double alignStep(final RandomAccessibleInterval<T> image) {
// compute error image = warped image - template
computeDifference(Views.extendBorder(image), currentTransform, template, error);
// compute transform parameter update
final double[] gradient = new double[numParameters];
for (int p = 0; p < numParameters; ++p) {
final Cursor<T> err = Views.flatIterable(error).cursor();
for (final T t : Views.flatIterable(Views.hyperSlice(descent, n, p)))
gradient[p] += t.getRealDouble() * err.next().getRealDouble();
}
final double[] dp = new double[numParameters];
LinAlgHelpers.mult(Hinv, gradient, dp);
// udpate transform
currentTransform.preConcatenate(warpFunction.getAffine(dp));
// return norm of parameter update vector
return LinAlgHelpers.length(dp);
}
/**
* 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;
}