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GlobalReg.cc
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//############################################################
// GlobalReg.cc
// Kari Pulli
// Tue Jun 23 11:54:00 PDT 1998
//
// Global registration of several scans simultaneously
//############################################################
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include <map>
#include <deque>
#include <iterator>
// G++ Update
#include <strstream>
#include <sys/stat.h>
#include "GlobalReg.h"
#include "absorient.h"
#include "TbObj.h"
#include "DisplayMesh.h"
#include "plvScene.h"
#include "ConnComp.h"
#include "Progress.h"
#include "BailDetector.h"
#include "DirEntries.h"
#include "FileNameUtils.h"
#include "ScanFactory.h"
#include "CyberScan.h"
#include "GroupScan.h"
#include "TclCmdUtils.h"
#include <math.h>
// TODO: make these sliders in globalreg window
#define VB_SIZE (100.0)
#define NOT_FOUND (-1)
#define THRESHOLD (700) // THIS SHOULD BE MUCH LARGER probably
#if defined(WIN32) || defined(i386)
#define LITTLE_ENDIAN
#endif
// setup file loading routines for a little endian machine
#ifdef LITTLE_ENDIAN
inline short swap_short(short x)
{
return ((x & 0xff) << 8) | ((unsigned short)x >> 8);
}
/* unsigned is essential, otherwise bitshift will
* sign extend and mess up the conversion.
*/
inline int swap_int(unsigned int x)
{
return (x << 24) |
((x << 8) & 0x00ff0000) |
((x >> 8) & 0x0000ff00) |
(x >> 24);
}
inline float swap_float(float x)
{
unsigned int y = (*((unsigned int *)&x));
y= (y << 24) |
((y << 8) & 0x00ff0000) |
((y >> 8) & 0x0000ff00) |
(y >> 24);
return (*((float *)&y));
}
inline short FixShort(short x)
{
return (swap_short(x));
}
inline int FixInt(int x)
{
return (swap_int(x));
}
inline float FixFloat(float x)
{
return (swap_float(x));
}
// otherwise set up file loading routines for a big endian machine
#else
inline short FixShort(short x)
{
return (x);
}
inline int FixInt(int x)
{
return (x);
}
inline float FixFloat(float x)
{
return (x);
}
#endif
// File writing routines
inline void WriteInt(int x, ofstream &out)
{
int temp = FixInt(x);
out.write((char*)&temp, 4);
}
inline void WriteFloat(float x, ofstream &out)
{
float temp = FixFloat(x);
out.write((char*)&temp, 4);
}
inline void WriteShort(short x, ofstream &out)
{
short temp = FixShort(x);
out.write((char*)&temp, 2);
}
/* There is no ReadChar since no special byte ordering is required for characters */
inline int ReadInt(ifstream &in)
{
int temp;
in.read((char*)&temp, 4);
return FixInt(temp);
}
inline short ReadShort(ifstream &in)
{
short temp;
in.read((char*)&temp, 2);
return FixShort(temp);
}
inline float ReadFloat(ifstream &in)
{
float temp;
in.read((char*)&temp, 4);
return FixFloat(temp);
}
inline void WriteSDRawPoints(vector<sd_raw_pnt> &rp, int n, ofstream &out)
{
for (int i=0; i<n; i++) {
WriteInt(rp[i].config, out);
WriteShort(rp[i].y, out);
WriteShort(rp[i].z, out);
WriteFloat(rp[i].nod, out);
WriteFloat(rp[i].turn, out);
WriteFloat(rp[i].tr_h, out);
}
}
inline void WritePnt3(vector<Pnt3> &pnt, int n, ofstream &out)
{
for (int i=0; i<n; i++) {
Pnt3 p = pnt[i];
WriteFloat(*(float *)p, out);
WriteFloat(*((float *)p + 1), out);
WriteFloat(*((float *)p + 2), out);
}
}
inline void ReadPnt3(vector<Pnt3> &pnt, int n, ifstream &in)
{
Pnt3 tempPnt;
for (int i=0; i<n; i++) {
float f1 = ReadFloat(in);
float f2 = ReadFloat(in);
float f3 = ReadFloat(in);
tempPnt.set(f1, f2, f3);
pnt[i] = tempPnt;
}
}
#define GR_MESHNAMES_SEP "^^^"
#define ECHO(x) cout << #x << endl; x
#define FOR_MAP_ENTRIES(key, data) \
for (ITT __m = hmm.begin(); __m != hmm.end(); __m++) {\
TbObj *key = (*__m).first;\
mapEntry *data = (*__m).second;
#define END_FOR_MAP }
#define FOR_MATCHING_KEYS(key, data) \
{ pair<ITT, ITT> __p = hmm.equal_range(key);\
for (ITT __i = __p.first; __i!=__p.second; __i++) {\
mapEntry *data = (*__i).second;
#define END_FOR_KEYS }}
#define CONTAINS(vec, item) \
(find(vec.begin(),vec.end(),item) != vec.end())
// this is ugly: it's linear time, which makes
// processing scans n^2 (though we have small n...)
inline int
scan_idx(const TbObj* a, const vector<TbObj*> &scan)
{
for (int i=scan.size()-1; i>=0; i--)
if (scan[i] == a) return i;
assert(0);
return 0;
}
inline float
dist2(const vector<Pnt3> &P, const vector<Pnt3> &Q)
{
float d = 0.0;
vector<Pnt3>::const_iterator ip = P.begin();
vector<Pnt3>::const_iterator iq = Q.begin();
while (ip != P.end()) {
d += dist2(*ip, *iq);
ip++; iq++;
}
assert(iq == Q.end());
return d;
}
static RigidScan*
createProxyScanNamed (const crope& name)
{
if (strcmp (Tcl_GetVar (g_tclInterp, "allowProxiesWithGR",
TCL_GLOBAL_ONLY), "0") == 0) {
return NULL;
}
// make sure we can find the scan, else it's pointless to try to
// globalreg it because we won't be able to use the results.
Tcl_VarEval (g_tclInterp, "file_locateScan ", name.c_str(), NULL);
char* filename = g_tclInterp->result;
if (!filename[0]) {
cerr << "Unable to locate scan for " << name << endl;
return NULL;
}
// create invisible scan with 0 bbox
RigidScan* rs = CreateScanFromBbox (filename, Pnt3(), Pnt3());
DisplayableMesh* dm = theScene->addMeshSet (rs);
//cerr << "creating proxy named " << name << " as "
// << dm->getName() << endl;
Tcl_VarEval (g_tclInterp, "addMeshToWindow ",
dm->getName(), " 0", NULL);
Tcl_VarEval (g_tclInterp, "changeVis ", dm->getName(), " 0", NULL);
return rs;
}
static void
calcPairwiseRmsErr(const vector<Pnt3> &ptsa,
const vector<Pnt3> &nrma,
const vector<Pnt3> &ptsb,
const vector<Pnt3> &nrmb,
const Xform<float> &rel_xf,
float &pw_point_rmsErr,
float &pw_plane_rmsErr)
{
assert(ptsa.size());
// calculate the rms for point pair distances
pw_point_rmsErr = pw_plane_rmsErr = 0.0;
Pnt3 p,nrm;
int n = ptsa.size();
bool do_tangents = (nrma.size() != 0);
float d;
for (int i=0; i<n; i++) {
rel_xf.apply(ptsa[i], p);
pw_point_rmsErr += dist2(p, ptsb[i]);
if (do_tangents) {
rel_xf.apply_nrm(nrma[i], nrm);
p -= ptsb[i];
d = dot(nrm, p);
pw_plane_rmsErr += d*d;
d = dot(nrmb[i], p);
pw_plane_rmsErr += d*d;
}
}
pw_point_rmsErr = sqrtf(pw_point_rmsErr / n);
pw_plane_rmsErr = sqrtf(pw_plane_rmsErr / (2*n));
}
void
GlobalReg::mapEntry::stats(void)
{
Xform<float> xf_a = xfa->getXform();
Xform<float> xf_b = xfb->getXform();
int n = ptsa.size();
Pnt3 first, second, nrm;
maxErr = avgErr = rmsErr = 0.0;
Xform<float> actual_rel_xf = xf_b;
actual_rel_xf.fast_invert();
actual_rel_xf = actual_rel_xf * xf_a;
for (int j=0; j<n; j++) {
// calculate the point wise distances
first = ptsa[j];
second = ptsa[j];
actual_rel_xf (first);
rel_xf (second);
float d = dist2(first, second);
if (d > maxErr) maxErr = d;
rmsErr += d;
avgErr += sqrtf(d);
}
for (int j=0; j<n; j++) {
// calculate the point wise distances
first = ptsb[j];
second = ptsb[j];
actual_rel_xf.apply_inv(first,first);
rel_xf.apply_inv(second,second);
float d = dist2(first, second);
if (d > maxErr) maxErr = d;
rmsErr += d;
avgErr += sqrtf(d);
}
n *= 2;
avgErr /= n;
rmsErr = sqrtf(rmsErr/n);
}
static bool
write_points(ofstream &out, vector<Pnt3> &pts, TbObj *scan)
{
CyberScan* cs = dynamic_cast<CyberScan*> (scan);
if (cs && GetTclGlobalBool ("writeGRsRaw")) {
//SHOW(cs);
// magic number (CyberScan point data 1)
out.write("cpd1", 4);
// point count
int n = pts.size();
WriteInt(n, out);
// the points
vector<sd_raw_pnt> cw(n);
for (int i=0; i<n; i++) {
if (cs->get_raw_data(pts[i], cw[i]) == false) {
cerr << "Problem in GlobalReg::write_points()"
<< endl;
return false;
}
}
WriteSDRawPoints(cw, n, out);
} else {
// magic number (general point data 1)
out.write("gpd1", 4);
// point count
int n = pts.size();
WriteInt(n, out);
// the points
WritePnt3(pts, n, out);
}
return !out.fail();
}
static bool
read_points (ifstream &in, vector<Pnt3> &pts)
{
// magic number (general point data 1)
char magic[4];
in.read(magic, 4);
if ( strncmp(magic, "cpd1", 4)==0 ) {
cout << "CyberScan raw data" << endl;
// CyberScan raw data
int n;
n = ReadInt(in);
pts.resize(n);
unsigned int config;
short yz[2];
float nt[2]; // nod, turn
float tr_h;
CyberXform xf;
for (int i=0; i<n; i++) {
config = ReadInt(in);
yz[0] = ReadShort(in);
yz[1] = ReadShort(in);
nt[0] = ReadFloat(in);
nt[1] = ReadFloat(in);
tr_h = ReadFloat(in);
int os = config&1; // other_screw
xf.setup(config, tr_h, nt[os]);
xf.set_screw(nt[!os], nt[!os]);
pts[i] = xf.apply_xform(yz[0],yz[1]);
if (! pts[i].isfinite()) {
SHOW(pts[i]);
SHOW(i);
SHOW(config);
SHOW(yz[0]);
SHOW(yz[1]);
SHOW(nt[0]);
SHOW(nt[1]);
SHOW(tr_h);
SHOW(os);
}
}
} else if (!strncmp (magic, "gpd1", 4)) {
// good old regular 3d points
// point count
int n;
n = ReadInt(in);
pts.resize(n);
// the points
ReadPnt3(pts, n, in);
} else {
cerr << "Bad magic field in .gr file!" << endl;
return false;
}
return !in.fail();
}
static struct {
char* magic; int ver;
} GRVersionTable[] = {
{ "GR01", 1 },
{ "GR02", 2 },
{ "GR03", 3 },
{ "GR04", 4 }
};
#define cGRVersionTableSize (sizeof(GRVersionTable)/sizeof(GRVersionTable[0]))
#define GRVersionCurrent (GRVersionTable[cGRVersionTableSize-1].magic)
int GetGRVersion (char* magic)
{
for (int i = 0; i < cGRVersionTableSize; i++) {
if (!strncmp (GRVersionTable[i].magic, magic, 4))
return GRVersionTable[i].ver;
}
return 0;
}
// try writing the mapEntry data into a single file
void
GlobalReg::mapEntry::export_to_file(const std::string &gr_dir)
{
// figure out the filename
const char *name1 = GetTbObjName(xfa);
const char *name2 = GetTbObjName(xfb);
if (!name1 || !name2) {
cerr << "Couldn't get names, not saving global"
<< " data" << endl;
return;
}
bool flip = false;
if (strcmp(name1, name2) == 1) {
flip = true;
const char *tmp = name2;
name2 = name1; name1 = tmp;
}
std::string path = gr_dir;
if (!manually_aligned) path += "/auto";
path += std::string("/") + name1 + GR_MESHNAMES_SEP + name2 + ".gr";
// just overwrite the file if it exists
#ifdef WIN32
ofstream out(path.c_str(), ios::binary);
#else
ofstream out(path.c_str());
#endif
if (!out) {
cerr << "Couldn't create file " << path.c_str() << endl;
return;
} else {
SHOW(path.c_str());
}
// fill the file with useful stuff
cout << "Writing correspondences between " << name1
<< " and " << name2 << " ... ";
out.write(GRVersionCurrent, 4); // magic number
//SHOW(name1);
//SHOW(name2);
//SHOW(dynamic_cast<CyberScan*> (xfa));
//SHOW(dynamic_cast<GroupScan*> (xfa));
if (flip) {
write_points(out, ptsb, xfb);
write_points(out, ptsa, xfa);
Xform<float> tmp_xf = rel_xf;
tmp_xf.fast_invert();
for (int i=0; i<16; i++)
WriteFloat(*((float*)tmp_xf + i), out);
} else {
write_points(out, ptsa, xfa);
write_points(out, ptsb, xfb);
for (int i=0; i<16; i++)
WriteFloat(*((float*)rel_xf + i), out);
}
WriteFloat(pw_point_rmsErr, out);
WriteFloat(pw_plane_rmsErr, out);
WriteInt(quality_grade, out);
out.write((char *)&manually_aligned, 1 /*sizeof(bool) */);
if (out.fail()) return;
cout << "success." << endl;
// currently saving:
// pairwiserms errors
// point count
// points
// registration xform
// whether manually aligned
// should also write:
// rmserror to tangent plane
// sampling density?
// or weight that would normalize based on area?
}
void
GlobalReg::mapEntry::export_cyber_raw(const char *fname)
{
// only work if both scans are CyberScans
CyberScan *csa = dynamic_cast<CyberScan*> (xfa);
CyberScan *csb = dynamic_cast<CyberScan*> (xfb);
if (!csa || !csb) return;
ofstream out(fname);
if (!out) {
cerr << "Couldn't create file " << fname << endl;
return;
} else {
SHOW(fname);
}
int cPnt = ptsa.size();
out.write ((char*)&cPnt, sizeof(cPnt));
//bool vert;
sd_raw_pnt cw;
for (int i=0; i<cPnt; i++) {
if (csa->get_raw_data(ptsa[i], cw) == false) {
cerr << "Problem in GlobalReg::mapEntry::export_cyber_raw()"
<< endl;
return;
}
int tmp = (cw.config & 0x00000001); // vert;
out.write((char*) &tmp, sizeof(int));
out.write((char*) &cw.y, 2*sizeof(short));
out.write((char*) &cw.nod, 2*sizeof(float));
}
for (int i=0; i<cPnt; i++) {
if (csb->get_raw_data(ptsb[i], cw) == false) {
cerr << "Problem in GlobalReg::mapEntry::export_cyber_raw()"
<< endl;
return;
}
int tmp = (cw.config & 0x00000001); // vert;
out.write((char*) &tmp, sizeof(int));
out.write((char*) &cw.y, 2*sizeof(short));
out.write((char*) &cw.nod, 2*sizeof(float));
}
out.write ((char*)(float*)rel_xf, 16 * sizeof(float));
if (g_verbose) {
if (out.fail()) cout << "failure." << endl;
else cout << "success." << endl;
}
}
// if partner == NULL, this fn will return the points from ALL
// the scans P is partnered with
void
GlobalReg::get_pts(TbObj *x, vector<Pnt3> &P, vector<Pnt3> &Q,
TbObj* partner)
{
P.clear(); Q.clear();
// find entries with key x
FOR_MATCHING_KEYS(x, data) {
TbObj *datap, *dataq;
XF_F dataxf = data->rel_xf;
vector<Pnt3> *pp;//, *qq;
if (x == data->xfa) {
datap = data->xfa; dataq = data->xfb;
pp = &data->ptsa;// qq = &data->ptsb;
} else {
datap = data->xfb; dataq = data->xfa;
pp = &data->ptsb;// qq = &data->ptsa;
dataxf.fast_invert();
}
if (partner != NULL && dataq != partner)
continue;
int ind = P.size();
P.insert(P.end(), pp->begin(), pp->end());
#if 1
// Q becomes "where P's points should be in Q's coords"
for (int i=0; i<pp->size(); i++) {
//Pnt3 p = data->ptsa[i];
Pnt3 p = (*pp)[i];
dataxf(p);
Q.push_back(p);
}
#else
Q.insert(Q.end(), qq->begin(), qq->end());
#endif
// then convert to world coordinates
for_each (P.begin() + ind, P.end(), datap->getXform());
for_each (Q.begin() + ind, Q.end(), dataq->getXform());
} END_FOR_KEYS
}
// used for global registration, and only Horn's version
void
GlobalReg::get_pts_within_group(TbObj *x,
vector<Pnt3> &P, vector<Pnt3> &Q,
vector<TbObj*> &group)
{
P.clear(); Q.clear();
// find entries with key x
FOR_MATCHING_KEYS(x, data) {
TbObj *datap, *dataq;
XF_F dataxf = data->rel_xf;
vector<Pnt3> *pp;//, *qq;
if (x == data->xfa) {
datap = data->xfa; dataq = data->xfb;
pp = &data->ptsa;// qq = &data->ptsb;
} else {
datap = data->xfb; dataq = data->xfa;
pp = &data->ptsb;// qq = &data->ptsa;
dataxf.fast_invert();
}
if (CONTAINS(group, dataq)) {
// copy the points (in local coordinates)
int ind = P.size();
P.insert(P.end(), pp->begin(), pp->end());
#if 1
// Q becomes "where P's points should be in Q's coords"
for (int i=0; i<pp->size(); i++) {
Pnt3 p = (*pp)[i];
dataxf(p);
Q.push_back(p);
}
#else
Q.insert(Q.end(), qq->begin(), qq->end());
#endif
// then convert to world coordinates
for_each (P.begin() + ind, P.end(), datap->getXform());
for_each (Q.begin() + ind, Q.end(), dataq->getXform());
}
} END_FOR_KEYS;
}
void
GlobalReg::evaluate(const vector<TbObj*> &group)
{
for (int i=0; i<group.size(); i++) {
FOR_MATCHING_KEYS(group[i], data) {
// TbObjs in a pair must be in the same group!
assert(data->xfa == group[i] ||
CONTAINS(group, data->xfa));
assert(data->xfb == group[i] ||
CONTAINS(group, data->xfb));
if (data->xfb == group[i]) continue;
data->stats();
} END_FOR_KEYS;
}
}
float
GlobalReg::evaluate(TbObj *one)
{
// calculate the mean distance between every point pair
int cnt = 0;
float sumSq = 0.0;
FOR_MATCHING_KEYS(one, data) {
data->stats();
int n = data->ptsa.size();
float rms = data->rmsErr;
cnt += n;
sumSq += n*rms*rms;
} END_FOR_KEYS;
if (cnt == 0) {
cerr << "GlobalReg::evaluate() didn't have entries to"
<< " evaluate" << endl;
return 0.0;
}
return sqrtf(sumSq/cnt);
}
static crope
nameFromTbObj (TbObj* tbo)
{
if (tbo) {
RigidScan* rs = dynamic_cast<RigidScan*> (tbo);
if (rs) {
DisplayableMesh* dm = FindMeshDisplayInfo (rs);
if (dm) return dm->getName();
else return rs->get_name();
}
return crope("(unknown)");
}
return crope("(NULL)");
}
void
GlobalReg::dump(void)
{
cout << endl;
FOR_MAP_ENTRIES(key, data) {
SHOW(key);
SHOW(data);
SHOW(data->xfa);
SHOW(data->xfb);
vector<Pnt3> &ptsa = data->ptsa;
cout << "-" << endl;
copy(ptsa.begin(), ptsa.end(),
ostream_iterator<Pnt3>(cout, "\n"));
vector<Pnt3> &ptsb = data->ptsb;
cout << "-" << endl;
copy(ptsb.begin(), ptsb.end(),
ostream_iterator<Pnt3>(cout, "\n"));
cout << "-" << endl;
copy(all_scans.begin(), all_scans.end(),
ostream_iterator<TbObj*>(cout, "\n"));
} END_FOR_MAP
cout << endl;
}
void
GlobalReg::move_back(const vector<TbObj*> &group,
const vector<XF_F> &old_xf)
{
cout << "Moving the scans back..." << flush;
// first, create point pairs
vector<Pnt3> P,Q;
XF_F xfp, xfq;
int i,j;
for (i=0; i<group.size(); i++) {
FOR_MATCHING_KEYS(group[i], data) {
// each entry twice in the map
if (group[i] == data->xfb) continue;
// points in data ptsa
int end = P.size();
for (j=0; j<data->ptsa.size(); j+=20) {
P.push_back(data->ptsa[j]);
Q.push_back(data->ptsa[j]);
}
xfp = data->xfa->getXform(); // current xf
xfq = old_xf[scan_idx(data->xfa, group)]; // old xf
for_each(P.begin() + end, P.end(), xfp);
for_each(Q.begin() + end, Q.end(), xfq);
// points in data ptsb
end = P.size();
for (j=0; j<data->ptsb.size(); j+=20) {
P.push_back(data->ptsb[j]);
Q.push_back(data->ptsb[j]);
}
xfp = data->xfb->getXform(); // current xf
xfq = old_xf[scan_idx(data->xfb, group)]; // old xf
for_each(P.begin() + end, P.end(), xfp);
for_each(Q.begin() + end, Q.end(), xfq);
} END_FOR_KEYS;
}
// find the motion that brings the group back close to
// where it was
double q[7];
horn_align(&P[0], &Q[0], P.size(), q);
xfp.fromQuaternion(q, q[4], q[5], q[6]);
// apply it
for (i=0; i<group.size(); i++) {
group[i]->setXform((xfp *
group[i]->getXform()).enforce_rigidity());
}
cout << "done." << endl;
}
Xform<float>
GlobalReg::compute_xform(vector<Pnt3> &P, vector<Pnt3> &Q)
{
Xform<float> xf;
double q[7];
horn_align (&P[0], &Q[0], P.size(), q);
xf.fromQuaternion (q, q[4], q[5], q[6]);
return xf;
}
void
GlobalReg::align_one_to_others (TbObj* one, TbObj* two)
{
vector<Pnt3> P,Q;
float sum = .5*FLT_MAX, oldsum;
one->save_for_undo();
do {
oldsum = sum;
get_pts (one, P, Q, two); // two==NULL means use all partners
if (P.size() == 0) continue;
one->setXform(compute_xform(P, Q) * one->getXform(),
false);
sum = evaluate(one);
cout << "The average point-to-point distance is "
<< sum << endl;
if (BailDetector::bail()) {
cerr << "global alignment cancelled." << endl;
break;
}
} while (2.0*(oldsum-sum) > ftol*(sum+oldsum+1.e-10));
}
#define FOR_ACTIVE_NBORS(scan, nbor) \
FOR_MATCHING_KEYS(scan, data) {\
TbObj *nbor = (data->xfa == scan ? data->xfb : data->xfa);\
if (active.end() != find(active.begin(),active.end(),nbor)){
#define END_FOR_NBORS }}}}
/* // get emacs identation working after above macro definition...
{
*/
// part covered by psuedo-code in the paper
void
GlobalReg::align_group(const vector<TbObj*> &group)
{
vector<Pnt3> P,Q;
int i;
assert (group.size() > 1);
vector<XF_F> old_xf(group.size());
for (i=0; i<group.size(); i++) {
old_xf[i] = group[i]->getXform();
group[i]->save_for_undo();
}
// new algorithm
//
// for each member of the group, calculate the number
// of links, choose the one with the most links as the seed
//
// push the seed to a queue and to the active set
//
// process the queue until empty
// take the scan at the front
// align it with the scans in the active set
// if it improves more than the threshold
// push all the neighbors in the active set to queue
//
// add to the queue and the active set the scan with the
// most links to scans in the active set
vector<TbObj*> active, dormant, nbors;
deque<TbObj*> que;
TbObj *seed;
int seed_links = 0;
// set the dormant and active sets...
if (dirty_scans.size()) {
for (i=0; i<group.size(); i++) {
if (dirty_scans.find(group[i]) != dirty_scans.end()) {
dormant.push_back(group[i]);
} else {
active.push_back(group[i]);
}
}
}
if (active.size() == 0) {
// active set is empty!
// initialize, find the seed (one with most links)
for (i=0; i<group.size(); i++) {
int links = 0;
FOR_MATCHING_KEYS(group[i], data) {
links++;
} END_FOR_KEYS;
if (links > seed_links) {
seed_links = links;
seed = group[i];
}
}
assert(seed_links);
// initialize the active and dormant sets
active.push_back(seed);
dormant.clear();
dormant.reserve(group.size()-1);
for (i=0; i<group.size(); i++) {
if (group[i] != seed) dormant.push_back(group[i]);
}
}
Progress progress (dormant.size(), "Global alignment");
// process all scans
while (!dormant.empty()) {
// find the dormant scan that has the most links to scans
// in active set
seed_links = 0;
vector<TbObj*>::iterator it, pos;
for (it = dormant.begin(); it != dormant.end(); it++) {
int links = 0;
FOR_ACTIVE_NBORS(*it, nbor) {
links++;
} END_FOR_NBORS;
if (links > seed_links) {
seed_links = links;
pos = it;
}
}
assert(seed_links);
// remove from dormant set
seed = *pos;
int dormant_size = dormant.size();
dormant.erase(pos);
assert(dormant_size - 1 == dormant.size());
// push to active and queue
active.push_back(seed);
assert(que.empty());
que.push_back(seed);
cout << "\n";
SHOW(active.size());
SHOW(dormant.size());
// process the queue