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

Example 1 with ControlPointCurve

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

the class XmlReader method getControlPointCurve.

/**
 * This method returns a ControlPointcurve object from a XML element.
 * Creation date: (5/22/2001 5:20:39 PM)
 * @return cbit.vcell.geometry.ControlPointCurve
 * @param param org.jdom.Element
 */
private ControlPointCurve getControlPointCurve(Element param) {
    ControlPointCurve curve = null;
    // get Attributes
    String type = param.getAttributeValue(XMLTags.TypeAttrTag);
    boolean closed = Boolean.valueOf(param.getAttributeValue(XMLTags.ClosedAttrTag)).booleanValue();
    List<Element> coordList = param.getChildren();
    // Upon de type, decide which Curve type to create
    if (type.equalsIgnoreCase(XMLTags.PolyLineTypeTag)) {
        if (coordList.size() == 2) {
            // I have a Line
            Coordinate begin = getCoordinate(coordList.get(0));
            Coordinate end = getCoordinate(coordList.get(1));
            // ****create new Line ****
            curve = new Line(begin, end);
        } else {
            // If it it is not a Line, then it is a SampledCurve
            Coordinate[] coords = new Coordinate[coordList.size()];
            for (int i = 0; i < coordList.size(); i++) {
                coords[i] = getCoordinate(coordList.get(i));
            }
            // ****create new SampledCurve ****
            curve = new SampledCurve(coords);
        }
    } else if (type.equalsIgnoreCase(XMLTags.SplineTypeTag)) {
        Coordinate[] coords = new Coordinate[coordList.size()];
        for (int i = 0; i < coordList.size(); i++) {
            coords[i] = getCoordinate(coordList.get(i));
        }
        // ****create new Spline ****
        curve = new Spline(coords);
    }
    // set Atributes
    curve.setClosed(closed);
    return curve;
}

Example 2 with ControlPointCurve

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

the class XmlReader method getGeometry.

/**
 * This method returns a Geometry object from a XML representation.
 * Creation date: (4/26/2001 12:12:18 PM)
 * @return cbit.vcell.geometry.Geometry
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
public Geometry getGeometry(Element param) throws XmlParseException {
    // Get the Extent object
    Extent newextent = getExtent(param.getChild(XMLTags.ExtentTag, vcNamespace));
    // Get VCimage information
    VCImage newimage = null;
    if (param.getChild(XMLTags.ImageTag, vcNamespace) != null) {
        try {
            newimage = getVCImage(param.getChild(XMLTags.ImageTag, vcNamespace), newextent);
        } catch (Throwable e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    int newdimension = Integer.parseInt(param.getAttributeValue(XMLTags.DimensionAttrTag));
    // Get Version
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Try to construct the geometry upon four different cases
    Geometry newgeometry = null;
    if (version != null && newimage != null) {
        newgeometry = new Geometry(version, newimage);
    } else if (version != null) {
        newgeometry = new Geometry(version, newdimension);
    } else if (newimage != null) {
        newgeometry = new Geometry(name, newimage);
    } else {
        newgeometry = new Geometry(name, newdimension);
    }
    // set attributes
    try {
        if (!newgeometry.getName().equalsIgnoreCase(name)) {
            newgeometry.setName(name);
        }
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // newgeometry.setDescription( unMangle(annotation) );
        // }
        // Add annotation
        String annotation = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotation != null && annotation.length() > 0) {
            newgeometry.setDescription(unMangle(annotation));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred when setting the name " + name + " to a Geometry object!", e);
    }
    // Add the Extent
    try {
        newgeometry.getGeometrySpec().setExtent(newextent);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException occurred while trying to set the Extent for the Geometry " + name, e);
    }
    // Add the Origin
    newgeometry.getGeometrySpec().setOrigin(getOrigin(param.getChild(XMLTags.OriginTag, vcNamespace)));
    // Add the SubVolumes
    List<Element> children = param.getChildren(XMLTags.SubVolumeTag, vcNamespace);
    SubVolume[] newsubvolumes = new SubVolume[children.size()];
    int subvolumeCounter = 0;
    for (Element child : children) {
        newsubvolumes[subvolumeCounter] = getSubVolume(child);
        subvolumeCounter++;
    }
    try {
        newgeometry.getGeometrySpec().setSubVolumes(newsubvolumes);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e);
    }
    if (newgeometry.getDimension() > 0) {
        // Add SurfaceClasses
        List<Element> surfaceClassChildren = param.getChildren(XMLTags.SurfaceClassTag, vcNamespace);
        SurfaceClass[] newSurfaceClassArr = new SurfaceClass[surfaceClassChildren.size()];
        int surfClassCounter = 0;
        for (Element surfClassChild : surfaceClassChildren) {
            newSurfaceClassArr[surfClassCounter] = getSurfaceClass(surfClassChild, newgeometry);
            surfClassCounter++;
        }
        try {
            newgeometry.getGeometrySurfaceDescription().setSurfaceClasses(newSurfaceClassArr);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace();
            throw new XmlParseException("A PropertyVetoException was generated when ading the subvolumes to the Geometry " + name, e);
        }
    }
    // read Filaments (if any)
    Iterator<Element> iterator = param.getChildren(XMLTags.FilamentTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = iterator.next();
        String filname = unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag));
        Iterator<Element> curveiterator = tempElement.getChildren().iterator();
        while (curveiterator.hasNext()) {
            ControlPointCurve curve = getControlPointCurve(curveiterator.next());
            newgeometry.getGeometrySpec().getFilamentGroup().addCurve(filname, curve);
        }
    }
    // read Surface description (if any)
    Element sd = param.getChild(XMLTags.SurfaceDescriptionTag, vcNamespace);
    if (sd != null) {
        GeometrySurfaceDescription dummy = getGeometrySurfaceDescription(sd, newgeometry);
    }
    try {
        newgeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), false, false);
    } catch (GeometryException e) {
        e.printStackTrace(System.out);
    } catch (ImageException e) {
        e.printStackTrace(System.out);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
    }
    return newgeometry;
}

Example 3 with ControlPointCurve

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML Element from a Filament object.
 * Creation date: (5/22/2001 4:03:13 PM)
 * @return Element
 * @param param cbit.vcell.geometry.Filament
 */
private Element getXML(Filament param) {
    // --- create Element
    Element filament = new Element(XMLTags.FilamentTag);
    // Add atributes
    filament.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
    // add curves
    Curve[] array = param.getCurves();
    for (int i = 0; i < array.length; i++) {
        filament.addContent(getXML((ControlPointCurve) array[i]));
    }
    return filament;
}

Example 4 with ControlPointCurve

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

the class PDEDataContextPanel method projectCurveOntoSlice.

/**
 * Insert the method's description here.
 * Creation date: (7/16/2003 1:05:56 PM)
 * @return cbit.vcell.geometry.ControlPointCurve
 * @param curve cbit.vcell.geometry.ControlPointCurve
 */
private ControlPointCurve projectCurveOntoSlice(ControlPointCurve curve) {
    // for SinglePoint(timepoint) and PolyLine(spatial) samplers(always stored in world coordinates),
    // convert the curve coordinates into view coordinates from the sliceviewer
    ControlPointCurve cpCurve = null;
    java.util.Vector<Coordinate> cpV = new java.util.Vector<Coordinate>();
    int normalAxis = getimagePlaneManager1().getNormalAxis();
    for (int i = 0; i < curve.getControlPointCount(); i += 1) {
        // convert curves that are always stored in world coordinates into coordinates that
        // represent how user sees them in the slice viewer
        double xCoord = Coordinate.convertAxisFromStandardXYZToNormal(curve.getControlPoint(i), Coordinate.X_AXIS, normalAxis);
        double yCoord = Coordinate.convertAxisFromStandardXYZToNormal(curve.getControlPoint(i), Coordinate.Y_AXIS, normalAxis);
        // Get z from slice
        double zCoord = Coordinate.convertAxisFromStandardXYZToNormal(getimagePlaneManager1().getWorldCoordinateFromUnitized2D(0, 0), Coordinate.Z_AXIS, normalAxis);
        // These are now the real coordinates as they are viewed in the slice viewer
        // Coordinate newCoord = new Coordinate(xCoord,yCoord,zCoord);
        Coordinate newCoord = Coordinate.convertCoordinateFromNormalToStandardXYZ(xCoord, yCoord, zCoord, normalAxis);
        cpV.add(newCoord);
    }
    if (cpV.size() > 0) {
        Coordinate[] cpArr = new Coordinate[cpV.size()];
        cpV.copyInto(cpArr);
        // Determine if curve has been projected down to a single point
        boolean bSinglePoint = true;
        for (int i = 0; i < cpArr.length; i += 1) {
            if (i > 0 && !cpArr[i].equals(cpArr[i - 1])) {
                bSinglePoint = false;
                break;
            }
        }
        // if(curve instanceof SinglePoint){
        if (bSinglePoint) {
            cpCurve = new SinglePoint(cpArr[0]);
        } else if (curve instanceof SampledCurve) {
            cpCurve = new PolyLine(cpArr);
        }
    }
    return cpCurve;
}

Example 5 with ControlPointCurve

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

the class PDEDataContextPanel method fetchSpatialSelections0.

/**
 * Insert the method's description here.
 * Creation date: (6/28/2003 4:57:18 PM)
 * @return cbit.vcell.simdata.gui.SpatialSelection[]
 */
private SpatialSelection[] fetchSpatialSelections0(Curve curveOfInterest, boolean bFetchOnlyVisible, VariableType vt) {
    // 
    java.util.Vector<SpatialSelection> spatialSelection = new java.util.Vector<SpatialSelection>();
    // 
    if (getPdeDataContext() != null && getPdeDataContext().getCartesianMesh() != null && getImagePlaneManagerPanel() != null && getImagePlaneManagerPanel().getCurveRenderer() != null) {
        // 
        CartesianMesh cm = getPdeDataContext().getCartesianMesh();
        Curve[] curves = getImagePlaneManagerPanel().getCurveRenderer().getAllCurves();
        // 
        if (curves != null && curves.length > 0) {
            for (int i = 0; i < curves.length; i += 1) {
                boolean bIsVisible = getImagePlaneManagerPanel().getCurveRenderer().getRenderPropertyVisible(curves[i]);
                if ((bFetchOnlyVisible && !bIsVisible) || (curveOfInterest != null && curves[i] != curveOfInterest)) {
                    continue;
                }
                // 
                if ((vt.equals(VariableType.POSTPROCESSING) || vt.equals(VariableType.VOLUME) || vt.equals(VariableType.VOLUME_REGION)) && curves[i] instanceof ControlPointCurve && !(curves[i] instanceof CurveSelectionCurve) && (curves[i].getDescription() == null || curves[i].getDescription().startsWith(CurveValueProvider.DESCRIPTION_VOLUME)) && (membranesAndIndexes == null || !membranesAndIndexes.containsKey(curves[i]))) {
                    // Volume
                    // 
                    Curve samplerCurve = null;
                    // if(isSpatial2D){
                    samplerCurve = projectCurveOntoSlice(curves[i].getSampledCurve());
                    // }
                    if (samplerCurve != null) {
                        samplerCurve.setDescription(curves[i].getDescription());
                        spatialSelection.add(new SpatialSelectionVolume(new CurveSelectionInfo(samplerCurve), vt, cm));
                    }
                } else if ((vt.equals(VariableType.MEMBRANE) || vt.equals(VariableType.MEMBRANE_REGION)) && membranesAndIndexes != null) {
                    // 
                    if (curves[i] instanceof CurveSelectionCurve) {
                        CurveSelectionCurve csCurve = (CurveSelectionCurve) curves[i];
                        if (csCurve.getSourceCurveSelectionInfo().getCurve() instanceof ControlPointCurve) {
                            int[] csisegsel = csCurve.getSourceCurveSelectionInfo().getSegmentsInSelectionOrder();
                            if (csisegsel != null) {
                                ControlPointCurve cscpcCurve = (ControlPointCurve) (csCurve.getSourceCurveSelectionInfo().getCurve());
                                Curve[] membraneCurves = (Curve[]) (membranesAndIndexes.keySet().toArray(new Curve[membranesAndIndexes.size()]));
                                // See if CurveSelectionCurve matches controlpoints in space of a membrane we have
                                for (int j = 0; j < membraneCurves.length; j += 1) {
                                    if (membraneCurves[j] instanceof ControlPointCurve) {
                                        // They should all be
                                        ControlPointCurve cpc = (ControlPointCurve) membraneCurves[j];
                                        boolean bSame = true;
                                        for (int k = 0; k < csisegsel.length; k += 1) {
                                            if (csisegsel[k] >= cpc.getControlPointCount() || csisegsel[k] >= cscpcCurve.getControlPointCount() || !Coordinate.get2DProjection(cpc.getControlPoint(csisegsel[k]), getNormalAxis()).equals(Coordinate.get2DProjection(cscpcCurve.getControlPoint(csisegsel[k]), getNormalAxis()))) {
                                                // 
                                                bSame = false;
                                                break;
                                            }
                                        }
                                        if (bSame) {
                                            int[] mi = (int[]) membranesAndIndexes.get(membraneCurves[j]);
                                            spatialSelection.add(new SpatialSelectionMembrane(new CurveSelectionInfo(membraneCurves[j], csisegsel[0], csisegsel[csisegsel.length - 1], csCurve.getSourceCurveSelectionInfo().getDirectionNegative()), vt, cm, mi, csCurve));
                                        }
                                    }
                                }
                            }
                        }
                    } else if (curves[i] instanceof SinglePoint && (curves[i].getDescription() == null || curves[i].getDescription().startsWith(CurveValueProvider.DESCRIPTION_MEMBRANE))) {
                        CurveSelectionInfo[] csiArr = getImagePlaneManagerPanel().getCurveRenderer().getCloseCurveSelectionInfos(curves[i].getBeginningCoordinate());
                        if (csiArr != null && csiArr.length > 0) {
                            for (int j = 0; j < csiArr.length; j += 1) {
                                if (membranesAndIndexes.containsKey(csiArr[j].getCurve())) {
                                    CurveSelectionInfo closestCSI = getImagePlaneManagerPanel().getCurveRenderer().getClosestSegmentSelectionInfo(curves[i].getBeginningCoordinate(), csiArr[j].getCurve());
                                    int[] mi = (int[]) membranesAndIndexes.get(csiArr[j].getCurve());
                                    spatialSelection.add(new SpatialSelectionMembrane(closestCSI, vt, cm, mi, (SinglePoint) curves[i]));
                                    break;
                                }
                            }
                        }
                    }
                }
            }
        }
    }
    // 
    if (spatialSelection.size() > 0) {
        SpatialSelection[] ss = new SpatialSelection[spatialSelection.size()];
        spatialSelection.copyInto(ss);
        return ss;
    }
    return null;
}