fiji.denoise

Class ROF_Denoise

java.lang.Object

fiji.denoise.ROF_Denoise

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter

public class ROF_Denoise
extends Object
implements ij.plugin.filter.PlugInFilter

This denoising method is based on total-variation, originally proposed by Rudin, Osher and Fatemi. In this particular case fixed point iteration is utilized.

For the included image, a fairly good result is obtained by using a theta value around 12-16. A possible addition would be to analyze the residual with an entropy function and add back areas that have a lower entropy, i.e. there are some correlation between the surrounding pixels.

Based on the Matlab code by Philippe Magiera and Carl Londahl.

Field Summary

Fields

Modifier and Type	Field and Description
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
ROF_Denoise()

Method Summary

Modifier and Type	Method and Description
static void	denoise(ij.process.FloatProcessor ip, float theta)
static void	denoise(ij.process.FloatProcessor ip, float theta, float g, float dt, int iterations)
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

Constructor Detail

ROF_Denoise

public ROF_Denoise()

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 (typically, plugins use the ImagePlus set above instead).

denoise

public static void denoise(ij.process.FloatProcessor ip,
                           float theta)

denoise

public static void denoise(ij.process.FloatProcessor ip,
                           float theta,
                           float g,
                           float dt,
                           int iterations)