void Connector::setup(QLabel *ql, QLineEdit *le, QPushButton *mBtn, QPushButton *dBtn, Canvas *c) {
status = ql;
ipBox = le;
modeBtn = mBtn;
delayBtn = dBtn;
canvas = c;
connect(this, SIGNAL(addY()), canvas, SLOT(addY()));
connect(this, SIGNAL(subY()), canvas, SLOT(subY()));
connect(this, SIGNAL(addX()), canvas, SLOT(addX()));
connect(this, SIGNAL(subX()), canvas, SLOT(subX()));
connect(this, SIGNAL(paint()), canvas, SLOT(paintClicked()));
}
void Connector::timesUp()
{
QPair<int, int> next = cmdQ.dequeue();
switch(next.first)
{
case CW:
axis_number = next.second;
canvas->rotateCW();
break;
case CCW:
axis_number = next.second;
canvas->rotateCCW();
break;
case ADDY:
emit addY();
break;
case SUBY:
emit subY();
break;
case ADDX:
emit addX();
break;
case SUBX:
emit subX();
break;
case PAINT:
emit paint();
break;
default:
qDebug() << "RECEIVE ERROR:" << next.first;
break;
}
}
int AnovaTest::anovacase(gsl_matrix *bY, gsl_matrix *bX)
{
unsigned int j;
// if Y col is all zeros
for ( j=0; j<nVars; j++ ){
gsl_vector_view colj = gsl_matrix_column(bY, j);
if ( gsl_vector_isnull(&colj.vector) == TRUE ) return GSL_ERANGE;
}
unsigned int i, hid, aid;
double *sj, *pj, *bj;
gsl_matrix *Z = gsl_matrix_alloc(nRows, nVars);
gsl_matrix_memcpy(Z, bY);
// Hats.X
for (i=0; i<nModels-1; i++){
hid = i+1; aid = i;
gsl_vector_view ref1 = gsl_matrix_row(inRef, aid);
subX(bX, &ref1.vector, Hats[aid].X);
gsl_vector_view ref0 = gsl_matrix_row(inRef, hid);
subX(bX, &ref0.vector, Hats[hid].X);
//Y = X*coef
gsl_blas_dgemm(CblasNoTrans,CblasNoTrans,-1.0,Hats[aid].X,Hats[aid].Coef,0.0,Z);
//Z = bY - Yhat;
gsl_matrix_add (Z, bY);
// calc teststats
calcSS(Z, &(Hats[hid]), mmRef);
calcSS(Z, &(Hats[aid]), mmRef);
testStatCalc(&(Hats[hid]), &(Hats[aid]), mmRef, TRUE, &(bMultStat), bStatj);
if (bMultStat >= multstat[i]) Pmultstat[i]++;
sj = gsl_matrix_ptr (statj, i, 0);
pj = gsl_matrix_ptr (Pstatj, i, 0);
bj = gsl_vector_ptr (bStatj, 0);
calcAdjustP(mmRef->punit, nVars, bj, sj, pj, sortid[i]);
}
gsl_matrix_free(Z);
return 0;
}
void Connector::readCommands() {
if (client)
{
qDebug() << "READ - NOT SERVER";
return;
}
char buf[2] = {0};
serverSock->read(buf, serverSock->bytesAvailable());
int command = int(buf[0]);
int axis = int(buf[1]);
if (delay)
{
cmdQ.enqueue(qMakePair(command, axis));
QTimer::singleShot(2000, this, SLOT(timesUp()));
}
else
{
switch(command)
{
case CW:
axis_number = next.second;
canvas->rotateCW();
break;
case CCW:
axis_number = next.second;
canvas->rotateCCW();
break;
case ADDY:
emit addY();
break;
case SUBY:
emit subY();
break;
case ADDX:
emit addX();
break;
case SUBX:
emit subX();
break;
case PAINT:
emit paint();
break;
default:
qDebug() << "RECEIVE ERROR:" << next.first;
break;
}
}
}
int GlmTest::anova(glm *fit, gsl_matrix *isXvarIn)
{
// Assume the models have been already sorted (in R)
Xin = isXvarIn;
nModels = Xin->size1;
double *rdf = new double [nModels];
unsigned int nP, i, j, k;
unsigned int ID0, ID1, nP0, nP1;
unsigned int nRows=tm->nRows, nVars=tm->nVars, nParam=tm->nParam;
unsigned int mtype = fit->mmRef->model-1;
dfDiff = new unsigned int [nModels-1];
anovaStat = gsl_matrix_alloc((nModels-1), nVars+1);
Panova = gsl_matrix_alloc((nModels-1), nVars+1);
gsl_vector *bStat = gsl_vector_alloc(nVars+1);
gsl_matrix_set_zero (anovaStat);
gsl_matrix_set_zero (Panova);
gsl_vector_set_zero (bStat);
PoissonGlm pNull(fit->mmRef), pAlt(fit->mmRef);
BinGlm binNull(fit->mmRef), binAlt(fit->mmRef);
NBinGlm nbNull(fit->mmRef), nbAlt(fit->mmRef);
PoissonGlm pNullb(fit->mmRef), pAltb(fit->mmRef);
BinGlm binNullb(fit->mmRef), binAltb(fit->mmRef);
NBinGlm nbNullb(fit->mmRef), nbAltb(fit->mmRef);
glm *PtrNull[3] = { &pNull, &nbNull, &binNull };
glm *PtrAlt[3] = { &pAlt, &nbAlt, &binAlt };
glm *bNull[3] = { &pNullb, &nbNullb, &binNullb };
glm *bAlt[3] = { &pAltb, &nbAltb, &binAltb };
double *suj, *buj, *puj;
gsl_vector_view teststat, unitstat,ref1, ref0;
gsl_matrix *X0=NULL, *X1=NULL, *L1=NULL, *tmp1=NULL, *BetaO=NULL;
gsl_matrix *bO=NULL, *bY=gsl_matrix_alloc(nRows, nVars);
bO = gsl_matrix_alloc(nRows, nVars);
gsl_permutation *sortid=NULL;
if (tm->punit==FREESTEP) sortid = gsl_permutation_alloc(nVars);
// ======= Fit the (first) Alt model =========//
for (i=0; i<nModels; i++) {
nP = 0;
for (k=0; k<nParam; k++)
if (gsl_matrix_get(Xin,i,k)!=FALSE) nP++;
rdf[i] = nRows-nP;
}
for (i=1; i<nModels; i++) {
// ======= Fit the Null model =========//
ID0 = i; ID1 = i-1;
nP0 = nRows - (unsigned int)rdf[ID0];
nP1 = nRows - (unsigned int)rdf[ID1];
// Degrees of freedom
dfDiff[i-1] = nP1 - nP0;
ref1=gsl_matrix_row(Xin, ID1);
ref0=gsl_matrix_row(Xin, ID0);
X0 = gsl_matrix_alloc(nRows, nP0);
subX(fit->Xref, &ref0.vector, X0);
X1 = gsl_matrix_alloc(nRows, nP1);
subX(fit->Xref, &ref1.vector, X1);
// ======= Get multivariate test statistics =======//
// Estimate shrinkage parametr only once under H1
// See "FW: Doubts R package "mvabund" (12/14/11)
teststat = gsl_matrix_row(anovaStat, (i-1));
PtrNull[mtype]->regression(fit->Yref, X0, fit->Oref, NULL);
if (tm->test == SCORE) {
lambda = gsl_vector_get(tm->anova_lambda, ID0);
GetR(PtrNull[mtype]->Res, tm->corr, lambda, Rlambda);
GeeScore(X1, PtrNull[mtype], &teststat.vector);
}
else if (tm->test==WALD) {
PtrAlt[mtype]->regression(fit->Yref, X1, fit->Oref, NULL);
L1 = gsl_matrix_alloc (nP1-nP0, nP1);
tmp1 = gsl_matrix_alloc (nParam, nP1);
subX(L, &ref1.vector, tmp1);
subXrow1(tmp1, &ref0.vector, &ref1.vector, L1);
lambda = gsl_vector_get(tm->anova_lambda, ID1);
GetR(PtrAlt[mtype]->Res, tm->corr, lambda, Rlambda);
GeeWald(PtrAlt[mtype], L1, &teststat.vector);
}
else {
BetaO = gsl_matrix_alloc(nP1, nVars);
addXrow2(PtrNull[mtype]->Beta, &ref1.vector, BetaO);
PtrAlt[mtype]->regression(fit->Yref, X1, fit->Oref, BetaO);
GeeLR(PtrAlt[mtype], PtrNull[mtype], &teststat.vector);
}
if (tm->resamp==MONTECARLO) {
lambda=gsl_vector_get(tm->anova_lambda,ID0);
GetR(fit->Res, tm->corr, lambda, Sigma);
setMonteCarlo (PtrNull[mtype], XBeta, Sigma);
}
// ======= Get univariate test statistics =======//
if (tm->punit == FREESTEP) {
unitstat=gsl_vector_subvector(&teststat.vector,1,nVars);
gsl_sort_vector_index (sortid, &unitstat.vector);
gsl_permutation_reverse(sortid);
}
// ======= Get resampling distribution under H0 ===== //
nSamp=0;
double dif, timelast=0;
clock_t clk_start=clock();
if (tm->showtime==TRUE)
printf("Resampling begins for test %d.\n", i);
for (j=0; j<tm->nboot; j++) {
// printf("simu %d :", j);
gsl_vector_set_zero (bStat);
if ( tm->resamp == CASEBOOT ) {
resampAnovaCase(PtrAlt[mtype],bY,X1,bO,j);
subX(X1, &ref0.vector, X0);
}
else {
resampNonCase(PtrNull[mtype], bY, j);
gsl_matrix_memcpy(bO, fit->Oref);
}
if ( tm->test == WALD ) {
bAlt[mtype]->regression(bY,X1,bO,NULL);
lambda = gsl_vector_get(tm->anova_lambda, ID1);
GetR(bAlt[mtype]->Res, tm->corr, lambda, Rlambda);
GeeWald(bAlt[mtype], L1, bStat);
}
else if ( tm->test == SCORE ) {
bNull[mtype]->regression(bY,X0,bO,NULL);
lambda = gsl_vector_get(tm->anova_lambda, ID0);
GetR(bNull[mtype]->Res, tm->corr, lambda, Rlambda);
GeeScore(X1, bNull[mtype], bStat);
}
else {
bNull[mtype]->regression(bY,X0,bO,NULL);
addXrow2(bNull[mtype]->Beta, &ref1.vector, BetaO);
bAlt[mtype]->regression(bY,X1,bO,BetaO);
GeeLR(bAlt[mtype], bNull[mtype], bStat);
}
// ----- get multivariate counts ------- //
buj = gsl_vector_ptr (bStat,0);
suj = gsl_matrix_ptr (anovaStat, i-1, 0);
puj = gsl_matrix_ptr (Panova, i-1, 0);
if ( *(buj) > (*(suj)-1e-8) ) *puj=*puj+1;
// ------ get univariate counts ---------//
calcAdjustP(tm->punit,nVars,buj+1,suj+1,puj+1,sortid);
nSamp++;
// Prompts
if ((tm->showtime==TRUE)&(j%100==0)) {
dif = (float)(clock() - clk_start)/(float)CLOCKS_PER_SEC;
timelast+=(double)dif/60;
printf("\tResampling run %d finished. Time elapsed: %.2f minutes...\n", j, timelast);
clk_start=clock();
}
} // end j for loop
// ========= get p-values ======== //
if ( tm->punit == FREESTEP) {
puj = gsl_matrix_ptr (Panova, i-1, 1);
reinforceP(puj, nVars, sortid);
}
if (BetaO!=NULL) gsl_matrix_free(BetaO);
if (X0!=NULL) gsl_matrix_free(X0);
if (X1!=NULL) gsl_matrix_free(X1);
if (tm->test == WALD) {
if (L1!=NULL) gsl_matrix_free(L1);
if (tmp1!=NULL) gsl_matrix_free(tmp1);
}
} // end i for loop and test for loop
// p = (#exceeding observed stat + 1)/(#nboot+1)
gsl_matrix_add_constant (Panova, 1.0);
gsl_matrix_scale (Panova, (double)1/(nSamp+1.0));
bAlt[mtype]->releaseGlm();
PtrAlt[mtype]->releaseGlm();
if ( tm->test!=WALD ) {
bNull[mtype]->releaseGlm();
PtrNull[mtype]->releaseGlm();
}
delete []rdf;
if (sortid != NULL )
gsl_permutation_free(sortid);
gsl_vector_free(bStat);
gsl_matrix_free(bY);
if (bO!=NULL) gsl_matrix_free(bO);
return SUCCESS;
}
void CStarCamera::setViewportAngle(const FPoint &angles) {
debug(DEBUG_DETAILED, "setViewportAngle %f %f", angles._x, angles._y);
if (isLocked())
return;
if (_matrixRow == -1) {
FPose subX(X_AXIS, angles._y);
FPose subY(Y_AXIS, angles._x);
FPose sub(subX, subY);
proc22(sub);
} else if (_matrixRow == 0) {
FVector row1 = _matrix._row1;
FPose subX(X_AXIS, angles._y);
FPose subY(Y_AXIS, angles._x);
FPose sub(subX, subY);
FMatrix m1 = _viewport.getOrientation();
FVector tempV1 = _viewport._position;
FVector tempV2, tempV3, tempV4, tempV5, tempV6;
tempV2._y = m1._row1._y * 100000.0;
tempV2._z = m1._row1._z * 100000.0;
tempV3._x = m1._row1._x * 100000.0 + tempV1._x;
tempV4._x = tempV3._x;
tempV3._y = tempV2._y + tempV1._y;
tempV4._y = tempV3._y;
tempV3._z = tempV2._z + tempV1._z;
tempV4._z = tempV3._z;
tempV2._x = m1._row2._x * 100000.0;
tempV2._y = m1._row2._y * 100000.0;
tempV2._z = m1._row2._z * 100000.0;
tempV2._x = m1._row3._x * 100000.0;
tempV2._y = m1._row3._y * 100000.0;
tempV2._z = m1._row3._z * 100000.0;
tempV2._x = tempV2._x + tempV1._x;
tempV2._y = tempV2._y + tempV1._y;
tempV2._z = tempV2._z + tempV1._z;
tempV3._x = tempV2._x + tempV1._x;
tempV3._y = tempV2._y + tempV1._y;
tempV5._x = tempV2._x;
tempV5._y = tempV2._y;
tempV3._z = tempV2._z + tempV1._z;
tempV5._z = tempV2._z;
tempV6._x = tempV3._x;
tempV6._y = tempV3._y;
tempV6._z = tempV3._z;
tempV1._x = tempV1._x - row1._x;
tempV1._y = tempV1._y - row1._y;
tempV1._z = tempV1._z - row1._z;
tempV4._x = tempV3._x - row1._x;
tempV4._y = tempV4._y - row1._y;
tempV4._z = tempV4._z - row1._z;
tempV5._x = tempV2._x - row1._x;
tempV5._y = tempV5._y - row1._y;
tempV5._z = tempV5._z - row1._z;
tempV6._x = tempV3._x - row1._x;
tempV6._y = tempV6._y - row1._y;
tempV6._z = tempV6._z - row1._z;
FVector modV1 = tempV1.fn5(sub);
FVector modV2 = tempV4.fn5(sub);
FVector modV3 = tempV5.fn5(sub);
FVector modV4 = tempV6.fn5(sub);
tempV1 = modV1;
tempV4 = modV2;
tempV5 = modV3;
tempV4 = modV4;
tempV2._x = tempV4._x - tempV1._x;
tempV2._y = tempV4._y - tempV1._y;
tempV2._z = tempV4._z - tempV1._z;
tempV4._x = tempV2._x;
tempV4._y = tempV2._y;
tempV2._x = tempV5._x - tempV1._x;
tempV4._z = tempV2._z;
tempV5._x = tempV2._x;
tempV2._y = tempV5._y - tempV1._y;
tempV5._y = tempV2._y;
tempV2._z = tempV5._z - tempV1._z;
tempV5._z = tempV2._z;
tempV2._x = tempV6._x - tempV1._x;
tempV2._y = tempV6._y - tempV1._y;
tempV2._z = tempV6._z - tempV1._z;
tempV6 = tempV2;
tempV4.normalize();
tempV5.normalize();
tempV6.normalize();
tempV1 += row1;
m1.set(tempV4, tempV5, tempV6);
_viewport.setOrientation(m1);
_viewport.setPosition(tempV1);
} else if (_matrixRow == 1) {
FVector tempV2;
DMatrix m1, m2, sub;
DVector mrow1, mrow2, mrow3;
DVector tempV1, diffV, multV, multV2, tempV3, tempV4, tempV5, tempV6, tempV7;
DVector tempV8, tempV9, tempV10, tempV11, tempV12;
DVector tempV13, tempV14, tempV15, tempV16;
DMatrix subX(0, _matrix._row1);
DMatrix subY(Y_AXIS, angles._y);
tempV1 = _matrix._row2 - _matrix._row1;
diffV = tempV1;
m1 = diffV.fn5();
m1 = m1.fn4(subX);
subX = m1.fn1();
subX = subX.fn4(subY);
FMatrix m3 = _viewport.getOrientation();
tempV2 = _viewport._position;
multV._x = m3._row1._x * 1000000.0;
multV._y = m3._row1._y * 1000000.0;
multV._z = m3._row1._z * 1000000.0;
tempV3._x = tempV2._x;
tempV3._y = tempV2._y;
tempV3._z = tempV2._z;
multV2._z = m3._row2._z * 1000000.0;
tempV1._x = multV._x + tempV3._x;
tempV1._y = multV._y + tempV3._y;
tempV1._z = multV._z + tempV3._z;
mrow3._z = 0.0;
mrow3._y = 0.0;
mrow3._x = 0.0;
multV2._x = m3._row2._x * 1000000.0;
multV2._y = m3._row2._y * 1000000.0;
mrow1 = tempV1;
multV = multV2 + tempV3;
mrow2 = multV;
tempV7._z = m3._row3._z * 1000000.0 + tempV3._z;
tempV7._y = m3._row3._y * 1000000.0 + tempV3._y;
tempV7._x = m3._row3._x * 1000000.0 + tempV3._x;
mrow3 = tempV8;
DVector *v = tempV3.fn1(tempV9, subX);
tempV3 = *v;
v = mrow1.fn1(tempV10, subX);
mrow1 = *v;
v = mrow2.fn1(tempV11, subX);
mrow2 = *v;
v = mrow3.fn1(tempV12, subX);
mrow3 = *v;
v = tempV3.fn1(tempV13, m1);
tempV3 = *v;
v = mrow1.fn1(tempV14, m1);
mrow1 = *v;
v = mrow2.fn1(tempV15, m1);
mrow2 = *v;
v = mrow3.fn1(tempV16, m1);
mrow3 = *v;
mrow1 -= tempV3;
mrow2 -= tempV3;
mrow3 -= tempV3;
mrow1.normalize();
mrow2.normalize();
mrow3.normalize();
tempV16 = tempV3;
m3.set(mrow1, mrow2, mrow3);
_viewport.setOrientation(m3);
_viewport.setPosition(tempV16);
}
}
AnovaTest::AnovaTest(mv_Method *mm, gsl_matrix *Y, gsl_matrix *X, gsl_matrix *isXvarIn):mmRef(mm), Yref(Y), Xref(X), inRef(isXvarIn)
{
unsigned int hid, aid;
unsigned int i, j, count;
nModels=inRef->size1, nParam=Xref->size2;
nRows=Yref->size1, nVars=Yref->size2;
// printf("initialize public variables: stats\n");
multstat=(double *)malloc((nModels-1)*sizeof(double));
Pmultstat = (double *)malloc((nModels-1)*sizeof(double));
for (j=0; j<nModels-1; j++) *(Pmultstat+j)=0.0;
dfDiff = (unsigned int *)malloc((nModels-1)*sizeof(unsigned int));
statj = gsl_matrix_alloc(nModels-1, nVars);
Pstatj = gsl_matrix_alloc(nModels-1, nVars);
gsl_matrix_set_zero(Pstatj);
bStatj = gsl_vector_alloc(nVars);
Hats = (mv_mat *)malloc(nModels*sizeof(mv_mat));
sortid = (gsl_permutation **)malloc((nModels-1)*sizeof(gsl_permutation *));
for (i=0; i<nModels; i++ ) {
// Hats[i]
Hats[i].mat=gsl_matrix_alloc(nRows, nRows);
Hats[i].SS=gsl_matrix_alloc(nVars, nVars);
Hats[i].R=gsl_matrix_alloc(nVars, nVars);
Hats[i].Res=gsl_matrix_alloc(nRows, nVars);
Hats[i].Y = gsl_matrix_alloc(nRows, nVars);
Hats[i].sd = gsl_vector_alloc(nVars);
count = 0;
for (j=0; j<nParam; j++){
count+=(unsigned int)gsl_matrix_get(inRef, i, j);
}
// printf("count=%d \n", count);
Hats[i].X = gsl_matrix_alloc(nRows, count);
Hats[i].Coef=gsl_matrix_alloc(count, nVars);
gsl_vector_view refi=gsl_matrix_row(inRef, i);
subX(Xref, &refi.vector, Hats[i].X);
calcSS(Yref, &(Hats[i]), mmRef);
// displaymatrix(Hats[i].SS, "SS");
}
for (i=1; i<nModels; i++) {
hid = i; aid = i-1;
if ( mmRef->resamp != CASEBOOT ) {
// fit = Y- resi
gsl_matrix_memcpy (Hats[i].Y, Yref);
gsl_matrix_sub (Hats[i].Y, Hats[i].Res);
}
gsl_vector_view statij = gsl_matrix_row(statj, aid);
testStatCalc(&(Hats[hid]), &(Hats[aid]), mmRef, TRUE, (multstat+aid), &statij.vector);
dfDiff[aid] = Hats[aid].X->size2-Hats[hid].X->size2;
// sortid
sortid[aid] = gsl_permutation_alloc(nVars);
gsl_sort_vector_index (sortid[aid], &statij.vector);
// rearrange sortid in descending order
gsl_permutation_reverse (sortid[aid]);
}
// initialize resampling indices
// getBootID(); done in R
bootID = NULL;
// Initialize GSL rnd environment variables
const gsl_rng_type *T;
gsl_rng_env_setup();
T = gsl_rng_default;
// an mt19937 generator with a seed of 0
rnd = gsl_rng_alloc(T);
if (mmRef->reprand!=TRUE){
struct timeval tv; // seed generation based on time
gettimeofday(&tv, 0);
unsigned long mySeed=tv.tv_sec + tv.tv_usec;
gsl_rng_set(rnd, mySeed); // reset seed
}
// printf("Anova test initialized.\n");
}