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Hey,
I'm trying to make a plugin that will export the coordinates of ROIs to a text file for further analysis in Mathematica. There's no issue deakling with one ROI. Things seem to go wrong when I try multiple (>1) ROIs. The group of ROIs becomes an array of ROIs. However, array[0].contains(x,y) returns false for all coordinates. Keep in mind that I primarily use Mathematica, so my Java programming is quite crude. I'm also not ruling out that I'm just overlooking a simple mistake. Here's the code:
public int[][] saveXYCoordinates(ImagePlus imp) {
Roi roi = imp.getRoi();
int count = 0;
if (roi==null)
throw new IllegalArgumentException("ROI required");
int i, j, height, width;
height= imp.getHeight();
width= imp.getWidth();
int[][] output = new int[height*width][2];
if (roi instanceof ShapeRoi) {
ShapeRoi p = (ShapeRoi)roi;
Roi[] rois = p.getRois();
IJ.log(Integer.toString(rois.length)); // returns the correct number of ROIs
if ((rois[0] instanceof PolygonRoi))
IJ.log("It's a polygon"); // Prints this
if (rois[0]!=null)
IJ.log("It's not null"); // This is also printed
PolygonRoi pr = (PolygonRoi)rois[0];
Rectangle r = pr.getBounds(); // This part is done so that I don't scan through the whole image
int xbase = r.x;
int ybase = r.y;
int xtop = r.width + xbase;
int ytop = r.height + ybase; // All these integers seem correct
IJ.log(Double.toString(rois[0].getLength()) ); // Both have perimeter > 0
IJ.log(Double.toString(rois[1].getLength()) );
for(i=xbase;i<=xtop;i++){
for(j=ybase;j<=ytop;j++){
if(pr.contains(i,j)){
IJ.log("HERE"); // Never prints this
output[count][0] = i;
output[count][1] = j;
count++;
}
}
return shorten(output,count);}
}
I apreciate any help.
Thanks,
David
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