Uses of Class
mgui.interfaces.shapes.Volume3DInt

Packages that use Volume3DInt

Package	Description
mgui.geometry.mesh	Provides classes representing and operating on 3D mesh shapes.
mgui.geometry.neuro.mesh
mgui.geometry.volume	Provides classes for representing and operating on 3D volume shapes.
mgui.interfaces.shapes	This package provides interfaces for user interaction with shapes and shape models.
mgui.interfaces.shapes.dynamic
mgui.interfaces.shapes.util
mgui.interfaces.shapes.volume
mgui.io.domestic.shapes
mgui.io.foreign.fsl
mgui.io.foreign.interfile
mgui.io.foreign.vol
mgui.io.foreign.wunil
mgui.io.standard.nifti
mgui.neuro.components
mgui.neuro.components.cortical

Uses of Volume3DInt in mgui.geometry.mesh

Methods in mgui.geometry.mesh that return Volume3DInt

Modifier and Type	Method	Description
Volume3DInt	MeshEngine.mapMeshToVolume(Mesh3DInt mesh, Volume3DInt volume, java.lang.String method, InterfaceProgressBar progress_bar)
Volume3DInt	MeshEngine.mapMeshToVolumeGaussian(Mesh3DInt mesh_int, Volume3DInt volume, InterfaceProgressBar progress_bar)
static Volume3DInt	MeshFunctions.mapMeshToVolumeGaussian(Mesh3DInt mesh_int, Volume3DInt volume, java.lang.String mesh_column, java.lang.String grid_channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, boolean normalize, boolean is_discrete, ProgressUpdater progress)	Projects vertex-wise data from a given Mesh3DInt data column to a Grid3D channel, normal and transverse (tangent) Gaussian functions.

Methods in mgui.geometry.mesh with parameters of type Volume3DInt

Modifier and Type	Method	Description
static Mesh3D	MeshFunctions.getIsosurfaceFromVolume(Volume3DInt volume, java.lang.String column, double iso_level)	Constructs an isosurface from volume; i.e., computes a mesh which represents the location where values in the 3D scalar field in volume are equal to iso_level.
Volume3DInt	MeshEngine.mapMeshToVolume(Mesh3DInt mesh, Volume3DInt volume, java.lang.String method, InterfaceProgressBar progress_bar)
Volume3DInt	MeshEngine.mapMeshToVolumeGaussian(Mesh3DInt mesh_int, Volume3DInt volume, InterfaceProgressBar progress_bar)
static Volume3DInt	MeshFunctions.mapMeshToVolumeGaussian(Mesh3DInt mesh_int, Volume3DInt volume, java.lang.String mesh_column, java.lang.String grid_channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, boolean normalize, boolean is_discrete, ProgressUpdater progress)	Projects vertex-wise data from a given Mesh3DInt data column to a Grid3D channel, normal and transverse (tangent) Gaussian functions.
java.util.ArrayList<MguiNumber>	MeshEngine.mapVolumeToMesh(Mesh3D mesh, Volume3DInt volume, java.lang.String method)
java.util.ArrayList<MguiNumber>	MeshEngine.mapVolumeToMesh(Mesh3D mesh, Volume3DInt volume, java.lang.String method, InterfaceProgressBar progress_bar)
static java.util.ArrayList<MguiNumber>	MeshFunctions.mapVolumeToMeshEV(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, float radius, int stat, ProgressUpdater progress)	Maps the values in channel of grid, an instance of Grid3D, to the vertices of mesh, using a containing-voxel(s) approach.
static java.util.ArrayList<MguiNumber>	MeshFunctions.mapVolumeToMeshEV(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, ProgressUpdater progress)	Maps the values in channel of grid, an instance of Grid3D, to the vertices of mesh, using a containing-voxel approach.
protected static java.util.ArrayList<MguiNumber>	MeshFunctions.mapVolumeToMeshEVBlocking(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, float radius, int stat, ProgressUpdater progress)	Maps the values in channel of grid, an instance of Grid3D, to the vertices of mesh, using a containing-voxel(s) approach.
static java.util.ArrayList<MguiNumber>	MeshFunctions.mapVolumeToMeshGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, java.lang.String setSigmaT, boolean normalize)
static java.util.ArrayList<MguiNumber>	MeshFunctions.mapVolumeToMeshGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, java.lang.String setSigmaT, boolean normalize, ProgressUpdater progress, boolean output_matrix, double normal_set_max_sigma, double tangent_set_max_sigma, java.lang.String matrix_file)	Maps values from a Grid3D object to a mesh object by applying a Gaussian kernal to voxels in the vicinity of each mesh vertex.

Uses of Volume3DInt in mgui.geometry.neuro.mesh

Fields in mgui.geometry.neuro.mesh declared as Volume3DInt

Modifier and Type	Field	Description
Volume3DInt	ScalpAndSkullModelOptions.t1_volume

Methods in mgui.geometry.neuro.mesh that return Volume3DInt

Modifier and Type	Method	Description
Volume3DInt	NeuroMeshEngine.mapCortexToVolume(Mesh3DInt mesh_int, Volume3DInt volume, java.lang.Object thickness, ProgressUpdater progress)	Maps cortical surface values to a volume

Methods in mgui.geometry.neuro.mesh with parameters of type Volume3DInt

Modifier and Type	Method	Description
Volume3DInt	NeuroMeshEngine.mapCortexToVolume(Mesh3DInt mesh_int, Volume3DInt volume, java.lang.Object thickness, ProgressUpdater progress)	Maps cortical surface values to a volume
static java.util.ArrayList<MguiNumber>	NeuroMeshFunctions.mapGrid3DToCortexGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, double thickness, boolean normalize)
java.util.ArrayList<MguiNumber>	NeuroMeshEngine.mapVolumeToCortex(Mesh3D mesh, Volume3DInt volume, java.lang.Object thickness, ProgressUpdater progress)	Maps a volume to a cortical surface
static java.util.ArrayList<MguiNumber>	NeuroMeshFunctions.mapVolumeToCortexGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, java.lang.Object _thickness, boolean normalize, ProgressUpdater progress, boolean output_matrix, java.lang.String matrix_file)	Maps values from a Grid3D object to a mesh object representing a middle cortical surface, by applying a Gaussian kernal to voxels in the vicinity of each mesh vertex.

Uses of Volume3DInt in mgui.geometry.volume

Methods in mgui.geometry.volume that return Volume3DInt

Modifier and Type	Method	Description
static Volume3DInt	VolumeFunctions.applyRotation(VolumeFunctions.VolumeAxis axis, VolumeFunctions.VolumeRotationAngle angle, Volume3DInt volume, InterfaceProgressBar progress_bar)	Rotates a Grid3D about one of its basis vectors (axes), either 90, 180, or 270 degrees, resizes the relevant dimensions, and returns the new grid.
static Volume3DInt	VolumeFunctions.applyRotationBlocking(VolumeFunctions.VolumeAxis axis, VolumeFunctions.VolumeRotationAngle angle, Volume3DInt volume)	Rotates a Grid3D about one of its basis vectors (axes), either 90, 180, or 270 degrees, resizes the relevant dimensions, and returns the new grid.
static Volume3DInt	VolumeFunctions.applyRotationBlocking(VolumeFunctions.VolumeAxis axis, VolumeFunctions.VolumeRotationAngle angle, Volume3DInt volume, InterfaceProgressBar progress_bar)	Rotates a Volume3DInt about one of its basis vectors (axes), either 90, 180, or 270 degrees, resizes the relevant dimensions, and returns the new grid.
static Volume3DInt	VolumeFunctions.getIntMaskedByValue(Volume3DInt volume, double comp_value)	Returns an integer mask of grid, where a voxel has value = 1, when grid(i,j,k,v) == comp_value (within tolerance), and 0 otherwise.
static Volume3DInt	VolumeFunctions.getIntMaskedByValue(Volume3DInt volume, double comp_value, boolean round)	Returns an integer mask of grid, where a voxel has value = 1, when grid(i,j,k,v) == comp_value (within tolerance), and 0 otherwise.
static Volume3DInt	VolumeFunctions.getInvertedVolume(Volume3DInt volume)	Returns a Grid3D object whose data is the inverse of grid.
static Volume3DInt	VolumeFunctions.getInvertedVolume(Volume3DInt volume, java.lang.String column)	Returns a Grid3D object whose data is the inverse of grid.
static Volume3DInt	VolumeFunctions.getInvertedVolume(Volume3DInt volume, java.lang.String column, ProgressUpdater progress)	Returns a Grid3D object whose data is the inverse of grid.
static Volume3DInt	VolumeFunctions.performOperationBlocking(Volume3DInt volume, java.lang.Double value, VolumeFunctions.Operation op, ProgressUpdater progress)	Performs the specified operation on one grid and a constant value, and returns and new volume.
static Volume3DInt	VolumeFunctions.performOperationBlocking(Volume3DInt volume1, Volume3DInt volume2, VolumeFunctions.Operation op, ProgressUpdater progress)	Performs the specified operation on the two volumes, and returns the result as a new Grid3D instance.

Methods in mgui.geometry.volume with parameters of type Volume3DInt

Modifier and Type	Method	Description
static Volume3DInt	VolumeFunctions.applyRotation(VolumeFunctions.VolumeAxis axis, VolumeFunctions.VolumeRotationAngle angle, Volume3DInt volume, InterfaceProgressBar progress_bar)	Rotates a Grid3D about one of its basis vectors (axes), either 90, 180, or 270 degrees, resizes the relevant dimensions, and returns the new grid.
static Volume3DInt	VolumeFunctions.applyRotationBlocking(VolumeFunctions.VolumeAxis axis, VolumeFunctions.VolumeRotationAngle angle, Volume3DInt volume)	Rotates a Grid3D about one of its basis vectors (axes), either 90, 180, or 270 degrees, resizes the relevant dimensions, and returns the new grid.
static Volume3DInt	VolumeFunctions.applyRotationBlocking(VolumeFunctions.VolumeAxis axis, VolumeFunctions.VolumeRotationAngle angle, Volume3DInt volume, InterfaceProgressBar progress_bar)	Rotates a Volume3DInt about one of its basis vectors (axes), either 90, 180, or 270 degrees, resizes the relevant dimensions, and returns the new grid.
static PointSet3DInt	VolumeFunctions.findMaximaBlocking(Volume3DInt volume, java.lang.String source_column, java.lang.String mask_column, java.lang.String label_column)	Returns a global maximum for a given volume or within a given mask, or mulitple maxima from a set of masks, specified by mask_column.
boolean	VolumeEngine.getBlobsFromVolume(Volume3DInt volume)	Extract blobs from a thresholded volume
static boolean	VolumeFunctions.getBlobsFromVolume(Volume3DInt volume, java.lang.String source_column, java.lang.String target_column, ProgressUpdater progress, int min_blob, double threshold)	Finds connected blobs in a thresholded volume.
static java.util.ArrayList<MguiNumber>	VolumeFunctions.getBlobsFromVolumeBlocking(Volume3DInt volume, java.lang.String column, ProgressUpdater progress, int min_blob, double threshold)	Finds connected blobs in a thresholded volume.
static java.awt.image.BufferedImage	VolumeFunctions.getCompositeRSliceImage(Volume3DInt volume, int r)	Returns a composite image from an R-slice plane and a volume
static java.awt.image.BufferedImage	VolumeFunctions.getCompositeRSliceImage(Volume3DInt volume, int r, java.util.ArrayList<java.lang.String> ordered_columns, java.util.ArrayList<WindowedColourModel> colour_models, java.util.ArrayList<java.lang.Double> alphas)	Returns a composite image from an R-slice plane, volume, and set of colour models and composite alphas.
static java.awt.image.BufferedImage	VolumeFunctions.getCompositeRSliceImage(Volume3DInt volume, int r, java.util.ArrayList<java.lang.String> ordered_columns, java.util.ArrayList<WindowedColourModel> colour_models, java.util.ArrayList<java.lang.Double> alphas, java.util.ArrayList<java.lang.Boolean> include)	Returns a composite image from an R-slice plane, volume, and set of colour models and composite alphas.
static java.awt.image.BufferedImage	VolumeFunctions.getCompositeSliceImage(Volume3DInt volume, int orientation, int section)	Returns a composite image from an S,T, or R-slice plane, determined by section, and volume.
static java.awt.image.BufferedImage	VolumeFunctions.getCompositeSliceImage(Volume3DInt volume, int orientation, int section, java.util.ArrayList<java.lang.String> ordered_columns, java.util.ArrayList<WindowedColourModel> colour_models, java.util.ArrayList<java.lang.Double> alphas, java.util.ArrayList<java.lang.Boolean> include)	Returns a composite image from an image plane, volume, determined by orientation, and set of colour models and composite alphas.
static double	VolumeFunctions.getGaussianSmoothedValue(Volume3DInt volume, int[] voxel, int channel, org.jogamp.vecmath.Vector3f normal, float sigma_normal, float sigma_tangent, float cutoff)	Computes a value for voxel which is the weighted average of a Gaussian sampling of its neighbouring voxels, where the Gaussian is defined by a normal vector, its corresponding plane, and the sigma parameters sigma_normal and sigma_tangent.
static Histogram	VolumeFunctions.getHistogram(Volume3DInt volume, int bins)	Returns a histogram for the current column of volume.
static Histogram	VolumeFunctions.getHistogram(Volume3DInt volume, int t, int bins, double min, double max)	Returns a histogram for the current column of volume.
static Histogram	VolumeFunctions.getHistogram(Volume3DInt volume, java.lang.String column, int t, int bins, double min, double max)	Returns a histogram for the vertex column column of volume.
static Volume2DInt	VolumeFunctions.getIntersectionCompositeImage(Volume3DInt volume, Plane3D plane, boolean setAlpha)	Returns an Volume2DInt object representing the intersection of the given 3D composite volume with plane.
static Volume2DInt	VolumeFunctions.getIntersectionImage(Volume3DInt volume, Plane3D plane, boolean setAlpha)	Returns an Volume2DInt object representing the intersection of the given 3D volume with plane.
static Volume2DInt	VolumeFunctions.getIntersectionImage(Volume3DInt volume, Plane3D plane, boolean setAlpha, org.jogamp.vecmath.Matrix4d transform)	Returns an Volume2DInt object representing the intersection of the given 3D volume with plane.
static Volume3DInt	VolumeFunctions.getIntMaskedByValue(Volume3DInt volume, double comp_value)	Returns an integer mask of grid, where a voxel has value = 1, when grid(i,j,k,v) == comp_value (within tolerance), and 0 otherwise.
static Volume3DInt	VolumeFunctions.getIntMaskedByValue(Volume3DInt volume, double comp_value, boolean round)	Returns an integer mask of grid, where a voxel has value = 1, when grid(i,j,k,v) == comp_value (within tolerance), and 0 otherwise.
static Volume3DInt	VolumeFunctions.getInvertedVolume(Volume3DInt volume)	Returns a Grid3D object whose data is the inverse of grid.
static Volume3DInt	VolumeFunctions.getInvertedVolume(Volume3DInt volume, java.lang.String column)	Returns a Grid3D object whose data is the inverse of grid.
static Volume3DInt	VolumeFunctions.getInvertedVolume(Volume3DInt volume, java.lang.String column, ProgressUpdater progress)	Returns a Grid3D object whose data is the inverse of grid.
boolean	VolumeEngine.getIsosurfaceFromVolume(Volume3DInt volume)	Creates an isosurface at a specified isovalue in volume.
static byte	VolumeFunctions.getMappedValueByte(Volume3DInt volume, int x, int y, int z)	Returns the value of voxel [i,j,k] mapped with its colour model, as a byte.
static double	VolumeFunctions.getMappedValueDouble(Volume3DInt volume, int x, int y, int z)
static java.awt.image.BufferedImage[]	VolumeFunctions.getMaskedCompositeImages(Volume3DInt volume)	Returns a set of composite images, comprised of all data columns specified for the composite, with alpha values and ordering as specified in the Volume3DInt object.
static java.awt.image.BufferedImage	VolumeFunctions.getMaskedCompositeRSliceImage(Volume3DInt volume, int r, boolean[][][] mask)	Returns a composite image from an R-slice plane, volume, and set of colour models and composite alphas.
static java.awt.image.BufferedImage[]	VolumeFunctions.getMaskedImages(Volume3DInt volume)	Produces a stack of R-planar images from volume, based upon the current data column and its associated colour map.
static java.awt.image.BufferedImage[]	VolumeFunctions.getMaskedImages(Volume3DInt volume, java.lang.String column)	Produces a stack of R-planar images from volume, based upon the data in column and its associated colour map.
static PointSet3DInt	VolumeFunctions.getRoiCentroidsBlocking(Volume3DInt volume, java.lang.String source_column, int[] value_range, int min_size, boolean map_values, java.lang.String label_column, ProgressUpdater progress)	Finds the centroids for all ROIs (identified as voxels with the same value).
boolean	VolumeEngine.mapVolumeToVolume(Volume3DInt source, Volume3DInt target, java.lang.String method, ProgressUpdater progress_bar)	Maps a column of source to a column of target, given the attributes corresponding to method.
static void	VolumeFunctions.mapVolumeToVolumeEV(Volume3DInt volume_source, Volume3DInt volume_target, java.lang.String column_source, java.lang.String column_target)	Maps volume_source to volume_target, using the enclosing voxel to assign the value.
static boolean	VolumeFunctions.mapVolumeToVolumeEV(Volume3DInt volume_source, Volume3DInt volume_target, java.lang.String column_source, java.lang.String column_target, double default_value, ProgressUpdater progress)	Maps volume_source to volume_target, using the enclosing voxel to assign the value.
static void	VolumeFunctions.mapVolumeToVolumeEV(Volume3DInt volume_source, Volume3DInt volume_target, java.lang.String column_source, java.lang.String column_target, ProgressUpdater progress)	Maps volume_source to volume_target, using the enclosing voxel to assign the value.
protected static boolean	VolumeFunctions.mapVolumeToVolumeEVBlocking(Volume3DInt volume_source, Volume3DInt volume_target, java.lang.String column_source, java.lang.String column_target, double default_value, ProgressUpdater progress)	Maps volume_source to volume_target, using the enclosing voxel to assign the value.
static void	VolumeFunctions.mapVolumeToVolumeInterp(Volume3DInt volume_source, Volume3DInt volume_target, java.lang.String column_source, java.lang.String column_target, java.lang.String method, java.util.ArrayList<java.lang.Object> parameters)	Maps volume_source to volume_target, using interpolation from all overlapping voxels to assign the value.
static boolean	VolumeFunctions.mapVolumeToVolumeInterp(Volume3DInt volume_source, Volume3DInt volume_target, java.lang.String column_source, java.lang.String column_target, java.lang.String method, java.util.ArrayList<java.lang.Object> parameters, double default_value, ProgressUpdater progress)	Maps volume_source to volume_target, using interpolation from all overlapping voxels to assign the value.
static void	VolumeFunctions.mapVolumeToVolumeInterp(Volume3DInt volume_source, Volume3DInt volume_target, java.lang.String column_source, java.lang.String column_target, java.lang.String method, java.util.ArrayList<java.lang.Object> parameters, ProgressUpdater progress)	Maps volume_source to volume_target, using interpolation from all overlapping voxels to assign the value.
protected static boolean	VolumeFunctions.mapVolumeToVolumeInterpBlocking(Volume3DInt volume_source, Volume3DInt volume_target, java.lang.String column_source, java.lang.String column_target, java.lang.String method, java.util.ArrayList<java.lang.Object> parameters, double default_value, ProgressUpdater progress)	Maps volume_source to volume_target, using interpolation from all overlapping voxels to assign the value.
static Volume3DInt	VolumeFunctions.performOperationBlocking(Volume3DInt volume, java.lang.Double value, VolumeFunctions.Operation op, ProgressUpdater progress)	Performs the specified operation on one grid and a constant value, and returns and new volume.
static Volume3DInt	VolumeFunctions.performOperationBlocking(Volume3DInt volume1, Volume3DInt volume2, VolumeFunctions.Operation op, ProgressUpdater progress)	Performs the specified operation on the two volumes, and returns the result as a new Grid3D instance.
boolean	VolumeEngine.smoothVolume(Volume3DInt volume, java.lang.String method, ProgressUpdater progress_bar)	Geometrically smooths values from source_column in volume with the smoothing kernel specified by method.
static boolean	VolumeFunctions.smoothVolumeGaussian(Volume3DInt volume, java.lang.String source_column, java.lang.String target_column, double fwhm, double max_radius)	Geometrically smooths values from source_column in volume with an isotropic Gaussian smoothing kernel with a full-width-at-half-maximum of fwhm.
static boolean	VolumeFunctions.smoothVolumeGaussian(Volume3DInt volume, java.lang.String source_column, java.lang.String target_column, double fwhm, double max_radius, ProgressUpdater progress, double default_value)	Geometrically smooths values from source_column in volume with an isotropic Gaussian smoothing kernel with a full-width-at-half-maximum of fwhm.
static boolean	VolumeFunctions.smoothVolumeGaussianBlocking(Volume3DInt volume, java.lang.String source_column, java.lang.String target_column, double fwhm, double max_radius, ProgressUpdater progress, double default_value)	Geometrically smooths values from source_column in volume with an isotropic Gaussian smoothing kernel with a full-width-at-half-maximum of fwhm.

Uses of Volume3DInt in mgui.interfaces.shapes

Subclasses of Volume3DInt in mgui.interfaces.shapes

Modifier and Type	Class	Description
class	TensorVolume3DInt
class	VolumeSet3DInt	A set of Volume3DInt objects which render as an overlay image.

Methods in mgui.interfaces.shapes that return Volume3DInt

Modifier and Type	Method	Description
Volume3DInt	VolumeSet3DInt.getMember(int i)	Gets the i'th member in this set

Methods in mgui.interfaces.shapes that return types with arguments of type Volume3DInt

Modifier and Type	Method	Description
java.util.ArrayList<Volume3DInt>	VolumeSet3DInt.getMembers()	Gets a list of this set's members

Methods in mgui.interfaces.shapes with parameters of type Volume3DInt

Modifier and Type	Method	Description
void	VolumeSet3DInt.addVolume(int index, float alpha, Volume3DInt volume, boolean update)	Adds volume at position index of this overlay set, with given alpha level, and redraws the overlay.
void	VolumeSet3DInt.addVolume(Volume3DInt volume, float alpha, boolean update)	Adds volume to top of this overlay set, with given alpha level, and redraws the overlay.
void	VolumeSet3DInt.removeVolume(Volume3DInt volume, boolean update)	Removes the given volume (actually the first volume having the identical name) from this set.
boolean	Volume3DInt.sampleFromVolume(Volume3DInt sample_volume)	Samples sample_volume where its geometric bounds cross the bounds of this volume.
boolean	Volume3DInt.sampleFromVolume(Volume3DInt sample_volume, double nan_value)	Samples sample_volume where its geometric bounds cross the bounds of this volume.
boolean	Volume3DInt.sampleFromVolume(Volume3DInt sample_volume, java.lang.String source_column, java.lang.String target_column)	Samples sample_volume where its geometric bounds cross the bounds of this volume.
boolean	Volume3DInt.sampleFromVolume(Volume3DInt sample_volume, java.lang.String source_column, java.lang.String target_column, double nan_value)	Samples sample_volume where its geometric bounds cross the bounds of this volume.
boolean	Volume3DInt.unionMaskWithVolume(java.lang.String name, Volume3DInt volume)	Sets mask name to a new mask which is a union between its current state and the mask specified by volume, where all zero-valued voxels are masked.
boolean	Volume3DInt.unionMaskWithVolume(java.lang.String name, Volume3DInt volume, java.lang.String column)	Sets mask name to a new mask which is a union between its current state and the mask specified by volume, where all zero-valued voxels are masked.

Uses of Volume3DInt in mgui.interfaces.shapes.dynamic

Subclasses of Volume3DInt in mgui.interfaces.shapes.dynamic

Modifier and Type	Class	Description
class	Volume4DInt	Volume with 3 space and 1 time dimension.

Uses of Volume3DInt in mgui.interfaces.shapes.util

Methods in mgui.interfaces.shapes.util with parameters of type Volume3DInt

Modifier and Type	Method	Description
static void	ShapeFunctions.unionMaskVolumeWithPlane(boolean[][][] mask, Volume3DInt volume, Plane3D plane, boolean is_above)	Returns a mask for volume which is above or below plane.

Uses of Volume3DInt in mgui.interfaces.shapes.volume

Fields in mgui.interfaces.shapes.volume declared as Volume3DInt

Modifier and Type	Field	Description
protected Volume3DInt	InterfaceVolumePanel.currentVolume
protected Volume3DInt	GridVertexDataColumn.volume
Volume3DInt	VolumeMaskOptions.volume
protected Volume3DInt	Volume3DRenderer.volume3D

Methods in mgui.interfaces.shapes.volume that return Volume3DInt

Modifier and Type	Method	Description
static Volume3DInt	InterfaceVolumePanel.getDefaultVolume()
protected Volume3DInt	InterfaceVolumePanel.getVolume(java.lang.String column)

Methods in mgui.interfaces.shapes.volume with parameters of type Volume3DInt

Modifier and Type	Method	Description
protected Histogram	InterfaceVolumePanel.getHistogramBlocking(Volume3DInt volume, int t, int bins, double min, double max)	Produces a histogram for the currently selected column of volume.
boolean	InterfaceVolumePanel.loadVolume(Volume3DInt volume, java.lang.String column, VolumeFileLoader loader, VolumeInputOptions options, ProgressUpdater progress_bar)
void	Volume3DTexture.setCurrentComposite(Volume3DInt volume)
protected void	InterfaceVolumePanel.setCurrentVolume(Volume3DInt volume)
boolean	Volume3DTexture.setFromVolume(Volume3DInt volume)	Set this volume from the specified grid.
boolean	Volume3DTexture.setFromVolume(Volume3DInt volume, boolean update)	Set this volume from the specified grid.
void	VolumeMetadata.setFromVolume(Volume3DInt volume)	Sets this metadata from volume.
void	VolumeMetadata.setFromVolume(Volume3DInt volume, java.lang.String column)	Sets this metadata from grid, for the specified column.
void	GridVertexDataColumn.setParent(Volume3DInt parent)	Sets the parent volume for this vertex data
void	Volume3DRenderer.setVolume(Volume3DInt volume)
void	VolumeMaskOptions.setVolume(Volume3DInt volume)
boolean	Volume3DTexture.updateFromVolume(Volume3DInt volume)	Set this volume from the specified grid.
boolean	Volume3DTexture.updateFromVolume(Volume3DInt volume, boolean update)	Updates this volume from the specified grid.

Constructors in mgui.interfaces.shapes.volume with parameters of type Volume3DInt

Constructor	Description
GridVertexDataColumn(java.lang.String name, Volume3DInt volume)
GridVertexDataColumn(java.lang.String name, Volume3DInt volume, java.util.ArrayList<MguiNumber> data)
Volume3DRenderer(Volume3DInt volume)
Volume3DTexture(Volume3DInt volume)
Volume3DTexture(Volume3DInt volume, ColourMap cmap)
Volume4DRenderer(Volume3DInt volume)

Uses of Volume3DInt in mgui.io.domestic.shapes

Fields in mgui.io.domestic.shapes declared as Volume3DInt

Modifier and Type	Field	Description
Volume3DInt[]	VolumeOutputOptions.volumes

Methods in mgui.io.domestic.shapes that return Volume3DInt

Modifier and Type	Method	Description
Volume3DInt	VolumeFileLoader.getVolume3D()
Volume3DInt	VolumeFileLoader.getVolume3D(int t)	Load the volume at time point t.
Volume3DInt	VolumeFileLoader.getVolume3D(int v, ProgressUpdater progress_bar)	Creates and returns a grid based on the metadata.
Volume3DInt	VolumeFileLoader.getVolume3D(VolumeInputOptions options)	Creates and returns a grid based on the parameters in options.
Volume3DInt	VolumeFileLoader.getVolume3D(VolumeInputOptions options, int v, ProgressUpdater progress_bar)	Creates and returns a grid based on the metadata.
protected Volume3DInt	VolumeFileLoader.getVolume3DCustom(VolumeInputOptions options, int v, ProgressUpdater progress_bar)	Creates and returns a grid based on the parameters in options.
Volume3DInt	VolumeFileInterface.getVolume3DInt(Volume3DInt volume)
Volume3DInt	VolumeFileLoader.loadVolume()	Load the volume at the current file, with default options.
Volume3DInt	VolumeFileLoader.loadVolume(ProgressUpdater progress_bar)	Load the volume at the current file.
Volume3DInt	VolumeFileLoader.loadVolume(VolumeInputOptions options, ProgressUpdater progress_bar)	Load the volume at the current file, with the given options.
static Volume3DInt	VolumeInputDialogBox.loadVolume(VolumeInputOptions options, InterfaceIOPanel panel)
static Volume3DInt	VolumeInputDialogBox.showDialog(InterfaceIOPanel panel, VolumeInputOptions opts, boolean show_checks)

Methods in mgui.io.domestic.shapes with parameters of type Volume3DInt

Modifier and Type	Method	Description
protected java.util.List<MguiDouble>	VolumeFileDataSource.getSourceSignalAsDouble(Volume3DInt volume)
Volume3DInt	VolumeFileInterface.getVolume3DInt(Volume3DInt volume)
protected byte[]	VolumeFileDataSource.getVolumeAsBytes(Volume3DInt volume)
boolean	VolumeFileLoader.setVolume3D(Volume3DInt volume, int v, VolumeInputOptions options)
boolean	VolumeFileLoader.setVolume3D(Volume3DInt volume, int v, VolumeInputOptions options, ProgressUpdater progress)
boolean	VolumeFileLoader.setVolume3D(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)
boolean	VolumeFileLoader.setVolume3D(Volume3DInt volume, VolumeInputOptions options)
protected abstract boolean	VolumeFileLoader.setVolume3DBlocking(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)
protected boolean	VolumeFileLoader.setVolume3DWorker(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)
boolean	VolumeFileWriter.writeVolume(Volume3DInt volume)	Writes volume to file using default parameters.
abstract boolean	VolumeFileWriter.writeVolume(Volume3DInt volume, VolumeOutputOptions options)	Writes a volume to file using the specified options.

Uses of Volume3DInt in mgui.io.foreign.fsl

Methods in mgui.io.foreign.fsl with parameters of type Volume3DInt

Modifier and Type	Method	Description
void	FSLVolumeMetadata.setFromVolume(Volume3DInt volume)
void	FSLVolumeMetadata.setFromVolume(Volume3DInt volume, java.lang.String column)
protected boolean	FSLVolumeLoader.setVolume3DBlocking(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)

Uses of Volume3DInt in mgui.io.foreign.interfile

Methods in mgui.io.foreign.interfile with parameters of type Volume3DInt

Modifier and Type	Method	Description
protected boolean	InterfileLoader.setVolume3DBlocking(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)

Uses of Volume3DInt in mgui.io.foreign.vol

Methods in mgui.io.foreign.vol that return Volume3DInt

Modifier and Type	Method	Description
Volume3DInt	VolFileLoader.getVolume3D()
Volume3DInt	VolFileLoader.getVolume3D(int v)	Return a Grid3D object representing the geometrical boundary of this volume

Methods in mgui.io.foreign.vol with parameters of type Volume3DInt

Modifier and Type	Method	Description
boolean	VolFileLoader.setVolume3D(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)	Fills a grid with this file's data.
protected boolean	VolFileLoader.setVolume3DBlocking(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)

Uses of Volume3DInt in mgui.io.foreign.wunil

Methods in mgui.io.foreign.wunil with parameters of type Volume3DInt

Modifier and Type	Method	Description
void	WunilDataset.setFromVolume(Volume3DInt volume)
void	WunilDataset.setFromVolume(Volume3DInt volume, java.lang.String column)
boolean	WunilVolumeLoader.setVolume3DBlocking(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)

Uses of Volume3DInt in mgui.io.standard.nifti

Methods in mgui.io.standard.nifti with parameters of type Volume3DInt

Modifier and Type	Method	Description
protected double[][][]	NiftiVolumeWriter.getDoubleArray(Volume3DInt volume, java.lang.String column)
void	NiftiMetadata.setFromVolume(Volume3DInt volume)
void	NiftiMetadata.setFromVolume(Volume3DInt volume, java.lang.String column)
boolean	NiftiVolumeWriter.setFromVolume(Volume3DInt volume)
protected boolean	NiftiVolumeLoader.setVolume3DBlocking(Volume3DInt volume3d, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)
boolean	NiftiVolumeWriter.writeVolume(Volume3DInt volume, java.lang.String column, NiftiMetadata dataset)	Writes volume to the current file, using the specified column and NiftiMetadata.
boolean	NiftiVolumeWriter.writeVolume(Volume3DInt volume, VolumeOutputOptions options)
boolean	NiftiVolumeWriter.writeVolume(Volume3DInt volume, NiftiMetadata dataset)	Writes volume to the current file, using the current column and NiftiMetadata.

Uses of Volume3DInt in mgui.neuro.components

Fields in mgui.neuro.components declared as Volume3DInt

Modifier and Type	Field	Description
Volume3DInt	CorticalVolume.volume

Methods in mgui.neuro.components that return Volume3DInt

Modifier and Type	Method	Description
Volume3DInt	CorticalVolume.getVolume()

Methods in mgui.neuro.components with parameters of type Volume3DInt

Modifier and Type	Method	Description
void	CorticalVolume.setVolume(Volume3DInt vol)

Constructors in mgui.neuro.components with parameters of type Volume3DInt

Constructor	Description
CorticalVolume(Volume3DInt vol)

Uses of Volume3DInt in mgui.neuro.components.cortical

Fields in mgui.neuro.components.cortical declared as Volume3DInt

Modifier and Type	Field	Description
Volume3DInt	CorticalVolume.volume

Methods in mgui.neuro.components.cortical that return Volume3DInt

Modifier and Type	Method	Description
Volume3DInt	CorticalVolume.getVolume()

Methods in mgui.neuro.components.cortical with parameters of type Volume3DInt

Modifier and Type	Method	Description
void	CorticalVolume.setVolume(Volume3DInt vol)

Constructors in mgui.neuro.components.cortical with parameters of type Volume3DInt

Constructor	Description
CorticalVolume(Volume3DInt vol)