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ij.plugin.ImageCalculator Maven / Gradle / Ivy
ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.
package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.plugin.filter.*;
import ij.measure.Calibration;
import ij.plugin.frame.Recorder;
import ij.macro.Interpreter;
/** This plugin implements the Process/Image Calculator command.
// test script
imp1 = IJ.openImage("http://imagej.nih.gov/ij/images/boats.gif")
imp2 = IJ.openImage("http://imagej.nih.gov/ij/images/bridge.gif")
imp3 = ImageCalculator.run(imp1, imp2, "add create 32-bit");
imp3.show();
*/
public class ImageCalculator implements PlugIn {
private static String[] operators = {"Add","Subtract","Multiply","Divide", "AND", "OR", "XOR", "Min", "Max", "Average", "Difference", "Copy", "Transparent-zero"};
private static String[] lcOperators = {"add","sub","mul","div", "and", "or", "xor", "min", "max", "ave", "diff", "copy", "zero"};
private static int operator;
private static String title1 = "";
private static String title2 = "";
private static boolean createWindow = true;
private static boolean floatResult;
private boolean processStack;
private boolean macroCall;
public void run(String arg) {
int[] wList = WindowManager.getIDList();
if (wList==null) {
IJ.noImage();
return;
}
IJ.register(ImageCalculator.class);
String[] titles = new String[wList.length];
for (int i=0; i
imp3 = ImageCalculator.run(imp1, imp2, "divide create 32-bit");
divides 'imp1' by 'imp2' and returns the result as a new 32-bit image.
*/
public static ImagePlus run(ImagePlus img1, ImagePlus img2, String operation) {
ImageCalculator ic = new ImageCalculator();
return ic.run(operation, img1, img2);
}
public ImagePlus run(String operation, ImagePlus img1, ImagePlus img2) {
if (img1==null || img2==null || operation==null) return null;
operator = getOperator(operation);
if (operator==-1)
throw new IllegalArgumentException("No valid operator");
createWindow = operation.indexOf("create")!=-1;
floatResult= operation.indexOf("32")!=-1 || operation.indexOf("float")!=-1;
processStack = operation.indexOf("stack")!=-1;
return calculate(img1, img2, true);
}
/**
* @deprecated
* replaced by run(String,ImagePlus,ImagePlus)
*/
public void calculate(String operation, ImagePlus img1, ImagePlus img2) {
if (img1==null || img2==null || operation==null) return;
operator = getOperator(operation);
if (operator==-1)
{IJ.error("Image Calculator", "No valid operator"); return;}
createWindow = operation.indexOf("create")!=-1;
floatResult = operation.indexOf("32")!=-1 || operation.indexOf("float")!=-1;
processStack = operation.indexOf("stack")!=-1;
macroCall = true;
ImagePlus img3 = calculate(img1, img2, true);
if (img3!=null) img3.show();
}
int getOperator(String options) {
options = options.toLowerCase();
int op= -1;
if (options.indexOf("xor")!=-1)
op = 6;
if (op==-1) {
for (int i=0; i
1||size2>1))
img3 = doStackOperation(img1, img2);
else
img3 = doOperation(img1, img2);
if (img3==null && !macroCall && (img1.getWindow()==null))
img3 = img1;
return img3;
}
boolean stackOp = false;
if (size1>1) {
int result = IJ.setupDialog(img1, PlugInFilter.NO_CHANGES);
if (result==PlugInFilter.DONE)
return null;
processStack = (result&PlugInFilter.DOES_STACKS)!=0;
if (processStack) {
if (img1.getStack().isVirtual())
createWindow = true;
img3 = doStackOperation(img1, img2);
stackOp = true;
} else
img3 = doOperation(img1, img2);
} else
img3 = doOperation(img1, img2);
if (Recorder.record) {
String options = operators[operator];
if (createWindow) options += " create";
if (floatResult) options += " 32-bit";
if (stackOp) options += " stack";
if (Recorder.scriptMode()) {
Recorder.recordCall("ImagePlus", "imp1 = WindowManager.getImage(\""+img1.getTitle()+"\");");
Recorder.recordCall("ImagePlus", "imp2 = WindowManager.getImage(\""+img2.getTitle()+"\");");
Recorder.recordCall("ImagePlus", "imp3 = ImageCalculator.run(imp1, imp2, \""+options+"\");");
Recorder.recordCall("imp3.show();");
} else
Recorder.record("imageCalculator", options, img1.getTitle(), img2.getTitle());
Recorder.setCommand(null); // don't record run(...)
}
return img3;
}
/** img1 = img2 op img2 (e.g. img1 = img2/img1) */
ImagePlus doStackOperation(ImagePlus img1, ImagePlus img2) {
ImagePlus img3 = null;
int size1 = img1.getStackSize();
int size2 = img2.getStackSize();
if (size1>1 && size2>1 && size1!=size2) {
IJ.error("Image Calculator", "'Image1' and 'image2' must be stacks with the same\nnumber of slices, or 'image2' must be a single image.");
return null;
}
if (createWindow) {
img1 = duplicateStack(img1);
if (img1==null) {
IJ.error("Calculator", "Out of memory");
return null;
}
img3 = img1;
}
int mode = getBlitterMode();
ImageWindow win = img1.getWindow();
if (win!=null)
WindowManager.setCurrentWindow(win);
else if (Interpreter.isBatchMode() && !createWindow && WindowManager.getImage(img1.getID())!=null)
IJ.selectWindow(img1.getID());
Undo.reset();
ImageStack stack1 = img1.getStack();
StackProcessor sp = new StackProcessor(stack1, img1.getProcessor());
try {
if (size2==1)
sp.copyBits(img2.getProcessor(), 0, 0, mode);
else
sp.copyBits(img2.getStack(), 0, 0, mode);
}
catch (IllegalArgumentException e) {
IJ.error("\""+img1.getTitle()+"\": "+e.getMessage());
return null;
}
img1.setStack(null, stack1);
if (img1.getType()!=ImagePlus.GRAY8) {
img1.getProcessor().resetMinAndMax();
}
if (img3==null)
img1.updateAndDraw();
return img3;
}
ImagePlus doOperation(ImagePlus img1, ImagePlus img2) {
ImagePlus img3 = null;
int mode = getBlitterMode();
ImageProcessor ip1 = img1.getProcessor();
ImageProcessor ip2 = img2.getProcessor();
Calibration cal1 = img1.getCalibration();
Calibration cal2 = img2.getCalibration();
if (createWindow)
ip1 = createNewImage(ip1, ip2);
else {
ImageWindow win = img1.getWindow();
if (win!=null)
WindowManager.setCurrentWindow(win);
else if (Interpreter.isBatchMode() && !createWindow && WindowManager.getImage(img1.getID())!=null)
IJ.selectWindow(img1.getID());
ip1.snapshot();
Undo.setup(Undo.FILTER, img1);
}
boolean rgb = ip2 instanceof ColorProcessor;
if (floatResult && !rgb)
ip2 = ip2.convertToFloat();
try {
ip1.copyBits(ip2, 0, 0, mode);
}
catch (IllegalArgumentException e) {
IJ.error("\""+img1.getTitle()+"\": "+e.getMessage());
return null;
}
if (floatResult && rgb)
ip1 = ip1.convertToFloat();
if (!(ip1 instanceof ByteProcessor))
ip1.resetMinAndMax();
if (createWindow) {
img3 = new ImagePlus("Result of "+img1.getTitle(), ip1);
img3.setCalibration(cal1);
} else
img1.updateAndDraw();
return img3;
}
ImageProcessor createNewImage(ImageProcessor ip1, ImageProcessor ip2) {
int width = Math.min(ip1.getWidth(), ip2.getWidth());
int height = Math.min(ip1.getHeight(), ip2.getHeight());
ImageProcessor ip3 = ip1.createProcessor(width, height);
if (floatResult && !(ip1 instanceof ColorProcessor)) {
ip1 = ip1.convertToFloat();
ip3 = ip3.convertToFloat();
}
ip3.insert(ip1, 0, 0);
return ip3;
}
private int getBlitterMode() {
int mode=0;
switch (operator) {
case 0: mode = Blitter.ADD; break;
case 1: mode = Blitter.SUBTRACT; break;
case 2: mode = Blitter.MULTIPLY; break;
case 3: mode = Blitter.DIVIDE; break;
case 4: mode = Blitter.AND; break;
case 5: mode = Blitter.OR; break;
case 6: mode = Blitter.XOR; break;
case 7: mode = Blitter.MIN; break;
case 8: mode = Blitter.MAX; break;
case 9: mode = Blitter.AVERAGE; break;
case 10: mode = Blitter.DIFFERENCE; break;
case 11: mode = Blitter.COPY; break;
case 12: mode = Blitter.COPY_ZERO_TRANSPARENT; break;
}
return mode;
}
ImagePlus duplicateStack(ImagePlus img1) {
Calibration cal = img1.getCalibration();
ImageStack stack1 = img1.getStack();
int width = stack1.getWidth();
int height = stack1.getHeight();
int n = stack1.getSize();
ImageStack stack2 = img1.createEmptyStack();
try {
for (int i=1; i<=n; i++) {
ImageProcessor ip1 = stack1.getProcessor(i);
ip1.resetRoi();
ImageProcessor ip2 = ip1.crop();
if (floatResult) {
ip2.setCalibrationTable(cal.getCTable());
ip2 = ip2.convertToFloat();
}
stack2.addSlice(stack1.getSliceLabel(i), ip2);
}
}
catch(OutOfMemoryError e) {
stack2.trim();
stack2 = null;
return null;
}
ImagePlus img3 = new ImagePlus("Result of "+img1.getTitle(), stack2);
img3.setCalibration(cal);
if (img3.getStackSize()==n) {
int[] dim = img1.getDimensions();
img3.setDimensions(dim[2], dim[3], dim[4]);
if (img1.isComposite()) {
img3 = new CompositeImage(img3, 0);
((CompositeImage)img3).copyLuts(img1);
}
if (img1.isHyperStack())
img3.setOpenAsHyperStack(true);
}
return img3;
}
}
