bergamaschi c6d383f770 Solved bug on number of measurements
git-svn-id: file:///afs/psi.ch/project/sls_det_software/svn/slsDetectorSoftware@250 951219d9-93cf-4727-9268-0efd64621fa3
2012-09-11 09:13:52 +00:00

953 lines
19 KiB
C++

#include "slsDetectorUtils.h"
#include "usersFunctions.h"
#include "slsDetectorCommand.h"
#include "postProcessing.h"
#include "enCalLogClass.h"
#include "angCalLogClass.h"
#include <cstdlib>
#include <sys/ipc.h>
#include <sys/shm.h>
using namespace std;
slsDetectorUtils::slsDetectorUtils() {
#ifdef VERBOSE
cout << "setting callbacks" << endl;
#endif
acquisition_finished=NULL;
acqFinished_p=NULL;
measurement_finished=NULL;
measFinished_p=NULL;
registerGetPositionCallback(&defaultGetPosition, NULL);
registerConnectChannelsCallback(&defaultConnectChannels,NULL);
registerDisconnectChannelsCallback(&defaultDisconnectChannels,NULL);
registerGoToPositionCallback(&defaultGoToPosition,NULL);
registerGoToPositionNoWaitCallback(&defaultGoToPositionNoWait,NULL);
registerGetI0Callback(&defaultGetI0,NULL);
#ifdef VERBOSE
registerAcquisitionFinishedCallback(&dummyAcquisitionFinished,this);
registerMeasurementFinishedCallback(&dummyMeasurementFinished,this);
cout << "done " << endl;
#endif
};
void slsDetectorUtils::acquire(int delflag){
// setTotalProgress();
//moved these 2 here for measurement change
progressIndex=0;
*stoppedFlag=0;
angCalLogClass *aclog=NULL;
enCalLogClass *eclog=NULL;
// int lastindex=startindex, nowindex=startindex;
int connectChannels=0;
#ifdef VERBOSE
cout << "Acquire function "<< delflag << endl;
cout << "Stopped flag is "<< stoppedFlag << delflag << endl;
#endif
void *status;
if ((*correctionMask&(1<< ANGULAR_CONVERSION)) || (*correctionMask&(1<< I0_NORMALIZATION)) || getActionMode(angCalLog) || (getScanMode(0)==positionScan)|| (getScanMode(0)==positionScan)) {
if (connectChannels==0)
if (connect_channels) {
connect_channels(CCarg);
connectChannels=1;
}
}
if (getActionMode(angCalLog))
aclog=new angCalLogClass(this);
if (getActionMode(enCalLog))
eclog=new enCalLogClass(this);
pthread_mutex_lock(&mp);
resetFinalDataQueue();
resetDataQueue();
jointhread=0;
queuesize=0;
posfinished=0;
pthread_mutex_unlock(&mp);
if (*threadedProcessing) {
startThread(delflag);
}
#ifdef VERBOSE
cout << " starting thread " << endl;
#endif
int nm=1;
if (timerValue[MEASUREMENTS_NUMBER]>0)
nm=timerValue[MEASUREMENTS_NUMBER];
for(int im=0;im<nm;im++) {
#ifdef VERBOSE
cout << " starting measurement "<< im << " of " << nm << endl;
#endif
//cout << "data thread started " << endl;
int np=1;
if (*numberOfPositions>0)
np=*numberOfPositions;
int ns0=1;
if (*actionMask & (1 << MAX_ACTIONS)) {
ns0=nScanSteps[0];
}
if (ns0<1)
ns0=1;
int ns1=1;
if (*actionMask & (1 << (MAX_ACTIONS+1))) {
ns1=nScanSteps[1];
}
if (ns1<1)
ns1=1;
//loop measurements
setStartIndex(*fileIndex);
//cout << "action at start" << endl;
if (*stoppedFlag==0) {
executeAction(startScript);
}
for (int is0=0; is0<ns0; is0++) {
// cout << "scan0 loop" << endl;
if (*stoppedFlag==0) {
executeScan(0,is0);
} else
break;
for (int is1=0; is1<ns1; is1++) {
// cout << "scan1 loop" << endl;
if (*stoppedFlag==0) {
executeScan(1,is1);
} else
break;
if (*stoppedFlag==0) {
executeAction(scriptBefore);
} else
break;
currentPositionIndex=0;
for (int ip=0; ip<np; ip++) {
// cout << "positions " << endl;
if (*stoppedFlag==0) {
if (*numberOfPositions>0) {
moveDetector(detPositions[ip]);
currentPositionIndex=ip+1;
#ifdef VERBOSE
std::cout<< "moving to position" << std::endl;
#endif
}
} else
break;
createFileName();
if (*stoppedFlag==0) {
executeAction(scriptBefore);
} else
break;
if (*stoppedFlag==0) {
executeAction(headerBefore);
if (*correctionMask&(1<< ANGULAR_CONVERSION)) {
pthread_mutex_lock(&mp);
currentPosition=getDetectorPosition();
posfinished=0;
pthread_mutex_unlock(&mp);
}
if (aclog) {
if ((*correctionMask&(1<< ANGULAR_CONVERSION))==0) {
pthread_mutex_lock(&mp);
currentPosition=getDetectorPosition();
posfinished=0;
pthread_mutex_unlock(&mp);
}
aclog->addStep(currentPosition, getCurrentFileName());
}
if (eclog)
eclog->addStep(setDAC(-1,THRESHOLD), getCurrentFileName());
if (*correctionMask&(1<< I0_NORMALIZATION)) {
if (get_i0)
get_i0(0, IOarg);
}
startAndReadAll();
if (*correctionMask&(1<< I0_NORMALIZATION)) {
if (get_i0)
currentI0=get_i0(1,IOarg); // this is the correct i0!!!!!
}
pthread_mutex_lock(&mp);
posfinished=1;
pthread_mutex_unlock(&mp);
if (*threadedProcessing==0){
#ifdef VERBOSE
cout << "start unthreaded process data " << endl;
#endif
processData(delflag);
}
} else
break;
// wait until data processing thread has finished the data
pthread_mutex_lock(&mp);
while (queuesize){
pthread_mutex_unlock(&mp);
usleep(100000);
pthread_mutex_lock(&mp);
}
pthread_mutex_unlock(&mp);
if (*stoppedFlag==0) {
executeAction(headerAfter);
setLastIndex(*fileIndex);
} else {
setLastIndex(*fileIndex);
break;
}
if (*stoppedFlag) {
#ifdef VERBOSE
std::cout<< "exiting since the detector has been stopped" << std::endl;
#endif
break;
} else if (ip<(np-1)) {
*fileIndex=setStartIndex();
}
} // loop on position finished
//script after
if (*stoppedFlag==0) {
executeAction(scriptAfter);
} else
break;
if (*stoppedFlag) {
#ifdef VERBOSE
std::cout<< "exiting since the detector has been stopped" << std::endl;
#endif
break;
} else if (is1<(ns1-1)) {
*fileIndex=setStartIndex();
}
}
//end scan1 loop is1
if (*stoppedFlag) {
#ifdef VERBOSE
std::cout<< "exiting since the detector has been stopped" << std::endl;
#endif
break;
} else if (is0<(ns0-1)) {
*fileIndex=setStartIndex();
}
} //end scan0 loop is0
*fileIndex=setLastIndex();
if (*stoppedFlag==0) {
executeAction(stopScript);
} else
break;
// loop measurements
if (measurement_finished)
measurement_finished(im,*fileIndex,measFinished_p);
if (*stoppedFlag) {
break;
}
}
// waiting for the data processing thread to finish!
if (*threadedProcessing) {
pthread_mutex_lock(&mp);
jointhread=1;
pthread_mutex_unlock(&mp);
pthread_join(dataProcessingThread, &status);
}
if (connectChannels) {
if (disconnect_channels)
disconnect_channels(DCarg);
}
if (aclog)
delete aclog;
if (eclog)
delete eclog;
if (acquisition_finished)
acquisition_finished(getCurrentProgress(),getDetectorStatus(),acqFinished_p);
}
//Naveen change
int slsDetectorUtils::setTotalProgress() {
int nf=1, npos=1, nscan[MAX_SCAN_LEVELS]={1,1}, nc=1, nm=1;
if (timerValue[FRAME_NUMBER])
nf=timerValue[FRAME_NUMBER];
if (timerValue[CYCLES_NUMBER]>0)
nc=timerValue[CYCLES_NUMBER];
if (timerValue[MEASUREMENTS_NUMBER]>0)
nm=timerValue[MEASUREMENTS_NUMBER];
if (*numberOfPositions>0)
npos=*numberOfPositions;
if ((nScanSteps[0]>0) && (*actionMask & (1 << MAX_ACTIONS)))
nscan[0]=nScanSteps[0];
if ((nScanSteps[1]>0) && (*actionMask & (1 << (MAX_ACTIONS+1))))
nscan[1]=nScanSteps[1];
totalProgress=nm*nf*nc*npos*nscan[0]*nscan[1];
#ifdef VERBOSE
cout << "nc " << nc << endl;
cout << "nm " << nm << endl;
cout << "nf " << nf << endl;
cout << "npos " << npos << endl;
cout << "nscan[0] " << nscan[0] << endl;
cout << "nscan[1] " << nscan[1] << endl;
cout << "Set total progress " << totalProgress << endl;
#endif
return totalProgress;
}
int slsDetectorUtils::setBadChannelCorrection(string fname, int &nbadtot, int *badchanlist, int off){
int nbad;
int badlist[MAX_BADCHANS];
ifstream infile;
string str;
int interrupt=0;
int ich;
int chmin,chmax;
#ifdef VERBOSE
std::cout << "Setting bad channel correction to " << fname << std::endl;
#endif
int modmi=0, modma=1;
int singlefile=0;
string fn;
int offset=off;
nbadtot=0;
if (fname=="" || fname=="none") {
;
} else {
if (fname.find(".sn")==string::npos && fname.find(".chans")==string::npos) {
modma=setNumberOfModules();
singlefile=1;
}
for (int im=0; im<modma; im++) {
if (singlefile) {
ostringstream ostfn;
ostfn << fname << ".sn" << setfill('0') << setw(3) << hex << getId(MODULE_SERIAL_NUMBER, im);
fn=ostfn.str();
} else
fn=fname;
infile.open(fn.c_str(), ios_base::in);
if (infile.is_open()==0) {
std::cout << "could not open file " << fname <<std::endl;
return -1;
}
nbad=setBadChannelCorrection(infile, nbad, badlist, offset);
infile.close();
for (int ich=0; ich<nbad; ich++) {
if (nbadtot<MAX_BADCHANS) {
badchanlist[nbadtot]=badlist[ich];
nbadtot++;
}
}
offset+=getChansPerMod(im);
}
}
if (nbadtot>0 && nbadtot<MAX_BADCHANS) {
return nbadtot;
} else
return 0;
}
double slsDetectorUtils::getCurrentProgress() {
#ifdef VERBOSE
cout << progressIndex << " / " << totalProgress << endl;
#endif
return 100.*((double)progressIndex)/((double)totalProgress);
}
void slsDetectorUtils::incrementProgress() {
progressIndex++;
cout << fixed << setprecision(2) << setw (6) << getCurrentProgress() << " \%";
#ifdef VERBOSE
cout << endl;
#else
cout << "\r" << flush;
#endif
};
int slsDetectorUtils::testFunction(int times) {
int i,count=0;
runStatus s;
char controlval[1000];
char statusval[1000];
int nchans = getTotalNumberOfChannels();
short int dataVals[nchans];
for(i=0;i<times;i++){
sprintf(statusval,"%x",readRegister(0x25));
std::cout<<std::endl<<dec<<i+1<<": stat:\t"<<statusval<<"\t";
sprintf(controlval,"%x",readRegister(0x24));
std::cout<<"cont:"<<controlval<<"\t"<<std::endl;
startAcquisition();
sprintf(controlval,"%x",readRegister(0x24));
std::cout<<"cont:"<<controlval<<"\t"<<std::endl;
//sprintf(statusval,"%x",readRegister(0x25));
//std::cout<<statusval<<std::endl;
s = getRunStatus();
if(s==IDLE){
std::cout<<"IDLE\t"<<std::endl;
s = getRunStatus();
if(s==IDLE){
std::cout<<"IDLE"<<std::endl;
exit(-1);
}
;
}
else {
if (s==RUNNING){
count=0;
while(s==RUNNING){
count++;//std::cout<<"count:"<<count<<std::endl;
if(count==4){
sprintf(statusval,"%x",readRegister(0x25));
std::cout<<"STUCK: stat"<<statusval<<std::endl;
exit(-1);
}
usleep(50000);
//val=readRegister(0x25);
s = getRunStatus();
}
}
}
/* else{
std::cout<<"\nWeird Status. "<<runStatusType(s)<<" Exit\n";
exit(-1);
}*/
system("rm ~/wORKSPACE/scratch/run* ");
//system("more ~/wORKSPACE/scratch/run* ");
usleep(1000000);
setFileIndex(0);
int b;
b=setThreadedProcessing(-1);
setThreadedProcessing(0);
readAll();
processData(1);
setThreadedProcessing(b);
if(!readDataFile("/home/l_maliakal_d/wORKSPACE/scratch/run_1.raw",dataVals)){
std::cout<< "Could not open file "<< std::endl;
exit(-1);
}
std::cout<<std::endl;
for(int j=1277;j< (nchans);j++)
std::cout<<"\t"<<j<<":"<<dataVals[j];
if(dataVals[1278]!=2558){
std::cout<< "DATA ERROR!! "<< std::endl;
exit(-1);
}
}
std::cout<<std::endl;
return 0;
}
int slsDetectorUtils::retrieveDetectorSetup(string const fname1, int level){
slsDetectorCommand *cmd;
char ext[100];
int skip=0;
string fname;
string str;
ifstream infile;
int iargval;
int interrupt=0;
char *args[10];
char myargs[10][1000];
//args[0]=myargs[0];
//args[1]=myargs[1];
string sargname, sargval;
int iline=0;
if (level==2) {
// fname=fname1+string(".config");
// readConfigurationFile(fname);
#ifdef VERBOSE
cout << "config file read" << endl;
#endif
fname=fname1+string(".det");
} else
fname=fname1;
infile.open(fname.c_str(), ios_base::in);
if (infile.is_open()) {
cmd=new slsDetectorCommand(this);
while (infile.good() and interrupt==0) {
sargname="none";
sargval="0";
getline(infile,str);
iline++;
#ifdef VERBOSE
std::cout<< str << std::endl;
#endif
if (str.find('#')!=string::npos) {
#ifdef VERBOSE
std::cout<< "Line is a comment " << std::endl;
std::cout<< str << std::endl;
#endif
continue;
} else {
istringstream ssstr(str);
iargval=0;
while (ssstr.good()) {
ssstr >> sargname;
// if (ssstr.good()) {
strcpy(myargs[iargval],sargname.c_str());
args[iargval]=myargs[iargval];
#ifdef VERBOSE
std::cout<< args[iargval] << std::endl;
#endif
iargval++;
// }
skip=0;
}
if (level!=2) {
if (string(args[0])==string("flatfield"))
skip=1;
else if (string(args[0])==string("badchannels"))
skip=1;
else if (string(args[0])==string("trimbits"))
skip=1;
}
if (skip==0)
cmd->executeLine(iargval,args,PUT_ACTION);
}
iline++;
}
delete cmd;
infile.close();
} else {
std::cout<< "Error opening " << fname << " for reading" << std::endl;
return FAIL;
}
#ifdef VERBOSE
std::cout<< "Read " << iline << " lines" << std::endl;
#endif
return iline;
}
int slsDetectorUtils::dumpDetectorSetup(string const fname, int level){
slsDetectorCommand *cmd;
string names[]={
"fname",\
"index",\
"flags",\
"dr",\
"settings",\
"threshold",\
"exptime",\
"period",\
"delay",\
"gates",\
"frames",\
"cycles",\
"probes",\
"timing",\
"fineoff",\
"startscript",\
"startscriptpar",\
"stopscript",\
"stopscriptpar",\
"scriptbefore",\
"scriptbeforepar",\
"scriptafter",\
"scriptafterpar",\
"scan0script",\
"scan0par",\
"scan0prec",\
"scan0steps",\
"scan1script",\
"scan1par",\
"scan1prec",\
"scan1steps",\
"ratecorr",\
"flatfield",\
"badchannels",\
"trimbits"
};
int nvar=35;
char ext[100];
int iv=0;
string fname1;
ofstream outfile;
char *args[2];
for (int ia=0; ia<2; ia++) {
args[ia]=new char[1000];
}
int nargs;
if (level==2)
nargs=2;
else
nargs=1;
if (level==2) {
fname1=fname+string(".config");
writeConfigurationFile(fname1);
fname1=fname+string(".det");
} else
fname1=fname;
outfile.open(fname1.c_str(),ios_base::out);
if (outfile.is_open()) {
cmd=new slsDetectorCommand(this);
for (iv=0; iv<nvar-3; iv++) {
strcpy(args[0],names[iv].c_str());
outfile << names[iv] << " " << cmd->executeLine(1,args,GET_ACTION) << std::endl;
}
strcpy(args[0],names[iv].c_str());
if (level==2) {
fname1=fname+string(".ff");
strcpy(args[1],fname1.c_str());
}
outfile << names[iv] << " " << cmd->executeLine(nargs,args,GET_ACTION) << std::endl;
iv++;
strcpy(args[0],names[iv].c_str());
if (level==2) {
fname1=fname+string(".bad");
strcpy(args[1],fname1.c_str());
}
outfile << names[iv] << " " << cmd->executeLine(nargs,args,GET_ACTION) << std::endl;
iv++;
if (level==2) {
strcpy(args[0],names[iv].c_str());
size_t c=fname.rfind('/');
if (c<string::npos) {
fname1=fname.substr(0,c+1)+string("trim_")+fname.substr(c+1);
} else {
fname1=string("trim_")+fname;
}
strcpy(args[1],fname1.c_str());
#ifdef VERBOSE
std::cout<< "writing to file " << fname1 << std::endl;
#endif
outfile << names[iv] << " " << cmd->executeLine(nargs,args,GET_ACTION) << std::endl;
iv++;
}
delete cmd;
outfile.close();
}
else {
std::cout<< "Error opening parameters file " << fname1 << " for writing" << std::endl;
return FAIL;
}
#ifdef VERBOSE
std::cout<< "wrote " <<iv << " lines to "<< fname1 << std::endl;
#endif
return 0;
}
// int slsDetectorUtils::setFlatFieldCorrectionFile(string fname){
// int tch=getTotalNumberOfChannels();
// double data[tch], xmed[tch];
// double ffcoefficients[tch], fferrors[tch];
// int nmed=0;
// int idet=0, ichdet=-1;
// char ffffname[MAX_STR_LENGTH*2];
// int nbad=0, nch;
// int badlist[MAX_BADCHANS];
// int im=0;
// if (fname=="default") {
// fname=string(flatFieldFile);
// }
// if (fname=="") {
// #ifdef VERBOSE
// std::cout<< "disabling flat field correction" << std::endl;
// #endif
// (*correctionMask)&=~(1<<FLAT_FIELD_CORRECTION);
// // strcpy(thisMultiDetector->flatFieldFile,"none");
// setFlatFieldCorrection(NULL, NULL);
// } else {
// #ifdef VERBOSE
// std::cout<< "Setting flat field correction from file " << fname << std::endl;
// #endif
// sprintf(ffffname,"%s/%s",flatFieldDir,fname.c_str());
// nch=readDataFile(string(ffffname),data);
// if (nch>tch)
// nch=tch;
// if (nch>0) {
// strcpy(flatFieldFile,fname.c_str());
// nbad=0;
// for (int ichan=0; ichan<nch; ichan++) {
// if (data[ichan]>0) {
// /* add to median */
// im=0;
// while ((im<nmed) && (xmed[im]<data[ichan]))
// im++;
// for (int i=nmed; i>im; i--)
// xmed[i]=xmed[i-1];
// xmed[im]=data[ichan];
// nmed++;
// } else {
// if (nbad<MAX_BADCHANS) {
// badlist[nbad]=ichan;
// nbad++;
// }
// }
// }
// if (nmed>1 && xmed[nmed/2]>0) {
// #ifdef VERBOSE
// std::cout<< "Flat field median is " << xmed[nmed/2] << " calculated using "<< nmed << " points" << std::endl;
// #endif
// thisMultiDetector->correctionMask|=(1<<FLAT_FIELD_CORRECTION);
// // add to ff coefficients and errors of single detectors
// for (int ichan=0; ichan<nch; ichan++) {
// setFlatFieldCorrection(ffcoefficients, fferrors);
// if (data[ichan]>0) {
// ffcoefficients[ichan]=xmed[nmed/2]/data[ichan];
// fferrors[ichan]=ffcoefficients[ichan]*sqrt(data[ichan])/data[ichan];
// } else {
// ffcoefficients[ichan]=0.;
// fferrors[ichan]=1.;
// }
// }
// setFlatFieldCorrection(ffcoefficients, fferrors);
// } else {
// std::cout<< "Flat field data from file " << fname << " are not valid (" << nmed << "///" << xmed[nmed/2] << std::endl;
// thisMultiDetector->correctionMask&=~(1<<FLAT_FIELD_CORRECTION);
// for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
// if (detectors[i])
// detectors[i]->setFlatFieldCorrection(NULL, NULL);
// }
// return -1;
// }
// } else {
// std::cout<< "Flat field from file " << fname << " is not valid " << nch << std::endl;
// thisMultiDetector->correctionMask&=~(1<<FLAT_FIELD_CORRECTION);
// for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
// if (detectors[i])
// detectors[i]->setFlatFieldCorrection(NULL, NULL);
// }
// return -1;
// }
// }
// return thisMultiDetector->correctionMask&(1<<FLAT_FIELD_CORRECTION);
// }