Examples with SampledCurve cbit.vcell.geometry.SampledCurve used on opensource projects

Example 16 with SampledCurve

use of cbit.vcell.geometry.SampledCurve in project vcell by virtualcell.

the class MeshDisplayAdapter method getCurvesAndMembraneIndexes.

/**
 * Insert the method's description here.
 * Creation date: (8/30/00 5:52:19 PM)
 * @return cbit.vcell.geometry.SampledCurve[]
 * @param normalAxis int
 */
public Hashtable<SampledCurve, int[]> getCurvesAndMembraneIndexes(int normalAxis, int slice) {
    Hashtable<SampledCurve, int[]> curvesAndValues = null;
    if (mesh.isChomboMesh()) {
        curvesAndValues = constructChomboCurves(normalAxis, slice);
    } else {
        // 
        // Finds individual curves given a normalAxis and slice
        // Also associates membrane indexes with each curve segment
        // 
        MembraneElement[] membraneElements = mesh.getMembraneElements();
        if (membraneElements == null) {
            return null;
        }
        if (mesh.isMembraneConnectivityOK() == false) {
            System.out.println("CartesianMesh.getCurvesFromMembranes(), MESH ERROR: membrane connectivity is bad");
        // throw new RuntimeException("membrane connectivity bad");
        }
        boolean[] bMembraneElementChecked = new boolean[membraneElements.length];
        for (int c = 0; c < membraneElements.length; c += 1) {
            bMembraneElementChecked[c] = false;
        }
        SampledCurve newCurve = null;
        // Stores (Integer) membrane indexes corresponding to each segment of curve
        Vector<Integer> resolvedMembraneIndexes = null;
        int c = 0;
        while (true) {
            for (; c < membraneElements.length; c += 1) {
                if (bMembraneElementChecked[c] == false && isMembraneElementVisible(membraneElements[c], normalAxis, slice)) {
                    newCurve = new SampledCurve();
                    resolvedMembraneIndexes = new Vector<Integer>();
                    ConstructCurveHelper pendingCCH = null;
                    ConstructCurveHelper currentCCH = new ConstructCurveHelper(membraneElements[c], newCurve, membraneElements[c], null, false, bMembraneElementChecked, normalAxis, slice, resolvedMembraneIndexes);
                    while (true) {
                        ConstructCurveHelper[] currentCCHArr = constructCurve(currentCCH);
                        if (currentCCHArr == null) {
                            if (pendingCCH == null) {
                                break;
                            } else {
                                currentCCH = pendingCCH;
                                pendingCCH = null;
                            }
                        } else if (currentCCHArr.length == 1) {
                            currentCCH = currentCCHArr[0];
                        } else if (currentCCHArr.length == 2) {
                            if (pendingCCH != null) {
                                throw new RuntimeException("MeshDisplayAdapter.getCurvesAndMembraneIndexes Error -- Only 1 Pending CurveConstructionHelper allowed.");
                            }
                            currentCCH = currentCCHArr[0];
                            pendingCCH = currentCCHArr[1];
                        }
                    }
                    break;
                }
            }
            if (newCurve == null) {
                break;
            }
            if (curvesAndValues == null) {
                curvesAndValues = new Hashtable<SampledCurve, int[]>();
            }
            // convert Vector to int[]
            int[] rmi = new int[resolvedMembraneIndexes.size()];
            for (int i = 0; i < resolvedMembraneIndexes.size(); i += 1) {
                rmi[i] = ((Integer) (resolvedMembraneIndexes.elementAt(i))).intValue();
            }
            curvesAndValues.put(newCurve, rmi);
            newCurve = null;
        }
    }
    return curvesAndValues;
}

Example 17 with SampledCurve

use of cbit.vcell.geometry.SampledCurve in project vcell by virtualcell.

the class SpatialSelectionVolume method sampleSymmetric.

/**
 * Insert the method's description here.
 * Creation date: (10/5/2004 7:19:49 AM)
 */
private SSHelper sampleSymmetric() throws Exception {
    // 
    if (!isSymmetric()) {
        return null;
    }
    SampledCurve ssCurve = getCurveSelectionInfo().getCurve().getSampledCurve();
    Vector pointsV = ssCurve.getControlPointsVector();
    if (pointsV.size() < 2) {
        return null;
    }
    final int INDEX_SPACE_INCR = 100;
    int[] indexes = new int[INDEX_SPACE_INCR];
    int indexCounter = 0;
    Vector snappedV = new Vector();
    CoordinateIndex lastCI = null;
    for (int i = 0; i < pointsV.size(); i += 1) {
        if (i > 0) {
            CoordinateIndex c1 = getMesh().getCoordinateIndexFromFractionalIndex(getMesh().getFractionalCoordinateIndex((Coordinate) pointsV.elementAt(i - 1)));
            CoordinateIndex c2 = getMesh().getCoordinateIndexFromFractionalIndex(getMesh().getFractionalCoordinateIndex((Coordinate) pointsV.elementAt(i)));
            int dx = c2.x - c1.x;
            if (dx != 0) {
                dx /= Math.abs(dx);
            }
            int dy = c2.y - c1.y;
            if (dy != 0) {
                dy /= Math.abs(dy);
            }
            int dz = c2.z - c1.z;
            if (dz != 0) {
                dz /= Math.abs(dz);
            }
            while (true) {
                if (!c1.compareEqual(lastCI)) {
                    if (indexCounter == indexes.length) {
                        // Make more space
                        int[] temp = new int[indexes.length + INDEX_SPACE_INCR];
                        System.arraycopy(indexes, 0, temp, 0, indexes.length);
                        indexes = temp;
                    }
                    indexes[indexCounter] = getConvertedIndexFromCI(c1);
                    snappedV.add(getMesh().getCoordinate(c1));
                    indexCounter += 1;
                }
                if (c1.compareEqual(c2)) {
                    break;
                }
                c1.x += dx;
                c1.y += dy;
                c1.z += dz;
                // sanity check to prevent infinite loop, this shouldn't happen
                if (c1.x < 0 || c1.y < 0 || c1.z < 0 || c1.x >= getMesh().getSizeX() || c1.y >= getMesh().getSizeY() || c1.z >= getMesh().getSizeZ()) {
                    throw new Exception(this.getClass().getName() + ".sampleSymmetric failed");
                }
            }
            ;
            lastCI = c2;
        }
    }
    if (indexCounter > 0) {
        return makeSSHelper(indexes, indexCounter, snappedV, false);
    }
    return null;
}

Example 18 with SampledCurve

use of cbit.vcell.geometry.SampledCurve in project vcell by virtualcell.

the class SpatialSelectionVolume method isSymmetric.

/**
 * Insert the method's description here.
 * Creation date: (10/3/2004 12:54:59 PM)
 * @return boolean
 */
private boolean isSymmetric() {
    if (!(getCurveSelectionInfo().getCurve() instanceof SampledCurve)) {
        return false;
    }
    SampledCurve ssCurve = getCurveSelectionInfo().getCurve().getSampledCurve();
    Vector pointsV = ssCurve.getControlPointsVector();
    if (pointsV.size() == 1) {
        return true;
    }
    for (int i = 0; i < pointsV.size(); i += 1) {
        if (i > 0) {
            CoordinateIndex c1 = getMesh().getCoordinateIndexFromFractionalIndex(getMesh().getFractionalCoordinateIndex((Coordinate) pointsV.elementAt(i - 1)));
            CoordinateIndex c2 = getMesh().getCoordinateIndexFromFractionalIndex(getMesh().getFractionalCoordinateIndex((Coordinate) pointsV.elementAt(i)));
            int dx = Math.abs(c1.x - c2.x);
            int dy = Math.abs(c1.y - c2.y);
            int dz = Math.abs(c1.z - c2.z);
            int symCount = 0;
            if (dx != 0 && dy != 0 && dx != dy) {
                symCount += 1;
            }
            if (dx != 0 && dz != 0 && dx != dz) {
                symCount += 1;
            }
            if (dy != 0 && dz != 0 && dy != dz) {
                symCount += 1;
            }
            if (symCount != 0) {
                return false;
            }
        }
    }
    return true;
}