void BigInt::ToComplement()
{
Refine();
for(long long i = 0; i < MAXBIT - 1; i++)
m_element[i] = JINZHI - 1 - m_element[i];
m_element[0] += 1;
Refine();
}
/* Refine a curve until it can be approximated with straight lines to within
** the given tolerance. Always does at least one refinement, even if the
** original curve is inside tolerance. */
void
CubicBspline::Refine_Tolerance(CubicBspline &result, const float tolerance)
{
Refine(result);
while ( ! result.Within_Tolerance(tolerance) )
result.Refine(result);
}
void Tile::Init(float roughness) {
// Zufallsgenerator initialisieren
srand(static_cast<unsigned int>(time(0)));
// x- und z-Koordinaten berechnen.
// Das Wurzel-Tile ersteckt sich entlang der x- und z-Achse immer im Bereich
// [-2.5, 2.5]
int i = 0;
for (int y = 0; y < size_; ++y) {
for (int x = 0; x < size_; ++x, ++i) {
vertices_[i].x = x * 5.0f / (size_ - 1) - 2.5f;
vertices_[i].z = y * 5.0f / (size_ - 1) - 2.5f;
}
}
// Ecken mit Zufallshöhenwerten initialisieren
int block_size = size_ - 1;
vertices_[I(0, 0)].y = randf();
vertices_[I(0, block_size)].y = randf();
vertices_[I(block_size, 0)].y = randf();
vertices_[I(block_size, block_size)].y = randf();
// Verfeinerungsschritte durchführen bis sämtliche Werte berechnet sind
while (block_size > 1) {
Refine(block_size, roughness);
block_size = block_size / 2;
}
}
BigInt::BigInt(const BigInt& x)
{
m_element = new unsigned long long[MAXBIT];
m_isRefined = false;
for(long long i = 0; i < MAXBIT; i++)
m_element[i] = x.GetElement(i);
Refine();
}
void Run()
{
SetStartTime();
Log("Started %s\n", GetTimeAsStr());
for (int i = 0; i < g_argc; ++i)
Log("%s ", g_argv[i]);
Log("\n");
#if TIMING
TICKS t1 = GetClockTicks();
#endif
if (g_bRefine)
Refine();
else if (g_bRefineW)
{
extern void DoRefineW();
DoRefineW();
}
else if (g_bProfDB)
ProfDB();
else if (g_bSW)
Local();
else if (0 != g_pstrSPFileName)
DoSP();
else if (g_bProfile)
Profile();
else if (g_bPPScore)
PPScore();
else if (g_bPAS)
ProgAlignSubFams();
else
DoMuscle();
#if TIMING
extern TICKS g_ticksDP;
extern TICKS g_ticksObjScore;
TICKS t2 = GetClockTicks();
TICKS TotalTicks = t2 - t1;
TICKS ticksOther = TotalTicks - g_ticksDP - g_ticksObjScore;
double dSecs = TicksToSecs(TotalTicks);
double PctDP = (double) g_ticksDP*100.0/(double) TotalTicks;
double PctOS = (double) g_ticksObjScore*100.0/(double) TotalTicks;
double PctOther = (double) ticksOther*100.0/(double) TotalTicks;
Log(" Ticks Secs Pct\n");
Log(" ============ ======= =====\n");
Log("DP %12ld %7.2f %5.1f%%\n",
(long) g_ticksDP, TicksToSecs(g_ticksDP), PctDP);
Log("OS %12ld %7.2f %5.1f%%\n",
(long) g_ticksObjScore, TicksToSecs(g_ticksObjScore), PctOS);
Log("Other %12ld %7.2f %5.1f%%\n",
(long) ticksOther, TicksToSecs(ticksOther), PctOther);
Log("Total %12ld %7.2f 100.0%%\n", (long) TotalTicks, dSecs);
#endif
ListDiagSavings();
Log("Finished %s\n", GetTimeAsStr());
}
bool RiemannianGeodesic<Real>::Subdivide (const GVector<Real>& end0,
GVector<Real>& mid, const GVector<Real>& end1)
{
mid = ((Real)0.5)*(end0 + end1);
RefineCallbackFunction save = RefineCallback;
RefineCallback = 0;
bool changed = Refine(end0, mid, end1);
RefineCallback = save;
return changed;
}
void RiemannianGeodesic<Real>::ComputeGeodesic (const GVector<Real>& point0,
const GVector<Real>& point1, int& quantity, GVector<Real>*& path)
{
assertion(Subdivisions < 32, "Exceeds maximum iterations\n");
quantity = (1 << Subdivisions) + 1;
path = new1<GVector<Real> >(quantity);
int i;
for (i = 0; i < quantity; ++i)
{
path[i].SetSize(mDimension);
}
mCurrentQuantity = 2;
path[0] = point0;
path[1] = point1;
for (mSubdivide = 1; mSubdivide <= Subdivisions; ++mSubdivide)
{
// A subdivision essentially doubles the number of points.
int newQuantity = 2*mCurrentQuantity - 1;
assertion(newQuantity <= quantity, "Unexpected condition.\n");
// Copy the old points so that there are slots for the midpoints
// during the subdivision, the slots interleaved between the old
// points.
for (i = mCurrentQuantity-1; i > 0; --i)
{
path[2*i] = path[i];
}
// Subdivide the polyline.
for (i = 0; i <= mCurrentQuantity-2; ++i)
{
Subdivide(path[2*i], path[2*i+1], path[2*i+2]);
}
mCurrentQuantity = newQuantity;
// Refine the current polyline vertices.
for (mRefine = 1; mRefine <= Refinements; ++mRefine)
{
for (i = 1; i <= mCurrentQuantity-2; ++i)
{
Refine(path[i-1], path[i], path[i+1]);
}
}
}
assertion(mCurrentQuantity == quantity, "Unexpected condition\n");
mSubdivide = 0;
mRefine = 0;
mCurrentQuantity = 0;
}
Tile::Tile(Tile *parent, Tile::Direction direction, float roughness,
Tile *north, Tile *west)
: lod_(parent->lod_ + 1),
size_(parent->size_),
num_lod_(parent->num_lod_ - 1),
index_buffer_(NULL),
direction_(direction),
parent_(parent) {
vertices_ = new Vector[size_*size_];
InitFromParent();
Refine(2, roughness);
FixEdges(north, west);
InitChildren(roughness, north, west);
}
void AdaptiveSparseGrid::BuildFirstLevel() {
AdaptiveARRAY<int>* px1 = AdaptiveCoordAllocator.NewItem(dim);
AdaptiveARRAY<int>* px2 = AdaptiveCoordAllocator.NewItem(dim);
px1 -> fill(1);
px2 -> fill(0);
//! The first level is always a single point.
AdaptiveARRAY<double> x;
x.redim(dim);
x.fill(0.5);
L = 0;
//! For the fisrt point, we always assign it to rank 0
if (rank == 0) {
EvaluateFunctionAtThisPoint(&x);
AdaptiveData* pData = AdaptiveDataAllocator.NewItem();
AdaptiveNodeData* pNodeData = AdaptiveNodeDataAllocator.NewItem();
pData->index = px1;
pNodeData->index = px2;
pNodeData->surplus = new double[TotalDof];
for ( int i = 0; i < TotalDof; i++) {
pNodeData->surplus[i] = surplus[i];
}
pData->NodeData.insert(pNodeData);
SparseGrid.push_front(pData);
}
MPI_Barrier(mpiCOMM);
//Generate New sons for each dimension
Refine(px1, px2);
// Compute the integration value
if ( type == 1)
{ UpdateError(); }
if ( rank != 0) {
AdaptiveCoordAllocator.DeleteItem(px1);
AdaptiveCoordAllocator.DeleteItem(px2);
}
}
void GenerateIcosphere(Grid& grid, const vector3& center, number radius,
int numRefinements, AVector3& aPos, Selector* psel)
{
Selector defSel;
if(!psel){
defSel.assign_grid(grid);
psel = &defSel;
}
Selector& sel = *psel;
// enable autoselection
bool autoselectionEnabled = sel.autoselection_enabled();
sel.enable_autoselection(true);
// clear the selector
sel.clear();
// create an icosahedron. All elements of the sphere will be selected, since we
// enabled autoselection
GenerateIcosahedron(grid, center, radius, aPos);
// perform refinement steps
// we need a temporary int attachment for the edges
AInt aInt;
grid.attach_to_edges(aInt);
// use a refinement callback to project the new vertices to the sphere
SphereProjector sphereProjecton(MakeGeometry3d(grid, aPos), center);
for(int i = 0; i < numRefinements; ++i)
Refine(grid, sel, aInt, &sphereProjecton);
// remove attachments
grid.detach_from_edges(aInt);
// restore autoselection
sel.enable_autoselection(autoselectionEnabled);
}
int main(int argc, char **argv)
{
char dcname[40];
AccMask setmask = 0;
AccMask clearmask = 0;
char *s;
PrgName = argv [0];
if( argc < (1 + 1))
{
printf("Usage: %s [[-+=][rwefghvxyzda]] <Objects>\n", PrgName);
exit(1);
}
argv++;
s = *argv;
if( *s == '+' || *s == '-' || *s == '=' )
{
AccMask *mask = &setmask;
if( *s == '-' ) mask = &clearmask;
elif( *s == '=' ) clearmask = 0xff;
s++;
while( *s != '\0' )
{
int bit = getbit(*s,FileChars);
if( bit == 0 ) bit = getbit(*s,DirChars);
if( bit == 0 ) printf("invalid bit character %c\n",*s);
*mask |= bit;
s++;
}
argv++;
}
for( ; *argv != NULL; argv++ )
{
char *name = *argv;
Object *o;
word e;
o = Locate(CurrentDir,name);
if( o == NULL )
{
fprintf(stderr,"could not locate %s : %x\n",name,Result2(CurrentDir));
continue;
}
if( clearmask || setmask )
{
AccMask mask = o->Access.Access;
mask &= ~clearmask;
mask |= setmask;
e = Refine(o,mask);
if( e < 0 )
fprintf(stderr,"refine of %s failed: %x\n",name,e);
}
DecodeCapability(dcname,&o->Access);
printf("%s%s\n",dcname,o->Name);
}
return 0;
}
/**
* Sample from the normal distribution with mean 0 and variance 1.
*
* @param[out] val the sample from the normal distribution
* @param[in,out] r a GMP random generator.
* @param[in] round the rounding direction.
* @return the MPFR ternary result (±1 if val is larger/smaller than
* the exact sample).
**********************************************************************/
int operator()(mpfr_t val, gmp_randstate_t r, mpfr_rnd_t round) const {
const double
s = 0.449871, // Constants from Leva
t = -0.386595,
a = 0.19600 ,
b = 0.25472 ,
r1 = 0.27597 ,
r2 = 0.27846 ,
u1 = 0.606530, // sqrt(1/e) rounded down and up
u2 = 0.606531,
scale = std::pow(2.0, -chunk_); // for turning randoms into doubles
while (true) {
mpz_urandomb(_vi, r, chunk_);
if (mpz_cmp_ui(_vi, m) >= 0) continue; // Very early reject
double vf = (mpz_get_ui(_vi) + 0.5) * scale;
mpz_urandomb(_ui, r, chunk_);
double uf = (mpz_get_ui(_ui) + 0.5) * scale;
double
x = uf - s,
y = vf - t,
Q = x*x + y * (a*y - b*x);
if (Q >= r2) continue; // Early reject
mpfr_set_ui_2exp(_eps, 1u, -chunk_, MPFR_RNDN);
mpfr_prec_t prec = chunk_;
mpfr_set_prec(_u, prec);
mpfr_set_prec(_v, prec);
// (u,v) = sw corner of range
mpfr_set_z_2exp(_u, _ui, -prec, MPFR_RNDN);
mpfr_set_z_2exp(_v, _vi, -prec, MPFR_RNDN);
mpfr_set_prec(_up, prec);
mpfr_set_prec(_vp, prec);
// (up,vp) = ne corner of range
mpfr_add(_up, _u, _eps, MPFR_RNDN);
mpfr_add(_vp, _v, _eps, MPFR_RNDN);
// Estimate how many extra bits will be needed to achieve the desired
// precision.
mpfr_prec_t prec_guard = 3 + chunk_ -
(std::max)(mpz_sizeinbase(_ui, 2), mpz_sizeinbase(_vi, 2));
if (Q > r1) {
int reject;
while (true) {
// Rejection curve v^2 + 4 * u^2 * log(u) < 0 has a peak at u =
// exp(-1/2) = 0.60653066. So treat uf in (0.606530, 0.606531) =
// (u1, u2) specially
// Try for rejection first
if (uf <= u1)
reject = Reject(_u, _vp, prec, MPFR_RNDU);
else if (uf >= u2)
reject = Reject(_up, _vp, prec, MPFR_RNDU);
else { // u in (u1, u2)
mpfr_set_prec(_vx, prec);
mpfr_add(_vx, _vp, _eps, MPFR_RNDN);
reject = Reject(_u, _vx, prec, MPFR_RNDU); // Could use _up too
}
if (reject < 0) break; // tried to reject but failed, so accept
// Try for acceptance
if (uf <= u1)
reject = Reject(_up, _v, prec, MPFR_RNDD);
else if (uf >= u2)
reject = Reject(_u, _v, prec, MPFR_RNDD);
else { // u in (u2, u2)
mpfr_sub(_vx, _v, _eps, MPFR_RNDN);
reject = Reject(_u, _vx, prec, MPFR_RNDD); // Could use _up too
}
if (reject > 0) break; // tried to accept but failed, so reject
prec = Refine(r, prec); // still can't decide, to refine
}
if (reject > 0) continue; // reject, back to outer loop
}
// Now evaluate v/u to the necessary precision
mpfr_prec_t prec0 = mpfr_get_prec (val);
// while (prec < prec0 + prec_guard) prec = Refine(r, prec);
if (prec < prec0 + prec_guard)
prec = Refine(r, prec,
(prec0 + prec_guard - prec + chunk_ - 1) / chunk_);
mpfr_set_prec(_x1, prec0);
mpfr_set_prec(_x2, prec0);
int flag;
while (true) {
int
f1 = mpfr_div(_x1, _v, _up, round), // min slope
f2 = mpfr_div(_x2, _vp, _u, round); // max slope
if (f1 == f2 && mpfr_equal_p(_x1, _x2)) {
flag = f1;
break;
}
prec = Refine(r, prec);
}
mpz_urandomb(_ui, r, 1);
if (mpz_tstbit(_ui, 0)) {
flag = -flag;
mpfr_neg(val, _x1, MPFR_RNDN);
} else
mpfr_set(val, _x1, MPFR_RNDN);
// std::cerr << uf << " " << vf << " " << Q << "\n";
return flag;
}
}
void AdaptiveSparseGrid::ConstructAdaptiveSparseGrid() {
//! Define a buffer deque to store all of the intermediate information
deque<AdaptiveData*> buffer;
//! iterator for transverse the active index
set<AdaptiveData*, AdaptiveDataCompare>::iterator it1;
set<AdaptiveNodeData*, AdaptiveNodeDataCompare>::iterator it2;
AdaptiveGrid OldIndex;
AdaptiveData* pData ;
AdaptiveNodeData* pNodeData;
//! Here we still keep a copy of active index for each processor for the purpose
//! of the easy implementation of the adaptivity
while ( !ActiveIndex.empty() && L <= Lmax ) {
int gnumber = NumberOfActivePoints();
if (rank == 0 && print) {
cout << "Now, it is in Level: " << L << endl;
cout << "The active number of points are: " << gnumber << endl;
}
//Copy the ActiveIndex to an oldIndex
OldIndex = ActiveIndex;
ActiveIndex.clear();
//! Define a temporary matrix to store all of the active point for parallel computation
Matrix1<double> gpoint;
gpoint.redim(gnumber, dim);
double time1, time;
time1 = MPI_Wtime();
int row = 1;
//! Extract the coordiante information
for (it1 = OldIndex.begin(); it1 != OldIndex.end(); ++it1) {
for (it2 = (*it1)->NodeData.begin(); it2 != (*it1)->NodeData.end(); ++it2) {
for ( int i = 1; i <= dim ; i++) {
gpoint(row, i) = IndextoCoordinate((*(*it1)->index)(i), (*(*it2)->index)(i));
}
row++;
}
}
// Parallel Implementation
int node;
AdaptiveARRAY<double> px;
px.redim(dim);
//! Distribute the points among the processors
int numNodesPerProcessor = 0;
for (int i = 0; i < gnumber; i++)
if ( (i % size) == rank)
{ numNodesPerProcessor++; }
int colnumber = TotalDof * numNodesPerProcessor;
//!Local value to store function value
double* local_value = new double[colnumber];
//! An array to store the nodes which belong to this processor
int* mynodes = new int[numNodesPerProcessor];
for ( int no = 1 ; no <= numNodesPerProcessor; no++) {
node = rank + size * (no - 1) + 1;
mynodes[no - 1] = node;
for ( int i = 1 ; i <= dim ; i++)
{ px(i) = gpoint(node, i); }
EvaluateFunctionAtThisPoint(&px);
for ( int i = 0; i < TotalDof ; i++) {
local_value[(no - 1)*TotalDof + i] = surplus[i] ;
}
}
/**
* EDIT BY ARYAN
*/
MPI_Barrier(mpiCOMM);
time = MPI_Wtime();
if (rank == 0 && print ) { cout << "Parallel Calculation using " << time - time1 << endl; }
gpoint.cleanup();
//! Set the action before storing the surplus
BeforeStoreSurplus();
int index = 1;
int cnt = 0, mynode;
//! Extract the coordiante information
for (it1 = OldIndex.begin(); it1 != OldIndex.end(); ++it1) {
int number = (*it1)->NodeData.size();
//! Define a temporary matrix to store all of the active point for parallel computation
Matrix1<double> point;
point.redim(number, dim);
int row = 1;
for (it2 = (*it1)->NodeData.begin(); it2 != (*it1)->NodeData.end(); ++it2) {
for ( int i = 1; i <= dim ; i++) {
point(row, i) = IndextoCoordinate((*(*it1)->index)(i), (*(*it2)->index)(i));
}
row++;
}
//! If there are points in this processor, generate a new data to store information
if ( numNodesPerProcessor != 0) {
pData = AdaptiveDataAllocator.NewItem();
pData->index = (*it1)->index;
buffer.push_front(pData);
}
double* temp = new double[TotalDof * number];
//! Calculate the hierarchical surplus
SpInterpolateLevel(point, temp);
//! Calculate the hierarchial surplus and generate the adaptivity information
Array<int> local_refine; local_refine.redim(number); local_refine.fill(0);
Array<int> global_refine; global_refine.redim(number);
int temp_index = index;
int temp_cnt = cnt;
it2 = (*it1)->NodeData.begin();
for ( int n = 1; n <= number; n++) {
if ( (temp_cnt != numNodesPerProcessor) && (temp_index == mynodes[temp_cnt]) ) {
for ( int i = 0; i < TotalDof; i++) {
local_value[temp_cnt * TotalDof + i] = surplus[i] = local_value[temp_cnt * TotalDof + i] - temp[(n - 1) * TotalDof + i];
}
//! Check the adaptivity criteria
local_refine(n) = IsRefine(surplus, (*it1)->index, (*it2)->index);
temp_cnt ++;
}
temp_index++;
++it2;
}
//! Free space
delete[] temp;
int error = MPI_Allreduce(local_refine.pData, global_refine.pData, number, MPI_INT, MPI_SUM, mpiCOMM);
//if (error) { cout << "ERORR 221 : " << error << "|" << rank << endl; }
//! Free space
local_refine.cleanup();
it2 = (*it1)->NodeData.begin();
// calculate herarchial surplus for each coordinate
for ( int n = 1 ; n <= number; n++) {
//! If this point belongs to this processor
if ( (cnt != numNodesPerProcessor) && (index == mynodes[cnt]) ) {
//Copy data to sparse grid
pNodeData = (*it2);
pNodeData->surplus = new double[TotalDof];
for ( int i = 0; i < TotalDof; i++) {
pNodeData->surplus[i] = local_value[cnt * TotalDof + i];
}
//! Refinement
if ( global_refine(n))
{ Refine((*it1)->index, (*it2)->index); }
cnt ++;
//! Insert the this nodadata to the buffer
pData->NodeData.insert(pNodeData);
}
//! the point doesn't belong to this processor
else {
if ( global_refine(n))
{ Refine((*it1)->index, (*it2)->index); }
//! If this point doesn't belong to this processor, delete the point.
AdaptiveCoordAllocator.DeleteItem((*it2)->index);
AdaptiveNodeDataAllocator.DeleteItem(*it2);
}
++it2;
index++;
}
//free space
global_refine.cleanup();
//! If there are no point for this processor, delete the data.
if ( numNodesPerProcessor == 0) {
AdaptiveCoordAllocator.DeleteItem((*it1)->index);
AdaptiveDataAllocator.DeleteItem(*it1);
}
}// End for
//free space
delete[] local_value;
delete[] mynodes;
/**
* EDIT BY ARYAN
*/
MPI_Barrier(mpiCOMM);
time1 = MPI_Wtime();
if (rank == 0 && print) { cout << "Surplus Calculation using " << time1 - time << endl; }
//! Insert all of the active points to the adaptive spare grid.
SparseGrid.insert(SparseGrid.begin(), buffer.begin(), buffer.end());
if ( type == 1)
{ UpdateError(); }
//free space
buffer.clear();
OldIndex.clear();
L += 1;
//! Set the action before storing the surplus
{ AfterStoreSurplus(); }
}//End for
}
bool AdaptSurfaceGridToCylinder(Selector& selOut, Grid& grid,
Vertex* vrtCenter, const vector3& normal,
number radius, number rimSnapThreshold, AInt& aInt,
APosition& aPos)
{
if(!grid.has_vertex_attachment(aPos)) {
UG_THROW("Position attachment required!");
}
Grid::VertexAttachmentAccessor<APosition> aaPos(grid, aPos);
if(rimSnapThreshold < 0)
rimSnapThreshold = 0;
if(rimSnapThreshold > (radius - SMALL))
rimSnapThreshold = radius - SMALL;
const number smallRadius = radius - rimSnapThreshold;
const number smallRadiusSq = smallRadius * smallRadius;
const number largeRadius = radius + rimSnapThreshold;
const number largeRadiusSq = largeRadius * largeRadius;
// the cylinder geometry
vector3 axis;
VecNormalize(axis, normal);
vector3 center = aaPos[vrtCenter];
// recursively select all vertices in the cylinder which can be reached from a
// selected vertex by following an edge. Start with the given one.
// We'll also select edges which connect inner with outer vertices. Note that
// some vertices are considered rim-vertices (those with a distance between
// smallRadius and largeRadius). Those are neither considered inner nor outer.
Selector& sel = selOut;
sel.clear();
sel.select(vrtCenter);
stack<Vertex*> vrtStack;
vrtStack.push(vrtCenter);
Grid::edge_traits::secure_container edges;
Grid::face_traits::secure_container faces;
vector<Quadrilateral*> quads;
while(!vrtStack.empty()) {
Vertex* curVrt = vrtStack.top();
vrtStack.pop();
// we have to convert associated quadrilaterals to triangles.
// Be careful not to alter the array of associated elements while we iterate
// over it...
quads.clear();
grid.associated_elements(faces, curVrt);
for(size_t i = 0; i < faces.size(); ++i) {
if(faces[i]->num_vertices() == 4) {
Quadrilateral* q = dynamic_cast<Quadrilateral*>(faces[i]);
if(q)
quads.push_back(q);
}
}
for(size_t i = 0; i < quads.size(); ++i) {
Triangulate(grid, quads[i], &aaPos);
}
// now check whether edges leave the cylinder and mark them accordingly.
// Perform projection of vertices to the cylinder rim for vertices which
// lie in the threshold area.
grid.associated_elements(edges, curVrt);
for(size_t i_edge = 0; i_edge < edges.size(); ++i_edge) {
Edge* e = edges[i_edge];
Vertex* vrt = GetConnectedVertex(e, curVrt);
if(sel.is_selected(vrt))
continue;
vector3 p = aaPos[vrt];
vector3 proj;
ProjectPointToRay(proj, p, center, axis);
number distSq = VecDistanceSq(p, proj);
if(distSq < smallRadiusSq) {
sel.select(vrt);
vrtStack.push(vrt);
}
else if(distSq < largeRadiusSq) {
sel.select(vrt);
// cut the ray from center through p with the cylinder hull to calculate
// the new position of vrt.
vector3 dir;
VecSubtract(dir, p, center);
number t0, t1;
if(RayCylinderIntersection(t0, t1, center, dir, center, axis, radius))
VecScaleAdd(aaPos[vrt], 1., center, t1, dir);
}
else {
// the edge will be refined later on
sel.select(e);
}
}
}
// refine selected edges and use a special refinement callback, which places
// new vertices on edges which intersect a cylinder on the cylinders hull.
CylinderCutProjector refCallback(MakeGeometry3d(grid, aPos),
center, axis, radius);
Refine(grid, sel, aInt, &refCallback);
// finally select all triangles which lie in the cylinder
sel.clear();
vrtStack.push(vrtCenter);
sel.select(vrtCenter);
while(!vrtStack.empty()) {
Vertex* curVrt = vrtStack.top();
vrtStack.pop();
grid.associated_elements(faces, curVrt);
for(size_t i_face = 0; i_face < faces.size(); ++i_face) {
Face* f = faces[i_face];
if(sel.is_selected(f))
continue;
sel.select(f);
for(size_t i = 0; i < f->num_vertices(); ++i) {
Vertex* vrt = f->vertex(i);
if(!sel.is_selected(vrt)) {
number dist = DistancePointToRay(aaPos[vrt], center, axis);
if(dist < (radius - SMALL)) {
sel.select(vrt);
vrtStack.push(vrt);
}
}
}
}
}
sel.clear<Vertex>();
return true;
}
int Execute(int argc,char* argv[])
{
int i;
cmdLineString In,Out;
cmdLineReadable Binary,Verbose,NoResetSamples,NoClipTree,Confidence,Manifold,PolygonMesh;
cmdLineInt Depth(8),SolverDivide(8),IsoDivide(8),Refine(3);
cmdLineInt KernelDepth;
cmdLineFloat SamplesPerNode(1.0f),Scale(1.1f);
char* paramNames[]=
{
"in","depth","out","refine","noResetSamples","noClipTree",
"binary","solverDivide","isoDivide","scale","verbose",
"kernelDepth","samplesPerNode","confidence","manifold","polygonMesh"
};
cmdLineReadable* params[]=
{
&In,&Depth,&Out,&Refine,&NoResetSamples,&NoClipTree,
&Binary,&SolverDivide,&IsoDivide,&Scale,&Verbose,
&KernelDepth,&SamplesPerNode,&Confidence,&Manifold,&PolygonMesh
};
int paramNum=sizeof(paramNames)/sizeof(char*);
int commentNum=0;
char **comments;
comments=new char*[paramNum+7];
for(i=0;i<paramNum+7;i++){comments[i]=new char[1024];}
const char* Rev = "Rev: V2 ";
const char* Date = "Date: 2006-11-09 (Thur, 09 Nov 2006) ";
cmdLineParse(argc-1,&argv[1],paramNames,paramNum,params,0);
if(Verbose.set){echoStdout=1;}
DumpOutput2(comments[commentNum++],"Running Multi-Grid Octree Surface Reconstructor (degree %d). Version 3\n", Degree);
if(In.set) {DumpOutput2(comments[commentNum++],"\t--in %s\n",In.value);}
if(Out.set) {DumpOutput2(comments[commentNum++],"\t--out %s\n",Out.value);}
if(Binary.set) {DumpOutput2(comments[commentNum++],"\t--binary\n");}
if(Depth.set) {DumpOutput2(comments[commentNum++],"\t--depth %d\n",Depth.value);}
if(SolverDivide.set) {DumpOutput2(comments[commentNum++],"\t--solverDivide %d\n",SolverDivide.value);}
if(IsoDivide.set) {DumpOutput2(comments[commentNum++],"\t--isoDivide %d\n",IsoDivide.value);}
if(Refine.set) {DumpOutput2(comments[commentNum++],"\t--refine %d\n",Refine.value);}
if(Scale.set) {DumpOutput2(comments[commentNum++],"\t--scale %f\n",Scale.value);}
if(KernelDepth.set) {DumpOutput2(comments[commentNum++],"\t--kernelDepth %d\n",KernelDepth.value);}
if(SamplesPerNode.set) {DumpOutput2(comments[commentNum++],"\t--samplesPerNode %f\n",SamplesPerNode.value);}
if(NoResetSamples.set) {DumpOutput2(comments[commentNum++],"\t--noResetSamples\n");}
if(NoClipTree.set) {DumpOutput2(comments[commentNum++],"\t--noClipTree\n");}
if(Confidence.set) {DumpOutput2(comments[commentNum++],"\t--confidence\n");}
if(Manifold.set) {DumpOutput2(comments[commentNum++],"\t--manifold\n");}
if(PolygonMesh.set) {DumpOutput2(comments[commentNum++],"\t--polygonMesh\n");}
double t;
double tt=Time();
Point3D<float> center;
Real scale=1.0;
Real isoValue=0;
//////////////////////////////////
// Fix courtesy of David Gallup //
TreeNodeData::UseIndex = 1; //
//////////////////////////////////
Octree<Degree> tree;
PPolynomial<Degree> ReconstructionFunction=PPolynomial<Degree>::GaussianApproximation();
center.coords[0]=center.coords[1]=center.coords[2]=0;
if(!In.set || !Out.set)
{
ShowUsage(argv[0]);
return 0;
}
TreeOctNode::SetAllocator(MEMORY_ALLOCATOR_BLOCK_SIZE);
t=Time();
int kernelDepth=Depth.value-2;
if(KernelDepth.set){kernelDepth=KernelDepth.value;}
tree.setFunctionData(ReconstructionFunction,Depth.value,0,Real(1.0)/(1<<Depth.value));
DumpOutput("Function Data Set In: %lg\n",Time()-t);
DumpOutput("Memory Usage: %.3f MB\n",float(MemoryInfo::Usage())/(1<<20));
if(kernelDepth>Depth.value){
fprintf(stderr,"KernelDepth can't be greater than Depth: %d <= %d\n",kernelDepth,Depth.value);
return EXIT_FAILURE;
}
t=Time();
#if 1
tree.setTree(In.value,Depth.value,Binary.set,kernelDepth,Real(SamplesPerNode.value),Scale.value,center,scale,!NoResetSamples.set,Confidence.set);
#else
if(Confidence.set){
tree.setTree(In.value,Depth.value,Binary.set,kernelDepth,Real(SamplesPerNode.value),Scale.value,center,scale,!NoResetSamples.set,0,1);
}
else{
tree.setTree(In.value,Depth.value,Binary.set,kernelDepth,Real(SamplesPerNode.value),Scale.value,center,scale,!NoResetSamples.set,0,0);
}
#endif
DumpOutput2(comments[commentNum++],"# Tree set in: %9.1f (s), %9.1f (MB)\n",Time()-t,tree.maxMemoryUsage);
DumpOutput("Leaves/Nodes: %d/%d\n",tree.tree.leaves(),tree.tree.nodes());
DumpOutput(" Tree Size: %.3f MB\n",float(sizeof(TreeOctNode)*tree.tree.nodes())/(1<<20));
DumpOutput("Memory Usage: %.3f MB\n",float(MemoryInfo::Usage())/(1<<20));
if(!NoClipTree.set){
t=Time();
tree.ClipTree();
DumpOutput("Tree Clipped In: %lg\n",Time()-t);
DumpOutput("Leaves/Nodes: %d/%d\n",tree.tree.leaves(),tree.tree.nodes());
DumpOutput(" Tree Size: %.3f MB\n",float(sizeof(TreeOctNode)*tree.tree.nodes())/(1<<20));
}
t=Time();
tree.finalize1(Refine.value);
DumpOutput("Finalized 1 In: %lg\n",Time()-t);
DumpOutput("Leaves/Nodes: %d/%d\n",tree.tree.leaves(),tree.tree.nodes());
DumpOutput("Memory Usage: %.3f MB\n",float(MemoryInfo::Usage())/(1<<20));
t=Time();
tree.maxMemoryUsage=0;
tree.SetLaplacianWeights();
DumpOutput2(comments[commentNum++],"#Laplacian Weights Set In: %9.1f (s), %9.1f (MB)\n",Time()-t,tree.maxMemoryUsage);
DumpOutput("Memory Usage: %.3f MB\n",float(MemoryInfo::Usage())/(1<<20));
t=Time();
tree.finalize2(Refine.value);
DumpOutput("Finalized 2 In: %lg\n",Time()-t);
DumpOutput("Leaves/Nodes: %d/%d\n",tree.tree.leaves(),tree.tree.nodes());
DumpOutput("Memory Usage: %.3f MB\n",float(MemoryInfo::Usage())/(1<<20));
tree.maxMemoryUsage=0;
t=Time();
tree.LaplacianMatrixIteration(SolverDivide.value);
DumpOutput2(comments[commentNum++],"# Linear System Solved In: %9.1f (s), %9.1f (MB)\n",Time()-t,tree.maxMemoryUsage);
DumpOutput("Memory Usage: %.3f MB\n",float(MemoryInfo::Usage())/(1<<20));
CoredVectorMeshData mesh;
tree.maxMemoryUsage=0;
t=Time();
isoValue=tree.GetIsoValue();
DumpOutput("Got average in: %f\n",Time()-t);
DumpOutput("Iso-Value: %e\n",isoValue);
DumpOutput("Memory Usage: %.3f MB\n",float(tree.MemoryUsage()));
t=Time();
if(IsoDivide.value) tree.GetMCIsoTriangles( isoValue , IsoDivide.value , &mesh , 0 , 1 , Manifold.set , PolygonMesh.set );
else tree.GetMCIsoTriangles( isoValue , &mesh , 0 , 1 , Manifold.set , PolygonMesh.set );
if( PolygonMesh.set ) DumpOutput2(comments[commentNum++],"# Got Polygons in: %9.1f (s), %9.1f (MB)\n",Time()-t,tree.maxMemoryUsage);
else DumpOutput2(comments[commentNum++],"# Got Triangles in: %9.1f (s), %9.1f (MB)\n",Time()-t,tree.maxMemoryUsage);
DumpOutput2(comments[commentNum++],"# Total Time: %9.1f (s)\n",Time()-tt);
PlyWritePolygons(Out.value,&mesh,PLY_BINARY_NATIVE,center,scale,comments,commentNum);
return 1;
}