Class ImageDataMeas

java.lang.Object
  ImageDataMeas

public class ImageDataMeas
extends java.lang.Object

ImageDataMeas class supports image data spot measurement object access.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Flicker Mozilla and Legal files are available on http://open2dprot.sourceforge.net/Flicker

Version:

$Date$ $Revision$

Author:

P. Lemkin (LECB/NCI), G. Thornwall (SAIC), Frederick, MD

See Also:

Flicker Home

Field Summary

float	bkgrdGrayValue Capture "background" pixel gray or OD value.
int	bkgrdObjX Capture "background" X coordinate
int	bkgrdObjY Capture "background" Y coordinate
Spot	curSpot Current spot set with showMeasValue if being measured.
static Flicker	flk Flicker global classes
ImageData	id Instance of ImageData for extended classes
static int[]	maskArea List of areas under each mask index by the mask radius
static int[][][]	maskNxN Array of masks [0:nMasks-1][0:Nr][0:Nr] where Nr is (2*radius+1)
static int[]	maskRadius Array of mask radius size where Nr is (2*radius+1)
static int[]	maskTotWeight List of total weights under each mask index by the mask radius
float	maxBkgrdGrayValue Capture max "background" pixel gray or OD value
float	maxGrayValue Capture max pixel gray or OD value within mask
float	maxMeasGrayValue Capture max "measurement" pixel gray or OD value
float	meanBkgrdGrayValue Capture mean "background" pixel gray or OD value.
float	meanGrayValue Capture mean pixel gray or OD value within mask
float	meanMeasGrayValue Capture mean "measurement" pixel gray or OD value.
float	measGrayValue Capture "measurement" pixel gray or OD value.
int	measObjX Capture "background" X coordinate
int	measObjY Capture "background" Y coordinate
float	minBkgrdGrayValue Capture min "background" pixel gray or OD value
float	minGrayValue Capture min pixel gray or OD value within mask
float	minMeasGrayValue Capture min "measurement" pixel gray or OD value
static int	nMasks number of masks [0:nMasks-1][0:Nr][0:Nr]
float	totGrayValue Capture total pixel gray or OD value within mask
float	totMeasGrayValue Capture total "measurement" pixel gray or OD value.
static Util	util extended Flicker state variable class

Constructor Summary

ImageDataMeas()
ImageData() - Constructor for creating spot masks Defaults to Flicker.MAX_CIRCLE_RADIUS # of masks

ImageDataMeas(ImageData iData)
ImageData() - Constructor for spot measurement extension

ImageDataMeas(int maxRadiusToCreate)
ImageData() - Constructor for creating spot masks of size 1x1 to (maxRadiusToCreate X maxRadiusToCreate)

Method Summary

boolean	calcHistogram(int x1, int y1, int x2, int y2) calcHistogram() - compute grayscale histogram under the specified computing window [x1:x2, y1:y2].
private static int	calcMaskArea(int[][] mask) calcMaskArea() - compute the area under the mask
private static int	calcMaskTotWeight(int[][] mask) calcMaskTotWeight() - compute the total weights under the mask
float	calcSumValuesUnderMask(int radius, int x0, int y0, boolean useTotDensityFlag) calcSumValuesUnderMask() - compute sum of pixel values under the mask corresponding to the mask set by the current radius.
float	captureBackgroundValue() captureBackgroundValue() - capture the values under the mask of the selected image if it is left or right and assign it to the background pixel value for the current image.
float	captureMeasCWvalue() captureMeasCWvalue() - capture the pixel values under the computing window of the selected image if it is left or right and assign it to the measurement pixel value for the current image.
float	captureMeasValue() captureMeasValue() - capture the pixel values under the mask of the selected image if it is left or right and assign it to the measurement pixel value for the current image.
void	clean() clean() - init the image data measurement state
static int	createMaskDatabase(int maxCircleRadius) createMaskDatabase() - create the set of circular masks of size NrxNr stored in a 3D array [0:nMasks-1][0:Nr][0:Nr] where Nr is (2*radius+1)
static java.lang.String	cvMaskToStr(int[][] mask, java.lang.String msg) cvMaskToStr() - convert a mask to a printable string
java.lang.String	cvtGrayValueToODstr(int g) cvtGrayValueToODstr() - convert gray value to OD string if the map has been defined for the ImageData instance
int	getPixelValue(int x, int y) getPixelValue() - get the pixel value for the image at (x,y).
java.lang.String	getPixelValueStr(int xObj, int yObj) getPixelValueStr() - get the pixel value string for the image where the trial object (xObj,yObj) is located.
static void	main(java.lang.String[] args) main() - createMaskDatabase function for debugging...
static void	setCircleMaskRadius(int radius, ImageData iData) setCircleMaskRadius() - set the circle radius for measurement and background, as well as the circle mask given the radius.
void	setupCircularMaskStatistics() setupCircularMaskStatistics()- compute the mask area and total weights for each mask.
java.lang.String	showBkgrdValue() showBkgrdValue() - print the background measurement value.
java.lang.String	showMeasValue(java.lang.String measMode) showMeasValue() - print the measurement value subtracting the background value.

Methods inherited from class java.lang.Object

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

Field Detail

flk

public static Flicker flk

Flicker global classes

util

public static Util util

extended Flicker state variable class

id

public ImageData id

Instance of ImageData for extended classes

maskNxN

public static int[][][] maskNxN

Array of masks [0:nMasks-1][0:Nr][0:Nr] where Nr is (2*radius+1)

nMasks

public static int nMasks

number of masks [0:nMasks-1][0:Nr][0:Nr]

maskRadius

public static int[] maskRadius

Array of mask radius size where Nr is (2*radius+1)

maskArea

public static int[] maskArea

List of areas under each mask index by the mask radius

maskTotWeight

public static int[] maskTotWeight

List of total weights under each mask index by the mask radius

maxGrayValue

public float maxGrayValue

Capture max pixel gray or OD value within mask

minGrayValue

public float minGrayValue

Capture min pixel gray or OD value within mask

curSpot

public Spot curSpot

Current spot set with showMeasValue if being measured.

totGrayValue

public float totGrayValue

Capture total pixel gray or OD value within mask

meanGrayValue

public float meanGrayValue

Capture mean pixel gray or OD value within mask

meanBkgrdGrayValue

public float meanBkgrdGrayValue

Capture mean "background" pixel gray or OD value.

meanMeasGrayValue

public float meanMeasGrayValue

Capture mean "measurement" pixel gray or OD value.

totMeasGrayValue

public float totMeasGrayValue

Capture total "measurement" pixel gray or OD value.

bkgrdGrayValue

public float bkgrdGrayValue

Capture "background" pixel gray or OD value. This is either mean or tottal integrated (sum over mask area) density.

measGrayValue

public float measGrayValue

Capture "measurement" pixel gray or OD value. This is either mean or tottal integrated (sum over mask area) density.

maxBkgrdGrayValue

public float maxBkgrdGrayValue

Capture max "background" pixel gray or OD value

maxMeasGrayValue

public float maxMeasGrayValue

Capture max "measurement" pixel gray or OD value

minBkgrdGrayValue

public float minBkgrdGrayValue

Capture min "background" pixel gray or OD value

minMeasGrayValue

public float minMeasGrayValue

Capture min "measurement" pixel gray or OD value

bkgrdObjX

public int bkgrdObjX

Capture "background" X coordinate

bkgrdObjY

public int bkgrdObjY

Capture "background" Y coordinate

measObjX

public int measObjX

Capture "background" X coordinate

measObjY

public int measObjY

Capture "background" Y coordinate

Constructor Detail

ImageDataMeas

public ImageDataMeas(ImageData iData)

ImageData() - Constructor for spot measurement extension

Parameters:

iData - is the ImageData instance

ImageDataMeas

public ImageDataMeas()

ImageData() - Constructor for creating spot masks Defaults to Flicker.MAX_CIRCLE_RADIUS # of masks

ImageDataMeas

public ImageDataMeas(int maxRadiusToCreate)

ImageData() - Constructor for creating spot masks of size 1x1 to (maxRadiusToCreate X maxRadiusToCreate)

Parameters:

maxRadiusToCreate -

Method Detail

clean

public void clean()

clean() - init the image data measurement state

createMaskDatabase

public static int createMaskDatabase(int maxCircleRadius)

createMaskDatabase() - create the set of circular masks of size NrxNr stored in a 3D array [0:nMasks-1][0:Nr][0:Nr] where Nr is (2*radius+1)

Parameters:

maxCircleRadius - is the maximum circle size radius

Returns:

the # of masks generated.

cvMaskToStr

public static java.lang.String cvMaskToStr(int[][] mask,
                                           java.lang.String msg)

cvMaskToStr() - convert a mask to a printable string

Parameters:

mask - is [nR][nR] to print

msg - is optional message to prefix out if not null

Returns:

string representing the matrix

setupCircularMaskStatistics

public void setupCircularMaskStatistics()

setupCircularMaskStatistics()- compute the mask area and total weights for each mask. Also set the current mask

calcMaskArea

private static int calcMaskArea(int[][] mask)

calcMaskArea() - compute the area under the mask

Parameters:

mask - is 2D mask

Returns:

total non-zero area under the mask

calcMaskTotWeight

private static int calcMaskTotWeight(int[][] mask)

calcMaskTotWeight() - compute the total weights under the mask

Parameters:

mask - is 2D mask

Returns:

total non-zero total weights under the mask

setCircleMaskRadius

public static void setCircleMaskRadius(int radius,
                                       ImageData iData)

setCircleMaskRadius() - set the circle radius for measurement and background, as well as the circle mask given the radius.

Parameters:

radius - - of the circle mask

iData - - if set to I1 or I2, null otherwise

calcSumValuesUnderMask

public float calcSumValuesUnderMask(int radius,
                                    int x0,
                                    int y0,
                                    boolean useTotDensityFlag)

calcSumValuesUnderMask() - compute sum of pixel values under the mask corresponding to the mask set by the current radius. If the gray to OD map exists, then map it and return integrated OD. eturn -1 if mask intersects the edge of the image.

Parameters:

radius - is mask radius to use (2*radius+1)

x0 - center of the mask'ed data

y0 - center of the mask'ed data

useTotFlag - to return total gray values else mean gray values.

Returns:

sum of pixels values, mapped to OD if map exists, else return -1.0 if therre is a problem.

getPixelValue

public final int getPixelValue(int x,
                               int y)

getPixelValue() - get the pixel value for the image at (x,y). Do not map grayscale to OD. That should be done by the caller.

 Notes: 
 1) because we only keep 24-bit (R,G,B) pixel image data, we only 
    report the least significant 8-bits (blue channel) for the gray value.
 2) If the original image data had > 8-bits, we still report it (for
    now) as 8-bits.

Returns:

grayscale value of pixel, -1 if a problem.

cvtGrayValueToODstr

public java.lang.String cvtGrayValueToODstr(int g)

cvtGrayValueToODstr() - convert gray value to OD string if the map has been defined for the ImageData instance

Parameters:

g - is the gray value to convert

Returns:

converted gray value

getPixelValueStr

public java.lang.String getPixelValueStr(int xObj,
                                         int yObj)

getPixelValueStr() - get the pixel value string for the image where the trial object (xObj,yObj) is located. If the gray to OD map exists, then compute it as OD else grayscale. If we are measuring spots in the spot list and they are viewable, then we can append the spot# and the spot.id (if not null).

 Notes: 
 1) because we only keep 24-bit (R,G,B) pixel image data, we only 
    report the least significant 8-bits (blue channel) for the gray value.
 2) If the original image data had > 8-bits, we still report it (for
    now) as 8-bits.
 3) [TODO] could remap RGB via NTSC mapping...

Parameters:

xObj - pixel coordinate

yObj - pixel coordinate

Returns:

string value of pixel

captureBackgroundValue

public float captureBackgroundValue()

captureBackgroundValue() - capture the values under the mask of the selected image if it is left or right and assign it to the background pixel value for the current image. If calibration is in effect, set the calibrated value.

Returns:

current pixel value, -1 if no image selected

showBkgrdValue

public java.lang.String showBkgrdValue()

showBkgrdValue() - print the background measurement value. These were added using the CTRL-B for background. It sends the string to the output.

Returns:

current background measurement string, null if no data

captureMeasValue

public float captureMeasValue()

captureMeasValue() - capture the pixel values under the mask of the selected image if it is left or right and assign it to the measurement pixel value for the current image. If calibration is in effect, set the calibrated value.

Returns:

current pixel value, -1 if no image selected

captureMeasCWvalue

public float captureMeasCWvalue()

captureMeasCWvalue() - capture the pixel values under the computing window of the selected image if it is left or right and assign it to the measurement pixel value for the current image. If calibration is in effect, set the calibrated value.

Returns:

current pixel value, -1 if no image selected

showMeasValue

public java.lang.String showMeasValue(java.lang.String measMode)

showMeasValue() - print the measurement value subtracting the background value. These were added using the CTRL-B for background and CTRL-M for measure. It sends the string to the output.

Parameters:

measMode - is "circleMask", "compROI", "boundary"

Returns:

current pixel measurement string, null if not data. If measuring spots in the spot list, then set curSpot to the current spot being measured, else set it to null.

calcHistogram

public boolean calcHistogram(int x1,
                             int y1,
                             int x2,
                             int y2)

calcHistogram() - compute grayscale histogram under the specified computing window [x1:x2, y1:y2]. The result is in this.hist[] which is created here.

Parameters:

x1 - - ULHC x coordinate

y1 - - ULHC y coordinate

x2 - - LRHC x coordinate

y2 - - LRHC y coordinate

main

public static void main(java.lang.String[] args)

main() - createMaskDatabase function for debugging...