Example 1 with VisLine
use of org.vcell.vis.vismesh.thrift.VisLine in project vcell by virtualcell.
the class ChomboMeshMapping method cropQuads.
private void cropQuads(VisMesh visMesh) {
if (visMesh.getDimension() != 2) {
throw new RuntimeException("expecting 2D mesh");
}
List<VisPolygon> polygons = visMesh.getPolygons();
List<VisPoint> points = visMesh.getPoints();
List<VisLine> lines = visMesh.getVisLines();
for (VisPolygon polygon : polygons) {
List<Integer> polygonPointIndices = polygon.getPointIndices();
double fraction = polygon.getChomboVolumeIndex().getFraction();
if (fraction < 1.0 && polygonPointIndices.size() == 4) {
int p0 = polygonPointIndices.get(0);
int p1 = polygonPointIndices.get(1);
int p2 = polygonPointIndices.get(2);
int p3 = polygonPointIndices.get(3);
VisPoint point0 = points.get(p0);
VisPoint point1 = points.get(p1);
VisPoint point2 = points.get(p2);
VisPoint point3 = points.get(p3);
double p0x = point0.x;
double p0y = point0.y;
double p1x = point1.x;
double p1y = point1.y;
double p2x = point2.x;
double p2y = point2.y;
double p3x = point3.x;
double p3y = point3.y;
double pLowX = p0x;
double pLowY = p0y;
double pHiX = p2x;
double pHiY = p2y;
for (VisLine segment : lines) {
VisPoint segpoint1 = points.get(segment.getP1());
double s1x = segpoint1.x;
double s1y = segpoint1.y;
if (s1x <= pHiX && s1x >= pLowX && s1y <= pHiY && s1y >= pLowY) {
VisPoint segpoint2 = points.get(segment.getP2());
double s2x = segpoint2.x;
double s2y = segpoint2.y;
if (s2x <= pHiX && s2x >= pLowX && s2y <= pHiY && s2y >= pLowY) {
//
if (p0x == s1x && p0y == s2y) {
if (fraction > 0.5) {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP2(), segment.getP1(), p1, p2, p3 }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP2(), p0, segment.getP1() }));
}
} else if (p0x == s2x && p0y == s1y) {
if (fraction > 0.5) {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP1(), segment.getP2(), p1, p2, p3 }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP1(), p0, segment.getP2() }));
}
// case 2) { (remove point one && replace with segment
//
// 0 3 0 3
// s1 => s1 or s1
// 1 s2 2 1 s2 s2 2
//
} else if (p1x == s1x && p1y == s2y) {
if (fraction > 0.5) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, segment.getP1(), segment.getP2(), p2, p3 }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP1(), p1, segment.getP2() }));
}
} else if (p1x == s2x && p1y == s1y) {
if (fraction > 0.5) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, segment.getP2(), segment.getP1(), p2, p3 }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP2(), p1, segment.getP1() }));
}
// case 3) { (remove point two && replace with segment
//
// 0 3 0 3
// s2 => s2 or s2
// 1 s1 2 s1 2 1 s1
//
} else if (p2x == s1x && p2y == s2y) {
if (fraction > 0.5) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, p1, segment.getP2(), segment.getP1(), p3 }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP2(), p2, segment.getP1() }));
}
} else if (p2x == s2x && p2y == s1y) {
if (fraction > 0.5) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, p1, segment.getP1(), segment.getP2(), p3 }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP1(), p2, segment.getP2() }));
}
// case 4) { (remove point three && replace with segment
//
// 0 s2 3 s2 3 0 s2
// s1 => s1 or s1
// 1 2 1 2
//
} else if (p3x == s1x && p3y == s2y) {
if (fraction > 0.5) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, p1, p2, segment.getP1(), segment.getP2() }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP1(), p3, segment.getP2() }));
}
} else if (p3x == s2x && p3y == s1y) {
if (fraction > 0.5) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, p1, p2, segment.getP2(), segment.getP1() }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP2(), p3, segment.getP1() }));
}
// case 5) { (remove points 0 && 1 verticle cut)
//
// 0 s1 3 0 s1 s1 3
// => or
// 1 s2 2 1 s2 s2 2
//
} else if (p0y == s1y && p1y == s2y) {
boolean bigleft = ((s1x - p0x) + (s2x - p0x) > p3x - p0x);
if ((fraction > 0.5 && bigleft) || (fraction <= 0.5 && !bigleft)) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, p1, segment.getP2(), segment.getP1() }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP1(), segment.getP2(), p2, p3 }));
}
} else if (p0y == s2y && p1y == s1y) {
boolean bigleft = ((s1x - p0x) + (s2x - p0x) > p3x - p0x);
if ((fraction > 0.5 && bigleft) || (fraction <= 0.5 && !bigleft)) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, p1, segment.getP1(), segment.getP2() }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP2(), segment.getP1(), p2, p3 }));
}
// case 6) { (remove points 0 && 1 horizontal cut)
//
// 0 3 0 3
// s1 s2 => s1 s2 or s1 s2
// 1 2 1 2
//
} else if (p0x == s1x && p3x == s2x) {
boolean bigtop = ((s1y - p0y) + (s2y - p0y) > p1y - p0y);
if ((fraction > 0.5 && bigtop) || (fraction <= 0.5 && !bigtop)) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, segment.getP1(), segment.getP2(), p3 }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP2(), segment.getP1(), p1, p2 }));
}
} else if (p0x == s2x && p3x == s1x) {
boolean bigtop = ((s1y - p0y) + (s2y - p0y) > p1y - p0y);
if ((fraction > 0.5 && bigtop) || (fraction <= 0.5 && !bigtop)) {
polygon.setPointIndices(Arrays.asList(new Integer[] { p0, segment.getP2(), segment.getP1(), p3 }));
} else {
polygon.setPointIndices(Arrays.asList(new Integer[] { segment.getP1(), segment.getP2(), p1, p2 }));
}
} else {
LG.warn("found the segment for this polygon, don't know how to crop this one yet");
}
}
}
}
}
}
}
Also used :
VisPolygon(org.vcell.vis.vismesh.thrift.VisPolygon)
VisLine(org.vcell.vis.vismesh.thrift.VisLine)
VisPoint(org.vcell.vis.vismesh.thrift.VisPoint)
VisPoint(org.vcell.vis.vismesh.thrift.VisPoint)
Example 2 with VisLine
use of org.vcell.vis.vismesh.thrift.VisLine in project vcell by virtualcell.
the class ChomboMeshMapping method fromMeshData2D.
private VisMesh fromMeshData2D(ChomboMeshData chomboMeshData) {
ChomboMesh chomboMesh = chomboMeshData.getMesh();
ChomboLevel finestLevel = chomboMesh.getLevel(chomboMesh.getNumLevels() - 1);
int finestAbsRefinement = finestLevel.getAbsoluteRefinement();
ISize size = finestLevel.getSize();
int numX = size.getX();
int numY = size.getY();
int numZ = size.getZ();
int dimension = chomboMeshData.getMesh().getDimension();
int z = 0;
// invoke VisMesh() constructor
VisMesh visMesh = new VisMesh(chomboMesh.getDimension(), toThrift(chomboMesh.getOrigin()), toThrift(chomboMesh.getExtent()));
int currPointIndex = 0;
HashMap<String, Integer> pointDict = new HashMap<String, Integer>();
double originX = chomboMesh.getOrigin().x;
double originY = chomboMesh.getOrigin().y;
double originZ = chomboMesh.getOrigin().z;
double extentX = chomboMesh.getExtent().x;
double extentY = chomboMesh.getExtent().y;
double extentZ = chomboMesh.getExtent().z;
ChomboBoundaries chomboBoundaries = chomboMesh.getBoundaries();
for (ChomboBoundaries.Point chomboPoint : chomboBoundaries.getPoints()) {
double px = chomboPoint.x;
double py = chomboPoint.y;
double pz = z;
px = (px - originX) * (numX) / extentX * 2 - 1;
py = (py - originY) * (numY) / extentY * 2 - 1;
pz = (pz - originZ) * (numZ) / extentZ * 2 - 1;
if (dimension == 2) {
pz = z;
}
VisPoint newVisPoint = new VisPoint(px, py, pz);
String coordKey = toStringKey(newVisPoint);
pointDict.put(coordKey, currPointIndex);
visMesh.addToPoints(newVisPoint);
visMesh.addToSurfacePoints(newVisPoint);
currPointIndex += 1;
}
for (ChomboBoundaries.Segment segment : chomboBoundaries.getSegments()) {
VisLine newVisLine = new VisLine(segment.getP1(), segment.getP2());
newVisLine.setChomboSurfaceIndex(new ChomboSurfaceIndex(segment.getChomboIndex()));
visMesh.addToVisLines(newVisLine);
}
for (int levelIndex = 0; levelIndex < chomboMesh.getNumLevels(); levelIndex++) {
ChomboLevelData chomboLevelData = chomboMeshData.getLevelData(levelIndex);
ChomboLevel currLevel = chomboMesh.getLevel(levelIndex);
int currAbsRefinement = currLevel.getAbsoluteRefinement();
Covering covering = currLevel.getCovering();
int[] levelMap = covering.getLevelMap();
int[] boxNumberMap = covering.getBoxNumberMap();
int[] boxIndexMap = covering.getBoxIndexMap();
int levelNumX = currLevel.getSize().getX();
int levelNumY = currLevel.getSize().getY();
for (int x = 0; x < levelNumX; x++) {
for (int y = 0; y < levelNumY; y++) {
int mapIndex = x + y * levelNumX;
if (levelMap[mapIndex] == levelIndex) {
//
// if fraction (volume fraction of element in box) is 0 ... then skip this element
//
int boxNumber = boxNumberMap[mapIndex];
int boxIndex = boxIndexMap[mapIndex];
double fraction = chomboLevelData.getCellFraction(currLevel, boxNumber, boxIndex);
if (fraction > 0) {
//
// add cell
//
ChomboBox chomboBox = new ChomboBox(currLevel, x, x, y, y, z, z, dimension).getProjectedBox(currAbsRefinement, finestAbsRefinement);
double minX = 2 * chomboBox.getMinX() - 1;
double maxX = 2 * chomboBox.getMaxX() + 1;
double minY = 2 * chomboBox.getMinY() - 1;
double maxY = 2 * chomboBox.getMaxY() + 1;
//
// counter clockwise points for a VisPolygon ... initially a quad ... then may be
//
// minX,minY
// minX,maxY
// maxX,maxY
// maxX,minY
//
VisPoint p1Coord = new VisPoint(minX, minY, z);
String p1Key = toStringKey(p1Coord);
Integer i1 = pointDict.get(p1Key);
if (i1 == null) {
pointDict.put(p1Key, currPointIndex);
i1 = currPointIndex;
visMesh.addToPoints(p1Coord);
currPointIndex++;
}
VisPoint p2Coord = new VisPoint(minX, maxY, z);
String p2Key = toStringKey(p2Coord);
Integer i2 = pointDict.get(p2Key);
if (i2 == null) {
pointDict.put(p2Key, currPointIndex);
i2 = currPointIndex;
visMesh.addToPoints(p2Coord);
currPointIndex++;
}
VisPoint p3Coord = new VisPoint(maxX, maxY, z);
String p3Key = toStringKey(p3Coord);
Integer i3 = pointDict.get(p3Key);
if (i3 == null) {
pointDict.put(p3Key, currPointIndex);
i3 = currPointIndex;
visMesh.addToPoints(p3Coord);
currPointIndex++;
}
VisPoint p4Coord = new VisPoint(maxX, minY, z);
String p4Key = toStringKey(p4Coord);
Integer i4 = pointDict.get(p4Key);
if (i4 == null) {
pointDict.put(p4Key, currPointIndex);
i4 = currPointIndex;
visMesh.addToPoints(p4Coord);
currPointIndex++;
}
VisPolygon quad = new VisPolygon(Arrays.asList(new Integer[] { i1, i2, i3, i4 }));
quad.setChomboVolumeIndex(new ChomboVolumeIndex(levelIndex, boxNumber, boxIndex, fraction));
// print('adding a cell at level '+str(currLevel.getLevel())+" from "+str(p1Coord)+" to "+str(p3Coord))
visMesh.addToPolygons(quad);
}
}
}
}
}
cropQuads(visMesh);
return visMesh;
}
Also used :
ChomboSurfaceIndex(org.vcell.vis.vismesh.thrift.ChomboSurfaceIndex)
HashMap(java.util.HashMap)
ISize(org.vcell.util.ISize)
VisLine(org.vcell.vis.vismesh.thrift.VisLine)
Covering(org.vcell.vis.chombo.ChomboLevel.Covering)
ChomboBoundaries(org.vcell.vis.chombo.ChomboBoundaries)
ChomboVolumeIndex(org.vcell.vis.vismesh.thrift.ChomboVolumeIndex)
VisPoint(org.vcell.vis.vismesh.thrift.VisPoint)
ChomboLevelData(org.vcell.vis.chombo.ChomboLevelData)
VisMesh(org.vcell.vis.vismesh.thrift.VisMesh)
VisPolygon(org.vcell.vis.vismesh.thrift.VisPolygon)
ChomboBox(org.vcell.vis.chombo.ChomboBox)
ChomboMesh(org.vcell.vis.chombo.ChomboMesh)
ChomboLevel(org.vcell.vis.chombo.ChomboLevel)
VisPoint(org.vcell.vis.vismesh.thrift.VisPoint)
Aggregations
VisLine (org.vcell.vis.vismesh.thrift.VisLine)2
VisPoint (org.vcell.vis.vismesh.thrift.VisPoint)2
VisPolygon (org.vcell.vis.vismesh.thrift.VisPolygon)2
HashMap (java.util.HashMap)1
ISize (org.vcell.util.ISize)1
ChomboBoundaries (org.vcell.vis.chombo.ChomboBoundaries)1
ChomboBox (org.vcell.vis.chombo.ChomboBox)1
ChomboLevel (org.vcell.vis.chombo.ChomboLevel)1
Covering (org.vcell.vis.chombo.ChomboLevel.Covering)1
ChomboLevelData (org.vcell.vis.chombo.ChomboLevelData)1
ChomboMesh (org.vcell.vis.chombo.ChomboMesh)1
ChomboSurfaceIndex (org.vcell.vis.vismesh.thrift.ChomboSurfaceIndex)1
ChomboVolumeIndex (org.vcell.vis.vismesh.thrift.ChomboVolumeIndex)1
VisMesh (org.vcell.vis.vismesh.thrift.VisMesh)1
