use of org.vcell.util.ISize 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 + "]");
}
}
}
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class CartesianMeshChombo method readMeshFile.
public static CartesianMeshChombo readMeshFile(File chomboMeshFile) throws Exception {
CartesianMeshChombo chomboMesh = new CartesianMeshChombo();
if (H5.H5open() < 0) {
throw new Exception("H5.H5open() failed");
}
FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
if (fileFormat == null) {
throw new Exception("FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5) failed, returned null.");
}
FileFormat meshFile = null;
try {
meshFile = fileFormat.createInstance(chomboMeshFile.getAbsolutePath(), FileFormat.READ);
meshFile.open();
DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) meshFile.getRootNode();
Group rootGroup = (Group) rootNode.getUserObject();
Group meshGroup = (Group) rootGroup.getMemberList().get(0);
List<Attribute> meshAttrList = meshGroup.getMetadata();
for (Attribute attr : meshAttrList) {
String attrName = attr.getName();
MeshAttribute mattr = null;
try {
mattr = MeshAttribute.valueOf(attrName);
} catch (IllegalArgumentException ex) {
}
if (mattr == null) {
// if not found, then we don't care about this attribute
logger.debug("mesh attribute " + attrName + " is not defined in Java");
continue;
}
Object value = attr.getValue();
switch(mattr) {
case dimension:
chomboMesh.dimension = ((int[]) value)[0];
break;
case numLevels:
chomboMesh.numLevels = ((int[]) value)[0];
break;
case viewLevel:
chomboMesh.viewLevel = ((int[]) value)[0];
break;
case refineRatios:
chomboMesh.refineRatios = (int[]) value;
break;
case Dx:
case extent:
case Nx:
case origin:
// these 4 has format of {};
String[] valueStrArray = (String[]) value;
String value0 = valueStrArray[0];
StringTokenizer st = new StringTokenizer(value0, "{,} ");
int numTokens = st.countTokens();
// we need 3 for 3d
double[] values = new double[Math.max(3, numTokens)];
for (int i = 0; i < Math.min(3, numTokens); ++i) {
String token = st.nextToken();
values[i] = Double.parseDouble(token);
}
switch(mattr) {
case Dx:
chomboMesh.dx = new double[3];
System.arraycopy(values, 0, chomboMesh.dx, 0, values.length);
break;
case extent:
chomboMesh.extent = new Extent(values[0], values[1], values[2] == 0 ? 1 : values[2]);
break;
case Nx:
chomboMesh.size = new ISize((int) values[0], (int) values[1], values[2] == 0 ? 1 : (int) values[2]);
break;
case origin:
chomboMesh.origin = new Origin(values[0], values[1], values[2]);
break;
}
break;
}
}
List<HObject> memberList = meshGroup.getMemberList();
for (HObject member : memberList) {
if (!(member instanceof Dataset)) {
continue;
}
Dataset dataset = (Dataset) member;
Vector vectValues = (Vector) dataset.read();
String name = dataset.getName();
MeshDataSet mdataset = null;
try {
mdataset = MeshDataSet.valueOfName(name);
} catch (IllegalArgumentException ex) {
logger.debug("mesh dataset " + name + " is not defined in Java");
}
if (mdataset == null) {
// if not found, then we don't care about this dataset
continue;
}
switch(mdataset) {
case vertices:
collectVertices(chomboMesh, vectValues);
break;
case segments:
collect2dSegments(chomboMesh, vectValues);
break;
case structures:
collectStructures(chomboMesh, vectValues);
break;
case featurephasevols:
collectFeaturePhaseVols(chomboMesh, vectValues);
break;
case membraneids:
collectMembraneIds(chomboMesh, vectValues);
break;
case membrane_elements:
case membrane_elements_old:
collectMembraneElements(chomboMesh, vectValues);
break;
case surface_triangles:
collect3dSurfaceTriangles(chomboMesh, vectValues);
break;
case slice_view:
collect3dSliceView(chomboMesh, vectValues);
break;
}
}
} finally {
if (meshFile != null) {
meshFile.close();
}
}
// set neighbors to membrane elements
if (chomboMesh.dimension == 2 && chomboMesh.membraneElements != null) {
for (int i = 0; i < chomboMesh.membraneElements.length; ++i) {
MembraneElement me = chomboMesh.membraneElements[i];
me.setConnectivity(chomboMesh.segments[i].prevNeigbhor, chomboMesh.segments[i].nextNeigbhor, -1, -1);
}
}
return chomboMesh;
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class ChomboBox method fromString.
public static ChomboBox fromString(String str) {
StringTokenizer st = new StringTokenizer(str);
if (st.countTokens() != 4 && st.countTokens() != 6) {
throw new RuntimeException("ChombBox::fromString(), wrong format");
}
if (st.countTokens() == 4) {
// 2d
ISize lo = new ISize(Integer.parseInt(st.nextToken()), Integer.parseInt(st.nextToken()), 1);
ISize hi = new ISize(Integer.parseInt(st.nextToken()), Integer.parseInt(st.nextToken()), 1);
return new ChomboBox(lo, hi);
} else {
// 3d
ISize lo = new ISize(Integer.parseInt(st.nextToken()), Integer.parseInt(st.nextToken()), Integer.parseInt(st.nextToken()));
ISize hi = new ISize(Integer.parseInt(st.nextToken()), Integer.parseInt(st.nextToken()), Integer.parseInt(st.nextToken()));
return new ChomboBox(lo, hi);
}
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class ChomboBox method readVCML.
public void readVCML(CommentStringTokenizer tokens) throws DataAccessException {
String token = tokens.nextToken();
if (token.equalsIgnoreCase(VCML.ChomboBox)) {
token = tokens.nextToken();
if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
throw new DataAccessException("unexpected token " + token + " expecting " + VCML.BeginBlock);
}
}
boxLo = new ISize(Integer.parseInt(tokens.nextToken()), Integer.parseInt(tokens.nextToken()), 1);
boxHi = new ISize(Integer.parseInt(tokens.nextToken()), Integer.parseInt(tokens.nextToken()), 1);
}
use of org.vcell.util.ISize in project vcell by virtualcell.
the class RefinementRoi method getDx.
public double getDx(Simulation simulation) {
Extent extent = simulation.getMathDescription().getGeometry().getExtent();
ISize levelSize = simulation.getSolverTaskDescription().getChomboSolverSpec().getLevelSamplingSize(simulation.getMeshSpecification().getSamplingSize(), level);
return extent.getX() / levelSize.getX();
}
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