/**
* Finds the position value in the image series map that is closest to the POI. This partially
* populates an Image object but does NOT include the image id.
*
* @param imageSeries
* @param poi
* @return
* @throws IOException
*/
private void getClosestPosition(ImageSeries imageSeries, Point3d poi100, Image image)
throws IOException {
URL u = new URL(assembleAtlasMapURI(imageSeries.imageSeriesId));
LOG.debug("Atlas map URI: {}", u.toString());
BufferedReader in = new BufferedReader(new InputStreamReader(u.openStream()));
String line = null;
// discard first 2 lines
in.readLine();
in.readLine();
double leastDistance = Double.POSITIVE_INFINITY;
String[] bestLineSegs = null;
int count = 2;
while ((line = in.readLine()) != null) {
String[] lineSegs = line.split(",");
Point3d abaCoordinates =
new Point3d(
Double.parseDouble(lineSegs[0]),
Double.parseDouble(lineSegs[1]),
Double.parseDouble(lineSegs[2]));
LOG.debug("lineSegs X: {}", lineSegs[0]);
LOG.debug("lineSegs Y: {}", lineSegs[1]);
LOG.debug("lineSegs Z: {}", lineSegs[2]);
if (poi100.distanceSquared(abaCoordinates) < leastDistance) {
leastDistance = poi100.distanceSquared(abaCoordinates);
bestLineSegs = lineSegs;
}
// debug
if ((++count % 1000) == 0) {
System.out.printf("%d%n", count);
}
}
in.close();
image.imagesCheckedForProximity = count;
image.abaCoordinates =
new Point3d(
Double.parseDouble(bestLineSegs[0]),
Double.parseDouble(bestLineSegs[1]),
Double.parseDouble(bestLineSegs[2]));
image.abaXPixelPosition = Integer.parseInt(bestLineSegs[3]);
image.abaYPixelPosition = Integer.parseInt(bestLineSegs[4]);
image.abaImagePosition = bestLineSegs[5];
LOG.debug("Points examined: {}", count);
}
private double calcSingleAsa(int i) {
Atom atom_i = atoms[i];
ArrayList<Integer> neighbor_indices = findNeighborIndices(i);
int n_neighbor = neighbor_indices.size();
int j_closest_neighbor = 0;
double radius = probe + radii[i];
int n_accessible_point = 0;
for (Point3d point : spherePoints) {
boolean is_accessible = true;
Point3d test_point =
new Point3d(
point.x * radius + atom_i.getX(),
point.y * radius + atom_i.getY(),
point.z * radius + atom_i.getZ());
int[] cycled_indices = new int[n_neighbor];
int arind = 0;
for (int ind = j_closest_neighbor; ind < n_neighbor; ind++) {
cycled_indices[arind] = ind;
arind++;
}
for (int ind = 0; ind < j_closest_neighbor; ind++) {
cycled_indices[arind] = ind;
arind++;
}
for (int j : cycled_indices) {
Atom atom_j = atoms[neighbor_indices.get(j)];
double r = radii[neighbor_indices.get(j)] + probe;
double diff_sq = test_point.distanceSquared(new Point3d(atom_j.getCoords()));
if (diff_sq < r * r) {
j_closest_neighbor = j;
is_accessible = false;
break;
}
}
if (is_accessible) {
n_accessible_point++;
}
}
return cons * n_accessible_point * radius * radius;
}