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SegmentationServiceNMCT Class Reference

Handles operation of the 3D Brain Atlas Tool. More...

Public Slots

void run ()
 Runs the tool.
 
bool openCustomAtlasWizard ()
 Create a new instance of the custom atlas wizard and show it. More...
 

Public Member Functions

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

Detailed Description

Handles operation of the 3D Brain Atlas Tool.

Please refer to ScriptMaster::BrainAtlasTool() to obtain this object.

Member Function Documentation

◆ createNewAtlas() [1/4]

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

Set up a new atlas in the atlas folder.

Parameters
nameStemThe name stem to be used to name all the atlas files
refFileThe path of the image to be used as an anatomical reference
roiFileThe path of the rmha to be used for the atlas ROIs
keyFile(optional) The paths of the keyfile CSVs. If none are provided, they will be automatically generated

◆ createNewAtlas() [2/4]

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
nameStemThe name stem to be used to name all the atlas files
refFileThe 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.
keyFile(optional) The paths of the keyfile CSVs. If none are provided, they will be automatically generated

◆ createNewAtlas() [3/4]

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

Set up a new atlas in the atlas folder.

Parameters
nameStemThe name stem to be used to name all the atlas files
refIdxThe index in the data list of the image to be used as an anatomical reference. (see ScriptMaster::index)
roiFileThe path of the rmha to be used for the atlas ROIs
keyFile(optional) The paths of the keyfile CSVs. If none are provided, they will be automatically generated

◆ createNewAtlas() [4/4]

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
nameStemThe name stem to be used to name all the atlas files
refIdxThe index in the data list of the image to be used as an anatomical reference. (see ScriptMaster::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.
keyFile(optional) The paths of the keyfile CSVs. If none are provided, they will be automatically generated

◆ getWidget()

Object getWidget ( string  name)

Gets a widget from the dialog widgets.

Parameters
nameThe 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
atlasNameThe 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
quietif true, prevents message windows and results loading

◆ setVisible()

void setVisible ( bool  visible)

Control whether or not the tool is visible.

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