Adding the AliAnalysisGUI class which is the main class that controls the GUI.
[u/mrichter/AliRoot.git] / ITS / AliITSClusterFinderSDD.cxx
1 /**************************************************************************
2  * Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
3  *                                                                        *
4  * Author: The ALICE Off-line Project.                                    *
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11  * appear in the supporting documentation. The authors make no claims     *
12  * about the suitability of this software for any purpose. It is          *
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14  **************************************************************************/
15 /*
16   $Id$
17  */
18 /////////////////////////////////////////////////////////////////////////// 
19 //  Cluster finder                                                       //
20 //  for Silicon                                                          //
21 //  Drift Detector                                                       //
22 ////////////////////////////////////////////////////////////////////////// 
23
24
25 #include "AliITSClusterFinderSDD.h"
26 #include "AliITSMapA1.h"
27 #include "AliITSRawClusterSDD.h"
28 #include "AliITSRecPoint.h"
29 #include "AliITSdigitSDD.h"
30 #include "AliITSDetTypeRec.h"
31 #include "AliITSCalibrationSDD.h"
32 #include "AliITSsegmentationSDD.h"
33 #include "AliLog.h"
34
35 ClassImp(AliITSClusterFinderSDD)
36
37 //______________________________________________________________________
38 AliITSClusterFinderSDD::AliITSClusterFinderSDD():
39 AliITSClusterFinder(),
40 fNclusters(0),
41 fDAnode(0.0),
42 fDTime(0.0),
43 fTimeCorr(0.0),
44 fCutAmplitude(0),
45 fMinPeak(0),
46 fMinCharge(0),
47 fMinNCells(0),
48 fMaxNCells(0){
49     // default constructor
50 }
51 //______________________________________________________________________
52 AliITSClusterFinderSDD::AliITSClusterFinderSDD(AliITSDetTypeRec* dettyp,
53                                                TClonesArray *digits,
54                                                TClonesArray *recp):
55 AliITSClusterFinder(dettyp),
56 fNclusters(0),
57 fDAnode(0.0),
58 fDTime(0.0),
59 fTimeCorr(0.0),
60 fCutAmplitude(0),
61 fMinPeak(0),
62 fMinCharge(0),
63 fMinNCells(0),
64 fMaxNCells(0){
65     // standard constructor
66
67     SetDigits(digits);
68     SetClusters(recp);
69     SetCutAmplitude(fDetTypeRec->GetITSgeom()->GetStartSDD());
70     SetDAnode();
71     SetDTime();
72     SetMinPeak((Int_t)((AliITSCalibrationSDD*)GetResp(fDetTypeRec->GetITSgeom()->GetStartSDD()))->GetNoiseAfterElectronics(0)*5);
73     SetMinNCells();
74     SetMaxNCells();
75     SetTimeCorr();
76     SetMinCharge();
77     SetMap(new AliITSMapA1(GetSeg(),Digits(),fCutAmplitude));
78 }
79 //______________________________________________________________________
80 void AliITSClusterFinderSDD::SetCutAmplitude(Int_t mod,Double_t nsigma){
81     // set the signal threshold for cluster finder
82     Double_t baseline,noiseAfterEl;
83
84     
85     Int_t nanodes = GetResp(mod)->Wings()*GetResp(mod)->Channels()*GetResp(mod)->Chips();
86     fCutAmplitude.Set(nanodes);
87     for(Int_t ian=0;ian<nanodes;ian++){
88       baseline=GetResp(mod)->GetBaseline(ian);
89       noiseAfterEl = ((AliITSCalibrationSDD*)GetResp(mod))->GetNoiseAfterElectronics(ian);
90       fCutAmplitude[ian] = (Int_t)((baseline + nsigma*noiseAfterEl));
91     }
92 }
93 //______________________________________________________________________
94 void AliITSClusterFinderSDD::Find1DClusters(){
95     // find 1D clusters
96   
97     // retrieve the parameters 
98     Int_t fNofMaps       = GetSeg()->Npz();
99     Int_t fMaxNofSamples = GetSeg()->Npx();
100     Int_t fNofAnodes     = fNofMaps/2;
101     Int_t dummy          = 0;
102     Double_t fTimeStep    = GetSeg()->Dpx(dummy);
103     Double_t fSddLength   = GetSeg()->Dx();
104     Double_t fDriftSpeed  = GetResp(fModule)->GetDriftSpeed();  
105     Double_t anodePitch   = GetSeg()->Dpz(dummy);
106
107     // map the signal
108     Map()->ClearMap();
109     Map()->SetThresholdArr(fCutAmplitude);
110     Map()->FillMap2();
111   
112     Int_t nofFoundClusters = 0;
113     Int_t i;
114     Double_t **dfadc = new Double_t*[fNofAnodes];
115     for(i=0;i<fNofAnodes;i++) dfadc[i] = new Double_t[fMaxNofSamples];
116     Double_t fadc  = 0.;
117     Double_t fadc1 = 0.;
118     Double_t fadc2 = 0.;
119     Int_t j,k,idx,l,m;
120     for(j=0;j<2;j++) {
121         for(k=0;k<fNofAnodes;k++) {
122             idx = j*fNofAnodes+k;
123             // signal (fadc) & derivative (dfadc)
124             dfadc[k][255]=0.;
125             for(l=0; l<fMaxNofSamples; l++) {
126                 fadc2=(Double_t)Map()->GetSignal(idx,l);
127                 if(l>0) fadc1=(Double_t)Map()->GetSignal(idx,l-1);
128                 if(l>0) dfadc[k][l-1] = fadc2-fadc1;
129             } // samples
130         } // anodes
131
132         for(k=0;k<fNofAnodes;k++) {
133             AliDebug(5,Form("Anode: %d, Wing: %d",k+1,j+1));
134             idx = j*fNofAnodes+k;
135             Int_t imax  = 0;
136             Int_t imaxd = 0;
137             Int_t it    = 0;
138             while(it <= fMaxNofSamples-3) {
139                 imax  = it;
140                 imaxd = it;
141                 // maximum of signal          
142                 Double_t fadcmax  = 0.;
143                 Double_t dfadcmax = 0.;
144                 Int_t lthrmina   = 1;
145                 Int_t lthrmint   = 3;
146                 Int_t lthra      = 1;
147                 Int_t lthrt      = 0;
148                 for(m=0;m<20;m++) {
149                     Int_t id = it+m;
150                     if(id>=fMaxNofSamples) break;
151                     fadc=(float)Map()->GetSignal(idx,id);
152                     if(fadc > fadcmax) { fadcmax = fadc; imax = id;}
153                     if(fadc > (float)fCutAmplitude[idx])lthrt++; 
154                     if(dfadc[k][id] > dfadcmax) {
155                         dfadcmax = dfadc[k][id];
156                         imaxd    = id;
157                     } // end if
158                 } // end for m
159                 it = imaxd;
160                 if(Map()->TestHit(idx,imax) == kEmpty) {it++; continue;}
161                 // cluster charge
162                 Int_t tstart = it-2;
163                 if(tstart < 0) tstart = 0;
164                 Bool_t ilcl = 0;
165                 if(lthrt >= lthrmint && lthra >= lthrmina) ilcl = 1;
166                 if(ilcl) {
167                     nofFoundClusters++;
168                     Int_t tstop      = tstart;
169                     Double_t dfadcmin = 10000.;
170                     Int_t ij;
171                     for(ij=0; ij<20; ij++) {
172                         if(tstart+ij > 255) { tstop = 255; break; }
173                         fadc=(float)Map()->GetSignal(idx,tstart+ij);
174                         if((dfadc[k][tstart+ij] < dfadcmin) && 
175                            (fadc > fCutAmplitude[idx])) {
176                             tstop = tstart+ij+5;
177                             if(tstop > 255) tstop = 255;
178                             dfadcmin = dfadc[k][it+ij];
179                         } // end if
180                     } // end for ij
181
182                     Double_t clusterCharge = 0.;
183                     Double_t clusterAnode  = k+0.5;
184                     Double_t clusterTime   = 0.;
185                     Int_t   clusterMult   = 0;
186                     Double_t clusterPeakAmplitude = 0.;
187                     Int_t its,peakpos     = -1;
188                     //Double_t n, baseline;
189                     //GetResp(fModule)->GetNoiseParam(n,baseline);
190                     Double_t baseline=GetResp(fModule)->GetBaseline(idx);
191                     for(its=tstart; its<=tstop; its++) {
192                         fadc=(float)Map()->GetSignal(idx,its);
193                         if(fadc>baseline) fadc -= baseline;
194                         else fadc = 0.;
195                         clusterCharge += fadc;
196                         // as a matter of fact we should take the peak
197                         // pos before FFT
198                         // to get the list of tracks !!!
199                         if(fadc > clusterPeakAmplitude) {
200                             clusterPeakAmplitude = fadc;
201                             //peakpos=Map()->GetHitIndex(idx,its);
202                             Int_t shift = (int)(fTimeCorr/fTimeStep);
203                             if(its>shift && its<(fMaxNofSamples-shift))
204                                 peakpos  = Map()->GetHitIndex(idx,its+shift);
205                             else peakpos = Map()->GetHitIndex(idx,its);
206                             if(peakpos<0) peakpos =Map()->GetHitIndex(idx,its);
207                         } // end if
208                         clusterTime += fadc*its;
209                         if(fadc > 0) clusterMult++;
210                         if(its == tstop) {
211                             clusterTime /= (clusterCharge/fTimeStep);   // ns
212                             if(clusterTime>fTimeCorr) clusterTime -=fTimeCorr;
213                             //ns
214                         } // end if
215                     } // end for its
216
217                     Double_t clusteranodePath = (clusterAnode - fNofAnodes/2)*
218                                                  anodePitch;
219                     Double_t clusterDriftPath = clusterTime*fDriftSpeed;
220                     clusterDriftPath = fSddLength-clusterDriftPath;
221                     if(clusterCharge <= 0.) break;
222                     AliITSRawClusterSDD clust(j+1,//i
223                                               clusterAnode,clusterTime,//ff
224                                               clusterCharge, //f
225                                               clusterPeakAmplitude, //f
226                                               peakpos, //i
227                                               0.,0.,clusterDriftPath,//fff
228                                               clusteranodePath, //f
229                                               clusterMult, //i
230                                               0,0,0,0,0,0,0);//7*i
231                     fDetTypeRec->AddCluster(1,&clust);
232                     it = tstop;
233                 } // ilcl
234                 it++;
235             } // while (samples)
236         } // anodes
237     } // detectors (2)
238
239     for(i=0;i<fNofAnodes;i++) delete[] dfadc[i];
240     delete [] dfadc;
241
242     return;
243 }
244 //______________________________________________________________________
245 void AliITSClusterFinderSDD::Find1DClustersE(){
246     // find 1D clusters
247     // retrieve the parameters 
248     Int_t fNofMaps = GetSeg()->Npz();
249     Int_t fMaxNofSamples = GetSeg()->Npx();
250     Int_t fNofAnodes = fNofMaps/2;
251     Int_t dummy=0;
252     Double_t fTimeStep = GetSeg()->Dpx( dummy );
253     Double_t fSddLength = GetSeg()->Dx();
254     Double_t fDriftSpeed = GetResp(fModule)->GetDriftSpeed();
255     Double_t anodePitch = GetSeg()->Dpz( dummy );
256
257     Map()->ClearMap();
258     Map()->SetThresholdArr( fCutAmplitude );
259     Map()->FillMap2();
260
261     Int_t nClu = 0;
262     //        cout << "Search  cluster... "<< endl;
263     for( Int_t j=0; j<2; j++ ){
264         for( Int_t k=0; k<fNofAnodes; k++ ){
265             Int_t idx = j*fNofAnodes+k;
266             Double_t baseline=GetResp(fModule)->GetBaseline(idx);
267             Bool_t on = kFALSE;
268             Int_t start = 0;
269             Int_t nTsteps = 0;
270             Double_t fmax = 0.;
271             Int_t lmax = 0;
272             Double_t charge = 0.;
273             Double_t time = 0.;
274             Double_t anode = k+0.5;
275             Int_t peakpos = -1;
276             for( Int_t l=0; l<fMaxNofSamples; l++ ){
277                 Double_t fadc = (Double_t)Map()->GetSignal( idx, l );
278                 if( fadc > 0.0 ){
279                     if( on == kFALSE && l<fMaxNofSamples-4){
280                         // star RawCluster (reset var.)
281                         Double_t fadc1 = (Double_t)Map()->GetSignal( idx, l+1 );
282                         if( fadc1 < fadc ) continue;
283                         start = l;
284                         fmax = 0.;
285                         lmax = 0;
286                         time = 0.;
287                         charge = 0.; 
288                         on = kTRUE; 
289                         nTsteps = 0;
290                     } // end if on...
291                     nTsteps++ ;
292                     if( fadc > baseline ) fadc -= baseline;
293                     else fadc=0.;
294                     charge += fadc;
295                     time += fadc*l;
296                     if( fadc > fmax ){ 
297                         fmax = fadc; 
298                         lmax = l; 
299                         Int_t shift = (Int_t)(fTimeCorr/fTimeStep + 0.5);
300                         if( l > shift && l < (fMaxNofSamples-shift) )  
301                             peakpos = Map()->GetHitIndex( idx, l+shift );
302                         else
303                             peakpos = Map()->GetHitIndex( idx, l );
304                         if( peakpos < 0) peakpos = Map()->GetHitIndex(idx,l);
305                     } // end if fadc
306                 }else{ // end fadc>0
307                     if( on == kTRUE ){        
308                         if( nTsteps > 2 ){
309                             //  min # of timesteps for a RawCluster
310                             // Found a RawCluster...
311                             Int_t stop = l-1;
312                             time /= (charge/fTimeStep);   // ns
313                                 // time = lmax*fTimeStep;   // ns
314                             if( time > fTimeCorr ) time -= fTimeCorr;   // ns
315                             Double_t anodePath =(anode-fNofAnodes/2)*anodePitch;
316                             Double_t driftPath = time*fDriftSpeed;
317                             driftPath = fSddLength-driftPath;
318                             AliITSRawClusterSDD clust(j+1,anode,time,charge,
319                                                       fmax, peakpos,0.,0.,
320                                                       driftPath,anodePath,
321                                                       nTsteps,start,stop,
322                                                       start, stop, 1, k, k );
323                             fDetTypeRec->AddCluster( 1, &clust );
324                             if(AliDebugLevel()>=5) clust.PrintInfo();
325                             nClu++;
326                         } // end if nTsteps
327                         on = kFALSE;
328                     } // end if on==kTRUE
329                 } // end if fadc>0
330             } // samples
331         } // anodes
332     } // wings
333     AliDebug(3,Form("# Rawclusters %d",nClu));         
334     return; 
335 }
336 //_______________________________________________________________________
337 Int_t AliITSClusterFinderSDD::SearchPeak(Double_t *spect,Int_t xdim,Int_t zdim,
338                                          Int_t *peakX, Int_t *peakZ, 
339                                          Double_t *peakAmp, Double_t minpeak ){
340     // search peaks on a 2D cluster
341     Int_t npeak = 0;    // # peaks
342     Int_t i,j;
343     // search peaks
344     for( Int_t z=1; z<zdim-1; z++ ){
345         for( Int_t x=1; x<xdim-2; x++ ){
346             Double_t sxz = spect[x*zdim+z];
347             Double_t sxz1 = spect[(x+1)*zdim+z];
348             Double_t sxz2 = spect[(x-1)*zdim+z];
349             // search a local max. in s[x,z]
350             if( sxz < minpeak || sxz1 <= 0 || sxz2 <= 0 ) continue;
351             if( sxz >= spect[(x+1)*zdim+z  ] && sxz >= spect[(x-1)*zdim+z  ] &&
352                 sxz >= spect[x*zdim    +z+1] && sxz >= spect[x*zdim    +z-1] &&
353                 sxz >= spect[(x+1)*zdim+z+1] && sxz >= spect[(x+1)*zdim+z-1] &&
354                 sxz >= spect[(x-1)*zdim+z+1] && sxz >= spect[(x-1)*zdim+z-1] ){
355                 // peak found
356                 peakX[npeak] = x;
357                 peakZ[npeak] = z;
358                 peakAmp[npeak] = sxz;
359                 npeak++;
360             } // end if ....
361         } // end for x
362     } // end for z
363     // search groups of peaks with same amplitude.
364     Int_t *flag = new Int_t[npeak];
365     for( i=0; i<npeak; i++ ) flag[i] = 0;
366     for( i=0; i<npeak; i++ ){
367         for( j=0; j<npeak; j++ ){
368             if( i==j) continue;
369             if( flag[j] > 0 ) continue;
370             if( peakAmp[i] == peakAmp[j] && 
371                 TMath::Abs(peakX[i]-peakX[j])<=1 && 
372                 TMath::Abs(peakZ[i]-peakZ[j])<=1 ){
373                 if( flag[i] == 0) flag[i] = i+1;
374                 flag[j] = flag[i];
375             } // end if ...
376         } // end for j
377     } // end for i
378     // make average of peak groups        
379     for( i=0; i<npeak; i++ ){
380         Int_t nFlag = 1;
381         if( flag[i] <= 0 ) continue;
382         for( j=0; j<npeak; j++ ){
383             if( i==j ) continue;
384             if( flag[j] != flag[i] ) continue;
385             peakX[i] += peakX[j];
386             peakZ[i] += peakZ[j];
387             nFlag++;
388             npeak--;
389             for( Int_t k=j; k<npeak; k++ ){
390                 peakX[k] = peakX[k+1];
391                 peakZ[k] = peakZ[k+1];
392                 peakAmp[k] = peakAmp[k+1];
393                 flag[k] = flag[k+1];
394             } // end for k        
395             j--;
396         } // end for j
397         if( nFlag > 1 ){
398             peakX[i] /= nFlag;
399             peakZ[i] /= nFlag;
400         } // end fi nFlag
401     } // end for i
402     delete [] flag;
403     return( npeak );
404 }
405 //______________________________________________________________________
406 void AliITSClusterFinderSDD::PeakFunc( Int_t xdim, Int_t zdim, Double_t *par,
407                                        Double_t *spe, Double_t *integral){
408     // function used to fit the clusters
409     // par -> parameters..
410     // par[0]  number of peaks.
411     // for each peak i=1, ..., par[0]
412     //                 par[i] = Ampl.
413     //                 par[i+1] = xpos
414     //                 par[i+2] = zpos
415     //                 par[i+3] = tau
416     //                 par[i+4] = sigma.
417     Int_t electronics = GetResp(fModule)->GetElectronics(); // 1 = PASCAL, 2 = OLA
418     const Int_t knParam = 5;
419     Int_t npeak = (Int_t)par[0];
420
421     memset( spe, 0, sizeof( Double_t )*zdim*xdim );
422
423     Int_t k = 1;
424     for( Int_t i=0; i<npeak; i++ ){
425         if( integral != 0 ) integral[i] = 0.;
426         Double_t sigmaA2 = par[k+4]*par[k+4]*2.;
427         Double_t t2 = par[k+3];   // PASCAL
428         if( electronics == 2 ) { t2 *= t2; t2 *= 2; } // OLA
429         for( Int_t z=0; z<zdim; z++ ){
430             for( Int_t x=0; x<xdim; x++ ){
431                 Double_t z2 = (z-par[k+2])*(z-par[k+2])/sigmaA2;
432                 Double_t x2 = 0.;
433                 Double_t signal = 0.;
434                 if( electronics == 1 ){ // PASCAL
435                     x2 = (x-par[k+1]+t2)/t2;
436                     signal = (x2>0.) ? par[k]*x2*exp(-x2+1.-z2) :0.0; // RCCR2
437                 //  signal =(x2>0.) ? par[k]*x2*x2*exp(-2*x2+2.-z2 ):0.0;//RCCR
438                 }else if( electronics == 2 ) { // OLA
439                     x2 = (x-par[k+1])*(x-par[k+1])/t2;
440                     signal = par[k]  * exp( -x2 - z2 );
441                 } else {
442                     Warning("PeakFunc","Wrong SDD Electronics = %d",
443                             electronics);
444                     // exit( 1 );
445                 } // end if electronicx
446                 spe[x*zdim+z] += signal;
447                 if( integral != 0 ) integral[i] += signal;
448             } // end for x
449         } // end for z
450         k += knParam;
451     } // end for i
452     return;
453 }
454 //__________________________________________________________________________
455 Double_t AliITSClusterFinderSDD::ChiSqr( Int_t xdim, Int_t zdim, Double_t *spe,
456                                         Double_t *speFit ) const{
457     // EVALUATES UNNORMALIZED CHI-SQUARED
458     Double_t chi2 = 0.;
459     for( Int_t z=0; z<zdim; z++ ){
460         for( Int_t x=1; x<xdim-1; x++ ){
461             Int_t index = x*zdim+z;
462             Double_t tmp = spe[index] - speFit[index];
463             chi2 += tmp*tmp;
464         } // end for x
465     } // end for z
466     return( chi2 );
467 }
468 //_______________________________________________________________________
469 void AliITSClusterFinderSDD::Minim( Int_t xdim, Int_t zdim, Double_t *param,
470                                     Double_t *prm0,Double_t *steprm,
471                                     Double_t *chisqr,Double_t *spe,
472                                     Double_t *speFit ){
473     // 
474     Int_t   k, nnn, mmm, i;
475     Double_t p1, delta, d1, chisq1, p2, chisq2, t, p3, chisq3, a, b, p0, chisqt;
476     const Int_t knParam = 5;
477     Int_t npeak = (Int_t)param[0];
478     for( k=1; k<(npeak*knParam+1); k++ ) prm0[k] = param[k];
479     for( k=1; k<(npeak*knParam+1); k++ ){
480         p1 = param[k];
481         delta = steprm[k];
482         d1 = delta;
483         // ENSURE THAT STEP SIZE IS SENSIBLY LARGER THAN MACHINE ROUND OFF
484         if( TMath::Abs( p1 ) > 1.0E-6 ) 
485             if ( TMath::Abs( delta/p1 ) < 1.0E-4 ) delta = p1/1000;
486             else  delta = (Double_t)1.0E-4;
487         //  EVALUATE CHI-SQUARED AT FIRST TWO SEARCH POINTS
488         PeakFunc( xdim, zdim, param, speFit );
489         chisq1 = ChiSqr( xdim, zdim, spe, speFit );
490         p2 = p1+delta;
491         param[k] = p2;
492         PeakFunc( xdim, zdim, param, speFit );
493         chisq2 = ChiSqr( xdim, zdim, spe, speFit );
494         if( chisq1 < chisq2 ){
495             // REVERSE DIRECTION OF SEARCH IF CHI-SQUARED IS INCREASING
496             delta = -delta;
497             t = p1;
498             p1 = p2;
499             p2 = t;
500             t = chisq1;
501             chisq1 = chisq2;
502             chisq2 = t;
503         } // end if
504         i = 1; nnn = 0;
505         do {   // INCREMENT param(K) UNTIL CHI-SQUARED STARTS TO INCREASE
506             nnn++;
507             p3 = p2 + delta;
508             mmm = nnn - (nnn/5)*5;  // multiplo de 5
509             if( mmm == 0 ){
510                 d1 = delta;
511                 // INCREASE STEP SIZE IF STEPPING TOWARDS MINIMUM IS TOO SLOW 
512                 delta *= 5;
513             } // end if
514             param[k] = p3;
515             // Constrain paramiters
516             Int_t kpos = (k-1) % knParam;
517             switch( kpos ){
518             case 0 :
519                 if( param[k] <= 20 ) param[k] = fMinPeak;
520                 break;
521             case 1 :
522                 if( TMath::Abs( param[k] - prm0[k] ) > 1.5 ) param[k] = prm0[k];
523                 break;
524             case 2 :
525                 if( TMath::Abs( param[k] - prm0[k] ) > 1. ) param[k] = prm0[k];
526                 break;
527             case 3 :
528                 if( param[k] < .5 ) param[k] = .5;        
529                 break;
530             case 4 :
531                 if( param[k] < .288 ) param[k] = .288;// 1/sqrt(12) = 0.288
532                 if( param[k] > zdim*.5 ) param[k] = zdim*.5;
533                 break;
534             }; // end switch
535             PeakFunc( xdim, zdim, param, speFit );
536             chisq3 = ChiSqr( xdim, zdim, spe, speFit );
537             if( chisq3 < chisq2 && nnn < 50 ){
538                 p1 = p2;
539                 p2 = p3;
540                 chisq1 = chisq2;
541                 chisq2 = chisq3;
542             }else i=0;
543         } while( i );
544         // FIND MINIMUM OF PARABOLA DEFINED BY LAST THREE POINTS
545         a = chisq1*(p2-p3)+chisq2*(p3-p1)+chisq3*(p1-p2);
546         b = chisq1*(p2*p2-p3*p3)+chisq2*(p3*p3-p1*p1)+chisq3*(p1*p1-p2*p2);
547         if( a!=0 ) p0 = (Double_t)(0.5*b/a);
548         else p0 = 10000;
549         //--IN CASE OF NEARLY EQUAL CHI-SQUARED AND TOO SMALL STEP SIZE PREVENT
550         //   ERRONEOUS EVALUATION OF PARABOLA MINIMUM
551         //---NEXT TWO LINES CAN BE OMITTED FOR HIGHER PRECISION MACHINES
552         //dp = (Double_t) max (TMath::Abs(p3-p2), TMath::Abs(p2-p1));
553         //if( TMath::Abs( p2-p0 ) > dp ) p0 = p2;
554         param[k] = p0;
555         // Constrain paramiters
556         Int_t kpos = (k-1) % knParam;
557         switch( kpos ){
558         case 0 :
559             if( param[k] <= 20 ) param[k] = fMinPeak;   
560             break;
561         case 1 :
562             if( TMath::Abs( param[k] - prm0[k] ) > 1.5 ) param[k] = prm0[k];
563             break;
564         case 2 :
565             if( TMath::Abs( param[k] - prm0[k] ) > 1. ) param[k] = prm0[k];
566             break;
567         case 3 :
568             if( param[k] < .5 ) param[k] = .5;        
569             break;
570         case 4 :
571             if( param[k] < .288 ) param[k] = .288;  // 1/sqrt(12) = 0.288
572             if( param[k] > zdim*.5 ) param[k] = zdim*.5;
573             break;
574         }; // end switch
575         PeakFunc( xdim, zdim, param, speFit );
576         chisqt = ChiSqr( xdim, zdim, spe, speFit );
577         // DO NOT ALLOW ERRONEOUS INTERPOLATION
578         if( chisqt <= *chisqr ) *chisqr = chisqt;
579         else param[k] = prm0[k];
580         // OPTIMIZE SEARCH STEP FOR EVENTUAL NEXT CALL OF MINIM
581         steprm[k] = (param[k]-prm0[k])/5;
582         if( steprm[k] >= d1 ) steprm[k] = d1/5;
583     } // end for k
584     // EVALUATE FIT AND CHI-SQUARED FOR OPTIMIZED PARAMETERS
585     PeakFunc( xdim, zdim, param, speFit );
586     *chisqr = ChiSqr( xdim, zdim, spe, speFit );
587     return;
588 }
589 //_________________________________________________________________________
590 Int_t AliITSClusterFinderSDD::NoLinearFit( Int_t xdim, Int_t zdim, 
591                                            Double_t *param, Double_t *spe, 
592                                            Int_t *niter, Double_t *chir ){
593     // fit method from Comput. Phys. Commun 46(1987) 149
594     const Double_t kchilmt = 0.01;  //        relative accuracy           
595     const Int_t   knel = 3;        //        for parabolic minimization  
596     const Int_t   knstop = 50;     //        Max. iteration number          
597     const Int_t   knParam = 5;
598     Int_t npeak = (Int_t)param[0];
599     // RETURN IF NUMBER OF DEGREES OF FREEDOM IS NOT POSITIVE 
600     if( (xdim*zdim - npeak*knParam) <= 0 ) return( -1 );
601     Double_t degFree = (xdim*zdim - npeak*knParam)-1;
602     Int_t   n, k, iterNum = 0;
603     Double_t *prm0 = new Double_t[npeak*knParam+1];
604     Double_t *step = new Double_t[npeak*knParam+1];
605     Double_t *schi = new Double_t[npeak*knParam+1]; 
606     Double_t *sprm[3];
607     sprm[0] = new Double_t[npeak*knParam+1];
608     sprm[1] = new Double_t[npeak*knParam+1];
609     sprm[2] = new Double_t[npeak*knParam+1];
610     Double_t  chi0, chi1, reldif, a, b, prmin, dp;
611     Double_t *speFit = new Double_t[ xdim*zdim ];
612     PeakFunc( xdim, zdim, param, speFit );
613     chi0 = ChiSqr( xdim, zdim, spe, speFit );
614     chi1 = chi0;
615     for( k=1; k<(npeak*knParam+1); k++) prm0[k] = param[k];
616         for( k=1 ; k<(npeak*knParam+1); k+=knParam ){
617             step[k] = param[k] / 20.0 ;
618             step[k+1] = param[k+1] / 50.0;
619             step[k+2] = param[k+2] / 50.0;                 
620             step[k+3] = param[k+3] / 20.0;                 
621             step[k+4] = param[k+4] / 20.0;                 
622         } // end for k
623     Int_t out = 0;
624     do{
625         iterNum++;
626             chi0 = chi1;
627             Minim( xdim, zdim, param, prm0, step, &chi1, spe, speFit );
628             reldif = ( chi1 > 0 ) ? ((Double_t) TMath::Abs( chi1-chi0)/chi1 ) : 0;
629         // EXIT conditions
630         if( reldif < (float) kchilmt ){
631             *chir  = (chi1>0) ? (float) TMath::Sqrt (chi1/degFree) :0;
632             *niter = iterNum;
633             out = 0;
634             break;
635         } // end if
636         if( (reldif < (float)(5*kchilmt)) && (iterNum > knstop) ){
637             *chir = (chi1>0) ?(float) TMath::Sqrt (chi1/degFree):0;
638             *niter = iterNum;
639             out = 0;
640             break;
641         } // end if
642         if( iterNum > 5*knstop ){
643             *chir  = (chi1>0) ?(float) TMath::Sqrt (chi1/degFree):0;
644             *niter = iterNum;
645             out = 1;
646             break;
647         } // end if
648         if( iterNum <= knel ) continue;
649         n = iterNum - (iterNum/knel)*knel; // EXTRAPOLATION LIMIT COUNTER N
650         if( n > 3 || n == 0 ) continue;
651         schi[n-1] = chi1;
652         for( k=1; k<(npeak*knParam+1); k++ ) sprm[n-1][k] = param[k];
653         if( n != 3 ) continue;
654         // -EVALUATE EXTRAPOLATED VALUE OF EACH PARAMETER BY FINDING MINIMUM OF
655         //    PARABOLA DEFINED BY LAST THREE CALLS OF MINIM
656         for( k=1; k<(npeak*knParam+1); k++ ){
657             Double_t tmp0 = sprm[0][k];
658             Double_t tmp1 = sprm[1][k];
659             Double_t tmp2 = sprm[2][k];
660             a  = schi[0]*(tmp1-tmp2) + schi[1]*(tmp2-tmp0);
661             a += (schi[2]*(tmp0-tmp1));
662             b  = schi[0]*(tmp1*tmp1-tmp2*tmp2);
663             b += (schi[1]*(tmp2*tmp2-tmp0*tmp0)+(schi[2]*
664                                              (tmp0*tmp0-tmp1*tmp1)));
665             if ((double)a < 1.0E-6) prmin = 0;
666             else prmin = (float) (0.5*b/a);
667             dp = 5*(tmp2-tmp0);
668             if( TMath::Abs(prmin-tmp2) > TMath::Abs(dp) ) prmin = tmp2+dp;
669             param[k] = prmin;
670             step[k]  = dp/10; // OPTIMIZE SEARCH STEP
671         } // end for k
672     } while( kTRUE );
673     delete [] prm0;
674     delete [] step;
675     delete [] schi; 
676     delete [] sprm[0];
677     delete [] sprm[1];
678     delete [] sprm[2];
679     delete [] speFit;
680     return( out );
681 }
682
683 //______________________________________________________________________
684 void AliITSClusterFinderSDD::ResolveClusters(){
685     // The function to resolve clusters if the clusters overlapping exists
686     Int_t i;
687     // get number of clusters for this module
688     Int_t nofClusters = NClusters();
689     nofClusters -= fNclusters;
690     Int_t fNofMaps = GetSeg()->Npz();
691     Int_t fNofAnodes = fNofMaps/2;
692     //Int_t fMaxNofSamples = GetSeg()->Npx();
693     Int_t dummy=0;
694     Double_t fTimeStep = GetSeg()->Dpx( dummy );
695     Double_t fSddLength = GetSeg()->Dx();
696     Double_t fDriftSpeed = GetResp(fModule)->GetDriftSpeed();
697     Double_t anodePitch = GetSeg()->Dpz( dummy );
698     //Double_t n, baseline;
699     //GetResp(fModule)->GetNoiseParam( n, baseline );
700     Int_t electronics =GetResp(fModule)->GetElectronics(); // 1 = PASCAL, 2 = OLA
701
702     for( Int_t j=0; j<nofClusters; j++ ){ 
703         // get cluster information
704         AliITSRawClusterSDD *clusterJ=(AliITSRawClusterSDD*) Cluster(j);
705         Int_t astart = clusterJ->Astart();
706         Int_t astop = clusterJ->Astop();
707         Int_t tstart = clusterJ->Tstartf();
708         Int_t tstop = clusterJ->Tstopf();
709         Int_t wing = (Int_t)clusterJ->W();
710         if( wing == 2 ){
711             astart += fNofAnodes; 
712             astop  += fNofAnodes;
713         } // end if 
714         Int_t xdim = tstop-tstart+3;
715         Int_t zdim = astop-astart+3;
716         if( xdim > 50 || zdim > 30 ) { 
717             Warning("ResolveClusters","xdim: %d , zdim: %d ",xdim,zdim);
718             continue;
719         }
720         Double_t *sp = new Double_t[ xdim*zdim+1 ];
721         memset( sp, 0, sizeof(Double_t)*(xdim*zdim+1) );
722         
723         // make a local map from cluster region
724         for( Int_t ianode=astart; ianode<=astop; ianode++ ){
725             for( Int_t itime=tstart; itime<=tstop; itime++ ){
726                 Double_t fadc = Map()->GetSignal( ianode, itime );
727                 Double_t baseline=GetResp(fModule)->GetBaseline(ianode);
728                 if( fadc > baseline ) fadc -= (Double_t)baseline;
729                 else fadc = 0.;
730                 Int_t index = (itime-tstart+1)*zdim+(ianode-astart+1);
731                 sp[index] = fadc;
732             } // time loop
733         } // anode loop
734         
735         // search peaks on cluster
736         const Int_t kNp = 150;
737         Int_t peakX1[kNp];
738         Int_t peakZ1[kNp];
739         Double_t peakAmp1[kNp];
740         Int_t npeak = SearchPeak(sp,xdim,zdim,peakX1,peakZ1,peakAmp1,fMinPeak);
741
742         // if multiple peaks, split cluster
743         if( npeak >= 1 ){
744             //        cout << "npeak " << npeak << endl;
745             //        clusterJ->PrintInfo();
746             Double_t *par = new Double_t[npeak*5+1];
747             par[0] = (Double_t)npeak;                
748             // Initial parameters in cell dimentions
749             Int_t k1 = 1;
750             for( i=0; i<npeak; i++ ){
751                 par[k1] = peakAmp1[i];
752                 par[k1+1] = peakX1[i]; // local time pos. [timebin]
753                 par[k1+2] = peakZ1[i]; // local anode pos. [anodepitch]
754                 if( electronics == 1 ) par[k1+3] = 2.; // PASCAL
755                 else if(electronics==2) par[k1+3] = 0.7;//tau [timebin] OLA 
756                 par[k1+4] = .4;    // sigma        [anodepich]
757                 k1 += 5;
758             } // end for i                        
759             Int_t niter;
760             Double_t chir;                        
761             NoLinearFit( xdim, zdim, par, sp, &niter, &chir );
762             Double_t peakX[kNp];
763             Double_t peakZ[kNp];
764             Double_t sigma[kNp];
765             Double_t tau[kNp];
766             Double_t peakAmp[kNp];
767             Double_t integral[kNp];
768             //get integrals => charge for each peak
769             PeakFunc( xdim, zdim, par, sp, integral );
770             k1 = 1;
771             for( i=0; i<npeak; i++ ){
772                 peakAmp[i] = par[k1];
773                 peakX[i]   = par[k1+1];
774                 peakZ[i]   = par[k1+2];
775                 tau[i]     = par[k1+3];
776                 sigma[i]   = par[k1+4];
777                 k1+=5;
778             } // end for i
779             // calculate parameter for new clusters
780             for( i=0; i<npeak; i++ ){
781                 AliITSRawClusterSDD clusterI( *clusterJ );
782             
783                 Int_t newAnode = peakZ1[i]-1 + astart;
784
785             //    Int_t newiTime = peakX1[i]-1 + tstart;
786             //    Int_t shift = (Int_t)(fTimeCorr/fTimeStep + 0.5);
787             //    if( newiTime > shift && newiTime < (fMaxNofSamples-shift) ) 
788             //        shift = 0;
789             //    Int_t peakpos = Map()->GetHitIndex(newAnode,newiTime+shift );
790             //    clusterI.SetPeakPos( peakpos );
791             
792                 clusterI.SetPeakAmpl( peakAmp1[i] );
793                 Double_t newAnodef = peakZ[i] - 0.5 + astart;
794                 Double_t newiTimef = peakX[i] - 1 + tstart;
795                 if( wing == 2 ) newAnodef -= fNofAnodes; 
796                 Double_t anodePath = (newAnodef - fNofAnodes/2)*anodePitch;
797                 newiTimef *= fTimeStep;
798                 if( newiTimef > fTimeCorr ) newiTimef -= fTimeCorr;
799                 if( electronics == 1 ){
800                 //    newiTimef *= 0.999438;    // PASCAL
801                 //    newiTimef += (6./fDriftSpeed - newiTimef/3000.);
802                 }else if( electronics == 2 )
803                     newiTimef *= 0.99714;    // OLA
804                     
805                 Int_t timeBin = (Int_t)(newiTimef/fTimeStep+0.5);    
806                 Int_t peakpos = Map()->GetHitIndex( newAnode, timeBin );
807                 if( peakpos < 0 ) { 
808                     for( Int_t ii=0; ii<3; ii++ ) {
809                         peakpos = Map()->GetHitIndex( newAnode, timeBin+ii );
810                         if( peakpos > 0 ) break;
811                         peakpos = Map()->GetHitIndex( newAnode, timeBin-ii );
812                         if( peakpos > 0 ) break;
813                     }
814                 }
815                 
816                 if( peakpos < 0 ) { 
817                     //Warning("ResolveClusters",
818                     //        "Digit not found for cluster");
819                     //if(AliDebugLevel()>=3) clusterI.PrintInfo(); 
820                    continue;
821                 }
822                 clusterI.SetPeakPos( peakpos );    
823                 Double_t driftPath = fSddLength - newiTimef * fDriftSpeed;
824                 Double_t sign = ( wing == 1 ) ? -1. : 1.;
825                 clusterI.SetX( driftPath*sign * 0.0001 );        
826                 clusterI.SetZ( anodePath * 0.0001 );
827                 clusterI.SetAnode( newAnodef );
828                 clusterI.SetTime( newiTimef );
829                 clusterI.SetAsigma( sigma[i]*anodePitch );
830                 clusterI.SetTsigma( tau[i]*fTimeStep );
831                 clusterI.SetQ( integral[i] );
832                 
833                 fDetTypeRec->AddCluster( 1, &clusterI );
834             } // end for i
835             Clusters()->RemoveAt( j );
836             delete [] par;
837         } else {  // something odd
838             Warning( "ResolveClusters",
839                      "--- Peak not found!!!!  minpeak=%d ,cluster peak= %f"
840                      " , module= %d",
841                      fMinPeak, clusterJ->PeakAmpl(),GetModule()); 
842             clusterJ->PrintInfo();
843             Warning( "ResolveClusters"," xdim= %d zdim= %d", xdim-2, zdim-2 );
844         }
845         delete [] sp;
846     } // cluster loop
847     Clusters()->Compress();
848 //    Map()->ClearMap(); 
849 }
850 //________________________________________________________________________
851 void  AliITSClusterFinderSDD::GroupClusters(){
852     // group clusters
853     Int_t dummy=0;
854     Double_t fTimeStep = GetSeg()->Dpx(dummy);
855     // get number of clusters for this module
856     Int_t nofClusters = NClusters();
857     nofClusters -= fNclusters;
858     AliITSRawClusterSDD *clusterI;
859     AliITSRawClusterSDD *clusterJ;
860     Int_t *label = new Int_t [nofClusters];
861     Int_t i,j;
862     for(i=0; i<nofClusters; i++) label[i] = 0;
863     for(i=0; i<nofClusters; i++) { 
864         if(label[i] != 0) continue;
865         for(j=i+1; j<nofClusters; j++) { 
866             if(label[j] != 0) continue;
867             clusterI = (AliITSRawClusterSDD*) Cluster(i);
868             clusterJ = (AliITSRawClusterSDD*) Cluster(j);
869             // 1.3 good
870             if(clusterI->T() < fTimeStep*60) fDAnode = 4.2;  // TB 3.2  
871             if(clusterI->T() < fTimeStep*10) fDAnode = 1.5;  // TB 1.
872             Bool_t pair = clusterI->Brother(clusterJ,fDAnode,fDTime);
873             if(!pair) continue;
874             if(AliDebugLevel()>=4){
875                 clusterI->PrintInfo();
876                 clusterJ->PrintInfo();
877             } // end if AliDebugLevel
878             clusterI->Add(clusterJ);
879             label[j] = 1;
880             Clusters()->RemoveAt(j);
881             j=i; // <- Ernesto
882         } // J clusters  
883         label[i] = 1;
884     } // I clusters
885     Clusters()->Compress();
886
887     delete [] label;
888     return;
889 }
890 //________________________________________________________________________
891 void AliITSClusterFinderSDD::SelectClusters(){
892     // get number of clusters for this module
893     Int_t nofClusters = NClusters();
894
895     nofClusters -= fNclusters;
896     Int_t i;
897     for(i=0; i<nofClusters; i++) { 
898         AliITSRawClusterSDD *clusterI =(AliITSRawClusterSDD*) Cluster(i);
899         Int_t rmflg = 0;
900         Double_t wy = 0.;
901         if(clusterI->Anodes() != 0.) {
902             wy = ((Double_t) clusterI->Samples())/clusterI->Anodes();
903         } // end if
904         Int_t amp = (Int_t) clusterI->PeakAmpl();
905         Int_t cha = (Int_t) clusterI->Q();
906         if(amp < fMinPeak) rmflg = 1;  
907         if(cha < fMinCharge) rmflg = 1;
908         if(wy < fMinNCells) rmflg = 1;
909         //if(wy > fMaxNCells) rmflg = 1;
910         if(rmflg) Clusters()->RemoveAt(i);
911     } // I clusters
912     Clusters()->Compress();
913     return;
914 }
915
916 //______________________________________________________________________
917 void AliITSClusterFinderSDD::GetRecPoints(){
918     // get rec points
919   
920     // get number of clusters for this module
921     Int_t nofClusters = NClusters();
922     nofClusters -= fNclusters;
923     const Double_t kconvGeV = 1.e-6; // GeV -> KeV
924     const Double_t kconv = 1.0e-4; 
925     const Double_t kRMSx = 38.0*kconv; // microns->cm ITS TDR Table 1.3
926     const Double_t kRMSz = 28.0*kconv; // microns->cm ITS TDR Table 1.3
927     Int_t i;
928     Int_t ix, iz, idx=-1;
929     AliITSdigitSDD *dig=0;
930     Int_t ndigits=NDigits();
931
932     Int_t lay,lad,det;
933     fDetTypeRec->GetITSgeom()->GetModuleId(fModule,lay,lad,det);
934     Int_t ind=(lad-1)*fDetTypeRec->GetITSgeom()->GetNdetectors(lay)+(det-1);
935     Int_t lyr=(lay-1);
936
937
938     for(i=0; i<nofClusters; i++) { 
939         AliITSRawClusterSDD *clusterI = (AliITSRawClusterSDD*)Cluster(i);
940         if(!clusterI) Error("SDD: GetRecPoints","i clusterI ",i,clusterI);
941         if(clusterI) idx=clusterI->PeakPos();
942         if(idx>ndigits) Error("SDD: GetRecPoints","idx ndigits",idx,ndigits);
943         // try peak neighbours - to be done 
944         if(idx&&idx<= ndigits) dig =(AliITSdigitSDD*)GetDigit(idx);
945         if(!dig) {
946             // try cog
947             GetSeg()->GetPadIxz(clusterI->X(),clusterI->Z(),ix,iz);
948             dig = (AliITSdigitSDD*)Map()->GetHit(iz-1,ix-1);
949             // if null try neighbours
950             if (!dig) dig = (AliITSdigitSDD*)Map()->GetHit(iz-1,ix); 
951             if (!dig) dig = (AliITSdigitSDD*)Map()->GetHit(iz-1,ix+1); 
952             if (!dig) printf("SDD: cannot assign the track number!\n");
953         } //  end if !dig
954         AliITSRecPoint rnew(fDetTypeRec->GetITSgeom());
955         rnew.SetXZ(fModule,clusterI->X(),clusterI->Z());
956         rnew.SetQ(clusterI->Q());   // in KeV - should be ADC
957         rnew.SetdEdX(kconvGeV*clusterI->Q());
958         rnew.SetSigmaDetLocX2(kRMSx*kRMSx);
959         rnew.SetSigmaZ2(kRMSz*kRMSz);
960
961         if(dig) rnew.SetLabel(dig->GetTrack(0),0);
962         if(dig) rnew.SetLabel(dig->GetTrack(1),1);
963         if(dig) rnew.SetLabel(dig->GetTrack(2),2);
964         rnew.SetDetectorIndex(ind);
965         rnew.SetLayer(lyr);
966         fDetTypeRec->AddRecPoint(rnew);        
967     } // I clusters
968 //    Map()->ClearMap();
969 }
970 //______________________________________________________________________
971 void AliITSClusterFinderSDD::FindRawClusters(Int_t mod){
972     // find raw clusters
973     
974     SetModule(mod);
975     SetCutAmplitude(mod);
976     Int_t nanodes=GetSeg()->Npz();
977     Int_t noise=0;
978     for(Int_t i=0;i<nanodes;i++){
979       noise+=(Int_t)(((AliITSCalibrationSDD*)GetResp(mod))->GetNoiseAfterElectronics(i));
980     }    
981     SetMinPeak((noise/nanodes)*5);
982     Find1DClustersE();
983     GroupClusters();
984     SelectClusters();
985     ResolveClusters();
986     GetRecPoints();
987 }
988 //_______________________________________________________________________
989 void AliITSClusterFinderSDD::PrintStatus() const{
990     // Print SDD cluster finder Parameters
991
992     cout << "**************************************************" << endl;
993     cout << " Silicon Drift Detector Cluster Finder Parameters " << endl;
994     cout << "**************************************************" << endl;
995     cout << "Number of Clusters: " << fNclusters << endl;
996     cout << "Anode Tolerance: " << fDAnode << endl;
997     cout << "Time  Tolerance: " << fDTime << endl;
998     cout << "Time  correction (electronics): " << fTimeCorr << endl;
999     cout << "Cut Amplitude (threshold): " << fCutAmplitude[0] << endl;
1000     cout << "Minimum Amplitude: " << fMinPeak << endl;
1001     cout << "Minimum Charge: " << fMinCharge << endl;
1002     cout << "Minimum number of cells/clusters: " << fMinNCells << endl;
1003     cout << "Maximum number of cells/clusters: " << fMaxNCells << endl;
1004     cout << "**************************************************" << endl;
1005 }