| ImageProcessor.java |
package ij.process;
import java.util.*;
import java.awt.*;
import java.awt.image.*;
import java.awt.geom.Rectangle2D;
import java.awt.font.GlyphVector;
import ij.gui.*;
import ij.util.*;
import ij.plugin.filter.GaussianBlur;
import ij.plugin.Binner;
import ij.plugin.Colors;
import ij.process.AutoThresholder.Method;
import ij.Prefs;
import ij.measure.Measurements;
/**
This abstract class is the superclass for classes that process
the four data types (byte, short, float and RGB) supported by ImageJ.
An ImageProcessor contains the pixel data of a 2D image and
some basic methods to manipulate it.
@see ByteProcessor
@see ShortProcessor
@see FloatProcessor
@see ColorProcessor
@see ij.ImagePlus
@see ij.ImageStack
*/
public abstract class ImageProcessor implements Cloneable {
/** Value of pixels included in masks. */
public static final int BLACK = 0xFF000000;
/** Value returned by getMinThreshold() when thresholding is not enabled. */
public static final double NO_THRESHOLD = -808080.0;
/** Left justify text. */
public static final int LEFT_JUSTIFY = 0;
/** Center justify text. */
public static final int CENTER_JUSTIFY = 1;
/** Right justify text. */
public static final int RIGHT_JUSTIFY = 2;
/** Isodata thresholding method */
public static final int ISODATA = 0;
/** Modified isodata method used in Image/Adjust/Threshold tool */
public static final int ISODATA2 = 1;
/** Composite image projection modes. */
public static final int UPDATE_RED=1, UPDATE_GREEN=2, UPDATE_BLUE=3, SET_FIRST_CHANNEL=4,
SUM_PROJECTION=5, MAX_PROJECTION=6, MIN_PROJECTION=7, INVERT_PROJECTION=8;
/** Interpolation methods */
public static final int NEAREST_NEIGHBOR=0, NONE=0, BILINEAR=1, BICUBIC=2;
public static final int BLUR_MORE=0, FIND_EDGES=1, MEDIAN_FILTER=2, MIN=3, MAX=4, CONVOLVE=5;
static public final int RED_LUT=0, BLACK_AND_WHITE_LUT=1, NO_LUT_UPDATE=2, OVER_UNDER_LUT=3;
static final int INVERT=0, FILL=1, ADD=2, MULT=3, AND=4, OR=5,
XOR=6, GAMMA=7, LOG=8, MINIMUM=9, MAXIMUM=10, SQR=11, SQRT=12, EXP=13, ABS=14, SET=15;
static final String WRONG_LENGTH = "width*height!=pixels.length";
int fgColor = 0;
protected int lineWidth = 1;
protected int cx, cy; //current drawing coordinates
protected Font font = ij.IJ.font12;
protected FontMetrics fontMetrics;
protected boolean antialiasedText;
protected boolean boldFont;
private static String[] interpolationMethods;
// Over/Under tresholding colors
private static int overRed, overGreen=255, overBlue;
private static int underRed, underGreen, underBlue=255;
private static boolean useBicubic;
private int sliceNumber;
private Overlay overlay;
private boolean noReset;
ProgressBar progressBar;
protected int width, snapshotWidth;
protected int height, snapshotHeight;
protected int roiX, roiY, roiWidth, roiHeight;
protected int xMin, xMax, yMin, yMax;
boolean snapshotCopyMode;
ImageProcessor mask;
protected ColorModel baseCM; // base color model
protected ColorModel cm;
protected byte[] rLUT1, gLUT1, bLUT1; // base LUT
protected byte[] rLUT2, gLUT2, bLUT2; // LUT as modified by setMinAndMax and setThreshold
protected boolean interpolate; // replaced by interpolationMethod
protected int interpolationMethod = NONE;
protected double minThreshold=NO_THRESHOLD, maxThreshold=NO_THRESHOLD;
protected int histogramSize = 256;
protected double histogramMin, histogramMax;
protected float[] cTable;
protected boolean lutAnimation;
protected MemoryImageSource source; //unused
protected Image img;
protected boolean newPixels; // unused
protected Color drawingColor = Color.black;
protected int clipXMin, clipXMax, clipYMin, clipYMax; // clip rect used by drawTo, drawLine, drawDot and drawPixel
protected int justification = LEFT_JUSTIFY;
protected int lutUpdateMode;
protected WritableRaster raster;
protected BufferedImage image;
protected BufferedImage fmImage;
protected Graphics2D fmGraphics;
protected ColorModel cm2;
protected SampleModel sampleModel;
protected static IndexColorModel defaultColorModel;
protected boolean minMaxSet;
protected static double seed = Double.NaN;
protected static Random rnd;
protected boolean fillValueSet;
protected void showProgress(double percentDone) {
if (progressBar!=null)
progressBar.show(percentDone);
}
/** @deprecated */
protected void hideProgress() {
showProgress(1.0);
}
/** Returns the width of this image in pixels. */
public int getWidth() {
return width;
}
/** Returns the height of this image in pixels. */
public int getHeight() {
return height;
}
/** Returns the bit depth, 8, 16, 24 (RGB) or 32. RGB images actually use 32 bits per pixel. */
public int getBitDepth() {
Object pixels = getPixels();
if (pixels==null)
return 0;
else if (pixels instanceof byte[])
return 8;
else if (pixels instanceof short[])
return 16;
else if (pixels instanceof int[])
return 24;
else if (pixels instanceof float[])
return 32;
else
return 0;
}
/** Returns this processor's color model. For non-RGB processors,
this is the base lookup table (LUT), not the one that may have
been modified by setMinAndMax() or setThreshold(). */
public ColorModel getColorModel() {
if (cm==null)
makeDefaultColorModel();
if (baseCM!=null)
return baseCM;
else
return cm;
}
private IndexColorModel getIndexColorModel() {
ColorModel cm2 = baseCM;
if (cm2==null)
cm2 = cm;
if (cm2!=null && (cm2 instanceof IndexColorModel))
return (IndexColorModel)cm2;
else
return null;
}
/** Returns the current color model, which may have
been modified by setMinAndMax() or setThreshold(). */
public ColorModel getCurrentColorModel() {
if (cm==null) makeDefaultColorModel();
return cm;
}
/** Sets the color model. Must be an IndexColorModel (aka LUT)
for all processors except the ColorProcessor. */
public void setColorModel(ColorModel cm) {
if (cm!=null && !(cm instanceof IndexColorModel))
throw new IllegalArgumentException("IndexColorModel required");
if (cm!=null && cm instanceof LUT)
cm = ((LUT)cm).getColorModel();
this.cm = cm;
baseCM = null;
rLUT1 = rLUT2 = null;
inversionTested = false;
minThreshold = NO_THRESHOLD;
}
public LUT getLut() {
ColorModel cm2 = getColorModel();
if (cm2!=null && (cm2 instanceof IndexColorModel))
return new LUT((IndexColorModel)cm2, getMin(), getMax());
else
return null;
}
public void setLut(LUT lut) {
if (lut==null)
setColorModel(null);
else {
setColorModel(lut.getColorModel());
if (lut.min!=0.0 || lut.max!=0.0)
setMinAndMax(lut.min, lut.max);
}
}
protected void makeDefaultColorModel() {
cm = getDefaultColorModel();
}
/** Inverts the values in this image's LUT (indexed color model).
Does nothing if this is a ColorProcessor. */
public void invertLut() {
IndexColorModel icm = (IndexColorModel)getColorModel();
int mapSize = icm.getMapSize();
byte[] reds = new byte[mapSize];
byte[] greens = new byte[mapSize];
byte[] blues = new byte[mapSize];
byte[] reds2 = new byte[mapSize];
byte[] greens2 = new byte[mapSize];
byte[] blues2 = new byte[mapSize];
icm.getReds(reds);
icm.getGreens(greens);
icm.getBlues(blues);
for (int i=0; i<mapSize; i++) {
reds2[i] = (byte)(reds[mapSize-i-1]&255);
greens2[i] = (byte)(greens[mapSize-i-1]&255);
blues2[i] = (byte)(blues[mapSize-i-1]&255);
}
ColorModel cm = new IndexColorModel(8, mapSize, reds2, greens2, blues2);
double min=getMin(), max=getMax();
setColorModel(cm);
setMinAndMax(min, max);
}
/** Returns the LUT index that's the best match for this color. */
public int getBestIndex(Color c) {
IndexColorModel icm;
if (cm==null)
makeDefaultColorModel();
if (minThreshold!=NO_THRESHOLD) {
double saveMin = getMinThreshold();
double saveMax = getMaxThreshold();
resetThreshold();
icm = (IndexColorModel)cm;
setThreshold(saveMin, saveMax, lutUpdateMode);
} else
icm = (IndexColorModel)cm;
int mapSize = icm.getMapSize();
byte[] rLUT = new byte[mapSize];
byte[] gLUT = new byte[mapSize];
byte[] bLUT = new byte[mapSize];
icm.getReds(rLUT);
icm.getGreens(gLUT);
icm.getBlues(bLUT);
int minDistance = Integer.MAX_VALUE;
int distance;
int minIndex = 0;
int r1 = c.getRed();
int g1 = c.getGreen();
int b1 = c.getBlue();
if (!(r1==g1&&g1==b1&&r1==b1) && icm==defaultColorModel) {
double[] w = ColorProcessor.getWeightingFactors();
r1 = (int)Math.round(3*r1*w[0]);
g1 = (int)Math.round(3*g1*w[1]);
b1 = (int)Math.round(3*b1*w[2]);
}
int r2,b2,g2;
for (int i=0; i<mapSize; i++) {
r2 = rLUT[i]&0xff; g2 = gLUT[i]&0xff; b2 = bLUT[i]&0xff;
distance = (r2-r1)*(r2-r1)+(g2-g1)*(g2-g1)+(b2-b1)*(b2-b1);
//ij.IJ.log(" "+i+" "+minIndex+" "+distance+" "+(rLUT[i]&255)+" "+(gLUT[i]&255)+" "+(bLUT[i]&255));
if (distance<minDistance) {
minDistance = distance;
minIndex = i;
}
if (minDistance==0.0)
break;
}
return minIndex;
}
protected boolean inversionTested = false;
protected boolean invertedLut;
/** Returns true if this image uses an inverting LUT
that displays zero as white and 255 as black. */
public boolean isInvertedLut() {
if (inversionTested)
return invertedLut;
IndexColorModel icm = getIndexColorModel();
if (icm==null)
return false;
boolean hasAscendingStep = false;
int v1, v2;
for (int i=1; i<255; i++) {
v1 = icm.getRed(i-1)+icm.getGreen(i-1)+icm.getBlue(i-1);
v2 = icm.getRed(i)+icm.getGreen(i)+icm.getBlue(i);
if (v1<v2) {
hasAscendingStep = true;
break;
}
}
invertedLut = !hasAscendingStep;
inversionTested = true;
return invertedLut;
}
/** Returns 'true' if this is an image with a grayscale LUT or an
* RGB image with identical red, green and blue channels.
*/
public boolean isGrayscale() {
return !isColorLut();
}
/** Returns true if this image uses a color LUT. */
public boolean isColorLut() {
IndexColorModel icm = getIndexColorModel();
if (icm==null)
return false;
int mapSize = icm.getMapSize();
byte[] reds = new byte[mapSize];
byte[] greens = new byte[mapSize];
byte[] blues = new byte[mapSize];
icm.getReds(reds);
icm.getGreens(greens);
icm.getBlues(blues);
boolean isColor = false;
for (int i=0; i<mapSize; i++) {
if ((reds[i] != greens[i]) || (greens[i] != blues[i])) {
isColor = true;
break;
}
}
return isColor;
}
/** Returns true if this image uses a pseudocolor or grayscale LUT,
in other words, is this an image that can be filtered. */
public boolean isPseudoColorLut() {
IndexColorModel icm = getIndexColorModel();
if (icm==null)
return false;
if (getMinThreshold()!=NO_THRESHOLD)
return true;
int mapSize = icm.getMapSize();
if (mapSize!=256)
return false;
byte[] reds = new byte[mapSize];
byte[] greens = new byte[mapSize];
byte[] blues = new byte[mapSize];
icm.getReds(reds);
icm.getGreens(greens);
icm.getBlues(blues);
int r, g, b, d;
int r2=reds[0]&255, g2=greens[0]&255, b2=blues[0]&255;
double sum=0.0, sum2=0.0;
for (int i=0; i<mapSize; i++) {
r=reds[i]&255; g=greens[i]&255; b=blues[i]&255;
d=r-r2; sum+=d; sum2+=d*d;
d=g-g2; sum+=d; sum2+=d*d;
d=b-b2; sum+=d; sum2+=d*d;
r2=r; g2=g; b2=b;
}
double stdDev = (768*sum2-sum*sum)/768.0;
if (stdDev>0.0)
stdDev = Math.sqrt(stdDev/(767.0));
else
stdDev = 0.0;
boolean isPseudoColor = stdDev<20.0;
if ((int)stdDev==67) isPseudoColor = true; // "3-3-2 RGB" LUT
return isPseudoColor;
}
/** Returns true if the image is using the default grayscale LUT. */
public boolean isDefaultLut() {
if (cm==null)
makeDefaultColorModel();
IndexColorModel icm = getIndexColorModel();
if (icm==null)
return false;
int mapSize = icm.getMapSize();
if (mapSize!=256)
return false;
byte[] reds = new byte[mapSize];
byte[] greens = new byte[mapSize];
byte[] blues = new byte[mapSize];
icm.getReds(reds);
icm.getGreens(greens);
icm.getBlues(blues);
boolean isDefault = true;
for (int i=0; i<mapSize; i++) {
if ((reds[i]&255)!=i || (greens[i]&255)!=i || (blues[i]&255)!=i) {
isDefault = false;
break;
}
}
return isDefault;
}
/** Sets the default fill/draw value to the pixel
value closest to the specified color. */
public abstract void setColor(Color color);
/** Sets the fill/draw color, where 'color' is
* "white", "black", "blue", etc., or a hex value
* like "#ff0000".
*/
public void setColor(String color) {
setColor(Colors.decode(color, Color.white));
}
/** Sets the background fill/draw color. */
public void setBackgroundColor(Color color) {
}
/** Sets the default fill/draw value. */
public void setColor(int value) {
setValue(value);
}
/** Sets the default fill/draw value. */
public void setColor(double value) {
setValue(value);
}
/** Sets the default fill/draw value. */
public abstract void setValue(double value);
/** Returns the default fill/draw value. */
public abstract double getForegroundValue();
/** Returns 'true' if the fill/draw value has been set. */
public boolean fillValueSet() {
return fillValueSet;
}
/** Sets the background fill value used by the rotate() and scale() methods. */
public abstract void setBackgroundValue(double value);
/** Returns the background fill value. */
public abstract double getBackgroundValue();
/** Sets the global (Color Picker) foreground color
* as the fill/draw color.
* @see ij.gui.Toolbar#setForegroundColor(Color)
* @see ij.gui.Toolbar#setForegroundValue(double)
*/
public void setGlobalForegroundColor() {
double value = Toolbar.getForegroundValue();
if (Double.isNaN(value))
setColor(Toolbar.getForegroundColor());
else
setValue(value);
}
/** Sets the global (Color Picker) background color
* as the fill/draw color.
* @see ij.gui.Toolbar#setBackgroundColor(Color)
* @see ij.gui.Toolbar#setBackgroundValue(double)
*/
public void setGlobalBackgroundColor() {
double value = Toolbar.getBackgroundValue();
if (Double.isNaN(value))
setColor(Toolbar.getBackgroundColor());
else
setValue(value);
}
/** Returns the smallest displayed pixel value. */
public abstract double getMin();
/** Returns the largest displayed pixel value. */
public abstract double getMax();
/** This image will be displayed by mapping pixel values in the
* range min-max to screen values in the range 0-255. For
* byte images, this mapping is done by updating the LUT. For
* short and float images, it's done by generating 8-bit AWT
* images. For RGB images, it's done by changing the pixel values.
* With signed 16-bit images, use IJ.setMinAndMax(imp,min,max).
* @see ij.IJ#setMinAndMax(ij.ImagePlus,double,double)
*/
public abstract void setMinAndMax(double min, double max);
/** For short and float images, recalculates the min and max
image values needed to correctly display the image. For
ByteProcessors, resets the LUT. */
public void resetMinAndMax() {}
/** Sets the lower and upper threshold levels using NO_LUT_UPDATE. */
public void setThreshold(double minThreshold, double maxThreshold) {
setThreshold(minThreshold, maxThreshold, NO_LUT_UPDATE);
}
/** Sets the lower and upper threshold levels. The 'lutUpdate' argument
can be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
Thresholding of RGB images is not supported. */
public void setThreshold(double minThreshold, double maxThreshold, int lutUpdate) {
//ij.IJ.log("setThreshold: "+" "+minThreshold+" "+maxThreshold+" "+lutUpdate);
if (this instanceof ColorProcessor)
return;
this.minThreshold = minThreshold;
this.maxThreshold = maxThreshold;
lutUpdateMode = lutUpdate;
if (minThreshold==NO_THRESHOLD) {
resetThreshold();
return;
}
if (lutUpdate==NO_LUT_UPDATE)
return;
if (rLUT1==null) {
if (cm==null)
makeDefaultColorModel();
baseCM = cm;
IndexColorModel m = (IndexColorModel)cm;
rLUT1 = new byte[256]; gLUT1 = new byte[256]; bLUT1 = new byte[256];
m.getReds(rLUT1); m.getGreens(gLUT1); m.getBlues(bLUT1);
rLUT2 = new byte[256]; gLUT2 = new byte[256]; bLUT2 = new byte[256];
}
int t1 = (int)minThreshold;
int t2 = (int)maxThreshold;
int index;
if (lutUpdate==RED_LUT)
for (int i=0; i<256; i++) {
if (i>=t1 && i<=t2) {
rLUT2[i] = (byte)255;
gLUT2[i] = (byte)0;
bLUT2[i] = (byte)0;
} else {
rLUT2[i] = rLUT1[i];
gLUT2[i] = gLUT1[i];
bLUT2[i] = bLUT1[i];
}
}
else if (lutUpdate==BLACK_AND_WHITE_LUT) {
// updated in v1.43i by Gabriel Lindini to use blackBackground setting
byte foreground = Prefs.blackBackground?(byte)255:(byte)0;
byte background = (byte)(255 - foreground);
for (int i=0; i<256; i++) {
if (i>=t1 && i<=t2) {
rLUT2[i] = foreground;
gLUT2[i] = foreground;
bLUT2[i] = foreground;
} else {
rLUT2[i] = background;
gLUT2[i] =background;
bLUT2[i] =background;
}
}
} else {
for (int i=0; i<256; i++) {
if (i>=t1 && i<=t2) {
rLUT2[i] = rLUT1[i];
gLUT2[i] = gLUT1[i];
bLUT2[i] = bLUT1[i];
} else if (i>t2) {
rLUT2[i] = (byte)overRed;
gLUT2[i] = (byte)overGreen;
bLUT2[i] = (byte)overBlue;
} else {
rLUT2[i] = (byte)underRed;
gLUT2[i] = (byte)underGreen;
bLUT2[i] = (byte)underBlue;
}
}
}
cm = new IndexColorModel(8, 256, rLUT2, gLUT2, bLUT2);
}
/** Automatically sets the lower and upper threshold levels, where 'method'
* must be "Default", "Huang", "Intermodes", "IsoData", "IJ_IsoData", "Li",
* "MaxEntropy", "Mean", "MinError", "Minimum", "Moments", "Otsu",
* "Percentile", "RenyiEntropy", "Shanbhag", "Triangle" or "Yen". The
* 'method' string may also include the keywords 'dark' (dark background)
* 'red' (red LUT, the default), 'b&w' (black and white LUT), 'over/under' (over/under LUT) or
* 'no-lut' (no LUT changes), for example "Huang dark b&w". The display range
* of 16-bit and 32-bit images is not reset if the 'method' string contains 'no-reset'.
* @see ImageProcessor#resetThreshold
* @see ImageProcessor#setThreshold
* @see ImageProcessor#createMask
*/
public void setAutoThreshold(String method) {
if (method==null)
throw new IllegalArgumentException("Null method");
boolean darkBackground = method.contains("dark");
noReset = method.contains("no-reset");
int lut = RED_LUT;
if (method.contains("b&w"))
lut = BLACK_AND_WHITE_LUT;
if (method.contains("over"))
lut = OVER_UNDER_LUT;
if (method.contains("no-lut"))
lut = NO_LUT_UPDATE;
int index = method.indexOf(" ");
if (index!=-1)
method = method.substring(0, index);
setAutoThreshold(method, darkBackground, lut);
noReset = false;
}
public void setAutoThreshold(String mString, boolean darkBackground, int lutUpdate) {
Method m = null;
try {
m = Method.valueOf(Method.class, mString);
} catch(Exception e) {
m = null;
}
if (m==null)
throw new IllegalArgumentException("Invalid method (\""+mString+"\")");
setAutoThreshold(m, darkBackground, lutUpdate);
}
public void setAutoThreshold(Method method, boolean darkBackground) {
setAutoThreshold(method, darkBackground, RED_LUT);
}
public void setAutoThreshold(Method method, boolean darkBackground, int lutUpdate) {
if (method==null || (this instanceof ColorProcessor))
return;
double min=0.0, max=0.0;
boolean notByteData = !(this instanceof ByteProcessor);
ImageProcessor ip2 = this;
if (notByteData) {
ImageProcessor mask = ip2.getMask();
Rectangle rect = ip2.getRoi();
if (!noReset || lutUpdate==OVER_UNDER_LUT)
ip2.resetMinAndMax();
noReset = false;
min = ip2.getMin(); max = ip2.getMax();
ip2 = ip2.convertToByte(true);
ip2.setMask(mask);
ip2.setRoi(rect);
}
ImageStatistics stats = ip2.getStats();
AutoThresholder thresholder = new AutoThresholder();
int threshold = thresholder.getThreshold(method, stats.histogram);
double lower, upper;
if (darkBackground) {
if (isInvertedLut())
{lower=0.0; upper=threshold;}
else
{lower=threshold+1; upper=255.0;}
} else {
if (isInvertedLut())
{lower=threshold+1; upper=255.0;}
else
{lower=0.0; upper=threshold;}
}
if (lower>255) lower = 255;
scaleAndSetThreshold(lower, upper, lutUpdate);
}
/** Automatically sets the lower and upper threshold levels, where 'method'
must be ISODATA or ISODATA2 and 'lutUpdate' must be RED_LUT,
BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
*/
public void setAutoThreshold(int method, int lutUpdate) {
if (method<0 || method>ISODATA2)
throw new IllegalArgumentException("Invalid thresholding method");
if (this instanceof ColorProcessor)
return;
boolean notByteData = !(this instanceof ByteProcessor);
ImageProcessor ip2 = this;
if (notByteData) {
ImageProcessor mask = ip2.getMask();
Rectangle rect = ip2.getRoi();
resetMinAndMax();
ip2 = convertToByte(true);
ip2.setMask(mask);
ip2.setRoi(rect);
}
ImageStatistics stats = ip2.getStats();
int[] histogram = stats.histogram;
int originalModeCount = histogram[stats.mode];
if (method==ISODATA2) {
int maxCount2 = 0;
for (int i = 0; i<stats.nBins; i++) {
if ((histogram[i] > maxCount2) && (i!=stats.mode))
maxCount2 = histogram[i];
}
int hmax = stats.maxCount;
if ((hmax>(maxCount2 * 2)) && (maxCount2 != 0)) {
hmax = (int)(maxCount2 * 1.5);
histogram[stats.mode] = hmax;
}
}
int threshold = ip2.getAutoThreshold(stats.histogram);
histogram[stats.mode] = originalModeCount;
float[] hist = new float[256];
for (int i=0; i<256; i++)
hist[i] = stats.histogram[i];
FloatProcessor fp = new FloatProcessor(256, 1, hist, null);
GaussianBlur gb = new GaussianBlur();
gb.blur1Direction(fp, 2.0, 0.01, true, 0);
float maxCount=0f, sum=0f, mean, count;
int mode = 0;
for (int i=0; i<256; i++) {
count = hist[i];
sum += count;
if (count>maxCount) {
maxCount = count;
mode = i;
}
}
double avg = sum/256.0;
double lower, upper;
if (maxCount/avg>1.5) {
if ((stats.max-mode)>(mode-stats.min))
{lower=threshold; upper=255.0;}
else
{lower=0.0; upper=threshold;}
} else {
if (isInvertedLut())
{lower=threshold; upper=255.0;}
else
{lower=0.0; upper=threshold;}
}
scaleAndSetThreshold(lower, upper, lutUpdate);
}
/** Set the threshold using a 0-255 range. For 16-bit and 32-bit images,
* this range is taken as relative with respect to the range between the
* current display min and max, but lower=0 and upper=255 are set to the
* full-range limits of 16-bit images and -/+1e30 for float images.
*/
public void scaleAndSetThreshold(double lower, double upper, int lutUpdate) {
int bitDepth = getBitDepth();
if (bitDepth!=8 && lower!=NO_THRESHOLD) {
double min = getMin();
double max = getMax();
if (max>min) {
if (lower==0.0) {
if (bitDepth==32)
lower = Math.min(min, -1e30); // can't set to -Float.MAX_VALUE; causes FloodFiller.particleAnalyzerFill to hang;
} else
lower = min + (lower/255.0)*(max-min);
if (upper==255.0) {
if (bitDepth==16)
upper = 65535;
else if (bitDepth==32)
upper = Math.max(max, 1e30);
} else
upper = min + (upper/255.0)*(max-min);
} else
lower = upper = min;
}
setThreshold(lower, upper, lutUpdate);
}
/** Disables thresholding. */
public void resetThreshold() {
minThreshold = NO_THRESHOLD;
if (baseCM!=null) {
cm = baseCM;
baseCM = null;
}
rLUT1 = rLUT2 = null;
inversionTested = false;
}
/** Returns the lower threshold level. Returns NO_THRESHOLD
if thresholding is not enabled. */
public double getMinThreshold() {
return minThreshold;
}
/** Returns the upper threshold level. */
public double getMaxThreshold() {
return maxThreshold;
}
/** Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT,
OVER_UNDER_LUT or NO_LUT_UPDATE. */
public int getLutUpdateMode() {
return lutUpdateMode;
}
/* Sets the threshold levels (non-visible) of an 8-bit mask based on
the state of Prefs.blackBackground and isInvertedLut().
@see ImageProcessor#resetBinaryThreshold
*/
public void setBinaryThreshold() {
//ij.IJ.log("setMaskThreshold1");
if (!(this instanceof ByteProcessor)) return;
double t1=255.0, t2=255.0;
boolean invertedLut = isInvertedLut();
if ((invertedLut&&ij.Prefs.blackBackground) || (!invertedLut&&!ij.Prefs.blackBackground)) {
t1 = 0.0;
t2 = 0.0;
}
//ij.IJ.log("setMaskThreshold2 "+t1+" "+t2);
setThreshold(t1, t2, ImageProcessor.NO_LUT_UPDATE);
}
/** Resets the threshold if minThreshold=maxThreshold and lutUpdateMode=NO_LUT_UPDATE.
This removes the invisible threshold set by the MakeBinary and Convert to Mask commands.
@see ImageProcessor#setBinaryThreshold
*/
public void resetBinaryThreshold() {
if (minThreshold==maxThreshold && lutUpdateMode==NO_LUT_UPDATE)
resetThreshold();
}
/** Defines a rectangular region of interest and sets the mask
to null if this ROI is not the same size as the previous one.
@see ImageProcessor#resetRoi
*/
public void setRoi(Rectangle roi) {
if (roi==null)
resetRoi();
else
setRoi(roi.x, roi.y, roi.width, roi.height);
}
/** Defines a rectangular region of interest and sets the mask to
null if this ROI is not the same size as the previous one.
@see ImageProcessor#resetRoi
*/
public void setRoi(int x, int y, int rwidth, int rheight) {
if (x<0 || y<0 || x+rwidth>width || y+rheight>height) {
//find intersection of roi and this image
Rectangle r1 = new Rectangle(x, y, rwidth, rheight);
Rectangle r2 = r1.intersection(new Rectangle(0, 0, width, height));
if (r2.width<=0 || r2.height<=0) {
roiX=0; roiY=0; roiWidth=0; roiHeight=0;
xMin=0; xMax=0; yMin=0; yMax=0;
mask=null;
return;
}
if (mask!=null && mask.getWidth()==rwidth && mask.getHeight()==rheight) {
Rectangle r3 = new Rectangle(0, 0, r2.width, r2.height);
if (x<0) r3.x = -x;
if (y<0) r3.y = -y;
mask.setRoi(r3);
if (mask!=null)
mask = mask.crop();
}
roiX=r2.x; roiY=r2.y; roiWidth=r2.width; roiHeight=r2.height;
} else {
roiX=x; roiY=y; roiWidth=rwidth; roiHeight=rheight;
}
if (mask!=null && (mask.getWidth()!=roiWidth||mask.getHeight()!=roiHeight))
mask = null;
//setup limits for 3x3 filters
xMin = Math.max(roiX, 1);
xMax = Math.min(roiX + roiWidth - 1, width - 2);
yMin = Math.max(roiY, 1);
yMax = Math.min(roiY + roiHeight - 1, height - 2);
}
/** Defines a non-rectangular region of interest that will consist of a
rectangular ROI and a mask. After processing, call <code>reset(mask)</code>
to restore non-masked pixels. Here is an example:
<pre>
ip.setRoi(new OvalRoi(50, 50, 100, 50));
ip.fill();
ip.reset(ip.getMask());
</pre>
The example assumes <code>snapshot()</code> has been called, which is the case
for code executed in the <code>run()</code> method of plugins that implement the
<code>PlugInFilter</code> interface.
@see ij.ImagePlus#getRoi
*/
public void setRoi(Roi roi) {
if (roi==null)
resetRoi();
else {
if ((roi instanceof PointRoi) && roi.size()==1) {
setMask(null);
Polygon p = roi.getPolygon();
setRoi(p.xpoints[0], p.ypoints[0], 1, 1);
} else {
setMask(roi.getMask());
setRoi(roi.getBounds());
}
}
}
/** Defines a polygonal region of interest that will consist of a
rectangular ROI and a mask. After processing, call <code>reset(mask)</code>
to restore non-masked pixels. Here is an example:
<pre>
Polygon p = new Polygon();
p.addPoint(50, 0); p.addPoint(100, 100); p.addPoint(0, 100);
ip.setRoi(triangle);
ip.invert();
ip.reset(ip.getMask());
</pre>
The example assumes <code>snapshot()</code> has been called, which is the case
for code executed in the <code>run()</code> method of plugins that implement the
<code>PlugInFilter</code> interface.
@see ij.gui.Roi#getPolygon
@see ImageProcessor#drawPolygon
@see ImageProcessor#fillPolygon
*/
public void setRoi(Polygon roi) {
if (roi==null)
{resetRoi(); return;}
Rectangle bounds = roi.getBounds();
for (int i=0; i<roi.npoints; i++) {
roi.xpoints[i] -= bounds.x;
roi.ypoints[i] -= bounds.y;
}
PolygonFiller pf = new PolygonFiller();
pf.setPolygon(roi.xpoints, roi.ypoints, roi.npoints);
ImageProcessor mask = pf.getMask(bounds.width, bounds.height);
setMask(mask);
setRoi(bounds);
for (int i=0; i<roi.npoints; i++) {
roi.xpoints[i] += bounds.x;
roi.ypoints[i] += bounds.y;
}
}
/** Sets the ROI (Region of Interest) and clipping rectangle to the entire image. */
public void resetRoi() {
roiX=0; roiY=0; roiWidth=width; roiHeight=height;
xMin=1; xMax=width-2; yMin=1; yMax=height-2;
mask=null;
clipXMin=0; clipXMax=width-1; clipYMin=0; clipYMax=height-1;
}
/** Returns a Rectangle that represents the current
region of interest. */
public Rectangle getRoi() {
return new Rectangle(roiX, roiY, roiWidth, roiHeight);
}
/** Defines a byte mask that limits processing to an
irregular ROI. Background pixels in the mask have
a value of zero. */
public void setMask(ImageProcessor mask) {
this.mask = mask;
}
/** For images with irregular ROIs, returns a mask, otherwise,
returns null. Pixels outside the mask have a value of zero. */
public ImageProcessor getMask() {
return mask;
}
/** Returns a reference to the mask pixel array, or null if there is no mask. */
public byte[] getMaskArray() {
return mask!=null?(byte[])mask.getPixels():null;
}
/** Assigns a progress bar to this processor. Set 'pb' to
null to disable the progress bar. */
public void setProgressBar(ProgressBar pb) {
progressBar = pb;
}
/** This method has been replaced by setInterpolationMethod(). */
public void setInterpolate(boolean interpolate) {
this.interpolate = interpolate;
if (interpolate)
interpolationMethod = useBicubic?BICUBIC:BILINEAR;
else
interpolationMethod = NONE;
}
/** Use this method to set the interpolation method (NONE,
BILINEAR or BICUBIC) used by scale(), resize() and rotate(). */
public void setInterpolationMethod(int method) {
if (method<NONE || method>BICUBIC)
throw new IllegalArgumentException("Invalid interpolation method");
interpolationMethod = method;
interpolate = method!=NONE?true:false;
}
/** Returns the current interpolation method (NONE, BILINEAR or BICUBIC). */
public int getInterpolationMethod() {
return interpolationMethod;
}
public static String[] getInterpolationMethods() {
if (interpolationMethods==null)
interpolationMethods = new String[] {"None", "Bilinear", "Bicubic"};
return interpolationMethods;
}
/** Returns the value of the interpolate field. */
public boolean getInterpolate() {
return interpolate;
}
/** @deprecated */
public boolean isKillable() {
return false;
}
private void process(int op, double value) {
double SCALE = 255.0/Math.log(255.0);
int v;
int[] lut = new int[256];
for (int i=0; i<256; i++) {
switch(op) {
case INVERT:
v = 255 - i;
break;
case FILL:
v = fgColor;
break;
case SET:
v = (int)value;
break;
case ADD:
v = i + (int)value;
break;
case MULT:
v = (int)Math.round(i * value);
break;
case AND:
v = i & (int)value;
break;
case OR:
v = i | (int)value;
break;
case XOR:
v = i ^ (int)value;
break;
case GAMMA:
v = (int)(Math.exp(Math.log(i/255.0)*value)*255.0);
break;
case LOG:
if (i==0)
v = 0;
else
v = (int)(Math.log(i) * SCALE);
break;
case EXP:
v = (int)(Math.exp(i/SCALE));
break;
case SQR:
v = i*i;
break;
case SQRT:
v = (int)Math.sqrt(i);
break;
case MINIMUM:
if (i<value)
v = (int)value;
else
v = i;
break;
case MAXIMUM:
if (i>value)
v = (int)value;
else
v = i;
break;
default:
v = i;
}
if (v < 0)
v = 0;
if (v > 255)
v = 255;
lut[i] = v;
}
applyTable(lut);
}
/**
* Returns an array containing the pixel values along the
* line starting at (x1,y1) and ending at (x2,y2). Pixel
* values are sampled using getInterpolatedValue(double,double)
* if interpolation is enabled or getPixelValue(int,int) if it is not.
* For byte and short images, returns calibrated values if a
* calibration table has been set using setCalibrationTable().
* The length of the returned array, minus one, is approximately
* equal to the length of the line.
* @see ImageProcessor#setInterpolate
* @see ImageProcessor#getPixelValue
* @see ImageProcessor#getInterpolatedValue
*/
public double[] getLine(double x1, double y1, double x2, double y2) {
double dx = x2-x1;
double dy = y2-y1;
int n = (int)Math.round(Math.sqrt(dx*dx + dy*dy));
double xinc = n>0?dx/n:0;
double yinc = n>0?dy/n:0;
if (!((xinc==0&&n==height) || (yinc==0&&n==width)))
n++;
double[] data = new double[n];
double rx = x1;
double ry = y1;
if (interpolate) {
for (int i=0; i<n; i++) {
data[i] = getInterpolatedValue(rx, ry);
rx += xinc;
ry += yinc;
}
} else {
for (int i=0; i<n; i++) {
data[i] = getPixelValue((int)Math.round(rx), (int)Math.round(ry));
rx += xinc;
ry += yinc;
}
}
return data;
}
/** Returns the pixel values along the horizontal line starting at (x,y). */
public void getRow(int x, int y, int[] data, int length) {
for (int i=0; i<length; i++)
data[i] = getPixel(x++, y);
}
/** Returns the pixel values along the horizontal line starting at (x,y). */
public float[] getRow(int x, int y, float[] data, int length) {
if (data==null)
data = new float[length];
for (int i=0; i<length; i++)
data[i] = getf(x++, y);
return data;
}
/** Returns the pixel values down the column starting at (x,y). */
public void getColumn(int x, int y, int[] data, int length) {
for (int i=0; i<length; i++)
data[i] = getPixel(x, y++);
}
/** Returns the pixel values down the column starting at (x,y). */
public float[] getColumn(int x, int y, float[] data, int length) {
if (data==null)
data = new float[length];
for (int i=0; i<length; i++)
data[i] = getf(x, y++);
return data;
}
/** Inserts the pixels contained in 'data' into a
horizontal line starting at (x,y). */
public void putRow(int x, int y, int[] data, int length) {
for (int i=0; i<length; i++)
putPixel(x++, y, data[i]);
}
/** Inserts the pixels contained in 'data' into a
horizontal line starting at (x,y). */
public void putRow(int x, int y, float[] data, int length) {
for (int i=0; i<length; i++)
setf(x++, y, data[i]);
}
/** Inserts the pixels contained in 'data' into a
column starting at (x,y). */
public void putColumn(int x, int y, int[] data, int length) {
for (int i=0; i<length; i++)
putPixel(x, y++, data[i]);
}
/** Inserts the pixels contained in 'data' into a
column starting at (x,y). */
public void putColumn(int x, int y, float[] data, int length) {
for (int i=0; i<length; i++)
setf(x, y++, data[i]);
}
/**
Sets the current drawing location.
@see ImageProcessor#lineTo
@see ImageProcessor#drawString
*/
public void moveTo(int x, int y) {
cx = x;
cy = y;
}
/** Sets the line width used by lineTo() and drawDot(). */
public void setLineWidth(int width) {
lineWidth = width;
if (lineWidth<1) lineWidth = 1;
}
/** Returns the current line width. */
public int getLineWidth() {
return lineWidth;
}
/** Draws a line from the current drawing location to (x2,y2). */
public void lineTo(int x2, int y2) {
int xMin = clipXMin-lineWidth/2-1; //need not draw dots outside of this rect
int xMax = clipXMax+lineWidth/2+1;
int yMin = clipYMin-lineWidth/2-1;
int yMax = clipYMax+lineWidth/2+1;
int dx = x2-cx;
int dy = y2-cy;
int absdx = dx>=0?dx:-dx;
int absdy = dy>=0?dy:-dy;
int n = absdy>absdx?absdy:absdx;
double xinc = dx!=0 ? (double)dx/n : 0; //single point (dx=dy=n=0): avoid division by zero
double yinc = dy!=0 ? (double)dy/n : 0;
double x = cx;
double y = cy;
cx = x2; cy = y2; //keep end point as starting for the next lineTo
int i1 = 0;
if (dx>0)
i1 = Math.max(i1, (int)((xMin-x)/xinc));
else if (dx<0)
i1 = Math.max(i1, (int)((xMax-x)/xinc));
else if (x<xMin || x>xMax)
return; // vertical line outside y range
if (dy>0)
i1 = Math.max(i1, (int)((yMin-y)/yinc));
else if (dy<0)
i1 = Math.max(i1, (int)((yMax-y)/yinc));
else if (y<yMin || y>yMax)
return; // horizontal line outside y range
int i2 = n;
if (dx>0)
i2 = Math.min(i2, (int)((xMax-x)/xinc));
else if (dx<0)
i2 = Math.min(i2, (int)((xMin-x)/xinc));
if (dy>0)
i2 = Math.min(i2, (int)((yMax-y)/yinc));
else if (dy<0)
i2 = Math.min(i2, (int)((yMin-y)/yinc));
x += i1*xinc;
y += i1*yinc;
for (int i=i1; i<=i2; i++) {
if (lineWidth==1)
drawPixel((int)Math.round(x), (int)Math.round(y));
else if (lineWidth==2)
drawDot2((int)Math.round(x), (int)Math.round(y));
else
drawDot((int)Math.round(x), (int)Math.round(y));
x += xinc;
y += yinc;
}
}
/** Draws a line from (x1,y1) to (x2,y2). */
public void drawLine(int x1, int y1, int x2, int y2) {
moveTo(x1, y1);
lineTo(x2, y2);
}
/* Draws a line using the Bresenham's algorithm that is 4-connected instead of 8-connected.<br>
Based on code from http://stackoverflow.com/questions/5186939/algorithm-for-drawing-a-4-connected-line<br>
Author: Gabriel Landini (G.Landini at bham.ac.uk)
*/
public void drawLine4(int x1, int y1, int x2, int y2) {
int dx = Math.abs(x2 - x1);
int dy = Math.abs(y2 - y1);
int sgnX = x1 < x2 ? 1 : -1;
int sgnY = y1 < y2 ? 1 : -1;
int e = 0;
for (int i=0; i < dx+dy; i++) {
putPixel(x1, y1, fgColor);
int e1 = e + dy;
int e2 = e - dx;
if (Math.abs(e1) < Math.abs(e2)) {
x1 += sgnX;
e = e1;
} else {
y1 += sgnY;
e = e2;
}
}
putPixel(x2, y2, fgColor);
}
/** Draws a rectangle. */
public void drawRect(int x, int y, int width, int height) {
if (width<1 || height<1)
return;
if (lineWidth==1) {
moveTo(x, y);
lineTo(x+width-1, y);
lineTo(x+width-1, y+height-1);
lineTo(x, y+height-1);
lineTo(x, y);
} else {
moveTo(x, y);
lineTo(x+width, y);
lineTo(x+width, y+height);
lineTo(x, y+height);
lineTo(x, y);
}
}
/** Fills a rectangle. */
public void fillRect(int x, int y, int width, int height) {
setRoi(x, y, width, height);
fill();
resetRoi();
}
/** Draws an elliptical shape. */
public void drawOval(int x, int y, int width, int height) {
if ((long)width*height>4L*this.width*this.height)
return;
OvalRoi oval = new OvalRoi(x, y, width, height);
drawPolygon(oval.getPolygon());
}
/** Fills an elliptical shape. */
public void fillOval(int x, int y, int width, int height) {
if ((long)width*height>4L*this.width*this.height)
return;
OvalRoi oval = new OvalRoi(x, y, width, height);
fillPolygon(oval.getPolygon());
}
/** Draws a polygon. */
public void drawPolygon(Polygon p) {
moveTo(p.xpoints[0], p.ypoints[0]);
for (int i=0; i<p.npoints; i++)
lineTo(p.xpoints[i], p.ypoints[i]);
lineTo(p.xpoints[0], p.ypoints[0]);
}
/** Fills a polygon. */
public void fillPolygon(Polygon p) {
setRoi(p);
fill(getMask());
resetRoi();
}
/** @deprecated */
public void drawDot2(int x, int y) {
drawPixel(x, y);
drawPixel(x-1, y);
drawPixel(x, y-1);
drawPixel(x-1, y-1);
}
/** Draws a dot using the current line width and fill/draw value. */
public void drawDot(int xcenter, int ycenter) {
double r = lineWidth/2.0;
int xmin=(int)(xcenter-r+0.5), ymin=(int)(ycenter-r+0.5);
int xmax=xmin+lineWidth, ymax=ymin+lineWidth;
//if (xcenter<clipXMin || ycenter<clipYMin || xcenter>clipXMax || ycenter>clipYMax ) {
if (xmin<clipXMin || ymin<clipYMin || xmax>clipXMax || ymax>clipYMax ) {
// draw edge dot
double r2 = r*r;
r -= 0.5;
double xoffset=xmin+r, yoffset=ymin+r;
double xx, yy;
for (int y=ymin; y<ymax; y++) {
for (int x=xmin; x<xmax; x++) {
xx = x-xoffset; yy = y-yoffset;
if (xx*xx+yy*yy<=r2)
drawPixel(x, y);
}
}
} else {
if (dotMask==null || lineWidth!=dotMask.getWidth()) {
OvalRoi oval = new OvalRoi(0, 0, lineWidth, lineWidth);
dotMask = oval.getMask();
}
setRoi(xmin, ymin, lineWidth, lineWidth);
fill(dotMask);
roiX=0; roiY=0; roiWidth=width; roiHeight=height;
xMin=1; xMax=width-2; yMin=1; yMax=height-2;
mask=null;
}
}
private ImageProcessor dotMask;
private void setupFontMetrics() {
if (fontMetrics==null) {
fmImage=new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
fmGraphics = (Graphics2D)fmImage.getGraphics();
fmGraphics.setFont(font);
Java2.setAntialiasedText(fmGraphics, antialiasedText);
fontMetrics = fmGraphics.getFontMetrics(font);
}
}
/** Draws a string at the current drawing location using the current fill/draw value.
* Draws multiple lines if the string contains newline characters.
* The current x coordinate is the left/center/right end of the string for
* left/center/right justification.
* The current y coordinate determines the bottommost position of the string,
* including the descent of the font (i.e., characters reaching below the baseline)
* For multi-line strings, the y coordinate applies to the first line.
* The y of the drawing position is incremented by the height of one text line,
* i.e. points at the drawing position for the next text line */
public void drawString(String s) {
if (s==null || s.equals("")) return;
setupFontMetrics();
if (s.indexOf("\n")==-1)
drawString2(s);
else {
String[] s2 = Tools.split(s, "\n");
for (int i=0; i<s2.length; i++)
drawString2(s2[i]);
}
}
/** Draws a single-line string at the current drawing location cx, cy and
* adds the line height (FontMetrics.getHeight) to the current y coordinate 'cy' */
private void drawString2(String s) {
int w = getStringWidth(s);
int cxx = cx;
if (justification==CENTER_JUSTIFY)
cxx -= w/2;
else if (justification==RIGHT_JUSTIFY)
cxx -= w;
int h = fontMetrics.getHeight();
if (w<=0 || h<=0) return;
Image bi = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB);
Graphics g = bi.getGraphics();
FontMetrics metrics = g.getFontMetrics(font);
int fontHeight = metrics.getHeight();
int descent = metrics.getDescent();
g.setFont(font);
if (antialiasedText && cxx>=0 && cy-h>=0) {
Java2.setAntialiasedText(g, true);
setRoi(cxx, cy-h, w, h);
ImageProcessor ip = crop();
resetRoi();
if (ip.getWidth()==0||ip.getHeight()==0)
return;
g.drawImage(ip.createImage(), 0, 0, null);
g.setColor(drawingColor);
g.drawString(s, 0, h-descent);
g.dispose();
ip = new ColorProcessor(bi);
if (this instanceof ByteProcessor) {
ip = ip.convertToByte(false);
if (isInvertedLut()) ip.invert();
}
//new ij.ImagePlus("ip",ip).show();
insert(ip, cxx, cy-h);
cy += h;
return;
}
Java2.setAntialiasedText(g, false);
g.setColor(Color.white);
g.fillRect(0, 0, w, h);
g.setColor(Color.black);
g.drawString(s, 0, h-descent);
g.dispose();
ImageProcessor ip = new ColorProcessor(bi);
ImageProcessor textMask = ip.convertToByte(false);
byte[] mpixels = (byte[])textMask.getPixels();
//new ij.ImagePlus("textmask",textMask).show();
textMask.invert();
if (cxx<width && cy-h<height) {
setMask(textMask);
setRoi(cxx,cy-h,w,h);
fill(getMask());
}
resetRoi();
cy += h;
}
/** Draws a string at the specified location using the current fill/draw value.
* Draws multiple lines if the string contains newline characters.
* The x coordinate is the left/center/right end of the string for left/center/right
* justification.
* The y coordinate determines the bottommost position of the string,
* including the descent of the font (i.e., characters reaching below the baseline)
* For multi-line strings, the y coordinate applies to the first line. */
public void drawString(String s, int x, int y) {
moveTo(x, y);
drawString(s);
}
/** Draws a string at the specified location with a filled background.
A JavaScript example is available at
http://imagej.nih.gov/ij/macros/js/DrawTextWithBackground.js
*/
public void drawString(String s, int x, int y, Color background) {
Color foreground = drawingColor;
FontMetrics metrics = getFontMetrics();
int w = 0;
int h = metrics.getAscent() + metrics.getDescent();
int y2 = y;
if (s.indexOf("\n")!=-1) {
String[] s2 = Tools.split(s, "\n");
for (int i=0; i<s2.length; i++) {
int w2 = getStringWidth(s2[i]);
if (w2>w) w = w2;
}
int h2 = metrics.getHeight();
y2 += h2*(s2.length-1);
h += h2*(s2.length-1);
} else
w = getStringWidth(s);
int x2 = x;
if (justification==CENTER_JUSTIFY)
x2 -= w/2;
else if (justification==RIGHT_JUSTIFY)
x2 -= w;
setColor(background);
setRoi(x2, y2-h, w, h);
fill();
resetRoi();
setColor(foreground);
drawString(s, x, y);
}
/** Sets the justification used by drawString(), where <code>justification</code>
is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY. The default is LEFT_JUSTIFY. */
public void setJustification(int justification) {
if (justification<LEFT_JUSTIFY || justification>RIGHT_JUSTIFY)
justification = LEFT_JUSTIFY;
this.justification = justification;
}
/** Sets the font used by drawString(). */
public void setFont(Font font) {
this.font = font;
boldFont = font.isBold();
setupFontMetrics();
fmGraphics.setFont(font);
Java2.setAntialiasedText(fmGraphics, antialiasedText);
fontMetrics = fmGraphics.getFontMetrics(font);
}
/** Sets the size of the font used by drawString(). */
public void setFontSize(int size) {
setFont(font.deriveFont(font.getStyle(), size));
if (size>15)
setAntialiasedText(true);
}
/** Specifies whether or not text is drawn using antialiasing. Antialiased
test requires an 8 bit or RGB image. Antialiasing does not
work with 8-bit images that are not using 0-255 display range. */
public void setAntialiasedText(boolean antialiasedText) {
setupFontMetrics();
if (antialiasedText && (((this instanceof ByteProcessor)&&getMin()==0.0&&getMax()==255.0) || (this instanceof ColorProcessor)))
this.antialiasedText = true;
else
this.antialiasedText = false;
Java2.setAntialiasedText(fmGraphics, this.antialiasedText);
fontMetrics = fmGraphics.getFontMetrics(font);
}
/** Returns the width in pixels of the specified string, including any background
* space (whitespace) between the x drawing coordinate and the string, not necessarily
* including all whitespace at the right. */
public int getStringWidth(String s) {
// Note that fontMetrics.getStringBounds often underestimates the width (worst for italic fonts on Macs)
// On the other hand, GlyphVector.getPixelBounds (returned by this.getStringBounds)
// does not include the full character width of e.g. the '1' character, which would make
// lists of right-justified numbers such as the y axis of plots look ugly.
// Thus, the maximum of both methods is returned.
Rectangle2D rect = getStringBounds(s);
return (int)Math.max(fontMetrics.getStringBounds(s, fmGraphics).getWidth(), rect.getX()+rect.getWidth());
}
/** Returns a rectangle enclosing the pixels affected by drawString
* assuming it is drawn at (x=0, y=0). As drawString draws above the drawing location,
* the y coordinate of the rectangle is negative. */
public Rectangle getStringBounds(String s) {
setupFontMetrics();
GlyphVector gv = font.createGlyphVector(fmGraphics.getFontRenderContext(), s);
Rectangle2D rect = gv.getPixelBounds(null, 0.f, -fontMetrics.getDescent());
return new Rectangle((int)rect.getX(), (int)rect.getY(), (int)rect.getWidth(), (int)rect.getHeight());
}
/** Returns the current font. */
public Font getFont() {
return font;
}
/** Returns the current FontMetrics. */
public FontMetrics getFontMetrics() {
setupFontMetrics();
return fontMetrics;
}
/** Replaces each pixel with the 3x3 neighborhood mean. */
public void smooth() {
if (width>1)
filter(BLUR_MORE);
}
/** Sharpens the image or ROI using a 3x3 convolution kernel. */
public void sharpen() {
if (width>1) {
int[] kernel = {-1, -1, -1,
-1, 12, -1,
-1, -1, -1};
convolve3x3(kernel);
}
}
/** Finds edges in the image or ROI using a Sobel operator. */
public void findEdges() {
if (width>1)
filter(FIND_EDGES);
}
/** Flips the image or ROI vertically. */
public abstract void flipVertical();
/** Flips the image or ROI horizontally. */
public void flipHorizontal() {
int[] col1 = new int[roiHeight];
int[] col2 = new int[roiHeight];
for (int x=0; x<roiWidth/2; x++) {
getColumn(roiX+x, roiY, col1, roiHeight);
getColumn(roiX+roiWidth-x-1, roiY, col2, roiHeight);
putColumn(roiX+x, roiY, col2, roiHeight);
putColumn(roiX+roiWidth-x-1, roiY, col1, roiHeight);
}
}
/** Rotates the entire image 90 degrees clockwise. Returns
a new ImageProcessor that represents the rotated image. */
public ImageProcessor rotateRight() {
int width2 = height;
int height2 = width;
ImageProcessor ip2 = createProcessor(width2, height2);
int[] arow = new int[width];
for (int row=0; row<height; row++) {
getRow(0, row, arow, width);
ip2.putColumn(width2-row-1, 0, arow, height2);
}
return ip2;
}
/** Rotates the entire image 90 degrees counter-clockwise. Returns
a new ImageProcessor that represents the rotated image. */
public ImageProcessor rotateLeft() {
int width2 = height;
int height2 = width;
ImageProcessor ip2 = createProcessor(width2, height2);
int[] arow = new int[width];
int[] arow2 = new int[width];
for (int row=0; row<height; row++) {
getRow(0, row, arow, width);
for (int i=0; i<width; i++) {
arow2[i] = arow[width-i-1];
}
ip2.putColumn(row, 0, arow2, height2);
}
return ip2;
}
/** Inserts the image contained in 'ip' at (xloc, yloc). */
public void insert(ImageProcessor ip, int xloc, int yloc) {
copyBits(ip, xloc, yloc, Blitter.COPY);
}
/** Returns a string containing information about this ImageProcessor. */
public String toString() {
return ("ip[width="+width+", height="+height+", bits="+getBitDepth()+", min="+getMin()+", max="+getMax()+"]");
}
/** Fills the image or ROI bounding rectangle with the current fill/draw value. Use
* fill(Roi) or fill(ip.getMask()) to fill non-rectangular selections.
* @see #setColor(Color)
* @see #setValue(double)
* @see #fill(Roi)
*/
public void fill() {
process(FILL, 0.0);
}
/** Fills pixels that are within the ROI bounding rectangle and part of
* the mask (i.e. pixels that have a value=BLACK in the mask array).
* Use ip.getMask() to acquire the mask.
* Throws and IllegalArgumentException if the mask is null or
* the size of the mask is not the same as the size of the ROI.
* @see #setColor(Color)
* @see #setValue(double)
* @see #getMask
* @see #fill(Roi)
*/
public abstract void fill(ImageProcessor mask);
/** Fills the ROI with the current fill/draw value.
* @see #setColor(Color)
* @see #setValue(double)
* @see #fill(Roi)
*/
public void fill(Roi roi) {
if (roi!=null && roi.isLine()) {
if ((roi instanceof Line) && roi.getStrokeWidth()>1 && !(roi instanceof Arrow))
fillPolygon(roi.getPolygon());
else
roi.drawPixels(this);
return;
}
ImageProcessor m = getMask();
Rectangle r = getRoi();
setRoi(roi);
fill(getMask());
setMask(m);
setRoi(r);
}
/** Fills outside an Roi. */
public void fillOutside(Roi roi) {
if (roi==null || !roi.isArea()) return;
ImageProcessor m = getMask();
Rectangle r = getRoi();
ShapeRoi s1, s2;
if (roi instanceof ShapeRoi)
s1 = (ShapeRoi)roi;
else
s1 = new ShapeRoi(roi);
s2 = new ShapeRoi(new Roi(0,0, width, height));
setRoi(s2.xor(s1));
fill(getMask());
setMask(m);
setRoi(r);
}
/** Draws the specified ROI on this image using the line
width and color defined by ip.setLineWidth() and ip.setColor().
@see ImageProcessor#drawRoi
*/
public void draw(Roi roi) {
roi.drawPixels(this);
}
/** Draws the specified ROI on this image using the stroke
width, stroke color and fill color defined by roi.setStrokeWidth,
roi.setStrokeColor() and roi.setFillColor(). Works with RGB
images. Does not work with 16-bit and float images.
@see ImageProcessor#draw
@see ImageProcessor#drawOverlay
*/
public void drawRoi(Roi roi) {
Image img = createImage();
Graphics g = img.getGraphics();
ij.ImagePlus imp = roi.getImage();
if (imp!=null) {
roi.setImage(null);
roi.drawOverlay(g);
roi.setImage(imp);
} else
roi.drawOverlay(g);
}
/** Draws the specified Overlay on this image. Works best
with RGB images. Does not work with 16-bit and float
images. Requires Java 1.6.
@see ImageProcessor#drawRoi
*/
public void drawOverlay(Overlay overlay) {
Roi[] rois = overlay.toArray();
for (int i=0; i<rois.length; i++)
drawRoi(rois[i]);
}
/** Set a lookup table used by getPixelValue(), getLine() and
convertToFloat() to calibrate pixel values. The length of
the table must be 256 for byte images and 65536 for short
images. RGB and float processors do not do calibration.
@see ij.measure.Calibration#setCTable
*/
public void setCalibrationTable(float[] cTable) {
this.cTable = cTable;
}
/** Returns the calibration table or null. */
public float[] getCalibrationTable() {
return cTable;
}
/** Set the number of bins to be used for histograms of float images. */
public void setHistogramSize(int size) {
histogramSize = size;
if (histogramSize<1) histogramSize = 1;
}
/** Returns the number of float image histogram bins. The bin
count is fixed at 256 for the other three data types. */
public int getHistogramSize() {
return histogramSize;
}
/** Set the range used for histograms of float images. The image range is
used if both <code>histMin</code> and <code>histMax</code> are zero. */
public void setHistogramRange(double histMin, double histMax) {
if (histMin>histMax) {
histMin = 0.0;
histMax = 0.0;
}
histogramMin = histMin;
histogramMax = histMax;
}
/** Returns the minimum histogram value used for histograms of float images. */
public double getHistogramMin() {
return histogramMin;
}
/** Returns the maximum histogram value used for histograms of float images. */
public double getHistogramMax() {
return histogramMax;
}
/** Returns a reference to this image's pixel array. The
array type (byte[], short[], float[] or int[]) varies
depending on the image type. */
public abstract Object getPixels();
/** Returns a copy of the pixel data. Or returns a reference to the
snapshot buffer if it is not null and 'snapshotCopyMode' is true.
@see ImageProcessor#snapshot
@see ImageProcessor#setSnapshotCopyMode
*/
public abstract Object getPixelsCopy();
/** Returns the value of the pixel at (x,y). For RGB images, the
* argb values are packed in an int. For float images, the
* the value must be converted using Float.intBitsToFloat().
* Returns zero if either the x or y coodinate is out of range.
* Use <i>getValue(x,y)</i> to get calibrated values from
* 8-bit and 16-bit images, to get intensity values from RGB
* images and to get float values from 32-bit images.
* @see ImageProcessor#getValue
*/
public abstract int getPixel(int x, int y);
/** This is a faster version of getPixel() that does not do bounds checking. */
public abstract int get(int x, int y);
public abstract int get(int index);
/** This is a faster version of putPixel() that does not clip
out of range values and does not do bounds checking. */
public abstract void set(int x, int y, int value);
public abstract void set(int index, int value);
/** Returns the value of the pixel at (x,y) as a float. Faster
* than getPixelValue() but does no bounds checking and
* does not return calibrated values.
*/
public abstract float getf(int x, int y);
public abstract float getf(int index);
/** Sets the value of the pixel at (x,y) to 'value'. Does no bounds
* checking or clamping, making it faster than putPixel(). Due to the lack
* of bounds checking, (x,y) coordinates outside the image may cause
* an exception. Due to the lack of clamping, values outside the 0-255
* range (for byte) or 0-65535 range (for short) are not handled correctly.
*/
public abstract void setf(int x, int y, float value);
public abstract void setf(int index, float value);
public int getPixelCount() {
return width*height;
}
/** Returns a copy of the pixel data as a 2D int array with
dimensions [x=0..width-1][y=0..height-1]. With RGB
images, the returned values are in packed ARGB format.
With float images, the returned values must be converted
to float using Float.intBitsToFloat(). */
public int[][] getIntArray() {
int[][] a = new int [width][height];
for(int y=0; y<height; y++) {
for(int x=0; x<width; x++)
a[x][y]=get(x,y);
}
return a;
}
/** Replaces the pixel data with contents of the specified 2D int array. */
public void setIntArray(int[][] a) {
for(int y=0; y<height; y++) {
for(int x=0; x<width; x++)
set(x, y, a[x][y]);
}
}
/** Returns a copy of the pixel data as a 2D float
array with dimensions [x=0..width-1][y=0..height-1]. */
public float[][] getFloatArray() {
float[][] a = new float[width][height];
for(int y=0; y<height; y++) {
for(int x=0; x<width; x++)
a[x][y]=getf(x,y);
}
return a;
}
/** Replaces the pixel data with contents of the specified 2D float array. */
public void setFloatArray(float[][] a) {
for(int y=0; y<height; y++) {
for(int x=0; x<width; x++)
setf(x, y, a[x][y]);
}
}
/** Experimental */
public void getNeighborhood(int x, int y, double[][] arr) {
int nx=arr.length;
int ny=arr[0].length;
int nx2 = (nx-1)/2;
int ny2 = (ny-1)/2;
if (x>=nx2 && y>=ny2 && x<width-nx2-1 && y<height-ny2-1) {
int index = (y-ny2)*width + (x-nx2);
for (int y2=0; y2<ny; y2++) {
for (int x2=0; x2<nx; x2++)
arr[x2][y2] = getf(index++);
index += (width - nx);
}
} else {
for (int y2=0; y2<ny; y2++) {
for (int x2=0; x2<nx; x2++)
arr[x2][y2] = getPixelValue(x2, y2);
}
}
}
/** Returns the samples for the pixel at (x,y) in an int array.
* RGB pixels have three samples, all others have one.
* Returns zeros if the the coordinates are not in bounds.
* iArray is an optional preallocated array.
*/
public int[] getPixel(int x, int y, int[] iArray) {
if (iArray==null) iArray = new int[1];
iArray[0] = getPixel(x, y);
return iArray;
}
/** Sets a pixel in the image using an int array of samples.
RGB pixels have three samples, all others have one. */
public void putPixel(int x, int y, int[] iArray) {
putPixel(x, y, iArray[0]);
}
/*
public int[] getRGBValue(int index, int[] rgb) {
if (rgb==null) rgb = new int[3];
if (this instanceof ColorProcessor)
return rgb;
if (rLUT1==null) {
if (cm==null)
makeDefaultColorModel();
baseCM = cm;
IndexColorModel m = (IndexColorModel)cm;
rLUT1 = new byte[256]; gLUT1 = new byte[256]; bLUT1 = new byte[256];
m.getReds(rLUT1); m.getGreens(gLUT1); m.getBlues(bLUT1);
}
int min2=(int)getMin(), max2=(int)getMax();
double scale = 256.0/(max2-min2+1);
double value = getf(index)-min2;
if (value<0.0) value = 0.0;
int v = (int)(value*scale+0.5);
if (v>255) v = 255;
rgb[0]=rLUT1[v]; rgb[1]=gLUT1[v]; rgb[2]=bLUT1[v];
return rgb;
}
*/
/** Uses the current interpolation method (bilinear or bicubic)
to find the pixel value at real coordinates (x,y). */
public abstract double getInterpolatedPixel(double x, double y);
/** Uses the current interpolation method to find the pixel value at real coordinates (x,y).
For RGB images, the argb values are packed in an int. For float images,
the value must be converted using Float.intBitsToFloat(). Returns zero
if the (x, y) is not inside the image. */
public abstract int getPixelInterpolated(double x, double y);
/** Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
Returns zero if the (x, y) is not inside the image. */
public final double getInterpolatedValue(double x, double y) {
if (useBicubic)
return getBicubicInterpolatedPixel(x, y, this);
if (x<0.0 || x>=width-1.0 || y<0.0 || y>=height-1.0) {
if (x<-1.0 || x>=width || y<-1.0 || y>=height)
return 0.0;
else
return getInterpolatedEdgeValue(x, y);
}
int xbase = (int)x;
int ybase = (int)y;
double xFraction = x - xbase;
double yFraction = y - ybase;
if (xFraction<0.0) xFraction = 0.0;
if (yFraction<0.0) yFraction = 0.0;
double lowerLeft = getPixelValue(xbase, ybase);
double lowerRight = getPixelValue(xbase+1, ybase);
double upperRight = getPixelValue(xbase+1, ybase+1);
double upperLeft = getPixelValue(xbase, ybase+1);
double upperAverage = upperLeft + xFraction * (upperRight - upperLeft);
double lowerAverage = lowerLeft + xFraction * (lowerRight - lowerLeft);
return lowerAverage + yFraction * (upperAverage - lowerAverage);
}
/** This method is from Chapter 16 of "Digital Image Processing:
An Algorithmic Introduction Using Java" by Burger and Burge
(http://www.imagingbook.com/). */
public double getBicubicInterpolatedPixel(double x0, double y0, ImageProcessor ip2) {
int u0 = (int) Math.floor(x0); //use floor to handle negative coordinates too
int v0 = (int) Math.floor(y0);
if (u0<=0 || u0>=width-2 || v0<=0 || v0>=height-2)
return ip2.getBilinearInterpolatedPixel(x0, y0);
double q = 0;
for (int j = 0; j <= 3; j++) {
int v = v0 - 1 + j;
double p = 0;
for (int i = 0; i <= 3; i++) {
int u = u0 - 1 + i;
p = p + ip2.get(u,v) * cubic(x0 - u);
}
q = q + p * cubic(y0 - v);
}
return q;
}
final double getBilinearInterpolatedPixel(double x, double y) {
if (x>=-1 && x<width && y>=-1 && y<height) {
int method = interpolationMethod;
interpolationMethod = BILINEAR;
double value = getInterpolatedPixel(x, y);
interpolationMethod = method;
return value;
} else
return getBackgroundValue();
}
static final double a = 0.5; // Catmull-Rom interpolation
public static final double cubic(double x) {
if (x < 0.0) x = -x;
double z = 0.0;
if (x < 1.0)
z = x*x*(x*(-a+2.0) + (a-3.0)) + 1.0;
else if (x < 2.0)
z = -a*x*x*x + 5.0*a*x*x - 8.0*a*x + 4.0*a;
return z;
}
private final double getInterpolatedEdgeValue(double x, double y) {
int xbase = (int)x;
int ybase = (int)y;
double xFraction = x - xbase;
double yFraction = y - ybase;
if (xFraction<0.0) xFraction = 0.0;
if (yFraction<0.0) yFraction = 0.0;
double lowerLeft = getEdgeValue(xbase, ybase);
double lowerRight = getEdgeValue(xbase+1, ybase);
double upperRight = getEdgeValue(xbase+1, ybase+1);
double upperLeft = getEdgeValue(xbase, ybase+1);
double upperAverage = upperLeft + xFraction * (upperRight - upperLeft);
double lowerAverage = lowerLeft + xFraction * (lowerRight - lowerLeft);
return lowerAverage + yFraction * (upperAverage - lowerAverage);
}
private float getEdgeValue(int x, int y) {
if (x<=0) x = 0;
if (x>=width) x = width-1;
if (y<=0) y = 0;
if (y>=height) y = height-1;
return getPixelValue(x, y);
}
/** Stores the specified value at (x,y). Does
nothing if (x,y) is outside the image boundary.
For 8-bit and 16-bit images, out of range values
are clamped. For RGB images, the
argb values are packed in 'value'. For float images,
'value' is expected to be a float converted to an int
using Float.floatToIntBits(). */
public abstract void putPixel(int x, int y, int value);
/** Returns the value of the pixel at <i>(x,y)</i>, a calibrated
* value from 8-bit and 16-bit images, an intensity value
* from RGB images and a double value from 32-bit images.
* This is an alias for getPixelValue(x,y).
* @see ImageProcessor#getPixel
* @see ImageProcessor#getPixelValue
* @see ImageProcessor#getf
*/
public double getValue(int x, int y) {
return getPixelValue(x,y);
}
/** Returns the value of the pixel at (x,y). For byte and short
* images, returns a calibrated value if a calibration table
* has been set using setCalibraionTable(). For RGB images,
* returns the luminance value.
* @see ImageProcessor#getPixel
* @see ImageProcessor#getValue
* @see ImageProcessor#getf
*/
public abstract float getPixelValue(int x, int y);
/** Stores the specified value at (x,y). */
public abstract void putPixelValue(int x, int y, double value);
/** Sets the pixel at (x,y) to the current fill/draw value. */
public abstract void drawPixel(int x, int y);
/** Sets a new pixel array for the image. The length of the array must be equal to width*height.
Use setSnapshotPixels(null) to clear the snapshot buffer. */
public abstract void setPixels(Object pixels);
/** Copies the image contained in 'ip' to (xloc, yloc) using one of
the transfer modes defined in the Blitter interface. */
public abstract void copyBits(ImageProcessor ip, int xloc, int yloc, int mode);
/** Transforms the image or ROI using a lookup table. The
length of the table must be 256 for byte images and
65536 for short images. RGB and float images are not
supported. */
public abstract void applyTable(int[] lut);
/** Inverts the image or ROI. */
public void invert() {process(INVERT, 0.0);}
/** Adds 'value' to each pixel in the image or ROI. */
public void add(int value) {process(ADD, value);}
/** Adds 'value' to each pixel in the image or ROI. */
public void add(double value) {process(ADD, value);}
/** Subtracts 'value' from each pixel in the image or ROI. */
public void subtract(double value) {
add(-value);
}
/** Multiplies each pixel in the image or ROI by 'value'. */
public void multiply(double value) {process(MULT, value);}
/** Assigns 'value' to each pixel in the image or ROI. */
public void set(double value) {process(SET, value);}
/** Binary AND of each pixel in the image or ROI with 'value'. */
public void and(int value) {process(AND, value);}
/** Binary OR of each pixel in the image or ROI with 'value'. */
public void or(int value) {process(OR, value);}
/** Binary exclusive OR of each pixel in the image or ROI with 'value'. */
public void xor(int value) {process(XOR, value);}
/** Performs gamma correction of the image or ROI. */
public void gamma(double value) {process(GAMMA, value);}
/** Does a natural logarithmic (base e) transform of the image or ROI. */
public void log() {process(LOG, 0.0);}
/** Does a natural logarithmic (base e) transform of the image or ROI. */
public void ln() {log();}
/** Performs a exponential transform on the image or ROI. */
public void exp() {process(EXP, 0.0);}
/** Performs a square transform on the image or ROI. */
public void sqr() {process(SQR, 0.0);}
/** Performs a square root transform on the image or ROI. */
public void sqrt() {process(SQRT, 0.0);}
/** If this is a 32-bit or signed 16-bit image, performs an
absolute value transform, otherwise does nothing. */
public void abs() {}
/** Pixels less than 'value' are set to 'value'. */
public void min(double value) {process(MINIMUM, value);}
/** Pixels greater than 'value' are set to 'value'. */
public void max(double value) {process(MAXIMUM, value);}
/** Returns a copy of this image is the form of an AWT Image. */
public abstract Image createImage();
/** Returns this image as a BufferedImage. */
public BufferedImage getBufferedImage() {
BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
Graphics2D g = (Graphics2D)bi.getGraphics();
g.drawImage(createImage(), 0, 0, null);
return bi;
}
/** Returns a new, blank processor with the specified width and height. */
public abstract ImageProcessor createProcessor(int width, int height);
/** Makes a copy of this image's pixel data that can be
later restored using reset() or reset(mask).
@see ImageProcessor#reset
@see ImageProcessor#reset(ImageProcessor)
*/
public abstract void snapshot();
/** Restores the pixel data from the snapshot (undo) buffer. */
public abstract void reset();
/** Swaps the pixel and snapshot (undo) buffers. */
public abstract void swapPixelArrays();
/** Restores pixels from the snapshot buffer that are
within the rectangular roi but not part of the mask. */
public abstract void reset(ImageProcessor mask);
/** Sets a new pixel array for the snapshot (undo) buffer. */
public abstract void setSnapshotPixels(Object pixels);
/** Returns a reference to the snapshot (undo) buffer, or null. */
public abstract Object getSnapshotPixels();
/** Convolves the image or ROI with the specified
3x3 integer convolution kernel. */
public abstract void convolve3x3(int[] kernel);
/** A 3x3 filter operation, where the argument (BLUR_MORE, FIND_EDGES,
MEDIAN_FILTER, MIN or MAX) determines the filter type. */
public abstract void filter(int type);
/** A 3x3 median filter. Requires 8-bit or RGB image. */
public abstract void medianFilter();
/** Adds pseudorandom, Gaussian ("normally") distributed values, with
mean 0.0 and the specified standard deviation, to this image or ROI. */
public abstract void noise(double standardDeviation);
/** Returns a new processor containing an image
that corresponds to the current ROI. */
public abstract ImageProcessor crop();
/** Sets pixels less than or equal to level to 0 and all other
pixels to 255. Only works with 8-bit and 16-bit images. */
public abstract void threshold(int level);
/** Returns a duplicate of this image. */
public abstract ImageProcessor duplicate();
/** Scales the image by the specified factors. Does not
change the image size.
@see ImageProcessor#setInterpolate
@see ImageProcessor#resize
*/
public abstract void scale(double xScale, double yScale);
/** Returns a new ImageProcessor containing a scaled copy of this image or ROI.
@see ij.process.ImageProcessor#setInterpolate
*/
public abstract ImageProcessor resize(int dstWidth, int dstHeight);
/** Returns a new ImageProcessor containing a scaled copy
of this image or ROI, with the aspect ratio maintained. */
public ImageProcessor resize(int dstWidth) {
return resize(dstWidth, (int)(dstWidth*((double)roiHeight/roiWidth)));
}
/** Returns a new ImageProcessor containing a scaled copy of this image or ROI.
@param dstWidth Image width of the resulting ImageProcessor
@param dstHeight Image height of the resulting ImageProcessor
@param useAverging True means that the averaging occurs to avoid
aliasing artifacts; the kernel shape for averaging is determined by
the interpolationMethod. False if subsampling without any averaging
should be used on downsizing. Has no effect on upsizing.
@see ImageProcessor#setInterpolationMethod
Author: Michael Schmid
*/
public ImageProcessor resize(int dstWidth, int dstHeight, boolean useAverging) {
Rectangle r = getRoi();
int rWidth = r.width;
int rHeight = r.height;
if ((dstWidth>=rWidth && dstHeight>=rHeight) || !useAverging)
return resize(dstWidth, dstHeight); //upsizing or downsizing without averaging
else { //downsizing with averaging in at least one direction: convert to float
ImageProcessor ip2 = createProcessor(dstWidth, dstHeight);
FloatProcessor fp = null;
int channels = getNChannels();
boolean showStatus = getProgressIncrement(width,height)>0;
boolean showProgress = showStatus && channels>1;
if (showProgress) showProgress(0.15);
for (int channelNumber=0; channelNumber<channels; channelNumber++) {
fp = toFloat(channelNumber, fp);
fp.setInterpolationMethod(interpolationMethod);
fp.setRoi(getRoi());
String msg = showStatus?" ("+(channelNumber+1)+"/"+channels+")":null;
FloatProcessor fp2 = fp.downsize(dstWidth, dstHeight, msg);
ip2.setPixels(channelNumber, fp2);
if (showProgress) showProgress(0.40+0.25*channelNumber);
}
if (showProgress) showProgress(1.0);
return ip2;
}
}
/** Use linear interpolation to resize images that have a width or height of one. */
protected ImageProcessor resizeLinearly(int width2, int height2) {
int bitDepth = getBitDepth();
ImageProcessor ip1 = this;
boolean rotate = width==1;
if (rotate) {
ip1=ip1.rotateLeft();
int w2 = width2;
width2 = height2;
height2 = w2;
}
ip1 = ip1.convertToFloat();
int width1 = ip1.getWidth();
int height1 = ip1.getHeight();
ImageProcessor ip2 = ip1.createProcessor(width2, height2);
double scale = (double)(width1-1)/(width2-1);
float[] data1 = new float[width1];
float[] data2 = new float[width2];
ip1.getRow(0, 0, data1, width1);
double fraction;
for (int x=0; x<width2; x++) {
int x1 = (int)(x*scale);
int x2 = x1+1;
if (x2==width1) x2=width1-1;
fraction = x*scale - x1;
//ij.IJ.log(x+" "+x1+" "+x2+" "+fraction+" "+width1+" "+width2);
data2[x] = (float)((1.0-fraction)*data1[x1] + fraction*data1[x2]);
}
for (int y=0; y<height2; y++)
ip2.putRow(0, y, data2, width2);
if (bitDepth==8)
ip2 = ip2.convertToByte(false);
else if (bitDepth==16)
ip2 = ip2.convertToShort(false);
if (rotate)
ip2=ip2.rotateRight();
return ip2;
}
/** Returns a copy of this image that has been reduced in size using binning. */
public ImageProcessor bin(int shrinkFactor) {
return new Binner().shrink(this, shrinkFactor, shrinkFactor, 0);
}
/** Rotates the image or selection 'angle' degrees clockwise.
@see ImageProcessor#setInterpolationMethod
@see ImageProcessor#setBackgroundValue
*/
public abstract void rotate(double angle);
/** Moves the image or selection vertically or horizontally by a specified
number of pixels. Positive x values move the image or selection to the
right, negative values move it to the left. Positive y values move the
image or selection down, negative values move it up.
*/
public void translate(double xOffset, double yOffset) {
ImageProcessor ip2 = this.duplicate();
ip2.setBackgroundValue(0.0);
boolean integerOffsets = xOffset==(int)xOffset && yOffset==(int)yOffset;
if (integerOffsets || interpolationMethod==NONE) {
for (int y=roiY; y<(roiY + roiHeight); y++) {
for (int x=roiX; x<(roiX + roiWidth); x++)
putPixel(x, y, ip2.getPixel(x-(int)xOffset, y-(int)yOffset));
}
} else {
if (interpolationMethod==BICUBIC && (this instanceof ColorProcessor))
((ColorProcessor)this).filterRGB(ColorProcessor.RGB_TRANSLATE, xOffset, yOffset);
else {
for (int y=roiY; y<(roiY + roiHeight); y++) {
for (int x=roiX; x<(roiX + roiWidth); x++)
putPixel(x, y, ip2.getPixelInterpolated(x-xOffset, y-yOffset));
}
}
}
}
/**
* @deprecated
* replaced by translate(x,y)
*/
public void translate(int xOffset, int yOffset, boolean eraseBackground) {
translate(xOffset, yOffset);
}
/** Returns the histogram of the image or ROI. Returns
a luminosity histogram for RGB images and null
for float images.
<p>
For 8-bit and 16-bit images, returns an array with one entry for each possible
value that a pixel can have, from 0 to 255 (8-bit image) or 0-65535 (16-bit image).
Thus, the array size is 256 or 65536, and the bin width in uncalibrated units is 1.
<p>
For RGB images, the brightness is evaluated using the color weights (which would result in a
float value) and rounded to an int. This gives 256 bins. FloatProcessor.getHistogram is not
implemented (returns null).
*/
public abstract int[] getHistogram();
/** Returns the histogram of the image or ROI, using the specified number of bins. */
public int[] getHistogram(int nBins) {
ImageProcessor ip;
if (((this instanceof ByteProcessor)||(this instanceof ColorProcessor)) && nBins!=256)
ip = convertToShort(false);
else
ip = this;
ip.setHistogramSize(nBins);
ip.setHistogramRange(0.0, 0.0);
ImageStatistics stats = ImageStatistics.getStatistics(ip);
ip.setHistogramSize(256);
return stats.histogram;
}
/** Erodes the image or ROI using a 3x3 maximum filter. Requires 8-bit or RGB image. */
public abstract void erode();
/** Dilates the image or ROI using a 3x3 minimum filter. Requires 8-bit or RGB image. */
public abstract void dilate();
/** For 16 and 32 bit processors, set 'lutAnimation' true
to have createImage() use the cached 8-bit version
of the image. */
public void setLutAnimation(boolean lutAnimation) {
this.lutAnimation = lutAnimation;
}
void resetPixels(Object pixels) {
if (pixels==null) {
if (img!=null) {
img.flush();
img = null;
}
}
}
/** Returns an 8-bit version of this image as a ByteProcessor. */
public ImageProcessor convertToByte(boolean doScaling) {
TypeConverter tc = new TypeConverter(this, doScaling);
return tc.convertToByte();
}
/** Returns a 16-bit version of this image as a ShortProcessor. */
public ImageProcessor convertToShort(boolean doScaling) {
TypeConverter tc = new TypeConverter(this, doScaling);
return tc.convertToShort();
}
/** Returns a 32-bit float version of this image as a FloatProcessor.
For byte and short images, converts using a calibration function
if a calibration table has been set using setCalibrationTable(). */
public ImageProcessor convertToFloat() {
TypeConverter tc = new TypeConverter(this, false);
return tc.convertToFloat(cTable);
}
/** Returns an RGB version of this image as a ColorProcessor. */
public ImageProcessor convertToRGB() {
TypeConverter tc = new TypeConverter(this, true);
return tc.convertToRGB();
}
/** Returns an 8-bit version of this image as a ByteProcessor. 16-bit and 32-bit
* pixel data are scaled from min-max to 0-255.
*/
public ByteProcessor convertToByteProcessor() {
return convertToByteProcessor(true);
}
/** Returns an 8-bit version of this image as a ByteProcessor. 16-bit and 32-bit
* pixel data are scaled from min-max to 0-255 if 'scale' is true.
*/
public ByteProcessor convertToByteProcessor(boolean scale) {
ByteProcessor bp;
if (this instanceof ByteProcessor)
bp = (ByteProcessor)this.duplicate();
else
bp = (ByteProcessor)this.convertToByte(scale);
return bp;
}
/** Returns a 16-bit version of this image as a ShortProcessor. 32-bit
* pixel data are scaled from min-max to 0-255.
*/
public ShortProcessor convertToShortProcessor() {
return convertToShortProcessor(true);
}
/** Returns a 16-bit version of this image as a ShortProcessor. 32-bit
* pixel data are scaled from min-max to 0-255 if 'scale' is true.
*/
public ShortProcessor convertToShortProcessor(boolean scale) {
ShortProcessor sp;
if (this instanceof ShortProcessor)
sp = (ShortProcessor)this.duplicate();
else
sp = (ShortProcessor)this.convertToShort(scale);
return sp;
}
/** Returns a 32-bit float version of this image as a FloatProcessor.
For byte and short images, converts using a calibration function
if a calibration table has been set using setCalibrationTable(). */
public FloatProcessor convertToFloatProcessor() {
FloatProcessor fp;
if (this instanceof FloatProcessor)
fp = (FloatProcessor)this.duplicate();
else
fp = (FloatProcessor)this.convertToFloat();
return fp;
}
/** Returns an RGB version of this image as a ColorProcessor. */
public ColorProcessor convertToColorProcessor() {
ColorProcessor cp;
if (this instanceof ColorProcessor)
cp = (ColorProcessor)this.duplicate();
else
cp = (ColorProcessor)this.convertToRGB();
return cp;
}
/** Performs a convolution operation using the specified kernel.
KernelWidth and kernelHeight must be odd. */
public abstract void convolve(float[] kernel, int kernelWidth, int kernelHeight);
/** Converts the image to binary using an automatically determined threshold.
For byte and short images, converts to binary using an automatically determined
threshold. For RGB images, converts each channel to binary. For
float images, does nothing.
*/
public void autoThreshold() {
threshold(getAutoThreshold());
}
/** Returns a pixel value (threshold) that can be used to divide the image into objects
and background. It does this by taking a test threshold and computing the average
of the pixels at or below the threshold and pixels above. It then computes the average
of those two, increments the threshold, and repeats the process. Incrementing stops
when the threshold is larger than the composite average. That is, threshold = (average
background + average objects)/2. This description was posted to the ImageJ mailing
list by Jordan Bevic. */
public int getAutoThreshold() {
return getAutoThreshold(getHistogram());
}
/** This is a version of getAutoThreshold() that uses a histogram passed as an argument. */
public int getAutoThreshold(int[] histogram) {
int level;
int maxValue = histogram.length - 1;
double result, sum1, sum2, sum3, sum4;
int count0 = histogram[0];
histogram[0] = 0; //set to zero so erased areas aren't included
int countMax = histogram[maxValue];
histogram[maxValue] = 0;
int min = 0;
while ((histogram[min]==0) && (min<maxValue))
min++;
int max = maxValue;
while ((histogram[max]==0) && (max>0))
max--;
if (min>=max) {
histogram[0]= count0; histogram[maxValue]=countMax;
level = histogram.length/2;
return level;
}
int movingIndex = min;
int inc = Math.max(max/40, 1);
do {
sum1=sum2=sum3=sum4=0.0;
for (int i=min; i<=movingIndex; i++) {
sum1 += (double)i*histogram[i];
sum2 += histogram[i];
}
for (int i=(movingIndex+1); i<=max; i++) {
sum3 += (double)i*histogram[i];
sum4 += histogram[i];
}
result = (sum1/sum2 + sum3/sum4)/2.0;
movingIndex++;
} while ((movingIndex+1)<=result && movingIndex<max-1);
histogram[0]= count0; histogram[maxValue]=countMax;
level = (int)Math.round(result);
return level;
}
/** Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
The clipping rectangle is reset by passing a null argument or by calling resetRoi(). */
public void setClipRect(Rectangle clipRect) {
if (clipRect==null) {
clipXMin = 0;
clipXMax = width-1;
clipYMin = 0;
clipYMax = height-1;
} else {
clipXMin = clipRect.x;
clipXMax = clipRect.x + clipRect.width - 1;
clipYMin = clipRect.y;
clipYMax = clipRect.y + clipRect.height - 1;
if (clipXMin<0) clipXMin = 0;
if (clipXMax>=width) clipXMax = width-1;
if (clipYMin<0) clipYMin = 0;
if (clipYMax>=height) clipYMax = height-1;
}
}
protected String maskSizeError(ImageProcessor mask) {
return "Mask size ("+mask.getWidth()+"x"+mask.getHeight()+") != ROI size ("+
roiWidth+"x"+roiHeight+")";
}
protected SampleModel getIndexSampleModel() {
if (sampleModel==null) {
IndexColorModel icm = getDefaultColorModel();
WritableRaster wr = icm.createCompatibleWritableRaster(1, 1);
sampleModel = wr.getSampleModel();
sampleModel = sampleModel.createCompatibleSampleModel(width, height);
}
return sampleModel;
}
/** Returns the default grayscale IndexColorModel. */
public IndexColorModel getDefaultColorModel() {
if (defaultColorModel==null) {
byte[] r = new byte[256];
byte[] g = new byte[256];
byte[] b = new byte[256];
for(int i=0; i<256; i++) {
r[i]=(byte)i;
g[i]=(byte)i;
b[i]=(byte)i;
}
defaultColorModel = new IndexColorModel(8, 256, r, g, b);
}
return defaultColorModel;
}
/** The getPixelsCopy() method returns a reference to the
snapshot buffer if it is not null and 'snapshotCopyMode' is true.
@see ImageProcessor#getPixelsCopy
@see ImageProcessor#snapshot
*/
public void setSnapshotCopyMode(boolean b) {
snapshotCopyMode = b;
}
/** Returns the number of color channels in the image. The color channels can be
* accessed by toFloat(channelNumber, fp) and written by setPixels(channelNumber, fp).
* @return 1 for grayscale images, 3 for RGB images
*/
public int getNChannels() {
return 1; /* superseded by ColorProcessor */
}
/** Returns a FloatProcessor with the image or one color channel thereof.
* The roi and mask are also set for the FloatProcessor.
* @param channelNumber Determines the color channel, 0=red, 1=green, 2=blue. Ignored for
* grayscale images.
* @param fp Here a FloatProcessor can be supplied, or null. The FloatProcessor
* is overwritten when converting data (re-using its pixels array
* improves performance).
* @return A FloatProcessor with the converted image data of the color channel selected
*/
public abstract FloatProcessor toFloat(int channelNumber, FloatProcessor fp);
/** Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
* @param channelNumber Determines the color channel, 0=red, 1=green, 2=blue.Ignored for
* grayscale images.
* @param fp The FloatProcessor where the image data are read from.
*/
public abstract void setPixels(int channelNumber, FloatProcessor fp);
/** Returns the minimum possible pixel value. */
public double minValue() {
return 0.0;
}
/** Returns the maximum possible pixel value. */
public double maxValue() {
return 255.0;
}
/** This method is used by CompositeImage.updateImage()
* to create RGB images (for display) of a multi-channel
* composite images.
*/
public void updateComposite(int[] rgbPixels, int mode) {
int redValue, greenValue, blueValue;
int size = width*height;
if (bytes==null || !lutAnimation)
bytes = create8BitImage();
if (cm==null)
makeDefaultColorModel();
if (reds==null || cm!=cm2)
updateLutBytes();
switch (mode) {
case UPDATE_RED: // update red channel
for (int i=0; i<size; i++)
rgbPixels[i] = (rgbPixels[i]&0xff00ffff) | (reds[bytes[i]&0xff]);
break;
case UPDATE_GREEN: // update green channel
for (int i=0; i<size; i++)
rgbPixels[i] = (rgbPixels[i]&0xffff00ff) | (greens[bytes[i]&0xff]);
break;
case UPDATE_BLUE: // update blue channel
for (int i=0; i<size; i++)
rgbPixels[i] = (rgbPixels[i]&0xffffff00) | blues[bytes[i]&0xff];
break;
case SET_FIRST_CHANNEL:
for (int i=0; i<size; i++) {
int index = bytes[i]&0xff;
rgbPixels[i] = reds[index] | greens[index] | blues[index];
}
break;
case SUM_PROJECTION:
for (int i=0; i<size; i++) {
int pixel = rgbPixels[i];
redValue = (pixel&0x00ff0000) + reds[bytes[i]&0xff];
greenValue = (pixel&0x0000ff00) + greens[bytes[i]&0xff];
blueValue = (pixel&0x000000ff) + blues[bytes[i]&0xff];
if (redValue>16711680) redValue = 16711680;
if (greenValue>65280) greenValue = 65280;
if (blueValue>255) blueValue = 255;
rgbPixels[i] = redValue | greenValue | blueValue;
}
break;
case MAX_PROJECTION:
for (int i=0; i<size; i++) {
int pixel = rgbPixels[i];
int index = bytes[i]&0xff;
redValue = reds[index]&0x00ff0000;
if (redValue>(pixel&0x00ff0000))
rgbPixels[i] = (rgbPixels[i]&0xff00ffff) | redValue;
greenValue = greens[index]&0x0000ff00;
if (greenValue>(pixel&0x0000ff00))
rgbPixels[i] = (rgbPixels[i]&0xffff00ff) | greenValue;
blueValue = blues[index]&0xff;
if (blueValue>(pixel&0xff))
rgbPixels[i] = (rgbPixels[i]&0xffffff00) | blueValue;
}
break;
case MIN_PROJECTION:
int pixel;
for (int i=0; i<size; i++) {
pixel = rgbPixels[i];
int index = bytes[i]&0xff;
redValue = reds[index]&0x00ff0000;
if (redValue<(pixel&0x00ff0000))
rgbPixels[i] = (rgbPixels[i]&0xff00ffff) | redValue;
greenValue = greens[index]&0x0000ff00;
if (greenValue<(pixel&0x0000ff00))
rgbPixels[i] = (rgbPixels[i]&0xffff00ff) | greenValue;
blueValue = blues[index]&0xff;
if (blueValue<(pixel&0xff))
rgbPixels[i] = (rgbPixels[i]&0xffffff00) | blueValue;
}
break;
}
lutAnimation = false;
}
// method and variables used by updateComposite()
byte[] create8BitImage() {return null;}
private byte[] bytes;
private int[] reds, greens, blues;
void updateLutBytes() {
IndexColorModel icm = (IndexColorModel)cm;
int mapSize = icm.getMapSize();
if (reds==null || reds.length!=mapSize) {
reds = new int[mapSize];
greens = new int[mapSize];
blues = new int[mapSize];
}
byte[] tmp = new byte[mapSize];
icm.getReds(tmp);
for (int i=0; i<mapSize; i++) reds[i] = (tmp[i]&0xff)<<16;
icm.getGreens(tmp);
for (int i=0; i<mapSize; i++) greens[i] = (tmp[i]&0xff)<<8;
icm.getBlues(tmp);
for (int i=0; i<mapSize; i++) blues[i] = tmp[i]&0xff;
cm2 = cm;
}
/** Sets the upper Over/Under threshold color. Can be called from a macro,
e.g., call("ij.process.ImageProcessor.setOverColor", 0,255,255). */
public static void setOverColor(int red, int green, int blue) {
overRed=red; overGreen=green; overBlue=blue;
}
/** Set the lower Over/Under thresholding color. */
public static void setUnderColor(int red, int green, int blue) {
underRed=red; underGreen=green; underBlue=blue;
}
/** Returns 'true' if this is a binary image (8-bit-image with only 0 and 255). */
public boolean isBinary() {
return false;
}
/** Returns 'true' if this is a signed 16-bit image. */
public boolean isSigned16Bit() {
return false;
}
/* This method is experimental and may be removed. */
public static void setUseBicubic(boolean b) {
useBicubic = b;
}
/** Calculates and returns uncalibrated statistics for this image or ROI,
* including histogram, area, mean, min and max, standard deviation,
* and mode. Use the setRoi(Roi) method to limit statistics to
* a non-rectangular area.
* @return an {@link ij.process.ImageStatistics} object
* @see #setRoi(Roi)
* @see #getStatistics
* @see ij.ImagePlus#getStatistics
*/
public ImageStatistics getStats() {
return ImageStatistics.getStatistics(this);
}
/** Calculates and returns complete uncalibrated (raw)
* statistics for this image or ROI but it is up to 70 times
* slower than getStats(). Use the setRoi(Roi) method to
* limit statistics to a non-rectangular area.
* @return an {@link ij.process.ImageStatistics} object
* @see #setRoi(Roi)
* @see #getStats
* @see ij.ImagePlus#getAllStatistics
*/
public ImageStatistics getStatistics() {
return ImageStatistics.getStatistics(this, Measurements.ALL_STATS, null);
}
/** Blurs the image by convolving with a Gaussian function. */
public void blurGaussian(double sigma) {
resetRoi();
GaussianBlur gb = new GaussianBlur();
gb.showProgress(false);
gb.blurGaussian(this, sigma);
}
/** Uses the Process/Math/Macro command to apply macro code to this image. */
public void applyMacro(String macro) {
ij.plugin.filter.ImageMath.applyMacro(this, macro, false);
}
/* Returns the PlugInFilter slice number. */
public int getSliceNumber() {
if (sliceNumber<1)
return 1;
else
return sliceNumber;
}
/** PlugInFilterRunner uses this method to set the slice number. */
public void setSliceNumber(int slice) {
sliceNumber = slice;
}
/** Returns a shallow copy of this ImageProcessor, where this
* image and the copy share pixel data. Use the duplicate() method
* to create a copy that does not share the pixel data.
* @see ImageProcessor#duplicate
*/
public Object clone() {
try {
return super.clone();
} catch (CloneNotSupportedException e) {
return null;
}
}
/** This method is used to display virtual stack overlays. */
public void setOverlay(Overlay overlay) {
this.overlay = overlay;
}
public Overlay getOverlay() {
return overlay;
}
protected int getProgressIncrement(int w, int h) {
if (progressBar==null)
return 0;
int inc = 0;
int threshold = 15000000;
if (interpolationMethod==BICUBIC)
threshold = 5000000;
boolean isBig = w*h>threshold;
if (isBig) {
inc = h/30;
if (inc<1) inc=1;
}
return inc;
}
public static void setRandomSeed(double randomSeed) {
seed = randomSeed;
}
/** Returns a binary mask, or null if a threshold is not set or this is an RGB image.
* @see ij.ImagePlus#createThresholdMask
* @see ij.ImagePlus#createRoiMask
*/
public ByteProcessor createMask() {
return null;
}
protected IndexColorModel getThresholdColorModel() {
byte[] r = new byte[256];
byte[] g = new byte[256];
byte[] b = new byte[256];
for(int i=0; i<255; i++) {
r[i]=(byte)i;
g[i]=(byte)i;
b[i]=(byte)i;
}
r[255] = (byte)255;
g[255] = (byte)0;
b[255] = (byte)0;
return new IndexColorModel(8, 256, r, g, b);
}
}