void mafAddIRows(char *mafIn, char *twoBitIn, char *mafOut, char *nBedFile)
/* mafAddIRows - Filter out maf files. */
{
FILE *f = mustOpen(mafOut, "w");
struct twoBitFile *twoBit = twoBitOpen(twoBitIn);
struct mafAli *mafList, *maf;
struct mafFile *mf = mafOpen(mafIn);
struct hash *bedHash = newHash(6);
if (nBedFile != NULL)
{
struct lineFile *lf = lineFileOpen(nBedFile, TRUE);
char *row[1];
while (lineFileRow(lf, row))
{
addBed(row[0], bedHash);
}
lineFileClose(&lf);
}
speciesHash = newHash(6);
mafList = readMafs(mf);
mafWriteStart(f, mf->scoring);
mafFileFree(&mf);
chainStrands(strandHeads, bedHash);
bridgeSpecies(mafList, speciesList);
fillHoles(mafList, speciesList, twoBit);
for(maf = mafList; maf ; maf = maf->next)
mafWrite(f, maf);
}
void FastThreePhase::decode() {
makeColor();
int n = width * height;
threePhaseWrap.setThreshold((unsigned char) rangeThreshold);
threePhaseWrap.makeWrappedPhase(phasePixels, qualityPixels,
graySequence[0], graySequence[1], graySequence[2]);
// this is used by getStart() to determine the center
for(int i = 0; i < n; i++)
ready[i] = qualityPixels[i] != LABEL_BACKGROUND;
partialQualityMap.makeQualityMap(phasePixels, qualityPixels);
scanlineOffset.makeOffset(phasePixels, qualityPixels, (char*) offsetPixels, getStart(), phasePersistence);
for(int i = 0; i < n; i++)
mask[i] = qualityPixels[i] != LABEL_UNWRAPPED;
for(int i = 0; i < n; i++) {
int cur = ((char*) offsetPixels)[i];
phase[i] = (cur * 256) + phasePixels[i];
phase[i] *= .002f; // this should be handled by skew/scale instead
}
makeDepth();
if(maxHoleSize > 0)
fillHoles();
}
void meshsurf3::buildSurface( std::vector<vec3d> &vertices, std::vector<vec3d> &normals, std::vector<vec3i> &faces, const levelset3 *fluid, const levelset3 *solid, bool enclose, FLOAT64 dpx, uint iteration, bool doFit ) {
// Save a reference to the mesher
const mesher3 &g = *this->g;
tick(); dump("Computing levelset for %d nodes...", g.nodes.size());
values.clear();
values.resize(g.nodes.size());
if( values.empty() ) {
email::print("Mesher Uninitialized !\n");
email::send();
exit(0);
}
// Compute levelset for each node
PARALLEL_FOR for( uint n=0; n<g.nodes.size(); n++ ) {
FLOAT64 phi = fluid->evalLevelset(g.nodes[n]);
if( enclose ) phi = fmax(phi,-dpx-solid->evalLevelset(g.nodes[n]));
values[n] = phi;
}
dump("Done. Took %s.\n",stock("meshsurf_levelset_sample"));
// Fill holes
fillHoles(values,solid,g.nodes,g.elements,g.node2node,fluid->dx);
// Calculate intersections on edges
tick(); dump("Computing cut edges for each tet...");
std::vector<vec3d> cutpoints(g.edges.size());
std::vector<int> cutIndices(g.edges.size());
uint index = 0;
for( int n=0; n<g.edges.size(); n++ ) {
FLOAT64 levelsets[2];
for( uint m=0; m<2; m++ ) levelsets[m] = values[g.edges[n][m]];
if( copysign(1.0,levelsets[0]) * copysign(1.0,levelsets[1]) <= 0 ) {
FLOAT64 det = levelsets[0]-levelsets[1];
if( fabs(det) < 1e-16 ) det = copysign(1e-16,det);
FLOAT64 a = fmin(0.99,fmax(0.01,levelsets[0]/det));
vec3d p = (1.0-a)*g.nodes[g.edges[n][0]]+a*g.nodes[g.edges[n][1]];
cutpoints[n] = p;
cutIndices[n] = index++;
} else {
cutIndices[n] = -1;
}
}
// Copy them to packed array
vertices.clear();
vertices.resize(index);
index = 0;
for( uint n=0; n<cutIndices.size(); n++ ) {
if( cutIndices[n] >= 0 ) vertices[index++] = cutpoints[n];
}
dump("Done. Took %s.\n",stock());
// Stitch faces (marching tet)
tick(); dump("Stitching edges...");
std::vector<std::vector<uint> > node_faces;
node_faces.resize(g.nodes.size());
faces.clear();
for( uint n=0; n<g.elements.size(); n++ ) {
std::vector<uint> nv;
for( uint m=0; m<g.element_edges[n].size(); m++ ) {
uint idx = g.element_edges[n][m];
if( cutIndices[idx] >= 0 ) {
nv.push_back(cutIndices[idx]);
}
}
if( nv.size() == 4 ) {
// Triangulate the veritces
int idx0 = -1;
int idx1 = -1;
for( uint m=0; m<g.element_edges[n].size(); m++ ) {
if( cutIndices[g.element_edges[n][m]] >= 0 ) {
idx0 = g.element_edges[n][m];
break;
}
}
// If found one intersection edge
if( idx0 >= 0 ) {
for( uint m=0; m<g.element_edges[n].size(); m++ ) {
uint opID = g.element_edges[n][m];
if( cutIndices[opID] >= 0 && isOpEdge(idx0,opID)) {
idx1 = opID;
break;
}
}
// If found opposite intersection edge
if( idx1 >= 0 ) {
vec3i v;
v[0] = cutIndices[idx0];
v[1] = cutIndices[idx1];
for( uint m=0; m<g.element_edges[n].size(); m++ ) {
uint idx2 = g.element_edges[n][m];
if( cutIndices[idx2] >= 0 && idx2 != idx0 && idx2 != idx1 ) {
v[2] = cutIndices[idx2];
faces.push_back(v);
for( uint m=0; m<g.elements[n].size(); m++ ) {
node_faces[g.elements[n][m]].push_back(faces.size()-1);
}
}
}
} else {
dump( "Opposite edge was not found !\n");
exit(0);
}
} else {
dump( "Ground edge was not found !\n");
exit(0);
}
} else if( nv.size() == 3 ) {
faces.push_back(vec3i(nv[0],nv[1],nv[2]));
for( uint m=0; m<g.elements[n].size(); m++ ) {
node_faces[g.elements[n][m]].push_back(faces.size()-1);
}
} else if( nv.size() == 0 ) {
// Empty surface. Do nothing...
} else {
dump( "\nBad stitch encounrtered: Element - edge count = %d.\n", g.element_edges[n].size() );
dump( "Unknown set found N(%e,%e,%e,%e) = %d.\n",
values[g.elements[n][0]], values[g.elements[n][1]], values[g.elements[n][2]], values[g.elements[n][3]], nv.size());
for( uint k=0; k<g.element_edges[n].size(); k++ ) {
uint vidx[2] = { g.edges[g.element_edges[n][k]][0], g.edges[g.element_edges[n][k]][1] };
dump( "Edge info[%d] = edge(%d,%d) = (%e,%e) = (%f,%f)\n", k, vidx[0], vidx[1], values[vidx[0]], values[vidx[1]], copysign(1.0,values[vidx[0]]), copysign(1.0,values[vidx[1]]) );
}
}
}
dump("Done. Took %s.\n",stock("meshsurf_stitch_mesh"));
// Find closest position
tick(); dump("Finding closest surface position at surface tets...");
surfacePos.clear();
surfacePos.resize(g.nodes.size());
for( uint n=0; n<g.nodes.size(); n++ ) {
FLOAT64 dist = 1e8;
vec3d p = g.nodes[n];
for( uint m=0; m<node_faces[n].size(); m++ ) {
vec3d p0 = vertices[faces[node_faces[n][m]][0]];
vec3d p1 = vertices[faces[node_faces[n][m]][1]];
vec3d p2 = vertices[faces[node_faces[n][m]][2]];
vec3d out = g.nodes[n];
vec3d src = out;
FLOAT64 d = fmax(1e-8,point_triangle_distance(src,p0,p1,p2,out));
if( d < dist ) {
p = out;
dist = d;
}
}
if( dist < 1.0 ) {
values[n] = (values[n]>=0 ? 1.0 : -1.0) * dist;
surfacePos[n].push_back(g.nodes[n]);
surfacePos[n].push_back(p);
} else {
values[n] = (values[n]>=0 ? 1.0 : -1.0) * 1e8;
}
}
dump("Done. Took %s.\n",stock("meshsurf_find_close_pos1"));
if( extrapolate_dist ) {
// Fast march
tick();
std::vector<fastmarch3<FLOAT64>::node3 *> fnodes(g.nodes.size());
for( uint n=0; n<g.nodes.size(); n++ ) fnodes[n] = new fastmarch3<FLOAT64>::node3;
for( uint n=0; n<g.nodes.size(); n++ ) {
vec3d p = g.nodes[n];
bool fixed = fabs(values[n]) < 1.0;
fnodes[n]->p = p;
fnodes[n]->fixed = fixed;
fnodes[n]->levelset = values[n];
fnodes[n]->value = 0.0;
fnodes[n]->p2p.resize(g.node2node[n].size());
for( uint m=0; m<g.node2node[n].size(); m++ ) {
fnodes[n]->p2p[m] = fnodes[g.node2node[n][m]];
}
}
fastmarch3<FLOAT64>::fastMarch(fnodes,extrapolate_dist,-extrapolate_dist,1);
// Pick up values
for( uint n=0; n<g.nodes.size(); n++ ) {
values[n] = fnodes[n]->levelset;
delete fnodes[n];
}
stock("meshsurf_fastmarch");
}
// Compute normal
tick(); dump("Computing normals...");
computeNormals(vertices,normals,faces,cutIndices);
dump("Done. Took %s.\n",stock("meshsurf_normal"));
// Flip facet rotation if necessary
flipFacet(vertices,normals,faces,0.1*fluid->dx);
#if 1
// Fit surface
if( doFit ) {
tick(); dump("Fitting %d surface vertices...", vertices.size() );
for( uint k=0; k<1; k++ ) {
smoothMesh(vertices,normals,faces,solid,dpx,1);
PARALLEL_FOR for( uint n=0; n<vertices.size(); n++ ) {
vec3d out = vertices[n];
if( solid->evalLevelset(out) > dpx && fluid->getClosestSurfacePos(out) ) {
vertices[n] = out;
}
}
}
dump("Done. Took %s.\n",stock("meshsurf_fit"));
}
#endif
// Smooth mesh
#if 1
tick(); dump("Smoothing faces...");
smoothMesh(vertices,normals,faces,solid,dpx,iteration);
dump("Done. Took %s.\n",stock("meshsurf_smooth"));
#endif
// Find closest position again
tick(); dump("Finding closest surface position at surface tets again...");
surfacePos.clear();
surfacePos.resize(g.nodes.size());
for( uint n=0; n<g.nodes.size(); n++ ) {
FLOAT64 dist = 1e8;
vec3d p = g.nodes[n];
for( uint m=0; m<node_faces[n].size(); m++ ) {
vec3d p0 = vertices[faces[node_faces[n][m]][0]];
vec3d p1 = vertices[faces[node_faces[n][m]][1]];
vec3d p2 = vertices[faces[node_faces[n][m]][2]];
vec3d out = g.nodes[n];
vec3d src = out;
FLOAT64 d = fmax(1e-8,point_triangle_distance(src,p0,p1,p2,out));
if( d < dist ) {
p = out;
dist = d;
}
}
if( dist < 1.0 ) {
values[n] = (values[n]>=0 ? 1.0 : -1.0) * dist;
}
}
dump("Done. Took %s.\n",stock("meshsurf_find_close_pos2"));
// Flip again
flipFacet(vertices,normals,faces,0.1*fluid->dx);
}
bool BkgdObsSplineLoader::loadBkgdObs(QList<real> &bgIn)
{
// Turn Debug on if there are problems with the vertical spline interpolation,
// Eventually this should be replaced with the internal spline code
// SplineD::Debug(1);
// Geographic functions
// GeographicLib::TransverseMercatorExact tm = GeographicLib::TransverseMercatorExact::UTM();
real referenceLon = configHash->value("ref_lon").toFloat();
int time;
real lat, lon, alt, u, v, w, t, qv, rhoa, qr;
real Pi = acos(-1);
bool debugDomain = isTrue("debug_domain");
// bgZ = -32768.; TODO. What was that about?
// background is in km, ROI is gridpoints
iROI = configHash->value("i_background_roi").toFloat() / iincr;
jROI = configHash->value("j_background_roi").toFloat() / jincr;
maxGridDist = 3.0;
QString interp_mode = configHash->value("bg_interpolation");
if (interp_mode == "Cressman")
maxGridDist = 1.0;
if (frameVector.size() == 0) {
std::cout << "Frame Vector is not initialized." << std::endl;
return false;
}
std::cout << "Loading background onto Gaussian mish with " << iROI
<< " grid length radius of influence in i direction" << std::endl;
std::cout << "and " << jROI << " grid length radius of influence in j direction" << std::endl;
QDateTime startTime = frameVector.front().getTime();
QDateTime endTime = frameVector.back().getTime();
std::cout << "Start time: " << startTime.toTime_t() << " "
<< startTime.toString("yyyy-MM-dd-HH:mm:ss").toLatin1().data() << std::endl;
std::cout << "End time: " << endTime.toTime_t() << " "
<< endTime.toString("yyyy-MM-dd-HH:mm:ss").toLatin1().data() << std::endl;
int timeProblem = 0;
int domainProblem = 0;
int radiusProblem = 0;
int levelProblem = 0;
int splineProblem = 0;
std::cout << "iROI: " << iROI << ", jROI: " << jROI << ", maxGridDist: "
<< maxGridDist << std::endl;
std::cout << "imin: " << imin << ", iincr: " << iincr << std::endl;
std::cout << "jmin: " << jmin << ", jincr: " << jincr << std::endl;
std::cout << "kmin: " << kmin << ", kincr: " << kincr << std::endl;
while( bkgdAdapter->next(time, lat, lon, alt, u, v, w, t, qv, rhoa, qr) ) {
int tci;
if (! timeCheck(time, startTime, endTime, tci)) {
timeProblem++;
continue;
}
real Um = frameVector[tci].getUmean();
real Vm = frameVector[tci].getVmean();
// Get the X, Y & Z
real tcX, tcY, metX, metY;
projection.Forward(referenceLon, frameVector[tci].getLat() , frameVector[tci].getLon(),
tcX, tcY);
projection.Forward(referenceLon, lat, lon , metX, metY);
bgX = (metX - tcX) / 1000.;
bgY = (metY - tcY) / 1000.;
real heightm = (alt > 10.0) ? alt : 10; // don't want to take log of zero below...
bgZ = heightm / 1000.;
bgRadius = sqrt(bgX * bgX + bgY * bgY);
bgTheta = 180.0 * atan2(bgY, bgX) / Pi;
if (configHash->value("allow_negative_angles") != "true")
if (bgTheta < 0)
bgTheta += 360.0;
// Make sure the ob is in the Interpolation domain
if (runMode == RUN_MODE_XYZ) {
if ((bgX < (imin - iincr - (iROI * iincr * maxGridDist))) or
(bgX > (imax + iincr + (iROI * iincr * maxGridDist))) or
(bgY < (jmin - jincr - (jROI * jincr * maxGridDist))) or
(bgY > (jmax + jincr + (jROI * jincr * maxGridDist))) or
(bgZ < kmin)) { //Allow for higher values for interpolation purposes
domainProblem++;
if (debugDomain)
std::cout << "bgX: " << bgX << " bgY: " << bgY << " bgZ: " << bgZ << std::endl;
continue;
}
} else if (runMode == RUN_MODE_RTZ) {
if ((bgRadius < (imin - iincr - (iROI * iincr * maxGridDist))) or
(bgRadius > (imax + iincr + (iROI * iincr * maxGridDist))) or
(bgTheta < jmin - jincr - (jROI * jincr * maxGridDist)) or
(bgTheta > jmax + jincr + (jROI * jincr * maxGridDist)) or
(bgZ < kmin)) { //Exceeding the Theta domain only makes sense for sectors
domainProblem++;
continue;
}
real cylUm = (Um * bgX + Vm * bgY) / bgRadius;
real cylVm = (-Um * bgY + Vm * bgX) / bgRadius;
Um = cylUm;
Vm = cylVm;
}
// Reference states
real rhoBar = refstate->getReferenceVariable(ReferenceVariable::rhoaref, heightm);
real qBar = refstate->getReferenceVariable(ReferenceVariable::qvbhypref, heightm);
real tBar = refstate->getReferenceVariable(ReferenceVariable::tempref, heightm);
real rho = rhoa + rhoa * qv / 1000.;
real rhou = rho * (u - Um);
real rhov = rho * (v - Vm);
real rhow = rho * w;
real tprime = t - tBar;
qv = refstate->bhypTransform(qv);
real qvprime = qv - qBar;
real rhoprime = (rhoa - rhoBar) * 100;
real logZ = log(bgZ);
if (configHash->value("qr_variable") == "qr")
qr = refstate->bhypTransform(qr);
// We assume here that the background precipitation field is always zero
// real qr = 0.;
if (runMode == RUN_MODE_XYZ) {
bgIn << bgX << bgY << logZ << time << rhou << rhov << rhow << tprime << qvprime << rhoprime << qr ;
} else if (runMode == RUN_MODE_RTZ)
bgIn << bgRadius << bgTheta << logZ << time << rhou << rhov << rhow << tprime
<< qvprime << rhoprime << qr ;
// Push values for an entire column, then solve for the spline
if ( (logheights.size() != 0) && (logZ <= logheights.back()) ) {
// Not first level, not same column, Solve for the spline
if (logheights.size() == 1) {
std::cerr << "Error at " << lat << ", " << lon << ", " << bgZ << std::endl
<< "Only one level found in background spline setup. " << std::endl
<< "Please check Background.in to ensure sorting by descending Z coordinate and re-run."
<< std::endl;
levelProblem++;
return false;
}
splineSolver(0); // This will also clear logheights, uBG, vBG, ...
}
logheights.push_back(logZ);
uBG.push_back(rhou);
vBG.push_back(rhov);
wBG.push_back(rhow);
tBG.push_back(tprime);
qBG.push_back(qvprime);
rBG.push_back(rhoprime);
zBG.push_back(qr);
} // each obs
std::cout << "timeProblem: " << timeProblem << ", domainProblem: " << domainProblem
<< ", radiusProblem: " << radiusProblem << ", levelProblem: " << levelProblem
<< ", splineProblem: " << splineProblem
<< std::endl;
if (!logheights.size()) {
// Error reading in the background field
std::cout << "No background estimates read in. "
<< "Please check the time and location of your background field.\n";
#if 0
std::cout << "Observation window: " << tcstart.toStdString() << " to " << tcend.toStdString() << "\n";
std::cout << "Background time: " << bgTimestring.toStdString() << "\n";
#endif
return false;
}
// std::cout << "------------------------2\n";
// Solve for the last spline
if (logheights.size() == 1) {
std::cerr << "Only one level found in background spline setup. "
<< "Please check Background.in to ensure sorting by Z coordinate and re-run." << std::endl;
return false;
}
// Exponential interpolation in horizontal, b-Spline interpolation on log height in vertical
splineSolver(2); // This will also clear logheights, uBG, vBG, ...
int numbgObs = bgIn.size() / 11; // 11 entries per ob
if (isTrue("debug_bgIn"))
dumpBgIn(0, numbgObs, bgIn);
QVector<int> emptybg;
// TODO Do we need to check interpolation and fill hole for KD too?
// bgWeight is a byproduct of calling the spline solver, so that's not available.
// what about fill holes? It depends on emptyBg which is also a byproduct of the spline solver.
// Check interpolation
if (numbgObs > 0) {
START_TIMER(timeci);
for (int ki = -1; ki < (kdim); ki++) {
for (int kmu = -1; kmu <= 1; kmu += 2) {
real kPos = kmin + kincr * (ki + (0.5 * sqrt(1. / 3.) * kmu + 0.5));
for (int ii = -1; ii < (idim); ii++) {
for (int imu = -1; imu <= 1; imu += 2) {
real iPos = imin + iincr * (ii + (0.5 * sqrt(1. / 3.) * imu + 0.5));
for (int ji = -1; ji < (jdim); ji++) {
for (int jmu = -1; jmu <= 1; jmu += 2) {
real jPos = jmin + jincr * (ji + (0.5 * sqrt(1. / 3.) * jmu + 0.5));
int bgI = (ii + 1) * 2 + (imu + 1) / 2;
int bgJ = (ji + 1) * 2 + (jmu + 1) / 2;
int bgK = (ki + 1) * 2 + (kmu + 1) / 2;
int bIndex = numVars * (idim + 1) * 2 * (jdim + 1) * 2 * bgK
+ numVars * (idim + 1) * 2 * bgJ + numVars * bgI;
for (unsigned int var = 0; var < numVars; var++) {
if (bgWeights[bIndex] != 0) {
bgU[bIndex + var] /= bgWeights[bIndex];
} else {
emptybg.push_back(bIndex);
if (emptybg.size() < 15) {
std::cout << "Empty background mish for variable "
<< var << " at " << iPos << ", " << jPos << ", " << kPos << std::endl;
} else if (emptybg.size() == 15) {
std::cout << "Too many empty mish points, will no longer report.\n";
}
}
}
if (configHash->value("qr_variable") == "dbz") {
if (bgU[bIndex + 6] > 0) {
real dbzavg = 10 * log10(bgU[bIndex + 6]);
bgU[bIndex + 6] = (dbzavg + 35.) * 0.1;
} else {
bgU[bIndex + 6] = 0.0;
}
}
}
}
}
}
}
}
fillHoles(emptybg);
PRINT_TIMER("Interpolation check", timeci);
} else {
std::cout << "No background observations loaded" << std::endl;
return false;
}
std::cout << numbgObs << " background observations loaded" << std::endl;
if (isTrue("debug_bgU")) {
dumpBgU(0, uStateSize, bgU);
}
if (configHash->contains("debug_bgU_nc"))
bgu2nc(configHash->value("debug_bgU_nc").toLatin1().data(), bgU);
return true;
}
