/**
* Rotate the oriented bounding box of the 3D image about the specified axis with the specified
* angle.
*
* @param transform The transform and its matrix by which to rotate the image.
*/
public void rotateFrameBy(Transform3D transform) {
double rY, rX, rZ;
double sinrX, sinrY, sinrZ, cosrX, cosrY, cosrZ;
Matrix3d matrix = new Matrix3d();
transform.get(matrix);
rY = -Math.asin(matrix.m02);
if (Math.cos(rY) != 0) {
rX = -Math.atan2(matrix.m12, matrix.m22);
rZ = Math.atan2(matrix.m01, matrix.m00);
} else {
rX = -Math.atan2(matrix.m10, matrix.m11);
rZ = 0;
}
cosrX = Math.cos(rX);
sinrX = Math.sin(rX);
cosrY = Math.cos(rY);
sinrY = Math.sin(rY);
cosrZ = Math.cos(rZ);
sinrZ = Math.sin(rZ);
matrix.m00 = cosrZ * cosrY;
matrix.m01 = -sinrZ * cosrY;
matrix.m02 = sinrY;
matrix.m10 = (cosrZ * sinrY * sinrX) + (sinrZ * cosrX);
matrix.m11 = (-sinrZ * sinrY * sinrX) + (cosrZ * cosrX);
matrix.m12 = -cosrY * sinrX;
matrix.m20 = (-cosrZ * sinrY * cosrX) + (sinrZ * sinrX);
matrix.m21 = (sinrZ * sinrY * cosrX) + (cosrZ * sinrX);
matrix.m22 = cosrY * cosrX;
m_kRotate.set(matrix);
m_akAxis[0] = new Vector3f(1.0f, 0.0f, 0.0f);
m_akAxis[1] = new Vector3f(0.0f, 1.0f, 0.0f);
m_akAxis[2] = new Vector3f(0.0f, 0.0f, 1.0f);
for (int i = 0; i < 3; i++) {
m_kRotate.transform(m_akAxis[i]);
}
orthonormalize(m_akAxis);
for (int i = 0; i < 3; i++) {
setAxis(i, m_akAxis[i]);
}
}
public static Vector3f rotate(Vector3f v, Vector3f axis, float angle) {
// Rotate the point (x,y,z) around the vector (u,v,w)
// Function RotatePointAroundVector(x#,y#,z#,u#,v#,w#,a#)
float ux = axis.x * v.x;
float uy = axis.x * v.y;
float uz = axis.x * v.z;
float vx = axis.y * v.x;
float vy = axis.y * v.y;
float vz = axis.y * v.z;
float wx = axis.z * v.x;
float wy = axis.z * v.y;
float wz = axis.z * v.z;
float sa = (float) Math.sin(angle);
float ca = (float) Math.cos(angle);
float x =
axis.x * (ux + vy + wz)
+ (v.x * (axis.y * axis.y + axis.z * axis.z) - axis.x * (vy + wz)) * ca
+ (-wy + vz) * sa;
float y =
axis.y * (ux + vy + wz)
+ (v.y * (axis.x * axis.x + axis.z * axis.z) - axis.y * (ux + wz)) * ca
+ (wx - uz) * sa;
float z =
axis.z * (ux + vy + wz)
+ (v.z * (axis.x * axis.x + axis.y * axis.y) - axis.z * (ux + vy)) * ca
+ (-vx + uy) * sa;
return new Vector3f(x, y, z);
}
/**
* Return a midpoint of a helix, calculated from three positions of three adjacent subunit
* centers.
*
* @param p1 center of first subunit
* @param p2 center of second subunit
* @param p3 center of third subunit
* @return midpoint of helix
*/
private Point3d getMidPoint(Point3d p1, Point3d p2, Point3d p3) {
Vector3d v1 = new Vector3d();
v1.sub(p1, p2);
Vector3d v2 = new Vector3d();
v2.sub(p3, p2);
Vector3d v3 = new Vector3d();
v3.add(v1);
v3.add(v2);
v3.normalize();
// calculat the total distance between to subunits
double dTotal = v1.length();
// calculate the rise along the y-axis. The helix axis is aligned with y-axis,
// therfore, the rise between subunits is the y-distance
double rise = p2.y - p1.y;
// use phythagorean theoremm to calculate chord length between two subunit centers
double chord = Math.sqrt(dTotal * dTotal - rise * rise);
// System.out.println("Chord d: " + dTotal + " rise: " + rise + "chord: " + chord);
double angle = helixLayers.getByLargestContacts().getAxisAngle().angle;
// using the axis angle and the chord length, we can calculate the radius of the helix
// http://en.wikipedia.org/wiki/Chord_%28geometry%29
double radius = chord / Math.sin(angle / 2) / 2; // can this go to zero?
// System.out.println("Radius: " + radius);
// project the radius onto the vector that points toward the helix axis
v3.scale(radius);
v3.add(p2);
// System.out.println("Angle: " +
// Math.toDegrees(helixLayers.getByLowestAngle().getAxisAngle().angle));
Point3d cor = new Point3d(v3);
return cor;
}
/** Move up/down a given distance. */
public void translateUpDown(double d) {
if (globe == null || d == 0) return;
double hDist = d * Math.cos(Math.PI / 2. + ha);
double vDist = d * Math.sin(Math.PI / 2. + ha);
lla = globe.getEllipsoid().forwGeodesic(lat, lon, hDist, az, lla);
lat = lla.lat;
lon = lla.lon;
az = Ellipsoid.adjlonPos(lla.az + Math.PI);
hEllps += vDist;
ele_changed = lat_changed = lon_changed = az_changed = true;
h = Double.MAX_VALUE;
}
public void translate(double d, double t_az, double t_ha, boolean correct_az) {
if (globe == null || d == 0) return;
double hDist = d * Math.cos(t_ha);
double vDist = d * Math.sin(t_ha);
lla = globe.getEllipsoid().forwGeodesic(lat, lon, hDist, t_az, lla);
lat = lla.lat;
lon = lla.lon;
hEllps += vDist;
if (correct_az) {
az = Ellipsoid.adjlonPos(az + lla.az + Math.PI - t_az);
az_changed = true;
}
ele_changed = lat_changed = lon_changed = true;
h = Double.MAX_VALUE;
}
protected void computeCircle() {
Vector3d center = new Vector3d((Vector3d) get(0));
Vector3d p2 = new Vector3d((Vector3d) get(1));
p2.sub(center);
double radius = p2.length();
removeAllElements();
double angle = 0;
double incAngle = 2 * Math.PI / sides;
for (int i = 0; i < sides; i++) {
super.add(
new Vector3d(
center.x + radius * Math.cos(angle), center.y + radius * Math.sin(angle), 0));
angle += incAngle;
}
super.add(new Vector3d(center.x + radius, center.y, 0));
}
public void rotateAroundPointer(double x_rot, double y_rot) {
if (hTerrain < 0) hTerrain = 0;
if (Math.abs(point_dist * Math.sin(x_rot)) > hTerrain / 10)
x_rot = Math.asin(hTerrain / point_dist / 10) * (x_rot >= 0 ? 1 : -1);
if (Math.abs(point_dist * Math.sin(y_rot)) > hTerrain / 10)
y_rot = Math.asin(hTerrain / point_dist / 10) * (y_rot >= 0 ? 1 : -1);
// translateSideway(dist*Math.sin(x_rot))
double d_x = point_dist * Math.sin(x_rot);
lla = globe.getEllipsoid().forwGeodesic(lat, lon, -d_x * Math.cos(ha), az + Math.PI / 2., lla);
lat = lla.lat;
lon = lla.lon;
az = Ellipsoid.adjlonPos(lla.az + Math.PI / 2.);
// translateUpDown(dist*Math.sin(y_rot));
double d_y = point_dist * Math.sin(y_rot);
hEllps += d_y * Math.sin(Math.PI / 2. + ha);
lla = globe.getEllipsoid().forwGeodesic(lat, lon, d_y * Math.cos(Math.PI / 2. + ha), az, lla);
lat = lla.lat;
lon = lla.lon;
az = Ellipsoid.adjlonPos(lla.az + Math.PI);
// translateForward(dist*(1-Math.cos(x_rot))*(1-Math.cos(y_rot)));
double d_xy = point_dist * (1 - Math.cos(x_rot)) * (1 - Math.cos(y_rot));
hEllps += d_xy * Math.sin(ha);
lla = globe.getEllipsoid().forwGeodesic(lat, lon, d_xy * Math.cos(ha), az, lla);
lat = lla.lat;
lon = lla.lon;
az = Ellipsoid.adjlonPos(lla.az + Math.PI + x_rot);
ha -= y_rot;
if (ha > Math.PI / 2) ha = Math.PI / 2;
if (ha < -Math.PI / 2) ha = -Math.PI / 2;
ele_changed = lat_changed = lon_changed = az_changed = ha_changed = true;
h = Double.MAX_VALUE;
}
private void createSections() {
float axonRadius = .5f;
Point3f posnEndPoint = new Point3f(0, -15, 0);
Segment rootAxon =
addAxonalSegment(axonRadius, "root", posnEndPoint, somaSection, 1, "axonRootSec");
Vector<Segment> layer = new Vector<Segment>();
layer.add(addRelativeAxon(rootAxon, new Point3f(-30, -20, -30), axonRadius));
layer.add(addRelativeAxon(rootAxon, new Point3f(-30, -20, 30), axonRadius));
layer.add(addRelativeAxon(rootAxon, new Point3f(30, -20, 30), axonRadius));
layer.add(addRelativeAxon(rootAxon, new Point3f(30, -20, -30), axonRadius));
for (int i = 0; i < layer.size(); i++) {
Segment axon = (Segment) layer.elementAt(i);
Segment a1 = addRelativeAxon(axon, new Point3f(-6, -4, -6), axonRadius);
Segment a2 = addRelativeAxon(axon, new Point3f(6, -4, -6), axonRadius);
Segment a3 = addRelativeAxon(axon, new Point3f(-6, -4, 6), axonRadius);
Segment a4 = addRelativeAxon(axon, new Point3f(6, -4, 6), axonRadius);
a1.getSection().addToGroup(axonSynGroup);
a2.getSection().addToGroup(axonSynGroup);
a3.getSection().addToGroup(axonSynGroup);
a4.getSection().addToGroup(axonSynGroup);
}
float dendriteDiam = 2;
int numDendrites = 6;
for (int i = 0; i < numDendrites; i++) {
double theta = ((2 * Math.PI) / numDendrites) * i;
float xFact = (float) Math.sin(theta);
float zFact = (float) Math.cos(theta);
posnEndPoint = new Point3f(60 * xFact, 60, 60 * zFact);
Segment radialDend =
addDendriticSegment(
dendriteDiam,
"radialDend_" + i,
posnEndPoint,
somaSection,
0,
"radialDend_" + i + "_Sec",
false);
Point3f posnNew = new Point3f(30 * xFact, 40, 30 * zFact);
Segment radialDend2 = addRelativeDendrite(radialDend, posnNew);
radialDend2.getSection().addToGroup(dendSynGroup);
Point3f posnNew2 = new Point3f(0, 30, 0);
Segment radialDend3 = addRelativeDendrite(radialDend2, posnNew2);
radialDend3.getSection().addToGroup(dendSynGroup);
Point3f posnNew3 = new Point3f(-10 * xFact, 30, -10 * zFact);
Segment radialDend4 = addRelativeDendrite(radialDend, posnNew3);
radialDend4.getSection().addToGroup(dendSynGroup);
Point3f posnNew4 = new Point3f(0, 25, 0);
Segment radialDend5 = addRelativeDendrite(radialDend4, posnNew4);
radialDend5.getSection().addToGroup(dendSynGroup);
}
}
