@Override
public void updateOverlay(final F figure, final OverlayView view) {
final Color strokeColor = figure.get(AttributeKeys.STROKE_COLOR);
final Overlay overlay = view.getData();
overlay.setLineColor(AWTColors.getColorRGB(strokeColor));
// The line style is intentionally omitted here because it is ambiguous and
// because there is no UI for setting it by the JHotDraw UI.
// FIXME - is this next line dangerous for drawing attributes? width could
// conceivably be 0.
overlay.setLineWidth(figure.get(AttributeKeys.STROKE_WIDTH));
final Color fillColor = figure.get(AttributeKeys.FILL_COLOR);
overlay.setFillColor(AWTColors.getColorRGB(fillColor));
overlay.setAlpha(fillColor.getAlpha());
}
@Override
public void run() {
if (!threshSrv.hasThreshold(input)) {
cancel("This command requires a thresholded image.");
return;
}
ThresholdOverlay thresh = threshSrv.getThreshold(input);
PointSetIterator iter = thresh.getPointsWithin().iterator();
if (!iter.hasNext()) {
cancel("No pixels are within the threshold");
return;
}
Dataset ds = dispSrv.getActiveDataset(input);
final int numDims = ds.numDimensions();
final long[] dimensions = new long[numDims];
final long[] min = new long[numDims];
/*
* First pass - find minima and maxima so we can use a shrunken image in some cases.
*/
for (int i = 0; i < numDims; i++) {
min[i] = (long) Math.floor(thresh.realMin(i));
dimensions[i] = (long) Math.floor(thresh.realMax(i) - thresh.realMin(i) + 1);
}
final ArrayImg<BitType, BitArray> arrayMask =
new ArrayImgFactory<BitType>().createBitInstance(dimensions, 1);
final BitType t = new BitType(arrayMask);
arrayMask.setLinkedType(t);
final Img<BitType> mask =
new ImgTranslationAdapter<BitType, ArrayImg<BitType, BitArray>>(arrayMask, min);
final RandomAccess<BitType> raMask = mask.randomAccess();
iter.reset();
while (iter.hasNext()) {
long[] pos = iter.next();
raMask.setPosition(pos);
raMask.get().set(true);
}
output =
new BinaryMaskOverlay(context, new BinaryMaskRegionOfInterest<BitType, Img<BitType>>(mask));
output.setAlpha(alpha);
output.setFillColor(color);
for (int i = 0; i < numDims; i++) {
output.setAxis(ds.getImgPlus().axis(i), i);
}
}