int fqAddNoiseE(float *aBlock, EFFECT *rEffect) {
udword i;
if (rEffect->fNoiseLev > 0.0)
for(i = rmin(rEffect->nFiltMinFreq, nBSize); i < rmin(rEffect->nFiltMaxFreq, nBSize); i++)
aBlock[i] += gaussian() * rEffect->fNoiseLev;
return OK;
}
static int fqIncEffect(float *aBlock, float *fVal, udword nDur, float *aBuf, sdword nSize, sdword *nPos, char aEffect) {
udword s;
sdword t;
if (aBlock == 0) {
if (nSize < FQ_SIZE) {
return ERR;
} else {
memset(aBuf, 0, nSize << 2);
*nPos = 0;
return OK;
}
}
if (nDur > 0) {
if (*nPos >= nSize)
*nPos = 0;
s = (udword)floor((float)nSize / (float)FQ_SIZE * FQ_SLICE);
t = *nPos - ((udword)floor((float)rmin(nDur, s) / FQ_SLICE) * FQ_SIZE);
if (t < 0)
t += nSize;
fqAdd(aBlock, &aBuf[t]);
memcpy(&aBuf[*nPos], aBlock, nBSize << 2);
switch (aEffect) {
case FQ_TIME_DELAY: fqScale(&aBuf[*nPos], *fVal); break;
case FQ_TIME_ACMODEL: fqEqualize(&aBuf[*nPos], fVal); break;
}
*nPos += FQ_SIZE;
}
return OK;
}
void CBaseAnimating::SetSequenceBox( void )
{
Vector mins, maxs;
// Get sequence bbox
if( ExtractBbox( pev->sequence, mins, maxs ) )
{
// expand box for rotation
// find min / max for rotations
float yaw = pev->angles.y * ( M_PI / 180.0 );
Vector xvector, yvector;
xvector.x = cos( yaw );
xvector.y = sin( yaw );
yvector.x = -sin( yaw );
yvector.y = cos( yaw );
Vector bounds[ 2 ];
bounds[ 0 ] = mins;
bounds[ 1 ] = maxs;
Vector rmin( 9999, 9999, 9999 );
Vector rmax( -9999, -9999, -9999 );
Vector base, transformed;
for( int i = 0; i <= 1; i++ )
{
base.x = bounds[ i ].x;
for( int j = 0; j <= 1; j++ )
{
base.y = bounds[ j ].y;
for( int k = 0; k <= 1; k++ )
{
base.z = bounds[ k ].z;
// transform the point
transformed.x = xvector.x*base.x + yvector.x*base.y;
transformed.y = xvector.y*base.x + yvector.y*base.y;
transformed.z = base.z;
if( transformed.x < rmin.x )
rmin.x = transformed.x;
if( transformed.x > rmax.x )
rmax.x = transformed.x;
if( transformed.y < rmin.y )
rmin.y = transformed.y;
if( transformed.y > rmax.y )
rmax.y = transformed.y;
if( transformed.z < rmin.z )
rmin.z = transformed.z;
if( transformed.z > rmax.z )
rmax.z = transformed.z;
}
}
}
rmin.z = 0;
rmax.z = rmin.z + 1;
SetSize( rmin, rmax );
}
}
void find(int i, int k){
if(k==1){
st[i][k]=stack[i];
return;
}
if(!st[i][k-1]) find(i,k-1);
if(!st[i+(1<<(k-1))][k-1]) find(i+(1<<(k-1)),k-1);
st[i][k]=rmin(st[i][k-1],st[i+(1<<(k-1))][k-1]);
}
void PrintDetectorGeometry() {
gSystem->Load("libITSUpgradeBase");
gSystem->Load("libITSUpgradeSim");
TArrayD rmin(0);
TArrayD rmax(0);
GetDetectorRadii(&rmin,&rmax);
for (Int_t i=0; i<rmin.GetSize(); i++) {
cout<<i<<": (rmin,rmax)=("<<rmin.At(i)<<","<<rmax.At(i)<<")cm"<<endl;
}
}
Geom::OptRect font_instance::BBox(int glyph_id)
{
int no = -1;
if ( id_to_no.find(glyph_id) == id_to_no.end() ) {
LoadGlyph(glyph_id);
if ( id_to_no.find(glyph_id) == id_to_no.end() ) {
// didn't load
} else {
no = id_to_no[glyph_id];
}
} else {
no = id_to_no[glyph_id];
}
if ( no < 0 ) {
return Geom::OptRect();
} else {
Geom::Point rmin(glyphs[no].bbox[0],glyphs[no].bbox[1]);
Geom::Point rmax(glyphs[no].bbox[2],glyphs[no].bbox[3]);
return Geom::Rect(rmin, rmax);
}
}
int fqLimitE(float *aBlock, EFFECT *rEffect) {
udword i;
if (rEffect->fLimitLev != 1.0) {
if (rEffect->fLimitLev == 0.0) {
memset(&aBlock[rmin(rEffect->nFiltMinFreq, nBSize)], 0, (rmin(rEffect->nFiltMaxFreq, nBSize) - rmin(rEffect->nFiltMinFreq, nBSize)) << 2);
} else {
for (i = rmin(rEffect->nFiltMinFreq, nBSize); i < rmin(rEffect->nFiltMaxFreq, nBSize); i++) {
if ((aBlock[i] > 0.0) && (aBlock[i] > rEffect->fLimitLev * 32767.0))
aBlock[i] = rEffect->fLimitLev * 32767.0;
if ((aBlock[i] < 0.0) && (aBlock[i] < rEffect->fLimitLev * -32767.0))
aBlock[i] = rEffect->fLimitLev * -32767.0;
}
if (1.0 / rEffect->fLimitLev * 3.0 < 1.0)
for (i = rmin(rEffect->nFiltMinFreq, nBSize); i < rmin(rEffect->nFiltMaxFreq, nBSize); i++)
if (aBlock[i] != 0.0)
aBlock[i] *= (1.0 / rEffect->fLimitLev * 3.0);
}
}
return OK;
}
int rmq(int l, int r){
int k=int(log((float)r-l+1)/log(2.0));
if(!st[l][k]) find(l,k);
if(!st[r-(1<<k)+1][k]) find(r-(1<<k)+1,k);
return rmin(st[l][k], st[r-(1<<k)+1][k]);
}
int main(int argc, char * argv[])
{
simplmat <double> data;
simplmat <double> dout;
SpectralAnalysis sa;
// Do 199 Simulations and takes the 5 lowest and 5 highest values
// to make the confidence envelopes. If the calculated value is
// between these highest or lowest values it is significative at 5% level
//
int numSimul=199,numExtreme=5,windowPos=0,numExtremeT=5;
char randz;
double probConf=0.05;
double probConfT=0.05;
double probOrig=0.05;
int bonfCorr=0,signif=0;
// OJO Falta agregar en parametros
int reaPer=0;
string fType="BI";
if( argc <3 )
{
cerr << "Usage: rnzSpectral inputFile.sed outFile fileType winPos{0,1,2,3} [R/A] [prob] [bonfCorr{0,1}] [numSimulations]" << endl;
exit(1);
}
if( argc >= 4)
{
fType = argv[3];
windowPos = atoi(argv[4]);
randz = toupper(argv[5][0]); // R=Randomizations, A=Asintotic chisqr.
if( windowPos > 3 || windowPos <0 )
{
cerr << "Out of range: 3 > windowPos > 0" << endl;
exit(1);
}
}
if( randz=='R' )
{
if( argc == 9)
{
probOrig = atof(argv[6]);
bonfCorr = atoi(argv[7]);
numSimul = atoi(argv[8]);
}
else
{
cerr << "Invalid number of arguments" << endl;
exit(1);
}
}
else
{
if( argc == 8 )
{
probOrig = atof(argv[6]);
bonfCorr = atoi(argv[7]);
}
else
{
cerr << "Invalid number of arguments" << endl;
exit(1);
}
}
RWFile file;
string fName = argv[1];
string outFName = argv[2];
if( fName.find(".sed")!=string::npos )
{
if(!file.ReadSeed(fName.c_str(), data, fType.c_str() ))
exit(1);
}
else if( fName.find(".img")!=string::npos )
{
if(!file.ReadIdrisi(fName.c_str(), data))
exit(1);
}
else
{
cerr << "File type not supported: " << fName << endl;
exit(1);
}
sa.Transpose(data); // Los datos leidos estan en formato (x,y) y las funciones
// tienen (y,x) o sea (row,col)
int rows=data.getRows();
int cols=data.getCols();
double var;
int s,l;
simplmat <double> origData(data);
sa.SetPow2(data,origData,windowPos);
int origRows = rows;
int origCols = cols;
rows=data.getRows();
cols=data.getCols();
var = sa.Spec2D(data,dout); // Calculates the periodogram usando FFT
simplmat<double> rper; // Rearranged periodogram
simplmat<double> polper; // Polar
sa.Spekout(rows,cols,dout,rper); // Rearranges the periodogram
ofstream fOut;
if(reaPer)
{
string rperOut="r."+outFName;
fOut.open(rperOut.c_str());
fOut << rper.getCols() << "\t" << rper.getRows() << endl;
fOut << "Rearranged periodogram" << endl;
for(l=0;l<rper.getRows();l++)
{
for(s=0;s<rper.getCols();s++)
fOut.form("%10.6f",rper(l,s)) << "\t";
fOut << endl;
}
fOut.close();
}
sa.Polar2D(rows,cols,rper,polper); // Calculates the Polar Spectrum
// OJO modifica rper!!!!!!!!!!!!
int d = int(0.5*sqrt(rows*rows + cols*cols)+1);
// Outputs the rearranged periodogram
//
//string rperOut("rper.");
//rperOut+=outFName;
//if(!file.WriteSeed(rperOut.c_str(), rper))
// exit(1);
fOut.open(outFName.c_str());
if( bonfCorr )
{
probConf=probOrig/d;
probConfT=probOrig/18;
}
else
{
probConf=probOrig;
probConfT=probOrig;
}
numExtreme = 1+probConf*numSimul/2;
if( numExtreme <=1 )
{
cerr << "numExtreme <= 1" << endl;
exit(1);
}
numExtremeT = 1+probConfT*numSimul/2;
if( numExtremeT <=1 )
{
cerr << "numExtremeT <= 1" << endl;
exit(1);
}
Randomizations rz;
simplmat<double> thetamin;
simplmat<double> thetamax;
simplmat<double> rmin;
simplmat<double> rmax;
simplmat<double> rpol; // Polar Spectrum for randomizations
thetamin.resize(18,numExtremeT,1000.0);
thetamax.resize(18,numExtremeT,0.0);
rmin.resize(d,numExtreme,1000.0);
rmax.resize(d,numExtreme,0.0);
for(s=0; s<numSimul; s++)
{
rz.Randomize(origData);
sa.SetPow2(data,origData);
sa.Spec2D(data,dout);
sa.Spekout(rows,cols,dout,rper);
sa.Polar2D(rows,cols,rper,rpol);
for(l=0;l<d;l++)
{
sa.spectMax(rpol(l,0),rmax,l,numExtreme);
sa.spectMin(rpol(l,0),rmin,l,numExtreme);
// cout << setw(2) << l+1 << "\t";
// cout.form("%8.5f", rpol(l,0)) << endl;
}
for(l=0;l<18;l++)
{
sa.spectMax(rpol(l,2),thetamax,l,numExtremeT);
sa.spectMin(rpol(l,2),thetamin,l,numExtremeT);
// cout << "\t\t" << setw(4) << l*10 << "\t";
// cout.form("%8.5f", rpol(l,2)) << endl;
}
}
fOut << "R Spectrum " << "\t" << outFName << endl;
fOut << "Randomizations: "<< "\t" << numSimul << "\t" << numExtreme << "\t" << probConf << endl;
fOut << "Data dim:" << "\t" << origRows << "\t" << origCols << endl;
fOut << "Window dim:" << "\t" << rows << "\t" << cols << "\tPosition:\t" << windowPos << endl;
for(l=0;l<d;l++)
{
signif = 0;
fOut << setw(2) << l+1 << "\t";
fOut.form("%8.5f", polper(l,0)) << "\t";
fOut.form("%8.5f", rmin(l,0)) << "\t";
fOut.form("%8.5f", rmax(l,0)) << "\t";
fOut.form("%8.5f", polper(l,1)) << "\t";
if( polper(l,0)<rmin(l,0) )
signif = -1;
if( polper(l,0)>rmax(l,0) )
signif = 1;
fOut << signif << endl;
}
fOut << "\nTheta Spectrum" << endl;
fOut << "Randomizations: "<< "\t" << numSimul << "\t" << numExtremeT << "\t" << probConfT << endl;
for(l=0;l<18;l++)
{
signif = 0;
fOut << setw(4) << l*10 << "\t";
fOut.form("%8.5f", polper(l,2)) << "\t";
fOut.form("%8.5f", thetamin(l,0)) << "\t";
fOut.form("%8.5f", thetamax(l,0)) << "\t";
fOut.form("%8.5f", polper(l,3)) << "\t";
if( polper(l,2)<thetamin(l,0) )
signif = -1;
if( polper(l,2)>thetamax(l,0) )
signif = 1;
fOut << signif << endl;
}
return 0;
}
void ViewSimple2D::redraw( bool paused )
{
vec2f ctr;
ctr = vec2f( 300, 300 );
// 2d part
glMatrixMode( GL_PROJECTION );
glLoadIdentity();
gluOrtho2D( 0, 800, 0, 600 ) ;
glMatrixMode( GL_MODELVIEW );
glLoadIdentity();
// Draw pumpkins in a ring
int i, j, k;
float t, sz=60;
int x, y;
Pumpkin p;
// the "board"
glDisable( GL_TEXTURE_2D );
glLineWidth( 3.0 );
vec4f fill = vec4f( 0.5f, 0.7f, 0.6f, 0.5f ),
line = vec4f( 0.8f, 0.3f, 0.8f, 1.0f ),
fill_dest = vec4f( 0.9f, 0.4f, 0.5f, 0.5f ),
line_dest = vec4f( 0.2f, 1.0f, 0.2f, 1.0f );
// The center "storage ring"
drawCircle( ctr, 50, SHAPE_LINE_AND_FILL,
fill, line, 100 );
// The outer ring
drawCircle( ctr, 250, SHAPE_LINE,
fill, line, 100 );
gfEnableFont( m_fontId, 25 );
// a bunch of dots for the board
vec2f freeze_pos, freeze_dir;
vec2f queue_pos, queue_dir;
vec2f station_pos;
vec4f color, linecolor;
char *label = NULL;
for (i = 0; i < MACHINE_SLOTS; i++) {
t = (2.0*M_PI)/MACHINE_SLOTS * i;
x = ctr[0] + cos(t)*250.0;
y = ctr[1] - sin(t)*250.0;
label = NULL;
if ((i >= DEST_SLOT_NDX) && (i < DEST_SLOT_NDX+5)) {
color = fill_dest;
linecolor = line_dest;
if (i==DEST_SLOT_NDX+2) label = "Destination";
} else if (i==FREEZER_NDX) {
color = vec4f( 0.0f, 1.0f, 1.0f, 0.6f );
linecolor = vec4f( 1.0f, 1.0f, 1.0f, 1.0f );
label = "Freeze";
// draw freezer slots
freeze_dir = vec2f( cos(t), -sin(t) );
freeze_pos = vec2f( x, y ) - freeze_dir*sz;
for (int j=0; j < FREEZER_CAPACITY; j++) {
drawCircle( freeze_pos - (freeze_dir*30*j),
15, SHAPE_LINE_AND_FILL,
vec4f( 1.0, 1.0, 1.0, 1.0 ),
vec4f( 0.0, 1.0, 1.0, 1.0), 12 );
}
} else if (i==PRODUCTION_NDX) {
color = fill;
linecolor = line;
// draw production slots
queue_dir = vec2f( cos(t), -sin(t) );
queue_pos = vec2f( x, y ) + queue_dir*sz*0.6f;
queue_dir = vec2f( 0.0, 1.0 ); // vertical queue
for (int j=0; j < PRODUCTION_CAPACITY; j++) {
drawCircle( queue_pos + (queue_dir*30*j),
15, SHAPE_LINE_AND_FILL,
vec4f( 1.0, 1.0, 1.0, 1.0 ),
vec4f( 0.5, 0.5, 0.5, 1.0), 12 );
}
} else if (i==TORCHY_NDX) {
color = vec4f( 1.0f, 0.0f, 0.0f, 0.6f );
linecolor = vec4f( 1.0f, 1.0f, 0.0f, 1.0f );
label = "Torchy";
} else {
color = fill;
linecolor = line;
}
// draw swap lines
if ((i==SWAP_NDX1)||(i==SWAP_NDX2)||(i==SWAP_NDX3)) {
glColor4f( linecolor[0], linecolor[1], linecolor[2], linecolor[3] );
glBegin( GL_LINES );
glVertex3f( ctr[0], ctr[1], 0 );
glVertex3f( x, y, 0 );
glEnd();
label = "Swap";
}
// draw circle
drawCircle( vec2f( x, y ), 25, SHAPE_LINE_AND_FILL,
color, linecolor, 8 );
// draw current station
if (m_station==i) {
station_pos = vec2f(x, y );
}
// draw label
if (label) {
glColor4f( linecolor[0], linecolor[1], linecolor[2], linecolor[3] );
gfBeginText();
float lx = x - (gfGetStringWidth( label )/2.0);
glTranslated( (lx<5.0)?5.0:lx, y, 0.0 );
gfDrawString( label );
gfEndText();
glDisable( GL_TEXTURE_2D );
}
}
// draw combos
color = fill;
linecolor = line;
vec2f rmin(610,545), rmax(795, 595);
for (i=0; i < m_game->getNumCombos(); i++)
{
Combo c = m_game->getCombo( i );
glDisable( GL_TEXTURE_2D );
drawRect( rmin, rmax, SHAPE_LINE_AND_FILL,
color, vec4f( 0.0, 0.9, 0.9, 1.0) );
gfEnableFont( m_fontId, 15 );
gfBeginText();
glTranslated( (rmin[0] + (rmax[0]-rmin[0])/2.0) -
gfGetStringWidth( c.m_name.c_str() )/2.0 , rmax[1]-12, 0.0 );
gfDrawString( c.m_name.c_str() );
gfEndText();
// draw combo Value
gfEnableFont( m_fontId, 25 );
gfBeginText();
glTranslated( rmax[0]-30 , rmax[1]-35, 0.0 );
gfDrawStringFmt( "%d", c.m_value );
gfEndText();
// draw combo pumpkins
glBindTexture( GL_TEXTURE_2D, m_texPumpkinIcons );
vec2f px(rmin[0]+5, rmin[1]+5);
for (j=0; j < c.m_groups.size(); j++) {
p = Pumpkin();
p.m_type = c.m_groups[j].m_item;
if ( (p.m_type == ANY_PUMPKIN) || (p.m_type == ANY_ITEM) ) {
glColor3f( m_groupColor[j][0], m_groupColor[j][1], m_groupColor[j][2] );
} else {
glColor3f( 1.0, 1.0, 1.0 );
}
for (k=0; k < c.m_groups[j].m_count; k++ ) {
drawPumpkin( px, p, sz*0.5, false );
px[0] = px[0] + sz*0.5;
}
}
rmin[1] = rmin[1] - 55;
rmax[1] = rmax[1] - 55;
}
gfEnableFont( m_fontId, 25 );
if (!paused) {
// Draw pumpkins in the machine
glEnable( GL_TEXTURE_2D );
glBindTexture( GL_TEXTURE_2D, m_texPumpkinIcons );
glColor3f( 1.0, 1.0, 1.0 );
vec2f v;
for (i = 0; i < MACHINE_SLOTS; i++) {
p = m_game->getPumpkin( i );
if (p.m_type == EMPTY) continue;
v = calcPosFromNdx( i );
x = v[0] - (sz/2);
y = v[1] - (sz/2);
drawPumpkin( vec2f( x, y ), p, sz );
}
// draw frozen pumpkins
for ( j=0; j < m_game->getFreezerUsage(); j++) {
p = m_game->getFrozenFood( j );
// shouldn't be empty, but...
if (p.m_type != EMPTY) {
drawPumpkin( (freeze_pos+ - (freeze_dir*30*j)) - vec2f(sz*0.25,sz*0.25), p, sz*0.5 );
}
}
// draw queued pumpkins
for ( j=0; j < m_game->getProdQueueSize(); j++) {
p = m_game->getQueuedPumpkin( j );
// shouldn't be empty, but...
if (p.m_type != EMPTY) {
drawPumpkin( (queue_pos+ (queue_dir*30*j)) - vec2f(sz*0.25,sz*0.25), p, sz*0.5 );
}
}
// draw center pumpkin
p = m_game->getCenterPumpkin();
if (p.m_type != EMPTY) {
drawPumpkin( vec2f( ctr[0]-(sz*1.5/2), ctr[1]-(sz*1.5/2)), p, sz*1.5 );
}
}
// Draw last combo acheived
if (m_lastComboAge < COMBO_DISPLAY_TIME) {
char buff[200];
t = 1.0 - (m_lastComboAge/COMBO_DISPLAY_TIME);
gfEnableFont( m_fontId, 25 );
gfBeginText();
sprintf( buff, "%d - %s - %d", m_lastCombo.m_value,
m_lastCombo.m_name.c_str(),
m_lastCombo.m_value );
glColor3f( 1.0, t, t );
glTranslated( ctr[0] - gfGetStringWidth( buff )/2,
ctr[1]+50-(50.0*t)+j*5, 0.0 );
gfDrawString( buff );
gfEndText();
}
glDisable( GL_TEXTURE_2D );
// draw cursor
drawCircle( station_pos, 30, SHAPE_LINE,
color, vec4f( 0.0, 1.0, 1.0, 1.0), 8 );
drawCircle( station_pos, 35, SHAPE_LINE,
color, vec4f( 0.0f, 0.8f, 0.8f, 1.0f), 8 );
// Draw animated pumpkins
if (!paused) {
glEnable( GL_TEXTURE_2D );
glBindTexture( GL_TEXTURE_2D, m_texPumpkinIcons );
PumpkinAnim pa;
for (i = 0; i < m_panim.size(); i++) {
pa = m_panim[i];
glPushMatrix();
glTranslated( pa.m_pos[0] - sz/2, pa.m_pos[1]-sz/2, 0.0 );
drawPumpkin( vec2f( 0.0, 0.0 ), pa, sz );
glPopMatrix();
}
}
// draw particles
drawParts();
}
void UnplacedTorus::Print(std::ostream &os) const {
os << "UnplacedTorus {" << rmin() << ", " << rmax() << ", " << rtor()
<< ", " << sphi() << ", " << dphi();
}
void CountTrackableMCs(TH1F *hAllMC, Bool_t onlyPrims,Bool_t onlyPion) {
gSystem->Load("libITSUpgradeBase");
gSystem->Load("libITSUpgradeSim");
// open run loader and load gAlice, kinematics and header
AliRunLoader* runLoader = AliRunLoader::Open("galice.root");
if (!runLoader) {
Error("Check kine", "getting run loader from file %s failed",
"galice.root");
return;
}
runLoader->LoadHeader();
runLoader->LoadKinematics();
runLoader->LoadTrackRefs();
AliLoader *dl = runLoader->GetDetectorLoader("ITS");
//Trackf
TTree *trackRefTree = 0x0;
TClonesArray *trackRef = new TClonesArray("AliTrackReference",1000);
// TH1F *hRef = new TH1F("","",100,0,100);
TH1F *hR = new TH1F("","",100,0,100);
if (hAllMC==0) hAllMC = new TH1F("","",100,0.1,2);
Float_t ptmin = hAllMC->GetBinCenter(1)-hAllMC->GetBinWidth(1)/2;
Float_t ptmax = hAllMC->GetBinCenter(hAllMC->GetNbinsX())+hAllMC->GetBinWidth(hAllMC->GetNbinsX())/2;
// Int_t nAllMC = 0;
// Detector geometry
TArrayD rmin(0); TArrayD rmax(0);
GetDetectorRadii(&rmin,&rmax);
TArrayI nLaySigs(rmin.GetSize());
printf("Counting trackable MC tracks ...\n");
for(Int_t iEv =0; iEv<runLoader->GetNumberOfEvents(); iEv++){
Int_t nTrackableTracks = 0;
runLoader->GetEvent(iEv);
AliStack* stack = runLoader->Stack();
printf("+++ event %i (of %d) +++++++++++++++++++++++ # total MCtracks: %d \n",iEv,runLoader->GetNumberOfEvents()-1,stack->GetNtrack());
trackRefTree=runLoader->TreeTR();
TBranch *br = trackRefTree->GetBranch("TrackReferences");
if(!br) {
printf("no TR branch available , exiting \n");
return;
}
br->SetAddress(&trackRef);
// init the trackRef tree
trackRefTree=runLoader->TreeTR();
trackRefTree->SetBranchAddress("TrackReferences",&trackRef);
// Count trackable MC tracks
for (Int_t iMC=0; iMC<stack->GetNtrack(); iMC++) {
TParticle* particle = stack->Particle(iMC);
if (TMath::Abs(particle->Eta())>etaCut) continue;
if (onlyPrims && !stack->IsPhysicalPrimary(iMC)) continue;
if (onlyPion && TMath::Abs(particle->GetPdgCode())!=211) continue;
Bool_t isTrackable = 0;
nLaySigs.Reset(0);
trackRefTree->GetEntry(stack->TreeKEntry(iMC));
Int_t nref=trackRef->GetEntriesFast();
for(Int_t iref =0; iref<nref; iref++){
AliTrackReference *trR = (AliTrackReference*)trackRef->At(iref);
if(!trR) continue;
if(trR->DetectorId()!=AliTrackReference::kITS) continue;
Float_t radPos = trR->R();
hR->Fill(radPos);
for (Int_t il=0; il<rmin.GetSize();il++) {
if (radPos>=rmin.At(il)-0.1 && radPos<=rmax.At(il)+0.1) {
// cout<<" in Layer "<<il<<" "<<radPos;
nLaySigs.AddAt(1.,il);
// cout<<" "<<nLaySigs.At(il)<<endl;
}
}
}
if (nLaySigs.GetSum()>=3) {
isTrackable =1;
// cout<<nLaySigs.GetSum()<<endl;
}
if (isTrackable) {
Double_t ptMC = particle->Pt();
// Double_t etaMC = particle->Eta();
// if (ptMC>ptmin&&ptMC<ptmax) {nTrackableTracks++;hAllMC->Fill(ptMC);}
if (ptMC>ptmin) {nTrackableTracks++;hAllMC->Fill(ptMC);}
}
} // entries tracks MC
printf(" -> trackable MC tracks: %d (%d)\n",nTrackableTracks,hAllMC->GetEntries());
}//entries Events
hR->DrawCopy();
hAllMC->DrawCopy();
runLoader->UnloadHeader();
runLoader->UnloadKinematics();
delete runLoader;
}
main (int argc, char *argv[]) {
int i, j, **seqs, **nall, ord=1, ns, **pij, lkf=0, npt=0, pnew=0, anc=0;
int tcat=1, rcat=0, verb=1, miss=0, *flocs;
int sw_flag=0, moment_flag=0, rmin_flag=0, sim_flag=0, test_flag=0;
char fname[MAXNAME+1], **seqnames;
long seed=-setseed();
extern int sizeofpset;
double *locs;
double **lkmat, *lkres;
FILE *ifp=NULL, *ifp2=NULL, *ifp3=NULL, *tfp;
struct site_type **pset;
struct data_sum *data;
int ask_questions = 1;
char *in_str;
print_help(argc, argv);
idum = &seed;
data = malloc((size_t) sizeof(struct data_sum));
data->exact = 0;
strcpy(data->prefix, "");
for(i = 0; i < argc; i++)
{
if(*argv[i] == '-')
{
in_str = argv[i];
ask_questions = 0;
if(strcmp(in_str, "-seq") == 0) ifp = fopen(argv[i+1], "r");
if(strcmp(in_str, "-loc") == 0) ifp2 = fopen(argv[i+1], "r");
if(strcmp(in_str, "-lk") == 0)
{
lkf = 1;
ifp3 = fopen(argv[i+1], "r");
}
if(strcmp(in_str, "-exact") == 0) data->exact = 1;
if(strcmp(in_str, "-concise") == 0) verb=0;
if(strcmp(in_str, "-window") == 0) sw_flag=1;
if(strcmp(in_str, "-moment") == 0) moment_flag=1;
if(strcmp(in_str, "-simulate") == 0) sim_flag=1;
if(strcmp(in_str, "-rmin_flag") == 0) rmin_flag=2;
if(strcmp(in_str, "-test") == 0) test_flag=1;
if(strcmp(in_str, "-prefix") == 0) strcpy(data->prefix, argv[i+1]);
}
}
if (ifp == NULL)
{
printf("\nCould not find seqs file in command line.\n");
printf("\nInput filename for seqs:\n");
scanf("%s", &fname);
ifp = fopen(fname, "r");
}
if (ifp == NULL) nrerror("Error in opening sequence file");
fscanf(ifp,"%i%i%i", &data->nseq, &data->lseq, &data->hd);
if ((data->nseq < 2) || (data->lseq < 2)) {printf("\n\nInsufficient data for analysis (n > 1, L > 1) \n\n"); exit(1);}
if (data->nseq > SEQ_MAX) {printf("\n\nMore than max no. sequences: Using first %i for analysis\n\n", SEQ_MAX); data->nseq=SEQ_MAX;}
printf("\nAnalysing %i (n=%i) sequences of length %i seg sites\n", data->nseq, data->hd, data->lseq);
seqs = imatrix(1, data->nseq, 1, data->lseq);
seqnames = cmatrix(1, data->nseq+11, 1, MAXNAME+11);
if (read_fasta(seqs, ifp, data->nseq, data->lseq, seqnames)) printf("\nSequences read succesfully\n");
fclose(ifp);
nall = imatrix(1, data->lseq, 1, 6);
allele_count(seqs, data->nseq, data->lseq, nall,1, data->hd, data->prefix);
/*Store lnfac values in array for speed of computation*/
lnfac_array = (double *) malloc((size_t) ((int) (data->nseq+2)*(data->hd))*sizeof(double));
lnfac_array[0]=lnfac_array[1]=0;
for (j=2;j<=((int) data->nseq*(data->hd));j++) lnfac_array[j]=(double) lnfac_array[j-1]+log(j);
/*Open file with location of seg sites and read in data*/
if (ifp2 == NULL)
{
printf("\nCould not find locs file in command line.\n");
printf("\nInput name of file containing location of seg sites\n\n");
scanf("%s", &fname);
ifp2 = fopen(fname, "r");
}
if (ifp2 == NULL) nrerror("Cannot open loc file");
fscanf(ifp2, "%i %lf %c", &ns, &data->tlseq, &data->lc);
if (ns != data->lseq) nrerror("Lseq and Locs disagree");
if ((data->lc != 'C')&&(data->lc != 'L')) nrerror("Must input linear(L)/conversion(C)");
if (data->lc == 'C') {
data->avc=0;
while (data->avc <= 0) {
printf("\n\nInput average tract length for conversion model: ");scanf("%lf", &(data->avc));
}
}
locs = dvector(1, data->lseq);
flocs = ivector(1, data->lseq); /*Array to use when simulating data*/
for (i=1; i<=data->lseq; i++) {
fscanf(ifp2, "%lf", &locs[i]);
if ((locs[i]==0)||(locs[i]>data->tlseq)) {printf("\n\nError in Loc file\n\n%lf\n", data->tlseq); exit(1);}
if (i>1 && locs[i]<=locs[i-1]) nrerror("Error in locs file: SNPs must be montonically increasing");
}
printf("\nLocation of seg sites\n\n");
for (i=1; i<=data->lseq; i++) printf("%3i %4.2lf\n", i, locs[i]);
fclose(ifp2);
/*Read in likelihood file where needed*/
if (ask_questions)
{
printf("\n\nUse existing likelihood file? (yes=1, no=0):");
scanf("%i", &lkf); /*lkf is a flag: 1 means use existing likelihood file as starting point*/
if (lkf)
{
printf("\n\nInput name of likelihood file: ");
scanf("%s", &fname);
ifp3 = fopen(fname, "r");
}
else
data->exact=0;
if (lkf == 1)
{
printf("\n\nIs likelihood file an exact match to data?(no=0/yes=1): ");
scanf("%i", &data->exact);
}
}
if (lkf && !ifp3) nrerror("Cannot open likelihood file");
if (!lkf && data->hd==2) nrerror("For diploid data need complete lookup table for sequences");
/*Store pair-types in pij matrix - classify in pair_spectrum routine*/
data->w = data->lseq; /*Note for this program use all data - pair_int restricts to a smaller window*/
pij = imatrix((int) 1,(int) data->lseq,(int) 1,(int) data->w);
for (i=1;i<=data->lseq;i++) for (j=1;j<=data->w;j++) pij[i][j]=0;
pset = init_pset(pset, lkf, ifp3, &npt, data); /*Reads in type configurations from likelihood file*/
printf("\n\n*** Calculating distribution of pair types ***\n\n");
pset = pair_spectrum(seqs, data, nall, pset, &npt, &pnew, &miss, anc, pij);
printf("\n\n *** Completed classification of pair types ***\n\n");
if (data->exact && (pnew || miss)) nrerror("Lookup table is not exact for sequences\n(possibly generated by interval)");
printf("\n\nOld = %i: New = %i: Missing = %i\n\n", npt,pnew,miss);
data->ptt = (int) npt+pnew+miss; /*npt is number from likelihood file, pnew is number new with no missing data, miss is # new with missing data*/
if (verb) {
strcpy(fname, data->prefix);
tfp = fopen(strcat(fname, "type_table.txt"), "w");
if (!tfp) nrerror("Cannot open type file");
type_print(pij, data->lseq, data->w,tfp);
fclose(tfp);
}
if (verb) print_pairs(stdout, pset, npt+pnew, data->hd, data->nseq);
/*Need a complete set for missing data or diploid data - check this*/
if (!data->exact && (data->hd ==2 || miss)) {
printf("\n\nMissing data or diploid: checking that likelihood table is exhaustive\n\n");
check_exhaustive(pset,npt,(data->nseq)*((int) data->hd));
}
/*Read parameters and likelihoods from likelihood file - where appropriate*/
if (lkf) {
read_pars(ifp3, &tcat, &data->th, &data->rcat, &data->rmax);
lkmat = dmatrix(1,npt+pnew+miss,1,data->rcat);
if (lkf) read_lk(ifp3, lkmat, npt, tcat, data->rcat);
}
/*If haploid, but novel types, need to calculate new likelihoods and input parameter values*/
if (data->hd ==1 && pnew) { /*Note can have pnew for diploid data, but this has been checked for already*/
if (!lkf) {
data->th=data->rmax=-1.0; data->rcat=0;
printf("\n\nInput theta per site (suggest Watterson estimate of %.5lf):",(double) data->lseq/(watterson(data->nseq*data->hd)*data->tlseq));
while (data->th<0.0) scanf("%lf", &data->th);
printf("\n\nMax 4Ner for grid (suggest 100):");
while(data->rmax<0.0) scanf("%lf", &data->rmax);
printf("\n\nNumber of points on grid (suggest 101, min=2):");
while(data->rcat<2) scanf("%i", &data->rcat);
lkmat = dmatrix(1,npt+pnew+miss,1,data->rcat);
}
lk_est(pset,npt,pnew,lkmat,data->th,data->rcat,data->rmax);
data->exact=1;
}
/*Sum over missing data or resolve genotypes and sum over missing data+configurations*/
else if (miss && data->hd==1) {
printf("\n\n*** Calculating likelihoods for missing data ***\n\n");
for (i=1;i<=miss;i++) {
lk_miss(pset[npt+i],lkmat[npt+i],lkmat,data);
printf("\rType %i", i);
}
printf(" ...Done!\n\n");
}
/*Sum over resolutions for diploid data*/
else if (data->hd==2 && !data->exact) {
printf("\n\n*** Resolving diploid data: %i ***\n\n",pnew+miss);
lkres = dvector(1,data->rcat);
for (i=1;i<=pnew+miss;i++) {
lk_resolve(lkres,pset[npt+i],lkmat[npt+i],lkmat,data);
printf("\rType %i", i);
}
free_dvector(lkres,1,data->rcat);
printf(" ...Done!\n\n");
}
/*If new likelihood generated can output likelihood file for future analyses*/
if (verb) print_lks(pset, data, npt+pnew+miss, lkmat);
/*Basic analysis - estimation of 4Ner asuming constant rate*/
data->rme=data->rmax; data->rce=data->rcat;
if (1) {
printf("\n\nDo you wish to change grid over which to estimate likelihoods for (default = %i points, 4Ner 0 - %.1lf) (1/0) :",data->rcat,data->rmax);
scanf("%i", &lkf);
if (lkf) {
data->rme=-10; data->rce=0;
printf("\n\nMax 4Ner for estimation : ");
while (data->rme < 0.0) scanf("%lf", &data->rme);
printf("\n\nNumber of classes to estimate for: ");
while (data->rce < 1) scanf("%i", &data->rce);
}
}
data->lksurf = dmatrix(1,data->rce,1,2);
lk_surf(pset, pij, data, lkmat, data->th, locs, 1);
/*Print marginal likelihood ratio test statistics for each pair of sites*/
printf("\n\nCalculating fits\n\n");
fit_pwlk(data,pij,locs,lkmat,verb);
/*Sliding windows version*/
if (1) {
printf("\n\nDo you wish to carry out a sliding windows analysis? (yes=1/no=0):");
scanf("%i", &sw_flag);
}
if (sw_flag) lk_win(pset,pij,data,lkmat,locs,nall);
/*Nonparametric estimation of recombination rate*/
if (1) {
printf("\n\nPrint out table of Rmin values?\n(0=No, 1=Total only, 2=Full table):");
scanf("%i", &rmin_flag);
}
if (rmin_flag) {
rmin(data, pset, pij, locs, lkf-1);
printf("\n\nLower bound on Rmin = %i\n\n",data->rmin);
}
/*Estimate 4Ner by Wakeley 1997 method*/
if (1) {
printf("\n\nEstimate 4Ner by moment method? (yes=1, no=0)");
scanf("%i", &moment_flag);
}
if (moment_flag) wakeley_est(data, seqs, locs);
/*Recombination tests - only available for haploid data!*/
if (data->hd==1) {
if (1) {
printf("\n\nDo you wish to test for recombination? (yes=1, no=0): ");
scanf("%i", &test_flag);
}
if (test_flag) {
rec_test(data, pij, locs, lkmat, pset, npt+pnew+miss);
}
}
/*Conditional simulation - only available for haploid data with a complete lk file*/
if (data->hd==1 && !(data->exact)) {
if (1) {
printf("\n\nDo you wish to test constant-rate model and estimate sampling distribution by simulation? (yes=1/no=0): ");
scanf("%i", &test_flag);
}
if (test_flag) {
freq_min(locs, flocs, nall, data);
printf("\n\nHow many simulations? ");
scanf("%i", &lkf);
snp_sim(locs, flocs, pset, lkmat, lkf, data);
}
}
free_imatrix(pij,1,data->lseq,1,data->w);
free_imatrix(seqs,1,data->nseq,1,data->lseq);
free_imatrix(nall,1,data->lseq,1,5);
for (i=1;i<sizeofpset;i++) free(pset[i]);
free(pset);
free(data);
free_dvector(locs, 1, data->lseq);
free_ivector(flocs, 1, data->lseq);
/* system("PAUSE"); */
}
/*************************************************************************
* This function is the entry point of the initial partitioning algorithm.
* This algorithm assembles the graph to all the processors and preceed
* serially.
**************************************************************************/
idx_t Mc_Diffusion(ctrl_t *ctrl, graph_t *graph, idx_t *vtxdist, idx_t *where,
idx_t *home, idx_t npasses)
{
idx_t h, i, j;
idx_t nvtxs, nedges, ncon, pass, iter, domain, processor;
idx_t nparts, mype, npes, nlinks, me, you, wsize;
idx_t nvisited, nswaps = -1, tnswaps, done, alldone = -1;
idx_t *rowptr, *colind, *diff_where, *sr_where, *ehome, *map, *rmap;
idx_t *pack, *unpack, *match, *proc2sub, *sub2proc;
idx_t *visited, *gvisited;
real_t *transfer, *npwgts, maxdiff, minflow, maxflow;
real_t lbavg, oldlbavg, ubavg, *lbvec;
real_t *diff_flows, *sr_flows;
real_t diff_lbavg, sr_lbavg, diff_cost, sr_cost;
idx_t *rbuffer, *sbuffer;
idx_t *rcount, *rdispl;
real_t *solution, *load, *workspace;
matrix_t matrix;
graph_t *egraph;
if (graph->ncon > 3)
return 0;
WCOREPUSH;
nvtxs = graph->nvtxs;
nedges = graph->nedges;
ncon = graph->ncon;
nparts = ctrl->nparts;
mype = ctrl->mype;
npes = ctrl->npes;
ubavg = ravg(ncon, ctrl->ubvec);
/* initialize variables and allocate memory */
lbvec = rwspacemalloc(ctrl, ncon);
diff_flows = rwspacemalloc(ctrl, ncon);
sr_flows = rwspacemalloc(ctrl, ncon);
load = rwspacemalloc(ctrl, nparts);
solution = rwspacemalloc(ctrl, nparts);
npwgts = graph->gnpwgts = rwspacemalloc(ctrl, ncon*nparts);
matrix.values = rwspacemalloc(ctrl, nedges);
transfer = matrix.transfer = rwspacemalloc(ctrl, ncon*nedges);
proc2sub = iwspacemalloc(ctrl, gk_max(nparts, npes*2));
sub2proc = iwspacemalloc(ctrl, nparts);
match = iwspacemalloc(ctrl, nparts);
rowptr = matrix.rowptr = iwspacemalloc(ctrl, nparts+1);
colind = matrix.colind = iwspacemalloc(ctrl, nedges);
rcount = iwspacemalloc(ctrl, npes);
rdispl = iwspacemalloc(ctrl, npes+1);
pack = iwspacemalloc(ctrl, nvtxs);
unpack = iwspacemalloc(ctrl, nvtxs);
rbuffer = iwspacemalloc(ctrl, nvtxs);
sbuffer = iwspacemalloc(ctrl, nvtxs);
map = iwspacemalloc(ctrl, nvtxs);
rmap = iwspacemalloc(ctrl, nvtxs);
diff_where = iwspacemalloc(ctrl, nvtxs);
ehome = iwspacemalloc(ctrl, nvtxs);
wsize = gk_max(sizeof(real_t)*nparts*6, sizeof(idx_t)*(nvtxs+nparts*2+1));
workspace = (real_t *)gk_malloc(wsize, "Mc_Diffusion: workspace");
graph->ckrinfo = (ckrinfo_t *)gk_malloc(nvtxs*sizeof(ckrinfo_t), "Mc_Diffusion: rinfo");
/* construct subdomain connectivity graph */
matrix.nrows = nparts;
SetUpConnectGraph(graph, &matrix, (idx_t *)workspace);
nlinks = (matrix.nnzs-nparts) / 2;
visited = iwspacemalloc(ctrl, matrix.nnzs);
gvisited = iwspacemalloc(ctrl, matrix.nnzs);
for (pass=0; pass<npasses; pass++) {
rset(matrix.nnzs*ncon, 0.0, transfer);
iset(matrix.nnzs, 0, gvisited);
iset(matrix.nnzs, 0, visited);
iter = nvisited = 0;
/* compute ncon flow solutions */
for (h=0; h<ncon; h++) {
rset(nparts, 0.0, solution);
ComputeLoad(graph, nparts, load, ctrl->tpwgts, h);
lbvec[h] = (rmax(nparts, load)+1.0/nparts) * (real_t)nparts;
ConjGrad2(&matrix, load, solution, 0.001, workspace);
ComputeTransferVector(ncon, &matrix, solution, transfer, h);
}
oldlbavg = ravg(ncon, lbvec);
tnswaps = 0;
maxdiff = 0.0;
for (i=0; i<nparts; i++) {
for (j=rowptr[i]; j<rowptr[i+1]; j++) {
maxflow = rmax(ncon, transfer+j*ncon);
minflow = rmin(ncon, transfer+j*ncon);
maxdiff = (maxflow - minflow > maxdiff) ? maxflow - minflow : maxdiff;
}
}
while (nvisited < nlinks) {
/* compute independent sets of subdomains */
iset(gk_max(nparts, npes*2), UNMATCHED, proc2sub);
CSR_Match_SHEM(&matrix, match, proc2sub, gvisited, ncon);
/* set up the packing arrays */
iset(nparts, UNMATCHED, sub2proc);
for (i=0; i<npes*2; i++) {
if (proc2sub[i] == UNMATCHED)
break;
sub2proc[proc2sub[i]] = i/2;
}
iset(npes, 0, rcount);
for (i=0; i<nvtxs; i++) {
domain = where[i];
processor = sub2proc[domain];
if (processor != UNMATCHED)
rcount[processor]++;
}
rdispl[0] = 0;
for (i=1; i<npes+1; i++)
rdispl[i] = rdispl[i-1] + rcount[i-1];
iset(nvtxs, UNMATCHED, unpack);
for (i=0; i<nvtxs; i++) {
domain = where[i];
processor = sub2proc[domain];
if (processor != UNMATCHED)
unpack[rdispl[processor]++] = i;
}
SHIFTCSR(i, npes, rdispl);
iset(nvtxs, UNMATCHED, pack);
for (i=0; i<rdispl[npes]; i++) {
ASSERT(unpack[i] != UNMATCHED);
domain = where[unpack[i]];
processor = sub2proc[domain];
if (processor != UNMATCHED)
pack[unpack[i]] = i;
}
/* Compute the flows */
if (proc2sub[mype*2] != UNMATCHED) {
me = proc2sub[2*mype];
you = proc2sub[2*mype+1];
ASSERT(me != you);
for (j=rowptr[me]; j<rowptr[me+1]; j++) {
if (colind[j] == you) {
visited[j] = 1;
rcopy(ncon, transfer+j*ncon, diff_flows);
break;
}
}
for (j=rowptr[you]; j<rowptr[you+1]; j++) {
if (colind[j] == me) {
visited[j] = 1;
for (h=0; h<ncon; h++) {
if (transfer[j*ncon+h] > 0.0)
diff_flows[h] = -1.0 * transfer[j*ncon+h];
}
break;
}
}
nswaps = 1;
rcopy(ncon, diff_flows, sr_flows);
iset(nvtxs, 0, sbuffer);
for (i=0; i<nvtxs; i++) {
if (where[i] == me || where[i] == you)
sbuffer[i] = 1;
}
egraph = ExtractGraph(ctrl, graph, sbuffer, map, rmap);
if (egraph != NULL) {
icopy(egraph->nvtxs, egraph->where, diff_where);
for (j=0; j<egraph->nvtxs; j++)
ehome[j] = home[map[j]];
RedoMyLink(ctrl, egraph, ehome, me, you, sr_flows, &sr_cost, &sr_lbavg);
if (ncon <= 4) {
sr_where = egraph->where;
egraph->where = diff_where;
nswaps = BalanceMyLink(ctrl, egraph, ehome, me, you, diff_flows, maxdiff,
&diff_cost, &diff_lbavg, 1.0/(real_t)nvtxs);
if ((sr_lbavg < diff_lbavg &&
(diff_lbavg >= ubavg-1.0 || sr_cost == diff_cost)) ||
(sr_lbavg < ubavg-1.0 && sr_cost < diff_cost)) {
for (i=0; i<egraph->nvtxs; i++)
where[map[i]] = sr_where[i];
}
else {
for (i=0; i<egraph->nvtxs; i++)
where[map[i]] = diff_where[i];
}
}
else {
for (i=0; i<egraph->nvtxs; i++)
where[map[i]] = egraph->where[i];
}
gk_free((void **)&egraph->xadj, &egraph->nvwgt, &egraph->adjncy, &egraph, LTERM);
}
/* Pack the flow data */
iset(nvtxs, UNMATCHED, sbuffer);
for (i=0; i<nvtxs; i++) {
domain = where[i];
if (domain == you || domain == me)
sbuffer[pack[i]] = where[i];
}
}
/* Broadcast the flow data */
gkMPI_Allgatherv((void *)&sbuffer[rdispl[mype]], rcount[mype], IDX_T,
(void *)rbuffer, rcount, rdispl, IDX_T, ctrl->comm);
/* Unpack the flow data */
for (i=0; i<rdispl[npes]; i++) {
if (rbuffer[i] != UNMATCHED)
where[unpack[i]] = rbuffer[i];
}
/* Do other stuff */
gkMPI_Allreduce((void *)visited, (void *)gvisited, matrix.nnzs,
IDX_T, MPI_MAX, ctrl->comm);
nvisited = isum(matrix.nnzs, gvisited, 1)/2;
tnswaps += GlobalSESum(ctrl, nswaps);
if (iter++ == NGD_PASSES)
break;
}
/* perform serial refinement */
Mc_ComputeSerialPartitionParams(ctrl, graph, nparts);
Mc_SerialKWayAdaptRefine(ctrl, graph, nparts, home, ctrl->ubvec, 10);
/* check for early breakout */
for (h=0; h<ncon; h++) {
lbvec[h] = (real_t)(nparts) *
npwgts[rargmax_strd(nparts,npwgts+h,ncon)*ncon+h];
}
lbavg = ravg(ncon, lbvec);
done = 0;
if (tnswaps == 0 || lbavg >= oldlbavg || lbavg <= ubavg + 0.035)
done = 1;
alldone = GlobalSEMax(ctrl, done);
if (alldone == 1)
break;
}
/* ensure that all subdomains have at least one vertex */
/*
iset(nparts, 0, match);
for (i=0; i<nvtxs; i++)
match[where[i]]++;
done = 0;
while (done == 0) {
done = 1;
me = iargmin(nparts, match);
if (match[me] == 0) {
if (ctrl->mype == PE) printf("WARNING: empty subdomain %"PRIDX" in Mc_Diffusion\n", me);
you = iargmax(nparts, match);
for (i=0; i<nvtxs; i++) {
if (where[i] == you) {
where[i] = me;
match[you]--;
match[me]++;
done = 0;
break;
}
}
}
}
*/
/* now free memory and return */
gk_free((void **)&workspace, (void **)&graph->ckrinfo, LTERM);
graph->gnpwgts = NULL;
graph->ckrinfo = NULL;
WCOREPOP;
return 0;
}
void UnplacedTorus::Print() const {
printf("UnplacedTorus {%.2f, %.2f, %.2f, %.2f, %.2f}",
rmin(), rmax(), rtor(), sphi(), dphi() );
}
int main ( int argc , char** argv )
{
int mtrx [ RW ][ CL ] , i , j , m , i1 , j1 , s , c ;
int rslt [ CL ] ;
int* rsli , * rslj , rsi , rsj ;
rsi = rsj = 0 ;
// copy matrix
for ( i = 0 ; i < RW ; i++ )
for ( j = 0 ; j < CL ; j++ ) mtrx [ i ][ j ] = matrix [ i ][ j ] ;
// print init matrix
printf ( "Init\n" ) ;
pmtr ( mtrx , RW , CL ) ;
printf ( "\n\n" ) ;
// Step 1. Find minimal elem in row and
// vichitaem from all elements of this row
l5:
s = 1 ;
for ( i = 0 ; i < RW ; i++ ) {
m = rmin ( mtrx , i , CL ) ;
for ( j = 0 ; j < CL ; j++ ) mtrx [ i ][ j ] -= m ;
}
#if ( DBG == 1 )
// print matrix
printf ( "Step 1\n" ) ;
pmtr ( mtrx , RW , CL ) ;
printf ( "\n\n" ) ;
#endif
l0:
for ( j = 0 ; j < CL ; j++ ) rslt [ j ] = -1 ;
// build result array
for ( j = 0 ; j < CL ; j++ ) {
for ( i = 0 ; i < RW ; i++ ) {
if ( ( mtrx [ i ][ j ] == 0 ) &&
( rslt [ j ] == -1 ) &&
( inar ( rslt , i , CL ) == -1 ) ) {
j1 = inrw ( mtrx , i , 0 , j , CL ) ;
if ( j1 == -1 ) { rslt [ j ] = i ; break ; }
if ( incl ( mtrx , j , 0 , i , RW ) == -1 ) { rslt [ j ] = i ; break; }
l1:
if ( incl ( mtrx , j1 , 0 , i , RW ) == -1 ) { rslt [ j1 ] = i ; break; }
j1 = inrw ( mtrx , i , 0 , j1 , CL ) ;
if ( j1 == -1 ) { rslt [ j ] = i ; break; }
goto l1 ;
}
}
}
// check if task solved
j1 = inar ( rslt , -1 , CL ) ;
if ( j1 == -1 ) goto l99 ;
else if ( s == 2 ) goto l2 ;
// Step 2. Use step for columns.
s++ ;
for ( j = j1 ; j < CL ; j++ ) {
if ( rslt [ j ] != -1 ) continue ;
m = cmin ( mtrx , j , RW ) ;
for ( i = 0 ; i < RW ; i++ ) mtrx [ i ][ j ] -= m ;
}
#if ( DBG == 1 )
printf ( "Step 2\n" ) ;
pmtr ( mtrx , RW , CL ) ;
printf ( "\n\n" ) ;
#endif
goto l0;
l2:
// Step 3. Find unused rows
c = 0 ;
for ( i = 0 ; i < RW ; i++ )
if ( inar ( rslt , i , CL ) == -1 ) {
rsi++ ; c++ ;
if ( ( rsi - 1 ) == 0 ) {
rsli = ( int* ) malloc ( rsi * sizeof ( *rsli ) ) ;
*rsli = i ;
} else {
rsli = realloc ( rsli , rsi * sizeof ( *rsli ) ) ;
*( rsli + ( rsi - 1 ) ) = i ;
}
}
if ( c == 0 ) goto l4 ;
l3:
// in all unused rows find columns' numbers with zero
c = 0 ;
for ( i = 0 ; i < rsi ; i++ ) {
j1 = inrw ( mtrx , *( rsli + i ) , 0 , -1 , CL ) ;
while ( j1 != -1 ) {
if ( !inpn ( rslj , j1 , rsj ) ) {
rsj++ ; c++ ;
if ( ( rsj - 1 ) == 0 ) {
rslj = ( int* ) malloc ( rsj * sizeof ( *rslj ) ) ;
*rslj = j1 ;
} else {
rslj = realloc ( rslj , rsj * sizeof ( *rslj ) ) ;
*( rslj + ( rsj - 1 ) ) = j1 ;
}
}
j1 = inrw ( mtrx , *( rsli + i ) , 0 , j1 , CL ) ;
}
}
if ( c == 0 ) goto l4 ;
// in all unused columns find rows' numbers with zero
c = 0 ;
for ( j = 0 ; j < rsj ; j++ ) {
i1 = incl ( mtrx , *( rslj + j ) , 0 , -1 , RW ) ;
while ( i1 != -1 ) {
if ( !inpn ( rsli , i1 , rsi ) ) {
rsi++ ; c++ ;
rsli = realloc ( rsli , rsi * sizeof ( *rsli ) ) ;
*( rsli + ( rsi - 1 ) ) = i1 ;
}
i1 = incl ( mtrx , *( rslj + j ) , 0 , i1 , RW ) ;
}
}
if ( c ) goto l3 ;
l4:
// Step 4. Vicherkivaem otmechennie stolbci
// i neotmechennie stroki
// for i == rsli , j != rslj
m = -1 ;
for ( i = 0 ; i < RW ; i++ ) {
if ( !inpn ( rsli , i , rsi ) ) continue ;
for ( j = 0 ; j < CL ; j++ ) {
if ( inpn ( rslj , j , rsj ) ) continue ;
m = ( mtrx [ i ][ j ] < m || m < 0 ) ? mtrx [ i ][ j ] : m ;
}
}
for ( i = 0 ; i < RW ; i++ ) {
for ( j = 0 ; j < CL ; j++ ) {
if ( inpn ( rsli , i , rsi ) && !inpn ( rslj , j , rsj ) )
mtrx [ i ][ j ] -= m ;
if ( !inpn ( rsli , i , rsi ) && inpn ( rslj , j , rsj ) )
mtrx [ i ][ j ] += m ;
}
}
free ( rsli ) ; free ( rslj ) ;
rsi = rsj = 0 ;
#if ( DBG == 1 )
printf ( "Step 4\n" ) ;
pmtr ( mtrx , RW , CL ) ;
printf ( "\n\n" ) ;
#endif
goto l5 ;
l99:
for ( j = 0 ; j < CL ; j++ ) printf ( "For task: %d use worker:%d\n" , j , rslt [ j ] ) ;
printf ( "\n" ) ;
return 0 ;
}
int fqFilterE(float *aBlock, EFFECT *rEffect) {
memset(aBlock, 0, rmin(rEffect->nFiltMinFreq, nBSize) << 2);
memset(&aBlock[rmin(rEffect->nFiltMaxFreq, nBSize) << 2], 0, (nBSize - rmin(rEffect->nFiltMaxFreq, nBSize)) << 2);
return OK;
}
void srcPositionStudy(Int_t binWidth, TString source, TString geometry) {
int numFiles = 200;
TString simLocation;
TChain *chain = new TChain("anaTree");
if (geometry==TString("2011-2012")) simLocation = TString(getenv("SIM_2011_2012"));
else if (geometry==TString("2012-2013")) simLocation = TString(getenv("SIM_2012_2013"));
else if (geometry==TString("2012-2013_ISOBUTANE")) simLocation = TString(getenv("SIM_2012_2013_ISOBUTANE"));
else { std::cout << "BAD GEOMETRY\n"; exit(0); }
for (int i=0; i<numFiles; i++) {
chain->AddFile(TString::Format("%s/%s/analyzed_%i.root",simLocation.Data(),source.Data(),i));
}
Double_t maxEn = 1500.;
Double_t minEn = 0.;
Double_t fidMax = 55.;
Int_t nHists = (int)(fidMax/binWidth);
std::vector <TH1D*> histsE(nHists, 0);
std::vector <TH1D*> histsW(nHists, 0);
std::vector <Double_t> rmin(nHists,0);
std::vector <Double_t> rmax(nHists,0);
std::vector <Double_t> rmid(nHists,0);
//final means and errors
std::vector < Double_t > EastMeans(nHists,0.);
std::vector < Double_t > WestMeans(nHists,0.);
std::vector < Double_t > EastMeanErrors(nHists,0.);
std::vector < Double_t > WestMeanErrors(nHists,0.);
for (Int_t i=0; i<nHists; i++) {
rmin[i] = i*binWidth;
rmax[i] = (i+1)*binWidth;
rmid[i] = (double)rmin[i] + (double)binWidth/2.;
histsE[i] = new TH1D(TString::Format("his%iE",i),
TString::Format("%s %i mm radius bins East", source.Data(),binWidth),
550, 0., 1100.);
histsW[i] = new TH1D(TString::Format("his%iW",i),
TString::Format("%s %i mm radius bins West", source.Data(),binWidth),
550, 0., 1100.);
histsE[i]->SetLineColor(i+1);
histsW[i]->SetLineColor(i+1);
}
Double_t primPos[4];
// Set the addresses of the information read in from the simulation file
chain->SetBranchAddress("MWPCEnergy",&mwpcE);
chain->SetBranchAddress("time",&Time);
chain->SetBranchAddress("Edep",&edep);
chain->SetBranchAddress("EdepQ",&edepQ);
chain->SetBranchAddress("MWPCPos",&mwpc_pos);
chain->SetBranchAddress("ScintPos",&scint_pos);
chain->SetBranchAddress("primKE",&primKE);
chain->SetBranchAddress("primTheta",&primTheta);
chain->SetBranchAddress("primPos",&primPos);
//Get total number of events in TChain
UInt_t nevents = chain->GetEntries();
cout << "events = " << nevents << endl;
for (Int_t i=0; i<nevents; i++) {
chain->GetEvent(i);
Int_t nBin = primPos[3]*1000./binWidth;
if (edepQ.EdepQE>0. && primKE<maxEn && primKE>minEn && mwpcE.MWPCEnergyE>0.1 && primTheta>TMath::Pi()/2.) histsE[nBin]->Fill(edepQ.EdepQE);
if (edepQ.EdepQW>0. && primKE<maxEn && primKE>minEn && mwpcE.MWPCEnergyW>0.1 && primTheta<TMath::Pi()/2.) histsW[nBin]->Fill(edepQ.EdepQW);
if (i%100000==0) std::cout << "*";
}
std::cout << std::endl;
TCanvas *c1 = new TCanvas("c1","c1",1600,1200);
c1->Divide(2,2);
//TCanvas *c2 = new TCanvas("c2");
//histsE[1]->Draw("SAME");
Double_t refMeanE = 0., refMeanW = 0.; //This will hold the mean of the center pixel
std::cout << nHists << endl;
for (Int_t i=0; i<nHists; i++) {
c1->cd(1);
histsE[i]->Draw("SAME");
EastMeans[i] = histsE[i]->GetMean();
EastMeanErrors[i] = EastMeans[i]>0. ? EastMeans[i]/sqrt(histsE[i]->GetEntries()) : 0.;
//cout << EastMeans[i][0] << " " << EastMeans[i][1] << endl;
c1->cd(2);
histsW[i]->Draw("SAME");
WestMeans[i] = histsW[i]->GetMean();
WestMeanErrors[i] = WestMeans[i]>0. ? WestMeans[i]/sqrt(histsW[i]->GetEntries()) : 0.;
if (i==0) { refMeanE = EastMeans[i], refMeanW = WestMeans[i]; }
}
//TCanvas *c3 = new TCanvas("c3");
c1->cd(3);
std::vector <Double_t> xerr(nHists,0.);
TGraphErrors *gEast = new TGraphErrors(11, &rmax[0],&EastMeans[0],&xerr[0],&EastMeanErrors[0]);
gEast->SetMarkerStyle(21);
gEast->SetTitle(TString::Format("East %s Mean EQ vs. position",source.Data()));
gEast->GetXaxis()->SetTitle("Position Bin Edge (mm)");
gEast->GetYaxis()->SetTitle("Energy (keV)");
gEast->Draw("AP");
TLine *eastLine = new TLine(gEast->GetXaxis()->GetXmin(),refMeanE,gEast->GetXaxis()->GetXmax(),refMeanE);
eastLine->SetLineStyle(2);
eastLine->Draw();
//TCanvas *c4 = new TCanvas("c4");
c1->cd(4);
TGraphErrors *gWest = new TGraphErrors(11, &rmax[0],&WestMeans[0],&xerr[0],&WestMeanErrors[0]);
gWest->SetMarkerStyle(21);
gWest->SetTitle(TString::Format("West %s Mean EQ vs. position",source.Data()));
gWest->GetXaxis()->SetTitle("Position Bin Edge (mm)");
gWest->GetYaxis()->SetTitle("Energy (keV)");
gWest->Draw("AP");
TLine *westLine = new TLine(gWest->GetXaxis()->GetXmin(),refMeanW,gWest->GetXaxis()->GetXmax(),refMeanW);
westLine->SetLineStyle(2);
westLine->Draw();
}