I don't really remember how this works anymore. Documentation is unlikely to occur. Here's the code though. It did work.
Align_Stack.java:
import ij.*;
import ij.plugin.filter.PlugInFilter;
import ij.plugin.*;
import ij.process.*;
import ij.gui.*;
import java.awt.event.*;
import java.io.*;
import java.awt.Color;
/**
* This plugin implements the KeyListener interface and listens
* for key events generated by the current image.
*/
public class Align_Stack implements PlugIn, KeyListener {
ImagePlus img;
ImageProcessor flatProcessor;
ImagePlus flatImg;
ImageStack stack;
String fileName;
int[] flatdisplacementX;
int[] flatdisplacementY;
int[] flatrotation;
int depth;
int currentSlice;
int stepSize;
void reConstruct() {
flatProcessor.multiply(0);
for(int z = 1; z<=depth; z++){
ImageProcessor tempIp = stack.getProcessor(z).duplicate();
if (z == currentSlice) {
tempIp.multiply(.5);
} else if (Math.abs(z-currentSlice)<3){
tempIp.multiply(.1);
} else {
tempIp.multiply(.1/(depth-5));
}
flatProcessor.copyBits(tempIp,flatdisplacementX[z],flatdisplacementY[z],Blitter.ADD);
}
flatImg.updateAndDraw();
IJ.log("Slice: "+currentSlice);
}
void loadData() {
try {
if (!( new File(fileName).exists() )) {IJ.error("No input file");return;}
BufferedReader br = new BufferedReader(new FileReader(fileName));
for(int i=1;i<=depth;i++) {
String[] line = br.readLine().split(",");
flatdisplacementX[i]= new Integer(line[0]).intValue();
flatdisplacementY[i]= new Integer(line[1]).intValue();
flatrotation[i]= new Integer(line[2]).intValue();
stack.getProcessor(i).insert(img.getStack().getProcessor(i),0,0);
stack.getProcessor(i).rotate(flatrotation[i]);
}
br.close();
reConstruct();
return;
} catch (IOException e) {
IJ.showMessage("FileIO Error On Load: ", ""+e);
return;
}
}
void saveData() {
try {
new File(fileName).delete();
PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(fileName)));
for(int i=1;i<=depth;i++) {
pw.print(flatdisplacementX[i]+","+flatdisplacementY[i]+","+flatrotation[i]+"\n");
}
pw.flush();
pw.close();
} catch (IOException e) {
IJ.showMessage("FileIO Error On Write: ", ""+e);
return;
}
}
public void run(String arg) {
img = WindowManager.getCurrentImage();
ImageWindow win = img.getWindow();
ImageCanvas canvas = win.getCanvas();
canvas.addKeyListener(this);
IJ.write(img.toString());
//fileName = "/Users/peter/Pictures/registerdata";
fileName = img.getOriginalFileInfo().directory+img.getOriginalFileInfo().fileName+".stackAlignData";
depth = img.getStackSize();
stack = new ImageStack(img.getWidth(),img.getHeight());
for (int i = 1;i<=depth;i++) {
stack.addSlice(null,img.getStack().getProcessor(i).duplicate());
stack.getProcessor(i).invertLut();
}
flatdisplacementX = new int[depth+1];
flatdisplacementY = new int[depth+1];
flatrotation = new int[depth+1];
flatProcessor = img.getStack().getProcessor(1).duplicate();
currentSlice = 1;
flatImg = new ImagePlus("Projection", flatProcessor);
ImageCanvas flatCanvas = new ImageCanvas(flatImg);
reConstruct();
new ImageWindow(flatImg, flatCanvas);
}
public void keyPressed(KeyEvent e) {
int keyCode = e.getKeyCode();
char keyChar = e.getKeyChar();
int flags = e.getModifiers();
IJ.log("keyCode=" + keyCode + " (" + KeyEvent.getKeyText(keyCode)
+ ") keyChar=\"" + keyChar + "\" (" + (int)keyChar + ") "
+ KeyEvent.getKeyModifiersText(flags));
if(keyCode==34 && currentSlice < img.getStackSize()) {
currentSlice = currentSlice+1;
reConstruct();
}
if(keyCode==33 && currentSlice>1) {
currentSlice = currentSlice-1;
reConstruct();
}
if ((flags & KeyEvent.SHIFT_MASK) != 0) {
stepSize = 10;
} else {
stepSize = 1;
}
if(keyCode==39) {
flatdisplacementX[currentSlice] = flatdisplacementX[currentSlice] + stepSize;
reConstruct();
}
if(keyCode==37) {
flatdisplacementX[currentSlice] = flatdisplacementX[currentSlice] - stepSize;
reConstruct();
}
if(keyCode==40) {
flatdisplacementY[currentSlice] = flatdisplacementY[currentSlice] + stepSize;
reConstruct();
}
if(keyCode==38) {
flatdisplacementY[currentSlice] = flatdisplacementY[currentSlice] - stepSize;
reConstruct();
}
if(keyCode==107) {
flatrotation[currentSlice] = flatrotation[currentSlice] + stepSize/10;
stack.getProcessor(currentSlice).insert(img.getStack().getProcessor(currentSlice),0,0);
stack.getProcessor(currentSlice).setValue(0);
stack.getProcessor(currentSlice).rotate(flatrotation[currentSlice]);
reConstruct();
}
if(keyCode==109) {
flatrotation[currentSlice] = flatrotation[currentSlice] - stepSize/10;
stack.getProcessor(currentSlice).insert(img.getStack().getProcessor(currentSlice),0,0);
stack.getProcessor(currentSlice).setValue(0);
stack.getProcessor(currentSlice).rotate(flatrotation[currentSlice]);
reConstruct();
}
if(keyCode==10) {
ImageStack newStack = new ImageStack(img.getWidth(),img.getHeight(),img.getStack().getColorModel());
for( int z = 1; z <=depth; z++){
IJ.write("Stanrting :"+z);
ImageProcessor tempProcessor = img.getStack().getProcessor(z).duplicate();
tempProcessor.invertLut();
tempProcessor.rotate(flatrotation[z]);
newStack.addSlice(img.getStack().getSliceLabel(z), tempProcessor.createProcessor(img.getWidth(),img.getHeight())); //lousy initialize
newStack.getProcessor(z).copyBits(tempProcessor,flatdisplacementX[z],flatdisplacementY[z],Blitter.ADD);
newStack.getProcessor(z).invertLut();
}
ImagePlus newImg = new ImagePlus( );
newImg.setStack("Aligned_stack",newStack);
ImageCanvas newCanvas = new ImageCanvas(newImg);
new ImageWindow(newImg, newCanvas);
IJ.write("Step4");
}
if(keyCode==76) {
loadData();
}
if(keyCode==106) {
saveData();
}
if(keyCode==86) {
IJ.write("##### View Results #####");
for(int i=1;i<=depth;i++){
IJ.write("Slice "+i+": "+flatdisplacementX[i]+","+flatdisplacementY[i]+","+flatrotation[i]);
}
IJ.write("########################");
IJ.write(" ");
IJ.write(" ");
}
}
public void keyReleased(KeyEvent e) {}
public void keyTyped(KeyEvent e) {}
/** Returns the current list of modifier keys. */
public String modifiers(int flags) {
String s = " [ ";
if (flags == 0) return "";
if ((flags & KeyEvent.SHIFT_MASK) != 0) s += "Shift ";
if ((flags & KeyEvent.CTRL_MASK) != 0) s += "Control ";
if ((flags & KeyEvent.META_MASK) != 0) s += "Meta ";
if ((flags & KeyEvent.ALT_MASK) != 0) s += "Alt ";
s += "] ";
return s;
}
}
Align_Colors.java:
import ij.*;
import ij.plugin.filter.PlugInFilter;
import ij.plugin.*;
import ij.process.*;
import ij.gui.*;
import java.awt.event.*;
import java.io.*;
/**
* This plugin implements the KeyListener interface and listens
* for key events generated by the current image.
*/
public class Align_Colors implements PlugIn, KeyListener {
ImagePlus img;
ImageStack originalStack;
String fileName;
int[][] displacementX;
int[][] displacementY;
int[][] rotation;
int depth,w,h;
int currentColor; //0-red 1-green 2-blue
int stepSize;
void loadData() {
try {
if (!( new File(fileName).exists() )) {IJ.error("No input file");return;}
int startColor = currentColor;
BufferedReader br = new BufferedReader(new FileReader(fileName));
for(int i=1;i<=depth;i++) {
img.setSlice(i);
for(int c=0;c<3;c++){
String[] line = br.readLine().split(",");
displacementX[i][c]= new Integer(line[0]).intValue();
displacementY[i][c]= new Integer(line[1]).intValue();
rotation[i][c]= new Integer(line[2]).intValue();
currentColor=c;
refreshView();
}
}
br.close();
currentColor = startColor;
return;
} catch (IOException e) {
IJ.showMessage("FileIO Error On Load: ", ""+e);
return;
}
}
void saveData() {
try {
new File(fileName).delete();
PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(fileName)));
for(int i=1;i<=depth;i++) {
for(int c=0;c<3;c++){
pw.print(displacementX[i][c]+","+displacementY[i][c]+","+rotation[i][c]+"\n");
}
}
pw.flush();
pw.close();
} catch (IOException e) {
IJ.showMessage("FileIO Error On Write: ", ""+e);
return;
}
}
void refreshView() {
int currentSlice = img.getCurrentSlice();
byte[][] cbytes = new byte[3][w*h];
byte[][] obytes = new byte[3][w*h];
((ColorProcessor)(img.getStack().getProcessor(currentSlice))).getRGB(cbytes[0],cbytes[1],cbytes[2]);
((ColorProcessor)(originalStack.getProcessor(currentSlice))).getRGB(obytes[0],obytes[1],obytes[2]);
ByteProcessor tempProcessor = new ByteProcessor(w,h,obytes[currentColor],null);
tempProcessor.invertLut();
tempProcessor.rotate(rotation[currentSlice][currentColor]);
ByteProcessor tempProcessor2 = new ByteProcessor(w,h);
tempProcessor2.insert(tempProcessor,displacementX[currentSlice][currentColor],displacementY[currentSlice][currentColor]);
cbytes[currentColor]=(byte[])tempProcessor2.getPixels();
((ColorProcessor)(img.getStack().getProcessor(currentSlice))).setRGB(cbytes[0],cbytes[1],cbytes[2]);
img.updateAndDraw();
}
public void run(String arg) {
img = WindowManager.getCurrentImage();
ImageWindow win = img.getWindow();
ImageCanvas canvas = win.getCanvas();
canvas.addKeyListener(this);
fileName = img.getOriginalFileInfo().directory+img.getOriginalFileInfo().fileName+".colorAlignData";
depth = img.getStackSize();
w = img.getWidth();
h = img.getHeight();
originalStack = new ImageStack(w,h);
for (int i = 1;i<=depth;i++) {
IJ.showProgress((i-1)/depth);
originalStack.addSlice(null,img.getStack().getProcessor(i).duplicate());
}
displacementX = new int[depth+1][3];
displacementY = new int[depth+1][3];
rotation = new int[depth+1][3];
}
public void keyPressed(KeyEvent e) {
int keyCode = e.getKeyCode();
char keyChar = e.getKeyChar();
int flags = e.getModifiers();
IJ.log("keyCode=" + keyCode + " (" + KeyEvent.getKeyText(keyCode)
+ ") keyChar=\"" + keyChar + "\" (" + (int)keyChar + ") "
+ KeyEvent.getKeyModifiersText(flags));
int currentSlice = img.getCurrentSlice();
if ((flags & KeyEvent.SHIFT_MASK) != 0) {
stepSize = 10;
} else {
stepSize = 1;
}
if(keyCode==39) {
displacementX[currentSlice][currentColor] = displacementX[currentSlice][currentColor] + stepSize;
refreshView();
}
if(keyCode==37) {
displacementX[currentSlice][currentColor] = displacementX[currentSlice][currentColor] - stepSize;
refreshView();
}
if(keyCode==40) {
displacementY[currentSlice][currentColor] = displacementY[currentSlice][currentColor] + stepSize;
refreshView();
}
if(keyCode==38) {
displacementY[currentSlice][currentColor] = displacementY[currentSlice][currentColor] - stepSize;
refreshView();
}
if(keyCode==107) {
rotation[currentSlice][currentColor] = rotation[currentSlice][currentColor] + stepSize/10;
refreshView();
}
if(keyCode==109) {
rotation[currentSlice][currentColor] = rotation[currentSlice][currentColor] - stepSize/10;
refreshView();
}
if(keyCode==76) {
loadData();
}
if(keyCode==106) {
saveData();
}
if(keyCode==82) {
currentColor=0;
}
if(keyCode==71) {
currentColor=1;
}
if(keyCode==66) {
currentColor=2;
}
if(keyCode==86) {
IJ.write("##### View Results #####");
for(int i=1;i<=depth;i++){
for(int c=0;c<3;c++){
IJ.write(displacementX[i][c]+","+displacementY[i][c]+","+rotation[i][c]);
}
}
IJ.write("########################");
IJ.write(" ");
IJ.write(" ");
}
}
public void keyReleased(KeyEvent e) {}
public void keyTyped(KeyEvent e) {}
/** Returns the current list of modifier keys. */
public String modifiers(int flags) {
String s = " [ ";
if (flags == 0) return "";
if ((flags & KeyEvent.SHIFT_MASK) != 0) s += "Shift ";
if ((flags & KeyEvent.CTRL_MASK) != 0) s += "Control ";
if ((flags & KeyEvent.META_MASK) != 0) s += "Meta ";
if ((flags & KeyEvent.ALT_MASK) != 0) s += "Alt ";
s += "] ";
return s;
}
}