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package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.measure.Calibration;
import ij.plugin.frame.Recorder;
import java.awt.AWTEvent;
import java.awt.geom.Rectangle2D;
/**
* The plugin implements the Image/Adjust/Coordinates command. It allows
* the user to set the corner coordinates of the selection bounds or the full image.
* This modifies the image scale (pixelWidth, pixelHeight) and the xOrigin, yOrigin.
* If a single point is selected, the coordinates of the point can be specified, which only
* sets the xOrigin and yOrigin.
* Units for x and y can be also selected (2016-08-30, Michael Schmid).
* Z unit of stacks can be selected (2019-09-30, Stein Rorvik).
*/
public class Coordinates implements PlugIn, DialogListener {
private static final String help = "<html>"
+"<h1>Image>Adjust>Coordinates</h1>"
+"<font size=+1>"
+"This command allows the user to set the corner coordinates of<br>the selection bounds "
+"or the full image. This modifies the image<br>scale (<i>pixelWidth</i>, <i>pixelHeight</i>) and <i>xOrigin</i> and <i>yOrigin</i>. "
+"If a<br>single point is selected, the coordinates of the point can be<br>specified, which only "
+"sets <i>xOrigin</i> and <i>yOrigin</i>. The units for X<br>and Y can be also selected.<br> "
+"</font>";
private final static String SAME_AS_X = "<same as x unit>";
private final static int IMAGE = 0, ROI_BOUNDS = 1, POINT = 2; //mode: coordinates of what to specify
private int mode = IMAGE;
private boolean isStack;
public void run(String arg) {
ImagePlus imp = IJ.getImage();
int imageHeight = imp.getHeight();
Calibration cal = imp.getCalibration();
Roi roi = imp.getRoi();
Rectangle2D.Double bounds = null;
int numSlices = imp.getNSlices();
int currSlice = imp.getCurrentSlice();
isStack = numSlices>1;
if (roi != null) {
bounds = roi.getFloatBounds();
if (bounds.width==0 && bounds.height==0)
mode = POINT;
else
mode = ROI_BOUNDS;
} else { //no Roi, use image bounds
bounds = new Rectangle2D.Double(0, 0, imp.getWidth(), imp.getHeight());
}
String title = (mode==IMAGE ? "Image" : "Selection") +" Coordinates";
if (mode == POINT)
title = "Point Coordinates";
GenericDialog gd = new GenericDialog(title);
if (mode == POINT) {
gd.addNumericField("X:", cal.getX(bounds.x), 2, 8, "");
gd.addNumericField("Y:", cal.getY(bounds.y, imageHeight), 2, 8, "");
if (isStack)
gd.addNumericField("Z:", cal.getZ(currSlice-1), 2, 8, "");
} else {
gd.addNumericField("Left:", cal.getX(bounds.x), 2, 8, "");
gd.addNumericField("Right:", cal.getX(bounds.x+bounds.width), 2, 8, "");
gd.addNumericField("Top:", cal.getY(bounds.y, imageHeight), 2, 8, "");
gd.addNumericField("Bottom:", cal.getY(bounds.y+bounds.height, imageHeight), 2, 8, "");
if (isStack) {
gd.addNumericField("Front:", cal.getZ(0), 2, 8, "");
gd.addNumericField("Back:", cal.getZ(numSlices), 2, 8, "");
}
}
String xUnit = cal.getUnit();
String yUnit = cal.getYUnit();
String zUnit = cal.getZUnit();
boolean xUnitChanged=false,yUnitChanged=false,zUnitChanged=false;
gd.addStringField("X_unit:", xUnit, 18);
gd.addStringField("Y_unit:", yUnit.equals(xUnit) ? SAME_AS_X : yUnit, 18);
if (isStack)
gd.addStringField("Z_unit:", zUnit.equals(xUnit) ? SAME_AS_X : zUnit, 18);
gd.addHelp(help);
gd.addDialogListener(this);
gd.showDialog();
if (gd.wasCanceled())
return;
if (mode == POINT) {
double x = gd.getNextNumber();
double y = gd.getNextNumber();
if (gd.invalidNumber()) {
IJ.error("Invalid number");
return;
}
cal.xOrigin = coordinate2offset(x, bounds.x, cal.pixelWidth);
cal.yOrigin = coordinate2offset(y, bounds.y, cal.getInvertY() ? -cal.pixelHeight : cal.pixelHeight);
if (isStack) {
double z = gd.getNextNumber();
if (gd.invalidNumber()) {
IJ.error("Invalid number");
return;
}
cal.zOrigin = coordinate2offset(z, currSlice-1, cal.pixelDepth);
}
} else {
double xl = gd.getNextNumber();
double xr = gd.getNextNumber();
double yt = gd.getNextNumber();
double yb = gd.getNextNumber();
if (gd.invalidNumber()) {
IJ.error("Invalid number");
return;
}
cal.pixelWidth = (xr-xl)/bounds.width;
cal.pixelHeight = (yb-yt)/bounds.height;
cal.xOrigin = coordinate2offset(xl, bounds.x, cal.pixelWidth);
cal.yOrigin = coordinate2offset(yt, bounds.y, cal.pixelHeight);
cal.setInvertY(cal.pixelHeight < 0);
if (isStack) {
double zf = gd.getNextNumber();
double zl = gd.getNextNumber();
cal.pixelDepth = (zl-zf)/numSlices;
cal.zOrigin = coordinate2offset(zf, 0, cal.pixelDepth);
}
if (cal.pixelHeight < 0)
cal.pixelHeight = -cal.pixelHeight;
}
String xUnit2 = gd.getNextString();
xUnitChanged = !xUnit2.equals(xUnit);
if (xUnitChanged)
cal.setXUnit(xUnit2);
String yUnit2 = gd.getNextString();
yUnitChanged = !yUnit2.equals(yUnit) && !yUnit2.equals(SAME_AS_X);
if (yUnitChanged)
cal.setYUnit(yUnit2);
String zUnit2 = null;
if (isStack) {
zUnit2 = gd.getNextString();
zUnitChanged = !zUnit2.equals(zUnit) && !zUnit2.equals(SAME_AS_X);
if (zUnitChanged)
cal.setZUnit(zUnit2);
}
ImageWindow win = imp.getWindow();
imp.repaintWindow();
if (Recorder.record) {
if (Recorder.scriptMode()) {
if (xUnitChanged)
Recorder.recordCall("imp.getCalibration().setXUnit(\""+xUnit2+"\");", true);
if (yUnitChanged)
Recorder.recordCall("imp.getCalibration().setYUnit(\""+yUnit2+"\");", true);
if (zUnitChanged)
Recorder.recordCall("imp.getCalibration().setZUnit(\""+zUnit2+"\");", true);
} else {
if (xUnitChanged)
Recorder.record("Stack.setXUnit", xUnit2);
if (yUnitChanged)
Recorder.record("Stack.setYUnit", yUnit2);
if (zUnitChanged)
Recorder.record("Stack.setZUnit", zUnit2);
}
}
}
public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
if (mode == POINT) {
gd.getNextNumber();
gd.getNextNumber();
if (isStack)
gd.getNextNumber();
return (!gd.invalidNumber());
} else {
double xl = gd.getNextNumber();
double xr = gd.getNextNumber();
double yt = gd.getNextNumber();
double yb = gd.getNextNumber();
if (isStack) {
double zf = gd.getNextNumber();
double zl = gd.getNextNumber();
return (!gd.invalidNumber() && (xr>xl) && (yt!=yb) && (zl>zf));
} else
return (!gd.invalidNumber() && xr>xl && yt!=yb);
}
}
// Calculates pixel offset from scaled coordinates of a point with given pixel position
private double coordinate2offset(double coordinate, double pixelPos, double pixelSize) {
return pixelPos - coordinate/pixelSize;
}
}
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