MeshImageStack (Deforming Mesh 0.9.4-SNAPSHOT API)

java.lang.Object
- deformablemesh.MeshImageStack

Direct Known Subclasses:

MeshImageSubStack
```
public class MeshImageStack
extends Object
```
This will setup normalized coordinates for an image. User: msmith Date: 7/3/13 Time: 1:55 PM To change this template use File | Settings | File Templates.

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`CURRENT`
`double[][][]`	`data`
`double`	`MAX_VALUE`
`double`	`MIN_VALUE`
`double[]`	`offsets`
`double[]`	`pixel_dimensions`
`double`	`SCALE`
`double[]`	`scale_values`

Constructor Summary

Constructors
Constructor and Description
`MeshImageStack()`
`MeshImageStack(ij.ImagePlus original)`
`MeshImageStack(ij.ImagePlus original, int frame, int channel)`
`MeshImageStack(Path path)` Creates an ImagePlus from the provided path.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`copyValues()` Copies the image data from the image stack to the double[][] backing the image data that is used for obtaining values.
`void`	`copyValues(ij.ImagePlus other)` For creating a backing double array of another ImagePlus that uses the same geometry as the original image plus.
`FurrowTransformer`	`createFurrowTransform(double[] pos, double[] normal)`
`Image`	`createSlice(double[] pos, double[] normal)`
`BufferedImage`	`createSlice(FurrowTransformer transformer)`
`MeshImageSubStack`	`createSubStack(Box3D box)`
`double[]`	`getCenterOfMass()`
`ij.ImagePlus`	`getCurrentFrame()` Returns a single channel image plus of the current frame.
`static MeshImageStack`	`getEmptyStack()`
`int`	`getHeightPx()`
`double[]`	`getImageCoordinates(double[] r)` Returns x, y, z in (px, px, slice) indexes of the backing data array.
`double[]`	`getIntensityValues()`
`double`	`getInterpolatedValue(double[] xyz)`
`double`	`getInterpolatedValue(double x, double y, double z)`
`Box3D`	`getLimits()`
`double`	`getMinPx()` Smallest pixel, in the x,y, or z direction from the input image.
`int`	`getNFrames()`
`double[]`	`getNormalizedCoordinate(double[] r)` Finds the position in normalized coordinates using.
`double`	`getNormalizedImageDepth()` Normalized length of the image along the z-axis.
`double`	`getNormalizedImageHeight()` Normalized length of the image along the y-axis.
`double`	`getNormalizedImageWidth()` Normalized length of the image along the x-axis.
`int`	`getNSlices()`
`ij.ImagePlus`	`getOriginalPlus()`
`String`	`getUnits()`
`double`	`getValue(int x, int y, int z)` Gets the value at the image coordintes x,y,z doesn't perform any sort of check.
`int`	`getWidthPx()`
`void`	`nextFrame()`
`void`	`previousFrame()`
`ij.ImagePlus`	`samplePlus(Box3D box)`
`double[]`	`scaleToNormalizedLength(double[] l)` given a length in px, px, slices this scales the length to normalized coordinate values.
`void`	`setChannel(int c)`
`void`	`setFrame(int i)`

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

- Field Detail
  - data
```
public double[][][] data
```
  - SCALE
```
public double SCALE
```
  - scale_values
```
public double[] scale_values
```
  - offsets
```
public double[] offsets
```
  - pixel_dimensions
```
public double[] pixel_dimensions
```
  - CURRENT
```
public int CURRENT
```
  - MIN_VALUE
```
public double MIN_VALUE
```
  - MAX_VALUE
```
public double MAX_VALUE
```
- Constructor Detail
  - MeshImageStack
```
public MeshImageStack()
```
  - MeshImageStack
```
public MeshImageStack(ij.ImagePlus original,
                      int frame,
                      int channel)
```
  - MeshImageStack
```
public MeshImageStack(ij.ImagePlus original)
```
  - MeshImageStack
```
public MeshImageStack(Path path)
```
    Creates an ImagePlus from the provided path.
    
    Parameters:
    
    path -
- Method Detail
  - getNFrames
```
public int getNFrames()
```
  - getNSlices
```
public int getNSlices()
```
  - getWidthPx
```
public int getWidthPx()
```
  - getHeightPx
```
public int getHeightPx()
```
  - getUnits
```
public String getUnits()
```
  - scaleToNormalizedLength
```
public double[] scaleToNormalizedLength(double[] l)
```
    given a length in px, px, slices this scales the length to normalized coordinate values.
    
    Parameters:
    
    l - px, px, slices (x,y,z lengths in image slices)
    
    Returns:
    
    scaled value.
  - getNormalizedCoordinate
```
public double[] getNormalizedCoordinate(double[] r)
```
    Finds the position in normalized coordinates using.
    
    Parameters:
    
    r - location in px,px,slice
    
    Returns:
    
    normalized coordinates where center of image is at 0 and the longest axis in real units is -0.5 0.5.
  - nextFrame
```
public void nextFrame()
```
  - previousFrame
```
public void previousFrame()
```
  - setFrame
```
public void setFrame(int i)
```
  - setChannel
```
public void setChannel(int c)
```
  - copyValues
```
public void copyValues()
```
    Copies the image data from the image stack to the double[][] backing the image data that is used for obtaining values.
  - copyValues
```
public void copyValues(ij.ImagePlus other)
```
    For creating a backing double array of another ImagePlus that uses the same geometry as the original image plus.
    
    Parameters:
    
    other -
  - getInterpolatedValue
```
public double getInterpolatedValue(double x,
                                   double y,
                                   double z)
```
  - getInterpolatedValue
```
public double getInterpolatedValue(double[] xyz)
```
  - getValue
```
public double getValue(int x,
                       int y,
                       int z)
```
    Gets the value at the image coordintes x,y,z doesn't perform any sort of check.
    
    Parameters:
    
    x -
    
    y -
    
    z -
    
    Returns:
  - createSlice
```
public BufferedImage createSlice(FurrowTransformer transformer)
```
  - createSlice
```
public Image createSlice(double[] pos,
                         double[] normal)
```
  - getNormalizedImageDepth
```
public double getNormalizedImageDepth()
```
    Normalized length of the image along the z-axis.
    
    Returns:
  - getNormalizedImageWidth
```
public double getNormalizedImageWidth()
```
    Normalized length of the image along the x-axis.
    
    Returns:
  - getNormalizedImageHeight
```
public double getNormalizedImageHeight()
```
    Normalized length of the image along the y-axis.
    
    Returns:
  - createFurrowTransform
```
public FurrowTransformer createFurrowTransform(double[] pos,
                                               double[] normal)
```
  - getCenterOfMass
```
public double[] getCenterOfMass()
```
  - getImageCoordinates
```
public double[] getImageCoordinates(double[] r)
```
    Returns x, y, z in (px, px, slice) indexes of the backing data array. The z index is in slices, but 0 indexed compared to the 1 indexed method in the ImagePlus.
    
    Parameters:
    
    r - x, y, z in normalized coordinates.
    
    Returns:
    
    closest double representation to the provided point in image coordinate space.
  - getMinPx
```
public double getMinPx()
```
    Smallest pixel, in the x,y, or z direction from the input image.
    
    Returns:
  - getLimits
```
public Box3D getLimits()
```
  - getEmptyStack
```
public static MeshImageStack getEmptyStack()
```
  - createSubStack
```
public MeshImageSubStack createSubStack(Box3D box)
```
  - samplePlus
```
public ij.ImagePlus samplePlus(Box3D box)
```
  - getCurrentFrame
```
public ij.ImagePlus getCurrentFrame()
```
    Returns a single channel image plus of the current frame.
    
    Returns:
    
    ImagePlus created by the original image contain one channel, all of the slices and a single time frame. Duplicate processors.
  - getIntensityValues
```
public double[] getIntensityValues()
```
  - getOriginalPlus
```
public ij.ImagePlus getOriginalPlus()
```

Class MeshImageStack

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

data

SCALE

scale_values

offsets

pixel_dimensions

CURRENT

MIN_VALUE

MAX_VALUE

Constructor Detail

MeshImageStack

MeshImageStack

MeshImageStack

MeshImageStack

Method Detail

getNFrames

getNSlices

getWidthPx

getHeightPx

getUnits

scaleToNormalizedLength

getNormalizedCoordinate

nextFrame

previousFrame

setFrame

setChannel

copyValues

copyValues

getInterpolatedValue

getInterpolatedValue

getValue

createSlice

createSlice

getNormalizedImageDepth

getNormalizedImageWidth

getNormalizedImageHeight

createFurrowTransform

getCenterOfMass

getImageCoordinates

getMinPx

getLimits

getEmptyStack

createSubStack

samplePlus

getCurrentFrame

getIntensityValues

getOriginalPlus