Class Normalize_

java.lang.Object
  |
  +--Normalize_

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter

public class Normalize_

extends java.lang.Object

implements ij.plugin.filter.PlugInFilter

This plugin simplifies the task of background subtraction and image normalization given a brightfield image and/or a background image. This plugin is currently limited to 16-bit images, but could easily be extended to 8-bit, 32-bit, or even color images.

Possible normalization methods:

If both BRIGHT and DARK images are specified

IMAGE = scale * (IMAGE - DARK) / (BRIGHT - DARK)

If only BRIGHT image is specified

IMAGE = scale * IMAGE / BRIGHT

If only DARK image is specified

IMAGE = IMAGE - DARK

Author:

Jeffrey Kuhn, The University of Texas at Austin, jkuhn@ccwf.cc.utexas.edu

Field Summary

private static double	dScale Number to scale resulting image by after division by BRIGHT
private int	iBrightID ImageJ ID of bright image
private int	iDarkID ImageJ ID of dark image
private ij.ImagePlus	impImage The image window to work on
private static java.lang.String	strBrightName Name of bright image
private static java.lang.String	strDarkName Name of dark image
private static java.lang.String	strNONE If "none" is selected, then that image is not used in the calculation

Fields inherited from interface ij.plugin.filter.PlugInFilter

DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, ROI_REQUIRED, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Normalize_()

Method Summary

boolean	getArguments() Request the user to specify the bright and dark images
(package private) void	processGray16Unsigned(double dScale, ij.ImagePlus impImage, ij.ImagePlus impBright, ij.ImagePlus impDark, int iLen) Normalize a 16-bit unsigned image
void	run(ij.process.ImageProcessor ip) Normalize the current image.
int	setup(java.lang.String arg, ij.ImagePlus imp) Report what kind of images this plugin can handle to ImageJ

Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait

Field Detail

strNONE

private static final java.lang.String strNONE

If "none" is selected, then that image is not used in the calculation

strBrightName

private static java.lang.String strBrightName

Name of bright image

strDarkName

private static java.lang.String strDarkName

Name of dark image

dScale

private static double dScale

Number to scale resulting image by after division by BRIGHT

iBrightID

private int iBrightID

ImageJ ID of bright image

iDarkID

private int iDarkID

ImageJ ID of dark image

impImage

private ij.ImagePlus impImage

The image window to work on

Constructor Detail

Normalize_

public Normalize_()

Method Detail

setup

public int setup(java.lang.String arg,
                 ij.ImagePlus imp)

Report what kind of images this plugin can handle to ImageJ

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

getArguments

public boolean getArguments()

Request the user to specify the bright and dark images

run

public void run(ij.process.ImageProcessor ip)

Normalize the current image.

Specified by:

run in interface ij.plugin.filter.PlugInFilter

processGray16Unsigned

void processGray16Unsigned(double dScale,
                           ij.ImagePlus impImage,
                           ij.ImagePlus impBright,
                           ij.ImagePlus impDark,
                           int iLen)

Normalize a 16-bit unsigned image