Volume (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ij3d.Volume

Direct Known Subclasses:

AreaListVolume, ImgLibVolume, VoltexVolume
```
public class Volume
extends Object
```
This class encapsulates an image stack and provides various methods for retrieving data. It is possible to control the loaded color channels of RGB images, and to specify whether or not to average several channels (and merge them in this way into one byte per pixel). Depending on these settings, and on the type of image given at construction time, the returned data type is one of INT_DATA or BYTE_DATA.

Author:

Benjamin Schmid

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected class`	`Volume.AverageByteLoader`
`protected class`	`Volume.ByteImage`
`protected class`	`Volume.ByteLoader`
`protected static interface`	`Volume.InputImage` Abstract interface for the input image.
`protected class`	`Volume.IntImage`
`protected class`	`Volume.IntLoader`
`protected static interface`	`Volume.Loader` Abstract interface for the loader classes.
`protected class`	`Volume.SaturatedIntLoader`

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`average` Flag indicating that the channels should be averaged
`static int`	`BYTE_DATA` Data is read as byte data.
`protected boolean[]`	`channels` Channels in RGB images which should be loaded
`protected int`	`dataType` Indicates in which format the data is loaded.
`protected Volume.InputImage`	`image` Wraping the ImagePlus
`protected ij.ImagePlus`	`imp` The image holding the data
`static int`	`INT_DATA` Data is read as int data.
`protected Volume.Loader`	`loader` The loader, initialized depending on the data type
`Point3d`	`maxCoord` The maximum coordinate of the data
`Point3d`	`minCoord` The minimum coordinate of the data
`double`	`pd` The calibration of the data
`double`	`ph` The calibration of the data
`double`	`pw` The calibration of the data
`protected boolean`	`saturatedVolumeRendering` Flag indicating that channels should be saturated
`int`	`xDim` The dimensions of the data
`int`	`yDim` The dimensions of the data
`int`	`zDim` The dimensions of the data

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`Volume()` Create instance with a null imp.
	`Volume(ij.ImagePlus imp)` Initializes this Volume with the specified image.
	`Volume(ij.ImagePlus imp, boolean[] ch)` Initializes this Volume with the specified image and channels.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clear()`
`void`	`getAlphaLUT(int[] lut)` Copies the current color table into the given array.
`byte`	`getAverage(int x, int y, int z)` Load the average value at the specified position
`void`	`getBlueLUT(int[] lut)` Copies the current color table into the given array.
`int`	`getDataType()` Get the current set data type.
`void`	`getGreenLUT(int[] lut)` Copies the current color table into the given array.
`ij.ImagePlus`	`getImagePlus()`
`void`	`getRedLUT(int[] lut)` Copies the current color table into the given array.
`protected boolean`	`initDataType()` Init the data type.
`protected void`	`initLoader()` Init the loader, based on the currently set data type, which is either INT_DATA or BYTE_DATA.
`boolean`	`isAverage()` Returns true if specified channels are being averaged when reading the image data.
`boolean`	`isDefaultLUT()` Checks if the LUTs of all the used color channels and of the alpha channel have a default LUT.
`boolean`	`isSaturatedVolumeRendering()` Returns whether if saturatedVolumeRendering is set to true.
`int`	`load(int x, int y, int z)` Load the value at the specified position
`int`	`loadWithLUT(int x, int y, int z)` Load the color at the specified position
`void`	`restore(String path)`
`void`	`set(int x, int y, int z, int v)`
`boolean`	`setAlphaLUTFullyOpaque()` Set the alpha channel to fully opaque.
`boolean`	`setAverage(boolean a)` If true, build an average byte from the specified channels (for each pixel).
`boolean`	`setChannels(boolean[] ch)` Specify the channels which should be read from the image.
`void`	`setImage(ij.ImagePlus imp, boolean[] ch)`
`boolean`	`setLUTs(int[] r, int[] g, int[] b, int[] a)` Set the lookup tables for this volume.
`void`	`setNoCheck(int x, int y, int z, int v)`
`boolean`	`setSaturatedVolumeRendering(boolean b)` If true, saturate the channels of RGB images; the RGB values of each pixels are scaled so that at least one of the values is 255, the alpha value is the average of the original RGB values.
`void`	`swap(String path)`

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

- Field Detail
  - INT_DATA
```
public static final int INT_DATA
```
    Data is read as int data. If the input image is RGB, this is the case if isDefaultLUT() returns false or more than a single channel is used. If the input image is 8 bit, again this is the case if isDefaultLUT() returns false.
    
    See Also:
    
    Constant Field Values
  - BYTE_DATA
```
public static final int BYTE_DATA
```
    Data is read as byte data. If the input image is RGB, this is the case if isDefaultLUT() returns true and only a single channel is used. If the input image is 8 bit, again this is the case if isDefaultLUT() returns true.
    
    See Also:
    
    Constant Field Values
  - imp
```
protected ij.ImagePlus imp
```
    The image holding the data
  - image
```
protected Volume.InputImage image
```
    Wraping the ImagePlus
  - loader
```
protected Volume.Loader loader
```
    The loader, initialized depending on the data type
  - dataType
```
protected int dataType
```
    Indicates in which format the data is loaded. This depends on the image type and on the number of selected channels. May be one of INT_DATA or BYTE_DATA
  - average
```
protected boolean average
```
    Flag indicating that the channels should be averaged
  - saturatedVolumeRendering
```
protected boolean saturatedVolumeRendering
```
    Flag indicating that channels should be saturated
  - channels
```
protected boolean[] channels
```
    Channels in RGB images which should be loaded
  - xDim
```
public int xDim
```
    The dimensions of the data
  - yDim
```
public int yDim
```
    The dimensions of the data
  - zDim
```
public int zDim
```
    The dimensions of the data
  - pw
```
public double pw
```
    The calibration of the data
  - ph
```
public double ph
```
    The calibration of the data
  - pd
```
public double pd
```
    The calibration of the data
  - minCoord
```
public final Point3d minCoord
```
    The minimum coordinate of the data
  - maxCoord
```
public final Point3d maxCoord
```
    The maximum coordinate of the data
- Constructor Detail
  - Volume
```
protected Volume()
```
    Create instance with a null imp.
  - Volume
```
public Volume(ij.ImagePlus imp)
```
    Initializes this Volume with the specified image. All channels are used.
    
    Parameters:
    
    imp -
  - Volume
```
public Volume(ij.ImagePlus imp,
              boolean[] ch)
```
    Initializes this Volume with the specified image and channels.
    
    Parameters:
    
    imp -
    
    ch - A boolean[] array of length three, which indicates whether the red, blue and green channel should be read. This has only an effect when reading color images.
- Method Detail
  - setImage
```
public void setImage(ij.ImagePlus imp,
                     boolean[] ch)
```
  - getImagePlus
```
public ij.ImagePlus getImagePlus()
```
  - clear
```
public void clear()
```
  - swap
```
public void swap(String path)
```
  - restore
```
public void restore(String path)
```
  - isDefaultLUT
```
public boolean isDefaultLUT()
```
    Checks if the LUTs of all the used color channels and of the alpha channel have a default LUT.
  - getDataType
```
public int getDataType()
```
    Get the current set data type. This is one of BYTE_DATA or INT_DATA. The data type specifies in which format the data is read.
  - setAverage
```
public boolean setAverage(boolean a)
```
    If true, build an average byte from the specified channels (for each pixel).
    
    Returns:
    
    true if the value for 'average' has changed.
  - isAverage
```
public boolean isAverage()
```
    Returns true if specified channels are being averaged when reading the image data.
    
    Returns:
  - setSaturatedVolumeRendering
```
public boolean setSaturatedVolumeRendering(boolean b)
```
    If true, saturate the channels of RGB images; the RGB values of each pixels are scaled so that at least one of the values is 255, the alpha value is the average of the original RGB values.
    
    Returns:
    
    true if the value for 'saturatedVolumeRendering' has changed
  - isSaturatedVolumeRendering
```
public boolean isSaturatedVolumeRendering()
```
    Returns whether if saturatedVolumeRendering is set to true.
  - getRedLUT
```
public void getRedLUT(int[] lut)
```
    Copies the current color table into the given array.
  - getGreenLUT
```
public void getGreenLUT(int[] lut)
```
    Copies the current color table into the given array.
  - getBlueLUT
```
public void getBlueLUT(int[] lut)
```
    Copies the current color table into the given array.
  - getAlphaLUT
```
public void getAlphaLUT(int[] lut)
```
    Copies the current color table into the given array.
  - setChannels
```
public boolean setChannels(boolean[] ch)
```
    Specify the channels which should be read from the image. This only affects RGB images.
    
    Returns:
    
    true if the channels settings has changed.
  - setLUTs
```
public boolean setLUTs(int[] r,
                       int[] g,
                       int[] b,
                       int[] a)
```
    Set the lookup tables for this volume. Returns true if the data type of the textures have changed.
  - setAlphaLUTFullyOpaque
```
public boolean setAlphaLUTFullyOpaque()
```
    Set the alpha channel to fully opaque. Returns true if the data type of the textures have changed.
  - initLoader
```
protected void initLoader()
```
    Init the loader, based on the currently set data type, which is either INT_DATA or BYTE_DATA.
  - initDataType
```
protected boolean initDataType()
```
    Init the data type. For 8 bit images, BYTE_DATA is used if isDefaultLUT() returns true. For RGB images, an additional condition is that only a single channel is used. For other cases, the data type is INT_DATA.
  - setNoCheck
```
public void setNoCheck(int x,
                       int y,
                       int z,
                       int v)
```
  - set
```
public void set(int x,
                int y,
                int z,
                int v)
```
  - load
```
public int load(int x,
                int y,
                int z)
```
    Load the value at the specified position
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
    
    value. Casted to int if it was a byte value before.
  - loadWithLUT
```
public int loadWithLUT(int x,
                       int y,
                       int z)
```
    Load the color at the specified position
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
    
    int-packed color
  - getAverage
```
public byte getAverage(int x,
                       int y,
                       int z)
```
    Load the average value at the specified position
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
    
    value.

Class Volume

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

INT_DATA

BYTE_DATA

imp

image

loader

dataType

average

saturatedVolumeRendering

channels

xDim

yDim

zDim

pw

ph

pd

minCoord

maxCoord

Constructor Detail

Volume

Volume

Volume

Method Detail

setImage

getImagePlus

clear

swap

restore

isDefaultLUT

getDataType

setAverage

isAverage

setSaturatedVolumeRendering

isSaturatedVolumeRendering

getRedLUT

getGreenLUT

getBlueLUT

getAlphaLUT

setChannels

setLUTs

setAlphaLUTFullyOpaque

initLoader

initDataType

setNoCheck

set

load

loadWithLUT

getAverage