOption()

void setOption	(	string	cbname,
		string	opt
	)

Set widget to given option; for use with widgets with multiple options (e.g. comboboxes)

Parameters

cbname	Name of widget
opt	Name of option

◆ setOptionObj()

void setOptionObj	(	Object	obj,
		string	opt
	)

Set widget to given option; for use with widgets with multiple options (e.g. comboboxes)

Note: Takes widget object as input (can be accessed by VQ.getWidget('widgetName'))

Parameters

obj	Widget object
opt	Name of option

◆ setTestMode()

void setTestMode ( bool b = true )

inline

Sets VivoQuant to test mode (or not)

Parameters

b	Determines whether VivoQuant is in test mode (1) or not (0)

◆ setVersion()

void setVersion ( string version )

Set a string representing the script version that will be used in audit log messages.

Parameters

version The version string

◆ showMessage()

void showMessage	(	string	msg,
		bool	modal = `true`
	)

Displays dialog box with user-defined message.

Parameters

msg	Message displayed in dialog box
modal	Determines whether VivoQuant is inaccessible while dialog box is open (true) or accessible (false)

◆ sin()

double sin ( double f )

inline

Returns sin of angle.

Parameters

f	Angle (in radians)

◆ splitROI2DICOM()

void splitROI2DICOM ( Index idx )

For each ROI in the 3D ROI Tool, creates a masked image of a given image in the Data Manager, where voxels outside the ROI are mapped to the given image's minimum.

Note: Example: Brain and Heart ROIs in the 3D ROI Tool. splitROI2DICOM(0) will create a masked image of the Reference image where all but the Brain ROI is masked out, and a masked image of the Reference image where all but the Heart ROI is masked out

Parameters

id	Index of image in Data Manager (see index())

◆ startTool()

string startTool	(	string	tool,
		string	baseDir = `"."`,
		Array< string >	args = `Array< string >()`
	)

Start an external tool.

Parameters

tool	The application or external script to start
key	baseDir The working directory for the tool
key	args The list of arguments for the tool

Returns: A string containing the status of the tool

◆ storeAsDICOM()

int storeAsDICOM	(	string	filepath,
		Index	idx,
		DICOMImageFormat	format,
		bool	compress = `false`,
		bool	quiet = `true`
	)

Stores data to disk in DICOM file format.

Parameters

filepath	Path of output file.
idx	Index of data to save in DataManager (see index())
format	A value of VQEnum::DICOMImageFormat
compress	Use JPEG2000 Lossless compression
quiet	Hide warning, error or information dialog

Note: Regarding format: 0 = Multi-Frame Module, 1 = Multi-Frame Functional Group, 2 = Single Frames

Returns: Success indicator: 0 = SaveOK, 1 = SaveAborted, 2 = SaveError

◆ storeAsDICOMByTimepoint()

int storeAsDICOMByTimepoint	(	string	filepath,
		int	idx,
		DICOMImageFormat	format,
		bool	compress = `false`,
		TimePointsSettings	timepointOption = `TimePointsSettings::AllTimePoints`,
		TimepointFilesSettings	timepointPerFileOption = `TimepointFilesSettings::SingleFileForAllTimepoints`
	)

Stores data to disk in DICOM file format, with the option to save by timepoint.

Parameters

filepath	Path of output file
idx	Index of data to save in DataManager
format	A value of VQEnum::DICOMImageFormat
compress	Use JPEG2000 Lossless compression
timepointOption	Selection of timepoints from VQEnum::TimePointsSettings
timepointPerFileOption	Selection of output files from VQEnum::TimepointFilesSettings To save current timepoint, first move to the desired timepoint using: VQ.dataManager().setDynamicActive(VQ.index(idx), timepoint_idx);

Returns: Success indicator: 0 = SaveOK, 1 = SaveAborted, 2 = SaveError

◆ storeAsRaw()

bool storeAsRaw	(	string	filepath,
		Index	idx
	)

Stores data to disk in MHD/RAW (or MHD/ZRAW) file format.

Parameters

filepath	Path of output file. Note: should end in .RAW or .ZRAW to output MHD/RAW or MHD/ZRAW pair, respectively.
idx	Index of data to save in Data Manager (see index())

◆ storeData()

int storeData	(	AbstractDicomRepository *	rep,
		Index	idx,
		DICOMImageFormat	format,
		bool	compress = `false`
	)

Stores DICOM data to a DICOM repository.

Parameters

rep	The DICOM repository object
idx	Index of data to save in DataManager (see index()) VQEnum::DICOMImageFormat
format	A value of VQEnum::DICOMImageFormat
compress	Use JPEG2000 Lossless compression

Returns: Success indicator: 0 = SaveOK, 1 = SaveAborted, 2 = SaveError.

See also: DICOMImageFormat

◆ storeDataByTimepoint()

int storeDataByTimepoint	(	AbstractDicomRepository *	rep,
		int	idx,
		DICOMImageFormat	format,
		bool	compress = `false`,
		TimePointsSettings	timepointOption = `TimePointsSettings::AllTimePoints`,
		TimepointFilesSettings	timepointPerFileOption = `TimepointFilesSettings::SingleFileForAllTimepoints`
	)

Stores DICOM data to a DICOM repository, with the option to save by timepoint.

Parameters

rep	The DICOM repository object
idx	Index of data to save in DataManager
format	A value of VQEnum::DICOMImageFormat
compress	Use JPEG2000 Lossless compression
timepointOption	For dynamic data, 0=Save all timepoints, 1=Save current timepoint. Ignored for static data.
timepointPerFileOption	For dynamic images, 0=In a single file, 1=One file per timepoint. Ignored for static data.

Returns: Success indicator: 0 = SaveOK, 1 = SaveAborted, 2 = SaveError

◆ storeHash()

bool storeHash ( string fileName )

Stores all keys and values in hash to local file.

Parameters

fileName Path to output file in which to store hash keys and values

◆ stripCredentials()

string stripCredentials ( string url_string )

Returns URL of DICOM repository with credentials (username and password) removed.

Parameters

url_string Full URL with credentials

◆ submitDataPoint()

Object submitDataPoint	(	AbstractDicomRepository *	rep,
		string	uid,
		Object &	data,
		string	type = `string()`
	)

Submits datapoint to DICOM repository.

Note: Example: VQ.submitDataPoint(rep,'1.2.3.4.5',{text: 'This is a datapoint!'},'annotation') submits an annotation datapoint to the study with StudyInstanceUID 1.2.3.4.5 in the DICOM repository rep with text 'This is a datapoint!'

Parameters

rep	DICOM repository
uid	UID of study, series, or image for which to submit datapoint. If submitting project-level datapoints, leave this field blank.
data	Object with datapoint fields as the object keys
type	Level at which to submit datapoint (e.g. project, studies, series, or image)

◆ suspend()

void suspend ( string message = string() )

Suspends script and opens a modeless "Resume" dialog.

Parameters

message String to display in dialog box

◆ webDisk()

Object webDisk ( string rep )

Return IPACS WebDisk object for project in given iPACS repository.

Parameters

rep	DICOM repository, including URL/path to repository and path to WebDisk directory

◆ writeFile()

bool writeFile	(	string	filepath,
		string	text
	)

Writes file to disk with given text.

Note: If file exists, will overwrite file.

Parameters

filepath	Path to output file
text	Text to write to output file

Public Member Functions

Detailed Description

Member Function Documentation

◆ appendFile()

◆ askForCancelReason()

◆ askYesNoQuestion()

◆ auditTrailMessage()

◆ availableItems()

◆ availableItemsObj()

◆ BrainAtlasTool()

◆ copyFile()

◆ cos()

◆ counter()

◆ dcmRep()

◆ debug()

◆ deleteFile()

◆ deletePath()

◆ dicomBrowser()

◆ dicomBrowserLoad() [1/2]

◆ dicomBrowserLoad() [2/2]

◆ downloadImages() [1/3]

◆ downloadImages() [2/3]

◆ downloadImages() [3/3]

◆ evalDialog()

◆ fileExists()

◆ flatIndex()

◆ folderExists()

◆ frand()

◆ getConfig()

◆ getDcmString()

◆ getDefaultPal()

◆ getEnv()

◆ getHalfLife()

◆ getHash()

◆ getHashNum()

◆ getIndexContainer() [1/2]

◆ getIndexContainer() [2/2]

◆ getLocalFiles()

◆ getLocalPath()

◆ getOS()

◆ getROIStats() [1/2]

◆ getROIStats() [2/2]

◆ getSavePath()

◆ getValues()

◆ getVersion()

◆ getWidget()

◆ index() [1/2]

◆ index() [2/2]

◆ loadHash()

◆ loadRepository()

◆ loadRGB()

◆ logMessage() [1/2]

◆ logMessage() [2/2]

◆ lsDir()

◆ MASTool()

◆ mkdir()

◆ openFileExternally()

◆ preProcess()

◆ PreProcessingTool()

◆ progressDialog()

◆ query()

◆ queryDataPoints()

◆ queryImages()

◆ querySeries()

◆ queryStudies()

◆ queryStudyPlan()

◆ rand() [1/2]

◆ rand() [2/2]

◆ readCSVFile()

◆ readFile()

◆ renameFile()

◆ rmDir()

◆ saveDataViaITK()

◆ saveDataViaITK4D()

◆ saveScreenshot()

◆ setConfig()

◆ setHash()

◆ setInteractive()

◆ setOption()

◆ setOptionObj()