Class Boundary

java.lang.Object
  Boundary

public class Boundary
extends java.lang.Object

Class Boundary performs boundary operations and its instance exists in the ImageData object.

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

(package private) int	area
java.awt.Point[]	bnd Boundary of object
(package private) java.awt.Color	bndColor color to draw boundary
boolean	bndOpenFlag boundary is active
(package private) double	density
(package private) double	densRaw
private Flicker	flk
(package private) int	iHeight height of image to measure
(package private) int	iWidth width of image to measure
(package private) float[]	mapGrayToOD gray scale to OD map
int	MAX_BND Max boundary size
(package private) int	maxBnd Max size of boundary array
(package private) double	maxd
java.lang.String	measType "Quant" or "Bkgrd"
(package private) int	measurementNbr measurement #
(package private) int	merx1
(package private) int	merx2
(package private) int	mery1
(package private) int	mery2
(package private) double	mind
(package private) double	mnbackground
(package private) int	nPoints # points drawn so far
(package private) int	perim
(package private) double	sdDensity
(package private) double	sx
(package private) double	sxy
(package private) double	sy
(package private) boolean	validFeaturesFlag Set object features as function of input pixels [] and boundary
(package private) double	xAbs
(package private) int[]	xPoints coordinates for drawing using polyline
(package private) double	yAbs
(package private) int[]	yPoints coordinates for drawing using polyline

Constructor Summary

Boundary(Flicker flk)
Boundary() - constructor.

Method Summary

void	clean() clean() - clean up before init or when kill instance before GC
java.lang.String	cvFeatures2str(java.lang.String imageFile) cvFeatures2str() - cvt object features to printable string
void	drawBoundary(java.awt.Graphics g) drawBoundary() - draw boundary backwards
void	drawBoundaryInImage(java.awt.Graphics g) drawBoundaryInImage() - redraw boundary in window if visible.
void	eraseBoundary() eraseBoundary() - erase boundary backwards one at a time.
boolean	finishMeasurement(int iWidth, int iHeight, int[] inputPix, int pixelMask) finishMeasurement() - finish measurement and compute features
java.awt.Point[]	getBoundary() getBoundary() - return boundary
int	getBoundaryLength() getBoundaryLength() - return nPoints for boundary
boolean	getValidFeaturesFlag() getValidFeaturesFlag() - get the valid features set after measurement
int	interpolatePoints(int xOld, int yOld, int xNew, int yNew) interpolatePoints() - interpolate (xOld,yOld) to (xNew,yNew) into list of x,y coordinates of maximum size maxN which are pushed onto the bnd[] point list.
void	measureRegion(int[] inputPixels, int pixelMask) measureRegion() - compute image features for object inside boundary.
void	processBoundaryMode(int x, int y, boolean shiftMod) processBoundaryMode() - process drawing mouse event if boundaryMode
int	pushBoundary(int x, int y) pushBoundary() - push unique boundary points from last point to current
void	regrowBoundary(int newSize) regrowBoundary() - increase boundary size
void	setBndColor(java.awt.Color c) setBndColor() - set the boundary drawing color
void	setBndState(boolean bndOpenFlag) setBndState() - set the boundary state in the imageCanvas
void	setMapGrayToOD(float[] mapGrayToOD) setMapGrayToOD() - set the MapGrayToOD[] table
void	startMeasurement(java.lang.String measType, int iWidth, int iHeight) startMeasurement() - start measurement of object.

Methods inherited from class java.lang.Object

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

Field Detail

flk

private Flicker flk

MAX_BND

public final int MAX_BND

Max boundary size

See Also:

Constant Field Values

measType

public java.lang.String measType

"Quant" or "Bkgrd"

bndOpenFlag

public boolean bndOpenFlag

boundary is active

mapGrayToOD

float[] mapGrayToOD

gray scale to OD map

bnd

public java.awt.Point[] bnd

Boundary of object

iWidth

int iWidth

width of image to measure

iHeight

int iHeight

height of image to measure

measurementNbr

int measurementNbr

measurement #

maxBnd

int maxBnd

Max size of boundary array

nPoints

int nPoints

# points drawn so far

bndColor

java.awt.Color bndColor

color to draw boundary

validFeaturesFlag

boolean validFeaturesFlag

Set object features as function of input pixels [] and boundary

mnbackground

double mnbackground

density

double density

sx

double sx

sy

double sy

sxy

double sxy

maxd

double maxd

mind

double mind

xAbs

double xAbs

yAbs

double yAbs

densRaw

double densRaw

sdDensity

double sdDensity

area

int area

perim

int perim

merx1

int merx1

merx2

int merx2

mery1

int mery1

mery2

int mery2

xPoints

int[] xPoints

coordinates for drawing using polyline

yPoints

int[] yPoints

coordinates for drawing using polyline

Constructor Detail

Boundary

public Boundary(Flicker flk)

Boundary() - constructor.

Method Detail

setMapGrayToOD

public void setMapGrayToOD(float[] mapGrayToOD)

setMapGrayToOD() - set the MapGrayToOD[] table

Parameters:

mapGrayToOD - map of grayscale to OD

drawBoundary

public void drawBoundary(java.awt.Graphics g)

drawBoundary() - draw boundary backwards

Parameters:

g - is graphics context where we draw the boundary

clean

public void clean()

clean() - clean up before init or when kill instance before GC

setBndState

public final void setBndState(boolean bndOpenFlag)

setBndState() - set the boundary state in the imageCanvas

Parameters:

bndOpenFlag - to toggle boundary drawing overlay

setBndColor

public final void setBndColor(java.awt.Color c)

setBndColor() - set the boundary drawing color

Parameters:

c - is boundary color

getValidFeaturesFlag

public final boolean getValidFeaturesFlag()

getValidFeaturesFlag() - get the valid features set after measurement

Returns:

true if features are valid (i.e. boundary defined and features computed)

startMeasurement

public final void startMeasurement(java.lang.String measType,
                                   int iWidth,
                                   int iHeight)

startMeasurement() - start measurement of object.

Parameters:

measType - is "Quant" or "Bkgrd"

iWidth - is width of image

iHeight - is height of image

See Also:

finishMeasurement(int, int, int[], int)

measureRegion

public void measureRegion(int[] inputPixels,
                          int pixelMask)

measureRegion() - compute image features for object inside boundary. Measure features (area, perimeter, centroid, and integrated density, if the PPX grayToNDmap[] is calibrated.

 ALGORITHM:
 [1] Given contiguous the convex hull list of points enclosing region.
 [2] Define the region by a run length map with one run/line.
 [3] When finished measuring, compute features as function of pixel
     data inside of the RLM. (Only count pixels INSIDE of boundary.)
 [4] Then conditionally print these out with the area, density, etc.

 This algorithm is the same used in the FLICKER program described
 in:
   Lemkin,P., Merril,C., Lipkin,L., etal. "Software Aids for
   the Analysis of 2D Gel Electrophoresis Images", Comp. Biomed.
   Res. 12, 517 (1979).

Parameters:

inputPixels - is array of pixels to use.

pixelMask - is pixel mask to use on inputPixels

regrowBoundary

public final void regrowBoundary(int newSize)

regrowBoundary() - increase boundary size

Parameters:

newSize - of boundary

interpolatePoints

public final int interpolatePoints(int xOld,
                                   int yOld,
                                   int xNew,
                                   int yNew)

interpolatePoints() - interpolate (xOld,yOld) to (xNew,yNew) into list of x,y coordinates of maximum size maxN which are pushed onto the bnd[] point list. Algorithm taken from Lemkin etal, Comput. in Biomed. Res., 12, 517-544 (1979). Compute the interpolated line from (xOld,yOld) to (xNew,yNew) storing it in the arrays and returning the number of points generated.

Parameters:

xOld - is starting coordinate

yOld - is starting coordinate

xNew - is final coordinate

yNew - is final coordinate

Returns:

the # of points generated this trip.

getBoundaryLength

public final int getBoundaryLength()

getBoundaryLength() - return nPoints for boundary

Returns:

length of boundary

getBoundary

public final java.awt.Point[] getBoundary()

getBoundary() - return boundary

Returns:

boundary points

pushBoundary

public final int pushBoundary(int x,
                              int y)

pushBoundary() - push unique boundary points from last point to current

Parameters:

x - is new boundary coordinate

y - is new boundary coordinate

Returns:

length of boundary or 0 if there is a problem

eraseBoundary

public final void eraseBoundary()

eraseBoundary() - erase boundary backwards one at a time.

finishMeasurement

public boolean finishMeasurement(int iWidth,
                                 int iHeight,
                                 int[] inputPix,
                                 int pixelMask)

finishMeasurement() - finish measurement and compute features

Parameters:

iWidth - is getSize().width of image

iHeight - is getSize().height of image

inputPix - is image buffer pixels from iData{1|2}. input pixels

pixelMask - to get gray value from low order inputPix bits

Returns:

true if ok.

cvFeatures2str

public java.lang.String cvFeatures2str(java.lang.String imageFile)

cvFeatures2str() - cvt object features to printable string

Parameters:

imageFile - is image file

Returns:

printable string

drawBoundaryInImage

public final void drawBoundaryInImage(java.awt.Graphics g)

drawBoundaryInImage() - redraw boundary in window if visible. If the boundary exists, then draw bnd[0:nPoints-1] in bndColor.

Parameters:

g - is graphics context

processBoundaryMode

public final void processBoundaryMode(int x,
                                      int y,
                                      boolean shiftMod)

processBoundaryMode() - process drawing mouse event if boundaryMode

Parameters:

x - is point to push

y - is point to push

shiftMod - status