scripting stuff added

git-svn-id: file:///afs/psi.ch/project/sls_det_software/svn/slsDetectorSoftware@26 951219d9-93cf-4727-9268-0efd64621fa3

slsDetectorSoftware/mythenDetector/mythenDetector.cpp

@@ -330,11 +330,12 @@ string mythenDetector::executeLine(int narg, char *args[], int action) {
   }  else if (var=="trimen") {
     if (action==PUT_ACTION) {
       sscanf(args[1],"%d",&ival);
-      std::cout<< ival << std::endl ;
+      //std::cout<< ival << std::endl ;
+      if (ival>narg-2)
+	ival=narg-2;
       int ene[ival];
       for (int ie=0; ie<ival; ie++) {
-	std::cout<< ie << " " << args[2+ie] ;
+	sscanf(args[2+ie],"%d",ene+ie);
-	std::cout<< sscanf(args[2+ie],"%d",ene+ie)<< std::endl;;
       }
       setTrimEn(ival,ene);
     }
@@ -363,6 +364,196 @@ string mythenDetector::executeLine(int narg, char *args[], int action) {
     sprintf(answer,"%d",setOnline());
     return string(answer);
   }
+  else if (var=="startscript") {
+    ival=startScript;
+    if (action==PUT_ACTION) {
+      setAction(ival,args[1]);
+    }
+    sprintf(answer,"%d %s",getActionMode(ival), getActionScript(ival).c_str());
+    return string(answer);
+  } else if (var=="startscriptpar") {
+    ival=startScript;
+    if (action==PUT_ACTION) {
+      setActionParameter(ival,args[1]);
+    }
+    
+    return getActionParameter(ival);
+
+
+  } else if (var=="stopscript") {
+    ival=stopScript;
+    if (action==PUT_ACTION) {
+      setAction(ival,args[1]);
+    }
+    sprintf(answer,"%d %s",getActionMode(ival), getActionScript(ival).c_str());
+    return string(answer);
+  } else if (var=="stopscriptpar") {
+    ival=stopScript;
+    if (action==PUT_ACTION) {
+      setActionParameter(ival,args[1]);
+    }
+    return getActionParameter(ival);
+
+  } else if (var=="scriptbefore") {
+    ival=scriptBefore;
+    if (action==PUT_ACTION) {
+      setAction(ival,args[1]);
+    }
+    sprintf(answer,"%d %s",getActionMode(ival), getActionScript(ival).c_str());
+    return string(answer);
+  } else if (var=="scriptbeforepar") {
+    ival=scriptBefore;
+    if (action==PUT_ACTION) {
+      setActionParameter(ival,args[1]);
+    }
+
+    return getActionParameter(ival);
+
+  } else if (var=="scriptafter") {
+    ival=scriptAfter;
+    if (action==PUT_ACTION) {
+      setAction(ival,args[1]);
+    }
+    sprintf(answer,"%d %s",getActionMode(ival), getActionScript(ival).c_str());
+    return string(answer);
+  } else if (var=="scriptafterpar") {
+    ival=scriptAfter;
+    if (action==PUT_ACTION) {
+      setActionParameter(ival,args[1]);
+    }
+    return getActionParameter(ival);
+    
+
+
+  } else if (var=="headerafter") {
+    ival=headerAfter;
+    if (action==PUT_ACTION) {
+      setAction(ival,args[1]);
+    }
+    sprintf(answer,"%d %s",getActionMode(ival), getActionScript(ival).c_str());
+    return string(answer);
+  } else if (var=="headerafterpar") {
+    ival=headerAfter;
+    if (action==PUT_ACTION) {
+      setActionParameter(ival,args[1]);
+    }
+    return getActionParameter(ival);
+    
+
+
+  } else if (var=="headerbefore") {
+    ival=headerBefore;
+    if (action==PUT_ACTION) {
+      setAction(ival,args[1]);
+    }
+    sprintf(answer,"%d %s",getActionMode(ival), getActionScript(ival).c_str());
+    return string(answer);
+  } else if (var=="headerbeforepar") {
+    ival=headerBefore;
+    if (action==PUT_ACTION) {
+      setActionParameter(ival,args[1]);
+    }
+    return getActionParameter(ival);
+  } 
+
+  else if (var=="scan0script") {
+    int ind=0;
+    if (action==PUT_ACTION) {
+      setScanScript(ind,args[1]);
+    }
+    return getScanScript(ind);
+  } else if (var=="scan0par") {
+    int ind=0;
+    if (action==PUT_ACTION) {
+      setScanParameter(ind,args[1]);
+    }
+    return getScanParameter(ind);
+  } else if (var=="scan0prec") {
+    int ind=0;
+    if (action==PUT_ACTION) {
+      sscanf(args[1],"%d",&ival);
+      setScanPrecision(ind,ival);
+    }
+    sprintf(answer,"%d",getScanPrecision(ind));
+    return string(answer);
+  } else if (var=="scan0steps") {
+    int ind=0;
+    if (action==PUT_ACTION) {
+      sscanf(args[1],"%d",&ival);
+      //cout << ival << " " << narg << endl;
+      if (ival>narg-2)
+	ival=narg-2;
+      float ene[ival];
+      for (int ie=0; ie<ival; ie++) {
+	sscanf(args[2+ie],"%f",ene+ie);
+      }
+      setScanSteps(ind,ival,ene);
+    }  
+    int nen=getScanSteps(ind);
+    sprintf(answer,"%d",nen);
+    float oen[nen];
+    getScanSteps(ind,oen);
+    char form[20];
+    sprintf(form,"%%s %%0.%df",getScanPrecision(ind));
+    for (int ie=0; ie<nen;ie++) {
+      sprintf(answer,form,answer,oen[ie]);
+    }
+    return string(answer);
+  } 
+
+
+  else if (var=="scan1script") {
+    int ind=1;
+    if (action==PUT_ACTION) {
+      setScanScript(ind,args[1]);
+    }
+    return getScanScript(ind);
+  } else if (var=="scan1par") {
+    int ind=1;
+    if (action==PUT_ACTION) {
+      setScanParameter(ind,args[1]);
+    }
+    return getScanParameter(ind);
+  } else if (var=="scan1prec") {
+    int ind=1;
+    if (action==PUT_ACTION) {
+      sscanf(args[1],"%d",&ival);
+      setScanPrecision(ind,ival);
+    }
+    sprintf(answer,"%d",getScanPrecision(ind));
+    return string(answer);
+  } else if (var=="scan1steps") {
+    int ind=1;
+    if (action==PUT_ACTION) {
+      sscanf(args[1],"%d",&ival);
+      if (ival>narg-2)
+	ival=narg-2;
+      float ene[ival];
+      for (int ie=0; ie<ival; ie++) {
+	sscanf(args[2+ie],"%f",ene+ie);
+      }
+      setScanSteps(ind,ival,ene);
+    }  
+    int nen=getScanSteps(ind);
+    sprintf(answer,"%d",nen);
+    float oen[nen];
+    getScanSteps(ind,oen);
+    char form[20];
+    sprintf(form,"%%s %%0.%df",getScanPrecision(ind));
+    for (int ie=0; ie<nen;ie++) {
+      sprintf(answer,form,answer,oen[ie]);
+    }
+    return string(answer);
+  } 
+
+
+
+
+
+
+
+
+
 
 
 
@@ -837,6 +1028,71 @@ string mythenDetector::helpLine( int action) {
     os << std::endl;
     os << "trimen nen [e0 e1...en] \t sets the number of energies for which trimbit files exist and their value"<< std::endl;
     os << std::endl;
+
+
+
+
+
+
+
+
+    os << "startscript script \t sets script to execute at the beginning of the measurements - \"none\" to unset - will be launched as a system call with arguments nrun=fileindex par=startscriptpar"<< std::endl;
+    os << std::endl;
+    os << "startscriptpar par \t sets start script parameter (see startscript)"<< std::endl;
+    os << std::endl;
+
+    os << "scan0script script \t sets script to launch at level 0 scan. If \"energy\" energy scan, if \"threshold\" threshold scan, if \"trimbits\" trimbits scan, \"none\" unsets otherwise will be launched as a system call with arguments nrun=fileindex fn=filename var=scan0var par=scan0par"<< std::endl;
+    os << std::endl;
+    os << "scan0par par\t sets the level 0 scan parameter. See scan0script"<< std::endl;
+    os << std::endl;
+    os << "scan0prec n \t sets the level 0 scan precision for the output file name. See scan0script"<< std::endl;
+    os << std::endl;
+    os << "scan0steps nsteps [s0 s1...] \t sets the level 0 scan steps. See scan0script - nsteps=0 unsets the scan level"<< std::endl;
+    os << std::endl;
+
+
+    os << "scan1script script \t sets script to launch at level 1 scan. If \"energy\" energy scan, if \"threshold\" threshold scan, if \"trimbits\" trimbits scan, \"none\" unsets otherwise will be launched as a system call with arguments nrun=fileindex fn=filename var=scan1var par=scan1par"<< std::endl;
+    os << std::endl;
+
+    os << "scan1par par\t sets the level 1 scan parameter. See scan1script"<< std::endl;
+    os << std::endl;
+    os << "scan1prec n \t sets the level 1 scan precision for the output file name. See scan1script"<< std::endl;
+    os << std::endl;
+    os << "scan1steps nsteps [s0 s1...] \t sets the level 1 scan steps. See scan1script - nsteps=0 unsets the scan level"<< std::endl;
+    os << std::endl;
+
+
+    os << "scriptbefore script \t sets script to execute at the beginning of the realtime acquisition - \"none\" to unset - will be launched as a system call with arguments nrun=fileindex fn=filename par=scriptbeforepar sv0=scan0var sv1=scan1var p0=scan0par p1=scan1par"<< std::endl;
+    os << std::endl;
+    os << "scriptbeforepar \t sets  script before parameter (see scriptbefore)"<< std::endl;
+    os << std::endl;
+
+    os << "headerbefore script \n script to launch to acquire the headerfile just before  the acquisition -  \"none\" to unset - will be launched as a system call with arguments nrun=fileindex fn=filename acqtime=t gainmode=sett threshold=thr badfile=badf angfile=angf bloffset=bloffset fineoffset=fineoffset fffile=ffile tau=taucorr par=headerbeforepar"<< std::endl;
+    os << std::endl;
+    os << "headerbeforepar \t sets header before parameter (see headerbefore)"<< std::endl;
+    os << std::endl;
+
+
+    os << "headerafter script \n script to launch to acquire the headerfile just after the acquisition -  \"none\" to unset - will be launched as a system call with arguments nrun=fileindex fn=filename acqtime=t gainmode=sett threshold=thr badfile=badf angfile=angf bloffset=bloffset fineoffset=fineoffset fffile=ffile tau=taucorr par=headerafterpar"<< std::endl;
+    os << std::endl;
+    os << "headerafterpar par \t sets header after parameter (see headerafter)"<< std::endl;
+    os << std::endl;
+
+    os << "scriptafter script \t sets script to execute at the end of the realtime acquisition - \"none\" to unset - will be launched as a system call with arguments nrun=fileindex fn=filename par=scriptafterpar sv0=scan0var sv1=scan1var p0=scan0par p1=scan1par"<< std::endl;
+    os << std::endl;
+    os << "scriptafterpar par \t sets  script after parameter (see scriptafter)"<< std::endl;
+    os << std::endl;
+
+
+    os << "stopscript script \t sets script to execute at the end of the measurements - \"none\" to unset - will be launched as a system call with arguments nrun=fileindex par=stopscriptpar"<< std::endl;
+    os << std::endl;
+    os << "stopscriptpar par\t sets stop script parameter (see stopscript)"<< std::endl;
+    os << std::endl;
+
+
+
+
+
     os << "outdir \t directory to which the files will be written by default" << std::endl;
     os << std::endl;
     os <<  "fname \t filename to which the files will be written by default (to which file and position indexes will eventually be attached)" << std::endl;
@@ -940,6 +1196,85 @@ string mythenDetector::helpLine( int action) {
     os << "trimdir \t Gets path of the trim files " << std::endl;
     os << std::endl;
     os << "trimen \t returns the number of energies for which trimbit files exist and their values"<< std::endl;
+
+
+
+
+
+
+    os << "startscript \t gets script to execute at the beginning of the measurements - \"none\" to unset - will be launched as a system call with arguments nrun=fileindex par=startscriptpar"<< std::endl;
+    os << std::endl;
+    os << "startscriptpar \t gets start script parameter (see startscript)"<< std::endl;
+    os << std::endl;
+
+    os << "scan0script \t gets script to launch at level 0 scan. If \"energy\" energy scan, if \"threshold\" threshold scan, if \"trimbits\" trimbits scan, \"none\" unsets otherwise will be launched as a system call with arguments nrun=fileindex fn=filename var=scan0var par=scan0par"<< std::endl;
+    os << std::endl;
+    os << "scan0par \t gets the level 0 scan parameter. See scan0script"<< std::endl;
+    os << std::endl;
+    os << "scan0prec \t gets the level 0 scan precision for the output file name. See scan0script"<< std::endl;
+    os << std::endl;
+    os << "scan0steps \t gets the level 0 scan steps. See scan0script - nsteps=0 unsets the scan level"<< std::endl;
+    os << std::endl;
+
+
+    os << "scan1script \t gets script to launch at level 1 scan. If \"energy\" energy scan, if \"threshold\" threshold scan, if \"trimbits\" trimbits scan, \"none\" unsets otherwise will be launched as a system call with arguments nrun=fileindex fn=filename var=scan1var par=scan1par"<< std::endl;
+    os << std::endl;
+
+    os << "scan1par \t gets the level 1 scan parameter. See scan1script"<< std::endl;
+    os << std::endl;
+    os << "scan1prec \t gets the level 1 scan precision for the output file name. See scan1script"<< std::endl;
+    os << std::endl;
+    os << "scan1steps \t gets the level 1 scan steps. See scan1script - nsteps=0 unsets the scan level"<< std::endl;
+    os << std::endl;
+
+
+    os << "scriptbefore \t gets script to execute at the beginning of the realtime acquisition - \"none\" to unset - will be launched as a system call with arguments nrun=fileindex fn=filename par=scriptbeforepar sv0=scan0var sv1=scan1var p0=scan0par p1=scan1par"<< std::endl;
+    os << std::endl;
+    os << "scriptbeforepar \t gets  script before parameter (see scriptbefore)"<< std::endl;
+    os << std::endl;
+
+    os << "headerbefore \n gets the script to launch to acquire the headerfile just before  the acquisition -  \"none\" to unset - will be launched as a system call with arguments nrun=fileindex fn=filename acqtime=t gainmode=sett threshold=thr badfile=badf angfile=angf bloffset=bloffset fineoffset=fineoffset fffile=ffile tau=taucorr par=headerbeforepar"<< std::endl;
+    os << std::endl;
+    os << "headerbeforepar \t gets header before parameter (see headerbefore)"<< std::endl;
+    os << std::endl;
+
+
+    os << "headerafter \n gets the script to launch to acquire the headerfile just after the acquisition -  \"none\" to unset - will be launched as a system call with arguments nrun=fileindex fn=filename acqtime=t gainmode=sett threshold=thr badfile=badf angfile=angf bloffset=bloffset fineoffset=fineoffset fffile=ffile tau=taucorr par=headerafterpar"<< std::endl;
+    os << std::endl;
+    os << "headerafterpar \t gets header after parameter (see headerafter)"<< std::endl;
+    os << std::endl;
+
+    os << "scriptafter \t gets script to execute at the end of the realtime acquisition - \"none\" to unset - will be launched as a system call with arguments nrun=fileindex fn=filename par=scriptafterpar sv0=scan0var sv1=scan1var p0=scan0par p1=scan1par"<< std::endl;
+    os << std::endl;
+    os << "scriptafterpar \t gets  script after parameter (see scriptafter)"<< std::endl;
+    os << std::endl;
+
+
+    os << "stopscript \t gets script to execute at the end of the measurements - \"none\" to unset - will be launched as a system call with arguments nrun=fileindex par=stopscriptpar"<< std::endl;
+    os << std::endl;
+    os << "stopscriptpar\t gets stop script parameter (see stopscript)"<< std::endl;
+    os << std::endl;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
     os << "outdir \t directory to which the files will be written by default" << std::endl;
     os << std::endl;
       os <<  "fname \t filename to which the files will be written by default (to which file and position indexes will eventually be attached)" << std::endl;
@@ -1564,7 +1899,7 @@ int mythenDetector::retrieveDetectorSetup(string fname1, int level){
       strcpy(thisDetector->trimFile,fname.c_str());
       return myMod;
     } else {
-      std::cout<< "could not open file " <<  myfname<< std::endl;
+      std::cout<< "could not open trim file " <<  myfname << std::endl;
       if (nflag)
 	deleteModule(myMod);
       return NULL;
@@ -1921,9 +2256,17 @@ int mythenDetector::setAngularConversion(string fname) {
   if (fname=="") {
     thisDetector->correctionMask&=~(1<< ANGULAR_CONVERSION);
     //strcpy(thisDetector->angConvFile,"none");
+    //#ifdef VERBOSE
+     std::cout << "Unsetting angular conversion" <<  std::endl;
+    //#endif
   } else {
-    if (fname=="default")
+    if (fname=="default") {
       fname=string(thisDetector->angConvFile);
+    }
+    
+    //#ifdef VERBOSE
+     std::cout << "Setting angular conversion to" << fname << std:: endl;
+    //#endif
     if (readAngularConversion(fname)>=0) {
       thisDetector->correctionMask|=(1<< ANGULAR_CONVERSION);
       strcpy(thisDetector->angConvFile,fname.c_str());
@@ -1932,6 +2275,12 @@ int mythenDetector::setAngularConversion(string fname) {
   return thisDetector->correctionMask&(1<< ANGULAR_CONVERSION);
 }
 
+
+
+
+
+
+
 int mythenDetector::getAngularConversion(int &direction,  angleConversionConstant *angconv) {
   direction=thisDetector->angDirection;
     if (angconv) {
@@ -2064,7 +2413,6 @@ int  mythenDetector::addToMerging(float *p1, float *v1, float *e1, float *mp, fl
   int ibin=0;
   int imod;
   float ang=0;
-
   if (thisDetector->binSize>0)
     binsize=thisDetector->binSize;
   else 
@@ -2133,10 +2481,19 @@ int  mythenDetector::addToMerging(float *p1, float *v1, float *e1, float *mp, fl
 
 void  mythenDetector::acquire(int delflag){
   void *status;
-#ifdef VERBOSE
+  //#ifdef VERBOSE
-  int iloop=0;
+  //int iloop=0;
-#endif
+  //#endif
+  int trimbit;
+  int startindex=thisDetector->fileIndex;
+  int lastindex=startindex;
+  char cmd[MAX_STR_LENGTH];
+  //string sett;
+
   thisDetector->progressIndex=0;
+  thisDetector->stoppedFlag=0;
+
+
 
   resetFinalDataQueue();
   resetDataQueue();
@@ -2144,6 +2501,11 @@ void  mythenDetector::acquire(int delflag){
 
   jointhread=0;
   queuesize=0;
+
+
+
+
+
   if (thisDetector->threadedProcessing) {
     startThread(delflag);
   }
@@ -2152,9 +2514,119 @@ void  mythenDetector::acquire(int delflag){
   if (thisDetector->numberOfPositions>0) 
     np=thisDetector->numberOfPositions;
 
+  int ns0=1;
+  if (thisDetector->actionMask & (1 << MAX_ACTIONS)) {
+    ns0=thisDetector->nScanSteps[0];
+  }
+  if (ns0<1)
+    ns0=1;
+
+
+  int ns1=1;
+  if (thisDetector->actionMask & (1 << (MAX_ACTIONS+1))) {
+    ns1=thisDetector->nScanSteps[1];
+  }
+  if (ns1<1)
+    ns1=1;
+
+
+
+
+
+  //action at start
+  if (thisDetector->stoppedFlag==0) {
+      if (thisDetector->actionMask & (1 << startScript)) {
+	//"Custom start script. The arguments are passed as nrun=n par=p.");
+	sprintf(cmd,"%s nrun=%d par=%s",thisDetector->actionScript[startScript],thisDetector->fileIndex,thisDetector->actionParameter[startScript]);
+#ifdef VERBOSE
+	cout << "Executing start script " << cmd << endl;
+#endif
+	system(cmd);
+      }
+  }
+
+  for (int is0=0; is0<ns0; is0++) {//scan0 loop
+
+  if (thisDetector->stoppedFlag==0) {
+
+    currentScanVariable[0]=thisDetector->scanSteps[0][is0];
+
+    switch(thisDetector->scanMode[0]) {
+    case 1:
+      setThresholdEnergy((int)currentScanVariable[0]); //energy scan
+      break;
+    case 2:
+      setDAC(currentScanVariable[0],THRESHOLD); // threshold scan
+      break;
+    case 3:
+      trimbit=(int)currentScanVariable[0];
+      setChannel((trimbit<<((int)TRIMBIT_OFF))|((int)COMPARATOR_ENABLE)); // trimbit scan
+      break;
+    case 0:
+       currentScanVariable[0]=0;
+       break;
+    default:
+    //Custom scan script level 0. The arguments are passed as nrun=n fn=filename var=v par=p"
+      sprintf(cmd,"%s nrun=%d fn=%s var=%f par=%s",thisDetector->scanScript[0],thisDetector->fileIndex,createFileName().c_str(),currentScanVariable[0],thisDetector->scanParameter[0]);
+#ifdef VERBOSE
+      cout << "Executing scan script 0 " << cmd << endl;
+#endif
+      system(cmd);
+     
+
+    }
+  } else
+    break;
+  
+
+  for (int is1=0; is1<ns0; is1++) {//scan0 loop
+
+     if (thisDetector->stoppedFlag==0) {
+
+    currentScanVariable[1]=thisDetector->scanSteps[1][is1];
+
+    switch(thisDetector->scanMode[1]) {
+    case 1:
+      setThresholdEnergy((int)currentScanVariable[1]); //energy scan
+      break;
+    case 2:
+      setDAC(currentScanVariable[1],THRESHOLD); // threshold scan
+      break;
+    case 3:
+      trimbit=(int)currentScanVariable[1];
+      setChannel((trimbit<<((int)TRIMBIT_OFF))|((int)COMPARATOR_ENABLE)); // trimbit scan
+      break;
+    case 0:
+       currentScanVariable[1]=0;
+       break;
+    default:
+    //Custom scan script level 1. The arguments are passed as nrun=n fn=filename var=v par=p"
+      sprintf(cmd,"%s nrun=%d fn=%s var=%f par=%s",thisDetector->scanScript[1],thisDetector->fileIndex,createFileName().c_str(),currentScanVariable[1],thisDetector->scanParameter[1]);
+#ifdef VERBOSE
+      cout << "Executing scan script 1 " << cmd << endl;
+#endif
+      system(cmd);
+    }
+  
+     } else
+       break;
+
+     if (thisDetector->stoppedFlag==0) {
+       if (thisDetector->actionMask & (1 << scriptBefore)) {
+	 //Custom script before each frame. The arguments are passed as nrun=n fn=filename par=p sv0=scanvar0 sv1=scanvar1 p0=par0 p1=par1"
+	 sprintf(cmd,"%s nrun=%d fn=%s par=%s sv0=%f sv1=%f p0=%s p1=%s",thisDetector->actionScript[scriptBefore],thisDetector->fileIndex,createFileName().c_str(),thisDetector->actionParameter[scriptBefore],currentScanVariable[0],currentScanVariable[1],thisDetector->scanParameter[0],thisDetector->scanParameter[1]);
+#ifdef VERBOSE
+	 cout << "Executing script before " << cmd << endl;
+#endif
+	 system(cmd);
+       }
+     } else
+       break;
+
      currentPositionIndex=0;
      
      for (int ip=0; ip<np; ip++) {
+       if (thisDetector->stoppedFlag==0) {
 	 if  (thisDetector->numberOfPositions>0) {
 	   go_to_position (thisDetector->detPositions[ip]);
 	   currentPositionIndex=ip+1;
@@ -2162,65 +2634,149 @@ void  mythenDetector::acquire(int delflag){
 	   std::cout<< "moving to position" << std::endl;
 #endif
 	 } 
+       } else
+	 break;
+       
+	 //write header before?
+	 //cmd=headerBeforeScript;
+	 //Custom script to write the header. \n The arguments will be passed as nrun=n fn=filenam acqtime=t gainmode=g threshold=thr badfile=badf angfile=angf bloffset=blo fineoffset=fo fffile=fffn tau=deadtau par=p")
+       
+       if (thisDetector->stoppedFlag==0) {
 	 if (thisDetector->correctionMask&(1<< I0_NORMALIZATION))
 	   currentI0=get_i0();
-    //write header before?
+	 if (thisDetector->actionMask & (1 << headerBefore)) {
+	   //Custom script after each frame. The arguments are passed as nrun=n fn=filename par=p sv0=scanvar0 sv1=scanvar1 p0=par0 p1=par1"
+	   sprintf(cmd,"%s nrun=%d fn=%s acqtime=%f gainmode=%d threshold=%d badfile=%s angfile=%s bloffset=%f fineoffset=%f fffile=%s/%s tau=%f par=%s",thisDetector->actionScript[headerBefore],thisDetector->fileIndex,createFileName().c_str(),((float)thisDetector->timerValue[ACQUISITION_TIME])*1E-9, thisDetector->currentSettings, thisDetector->currentThresholdEV, getBadChannelCorrectionFile().c_str(), getAngularConversion().c_str(), thisDetector->globalOffset, thisDetector->fineOffset,getFlatFieldCorrectionDir(),getFlatFieldCorrectionFile(), getRateCorrectionTau(), thisDetector->actionParameter[headerBefore]);
+#ifdef VERBOSE
+	   cout << "Executing header after " << cmd << endl;
+#endif
+	   system(cmd);
+	 }
+       } else
+	 break;
        
+       
+       
+       if (thisDetector->stoppedFlag==0) {
 	 startAndReadAll();
 	 
-    //write header after?
-    if (thisDetector->correctionMask&(1<< I0_NORMALIZATION))
-      currentI0=get_i0();
 	 if (thisDetector->correctionMask&(1<< ANGULAR_CONVERSION))
 	   currentPosition=get_position();  
 	 
+	 if (thisDetector->correctionMask&(1<< I0_NORMALIZATION))
+	   currentI0=get_i0()-currentI0;
+	 
 	 
 	 if (thisDetector->threadedProcessing==0)
 	   processData(delflag); 
 	 
-#ifdef ACQVERBOSE
+	 
-    std::cout<< "--------------------------------------------------waiting to empty raw data queue " << queuesize << std::endl ;
+       } else
-#endif
+	 break;
+       
        //while (!dataQueue.empty()){
        while (queuesize){
 	 usleep(100);
-// #ifdef VERBOSE
-//        if (iloop%10000==0)
-//  	std::cout<< "--------------------------------------------------looping raw data queue " << queuesize << std::endl ;
-//        // 	//std::cout<< "--------------------------------------------------looping raw data queue " << dataQueue.size() << std::endl ;
-//       iloop++;
-//       //usleep(100000);
-// #endif
        }
     
-#ifdef ACQVERBOSE
+
-    std::cout<< "----------------------------------------------------raw data queue is empty!" << std::endl ;
+    if (thisDetector->fileIndex>lastindex)
+      lastindex=thisDetector->fileIndex;
+
+    if (thisDetector->stoppedFlag==0) {
+      if (thisDetector->actionMask & (1 << headerAfter)) {
+	//Custom script after each frame. The arguments are passed as nrun=n fn=filename par=p sv0=scanvar0 sv1=scanvar1 p0=par0 p1=par1"
+	sprintf(cmd,"%s nrun=%d fn=%s acqtime=%f gainmode=%d threshold=%d badfile=%s angfile=%s bloffset=%f fineoffset=%f fffile=%s/%s tau=%f par=%s", \
+		thisDetector->actionScript[headerAfter],		\
+	      thisDetector->fileIndex,\
+		createFileName().c_str(),				\
+		((float)thisDetector->timerValue[ACQUISITION_TIME])*1E-9, \
+		thisDetector->currentSettings,				\
+		thisDetector->currentThresholdEV,			\
+		getBadChannelCorrectionFile().c_str(),			\
+		getAngularConversion().c_str(),				\
+		thisDetector->globalOffset,				\
+		thisDetector->fineOffset,				\
+		getFlatFieldCorrectionDir(),				\
+		getFlatFieldCorrectionFile(),				\
+		getRateCorrectionTau(),					\
+		thisDetector->actionParameter[headerAfter]);
+#ifdef VERBOSE
+	cout << "Executing header after " << cmd << endl;
 #endif
+	system(cmd);
+      }
+    } else
+      break;
+     
+
+    
     if (thisDetector->stoppedFlag) {
 #ifdef VERBOSE
       std::cout<< "exiting since the detector has been stopped" << std::endl;
 #endif
       break;
-    } else if (ip<(np-1))
+    } else if (ip<(np-1)) {
-      thisDetector->fileIndex=thisDetector->fileIndex-thisDetector->timerValue[FRAME_NUMBER]; 
+      thisDetector->fileIndex=startindex; 
+    }
+     } // loop on position finished
+
+  //script after
+        if (thisDetector->stoppedFlag==0) {
+	  if (thisDetector->actionMask & (1 << scriptAfter)) {
+	    //Custom script after each frame. The arguments are passed as nrun=n fn=filename par=p sv0=scanvar0 sv1=scanvar1 p0=par0 p1=par1"
+	    sprintf(cmd,"%s nrun=%d fn=%s par=%s sv0=%f sv1=%f p0=%s p1=%s",thisDetector->actionScript[scriptAfter],thisDetector->fileIndex,createFileName().c_str(),thisDetector->actionParameter[scriptAfter],currentScanVariable[0],currentScanVariable[1],thisDetector->scanParameter[0],thisDetector->scanParameter[1]);
 #ifdef VERBOSE
-    cout << "------------------------------------------------------Setting file index to " << thisDetector->fileIndex << endl;
+	    cout << "Executing script after " << cmd << endl;
 #endif
+	    system(cmd);
+	  } 
+	} else
+	    break;
+  
+
+    if (thisDetector->stoppedFlag) {
+#ifdef VERBOSE
+      std::cout<< "exiting since the detector has been stopped" << std::endl;
+#endif
+      break;
+    } else if (is1<(ns1-1)) {
+      thisDetector->fileIndex=startindex; 
     }
 
-#ifdef ACQVERBOSE
+
-  std::cout<< "------------------------------------------------------cancelling data processing thread " << std::endl ;
+  } 
+
+  //end scan1 loop is1
+  //currentScanVariable[MAX_SCAN_LEVELS];
+  
+
+    if (thisDetector->stoppedFlag) {
+#ifdef VERBOSE
+      std::cout<< "exiting since the detector has been stopped" << std::endl;
 #endif
+      break;
+    } else if (is0<(ns0-1)) {
+      thisDetector->fileIndex=startindex; 
+    }
+  } //end scan0 loop is0
+
+  thisDetector->fileIndex=lastindex;
+  if (thisDetector->stoppedFlag==0) {
+    if (thisDetector->actionMask & (1 << stopScript)) {
+      //Custom stop script. The arguments are passed as nrun=n par=p.
+      sprintf(cmd,"%s nrun=%d par=%s",thisDetector->actionScript[stopScript],thisDetector->fileIndex,thisDetector->actionParameter[stopScript]);
+#ifdef VERBOSE
+      cout << "Executing stop script " << cmd << endl;
+#endif
+      system(cmd);
+    }
+  } 
+
+
    if (thisDetector->threadedProcessing) { 
      jointhread=1;
      pthread_join(dataProcessingThread, &status);
-
-     /*  while (pthread_cancel(dataProcessingThread)) {
-      ;  
-}*/
-#ifdef ACQVERBOSE
-      std::cout<< "----------------------------------------------------process canceled" << std::endl;
-#endif
    }
 
 }
@@ -2240,21 +2796,11 @@ void* mythenDetector::processData(int delflag) {
   int np;
   detectorData *thisData;
   int dum=1;
-  //  thisDetector->progressIndex=0;
-
-#ifdef VERBOSE
-  int iloop=0;
-#endif
 
 #ifdef ACQVERBOSE
   std::cout<< " processing data - threaded mode " << thisDetector->threadedProcessing;
 #endif
 
-  //pthread_setcanceltype(PTHREAD_CANCEL_DEFERRED,&outer_c_s );
-  //#ifdef VERBOSE
-  //	std::cout<< "impossible to cancel process " << std::endl;
-  //#endif
-  //    pthread_setcancelstate (PTHREAD_CANCEL_DISABLE, &outer_c_s);
 
   while(dum | thisDetector->threadedProcessing) { // ????????????????????????
     
@@ -2264,29 +2810,20 @@ void* mythenDetector::processData(int delflag) {
 
       /** Pop data queue */
       myData=dataQueue.front(); // get the data from the queue 
-      //dataQueue.pop(); //remove the data from the queue
       if (myData) {
 	//process data
 	/** decode data */
 	fdata=decodeData(myData);
 
-      //delete [] myData;
-      //	myData=NULL;
 	/** write raw data file */	   
 	if (thisDetector->correctionMask==0 && delflag==1) {
-#ifdef ACQVERBOSE
+
-	  std::cout<< "------------------------------------no processing "<< delflag <<std::endl;
+
-#endif 
-#ifdef VERBOSE
-	  cout << "********************** no processing: writing file " << createFileName().append(".raw") << endl;
-#endif 
 	  writeDataFile (createFileName().append(".raw"), fdata, NULL, NULL, 'i'); 
 	  delete [] fdata;
 	} else {
 	  writeDataFile (createFileName().append(".raw"), fdata, NULL, NULL, 'i');
-#ifdef VERBOSE
+
-	  std::cout << "********************** if (thisDetector->correctionMask!=0 || delflag==0) { writing raw data file " << createFileName() <<" " << thisDetector->correctionMask<< " " << delflag << endl;
-#endif
 	  /** rate correction */
 	  if (thisDetector->correctionMask&(1<<RATE_CORRECTION)) {
 	    rcdata=new float[thisDetector->nChans*thisDetector->nChips*thisDetector->nMods]; 
@@ -2315,10 +2852,6 @@ void* mythenDetector::processData(int delflag) {
 	  
 	  if (thisDetector->correctionMask&(1<< ANGULAR_CONVERSION)) {
 
-	  /** angular conversion */
-	  /** data merging */
-	  // if (thisDetector->numberOfPositions) {
-	    
 	    if (currentPositionIndex<=1) {     
 	      if (thisDetector->binSize>0)
 		bs=thisDetector->binSize;
@@ -2347,27 +2880,13 @@ void* mythenDetector::processData(int delflag) {
 	    }
 	    
 	    if (thisDetector->correctionMask!=0)
-#ifdef VERBOSE
-	      std::cout << "********************** writing dat data file  if (thisDetector->correctionMask!=0) { " << createFileName() <<" " << thisDetector->correctionMask << endl;
-#endif
 	    writeDataFile (createFileName().append(".dat"), ffcdata, ffcerr,ang);
-	    
-	    
 	    addToMerging(ang, ffcdata, ffcerr, mergingBins, mergingCounts,mergingErrors, mergingMultiplicity);
-	    
-	    
-	    
-	    
 	    if ((currentPositionIndex==thisDetector->numberOfPositions) || (currentPositionIndex==0)) {
-	      
 	      np=finalizeMerging(mergingBins, mergingCounts,mergingErrors, mergingMultiplicity);
-	      
 	      /** file writing */
 	      currentPositionIndex++;
 	      if (thisDetector->correctionMask!=0)
-#ifdef VERBOSE
-		std::cout << "********************** writing dat data file if ((currentPositionIndex==thisDetector->numberOfPositions) || (currentPositionIndex==0))" << createFileName() << endl;
-#endif
 		writeDataFile (createFileName().append(".dat"),mergingCounts, mergingErrors, mergingBins,'f',np);
 	      if (delflag) {
 		delete [] mergingBins;
@@ -2381,9 +2900,6 @@ void* mythenDetector::processData(int delflag) {
 		  thisData=new detectorData(mergingCounts,mergingErrors,mergingBins,thisDetector->progressIndex+1,(createFileName().append(".raw")).c_str(),np);
 		
 		finalDataQueue.push(thisData);
-#ifdef ACQVERBOSE
-		std::cout<< "------------------------------------pushing final data queue " << finalDataQueue.size() << " " << createFileName() << std::endl;
-#endif
 	      }
 	    }
 	    
@@ -2393,13 +2909,9 @@ void* mythenDetector::processData(int delflag) {
 	      delete [] ffcerr;
 	    if (ang)
 	      delete [] ang;
-	    //}
 	  } else {
 	    if (thisDetector->correctionMask!=0) {
 	      writeDataFile (createFileName().append(".dat"), ffcdata, ffcerr);
-#ifdef VERBOSE
-	      std::cout << "********************** if (thisDetector->correctionMask!=0) writing dat data file " << createFileName() << endl;
-#endif
 	    }
 	    if (delflag) {
 	      if (ffcdata)
@@ -2415,50 +2927,18 @@ void* mythenDetector::processData(int delflag) {
 		thisData=new detectorData(ffcdata,ffcerr,NULL,thisDetector->progressIndex+1,(createFileName().append(".raw")).c_str(),thisDetector->nChans*thisDetector->nChips*thisDetector->nMods);
 	      }
 	      finalDataQueue.push(thisData);  
-#ifdef VERBOSE
-	      std::cout<< "------------------------------------pushing final data queue with " << createFileName() << " " <<finalDataQueue.size() << std::endl;
-#endif 
 	    }  
 	  }
 	}
 	thisDetector->fileIndex++;
-#ifdef VERBOSE
-	cout << "setting file index to "<< thisDetector->fileIndex << endl;
-#endif
 	thisDetector->progressIndex++;
-#ifdef ACQVERBOSE
-	std::cout<< "------------------------------------raw data queueto be popped " << dataQueue.size() << " empty " << !dataQueue.empty() << std::endl;
-#endif
 	delete [] myData;
 	myData=NULL;
 	dataQueue.pop(); //remove the data from the queue
 	queuesize=dataQueue.size();
-#ifdef ACQVERBOSE
-	std::cout<< "------------------------------------raw data queue popped " << dataQueue.size() << " var " << queuesize << std::endl;
-#endif
       }
-#ifdef ACQVERBOSE
-      else
-	std::cout<< "could not pop data queue " << std::endl;
-#endif
-      //#ifdef VERBOSE
-      //	std::cout<< "possible to cancel process " << std::endl;
-      //#endif
-      //	pthread_setcancelstate (PTHREAD_CANCEL_ENABLE, &outer_c_s);
-      //	pthread_testcancel();
     }
-    
-// #ifdef VERBOSE
-//       if (iloop%10000==0) 
-// 	std::cout<< "------------------------------------process idle " << dataQueue.size() << " empty " << !dataQueue.empty()  << std::endl;
-//       iloop++;
-// #endif
-
-
     if (jointhread) {
-#ifdef VERBOSE
-	std::cout<< "acquisition finished " << dataQueue.size() << " empty " << !dataQueue.empty()  << "final data queue size: " << finalDataQueue.size() <<std::endl;
-#endif
       if (dataQueue.size()==0)
 	break;
     }

slsDetectorSoftware/slsDetector/slsDetector.cpp

@@ -241,6 +241,30 @@ int slsDetector::initializeDetectorSize(detectorType type) {
      thisDetector->binSize=0;
      thisDetector->stoppedFlag=0;
      
+     thisDetector->actionMask=0;
+
+
+     for (int ia=0; ia<MAX_ACTIONS; ia++) {
+       thisDetector->actionMode[ia]=0;
+       strcpy(thisDetector->actionScript[ia],"none");
+       strcpy(thisDetector->actionParameter[ia],"none");
+     }
+
+
+     for (int iscan=0; iscan<MAX_SCAN_LEVELS; iscan++) {
+       
+       thisDetector->scanMode[iscan]=0;
+       strcpy(thisDetector->scanScript[iscan],"none");
+       strcpy(thisDetector->scanParameter[iscan],"none");
+       thisDetector->nScanSteps[iscan]=0;
+       thisDetector->scanPrecision[iscan]=0;
+     }
+
+
+     
+
+
+
 
      
      /** calculates the memory offsets for flat field coefficients and errors, module structures, dacs, adcs, chips and channels */ 
@@ -627,11 +651,27 @@ string slsDetector::createFileName() {
   /*directory name +root file name */
   osfn << thisDetector->filePath << "/" << thisDetector->fileName;
   
+  // scan level 0
+  if (thisDetector->actionMask & (1 << (MAX_ACTIONS)))
+    osfn << "_S" << fixed << setprecision(thisDetector->scanPrecision[0]) << currentScanVariable[0];
+
+  //scan level 1
+  if (thisDetector->actionMask & (1 << (MAX_ACTIONS+1)))
+    osfn << "_s" << fixed << setprecision(thisDetector->scanPrecision[1]) << currentScanVariable[1];
+  
+
+  //position
   if (currentPositionIndex>0 && currentPositionIndex<=thisDetector->numberOfPositions)
     osfn << "_p" << currentPositionIndex;
 
+  // file index
   osfn << "_" << thisDetector->fileIndex;
 
+
+#ifdef VERBOSE
+  cout << "created file name " << osfn.str() << endl;
+#endif
+
   return osfn.str();
 
 }
@@ -3094,11 +3134,11 @@ int slsDetector::setFlatFieldCorrection(string fname){
 	fillBadChannelMask();
 
       } else {
-	std::cout<< "Flat field data from file " << fname << " are not valid " << std::endl;
+	std::cout<< "Flat field data from file " << fname << " are not valid (" << nmed << "///" << xmed[nmed/2] << std::endl;
 	return -1;
       }
     } else {
-	std::cout<< "Flat field from file " << fname << " is not valid " << std::endl;
+      std::cout<< "Flat field from file " << fname << " is not valid " << nch << std::endl;
 	return -1;
     } 
   }
@@ -3216,6 +3256,27 @@ int slsDetector::getRateCorrection(float &t){
     return 0;
 };
 
+float slsDetector::getRateCorrectionTau(){
+
+  if (thisDetector->correctionMask&(1<<RATE_CORRECTION)) {
+#ifdef VERBOSE
+    std::cout<< "Rate correction is enabled with dead time "<< thisDetector->tDead << std::endl;
+#endif
+    return thisDetector->tDead;
+    //return 1;
+  } else
+#ifdef VERBOSE
+    std::cout<< "Rate correction is disabled " << std::endl;
+#endif
+    return 0;
+};
+
+
+
+
+
+
+
 int slsDetector::getRateCorrection(){
 
   if (thisDetector->correctionMask&(1<<RATE_CORRECTION)) {
@@ -3428,6 +3489,392 @@ int slsDetector::exitServer(){
 };
 
 
+
+
+
+
+
+
+
+
+  /** 
+      set action 
+      \param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript, MAX_ACTIONS}
+      \param fname for script ("" disable but leaves script unchanged, "none" disables and overwrites)
+      \returns 0 if action disabled, >0 otherwise
+  */
+int slsDetector::setAction(int iaction, string fname, string par) {
+
+  if (iaction>=0 && iaction<MAX_ACTIONS) {
+
+    if (fname=="") {
+      thisDetector->actionMode[iaction]=0;
+    } else if (fname=="none") {
+      thisDetector->actionMode[iaction]=0;
+      strcpy(thisDetector->actionScript[iaction],fname.c_str());
+    } else {
+      strcpy(thisDetector->actionScript[iaction],fname.c_str());
+      thisDetector->actionMode[iaction]=1;
+    }
+    
+    if (par!="") {
+      strcpy(thisDetector->actionParameter[iaction],par.c_str());
+    }
+    
+    if (thisDetector->actionMode[iaction]) {
+
+#ifdef VERBOSE
+      cout << iaction << "  " << hex << (1 << iaction) << " " << thisDetector->actionMask << dec;
+#endif
+    
+      thisDetector->actionMask |= (1 << iaction);
+
+#ifdef VERBOSE
+    cout << " set " << hex << thisDetector->actionMask << dec << endl;
+#endif
+    
+    } else {
+#ifdef VERBOSE
+    cout << iaction << "  " << hex << thisDetector->actionMask << dec;
+#endif
+    
+    thisDetector->actionMask &= ~(1 << iaction);
+
+#ifdef VERBOSE
+    cout << "  unset " << hex << thisDetector->actionMask << dec << endl;
+#endif
+    }
+#ifdef VERBOSE
+    cout << iaction << " Action mask set to " << hex << thisDetector->actionMask << dec << endl;
+#endif
+    
+    return thisDetector->actionMode[iaction]; 
+  } else
+    return -1;
+}
+
+
+int slsDetector::setActionScript(int iaction, string fname) {
+#ifdef VERBOSE
+  
+#endif
+  return setAction(iaction,fname,"");
+}
+
+
+
+int slsDetector::setActionParameter(int iaction, string par) {
+  if (iaction>=0 && iaction<MAX_ACTIONS) {
+
+    if (par!="") {
+      strcpy(thisDetector->actionParameter[iaction],par.c_str());
+    }
+    
+    if (thisDetector->actionMode[iaction]) {
+      thisDetector->actionMask |= (1 << iaction);
+    } else {
+      thisDetector->actionMask &= ~(1 << iaction);
+    }
+    
+    return thisDetector->actionMode[iaction]; 
+  } else
+    return -1; 
+}
+
+  /** 
+      returns action script
+      \param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript}
+      \returns action script
+  */
+string slsDetector::getActionScript(int iaction){
+  if (iaction>=0 && iaction<MAX_ACTIONS) 
+    return string(thisDetector->actionScript[iaction]);
+  else
+    return string("wrong index");
+};
+
+    /** 
+	returns action parameter
+	\param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript}
+	\returns action parameter
+    */
+string slsDetector::getActionParameter(int iaction){
+  if (iaction>=0 && iaction<MAX_ACTIONS) 
+    return string(thisDetector->actionParameter[iaction]);
+  else
+    return string("wrong index");
+}
+
+   /** 
+	returns action mode
+	\param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript}
+	\returns action mode
+    */
+int slsDetector::getActionMode(int iaction){
+  if (iaction>=0 && iaction<MAX_ACTIONS) {
+#ifdef VERBOSE
+    cout << "slsDetetctor : action " << iaction << " mode is " <<  thisDetector->actionMode[iaction] << endl;
+#endif
+    return thisDetector->actionMode[iaction];
+  } else {
+#ifdef VERBOSE
+    cout << "slsDetetctor : wrong action index " << iaction <<  endl;
+#endif
+    return -1;
+  }
+}
+
+
+  /** 
+      set scan 
+      \param index of the scan (0,1)
+      \param fname for script ("" disable)
+      \returns 0 if scan disabled, >0 otherwise
+  */
+int slsDetector::setScan(int iscan, string script, int nvalues, float *values, string par, int precision) {
+  if (iscan>=0 && iscan<MAX_SCAN_LEVELS) {
+
+    if (script=="") {
+      thisDetector->scanMode[iscan]=0;
+    } else {
+      strcpy(thisDetector->scanScript[iscan],script.c_str());
+      if (script=="none") {
+	thisDetector->scanMode[iscan]=0;
+      } else if (script=="energy") {
+	thisDetector->scanMode[iscan]=1;
+      }  else if (script=="threshold") {
+	thisDetector->scanMode[iscan]=2;
+      } else if (script=="trimbits") {
+	thisDetector->scanMode[iscan]=3;
+      } else {
+	thisDetector->scanMode[iscan]=4;
+      }  
+    }
+    
+    
+
+    
+
+    
+    if (par!="")
+      strcpy(thisDetector->scanParameter[iscan],par.c_str());
+      
+      if (nvalues>=0) {    
+	if (nvalues==0)
+	  thisDetector->scanMode[iscan]=0;
+	else {
+	  thisDetector->nScanSteps[iscan]=nvalues;
+	  if (nvalues>MAX_SCAN_STEPS)
+	    thisDetector->nScanSteps[iscan]=MAX_SCAN_STEPS;
+	}
+      }
+      
+      if (values) {
+	for (int iv=0; iv<thisDetector->nScanSteps[iscan]; iv++) {
+	  thisDetector->scanSteps[iscan][iv]=values[iv];
+	}
+      }
+      if (precision>=0)
+	thisDetector->scanPrecision[iscan]=precision;
+      
+      if (thisDetector->scanMode[iscan]>0){
+	thisDetector->actionMask |= 1 >> (iscan+MAX_ACTIONS);
+      } else {
+	thisDetector->actionMask &= ~(1 >>  (iscan+MAX_ACTIONS));
+      }
+
+
+      return thisDetector->scanMode[iscan];
+  }  else 
+    return -1;
+  
+}
+
+int slsDetector::setScanScript(int iscan, string script) {
+ if (iscan>=0 && iscan<MAX_SCAN_LEVELS) {
+    if (script=="") {
+      thisDetector->scanMode[iscan]=0;
+    } else {
+      strcpy(thisDetector->scanScript[iscan],script.c_str());
+      if (script=="none") {
+	thisDetector->scanMode[iscan]=0;
+      } else if (script=="energy") {
+	thisDetector->scanMode[iscan]=1;
+      }  else if (script=="threshold") {
+	thisDetector->scanMode[iscan]=2;
+      } else if (script=="trimbits") {
+	thisDetector->scanMode[iscan]=3;
+      } else {
+	thisDetector->scanMode[iscan]=4;
+      }  
+    }
+    
+    if (thisDetector->scanMode[iscan]>0){
+      thisDetector->actionMask |= (1 << (iscan+MAX_ACTIONS));
+    } else {
+      thisDetector->actionMask &= ~(1 <<  (iscan+MAX_ACTIONS));
+    }
+
+    
+    return thisDetector->scanMode[iscan];
+    
+    
+ } else 
+   return -1;
+ 
+}
+
+
+
+int slsDetector::setScanParameter(int iscan, string par) {
+
+
+  if (iscan>=0 && iscan<MAX_SCAN_LEVELS) {
+      if (par!="")
+	strcpy(thisDetector->scanParameter[iscan],par.c_str());
+      return thisDetector->scanMode[iscan];
+  } else
+    return -1;
+
+}
+
+
+int slsDetector::setScanPrecision(int iscan, int precision) {
+  if (iscan>=0 && iscan<MAX_SCAN_LEVELS) {
+    if (precision>=0)
+      thisDetector->scanPrecision[iscan]=precision;
+    return thisDetector->scanMode[iscan];
+  } else
+    return -1;
+
+}
+
+int slsDetector::setScanSteps(int iscan, int nvalues, float *values) {
+
+  if (iscan>=0 && iscan<MAX_SCAN_LEVELS) {
+  
+      if (nvalues>=0) {    
+	if (nvalues==0)
+	  thisDetector->scanMode[iscan]=0;
+	else {
+	  thisDetector->nScanSteps[iscan]=nvalues;
+	  if (nvalues>MAX_SCAN_STEPS)
+	    thisDetector->nScanSteps[iscan]=MAX_SCAN_STEPS;
+	}
+      }
+      
+      if (values) {
+	for (int iv=0; iv<thisDetector->nScanSteps[iscan]; iv++) {
+	  thisDetector->scanSteps[iscan][iv]=values[iv];
+	}
+      }
+     
+      if (thisDetector->scanMode[iscan]>0){
+	thisDetector->actionMask |= (1 << (iscan+MAX_ACTIONS));
+      } else {
+	thisDetector->actionMask &= ~(1 <<  (iscan+MAX_ACTIONS));
+      }
+
+
+      return thisDetector->scanMode[iscan];
+  
+
+  } else 
+      return -1;
+  
+  
+  
+  
+}
+
+
+
+  /** 
+      returns scan script
+      \param iscan can be (0,1) 
+      \returns scan script
+  */
+string slsDetector::getScanScript(int iscan){
+    if (iscan>=0 && iscan<MAX_SCAN_LEVELS)
+      return string(thisDetector->scanScript[iscan]);
+    else
+      return string("wrong index");
+      
+};
+
+    /** 
+	returns scan parameter
+	\param iscan can be (0,1)
+	\returns scan parameter
+    */
+string slsDetector::getScanParameter(int iscan){
+    if (iscan>=0 && iscan<MAX_SCAN_LEVELS)
+      return string(thisDetector->scanParameter[iscan]);
+    else
+      return string("wrong index");
+}
+
+
+   /** 
+	returns scan mode
+	\param iscan can be (0,1)
+	\returns scan mode
+    */
+int slsDetector::getScanMode(int iscan){
+  if (iscan>=0 && iscan<MAX_SCAN_LEVELS)
+    return thisDetector->scanMode[iscan];
+  else
+    return -1;
+}
+
+
+   /** 
+	returns scan steps
+	\param iscan can be (0,1)
+	\param v is the pointer to the scan steps
+	\returns scan steps
+    */
+int slsDetector::getScanSteps(int iscan, float *v) {
+
+  if (iscan>=0 && iscan<MAX_SCAN_LEVELS) {
+    if (v) {
+      for (int iv=0; iv<thisDetector->nScanSteps[iscan]; iv++) {
+	v[iv]=thisDetector->scanSteps[iscan][iv];
+      }
+    }
+
+    return thisDetector->nScanSteps[iscan];
+  } else
+    return -1;
+}
+
+
+int slsDetector::getScanPrecision(int iscan){
+  if (iscan>=0 && iscan<MAX_SCAN_LEVELS) {
+    return thisDetector->scanPrecision[iscan];
+  } else
+    return -1;
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 
 /*
 void slsDetector::startThread() {

slsDetectorSoftware/slsDetector/slsDetector.h

@@ -28,6 +28,8 @@ extern "C" {
 #define MAX_ROIS 100
 #define MAX_BADCHANS 2000
 #define MAXPOS 50
+#define MAX_SCAN_LEVELS 2
+#define MAX_SCAN_STEPS 2000
 
 #define NMODMAXX 24
 #define NMODMAXY 24
@@ -43,6 +45,9 @@ extern "C" {
 
 
 
+enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript, MAX_ACTIONS};
+
+
 /**
    data structure to hold the detector data after postprocessing (e.g. to plot, store in a root tree etc.)
  */
@@ -243,6 +248,7 @@ typedef  struct sharedSlsDetector {
     /** readout flags */
     readOutFlags roFlags;
 
+
  /* detector setup - not needed */
   /** name root of the output files */  
   char trimFile[MAX_STR_LENGTH];
@@ -255,8 +261,27 @@ typedef  struct sharedSlsDetector {
   /** clock divider */
   //int clkDiv;
 
+
+  /** Scans and scripts */
+
+  int actionMask;
+  
+  int actionMode[MAX_ACTIONS];
+  char actionScript[MAX_ACTIONS][MAX_STR_LENGTH];
+  char actionParameter[MAX_ACTIONS][MAX_STR_LENGTH];
+
+
+  int scanMode[MAX_SCAN_LEVELS];
+  char scanScript[MAX_SCAN_LEVELS][MAX_STR_LENGTH];
+  char scanParameter[MAX_SCAN_LEVELS][MAX_STR_LENGTH];
+  int nScanSteps[MAX_SCAN_LEVELS];
+  float scanSteps[MAX_SCAN_LEVELS][MAX_SCAN_STEPS];
+  int scanPrecision[MAX_SCAN_LEVELS];
+  
+
+    
   /*offsets*/
-    /** memory offsets for the flat filed coefficients */
+    /** memory offsets for the flat field coefficients */
     int ffoff;
     /** memory offsets for the flat filed coefficient errors */
     int fferroff;
@@ -1079,7 +1104,7 @@ s
       get flat field corrections file name
       \returns flat field correction file name
   */
-  char *getFlatFieldCorrectionFile(){return thisDetector->flatFieldFile;};
+  char *getFlatFieldCorrectionFile(){  if (thisDetector->correctionMask&(1<<FLAT_FIELD_CORRECTION)) return thisDetector->flatFieldFile; else return "none";};
 
   /** 
       set rate correction
@@ -1096,6 +1121,12 @@ s
   */
   int getRateCorrection(float &t);
 
+  
+  /** 
+      get rate correction tau
+      \returns 0 if rate correction disabled, otherwise the tau used for the correction
+  */
+  float getRateCorrectionTau();
   /** 
       get rate correction
       \returns 0 if rate correction disabled, >0 otherwise
@@ -1210,6 +1241,106 @@ s
 
 
 
+  /** 
+      set action 
+      \param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript, MAX_ACTIONS}
+      \param fname for script ("" disable)
+      \param par for script 
+      \returns 0 if action disabled, >0 otherwise
+  */
+  int setAction(int iaction, string fname="", string par="");
+
+  /** 
+      set action 
+      \param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript, MAX_ACTIONS}
+      \param fname for script ("" disable)
+      \returns 0 if action disabled, >0 otherwise
+  */
+  int setActionScript(int iaction, string fname="");
+  /** 
+      set action 
+      \param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript, MAX_ACTIONS}
+      \param par for script ("" disable)
+      \returns 0 if action disabled, >0 otherwise
+  */
+  int setActionParameter(int iaction, string par="");
+
+  /** 
+      returns action script
+      \param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript}
+      \returns action script
+  */
+  string getActionScript(int iaction);
+
+    /** 
+	returns action parameter
+	\param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript}
+	\returns action parameter
+    */
+  string getActionParameter(int iaction);
+
+   /** 
+	returns action mode
+	\param iaction can be enum {startScript, scriptBefore, headerBefore, headerAfter,scriptAfter, stopScript}
+	\returns action mode
+    */
+  int getActionMode(int iaction);
+
+
+  /** 
+      set scan 
+      \param index of the scan (0,1)
+      \param fname for script ("" disables, "none" disables and overwrites current)
+      \param nvalues number of steps (0 disables, -1 leaves current value)
+      \param values pointer to steps (if NULL leaves current values)
+      \param par parameter for the scan script ("" leaves unchanged)
+      \returns 0 is scan disabled, >0 otherwise
+  */
+  int setScan(int index, string script="", int nvalues=-1, float *values=NULL, string par="", int precision=-1);
+  
+  int setScanScript(int index, string script="");
+  int setScanParameter(int index, string par="");
+  int setScanPrecision(int index, int precision=-1);
+  int setScanSteps(int index, int nvalues=-1, float *values=NULL);
+  /** 
+      returns scan script
+      \param iscan can be (0,1) 
+      \returns scan script
+  */
+  string getScanScript(int iscan);
+
+    /** 
+	returns scan parameter
+	\param iscan can be (0,1)
+	\returns scan parameter
+    */
+  string getScanParameter(int iscan);
+
+   /** 
+	returns scan mode
+	\param iscan can be (0,1)
+	\returns scan mode
+    */
+  int getScanMode(int iscan);
+
+   /** 
+	returns scan steps
+	\param iscan can be (0,1)
+	\param v is the pointer to the scan steps
+	\returns scan steps
+    */
+  int getScanSteps(int iscan, float *v=NULL);
+
+
+   /** 
+	returns scan precision
+	\param iscan can be (0,1)
+	\returns scan precision
+    */
+  int getScanPrecision(int iscan);
+
+
+
 
   /** 
      decode data from the detector converting them to an array of floats, one for each channle
@@ -1409,6 +1540,20 @@ s
   
   
 
+
+  /**
+     current scan variable of the detector
+  */
+  float currentScanVariable[MAX_SCAN_LEVELS];
+  
+  /**
+     current scan variable index of the detector
+  */
+  int currentScanIndex[MAX_SCAN_LEVELS];
+  
+  
+
+
   /** merging bins */
   float *mergingBins;
 
@@ -1422,11 +1567,6 @@ s
   int *mergingMultiplicity;
   
  
-
-
-
-
- 
   /** pointer to flat field coefficients */
   float *ffcoefficients;
   /** pointer to flat field coefficient errors */