int
main()
{
PdmSuperClusterer super;
PdmCWDClusterer clust(&super, POL_LEFTCIRCULAR);
// guestimates for TSS; match test data
super.setObsParams(2289 - 5.034399, 64, 0.6958917);
while(cin)
{
int count, bin, drift, power;
cin >> count;
cin >> bin;
cin >> drift;
cin >> power;
clust.recordHit(bin,drift,power);
}
clust.allHitsLoaded();
super.compute();
printf("found %d superclusters:\n", super.getCount());
for (int i = 0; i < super.getCount(); i++)
{
const PdmClusterTag &tag = super.getNthMainSignal(i);
dumpTag("SUPER ",tag);
for (int j = 0; j < super.getNthClusterCount(i); j++)
{
const PdmClusterTag &tag2 = super.getNthMthCluster(i,j);
dumpTag(" ",tag2);
}
}
return 0;
}
void FExtrudeMod::ModifyObject(
TimeValue t, ModContext &mc, ObjectState *os, INode *node)
{
if (os->obj->IsSubClassOf(triObjectClassID)) {
TriObject *tobj = (TriObject*)os->obj;
Mesh &mesh = tobj->GetMesh();
Interval iv = FOREVER;
float a, s;
Point3 pt, center;
int c;
pblock->GetValue(PB_AMOUNT,t,a,iv);
pblock->GetValue(PB_SCALE,t,s,iv);
pblock->GetValue(PB_CENTER,t,c,iv);
base->GetValue(t,&pt,iv,CTRL_ABSOLUTE);
// Extrude the faces -- this just creates the new faces
mesh.ExtrudeFaces();
// Build normals of selected faces only
Tab<Point3> normals;
if (!c) {
normals.SetCount(mesh.getNumVerts());
for (int i=0; i<mesh.getNumVerts(); i++) {
normals[i] = Point3(0,0,0);
}
for (int i=0; i<mesh.getNumFaces(); i++) {
if (mesh.faceSel[i]) {
Point3 norm =
(mesh.verts[mesh.faces[i].v[1]]-mesh.verts[mesh.faces[i].v[0]]) ^
(mesh.verts[mesh.faces[i].v[2]]-mesh.verts[mesh.faces[i].v[1]]);
for (int j=0; j<3; j++) {
normals[mesh.faces[i].v[j]] += norm;
}
}
}
for (int i=0; i<mesh.getNumVerts(); i++) {
normals[i] = Normalize(normals[i]);
}
} else {
// Compute the center point
base->GetValue(t,¢er,iv,CTRL_ABSOLUTE);
}
// Mark vertices used by selected faces
BitArray sel;
sel.SetSize(mesh.getNumVerts());
for (int i=0; i<mesh.getNumFaces(); i++) {
if (mesh.faceSel[i]) {
for (int j=0; j<3; j++) sel.Set(mesh.faces[i].v[j],TRUE);
}
}
// Move selected verts
for (int i=0; i<mesh.getNumVerts(); i++) {
if (sel[i]) {
if (!c) {
mesh.verts[i] += normals[i]*a;
} else {
Point3 vect = Normalize((mesh.verts[i] * (*mc.tm))
- center);
mesh.verts[i] += vect*a;
}
}
}
// Scale verts
if (s!=100.0f) {
s /= 100.0f;
AdjEdgeList ae(mesh);
AdjFaceList af(mesh,ae);
FaceClusterList clust(mesh.faceSel,af);
// Make sure each vertex is only scaled once.
BitArray done;
done.SetSize(mesh.getNumVerts());
// scale each cluster independently
for (int i=0; (DWORD)i<clust.count; i++) {
// First determine cluster center
Point3 cent(0,0,0);
int ct=0;
for (int j=0; j<mesh.getNumFaces(); j++) {
if (clust[j]==(DWORD)i) {
for (int k=0; k<3; k++) {
cent += mesh.verts[mesh.faces[j].v[k]];
ct++;
}
}
}
if (ct) cent /= float(ct);
// Now scale the cluster about its center
for (int j=0; j<mesh.getNumFaces(); j++) {
if (clust[j]==(DWORD)i) {
for (int k=0; k<3; k++) {
int index = mesh.faces[j].v[k];
if (done[index]) continue;
done.Set(index);
mesh.verts[index] =
(mesh.verts[index]-cent)*s + cent;
}
}
}
}
}
mesh.InvalidateTopologyCache ();
os->obj->UpdateValidity(GEOM_CHAN_NUM,iv);
}
}
void
testCWDCluster()
{
PdmSuperClusterer super;
PdmCWDClusterer clust(&super, POL_LEFTCIRCULAR);
// with nothing added, should return empty vector
clust.allHitsLoaded();
super.compute();
int count = super.getCount();
ASSERT_EQ(0, count);
// with one hit added, should return 1 supercluster describing that hit
super.clear();
clust.recordHit(100,5,50);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// after clear, should return empty vector
super.clear();
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(0, count);
// with two hits added far apart,
// should return 2 superclusters describing each hit
super.clear();
clust.recordHit(100,5,50);
clust.recordHit(2100,5,50);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(2, count);
// verify description
PdmClusterTag tag;
tag = super.getNthMainSignal(0);
CwPowerSignal cw = tag.holder->getCWD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(100), cw.sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(5)/clust.getSecondsPerObs(),
cw.sig.drift, D_FREQ);
ASSERT_EQ_F(50, cw.sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), cw.sig.width, D_FREQ);
tag = super.getNthMainSignal(1);
cw = tag.holder->getCWD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(2100), cw.sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(5)/clust.getSecondsPerObs(),
cw.sig.drift, D_FREQ);
ASSERT_EQ_F(50, cw.sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), cw.sig.width, D_FREQ);
// with two equally powered hits added within the lev1 range
// should return 1 supercluster describing first hit, with
// width set to number of bins from lowest to highest hit, inclusive
super.clear();
clust.recordHit(100,5,50);
clust.recordHit(102,5,50);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// verify description
tag = super.getNthMainSignal(0);
cw = tag.holder->getCWD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(100), cw.sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(5)/clust.getSecondsPerObs(),
cw.sig.drift, D_FREQ);
ASSERT_EQ_F(50, cw.sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(3), cw.sig.width, D_FREQ);
// with three unequally powered hits added within the lev1 range
// should return 1 supercluster describing highest power hit, with
// width set to number of bins from lowest to highest hit, inclusive
super.clear();
clust.recordHit(100,5,50);
clust.recordHit(102,5,52);
clust.recordHit(104,5,51);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// verify description
tag = super.getNthMainSignal(0);
cw = tag.holder->getCWD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(102), cw.sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(5)/clust.getSecondsPerObs(),
cw.sig.drift, D_FREQ);
ASSERT_EQ_F(52, cw.sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(5), cw.sig.width, D_FREQ);
// with two equally powered hits added outside the lev1 range but
// within the lev2 range
// should return 1 supercluster describing first hit
super.clear();
clust.recordHit(100,5,50);
clust.recordHit(200,5,50);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// verify description
tag = super.getNthMainSignal(0);
cw = tag.holder->getCWD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(100), cw.sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(5)/clust.getSecondsPerObs(),
cw.sig.drift, D_FREQ);
ASSERT_EQ_F(50, cw.sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), cw.sig.width, D_FREQ);
// with unequally powered hits added outside the lev1 range but
// within the lev2 range
// should return 1 supercluster describing highest power hit
super.clear();
clust.recordHit(100,5,50);
clust.recordHit(200,5,52);
clust.recordHit(300,5,51);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// verify description
tag = super.getNthMainSignal(0);
cw = tag.holder->getCWD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(200), cw.sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(5)/clust.getSecondsPerObs(),
cw.sig.drift, D_FREQ);
ASSERT_EQ_F(52, cw.sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), cw.sig.width, D_FREQ);
super.clear();
}
void
testPDCluster()
{
PdmSuperClusterer super;
PdmPDClusterer clust(&super, RES_1HZ);
// with nothing added, should return empty vector
clust.allHitsLoaded();
super.compute();
int count = super.getCount();
ASSERT_EQ(0, count);
// with one hit added, should return 1 supercluster describing that hit
// "bogus" triplets should get stripped
super.clear();
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 101, 50,
4, 102, 50,
6, 103, 50);
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 101, 0,
4, 102, 50,
6, 103, 50);
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 101, 50,
4, 102, 0,
6, 103, 50);
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 101, 50,
4, 102, 50,
6, 103, 0);
clust.recordTriplet(POL_LEFTCIRCULAR,
4, 101, 50,
4, 102, 50,
4, 103, 50);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// after clear, should return empty vector
super.clear();
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(0, count);
// with two hits added far apart,
// should return 2 superclusters describing each hit
super.clear();
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 101, 50,
4, 102, 50,
6, 103, 50);
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 2101, 50,
4, 2102, 50,
6, 2103, 50);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(2, count);
// verify description
PdmClusterTag tag;
tag = super.getNthMainSignal(0);
const PulseSignalHeader *pd = &tag.holder->getPD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(100), pd->sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(32)/clust.getSecondsPerObs(),
pd->sig.drift, D_FREQ);
ASSERT_EQ_F(3*50, pd->sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), pd->sig.width, D_FREQ);
tag = super.getNthMainSignal(1);
pd = &tag.holder->getPD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(2100), pd->sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(32)/clust.getSecondsPerObs(),
pd->sig.drift, D_FREQ);
ASSERT_EQ_F(3*50, pd->sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), pd->sig.width, D_FREQ);
// with three triplets in the lev1 range, should calculate a path
// through all pulses with unique spectra. Only the strongest
// pulse for a given spectrum number is retained. Power should
// sum over all included pulses
super.clear();
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 101, 8,
4, 102, 2,
6, 103, 4);
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 111, 1,
4, 102, 16,
6, 113, 32);
clust.recordTriplet(POL_LEFTCIRCULAR,
6, 103, 64,
8, 104, 128,
10, 105, 256);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// verify description
tag = super.getNthMainSignal(0);
pd = &tag.holder->getPD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(100), pd->sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(32)/clust.getSecondsPerObs(),
pd->sig.drift, D_FREQ);
ASSERT_EQ_F(8+16+64+128+256, pd->sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1+10*((float)2/3)),
pd->sig.width, D_FREQ);
// check pulse period
ASSERT_EQ_F(2.0 * clust.getSecondsPerObs() / clust.getSpectraPerObs(),
pd->train.pulsePeriod, D_PERIOD);
// check individual pulses
ASSERT_EQ(5, pd->train.numberOfPulses);
Pulse *p = (Pulse *)(pd+1);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(101), p[0].frequency, D_FREQ);
ASSERT_EQ(8, (int)p[0].power);
ASSERT_EQ(2, p[0].spectrumNumber);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(102), p[1].frequency, D_FREQ);
ASSERT_EQ(16, (int)p[1].power);
ASSERT_EQ(4, p[1].spectrumNumber);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(103), p[2].frequency, D_FREQ);
ASSERT_EQ(64, (int)p[2].power);
ASSERT_EQ(6, p[2].spectrumNumber);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(104), p[3].frequency, D_FREQ);
ASSERT_EQ(128, (int)p[3].power);
ASSERT_EQ(8, p[3].spectrumNumber);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(105), p[4].frequency, D_FREQ);
ASSERT_EQ(256, (int)p[4].power);
ASSERT_EQ(10, p[4].spectrumNumber);
// with two equally powered hits added outside the lev1 range but
// within the lev2 range
// should return 1 supercluster describing first hit
super.clear();
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 101, 50,
4, 102, 50,
6, 103, 50);
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 201, 50,
4, 202, 50,
6, 203, 50);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// verify description
tag = super.getNthMainSignal(0);
pd = &tag.holder->getPD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(100), pd->sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(32)/clust.getSecondsPerObs(),
pd->sig.drift, D_FREQ);
ASSERT_EQ_F(3*50, pd->sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), pd->sig.width, D_FREQ);
// with unequally powered hits added outside the lev1 range but
// within the lev2 range
// should return 1 supercluster describing highest power hit
super.clear();
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 101, 50,
4, 102, 50,
6, 103, 50);
clust.recordTriplet(POL_LEFTCIRCULAR,
2, 201, 60,
4, 202, 60,
6, 203, 60);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// verify description
tag = super.getNthMainSignal(0);
pd = &tag.holder->getPD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(200), pd->sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(32)/clust.getSecondsPerObs(),
pd->sig.drift, D_FREQ);
ASSERT_EQ_F(3*60, pd->sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), pd->sig.width, D_FREQ);
// check pulse period
ASSERT_EQ_F(2.0 * clust.getSecondsPerObs() / clust.getSpectraPerObs(),
pd->train.pulsePeriod, D_PERIOD);
// check individual pulses
ASSERT_EQ(3, pd->train.numberOfPulses);
p = (Pulse *)(pd+1);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(201), p[0].frequency, D_FREQ);
ASSERT_EQ(60, (int)p[0].power);
ASSERT_EQ(2, p[0].spectrumNumber);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(202), p[1].frequency, D_FREQ);
ASSERT_EQ(60, (int)p[1].power);
ASSERT_EQ(4, p[1].spectrumNumber);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(203), p[2].frequency, D_FREQ);
ASSERT_EQ(60, (int)p[2].power);
ASSERT_EQ(6, p[2].spectrumNumber);
// pulse period test -- 3 triplets; two with one period and one with
// another; should take most common period
super.clear();
clust.recordTriplet(POL_LEFTCIRCULAR,
8, 104, 10,
10, 105, 10,
12, 106, 10);
clust.recordTriplet(POL_LEFTCIRCULAR,
14, 107, 10,
18, 109, 10,
22, 111, 10);
clust.recordTriplet(POL_LEFTCIRCULAR,
26, 113, 10,
30, 115, 10,
34, 117, 10);
clust.allHitsLoaded();
super.compute();
count = super.getCount();
ASSERT_EQ(1, count);
// verify description
tag = super.getNthMainSignal(0);
pd = &tag.holder->getPD()->getNth(tag.index);
ASSERT_EQ_F(clust.binsToAbsoluteMHz(100), pd->sig.rfFreq, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(32)/clust.getSecondsPerObs(),
pd->sig.drift, D_FREQ);
ASSERT_EQ_F(9*10, pd->sig.power, D_FREQ);
ASSERT_EQ_F(clust.binsToRelativeHz(1), pd->sig.width, D_FREQ);
// check pulse period
ASSERT_EQ_F(4.0 * clust.getSecondsPerObs() / clust.getSpectraPerObs(),
pd->train.pulsePeriod, D_PERIOD);
super.clear();
}
int main() {
std::shared_ptr<util::DissimMatrix> l1ptr = parseFile("/home/srmq/Dropbox/CIn/research/inria/dados/iris-L1-1-N.csv");
std::shared_ptr<util::DissimMatrix> l2ptr = parseFile("/home/srmq/Dropbox/CIn/research/inria/dados/iris-L1-2-N.csv");
std::shared_ptr<util::DissimMatrix> l3ptr = parseFile("/home/srmq/Dropbox/CIn/research/inria/dados/iris-L1-3-N.csv");
std::shared_ptr<util::DissimMatrix> l4ptr = parseFile("/home/srmq/Dropbox/CIn/research/inria/dados/iris-L1-4-N.csv");
std::vector<std::shared_ptr<util::DissimMatrix>> dissimMatrices = {l1ptr, l2ptr, l3ptr, l4ptr};
const int NUMBER_OF_RUNS = 100;
int k = 3;
bool possibilisticMode = false;
double bestJ = std::numeric_limits<double>::max();
std::shared_ptr<std::vector<util::FuzzyCluster> > bestClusters;
const int classLabelLength = 150;
int classlabels[classLabelLength];
for (int i = 0; i < classLabelLength; i++) {
classlabels[i] = i/50;
}
const unsigned int procCount = std::thread::hardware_concurrency();
if (procCount > 1) {
unsigned int procId = 0;
bool quitwhile = false;
int pipeParentChild[procCount][2]; // PARENT WRITES to CHILD, CHILD READS from PARENT
int pipeChildParent[procCount][2]; // PARENT READS from CHILD, CHILD WRITES to PARENT
pid_t cpid;
do {
if (pipe(pipeParentChild[procId]) == -1) {
perror("pipe");
exit(EXIT_FAILURE);
}
if (pipe(pipeChildParent[procId]) == -1) {
perror("pipe");
exit(EXIT_FAILURE);
}
cpid = fork();
if (cpid == -1) {
perror("fork");
exit(EXIT_FAILURE);
}
if (cpid == 0) { /* I am the child */
// close WRITE in pipeParentChild
close(pipeParentChild[procId][1]);
// close READ in pipeChildParent
close(pipeChildParent[procId][0]);
quitwhile = true;
} else { /* I am the master */
// close READ in pipeParentChild
close(pipeParentChild[procId][0]);
// close WRITE in pipeChildParent
close(pipeChildParent[procId][1]);
procId++;
}
} while (procId < procCount && !quitwhile);
if (cpid == 0) { /* I am the child do stuff */
clustering::FWRDCA::seed_random_engine(2u*procId + 1u);
for (int i = procId; i < NUMBER_OF_RUNS; i=i+procCount) {
std::cout << "Run number ";
std::cout << i;
std::cout << std::endl;
clustering::FWRDCA clust(dissimMatrices);
clust.setPossibilisticMode(possibilisticMode);
clust.cluster(k);
std::shared_ptr<std::vector<util::FuzzyCluster> > const myClusters = clust.getClusters();
const double myJ = clust.calcJ(myClusters);
std::cout << "J: ";
std::cout << myJ;
std::cout << std::endl;
if (myJ < bestJ) {
bestJ = myJ;
bestClusters = clust.getClustersCopy();
}
}
write(pipeChildParent[procId][1], &bestJ, sizeof(double));
close(pipeChildParent[procId][1]);
bool amITheBest;
read(pipeParentChild[procId][0], &amITheBest, sizeof(bool)); // le resultado
if (amITheBest) {
printIndices(k, classLabelLength, bestClusters, classlabels);
}
} else { /* I am the master get results */
double overallBestJ;
read(pipeChildParent[0][0], &overallBestJ, sizeof(double)); // le resultado
unsigned int bestIndex = 0;
for (unsigned int i = 1; i < procCount; i++) {
double procBestJ;
read(pipeChildParent[i][0], &procBestJ, sizeof(double)); // le resultado
if (procBestJ > overallBestJ) {
overallBestJ = procBestJ;
bestIndex = i;
}
}
const bool falseConst = false;
const bool trueConst = true;
for (unsigned int i = 0; i < procCount; i++) {
if (i != bestIndex) {
write(pipeParentChild[i][1], &falseConst, sizeof(bool));
close(pipeParentChild[i][1]);
} else {
write(pipeParentChild[i][1], &trueConst, sizeof(bool));
close(pipeParentChild[i][1]);
}
}
}
} else {
for (int i = 0; i < NUMBER_OF_RUNS; i++) {
std::cout << "Run number ";
std::cout << i;
std::cout << std::endl;
clustering::FWRDCA clust(dissimMatrices);
clust.setPossibilisticMode(possibilisticMode);
clust.cluster(k);
std::shared_ptr<std::vector<util::FuzzyCluster> > const myClusters = clust.getClusters();
const double myJ = clust.calcJ(myClusters);
std::cout << "J: ";
std::cout << myJ;
std::cout << std::endl;
if (myJ < bestJ) {
bestJ = myJ;
bestClusters = clust.getClustersCopy();
}
}
printIndices(k, classLabelLength, bestClusters, classlabels);
}
return(0);
}
SEXP kmeansMatrixEuclid(MatrixType x, index_type n, index_type m,
SEXP pcen, SEXP pclust, SEXP pclustsizes,
SEXP pwss, SEXP itermax)
{
index_type j, col, nchange;
int maxiters = Rf_asInteger(itermax);
SEXP Riter;
Rf_protect(Riter = Rf_allocVector(INTSXP, 1));
int *iter = INTEGER(Riter);
iter[0] = 0;
BigMatrix *pcent = reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(pcen));
MatrixAccessor<double> cent(*pcent);
BigMatrix *Pclust = reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(pclust));
MatrixAccessor<int> clust(*Pclust);
BigMatrix *Pclustsizes = reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(pclustsizes));
MatrixAccessor<double> clustsizes(*Pclustsizes);
BigMatrix *Pwss = reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(pwss));
MatrixAccessor<double> ss(*Pwss);
int k = (int) pcent->nrow(); // number of clusters
int cl, bestcl, oldcluster, newcluster;
int done = 0;
double temp;
vector<double> d(k); // Vector of distances, internal only.
vector<double> temp1(k);
vector<vector<double> > tempcent(m, temp1); // For copy of global centroids k x m
// At this point I can use [][] to access things, with ss[0][cl]
// being used for the vectors, for example.
// Before starting the loop, we only have cent (centers) as passed into the function.
// Calculate clust and clustsizes, then update cent as centroids.
for (cl=0; cl<k; cl++) clustsizes[0][cl] = 0.0;
for (j=0; j<n; j++) {
bestcl = 0;
for (cl=0; cl<k; cl++) {
d[cl] = 0.0;
for (col=0; col<m; col++) {
temp = (double)x[col][j] - cent[col][cl];
d[cl] += temp * temp;
}
if (d[cl]<d[bestcl]) bestcl = cl;
}
clust[0][j] = bestcl + 1; // Saving the R cluster number, not the C index.
clustsizes[0][bestcl]++;
for (col=0; col<m; col++)
tempcent[col][bestcl] += (double)x[col][j];
}
for (cl=0; cl<k; cl++)
for (col=0; col<m; col++)
cent[col][cl] = tempcent[col][cl] / clustsizes[0][cl];
do {
nchange = 0;
for (j=0; j<n; j++) { // For each of my points, this is offset from hash position
oldcluster = clust[0][j] - 1;
bestcl = 0;
for (cl=0; cl<k; cl++) { // Consider each of the clusters
d[cl] = 0.0; // We'll get the distance to this cluster.
for (col=0; col<m; col++) { // Loop over the dimension of the data
temp = (double)x[col][j] - cent[col][cl];
d[cl] += temp * temp;
}
if (d[cl]<d[bestcl]) bestcl = cl;
} // End of looking over the clusters for this j
if (d[bestcl] < d[oldcluster]) { // MADE A CHANGE!
newcluster = bestcl;
clust[0][j] = newcluster + 1;
nchange++;
clustsizes[0][newcluster]++;
clustsizes[0][oldcluster]--;
for (col=0; col<m; col++) {
cent[col][oldcluster] += ( cent[col][oldcluster] - (double)x[col][j] ) / clustsizes[0][oldcluster];
cent[col][newcluster] += ( (double)x[col][j] - cent[col][newcluster] ) / clustsizes[0][newcluster];
}
}
} // End of this pass over my points.
iter[0]++;
if ( (nchange==0) || (iter[0]>=maxiters) ) done = 1;
} while (done==0);
// Collect the sums of squares now that we're done.
for (cl=0; cl<k; cl++) ss[0][cl] = 0.0;
for (j=0; j<n; j++) {
for (col=0; col<m; col++) {
cl = clust[0][j]-1;
temp = (double)x[col][j] - cent[col][cl];
ss[0][cl] += temp * temp;
}
}
Rf_unprotect(1);
return(Riter);
}