Examples with Coordinate org.vcell.util.Coordinate used on opensource projects

Example 11 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class ImagePlaneManager method snapWorldCoordinateFace.

/**
 * Insert the method's description here.
 * Creation date: (7/13/2004 4:27:15 PM)
 */
public Coordinate snapWorldCoordinateFace(Coordinate targetC) {
    if (getSourceDataInfo().isCellCentered()) {
        return targetC;
    }
    org.vcell.util.CoordinateIndex centerCI = getSourceDataInfo().getDataIndexFromWorldCoordinate(targetC);
    Coordinate centerCoord = getSourceDataInfo().getWorldCoordinateFromIndex(centerCI);
    double diffX = centerCoord.getX() - targetC.getX();
    double diffY = centerCoord.getY() - targetC.getY();
    double diffZ = centerCoord.getZ() - targetC.getZ();
    if (Math.abs(diffX) >= Math.abs(diffY) && Math.abs(diffX) >= Math.abs(diffZ)) {
        diffY = 0;
        diffZ = 0;
    } else if (Math.abs(diffY) >= Math.abs(diffX) && Math.abs(diffY) >= Math.abs(diffZ)) {
        diffX = 0;
        diffZ = 0;
    } else {
        diffX = 0;
        diffY = 0;
    }
    CoordinateIndex offsetCI = new CoordinateIndex(centerCI.x - (new java.math.BigDecimal(diffX).signum()), centerCI.y - (new java.math.BigDecimal(diffY).signum()), centerCI.z - (new java.math.BigDecimal(diffZ).signum()));
    Coordinate offsetCoord = getSourceDataInfo().getWorldCoordinateFromIndex(offsetCI);
    Coordinate faceCoord = new Coordinate((centerCoord.getX() + offsetCoord.getX()) / 2.0, (centerCoord.getY() + offsetCoord.getY()) / 2.0, (centerCoord.getZ() + offsetCoord.getZ()) / 2.0);
    return faceCoord;
}

Example 12 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class RegionImage method sortSurfaceCollection.

public static void sortSurfaceCollection(SurfaceCollection surfCollection) {
    // Sort nodes
    Object[] nodeObjArr = new Object[surfCollection.getNodes().length];
    for (int i = 0; i < nodeObjArr.length; i++) {
        Object[] temp = new Object[2];
        temp[0] = new Integer(i);
        temp[1] = surfCollection.getNodes()[i];
        nodeObjArr[i] = temp;
    }
    Arrays.sort(nodeObjArr, new Comparator<Object>() {

        public int compare(Object obj1, Object obj2) {
            cbit.vcell.geometry.surface.Node o1 = (cbit.vcell.geometry.surface.Node) ((Object[]) obj1)[1];
            cbit.vcell.geometry.surface.Node o2 = (cbit.vcell.geometry.surface.Node) ((Object[]) obj2)[1];
            double xdiff = o1.getX() - o2.getX();
            double xmin = Math.min(Math.abs(o1.getX()), Math.abs(o2.getX()));
            double xlimit = (1e-12 * (xmin >= 1.0 ? (Math.pow(10, (int) Math.log10(xmin) + 1)) : 1));
            double ydiff = o1.getY() - o2.getY();
            double ymin = Math.min(Math.abs(o1.getY()), Math.abs(o2.getY()));
            double ylimit = (1e-12 * (ymin >= 1.0 ? (Math.pow(10, (int) Math.log10(ymin) + 1)) : 1));
            double zdiff = o1.getZ() - o2.getZ();
            double zmin = Math.min(Math.abs(o1.getZ()), Math.abs(o2.getZ()));
            double zlimit = (1e-12 * (zmin >= 1.0 ? (Math.pow(10, (int) Math.log10(zmin) + 1)) : 1));
            if (Math.abs(zdiff) < zlimit) {
                if (Math.abs(ydiff) < ylimit) {
                    return (int) Math.signum((Math.abs(xdiff) < xlimit ? 0 : xdiff));
                }
                return (int) Math.signum((Math.abs(ydiff) < ylimit ? 0 : ydiff));
            }
            return (int) Math.signum((Math.abs(zdiff) < zlimit ? 0 : zdiff));
        }
    });
    int[] remap = new int[nodeObjArr.length];
    Arrays.fill(remap, -1);
    cbit.vcell.geometry.surface.Node[] sortedNodes = new cbit.vcell.geometry.surface.Node[nodeObjArr.length];
    for (int i = 0; i < nodeObjArr.length; i++) {
        sortedNodes[i] = (cbit.vcell.geometry.surface.Node) ((Object[]) nodeObjArr[i])[1];
        if (remap[sortedNodes[i].getGlobalIndex()] == -1) {
            remap[sortedNodes[i].getGlobalIndex()] = i;
        } else {
            throw new RuntimeException("SORT error: duplicate nodes");
        }
    }
    // surfCollection.setNodes(sortedNodes);
    System.arraycopy(sortedNodes, 0, surfCollection.getNodes(), 0, sortedNodes.length);
    HashSet<cbit.vcell.geometry.surface.Node> remapHashSet = new HashSet<cbit.vcell.geometry.surface.Node>();
    for (int i = 0; i < surfCollection.getSurfaceCount(); i++) {
        Surface surf = surfCollection.getSurfaces(i);
        Polygon[] sortedPolygonArr = new Polygon[surf.getPolygonCount()];
        for (int j = 0; j < surf.getPolygonCount(); j++) {
            Polygon poly = surf.getPolygons(j);
            for (int k = 0; k < poly.getNodes().length; k++) {
                cbit.vcell.geometry.surface.Node node = poly.getNodes(k);
                if (!remapHashSet.contains(node)) {
                    node.setGlobalIndex(remap[node.getGlobalIndex()]);
                    remapHashSet.add(node);
                }
            }
            sortedPolygonArr[j] = poly;
        }
        Arrays.sort(sortedPolygonArr, new Comparator<Polygon>() {

            public int compare(Polygon obj1, Polygon obj2) {
                Coordinate o1 = ((Quadrilateral) obj1).calculateCentroid();
                Coordinate o2 = ((Quadrilateral) obj2).calculateCentroid();
                double xdiff = o1.getX() - o2.getX();
                double xmin = Math.min(Math.abs(o1.getX()), Math.abs(o2.getX()));
                double xlimit = (1e-12 * (xmin >= 1.0 ? (Math.pow(10, (int) Math.log10(xmin) + 1)) : 1));
                double ydiff = o1.getY() - o2.getY();
                double ymin = Math.min(Math.abs(o1.getY()), Math.abs(o2.getY()));
                double ylimit = (1e-12 * (ymin >= 1.0 ? (Math.pow(10, (int) Math.log10(ymin) + 1)) : 1));
                double zdiff = o1.getZ() - o2.getZ();
                double zmin = Math.min(Math.abs(o1.getZ()), Math.abs(o2.getZ()));
                double zlimit = (1e-12 * (zmin >= 1.0 ? (Math.pow(10, (int) Math.log10(zmin) + 1)) : 1));
                if (Math.abs(zdiff) < zlimit) {
                    if (Math.abs(ydiff) < ylimit) {
                        return (int) Math.signum((Math.abs(xdiff) < xlimit ? 0 : xdiff));
                    }
                    return (int) Math.signum((Math.abs(ydiff) < ylimit ? 0 : ydiff));
                }
                return (int) Math.signum((Math.abs(zdiff) < zlimit ? 0 : zdiff));
            }
        });
        OrigSurface sortedSurface = new OrigSurface(surf.getInteriorRegionIndex(), surf.getExteriorRegionIndex());
        for (int k = 0; k < sortedPolygonArr.length; k++) {
            int minGlobalIndex = sortedPolygonArr[k].getNodes(0).getGlobalIndex();
            // System.out.print("Surf "+i+" poly "+k+" nodeGI - ");
            for (int j = 0; j < sortedPolygonArr[k].getNodeCount(); j++) {
                if (sortedPolygonArr[k].getNodes(j).getGlobalIndex() < minGlobalIndex) {
                    minGlobalIndex = sortedPolygonArr[k].getNodes(j).getGlobalIndex();
                }
            // System.out.print(sortedPolygonArr[k].getNodes(j).getGlobalIndex()+" ");
            }
            while (sortedPolygonArr[k].getNodes(0).getGlobalIndex() != minGlobalIndex) {
                cbit.vcell.geometry.surface.Node lastNode = sortedPolygonArr[k].getNodes(sortedPolygonArr[k].getNodeCount() - 1);
                System.arraycopy(sortedPolygonArr[k].getNodes(), 0, sortedPolygonArr[k].getNodes(), 1, sortedPolygonArr[k].getNodeCount() - 1);
                sortedPolygonArr[k].getNodes()[0] = lastNode;
            }
            // System.out.println();
            sortedSurface.addPolygon(sortedPolygonArr[k]);
        }
        surfCollection.setSurfaces(i, sortedSurface);
    }
}

Example 13 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class SampledCurve method isSampledCurveInside.

/**
 * Insert the method's description here.
 * Creation date: (10/9/00 7:00:19 PM)
 */
protected boolean isSampledCurveInside(org.vcell.util.Origin origin, org.vcell.util.Extent extent, Coordinate delta) {
    // 
    // This util. checks sample of this curve that are straight line segments and that if their endpoints
    // are inside the the whole thing is inside.
    // 
    int controlPointCount = getControlPointCount();
    java.util.Vector controlPointsV = getControlPointsVector();
    for (int c = 0; c < controlPointCount; c += 1) {
        Coordinate curveCoord = (Coordinate) controlPointsV.elementAt(c);
        if (!Coordinate.isCoordinateInBounds(curveCoord, origin, extent, delta)) {
            return false;
        }
    }
    return true;
}

Example 14 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class SampledCurve method pickSegment.

/**
 * Insert the method's description here.
 * Creation date: (10/10/00 12:54:48 PM)
 */
public int pickSegment(Coordinate pickCoord, double minPickDistance) {
    int segmentCount = getSegmentCount();
    int controlPointCount = getControlPointCount();
    double shortestDistance = Double.MAX_VALUE;
    int closestSegment = Curve.NONE_SELECTED;
    Coordinate p0 = null;
    Coordinate p1 = null;
    for (int i = 0; i < segmentCount; i += 1) {
        p0 = getControlPoint(i);
        p1 = getControlPoint((i + 1) % controlPointCount);
        double distance = getDistanceToLine(p0, p1, pickCoord);
        if (distance <= minPickDistance && distance < shortestDistance) {
            shortestDistance = distance;
            closestSegment = i;
        }
    }
    return closestSegment;
}

Example 15 with Coordinate

use of org.vcell.util.Coordinate in project vcell by virtualcell.

the class SampledCurve method pickUSampledCurve.

/**
 * Insert the method's description here.
 * Creation date: (10/10/00 4:23:11 PM)
 */
protected double pickUSampledCurve(Coordinate pickCoord, double minPickDistance) {
    int segmentCount = getSegmentCount();
    int controlPointCount = getControlPointCount();
    double shortestDistance = Double.MAX_VALUE;
    int closestSegment = Curve.NONE_SELECTED;
    double closestSegmentU = Curve.NONE_SELECTED;
    Coordinate p0 = null;
    Coordinate p1 = null;
    for (int i = 0; i < segmentCount; i += 1) {
        p0 = getControlPoint(i);
        p1 = getControlPoint((i + 1) % controlPointCount);
        double u = calculateUOfV1AlongV2(p0, pickCoord, p1);
        if (u >= 0.0 && u <= 1.0) {
            double uX = p0.getX() + ((p1.getX() - p0.getX()) * u);
            double uY = p0.getY() + ((p1.getY() - p0.getY()) * u);
            double uZ = p0.getZ() + ((p1.getZ() - p0.getZ()) * u);
            double distance = pickCoord.distanceTo(uX, uY, uZ);
            if (distance <= minPickDistance && distance < shortestDistance) {
                shortestDistance = distance;
                closestSegment = i;
                closestSegmentU = u;
            }
        }
    }
    if (closestSegment != Curve.NONE_SELECTED) {
        // Calculate Non-LengthNormalized U
        double finalU = (closestSegment + closestSegmentU) / getSegmentCount();
        return finalU;
    } else {
        return Curve.NONE_SELECTED;
    }
}