Object for managing and querying all image data and meta-information in VivoQuant. More...

Public Member Functions
bool	openDat (int type, Array< string > fileNames, bool forcePlanar=false, bool embedSliceDefault=false)
	Load a new image into VivoQuant from a list of filenames. More...

int	numROIs ()
	Get number of regions of interest currently specified, including background Always greater than 1. More...

int	getDimX (Index idx)
	Get the number of sagittal slices ("X" dimension) in an image. More...

int	getDimY (Index idx)
	Get the number of coronal slices ("Y" dimension) in an image. More...

int	getDimZ (Index idx)
	Get the number of transverse/axial slices ("Z" dimension) in an image. More...

int	getDim (int id, Index idx)
	Get number of slices in an image along specified dimension. More...

int	getSize (Index idx)
	Get total number of voxels in an image. More...

float	getValue (int x, int y, int z, Index idx)
	Return the raw pixel value at provided voxel/pixel location. More...

float	getMin (Index idx)
	Get minimum raw voxel/pixel value of an image. More...

float	getMax (Index idx)
	Get maximum raw voxel/pixel value of an image. More...

void	setDynamicActive (Index idx, int activeId)
	Set the activated index for dynamic data. More...

int	getDynamicActive (Index idx)
	Get the activated child index for dynamic data. More...

bool	copyAsNewSeries (Index idx)
	Copy a given data set timepoint from a dynamic collapsed data set. More...

float	getMinCached (Index idx)
	Get the cached min intensity value of an image. More...

float	getMaxCached (Index idx)
	Get the cached max intensity value of an image. More...

void	setMinMaxCache (Index idx, float min, float max)
	Set the cached min/max intensity value of an image. More...

float	getLevelCached (Index idx)
	Get the cached window level itensity value of an image. More...

float	getWidthCached (Index idx)
	Get the cached window width itensity value of an image. More...

void	setLevelWidthCache (Index idx, float level, float width)
	Set the cached window level/width intensity value of an image. More...

bool	isPlanar (Index idx)
	Check if a given data set is planar or not. More...

string	getDataTypeString (Index idx)
	Get a string containing the data type of a given data set. More...

float	voxelSizeDim (int dim, Index idx)
	Get the voxel size of a given data set for a given dimension. More...

float	voxelSizeX (Index idx)
	Get the X voxel size of a given data set. More...

float	voxelSizeY (Index idx)
	Get the Y voxel size of a given data set. More...

float	voxelSizeXY (Index idx)
	Get the XY voxel size of a given data set. More...

float	voxelSizeZ (Index idx)
	Get the Z voxel size of a given data set. More...

string	getDesc (Index idx, string key)
	Get a DICOM tag value from a given data set. More...

void	setDesc (Index idx, string key, string val)
	Set a DICOM tag value to a given data set. More...

void	setDescs (Index idx, Array< string > keys, Array< string > vals)
	Set a list of DICOM tag value to a given data set. More...

double	getSUL (Index idx)
	Get the SUL value of a given data set. More...

string	getDcmString (Index idx, string key)
	Get a DICOM tag string value from a given data set. More...

string	getSOPUID (Index idx)
	Get the SOP UID of a given data set. More...

string	getSeriesUID (Index idx)
	Get the Series ID of a given data set. More...

string	getStudyUID (Index idx)
	Get the Study ID of a given data set. More...

void	setUniqueStudyID (Index idx)
	Set a unique Study ID to a given data set. More...

void	setUniqueStudyID (Index idx, string id)
	Set the given unique Study ID to a given data set. More...

Index	getParentImageIndex (DcmDataset *childImageHeader)
	Finds the index in the DataManager for a possible parent image to a dependent DICOM, for example the original image an RTSTRUCT would have been drawn on. We can match on either of the following: More...

string	getDataDetailsString (Index idx)
	Return a string with image details (original vs loaded for current voxel sizes, dimensions, and direction cosines matrix.) More...

string	getHeaderSummary (Index idx)
	Return a string with the header summary ( modality, patient name, and series description) More...

int	size ()
	Return number of data in first level.

int	count (Index parent=Index())
	Return number of dynamic data set contained at given index. More...

int	maxVis ()
	Return the maximum number size that can be visualized.

bool	hasValid (Index idx)
	Check if the Data Manager holds valid data at the given index. More...

void	setPaletteParameters (Index idx, float param1, float param2)
	Set the palette values for the given data in Data Manager This function independent of the palette type. More...

void	setPaletteFromTo (Index idx, float from, float to)
	Set the palette "from" and "to" value for the given data in Data Manager. More...

void	setPaletteFrom (Index idx, float from)
	Set the palette "from" value for the given data in Data Manager. More...

void	setPaletteTo (Index idx, float to)
	Set the palette "to" value for the given data in Data Manager. More...

void	setPaletteLevel (Index idx, float level)
	Set the palette "level" value for the given data in Data Manager. More...

void	setPaletteWidth (Index idx, float width)
	Set the palette "width" value for the given data in Data Manager. More...

void	setPalette (Index idx, string name)
	Set the palette for the given data in Data Manager. More...

void	invertPalette (Index idx)
	Invert the palette for the given data in Data Manager. More...

void	saveDataPaletteParameter (string name)
	Save palette parameter to disk. More...

void	loadDataPaletteParameter (string name)
	load palette parameter from file More...

float	getPaletteFrom (Index idx)
	Get the palette "from" value for the given data in Data Manager. More...

float	getPaletteTo (Index idx)
	Get the palette "to" value for the given data in Data Manager. More...

float	getPaletteLevel (Index idx)
	Get the palette window "level" value for the given data in Data Manager. More...

float	getPaletteWidth (Index idx)
	Get the palette window "width" value for the given data in Data Manager. More...

string	getPaletteName (Index idx)
	Get the palette name for the given data in Data Manager. More...

bool	isPaletteInverted (Index idx)
	Get the inverted status of the palette for the given data in Data Manager. More...

void	unloadData (Index idx, int num=1)
	Unloads data. More...

void	unloadData (Array< Index > indices)
	Unloads a list of data. More...

void	swapData (Index a, Index b)
	Swap the position of two data set in the Data Manager. More...

void	moveData (Array< Index > list, int dst)
	Move data set in the Data Manager. More...

bool	mergeData (Array< Index > list, bool quiet=true)
	Create a collapsed data set with the selected data. More...

void	removeTag (Index idx, string key)
	Remove a DICOM tag or sequence item from a given data set. More...

void	stackData (Array< int > &list, bool quiet=true)
	Create and append an image using multiple single-slice images and unload the images it was created from. More...

void	stackDataMultiple (QList< Variant > &list, bool quiet=true)
	Create and append images using multiple single-slice images and unload the images they were created from. More...

Protected Attributes
QVector< TPointAndMode >	m_paths
	list of annotation graphs

Friends
class	ImageSelectorWidget

Detailed Description

Object for managing and querying all image data and meta-information in VivoQuant.

This object can be used to query meta-information from an image, including the DICOM header. It can also be used to open/append new images into VQ and remove/unload images that are currently loaded.

Image data are indexed starting at zero. See also ScriptMaster::dataManager() to obtain this object.

Member Function Documentation

◆ copyAsNewSeries()

bool copyAsNewSeries ( Index idx )

Copy a given data set timepoint from a dynamic collapsed data set.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ count()

int count ( Index parent = Index() )

Return number of dynamic data set contained at given index.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getDataDetailsString()

string getDataDetailsString ( Index idx )

Return a string with image details (original vs loaded for current voxel sizes, dimensions, and direction cosines matrix.)

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getDataTypeString()

string getDataTypeString ( Index idx )

Get a string containing the data type of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ getDcmString()

string getDcmString	(	Index	idx,
		string	key
	)

Get a DICOM tag string value from a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

Note: For all non-dynamic tag, use the top level parent index, only dynamic tags should be used with child index.

◆ getDesc()

string getDesc	(	Index	idx,
		string	key
	)

Get a DICOM tag value from a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())
keys	The tag/key
vals	The value

Note: For all non-dynamic tag, use the top level parent index, only dynamic tags should be used with child index.

◆ getDim()

int getDim	(	int	id,
		Index	idx
	)

Get number of slices in an image along specified dimension.

Parameters

id	Plane/dimension to query: 0=Sagittal, 1=Coronal, 2=Transverse/Axial
idx	Index of data (see ScriptMaster::index())

Returns: Dimension size, zero if no data are loaded at position i

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ getDimX()

int getDimX ( Index idx )

Get the number of sagittal slices ("X" dimension) in an image.

Parameters

idx	Index of data (see ScriptMaster::index())

Returns: Number of sagittal slices, zero if no data are loaded at position i

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ getDimY()

int getDimY ( Index idx )

Get the number of coronal slices ("Y" dimension) in an image.

Parameters

idx	Index of data (see ScriptMaster::index())

Returns: Number of coronal slices, zero if no data are loaded at position i

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ getDimZ()

int getDimZ ( Index idx )

Get the number of transverse/axial slices ("Z" dimension) in an image.

Parameters

idx	Index of data (see ScriptMaster::index())

Returns: Number of transverse/axial slices, zero if no data are loaded at position i

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ getDynamicActive()

int getDynamicActive ( Index idx )

Get the activated child index for dynamic data.

Parameters

idx	Index of data (see ScriptMaster::index())

Returns: Child index if any, -1 otherwise

◆ getHeaderSummary()

string getHeaderSummary ( Index idx )

Return a string with the header summary ( modality, patient name, and series description)

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getLevelCached()

float getLevelCached ( Index idx )

Get the cached window level itensity value of an image.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getMax()

float getMax ( Index idx )

Get maximum raw voxel/pixel value of an image.

Parameters

idx	Index of data (see ScriptMaster::index())

Returns: Maximum or NaN if no image exists at provided index, in native data units

◆ getMaxCached()

float getMaxCached ( Index idx )

Get the cached max intensity value of an image.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getMin()

float getMin ( Index idx )

Get minimum raw voxel/pixel value of an image.

Parameters

idx	Index of data (see ScriptMaster::index())

Returns: Minimum or NaN if no image exists at provided index, in native data units

◆ getMinCached()

float getMinCached ( Index idx )

Get the cached min intensity value of an image.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getPaletteFrom()

float getPaletteFrom ( Index idx )

Get the palette "from" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getPaletteLevel()

float getPaletteLevel ( Index idx )

Get the palette window "level" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getPaletteName()

string getPaletteName ( Index idx )

Get the palette name for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getPaletteTo()

float getPaletteTo ( Index idx )

Get the palette "to" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getPaletteWidth()

float getPaletteWidth ( Index idx )

Get the palette window "width" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getParentImageIndex()

Index getParentImageIndex ( DcmDataset * childImageHeader )

Finds the index in the DataManager for a possible parent image to a dependent DICOM, for example the original image an RTSTRUCT would have been drawn on. We can match on either of the following:

ReferencedSOPInstanceUID child string including a SOPInstanceUID parent string
Same study ID

Parameters

childImageHeader the DICOM header for the child image

Returns: -1 if image not found, otherwise the index of a matching image in the DataManager.

◆ getSeriesUID()

string getSeriesUID ( Index idx )

Get the Series ID of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getSize()

int getSize ( Index idx )

Get total number of voxels in an image.

Parameters

idx	Index of data (see ScriptMaster::index())

Returns: Dimension size, zero if no data are loaded at position i

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ getSOPUID()

string getSOPUID ( Index idx )

Get the SOP UID of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getStudyUID()

string getStudyUID ( Index idx )

Get the Study ID of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getSUL()

double getSUL ( Index idx )

Get the SUL value of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ getValue()

float getValue	(	int	x,
		int	y,
		int	z,
		Index	idx
	)

Return the raw pixel value at provided voxel/pixel location.

Parameters

x	Sagittal slice index
y	Coronal slice index
z	Transverse/Axial slice index
idx	Index of data (see ScriptMaster::index())

Returns: Dimension size, zero if no data are loaded at the given index position

◆ getWidthCached()

float getWidthCached ( Index idx )

Get the cached window width itensity value of an image.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ hasValid()

bool hasValid ( Index idx )

inline

Check if the Data Manager holds valid data at the given index.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ invertPalette()

void invertPalette ( Index idx )

Invert the palette for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ isPaletteInverted()

bool isPaletteInverted ( Index idx )

Get the inverted status of the palette for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ isPlanar()

bool isPlanar ( Index idx )

Check if a given data set is planar or not.

Parameters

idx	Index of data (see ScriptMaster::index())

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ loadDataPaletteParameter()

void loadDataPaletteParameter ( string name )

load palette parameter from file

Parameters

path	with file name(*.txt)

◆ mergeData()

bool mergeData	(	Array< Index >	list,
		bool	quiet = `true`
	)

Create a collapsed data set with the selected data.

Parameters

list	List of data index to be grouped (see ScriptMaster::index())

◆ moveData()

void moveData	(	Array< Index >	list,
		int	dst
	)

Move data set in the Data Manager.

Parameters

a	List of data index to moved (see ScriptMaster::index())
b	Index of the parent destination to be moved.

Note: When using dynamic data, only parent index can be moved and used as a destination.

◆ numROIs()

int numROIs ( )

Get number of regions of interest currently specified, including background Always greater than 1.

Returns: Number of ROIs

◆ openDat()

bool openDat	(	int	type,
		Array< string >	fileNames,
		bool	forcePlanar = `false`,
		bool	embedSliceDefault = `false`
	)

Load a new image into VivoQuant from a list of filenames.

Parameters

type	Position where image will be loaded into the list. 0=Reference, 1=Input 1, etc.
fileNames	Array of filenames containing full paths or path relative to current working directory where VQ was started from
forcePlanar	(Optional) Indicates whether image should be forced into "Planar" mode upon loading https://www.vivoquant.com/cgi-bin/manual.cgi?config-data.html
embedSliceDefault	(Optional) Indicates whether default values for embed slice (embedded in the center of the reference data) should be used or a dialog prompt will appear to define it. Only applies for plannar data.

Returns: true if data is loaded successfully, otherwise returns false

◆ removeTag()

void removeTag	(	Index	idx,
		string	key
	)

Remove a DICOM tag or sequence item from a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())
key	The tag/key

◆ saveDataPaletteParameter()

void saveDataPaletteParameter ( string name )

Save palette parameter to disk.

Parameters

output path with file name(*.txt)

◆ setDesc()

void setDesc	(	Index	idx,
		string	key,
		string	val
	)

Set a DICOM tag value to a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())
keys	The tag/key
vals	The value

Note: For all non-dynamic tag, use the top level parent index, only dynamic tags should be used with child index.

◆ setDescs()

void setDescs	(	Index	idx,
		Array< string >	keys,
		Array< string >	vals
	)

Set a list of DICOM tag value to a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())
keys	The list of tags/keys
vals	The list of values

Note: For all non-dynamic tag, use the top level parent index, only dynamic tags should be used with child index.

◆ setDynamicActive()

void setDynamicActive	(	Index	idx,
		int	activeId
	)

Set the activated index for dynamic data.

Parameters

idx	Index of data (see ScriptMaster::index())
activeId	indicate the number of child to be displayed.

◆ setLevelWidthCache()

void setLevelWidthCache	(	Index	idx,
		float	level,
		float	width
	)

Set the cached window level/width intensity value of an image.

Parameters

idx	Index of data (see ScriptMaster::index())
level	Window level or center
width	Window width

◆ setMinMaxCache()

void setMinMaxCache	(	Index	idx,
		float	min,
		float	max
	)

Set the cached min/max intensity value of an image.

Parameters

idx	Index of data (see ScriptMaster::index())
level	Window min
width	Window max

◆ setPalette()

void setPalette	(	Index	idx,
		string	name
	)

Set the palette for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())
name	Name of the palette

◆ setPaletteFrom()

void setPaletteFrom	(	Index	idx,
		float	from
	)

Set the palette "from" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())
from	From parameter value from 0-1.0

◆ setPaletteFromTo()

void setPaletteFromTo	(	Index	idx,
		float	from,
		float	to
	)

Set the palette "from" and "to" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())
from	From parameter value from 0-1.0
to	for right parameter from 0-1.0

◆ setPaletteLevel()

void setPaletteLevel	(	Index	idx,
		float	level
	)

Set the palette "level" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())
level	Level parameter value from 0-1.0

◆ setPaletteParameters()

void setPaletteParameters	(	Index	idx,
		float	param1,
		float	param2
	)

Set the palette values for the given data in Data Manager This function independent of the palette type.

Parameters

idx	Index of data (see ScriptMaster::index())
param1	First parameter value from 0-1.0
param2	Second parameter value from 0-1.0

Note: If the palette type is Min/Max the param1 and param2 are expected to be from and to respectively. If the palette type is Window Width/Level the param1 and param2 are expected to be width and level respectively.

◆ setPaletteTo()

void setPaletteTo	(	Index	idx,
		float	to
	)

Set the palette "to" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())
to	To parameter value from 0-1.0

◆ setPaletteWidth()

void setPaletteWidth	(	Index	idx,
		float	width
	)

Set the palette "width" value for the given data in Data Manager.

Parameters

idx	Index of data (see ScriptMaster::index())
width	Width parameter value from 0-1.0

◆ setUniqueStudyID() [1/2]

void setUniqueStudyID ( Index idx )

Set a unique Study ID to a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ setUniqueStudyID() [2/2]

void setUniqueStudyID	(	Index	idx,
		string	id
	)

Set the given unique Study ID to a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

◆ stackData()

void stackData	(	Array< int > &	list,
		bool	quiet = `true`
	)

Create and append an image using multiple single-slice images and unload the images it was created from.

Parameters

list	The indices of the data to be stacked
quiet	(optional) If true, warnings are displayed in a UI popup, if false they are printed to the debug output.

◆ stackDataMultiple()

void stackDataMultiple	(	QList< Variant > &	list,
		bool	quiet = `true`
	)

Create and append images using multiple single-slice images and unload the images they were created from.

Parameters

list	A list of lists, where each list contains indices of data that will be stacked into one image
quiet	(optional) If true, warnings are displayed in a UI popup, if false they are printed to the debug output.

◆ swapData()

void swapData	(	Index	a,
		Index	b
	)

Swap the position of two data set in the Data Manager.

Parameters

a	Frist data index to swap (see ScriptMaster::index())
b	Second data index to swap (see ScriptMaster::index())

Note: When using dynamic data, only parent index can be swapped

◆ unloadData() [1/2]

void unloadData ( Array< Index > indices )

Unloads a list of data.

Parameters

indices A list containing the indices to unload (see ScriptMaster::index())

◆ unloadData() [2/2]

void unloadData	(	Index	idx,
		int	num = `1`
	)

Unloads data.

Parameters

from	Index at which to start unloading (see ScriptMaster::index())
num	Number of consecutive datasets to unload at the same level, starting with and including startIndex

◆ voxelSizeDim()

float voxelSizeDim	(	int	dim,
		Index	idx
	)

Get the voxel size of a given data set for a given dimension.

Parameters

dim	the Dimension (x:0, y:1, z:2)
idx	Index of data (see ScriptMaster::index())

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ voxelSizeX()

float voxelSizeX ( Index idx )

Get the X voxel size of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ voxelSizeXY()

float voxelSizeXY ( Index idx )

Get the XY voxel size of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ voxelSizeY()

float voxelSizeY ( Index idx )

Get the Y voxel size of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

Note: The index parameter is optional. If not specified, it will return the value for the first data set

◆ voxelSizeZ()

float voxelSizeZ ( Index idx )

Get the Z voxel size of a given data set.

Parameters

idx	Index of data (see ScriptMaster::index())

Note: The index parameter is optional. If not specified, it will return the value for the first data set

Public Member Functions

Protected Attributes

Friends

Detailed Description

Member Function Documentation

◆ copyAsNewSeries()

◆ count()

◆ getDataDetailsString()

◆ getDataTypeString()

◆ getDcmString()

◆ getDesc()

◆ getDim()

◆ getDimX()

◆ getDimY()

◆ getDimZ()

◆ getDynamicActive()

◆ getHeaderSummary()

◆ getLevelCached()

◆ getMax()

◆ getMaxCached()

◆ getMin()

◆ getMinCached()

◆ getPaletteFrom()

◆ getPaletteLevel()

◆ getPaletteName()

◆ getPaletteTo()

◆ getPaletteWidth()

◆ getParentImageIndex()

◆ getSeriesUID()

◆ getSize()

◆ getSOPUID()

◆ getStudyUID()

◆ getSUL()

◆ getValue()

◆ getWidthCached()

◆ hasValid()

◆ invertPalette()

◆ isPaletteInverted()

◆ isPlanar()

◆ loadDataPaletteParameter()

◆ mergeData()

◆ moveData()

◆ numROIs()

◆ openDat()

◆ removeTag()

◆ saveDataPaletteParameter()

◆ setDesc()

◆ setDescs()

◆ setDynamicActive()

◆ setLevelWidthCache()

◆ setMinMaxCache()

◆ setPalette()

◆ setPaletteFrom()

◆ setPaletteFromTo()

◆ setPaletteLevel()

◆ setPaletteParameters()

◆ setPaletteTo()

◆ setPaletteWidth()

◆ setUniqueStudyID() [1/2]

◆ setUniqueStudyID() [2/2]

◆ stackData()

◆ stackDataMultiple()

◆ swapData()

◆ unloadData() [1/2]

◆ unloadData() [2/2]

◆ voxelSizeDim()

◆ voxelSizeX()

◆ voxelSizeXY()

◆ voxelSizeY()

◆ voxelSizeZ()