Examples with GeometrySurfaceDescription cbit.vcell.geometry.surface.GeometrySurfaceDescription used on opensource projects

Example 16 with GeometrySurfaceDescription

use of cbit.vcell.geometry.surface.GeometrySurfaceDescription in project vcell by virtualcell.

the class SurfaceEditor method setgeometrySurfaceDescription1.

/**
 * Set the geometrySurfaceDescription1 to a new value.
 * @param newValue cbit.vcell.geometry.surface.GeometrySurfaceDescription
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setgeometrySurfaceDescription1(GeometrySurfaceDescription newValue) {
    if (ivjgeometrySurfaceDescription1 != newValue) {
        try {
            GeometrySurfaceDescription oldValue = getgeometrySurfaceDescription1();
            /* Stop listening for events from the current object */
            if (ivjgeometrySurfaceDescription1 != null) {
                ivjgeometrySurfaceDescription1.removePropertyChangeListener(ivjEventHandler);
            }
            ivjgeometrySurfaceDescription1 = newValue;
            /* Listen for events from the new object */
            if (ivjgeometrySurfaceDescription1 != null) {
                ivjgeometrySurfaceDescription1.addPropertyChangeListener(ivjEventHandler);
            }
            connPtoP1SetSource();
            connEtoM1(ivjgeometrySurfaceDescription1);
            connEtoM6(ivjgeometrySurfaceDescription1);
            connEtoC2(ivjgeometrySurfaceDescription1);
            firePropertyChange("geometrySurfaceDescription", oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}

Example 17 with GeometrySurfaceDescription

use of cbit.vcell.geometry.surface.GeometrySurfaceDescription in project vcell by virtualcell.

the class SurfaceEditor method setGeometrySurfaceDescription.

/**
 * Sets the geometrySurfaceDescription property (cbit.vcell.geometry.surface.GeometrySurfaceDescription) value.
 * @param geometrySurfaceDescription The new value for the property.
 * @see #getGeometrySurfaceDescription
 */
public void setGeometrySurfaceDescription(GeometrySurfaceDescription geometrySurfaceDescription) {
    GeometrySurfaceDescription oldValue = fieldGeometrySurfaceDescription;
    fieldGeometrySurfaceDescription = geometrySurfaceDescription;
    firePropertyChange("geometrySurfaceDescription", oldValue, geometrySurfaceDescription);
}

Example 18 with GeometrySurfaceDescription

use of cbit.vcell.geometry.surface.GeometrySurfaceDescription in project vcell by virtualcell.

the class XmlReader method getGeometrySurfaceDescription.

private GeometrySurfaceDescription getGeometrySurfaceDescription(Element param, Geometry geom) throws XmlParseException {
    GeometrySurfaceDescription gsd = geom.getGeometrySurfaceDescription();
    String cutoffStr = param.getAttributeValue(XMLTags.CutoffFrequencyAttrTag);
    String xDim = param.getAttributeValue(XMLTags.NumSamplesXAttrTag);
    String yDim = param.getAttributeValue(XMLTags.NumSamplesYAttrTag);
    String zDim = param.getAttributeValue(XMLTags.NumSamplesZAttrTag);
    if (cutoffStr == null || xDim == null || yDim == null || zDim == null) {
        throw new XmlParseException("Attributes for element Surface Description not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
    }
    try {
        ISize isize = new ISize(Integer.parseInt(xDim), Integer.parseInt(yDim), Integer.parseInt(zDim));
        gsd.setVolumeSampleSize(isize);
        gsd.setFilterCutoffFrequency(new Double(cutoffStr));
        // these lists are allowed to be empty.
        ArrayList<Element> memRegions = new ArrayList<Element>(param.getChildren(XMLTags.MembraneRegionTag, vcNamespace));
        ArrayList<Element> volRegions = new ArrayList<Element>(param.getChildren(XMLTags.VolumeRegionTag, vcNamespace));
        ArrayList<GeometricRegion> regions = new ArrayList<GeometricRegion>();
        GeometryUnitSystem geometryUnitSystem = geom.getUnitSystem();
        for (Element temp : volRegions) {
            String regionID = temp.getAttributeValue(XMLTags.RegionIDAttrTag);
            String name = temp.getAttributeValue(XMLTags.NameAttrTag);
            String subvolumeRef = temp.getAttributeValue(XMLTags.SubVolumeAttrTag);
            if (regionID == null || name == null || subvolumeRef == null) {
                throw new XmlParseException("Attributes for element Volume Region not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            SubVolume subvolume = geom.getGeometrySpec().getSubVolume(subvolumeRef);
            if (subvolume == null) {
                throw new XmlParseException("The subvolume " + subvolumeRef + " could not be resolved.");
            }
            double size = -1;
            VCUnitDefinition unit = null;
            String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag);
            if (sizeStr != null) {
                size = Double.parseDouble(sizeStr);
                String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                if (unitSymbol != null) {
                    unit = geometryUnitSystem.getInstance(unitSymbol);
                }
            }
            VolumeGeometricRegion vgr = new VolumeGeometricRegion(name, size, unit, subvolume, Integer.parseInt(regionID));
            regions.add(vgr);
        }
        for (Element temp : memRegions) {
            String volRegion_1 = temp.getAttributeValue(XMLTags.VolumeRegion_1AttrTag);
            String volRegion_2 = temp.getAttributeValue(XMLTags.VolumeRegion_2AttrTag);
            String name = temp.getAttributeValue(XMLTags.NameAttrTag);
            if (volRegion_1 == null || volRegion_2 == null || name == null) {
                throw new XmlParseException("Attributes for element Membrane Region not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            VolumeGeometricRegion region1 = getAdjacentVolumeRegion(regions, volRegion_1);
            VolumeGeometricRegion region2 = getAdjacentVolumeRegion(regions, volRegion_2);
            if (region1 == null || region2 == null) {
                throw new XmlParseException("Element Membrane Region refernces invalid volume regions, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            double size = -1;
            VCUnitDefinition unit = null;
            String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag);
            if (sizeStr != null) {
                size = Double.parseDouble(sizeStr);
                String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                if (unitSymbol != null) {
                    unit = geometryUnitSystem.getInstance(unitSymbol);
                }
            }
            SurfaceGeometricRegion rsl = new SurfaceGeometricRegion(name, size, unit);
            rsl.addAdjacentGeometricRegion(region1);
            region1.addAdjacentGeometricRegion(rsl);
            rsl.addAdjacentGeometricRegion(region2);
            region2.addAdjacentGeometricRegion(rsl);
            regions.add(rsl);
        }
        if (regions.size() > 0) {
            gsd.setGeometricRegions((GeometricRegion[]) regions.toArray(new GeometricRegion[regions.size()]));
        }
    } catch (Exception e) {
        System.err.println("Unable to read geometry surface description from XML, for geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
        e.printStackTrace();
    }
    return gsd;
}

Example 19 with GeometrySurfaceDescription

use of cbit.vcell.geometry.surface.GeometrySurfaceDescription in project vcell by virtualcell.

the class GeometryFileWriter method write.

/**
 * Insert the method's description here.
 * Creation date: (7/19/2004 10:54:30 AM)
 * @param geometrySurfaceDescription cbit.vcell.geometry.surface.GeometrySurfaceDescription
 * @throws IOException
 */
public static void write(Writer writer, Geometry resampledGeometry) throws IOException {
    // 
    // "name" name
    // "dimension" dimension
    // "extent" extentx extenty extentz
    // "origin" originx originy originz
    // "volumeRegions" num
    // name totalVolume featureHandle
    // "membraneRegions" num
    // name totalArea volumeRegionIndex1 volumeRegionIndex2
    // "volumeSamples" numX, numY, numZ
    // uncompressed regionIndexs for each volume element
    // compressed regionIndexs for each volume element
    // "nodes" num
    // nodeIndex x y z
    // "cells" num
    // cellIndex patchIndex node1 node2 node3 node4
    // "celldata"
    // insideVolumeIndex outsideVolumeIndex area normalx normaly normalz
    // 
    // 
    // When we are writing volume regions, we sort regions so that ID is equal to index
    // 
    writer.write("name " + resampledGeometry.getName() + "\n");
    writer.write("dimension " + resampledGeometry.getDimension() + "\n");
    org.vcell.util.Extent extent = resampledGeometry.getExtent();
    org.vcell.util.Origin origin = resampledGeometry.getOrigin();
    switch(resampledGeometry.getDimension()) {
        case 1:
            writer.write("size " + extent.getX() + "\n");
            writer.write("origin " + origin.getX() + "\n");
            break;
        case 2:
            writer.write("size " + extent.getX() + " " + extent.getY() + "\n");
            writer.write("origin " + origin.getX() + " " + origin.getY() + "\n");
            break;
        case 3:
            writer.write("size " + extent.getX() + " " + extent.getY() + " " + extent.getZ() + "\n");
            writer.write("origin " + origin.getX() + " " + origin.getY() + " " + origin.getZ() + "\n");
            break;
    }
    GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
    RegionImage regionImage = geoSurfaceDesc.getRegionImage();
    SurfaceCollection surfaceCollection = geoSurfaceDesc.getSurfaceCollection();
    GeometricRegion[] geometricRegions = geoSurfaceDesc.getGeometricRegions();
    int numVolumeRegions = 0;
    int numMembraneRegions = 0;
    Vector<VolumeGeometricRegion> volRegionList = new Vector<VolumeGeometricRegion>();
    if (geometricRegions != null) {
        for (int i = 0; i < geometricRegions.length; i++) {
            if (geometricRegions[i] instanceof VolumeGeometricRegion) {
                numVolumeRegions++;
                volRegionList.add((VolumeGeometricRegion) geometricRegions[i]);
            } else if (geometricRegions[i] instanceof SurfaceGeometricRegion) {
                numMembraneRegions++;
            }
        }
    }
    // 
    // get ordered array of volume regions (where "id" == index into array)... fail if impossible
    // 
    java.util.Collections.sort(volRegionList, new Comparator<VolumeGeometricRegion>() {

        public int compare(VolumeGeometricRegion reg1, VolumeGeometricRegion reg2) {
            if (reg1.getRegionID() < reg2.getRegionID()) {
                return -1;
            } else if (reg1.getRegionID() > reg2.getRegionID()) {
                return 1;
            } else {
                return 0;
            }
        }

        public boolean equals(Object obj) {
            return this == obj;
        }
    });
    VolumeGeometricRegion[] volRegions = (VolumeGeometricRegion[]) org.vcell.util.BeanUtils.getArray(volRegionList, VolumeGeometricRegion.class);
    writer.write("volumeRegions " + numVolumeRegions + "\n");
    for (int i = 0; i < volRegions.length; i++) {
        if (volRegions[i].getRegionID() != i) {
            throw new RuntimeException("Region ID != Region Index, they must be the same!");
        }
        writer.write(volRegions[i].getName() + " " + volRegions[i].getSize() + " " + volRegions[i].getSubVolume().getHandle() + "\n");
    }
    writer.write("membraneRegions " + numMembraneRegions + "\n");
    if (geometricRegions != null) {
        for (int i = 0; i < geometricRegions.length; i++) {
            if (geometricRegions[i] instanceof SurfaceGeometricRegion) {
                SurfaceGeometricRegion surfaceRegion = (SurfaceGeometricRegion) geometricRegions[i];
                GeometricRegion[] neighbors = surfaceRegion.getAdjacentGeometricRegions();
                VolumeGeometricRegion insideRegion = (VolumeGeometricRegion) neighbors[0];
                VolumeGeometricRegion outsideRegion = (VolumeGeometricRegion) neighbors[1];
                writer.write(surfaceRegion.getName() + " " + surfaceRegion.getSize() + " " + insideRegion.getRegionID() + " " + outsideRegion.getRegionID() + "\n");
            }
        }
    }
    // 
    // write volume samples
    // 
    ISize volumeSampleSize = geoSurfaceDesc.getVolumeSampleSize();
    switch(resampledGeometry.getDimension()) {
        case 1:
            writer.write("volumeSamples " + volumeSampleSize.getX() + "\n");
            break;
        case 2:
            writer.write("volumeSamples " + volumeSampleSize.getX() + " " + volumeSampleSize.getY() + "\n");
            break;
        case 3:
            writer.write("volumeSamples " + volumeSampleSize.getX() + " " + volumeSampleSize.getY() + " " + volumeSampleSize.getZ() + "\n");
            break;
    }
    // regionImage
    if (regionImage != null) {
        if (regionImage.getNumRegions() > 65536) {
            throw new RuntimeException("cannot process a geometry with more than 65536 volume regions");
        }
        byte[] uncompressedRegionIDs = new byte[2 * regionImage.getNumX() * regionImage.getNumY() * regionImage.getNumZ()];
        for (int i = 0, j = 0; i < uncompressedRegionIDs.length; i += 2, j++) {
            int regindex = regionImage.getRegionInfoFromOffset(j).getRegionIndex();
            uncompressedRegionIDs[i] = (byte) (regindex & 0x000000ff);
            uncompressedRegionIDs[i + 1] = (byte) ((regindex & 0x0000ff00) >> 8);
        }
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        DeflaterOutputStream dos = new DeflaterOutputStream(bos);
        dos.write(uncompressedRegionIDs, 0, uncompressedRegionIDs.length);
        dos.close();
        byte[] compressedRegionIDs = bos.toByteArray();
        writer.write(org.vcell.util.Hex.toString(compressedRegionIDs) + "\n");
    } else {
        writer.write("\n");
    }
    // 
    if (surfaceCollection == null) {
        throw new RuntimeException("geometry is not updated");
    }
    int numCells = surfaceCollection.getTotalPolygonCount();
    writer.write("cells " + numCells + "\n");
    // "celldata"
    // insideVolumeIndex outsideVolumeIndex area normalx normaly normalz
    // 
    int cellID = 0;
    int dimension = resampledGeometry.getDimension();
    double correctCoeff = 1;
    if (dimension == 1) {
        correctCoeff = extent.getY() * extent.getZ();
    } else if (dimension == 2) {
        correctCoeff = extent.getZ();
    }
    if (surfaceCollection != null) {
        for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
            Surface surface = surfaceCollection.getSurfaces(i);
            int region1Outside = 0;
            int region1Inside = 0;
            for (int j = 0; j < surface.getPolygonCount(); j++) {
                Quadrilateral polygon = (Quadrilateral) surface.getPolygons(j);
                Node[] node = polygon.getNodes();
                cbit.vcell.render.Vect3d elementCoord = new cbit.vcell.render.Vect3d();
                int nodesOnBoundary = 0;
                for (int k = 0; k < node.length; k++) {
                    if (!node[k].getMoveX() || (dimension > 1 && !node[k].getMoveY()) || (dimension == 3 && !node[k].getMoveZ())) {
                        nodesOnBoundary++;
                    }
                }
                if (nodesOnBoundary == 0) {
                    for (int k = 0; k < node.length; k++) {
                        elementCoord.add(new cbit.vcell.render.Vect3d(node[k].getX(), node[k].getY(), node[k].getZ()));
                    }
                    elementCoord.scale(0.25);
                } else if (nodesOnBoundary == 2) {
                    for (int k = 0; k < node.length; k++) {
                        if (!node[k].getMoveX() || !node[k].getMoveY() || !node[k].getMoveZ()) {
                            elementCoord.add(new cbit.vcell.render.Vect3d(node[k].getX(), node[k].getY(), node[k].getZ()));
                        }
                    }
                    elementCoord.scale(0.5);
                } else if (nodesOnBoundary == 3) {
                    for (int k = 0; k < node.length; k++) {
                        if (!node[k].getMoveX() && !node[k].getMoveY() || !node[k].getMoveY() && !node[k].getMoveZ() || !node[k].getMoveX() && !node[k].getMoveZ()) {
                            elementCoord.set(node[k].getX(), node[k].getY(), node[k].getZ());
                        }
                    }
                } else {
                    throw new RuntimeException("Unexcepted number of nodes on boundary for a polygon: " + nodesOnBoundary);
                }
                cbit.vcell.render.Vect3d unitNormal = new cbit.vcell.render.Vect3d();
                polygon.getUnitNormal(unitNormal);
                int volNeighbor1Region = regionImage.getRegionInfoFromOffset(polygon.getVolIndexNeighbor1()).getRegionIndex();
                int volNeighbor2Region = regionImage.getRegionInfoFromOffset(polygon.getVolIndexNeighbor2()).getRegionIndex();
                if (surface.getExteriorRegionIndex() == volNeighbor1Region && surface.getInteriorRegionIndex() == volNeighbor2Region) {
                    region1Outside++;
                }
                if (surface.getExteriorRegionIndex() == volNeighbor2Region && surface.getInteriorRegionIndex() == volNeighbor1Region) {
                    region1Inside++;
                }
                writer.write(cellID + " " + polygon.getVolIndexNeighbor1() + " " + polygon.getVolIndexNeighbor2() + " " + polygon.getArea() / correctCoeff + " " + elementCoord.getX() + " " + elementCoord.getY() + " " + elementCoord.getZ() + " " + unitNormal.getX() + " " + unitNormal.getY() + " " + unitNormal.getZ() + "\n");
                cellID++;
            }
            if (region1Inside != surface.getPolygonCount() && region1Outside != surface.getPolygonCount()) {
                throw new RuntimeException("Volume neighbor regions not consistent: [total, inside, outside]=" + surface.getPolygonCount() + "," + region1Inside + "," + region1Outside + "]");
            }
        }
    }
}

Example 20 with GeometrySurfaceDescription

use of cbit.vcell.geometry.surface.GeometrySurfaceDescription in project vcell by virtualcell.

the class OptXmlWriter method getModelXML.

public static Element getModelXML(PdeObjectiveFunction pdeObjectiveFunction, String[] parameterNames) {
    Element modelElement = new Element(OptXmlTags.Model_Tag);
    try {
        SpatialReferenceData refData = pdeObjectiveFunction.getReferenceData();
        double refDataEndTime = refData.getDataByRow(refData.getNumDataRows() - 1)[0];
        // 
        // post the problem either as an IDA or CVODE model
        // 
        org.vcell.util.document.SimulationVersion simVersion = new org.vcell.util.document.SimulationVersion(new KeyValue("12345"), "name", new org.vcell.util.document.User("user", new KeyValue("123")), new org.vcell.util.document.GroupAccessNone(), // versionBranchPointRef
        null, // branchID
        new java.math.BigDecimal(1.0), new java.util.Date(), org.vcell.util.document.VersionFlag.Archived, "", null);
        Simulation simulation = new Simulation(simVersion, pdeObjectiveFunction.getMathDescription());
        simulation.getMeshSpecification().setSamplingSize(refData.getDataISize());
        double[] times = refData.getDataByColumn(0);
        double minDt = Double.POSITIVE_INFINITY;
        for (int i = 1; i < times.length; i++) {
            minDt = Math.min(minDt, times[i] - times[i - 1]);
        }
        simulation.getSolverTaskDescription().setTimeBounds(new cbit.vcell.solver.TimeBounds(0.0, refDataEndTime));
        simulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolume);
        simulation.getSolverTaskDescription().setTimeStep(new TimeStep(minDt / 5, minDt / 5, minDt / 5));
        // clone and resample geometry
        Geometry resampledGeometry = null;
        try {
            resampledGeometry = (Geometry) BeanUtils.cloneSerializable(simulation.getMathDescription().getGeometry());
            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
            ISize newSize = simulation.getMeshSpecification().getSamplingSize();
            geoSurfaceDesc.setVolumeSampleSize(newSize);
            geoSurfaceDesc.updateAll();
        } catch (Exception e) {
            e.printStackTrace();
            throw new SolverException(e.getMessage());
        }
        SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, pdeObjectiveFunction.getFieldDataIDSs()), 0);
        StringWriter simulationInputStringWriter = new StringWriter();
        FiniteVolumeFileWriter fvFileWriter = new FiniteVolumeFileWriter(new PrintWriter(simulationInputStringWriter, true), simTask, resampledGeometry, pdeObjectiveFunction.getWorkingDirectory());
        fvFileWriter.write(parameterNames);
        simulationInputStringWriter.close();
        modelElement.setAttribute(OptXmlTags.ModelType_Attr, OptXmlTags.ModelType_Attr_FVSOLVER);
        CDATA simulationInputText = new CDATA(simulationInputStringWriter.getBuffer().toString());
        modelElement.addContent(simulationInputText);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new OptimizationException("failed to create fv input file: " + e.getMessage());
    }
    return modelElement;
}