gov.nih.mipav.model.algorithms.AlgorithmAHElocal

All Implemented Interfaces:: ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmAHElocal extends AlgorithmBase

algorithm to apply an adaptive histogram to an image, placing it in a new ModelImage, or returning the changed picture to the same image.

This is an algorithm to apply within a neighborhood, that is it selects a region of adjacent pixels, the number of adjacent pixels is of a user-selected size, and forms the histogram from that region. The region selection routine is adopted from AlgorithmMedian. The value of the cell (the brightness of the pixel at a particular location) is then mapped to the region. Over the entire image, this means that all pixels will still be brighter or darker than other pixels, but the brightness has been shifted making minor variations more apparent. The cumulative distribution is changed so that it becomes step-wise linear, making the darker pixels use the lowest possible values available to the image, the brightest use the highest possible values.

This algorithm may be used to perform a contrast-limited or 'clamped' histogram equalization. It is set by supplying a percentage of the maximum number of pixels in any particular brightness level. As the regional histograms are tabulated, the brightness with the maximum number of pixels attributed to it is remembered. The algorithm will then evenly redistribute the total number of pixels from any brightness which has a greater number than the max times this fraction to all other (less populous) brightnesses. (If the supplied percentage is 80, for instance, the maximum number of pixels to any brightness level, will be four-fifths the largest number number of pixels of any shade found.

The principle methodology of this algorithm, is to take each window, form a histogram; clamp so there is no brightness which can have more than a certain number of pixels; scale the brightnesses so that the values are spread evenly from the maximum to the minimum brightness. (ie., scale * histogram(i)).

Primary source: Stark, J Alex. Adaptive Image Contrast Enhancement Using Generalizations of Histogram Equalization.
Background Information:
- Russ, John. Image Processing HandbookM.
- Tidestav, Claes. Short Introduction to Adaptive Equalization.
- Rabie, Tamer; Rangayan, Rangaraj; Paranjape, Raman. Adaptive-Neighborhood Image Deblurring.

According to Freedman and Diaconis as summarized in "Recent Developments in NonParametric Density Estimation" by Alan Julian Izenman, Journal of the American Statistical Association, March, 1991, Vol. 86, No. 413, pp. 205 - 224: The ideal histogram bin width W is given by W = 2(IQR)pow(N,-1/3) where IQR is the interquartile range(the 75 percentile minus the 25th percentile) and N is the number of available samples.

The three coordinates of CIELAB represent the lightness of the color(L* = 0 yields black and L* = 100 indicates diffuse white; specular white may be higher), its position between red/magenta and green(a*, negative values indicate green while positive values indicate magenta) and its position between yellow and blue(b*, negative values indicate blue and positive values indicate yellow). The asterisk(*) after L, a, and b are part of the full name, since they represent L*, a*, and b*, to distinguish them from Hunter's L, a, and b. The L* coordinate ranges from 0 to 100. The possible range of a* and b* coordinates depends on the color space that one is converting from. R = 0, G = 0, B = 0 => L* = 0, a* = 0, b* = 0 R = 255, G = 0, B = 0 => L* = 53.2, a* = 80.1, b* = 67.22 R = 0, G = 255, B = 0 => L* = 87.7, a* = -86.2, b* = 83.2 R = 0, G = 0, B = 255 => L* = 32.3, a* = 79.2, b* = -107.9 R = 255, G = 255, B = 0 => L* = 97.1, a* = -21.6, b* = 94.5 R = 255, G = 0, B = 255 => L* = 60.3, a* = 98.3, b* = -60.8 R = 0, G = 255, B = 255 => L* = 91.1, a* = -48.1, b* = -14.1 R = 255, G = 255, B = 255 => L* = 100.0, a* = 0.00525, b* = -0.0104 so the range of a* equals about the range of b* and the range of a* equals about twice the range of L*. The simplest distance metric delta E is CIE76 = sqrt((L2* - L1*)**2 + (a2* - a1*)**2 + (b2* - b1*)**2) XW, YW, and ZW (also called XN, YN, ZN or X0, Y0, Z0) are reference white tristimulus values - typically the white of a perfectly reflecting diffuser under CIE standard D65 illumination(defined by x = 0.3127 and y = 0.3291 in the CIE chromatcity diagram). The 2 degrees, D65 reference tristimulus values are: XN = 95.047, YN = 100.000, and ZN = 1 http://www.easyrgb.com has XYZ -> RGB, RGB -> XYZ, XYZ -> CIEL*ab, CIEL*ab -> XYZ, and XYZ(Tristimulus) Reference values of a perfect reflecting diffuser. Smoothing vs. sharpening of color images - Together or separated by Cristina Perez, Samuel Morillas, and Alberto Conejero, June, 2017. "Histogram equalization is a non-linear process and involves intensity values of the image and not the color components For these reasons, channel splitting and equalizing each channel separately is not the proper way for equalization of contrast. So, the first step is to convert the color space of the image from RGB into other color space which separates intensity values from color components such as HSV, YCbCr, or Lab, and apply equalization over the H, Y, or L channel respectively."

Version:

1.00; 24 Sep 2001

Author:

David Parsons (parsonsd), Matthew J. McAuliffe, Ph.D.

See Also:

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread
Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler
Field Summary

Fields

Modifier and Type

Field

Description

protected float

absMinThreshold

pixel does not get remapped when pixel is below threshold.

static final int

AXIAL_KERNEL

along the major axis (+).

protected boolean

bChannel

the blue channel.

protected int

brightnessLevel

a pixel (no matter whether represented as a float or int), has a brightnessLevel, which is in the histogram as a value between 0 and totalBins.

protected float

bufMax

maximum of the image buffer.

protected float

bufMin

minimum of the image buffer.

protected boolean

clampingIsNecessary

perform a "contrast limited" AHE.

protected float

clipLevel

DOCUMENT ME!

(package private) int

colorUsed

static final int

CROSS_KERNEL

cross (+).

protected int

currentSlice

DOCUMENT ME!

protected boolean

entireImage

true means apply to entire image, false only region.

protected boolean

gChannel

the green channel.

protected int

halfK

DOCUMENT ME!

protected int[]

histogram

(cumulative) histogram.

protected float[]

histomap

the scaled histogram.

private double

imageMax

protected float

imageOffset

image minimum; used as offset for images to build histogram.

protected boolean

isColorImage

indicates the image is a color image.

protected float[]

kernel

DOCUMENT ME!

protected int

kernelCenter

DOCUMENT ME!

protected byte[]

kernelMask

mask to determine the region of pixels used in a median filter.

protected int

kernelShape

user-selectable shape of the region for neighbor-selection.

protected int

kernelSize

dimension of the kernel (ie., 5 = 5x5, 7 = 7x7, 9 = 9x9, etc.).

(package private) float[]

Lmax

(package private) float[]

Lmin

protected BitSet

mask

DOCUMENT ME!

protected int

maskCenter

DOCUMENT ME!

protected float

maxScale

range of max - min over local kernel, slice, or entire image.

protected int

maxScaleRule

flag how/when to set the maximum scale. default per slice

protected float

minThreshold

DOCUMENT ME!

protected float

minValue

min over local kernel, slice, or entire image.

protected int

numberOfSlices

DOCUMENT ME!

(package private) int

numColors

protected boolean

rChannel

if T, filter the red channel.

private double

scaleMaxCIELab

static final int

scaleOnImage

DOCUMENT ME!

static final int

scaleOnLocal

DOCUMENT ME!

static final int

scaleOnSlice

DOCUMENT ME!

protected float[]

sortBuffer

here for memory/speed concerns.

static final int

SQUARE_KERNEL

square kernel.

protected boolean

thresholdingIsNecessary

threshold the image while processing.

protected int

totalBins

number of histogram and histomap values actually used.

protected float

unitSize

one unit is one totalBin-th of the distance between max invalid input: '&' min brightness.

private boolean

useCIELab

protected int

valuesPerPixel

number of elements in a pixel.

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY
Constructor Summary

Constructors

Constructor

Description

AlgorithmAHElocal(ModelImage srcImg, int kSize, int kShape, boolean wholeImage, boolean useCIELab, float[] Lmin, float[] Lmax)

Constructor for images in which changes are returned to the source image.

AlgorithmAHElocal(ModelImage destImg, ModelImage srcImg, int kSize, int kShape, boolean wholeImage, boolean useCIELab, float[] Lmin, float[] Lmax)

Constructor for images in which changes are placed in a predetermined destination image.
Method Summary

Modifier and Type

Method

Description

protected int

buildHistogram()

make histogram uses the class-global vars kernel and histogram.

protected void

calcInPlace2D()

Histogram equalization on the source image.

protected void

calcInPlace3D()

Histogram Equalization on the source image and replaces the source image with the processed image.

protected void

calcStoreInDest2D()

This function produces a new image that has had itself histogram equalized. places filtered image in the destination image.

protected void

calcStoreInDest3D()

This function produces a new volume image that has been histogram equalized.

protected final void

clip(int[] histogram, int clipLimit)

after generating a histogram, clip will reduce the number of pixels attributed to that brightness level.

private void

convertCIELabtoRGB(float[] L, float[] a, float[] b, float[] buffer)

private void

convertRGBtoCIELab(float[] buffer, float[] L, float[] a, float[] b)

protected final void

copyBuffers(float[] dest, float[] src)

Copies all values from the srcbuffer to the destination buffer. the format is intended to envision the Organization of dest[i] := src[i] float dest destination array float src source array

void

finalize()

Prepares this class for destruction.

protected final void

findBufferMinMax(float[] buf, int bufStart, int bufEnd)

Finds the local maximum and minimum values in the given range in order, as given by the starting and stoping values.

protected final void

findImageOffset(int type)

gets the bottom end of the image. for any image but color images, the bottom end is defined as the buffer minimum for all images except color images; there the offset is defined to be zero

protected final int

findTotalBins(int type, int ideal)

finds the total number of bins based on the type of image.

protected final float

getMax(int color)

gets the image max based on 1st) whether or not the image is color. 2) the color.

protected final float

getMin(int color)

gets the image max based on 1st) whether or not the image is color. 2) the color.

protected final void

getNeighborList(int i, float[] data)

Compiles a list of the values neighboring the desired pixel, that are defined in the kernel.

protected final boolean

getThresholdNeighborList(int i, float[] data)

Compiles a list of the values neighboring the desired pixel, that are defined in the kernel.

protected void

makeKernel()

Makes the kernel.

protected void

makeKernelMask()

Forms kernel.

protected final void

monoSliceEqualizer(float[] srcBuffer, float[] destBuffer)

Allows a single monochrome image slice to be filtered.

protected final void

printhisto(int[] histo)

a debug tool.

protected final float

procPixel(int pix, float[] srcBuffer)

process pixel at pixel pix using data from the srcBuffer. builds a list of monochromatic image values of the neighboring pixels image values (using a map generated by the kernelMask), builds the histogram of those values, clamps when necessary, then scales the cumulative histogram, getting the brightness back out.

void

runAlgorithm()

starts the algorithm.

void

setClipLevel(int sectorPercentage)

The Clip Level is a percentage of the maximum number of pixels in any particular brightness level.

void

setContrastLimited(boolean beClamped)

Redistribute from brightnesses with at a least a specified percentage of the brightness with the maximum number of pixels.

private void

setCopyColorText(String colorText)

If the progress bar is visible, sets the text to:
Copying all color values ...

void

setHistogramScaleRule(int scaleRule)

permit the user to select the scale on which the algorithm forms the brightness pattern of the histogram.

protected void

setKernelMask()

Fill in the mask for which pixels are used in filtering.

void

setMinimumThreshold(float minThresh)

sets minimum threshold values.

void

setRGBChannelFilter(boolean r, boolean g, boolean b)

RGB images are histogram equalized by 'channel.'

void

setThresholdImage(boolean useThreshold)

If useThreshold true only copy when both the source pixel and its local neighborhoold are are less than minThreshold.

protected final float

thresholdProcPixel(int pix, float[] srcBuffer)

process pixel at pixel pix using data from the srcBuffer. builds a list of monochromatic image values of the neighboring pixels image values (using a map generated by the kernelMask), builds the histogram of those values, clamps when necessary, then scales the cumulative histogram, getting the brightness back out.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

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

Field Details
- SQUARE_KERNEL
  
  public static final int SQUARE_KERNEL
  
  square kernel.
  See Also:
  
  Constant Field Values
- CROSS_KERNEL
  
  public static final int CROSS_KERNEL
  
  cross (+).
  See Also:
  
  Constant Field Values
- AXIAL_KERNEL
  
  public static final int AXIAL_KERNEL
  
  along the major axis (+).
  See Also:
  
  Constant Field Values
- scaleOnLocal
  
  public static final int scaleOnLocal
  
  DOCUMENT ME!
  See Also:
  
  Constant Field Values
- scaleOnSlice
  
  public static final int scaleOnSlice
  
  DOCUMENT ME!
  See Also:
  
  Constant Field Values
- scaleOnImage
  
  public static final int scaleOnImage
  
  DOCUMENT ME!
  See Also:
  
  Constant Field Values
- absMinThreshold
  
  protected float absMinThreshold
  
  pixel does not get remapped when pixel is below threshold.
- bChannel
  
  protected boolean bChannel
  
  the blue channel.
- brightnessLevel
  
  protected int brightnessLevel
  
  a pixel (no matter whether represented as a float or int), has a brightnessLevel, which is in the histogram as a value between 0 and totalBins.
- bufMax
  
  protected float bufMax
  
  maximum of the image buffer.
- bufMin
  
  protected float bufMin
  
  minimum of the image buffer.
- clampingIsNecessary
  
  protected boolean clampingIsNecessary
  
  perform a "contrast limited" AHE.
- clipLevel
  
  protected float clipLevel
  
  DOCUMENT ME!
- currentSlice
  
  protected int currentSlice
  
  DOCUMENT ME!
- entireImage
  
  protected boolean entireImage
  
  true means apply to entire image, false only region.
- gChannel
  
  protected boolean gChannel
  
  the green channel.
- halfK
  
  protected int halfK
  
  DOCUMENT ME!
- histogram
  
  protected int[] histogram
  
  (cumulative) histogram.
- histomap
  
  protected float[] histomap
  
  the scaled histogram.
- imageOffset
  
  protected float imageOffset
  
  image minimum; used as offset for images to build histogram.
- isColorImage
  
  protected boolean isColorImage
  
  indicates the image is a color image.
- kernel
  
  protected float[] kernel
  
  DOCUMENT ME!
- kernelCenter
  
  protected int kernelCenter
  
  DOCUMENT ME!
- kernelMask
  
  protected byte[] kernelMask
  
  mask to determine the region of pixels used in a median filter.
- kernelShape
  
  protected int kernelShape
  
  user-selectable shape of the region for neighbor-selection.
- kernelSize
  
  protected int kernelSize
  
  dimension of the kernel (ie., 5 = 5x5, 7 = 7x7, 9 = 9x9, etc.).
- mask
  
  protected BitSet mask
  
  DOCUMENT ME!
- maskCenter
  
  protected int maskCenter
  
  DOCUMENT ME!
- maxScale
  
  protected float maxScale
  
  range of max - min over local kernel, slice, or entire image.
- maxScaleRule
  
  protected int maxScaleRule
  
  flag how/when to set the maximum scale. default per slice
- minThreshold
  
  protected float minThreshold
  
  DOCUMENT ME!
- minValue
  
  protected float minValue
  
  min over local kernel, slice, or entire image.
- numberOfSlices
  
  protected int numberOfSlices
  
  DOCUMENT ME!
- rChannel
  
  protected boolean rChannel
  
  if T, filter the red channel.
- useCIELab
  
  private boolean useCIELab
- sortBuffer
  
  protected float[] sortBuffer
  
  here for memory/speed concerns.
- thresholdingIsNecessary
  
  protected boolean thresholdingIsNecessary
  
  threshold the image while processing.
- totalBins
  
  protected int totalBins
  
  number of histogram and histomap values actually used.
- unitSize
  
  protected float unitSize
  
  one unit is one totalBin-th of the distance between max invalid input: '&' min brightness.
- valuesPerPixel
  
  protected int valuesPerPixel
  
  number of elements in a pixel. Monochrome = 1, Color = 4. (a, R, G, B)
- numColors
  
  int numColors
- colorUsed
  
  int colorUsed
- imageMax
  
  private double imageMax
- scaleMaxCIELab
  
  private double scaleMaxCIELab
- Lmin
  
  float[] Lmin
- Lmax
  
  float[] Lmax
Constructor Details
- AlgorithmAHElocal
  
  public AlgorithmAHElocal(ModelImage srcImg, int kSize, int kShape, boolean wholeImage, boolean useCIELab, float[] Lmin, float[] Lmax)
  
  Constructor for images in which changes are returned to the source image.
  
  Parameters:
  
  srcImg - source image model
  
  kSize - size of kernel
  
  kShape - shape of kernel
  
  wholeImage - If true whole image used
  
  useCIELab - If color, use intensity L in CIELab space
  
  Lmin - [0] is lowest color image L value in CIELab space
  
  Lmax - [0] is highest color image L value in CIELab space
- AlgorithmAHElocal
  
  public AlgorithmAHElocal(ModelImage destImg, ModelImage srcImg, int kSize, int kShape, boolean wholeImage, boolean useCIELab, float[] Lmin, float[] Lmax)
  
  Constructor for images in which changes are placed in a predetermined destination image.
  
  Parameters:
  
  destImg - image model where result image is to stored
  
  srcImg - source image model
  
  kSize - size of kernel
  
  kShape - shape of kernel
  
  wholeImage - If true whole image used
  
  useCIELab - If color, use intensity L in CIELab space
  
  Lmin - [0] is lowest color image L value in CIELab space
  
  Lmax - [0] is highest color image L value in CIELab space
Method Details
- finalize
  
  public void finalize()
  
  Prepares this class for destruction.
  
  Overrides:
  
  finalize in class AlgorithmBase
- runAlgorithm
  
  public void runAlgorithm()
  
  starts the algorithm.
  
  Specified by:
  
  runAlgorithm in class AlgorithmBase
- setClipLevel
  
  public void setClipLevel(int sectorPercentage)
  
  The Clip Level is a percentage of the maximum number of pixels in any particular brightness level. This method allows one to set that percentage. As the regional histograms are tabulated, the brightness with the maximum number of pixels attributed to it is remembered. The algorithm will then evenly redistibute the total number of pixels from any brightness which has a greater number than the max times this fraction to all other (less populous) brightnesses.
  
  Parameters:
  
  sectorPercentage - DOCUMENT ME!
- setContrastLimited
  
  public void setContrastLimited(boolean beClamped)
  
  Redistribute from brightnesses with at a least a specified percentage of the brightness with the maximum number of pixels.
  
  Parameters:
  
  beClamped - DOCUMENT ME!
- setHistogramScaleRule
  
  public void setHistogramScaleRule(int scaleRule)
  permit the user to select the scale on which the algorithm forms the brightness pattern of the histogram. The default is scaleOnSlice.
  The options are:
  
  scale On Local neighborhood
  
  scale on Slice
  
  scale on image
  Parameters:
  
  scaleRule - DOCUMENT ME!
- setMinimumThreshold
  
  public void setMinimumThreshold(float minThresh)
  
  sets minimum threshold values. Pixels are copied over when both the source pixel and the local neighborhood surrounding the pixel are all less than the given minimum pixel value.
  
  Parameters:
  
  minThresh - DOCUMENT ME!
- setRGBChannelFilter
  
  public void setRGBChannelFilter(boolean r, boolean g, boolean b)
  
  RGB images are histogram equalized by 'channel.' That is, each color, red, blue and green, is run independently of the other two colors. This permits selectively filtering any combination of the three channels instead of simply trying to handle all three at once. True filters that channel.
  
  Parameters:
  
  r - DOCUMENT ME!
  
  g - DOCUMENT ME!
  
  b - DOCUMENT ME!
- setThresholdImage
  
  public void setThresholdImage(boolean useThreshold)
  
  If useThreshold true only copy when both the source pixel and its local neighborhoold are are less than minThreshold.
  
  Parameters:
  
  useThreshold - DOCUMENT ME!
- buildHistogram
  
  protected int buildHistogram()
  
  make histogram uses the class-global vars kernel and histogram.
  
  Returns:
  
  the index to the bin with the highest count.
- calcInPlace2D
  
  protected void calcInPlace2D()
  
  Histogram equalization on the source image. Replaces the original image with the filtered image.
- calcInPlace3D
  
  protected void calcInPlace3D()
  
  Histogram Equalization on the source image and replaces the source image with the processed image.
- calcStoreInDest2D
  
  protected void calcStoreInDest2D()
  
  This function produces a new image that has had itself histogram equalized. places filtered image in the destination image.
- calcStoreInDest3D
  
  protected void calcStoreInDest3D()
  
  This function produces a new volume image that has been histogram equalized. The Image is changed by filtering each slice individually.
- clip
  
  protected final void clip(int[] histogram, int clipLimit)
  
  after generating a histogram, clip will reduce the number of pixels attributed to that brightness level.
  The idea is to limit any brightness level in the histogram to a set value; the number of pixels that are above the limit are tallied. The total number of pixels that were found above the limit, is then spread evenly among the brightnesses that are below limit.
  
  Parameters:
  
  histogram - array where the brightness values of all pixels in the image have been counted.
  
  clipLimit - no brightness may have any more than this number of pixels. Obviously, this method will not achieve anything when clipLimit is as large or larger than the largest brightness in histogram.
- copyBuffers
  
  protected final void copyBuffers(float[] dest, float[] src)
  
  Copies all values from the srcbuffer to the destination buffer. the format is intended to envision the Organization of dest[i] := src[i] float dest destination array float src source array
  
  Parameters:
  
  dest - DOCUMENT ME!
  
  src - DOCUMENT ME!
- findBufferMinMax
  
  protected final void findBufferMinMax(float[] buf, int bufStart, int bufEnd)
  
  Finds the local maximum and minimum values in the given range in order, as given by the starting and stoping values.
  
  Parameters:
  
  buf - float array of values
  
  bufStart - where to begin looking
  
  bufEnd - where to stop
- findImageOffset
  
  protected final void findImageOffset(int type)
  
  gets the bottom end of the image. for any image but color images, the bottom end is defined as the buffer minimum for all images except color images; there the offset is defined to be zero
  
  Parameters:
  
  type - DOCUMENT ME!
- findTotalBins
  
  protected final int findTotalBins(int type, int ideal)
  
  finds the total number of bins based on the type of image.
  
  Parameters:
  
  type - DOCUMENT ME!
  
  ideal - DOCUMENT ME!
  
  Returns:
  
  the total number of bins.
- getMax
  
  protected final float getMax(int color)
  
  gets the image max based on 1st) whether or not the image is color. 2) the color.
  
  Parameters:
  
  color - DOCUMENT ME!
  
  Returns:
  
  DOCUMENT ME!
- getMin
  
  protected final float getMin(int color)
  
  gets the image max based on 1st) whether or not the image is color. 2) the color.
  
  Parameters:
  
  color - DOCUMENT ME!
  
  Returns:
  
  DOCUMENT ME!
- getNeighborList
  
  protected final void getNeighborList(int i, float[] data)
  
  Compiles a list of the values neighboring the desired pixel, that are defined in the kernel.
  The Neighbor list reports the monochromatic brightness values. returned in the neighbor list's kernel.
  
  Parameters:
  
  i - The central pixel to find neighbors for.
  
  data - Image data. The data is to be arranged always as a monochromatic, 2d set. Returned in kernel: The neighboring pixel list
- getThresholdNeighborList
  
  protected final boolean getThresholdNeighborList(int i, float[] data)
  
  Compiles a list of the values neighboring the desired pixel, that are defined in the kernel.
  The Neighbor list reports the monochromatic brightness values. returned in the neighbor list's kernel.
  
  Parameters:
  
  i - The central pixel to find neighbors for.
  
  data - Image data. The data is to be arranged always as a monochromatic, 2d set.
  
  Returns:
  
  aboveThreshold
- makeKernel
  
  protected void makeKernel()
  
  Makes the kernel. Creates out of memory, sets the center and the size.
- makeKernelMask
  
  protected void makeKernelMask()
  
  Forms kernel.
- monoSliceEqualizer
  
  protected final void monoSliceEqualizer(float[] srcBuffer, float[] destBuffer)
  
  Allows a single monochrome image slice to be filtered. Any color image may be processed in this so long as each color plane is separate and provided one at a time. This means, extract [aRGB aRGB ...] buffer into 3 seperate buffers [RRRRRRRRRRR...] , [GGGGGG....] and [BBBBBBBB] and feed each into the sliceFilter one-at-a-time.
  The benefit is one sliceFilter for all image types; just break up each RGB image into these seperate monochrome images sliceFilter and then reassemble int aRGB.
  
  Only length of one slice (image.getExtents[0] * image.getExtents[1]) Will be copied at a time. Note that a progressBar must be created first.
  
  Parameters:
  
  srcBuffer - source buffer
  
  destBuffer - destination Buffer
- printhisto
  
  protected final void printhisto(int[] histo)
  
  a debug tool.
  
  Parameters:
  
  histo - DOCUMENT ME!
- procPixel
  
  protected final float procPixel(int pix, float[] srcBuffer)
  
  process pixel at pixel pix using data from the srcBuffer. builds a list of monochromatic image values of the neighboring pixels image values (using a map generated by the kernelMask), builds the histogram of those values, clamps when necessary, then scales the cumulative histogram, getting the brightness back out.
  This is the entire algorithm on one pixel.
  
  Parameters:
  
  pix - the pixel to process; generates the histogram from the neighbors around this image-data element.
  
  srcBuffer - all the monochromatic image data -- which means that 4-color image data must be seperated out into monochrome color slices for this method.
  
  Returns:
  
  DOCUMENT ME!
- setKernelMask
  
  protected void setKernelMask()
  
  Fill in the mask for which pixels are used in filtering.
- thresholdProcPixel
  
  protected final float thresholdProcPixel(int pix, float[] srcBuffer)
  
  process pixel at pixel pix using data from the srcBuffer. builds a list of monochromatic image values of the neighboring pixels image values (using a map generated by the kernelMask), builds the histogram of those values, clamps when necessary, then scales the cumulative histogram, getting the brightness back out.
  This is the entire algorithm on one pixel.
  
  Parameters:
  
  pix - the pixel to process; generates the histogram from the neighbors around this image-data element.
  
  srcBuffer - all the monochromatic image data -- which means that 4-color image data must be separated out into monochrome color slices for this method.
  
  Returns:
  
  DOCUMENT ME!
- setCopyColorText
  
  private void setCopyColorText(String colorText)
  
  If the progress bar is visible, sets the text to:
  Copying all color values ...
  
  Parameters:
  
  colorText - the color to use. Eg., "red" or "blue"
- convertRGBtoCIELab
  
  private void convertRGBtoCIELab(float[] buffer, float[] L, float[] a, float[] b)
- convertCIELabtoRGB
  
  private void convertCIELabtoRGB(float[] L, float[] a, float[] b, float[] buffer)

Class AlgorithmAHElocal

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Details

SQUARE_KERNEL

CROSS_KERNEL

AXIAL_KERNEL

scaleOnLocal

scaleOnSlice

scaleOnImage

absMinThreshold

bChannel

brightnessLevel

bufMax

bufMin

clampingIsNecessary

clipLevel

currentSlice

entireImage

gChannel

halfK

histogram

histomap

imageOffset

isColorImage

kernel

kernelCenter

kernelMask

kernelShape

kernelSize

mask

maskCenter

maxScale

maxScaleRule

minThreshold

minValue

numberOfSlices

rChannel

useCIELab

sortBuffer

thresholdingIsNecessary

totalBins

unitSize

valuesPerPixel

numColors

colorUsed

imageMax

scaleMaxCIELab

Lmin

Lmax

Constructor Details

AlgorithmAHElocal

AlgorithmAHElocal

Method Details

finalize

runAlgorithm

setClipLevel

setContrastLimited

setHistogramScaleRule

setMinimumThreshold

setRGBChannelFilter

setThresholdImage

buildHistogram

calcInPlace2D

calcInPlace3D

calcStoreInDest2D

calcStoreInDest3D

clip

copyBuffers

findBufferMinMax

findImageOffset

findTotalBins