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BrainSet Class Reference

#include <BrainSet.h>

List of all members.


Detailed Description

Brain Set contains all Surfaces (topology and coordinates) and all attribute data (paint files, metric files, etc).

Definition at line 136 of file BrainSet.h.


Public Types

enum  SPEC_FILE_READ_MODE { SPEC_FILE_READ_MODE_NORMAL, SPEC_FILE_READ_MODE_APPEND }
 spec file read mode

Public Slots

void clearAreaColorFile ()
 clear the file
void clearArealEstimationFile ()
 clear the file
void clearBorderColorFile ()
 clear the file
void clearCellColorFile ()
 clear the file
void clearCocomacConnectivityFile ()
 clear the file
void clearContourCellColorFile ()
 clear the file
void clearContourCellFile ()
 clear the file
void clearContourFile (const bool deleteBrainModelContoursFlag=true)
 clear the file
void clearCutsFile ()
 clear the file
void clearDeformationFieldFile ()
 clear the file
void clearDeformationMapFile ()
 clear the file
void clearFociColorFile ()
 clear the file
void clearFociSearchFile ()
 clear the file
void clearGeodesicDistanceFile ()
 clear the file
void clearLatLonFile ()
 clear the file
void clearMetricFile ()
 clear the file
void clearPaintFile ()
 clear the file
void clearPaletteFile ()
 clear the file
void clearParamsFile ()
 clear the file
void clearProbabilisticAtlasFile ()
 clear the file
void clearRgbPaintFile ()
 clear the file
void clearSceneFile ()
 clear the file
void clearSectionFile ()
 clear the file
void clearStudyCollectionFile ()
 clear the study collection file
void clearStudyMetaDataFile ()
 clear the study metadata file
void clearSurfaceShapeFile ()
 clear the file
void clearTopographyFile ()
 clear the file
void clearTransformationDataFiles ()
 clear the transformation data files
void clearTransformationMatrixFile ()
 clear the file
void clearVectorFiles ()
 clear the file
void clearVocabularyFile ()
 clear the vocabulary file
void clearVolumeAnatomyFiles ()
 clear the anatomy volume files
void clearVolumeFunctionalFiles ()
 clear the functional volume files
void clearVolumePaintFiles ()
 clear the paint volume files
void clearVolumeProbabilisticAtlasFiles ()
 clear the prob atlasvolume files
void clearVolumeRgbFiles ()
 clear the rgb volume files
void clearVolumeSegmentationFiles ()
 clear the segmentation volume files
void clearVolumeVectorFiles ()
 clear the vector volume files
void clearWustlRegionFile ()
 clear the file

Signals

void signalBrainSetChanged ()
 signal that the brain set has changed
void signalDisplayBrainModel (int brainModelIndex)
 signal that requests a brain model be displayed and drawn
void signalGraphicsUpdate (BrainSet *bs)
 signal that graphics windows should be redrawn

Public Member Functions

void addBrainModel (BrainModel *bm, const bool readingSpecFile=false)
 add a brain model
void addDocumentFile (const QString &documentFileName)
 add a document file
void addImageFile (ImageFile *img)
 add an image file
void addNodes (const int numNodesToAdd)
 add nodes to all surfaces at the origin
void addTopologyFile (TopologyFile *tf)
 add a topology file
void addToSpecFile (const QString &specFileTag, const QString &fileName, const QString &fileName2="")
 add a tag and file pair to the spec file
void addVectorFile (VectorFile *vf)
 add a vector file
void addVolumeFile (const VolumeFile::VOLUME_TYPE vt, VolumeFile *vf, const QString &name, const bool append, const bool updateSpec) throw (FileException)
 add a volume file of the specified type
void addVtkModelFile (VtkModelFile *vmf)
 add a VTK model file
void applyAllProjectedFiles ()
 apply all projected files (foci, cells, borders)
void assignBorderColors ()
 Assign border colors to border projections and borders.
void assignCellColors ()
 Assign cell colors to cell and cell projection files.
void assignContourCellColors ()
 Assign contour cell colors to contour cells.
void assignFociColors ()
 Assign foci colors to foci and foci projection files.
void assignTransformationDataFileColors ()
 assign transformation data file colors
 BrainSet (const QString &vtkSurfaceFileName, const BrainModelSurface::SURFACE_TYPES surfaceType=BrainModelSurface::SURFACE_TYPE_UNKNOWN, const TopologyFile::TOPOLOGY_TYPES topologyType=TopologyFile::TOPOLOGY_TYPE_UNKNOWN)
 Construct a brain set from a vtk surface file.
 BrainSet (const QString &topoFileName, const QString &coordFileName1, const QString &coordFileName2="", const bool primaryBrainSetFlagIn=false)
 Construct a brain set from a topology file and one or more coordinate files.
 BrainSet (const QString &specFileNameIn, const bool readAllFilesInSpecFile, const bool primaryBrainSetFlagIn)
 Read in the brain set contained in the spec file.
 BrainSet (const bool primaryBrainSetFlagIn=false)
 Constructor (using only the caret main sets the primaryBrainSetFlagIn).
void classifyNodes (TopologyFile *tf=NULL, const bool onlyDoClassificationIfNeeded=false)
 classify the nodes as interior and edges
void clearAllDisplayLists ()
 Clear all display list.
void clearNodeAttributes ()
 clear the node attributes
void clearNodeHighlightSymbols ()
 clear all node highlight symbols
void convertDisplayedBordersToVtkModel (const BrainModelSurface *bms)
 convert displayed borders into a VTK model.
void convertDisplayedCellsToVtkModel (const BrainModelSurface *bms)
 convert displayed cells into a VTK model.
void convertDisplayedFociToVtkModel (const BrainModelSurface *bms)
 convert displayed foci into a VTK model.
vtkPolyData * convertToVtkPolyData (const BrainModelSurface *bms, const bool useNodeColors)
 Convert a BrainModelSurface to a vtkPolyData file with option of node colors.
void convertVolumeBordersToFiducialCells ()
 convert volume borders to cells
void copyOverlaysFromSurface (const int surfaceModelIndex)
 copy the overlay selections from specified surface to all other surfaces
void createSpecFromScenes (const std::vector< int > &sceneIndices, const QString &newSpecFileName, const QString &newSceneFileName, QString &errorMessageOut)
 create a spec file from all files in the selected scenes
void deleteAllBorders ()
 delete all borders
void deleteAllBrainModels ()
 delete all brain models
void deleteAllBrainModelSurfaces ()
 delete all brain model surfaces
void deleteAllCellProjections ()
 delete all cell projections (including those in cell files)
void deleteAllCells (const bool deleteCellProjections, const bool deleteVolumeCells)
 delete all cells and cell projections
void deleteAllFociProjections ()
 delete all foci projections (including those in foci files)
void deleteAllImageFiles ()
 delete all image files
void deleteAllTopologyFiles ()
 delete all topology files
void deleteAllVtkModelFiles ()
 delete all of the VTK model files
void deleteBrainModel (const BrainModel *bm)
 delete a brain model
void deleteBrainModelSurface (BrainModelSurface *bms)
 delete a brain model surface
void deleteCell (const int cellNumber)
 delete a cell
void deleteFocus (const int focusNumber)
 delete a focus
void deleteImageFile (ImageFile *img)
 delete an image file
void deleteTopologyFile (TopologyFile *tf)
 delete topology file
void deleteTransformationDataFile (AbstractFile *af)
 delete a transformation data file
void deleteTransformationDataFile (const int fileIndex)
 delete a transformation data file
void deleteVolumeFile (const VolumeFile *vf)
 delete a volume file
void deleteVtkModelFile (VtkModelFile *vmf)
 delete a VTK model file
void disconnectNodes (TopologyFile *tf, const std::vector< int > &paintIndices, const int paintColumn)
 disconnect the nodes with the specified paint indices in the specified paint column
void disconnectNodes (TopologyFile *tf, const std::vector< QString > &paintNames, const int paintColumn)
 disconnect the nodes with the specified paint names in the specified paint column
void disconnectNodes (TopologyFile *tf, const std::vector< bool > &nodesToDisconnect)
void drawBrainModel (const BrainModel *bm, const int currentAlgorithmIteration=-1)
 request that a brain model be displayed and drawn by the user of this brain set
void drawBrainModel (const int brainModelIndex, const int currentAlgorithmIteration=-1)
 request that a brain model be displayed and drawn by the user of this brain set
void export3DStudioASESurfaceFile (const BrainModelSurface *bms, const QString &filename) throw (FileException)
 export 3dStudio ASE surface file
void exportAnalyzeVolumeFile (VolumeFile *vf, const QString &filename) throw (FileException)
 Export Analyze volume file.
void exportByuSurfaceFile (const BrainModelSurface *bms, const QString &filename) throw (FileException)
 export byu surface file
void exportFreeSurferAsciiSurfaceFile (BrainModelSurface *bms, const QString &filename) throw (FileException)
 Export to a free surfer ascii surface file.
void exportInventorSurfaceFile (const BrainModelSurface *bms, const QString &filename) throw (FileException)
 export inventor surface file
void exportMincVolumeFile (VolumeFile *vf, const QString &filename) throw (FileException)
 Export MINC volume file.
void exportStlSurfaceFile (const BrainModelSurface *bms, const QString &filename) throw (FileException)
 export stl surface file
void exportVrmlSurfaceFile (const BrainModelSurface *bms, const QString &filename) throw (FileException)
 export vrml surface file
void exportVtkStructuredPointsVolumeFile (VolumeFile *vf, const QString &filename) throw (FileException)
 Export VTK structured points volume file.
void exportVtkSurfaceFile (const BrainModelSurface *bms, const QString &filename, const bool exportColors) throw (FileException)
 export vtk surface file
void exportVtkXmlSurfaceFile (const BrainModelSurface *bms, const QString &filename, const bool exportColors) throw (FileException)
 export vtk XML surface file
void exportWavefrontSurfaceFile (const BrainModelSurface *bms, const QString &filename) throw (FileException)
 export wavefront object surface file
void generateCerebralHullVtkFile (const VolumeFile *segmentationVolumeIn, VolumeFile *&cerebralHullVolumeOut, vtkPolyData *&cerebralHullVtkPolyDataOut) throw (BrainModelAlgorithmException)
void generateCerebralHullVtkFile (const VolumeFile *segmentationVolume, const bool saveHullVolumeFileFlag) throw (BrainModelAlgorithmException)
 generate the cerebral hull vtk file from the segmentation volume
BrainModelSurfacegetActiveFiducialSurface ()
 get the "active" fiducial surface
AreaColorFilegetAreaColorFile ()
 get the area color file
ArealEstimationFilegetArealEstimationFile ()
 get the areal estimation file
BrainSetAutoLoaderManagergetAutoLoaderManager ()
 get the brain set auto loader manager
BorderColorFilegetBorderColorFile ()
 get the border color file
BrainModelBorderSetgetBorderSet ()
 get the border set
const BrainModelgetBrainModel (const int modelIndex) const
 get a brain model (constant method)
BrainModelgetBrainModel (const int modelIndex)
 get a brain model
const BrainModelContoursgetBrainModelContours (const int modelIndex=-1) const
 get a brain model contours (const method) (if negative index first one found is returned)
BrainModelContoursgetBrainModelContours (const int modelIndex=-1)
 get a brain model contours (if negative index first one found is returned)
BrainModelIdentificationgetBrainModelIdentification ()
 get the identification object
int getBrainModelIndex (const BrainModel *bm) const
 get the index for a brain model
const BrainModelSurfacegetBrainModelSurface (const int modelIndex) const
 get a brain model surface (const method)
BrainModelSurfacegetBrainModelSurface (const int modelIndex)
 get a brain model surface
const BrainModelSurfaceAndVolumegetBrainModelSurfaceAndVolume (const int modelIndex=-1) const
 get a brain model surface and volume (if negative index first one found is returned) CONST method
BrainModelSurfaceAndVolumegetBrainModelSurfaceAndVolume (const int modelIndex=-1)
 get a brain model surface and volume (if negative index first one found is returned)
BrainModelSurfacegetBrainModelSurfaceOfType (const BrainModelSurface::SURFACE_TYPES st)
 get a brain model surface of the specified type
const
BrainModelSurfaceROINodeSelection
getBrainModelSurfaceRegionOfInterestNodeSelection () const
 get the region of interest node selection object const method
BrainModelSurfaceROINodeSelectiongetBrainModelSurfaceRegionOfInterestNodeSelection ()
 get the region of interest node selection object
BrainModelSurfacegetBrainModelSurfaceWithCoordinateFileName (const QString &fileName)
 get a brain model surface with the specified coordinate file name (NULL if not found)
const BrainModelVolumegetBrainModelVolume (const int modelIndex=-1) const
 get a brain model volume (if negative index first one found is returned) CONST method
BrainModelVolumegetBrainModelVolume (const int modelIndex=-1)
 get a brain model volume (if negative index first one found is returned)
CellColorFilegetCellColorFile ()
 cell color file
CellProjectionFilegetCellProjectionFile ()
 get the cell projection file
BrainModelSurfacegetCerebellumFiducialVolumeInteractionSurface ()
 get the cerebellum fiducial volume interaction surface
QString getCerebralHullFileName () const
 get the name of the cerebral hull file
CocomacConnectivityFilegetCocomacFile ()
 get the cocomac file
ContourCellColorFilegetContourCellColorFile ()
 get the contour cell color file
ContourCellFilegetContourCellFile ()
 get the contour cell file
CutsFilegetCutsFile ()
 get the cuts file
DeformationFieldFilegetDeformationFieldFile ()
 get the deformation field file
QString getDeformationMapFileName () const
 get the name of the deformation map file
bool getDisplayAllNodes () const
 get the display all nodes flag
int getDisplayCrossForNode () const
 get display cross for node
BrainModelSurfacegetDisplayCrossSurface () const
 get surface on which identification was made
int getDisplayedModelIndexForWindow (const BrainModel::BRAIN_MODEL_VIEW_NUMBER windowNumber) const
 get the displayed model index for a window
DisplaySettingsArealEstimationgetDisplaySettingsArealEstimation ()
 get the areal estimation settings
DisplaySettingsBordersgetDisplaySettingsBorders ()
 get the border display settings
DisplaySettingsCellsgetDisplaySettingsCells ()
 get the cell display settings
DisplaySettingsCoCoMacgetDisplaySettingsCoCoMac ()
 get the cocomac display settings
DisplaySettingsContoursgetDisplaySettingsContours ()
 get the contour display settings
DisplaySettingsCutsgetDisplaySettingsCuts ()
 get the cuts display settings
DisplaySettingsDeformationFieldgetDisplaySettingsDeformationField ()
 get the deformation field display settings
DisplaySettingsFocigetDisplaySettingsFoci ()
 get the foci display settings
DisplaySettingsGeodesicDistancegetDisplaySettingsGeodesicDistance ()
 get the geodesic distance display settings
DisplaySettingsImagesgetDisplaySettingsImages ()
 get the images display settings
DisplaySettingsMetricgetDisplaySettingsMetric ()
 get the metric display settings
DisplaySettingsModelsgetDisplaySettingsModels ()
 get the model display settings
DisplaySettingsPaintgetDisplaySettingsPaint ()
 get the paint display settings
DisplaySettingsProbabilisticAtlasgetDisplaySettingsProbabilisticAtlasSurface ()
 get the prob atlas display settings
DisplaySettingsProbabilisticAtlasgetDisplaySettingsProbabilisticAtlasVolume ()
 get the volume prob atlas display settings
DisplaySettingsRgbPaintgetDisplaySettingsRgbPaint ()
 get the rgb paint display settings
DisplaySettingsScenegetDisplaySettingsScene ()
 get the scene display settings
DisplaySettingsSectiongetDisplaySettingsSection ()
 get the section display settings
DisplaySettingsStudyMetaDatagetDisplaySettingsStudyMetaData ()
 get the study metadata display settings
DisplaySettingsSurfacegetDisplaySettingsSurface ()
 get the node display settings
DisplaySettingsSurfaceShapegetDisplaySettingsSurfaceShape ()
 get the surface shape display settings
DisplaySettingsTopographygetDisplaySettingsTopography ()
 get the topography file display settings
DisplaySettingsVectorsgetDisplaySettingsVectors ()
 get the surface display settings
const DisplaySettingsVolumegetDisplaySettingsVolume () const
 get the volume display settings (const method)
DisplaySettingsVolumegetDisplaySettingsVolume ()
 get the volume display settings
DisplaySettingsWustlRegiongetDisplaySettingsWustlRegion ()
 get the wustl region display settings
bool getDisplaySplashImage () const
 get display splash image
int getFirstBrainModelSurfaceIndex () const
 get the index of the first brain model surface (returns -1 if not found)
FociColorFilegetFociColorFile ()
 get the foci color file
FociProjectionFilegetFociProjectionFile ()
 get the foci projection file
FociSearchFilegetFociSearchFile ()
 get the foci search file
GeodesicDistanceFilegetGeodesicDistanceFile ()
 get the geodesic distance file
bool getHaveTransformationDataCellFiles () const
 get have transformation data cell files
bool getHaveTransformationDataContourCellFiles () const
 get have transformation data contour cell files
bool getHaveTransformationDataContourFiles () const
 get have transformation data contour files
bool getHaveTransformationDataFociFiles () const
 get have transformation data foci files
bool getHaveTransformationDataVtkFiles () const
 get have transformation data vtk files
ImageFilegetImageFile (const QString &filename)
 get an image file based upon the image's name
ImageFilegetImageFile (const int fileNum)
 get an image file
bool getImageFileValid (const ImageFile *img) const
 see if an image file is valid
LatLonFilegetLatLonFile ()
 get the lat/lon file
BrainModelSurfacegetLeftFiducialVolumeInteractionSurface ()
 get the left fiducial volume interaction surface
const SpecFilegetLoadedFilesSpecFile () const
 get the spec file (const method)
SpecFilegetLoadedFilesSpecFile ()
 get the spec file that keeps track of loaded files
MetricFilegetMetricFile ()
 get the metric file
const BrainSetNodeAttributegetNodeAttributes (const int nodeNum) const
 get the common node attributes for a node (const method)
BrainSetNodeAttributegetNodeAttributes (const int nodeNum)
 get the common node attributes for a node
BrainModelSurfaceNodeColoringgetNodeColoring ()
 get access to node coloring
bool getNodesHaveBeenClassified () const
 find out if nodes have been classified
int getNodeWithMorphRowColumn (const int row, const int column, const int startAtNode=0) const
 find a node with the specified morph row and column (returns -1 if not found)
int getNumberOfBrainModels () const
 get the number of brain models
int getNumberOfImageFiles () const
 get number of image files
int getNumberOfNodes () const
 get the number of nodes
int getNumberOfSurfaceOverlays () const
 get the number of surface overlays
int getNumberOfTopologyFiles () const
 get the number of topology files
int getNumberOfTransformationDataFiles () const
 get the number of transformation data files
int getNumberOfVectorFiles () const
 get the number of vector files
int getNumberOfVolumeAnatomyFiles () const
 get the number of volume anatomy files
int getNumberOfVolumeFunctionalFiles () const
 get the number of volume functional files
int getNumberOfVolumePaintFiles () const
 get the number of paint volume files
int getNumberOfVolumeProbAtlasFiles () const
 get the number of prob atlas volume files
int getNumberOfVolumeRgbFiles () const
 get the number of rgb volume files
int getNumberOfVolumeSegmentationFiles () const
 get the number of volume segmentation files
int getNumberOfVolumeVectorFiles () const
 get the number of volume vector files
int getNumberOfVtkModelFiles () const
 get the number of vtk model files
PaintFilegetPaintFile ()
 get the paint file
PaletteFilegetPaletteFile ()
 get the palette file
ParamsFilegetParamsFile ()
 get the parameters file
const BrainModelSurfaceOverlaygetPrimarySurfaceOverlay () const
 get the primary surface overlay (const method)
BrainModelSurfaceOverlaygetPrimarySurfaceOverlay ()
 get the primary surface overlay
ProbabilisticAtlasFilegetProbabilisticAtlasSurfaceFile ()
 get the probabilistic atlas file
QWidget * getProgressDialogParent ()
 get the progress dialog parent
RgbPaintFilegetRgbPaintFile ()
 get the RGB Paint file
BrainModelSurfacegetRightFiducialVolumeInteractionSurface ()
 get the right fiducial volume interaction surface
SceneFilegetSceneFile ()
 get the scene file
const BrainModelSurfaceOverlaygetSecondarySurfaceOverlay () const
 get the secondary surface overlay (const method)
BrainModelSurfaceOverlaygetSecondarySurfaceOverlay ()
 get the secondary surface overlay
SectionFilegetSectionFile ()
 get the section file
QString getSpecFileName () const
 get the spec file name
QDateTime getSpecFileTimeOfLoading () const
 get the time the spec file was loaded
Species getSpecies () const
 get the species
QImage * getSplashImage ()
 get the splash image
StereotaxicSpace getStereotaxicSpace () const
 get the stereotaxic space
Structure getStructure () const
 get the structure
StudyCollectionFilegetStudyCollectionFile ()
 get the study collection file
StudyMetaDataFilegetStudyMetaDataFile ()
 get the study metadata file
QString getSubject () const
 get the subject
const BrainModelSurfaceOverlaygetSurfaceOverlay (const int overlayNumber) const
 get a surface overlay (const method)
BrainModelSurfaceOverlaygetSurfaceOverlay (const int overlayNumber)
 get a surface overlay
SurfaceShapeFilegetSurfaceShapeFile ()
 get the surface shape file
const BrainModelSurfaceOverlaygetSurfaceUnderlay () const
 get the surface underlay (const method)
BrainModelSurfaceOverlaygetSurfaceUnderlay ()
 get the surface underlay
TopographyFilegetTopographyFile ()
 get the topography file
TopologyFilegetTopologyClosed ()
 get the closed topology
TopologyFilegetTopologyCut ()
 get the cut topology
TopologyFilegetTopologyFile (const int index)
 get a topology file by its index
TopologyFilegetTopologyLobarCut ()
 get the lobar cut topology
TopologyFilegetTopologyOpen ()
 get the open topology
TopologyFilegetTopologyUnknown ()
 get the unknown topology
const AbstractFilegetTransformationDataFile (const int indx) const
 get a transformation data file (const method)
AbstractFilegetTransformationDataFile (const int indx)
 get a transformation data file
TransformationMatrixFilegetTransformationMatrixFile ()
 get the transformation matrix file
const VectorFilegetVectorFile (const int indx) const
 get the vector file (const method)
VectorFilegetVectorFile (const int indx)
 get the vector file
int getVectorFileIndex (VectorFile *vf)
 get vector file's index
VocabularyFilegetVocabularyFile ()
 get the vocabulary file
const VolumeFilegetVolumeAnatomyFile (const int index) const
 get the volume anatomy file (const method)
VolumeFilegetVolumeAnatomyFile (const int index)
 get the volume anatomy file
void getVolumeAnatomyFiles (std::vector< VolumeFile * > &files)
 get the volume anatomy files
VolumeFilegetVolumeAnatomyFileWithName (const QString &name)
 get the anatomy volume file with the specified name (NULL if not found)
const BorderFilegetVolumeBorderFile () const
 get the volume borders const method
BorderFilegetVolumeBorderFile ()
 get the volume borders
const CellFilegetVolumeCellFile () const
 get the volume cell file (const method)
CellFilegetVolumeCellFile ()
 get the volume cell file
VolumeFilegetVolumeFileWithName (const std::vector< VolumeFile * > &files, const QString &fileName)
 Get the volume file name with the specified name (NULL if not found).
const VolumeFilegetVolumeFunctionalFile (const int index) const
 get the volume functional file (const method)
VolumeFilegetVolumeFunctionalFile (const int index)
 get the volume functional file
void getVolumeFunctionalFiles (std::vector< VolumeFile * > &files)
 get the volume functional files
VolumeFilegetVolumeFunctionalFileWithName (const QString &name)
 get the functional volume file with the specified name (NULL if not found)
const VolumeFilegetVolumePaintFile (const int index) const
 get the volume paint file (const method)
VolumeFilegetVolumePaintFile (const int index)
 get the volume paint file
void getVolumePaintFiles (std::vector< VolumeFile * > &files)
 get the volume paint files
VolumeFilegetVolumePaintFileWithName (const QString &name)
 get the paint volume file with the specified name (NULL if not found)
const VolumeFilegetVolumeProbAtlasFile (const int index) const
 get the volume prob atlas file (const method)
VolumeFilegetVolumeProbAtlasFile (const int index)
 get the volume prob atlas file
void getVolumeProbAtlasFiles (std::vector< VolumeFile * > &files)
 get the volume prob atlas files
VolumeFilegetVolumeProbAtlasFileWithName (const QString &name)
 get the prob atlas volume file with the specified name (NULL if not found)
BrainModelVolumeRegionOfInterestgetVolumeRegionOfInterestController ()
 get the volume region of interest controller
const VolumeFilegetVolumeRgbFile (const int index) const
 get the volume rgb file (const method)
VolumeFilegetVolumeRgbFile (const int index)
 get the volume rgb file
void getVolumeRgbFiles (std::vector< VolumeFile * > &files)
 get the volume rgb files
VolumeFilegetVolumeRgbFileWithName (const QString &name)
 get the RGB volume file with the specified name (NULL if not found)
const VolumeFilegetVolumeSegmentationFile (const int index) const
 get the volume segmentation file (const method)
VolumeFilegetVolumeSegmentationFile (const int index)
 get the volume segmentation file
void getVolumeSegmentationFiles (std::vector< VolumeFile * > &files)
 get the volume segmentation files
VolumeFilegetVolumeSegmentationFileWithName (const QString &name)
 get the segmentation volume file with the specified name (NULL if not found)
const VolumeFilegetVolumeVectorFile (const int index) const
 get the volume vector file (const method)
VolumeFilegetVolumeVectorFile (const int index)
 get the volume vector file
void getVolumeVectorFiles (std::vector< VolumeFile * > &files)
 get the volume vector files
VolumeFilegetVolumeVectorFileWithName (const QString &name)
 get the vector volume file with the specified name (NULL if not found)
BrainModelVolumeVoxelColoringgetVoxelColoring ()
 get access to the voxel coloring
VtkModelFilegetVtkModelFile (const int modelNum)
 get a vtk model file
bool getWebCaretFlag () const
 get the web caret flag
WustlRegionFilegetWustlRegionFile ()
 get the wustl region file
void guessSubjectSpeciesStructureFromCoordTopoFileNames ()
 guess subject, species, and structure if not specified
void importAnalyzeVolumeFile (const QString &filename, const VolumeFile::VOLUME_TYPE volumeType) throw (FileException)
 Import Analyze volume file.
void importBrainVoyagerFile (const QString &filename, const bool importCoordinates, const bool importTopology, const bool importColors, const BrainModelSurface::SURFACE_TYPES surfaceType=BrainModelSurface::SURFACE_TYPE_FIDUCIAL, const TopologyFile::TOPOLOGY_TYPES topologyType=TopologyFile::TOPOLOGY_TYPE_CLOSED) throw (FileException)
 import brain voyager file
void importByuSurfaceFile (const QString &filename, const bool importCoordinates, const bool importTopology, const BrainModelSurface::SURFACE_TYPES surfaceType, const TopologyFile::TOPOLOGY_TYPES topologyType) throw (FileException)
 import byu surface file
void importFreeSurferSurfaceFile (const QString &filename, const bool importCoordinates, const bool importTopology, const AbstractFile::FILE_FORMAT fileFormat=AbstractFile::FILE_FORMAT_ASCII, const BrainModelSurface::SURFACE_TYPES surfaceType=BrainModelSurface::SURFACE_TYPE_FIDUCIAL, const TopologyFile::TOPOLOGY_TYPES topologyType=TopologyFile::TOPOLOGY_TYPE_CLOSED) throw (FileException)
 import a free surfer ascii surface file
void importMDPlotFile (const QString &filename, const bool importPointsAsContourCells, const bool importLinesAsContours, const bool appendToExistingContours, const bool appendToExistingContourCells) throw (FileException)
 import MD Plot file
void importMincVolumeFile (const QString &filename, const VolumeFile::VOLUME_TYPE volumeType) throw (FileException)
 Import MINC volume file.
void importMniObjSurfaceFile (const QString &filename, const bool importCoordinates, const bool importTopology, const bool importColors, const BrainModelSurface::SURFACE_TYPES surfaceType=BrainModelSurface::SURFACE_TYPE_FIDUCIAL, const TopologyFile::TOPOLOGY_TYPES topologyType=TopologyFile::TOPOLOGY_TYPE_CLOSED) throw (FileException)
 import mni obj surface file
void importNeurolucidaFile (const QString &filename, const bool importMarkersAsCells, const bool importContours, const bool appendToExistingContours, const bool appendToExistingContourCells) throw (FileException)
 import Neurolucida file
void importRawVolumeFile (const QString &filename, const VolumeFile::VOLUME_TYPE volumeType, const int dimensions[3], const VolumeFile::VOXEL_DATA_TYPE voxelDataType, const bool byteSwap) throw (FileException)
 Import Raw volume file.
void importStlSurfaceFile (const QString &filename, const bool importCoordinates, const bool importTopology, const BrainModelSurface::SURFACE_TYPES surfaceType, const TopologyFile::TOPOLOGY_TYPES topologyType) throw (FileException)
 import stl surface file
void importVtkStructuredPointsVolumeFile (const QString &filename, const VolumeFile::VOLUME_TYPE volumeType) throw (FileException)
 Import VTK structured points volume file.
void importVtkSurfaceFile (const QString &filename, const bool importCoordinates, const bool importTopology, const bool importColors, const BrainModelSurface::SURFACE_TYPES surfaceType, const TopologyFile::TOPOLOGY_TYPES topologyType) throw (FileException)
 import vtk surface file
void importVtkTypeFileHelper (const QString &filename, vtkPolyData *polyData, const bool importCoordinates, const bool importTopology, const bool importColors, const BrainModelSurface::SURFACE_TYPES surfaceType, const TopologyFile::TOPOLOGY_TYPES topologyType) throw (FileException)
 Import vtk type files (vtk, stl, byu).
void importVtkXmlSurfaceFile (const QString &filename, const bool importCoordinates, const bool importTopology, const bool importColors, const BrainModelSurface::SURFACE_TYPES surfaceType, const TopologyFile::TOPOLOGY_TYPES topologyType) throw (FileException)
 import vtk XML surface file
void insertScene (SceneFile *sf, const int insertAfterIndex, const std::vector< SceneFile::SceneClass > &mainWindowSceneClasses, const QString &sceneName, const bool onlyIfSelectedFlag, QString &errorMessageOut, QString &warningMessageOut)
 insert after scene (read display settings)
bool isASurfaceOverlay (const int model, const BrainModelSurfaceOverlay::OVERLAY_SELECTIONS os) const
 get something is an overlay
bool isASurfaceOverlayForAnySurface (const BrainModelSurfaceOverlay::OVERLAY_SELECTIONS os) const
 get something is an overlay for any model
bool isIterationUpdate (const int currentAlgorithmIteration) const
 See if this iteration is one in which the brain model should be redrawn.
void moveFociStudyInfoToStudyMetaDataFile ()
 move foci study info to the study meta data file
void postSpecFileReadInitializations ()
 Initalize things after reading a spec file or initial surface into caret.
void readAreaColorFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the area color data file file
void readArealEstimationFile (const QString &name, const std::vector< int > &columnDestination, const std::vector< QString > &fileBeingReadColumnNames, const AbstractFile::FILE_COMMENT_MODE fcm, const bool updateSpec) throw (FileException)
 read the areal estimation data file (only selected columns)
void readArealEstimationFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the areal estimation data file
void readBorderColorFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the border color data file
void readBorderFile (const QString &name, const BrainModelSurface::SURFACE_TYPES st, const bool append, const bool updateSpec) throw (FileException)
 read the border data file
void readBorderProjectionFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the border projection data file
void readCellColorFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the cell color data file
void readCellFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the cell data file
void readCellProjectionFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the cell projection data file
void readCocomacConnectivityFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the cocomac connectivity file
void readContourCellColorFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read a contour cell color file
void readContourCellFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read a contour cell file
void readContourFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read a contour file
void readCoordinateFile (const QString &name, const BrainModelSurface::SURFACE_TYPES st, const bool readingSpecFile, const bool append, const bool updateSpec) throw (FileException)
 read the coordinate data file file
void readCutsFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the cuts file
void readDeformationFieldFile (const QString &name, const std::vector< int > &columnDestination, const std::vector< QString > &fileBeingReadColumnNames, const AbstractFile::FILE_COMMENT_MODE fcm, const bool updateSpec) throw (FileException)
 read the deformation field file (only selected columns)
void readDeformationFieldFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the deformation field file
void readFociColorFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the foci color data file file
void readFociFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the foci data file file
void readFociProjectionFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the foci projection data file file
void readFociSearchFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the foci search file
void readGeodesicDistanceFile (const QString &name, const std::vector< int > &columnDestination, const std::vector< QString > &fileBeingReadColumnNames, const AbstractFile::FILE_COMMENT_MODE fcm, const bool updateSpec) throw (FileException)
 read the geodesic distance data file file (only selected columns)
void readGeodesicDistanceFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the geodesic distance data file file
void readImageFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the image data file
void readLatLonFile (const QString &name, const std::vector< int > &columnDestination, const std::vector< QString > &fileBeingReadColumnNames, const AbstractFile::FILE_COMMENT_MODE fcm, const bool updateSpec) throw (FileException)
 read the lat lon data file file (only selected columns)
void readLatLonFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the lat lon data file file
void readMetricFile (const QString &name, const std::vector< int > &columnDestination, const std::vector< QString > &fileBeingReadColumnNames, const AbstractFile::FILE_COMMENT_MODE fcm, const bool updateSpec) throw (FileException)
 read the metric data file file (only selected columns)
void readMetricFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the metric data file file
void readPaintFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the paint data file file
void readPaintFile (const QString &name, const std::vector< int > &columnDestination, const std::vector< QString > &fileBeingReadColumnNames, const AbstractFile::FILE_COMMENT_MODE fcm, const bool updateSpec) throw (FileException)
 read the paint data file file (only selected columns)
void readPaletteFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the palette data file file
void readParamsFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the params data file file
void readProbabilisticAtlasFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the prob atlas data file file
void readRgbPaintFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the rgb paint data file file
void readSceneFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the scene data file file
void readSectionFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the section data file file
bool readSpecFile (const SPEC_FILE_READ_MODE specReadMode, const SpecFile &specFileIn, const QString &specFileNameIn, QString &errorMessageOut, const TransformationMatrix *specTransformationMatrixIn, QProgressDialog *progressDialog)
 read the spec file (returns true if reading was aborted by user)
bool readSpecFile (const SPEC_FILE_READ_MODE specReadMode, const SpecFile &specFileIn, const QString &specFileNameIn, std::vector< QString > &errorMessagesOut, const TransformationMatrix *specTransformationMatrixIn, QProgressDialog *progressDialog)
 read the spec file (returns true if reading was aborted by user)
bool readSpecFile (const SpecFile &specFileIn, const QString &specFileNameIn, QString &errorMessagesOut)
 read the spec file (returns true if reading was aborted by user)
bool readSpecFileMultiThreaded (const SPEC_FILE_READ_MODE specReadMode, const SpecFile &specFileIn, const QString &specFileNameIn, std::vector< QString > &errorMessagesOut, const TransformationMatrix *specTransformationMatrixIn, QProgressDialog *progressDialog)
 read the spec file (returns true if reading was aborted by user)
void readStudyCollectionFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the study collection file
void readStudyMetaDataFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the study metadata file
void readSurfaceFile (const QString &name, const BrainModelSurface::SURFACE_TYPES st, const bool readingSpecFile, const bool append, const bool updateSpec) throw (FileException)
 read the surface data file file
void readSurfaceShapeFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the surface shape data file file
void readSurfaceShapeFile (const QString &name, const std::vector< int > &columnDestination, const std::vector< QString > &fileBeingReadColumnNames, const AbstractFile::FILE_COMMENT_MODE fcm, const bool updateSpec) throw (FileException)
 read the surface shape data file file (only selected columns)
void readTopographyFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the topography data file file
void readTopologyFile (const QString &name, const TopologyFile::TOPOLOGY_TYPES tt, const bool append, const bool updateSpec) throw (FileException)
 read the topology data file file
void readTransformationDataFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the transformation data file
void readTransformationMatrixFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the transformation matrix file
void readVectorFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the vector data file file
void readVocabularyFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the vocabulary file
void readVolumeBorderFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read a volume border file
void readVolumeCellFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the volume cell data file
void readVolumeFile (const QString &name, const VolumeFile::VOLUME_TYPE vt, const bool append, const bool updateSpec) throw (FileException)
 read volume data file
void readVtkModelFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the vtk model data file
void readWustlRegionFile (const QString &name, const bool append, const bool updateSpec) throw (FileException)
 read the wustl region file
void removeCoordAndTopoFromSpecFile ()
 remove coordinate and topoology files from spec file
int removeUnlinkedStudiesFromStudyMetaDataFile ()
 remove unlinked studies from study meta data file
void removeVectorFile (VectorFile *vf)
 remove a vector file
void removeVectorFile (const int indx)
 remove a vector file
void replaceScene (SceneFile *sf, const int sceneIndex, const std::vector< SceneFile::SceneClass > &mainWindowSceneClasses, const QString &sceneName, const bool onlyIfSelectedFlag, QString &errorMessageOut, QString &warningMessageOut)
 replace a scene (read display settings)
void reset (const bool keepSceneData=false)
 reset the Brain Surfaces
void resetDataFiles (const bool keepSceneData, const bool keepFociAndFociColorsAndStudyMetaData)
 reset all data files
void resetNodeAttributeFiles ()
 reset all node attribute files
void resetNodeAttributes ()
 reset node attributes (ensures number of attributes == num nodes)
void saveScene (SceneFile *sf, const std::vector< SceneFile::SceneClass > &mainWindowSceneClasses, const QString &sceneName, const bool onlyIfSelectedFlag, QString &errorMessageOut, QString &warningMessageOut)
 create a scene (read display settings)
void saveSceneForBrainModelWindow (const int viewingWindowNumber, const int geometry[4], const int glWidthHeight[2], const BrainModel *bm, const bool yokeIn, SceneFile::SceneClass &sceneClass)
 Save the model for a window from a scene.
void setActiveFiducialSurface (BrainModelSurface *bms)
 set the "active" fiducial surface
void setAllNodesVisited (const bool value)
 set the visited flag on all node attributes
void setCerebellumFiducialVolumeInteractionSurface (BrainModelSurface *bms)
 set the cerebellum fiducial volume interaction surface
void setDefaultScaling (const float orthoRight, const float orthoTop)
 Set the default scaling for all surfaces.
void setDeformationMapFileName (const QString &name, const bool updateSpec)
 set the deformation map file name
void setDisplayAllNodes (const bool dan)
 set the display all nodes flag
void setDisplayCrossForNode (const int nodeNumber, BrainModelSurface *surface)
 set display cross for node
void setDisplayedModelIndexForWindow (const BrainModel::BRAIN_MODEL_VIEW_NUMBER windowNumber, const int modelIndex)
 set the displayed model index for a window
void setDisplaySplashImage (const bool b)
 set display splash image
void setIgnoreTopologyFileInCoordinateFileHeaderFlag (const bool b)
 set when reading coordinate files DO NOT use topology file in coord file header
void setLeftFiducialVolumeInteractionSurface (BrainModelSurface *bms)
 set the left fiducial volume interaction surface
void setProgressDialogParent (QWidget *parent)
void setRightFiducialVolumeInteractionSurface (BrainModelSurface *bms)
 set the right fiducial volume interaction surface
void setSpecFileName (const QString &name, const bool readOldSpecFileFlag=true)
 set the spec file name
void setSpecies (const Species &s)
 set the species
void setStereotaxicSpace (const StereotaxicSpace &ss)
 set the stereotaxic space (const method)
void setStructure (const Structure &s)
 set the structure
void setStructure (const Structure::STRUCTURE_TYPE s)
 set the structure
void setSubject (const QString &s)
 set the subject
void setWebCaretFlag (const bool flag)
 set the web caret flag
void showScene (const int sceneIndex, QString &errorMessage, QString &warningMessage)
 apply a scene (set display settings)
void showScene (const SceneFile::Scene *ss, const bool checkSpecFlag, QString &errorMessage, QString &warningMessage)
 apply a scene (set display settings)
BrainModelshowSceneGetBrainModel (const SceneFile::Scene *scene, const int viewingWindowNumberIn, int geometryOut[4], int glWidthHeightOut[2], bool &yokeOut, QString &errorMessageOut)
 Get the model for a window from a scene.
BrainModelshowSceneGetBrainModel (const int sceneIndex, const int viewingWindowNumberIn, int geometryOut[4], int glWidthHeightOut[2], bool &yokeOut, QString &errorMessageOut)
 Get the model for a window from a scene.
void showSceneIdentificationFilters (const SceneFile::Scene *ss, QString &errorMessage)
 load identification filters from a scene
void simplifySurface (const BrainModelSurface *bms, const int maxPolygons) throw (FileException)
 Simplify the surface (this also removed all other surfaces and volumes).
void sortBrainModels ()
 sort the brain models (raw, fiducial, ..., volume, surf&vol, contours)
void synchronizeProbAtlasVolumeRegionNames ()
 synchronize prob atlas volume region names
void updateDefaultFileNamePrefix ()
 update the default file naming prefix
void updateNodeDisplayFlags ()
 Set node display flags based upon sections and other criteria.
void updateSurfaceOverlaysDueToChangeInBrainModels ()
 update the surface overlays due to change in brain models
void writeAreaColorFile (const QString &name) throw (FileException)
 write the NodeColor data file
void writeArealEstimationFile (const QString &name) throw (FileException)
 write the ArealEstimation data file
void writeBorderColorFile (const QString &name) throw (FileException)
 write the BorderColor data file
void writeBorderFile (const QString &name, const BrainModelSurface *bms, const BrainModelSurface::SURFACE_TYPES borderFileType, const QString &commentText, const QString &pubMedID, const bool removeDuplicates=false) throw (FileException)
 write the Border data file
void writeBorderProjectionFile (const QString &name, const QString &commentText, const QString &pubMedID, const bool removeDuplicates=false) throw (FileException)
 write the BorderProjection data file
void writeCellColorFile (const QString &name) throw (FileException)
 write the CellColor data file
void writeCellFile (const QString &name, const BrainModelSurface *bms, const AbstractFile::FILE_FORMAT fileFormat, const QString &commentText) throw (FileException)
 write the Cell data file
void writeCellProjectionFile (const QString &name) throw (FileException)
 write the CellProjection data file
void writeCocomacConnectivityFile (const QString &name) throw (FileException)
 write the CocomacConnectivity data file
void writeContourCellColorFile (const QString &name) throw (FileException)
 write the Contour Cell Color data file
void writeContourCellFile (const QString &name) throw (FileException)
 write the Contour Cell data file
void writeContourFile (const QString &name, ContourFile *cf) throw (FileException)
 write the Contour data file
void writeCoordinateFile (const QString &name, const BrainModelSurface::SURFACE_TYPES st, CoordinateFile *cf, const bool updateSpecFile=true) throw (FileException)
 write the coordinate data file
void writeCutsFile (const QString &name) throw (FileException)
 write the Cuts data file
void writeDeformationFieldFile (const QString &name) throw (FileException)
 write the deformation field data file
void writeFociColorFile (const QString &name) throw (FileException)
 write the FociColor data file
void writeFociFile (const QString &name, const BrainModelSurface *leftBms, const BrainModelSurface *rightBms, const BrainModelSurface *cerebellumBMS, const AbstractFile::FILE_FORMAT fileFormat, const QString &commentText) throw (FileException)
 write the Foci data file
void writeFociFileOriginalCoordinates (const QString &name, const AbstractFile::FILE_FORMAT fileFormat, const QString &commentText) throw (FileException)
 write the Foci data file
void writeFociProjectionFile (const QString &name) throw (FileException)
 write the FociProjection data file
void writeFociSearchFile (const QString &name) throw (FileException)
 write the foci search file
void writeGeodesicDistanceFile (const QString &name) throw (FileException)
 write the geodesic distance data file
void writeImageFile (const QString &name, ImageFile *img) throw (FileException)
 write the image data file
void writeLatLonFile (const QString &name) throw (FileException)
 write the LatLon data file
void writeMetricFile (const QString &name) throw (FileException)
 write the Metric data file
void writeMultiVolumeFile (const QString &name, const VolumeFile::VOLUME_TYPE volumeType, const QString &comment, std::vector< VolumeFile * > &subVolumes, const VolumeFile::VOXEL_DATA_TYPE voxelDataTypeToWrite=VolumeFile::VOXEL_DATA_TYPE_UNKNOWN, const bool zipAfniVolumeFile=false) throw (FileException)
 Write the multi-volume file data.
void writePaintFile (const QString &name) throw (FileException)
 write the Paint data file
void writePaletteFile (const QString &name) throw (FileException)
 write the Palette data file
void writeParamsFile (const QString &name) throw (FileException)
 write the Params data file
void writeProbabilisticAtlasFile (const QString &name) throw (FileException)
 write the ProbabilisticAtlas data file
void writeRgbPaintFile (const QString &name) throw (FileException)
 write the RgbPaint data file
void writeSceneFile (const QString &name) throw (FileException)
 write the scene data file
void writeSectionFile (const QString &name) throw (FileException)
 write the Section data file
void writeStudyCollectionFile (const QString &name) throw (FileException)
 write the study collection file
void writeStudyMetaDataFile (const QString &name) throw (FileException)
 write the study metadata file
void writeSurfaceFile (const QString &name, const BrainModelSurface::SURFACE_TYPES st, BrainModelSurface *bms, const bool updateSpecFile=true, const AbstractFile::FILE_FORMAT fileFormat=AbstractFile::FILE_FORMAT_XML) throw (FileException)
 write the surface data file
void writeSurfaceShapeFile (const QString &name) throw (FileException)
 write the SurfaceShape data file
void writeTopographyFile (const QString &name) throw (FileException)
 write the Topography data file
void writeTopologyFile (const QString &name, const TopologyFile::TOPOLOGY_TYPES tt, TopologyFile *tf) throw (FileException)
 write theTopology data file
void writeTransformationMatrixFile (const QString &name) throw (FileException)
 write the transformation matrix file
void writeVectorFile (VectorFile *vf, const QString &name) throw (FileException)
 write the Vector data file
void writeVocabularyFile (const QString &name) throw (FileException)
 write the vocabulary file
void writeVolumeBorderFile (const QString &name, const bool removeDuplicates=false) throw (FileException)
 write a volume border file
void writeVolumeCellFile (const QString &name) throw (FileException)
 write the Volume Cell data file
void writeVolumeFile (const QString &name, const VolumeFile::FILE_READ_WRITE_TYPE writeFileType, const VolumeFile::VOLUME_TYPE volumeType, VolumeFile *vf, const VolumeFile::VOXEL_DATA_TYPE voxelDataTypeToWrite=VolumeFile::VOXEL_DATA_TYPE_UNKNOWN, const bool zipAfniVolumeFile=false) throw (FileException)
 write the volume data file
void writeVtkModelFile (const QString &name, VtkModelFile *vmf) throw (FileException)
 write the vtk model data file
void writeWustlRegionFile (const QString &name) throw (FileException)
 write the wustl region file
virtual ~BrainSet ()
 Destructor.

Static Public Member Functions

static QString getBinDirectoryName ()
 get the name of the bin directory
static QString getCaretHomeDirectory ()
 get caret's home directory
static PreferencesFilegetPreferencesFile ()
 get the preferences file
static void initializeDataFileStaticMembers ()
 initialize data file static members
static void initializeStaticStuff ()
static void setRandomSeed (unsigned int randomSeed)
 set the random seed

Protected Slots

void slotDisplayCrossTimerTimeout ()

Private Member Functions

void checkNodeAttributeFilesForDuplicateColumnNames (QString &errorMessageOut)
 check node attribute columns for columns with same name
void constructBrainSet ()
 construct the brain set
void createBrainModelSurfaceAndVolume ()
 create a brain model surface and volume
void deleteSurfacesOfType (const BrainModelSurface::SURFACE_TYPES st)
 delete surface that are of the specified type
void getSectionsFromTopology ()
 if section file empty, look for sections in topology files
void niftiNodeDataFileDuplicateNamesHelper (const QString &fileTypeName, GiftiNodeDataFile *naf, QString &errorMessageOut) const
 check for duplicate column names in a mode attribute file
void nodeAttribteDuplicateNamesHelper (const QString &fileTypeName, NodeAttributeFile *naf, QString &errorMessageOut) const
 check for duplicate column names in a mode attribute file
bool readBorderFiles (const SpecFile::Entry &borderFilesToRead, const BrainModelSurface::SURFACE_TYPES bt, std::vector< QString > &errorMessages, int &progressFileCounter, QProgressDialog *progressDialog)
 Read in border files.
bool readCoordinateFileGroup (const SpecFile::Entry &coordFile, const BrainModelSurface::SURFACE_TYPES surfaceType, std::vector< QString > &errorMessages, int &progressFileCounter, QProgressDialog *progressDialog)
 Read in coordinate file group.
bool readImage (const QString &filename, const QString &format, QImage &image)
 read an image (returns true if read successfully)
bool readSurfaceFileGroup (const SpecFile::Entry &surfaceFile, const BrainModelSurface::SURFACE_TYPES surfaceType, std::vector< QString > &errorMessages, int &progressFileCounter, QProgressDialog *progressDialog)
 Read in surface file group.
void saveReplaceSceneHelper (SceneFile::Scene &scene, const std::vector< SceneFile::SceneClass > &mainWindowSceneClasses, const bool onlyIfSelectedFlag, QString &errorMessageOut, QString &warningMessageOut)
 save/replace scene helper
void setSelectedTopologyFiles ()
 set the selected topology files
void updateAllDisplaySettings ()
 Update all display settings.
void updateDisplayedModelIndices ()
 update displayed model indices
bool updateFileReadProgressDialog (const QString &filename, int &progressFileCounter, QProgressDialog *progressDialog)
 Update the file reading progress dialog.

Private Attributes

BrainModelSurfaceactiveFiducialSurface
 the active fiducial surface
AreaColorFileareaColorFile
 area color file
ArealEstimationFilearealEstimationFile
 areal estimation file
BorderColorFileborderColorFile
 Border color file.
BrainModelBorderSetbrainModelBorderSet
 the border set
BrainModelIdentificationbrainModelIdentification
 the identification object
std::vector< BrainModel * > brainModels
 storage for all surfaces
BrainModelSurfaceROINodeSelectionbrainModelSurfaceRegionOfInterestNodeSelection
 region of interest node selection object
BrainModelVolumeRegionOfInterestbrainModelVolumeRegionOfInterest
 volume region of interest controller
BrainSetAutoLoaderManagerbrainSetAutoLoaderManager
 the auto loader manager
CellColorFilecellColorFile
 Cell color file.
CellProjectionFilecellProjectionFile
 Cell Projection File.
BrainModelSurfacecerebellumFiducialVolumeInteractionSurface
 the cerebellum fiducial volume interaction surface
QString cerebralHullFileName
 name of cerebral hull file name
CocomacConnectivityFilecocomacFile
 cocomac file
ContourCellColorFilecontourCellColorFile
 contour cell color file
ContourCellFilecontourCellFile
 contour cell file
CutsFilecutsFile
 cuts file (cuts are same as borders)
DeformationFieldFiledeformationFieldFile
 deformation field file
QString deformationMapFileName
 name of deformation map file
bool displayAllNodesFlag
 display all nodes flag
int displayCrossForNode
 display a cross for this node
QTimer * displayCrossTimer
 display cross timer
int displayedModelIndices [BrainModel::NUMBER_OF_BRAIN_MODEL_VIEW_WINDOWS]
 index of model in each window
BrainModelSurfacedisplayNoCrossForSurface
 surface on which no cross should be shown
DisplaySettingsArealEstimationdisplaySettingsArealEstimation
 Areal Estimation display settings.
DisplaySettingsBordersdisplaySettingsBorders
 Border display settings.
DisplaySettingsCellsdisplaySettingsCells
 Cell display settings.
DisplaySettingsCoCoMacdisplaySettingsCoCoMac
 CoCoMac display settings.
DisplaySettingsContoursdisplaySettingsContours
 Contour display settings.
DisplaySettingsCutsdisplaySettingsCuts
 Cuts display settings.
DisplaySettingsDeformationFielddisplaySettingsDeformationField
 deformation field display settings
DisplaySettingsFocidisplaySettingsFoci
 Foci display settings.
DisplaySettingsGeodesicDistancedisplaySettingsGeodesicDistance
 Geodesic distance file Display Settings.
DisplaySettingsImagesdisplaySettingsImages
 images display settings
DisplaySettingsMetricdisplaySettingsMetric
 Metric display settings.
DisplaySettingsModelsdisplaySettingsModels
 Models display settings.
DisplaySettingsPaintdisplaySettingsPaint
 Paint settings.
DisplaySettingsProbabilisticAtlasdisplaySettingsProbabilisticAtlasSurface
 Probabilistic Atlas settings for surface.
DisplaySettingsProbabilisticAtlasdisplaySettingsProbabilisticAtlasVolume
 Probabilistic Atlas settings for volume.
DisplaySettingsRgbPaintdisplaySettingsRgbPaint
 RGB Paint display settings.
DisplaySettingsScenedisplaySettingsScene
 Scene display settings.
DisplaySettingsSectiondisplaySettingsSection
 section display settings
DisplaySettingsStudyMetaDatadisplaySettingsStudyMetaData
 study metadata display settings
DisplaySettingsSurfacedisplaySettingsSurface
 node display settings
DisplaySettingsSurfaceShapedisplaySettingsSurfaceShape
 Surface shape display settings.
DisplaySettingsTopographydisplaySettingsTopography
 Topography display settings.
DisplaySettingsVectorsdisplaySettingsVectors
 vector display settings
DisplaySettingsVolumedisplaySettingsVolume
 Volume display settings.
DisplaySettingsWustlRegiondisplaySettingsWustlRegion
 Wustl Region Display Settings.
bool displaySplashImage
 display splash image
FociColorFilefociColorFile
 foci color file
FociProjectionFilefociProjectionFile
 foci projection file
FociSearchFilefociSearchFile
 foci search file
GeodesicDistanceFilegeodesicDistanceFile
 geodesic distance file
bool ignoreTopologyFileInCoordinateFileHeaderFlag
 when reading coordinate files DO NOT use topology file in coord file header
std::vector< ImageFile * > imageFiles
 the image files
LatLonFilelatLonFile
 lat/lon files
BrainModelSurfaceleftFiducialVolumeInteractionSurface
 the left fiducial volume interaction surface
SpecFile loadedFilesSpecFile
 the spec file that keeps track of loaded files for this brain set
MetricFilemetricFile
 metric file
QMutex mutexAddBrainModel
 mutex for adding brain model
QMutex mutexAddToSpecFile
 mutex for add to spec file
QMutex mutexAddVolumeFile
 mutex for adding volume file
QMutex mutexAreaColorFile
 mutex for reading area color file
QMutex mutexArealEstimationFile
 mutex for reading areal estimation file
QMutex mutexBorderAndBorderProjectionFile
 mutex for reading surface border and border projection files
QMutex mutexBorderColorFile
 mutex for reading border color file
QMutex mutexCellAndCellProjectionFile
 mutex for reading cell and cell projection file
QMutex mutexCellColorFile
 mutex for reading cell color file
QMutex mutexCocomacFile
 mutex for reading cocomac file
QMutex mutexContourCellColorFile
 mutex for reading contour cell color file
QMutex mutexContourCellFile
 mutex for reading contour cell file
QMutex mutexContourFile
 mutex for reading contour file
QMutex mutexCreateSurfaceAndVolume
 mutex for creating surface and volume
QMutex mutexCutsFile
 mutex for reading cuts file
QMutex mutexDeformationFieldFile
 mutex for reading deformation field file
QMutex mutexFociAndFociProjectionFile
 mutex for reading foci and foci projection file
QMutex mutexFociColorFile
 mutex for reading foci color file
QMutex mutexFociSearchFile
 mutex for reading foci search file
QMutex mutexGeodesicDistanceFile
 mutex for reading geodesic distance file
QMutex mutexImageFile
 mutex for reading image files
QMutex mutexLatLonFile
 mutex for reading lat lon file
QMutex mutexMetricFile
 mutex for reading metric file
QMutex mutexPaintFile
 mutex for reading paint file
QMutex mutexPaletteFile
 mutex for reading palette file
QMutex mutexParamsFile
 mutex for reading params file
QMutex mutexProbAtlasFile
 mutex for reading prob atlas file
QMutex mutexReadCoordinateFile
 mutex for reading coordinate files
QMutex mutexReadSurfaceFile
 mutex for reading surface files
QMutex mutexReadTopologyFile
 mutex for reading topology files
QMutex mutexRgbPaintFile
 mutex for reading rgb paint file
QMutex mutexSceneFile
 mutex for reading scene file
QMutex mutexSectionFile
 mutex for reading section file
QMutex mutexStudyCollectionFile
 mutex for reading study collection file
QMutex mutexStudyMetaDataFile
 mutex for reading study meta data file
QMutex mutexSurfaceShapeFile
 mutex for reading surface shape file
QMutex mutexTopographyFile
 mutex for reading topography file
QMutex mutexTransformationDataFile
 mutex for reading transformation data file
QMutex mutexTransformationMatrixFile
 mutex for reading transformation matrix file
QMutex mutexVectorFile
 mutex for reading vector file
QMutex mutexVocabularyFile
 mutex for reading vocabulary file
QMutex mutexVolumeBorderFile
 mutex for reading volume border file
QMutex mutexVolumeCellFile
 mutex for reading volume cell file
QMutex mutexVtkModelFile
 mutex for reading vtk models
QMutex mutexWustlRegionFile
 mutex for reading wustl region file
std::vector
< BrainSetNodeAttribute
nodeAttributes
 node
BrainModelSurfaceNodeColoringnodeColoring
 node coloring class
bool nodesHaveBeenClassified
 nodes have been classified flag
int numberOfSurfaceOverlays
 the number of surface overlays
QString numNodesMessage
 number of nodes message when reading files
PaintFilepaintFile
 paint file
PaletteFilepaletteFile
 Palette File.
ParamsFileparamsFile
 Params File.
bool primaryBrainSetFlag
 primary brain set flag (allows setting of AbstractFile default names)
ProbabilisticAtlasFileprobabilisticAtlasSurfaceFile
QWidget * progressDialogParent
 parent for progress dialogs
bool readingSpecFileFlag
 reading a spec file flag (do not update the spec file)
RgbPaintFilergbPaintFile
 RGB Paint file.
BrainModelSurfacerightFiducialVolumeInteractionSurface
 the right fiducial volume interaction surface
SceneFilesceneFile
 scene file
SectionFilesectionFile
 section file
TransformationMatrix specDataFileTransformationMatrix
 a transformation matrix that is applied to "fiducial" files while reading a spec file
QString specFileName
 name of the spec file
QDateTime specFileTimeOfLoading
 time of spec file loading
Species species
 the species
QImage splashImage
 splash image
StereotaxicSpace stereotaxicSpace
 the stereotaxic space
Structure structure
 hemisphere
StudyCollectionFilestudyCollectionFile
 study collection file
StudyMetaDataFilestudyMetaDataFile
 study metadata file
QString subject
 the subject
std::vector
< BrainModelSurfaceOverlay * > 
surfaceOverlays
 the overlays
SurfaceShapeFilesurfaceShapeFile
 Surface Shape file.
TopographyFiletopographyFile
 Topography File.
TopologyFiletopologyClosed
 active closed topology file
TopologyFiletopologyCut
 active cut topology file
std::vector< TopologyFile * > topologyFiles
 topology files
TopologyFiletopologyLobarCut
 active lobar cut topology file
TopologyFiletopologyOpen
 active open topology file
TopologyFiletopologyUnknown
 active unknown topology file
std::vector< AbstractFile * > transformationDataFiles
 the transformation matrix data files
TransformationMatrixFiletransformationMatrixFile
 transformation matrix file
std::vector< VectorFile * > vectorFiles
 vector file
VocabularyFilevocabularyFile
 vocabulary file
std::vector< VolumeFile * > volumeAnatomyFiles
 anatomy volume files
CellFilevolumeCellFile
 volume cell file
std::vector< VolumeFile * > volumeFunctionalFiles
 functional volume files
std::vector< VolumeFile * > volumePaintFiles
 paint volume files
std::vector< VolumeFile * > volumeProbAtlasFiles
 prob atlas volume files
std::vector< VolumeFile * > volumeRgbFiles
 rgb paint volume files
std::vector< VolumeFile * > volumeSegmentationFiles
 segmentation volume files
std::vector< VolumeFile * > volumeVectorFiles
 vector volume files
BrainModelVolumeVoxelColoringvoxelColoring
 voxel coloring class
std::vector< VtkModelFile * > vtkModelFiles
 the vtk model files
bool webCaretFlag
 the web caret flag
WustlRegionFilewustlRegionFile
 wustl region file

Static Private Attributes

static PreferencesFilepreferencesFile
 the preferences file (DO NOT USE THIS DIRECTLY, use getPreferencesFile())
static bool staticStuffInitialized
 initialize static stuff flag

Friends

class BrainSetMultiThreadedSpecFileReader

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

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