SegmentationServiceNMCT Class Reference

Description

Handles operation of the 3D Brain Atlas Tool.

Please refer to VQ.BrainAtlasTool() to obtain this object.

Public Slots
void	run ()
	Runs the tool.
bool	openCustomAtlasWizard ()
	Create a new instance of the custom atlas wizard and show it.
Array< string >	getAllAnimalNames ()

Public Member Functions
Object	getWidget (string name)
	Gets a widget from the dialog widgets Widget Reference - BrainAtlasTool.
void	setQuietMode (bool quiet)
	Control whether or not the tool produces message windows.
void	setVisible (bool visible)
	Control whether or not the tool is visible.
void	setOutputFormat (string format)
	Choose the style of output.
Array< string >	createNewAtlas (string nameStem, string refFile, string roiFile, Array< string > keyFiles=Array< string >())
	Set up a new atlas in the atlas folder.
Array< string >	createNewAtlas (string nameStem, string refFile, int layer=-1, Array< string > keyFiles=Array< string >())
	Set up a new atlas in the atlas folder.
Array< string >	createNewAtlas (string nameStem, Index refIdx, string roiFile, Array< string > keyFiles=Array< string >())
	Set up a new atlas in the atlas folder.
Array< string >	createNewAtlas (string nameStem, Index refIdx, int layer=-1, Array< string > keyFiles=Array< string >())
	Set up a new atlas in the atlas folder.
void	removeAtlas (string atlasName)
	Remove an atlas from the atlas folder.

Member Function Documentation

createNewAtlas() [1/4]

Array< string > createNewAtlas	(	string	nameStem,
		Index	refIdx,
		int	layer = -1,
		Array< string >	keyFiles = Array< string >() )

Set up a new atlas in the atlas folder.

Parameters

nameStem	The name stem to be used to name all the atlas files, which should include the species name at the end (ex: ExampleMouse)
refIdx	The index in the data list of the image to be used as an anatomical reference. (see VQ.index())
layer	(optional) The ROI layer to be saved to an rmha to use for the atlas ROIs. To use all layers set this to -1. If no argument is provided, all layers will be used.
keyFiles	(optional) The paths of the keyfile CSVs. If none are provided, they will be automatically generated

createNewAtlas() [2/4]

Array< string > createNewAtlas	(	string	nameStem,
		Index	refIdx,
		string	roiFile,
		Array< string >	keyFiles = Array< string >() )

Set up a new atlas in the atlas folder.

Parameters

nameStem	The name stem to be used to name all the atlas files, which should include the species name at the end (ex: ExampleMouse)
refIdx	The index in the data list of the image to be used as an anatomical reference. (see VQ.index())
roiFile	The path of the rmha to be used for the atlas ROIs
keyFiles	(optional) The paths of the keyfile CSVs. If none are provided, they will be automatically generated

createNewAtlas() [3/4]

Array< string > createNewAtlas	(	string	nameStem,
		string	refFile,
		int	layer = -1,
		Array< string >	keyFiles = Array< string >() )

Set up a new atlas in the atlas folder.

Parameters

nameStem	The name stem to be used to name all the atlas files, which should include the species name at the end (ex: ExampleMouse)
refFile	The path of the image to be used as an anatomical reference
layer	(optional) The ROI layer to be saved to an rmha to use for the atlas ROIs. To use all layers set this to -1. If no argument is provided, all layers will be used.
keyFiles	(optional) The paths of the keyfile CSVs. If none are provided, they will be automatically generated

createNewAtlas() [4/4]

Array< string > createNewAtlas	(	string	nameStem,
		string	refFile,
		string	roiFile,
		Array< string >	keyFiles = Array< string >() )

Set up a new atlas in the atlas folder.

Parameters

nameStem	The name stem to be used to name all the atlas files, which should include the species name at the end (ex: ExampleMouse)
refFile	The path of the image to be used as an anatomical reference
roiFile	The path of the rmha to be used for the atlas ROIs
keyFiles	(optional) The paths of the keyfile CSVs. If none are provided, they will be automatically generated

getAllAnimalNames

Array< string > getAllAnimalNames ( )

slot

Returns

List of supported animal names.

getWidget()

Object getWidget

(

string

name

)

Gets a widget from the dialog widgets Widget Reference - BrainAtlasTool.

Parameters

name	The name of the widget to get

Returns

A widget object

openCustomAtlasWizard

bool openCustomAtlasWizard ( )

slot

Create a new instance of the custom atlas wizard and show it.

Returns

False if the wizard was closed with Cancel, True if the wizard was successful

removeAtlas()

void removeAtlas

(

string

atlasName

)

Remove an atlas from the atlas folder.

Parameters

atlasName

The name stem of the atlas to remove.

setOutputFormat()

void setOutputFormat

(

string

format

)

Choose the style of output.

Parameters

format

"Standard" or "Master"

setQuietMode()

void setQuietMode ( bool quiet )

inline

Control whether or not the tool produces message windows.

Parameters

quiet

if true, prevents message windows and results loading

setVisible()

void setVisible

(

bool

visible

)

Control whether or not the tool is visible.

Parameters

visible

if true, tool will be shown, and if false, tool will be hidden