My3DData (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- view5d.My3DData

```
public class My3DData
extends Object
```

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`ActiveElement`
`int`	`ActiveTime`
`int`	`AppendTo`
`Container`	`applet`
`int`	`DimensionOrder`
`int`	`Elements`
`String`	`markerInfilename`
`String`	`markerOutfilename`
`view5d.ASlice[]`	`MyColorProjection`
`view5d.ASlice[]`	`MyColorSlice`
`Vector<AnElement>`	`MyElements`
`MarkerLists`	`MyMarkers`
`Vector<view5d.ASlice>[]`	`MyProjections`
`view5d.ASlice[]`	`MySlice`
`Vector<view5d.ASlice[]>`	`MyTimeColorProj`
`Vector<Vector<view5d.ASlice>[]>`	`MyTimeProj`
`Vector<Vector<AnElement>>`	`MyTimes`
`int`	`SizeX`
`int`	`SizeY`
`int`	`SizeZ`
`int`	`Times`

Constructor Summary

Constructors
Constructor and Description
`My3DData(Container myapp, int sizex, int sizey, int sizez, int elements, int times, int redEl, int greenEl, int blueEl, int hisx, int hisy, int hisz, int myType, int NumBytes, int NumBits, double[] Scales, double[] Offsets, double ScaleV, double OffsetV, String[] Names, String[] Units)`
`My3DData(My3DData other)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`AnElement`	`ActElement()`
`int`	`AddLookUpTable(int MapSize, byte[] Reds, byte[] Greens, byte[] Blues)`
`void`	`addLThresh(double howmuch)`
`void`	`AddMarkedElement()`
`void`	`addUThresh(double howmuch)`
`void`	`adjustColorMapLThresh(double howmuch)`
`void`	`adjustColorMapUThresh(double howmuch)`
`void`	`AdjustOffsetToROIMean()`
`void`	`AdjustThresh()`
`void`	`AdjustThresh(boolean allelements)`
`boolean`	`AdjustThresh(int elementNum)`
`boolean`	`AdjustThreshGlobal()`
`void`	`advanceElement(int howmany)`
`void`	`advanceTime(int howmany)`
`void`	`ApplyHistSelection()`
`void`	`ClearChannel(int col)`
`void`	`ClearLineROIs()`
`void`	`ClearPolyROIs()`
`void`	`ClearPolyROIs(int dir)`
`void`	`CloneElement(AnElement oldelem)`
`void`	`CloneFloat()`
`void`	`CloneLastElements()`
`void`	`CloneShort()`
`view5d.ASlice[]`	`ColorProjsAtTime(int atime)`
`void`	`ComputeColorProj(int dim)`
`void`	`copyLinkedProperties(int anElement)`
`void`	`CThreshToValThresh(int elem, double facmin, double facmax)`
`void`	`DeleteActElement()`
`void`	`DeleteActElement(Vector<AnElement> ElementList)`
`void`	`DivMarkedElement()`
`AnElement`	`ElementAt(int num)`
`AnElement`	`ElementAt(int num, int time)`
`Vector<AnElement>`	`ElementsAtTime(int atime)`
`void`	`GenerateMask(int dim)`
`int`	`GenerateNewElement(int DataType, int NumBytes, int NumBits, double[] Scales, double[] Offsets, double ScaleV, double OffsetV, String[] Names, String[] Units)`
`int`	`GenerateNewTime(int DataType, int NumBytes, int NumBits, double[] Scales, double[] Offsets, double ScaleV, double OffsetV, String[] Names, String[] Units, int NewElements)`
`int`	`GetActiveColorModelNr()`
`int`	`GetActiveElement()`
`int`	`GetActiveTime()`
`String[]`	`GetAxisNames()`
`String[]`	`GetAxisUnits()`
`Bundle`	`GetBundleAt(int e)`
`int`	`GetChannel(int col)`
`Color`	`GetCMapColor(int e, int pos, int mysize)`
`Color`	`GetColColor(int e, int x, int y, int z)`
`boolean`	`GetColorMode()`
`int`	`GetColorModelNr(int e)`
`String`	`GetDataTypeName(int elem)`
`double[]`	`GetDisplayOffset(int elem)`
`void`	`GetElementsFromTime()`
`double`	`GetGamma(int e)`
`int`	`GetIntValueAt(int x, int y, int z, int e)`
`boolean`	`GetLogMode()`
`Color`	`GetMarkerColor(int e)`
`double`	`GetMaxThresh(int elem)`
`double`	`GetMinThresh(int elem)`
`boolean`	`GetMIPMode(int DimNr)`
`int`	`GetNumElements()`
`int`	`GetNumTimes()`
`double[]`	`GetOffset(int elem)`
`double`	`GetOffset(int elem, int dim)`
`void`	`GetPolyROICoords(int dir, int segment, float[] coords)`
`int`	`GetPolyROISize(int dir)`
`boolean`	`GetProjectionMode(int DimNr)`
`void`	`GetProjsFromTime()`
`double`	`GetROIAvg(int elem)`
`double`	`GetROIMax(int elem)`
`double`	`GetROIMin(int elem)`
`double`	`GetROISize(int elem, int dim)`
`double`	`GetROISum(int elem)`
`double`	`GetROIVal(int elem)`
`double`	`GetROIVoxels(int elem)`
`double[]`	`GetScale(int elem)`
`double`	`GetScale(int elem, int dim)`
`double`	`GetScaledMaxcs(int elem)`
`double`	`GetScaledMincs(int elem)`
`double`	`GetScaledRange(int elem)`
`int`	`GetSize(int DimNr)`
`Rectangle`	`GetSqrROI(int dim)`
`String`	`GetValueName(int elem)`
`double`	`GetValueOffset(int elem)`
`double`	`GetValueScale(int elem)`
`String`	`GetValueUnit(int elem)`
`double`	`GlobalMax()`
`double`	`GlobalMin()`
`void`	`initGlobalThresh()`
`void`	`initThresh()`
`void`	`InvalidateColor()`
`void`	`InvalidateColor(int time)`
`void`	`InvalidateProjs(int which)`
`void`	`InvalidateProjs(int which, int time)`
`void`	`InvalidateSlices()`
`void`	`InvertCMap()`
`void`	`Load(int DataType, int NumBytes, int NumBits, String URLname)`
`void`	`LoadMarkers()`
`void`	`MarkAsHistoDim(int dim)`
`void`	`MarkChannel(int col)`
`void`	`MarkChannel(int elem, int col)`
`void`	`MovePolyROI(int DX, int DY, int dir)`
`void`	`MoveROI(int DX, int DY, int dir)`
`void`	`MoveSqrROI(int DX, int DY, int dir)`
`void`	`MulMarkedElement()`
`void`	`NewMarkerList()`
`void`	`NewMarkerList(int linkTo, String NameExtension)`
`void`	`nextTime(int num)`
`double`	`Normalize(double val, int e)`
`double`	`NormedProjValueAt(int dir, int pos, int e)`
`double`	`NormedValueAt(int x, int y, int z, int e)`
`Vector<view5d.ASlice>[]`	`ProjsAtTime(int atime)`
`double`	`ProjValueAt(int dir, int pos, int e)`
`void`	`SaveMarkers()`
`void`	`setColorMapThresh(int elem, int low, int high)`
`void`	`SetColorModelNr(int e, int actModel)`
`void`	`setElement(int num)`
`void`	`setElementsLinked(boolean v)`
`void`	`setFontSize(int FS)`
`void`	`SetGamma(int e, double gamma)`
`void`	`setGate()`
`void`	`setModelThresh()`
`void`	`setModelThresh(int e)`
`void`	`SetOffsets(int elem, double OfX, double OfY, double OfZ)`
`boolean`	`SetScaledMinMaxcs(int elem, double Min, double Max)`
`boolean`	`SetThresh(double min, double max)`
`boolean`	`SetThresh(int e, double min, double max)`
`void`	`setTime(int num)`
`void`	`setTimesLinked(boolean v)`
`void`	`SetUp(int DataType, View5D_ myv3d, int elements, int times, int ImageType)`
`void`	`SetValueOffset(int elem, double value)`
`void`	`SetValueScale(int elem, double ScaleV, double Off, String NameV, String UnitV)`
`boolean`	`SquareROIs()`
`void`	`SubMarkedElement()`
`void`	`TakeDataToHistogram(My3DData data)`
`void`	`TakeLineROI(int ROIX, int ROIY, int ROIXe, int ROIYe, int dir)`
`void`	`TakePolyROI(Polygon myNewROI, int dir)`
`void`	`TakeROI(int ROIX, int ROIY, int ROIXe, int ROIYe, int dir)`
`void`	`ToggleColor()`
`void`	`ToggleColor(boolean set)`
`void`	`ToggleConnection(int newVal)`
`void`	`toggleGate(int toggle)`
`void`	`ToggleLog(int newVal)`
`void`	`ToggleLog(int e, int newVal)`
`void`	`ToggleModel(int newModel)`
`void`	`ToggleModel(int elem, int newModel)`
`void`	`ToggleMulDispl(int val)`
`void`	`ToggleOverlayDispl(int val)`
`void`	`ToggleOvUn(int newVal)`
`void`	`ToggleProj(int DimNr, boolean mipmode)`
`void`	`ToggleSquareROIs()`
`void`	`transferThresh(int elem)`
`double`	`ValueAt(int x, int y, int z, int e)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

markerInfilename
```
public String markerInfilename
```

markerOutfilename
```
public String markerOutfilename
```

MyElements
```
public Vector<AnElement> MyElements
```

MyProjections

public Vector<view5d.ASlice>[] MyProjections

MyColorProjection

public view5d.ASlice[] MyColorProjection

MySlice
```
public view5d.ASlice[] MySlice
```

MyColorSlice
```
public view5d.ASlice[] MyColorSlice
```

MyMarkers
```
public MarkerLists MyMarkers
```

SizeX
```
public int SizeX
```

SizeY
```
public int SizeY
```

SizeZ
```
public int SizeZ
```

Elements
```
public int Elements
```

ActiveElement
```
public int ActiveElement
```

DimensionOrder
```
public int DimensionOrder
```

AppendTo
```
public int AppendTo
```

MyTimes

public Vector<Vector<AnElement>> MyTimes

MyTimeProj

public Vector<Vector<view5d.ASlice>[]> MyTimeProj

Times
```
public int Times
```

ActiveTime
```
public int ActiveTime
```

MyTimeColorProj

public Vector<view5d.ASlice[]> MyTimeColorProj

applet
```
public Container applet
```

Constructor Detail

My3DData
```
public My3DData(My3DData other)
```

My3DData

public My3DData(Container myapp,
                int sizex,
                int sizey,
                int sizez,
                int elements,
                int times,
                int redEl,
                int greenEl,
                int blueEl,
                int hisx,
                int hisy,
                int hisz,
                int myType,
                int NumBytes,
                int NumBits,
                double[] Scales,
                double[] Offsets,
                double ScaleV,
                double OffsetV,
                String[] Names,
                String[] Units)

Method Detail

setElementsLinked

public void setElementsLinked(boolean v)

setTimesLinked

public void setTimesLinked(boolean v)

setFontSize
```
public void setFontSize(int FS)
```

NewMarkerList
```
public void NewMarkerList()
```

NewMarkerList

public void NewMarkerList(int linkTo,
                          String NameExtension)

AddLookUpTable

public int AddLookUpTable(int MapSize,
                          byte[] Reds,
                          byte[] Greens,
                          byte[] Blues)

toggleGate
```
public void toggleGate(int toggle)
```

setGate
```
public void setGate()
```

setModelThresh
```
public void setModelThresh()
```

setModelThresh
```
public void setModelThresh(int e)
```

GetActiveColorModelNr
```
public int GetActiveColorModelNr()
```

GetColorModelNr
```
public int GetColorModelNr(int e)
```

SetColorModelNr

public void SetColorModelNr(int e,
                            int actModel)

GetBundleAt
```
public Bundle GetBundleAt(int e)
```

ToggleLog
```
public void ToggleLog(int newVal)
```

ToggleConnection

public void ToggleConnection(int newVal)

ToggleLog

public void ToggleLog(int e,
                      int newVal)

SetGamma

public void SetGamma(int e,
                     double gamma)

GetGamma
```
public double GetGamma(int e)
```

ToggleOvUn
```
public void ToggleOvUn(int newVal)
```

ToggleModel

public void ToggleModel(int elem,
                        int newModel)

ToggleModel

public void ToggleModel(int newModel)

InvertCMap
```
public void InvertCMap()
```

GetScaledMincs

public double GetScaledMincs(int elem)

GetScaledMaxcs

public double GetScaledMaxcs(int elem)

GetScaledRange

public double GetScaledRange(int elem)

transferThresh
```
public void transferThresh(int elem)
```

SetThresh

public boolean SetThresh(double min,
                         double max)

SetThresh

public boolean SetThresh(int e,
                         double min,
                         double max)

SetScaledMinMaxcs

public boolean SetScaledMinMaxcs(int elem,
                                 double Min,
                                 double Max)

AdjustThresh

public boolean AdjustThresh(int elementNum)

AdjustThresh

public void AdjustThresh(boolean allelements)

AdjustThresh
```
public void AdjustThresh()
```

GlobalMin
```
public double GlobalMin()
```

GlobalMax
```
public double GlobalMax()
```

AdjustThreshGlobal
```
public boolean AdjustThreshGlobal()
```

copyLinkedProperties

public void copyLinkedProperties(int anElement)

setColorMapThresh

public void setColorMapThresh(int elem,
                              int low,
                              int high)

adjustColorMapLThresh

public void adjustColorMapLThresh(double howmuch)

adjustColorMapUThresh

public void adjustColorMapUThresh(double howmuch)

GetMinThresh
```
public double GetMinThresh(int elem)
```

GetMaxThresh
```
public double GetMaxThresh(int elem)
```

CThreshToValThresh

public void CThreshToValThresh(int elem,
                               double facmin,
                               double facmax)

addLThresh

public void addLThresh(double howmuch)

addUThresh

public void addUThresh(double howmuch)

initThresh
```
public void initThresh()
```

initGlobalThresh
```
public void initGlobalThresh()
```

ElementsAtTime

public Vector<AnElement> ElementsAtTime(int atime)

ProjsAtTime

public Vector<view5d.ASlice>[] ProjsAtTime(int atime)

ColorProjsAtTime

public view5d.ASlice[] ColorProjsAtTime(int atime)

GetElementsFromTime
```
public void GetElementsFromTime()
```

GetProjsFromTime
```
public void GetProjsFromTime()
```

setTime
```
public void setTime(int num)
```

nextTime
```
public void nextTime(int num)
```

advanceTime
```
public void advanceTime(int howmany)
```

setElement
```
public void setElement(int num)
```

advanceElement

public void advanceElement(int howmany)

GetNumElements
```
public int GetNumElements()
```

GetNumTimes
```
public int GetNumTimes()
```

GetSize
```
public int GetSize(int DimNr)
```

GetROISize

public double GetROISize(int elem,
                         int dim)

GetROISum
```
public double GetROISum(int elem)
```

GetROIVoxels
```
public double GetROIVoxels(int elem)
```

GetROIAvg
```
public double GetROIAvg(int elem)
```

GetROIMax
```
public double GetROIMax(int elem)
```

GetROIMin
```
public double GetROIMin(int elem)
```

GetROIVal
```
public double GetROIVal(int elem)
```

GetDataTypeName

public String GetDataTypeName(int elem)

GetValueScale

public double GetValueScale(int elem)

GetScale

public double GetScale(int elem,
                       int dim)

GetScale
```
public double[] GetScale(int elem)
```

GetOffset

public double GetOffset(int elem,
                        int dim)

GetOffset
```
public double[] GetOffset(int elem)
```

SetValueScale

public void SetValueScale(int elem,
                          double ScaleV,
                          double Off,
                          String NameV,
                          String UnitV)

SetOffsets

public void SetOffsets(int elem,
                       double OfX,
                       double OfY,
                       double OfZ)

GetValueName
```
public String GetValueName(int elem)
```

GetValueUnit
```
public String GetValueUnit(int elem)
```

GetAxisUnits
```
public String[] GetAxisUnits()
```

GetAxisNames
```
public String[] GetAxisNames()
```

GetValueOffset

public double GetValueOffset(int elem)

GetDisplayOffset

public double[] GetDisplayOffset(int elem)

SetValueOffset

public void SetValueOffset(int elem,
                           double value)

GetActiveElement
```
public int GetActiveElement()
```

GetActiveTime
```
public int GetActiveTime()
```

GetColorMode
```
public boolean GetColorMode()
```

GetChannel
```
public int GetChannel(int col)
```

InvalidateColor

public void InvalidateColor(int time)

InvalidateColor
```
public void InvalidateColor()
```

InvalidateSlices
```
public void InvalidateSlices()
```

InvalidateProjs

public void InvalidateProjs(int which,
                            int time)

InvalidateProjs

public void InvalidateProjs(int which)

ClearChannel
```
public void ClearChannel(int col)
```

MarkChannel
```
public void MarkChannel(int col)
```

MarkChannel

public void MarkChannel(int elem,
                        int col)

MarkAsHistoDim
```
public void MarkAsHistoDim(int dim)
```

ToggleSquareROIs
```
public void ToggleSquareROIs()
```

SquareROIs
```
public boolean SquareROIs()
```

ToggleColor
```
public void ToggleColor(boolean set)
```

ToggleColor
```
public void ToggleColor()
```

ComputeColorProj

public void ComputeColorProj(int dim)

CloneElement

public void CloneElement(AnElement oldelem)

CloneLastElements
```
public void CloneLastElements()
```

GenerateNewElement

public int GenerateNewElement(int DataType,
                              int NumBytes,
                              int NumBits,
                              double[] Scales,
                              double[] Offsets,
                              double ScaleV,
                              double OffsetV,
                              String[] Names,
                              String[] Units)

GenerateNewTime

public int GenerateNewTime(int DataType,
                           int NumBytes,
                           int NumBits,
                           double[] Scales,
                           double[] Offsets,
                           double ScaleV,
                           double OffsetV,
                           String[] Names,
                           String[] Units,
                           int NewElements)

AdjustOffsetToROIMean
```
public void AdjustOffsetToROIMean()
```

AddMarkedElement
```
public void AddMarkedElement()
```

SubMarkedElement
```
public void SubMarkedElement()
```

MulMarkedElement
```
public void MulMarkedElement()
```

DivMarkedElement
```
public void DivMarkedElement()
```

DeleteActElement

public void DeleteActElement(Vector<AnElement> ElementList)

DeleteActElement
```
public void DeleteActElement()
```

GetMarkerColor
```
public Color GetMarkerColor(int e)
```

GetCMapColor

public Color GetCMapColor(int e,
                          int pos,
                          int mysize)

Normalize

public double Normalize(double val,
                        int e)

NormedValueAt

public double NormedValueAt(int x,
                            int y,
                            int z,
                            int e)

GetIntValueAt

public int GetIntValueAt(int x,
                         int y,
                         int z,
                         int e)

GetColColor

public Color GetColColor(int e,
                         int x,
                         int y,
                         int z)

NormedProjValueAt

public double NormedProjValueAt(int dir,
                                int pos,
                                int e)

ProjValueAt

public double ProjValueAt(int dir,
                          int pos,
                          int e)

ValueAt

public double ValueAt(int x,
                      int y,
                      int z,
                      int e)

ApplyHistSelection
```
public void ApplyHistSelection()
```

CloneFloat
```
public void CloneFloat()
```

CloneShort
```
public void CloneShort()
```

GenerateMask
```
public void GenerateMask(int dim)
```

ElementAt

public AnElement ElementAt(int num,
                           int time)

ElementAt
```
public AnElement ElementAt(int num)
```

ActElement
```
public AnElement ActElement()
```

GetPolyROISize
```
public int GetPolyROISize(int dir)
```

GetPolyROICoords

public void GetPolyROICoords(int dir,
                             int segment,
                             float[] coords)

MovePolyROI

public void MovePolyROI(int DX,
                        int DY,
                        int dir)

MoveSqrROI

public void MoveSqrROI(int DX,
                       int DY,
                       int dir)

MoveROI

public void MoveROI(int DX,
                    int DY,
                    int dir)

TakePolyROI

public void TakePolyROI(Polygon myNewROI,
                        int dir)

ClearPolyROIs
```
public void ClearPolyROIs(int dir)
```

ClearPolyROIs
```
public void ClearPolyROIs()
```

TakeLineROI

public void TakeLineROI(int ROIX,
                        int ROIY,
                        int ROIXe,
                        int ROIYe,
                        int dir)

ClearLineROIs
```
public void ClearLineROIs()
```

GetSqrROI
```
public Rectangle GetSqrROI(int dim)
```

TakeROI

public void TakeROI(int ROIX,
                    int ROIY,
                    int ROIXe,
                    int ROIYe,
                    int dir)

TakeDataToHistogram

public void TakeDataToHistogram(My3DData data)

SetUp

public void SetUp(int DataType,
                  View5D_ myv3d,
                  int elements,
                  int times,
                  int ImageType)

SaveMarkers
```
public void SaveMarkers()
```

LoadMarkers
```
public void LoadMarkers()
```

Load

public void Load(int DataType,
                 int NumBytes,
                 int NumBits,
                 String URLname)

GetProjectionMode

public boolean GetProjectionMode(int DimNr)

GetMIPMode
```
public boolean GetMIPMode(int DimNr)
```

GetLogMode
```
public boolean GetLogMode()
```

ToggleProj

public void ToggleProj(int DimNr,
                       boolean mipmode)

ToggleOverlayDispl

public void ToggleOverlayDispl(int val)

ToggleMulDispl
```
public void ToggleMulDispl(int val)
```

Class My3DData

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

markerInfilename

markerOutfilename

MyElements

MyProjections

MyColorProjection

MySlice

MyColorSlice

MyMarkers

SizeX

SizeY

SizeZ

Elements

ActiveElement

DimensionOrder

AppendTo

MyTimes

MyTimeProj

Times

ActiveTime

MyTimeColorProj

applet

Constructor Detail

My3DData

My3DData

Method Detail

setElementsLinked

setTimesLinked

setFontSize

NewMarkerList

NewMarkerList

AddLookUpTable

toggleGate

setGate

setModelThresh

setModelThresh

GetActiveColorModelNr

GetColorModelNr

SetColorModelNr

GetBundleAt

ToggleLog

ToggleConnection

ToggleLog

SetGamma

GetGamma

ToggleOvUn

ToggleModel

ToggleModel

InvertCMap

GetScaledMincs

GetScaledMaxcs

GetScaledRange

transferThresh

SetThresh

SetThresh

SetScaledMinMaxcs

AdjustThresh

AdjustThresh

AdjustThresh

GlobalMin

GlobalMax

AdjustThreshGlobal

copyLinkedProperties

setColorMapThresh

adjustColorMapLThresh

adjustColorMapUThresh

GetMinThresh

GetMaxThresh

CThreshToValThresh

addLThresh

addUThresh

initThresh

initGlobalThresh

ElementsAtTime

ProjsAtTime