Shape_Index_Map (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.geom.Shape_Index_Map

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter
```
public class Shape_Index_Map
extends Object
implements ij.plugin.filter.PlugInFilter
```
Calculate the shape index as defined in J Koenderink and A van Doorn, “Surface shape and curvature scales,” Image Vision Comput, vol. 10, no. 8, pp. 557–565, 1992

Field Summary

Fields
Modifier and Type Field and Description

protected static ij.plugin.filter.GaussianBlur gaussianBlur

protected ij.ImagePlus image
- Fields inherited from interface ij.plugin.filter.PlugInFilter
  CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, NO_UNDO_RESET, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Fields
Modifier and Type	Field and Description
`protected static ij.plugin.filter.GaussianBlur`	`gaussianBlur`
`protected ij.ImagePlus`	`image`

Constructor Summary

Constructors
Constructor and Description

Shape_Index_Map()

Constructors
Constructor and Description
`Shape_Index_Map()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static ij.process.ImageProcessor`	`deriveX(ij.process.ImageProcessor ip)`
`static ij.process.ImageProcessor`	`deriveY(ij.process.ImageProcessor ip)`
`static ij.process.ImageProcessor`	`getShapeIndex(ij.process.ImageProcessor ip)` The formula is:
`static ij.ImagePlus`	`getShapeIndexMap(ij.ImagePlus image, double gaussianBlurRadius)`
`void`	`run(ij.process.ImageProcessor ip)` This method is run when the current image was accepted.
`int`	`setup(String arg, ij.ImagePlus image)` This method gets called by ImageJ / Fiji to determine whether the current image is of an appropriate type.

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

- Field Detail
  - image
```
protected ij.ImagePlus image
```
  - gaussianBlur
```
protected static ij.plugin.filter.GaussianBlur gaussianBlur
```
- Constructor Detail
  - Shape_Index_Map
```
public Shape_Index_Map()
```
- Method Detail
  - setup
```
public int setup(String arg,
                 ij.ImagePlus image)
```
    This method gets called by ImageJ / Fiji to determine whether the current image is of an appropriate type.
    
    Specified by:
    
    setup in interface ij.plugin.filter.PlugInFilter
    
    Parameters:
    
    arg - can be specified in plugins.config
    
    image - is the currently opened image
  - run
```
public void run(ij.process.ImageProcessor ip)
```
    This method is run when the current image was accepted.
    
    Specified by:
    
    run in interface ij.plugin.filter.PlugInFilter
    
    Parameters:
    
    ip - is the current slice (we use the ImagePlus set above instead).
  - getShapeIndexMap
```
public static ij.ImagePlus getShapeIndexMap(ij.ImagePlus image,
                                            double gaussianBlurRadius)
```
  - getShapeIndex
```
public static ij.process.ImageProcessor getShapeIndex(ij.process.ImageProcessor ip)
```
    The formula is:
```
                                 dnx_x + dny_y
 s = 2 / PI * arctan ---------------------------------------
                     sqrt((dnx_x - dny_y)^2 + 4 dny_x dnx_y)
 
```
    where _x and _y are the x and y components of the partial derivatives of the normal vector of the surface defined by the intensities of the image.
    n_x and n_y are the negative partial derivatives of the intensity, approximated by simple differences.
    Parameters:
    
    ip - the source image processor.
    
    Returns:
    
    the shape index in a new image processor.
  - deriveX
```
public static ij.process.ImageProcessor deriveX(ij.process.ImageProcessor ip)
```
  - deriveY
```
public static ij.process.ImageProcessor deriveY(ij.process.ImageProcessor ip)
```

Class Shape_Index_Map

Field Summary

Fields inherited from interface ij.plugin.filter.PlugInFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

image

gaussianBlur

Constructor Detail

Shape_Index_Map

Method Detail

setup

run

getShapeIndexMap

getShapeIndex

deriveX

deriveY