Class TiffLoader

java.lang.Object
  TiffLoader

public class TiffLoader
extends java.lang.Object

Class TiffLoader reads Tiff image into the class instance. variables.

 It uses class Raster when reading the image.
 All image data is expressed as a collection of pixels. Each pixel consists
 of a number of samples. A sample is a datum for one band of an image
 and a band consists of all samples of a particular type in an image. For
 example, a pixel might contain three samples representing its red, green
 and blue components. There are three bands in the image containing this
 pixel. One band consists of all the red samples from all pixels in the
 image. The second band consists of all the green samples and the 
 remaining band consists of all of the blue samples. The pixel can be 
 stored in various formats. For example, all samples from a particular
 band can be stored contiguously or all samples from a single pixel can
 be stored contiguously. In the Java 2D(tm) API, all built-in image 
 processing and display operators process samples which represent
 unsigned integral values.

 A collection of pixels is represented as a Raster, which consists of a
 DataBuffer and a SampleModel. The SampleModel allows access to samples 
 in the DataBuffer and may provide low-level information that a programmer
 can use to directly manipulate samples and pixels in the DataBuffer.

 This class is generally a fall back method for dealing with images. More
 efficient code will cast the SampleModel to the appropriate subclass and
 extract the information needed to directly manipulate pixels in the 
 DataBuffer.

 There is an option useLogInputFlag to add Log(grayscale) to take scaled
 log of grayscale data for maxBits>8-bits (e.g., 10-bits or 16-bits) for
 TIFF images prior to reading them. Scale log((2**nBitsPerPixel)-1) to 255:
   f'(g) = 255*log(g+1)/log((2**nBitsPerPixel)-1).

 This requires two JAI jar files: jai_core.jar and jai_codec.jar
 for TiffLoader.java to compile. These should be in the same class path
 as the Flicker.jar file.




Version:
  
$Date$   $Revision$
Author:
  
Jai Evans, CIT, NIH; Peter Lemkin, LECB/NCI, Frederick, MD
See Also:
http://java.sun.com/products/java-media/jai/forDevelopers/jai-apidocs/, 
See the SUN license file for JAI at these web sites.

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

, Flicker Home Original: Date: 8-13-2003, Jai Evans.

Field Summary

private static boolean	ALWAYS Fixed value of true for DEBUGGING
boolean	blackIsZeroFlag Black is Zero flag
java.awt.image.ColorModel	cm
static int	count instance # of TiffLoader
int	dataType data type from sampleModel.getDataType() The types are defined as DataBuffer.TYPE_xxxx where xxxx is (BYTE, DOUBLE, FLOAT, INT, SHORT, UNDEFINED, USHORT)
private static boolean	dbugFlag debugging flag
ImageDecoder	decoder Tiff Image Decoder
java.lang.String	fatalMsg Msg why failed if not null
java.lang.String	fileName filename path of image file
float[]	gray2OD [FUTURE] grayscale to OD lookup table [0:maxGray-1] if supplied as additional TIFF tags.
java.awt.Image	img Image structure required for Flicker
boolean	isComponentCMflag set if has ComponentColorModel
boolean	isComponentSMflag set if has ComponentSampleModel
boolean	isMultiplePixelPackedSMflag set if has a MultiplePixelPackedSampleModel
boolean	isPackedCMflag set if PackedColorModel
boolean	isPackedFlag set if pixel can be packed into a byte array
boolean	isRGBcolorImageFlag set if this is a RGB color image
boolean	isSinglePixelPackedSMflag set if has a SinglePixelPackedSampleModel
int	maxGray maximum gray value
int	minX X upper left hand corner of image origin
int	minY Y upper left hand corner of image origin
int	nBands # of samples/pixel
int	nBitsPerPixel # bits/pixel is sampleModel.sampleSize[0]
int	nCols # of columns in the image
private static boolean	NEVER Fixed value of false for DEBUGGING
int	nPixels # of pixels/image (is nRows*nCols)
int	nRows # of rows in the image
int	numDataElements # raster DataBuffer data elements/pixel
int	numPages # of TIFF pages
PixelAccessor[]	pi List of PixelAccessors from the RenderedImages'
private int[]	pixels image of size nRows of nCols pixels.
java.awt.image.Raster	ras Raster image read
java.awt.image.RenderedImage[]	ri List of Rendered images that was read in the tiff file
java.awt.image.SampleModel	sampleModel Tiff sample model name
int[]	sampleSizes bits/pixel is sample sizes [0:nBands-1] from sampleModel.getSampleSize()
boolean	useLogInputFlag "Use log of pixels if > 8-bits grayscale image"

Constructor Summary

TiffLoader()
TiffLoader() - constructor

TiffLoader(boolean flag)
TiffLoader() - constructor where set the debug flag

Method Summary

java.lang.String	doTiffLoad(java.lang.String path, boolean checkCacheFlag) doTiffLoad() - load the image and array grab of TIFF files
java.awt.Image	getImage() getImage() - get pixels from the raster
int	getNbrRGBpixels(int[] pixels, int nPixels) getNbrRGBpixels() - test if red==green==blue for all pixels
int[]	getTiffPixels(java.awt.image.Raster r, boolean checkCacheFlag) getTiffPixels() - get pixels from the raster
void	getTiffProperties(java.awt.image.Raster r) getTiffProperties() - get properties of the Tiff image
static void	main(java.lang.String[] args) main() - test loader.
java.awt.image.RenderedImage[]	readTiff(java.lang.String fileName) readTiff() - read a tiff image file
void	setDbugFlag(boolean flag) setDbugFlag() - flag
void	setUseLogFlag(boolean flag) setUseLogFlag() - flag to set the log flag This is used if the data has more than 8-bits of grayscale so the data is transformed by the log over the range of 255*log(10**nBits-1) to 0
java.lang.String	toString() toString() - return string representation of this instance

Methods inherited from class java.lang.Object

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

Field Detail

ALWAYS

private static boolean ALWAYS

Fixed value of true for DEBUGGING

NEVER

private static boolean NEVER

Fixed value of false for DEBUGGING

dbugFlag

private static boolean dbugFlag

debugging flag

count

public static int count

instance # of TiffLoader

fileName

public java.lang.String fileName

filename path of image file

sampleModel

public java.awt.image.SampleModel sampleModel

Tiff sample model name

ri

public java.awt.image.RenderedImage[] ri

List of Rendered images that was read in the tiff file

pi

public PixelAccessor[] pi

List of PixelAccessors from the RenderedImages'

ras

public java.awt.image.Raster ras

Raster image read

decoder

public ImageDecoder decoder

Tiff Image Decoder

cm

public java.awt.image.ColorModel cm

nRows

public int nRows

# of rows in the image

nCols

public int nCols

# of columns in the image

minX

public int minX

X upper left hand corner of image origin

minY

public int minY

Y upper left hand corner of image origin

nBands

public int nBands

# of samples/pixel

numPages

public int numPages

# of TIFF pages

numDataElements

public int numDataElements

# raster DataBuffer data elements/pixel

pixels

private int[] pixels

image of size nRows of nCols pixels. This is either 8-bit, 16-bit, 24-bit RGB, etc. If the data is 8-bits, 12-bits or 16-bits then the (R,G,B) channels of the pixels[] array data are scaled to 8-bits and are set to be the same. [TODO] If the image is 24-bit (R,G,B) or an index-colormap 8-bit RGB, then set the (R,G,B) channels separately to preserve the colors.

img

public java.awt.Image img

Image structure required for Flicker

dataType

public int dataType

data type from sampleModel.getDataType() The types are defined as DataBuffer.TYPE_xxxx where xxxx is (BYTE, DOUBLE, FLOAT, INT, SHORT, UNDEFINED, USHORT)

sampleSizes

public int[] sampleSizes

bits/pixel is sample sizes [0:nBands-1] from sampleModel.getSampleSize()

isPackedFlag

public boolean isPackedFlag

set if pixel can be packed into a byte array

isPackedCMflag

public boolean isPackedCMflag

set if PackedColorModel

isComponentCMflag

public boolean isComponentCMflag

set if has ComponentColorModel

isComponentSMflag

public boolean isComponentSMflag

set if has ComponentSampleModel

isSinglePixelPackedSMflag

public boolean isSinglePixelPackedSMflag

set if has a SinglePixelPackedSampleModel

isMultiplePixelPackedSMflag

public boolean isMultiplePixelPackedSMflag

set if has a MultiplePixelPackedSampleModel

nBitsPerPixel

public int nBitsPerPixel

# bits/pixel is sampleModel.sampleSize[0]

nPixels

public int nPixels

# of pixels/image (is nRows*nCols)

blackIsZeroFlag

public boolean blackIsZeroFlag

Black is Zero flag

isRGBcolorImageFlag

public boolean isRGBcolorImageFlag

set if this is a RGB color image

gray2OD

public float[] gray2OD

[FUTURE] grayscale to OD lookup table [0:maxGray-1] if supplied as additional TIFF tags. Format specific....

maxGray

public int maxGray

maximum gray value

useLogInputFlag

public boolean useLogInputFlag

"Use log of pixels if > 8-bits grayscale image"

fatalMsg

public java.lang.String fatalMsg

Msg why failed if not null

Constructor Detail

TiffLoader

public TiffLoader()

TiffLoader() - constructor

TiffLoader

public TiffLoader(boolean flag)

TiffLoader() - constructor where set the debug flag

Method Detail

setDbugFlag

public void setDbugFlag(boolean flag)

setDbugFlag() - flag

setUseLogFlag

public void setUseLogFlag(boolean flag)

setUseLogFlag() - flag to set the log flag This is used if the data has more than 8-bits of grayscale so the data is transformed by the log over the range of 255*log(10**nBits-1) to 0

readTiff

public java.awt.image.RenderedImage[] readTiff(java.lang.String fileName)
                                        throws java.io.IOException

readTiff() - read a tiff image file

Parameters:

fileName - is the file to be read

Returns:

image rendered raster instance that may be an array of images

Throws:

java.io.IOException

getTiffPixels

public int[] getTiffPixels(java.awt.image.Raster r,
                           boolean checkCacheFlag)

getTiffPixels() - get pixels from the raster

Parameters:

r - is the image raster instance

checkCacheFlag - to see if pixels data exists, then return it

Returns:

1D array encoding a raster 2D image of size width X height.

getTiffProperties

public void getTiffProperties(java.awt.image.Raster r)

getTiffProperties() - get properties of the Tiff image

Parameters:

r - is the image raster instance

getImage

public java.awt.Image getImage()

getImage() - get pixels from the raster

Parameters:

r - is the image raster instance

Returns:

1D array encoding a raster 2D image of size width X height.

doTiffLoad

public java.lang.String doTiffLoad(java.lang.String path,
                                   boolean checkCacheFlag)

doTiffLoad() - load the image and array grab of TIFF files

Parameters:

path - of the image

checkCacheFlag - to see if pixels data exists, then return it

Returns:

null if succeed, else error message

getNbrRGBpixels

public int getNbrRGBpixels(int[] pixels,
                           int nPixels)

getNbrRGBpixels() - test if red==green==blue for all pixels

Returns:

# of color pixels. 0 means gray value image

toString

public java.lang.String toString()

toString() - return string representation of this instance

Overrides:

toString in class java.lang.Object

Returns:

string instance

main

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

main() - test loader. Replace hard code here with local path for testing