Bad channels correction separated from postProcessing

git-svn-id: file:///afs/psi.ch/project/sls_det_software/svn/slsDetectorSoftware@241 951219d9-93cf-4727-9268-0efd64621fa3

slsDetectorSoftware/slsDetectorAnalysis/angleConversionConstant.h

@@ -14,6 +14,25 @@ class angleConversionConstant {
   double tilt; /**< ossible tilt in the orthogonal direction (unused)*/
   double etilt; /**< error in the tilt determination */
 //} angleConversionConstant;
+
+  double getCenter(){return center;};
+  double getConversion(){return r_conversion;};
+  double getOffset(){return offset;};
+  double getTilt(){return tilt;};
+  
+  int setAngConvConstant(angleConversionConstant *acc) {\
+    center=acc->center;					\
+    ecenter=acc->ecenter;				\
+    r_conversion=acc->r_conversion;			\
+    er_conversion=acc->er_conversion;			\
+    offset=acc->offset;					\
+    eoffset=acc->eoffset;				\
+    tilt=acc->tilt;					\
+    etilt=acc->etilt;					\
+  };
+
+
+
 };
 
 #endif

slsDetectorSoftware/slsDetectorAnalysis/angularCalibration.h

@@ -16,22 +16,6 @@ class TH1;
 
 
 
-/**
-   angular conversion constant for a module
- */
-typedef struct  {
-  double center;  /**< center of the module (channel at which the radius is perpendicular to the module surface) */
-  double ecenter; /**< error in the center determination */
-  double r_conversion;  /**<  detector pixel size (or strip pitch) divided by the diffractometer radius */
-  double er_conversion;  /**< error in the r_conversion determination */
-  double offset; /**< the module offset i.e. the position of channel 0 with respect to the diffractometer 0 */
-  double eoffset; /**< error in the offset determination */
-  double tilt; /**< ossible tilt in the orthogonal direction (unused)*/
-  double etilt; /**< error in the tilt determination */
-} angleConversionConstant;
-
-
-
 class angularCalibration {
 
  public:
@@ -155,7 +139,7 @@ class angularCalibration {
   int nmod;
   int nchmod;
 
-  angleConversionConstant *angConv;
+  angleConversionConstant angConv[MAXMOD*MAXDET];
 
   
 

slsDetectorSoftware/slsDetectorAnalysis/angularConversion.h

@@ -49,7 +49,9 @@ class angularConversion : public virtual slsDetectorBase, public virtual angular
 
   //virtual int readAngularConversion(string fname)=0;
 
-
+  using angularConversionStatic::writeAngularConversion;
+  using angularConversionStatic::readAngularConversion;
+  
 
 
    /** 

slsDetectorSoftware/slsDetectorAnalysis/angularConversionStatic.h

@@ -15,6 +15,7 @@
 
 #include "angleConversionConstant.h"
 
+
   //double angle(int ichan, double encoder, double totalOffset, double conv_r, double center, double offset, double tilt, int direction)
 
 
@@ -147,12 +148,12 @@ class angularConversionStatic : public virtual slsDetectorDefs
   int registerAngleFunctionCallback(double (*fun)(double, double, double, double, double, double, double, int)) {angle = fun; return 0;};
   
   
-
- private:
-
-  
   double (*angle)(double, double, double, double, double, double, double, int);
 
+
+  // private:
+
+  
 };
 
 #endif

slsDetectorSoftware/slsDetectorAnalysis/angularConversionStatic.h~

@@ -34,19 +34,14 @@ class containing the methods to set/unset the angular conversion and merge the d
 The angular conversion itself is defined by the angle() function defined in usersFunctions.cpp
    
 */
-class angularConversion 
+class angularConversionStatic : public virtual slsDetectorDefs
-#ifndef MYROOT
-: public virtual slsDetectorBase 
-#else
-: public virtual slsDetectorDefs
-#endif
 {
 
  public:
   /** default constructor */
-  angularConversion();
+  angularConversionStatic();
   /** virtual destructor */
-  virtual ~angularConversion();
+  virtual ~angularConversionStatic();
  
 
 
@@ -92,12 +87,6 @@ class angularConversion
   */
    static int writeAngularConversion(ofstream& ofs, int nmod, angleConversionConstant *angOff);
 
-   /** 
-       pure virtual function
-       \param file name to be written (nmod and array of angular conversion constants default to the ones ot the slsDetector
-   */
-   virtual int writeAngularConversion(string fname)=0;
-
    /** 
        sets the arrays of the merged data to 0. NB The array should be created with size nbins >= 360./getBinSize(); 
        \param mp already merged postions
@@ -108,20 +97,6 @@ class angularConversion
        \returns OK or FAIL
    */
    static int resetMerging(double *mp, double *mv,double *me, int *mm, int nbins);
-   /** 
-       sets the arrays of the merged data to 0. NB The array should be created with size >= 360./getBinSize(); 
-       \param mp already merged postions
-       \param mv already merged data
-       \param me already merged errors (squared sum)
-       \param mm multiplicity of merged arrays
-       \returns OK or FAIL
-   */
-   int resetMerging(double *mp, double *mv,double *me, int *mm);
-  
-   /** 
-       creates the arrays for merging the data and sets them to 0. 
-   */
-   int resetMerging();
 
   /** 
       merge dataset
@@ -141,30 +116,6 @@ class angularConversion
 
    static int  addToMerging(double *p1, double *v1, double *e1, double *mp, double *mv,double *me, int *mm, int nchans, double binsize,int nb, int *badChanMask );
    
-  /** 
-      merge dataset
-      \param p1 angular positions of dataset
-      \param v1 data
-      \param e1 errors
-      \param mp already merged postions
-      \param mv already merged data
-      \param me already merged errors (squared sum)
-      \param mm multiplicity of merged arrays
-      \param badChanMask badchannelmask (if NULL does not correct for bad channels)
-      \returns OK or FAIL
-  */
-
-   int  addToMerging(double *p1, double *v1, double *e1, double *mp, double *mv,double *me, int *mm, int *badChanMask);
-  /** 
-      merge dataset
-      \param p1 angular positions of dataset
-      \param v1 data
-      \param e1 errors
-      \param badChanMask badchannelmask (if NULL does not correct for bad channels)
-      \returns OK or FAIL
-  */
-
-   int addToMerging(double *p1, double *v1, double *e1,int *badChanMask);
 
    /**
       calculates the "final" positions, data value and errors for the merged data
@@ -177,307 +128,28 @@ class angularConversion
   */
 
    static int finalizeMerging(double *mp, double *mv,double *me, int *mm, int nb);
-   /**
-      calculates the "final" positions, data value and errors for the merged data
-      \param mp already merged postions
-      \param mv already merged data
-      \param me already merged errors (squared sum)
-      \param mm multiplicity of merged arrays
-      \returns FAIL or the number of non empty bins (i.e. points belonging to the pattern)
-  */
-
-   int finalizeMerging(double *mp, double *mv,double *me, int *mm);
-
-/**
-      calculates the "final" positions, data value and errors for the merged data
-      \returns FAIL or the number of non empty bins (i.e. points belonging to the pattern)
-  */
-
-   int finalizeMerging();
-
-
-  /**
-      set detector global offset
-      \param f global offset to be set
-      \returns actual global offset
-  */
-  double setGlobalOffset(double f){return setAngularConversionParameter(GLOBAL_OFFSET,f);};
-
  
-  /**
-      set detector fine offset
-      \param f global fine to be set
-      \returns actual fine offset
-  */
-  double setFineOffset(double f){return setAngularConversionParameter(FINE_OFFSET,f);};
-  
-  /**
-      get detector fine offset
-      \returns actual fine offset
-  */
-  double getFineOffset(){return getAngularConversionParameter(FINE_OFFSET);};
-  
-  /**
-      get detector global offset
-      \returns actual global offset
-  */
-  double getGlobalOffset(){return getAngularConversionParameter(GLOBAL_OFFSET);};
-
-  /** 
-      
-      set detector bin size
-      \param bs bin size to be set
-      \returns actual bin size
-  */
-  double setBinSize(double bs){if (bs>0) nBins=360/bs; return setAngularConversionParameter(BIN_SIZE,bs);};
-
-  /** 
-      get detector bin size
-      \returns detector bin size used for merging (approx angular resolution)
-  */
-  double getBinSize() {return getAngularConversionParameter(BIN_SIZE);};
-
-
-
-  /** 
-      
-      get angular direction
-      \returns actual angular direction (1 is channel number increasing with angle, -1 decreasing)
-  */
-  int getAngularDirection(){return (int)getAngularConversionParameter(ANGULAR_DIRECTION);};
-
-  
-  /** 
-      
-      set angular direction
-      \param d angular direction to be set (1 is channel number increasing with angle, -1 decreasing)
-      \returns actual angular direction (1 is channel number increasing with angle, -1 decreasing)
-  */
-  int setAngularDirection(int d){return (int)setAngularConversionParameter(ANGULAR_DIRECTION, (double)d);};
-
-  /**
-     \returns  number of angular bins in the merging (360./binsize)
-  */
-  int getNumberOfAngularBins(){return nBins;};
-
-  /**
-     get angular conversion
-     \param direction reference to diffractometer direction
-      \param angconv array that will be filled with the angular conversion constants
-      \returns 0 if angular conversion disabled, >0 otherwise
-  */
-  virtual int getAngularConversion(int &direction,  angleConversionConstant *angconv=NULL)=0;
-
-
-  /**
-     set angular conversion parameter
-     \param c parameter type (globaloffset, fineoffset, binsize, angular direction, move flag)
-     \param v value to be set
-     \returns actual value
-  */
-   double setAngularConversionParameter(angleConversionParameter c, double v);
- /**
-     get angular conversion parameter
-     \param c parameter type (globaloffset, fineoffset, binsize, angular direction, move flag)
-     \returns actual value
-  */
-   double getAngularConversionParameter(angleConversionParameter c);
-   
- 
-
-
-  /** 
-      set  positions for the acquisition
-      \param nPos number of positions
-      \param pos array with the encoder positions
-      \returns number of positions
-  */
-  virtual int setPositions(int nPos, double *pos);
-   /** 
-      get  positions for the acquisition
-      \param pos array which will contain the encoder positions
-      \returns number of positions
-  */
-  virtual int getPositions(double *pos=NULL);
- 
-  /**
-     deletes the array of merged data
-     \returns OK
-  */
-  int deleteMerging();
-
-  /**
-     \returns pointer to the array o merged positions
-  */
-  double *getMergedPositions(){return mergingBins;};
-  /**
-     \returns pointer to the array of merged counts
-  */
-  double *getMergedCounts(){return mergingCounts;};
-  /**
-     \returns pointer to the array of merged errors
-  */
-  double *getMergedErrors(){return mergingErrors;};
-  
-
-
-  /**
-     sets  the angular conversion file
-     \param fname file to read
-     \returns angular conversion flag
-  */
-
-  int setAngularConversionFile(string fname);
-
-  
-  /**
-      returns the angular conversion file
-     */
-  string getAngularConversionFile(){if (setAngularCorrectionMask()) return string(angConvFile); else return string("none");};
-
-
-  /**
-     reads teh angular conversion file for the (multi)detector and writes it to shared memory
-  */
-  virtual int readAngularConversionFile(string fname="")=0;
-
-
-
-
-
-  /**
-     \returns number of modules of the (multi)detector
-  */
-  virtual int getNMods()=0;
-
-  /**
-     returns number of channels in the module
-     \param imod module number
-     \returns number of channels in the module
-  */
-  virtual int getChansPerMod(int imod=0)=0;
-
-  /**
-     get the angular conversion  contant of one modules
-     \param imod module number
-     \returns pointer to the angular conversion constant
-  */
-  virtual angleConversionConstant *getAngularConversionPointer(int imod=0)=0;
-  
   /**
      converts channel number to angle
      \param pos encoder position
      \returns array of angles corresponding to the channels
   */
-  double* convertAngles(double pos){return convertAngles(pos, getTotalNumberOfChannels());}
 
-
+  double* convertAngles(double pos, int nch, int *chansPerMod, angleConversionConstant **angOff, int *mF, double fo, double go, int angdir);
-  double* convertAngles(double pos, int nch);
-
-  /**
-     converts channel number to angle for the current encoder position
-     \returns array of angles corresponding to the channels
-  */
-  double *convertAngles(){return convertAngles(currentPosition);};
-  
-  /**
-     \param imod module number
-     \returns move flag of the module (1 encoder is added to the angle, 0 not)
-     Shold be module dependent!
-  */
-  virtual int getMoveFlag(int imod)=0;
-
-  /**
-     returns number of positions
-  */
-  int getNumberOfPositions() {return *numberOfPositions;};
 
 
 
  protected:
     
 
-  /** pointer to number of positions for the acquisition*/
-   int *numberOfPositions;
-   
-  /** pointer to the detector positions for the acquisition*/
-   double *detPositions;
-      
-   /** pointer to angular conversion file name*/
-   char *angConvFile;
-   
-   /** pointer to angular bin size*/
-   double *binSize;
-
-   /** pointer to beamlien fine offset*/
-   double *fineOffset;
-   /** pointer to beamlien global offset*/
-   double *globalOffset;
-   /** pointer to beamlien angular direction*/
-   int *angDirection;
-   /** pointer to detector move flag (1 moves with encoder, 0 not)*/
-   int *moveFlag;
-
-   /** number of bins for angular conversion (360./binsize)*/
-   int nBins;
-   
-   
-
-  /**
-     current position of the detector
-  */
-  double currentPosition;
-  /**
-     current position index of the detector
-  */
-  int currentPositionIndex;
-  
-
-  /**
-     enables/disable the angular conversion
-     \param i 1 sets, 0 unsets,, -1 gets
-     \returns actual angular conversion flag
-  */
-  virtual int setAngularCorrectionMask(int i=-1)=0;
-  
-  /**
-     returns current position index
-  */
-  int getCurrentPositionIndex() {return currentPositionIndex;};
-  void incrementPositionIndex() {currentPositionIndex++;};
-
- 
 
 
-  void registerAngleFunctionCallback(double( *fun)(double, double, double, double, double, double, double, int)) {angle = fun;};
+  int registerAngleFunctionCallback(double (*fun)(double, double, double, double, double, double, double, int)) {angle = fun; return 0;};
   
   
 
  private:
 
-
-
-
-  // int nChans;
-  // int nMods;
-  // int chansPerMod;
-  // int moveFlag;
-
-
-
-
-
-  /** merging bins */
-  double *mergingBins;
-  
-  /** merging counts */
-  double *mergingCounts;
-  
-  /** merging errors */
-  double *mergingErrors;
-  
-  /** merging multiplicity */
-  int *mergingMultiplicity;
   
   double (*angle)(double, double, double, double, double, double, double, int);
 

slsDetectorSoftware/slsDetectorAnalysis/badChannelCorrections.h

@@ -0,0 +1,59 @@
+#ifndef BAD_CHANNEL_CORRECTIONS_H
+#define BAD_CHANNEL_CORRECTIONS_H
+
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+
+using namespace std;
+class badChannelCorrections{
+
+ public:
+
+  
+
+  static int readBadChannelCorrectionFile(ifstream &infile, int &nbad, int *badlist, int moff=0){ \
+    int interrupt=0;							\
+    int ich;							\
+    int chmin,chmax;						\
+    string str;							\
+    nbad=0;							\
+    while (infile.good() and interrupt==0) {			\
+      getline(infile,str);					\
+      istringstream ssstr;					\
+      ssstr.str(str);						\
+      if (ssstr.bad() || ssstr.fail() || infile.eof()) {	\
+	interrupt=1;						\
+	break;							\
+      }								\
+      if (str.find('-')!=string::npos) {			\
+	ssstr >> chmin ;					\
+	ssstr.str(str.substr(str.find('-')+1,str.size()));	\
+	ssstr >> chmax;						\
+	for (ich=chmin; ich<=chmax; ich++) {			\
+	  badlist[nbad]=ich;					\
+	  nbad++;							\
+	}								\
+      } else {								\
+	ssstr >> ich;							\
+	badlist[nbad]=ich;						\
+	nbad++;								\
+      }									\
+    }									\
+    return nbad;  };
+  
+ protected:
+  
+
+  char *badChanFile;
+  int *nBadChans;
+  int *badChansList;
+  int *nBadFF;
+  int *badFFList;
+
+
+
+
+};
+#endif

slsDetectorSoftware/slsDetectorAnalysis/postProcessing.cpp

@@ -66,69 +66,6 @@ int postProcessing::flatFieldCorrect(double datain, double errin, double &dataou
 
 
 
-int postProcessing::setBadChannelCorrection(ifstream &infile, int &nbad, int *badlist, int moff){
-  
-  int interrupt=0;
-  int ich;
-  int chmin,chmax;
-  string str;
-
-
-  
-  nbad=0;
-  while (infile.good() and interrupt==0) {
-    getline(infile,str);
-#ifdef VERBOSE
-    std::cout << str << std::endl;
-#endif
-    istringstream ssstr;
-    ssstr.str(str);
-      if (ssstr.bad() || ssstr.fail() || infile.eof()) {
-	interrupt=1;
-	break;
-      }
-      if (str.find('-')!=string::npos) {
-	ssstr >> chmin ;
-	ssstr.str(str.substr(str.find('-')+1,str.size()));
-	ssstr >> chmax;
-#ifdef VERBOSE
-	std::cout << "channels between"<< chmin << " and " << chmax << std::endl;
-#endif
-	for (ich=chmin; ich<=chmax; ich++) {
-	  if (nbad<MAX_BADCHANS) {
-	    badlist[nbad]=ich;
-	    nbad++;
-#ifdef VERBOSE
-	    std::cout<< nbad << " Found bad channel "<< ich << std::endl;
-#endif
-	  } else
-	    interrupt=1;
-	}
-      } else {
-	ssstr >> ich;
-#ifdef VERBOSE
-	std::cout << "channel "<< ich << std::endl;
-#endif
-	if (nbad<MAX_BADCHANS) {
-	  badlist[nbad]=ich;
-	  nbad++;
-#ifdef VERBOSE
-	  std::cout << nbad << " Found bad channel "<< ich << std::endl;
-#endif
-	} else
-	  interrupt=1;
-      }
-  }
-
-  for (int ich=0; ich<nbad; ich++) {
-    badlist[ich]=badlist[ich]+moff;
-  }
-  return nbad;
-}
-
-
-
-
 
 
 

slsDetectorSoftware/slsDetectorAnalysis/postProcessing.h

@@ -5,6 +5,7 @@
 #include "detectorData.h"
 #include "slsDetectorBase.h"
 #include "angularConversion.h"
+#include "badChannelCorrections.h"
 #include "fileIO.h"
 #include <string>
 
@@ -20,7 +21,7 @@
 
 using namespace std;
 
-#define MAX_BADCHANS 2000
+#define MAX_BADCHANS 20000
 
 
 #define defaultTDead {170,90,750} /**< should be changed in order to have it separate for the different detector types */
@@ -32,7 +33,7 @@ using namespace std;
    (including thread for writing data files and plotting in parallel with the acquisition) 
 */
 
-class postProcessing : public angularConversion, public fileIO {
+class postProcessing : public angularConversion, public fileIO, public badChannelCorrections {
 
 //public virtual angularConversion, public virtual fileIO  {
 
@@ -73,8 +74,9 @@ class postProcessing : public angularConversion, public fileIO {
       \returns 0 if bad channel disabled, >0 otherwise
   */
   virtual int setBadChannelCorrection(string fname="")=0;
-  
+
-  static int setBadChannelCorrection(ifstream &infile, int &nbad, int *badlist, int moff=0);
+  static int setBadChannelCorrection(ifstream &infile, int &nbad, int *badlist, int moff){int retval=readBadChannelCorrectionFile(infile,nbad,badlist); for (int ich=0; ich<nbad; ich++)    badlist[ich]=badlist[ich]+moff;	return retval;};
+ 
   /** 
       set bad channels correction
       \param fname file with bad channel list ("" disable)
@@ -244,40 +246,6 @@ s
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
  protected:
      
   int *threadedProcessing;
@@ -287,12 +255,6 @@ s
   char *flatFieldDir;
   char *flatFieldFile;
 
-  char *badChanFile;
-  int *nBadChans;
-  int *badChansList;
-  int *nBadFF;
-  int *badFFList;
-
 
   /** mutex to synchronize main and data processing threads */
   pthread_mutex_t mp;