/**
* Test whether the {@code containing} interval completely contains the {@code contained}
* interval.
*
* <p>TODO: move to {@link Intervals}
*
* @param containing
* @param contained
* @return
*/
public static final boolean contains(final Interval containing, final Interval contained) {
assert containing.numDimensions() == contained.numDimensions();
final int n = containing.numDimensions();
for (int d = 0; d < n; ++d) {
if (containing.min(d) > contained.min(d) || containing.max(d) < contained.max(d))
return false;
}
return true;
}
public static String printInterval(final Interval interval) {
String out = "(Interval empty)";
if (interval == null || interval.numDimensions() == 0) return out;
out = "[" + interval.min(0);
for (int i = 1; i < interval.numDimensions(); i++) out += ", " + interval.min(i);
out += "] -> [" + interval.max(0);
for (int i = 1; i < interval.numDimensions(); i++) out += ", " + interval.max(i);
out += "], dimensions (" + interval.dimension(0);
for (int i = 1; i < interval.numDimensions(); i++) out += ", " + interval.dimension(i);
out += ")";
return out;
}
/**
* Create a long[] with the max coordinates of an {@link Interval}.
*
* <p>Keep in mind that creating arrays wildly is not good practice and consider using the
* interval directly.
*
* @param interval
* @return dimensions of the interval as a new long[]
*/
public static final long[] intervalMax(final Interval interval) {
final long[] max = new long[interval.numDimensions()];
interval.max(max);
return max;
}
/**
* Get a "good" initial viewer transform. The viewer transform is chosen such that for the first
* source,
*
* <ul>
* <li>the XY plane is aligned with the screen plane,
* <li>the <em>z = dim_z / 2</em> slice is shown,
* <li>centered and scaled such that the full <em>dim_x</em> by <em>dim_y</em> is visible.
* </ul>
*
* @param viewerWidth width of the viewer display
* @param viewerHeight height of the viewer display
* @param state the {@link ViewerState} containing at least one source.
* @return proposed initial viewer transform.
*/
public static AffineTransform3D initTransform(
final int viewerWidth,
final int viewerHeight,
final boolean zoomedIn,
final ViewerState state) {
final int cX = viewerWidth / 2;
final int cY = viewerHeight / 2;
final Source<?> source = state.getSources().get(state.getCurrentSource()).getSpimSource();
final int timepoint = state.getCurrentTimepoint();
if (!source.isPresent(timepoint)) return new AffineTransform3D();
final AffineTransform3D sourceTransform = new AffineTransform3D();
source.getSourceTransform(timepoint, 0, sourceTransform);
final Interval sourceInterval = source.getSource(timepoint, 0);
final double sX0 = sourceInterval.min(0);
final double sX1 = sourceInterval.max(0);
final double sY0 = sourceInterval.min(1);
final double sY1 = sourceInterval.max(1);
final double sZ0 = sourceInterval.min(2);
final double sZ1 = sourceInterval.max(2);
final double sX = (sX0 + sX1 + 1) / 2;
final double sY = (sY0 + sY1 + 1) / 2;
final double sZ = (sZ0 + sZ1 + 1) / 2;
final double[][] m = new double[3][4];
// rotation
final double[] qSource = new double[4];
final double[] qViewer = new double[4];
Affine3DHelpers.extractApproximateRotationAffine(sourceTransform, qSource, 2);
LinAlgHelpers.quaternionInvert(qSource, qViewer);
LinAlgHelpers.quaternionToR(qViewer, m);
// translation
final double[] centerSource = new double[] {sX, sY, sZ};
final double[] centerGlobal = new double[3];
final double[] translation = new double[3];
sourceTransform.apply(centerSource, centerGlobal);
LinAlgHelpers.quaternionApply(qViewer, centerGlobal, translation);
LinAlgHelpers.scale(translation, -1, translation);
LinAlgHelpers.setCol(3, translation, m);
final AffineTransform3D viewerTransform = new AffineTransform3D();
viewerTransform.set(m);
// scale
final double[] pSource = new double[] {sX1 + 0.5, sY1 + 0.5, sZ};
final double[] pGlobal = new double[3];
final double[] pScreen = new double[3];
sourceTransform.apply(pSource, pGlobal);
viewerTransform.apply(pGlobal, pScreen);
final double scaleX = cX / pScreen[0];
final double scaleY = cY / pScreen[1];
final double scale;
if (zoomedIn) scale = Math.max(scaleX, scaleY);
else scale = Math.min(scaleX, scaleY);
viewerTransform.scale(scale);
// window center offset
viewerTransform.set(viewerTransform.get(0, 3) + cX, 0, 3);
viewerTransform.set(viewerTransform.get(1, 3) + cY, 1, 3);
return viewerTransform;
}