Class ImageData

java.lang.Object
  ImageData

public class ImageData
extends java.lang.Object

ImageData class supports image data object access. This is the top level data structure for a basic image object (left or right). It contains the input and output Image objects and input and output int[] pix arrays.

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

java.awt.Image	bcImg brightness contrast filtered image if used.
boolean	blackIsZeroFlag Is true if original input image has BLACK as gray value 0, else WHITE is gray value 0
Boundary	bnd This boundary boundary is ImageData specific.
CalibrateOD	calib calibration data is ImageData specific
(package private) boolean	doingTransform set by doXform, cleared by doneWithXform
DrawHistogram	dwCalHist generic Calibration popup histogram for image
DrawHistogram	dwHist generic ROI popup histogram for image
long	endTime ending time of last transform
java.lang.String	errStr last error message associated with obj
static Flicker	flk Flicker global classes
boolean	hasODmapFlag Indicates that there is an valid mapGrayToOD map else if it was set to 1:1 the flag is set false.
int[]	hist Histogram of data [0:maxGray]
private java.awt.image.IndexColorModel	icm Index Color map
ImageDataMeas	idM Current measured circular mask spot for this image
ImageDataROI	idROI Region(s) Of Interest (ROI).
ImageDataSpotList	idSL Spot list (measured spots) for this image
int	iHeight height of original input image
java.awt.Image	iImg input image.
java.lang.String	imageFile full-path input image file name
int	IMG_TYPE_GIF GIF image type
int	IMG_TYPE_J2K [FUTURE] JPEG2000 image type.
int	IMG_TYPE_JPG JPEG image type
int	IMG_TYPE_PPX GELLAB-II PPX image type
int	IMG_TYPE_TIF TIFF image type
int	IMG_TYPE_UNKNOWN Unknown image type
int	imgType image type is one of IMG_TYPE_xxx
int[]	iPix For ImageXform and display - input image pixel data for display.
boolean	isClickableDBflag flag set if currently selected image is clickable
boolean	isColorImgFlag Is true if it is a color image where red!=green or red!=blue or when it is read in.
int	iWidth width of original input image
(package private) double	mag magnification factor
(package private) float	magVal
float[]	mapGrayToOD mapGrayToOD data if not null
int	maxG maximum Gray value seen in the original iPix[].
int	minG minimum Gray value seen in the original iPix[].
int	nBitsPerPixel # of bits/pixel.
java.awt.Image	oImg output image generated by ImageXform.
int	pixelMask bit mask to get the pixel (1 << nBitsPerPixel) -1
static boolean	reportErrorMsgsFlag report errors on loading else ignore messages
int	runTimeMsec # of milli-seconds to process last transform
long	startTime starting time of last transform
SliderState	state SliderState threshold parameters associated with the image
(package private) boolean	threadIsPaintFlag Ok to paint ImageScroller
java.lang.String	title current title for image scroller associated with iData
boolean	userClickableImageDBflag User enabled image as clickable DB checkbox to get DB entry
static Util	util extended Flicker state variable class
int	xObj Image current object mark
int	yObj Image current object mark
java.awt.Image	zImg ZoomMag filtered image if used.
int	zoomedHeight zoomed height
int	zoomedWidth zoomed width
(package private) int	zoomMagScr zoom value

Constructor Summary

ImageData()
ImageData() - Constructor for extensions

ImageData(java.lang.String iName, java.awt.Image newImg, java.awt.Dimension iSize, boolean blackIsZeroFlag, float[] mapGrayToOD, Flicker flkS)
ImageData() - Constructor.

Method Summary

boolean	applyNTSCrgb2grayTransform() applyNTSCrgb2grayTransform() - optionally convert RGT to grayscale for the iPix[] data.
void	changeImageData(java.lang.String iName, java.awt.Image newImg, java.awt.Dimension iSize, boolean blackIsZeroFlag, float[] mapGrayToOD) changeImageData() - change values of this ImageData object
boolean	checkAndMakeIpix(boolean reportErrorMsgsFlag) checkAndMakeIpix() - check & make iData.iPix if !exists.
boolean	checkAndMakeIpix(java.lang.String useXform, boolean reportErrorMsgsFlag) checkAndMakeIpix() - check & make iData.iPix if it does not exist.
static int	cvtRGBvalToNTSCgrayVal(int rgbPixelVal) cvtRGBvalToNTSCgrayVal() - convert RGB value to NTSC grayscale value.
java.awt.Image	getImageForBCInput() getImageForBCInput() - get image for input to Brightness/Contrast filter.
java.awt.Image	getImageForDisplayInput() getImageForDisplayInput() - get image for input to display painting.
java.awt.Image	getImageForXformInput() getImageForXformInput() - get the image for input to image transform.
java.awt.Image	getImageForZoomInput() getImageForZoomInput() - get image for input to ZoomMag filter.
int	getImgType() getImgType() - get image type from IMG_TYPE_xxx
private static int[]	getPixelDataFromImage(java.awt.Image img, int width, int height) getPixelDataFromImage() - get the pixel data from the image
boolean	isRGBcolorImage() isRGBcolorImage() - test if red!=green!=blue for any pixels
ImageData	loadBlankImageData(java.lang.String name, int w, int h) loadBlankImageData() - create and return a blank ImageData object [NOTE] This code has a bug since it does not create the empty window correctly.
java.awt.Point	mapStateToZoom(java.awt.Point XYobjToMap) mapStateToZoom() - map state point to zoomed/dezoomed point based on zoomMagVal.
java.awt.Point	mapZoomToState(java.awt.Point zoomedXYobjToMap) mapZoomToState() - map zoom point to state point based on zoomMagVal.
java.awt.Point	mapZoomToState(java.awt.Point zoomedXYobjToMap, int gw, int gh) mapZoomToState() - map zoom point to state point with Guard Region factored in.
void	printImgDebugState(java.lang.String msg) printImgDebugState() - Debugging print (iImg,oImg,zImg) object Java pointers.
void	printProperties(java.lang.String msg, java.awt.Image img, java.awt.Image zoomInputImg) printProperties() - Debugging print (iImg,oImg,zImg) object Java pointers, and img width & height.
void	resetImageData(boolean iImgFlushFlag) resetImageData() - reset this ImageData object.
static java.awt.Image	resizeImageToTargetSize(java.awt.Image img, int w, int h, int minTargetSize, int maxTargetSize, int targetSize) resizeImageToTargetSize() - resize image to target size if the w or h is outside the range [minTargetSize : maxTargetSize].
void	setDefaultGrayscaleIndexColorMap() setDefaultGrayscaleIndexColorMap() - set the default grayscale colormap to a RGB IndexColorMap with all colors the same
void	setDefaultGrayscaleIndexColorMap(byte[] r, byte[] g, byte[] b) setDefaultGrayscaleIndexColorMap() - set the RGB IndexColorMap from (r,g,b) maps Note: see Hacking Java, pg 90 on cycling color palette [TODO] Update the display...
void	setOrigInputPixels(int[] origInputPixels, int nBitsPerPixel, boolean blackIsZeroFlag) setOrigInputPixels() - set the original image iPix[] pixels and associated flags.
void	setTitle(java.lang.String title) setTitle() - change the title for the ImageData instance.

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

IMG_TYPE_UNKNOWN

public final int IMG_TYPE_UNKNOWN

Unknown image type

See Also:

Constant Field Values

IMG_TYPE_GIF

public final int IMG_TYPE_GIF

GIF image type

See Also:

Constant Field Values

IMG_TYPE_JPG

public final int IMG_TYPE_JPG

JPEG image type

See Also:

Constant Field Values

IMG_TYPE_TIF

public final int IMG_TYPE_TIF

TIFF image type

See Also:

Constant Field Values

IMG_TYPE_PPX

public final int IMG_TYPE_PPX

GELLAB-II PPX image type

See Also:

Constant Field Values

IMG_TYPE_J2K

public final int IMG_TYPE_J2K

[FUTURE] JPEG2000 image type. Could possibly use JJ2000 at http://jj2000.epfl.ch/

See Also:

Constant Field Values

iImg

public java.awt.Image iImg

input image. This is the original image and does NOT change.

oImg

public java.awt.Image oImg

output image generated by ImageXform. If sequential transforms are used, then this will also be used for the next round of tranform as the input image and then replaced with the computed output image.

zImg

public java.awt.Image zImg

ZoomMag filtered image if used.

bcImg

public java.awt.Image bcImg

brightness contrast filtered image if used.

xObj

public int xObj

Image current object mark

yObj

public int yObj

Image current object mark

iWidth

public int iWidth

width of original input image

iHeight

public int iHeight

height of original input image

zoomedWidth

public int zoomedWidth

zoomed width

zoomedHeight

public int zoomedHeight

zoomed height

imgType

public int imgType

image type is one of IMG_TYPE_xxx

isColorImgFlag

public boolean isColorImgFlag

Is true if it is a color image where red!=green or red!=blue or when it is read in. This flag can then be tested if we want to map the (R,G,B) to NTSC(R,G,B) grayscale on a pixel level so we could quantify the color data.

blackIsZeroFlag

public boolean blackIsZeroFlag

Is true if original input image has BLACK as gray value 0, else WHITE is gray value 0

nBitsPerPixel

public int nBitsPerPixel

# of bits/pixel. E.g., 8, 12, 16 bits

pixelMask

public int pixelMask

bit mask to get the pixel (1 << nBitsPerPixel) -1

maxG

public int maxG

maximum Gray value seen in the original iPix[]. -1 means it is not defined.

minG

public int minG

minimum Gray value seen in the original iPix[]. -1 means it is not defined.

iPix

public int[] iPix

For ImageXform and display - input image pixel data for display. Although the original image can be 8, 12, 16-bits, it is scaled in the image loaders to 8-bits if it is a grayscale image. By default we get the 8-bit data from the LSB or blue 8-bit channel.

reportErrorMsgsFlag

public static boolean reportErrorMsgsFlag

report errors on loading else ignore messages

errStr

public java.lang.String errStr

last error message associated with obj

imageFile

public java.lang.String imageFile

full-path input image file name

startTime

public long startTime

starting time of last transform

endTime

public long endTime

ending time of last transform

runTimeMsec

public int runTimeMsec

# of milli-seconds to process last transform

userClickableImageDBflag

public boolean userClickableImageDBflag

User enabled image as clickable DB checkbox to get DB entry

isClickableDBflag

public boolean isClickableDBflag

flag set if currently selected image is clickable

icm

private java.awt.image.IndexColorModel icm

Index Color map

doingTransform

boolean doingTransform

set by doXform, cleared by doneWithXform

threadIsPaintFlag

boolean threadIsPaintFlag

Ok to paint ImageScroller

title

public java.lang.String title

current title for image scroller associated with iData

zoomMagScr

int zoomMagScr

zoom value

mag

double mag

magnification factor

magVal

float magVal

state

public SliderState state

SliderState threshold parameters associated with the image

bnd

public Boundary bnd

This boundary boundary is ImageData specific.

calib

public CalibrateOD calib

calibration data is ImageData specific

mapGrayToOD

public float[] mapGrayToOD

mapGrayToOD data if not null

hasODmapFlag

public boolean hasODmapFlag

Indicates that there is an valid mapGrayToOD map else if it was set to 1:1 the flag is set false.

hist

public int[] hist

Histogram of data [0:maxGray]

dwHist

public DrawHistogram dwHist

generic ROI popup histogram for image

dwCalHist

public DrawHistogram dwCalHist

generic Calibration popup histogram for image

idSL

public ImageDataSpotList idSL

Spot list (measured spots) for this image

idM

public ImageDataMeas idM

Current measured circular mask spot for this image

idROI

public ImageDataROI idROI

Region(s) Of Interest (ROI). Note that the ND step wedge ROI is kept in and maintained by calib.{ndcwx1,ndcwx2,ndcwy1,ndcwy2}

Constructor Detail

ImageData

public ImageData(java.lang.String iName,
                 java.awt.Image newImg,
                 java.awt.Dimension iSize,
                 boolean blackIsZeroFlag,
                 float[] mapGrayToOD,
                 Flicker flkS)

ImageData() - Constructor. Obj keeps all image data together. Assumption: image, widthA, heightA and iPixA must exist before the class instance is created. Note: newImg must exist completely in memory at this point. Setup up a 1:1 mapGrayToOD[0:maxGray] if mapGrayToOD is null.

Parameters:

iName - is name of image

newImg - is existing input image to setthis.iImg.

iSize - is size of image

blackIsZeroFlag - is true if image has black as 0 gray value

mapGrayToOD - is Map of Gray to OD if exists

flk - is instance of Flicker

ImageData

public ImageData()

ImageData() - Constructor for extensions

Method Detail

getImgType

public int getImgType()

getImgType() - get image type from IMG_TYPE_xxx

Returns:

image type

setTitle

public void setTitle(java.lang.String title)

setTitle() - change the title for the ImageData instance. You can do a temporary change or a permanent change.

Parameters:

title - to use

setDefaultGrayscaleIndexColorMap

public void setDefaultGrayscaleIndexColorMap(byte[] r,
                                             byte[] g,
                                             byte[] b)

setDefaultGrayscaleIndexColorMap() - set the RGB IndexColorMap from (r,g,b) maps Note: see Hacking Java, pg 90 on cycling color palette [TODO] Update the display...

Parameters:

r - is red map

g - is green map

b - is blue map

setDefaultGrayscaleIndexColorMap

public void setDefaultGrayscaleIndexColorMap()

setDefaultGrayscaleIndexColorMap() - set the default grayscale colormap to a RGB IndexColorMap with all colors the same

resetImageData

public void resetImageData(boolean iImgFlushFlag)

resetImageData() - reset this ImageData object. It does not change the name of the file, black is white flag nor mapGrayToOD.

Parameters:

iImgFlushFlag - to flush iImg if true

changeImageData

public void changeImageData(java.lang.String iName,
                            java.awt.Image newImg,
                            java.awt.Dimension iSize,
                            boolean blackIsZeroFlag,
                            float[] mapGrayToOD)

changeImageData() - change values of this ImageData object

Parameters:

iName - is name of image

newImg - is existing input image to set to this ImageData instance

iSize - is size of image

blackIsZeroFlag - is true if image has black as 0 gray value

mapGrayToOD - is Map of Gray to OD if exists and is not null

resizeImageToTargetSize

public static java.awt.Image resizeImageToTargetSize(java.awt.Image img,
                                                     int w,
                                                     int h,
                                                     int minTargetSize,
                                                     int maxTargetSize,
                                                     int targetSize)

resizeImageToTargetSize() - resize image to target size if the w or h is outside the range [minTargetSize : maxTargetSize]. We resize if we DO need to resize AND (targetSize!=0). Also keep the (h/w) aspect ratio the same.

Parameters:

img - is image to resize

w - is actual width

h - is actual height

minTargetSize - allowed

maxTargetSize - allowed

targetSize - to set the image to if resizing and it is not 0

Returns:

new image if had to resize it, else return the old image

getPixelDataFromImage

private static int[] getPixelDataFromImage(java.awt.Image img,
                                           int width,
                                           int height)

getPixelDataFromImage() - get the pixel data from the image

Parameters:

img - image to use

width - of image

height - of image

Returns:

int[] array of pixel data,

loadBlankImageData

public ImageData loadBlankImageData(java.lang.String name,
                                    int w,
                                    int h)

loadBlankImageData() - create and return a blank ImageData object [NOTE] This code has a bug since it does not create the empty window correctly. It could be called initially from flk.initialImageLoad() if the call to load an initial image using loadPixIntoImageData() fails.

Parameters:

name - of empty image to create

w - is width of empty image

h - is height of empty image

Returns:

ImageData instance

checkAndMakeIpix

public boolean checkAndMakeIpix(boolean reportErrorMsgsFlag)

checkAndMakeIpix() - check & make iData.iPix if !exists. This gets the generic iImg or oImg data.

Parameters:

reportErrorMsgsFlag - to report error it it occurs on load

Returns:

false if an error.

checkAndMakeIpix

public boolean checkAndMakeIpix(java.lang.String useXform,
                                boolean reportErrorMsgsFlag)

checkAndMakeIpix() - check & make iData.iPix if it does not exist. If we are zooming, it gets the zoom input else the image Xform image which could be either iImg or oImg (if the latter exists and the switches are set according to the getImageForXformInput() rules.

Parameters:

useXform - to check for "DeZoom" transform.

reportErrorMsgsFlag - to report error it it occurs on load

Returns:

false if an error.

isRGBcolorImage

public boolean isRGBcolorImage()

isRGBcolorImage() - test if red!=green!=blue for any pixels

Returns:

true if RGB color pixels.

cvtRGBvalToNTSCgrayVal

public static final int cvtRGBvalToNTSCgrayVal(int rgbPixelVal)

cvtRGBvalToNTSCgrayVal() - convert RGB value to NTSC grayscale value. The NTSC standard to convert RGB to Grayscale is grayscale = 0.33Red + 0.5Green + 0.17Blue.

Parameters:

rgbPixelVal -

applyNTSCrgb2grayTransform

public boolean applyNTSCrgb2grayTransform()

applyNTSCrgb2grayTransform() - optionally convert RGT to grayscale for the iPix[] data. If the iPix[] data is color RGB, then apply the NTSC rgb to grayscale transform to the iPix[] data.

First we recompute the isColorImgFlag status. If it is true, it is a color image where red!=green or red!=blue. This flag is then be tested if we want to map the (R,G,B) to NTSC(R,G,B) grayscale on a pixel level so we could quantify the color data.

This is only applied if the flk.useNTSCrgbTograyCvtFlag and the iData.isColorImgFlag was recomputed as true. It always computes (minG, maxG) for the iPix[] LSB 8-bit data (AFTER the NTSC conversion if required).

Returns:

true if did conversion, else false

getImageForXformInput

public java.awt.Image getImageForXformInput()

getImageForXformInput() - get the image for input to image transform. If are not allowing image transforms (i.e. !flk.allowXformFlag), then use the iImg. Otherwise, if we are composing output images (flk.composeXformFlag and oImg exists) then use oImg else iImg.

Returns:

the Image to use, else null if error

getImageForZoomInput

public java.awt.Image getImageForZoomInput()

getImageForZoomInput() - get image for input to ZoomMag filter. If allowing image transforms (i.e. flk.allowXformFlag) and oImg exists, then use oImg, else use iImg. Note: we do not care whether the oImg was composed or not - just whether it exists!

Returns:

the Image to use, else null if error

getImageForBCInput

public java.awt.Image getImageForBCInput()

getImageForBCInput() - get image for input to Brightness/Contrast filter. If zImg exists, then use that. Else if we are allowing image transforms (i.e. flk.allowXformFlag) and oImg exists, then use oImg, else use iImg. Note: if change flk.allowXformFlag status, MUST resync zImg if zoomMagVal is not 1.0X since different data source.

Returns:

the Image to use, else null if error

getImageForDisplayInput

public java.awt.Image getImageForDisplayInput()

getImageForDisplayInput() - get image for input to display painting. If bcImg exists, then use it. Else if zImg exists, then use that. Else if we are allowing image transforms (i.e. flk.allowXformFlag) and oImg exists, then use oImg, else use iImg.

Returns:

the Image to use, else null if error

printImgDebugState

public void printImgDebugState(java.lang.String msg)

printImgDebugState() - Debugging print (iImg,oImg,zImg) object Java pointers. This is useful for debugging transforms etc.

Parameters:

msg - - to print if any

setOrigInputPixels

public final void setOrigInputPixels(int[] origInputPixels,
                                     int nBitsPerPixel,
                                     boolean blackIsZeroFlag)

setOrigInputPixels() - set the original image iPix[] pixels and associated flags.

Parameters:

origInputPixels - is the original pixels array data

nBitsPerPixel - is # bits/pixel in the original pixels

blackIsZeroFlag - is true if original input image has BLACK as gray value 0, else WHITE is gray value 0

printProperties

public void printProperties(java.lang.String msg,
                            java.awt.Image img,
                            java.awt.Image zoomInputImg)

printProperties() - Debugging print (iImg,oImg,zImg) object Java pointers, and img width & height. This is useful for debugging transforms etc.

Parameters:

msg - - to print if any

img - - to print if any

zoomInputImg - - to print if any

mapStateToZoom

public java.awt.Point mapStateToZoom(java.awt.Point XYobjToMap)

mapStateToZoom() - map state point to zoomed/dezoomed point based on zoomMagVal. This can be used for remapping overlays.

Parameters:

mappedXYobj - to use if not null, else create one.

Returns:

zoomed point

mapZoomToState

public java.awt.Point mapZoomToState(java.awt.Point zoomedXYobjToMap,
                                     int gw,
                                     int gh)

mapZoomToState() - map zoom point to state point with Guard Region factored in. This can be used for remapping overlays.

Parameters:

mappedXYobj - to use if not null, else create one.

gw - guard width

gh - guard height

Returns:

zoomed point, -1 if out of bounds

mapZoomToState

public java.awt.Point mapZoomToState(java.awt.Point zoomedXYobjToMap)

mapZoomToState() - map zoom point to state point based on zoomMagVal. This can be used for remapping overlays.

Parameters:

mappedXYobj - to use if not null, else create one.

Returns:

zoomed point, -1 if out of bounds