fiji.geom

Class Shape_Index_Map

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

Constructor Summary

Constructors

Constructor and Description
Shape_Index_Map()

Method Summary

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: 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.
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)