Interpolation has problems. To be checked

.travis.yml

@@ -0,0 +1,45 @@
+sudo: false
+
+language: cpp
+
+matrix:
+  include:
+    - os: linux
+      env: CONDA_PY=3.6
+
+dist: trusty
+
+install:
+  - sudo apt-get update
+  - ldd --version
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - rm -f miniconda.sh
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda config --add channels conda-forge
+  - conda config --add channels slsdetectorgroup
+  - conda update conda
+  - conda update --all
+  - conda install conda-build anaconda-client
+
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+
+  # Replace dep1 dep2 ... with your dependencies
+  - conda create -q -n test-environment python=$CONDA_PY
+  - source activate test-environment
+  - conda-build .
+
+script:
+ - echo "No test scripts to be run!"
+
+
+deploy:
+  provider: script
+  script: find $HOME/miniconda/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -t $CONDA_TOKEN upload --force {} \;
+  on:
+    branch: developer
+

examples/moench03_T1_lab.config

@@ -1,4 +1,4 @@
-hostname bchip011
+hostname bchip020+
 
 patword 0000 0000000000000000
 patword 0001 0000000000000000
@@ -415,27 +415,49 @@ patwait2 0400
 patwaittime2 0
 
 
-
+####mcp2011
+0:rx_tcpport 1954
 0:rx_udpip 10.1.1.102
 0:detectorip 10.1.1.19
-0:rx_udpport 32410
-#0:detectormac 00:ab:bc:cd:de:ef
-#0:rx_udpmac 70:10:6f:a0:b5:b1
-
-#gui listening to
-zmqip 129.129.202.131
-zmqport 30001
-
-#data streaming out of
+0:rx_udpport 32411
+####gui listening to 
+zmqip 129.129.202.106
+zmqport 50001
+####data streaming out of
 rx_zmqip 10.1.2.103
-rx_zmqport 30003
+rx_zmqport 50003
+
+0:rx_hostname mpc2011
+
+
+####pcmoench01
+#0:rx_tcpport 1977
+#0:rx_udpip 10.1.1.100
+#0:detectorip 10.1.1.19
+#0:rx_udpport 32410
+####gui listening to (on receiver pc)
+#zmqip 129.129.202.92
+#zmqport 50001
+####data streaming out of
+#rx_zmqip 10.1.1.100
+#rx_zmqport 50003
+#0:rx_hostname mx-test-1
+
+
+
+
+
+
+
+
+
+
 
 #turn on datastream from commandline
 rx_datastream 1
 
 r_readfreq 1
 
-0:rx_hostname mpc2011
 #0:configuremac -1
 rx_datastream 1
 

manual/manual-client/Eiger_short.tex

@@ -64,7 +64,8 @@ The directory contains some executables that are needed to make your detector to
  \begin{verbatim}
 ./on #to switch modules on
 ./off #to switch modules off
-./hvget #gets the current HV value
+./state #tells you if is ON or OFF
+cat /var/log/pcu.log #displays the log if there are problem
 ./waterflow #returns the current waterflow returned by the flowmeter
 ./temp #returns the water temperature returned by the flowmeter
  \end{verbatim}
@@ -560,12 +561,23 @@ Here are the implemented options so far:
 \item {\tt{auto}} is the software controlled acquisition (does not use triggers), where {\tt{exptime}} and {\tt{period}} have to be set. Set number of cycles (i.e. triggers) to 1 using {\tt{cycles}}. Set number of frames using {\tt{frames}}.
 \item {\tt{trigger}} 1 frame taken for 1 trigger. Your {\tt{frames}} needs to be  1 always, {\tt{cycles}} can be changed and defines how many triggers are considered.  {\tt{exptime}} needs to be set. In the GUI this is called trigger exposure series.  
 \item {\tt{burst\_trigger}} gets only 1 trigger, but allows to take many frames. With {\tt{frames}} one can change the number of frames. {\tt{cycles}} needs to be 1.  {\tt{exptime}} and {\tt{period}} have to be set. In the gui it is called trigger readout.
-\item{\tt{gating}} allows to get a frame only when the trigger pulse is gating. Note that in this case the exp time and period only depend on the gating signal. {\tt{cycles}} allows to select how many gates to consider.  Set number of frames to 1 using {\tt{frames}}.
+\item{\tt{gating}} allows to get a frame only when the trigger pulse is gating. Note that in this case the exp time and period only depend on the gating signal. {\tt{cycles}} allows to select how many gates to consider.  Set number of frames to 1 using {\tt{frames}}. ATTENTION: if you are in 16 bit mode and you are applying online rate corrections, as now the exptime is generated by the trigger, you might not have correct rate corrections. If you know what the exposure time is in the gating signal, then you can set the {\tt{exptime}} once and the rate corrections will be correct. If the exposure time is unknow, it is recommended that you switch off the rate corrections. In 32 bit mode, it does not matter as the rate corrections depends on the {\tt{subexptime}} which is software set independently from the gate exptime.
+
 \end{itemize}
 
 Hardware-wise, the ENABLE OUT signal outputs when the chips are really acquiring. This means that the single subframes will be output in 32 bit mode. The TRIGGER OUT outputs the sum-up-signal at the moment (which is useless). This will be changed in the future to output the envelop of the enable signal. 
 
-We are planning to change some functionality, i.e. unify the {\tt{trigger}} and {\tt{burst}} trigger modes and make both {\tt{frames}} and {\tt{cycles}} configurable at the same time.
+We are planning to change some functionality, i.e. unify the {\tt{trigger}} and {\tt{burst\_trigger}} trigger modes and make both {\tt{frames}} and {\tt{cycles}} configurable at the same time.
+
+There is the possibility to use {\tt{timing trigger/burst\_trigger}} and send software single commands to fake the trigger. This is done with:
+\begin{verbatim}
+sls_detector_put 0-timing [trigger/burst_trigger]
+sls_detector_put 0-frames x
+sls_detector_put 0-cycles y
+sls_detector_status trigger
+\end{verbatim}
+ Note that this functionality is very (!) useful if you need to do something between and acquisition and the next. This can be used to do a fast threshold scan for example. See section~\ref{Sec:fastthresholdscan}.
+
 
 \section{Autosumming and rate corrections} \label{advanced}
 
@@ -1046,6 +1058,12 @@ To load the special noise file look at {\tt{settingsdir/eiger/standard/eigernois
 \begin{verbatim}
 sls_detector_put trimbits ../settingsdir/eiger/standard/eigernoise
 \end{verbatim}
+To exit from this pattern noise, just set the theshold to something known. 
+\begin{verbatim}
+\item sls_detector_put threshold 50000 standard
+\end{verbatim}
+where 5000 would be a value in eV and {/tt{standard}} is important in this case.
+
 
 \section{Troubleshooting}
 \subsection{Cannot successfully finish an acquisition}
@@ -1167,6 +1185,13 @@ If you see strange lines in vertical occurring at period patterns, it is a memor
 \subsection{ssh to the boards takes long}
 Depending on your network setup,  to speed up the ssh to the boards from a pc with internal dhcp server running: \textbf{iptables -t nat -A POSTROUTING -o eth1 -j MASQUERADE; echo "1" > /proc/sys/net/ipv4/ip\_forward}, where eth1 has to be the 1Gb network device on the pc
 
+\subsection{Generate keys on the boards not to have to type the password}
+\begin{verbatim}
+export AFSDIRS64=/afs/psi.ch/intranet/Controls/Software/Trolltech/SL6-x86_64
+ssh-copy-id -i /afs/psi.ch/user/t/tinti_g/.ssh/id_rsa.pub  root@beb100
+ssh-keygen
+\end{verbatim}
+
 \subsection{Check firmware version installed on BEB}
 You can either ask in the client as described in section~\ref{api}, or login to the boards directly. Follow some steps described in Section~\ref{server}. 
 \begin{verbatim}
@@ -1190,6 +1215,13 @@ Scroll up in the terminal till you find:\\
 *************** MASTER/SLAVE ***************\\
 *************** NORMAL/SPECIAL ***************\\
 
+There is also an easier way, that is that only the master module will reaturn the real value of the HV. If you have more than 1 detector system, then you will have more than 1 physical master, as the HV needs to be applied to all the systems.
+
+\begin{verbatim}
+for i in $(seq 0 36); do sls_detector_put $i:vhighvoltage; done
+\end{verbatim}
+ Only the master will return to you a sensible number (150 normally). the others will return -999.
+
 \subsection{'Cannot connect to socket'}
 This error is typically due to the detector server not running. For why, see section~\ref{servernot}.
 

recipe/build.sh

@@ -0,0 +1,15 @@
+mkdir build
+mkdir install
+cd build
+cmake .. \
+      -DCMAKE_PREFIX_PATH=$CONDA_PREFIX \
+      -DCMAKE_INSTALL_PREFIX=install \
+      -DUSE_TEXTCLIENT=ON \
+      -DUSE_RECEIVER=ON \
+      -DUSE_GUI=ON \
+      -DCMAKE_BUILD_TYPE=Release \
+      -DUSE_HDF5=OFF\
+     
+
+cmake --build . -- -j10
+cmake --build . --target install

recipe/copy_gui.sh

@@ -0,0 +1,15 @@
+
+mkdir $PREFIX/lib
+mkdir $PREFIX/bin
+mkdir $PREFIX/include
+
+#No libs for gui?
+
+#Binaries
+cp build/bin/gui_client $PREFIX/bin/.
+cp build/bin/slsDetectorGui $PREFIX/bin/.
+
+
+#Which headers do we need for development??
+
+# cp include/some_lib.h $PREFIX/include/.

recipe/copy_lib.sh

@@ -0,0 +1,23 @@
+
+mkdir $PREFIX/lib
+mkdir $PREFIX/bin
+mkdir $PREFIX/include
+mkdir $PREFIX/include/slsDetectorPackage
+
+#Shared and static libraries
+cp build/bin/libSlsDetector.so $PREFIX/lib/.
+cp build/bin/libSlsDetector.a $PREFIX/lib/.
+cp build/bin/libSlsReceiver.so $PREFIX/lib/.
+cp build/bin/libSlsReceiver.a $PREFIX/lib/.
+
+#Binaries
+cp build/bin/sls_detector_acquire $PREFIX/bin/.
+cp build/bin/sls_detector_get $PREFIX/bin/.
+cp build/bin/sls_detector_put $PREFIX/bin/.
+cp build/bin/sls_detector_help $PREFIX/bin/.
+cp build/bin/slsReceiver $PREFIX/bin/.
+cp build/bin/slsMultiReceiver $PREFIX/bin/.
+
+#Which headers do we need for development??
+cp build/install/include/* $PREFIX/include/slsDetectorPackage/
+# cp include/some_lib.h $PREFIX/include/.

recipe/meta.yaml

@@ -0,0 +1,89 @@
+
+package:
+  name: sls_detector_software
+  version: "developer"
+
+source:
+  - path: ..
+
+build:
+  number: 0
+  rpaths:
+    - lib/
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{compiler('cxx')}}
+    - cmake
+    - qwt 6.*
+    - qt=4.8.7=7
+    - zeromq=4.2.5=hfc679d8_5
+    - pyzmq
+    - xorg-libx11
+    - xorg-libice
+    - xorg-libxext
+    - xorg-libsm
+    - xorg-libxau
+    - xorg-libxrender
+    - xorg-libxfixes
+    - {{ cdt('mesa-libgl-devel') }}      # [linux]
+    - {{ cdt('mesa-libegl-devel') }}     # [linux]
+    - {{ cdt('mesa-dri-drivers') }}      # [linux]
+    - {{ cdt('libselinux') }}      # [linux]
+    - {{ cdt('libxdamage') }}            # [linux]
+    - {{ cdt('libxxf86vm') }}            # [linux]
+
+  host:
+    - libstdcxx-ng
+    - libgcc-ng
+    - libpng >=1.6.32,<1.6.35
+    - xorg-libx11
+    - xorg-libice
+    - xorg-libxext
+    - xorg-libsm
+    - xorg-libxau
+    - xorg-libxrender
+    - xorg-libxfixes
+
+  run:
+    - libstdcxx-ng
+    - libgcc-ng 
+
+outputs:
+  - name: sls_detector_lib
+    version: "developer"
+    script: copy_lib.sh
+    requirements:
+      build:
+        - {{ compiler('c') }}
+        - {{compiler('cxx')}}
+  - name: sls_detector_gui
+    version: "developer"
+    script: copy_gui.sh
+    requirements:
+      build:
+      - {{ compiler('c') }}
+      - {{compiler('cxx')}}
+      - cmake
+      - qwt 6.*
+      - qt=4.8.7=7
+      - zeromq=4.2.5=hfc679d8_5
+      - pyzmq
+      - xorg-libx11
+      - xorg-libice
+      - xorg-libxext
+      - xorg-libsm
+      - xorg-libxau
+      - xorg-libxrender
+      - xorg-libxfixes
+      - {{ cdt('mesa-libgl-devel') }}      # [linux]
+      - {{ cdt('mesa-libegl-devel') }}     # [linux]
+      - {{ cdt('mesa-dri-drivers') }}      # [linux]
+      - {{ cdt('libselinux') }}      # [linux]
+      - {{ cdt('libxdamage') }}            # [linux]
+      - {{ cdt('libxxf86vm') }}            # [linux]
+      run:
+        - sls_detector_lib=developer
+        - qwt 6.*
+        - qt=4.8.7=7

slsDetectorCalibration/.gitignore

@@ -1,2 +0,0 @@
-*.o
-*.*~

slsDetectorCalibration/MovingStat.h

@@ -31,18 +31,19 @@ class MovingStat
 	*/
         void Set(double val, double rms=0, int m=-1)
         {
-	  if (m>=0) m_n = m;  else m_n = n; 
+	  if (m>0) m_n = m;  else m_n = n; 
 	  m_newM=val*m_n; 
+	  // cout << "set " << val << " " << m << " " << m_n << " " << m_newM << endl;
 	  SetRMS(rms);
         }
-		/**
+	/**
 	   clears the moving average number of samples parameter, mean and standard deviation
 	*/
         void SetRMS(double rms)
         {
 	  if (rms<=0) {
 	    m_newM2=m_newM*m_newM/n;
-	    m_n=0;
+	    //m_n=0;
 	  } else {
 	    if (m_n>0)
 	      m_newM2=(m_n*rms*rms+m_newM*m_newM/m_n);
@@ -120,6 +121,7 @@ class MovingStat
 	 */
         inline double Mean() const
         {
+	  //  cout << "get " <<  m_n << " " << m_newM << " " << m_newM/m_n << endl;
             return (m_n > 0) ? m_newM/m_n : 0.0;
         }
 

slsDetectorCalibration/Stat.h

@@ -0,0 +1,45 @@
+class Stat
+  {
+  public:
+    
+  Stat() : n(0), m(0.), m2(0.) {}
+    
+    void Clear()
+    {
+      n = 0;
+      m=0;
+      m2=0;
+    }
+    
+        void Push(double x)
+        {
+	  
+	  m+=x;
+	  m2+=x*x;
+            n++;
+        }
+
+        int NumDataValues() const
+        {
+            return n;
+        }
+
+        double Mean() const
+        {
+            return (n > 0) ? m/n : 0.0;
+        }
+
+        double Variance() const
+        {
+	  return ( (n >0 ) ? (m2/n-m*m/(n*n)) : 0.0 );
+        }
+
+        double StandardDeviation() const
+        {
+            return sqrt( Variance() );
+        }
+
+    private:
+        int n;
+        double m, m2;
+    };

slsDetectorCalibration/analogDetector.h

@@ -6,7 +6,8 @@
 #include <pthread.h>
 #include "slsDetectorData.h"
 #include "pedestalSubtraction.h"
-#include "commonModeSubtraction.h"
+#include "commonModeSubtractionNew.h"
+#include "ghostSummation.h"
 #include "tiffIO.h"
 #include "slsInterpolation.h"
 
@@ -61,7 +62,7 @@ template <class dataType> class analogDetector {
   
 
  analogDetector(slsDetectorData<dataType> *d, int sign=1, 
-		commonModeSubtraction *cm=NULL, int nped=1000, int nnx=-1, int nny=-1, double *gm=NULL) : det(d), nx(nnx), ny(nny), stat(NULL), cmSub(cm),  iframe(-1), dataSign(sign), gmap(gm), id(0) {
+		commonModeSubtraction *cm=NULL, int nped=1000, int nnx=-1, int nny=-1, double *gm=NULL, ghostSummation<dataType> *gs=NULL) : det(d), nx(nnx), ny(nny), stat(NULL), cmSub(cm), dataSign(sign), iframe(-1), gmap(gm), ghSum(gs), id(0) {
     
     if (det)
       det->getDetectorSize(nx,ny);
@@ -118,7 +119,7 @@ template <class dataType> class analogDetector {
     dataSign=orig->dataSign;
     iframe=orig->iframe;
     gmap=orig->gmap;
-    cmSub=orig->cmSub;
+    //  cmSub=orig->cmSub;
     id=orig->id;
     xmin=orig->xmin;
     xmax=orig->xmax;
@@ -153,7 +154,16 @@ template <class dataType> class analogDetector {
      hs9=(TH2F*)(orig->hs9)->Clone();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5); 
 #endif
 #endif
-
+     if (orig->cmSub) {
+       cmSub=(orig->cmSub)->Clone();
+       cout <<"cloning cm" << endl;
+     }
+     else cmSub=NULL;
+     if (orig->ghSum) {
+       ghSum=(orig->ghSum)->Clone();
+       cout <<"cloning gs" << endl;
+     }
+     else ghSum=NULL;
   }
 
 
@@ -221,9 +231,10 @@ template <class dataType> class analogDetector {
     if (gm) {
       if (gmap) delete [] gmap; 
       gmap=new double[nnx*nny];
-      for (int ix=0; ix<nnx; ix++) {
-	for (int iy=0; iy<nny; iy++) {
+      for (int iy=0; iy<nny; iy++) {
+	for (int ix=0; ix<nnx; ix++) {
 	  gmap[iy*nnx+ix]=gm[iy*nnx+ix];
+	  // cout << gmap[iy*nnx+ix] << " " ;
 	}
       }
       return gmap;
@@ -240,8 +251,8 @@ template <class dataType> class analogDetector {
     void *ret;
     if (gmap)  {
       gm=new float[nx*ny];
-      for (int ix=0; ix<nx; ix++) {
 	for (int iy=0; iy<ny; iy++) {
+      for (int ix=0; ix<nx; ix++) {
 	  gm[iy*nx+ix]=gmap[iy*nx+ix];
 	}
       }
@@ -275,6 +286,14 @@ template <class dataType> class analogDetector {
   
   /** resets the commonModeSubtraction and increases the frame index */
   virtual void newFrame(){iframe++; if (cmSub) cmSub->newFrame();};
+
+  /** resets the commonModeSubtraction and increases the frame index */
+  virtual void newFrame(char *data){
+    iframe++; 
+    if (cmSub) cmSub->newFrame(); 
+    calcGhost(data); 
+    //    cout << getId() << " Calc ghost " <<  getGhost(15,15) << endl;
+      };
   
 
     /** sets the commonModeSubtraction algorithm to be used 
@@ -289,6 +308,11 @@ template <class dataType> class analogDetector {
     commonModeSubtraction *getCommonModeSubtraction() {return cmSub;};
 
 
+    ghostSummation<dataType> *getGhostSummation(){return ghSum;};
+    ghostSummation<dataType> *setGhostSummation(ghostSummation<dataType> *gs){ghSum=gs; return ghSum;}; 
+
+
+
     /**
        sets the sign of the data
        \param sign 1 means positive values for photons, -1 negative, 0 gets
@@ -304,11 +328,17 @@ template <class dataType> class analogDetector {
        \param iy pixel y coordinate
        \param cm 1 adds the value to common mod, 0 skips it. Defaults to 0. - not properly implemented
     */
-    virtual void addToPedestal(double val, int ix, int iy=0, int cm=0){ 
+    virtual void addToPedestal(double val, int ix, int iy, int cm=0){ 
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) { 
+	
+	//	cout << val << " " ;
 	if (cmSub && cm>0)  { 
 	  val-=	getCommonMode(ix, iy);
 	}
+	//	cout << val << " " ;
+	val+=getGhost(ix,iy);
+	//	cout << val ;
+	//	cout << endl;
 	stat[iy][ix].addToPedestal(val); 
 	/* if (cmSub && cm>0)  { */
 	/*   if (det) if (det->isGood(ix, iy)==0) return; */
@@ -318,29 +348,47 @@ template <class dataType> class analogDetector {
     }
     
     double getCommonMode(int ix, int iy) {
-      if (cmSub) return cmSub->getCommonMode(ix, iy);
-      else return 0;
+      if (cmSub) {
+	return cmSub->getCommonMode(ix, iy);
+      }
+      return 0;
     }
 
 
     virtual void addToCommonMode(char *data){ 
+      // cout << "+"<< getId() << endl;
       if (cmSub) {
-	for (int ix=xmin; ix<xmax; ix++) {
+	//cout << "*" << endl;
 	  for (int iy=ymin; iy<ymax; iy++) { 
+	for (int ix=xmin; ix<xmax; ix++) {
 	    // if (getNumpedestals(ix,iy)>0) 
-	    if (det->isGood(ix,iy))
+	  //  if (det->isGood(ix,iy)) {
 	      addToCommonMode(data, ix, iy);
-	  }
+	      //  cout << ":";
+	      // }
 	}
+	  }
 	//cout << "cm " << getCommonMode(0,0) << " " << getCommonMode(1,0) << endl;
       }
     }      
+
     virtual void addToCommonMode(char *data, int ix, int iy=0){ 
+      //  cout <<".";
       if (cmSub) {
+	//cout <<":";
 	if (det) if (det->isGood(ix, iy)==0) return;
 	if (getNumpedestals(ix,iy)>0){
-	    cmSub->addToCommonMode(subtractPedestal(data,ix,iy,0), ix, iy);
-	    // cout << ix << " " <<subtractPedestal(data,ix,iy,0)  << endl;
+	  double val;
+	  if (det) {
+	  /* if (det->getChannel(data, ix, iy)>=0x3fff) */
+	  /*   cout << ix << " " << iy << " " << det->getChannel(data, ix, iy) <<endl; */
+	    val= (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy,0));
+	  }	else
+	    val= (((double*)data)[iy*nx+ix]-getPedestal(ix,iy));
+	  	val+=getGhost(ix,iy);
+	
+	  cmSub->addToCommonMode(val, ix, iy);
+	  //cout << ":";
 	}
       }
     }      
@@ -351,12 +399,13 @@ template <class dataType> class analogDetector {
        \param cm 0 (default) without common mode subtraction, 1 with common mode subtraction (if defined)
        \returns pedestal value
     */
-    virtual double getPedestal(int ix, int iy, int cm=0){
-      if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
-	if (cmSub && cm>0) 
+    virtual double getPedestal (int ix, int iy, int cm=0){
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
+	if (cmSub && cm>0) {
 	  return stat[iy][ix].getPedestal()+getCommonMode(ix,iy); 
-	else return stat[iy][ix].getPedestal(); 
-      else return -1;
+	  
+	}     	else return stat[iy][ix].getPedestal(); 
+      } else return -1;
     };
 
 
@@ -367,15 +416,22 @@ template <class dataType> class analogDetector {
        \returns pedestal rms
     */
     virtual double getPedestalRMS(int ix, int iy){
-      if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
-	return stat[iy][ix].getPedestalRMS();
-      else return -1;
+      double g=1;
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
+	if (gmap) {
+	  g=gmap[iy*nx+ix];
+	  if (g==0) g=-1.;
+	}
+      
+	return stat[iy][ix].getPedestalRMS()/g;//divide by gain?
+      }
+      return -1;
     };
 
      virtual int getNumpedestals(int ix, int iy){
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
 	return stat[iy][ix].getNumpedestals();
-      else return -1;
+      return -1;
     };
     /**
        gets  pedestal (and common mode)
@@ -387,10 +443,10 @@ template <class dataType> class analogDetector {
     virtual double* getPedestal(double *ped){
       if (ped==NULL)
 	ped=new double[nx*ny];
-      for (int ix=0; ix<nx; ix++) {
-	for (int iy=0; iy<ny; iy++) {
+      for (int iy=0; iy<ny; iy++) {
+	for (int ix=0; ix<nx; ix++) {
 	  ped[iy*nx+ix]=stat[iy][ix].getPedestal();
-	  //cout << ped[iy*nx+ix] << " " ;
+	    //cout << ped[iy*nx+ix] << " " ;
 	}
       }
       return ped;
@@ -405,8 +461,8 @@ template <class dataType> class analogDetector {
     virtual double* getPedestalRMS(double *ped=NULL){
       if (ped==NULL)
 	ped=new double[nx*ny];
-      for (int ix=0; ix<nx; ix++) {
 	for (int iy=0; iy<ny; iy++) {
+      for (int ix=0; ix<nx; ix++) {
 	  ped[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
 	}
       }
@@ -445,13 +501,14 @@ template <class dataType> class analogDetector {
     */
     virtual void setPedestal(double *ped, double *rms=NULL, int m=-1){
       double rr=0;
-      for (int ix=xmin; ix<xmax; ix++) {
-	for (int iy=ymin; iy<ymax; iy++) {
+      for (int iy=ymin; iy<ymax; iy++) {
+	for (int ix=xmin; ix<xmax; ix++) {
 	  if (rms) rr=rms[iy*nx+ix];
 	  stat[iy][ix].setPedestal(ped[iy*nx+ix],rr, m);
+	  //  cout << ix << " " << iy << " " << ped[iy*nx+ix] << " " << stat[iy][ix].getPedestal() << endl;
 	};
       };
-
+      
     }
     
 
@@ -474,15 +531,32 @@ template <class dataType> class analogDetector {
        \param rms pointer to array of pedestal rms
     */
  virtual void setPedestalRMS(double *rms){
-      for (int ix=xmin; ix<xmax; ix++) {
 	for (int iy=ymin; iy<ymax; iy++) {
+      for (int ix=xmin; ix<xmax; ix++) {
 	  stat[iy][ix].setPedestalRMS(rms[iy*nx+ix]);
 	};
       };
 
     }
     
+ virtual void calcGhost(char *data, int ix, int iy=1) {
+   if (ghSum) {
+     ghSum->calcGhost(data, ix, iy);
+   }
+     
+};
 
+ virtual void calcGhost(char *data){if (ghSum) {
+     ghSum->calcGhost(data);
+     
+     //  cout << getId() << " @ " << ghSum->getXTalk() << " " <<  ghSum->getGhost(15,15) << endl;
+   }
+     
+
+};
+
+
+ virtual double getGhost(int ix, int iy) {if (ghSum) return ghSum->getGhost(ix, iy); return 0;};
 
      /**
        write 32bit tiff file with detector image data
@@ -498,8 +572,8 @@ template <class dataType> class analogDetector {
 
 #endif
       gm=new float[nx*ny];
-      for (int ix=0; ix<nx; ix++) {
 	for (int iy=0; iy<ny; iy++) {
+      for (int ix=0; ix<nx; ix++) {
 	    gm[iy*nx+ix]=image[iy*nx+ix];
 #ifdef ROOTSPECTRUM
 	    hmap->SetBinContent(ix+1, iy+1,image[iy*nx+ix]);
@@ -546,8 +620,8 @@ template <class dataType> class analogDetector {
       TH2F *hmap=new TH2F("hmap","hmap",nx, -0.5,nx-0.5, ny, -0.5, ny-0.5);
 
 #endif
-    for (int ix=0; ix<nx; ix++) {
       for (int iy=0; iy<ny; iy++) {
+    for (int ix=0; ix<nx; ix++) {
 	/* if (cmSub)  */
 	/*     gm[iy*nx+ix]=stat[iy][ix].getPedestal()-cmSub->getCommonMode(); */
 	/* else */
@@ -593,15 +667,15 @@ template <class dataType> class analogDetector {
 
 
     if (gm) {
-      for (int ix=0; ix<nnx; ix++) {
 	for (int iy=0; iy<nny; iy++) {
+      for (int ix=0; ix<nnx; ix++) {
 	  stat[iy][ix].setPedestal(gm[iy*nx+ix],-1,-1);
 	}
       }
       delete [] gm;
       return 1;
     }
-    return NULL;
+    return 0;
   }
   
  /**
@@ -618,15 +692,15 @@ template <class dataType> class analogDetector {
 
 
     if (gm) {
-      for (int ix=0; ix<nnx; ix++) {
 	for (int iy=0; iy<nny; iy++) {
+      for (int ix=0; ix<nnx; ix++) {
 	  image[iy*nx+ix]=gm[iy*nx+ix];
 	}
       }
       delete [] gm;
       return 1;
     }
-    return NULL;
+    return 0;
   }
   
    
@@ -644,8 +718,8 @@ template <class dataType> class analogDetector {
     float *gm=NULL;
     void *ret;
       gm=new float[nx*ny];
-      for (int ix=0; ix<nx; ix++) {
 	for (int iy=0; iy<ny; iy++) {
+      for (int ix=0; ix<nx; ix++) {
 	    gm[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
 	}
       }
@@ -666,8 +740,8 @@ template <class dataType> class analogDetector {
     if (nnx>nx) nnx=nx;
     if (nny>ny) nny=ny;
     if (gm) {
-      for (int ix=0; ix<nnx; ix++) {
 	for (int iy=0; iy<nny; iy++) {
+      for (int ix=0; ix<nnx; ix++) {
 	  stat[iy][ix].setPedestalRMS(gm[iy*nx+ix]);
 	}
       }
@@ -690,19 +764,24 @@ template <class dataType> class analogDetector {
     
     virtual void addToPedestal(char *data, int cm=0) {
       
-      //    cout << "add to pedestal " << endl;
-      newFrame();
+      // cout << "add to pedestal " << endl;
+      newFrame(data);
       
-      if (cmSub) {
+      //calcGhost(data);
+
+
+      if (cmSub && cm) {
+	//	cout <<",";
 	addToCommonMode(data);
-      }
+      } 
             
       //cout << xmin << " " << xmax << endl;
       // cout << ymin << " " << ymax << endl;
-      for (int ix=xmin; ix<xmax; ix++) {
-	for (int iy=ymin; iy<ymax; iy++) {
+      for (int iy=ymin; iy<ymax; iy++) {
+	for (int ix=xmin; ix<xmax; ix++) {
 	  if (det->isGood(ix,iy)) {
-	    addToPedestal(data,ix,iy,1);
+	    // addToPedestal(data,ix,iy,1);
+	    addToPedestal(data,ix,iy,cm);
 	  //if (ix==10 && iy==10) 
 	  // cout <<ix << " " << iy << " " << getPedestal(ix,iy)<< endl;
 #ifdef ROOTSPECTRUM 
@@ -782,7 +861,7 @@ template <class dataType> class analogDetector {
     */
 
 
-    virtual void addToPedestal(char *data, int ix, int iy=0, int cm=0) {
+    virtual void addToPedestal(char *data, int ix, int iy, int cm=0) {
       
       
       double val;
@@ -792,12 +871,13 @@ template <class dataType> class analogDetector {
 	  val=dataSign*det->getValue(data, ix, iy);
 	else
 	  val=((double*)data)[iy*nx+ix];
-	
+	//	cout << val << endl;
 	 /* if (ix==10 && iy==10)  */
 	 /*     cout << ix << " " << iy << " " << val ;  */
 	  /* if (ix==100 && iy==100) */
 	  /*   cout << ix << " " << iy << " " << val; */
 	addToPedestal(val,ix,iy);
+	//	cout << val << endl;
 	  /* if (ix==10 && iy==10)  */
 	  /*   cout <<" " << getPedestal(ix,iy)<< endl; */
 	  /* if (ix==100 && iy==100) */
@@ -818,15 +898,17 @@ template <class dataType> class analogDetector {
       
     virtual  int *subtractPedestal(char *data, int *val=NULL, int cm=0) {
       
-      newFrame();
+      newFrame(data);
       
       if (val==NULL)
 	val=image;//new double[nx*ny];
       
-      for (int ix=xmin; ix<xmax; ix++) {
-	for (int iy=ymin; iy<ymax; iy++) {
-	    if (det->isGood(ix,iy))
-	      val[iy*nx+ix]+=subtractPedestal(data, ix, iy,cm);
+      //calcGhost(data);
+
+      for (int iy=ymin; iy<ymax; iy++) {
+	for (int ix=xmin; ix<xmax; ix++) {
+	  if (det->isGood(ix,iy))
+	    val[iy*nx+ix]+=subtractPedestal(data, ix, iy,cm);
 	}
       }
       return  val;
@@ -847,18 +929,25 @@ template <class dataType> class analogDetector {
 
    virtual  double subtractPedestal(char *data, int ix, int iy=0, int cm=0) {
      double g=1.;
-     double val;
+     double val =0;
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
 	if (gmap) {
 	  g=gmap[iy*nx+ix];
 	  if (g==0) g=-1.;
 	}
 
-	if (det)
+	if (det) {
+	  /* if (det->getChannel(data, ix, iy)>=0x3fff) */
+	  /*   cout << ix << " " << iy << " " << det->getChannel(data, ix, iy) <<endl; */
 	  val= (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy,cm))/g;
-	else
+	}	else
 	  val= (((double*)data)[iy*nx+ix]-getPedestal(ix,iy))/g;
-    
+	
+	//if (val>=0.5*thr)
+	// cout << val << " " << (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy,cm)) << " " << g << " ";
+
+	val+=getGhost(ix,iy)/g;
+
 #ifdef ROOTSPECTRUM
 	hs->Fill(val,(iy-ymin)*(xmax-xmin)+(ix-xmin));
 #ifdef ROOTCLUST
@@ -890,6 +979,7 @@ template <class dataType> class analogDetector {
 #endif
 	return val;
       }	  
+      return val;
    };
       
 
@@ -917,8 +1007,7 @@ template <class dataType> class analogDetector {
      int nph=0;
      double v;
      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
-       v=subtractPedestal(data,ix,iy);
-
+       v=subtractPedestal(data,ix,iy,1);
 /*        // cout << v << " " ; */
 /* #ifdef ROOTSPECTRUM */
 /*        // cout << (iy-ymin)*(xmax-xmin)+(ix-xmin) << endl; */
@@ -927,8 +1016,14 @@ template <class dataType> class analogDetector {
        if (thr>0) {
 	 v+=0.5*thr;
 	 nph=v/thr;
-	 if (nph>0)
+	 
+	 /* if (ix ==10 && iy<20) */
+	 /*   cout << det->getValue(data,ix,iy) << " " << stat[iy][ix].getPedestal() << " " << getCommonMode(ix,iy) << " " << getPedestal(ix,iy,0)<< " "  << getPedestal(ix,iy,1) << endl; */
+	 // cout << subtractPedestal(data,ix,iy,0) << " " << subtractPedestal(data,ix,iy,1) << " " << nph << endl;
+	 if (nph>0) {
+	   //cout << " " << nph << endl;
 	   return nph;
+	 }
 	 return 0;
        } 
        return v;
@@ -944,15 +1039,16 @@ template <class dataType> class analogDetector {
    */
      int *getNPhotons(char *data,  int *nph=NULL) {
        
-       double val;
+       //double val;
        if (nph==NULL)
 	 nph=image;
-       newFrame();
+       
+       newFrame(data);
 
+       //calcGhost(data);
        addToCommonMode(data);
-
-       for (int ix=xmin; ix<xmax; ix++) {
-	 for (int iy=ymin; iy<ymax; iy++) {
+       for (int iy=ymin; iy<ymax; iy++) {
+	 for (int ix=xmin; ix<xmax; ix++) {
 	   if (det->isGood(ix,iy))
 	     nph[iy*nx+ix]+=getNPhotons(data, ix, iy);
 	 }
@@ -966,8 +1062,8 @@ template <class dataType> class analogDetector {
      
     */
    virtual void clearImage(){  
-     for (int ix=0; ix<nx; ix++) {
        for (int iy=0; iy<ny; iy++) { 
+     for (int ix=0; ix<nx; ix++) {
 	 image[iy*nx+ix]=0;
        }
      }
@@ -997,8 +1093,8 @@ template <class dataType> class analogDetector {
     int SetNPedestals(int i=-1) {
       int ix=0, iy=0; 
       if (i>0) 
-	for (ix=0; ix<nx; ix++) 
 	  for (iy=0; iy<ny; iy++) 
+	for (ix=0; ix<nx; ix++) 
 	    stat[iy][ix].SetNPedestals(i); 
       return stat[0][0].SetNPedestals();
     };
@@ -1030,13 +1126,16 @@ template <class dataType> class analogDetector {
       if (ymi<0) ymi=ymin;
       if (yma<0) yma=ymax;
       
-      for (int ix=xmi; ix<xma; ix++)
-	for (int iy=ymi; iy<yma; iy++)
+      newFrame(data);
+      //calcGhost(data);
+      addToCommonMode(data);
+      for (int iy=ymi; iy<yma; iy++)
+	for (int ix=xmi; ix<xma; ix++)
 	  if (det->isGood(ix,iy)) {
 	    if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
 	      val+=getNPhotons(data, ix, iy);
 	  }
-
+      
       return val;
       
     };
@@ -1054,7 +1153,7 @@ template <class dataType> class analogDetector {
       switch(fMode) {
       case ePedestal:
 	//cout << "analog ped " << endl;
-	addToPedestal(data);
+	addToPedestal(data,1);
 	break;
       default:
 	//	cout << "analog " << endl;
@@ -1138,6 +1237,7 @@ FILE *getFilePointer(){return myFile;};
     int dataSign; /**< sign of the data i.e. 1 if photon is positive, -1 if negative */
     int iframe;  /**< frame number (not from file but incremented within the dataset every time newFrame is called */
     double *gmap;
+    ghostSummation<dataType> *ghSum;/**< ghostSummation class */
     int *image;
     int id;
     //int xmin, xmax, ymin, ymax;  int xmin; /**< minimum x of the region of interest */

slsDetectorCalibration/commonModeSubtractionNew.h

@@ -0,0 +1,127 @@
+#ifndef COMMONMODESUBTRACTION_H
+#define COMMONMODESUBTRACTION_H
+
+#include <cmath>
+
+class commonModeSubtraction {
+
+  /** @short class to calculate the common mode of the pedestals based on an approximated moving average*/ 
+
+ public:
+  
+  /** constructor
+      \param nn number of samples for the moving average to calculate the average common mode
+      \param iroi number of regions on which one can calculate the common mode separately. Defaults to 1 i.e. whole detector
+
+  */
+ commonModeSubtraction(int iroi=1, int ns=3) : nsigma(ns), nROI(iroi)  {
+    mean=new double[nROI];  
+    mean2=new double[nROI]; 
+    nCm=new double[nROI];
+  };
+
+    /** destructor - deletes the moving average(s) and the sum of pedestals calculator(s) */
+    virtual ~commonModeSubtraction() {delete [] mean; delete [] mean2; delete [] nCm;};
+    
+    /* commonModeSubtraction(commonModeSubtraction *cs) { */
+    /*   if (cs) new commonModeSubtraction(cs->getNRoi(), cs->nsigma); */
+    /* } */
+    
+    virtual commonModeSubtraction *Clone() {
+      return new commonModeSubtraction(this->nROI, this->nsigma);
+    }
+
+    /** clears the moving average and the sum of pedestals calculation - virtual func*/
+    virtual void  Clear(){
+      for (int i=0; i<nROI; i++) {
+	mean[i]=0;  
+	nCm[i]=0; 
+	mean2[i]=0;
+      }};
+    
+    /** adds the average of pedestals to the moving average and reinitializes the calculation of the sum of pedestals for all ROIs. - virtual func*/
+    virtual void  newFrame(){
+      //cout << "Reset CM" << endl;
+      for (int i=0; i<nROI; i++) {
+	//	if (nCm[i]>0) cmStat[i].Calc(cmPed[i]/nCm[i]); 
+	nCm[i]=0; 
+	mean[i]=0;
+	mean2[i]=0;
+      }};
+    
+    /** adds the pixel to the sum of pedestals -- virtual func must be overloaded to define the regions of interest
+	\param val value to add
+	\param ix pixel x coordinate
+	\param iy pixel y coordinate
+    */
+    virtual void addToCommonMode(double val, int ix=0, int iy=0) {
+      
+      int iroi=getROI(ix,iy);
+      // if (iroi==0) val=100;
+      // else val=-100;
+      // if (isc>=0 && isc<nROI) {
+      //	cout << ix << " " << iy << " " << iroi << endl;
+      //if (ix==15 && iy==15) cout << "=" << val << endl;
+      if (iroi>=0 && iroi<nROI) {
+	//	cout << ix << " " << iy << " " << iroi << endl;
+	mean[iroi]+=val; 
+	mean2[iroi]+=val*val; 
+	nCm[iroi]++;
+      }
+    };
+
+    /** gets the common mode i.e. the difference between the current average sum of pedestals mode and the average pedestal 
+	\param ix pixel x coordinate
+	\param iy pixel y coordinate
+	\return the difference  between the current average sum of pedestals and the average pedestal
+    */
+    virtual double getCommonMode(int ix=0, int iy=0) {
+      int iroi=getROI(ix,iy); 
+      /* if (iroi==0) */
+      /* 	return 100; */
+      /* else */
+      /* 	return -100; */
+      // cout << "*" << ix << " " << iy << " " << iroi << " " << mean[iroi] << " " << nCm[iroi]<< endl;
+      // if (ix==15 && iy==15) cout << "-" << mean[iroi]/nCm[iroi] << endl;
+      if (iroi>=0 && iroi<nROI) {
+	if (nCm[iroi]>0)  
+	  return mean[iroi]/nCm[iroi]; 
+      }
+      return 0;
+    };
+    
+    /** gets the common mode i.e. the difference between the current average sum of pedestals mode and the average pedestal 
+	\param ix pixel x coordinate
+	\param iy pixel y coordinate
+	\return the difference  between the current average sum of pedestals and the average pedestal
+    */
+    virtual double getCommonModeRMS(int ix=0, int iy=0) {
+      int iroi=getROI(ix,iy);
+      if (iroi>=0 && iroi<nROI) {
+	if (nCm[iroi]>0) 
+	  return sqrt(mean2[iroi]/nCm[iroi]-(mean[iroi]/nCm[iroi])*(mean[iroi]/nCm[iroi])); 
+      }
+      return 0;
+    };
+
+    /** 
+	gets the common mode ROI for pixel ix, iy -should be overloaded!
+     */
+    virtual int getROI(int ix, int iy){ (void) ix; (void) iy; return 0;};
+    int getNRoi(){return nROI;};
+
+ protected:
+  double *mean; /**<array of moving average of the pedestal average per region of interest */
+  double *mean2; /**< array storing the sum of pedestals per region of interest */
+  double *nCm; /**< array storing the number of pixels currently contributing to the pedestals */
+  int nsigma; /** number of rms above which the pedestal should be considered as a photon */
+  const int nROI; /**< constant parameter for number of regions on which the common mode should be calculated separately e.g. supercolumns */
+
+
+};
+
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/Mythen3_01_jctbData.h

@@ -45,7 +45,7 @@ class mythen3_01_jctbData : public slsDetectorData<short unsigned int> {
 
  virtual short unsigned int* mythen03_frame(char *ptr, int dr=24,  int nch=64*3, int off=5) {
    // off=0;
-    int iarg;
+    //int iarg;
     int64_t word, *wp;
     short unsigned int* val=new short unsigned int[nch];
     int bit[64];
@@ -74,7 +74,7 @@ class mythen3_01_jctbData : public slsDetectorData<short unsigned int> {
 	  for (ib=0; ib<nb; ib++) {
 	    if (word&(1<<bit[ib]))  {
 	      cout << "+" ;
-	      val[iw+nch*(ib/nb)]|=(1<<idr);
+	      val[iw+nch/nb*(ib)]|=(1<<idr);
 	    }  else { 
 	      	cout << "-" ; 
 	       } 
@@ -96,8 +96,8 @@ class mythen3_01_jctbData : public slsDetectorData<short unsigned int> {
       ii++;
     }//end for
     
-    cout << "Decoded "<<ii << " samples"<< endl;
-    cout << "Should be "<< nch/nb*dr+off << " samples"<< endl;
+    cout << "M3.01 Decoded "<<ii << " samples"<< endl;
+    cout << "M3.01 Should be "<< nch/nb*dr+off << " samples"<< endl;
   
     return val;
  }

slsDetectorCalibration/dataStructures/Mythen3_02_jctbData.h

@@ -49,7 +49,7 @@ class mythen3_02_jctbData : public mythen3_01_jctbData {
 
  virtual short unsigned int* mythen03_frame(char *ptr, int dr=24,  int nch=64*3, int off=5) {
    // off=0;
-    int iarg;
+    //int iarg;
     int64_t word, *wp;
     short unsigned int* val=new short unsigned int[nch];
     int bit[64];
@@ -57,8 +57,9 @@ class mythen3_02_jctbData : public mythen3_01_jctbData {
     int ioff=0;
     int idr=0;
     int ib=0;
-    int iw=0;
+    //int ich=0;
     int ii=0;
+    int iw=0;
     bit[0]=17;//19;
     bit[1]=6;//8;
     idr=0;
@@ -68,7 +69,8 @@ class mythen3_02_jctbData : public mythen3_01_jctbData {
     wp=(int64_t*)ptr;
     
     for (iw=0; iw<nch/nb; iw) {
-      word=*wp;;
+      word=*wp;
+
       if (ioff<off) {
 	ioff++;
 	 cout <<"*";
@@ -78,10 +80,11 @@ class mythen3_02_jctbData : public mythen3_01_jctbData {
 	  for (ib=0; ib<nb; ib++) {
 	    if (word&(1<<bit[ib]))  {
 	      cout << "+" ;
-	      val[iw+nch*(ib/nb)]|=(1<<idr);
+	      val[iw+nch/nb*(ib)]|=(1<<idr);
 	    }  else { 
 	      	cout << "-" ; 
-	       } 
+	    } 
+	    //    cout <<  iw+nch/nb*(ib)<< " " ;
 	  }//end for()
 	}
 	
@@ -94,14 +97,14 @@ class mythen3_02_jctbData : public mythen3_01_jctbData {
 	  cout <<dec << iw<<endl;
 	  iw++;
 	}//end if()
-
+	
       }//end else()
       wp+=1;
       ii++;
     }//end for
     
-    cout << "Decoded "<<ii << " samples"<< endl;
-    cout << "Should be "<< nch/nb*dr+off << " samples"<< endl;
+    cout << "M3.02 Decoded "<<ii << " samples"<< endl;
+    cout << "M3.02 Should be "<< nch/nb*dr+off << " samples"<< endl;
   
     return val;
  }

slsDetectorCalibration/dataStructures/deserializer.h

@@ -0,0 +1,171 @@
+#ifndef DESERIALIZER_H
+#define DESERIALIZER_H
+#include <vector>
+
+class deserializer : public slsDetectorData<int> {
+
+
+ public:
+
+
+ deserializer( std::vector <int> dbl, int nch=64*3,int dr=24, int off=2): slsDetectorData<int>(nch,1,nch*dr*8+off*8,NULL,NULL,NULL), dynamicRange(dr), serialOffset(off), frameNumber(0), numberOfCounters(nch), dbitlist(dbl) {};
+
+ deserializer( std::vector <int> dbl, int nch,int dr, int off, int ds): slsDetectorData<int>(nch,1,ds,NULL,NULL,NULL), dynamicRange(dr), serialOffset(off), frameNumber(0), numberOfCounters(nch),  dbitlist(dbl) {};
+
+  virtual void getPixel(int ip, int &x, int &y) {x=-1; y=-1;};
+  
+  virtual int getChannel(char *data, int ix, int iy=0) {
+    int ret=-1;
+    if (ix>=0 && ix<numberOfCounters) {
+      int *val=deserializeAll(data,dbitlist,dynamicRange,numberOfCounters,serialOffset); 
+      ret=val[ix];
+      delete [] val;
+    }
+    return ret;
+  };
+  
+  virtual int getFrameNumber(char *buff) {return frameNumber;};
+ 
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize) {
+    ndata=dsize;
+    return data;
+  }
+  
+ virtual char *readNextFrame(ifstream &filebin) {
+    char *data=NULL;
+    if (filebin.is_open()) {
+      data=new char[dataSize];
+      filebin.read(data,dataSize);
+    }
+    return data;
+  }
+ 
+ virtual int **getData(char *ptr, int dsize=-1) {
+   int **val;
+   val=new int*[1];
+   val[0]=deserializeAll(ptr,dbitlist,dynamicRange,nx,serialOffset);
+   return val;
+   
+ }
+ 
+
+ static int* deserializeAll(char *ptr, std::vector <int> dbl, int dr=24,  int nch=64*3, int off=5) {
+   // off=0;
+   //int iarg;
+   int64_t word, *wp;
+   int* val=new int[nch];
+   int ioff=0;
+   int idr=0;
+   int ib=0;
+   int iw=0;
+   int ii=0;
+   int ich;
+   int nb=dbl.size();
+   idr=0;
+   for (ib=0; ib<nch; ib++) {
+     val[ib]=0;
+   }
+   wp=(int64_t*)ptr;
+   
+   for (iw=0; iw<nch/nb; iw) {
+     word=*wp;;
+     if (ioff<off) {
+       ioff++;
+       // cout <<"*";
+     }  else {
+       //if (idr<16) {
+       ib=0;
+	for (const auto &bit : dbl) {
+	  ich=iw+nch/nb*(ib);
+	  if (word&(1<<bit) && ich<nch)  {
+	    //cout << "+" ;
+	    val[ich]|=(1<<idr);
+	  }  //else { 
+	  //cout << "-" ; 
+	  //}
+	  ib++;
+	}
+	
+     }
+     
+     idr++; 
+     if (idr==dr) {
+       idr=0;
+	//  cout << dec << " " << iw << " " << val[iw] << " " << val[iw+nch/2] << endl;
+       cout <<dec << iw<<endl;
+       iw++;
+     }//end if()
+     
+      //end else()
+     wp+=1;
+     ii++;
+   }//end for
+   
+    
+    return val;
+ }
+
+ static int* deserializeList(char *ptr, std::vector <int> dbl, int dr=24,  int nch=64*3, int off=5) {
+   // off=0;
+   //int iarg;
+  // int64_t word;
+   int* val=new int[nch];
+   //int ioff=0;
+   int idr=0;
+   int ib=0;
+   int iw=0;
+   int ii=0;
+   int ich;
+   int nb=dbl.size();
+
+   char *dval;
+
+   idr=0;
+   for (ib=0; ib<nch; ib++) {
+     val[ib]=0;
+   }
+   dval=ptr;
+   
+   ib=0;
+   ich=0;
+   for (const auto &bit : dbl) {
+     //ioff=off;
+     idr=0;
+     for (iw=0; iw<(nch*dr/nb)/8; iw++) {
+       val[ich]|=(*dval)<<idr;
+       idr+=8;
+       dval++;
+       if (idr>=dr) {
+	 idr=0;
+	 ich++;
+       }	
+     }
+     ii++;
+     ib++;
+   }//end for
+   
+    
+    return val;
+ }
+
+ virtual int setFrameNumber(int f=0) {if (f>=0) frameNumber=f; return frameNumber; };
+ virtual int setDynamicRange(int d=-1) {if (d>0 && d<=24) dynamicRange=d; return dynamicRange;};
+ virtual int setSerialOffset(int d=-1) {if (d>=0) serialOffset=d; return serialOffset;};
+ virtual int setNumberOfCounters(int d=-1) {if (d>=0) numberOfCounters=d; return numberOfCounters;};
+ virtual  std::vector <int> setDBitList(std::vector <int> dbl) {dbitlist=dbl; return dbitlist;};
+ virtual  std::vector <int> getDBitList() {return dbitlist;};
+ 
+ 
+ private:
+ 
+ int dynamicRange;
+ int serialOffset;
+ int frameNumber;
+ int numberOfCounters;
+ std::vector <int> dbitlist;
+   
+
+ 
+};
+
+#endif

slsDetectorCalibration/dataStructures/eigerHalfModuleData.h

@@ -1,470 +0,0 @@
-#ifndef EIGERMODULEDATA_H
-#define  EIGERMODULEDATA_H
-#include "slsReceiverData.h"
-
-
-
-class eigerHalfModuleData : public slsReceiverData<uint32_t> {
-public:
-
-
-
-
-	/**
-     Implements the slsReceiverData structure for the eiger prototype read out by a half module i.e. using the slsReceiver
-     (256*256 pixels, 512 packets for 16 bit mode, 256 for 8, 128 for 4, 1024 for 32, 1040  etc.)
-     \param d dynamic range
-     \param c crosstalk parameter for the output buffer
-
-	 */
-
-
-	eigerHalfModuleData(bool t, bool l, int dr, int tg, int psize, int dsize, int npf, int x, int y, double c=0):
-		slsReceiverData<uint32_t>(x, y, npf, psize),
-		top(t), left(l),
-		dynamicRange(dr), tenGiga(tg),
-		packetSize(psize), onepacketdataSize(dsize), numberofPacketsPerFrame(npf),
-		xtalk(c),
-		header_t(0), footer_t(0){
-
-
-		int **dMap;
-		uint32_t **dMask;
-
-		dMap=new int*[ny];
-		dMask=new uint32_t*[ny];
-
-
-		for (int i = 0; i < ny; i++) {
-			dMap[i] = new int[nx];
-			dMask[i] = new uint32_t[nx];
-		}
-
-		//Map
-		int totalNumberOfBytes = numberofPacketsPerFrame * packetSize;
-		int iPacket = 8;
-		int iData = 0;
-		int increment = (dynamicRange/8);
-		int ic_increment = 1;
-		if (dynamicRange == 4) {
-			increment = 1;
-			ic_increment = 2;
-		}
-
-		if(top){
-			for (int ir=0; ir<ny; ir++) {
-				for (int ic=0; ic<nx; ic = ic + ic_increment) {
-					dMap[ir][ic]  = iPacket;
-					iPacket += increment;
-					iData += increment;
-					//increment header
-					if(iData >= onepacketdataSize){
-						iPacket += 16;
-						iData = 0;
-					}
-
-				}
-			}
-		}
-
-		//bottom
-		else{
-			iData = 0;
-			int numbytesperline;
-			switch(dynamicRange){
-				case 4: numbytesperline = 256; break;
-				case 8:	numbytesperline = 512; break;
-				case 16:numbytesperline = 1024; break;
-				case 32:numbytesperline = 2048; break;
-			}
-			iPacket = totalNumberOfBytes - numbytesperline - 8;
-			if((dynamicRange == 32) && (!tenGiga))
-					iPacket -= 16;
-
-			for (int ir=0; ir<ny; ir++) {
-				for (int ic=0; ic<nx; ic = ic + ic_increment) {
-					dMap[ir][ic]  = iPacket;
-					iPacket += increment;
-					iData += increment;
-					//--------------------32 bit 1giga -------------------
-					if((dynamicRange == 32) && (!tenGiga)){
-						if(iData == numbytesperline){
-							iPacket -= (numbytesperline*2 + 16*3);
-							iData = 0;
-						}
-						if(iData == onepacketdataSize){
-							iPacket += 16;
-						}
-					}//------------end of 32 bit -------------------------
-					else if((iData % numbytesperline) == 0){
-						iPacket -= (numbytesperline*2);
-						if(iData == onepacketdataSize){
-							iPacket -= 16;
-							iData = 0;
-						}
-					}
-					//---------------------------------------------------
-				}
-			}
-		}
-
-
-
-
-		//Mask
-		for(int ir=0; ir<ny; ++ir)
-			for(int ic=0; ic<nx; ++ic)
-				dMask[ir][ic] = 0x0;
-
-		setDataMap(dMap);
-		setDataMask(dMask);
-
-	};
-
-
-
-
-
-	/** Returns the frame number for the given dataset.
-	     \param buff pointer to the dataset
-	     \returns frame number
-	 */
-	int getFrameNumber(char *buff){
-		footer_t = (eiger_packet_footer_t*)(buff + onepacketdataSize + sizeof(eiger_packet_header_t));
-		return ((uint32_t)(*( (uint64_t*) footer_t)));
-	};
-
-
-
-
-
-	/** gets the packets number
-     	 \param buff pointer to the memory
-     	 \returns packet number
-	 */
-	int getPacketNumber(char *buff){
-		footer_t = (eiger_packet_footer_t*)(buff + onepacketdataSize + sizeof(eiger_packet_header_t));
-		return(*( (uint16_t*) footer_t->packetnum));
-	};
-
-
-
-	/**
-    returns the pixel value as double correcting for the output buffer crosstalk
-     \param data pointer to the memory
-     \param ix coordinate in the x direction
-     \param iy coordinate in the y direction
-     \returns channel value as double
-
-	 */
-	double getValue(char *data, int ix, int iy=0) {
-		//  cout << "##" << (void*)data << " " << ix << " " <<iy << endl;
-		if (xtalk==0)
-			return getChannelwithMissingPackets(data, ix, iy);
-		else
-			return getChannelwithMissingPackets(data, ix, iy)-xtalk * getChannelwithMissingPackets(data, ix-1, iy);
-	};
-
-
-	/**
-
-	     Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
-	     \param data pointer to the dataset (including headers etc)
-	     \param ix pixel number in the x direction
-	     \param iy pixel number in the y direction
-	     \returns data for the selected channel, with inversion if required
-
-	 */
-
-	virtual int getChannelwithMissingPackets(char *data, int ix, int iy) {
-		uint32_t m=0, n = 0;
-		int linesperpacket,newix, newiy,origX;
-
-
-		//cout <<"ix:"<<ix<<" nx:"<<nx<<" iy:"<<iy<<" ny:"<<ny<<" datamap[iy][ix]:"<< dataMap[iy][ix] <<" datasize:"<< dataSize <<endl;
-		if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
-			m=dataMask[iy][ix];
-
-
-			//pixelpos1d = (nx * iy + ix);
-
-			switch(dynamicRange){
-			case 4: 	if(tenGiga) linesperpacket=16;	else linesperpacket=4;break;
-			case 8: 	if(tenGiga) linesperpacket=8; 	else linesperpacket=2;break;
-			case 16: 	if(tenGiga) linesperpacket=4; 	else linesperpacket=1;break;
-			case 32:	if(tenGiga) linesperpacket=2; 	else linesperpacket=1;break;
-			}
-
-
-
-			//each byte is shared by 2 pixels for 4 bit mode
-			origX = ix;
-			if((dynamicRange == 4) && (ix%2))
-				ix--;
-
-
-
-			// ------check if missing packet, get to pixel at start of packet-----------------
-
-			//to get the starting of a packet (except 1g 32 bit)
-			newix = 0;
-			// 0.5 Lines per packet for 1g 32 bit
-			if(dynamicRange == 32 && !tenGiga)
-				newix = ix - (ix%256);
-
-			//iy divided by linesperpacket depending on bitmode
-			if(!(iy%linesperpacket))
-				newiy = iy;
-			else
-				newiy = (iy - (iy%linesperpacket));
-
-			header_t = (eiger_packet_header_t*)((char*)(data +(dataMap[newiy][newix]-8)));
-			uint16_t identifier = (uint16_t)*( (uint16_t*) header_t->missingpacket);
-
-			if(identifier==deactivatedPacketValue){
-				//	cprintf(RED,"deactivated packet\n");
-				return -2;
-			}
-			// -----END OF CHECK -------------------------------------------------------------
-
-
-		}else{
-			cprintf(RED,"outside limits\n");
-			return -99;
-		}
-
-		//get proper data
-		n = ((uint32_t)(*((uint32_t*)(((char*)data)+(dataMap[iy][ix])))));
-
-		//each byte is shared by 2 pixels for 4 bit mode
-		if(dynamicRange == 4){
-			if(ix != origX)
-				return ((n & 0xf0)>>4)^m;
-			return (n & 0xf)^m;
-		}
-		else if(dynamicRange == 8)	return (n & 0xff)^m;
-		else if(dynamicRange == 16)	return (n & 0xffff)^m;
-		else				return (n & 0xffffffff)^m;
-
-
-	};
-
-
-	/** sets the output buffer crosstalk correction parameter
-      \param c output buffer crosstalk correction parameter to be set
-      \returns current value for the output buffer crosstalk correction parameter
-
-	 */
-	double setXTalk(double c) {xtalk=c; return xtalk;}
-
-
-	/** gets the output buffer crosstalk parameter
-      \returns current value for the output buffer crosstalk correction parameter
-	 */
-	double getXTalk() {return xtalk;}
-
-	void getChannelArray(double* data, char* buffer){
-		for(int iy = 0; iy < ny; iy++){
-			for(int ix = 0; ix < nx; ix++){
-				data[iy*nx+ix] = getValue((char*)buffer,ix,iy);
-				//cprintf(BLUE,"%d,%d :%f\n",ix,iy,value);
-			}
-		}
-	}
-
-
-	int* decodeData(int *datain) {
-
-		int dataBytes = numberofPacketsPerFrame * onepacketdataSize;
-		int nch = nx*ny;
-		int* dataout = new int [nch];
-		char *ptr=(char*)datain;
-		char iptr;
-
-		const int bytesize=8;
-		int ival=0;
-		int  ipos=0, ichan=0, ibyte;
-
-		switch (dynamicRange) {
-		case 4:
-			for (ibyte=0; ibyte<dataBytes; ++ibyte) {//for every byte (1 pixel = 1/2 byte)
-				iptr=ptr[ibyte]&0xff;				//???? a byte mask
-				for (ipos=0; ipos<2; ++ipos) {		//loop over the 8bit (twice)
-					ival=(iptr>>(ipos*4))&0xf;		//pick the right 4bit
-					dataout[ichan]=ival;
-					ichan++;
-				}
-			}
-			break;
-		case 8:
-			for (ichan=0; ichan<dataBytes; ++ichan) {//for every pixel (1 pixel = 1 byte)
-				ival=ptr[ichan]&0xff;				//????? a byte mask
-				dataout[ichan]=ival;
-			}
-			break;
-		case 16:
-			for (ichan=0; ichan<nch; ++ichan) { 	//for every pixel
-				ival=0;
-				for (ibyte=0; ibyte<2; ++ibyte) { 	//for each byte (concatenate 2 bytes to get 16 bit value)
-					iptr=ptr[ichan*2+ibyte];
-					ival|=((iptr<<(ibyte*bytesize))&(0xff<<(ibyte*bytesize)));
-				}
-				dataout[ichan]=ival;
-			}
-			break;
-		default:
-													//for every 32 bit (every element in datain array)
-			for (ichan=0; ichan<nch; ++ichan) { 	//for every pixel
-				ival=datain[ichan]&0xffffff;
-				dataout[ichan]=ival;
-			}
-		}
-
-
-
-		return dataout;
-
-	};
-
-
-	int* readNextFrameOnlyData(ifstream &filebin, int& fnum) {
-		int framesize = numberofPacketsPerFrame * onepacketdataSize;
-
-		int* data = new int[framesize/(sizeof(int))];
-		char *packet=new char[packetSize];
-		fnum = -1;
-		int pn=-1;
-		int dataoffset = 0;
-
-		if (filebin.is_open()) {
-
-			while (filebin.read(packet,packetSize)) {
-
-				fnum = getFrameNumber(packet); //cout << "fn:"<<fn<<endl;
-				pn = getPacketNumber(packet); //cout << "pn:"<<pn<<endl;
-
-				memcpy(((char*)data)+dataoffset,packet+DATA_PACKET_HEADER_SIZE,onepacketdataSize);
-				dataoffset+=onepacketdataSize;
-				if(pn == numberofPacketsPerFrame)
-					break;
-			}
-		}
-
-		delete [] packet;
-		if(!dataoffset){
-			delete [] data;
-			return NULL;
-		}
-
-		return data;
-
-	}
-	/*
-	when u get packet form next frames
-	//to remember the position to read next frame
-	filebin.seekg (position, filebin.beg);
-	position = filebin.tellg();
-
-	*/
-
-	int *readNextFramewithMissingPackets(ifstream &filebin, int& fnum) {
-
-		int* data = new int[(numberofPacketsPerFrame * onepacketdataSize)/(sizeof(int))];
-		char *packet=new char[packetSize];
-		fnum = -1;
-		int pnum = 0;
-		int fn = -1;
-		int pn =-1;
-		int dataoffset = 0;
-		int missingpackets;
-
-
-		if (filebin.is_open()) {
-
-			while (filebin.read(packet,packetSize)) {
-
-				fn = getFrameNumber(packet); //cout << "fn:"<<fn<<endl;
-				pn = getPacketNumber(packet); //cout << "pn:"<<pn<<endl;
-
-				//first packet
-				if(fnum == -1){
-					fnum = fn;
-				}
-				//next frame packet
-				else if (fnum != fn){
-					//set file reading to the last frame's packet in file
-					filebin.seekg(-packetSize, ios::cur);//filebin.beg
-					break;
-				}
-
-				//missing packets
-				missingpackets = pn - pnum - 1;
-				if(missingpackets){
-					memset(((char*)data)+dataoffset,0xFF,missingpackets*onepacketdataSize);
-					dataoffset+=(missingpackets*onepacketdataSize);
-					pnum+=missingpackets;
-				}
-
-				memcpy(((char*)data)+dataoffset,packet+DATA_PACKET_HEADER_SIZE,onepacketdataSize);
-				dataoffset+=onepacketdataSize;
-				pnum++;
-				if(pnum == numberofPacketsPerFrame)
-					break;
-
-			}
-		}
-
-		delete [] packet;
-		if(!pnum){
-			delete [] data;
-			return NULL;
-		}
-
-		//missing packets (added here to also catch end of file)
-		missingpackets = numberofPacketsPerFrame - pnum;
-		if(missingpackets){
-			memset(((char*)data)+dataoffset,0xFF,missingpackets*onepacketdataSize);
-			dataoffset+=(missingpackets*onepacketdataSize);
-		}
-
-		return data;
-	}
-
-
-
-private:
-	/** Missing Packet identifier value */
-	const static uint16_t deactivatedPacketValue = 0xFEFE;
-
-	const static int DATA_PACKET_HEADER_SIZE = 8;
-	const bool top;
-	const bool left;
-	const int dynamicRange;
-	const bool tenGiga;
-	const int packetSize;
-	const int onepacketdataSize;
-	const int numberofPacketsPerFrame;
-	double xtalk; /**<output buffer crosstalk correction parameter */
-
-
-	/** structure of an eiger packet*/
-	typedef struct{
-		unsigned char subframenum[4];
-		unsigned char missingpacket[2];
-		unsigned char portnum[1];
-		unsigned char dynamicrange[1];
-	} eiger_packet_header_t;
-
-	typedef struct{
-		unsigned char framenum[6];
-		unsigned char packetnum[2];
-	} eiger_packet_footer_t;
-
-	eiger_packet_header_t* header_t;
-	eiger_packet_footer_t* footer_t;
-};
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/gotthardModuleData.h

@@ -1,148 +0,0 @@
-#ifndef GOTTHARDMODULEDATA_H
-#define  GOTTHARDMODULEDATA_H
-#include "slsReceiverData.h"
-
-
-
-
-
-#define FRAMEMASK 0xFFFFFFFE
-#define PACKETMASK 1
-#define FRAMEOFFSET 0x1
-
-
-class gotthardModuleData : public slsReceiverData<uint16_t> {
-public:
-
-
-
-
-	/**
-     Implements the slsReceiverData structure for the gotthard read out by a module i.e. using the slsReceiver
-     (1x1280 pixels, 2 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-	 */
-
-
-	gotthardModuleData(double c=0): slsReceiverData<uint16_t>(xpixels, ypixels, npackets, buffersize), xtalk(c) {
-
-		uint16_t **dMask;
-		int **dMap;
-		int ix, iy;
-		int initial_offset = 2;
-		int offset = initial_offset;
-
-		dMask=new uint16_t*[ypixels];
-		dMap=new int*[ypixels];
-		for (int i = 0; i < ypixels; i++) {
-			dMap[i] = new int[xpixels];
-			dMask[i] = new uint16_t[xpixels];
-		}
-
-		for(ix=0; ix<ypixels; ++ix)
-			for(iy=0; iy<xpixels; ++iy)
-				dMask[ix][iy] = 0x0;
-
-		for(ix=0; ix<ypixels; ++ix){
-			if(ix == (ypixels/2)){
-				offset += initial_offset;//2
-				offset++;
-			}
-			for(iy=0; iy<xpixels; ++iy){
-				dMap[ix][iy] = offset;
-				offset++;
-			}
-		}
-
-		setDataMap(dMap);
-		setDataMask(dMask);
-
-	};
-
-
-	  /**
-
-	     Returns the frame number for the given dataset.
-	     \param buff pointer to the dataset
-	     \returns frame number
-
-	   */
-
-	int getFrameNumber(char *buff){
-		int np=(*(int*)buff);
-		//gotthards frame header must be incremented
-		++np;
-		//packet index should be 1 or 2
-		return ((np&FRAMEMASK)>>FRAMEOFFSET);
-	};
-
-
-
-	/**
-     gets the packets number (last packet is labelled with 0 and is replaced with 40)
-     \param buff pointer to the memory
-     \returns packet number
-
-	 */
-
-	int getPacketNumber(char *buff){
-		int np=(*(int*)buff);
-		//gotthards frame header must be incremented
-		++np;
-		//packet index should be 1 or 2
-		return ((np&PACKETMASK)+1);
-	};
-
-
-	/**
-    returns the pixel value as double correcting for the output buffer crosstalk
-     \param data pointer to the memory
-     \param ix coordinate in the x direction
-     \param iy coordinate in the y direction
-     \returns channel value as double
-
-	 */
-	double getValue(char *data, int ix, int iy=0) {
-		//check how it is for gotthard
-	    if (xtalk==0)
-	      return  slsDetectorData<uint16_t>::getValue(data, ix, iy);
-	    else
-	      return slsDetectorData<uint16_t>::getValue(data, ix, iy)-xtalk*slsDetectorData<uint16_t>::getValue(data, ix-1, iy);
-	};
-
-
-
-	/** sets the output buffer crosstalk correction parameter
-      \param c output buffer crosstalk correction parameter to be set
-      \returns current value for the output buffer crosstalk correction parameter
-
-	 */
-	double setXTalk(double c) {xtalk=c; return xtalk;}
-
-
-	/** gets the output buffer crosstalk parameter
-      \returns current value for the output buffer crosstalk correction parameter
-	 */
-	double getXTalk() {return xtalk;}
-
-
-
-
-
-
-
-private:
-
-	double xtalk; /**<output buffer crosstalk correction parameter */
-	const static int xpixels = 1280;
-	const static int ypixels = 1;
-	const static int npackets = 2;
-	const static int buffersize = 1286;
-};
-
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/gotthardModuleDataNew.h

@@ -1,170 +0,0 @@
-#ifndef GOTTHARDMODULEDATANEW_H
-#define  GOTTHARDMODULEDATANEW_H
-#include "slsDetectorData.h"
-
-
-
-
-
-    typedef struct {
-        uint64_t frameNumber;    /**< is the frame number */
-        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
-        uint32_t packetNumber;    /**< is the packet number */
-        uint64_t bunchId;        /**< is the bunch id from beamline */
-        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
-        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
-        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
-        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
-        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
-        uint32_t debug;            /**< is for debugging purposes */
-        uint16_t roundRNumber;    /**< is the round robin set number */
-        uint8_t detType;        /**< is the detector type see :: detectorType */
-        uint8_t version;        /**< is the version number of this structure format */
-    } sls_detector_header;
-
-
-
-
-
-
-
-
-class gotthardModuleDataNew : public slsDetectorData<uint16_t> {
-
- private:
-  
-  int iframe;
-  const int offset;
-
-
-public:
-
-
-
-	/**
-     Implements the slsReceiverData structure for the gotthard read out by a module i.e. using the slsReceiver
-     (1x1280 pixels, 2 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-	 */
-
-
-    gotthardModuleDataNew(int off=24*2, int nch=1280): slsDetectorData<uint16_t>(nch, 1, nch*2+off), offset(off) {
-
-		uint16_t **dMask;
-		int **dMap;
-		int ix, iy;
-		int ypixels=1;
-		int xpixels=nch;
-
-		dMask=new uint16_t*[1];
-		dMap=new int*[1];
-		dMap[0] = new int[nch];
-		dMask[0] = new uint16_t[nch];
-
-		for(int ix=0; ix<xpixels; ix++) {
-		  dMap[0][ix] = 2*ix+offset; 
-		  dMask[0][ix] = 0x0;
-		}
-
-		setDataMap(dMap);
-		setDataMask(dMask);
-
-	};
-
-
-	  /**
-
-	     Returns the frame number for the given dataset.
-	     \param buff pointer to the dataset
-	     \returns frame number
-
-	   */
-
-
-  int getFrameNumber(char *buff){if (offset>=sizeof(sls_detector_header)) return ((sls_detector_header*)buff)->frameNumber; return iframe;};//*((int*)(buff+5))&0xffffff;};   
-
-
-
-	/**
-     gets the packets number (last packet is labelled with 0 and is replaced with 40)
-     \param buff pointer to the memory
-     \returns packet number
-
-	 */
-
-  int getPacketNumber(char *buff){if (offset>=sizeof(sls_detector_header))return ((sls_detector_header*)buff)->packetNumber;};
-
-
-
-
-  /**
-
-     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
-     \param data pointer to the memory to be analyzed
-     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
-     \param dsize size of the memory slot to be analyzed
-     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
-     
-  */
-  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
-    if (dsize<dataSize) ndata=dsize;
-    else ndata=dataSize;
-    return data;
-
-  }
-
-  virtual char *readNextFrame(ifstream &filebin) {
-    int ff=-1, np=-1;
-    return readNextFrame(filebin, ff, np);
-  };
-
-  virtual char *readNextFrame(ifstream &filebin, int &ff) {
-    int np=-1;
-    return readNextFrame(filebin, ff, np);
-  };
-
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
-	  char *data=new char[dataSize];
-	  char *d=readNextFrame(filebin, ff, np, data);
-	  if (d==NULL) {delete [] data; data=NULL;}
-	  return data;
-  }
-
-
-
-
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-	  char *retval=0;
-	  int  nd;
-	  int fnum = -1;
-	  np=0;
-	  int  pn;
-	  
-	  //  cout << dataSize << endl;
-	  if (ff>=0)
-	    fnum=ff;
-
-	  if (filebin.is_open()) {
-	    if (filebin.read(data, dataSize) ){
-	      ff=getFrameNumber(data);
-	      np=getPacketNumber(data);
-	      return data;
-	    }
-	  }
-	    return NULL;
-	    
-	    
-	  
-  };
-
-  
-
-
-};
-
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/jungfrau02Data.h

@@ -1,156 +0,0 @@
-#ifndef JUNGFRAU02DATA_H
-#define JUNGFRAU02DATA_H
-
-#include "chiptestBoardData.h"
-
-
-
-class jungfrau02Data : public chiptestBoardData {
- public:
-
-/* test :) */
-
-
-  /**
-     Implements the chiptestBoardData structure for the jungfrau02 prototype 
-     (48x48 pixels, ADC2 for analog output, 2 more ADCs used for readout of digital bits, pixel offset configurable.)
-     \param c crosstalk parameter for the output buffer
-
-  */
-  
-
-  jungfrau02Data(int nadc, int offset, double c=0): chiptestBoardData(48, 48, nadc, offset), 
-    xtalk(c) {
-
-
-
-
-    uint16_t **dMask;
-    int **dMap;
-
-
-
-    dMask=new uint16_t*[48];
-    dMap=new int*[48];
-    for (int i = 0; i < 48; i++) {
-      dMap[i] = new int[48];
-      dMask[i] = new uint16_t[48];
-    }
-
-
-    for (int iy=0; iy<48; iy++) {
-      for (int ix=0; ix<48; ix++) {
-	
-	dMap[ix][iy]=offset+(iy*48+ix)*nAdc;//dMap[iy][ix]=offset+(iy*48+ix)*nAdc;
-	// cout << ix << " " << iy << " " << dMap[ix][iy] << endl;
-      }
-    }
-
-    cout << (0,0) << " " << dMap[0][0] << endl;
-    cout << (47,47) << " " << dMap[47][47] << endl;
-	
-
-    for (int ix=0; ix<48; ix++) {
-      for (int iy=0; iy<48; iy++)
-	dMask[iy][ix]=0x0; 
-
-    setDataMap(dMap);
-    setDataMask(dMask);
-    }
-
-
-
-  };
-    
-   /**
-
-     Returns the value of the selected channel for the given dataset. Since the ADC is only 14bit wide, only bit 0-13 are occupied. If the gain bits are read out, they are returned in bit 14-15.
-     \param data pointer to the dataset (including headers etc)
-     \param ix pixel number in the x direction
-     \param iy pixel number in the y direction
-     \returns data for the selected channel, with inversion if required
-
-  */
- 
- virtual uint16_t getChannel(char *data, int ix, int iy=0) { 
-    uint16_t m=0, d=0;
-    if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) { 
-          m=dataMask[iy][ix]; 
-          d=*(((uint16_t*)(data))+dataMap[iy][ix]); 
-      // cout << ix << " " << iy << " " << (uint16_t*)data << " " << ((uint16_t*)(data))+dataMap[iy][ix] << " " << d << endl;
-	if (nAdc==3) {
-	  //cout << "Gain bit!" << endl;
-	  if (*((uint16_t*)(data)+dataMap[iy][ix]+2)>8000) //exchange if gainBits==2 is returned!
-		d|=(1<<14); // gain bit 1
-	  if (*((uint16_t*)(data)+dataMap[iy][ix]+1)>8000) //exchange if gainBits==2 is returned!
-		d|=(1<<15); // gain bit 0
-	  
-        }
-
-    }  
-    return d^m;
-  };
-
-  /**
-    returns the pixel value as double correcting for the output buffer crosstalk
-     \param data pointer to the memory
-     \param ix coordinate in the x direction
-     \param iy coordinate in the y direction
-     \returns channel value as double
-
-  */
-  double getValue(char *data, int ix, int iy=0) { 
-    //  cout << "##" << (void*)data << " " << ix << " " <<iy << endl;
-    uint16_t d=getChannel(data, ix, iy);
-    // cout << d << " " << (d&0x3fff) << endl;
-    if (xtalk==0 || ix==0)
-      return  (double)(getChannel(data, ix, iy)&0x3fff);
-    else
-      return  (double)(getChannel(data, ix, iy)&0x3fff)-xtalk* (double)(getChannel(data, ix, iy)&0x3fff);
-  };
-  
-  /**
-    returns the gain bit value, i.e. returns 0 if(GB0==0 && GB1==0), returns 1 if(GB0==1 && GB1==0), returns 3 if(GB0==1 && GB1==1), if it returns 2 -> the gain bits are read out the wrong way around (i.e. GB0 and GB1 have to be reversed!)
-     \param data pointer to the memory
-     \param ix coordinate in the x direction
-     \param iy coordinate in the y direction
-     \returns gain bits as int
-  */
-  int getGainBits(char *data, int ix, int iy=0) { 
-  	uint16_t d=getChannel(data, ix, iy);
-  	return ((d&0xc000)>>14); 
-  };
-  //*/
- 
-
-  
-
-  /** sets the output buffer crosstalk correction parameter
-      \param c output buffer crosstalk correction parameter to be set
-      \returns current value for the output buffer crosstalk correction parameter
-
-  */
-  double setXTalk(double c) {xtalk=c; return xtalk;}
-
-
-  /** gets the output buffer crosstalk parameter
-      \returns current value for the output buffer crosstalk correction parameter
-  */
-  double getXTalk() {return xtalk;}
-  
-
-
-
-
-  
-
- private:
-  
-  double xtalk; /**<output buffer crosstalk correction parameter */
-
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/jungfrau10ModuleData.h

@@ -1,217 +0,0 @@
-#ifndef JUNGFRAU10MODULEDATA_H
-#define  JUNGFRAU10MODULEBDATA_H
-#include "slsDetectorData.h"
-
-
-
-class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
-
- private:
-
-     typedef struct {
-        uint64_t frameNumber;    /**< is the frame number */
-        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
-        uint32_t packetNumber;    /**< is the packet number */
-        uint64_t bunchId;        /**< is the bunch id from beamline */
-        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
-        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
-        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
-        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
-        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
-        uint32_t debug;            /**< is for debugging purposes */
-        uint16_t roundRNumber;    /**< is the round robin set number */
-        uint8_t detType;        /**< is the detector type see :: detectorType */
-        uint8_t version;        /**< is the version number of this structure format */
-    } sls_detector_header;
-
-
-  int iframe;
-  int nadc;
-  int sc_width;
-  int sc_height;
- public:
-
-
-
-
-  /**
-     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
-     (160x160 pixels, 40 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-  */
-  
-
- jungfrau10ModuleData(int ns=16384): slsDetectorData<uint16_t>(256*4, 256*2, 256*256*8*2+48, NULL, NULL, NULL) , iframe(0) {
-
-    
-   
-    int row, col;
-
-    int isample;
-    int iadc;
-    int ix, iy;
-
-    int ichip;
-
-    // cout << sizeof(uint16_t) << endl;
-    int ip=0;
-    for (int iy=0; iy<256*2; iy++) {
-      for (int ix=0; ix<256*4; ix++){
-	dataMap[iy][ix]=ip*2+48;
-	ip++;
-      }
-    }
-      
-
-    /* for (iadc=0; iadc<nadc; iadc++) { */
-    /*   ichip=iadc/4; */
-
-    /*   for (int i=0; i<sc_width*sc_height; i++) { */
-
-/* 	if (ichip%2==0) { */
-/* 	  row=sc_height+i/sc_width; */
-/* 	  col=(ichip/2)*256+iadc%4*sc_width+(i%sc_width); */
-/* 	} else {  */
-/* 	  row=sc_height-1-i/sc_width;  */
-/* 	  col=((ichip/2)*256+iadc%4*sc_width)+sc_width-(i%sc_width)-1; */
-/* 	} */
-	  
-
-	
-/* /\* 	if (iadc<nadc/2) { *\/ */
-/* /\* 	  row=sc_height+i/sc_width; *\/ */
-/* /\* 	  col=iadc*sc_width+(i%sc_width); *\/ */
-/* /\* 	} else { *\/ */
-/* /\* 	  row=sc_height-1-i/sc_width; *\/ */
-/* /\* 	  col=(nx-1)-((iadc-16)*sc_width)-(i%sc_width); *\/ */
-/* /\* 	} *\/ */
-/* 	if (row<0 || row>=ny ||  col<0 || col>=nx) { */
-/* 	    cout << "Wrong row, column " << row << " " << col << " " << iadc << " " << i << endl; */
-/* 	} else */
-/* 	  dataMap[row][col]=(nadc*i+iadc)*2; */
-      /* 	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize) */
-      /* 	   cout << "Error: pointer " << dataMap[row][col] << " out of range " << row << " " << col  <<" " << iadc << " " << i << endl; */
-      /* 	else { */
-      /* 	  xmap[nadc*i+iadc]=col; */
-      /* 	  ymap[nadc*i+iadc]=row; */
-
-      /* 	} */
-      /* } */
-
-    //  }
-
-    
-    
-  };
-  
-  
-
-     /**
-
-     Returns the frame number for the given dataset. Purely virtual func.
-     \param buff pointer to the dataset
-     \returns frame number
-
-  */
-
-
-  int getFrameNumber(return (sls_detector_header*)buff)->frameNumber;};   
-
-  /**
-
-     Returns the packet number for the given dataset. purely virtual func
-     \param buff pointer to the dataset
-     \returns packet number number
-
-
-  virtual int getPacketNumber(char *buff)=0;
-
-  */
-
-   /**
-
-     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
-     \param data pointer to the memory to be analyzed
-     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
-     \param dsize size of the memory slot to be analyzed
-     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
-
-  */
-   char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;};
-
-
-   /**
-
-     Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors! 
-     \param filebin input file stream (binary)
-     \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete
-
-  */
-  virtual char *readNextFrame(ifstream &filebin) {
-    int ff=-1, np=-1;
-    return readNextFrame(filebin, ff, np);
-  };
-
-  virtual char *readNextFrame(ifstream &filebin, int &ff) {
-    int np=-1;
-    return readNextFrame(filebin, ff, np);
-  };
-
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
-	  char *data=new char[dataSize];
-	  char *d=readNextFrame(filebin, ff, np, data);
-	  if (d==NULL) {delete [] data; data=NULL;}
-	  return data;
-  }
-
-
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-    // char *readNextFrame(ifstream &filebin){
-      //	int afifo_length=0;  
-    /*   uint16_t *afifo_cont;  */
-    /*   int ib=0; */
-    /*   if (filebin.is_open()) { */
-    /* 	afifo_cont=new uint16_t[dataSize/2]; */
-    /* 	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
-    /* 	  ib+=2; */
-    /* 	  if (ib==dataSize) break; */
-    /* 	} */
-    /* 	if (ib>0) { */
-    /* 	  iframe++; */
-    /* 	  // cout << ib << "-" << endl; */
-    /* 	  return (char*)afifo_cont; */
-    /* 	} else { */
-    /* 	  delete [] afifo_cont; */
-    /* 	  return NULL; */
-    /* 	} */
-    /*   }      */
-    /*   return NULL; */
-    /* }; */
-
- char *retval=0;
-	  int  nd;
-	  int fnum = -1;
-	  np=0;
-	  int  pn;
-	  
-	  //  cout << dataSize << endl;
-	  if (ff>=0)
-	    fnum=ff;
-
-	  if (filebin.is_open()) {
-	    if (filebin.read(data, dataSize) ){
-	      ff=getFrameNumber(data);
-	      np=getPacketNumber(data);
-	      return data;
-	    }
-	  }
-	    return NULL;
-	    
-  
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench02Ctb10GbData.h

@@ -1,246 +0,0 @@
-#ifndef MOENCH02CTB10GBDATA_H
-#define  MOENCH02CTB10GBDATA_H
-#include <stdio.h>
-#include "slsDetectorData.h"
-#include "slsReceiverData.h"
-
-
-class moench02Ctb10GbData : public slsReceiverData<uint16_t> {
-
- private:
-  
-  int iframe;
-  // int *xmap, *ymap;
-  int nadc;
-  int sc_width;
-  int sc_height;
-
-  int maplength;
-
-
-
- public:
-
-
-
-
-  /**
-     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
-     (160x160 pixels, 40 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-  */
-  
-
- moench02Ctb10GbData(int ns=6400): slsReceiverData<uint16_t>(160, 160, 50, 8208) , nadc(4), sc_width(40), sc_height(160) {
-
-    
-    int adc_nr[4]={120,0,80,40};
-    int row, col;
-
-    int isample;
-    int iadc;
-    int ix, iy;
-    int i;
-    int npackets=50;
-    maplength = 8208*npackets;
-    //this->setDataSize(maplength);
-    /* maplength=this->getDataSize()/2; */
-    
-    for (int ip=0; ip<npackets; ip++) {
-      for (int is=0; is<128; is++) {
-
-	for (iadc=0; iadc<nadc; iadc++) {
-	  i=128*ip+is;
-	  if (i<sc_width*sc_height) {
-	    col=adc_nr[iadc]+(i%sc_width);
-	    row=i/sc_width;
-	    dataMap[row][col]=(32*i+iadc+2)*2+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8208*npackets) {
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;	  
-	    }
-	  
-	  }
-	}
-      }
-    }
-    int ibyte;
-    int ii=0;
-
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8208/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	if(ibyte<8){
-	  xmap[i]=-1;
-	  ymap[i]=-1;
-	}else{
-	  isample=ii/32;
-	  iadc=ii%32;
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if(iadc>=2 && iadc<=5){
-	    xmap[i]=adc_nr[iadc-2]+ix;
-	    ymap[i]=iy;
-	  }else{
-	    xmap[i]=-1;
-	    ymap[i]=-1;
-	  }
-	  ii++;
-	}
-      }//end loop on bytes
-    }//end loop on packets
-
-    iframe=0;
-    cout << "data struct created" << endl;
-  };
-    
-  void getPixel(int ip, int &x, int &y) {
-    if(ip>=0 && ip<maplength){
-      x=xmap[ip]; 
-      y=ymap[ip];
-    }else{
-      cerr<<"WRONG ARRAY LENGTH"<<endl;
-      cerr<<"Trying to access the "<<ip<<"-th element"<<endl;
-    }
-
-  };
-  
-
-  /**
-
-     Returns the frame number for the given dataset. Purely virtual func.
-     \param buff pointer to the dataset
-     \returns frame number
-
-  */
-
-  int getFrameNumber(char *buff){return *((int*)buff)&0xffffffff;};  
-  /* virtual  int getFrameNumber(char *buff){(void)buff; return iframe;};    */
-
-  /**
-
-     Returns the packet number for the given dataset. purely virtual func
-     \param buff pointer to the dataset
-     \returns packet number number
-
- 
-     virtual int getPacketNumber(char *buff)=0;
-
-  */
-  int getPacketNumber(char *buff){return ((*(((int*)(buff+4))))&0xff)+1;};  
-  /**
-
-     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
-     \param data pointer to the memory to be analyzed
-     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
-     \param dsize size of the memory slot to be analyzed
-     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
-
-  */
-  //virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;};
-
-
-  /**
-
-     Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors! 
-     \param filebin input file stream (binary)
-     \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete
-
-  */
-  /* virtual char *readNextFrame(ifstream &filebin){ */
-  /*   //	int afifo_length=0;   */
-  /*   uint16_t *afifo_cont;  */
-  /*   int ib=0; */
-  /*   if (filebin.is_open()) { */
-  /* 	afifo_cont=new uint16_t[dataSize/2]; */
-  /* 	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
-  /* 	  ib+=2; */
-  /* 	  if (ib==dataSize) break; */
-  /* 	} */
-  /* 	if (ib>0) { */
-  /* 	  iframe++; */
-  /* 	  //cout << ib << "-" << endl; */
-  /* 	  return (char*)afifo_cont; */
-  /* 	} else { */
-  /* 	  delete [] afifo_cont; */
-  /* 	  return NULL; */
-  /* 	} */
-  /*   }      */
-  /*   return NULL; */
-  /* }; */
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
-    char *data=new char[packetSize*nPackets];
-    char *retval=0;
-    int nd;
-    np=0;
-    int  pn;
-    char aa[8224]={0};
-    char *packet=(char *)aa;
-    int  fnum = -1;
-    if (ff>=0)
-      fnum=ff;
-
-    if (filebin.is_open()) {
-
-
-      cout << "+";
-
-      while(filebin.read((char*)packet, 8208)){
-	      
-	pn=getPacketNumber(packet);
-	if (fnum<0)
-	  fnum= getFrameNumber(packet);
-	
-
-	if (fnum>=0) {
-	  if (getFrameNumber(packet) !=fnum) { 
-	    
-	    if (np==0){
-	      cout << "-";
-	      delete [] data;
-	      return NULL;
-	    } else
-	      filebin.seekg(-8208,ios_base::cur);
-	    return data;
-	  }
-	
-	  memcpy(data+(pn-1)*packetSize, packet, packetSize);
-
-	  np++;
-	  if (np==nPackets)
-	    break;
-	  if (pn==nPackets)
-	    break;
-	}
-      }	    
-    }else{
-      cerr<<filebin<<" not open!!!"<<endl;
-      return NULL;
-    }
-	  
-    if (np==0){
-      cout << "?";
-      delete [] data;
-      return NULL;
-    }// else if (np<nPackets)
-    //  cout << "Frame " << fnum << " lost "  << nPackets-np << " packets " << endl;
-
-    
-    return data;
-	  
-  };
-
-
-
-  virtual char *readNextFrame(ifstream &filebin) {
-    int fnum=-1, np;
-    return readNextFrame(filebin, fnum, np);
-  };
-
-  
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench02CtbData.h

@@ -35,7 +35,7 @@ class moench02CtbData : public slsDetectorData<uint16_t> {
 
     
     int adc_off[4]={40,0,120,80};
-    int adc_nr[4]={8,10,20,23};
+    int adc_nr[4]={8,10,20,22};
     int row, col;
 
     int isample;

slsDetectorCalibration/dataStructures/moench02CtbDataDGS.h

@@ -1,187 +0,0 @@
-#ifndef MOENCH02CTBDATADGS_H
-#define  MOENCH02CTBDATADGS_H
-#include "slsDetectorData.h"
-
-
-
-class moench02CtbData : public slsDetectorData<uint16_t> {
-
- private:
-  
-  int iframe;
-  // int *xmap, *ymap;
-  //int nadc;
-  int sc_width;
-  int sc_height;
-
-  int maplength;
-
-
-
- public:
-
-
-
-
-  /**
-     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
-     (160x160 pixels, 40 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-  */
-  
-
- moench02CtbDataDGS(int ns=6400): slsDetectorData<uint16_t>(160, 160, ns*(2*32+8), NULL, NULL) ,  sc_width(40), sc_height(160) {
-
-    
-    int adc_off[4]={40,0,120,80};
-    int adc_nr[4]={8,10,20,23};
-    int row, col;
-
-    int isample;
-    int iadc, iiadc;
-    int ix, iy;
-    maplength=this->getDataSize()/2;
-    //cout << maplength << endl;
-
-    for (iiadc=0; iiadc<4; iiadc++) {
-      
-      iadc=adc_nr[iiadc];
-      //cout << iiadc << endl;
-      for (int i=0; i<sc_width*sc_height; i++) {
-	col=adc_off[iiadc]+(i%sc_width);
-	row=i/sc_width;
-	dataMap[row][col]=(32*i+iadc)*2;
-	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize) {
-	  cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;	  
-	}
-	  
-      }
-    }
-    
-    for (int i=0; i<maplength; i++) {
-      //cout << i << endl;
-      isample=i/32;
-      iiadc=i%32;
-      iadc=-1;
-      for (int iii=0; iii<4; iii++) {
-	if (iiadc==adc_nr[iii]) iadc=iii;
-      }
-      ix=isample%sc_width;
-      iy=isample/sc_width;
-      if(iadc>=0){
-	xmap[i]=adc_off[iadc]+ix;
-	ymap[i]=iy;
-      }else{
-	xmap[i]=-1;
-	ymap[i]=-1;
-      }
-    }
-    iframe=0;
-    cout << "data struct created" << endl;
-  };
-  
-  void getPixel(int ip, int &x, int &y) {
-    if(ip>=0 && ip<maplength){
-      x=xmap[ip]; 
-      y=ymap[ip];
-    }/*else{
-      cerr<<"WRONG ARRAY LENGTH"<<endl;
-      cerr<<"Trying to access the "<<ip<<"-th element"<<endl;
-      }*/
-
-  };
-  
-  /**
-     Returns the gain for the selected pixel (at the moemnt only 3rd supercolumn)
-     \param buff pointer to the dataset
-     \param ix x coordinate 
-     \param iy y coordinate
-     \returns gain value
-   */
-
-  int getGain(char *buff, int ix, int iy) {
-    int isample=iy*sc_width+iy;
-    if (ix<sc_width) return 0; //first supercolumn no gain switching - could return the static gain if wished
-    if (ix<2*sc_width) return 0; //second supercolumn no gain switching  - could return the static gain if wished
-    if (ix<3*sc_width){ 
-      if(*((long*)(buff+(32*2*isample+8*(isample-1)))&(1>>31)) return 1;
-      return 0;
-    }
-    return 0; //not yet implemented for 4th supercolumn
-  }
-
-
-     /**
-
-     Returns the frame number for the given dataset. Purely virtual func.
-     \param buff pointer to the dataset
-     \returns frame number
-
-  */
-
-
-    virtual  int getFrameNumber(char *buff){(void)buff; return iframe;};   
-
-  /**
-
-     Returns the packet number for the given dataset. purely virtual func
-     \param buff pointer to the dataset
-     \returns packet number number
-
-
-  virtual int getPacketNumber(char *buff)=0;
-
-  */
-
-   /**
-
-     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
-     \param data pointer to the memory to be analyzed
-     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
-     \param dsize size of the memory slot to be analyzed
-     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
-
-  */
-    virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;};
-
-
-   /**
-
-     Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors! 
-     \param filebin input file stream (binary)
-     \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete
-
-  */
-    virtual char *readNextFrame(ifstream &filebin){
-      //	int afifo_length=0;  
-      uint16_t *afifo_cont; 
-      int ib=0;
-      if (filebin.is_open()) {
-	afifo_cont=new uint16_t[dataSize/2];
- 	while (filebin.read(((char*)afifo_cont)+ib,2)) {
-	  ib+=2;
-	  if (ib==dataSize) break;
-	}
-	if (ib>0) {
-	  iframe++;
-	  //cout << ib/2 << "-" << endl;
-	  //for (int i=0; i<ib/2; i++)
-	  //cout << i << " " << afifo_cont[i] << endl;
-	  return (char*)afifo_cont;
-	} else {
-	  delete [] afifo_cont;
-	  return NULL;
-	}
-      }     
-      return NULL;
-    };
-
-
-  
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench02ModuleData.h

@@ -1,137 +0,0 @@
-#ifndef MOENCH02MODULEDATA_H
-#define  MOENCH02MODULEDATA_H
-#include "slsReceiverData.h"
-
-
-
-class moench02ModuleData : public slsReceiverData<uint16_t> {
- public:
-
-
-
-
-  /**
-     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
-     (160x160 pixels, 40 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-  */
-  
-
-  moench02ModuleData(double c=0): slsReceiverData<uint16_t>(160, 160, 40, 1286), 
-    xtalk(c) {
-
-
-
-
-    uint16_t **dMask;
-    int **dMap;
-    int ix, iy;
-
-
-
-    dMask=new uint16_t*[160];
-    dMap=new int*[160];
-    for (int i = 0; i < 160; i++) {
-      dMap[i] = new int[160];
-      dMask[i] = new uint16_t[160];
-    }
-
-    for (int isc=0; isc<4; isc++) {
-      for (int ip=0; ip<10; ip++) {
-
-	for (int ir=0; ir<16; ir++) {
-	  for (int ic=0; ic<40; ic++) {
-
-	    ix=isc*40+ic;
-	    iy=ip*16+ir;
-
-	    dMap[iy][ix]=1286*(isc*10+ip)+2*ir*40+2*ic+4; 
-	    // cout << ix << " " << iy << " " << dMap[ix][iy] << endl;
-	  }
-	}
-      }
-    }
-
-    for (ix=0; ix<120; ix++) {
-      for (iy=0; iy<160; iy++)
-	dMask[iy][ix]=0x3fff;
-    }
-    for (ix=120; ix<160; ix++) {
-      for (iy=0; iy<160; iy++)
-	dMask[iy][ix]=0x0;
-    }
-
-
-    setDataMap(dMap);
-    setDataMask(dMask);
-
-
-    
-
-  };
-    
-  
-  
-  /**
-     gets the packets number (last packet is labelled with 0 and is replaced with 40)
-     \param buff pointer to the memory
-     \returns packet number
-
-  */
-  
-  int getPacketNumber(char *buff){
-    int np=(*(int*)buff)&0xff;
-    if (np==0)
-      np=40;
-    return np;
-  };
-
-
-  /**
-    returns the pixel value as double correcting for the output buffer crosstalk
-     \param data pointer to the memory
-     \param ix coordinate in the x direction
-     \param iy coordinate in the y direction
-     \returns channel value as double
-
-  */
-  double getValue(char *data, int ix, int iy=0) {
-    //  cout << "##" << (void*)data << " " << ix << " " <<iy << endl;
-    if (xtalk==0 || ix%40==0)
-      return  slsDetectorData<uint16_t>::getValue(data, ix, iy);
-    else
-      return slsDetectorData<uint16_t>::getValue(data, ix, iy)-xtalk*slsDetectorData<uint16_t>::getValue(data, ix-1, iy);
-  };
-  
-  
-
-  /** sets the output buffer crosstalk correction parameter
-      \param c output buffer crosstalk correction parameter to be set
-      \returns current value for the output buffer crosstalk correction parameter
-
-  */
-  double setXTalk(double c) {xtalk=c; return xtalk;}
-
-
-  /** gets the output buffer crosstalk parameter
-      \returns current value for the output buffer crosstalk correction parameter
-  */
-  double getXTalk() {return xtalk;}
-  
-
-
-
-
-  
-
- private:
-  
-  double xtalk; /**<output buffer crosstalk correction parameter */
-
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench03Ctb10GbData.h

@@ -1,285 +0,0 @@
-#ifndef MOENCH03CTB10GBDATA_H
-#define  MOENCH03CTB10GBDATA_H
-#include "slsReceiverData.h"
-
-
-
-class moench03Ctb10GbData : public slsReceiverData<uint16_t> {
- 
- protected:
-  
-  int iframe;
-  int nadc;
-  int sc_width;
-  int sc_height;
-
- public:
-
-
-
-
-  /**
-     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
-     (160x160 pixels, 40 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-  */
-  
-
-  //  moench03Ctb10GbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, 8208*40, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
- moench03Ctb10GbData(int ns=5000): slsReceiverData<uint16_t>(400, 400, 40, 8208), nadc(32), sc_width(25), sc_height(200) {
-
-    int adc_nr[32]={200,225,250,275,300,325,350,375,\
-		    0,25,50,75,100,125,150,175,\
-		    175,150,125,100,75,50,25,0,\
-		    375,350,325,300,275,250,225,200};
-    int row, col;
-
-    int isample;
-    int iadc;
-    int ix, iy;
-    
-    int npackets=40;
-    int i;
-
-
-    for (int ip=0; ip<npackets; ip++) {
-      for (int is=0; is<128; is++) {
-
-	for (iadc=0; iadc<nadc; iadc++) {
-	  i=128*ip+is;
-	  if (i<sc_width*sc_height) {
-	    //  for (int i=0; i<sc_width*sc_height; i++) {
-	    col=adc_nr[iadc]+(i%sc_width);
-	    if (iadc<16) {
-	      row=199-i/sc_width;
-	    } else {
-	      row=200+i/sc_width;
-	    }
-	    dataMap[row][col]=(nadc*i+iadc)*2+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8208*40)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
-	  }
-	}
-      }
-    }
-
-    int ipacket;
-    int ibyte;
-    int ii=0;
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8208/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	if (ibyte<8) {
-	//header!
-	  xmap[i]=-1;
-	  ymap[i]=-1;
-	} else {
-	  // ii=ibyte+128*32*ipacket;
-	  isample=ii/nadc;
-	  iadc=ii%nadc;
-	
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if (iadc<(nadc/2)) {
-	    xmap[i]=adc_nr[iadc]+ix;
-	    ymap[i]=ny/2-1-iy;
-	  } else {
-	    xmap[i]=adc_nr[iadc]+ix;
-	    ymap[i]=ny/2+iy;
-	  }
-	  
-	ii++;
-	}
-      }
-    }
-    
-
-    
-    
-    iframe=0;
-    //  cout << "data struct created" << endl;
-  };
-    
-
-     /**
-
-     Returns the frame number for the given dataset. Purely virtual func.
-     \param buff pointer to the dataset
-     \returns frame number
-
-  */
-
-
-  int getFrameNumber(char *buff){return *((int*)buff)&0xffffffff;};   
-
-  /**
-
-     Returns the packet number for the given dataset. purely virtual func
-     \param buff pointer to the dataset
-     \returns packet number number
-
-
-
-  */
-  int getPacketNumber(char *buff){return ((*(((int*)(buff+4))))&0xff)+1;};   
-
-/*    /\** */
-
-/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
-/*      \param data pointer to the memory to be analyzed */
-/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
-/*      \param dsize size of the memory slot to be analyzed */
-/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
-
-/*   *\/ */
-/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
-
-
-/*    /\** */
-
-/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
-/*      \param filebin input file stream (binary) */
-/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
-
-/*   *\/ */
-/*     virtual char *readNextFrame(ifstream &filebin){ */
-/*       //	int afifo_length=0;   */
-/*       uint16_t *afifo_cont;  */
-/*       int ib=0; */
-/*       if (filebin.is_open()) { */
-/* 	afifo_cont=new uint16_t[dataSize/2]; */
-/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
-/* 	  ib+=2; */
-/* 	  if (ib==dataSize) break; */
-/* 	} */
-/* 	if (ib>0) { */
-/* 	  iframe++; */
-/* 	  // cout << ib << "-" << endl; */
-/* 	  return (char*)afifo_cont; */
-/* 	} else { */
-/* 	  delete [] afifo_cont; */
-/* 	  return NULL; */
-/* 	} */
-/*       }      */
-/*       return NULL; */
-/*     }; */
-
-
-  virtual char *readNextFrame(ifstream &filebin, int& fnum, char *data=NULL) {
-    int dd=0;
-    if (data==NULL) {
-      data=new char[packetSize*nPackets];
-      dd=1;
-    }
-      char *retval=0;
-      int np=0, nd;
-      fnum = -1;
-      int  pn;
-      char aa[8224];
-      char *packet=(char *)aa;
-      int place;
-      
-      if (filebin.is_open()) {
-
-
-
-        place=filebin.tellg();
-        while(filebin.read((char*)packet, 8208) && np<nPackets){
-          pn=getPacketNumber(packet);
-          if (pn==1 && fnum<0)
-	    fnum= getFrameNumber(packet);
-          
-	  //	  cout <<getFrameNumber(packet)<< " fn: " << fnum << "\t pn: " << pn << " np " << np << endl;
-          if (fnum>=0) {
-	    if (getFrameNumber(packet) !=fnum) {
-	      cout << "-"<<endl;
-	      filebin.seekg(place);
-	      if (np==0){
-		if (dd)
-		  delete [] data;
-		return NULL;
-	      } else {
-		return data;
-	      }
-	    }
-        
-	    memcpy(data+(pn-1)*packetSize, packet, packetSize);
-	    np++;
-	    if (np==nPackets)
-	      return data;
-        
-          }
-          place=filebin.tellg();
-        }
-        
-      }
-
-	      
-      if (np==0){
-	cout << "-"<<endl;
-        filebin.seekg(place);
-	if (dd)
-	  delete [] data;
-        return NULL;
-      }
-
-      //filebin.seekg(place);
-      return data;
-    };
-
-/*   	virtual char *readNextFrame(ifstream &filebin, int& fnum) { */
-/* 	  char *data=new char[packetSize*nPackets]; */
-/* 	  char *retval=0; */
-/* 	  int np=0, nd; */
-/* 	  fnum = -1; */
-/* 	  int  pn; */
-/* 	  char aa[8224]; */
-/* 	  char *packet=(char *)aa; */
-
-/* 	  if (filebin.is_open()) { */
-
-
-
-
-/* 	    while(filebin.read((char*)packet, 8208) && np<nPackets){ */
-/* 	      pn=getPacketNumber(packet); */
-	      
-/* 	      if (pn==1 && fnum<0) */
-/* 		fnum= getFrameNumber(packet); */
-	      
-/* 	      // cout << "fn: " << fnum << "\t pn: " << pn << endl; */
-/* 	      if (fnum>=0) { */
-/* 		if (getFrameNumber(packet) !=fnum) {  */
-		  
-/* 		  if (np==0){ */
-/* 		    delete [] data; */
-/* 		    return NULL; */
-/* 		  } else */
-/* 		    return data; */
-/* 		} */
-		
-/* 		memcpy(data+(pn-1)*packetSize, packet, packetSize); */
-/* 		np++; */
-		
-/* 	      } */
-/* 	    } */
-	    
-/* 	  } */
-
-/* 	  if (np==0){ */
-/* 	    delete [] data; */
-/* 	    return NULL; */
-/* 	  } */
-
-/* 	}; */
-
-int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;};
-
-
-};
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h

@@ -2,6 +2,7 @@
 #define  MOENCH03T1RECDATANEW_H
 #include "slsDetectorData.h"
 
+//#define VERSION_V2
     /**
         @short  structure for a Detector Packet or Image Header
         @li frameNumber is the frame number
@@ -32,6 +33,10 @@
         uint16_t roundRNumber;    /**< is the round robin set number */
         uint8_t detType;        /**< is the detector type see :: detectorType */
         uint8_t version;        /**< is the version number of this structure format */
+#ifndef VERSION_V1
+      uint64_t packetCaught[8];        /**< is the version number of this structure format */
+#endif
+
     } sls_detector_header;
 
 
@@ -95,6 +100,9 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
 	      row=200+i/sc_width;
 	    }
 	    dataMap[row][col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
+#ifdef HIGHZ
+	    dataMask[row][col]=0x3fff;
+#endif
 	    if (dataMap[row][col]<0 || dataMap[row][col]>=nSamples*2*32)
 	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
 	  }

slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNewRect.h

@@ -34,6 +34,9 @@
         uint16_t roundRNumber;    /**< is the round robin set number */
         uint8_t detType;        /**< is the detector type see :: detectorType */
         uint8_t version;        /**< is the version number of this structure format */
+#ifndef VERSION_V1
+      uint64_t packetCaught[8];        /**< is the version number of this structure format */
+#endif
     } sls_detector_header;
 
 

slsDetectorCalibration/dataStructures/moench03T1ReorderedData.h

@@ -0,0 +1,176 @@
+#ifndef MOENCH03T1REORDERED_H
+#define  MOENCH03T1REORDERED_H
+#include "slsDetectorData.h"
+
+
+class moench03T1ReorderedData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+	fwrite(&ff, 8, 1,of);//write detector frame number
+	fwrite(&ifr, 8, 1,of);//write datset frame number
+	fwrite(data,2,NX*NY,of);//write reordered data
+  */
+ moench03T1ReorderedData(): slsDetectorData<uint16_t>(400, 400, 2*400*400+2*8) {
+    for (int iy=0; iy<400; iy++)
+      for (int ix=0; ix<400; ix++)
+	dataMap[iy][ix]=2*8+2*(iy*400+ix);
+    
+    int ibyte;
+    for (ibyte=0; ibyte<8; ibyte++){
+      xmap[ibyte]=-1;
+      ymap[ibyte]=-1;
+    }
+    for (ibyte=0; ibyte<400*400; ibyte++){
+      xmap[ibyte+8]=ibyte%400;
+      ymap[ibyte+8]=ibyte/400;
+    }
+    
+    //  cout << "data struct created" << endl;
+  };
+  
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return *((int*)buff);};
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=40;
+	      return data;
+	    }
+	  }
+	  return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h

@@ -3,16 +3,16 @@
 #include "slsDetectorData.h"
 
 
-
 class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
  
  private:
   
-  int iframe;
+  // int iframe;
   int nadc;
   int sc_width;
   int sc_height;
   const int nSamples;
+  const int offset;
 
  public:
 
@@ -25,7 +25,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
      \param c crosstalk parameter for the output buffer
 
   */
- moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*32*2), nSamples(ns) {
+ moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*32*2+sizeof(int)), nSamples(ns), offset(sizeof(int)) {
 
     int nadc=32;
     int sc_width=25;
@@ -37,7 +37,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
     		    0,25,50,75,0,25,50,75};
 
     int row, col;
-
+    
     int isample;
     int iadc;
     int ix, iy;
@@ -60,50 +60,51 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 	    } else {
 	      row=200+i/sc_width;
 	    }
-	    dataMap[row][col]=(nadc*i+iadc)*2;//+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=nSamples*2*32)
+	    dataMap[row][col]=(nadc*i+iadc)*2+offset;//+16*(ip+1);
+#ifdef HIGHZ
+	    dataMask[row][col]=0x3fff;
+#endif
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize)
 	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
 	  }
 	}
       }
     }
 
-    int ipacket;
-    int ibyte;
+    
     int ii=0;
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8192/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	/* if (ibyte<8) { */
-	/* //header! */
-	/*   xmap[i]=-1; */
-	/*   ymap[i]=-1; */
-	/* } else { */
-	  // ii=ibyte+128*32*ipacket;
-	  isample=ii/nadc;
-	  if (isample<nSamples) {
-	  iadc=ii%nadc;
-	  adc4 = (int)iadc/4;
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if (adc4%2==0) {
-	    xmap[i]=adc_nr[iadc]+ix;
-	    ymap[i]=ny/2-1-iy;
-	  } else {
-	    xmap[i]=adc_nr[iadc]+ix;
-	    ymap[i]=ny/2+iy;
-	  }
-	  }
+    
+    for (i=0; i<  dataSize; i++) {
+      if (i<offset) {
+    	//header! */
+    	xmap[i]=-1;
+    	ymap[i]=-1;
+      } else {
+    	  // ii=ibyte+128*32*ipacket;
+    	isample=ii/nadc;
+    	if (isample<nSamples) {
+    	  iadc=ii%nadc;
+    	  adc4 = (int)iadc/4;
+    	  ix=isample%sc_width;
+    	  iy=isample/sc_width;
+    	  if (adc4%2==0) {
+    	    xmap[i]=adc_nr[iadc]+ix;
+    	    ymap[i]=ny/2-1-iy;
+    	  } else {
+    	    xmap[i]=adc_nr[iadc]+ix;
+    	    ymap[i]=ny/2+iy;
+    	  }
+    	}
 	  
-	ii++;
-	//	}
+    	ii++;
       }
+  
     }
     
 
     
     
-    iframe=0;
+    // iframe=0;
     //  cout << "data struct created" << endl;
   };
     
@@ -127,7 +128,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 
 
 
-  int getFrameNumber(char *buff){return iframe;};//*((int*)(buff+5))&0xffffff;};   
+  int getFrameNumber(char *buff){return *((int*)buff);};//*((int*)(buff+5))&0xffffff;};   
 
   /**
 
@@ -203,24 +204,24 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 
 
   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-	  char *retval=0;
-	  int  nd;
-	  int fnum = -1;
+	  /* char *retval=0; */
+	  /* int  nd; */
+	  /* int fnum = -1; */
 	  np=0;
-	  int  pn;
+	  /* int  pn; */
 	  
 
-	  if (ff>=0)
-	    fnum=ff;
+	  /* if (ff>=0) */
+	  /*   fnum=ff; */
 
 	  if (filebin.is_open()) {
 	    if (filebin.read(data, 32*2*nSamples) ){
-	      iframe++;
-	      ff=iframe;
+	      // iframe++;
+	      //ff=iframe;
 	      return data;
 	    }
 	  }
-	    return NULL;
+	  return NULL;
 	    
 	    
 	  
@@ -249,6 +250,8 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 
 
 
+  // virtual int setFrameNumber(int ff){iframe=ff};
+
 
 
 

slsDetectorCalibration/dataStructures/moench03T1ZmqDataNewRect.h

@@ -1,10 +1,12 @@
-#ifndef MOENCH03CTB10GBT1DATA_H
-#define  MOENCH03CTB10GBT1DATA_H
-#include "slsReceiverData.h"
+#ifndef MOENCH03T1ZMQNEWRECT_H
+#define  MOENCH03T1ZMQNEWRECT_H
+#include "slsDetectorData.h"
+
+#define VERT 1
 
 
 
-class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
+class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
  
  private:
   
@@ -12,9 +14,12 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
   int nadc;
   int sc_width;
   int sc_height;
- public:
+  const int nSamples;
+  const int offset;
 
 
+ public:
+
 
 
   /**
@@ -23,9 +28,16 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
      \param c crosstalk parameter for the output buffer
 
   */
-   moench03Ctb10GbT1Data(int ns=5000): slsReceiverData<uint16_t>(400, 400, 40, 8208), nadc(32), sc_width(25), sc_height(200) {
-
+#ifdef HOR
+ moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(800, 200, ns*2*32), nSamples(ns), offset(sizeof(int)) {
+#endif
+#ifdef VERT
+   moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(200, 800, ns*2*32), nSamples(ns), offset(sizeof(int)) {
+#endif
 
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
 
     int adc_nr[32]={300,325,350,375,300,325,350,375,		\
     		    200,225,250,275,200,225,250,275,\
@@ -38,9 +50,17 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
     int iadc;
     int ix, iy;
     
-    int npackets=40;
+     int npackets=40;
     int i;
     int adc4(0);
+    int pix;
+
+
+    int off=0;
+#ifdef OFF_1
+    off=1;
+#endif
+    cout << "This is a MOENCH with rectangular pixels!" << endl;
 
     for (int ip=0; ip<npackets; ip++) {
       for (int is=0; is<128; is++) {
@@ -56,46 +76,67 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 	    } else {
 	      row=200+i/sc_width;
 	    }
-	    dataMap[row][col]=(nadc*i+iadc)*2+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8208*40)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	    pix=(nadc*i+iadc)*2+offset;//+16*(ip+1);
+	    if (pix<0 || pix>=nSamples*2*32)
+	      cout << "Error: pointer " << pix << " out of range "<< endl;
+	    ix=col;
+	    iy=row;
+	    //col and row have to do with data sequence
+	    //ix and iy have to do with implant position
+#ifdef HOR
+	    if (row%2==off) {
+	      ix=2*col;
+	      iy=row/2;
+	    } else {
+	      ix=2*col+1;
+	      iy=row/2;
+	    }
+#endif
+
+#ifdef VERT
+	    if (col%2==off) {
+	      ix=col/2;
+	      iy=row*2+1;
+	    } else {
+	      ix=col/2;
+	      iy=row*2;
+	    }
+#endif
+	    dataMap[iy][ix]=pix;
 	  }
 	}
       }
     }
 
-    int ipacket;
-    int ibyte;
-    int ii=0;
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8208/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	if (ibyte<8) {
-	//header!
-	  xmap[i]=-1;
-	  ymap[i]=-1;
-	} else {
-	  // ii=ibyte+128*32*ipacket;
-	  isample=ii/nadc;
-	  iadc=ii%nadc;
-	  adc4 = (int)iadc/4;
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if (adc4%2==0) {
-	    xmap[i]=adc_nr[iadc]+ix;
-	    ymap[i]=ny/2-1-iy;
-	  } else {
-	    xmap[i]=adc_nr[iadc]+ix;
-	    ymap[i]=ny/2+iy;
-	  }
-	  
-	ii++;
-	}
-      }
-    }
-    
-
-    
+    /* int ipacket; */
+    /* int ibyte; */
+    /* int ii=0; */
+    /* for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){ */
+    /*   xmap[ibyte]=-1; */
+    /*   ymap[ibyte]=-1; */
+    /* } */
+    /* int off=sizeof(sls_detector_header)/2; */
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
     
     iframe=0;
     //  cout << "data struct created" << endl;
@@ -121,8 +162,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
 
 
-  // int getFrameNumber(char *buff){return *((int*)buff)&0xffffffff;}; 
-   int getFrameNumber(char *buff){return *((int*)(buff+5))&0xffffff;};   
+  int getFrameNumber(char *buff){return *((int*)buff);};//*((int*)(buff+5))&0xffffff;};   
 
   /**
 
@@ -133,7 +173,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
 
   */
-  int getPacketNumber(char *buff){return ((*(((int*)(buff+4))))&0xff)+1;};   
+  int getPacketNumber(char *buff){return 0;}//((*(((int*)(buff+4))))&0xff)+1;};   
 
 /*    /\** */
 
@@ -188,79 +228,63 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
   };
 
   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
-	  char *data=new char[packetSize*nPackets];
+	  char *data=new char[32*2*nSamples];
 	  char *d=readNextFrame(filebin, ff, np, data);
 	  if (d==NULL) {delete [] data; data=NULL;}
 	  return data;
-
   }
 
+
+
+
   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-	  char *retval=0;
-	  int  nd;
-	  int fnum = -1;
+	  /* char *retval=0; */
+	  /* int  nd; */
+	  /* int fnum = -1; */
 	  np=0;
-	  int  pn, po=0;
-	  char aa[8224];
-	  char *packet=(char *)aa;
-	  //  cout << packetSize*nPackets << endl;
-	  if (ff>=0)
-	    fnum=ff;
+	  /* int  pn; */
+	  
+
+	  /* if (ff>=0) */
+	  /*   fnum=ff; */
 
 	  if (filebin.is_open()) {
-
-
-
-
-	    while(filebin.read((char*)packet, 8208) ){
-	      pn=getPacketNumber(packet);
-	      
-	      if (fnum<0)
-		fnum= getFrameNumber(packet);
-	      
-	      //   cout << "fn: " << fnum << "\t pn: " << pn << endl;
-	      if (fnum>=0) {
-		if (getFrameNumber(packet) !=fnum || pn<po) { 
-		  
-		  if (np==0){
-		    // delete [] data;
-		    return NULL;
-		  } else
-		    filebin.seekg(-8208,ios_base::cur);
-		  po =pn;
-		    return data;
-		}
-		if (pn>nPackets) {
-		  cout << "Bad packet number " << pn << endl;
-		}
-
-		memcpy(data+(pn-1)*packetSize, packet, packetSize);
-		np++;
-		po =pn;
-
-		if (np==nPackets)
-		  break;
-
-		if (pn==nPackets)
-		  break;
-		
-	      }
+	    if (filebin.read(data, 32*2*nSamples) ){
+	      // iframe++;
+	      //ff=iframe;
+	      return data;
 	    }
+	  }
+	  return NULL;
+	    
 	    
-	  }
-
-	  if (np==0){
-	    // delete [] data;
-	    return NULL;
-	  }
-
-	  ff=fnum;
-	  return data;
 	  
   };
 
 
 
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<32*2*nSamples) ndata=dsize;
+    else ndata=32*2*nSamples;
+    return data;
+
+  }
+  
+
+
+
+
+
+  // virtual int setFrameNumber(int ff){iframe=ff};
 
 
 
@@ -271,13 +295,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
 
 
-
-
-
-
-
-int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;};
-
+int getPacketNumber(int x, int y) {return 0;};
 
 };
 
@@ -285,3 +303,4 @@ int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;};
 
 
 #endif
+

slsDetectorCalibration/dataStructures/moench03TCtb10GbData.h

@@ -1,285 +0,0 @@
-#ifndef MOENCH03TCTB10GBDATA_H
-#define  MOENCH03TCTB10GBDATA_H
-#include "moench03Ctb10GbData.h"
-
-
-
-class moench03TCtb10GbData : public moench03Ctb10GbData { //slsReceiverData<uint16_t> {
- 
-
- public:
-
-
-
-
-  /**
-     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
-     (160x160 pixels, 40 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-  */
-  
-
-  //  moench03TCtb10GbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, 8208*40, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
- moench03TCtb10GbData(int ns=5000): moench03Ctb10GbData(ns) {//slsReceiverData<uint16_t>(400, 400, 40, 8208), nadc(32), sc_width(25), sc_height(200) {
-    // cout <<"constructor"<< endl;
-      // nadc=32;
-    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
-		    200,225,250,275,200,225,250,275,\
-		    100,125,150,175,100,125,150,175,\
-		    0,25,50,75,0,25,50,75};
-    int row, col;
-
-    int isample;
-    int iadc;
-    int ix, iy;
-    
-    int npackets=40;
-    int i;
-    int adc4(0);
-
-    for (int ip=0; ip<npackets; ip++) {
-      for (int is=0; is<128; is++) {
-
-	for (iadc=0; iadc<nadc; iadc++) {
-	  i=128*ip+is;
-	  //cout << i << endl;
-	   adc4=(int)iadc/4;
-	  if (i<sc_width*sc_height) {
-	    //  for (int i=0; i<sc_width*sc_height; i++) {
-	    col=adc_nr[iadc]+(i%sc_width);
-	    if (adc4%2==0) {
-	      // if (iadc<(nadc/2)) {
-	      row=199-i/sc_width; 	            
-	    } else {
-	      row=200+i/sc_width;
-	    }
-	    dataMap[row][col]=(nadc*i+iadc)*2+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8208*40)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
-	  }
-	}
-      }
-    }
-    //  cout <<"map"<< endl;
-    int ipacket;
-    int ibyte;
-    int ii=0;
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8208/2; ibyte++) {
-    	i=ipacket*8208/2+ibyte;
-    	//	cout << i << " ";
-    	if (ibyte<8) {
-    	//header!
-    	  xmap[i]=-1;
-    	  ymap[i]=-1;
-    	} else {
-    	  // ii=ibyte+128*32*ipacket;
-    	  // cout << nadc << endl;
-    	  isample=ii/nadc;
-    	  iadc=ii%nadc;
-	
-    	  adc4 = (int)iadc/4;
-
-    	  ix=isample%sc_width;
-    	  iy=isample/sc_width;
-    	  //  cout << isample << " " << iadc << " " << ix << " " << iy ;//<< endl;
-    	  if (adc4%2==0) {//iadc<(nadc/2)) {
-    	  //if (iadc<(nadc/2)) {
-    	    xmap[i]=adc_nr[iadc]+ix;
-    	    ymap[i]=ny/2-1-iy;
-    	  } else {
-    	    xmap[i]=adc_nr[iadc]+ix;
-    	    ymap[i]=ny/2+iy;
-    	  }
-	  
-    	ii++;
-    	}
-      }
-    }
-    
-
-    
-    /* int ipacket; */
-    /* int ibyte; */
-    /* int ii=0; */
-    
-    /* for (int ipacket=0; ipacket<npackets; ipacket++) { */
-    /*   for (int ibyte=0;  ibyte< 8208/2; ibyte++) { */
-    /* 	i=ipacket*8208/2+ibyte; */
-    /* 	cout << i << endl; */
-    /* 	if (ibyte<8) { */
-    /* 	//header! */
-    /* 	  xmap[i]=-1; */
-    /* 	  ymap[i]=-1; */
-    /* 	} else { */
-    /* 	  ii=ibyte+128*32*ipacket; */
-    /* 	  isample=ii/nadc; */
-    /* 	  iadc=ii%nadc; */
-    /* 	  adc4 = (int)iadc/4; */
-
-    /* 	  ix=isample%sc_width; */
-    /* 	  iy=isample/sc_width; */
-    /* 	  if (adc4%2==0) { */
-    /* 	    xmap[i]=adc_nr[iadc]+ix; */
-    /* 	    ymap[i]=ny/2-1-iy; */
-
-
-
-    /* 	  } else { */
-    /* 	    xmap[i]=adc_nr[iadc]+ix; */
-    /* 	    ymap[i]=ny/2+iy; */
-
-    /* 	  } */
-	  
-    /* 	ii++; */
-    /* 	} */
-    /*   } */
-    /* } */
-    
-
-    
-    //  cout <<"done"<< endl;
-    
-    iframe=0;
-    //  cout << "data struct created" << endl;
-  };
-    
-
-/*      /\** */
-
-/*      Returns the frame number for the given dataset. Purely virtual func. */
-/*      \param buff pointer to the dataset */
-/*      \returns frame number */
-
-/*   *\/ */
-
-
-/*   int getFrameNumber(char *buff){return *((int*)buff)&0xffffffff;};    */
-
-/*   /\** */
-
-/*      Returns the packet number for the given dataset. purely virtual func */
-/*      \param buff pointer to the dataset */
-/*      \returns packet number number */
-
-
-
-/*   *\/ */
-/*   int getPacketNumber(char *buff){return ((*(((int*)(buff+4))))&0xff)+1;};    */
-
-/* /\*    /\\** *\/ */
-
-/* /\*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func *\/ */
-/* /\*      \param data pointer to the memory to be analyzed *\/ */
-/* /\*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot *\/ */
-/* /\*      \param dsize size of the memory slot to be analyzed *\/ */
-/* /\*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  *\/ */
-
-/* /\*   *\\/ *\/ */
-/* /\*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; *\/ */
-
-
-/* /\*    /\\** *\/ */
-
-/* /\*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  *\/ */
-/* /\*      \param filebin input file stream (binary) *\/ */
-/* /\*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete *\/ */
-
-/* /\*   *\\/ *\/ */
-/* /\*     virtual char *readNextFrame(ifstream &filebin){ *\/ */
-/* /\*       //	int afifo_length=0;   *\/ */
-/* /\*       uint16_t *afifo_cont;  *\/ */
-/* /\*       int ib=0; *\/ */
-/* /\*       if (filebin.is_open()) { *\/ */
-/* /\* 	afifo_cont=new uint16_t[dataSize/2]; *\/ */
-/* /\*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { *\/ */
-/* /\* 	  ib+=2; *\/ */
-/* /\* 	  if (ib==dataSize) break; *\/ */
-/* /\* 	} *\/ */
-/* /\* 	if (ib>0) { *\/ */
-/* /\* 	  iframe++; *\/ */
-/* /\* 	  // cout << ib << "-" << endl; *\/ */
-/* /\* 	  return (char*)afifo_cont; *\/ */
-/* /\* 	} else { *\/ */
-/* /\* 	  delete [] afifo_cont; *\/ */
-/* /\* 	  return NULL; *\/ */
-/* /\* 	} *\/ */
-/* /\*       }      *\/ */
-/* /\*       return NULL; *\/ */
-/* /\*     }; *\/ */
-
-
-/*   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) { */
-/* 	  char *data=new char[packetSize*nPackets]; */
-/* 	  char *retval=0; */
-/* 	  int nd; */
-/* 	  np=0; */
-/* 	  int  pn; */
-/* 	  char aa[8224]={0}; */
-/* 	  char *packet=(char *)aa; */
-/* 	  int  fnum = -1; */
-	  
-/* 	  if (ff>=0) */
-/* 	    fnum=ff; */
-
-/* 	  if (filebin.is_open()) { */
-
-
-/* 	    cout << "+"; */
-
-/* 	    while(filebin.read((char*)packet, 8208)){ */
-	      
-/* 	      pn=getPacketNumber(packet); */
-	      
-/* 	      if (fnum<0) */
-/* 		fnum= getFrameNumber(packet); */
-	      
-/* 	      if (fnum>=0) { */
-/* 		if (getFrameNumber(packet) !=fnum) {  */
-		  
-/* 		  if (np==0){ */
-/* 		    cout << "-"; */
-/* 		    delete [] data; */
-/* 		    return NULL; */
-/* 		  } else */
-/* 		    filebin.seekg(-8208,ios_base::cur); */
-
-/* 		    return data; */
-/* 		} */
-		
-/* 		memcpy(data+(pn-1)*packetSize, packet, packetSize); */
-/* 		np++; */
-/* 		if (np==nPackets) */
-/* 		  break; */
-/* 		if (pn==nPackets) */
-/* 		  break; */
-/* 	      } */
-/* 	    } */
-	    
-/* 	  } */
-	  
-/* 	  if (np==0){ */
-/* 	    cout << "?"; */
-/* 	    delete [] data; */
-/* 	    return NULL; */
-/* 	  }// else if (np<nPackets) */
-/* 	    //  cout << "Frame " << fnum << " lost "  << nPackets-np << " packets " << endl; */
-
-/* 	  return data; */
-	  
-/* 	}; */
-
-/* int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;}; */
-
-/*   	virtual char *readNextFrame(ifstream &filebin) { */
-/* 	  int fnum=-1, np; */
-/* 	  return readNextFrame(filebin, fnum, np); */
-/* 	}; */
-
-};
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench04CtbReceiver10GbData.h

@@ -0,0 +1,294 @@
+#ifndef MOENCH04REC10GBDATA_H
+#define  MOENCH04REC10GBDATA_H
+#include "slsDetectorData.h"
+
+//#define VERSION_V2
+    /**
+        @short  structure for a Detector Packet or Image Header
+        @li frameNumber is the frame number
+        @li expLength is the subframe number (32 bit eiger) or real time exposure time in 100ns (others)
+        @li packetNumber is the packet number
+        @li bunchId is the bunch id from beamline
+        @li timestamp is the time stamp with 10 MHz clock
+        @li modId is the unique module id (unique even for left, right, top, bottom)
+        @li xCoord is the x coordinate in the complete detector system
+        @li yCoord is the y coordinate in the complete detector system
+        @li zCoord is the z coordinate in the complete detector system
+        @li debug is for debugging purposes
+        @li roundRNumber is the round robin set number
+        @li detType is the detector type see :: detectorType
+        @li version is the version number of this structure format
+    */
+    typedef struct {
+        uint64_t frameNumber;    /**< is the frame number */
+        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
+        uint32_t packetNumber;    /**< is the packet number */
+        uint64_t bunchId;        /**< is the bunch id from beamline */
+        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
+        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
+        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
+        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
+        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
+        uint32_t debug;            /**< is for debugging purposes */
+        uint16_t roundRNumber;    /**< is the round robin set number */
+        uint8_t detType;        /**< is the detector type see :: detectorType */
+        uint8_t version;        /**< is the version number of this structure format */
+      uint64_t packetCaught[8];        /**< is the version number of this structure format */
+
+    } sls_detector_header;
+
+
+
+
+class moench04CtbReceiver10GbData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int aSamples;
+  const int dSamples;
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+ moench04CtbReceiver10GbData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, nas*2*32+sizeof(sls_detector_header)+nds*8), aSamples(nas), dSamples(nds) {
+
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
+
+    int adc_nr[32]={9, 8,11,10,13,12,15,14,1,0,3,2,5,4,7,6,23,22,21,20,19,18,17,16,31,30,29,28,27,26,25,24 };
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+    
+     int npackets=40;
+    int i;
+    int adc4(0);
+
+    for (int ip=0; ip<npackets; ip++) {
+      for (int is=0; is<128; is++) {
+
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=128*ip+is;
+	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=(adc_nr[iadc]%16)*sc_width+(i%sc_width);
+	    // if (adc4%2==0) {
+	    if (iadc/16>0) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    if (nds>0)
+	      dataMap[row][col]=sizeof(sls_detector_header)+((nadc+4)*i+iadc)*2;//+16*(ip+1); 
+	    else
+	    dataMap[row][col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=aSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+    }
+
+    int ipacket;
+    int ibyte;
+    int ii=0;
+    for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){
+      xmap[ibyte]=-1;
+      ymap[ibyte]=-1;
+    }
+    /* int off=sizeof(sls_detector_header)/2; */
+    
+    /*   for (ibyte=0;  ibyte<dataSize; ibyte++) { */
+
+
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+    
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return ((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench04CtbReceiverData.h

@@ -1,7 +1,8 @@
-#ifndef MOENCH03T1ZMQDATA_H
-#define  MOENCH03T1ZMQDATA_H
+#ifndef MOENCH04RECDATA_H
+#define  MOENCH04RECDATA_H
 #include "slsDetectorData.h"
 
+//#define VERSION_V2
     /**
         @short  structure for a Detector Packet or Image Header
         @li frameNumber is the frame number
@@ -32,12 +33,14 @@
         uint16_t roundRNumber;    /**< is the round robin set number */
         uint8_t detType;        /**< is the detector type see :: detectorType */
         uint8_t version;        /**< is the version number of this structure format */
+      uint64_t packetCaught[8];        /**< is the version number of this structure format */
+
     } sls_detector_header;
 
 
 
 
-class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
+class moench04CtbReceiverData : public slsDetectorData<uint16_t> {
  
  private:
   
@@ -45,8 +48,8 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
   int nadc;
   int sc_width;
   int sc_height;
-  const int nPackets; /**<number of UDP packets constituting one frame */
-  const int packetSize; /**< size of a udp packet */
+  const int aSamples;
+  const int dSamples;
 
 
  public:
@@ -60,16 +63,13 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
      \param c crosstalk parameter for the output buffer
 
   */
-    moench03T1ReceiverData(int npackets=40, int ps=8192): slsDetectorData<uint16_t>(400, 400, ps*npackets+sizeof(sls_detector_header)), packetSize(ps), nPackets(npackets) {
+ moench04CtbReceiverData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, nas*2*32+sizeof(sls_detector_header)+nds*8), aSamples(nas), dSamples(nds) {
 
     int nadc=32;
     int sc_width=25;
     int sc_height=200;
 
-    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
-    		    200,225,250,275,200,225,250,275,\
-    		    100,125,150,175,100,125,150,175,\
-    		    0,25,50,75,0,25,50,75};
+    int adc_nr[32]={9, 8,11,10,13,12,15,14,1,0,3,2,5,4,7,6,23,22,21,20,19,18,17,16,31,30,29,28,27,26,25,24 };
 
     int row, col;
 
@@ -77,7 +77,7 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
     int iadc;
     int ix, iy;
     
-    // int npackets=40;
+     int npackets=40;
     int i;
     int adc4(0);
 
@@ -89,14 +89,15 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
 	  adc4=(int)iadc/4;
 	  if (i<sc_width*sc_height) {
 	    //  for (int i=0; i<sc_width*sc_height; i++) {
-	    col=adc_nr[iadc]+(i%sc_width);
-	    if (adc4%2==0) {
+	    col=(adc_nr[iadc]%16)*sc_width+(i%sc_width);
+	    // if (adc4%2==0) {
+	    if (iadc/16>0) {
 	      row=199-i/sc_width;
 	    } else {
 	      row=200+i/sc_width;
 	    }
 	    dataMap[row][col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8192*40)
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=aSamples*2*32)
 	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
 	  }
 	}
@@ -110,27 +111,32 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
       xmap[ibyte]=-1;
       ymap[ibyte]=-1;
     }
-    int off=sizeof(sls_detector_header)/2;
-    for (ipacket=0; ipacket<npackets; ipacket++) {
-      for (ibyte=0;  ibyte< 8192/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	  isample=ii/nadc;
-	  iadc=ii%nadc;
-	  adc4 = (int)iadc/4;
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if (adc4%2==0) {
-	    xmap[i+off]=adc_nr[iadc]+ix;
-	    ymap[i+off]=ny/2-1-iy;
-	  } else {
-	    xmap[i+off]=adc_nr[iadc]+ix;
-	    ymap[i+off]=ny/2+iy;
-	  }
-	  
-	ii++;
-	//	}
-      }
-    }
+    /* int off=sizeof(sls_detector_header)/2; */
+    
+    /*   for (ibyte=0;  ibyte<dataSize; ibyte++) { */
+
+
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
     
     iframe=0;
     //  cout << "data struct created" << endl;
@@ -167,7 +173,7 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
 
 
   */
-  int getPacketNumber(char *buff){((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+  int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
 
 /*    /\** */
 
@@ -275,7 +281,7 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
 
 
 
-int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
 
 };
 

slsDetectorCalibration/dataStructures/moench04CtbZmq10GbData.h

@@ -0,0 +1,290 @@
+#ifndef MOENCH04ZMQ10GBDATA_H
+#define  MOENCH04ZMQ10GBDATA_H
+#include "slsDetectorData.h"
+
+
+
+
+class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int aSamples;
+  const int dSamples;
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+  //moench04CtbZmq10GbData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, nas*2*32+nds*8), aSamples(nas), dSamples(nds), nadc(32), sc_width(25), sc_height(200) {
+ moench04CtbZmq10GbData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, (nas > 0) && (nds>0) ? max(nas,nds)*(32*2+8) : nas*32*2+nds*8), nadc(32), sc_width(25), sc_height(200), aSamples(nas), dSamples(nds) {
+
+    /* int ds; */
+    /* if (nas && nds) */
+    /*   if (nds>nas) */
+    /* 	ds=nds*(32*2+8); */
+    /*   else */
+    /* 	ds=nas*(32*2+8); */
+    /* else */
+    /*   ds=nas*32*2+nds*8; */
+
+    /* new slsDetectorData<uint16_t>(400, 400, ds); */
+
+    int adc_nr[32]={9, 8,11,10,13,12,15,14,1,0,3,2,5,4,7,6,23,22,21,20,19,18,17,16,31,30,29,28,27,26,25,24 };
+
+    int row, col;
+
+    //int isample;
+    int iadc;
+   // int ix, iy;
+    
+    // int npackets=40;
+    int i;
+    //int adc4(0);
+
+      for (int is=0; is<aSamples; is++) {
+	
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=is;
+	  //	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=(adc_nr[iadc]%16)*sc_width+(i%sc_width);
+	    // if (adc4%2==0) {
+	    if (iadc<16) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    if (nds>0)
+	      dataMap[row][col]=((nadc+4)*i+iadc)*2;//+16*(ip+1);
+	    else
+	      dataMap[row][col]=(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=aSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+  
+
+    /* for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){ */
+    /*   xmap[ibyte]=-1; */
+    /*   ymap[ibyte]=-1; */
+    /* } */
+    /* int off=sizeof(sls_detector_header)/2; */
+    
+    /*   for (ibyte=0;  ibyte<dataSize; ibyte++) { */
+
+
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  }
+    
+  int getGain(char *data, int x, int y) {
+   // int aoff=aSamples*2*32;
+    int irow;
+    int isc=x/sc_width;
+    int icol=x%sc_width;
+    if (y<200) irow=sc_height-1-y;
+    else {
+      irow=y-sc_height;
+      isc++;
+    }
+    int ibit[32]={-1,-1,-1,-1,-1,-1,1,3,5,7,-1,-1,-1,-1,-1,-1,62,60,58,56,54,52,50,48,63,61,59,57,55,53,51,49};
+    int isample=irow*sc_width+icol;
+   
+    uint64_t sample;
+    char *ptr;
+    if (isc<0 || isc>=32) return 0;
+    if (ibit[isc]<0 || ibit[isc]>=64) return 0;
+    if (dSamples>isample) {
+      ptr=data+32*(isample+1)+8*isample;
+      sample=*((uint64_t*)ptr);
+    cout << isc << " " << ibit[isc] << " " << isample << hex << sample << dec << endl;
+    if (sample & (1<<ibit[isc]))
+      return 1;
+    else
+      return 0;
+    } else
+      return 0;
+  }
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return iframe;};//((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  //int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	 // char *retval=0;
+	 // int  nd;
+	 // int fnum = -1;
+	  np=0;
+	  //int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	   // fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      //     np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench04CtbZmqData.h

@@ -0,0 +1,276 @@
+#ifndef MOENCH04ZMQDATA_H
+#define  MOENCH04ZMQDATA_H
+#include "slsDetectorData.h"
+
+
+
+
+class moench04CtbZmqData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int aSamples;
+  const int dSamples;
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+ moench04CtbZmqData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, nas*2*32+nds*8), nadc(32), sc_width(25), sc_height(200), aSamples(nas), dSamples(nds) {
+    
+
+    int adc_nr[32]={9, 8,11,10,13,12,15,14,1,0,3,2,5,4,7,6,23,22,21,20,19,18,17,16,31,30,29,28,27,26,25,24 };
+
+    int row, col;
+
+    //int isample;
+    int iadc;
+    //int ix, iy;
+    
+    // int npackets=40;
+    int i;
+    //int adc4(0);
+
+      for (int is=0; is<aSamples; is++) {
+	
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=is;
+	  //	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=(adc_nr[iadc]%16)*sc_width+(i%sc_width);
+	    // if (adc4%2==0) {
+	    if (iadc<16) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    dataMap[row][col]=(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=aSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+  
+
+    /* for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){ */
+    /*   xmap[ibyte]=-1; */
+    /*   ymap[ibyte]=-1; */
+    /* } */
+    /* int off=sizeof(sls_detector_header)/2; */
+    
+    /*   for (ibyte=0;  ibyte<dataSize; ibyte++) { */
+
+
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  }
+    
+  int getGain(char *data, int x, int y) {
+    int aoff=aSamples*2*32;
+    int irow;
+    int isc=x/sc_width;
+    int icol=x%sc_width;
+    if (y<200) irow=sc_height-1-y;
+    else {
+      irow=y-sc_height;
+      isc++;
+    }
+    int ibit[32]={-1,-1,-1,-1,-1,-1,1,3,5,7,-1,-1,-1,-1,-1,-1,62,60,58,56,54,52,50,48,63,61,59,57,55,53,51,49};
+    int isample=irow*sc_width+icol;
+   
+    uint64_t sample;
+    char *ptr;
+    if (isc<0 || isc>=32) return 0;
+    if (ibit[isc]<0 || ibit[isc]>=64) return 0;
+    if (dSamples>isample) {
+      ptr=data+aoff+8*isample;
+      sample=*((uint64_t*)ptr);
+    cout << isc << " " << ibit[isc] << " " << isample << hex << sample << dec << endl;
+    if (sample & (1<<ibit[isc]))
+      return 1;
+    else
+      return 0;
+    } else
+      return 0;
+  }
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return iframe;};//((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  //int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	 // char *retval=0;
+	  //int  nd;
+	  //int fnum = -1;
+	  np=0;
+	  //int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	   // fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      //     np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/slsDetectorData.h

@@ -261,6 +261,8 @@ class slsDetectorData {
     return d^m;
   };
 
+  virtual int getGain(char *data, int ix, int iy=0){return 0;};
+
   /**
 
      Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
@@ -331,8 +333,6 @@ class slsDetectorData {
    */
   virtual char *readNextFrame(ifstream &filebin)=0;
   
-  
-
 };
 
 

slsDetectorCalibration/energyCalibration.cpp

@@ -1,534 +0,0 @@
-#include "energyCalibration.h"
-
-#ifdef __CINT
-#define MYROOT
-#endif
-
-
-#ifdef MYROOT
-#include <TMath.h>
-#include <TH1F.h>
-#include <TH2F.h>
-#include <TGraphErrors.h>
-#endif
-
-#include <iostream>
-
-#define max(a,b) ((a) > (b) ? (a) : (b))
-#define min(a,b) ((a) < (b) ? (a) : (b))
-#define ELEM_SWAP(a,b) { register int t=(a);(a)=(b);(b)=t; }
-
-
-using namespace std;
-
-#ifdef MYROOT
-
-Double_t energyCalibrationFunctions::pedestal(Double_t *x, Double_t *par) { 
-    return par[0]-par[1]*sign*x[0];                                      
-}
-
-
-Double_t energyCalibrationFunctions::gaussChargeSharing(Double_t *x, Double_t *par) { 
-  Double_t f, arg=0;
-  if (par[3]!=0) arg=sign*(x[0]-par[2])/par[3];
-    f=TMath::Exp(-1*arg*arg/2.); 
-    f=f+par[5]/2.*(TMath::Erfc(arg/(TMath::Sqrt(2.)))); 
-    return par[4]*f+pedestal(x,par);                                       
-}
-
-Double_t energyCalibrationFunctions::gaussChargeSharingPixel(Double_t *x, Double_t *par) { 
-  Double_t f;
-  if (par[3]<=0 || par[2]*(*x)<=0 || par[5]<0 || par[4]<=0) return 0;
-
-  Double_t pp[3];
-
-  pp[0]=0;
-  pp[1]=par[2];
-  pp[2]=par[3];
-  
-
-  f=(par[5]-par[6]*(TMath::Log(*x/par[2])))*erfBox(x,pp);
-  f+=par[4]*TMath::Gaus(*x, par[2], par[3], kTRUE);
-  return f+pedestal(x,par);                                       
-}
-
-Double_t energyCalibrationFunctions::erfBox(Double_t *z, Double_t *par) {
-
-  
-  
-  Double_t m=par[0];
-  Double_t M=par[1];
-  
-  if (par[0]>par[1]) {
-    m=par[1];
-    M=par[0];
-  }
-  
-  if (m==M)
-    return 0;
-
-
-  if (par[2]<=0) {
-    if (*z>=m && *z<=M)
-      return 1./(M-m);
-    else
-      return 0;
-
-  }
-
-  return (TMath::Erfc((z[0]-M)/par[2])-TMath::Erfc((z[0]-m)/par[2]))*0.5/(M-m);
-
-}
-
-
-// basic erf function
-Double_t energyCalibrationFunctions::erfFunction(Double_t *x, Double_t *par) {	
-  double arg=0;
-  if (par[1]!=0) arg=(par[0]-x[0])/par[1];
-  return ((par[2]/2.*(1+TMath::Erf(sign*arg/(TMath::Sqrt(2))))));  
-};
-  
-
-Double_t energyCalibrationFunctions::erfFunctionChargeSharing(Double_t *x, Double_t *par) {	       
-  Double_t f;		
-  
-  f=erfFunction(x, par+2)*(1+par[5]*(par[2]-x[0]))+par[0]-par[1]*x[0]*sign;		
-  return f;								
-};
-  
-  
-Double_t energyCalibrationFunctions::erfFuncFluo(Double_t *x, Double_t *par) {
-  Double_t f;							       
-  f=erfFunctionChargeSharing(x, par)+erfFunction(x, par+6)*(1+par[9]*(par[6]-x[0])); 
-  return f;							
-};
-#endif
-
-double energyCalibrationFunctions::median(double *x, int n){
-  // sorts x into xmed array and returns median 
-  // n is number of values already in the xmed array
-  double xmed[n];
-  int k,i,j;
-
-  for (i=0; i<n; i++) {
-    k=0;
-    for (j=0; j<n; j++) {
-      if(*(x+i)>*(x+j))
-	k++;
-      if (*(x+i)==*(x+j)) {
-	if (i>j) 
-	  k++;
-      }
-    }
-    xmed[k]=*(x+i);
-  }
-  k=n/2;
-  return xmed[k];
-}
-
-
-int energyCalibrationFunctions::quick_select(int arr[], int n){
-    int low, high ;
-    int median;
-    int middle, ll, hh;
-
-    low = 0 ; high = n-1 ; median = (low + high) / 2;
-    for (;;) {
-        if (high <= low) /* One element only */
-            return arr[median] ;
-
-        if (high == low + 1) {  /* Two elements only */
-            if (arr[low] > arr[high])
-                ELEM_SWAP(arr[low], arr[high]) ;
-            return arr[median] ;
-        }
-
-    /* Find median of low, middle and high items; swap into position low */
-    middle = (low + high) / 2;
-    if (arr[middle] > arr[high])    ELEM_SWAP(arr[middle], arr[high]) ;
-    if (arr[low] > arr[high])       ELEM_SWAP(arr[low], arr[high]) ;
-    if (arr[middle] > arr[low])     ELEM_SWAP(arr[middle], arr[low]) ;
-
-    /* Swap low item (now in position middle) into position (low+1) */
-    ELEM_SWAP(arr[middle], arr[low+1]) ;
-
-    /* Nibble from each end towards middle, swapping items when stuck */
-    ll = low + 1;
-    hh = high;
-    for (;;) {
-        do ll++; while (arr[low] > arr[ll]) ;
-        do hh--; while (arr[hh]  > arr[low]) ;
-
-        if (hh < ll)
-        break;
-
-        ELEM_SWAP(arr[ll], arr[hh]) ;
-    }
-
-    /* Swap middle item (in position low) back into correct position */
-    ELEM_SWAP(arr[low], arr[hh]) ;
-
-    /* Re-set active partition */
-    if (hh <= median)
-        low = ll;
-        if (hh >= median)
-        high = hh - 1;
-    }
-}
-
-int energyCalibrationFunctions::kth_smallest(int *a, int n, int k){
-    register int i,j,l,m ;
-    register double x ;
-
-    l=0 ; m=n-1 ;
-    while (l<m) {
-        x=a[k] ;
-        i=l ;
-        j=m ;
-        do {
-            while (a[i]<x) i++ ;
-            while (x<a[j]) j-- ;
-            if (i<=j) {
-                ELEM_SWAP(a[i],a[j]) ;
-                i++ ; j-- ;
-            }
-        } while (i<=j) ;
-        if (j<k) l=i ;
-        if (k<i) m=j ;
-    }
-    return a[k] ;
-}
-
-
-
-#ifdef MYROOT
-Double_t energyCalibrationFunctions::spectrum(Double_t *x, Double_t *par) {
-  return gaussChargeSharing(x,par);	
-}
-
-Double_t energyCalibrationFunctions::spectrumPixel(Double_t *x, Double_t *par) {
-  return gaussChargeSharingPixel(x,par);	
-}
-
-
-Double_t energyCalibrationFunctions::scurve(Double_t *x, Double_t *par) {
-  return erfFunctionChargeSharing(x,par);
-}
-
-
-Double_t energyCalibrationFunctions::scurveFluo(Double_t *x, Double_t *par) {
-  return erfFuncFluo(x,par);						
-}
-#endif
-
-energyCalibration::energyCalibration() : 
-#ifdef MYROOT	
-					 fit_min(-1),	
-					 fit_max(-1),	
-					 bg_offset(-1),	
-					 bg_slope(-1),	
-					 flex(-1),
-					 noise(-1),
-					 ampl(-1),
-					 cs_slope(-1),
-					 fscurve(NULL),
-					 fspectrum(NULL),
-#endif
-					 funcs(NULL),
-					 plot_flag(1), // fit parameters output to screen
-					 cs_flag(1)
-{
-
-#ifdef MYROOT	
-  funcs=new energyCalibrationFunctions();
-  
-  fscurve=new TF1("fscurve",funcs,&energyCalibrationFunctions::scurve,0,1000,6,"energyCalibrationFunctions","scurve");	
-  fscurve->SetParNames("Background Offset","Background Slope","Inflection Point","Noise RMS", "Number of Photons","Charge Sharing Slope");
-
-  fspectrum=new TF1("fspectrum",funcs,&energyCalibrationFunctions::spectrum,0,1000,6,"energyCalibrationFunctions","spectrum");	
-  fspectrum->SetParNames("Background Pedestal","Background slope", "Peak position","Noise RMS", "Number of Photons","Charge Sharing Pedestal");
-
-  fspixel=new TF1("fspixel",funcs,&energyCalibrationFunctions::spectrumPixel,0,1000,7,"energyCalibrationFunctions","spectrumPixel");	
-  fspixel->SetParNames("Background Pedestal","Background slope", "Peak position","Noise RMS", "Number of Photons","Charge Sharing Pedestal","Corner");
-
-#endif
-
-
-}
-
-
-
-void energyCalibration::fixParameter(int ip, Double_t val){
-  
-  fscurve->FixParameter(ip, val);
-  fspectrum->FixParameter(ip, val);
-}
-
-
-void energyCalibration::releaseParameter(int ip){
-
-  fscurve->ReleaseParameter(ip);
-  fspectrum->ReleaseParameter(ip);
-}
-
-
-
-
-
-
-
-energyCalibration::~energyCalibration(){ 
-#ifdef MYROOT
-  delete fscurve;
-  delete fspectrum;
-#endif
-  
-}
-
-#ifdef MYROOT
-
-
-
-
-
-TH1F* energyCalibration::createMedianHistogram(TH2F* h2, int ch0, int nch, int direction) {
-
-  if (h2==NULL || nch==0)
-    return NULL;
-
-  double *x=new double[nch];
-  TH1F *h1=NULL;
-  
-  double val=-1;
-
-  if (direction==0) {
-    h1=new TH1F("median","Median",h2->GetYaxis()->GetNbins(),h2->GetYaxis()->GetXmin(),h2->GetYaxis()->GetXmax());
-    for (int ib=0; ib<h1->GetXaxis()->GetNbins(); ib++) {
-      for (int ich=0; ich<nch; ich++) {
-	x[ich]=h2->GetBinContent(ch0+ich+1,ib+1);
-      }
-      val=energyCalibrationFunctions::median(x, nch);
-      h1->SetBinContent(ib+1,val);
-    }
-  } else if (direction==1) {   
-    h1=new TH1F("median","Median",h2->GetXaxis()->GetNbins(),h2->GetXaxis()->GetXmin(),h2->GetXaxis()->GetXmax());
-    for (int ib=0; ib<h1->GetYaxis()->GetNbins(); ib++) {
-      for (int ich=0; ich<nch; ich++) {
-	x[ich]=h2->GetBinContent(ib+1,ch0+ich+1);
-      }
-      val=energyCalibrationFunctions::median(x, nch);
-      h1->SetBinContent(ib+1,val);
-    }
-  }
-  delete [] x;
-
-  return h1;
-
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-void energyCalibration::setStartParameters(Double_t *par){	
-  bg_offset=par[0];						
-  bg_slope=par[1];						
-  flex=par[2];							
-  noise=par[3];							
-  ampl=par[4];							
-  cs_slope=par[5];						
-}
-
-
-void energyCalibration::getStartParameters(Double_t *par){	
-  par[0]=bg_offset;
-  par[1]=bg_slope;
-  par[2]=flex;
-  par[3]=noise;
-  par[4]=ampl;				
-  par[5]=cs_slope;				
-}
-
-#endif
-int energyCalibration::setChargeSharing(int p) {
-  if (p>=0) {
-    cs_flag=p; 
-#ifdef MYROOT  
-    if (p) {
-      fscurve->ReleaseParameter(5);
-      fspectrum->ReleaseParameter(1);
-    } else {
-      fscurve->FixParameter(5,0);
-      fspectrum->FixParameter(1,0);
-    }
-#endif
-  } 
-  
-  return cs_flag;
-}
-
- 
-#ifdef MYROOT  
-void energyCalibration::initFitFunction(TF1 *fun, TH1 *h1) {
-
- Double_t min=fit_min, max=fit_max; 
-
- Double_t mypar[6];
-  
- if (max==-1) 
-    max=h1->GetXaxis()->GetXmax();
- 
-  if (min==-1) 
-    min=h1->GetXaxis()->GetXmin();
-
-  
-  if (bg_offset==-1)
-    mypar[0]=0;
-  else
-    mypar[0]=bg_offset;
-
-
-  if (bg_slope==-1)
-    mypar[1]=0;
-  else
-    mypar[1]=bg_slope;
-
-
-  if (flex==-1)
-    mypar[2]=(min+max)/2.;
-  else
-    mypar[2]=flex;
-
-
-  if (noise==-1)
-    mypar[3]=0.1;
-  else
-    mypar[3]=noise;
-
-  if (ampl==-1)
-    mypar[4]=h1->GetBinContent(h1->GetXaxis()->FindBin(0.5*(max+min)));
-  else
-    mypar[4]=ampl;
-
-  if (cs_slope==-1)
-    mypar[5]=0;
-  else
-    mypar[5]=cs_slope;
- 
-  fun->SetParameters(mypar);
-
-  fun->SetRange(min,max);
-
-}
-
-
-TF1* energyCalibration::fitFunction(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t *emypar) {
-
-
-  TF1* fitfun;
-
-  char fname[100];
-
-  strcpy(fname, fun->GetName());
-
-  if (plot_flag) {
-    h1->Fit(fname,"R0Q");
-  } else
-    h1->Fit(fname,"R0Q");
-
-
-  fitfun= h1->GetFunction(fname);
-  fitfun->GetParameters(mypar);
-  for (int ip=0; ip<6; ip++) {
-    emypar[ip]=fitfun->GetParError(ip);
-  }
-  return fitfun;
-}
-
-TF1* energyCalibration::fitSCurve(TH1 *h1, Double_t *mypar, Double_t *emypar) {
-  initFitFunction(fscurve,h1);
-  return fitFunction(fscurve, h1, mypar, emypar);
-}
-
-
-
-
-
-TF1* energyCalibration::fitSpectrum(TH1 *h1, Double_t *mypar, Double_t *emypar) {
-  initFitFunction(fspectrum,h1);
-  return fitFunction(fspectrum, h1, mypar, emypar);
-}
-
-
-
-TF1* energyCalibration::fitSpectrumPixel(TH1 *h1, Double_t *mypar, Double_t *emypar) {
-  initFitFunction(fspixel,h1);
-  return fitFunction(fspixel, h1, mypar, emypar);
-}
-
-
-
-TGraphErrors* energyCalibration::linearCalibration(int nscan, Double_t *en, Double_t *een, Double_t *fl, Double_t *efl, Double_t &gain, Double_t &off, Double_t &egain, Double_t &eoff) { 
- 
-  TGraphErrors *gr;
- 
-  Double_t  mypar[2];
- 
-  gr = new TGraphErrors(nscan,en,fl,een,efl);
-
-  if (plot_flag) {
-    gr->Fit("pol1");
-    gr->SetMarkerStyle(20);
-  } else
-    gr->Fit("pol1","0Q");
-        
-  TF1 *fitfun= gr->GetFunction("pol1"); 
-  fitfun->GetParameters(mypar);
-
-  egain=fitfun->GetParError(1);
-  eoff=fitfun->GetParError(0);
-
-  gain=funcs->setScanSign()*mypar[1];
-  
-  off=mypar[0]; 
-  
-  return gr;
-}
-
-
-TGraphErrors* energyCalibration::calibrate(int nscan, Double_t *en, Double_t *een, TH1F **h1, Double_t &gain, Double_t &off, Double_t &egain, Double_t &eoff, int integral) {
-
-  TH1F *h;
-
-  Double_t mypar[6], emypar[6];
-  Double_t fl[nscan], efl[nscan];
-  
-
-  for (int ien=0; ien<nscan; ien++) {
-    h=h1[ien];
-    if (integral)
-      fitSCurve(h,mypar,emypar);
-    else
-      fitSpectrum(h,mypar,emypar);
-
-    fl[ien]=mypar[2];
-    efl[ien]=emypar[2];
-  }
-  return linearCalibration(nscan,en,een,fl,efl,gain,off, egain, eoff);
-
-}
-
-#endif
-
-
-
-

slsDetectorCalibration/ghostSummation.h

@@ -0,0 +1,62 @@
+#ifndef GHOSTSUMMATION_H
+#define GHOSTSUMMATION_H
+
+#include <cmath>
+#include "slsDetectorData.h"
+
+template <class dataType> class ghostSummation {
+
+  /** @short virtual calss to handle ghosting*/ 
+
+ public:
+  
+  /** constructor
+      \param xt crosstalk
+  */
+ ghostSummation(slsDetectorData<dataType> *d, double xt) : xtalk(xt),det(d)  {
+    if (det)
+      det->getDetectorSize(nx,ny);
+    ghost=new double[nx*ny];
+  };
+
+  ghostSummation(ghostSummation *orig) {
+    xtalk=orig->xtalk; 
+    det=orig->det;
+    ghost=new double[nx*ny];
+    
+  }
+  ~ghostSummation() {delete [] ghost;};
+
+  virtual ghostSummation *Clone() {
+    return new ghostSummation(this);
+  }
+
+  double getXTalk(){return xtalk;};
+  void setXTalk(double g) {xtalk=g;};
+
+  virtual double calcGhost(char *data, int ix, int iy=1){ghost[iy*nx+ix]=0; return 0;};
+
+  virtual void calcGhost(char *data){
+    for (int iy=0; iy<ny; iy++)
+      for (int ix=0; ix<nx; ix++)
+	ghost[iy*nx+ix]=calcGhost(data, ix, iy);
+  }
+
+  virtual double getGhost(int ix, int iy) {
+    if (ix<0 || ix>=nx || iy<0 || iy>=ny) return 0;
+    return ghost[iy*nx+ix];
+  }
+
+ protected:
+    double xtalk;
+    slsDetectorData<dataType> *det;
+    double *ghost;
+    int nx, ny;
+
+};
+
+
+
+
+
+#endif

slsDetectorCalibration/gotthardDoubleModuleCommonModeSubtractionNew.h

@@ -1,30 +0,0 @@
-#ifndef GOTTHARDDOUBLECOMMONMODESUBTRACTION_H
-#define GOTTHARDDOUBLECOMMONMODESUBTRACTION_H
-
-
-#include "commonModeSubtractionNew.h"
-
-class gotthardDoubleModuleCommonModeSubtraction : public commonModeSubtraction {
-
-  /** @short class to calculate the common mode of the pedestals based on an approximated moving average*/ 
-
- public:
-  
-  /** constructor
-      \param nn number of samples for the moving average to calculate the average common mode
-      \param iroi number of regions on which one can calculate the common mode separately. Defaults to 1 i.e. whole detector
-
-  */
- gotthardDoubleModuleCommonModeSubtraction(int ns=3) : commonModeSubtraction(2, ns) {};
-
-    /** 
-	gets the common mode ROI for pixel ix, iy 
-     */
-  virtual int getROI(int ix, int iy){return ix%2;};
-
-
-};
-
-
-
-#endif

slsDetectorCalibration/gotthardExecutables/Makefile.onTheFly

@@ -1,22 +0,0 @@
-
-CBFLIBDIR=/afs/psi.ch/project/sls_det_software/CBFlib-0.9.5
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o ../tiffIO.cpp
-ZMQLIB=../../slsReceiverSoftware/include
-INCDIR=-I.. -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ -I. -I../interpolations  -I../dataStructures
-LIBHDF5=-L$(CBFLIBDIR)/lib/ -lhdf5
-LDFLAG= -L/usr/lib64/ -lpthread
-#-L../../bin 
-MAIN=gotthard25umZmqAnalysis.C
-
-#DESTDIR?=../bin
-
-all: gotthard25umOnTheFlyAnalysis gotthard25umZmq
-
-gotthard25umOnTheFlyAnalysis:  $(MAIN)  $(INCS) clean
-			   g++ -o gotthard25umOnTheAnalysis  $(MAIN)  -lm -ltiff -lstdc++ $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
-
-gotthard25umZmq:  $(MAIN)  $(INCS) clean
-			   g++ -o gotthard25umZmq  $(MAIN)  -lm -ltiff -lstdc++ $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DZMQ  -L$(ZMQLIB) -lzmq
-
-clean:
-	rm -f gotthard25umOnTheFlyAnalysis

slsDetectorCalibration/gotthardExecutables/bchip2modules_pc8829.config

@@ -0,0 +1,40 @@
+detsizechan 2560 1
+
+hostname bchip074+bchip075+
+#hostname bchip092+bchip093+
+
+settingsdir settingsdir/gotthard
+angdir 1.000000
+caldir settingsdir/gotthard
+
+0:extsig:0 trigger_in_rising_edge
+0:rx_tcpport 1954
+0:rx_udpport 50001
+0:vhighvoltage 0
+
+#0:rx_zmqip pc8829
+#0:rx_zmqport 30003
+#0:zmqip pc8829
+#0:zmqport  40003
+
+1:extsig:0 trigger_in_rising_edge
+1:rx_tcpport 1955
+1:rx_udpport 50002
+#1:detectorip 10.1.1.52
+1:vhighvoltage 0
+
+#1:rx_zmqip pc8829
+#1:rx_zmqport 30004
+#1:zmqip pc8829
+#1:zmqport  40004
+
+
+r_readfreq 1
+rx_datastream 1
+
+#rx_udpip 10.1.1.100
+rx_hostname pc8498
+rx_datastream 1
+outdir /tmp/
+angconv none
+threaded 1

slsDetectorCalibration/gotthardExecutables/gotthard25umZmqAnalysis.C

@@ -1,517 +0,0 @@
-#include "sls_receiver_defs.h"
-//#ifdef ZMQ
-#include "ZmqSocket.h"
-//#endif
-#include <vector>
-#include <string>
-#include <sstream>
-#include <iomanip>
-#include <fstream>
-#include <stdio.h>
-//#include <deque>
-//#include <list>
-//#include <queue>
-#include <fstream>
-#include <cstring>
-
-//#define BCHIP074_BCHIP075
-
-#include "gotthardModuleDataNew.h"
-#include "gotthardDoubleModuleDataNew.h"
-#include "gotthardDoubleModuleCommonModeSubtractionNew.h"
-
-#include "singlePhotonDetector.h"
-//#include "interpolatingDetector.h"
-//#include "linearInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-
-#include <ctime>
-
-#define NC 1280
-#define NR 1
-
-//#include "tiffIO.h"
-
-
-
-
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
-int main(int argc, char *argv[]){
-  //void *gotthardProcessFrame() {
-
-
-
-  int fifosize=1000;
-  int nthreads=1;
-  int nph, nph1;
-  int etabins=550;
-  double etamin=-1, etamax=2;
-  int nsubpix=1;
-  float *etah=new float[etabins*etabins];
-  int *heta, *himage;
-  int offset=48;
-  #ifdef ZMQ
-  offset=0;
-  #endif
-  #ifndef ZMQ
-  offset=48;
-  #endif
- 
-  //commonModeSubtraction *cm=NULL;
-
-  gotthardDoubleModuleCommonModeSubtraction *cm=new gotthardDoubleModuleCommonModeSubtraction();
-  gotthardModuleDataNew *decoder=new   gotthardModuleDataNew();
-  gotthardDoubleModuleDataNew *det=new   gotthardDoubleModuleDataNew(offset);
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, cm, 1000, 100);
-  // analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det, 1, cm, 1000);
-  // analogDetector<uint16_t> *filter_nocm=new analogDetector<uint16_t>(det, 1, NULL, 1000);
-  filter->setROI(0,2560,0,1);
-  char *buff;//[2*(48+1280*2)];
-  char *buff0;
-  char *buff1;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-  mt->setFrameMode(eFrame);
-  // mt->setFrameMode(eFrame);
-  // mt->setFrameMode(ePedestal);
-  mt->StartThreads();
-  mt->popFree(buff);
-  buff0=buff;
-  buff1=buff+offset*2+1280*2;
-  int photons[1280*2];
-  int nf=0;
-  int ok=0;
-  std::time_t end_time;
-  //int16_t dout[1280*2];
-  int iFrame=-1;
-  int np=-1;
-  nph=0;
-  nph1=0;
-  //int np;
-  int iph;
-  int data_ready=1;
-  int *image;
-
-
-
-	int length;
-	int nnx, nny,nns;
-	int nix, niy,nis;
-	// infinite loop
-	int ix, iy, isx, isy;
-
-  filter->getImageSize(nnx, nny,nns);
-  int16_t *dout=new int16_t [nnx*nny];
-
-
-
-#ifdef ZMQ
-	if (argc < 3 ) {
-	  cprintf(RED, "Help: %s [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number]\n",argv[0]);
-		return EXIT_FAILURE;
-	}
-
-	// receive parameters
-	bool send = false;
-	  char* socketip=argv[1];
-	uint32_t portnum = atoi(argv[2]);
-	int size = nnx*nny*2;
-
-	// send parameters if any
-	char* socketip2 = 0;
-	uint32_t portnum2 = 0;
-	if (argc > 3) {
-		send = true;
-		socketip2 = argv[3];
-		portnum2 = atoi(argv[4]);
-	}
-	cout << "\nrx socket ip : " << socketip <<
-	  "\nrx port num  : " <<  portnum ;
-	if (send) {
-	  cout << "\nsd socket ip : " << socketip2 <<
-	    "\nsd port num  : " <<  portnum2;
-	}
-	cout << endl;
-
-
-
-	// receive socket
-	  ZmqSocket* zmqsocket0 = new ZmqSocket(socketip,portnum); 
-	if (zmqsocket0->IsError()) {
-	  cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-	  delete zmqsocket0;
-	  return EXIT_FAILURE;
-	}
-
-	  ZmqSocket* zmqsocket1 = new ZmqSocket(socketip,portnum+1); 
-	if (zmqsocket1->IsError()) {
-	  cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum+1, socketip);
-	  delete zmqsocket1;
-	  delete zmqsocket0;
-	  return EXIT_FAILURE;
-	}
-
-
-	zmqsocket0->Connect();
-	printf("Zmq Client 0 at %s\n", zmqsocket0->GetZmqServerAddress());
-	zmqsocket1->Connect();
-	printf("Zmq Client 1 at %s\n", zmqsocket1->GetZmqServerAddress());
-
-	// send socket
-	ZmqSocket* zmqsocket2 = 0;
-	ZmqSocket* zmqsocket3 = 0;
-	if (send) {
-	  zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-	  if (zmqsocket2->IsError()) {
-	    bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-	    delete zmqsocket2;
-	    delete zmqsocket1;
-	    delete zmqsocket0;
-	    return EXIT_FAILURE;
-	  }
-	  
-	  zmqsocket3 = new ZmqSocket(portnum2+1, socketip2);
-	  if (zmqsocket3->IsError()) {
-	    bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2+1, socketip2);
-	    delete zmqsocket3;
-	    delete zmqsocket2;
-	    delete zmqsocket1;
-	    delete zmqsocket0;
-	    return EXIT_FAILURE;
-	  }
-	  
-	  zmqsocket2->Connect();
-	  printf("Zmq Server 0 started at %s\n", zmqsocket2->GetZmqServerAddress());
-	  zmqsocket3->Connect();
-	  printf("Zmq Server 1 started at %s\n", zmqsocket3->GetZmqServerAddress());
-	}
-
-
-
-
-
-
-
-	uint64_t acqIndex1 = -1;
-	uint64_t frameIndex1 = -1;
-	uint32_t subframeIndex1 = -1;
-	uint64_t fileindex1 = -1;
-	string filename1 = "";
-
-	uint64_t acqIndex0 = -1;
-	uint64_t frameIndex0 = -1;
-	uint32_t subframeIndex0 = -1;
-	uint64_t fileindex0 = -1;
-	string filename0 = "";
-
-
-	int eoa0=0;
-	int eoa1=0;
-
-
-
-
-
-  #endif
-
-
-
-
-
-
-
-
-
-
-
-
-	char ofname[10000];
-	char fn0[10000], fn1[10000];
-	FILE *fout=NULL;
-	FILE *fclust=NULL;
-	for (int i=0; i<nnx; i++)
-	  dout[i]=0;
-	char fname0[10000], fname1[10000];
-	int irun;
-
-#ifndef ZMQ
-
-	char ff[10000];
-  if (argc < 6 ) {
-    cprintf(RED, "Help: %s [indir] [fformat] [runmin] [runmax] [out file format]\n",argv[0]);
-    return EXIT_FAILURE;
-  }
-  char *indir=argv[1];
-  char *fformat=argv[2];
-  int runmin=atoi(argv[3]);
-  int runmax=atoi(argv[4]);
-  char *outdir=argv[5];
-  sprintf(ff,"%s/%s",indir,fformat);
-  // strcpy(fformat,"/external_pool/gotthard_data/datadir_gotthardI/bchip074075/20170731/Xray/xray_15kV_200uA_5us_d%d_f000000000000_0.raw");
-  // sprintf(fname0,fformat,0,0);
-  // sprintf(fname1,fformat,1,1);
-  
-  ifstream filebin0,filebin1;
-  for (irun=runmin; irun<runmax; irun++) {
-
-    sprintf(fname0,ff,0,irun);
-    sprintf(fname1,ff,1,irun);
-    sprintf(ofname,outdir,irun);
-
-    filebin0.open((const char *)(fname0), ios::in | ios::binary);
-    filebin1.open((const char *)(fname1), ios::in | ios::binary);
-    if (filebin0.is_open() && filebin1.is_open()) {
-      cout << "Opened file " << fname0<< endl;
-      cout << "Opened file " << fname1<< endl;
-      nf=0;
-      iFrame=-1;
-      while ((decoder->readNextFrame(filebin0, iFrame, np, buff0)) && (decoder->readNextFrame(filebin1, iFrame, np, buff1))) {
-#endif
-
-
-
-
-
-#ifdef ZMQ
-
-	int end_of_acquisition;
-	while(1) {
-	  end_of_acquisition=0;
-	  eoa0=0;
-	  eoa1=0;
-	  
-	  //  cout << "Receive header " << nf << endl;
-	  if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
-	    
-	    //   cout << "************************************************************************** packet0!*****************************"<< endl;
-	    eoa0=1;
-	    end_of_acquisition++;
-	  } 
-	  if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
-	    //cout << "************************************************************************** packet1!*****************************"<< endl;
-	    eoa1=1;
-	    end_of_acquisition++;
-	  }
-
-
-
-
-
-	  //	  if ((!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) && (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1))){
-	  if (end_of_acquisition==0) {
-	    
-	    if (acqIndex0!=acqIndex1)
-	      cout << "different acquisition indexes " << acqIndex0 << " and " << acqIndex1 << endl;
-	    if (frameIndex0!=frameIndex1)
-	      cout << "different frame indexes " << frameIndex0 << " and " << frameIndex1 << endl;
-	    
-	    
-	    while (frameIndex0<frameIndex1) {
-	      cout << "aligning det 0 " << endl; 
-	      length = zmqsocket0->ReceiveData(0, buff0, size/2);
-	      if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
-		end_of_acquisition++;
-		eoa0=1;
-		break;
-	      } 
-	    }
-	    
-	    while (frameIndex1<frameIndex0) {
-	      cout << "aligning det 1 " << endl; 
-	      length = zmqsocket1->ReceiveData(0, buff1, size/2);
-	      if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
-		end_of_acquisition++;
-		eoa1=1;
-		break;
-	      } 
-	    }
-	  }
-
-
-
-	  if (eoa0!=eoa1) {
-
-	    while (eoa0<1) {
-	      length = zmqsocket0->ReceiveData(0, buff0, size/2);
-	      if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
-		end_of_acquisition++;
-		eoa0=1;
-	      }
-	    }
-
-
-	    while (eoa1<1) {
-	      length = zmqsocket1->ReceiveData(0, buff1, size/2);
-	      if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
-		end_of_acquisition++;
-		eoa1=1;
-	      }
-	    }
-	  }
-
-	  
-
-
-
-	  
-	  if (end_of_acquisition) {
-	    // cout << "************************************************************************** END OF FRAME" << end_of_acquisition << " !*****************************"<< endl;
-	    //  return 0;
-	    
-	    sprintf(ofname,"%s_%d.ph",fn0,irun);
-	    while (mt->isBusy()) {;}
-	    image=filter->getImage();
-	    if (image) {
-	      fout=fopen(ofname,"w");
-	      cout << nf << "*****************" << endl;
-	      for (int i=0; i<2560; i++) {
-		fprintf(fout,"%d %d\n",i,image[i]);
-		dout[i]=image[i];
-		if (dout[i]<0)
-		   dout[i]=0;
-	      }
-	      fclose(fout);
-	    }
-	    
-
-	    if (send) {
-	      
-	      zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fn0, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-	      zmqsocket3->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fn1, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-	      
-	      zmqsocket2->SendData((char*)dout,size/2);
-	      zmqsocket3->SendData(((char*)dout)+size/2,size/2);
-	      //    	//	cprintf(GREEN, "Sent Data\n");
-
-	      
-	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	      zmqsocket3->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	    }
-	    
-	    
-	    //mt->setFrameMode(eFrame);
-	    filter->clearImage();
-	    // std::time(&end_time);
-	    // cout << std::ctime(&end_time) << " " << nf <<   endl;
-	    fclose(fclust);
-	    fclust=NULL;
-	    
-	    
-	    
-	    continue; 
-	  }
-	  
-	  if (fclust==NULL) {
-
-	    strcpy(fn0,filename0.c_str());
-	    strcpy(fn1,filename1.c_str());
-	    sprintf(ofname,"%s_%d.clust",fn0,irun);
-	    fclust=fopen(ofname,"w");
-	    while (mt->isBusy()) {;}
-	    mt->setFilePointer(fclust);
-	  }
-
-	  // strcpy(fn0,filename0.c_str());
-	  // strcpy(fn1,filename1.c_str());
-	  
-	  //	  cout << "Receive data " << nf << endl;
-	  length = zmqsocket0->ReceiveData(0, buff0, size/2);
-	  length += zmqsocket1->ReceiveData(0, buff1, size/2);  
-	  
-	  irun=fileindex0;
-	  
-	  
-	    
-	    // //  if (nf>100)
-	    // //  mt->setFrameMode(eFrame);
-	    // //filter->clearImage();
-
-
-#endif
-
-
-	mt->pushData(buff);
-	mt->nextThread();
-	// cout << "==" << nf << endl;
-
-	    // while (mt->isBusy()) {;}
-	    // image=filter->getImage();
-	    // if (image) {
-	    //   for (int i=0; i<2560; i++) {
-	    // 	//	if (i<512)
-	
-	    // 	//  	fprintf(fout,"%d %d\n",i,image[i]);
-	    //   	dout[i]=filter->subtractPedestal(buff,i,0,1);//image[i];//filter->getPedestal(i,0);//
-	    // 	if (dout[i]<0)
-	    // 	   dout[i]=0;
-	    // 	//	cout << i << " " << image[i] << " " << dout[i] << endl;
-	    //   }
-	    // }
-
-
-	    // if (send) {
-	    // 	strcpy(fname0,filename0.c_str());
-	    // 	strcpy(fname1,filename1.c_str());
-	    // 	//  zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,16,fileindex,400,400,400*400, acqIndex,frameIndex,fname, acqIndex, 0,0,0,0,0,0,0,0,0,0,0,1);
-	    // 	zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname0, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-	    // 	zmqsocket3->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname1, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-		
-	    // 	zmqsocket2->SendData((char*)dout,size/2);
-	    // 	zmqsocket3->SendData(((char*)dout)+size/2,size/2);
-	    // 	//	cprintf(GREEN, "Sent Data\n");
-
-
-	    // 	// zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	    // 	// zmqsocket3->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-
-	    // 	//	cprintf(RED, "Received %d frames\n", nf);
-
-	    // }
-	    
-
-	mt->popFree(buff);
-	buff0=buff;
-	buff1=buff+offset*2+1280*2;
-	  
-
-
-	nf++;
-	
-
-
-
-#ifndef ZMQ
-
-
-	 
-
-	  while (mt->isBusy()) {;}
-	  image=filter->getImage();
-	  if (image) {
-	      fout=fopen(ofname,"w");
-	      //cout << nf << "*****************" << endl;
-	      for (int i=0; i<512; i++) {
-		fprintf(fout,"%d %d\n",i,image[i]);
-	      }
-	      fclose(fout);
-	  }
-	  filter->clearImage();
-      
-
-
-	  iFrame=-1;
-      }
-      
-      filebin0.close();
-      filebin1.close();
-    }
-    else
-      cout << "Could not open file " << fname0<< " or " << fname1 <<  endl;
-#endif
-
-    }
-  return NULL;
-
-
-
-}

slsDetectorCalibration/gotthardExecutables/howto_gotthatd_twomodules.txt

@@ -0,0 +1,14 @@
+slsReceiver --rx_tcpport 1954 &
+slsReceiver --rx_tcpport 1955 &
+
+./gotthard25umZmq pc8829 30003 129.129.202.98 40003 &
+slsDetectorGui -f examples/bchip2modules_pc8829.config &
+
+
+sls_detector_put settings veryhighgain
+sls_detector_put exptime 0.000005
+sls_detector_put period 0.01
+
+
+sls_detector_put vhighvoltage 90
+

slsDetectorCalibration/interpolatingDetector.h

@@ -46,8 +46,8 @@ class interpolatingDetector : public singlePhotonDetector {
 		       int sign=1, 
 		       commonModeSubtraction *cm=NULL,
 		       int nped=1000, 
-		       int nd=100, int nnx=-1, int nny=-1) : 
-  singlePhotonDetector(d, 3,nsigma,sign, cm, nped, nd, nnx, nny) , interp(inte), id(0)  {
+		       int nd=100, int nnx=-1, int nny=-1, double *gm=NULL, ghostSummation<uint16_t> *gs=NULL) : 
+  singlePhotonDetector(d, 3,nsigma,sign, cm, nped, nd, nnx, nny, gm, gs) , interp(inte), id(0)  {
     //cout << "**"<< xmin << " " << xmax << " " << ymin << " " << ymax << endl;
     fi=new pthread_mutex_t ;
 
@@ -139,8 +139,8 @@ class interpolatingDetector : public singlePhotonDetector {
     nph=addFrame(data,val,0); 
     if (interp)
       return interp->getInterpolatedImage();
-    else
-      singlePhotonDetector::getImage();
+    //else
+    return singlePhotonDetector::getImage();
       //return NULL;
   };
   
@@ -178,7 +178,7 @@ int addFrame(char *data,  int *ph=NULL, int ff=0) {
   double int_x, int_y;
   double eta_x, eta_y;
   if (interp) {
-  cout << "int" << endl;
+    // cout << "int" << endl;
   pthread_mutex_lock(fi); 
     for (nph=0; nph<nphFrame; nph++) {
       if (ff) {
@@ -233,13 +233,13 @@ int addFrame(char *data,  int *ph=NULL, int ff=0) {
     };
     
     virtual slsInterpolation *setInterpolation(slsInterpolation *ii){
-      int ok; 
+      // int ok; 
       interp=ii; 
       /*  pthread_mutex_lock(fi);
       if (interp)
 	interp->prepareInterpolation(ok);
 	pthread_mutex_unlock(fi);  */
-      cout << "det" << endl;
+      // cout << "det" << endl;
       return interp;
     };
   

slsDetectorCalibration/interpolations/eta2InterpolationBase.h

@@ -1,434 +0,0 @@
-#ifndef ETA2_INTERPOLATION_BASE_H
-#define ETA2_INTERPOLATION_BASE_H
-
-#ifdef MYROOT1
-#include <TObject.h>
-#include <TTree.h>
-#include <TH2D.h>
-#include <TH2F.h>
-#endif
-
-#include "etaInterpolationBase.h"
-
-class eta2InterpolationBase : public virtual etaInterpolationBase {
-  
- public:
- eta2InterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) :  etaInterpolationBase(nx,ny, ns, nb, emin, emax) {
-    // cout << "e2ib " << nb << " " << emin << " " << emax << endl; 
-
-    /* if (nbeta<=0) { */
-    /*   nbeta=nSubPixels*10;  */
-    /* } */
-    if (etamin>=etamax) {
-      etamin=-1;
-      etamax=2; 
-      //  cout << ":" <<endl;
-    }
-    etastep=(etamax-etamin)/nbeta;
-#ifdef MYROOT1
-    delete heta;
-    delete hhx;
-    delete hhy;
-    heta=new TH2D("heta","heta",nbeta,etamin,etamax,nbeta,etamin,etamax);
-    hhx=new TH2D("hhx","hhx",nbeta,etamin,etamax,nbeta,etamin,etamax);
-    hhy=new TH2D("hhy","hhy",nbeta,etamin,etamax,nbeta,etamin,etamax);
-#endif
-#ifndef MYROOT1
-    /* delete [] heta; */
-    /* delete [] hhx; */
-    /* delete [] hhy; */
-    /* heta=new int[nbeta*nbeta]; */
-    /* hhx=new float[nbeta*nbeta]; */
-    /* hhy=new float[nbeta*nbeta]; */
-    
-#endif
-    
-    //   cout << nbeta << " " << etamin << " " << etamax << endl;
-  };
-  
- eta2InterpolationBase(eta2InterpolationBase *orig): etaInterpolationBase(orig){ };
-
-/*  virtual eta2InterpolationBase* Clone()=0; {
-
-    return new eta2InterpolationBase(this);
-
-  };
-
-					   */
- 
-  //////////////////////////////////////////////////////////////////////////////
-  //////////// /*It return position hit for the event in input */ //////////////
-  virtual void getInterpolatedPosition(int x, int y, int *data, double &int_x, double &int_y)
-  {
-    double sDum[2][2];
-    double tot, totquad;
-    double etax,etay;
-    
-    int corner;
-    corner=calcQuad(data, tot, totquad, sDum); 
-    if (nSubPixels>2) 
-      calcEta(totquad, sDum, etax, etay); 
-    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
-
-    return;
-  };
-  
-
-  virtual void getInterpolatedPosition(int x, int y, double *data, double &int_x, double &int_y)
-  {
-    double sDum[2][2];
-    double tot, totquad;
-    double etax,etay;
-    
-    int corner;
-    corner=calcQuad(data, tot, totquad, sDum); 
-    if (nSubPixels>2) 
-      calcEta(totquad, sDum, etax, etay); 
-    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
-
-    return;
-  };
-  
-
-
-
-
-
-
-
-
-  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,double *cl,double &int_x, double &int_y) {
-    
-     double cc[2][2];
-     double *cluster[3];
-     int xoff, yoff;
-     cluster[0]=cl;
-     cluster[1]=cl+3;
-     cluster[2]=cl+6;
-     
-     switch (quad) {
-     case BOTTOM_LEFT:
-       xoff=0;
-       yoff=0;
-       break;
-     case BOTTOM_RIGHT:
-       xoff=1;
-       yoff=0;
-       break;
-     case TOP_LEFT:
-       xoff=0;
-       yoff=1;
-       break;
-     case TOP_RIGHT:
-       xoff=1;
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-     double etax, etay;
-     if (nSubPixels>2) { 
-       cc[0][0]=cluster[yoff][xoff];
-       cc[1][0]=cluster[yoff+1][xoff];
-       cc[0][1]=cluster[yoff][xoff+1];
-       cc[1][1]=cluster[yoff+1][xoff+1];
-       calcEta(totquad,cc,etax,etay);
-     }
-     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
-
-  }
-
-
-
-  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,int *cl,double &int_x, double &int_y) {
-    
-     double cc[2][2];
-     int *cluster[3];
-     int xoff, yoff;
-     cluster[0]=cl;
-     cluster[1]=cl+3;
-     cluster[2]=cl+6;
-     
-     switch (quad) {
-     case BOTTOM_LEFT:
-       xoff=0;
-       yoff=0;
-       break;
-     case BOTTOM_RIGHT:
-       xoff=1;
-       yoff=0;
-       break;
-     case TOP_LEFT:
-       xoff=0;
-       yoff=1;
-       break;
-     case TOP_RIGHT:
-       xoff=1;
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-     double etax, etay;
-     if (nSubPixels>2) { 
-       cc[0][0]=cluster[yoff][xoff];
-       cc[1][0]=cluster[yoff+1][xoff];
-       cc[0][1]=cluster[yoff][xoff+1];
-       cc[1][1]=cluster[yoff+1][xoff+1];
-       calcEta(totquad,cc,etax,etay);
-     }
-     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
-
-  }
-
-
-
-
-
-
-  virtual void getInterpolatedPosition(int x, int y, double etax, double etay, int corner, double &int_x, double &int_y)
-  {
-
-
-    double xpos_eta=0,ypos_eta=0;
-    double dX,dY;
-    int ex,ey;
-    switch (corner)
-      {
-      case TOP_LEFT:
-	dX=-1.;
-	dY=0;
-	break;
-      case TOP_RIGHT:
-	;
-	dX=0;
-	dY=0;
-	break;
-      case BOTTOM_LEFT:
-	dX=-1.;
-	dY=-1.;
-	break;
-      case BOTTOM_RIGHT:
-	dX=0;
-	dY=-1.;
-	break;
-      default:
-	cout << "bad quadrant" << endl;
-	dX=0.; 
-	dY=0.;
-      }
-    
-
-     if (nSubPixels>2) { 
-
-#ifdef MYROOT1
-    xpos_eta=(hhx->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
-    ypos_eta=(hhy->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
-#endif
-#ifndef MYROOT1
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ex<0) {
-      cout << "x*"<< ex << endl;
-      ex=0;
-	} 
-    if (ex>=nbeta) {
-      cout << "x?"<< ex << endl;
-      ex=nbeta-1;
-      
-    }
-    if (ey<0) {
-      cout << "y*"<< ey << endl;
-      ey=0;
-	} 
-    if (ey>=nbeta) {
-      cout << "y?"<< ey << endl;
-      ey=nbeta-1;
-      
-    }
-    
-    
-   
-    xpos_eta=(((double)hhx[(ey*nbeta+ex)]))+dX ;///((double)nSubPixels);
-    ypos_eta=(((double)hhy[(ey*nbeta+ex)]))+dY ;///((double)nSubPixels);
-    //else
-    //return 0;
-    
-#endif
-     } else {
-       xpos_eta=0.5*dX+0.25;
-       ypos_eta=0.5*dY+0.25;
-     }
-       
-       int_x=((double)x) + xpos_eta+0.5;
-       int_y=((double)y) +  ypos_eta+0.5;
-    
-
-  }
-
-
-  
-   virtual int addToFlatField(double totquad,int quad,int *cl,double &etax, double &etay) {
-     double cc[2][2];
-     int *cluster[3];
-     int xoff, yoff;
-     cluster[0]=cl;
-     cluster[1]=cl+3;
-     cluster[2]=cl+6;
-     
-     switch (quad) {
-     case BOTTOM_LEFT:
-       xoff=0;
-       yoff=0;
-       break;
-     case BOTTOM_RIGHT:
-       xoff=1;
-       yoff=0;
-       break;
-     case TOP_LEFT:
-       xoff=0;
-       yoff=1;
-       break;
-     case TOP_RIGHT:
-       xoff=1;
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-     cc[0][0]=cluster[yoff][xoff];
-     cc[1][0]=cluster[yoff+1][xoff];
-     cc[0][1]=cluster[yoff][xoff+1];
-     cc[1][1]=cluster[yoff+1][xoff+1];
-     
-      /* cout << cl[0] << " " << cl[1] << " " << cl[2] << endl;   */
-      /* cout << cl[3] << " " << cl[4] << " " << cl[5] << endl;   */
-      /* cout << cl[6] << " " << cl[7] << " " << cl[8] << endl;   */
-      /* cout <<"******"<<totquad << " " << quad << endl;  */
-      /* cout << cc[0][0]<< " " << cc[0][1] << endl;  */
-      /* cout << cc[1][0]<< " " << cc[1][1] << endl;  */
-     //calcMyEta(totquad,quad,cl,etax, etay);
-     calcEta(totquad, cc,etax, etay);
-
-     //     cout <<"******"<< etax << " " << etay << endl;
-
-
-     return addToFlatField(etax,etay);
-   }
-
-   virtual int addToFlatField(double totquad,int quad,double *cl,double &etax, double &etay) {
-     double cc[2][2];
-     double *cluster[3];
-     int xoff, yoff;
-     cluster[0]=cl;
-     cluster[1]=cl+3;
-     cluster[2]=cl+6;
-     
-     switch (quad) {
-     case BOTTOM_LEFT:
-       xoff=0;
-       yoff=0;
-       break;
-     case BOTTOM_RIGHT:
-       xoff=1;
-       yoff=0;
-       break;
-     case TOP_LEFT:
-       xoff=0;
-       yoff=1;
-       break;
-     case TOP_RIGHT:
-       xoff=1;
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-     cc[0][0]=cluster[yoff][xoff];
-     cc[1][0]=cluster[yoff+1][xoff];
-     cc[0][1]=cluster[yoff][xoff+1];
-     cc[1][1]=cluster[yoff+1][xoff+1];
-     
-      /* cout << cl[0] << " " << cl[1] << " " << cl[2] << endl;   */
-      /* cout << cl[3] << " " << cl[4] << " " << cl[5] << endl;   */
-      /* cout << cl[6] << " " << cl[7] << " " << cl[8] << endl;   */
-      /* cout <<"******"<<totquad << " " << quad << endl;  */
-      /* cout << cc[0][0]<< " " << cc[0][1] << endl;  */
-      /* cout << cc[1][0]<< " " << cc[1][1] << endl;  */
-     //calcMyEta(totquad,quad,cl,etax, etay);
-     calcEta(totquad, cc,etax, etay);
-
-     //     cout <<"******"<< etax << " " << etay << endl;
-
-
-     return addToFlatField(etax,etay);
-   }
-
-
-
-  //////////////////////////////////////////////////////////////////////////////////////
-  virtual int addToFlatField(double *cluster, double &etax, double &etay){
-    double sDum[2][2];
-    double tot, totquad;
-    int corner;
-    corner=calcQuad(cluster, tot, totquad, sDum); 
-    
-    double xpos_eta,ypos_eta;
-    double dX,dY;
-  
-    
-    calcEta(totquad, sDum, etax, etay); 
-   
-    return addToFlatField(etax,etay);
-
-    };
-
-  virtual int addToFlatField(int *cluster, double &etax, double &etay){
-    double sDum[2][2];
-    double tot, totquad;
-    int corner;
-    corner=calcQuad(cluster, tot, totquad, sDum); 
-    
-    double xpos_eta,ypos_eta;
-    double dX,dY;
-  
-    
-    calcEta(totquad, sDum, etax, etay); 
-   
-    return addToFlatField(etax,etay);
-
-    };
-
-
-  virtual int addToFlatField(double etax, double etay){
-#ifdef MYROOT1
-    heta->Fill(etax,etay);
-#endif
-#ifndef MYROOT1
-    int ex,ey; 
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
-      heta[ey*nbeta+ex]++; 
-#endif
-    return 0;    
-  };
-  
-/*  protected: */
-  
-/* #ifdef MYROOT1 */
-/*   TH2D *heta; */
-/*   TH2D *hhx; */
-/*   TH2D *hhy; */
-/* #endif */
-/* #ifndef MYROOT1 */
-/*   int *heta; */
-/*   float *hhx; */
-/*   float *hhy; */
-/* #endif */
-/*   int nbeta; */
-/*   double etamin, etamax, etastep; */
-
-};
-
-#endif

slsDetectorCalibration/interpolations/eta3InterpolationBase.h

@@ -1,294 +0,0 @@
-#ifndef ETA3_INTERPOLATION_BASE_H
-#define ETA3_INTERPOLATION_BASE_H
-
-#ifdef MYROOT1
-#include <TObject.h>
-#include <TTree.h>
-#include <TH2D.h>
-#include <TH2F.h>
-#endif
-
-#include "etaInterpolationBase.h"
-
-class eta3InterpolationBase : public virtual etaInterpolationBase  {
-  
- public:
- eta3InterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx, ny, ns, nb, emin, emax) {
-    //  cout << "e3ib " << nb << " " << emin << " " << emax << endl; 
-    /* if (nbeta<=0) { */
-    /*   nbeta=nSubPixels*10;    */
-    /* } */
-    if (etamin>=etamax) {
-      etamin=-1;
-      etamax=1; 
-    }
-    
-    etastep=(etamax-etamin)/nbeta;
-#ifdef MYROOT1
-    delete heta;
-    delete hhx;
-    delete hhy;
-    heta=new TH2D("heta","heta",nbeta,etamin,etamax,nbeta,etamin,etamax);
-    hhx=new TH2D("hhx","hhx",nbeta,etamin,etamax,nbeta,etamin,etamax);
-    hhy=new TH2D("hhy","hhy",nbeta,etamin,etamax,nbeta,etamin,etamax);
-#endif
-#ifndef MYROOT1
-    /* delete [] heta; */
-    /* delete [] hhx; */
-    /* delete [] hhy; */
-
-    /* heta=new int[nbeta*nbeta]; */
-    /* hhx=new float[nbeta*nbeta]; */
-    /* hhy=new float[nbeta*nbeta]; */
-    
-#endif
-    //   cout << nbeta << " " << etamin << " " << etamax << endl;
-};
-  
- eta3InterpolationBase(eta3InterpolationBase *orig): etaInterpolationBase(orig){ };
-
-  /* virtual eta3InterpolationBase* Clone()=0; */
-  
-  
-
-  
-  // virtual void prepareInterpolation(int &ok){};
- 
-
-  //////////////////////////////////////////////////////////////////////////////
-  //////////// /*It return position hit for the event in input */ //////////////
-  virtual void getInterpolatedPosition(int x, int y, int *data, double &int_x, double &int_y)
-  {
-   double tot, totquad;
-    double etax,etay;
-    
-    int corner=calcEta3(data,etax,etay, totquad);
-    
-    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
-
-    return;
-  };
-  
-
-  virtual void getInterpolatedPosition(int x, int y, double *data, double &int_x, double &int_y)
-  {
-    double sDum[2][2];
-    double tot, totquad;
-    double etax,etay;
-    
-    int corner=calcEta3(data,etax,etay, totquad);
-    
-    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
-
-    return;
-  };
-  
-
-  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,double *cl,double &int_x, double &int_y) {
-    
-  
-    double etax, etay;
-     if (nSubPixels>2) { 
-       calcEta3(cl,etax,etay, totquad);
-     } 
-     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
-
-  }
-
-
-
-  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,int *cl,double &int_x, double &int_y) {
-    
-    
-     double etax, etay;
-     if (nSubPixels>2) { 
-       calcEta3(cl,etax,etay, totquad);
-     }
-     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
-
-  }
-
-
-
-  virtual void getInterpolatedPosition(int x, int y, double etax, double etay, int corner, double &int_x, double &int_y)
-  {
-
-
-    double xpos_eta=0,ypos_eta=0;
-    int ex,ey;
-
-     if (nSubPixels>2) { 
-
-#ifdef MYROOT1
-    xpos_eta=(hhx->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
-    ypos_eta=(hhy->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
-#endif
-#ifndef MYROOT1
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ex<0) {
-      /* cout << etax << " " << etamin << " "; */
-      /*  cout << "3x*"<< ex << endl; */
-      ex=0;
-	} 
-    if (ex>=nbeta) {
-      /* cout << etax << " " << etamin << " "; */
-      /* cout << "3x?"<< ex << endl; */
-      ex=nbeta-1;
-    }
-    if (ey<0) {
-      /* cout << etay << " " << etamin << " "; */
-      /* cout << "3y*"<< ey << endl; */
-      ey=0;
-	} 
-    if (ey>=nbeta) {
-      /* cout << etay << " " << etamin << " "; */
-      /* cout << "3y?"<< ey << endl; */
-      ey=nbeta-1;
-      
-    }
-    xpos_eta=(((double)hhx[(ey*nbeta+ex)]));///((double)nSubPixels);
-    ypos_eta=(((double)hhy[(ey*nbeta+ex)]));///((double)nSubPixels);
-
-#endif
-   
-     } else {
-         switch (corner) {
-     case BOTTOM_LEFT:
-       xpos_eta=-0.25;
-       ypos_eta=-0.25;
-       break;
-     case BOTTOM_RIGHT:
-       xpos_eta=0.25;
-       ypos_eta=-0.25;
-       break;
-     case TOP_LEFT:
-       xpos_eta=-0.25;
-       ypos_eta=0.25;
-       break;
-     case TOP_RIGHT:
-       xpos_eta=0.25;
-       ypos_eta=0.25;
-       break;
-     default:
-       xpos_eta=0;
-       ypos_eta=0;
-     } 
-	 
-     }
-    int_x=((double)x) + xpos_eta;
-    int_y=((double)y) + ypos_eta;
-     // int_x=5. + xpos_eta;
-     //  int_y=5. + ypos_eta;
-    
-
-  }
-
-
-
-
-
-
-/*   ///////////////////////////////////////////////////////////////////////////////////////////////// */
-/*    virtual void getPositionETA3(int x, int y, double *data, double &int_x, double &int_y) */
-/*    { */
-/*     double sDum[2][2]; */
-/*     double tot, totquad; */
-/*     double eta3x,eta3y; */
-/*     double ex,ey; */
-    
-/*     calcQuad(data, tot, totquad, sDum);  */
-/*     calcEta3(data,eta3x, eta3y,tot);  */
-    
-/*     double xpos_eta,ypos_eta; */
-    
-/* #ifdef MYROOT1 */
-/*     xpos_eta=((hhx->GetBinContent(hhx->GetXaxis()->FindBin(eta3x),hhy->GetYaxis()->FindBin(eta3y))))/((double)nSubPixels); */
-/*     ypos_eta=((hhy->GetBinContent(hhx->GetXaxis()->FindBin(eta3x),hhy->GetYaxis()->FindBin(eta3y))))/((double)nSubPixels); */
-    
-/* #endif */
-/* #ifndef MYROOT1 */
-/*     ex=(eta3x-etamin)/etastep; */
-/*     ey=(eta3y-etamin)/etastep; */
-    
-/*     if (ex<0) ex=0; */
-/*     if (ex>=nbeta) ex=nbeta-1; */
-/*     if (ey<0) ey=0; */
-/*     if (ey>=nbeta) ey=nbeta-1; */
-
-/*     xpos_eta=(((double)hhx[(int)(ey*nbeta+ex)]))/((double)nSubPixels); */
-/*     ypos_eta=(((double)hhy[(int)(ey*nbeta+ex)]))/((double)nSubPixels); */
-/* #endif */
-    
-/*     int_x=((double)x) + xpos_eta; */
-/*     int_y=((double)y) + ypos_eta; */
-    
-/*     return; */
-/*   }; */
-  
-   virtual int addToFlatField(double totquad,int quad,int *cl,double &etax, double &etay) {
-   
-     calcEta3(cl, etax, etay, totquad);
-     return addToFlatField(etax,etay);
-   }
-
-   virtual int addToFlatField(double totquad,int quad,double *cl,double &etax, double &etay) {
-    
-
-     calcEta3(cl, etax, etay, totquad);
-     return addToFlatField(etax,etay);
-   }
-
-
-
-  //////////////////////////////////////////////////////////////////////////////////////
-  virtual int addToFlatField(double *cluster, double &etax, double &etay){
-    double totquad;
-     calcEta3(cluster, etax, etay, totquad);
-    return addToFlatField(etax,etay);
-
-    };
-
-  virtual int addToFlatField(int *cluster, double &etax, double &etay){
-  
-    double totquad;
-   
-     calcEta3(cluster, etax, etay, totquad);
-    return addToFlatField(etax,etay);
-
-    };
-
-
-  virtual int addToFlatField(double etax, double etay){
-#ifdef MYROOT1
-    heta->Fill(etax,etay);
-#endif
-#ifndef MYROOT1
-    int ex,ey; 
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
-      heta[ey*nbeta+ex]++; 
-#endif
-    return 0;    
-  };
-  
-  
-/*  protected: */
-  
-/* #ifdef MYROOT1 */
-/*   TH2D *heta; */
-/*   TH2D *hhx; */
-/*   TH2D *hhy; */
-/* #endif */
-/* #ifndef MYROOT1 */
-/*   int *heta; */
-/*   float *hhx; */
-/*   float *hhy; */
-/* #endif */
-/*   int nbeta; */
-/*   double etamin, etamax, etastep; */
-
-};
-
-#endif

slsDetectorCalibration/interpolations/etaInterpolationAdaptiveBins.h

@@ -1,131 +1,137 @@
 #ifndef ETA_INTERPOLATION_ADAPTIVEBINS_H
 #define ETA_INTERPOLATION_ADAPTIVEBINS_H
 
-
+#include <cmath>
 #include "tiffIO.h"
 //#include "etaInterpolationBase.h"
 #include "etaInterpolationPosXY.h"
 
+
+
 class etaInterpolationAdaptiveBins : public etaInterpolationPosXY {
 
- private:
-  double calcDiff(double avg, float *hx, float *hy) {
-    double p_tot=0;
-    double diff=0;
-    double bsize=1./nSubPixels;
-    
-    for (int ipx=0; ipx<nSubPixels; ipx++) {
-      for (int ipy=0; ipy<nSubPixels; ipy++) {
-	p_tot=0;
-	for (int ibx=0; ibx<nbeta; ibx++) {
-	  for (int iby=0; iby<nbeta; iby++) {
-	    if ( hx[ibx+iby*nbeta]>=((ipx)*bsize) && hx[ibx+iby*nbeta]<((ipx+1)*bsize) &&  hy[ibx+iby*nbeta]>=((ipy)*bsize) && hy[ibx+iby*nbeta]<((ipy+1)*bsize)) {
-	      p_tot+=heta[ibx+iby*nbeta];
-	    } 
-	  }
-	}
-	
-	cout <<  p_tot << " \t ";
+  // protected:
 
 
+ private: 
 
-	diff+=(p_tot-avg)*(p_tot-avg);
-	
-      }
-      cout << "\n";
-    }
-    return diff;
-  }
-  
-  void iterate(float *newhhx, float *newhhy) {
+  virtual void iterate(float *newhhx, float *newhhy) {
 
     double bsize=1./nSubPixels;
     
-    double hy[nbeta]; //profile y
-    double hx[nbeta]; //profile x
-    double hix[nbeta]; //integral of projection x
-    double hiy[nbeta]; //integral of projection y
-    
-   double tot_eta_x=0;
-   double tot_eta_y=0;
-    for (int ipy=0; ipy<nSubPixels; ipy++) {
+    double hy[nSubPixels][nbeta]; //profile y
+    double hx[nSubPixels][nbeta]; //profile x
+    double hix[nSubPixels][nbeta]; //integral of projection x
+    double hiy[nSubPixels][nbeta]; //integral of projection y
+    int ipy, ipx;
+   double tot_eta_x[nSubPixels];
+   double tot_eta_y[nSubPixels];
+   //for (int ipy=0; ipy<nSubPixels; ipy++) {
      
-      for (int ibx=0; ibx<nbeta; ibx++) {
-	hx[ibx]=0;
-	hy[ibx]=0;
+       for (ipy=0; ipy<nSubPixels; ipy++) {
+     for (int ibx=0; ibx<nbeta; ibx++) { 
+      	hx[ipy][ibx]=0; 
+      	hy[ipy][ibx]=0;
       }
+       }
 
-      tot_eta_x=0;
-      tot_eta_y=0;
       // cout << ipy << " " << ((ipy)*bsize) << " " << ((ipy+1)*bsize) << endl;
        for (int ibx=0; ibx<nbeta; ibx++) {
 	 for (int iby=0; iby<nbeta; iby++) {
-	   
-	  if (hhy[ibx+iby*nbeta]>=((ipy)*bsize) && hhy[ibx+iby*nbeta]<=((ipy+1)*bsize)) {
-	    hx[ibx]+=heta[ibx+iby*nbeta];
-	    tot_eta_x+=heta[ibx+iby*nbeta];
-	  } 
-	  
-	  
-	  if (hhx[ibx+iby*nbeta]>=((ipy)*bsize) && hhx[ibx+iby*nbeta]<=((ipy+1)*bsize)) {
-	    hy[iby]+=heta[ibx+iby*nbeta];
-	    tot_eta_y+=heta[ibx+iby*nbeta];
-	  } 
-	 }
+	   ipy=hhy[ibx+iby*nbeta]*nSubPixels;
+	   if (ipy<0) ipy=0;
+	   if (ipy>=nSubPixels) ipy=nSubPixels-1;
+	   hx[ipy][ibx]+=heta[ibx+iby*nbeta];
+
+
+	   ipx=hhx[ibx+iby*nbeta]*nSubPixels;
+	   if (ipx<0) ipx=0;
+	   if (ipx>=nSubPixels) ipx=nSubPixels-1;
+	   hy[ipx][iby]+=heta[ibx+iby*nbeta];
+	 } 
        }
       
  
-       hix[0]=hx[0];
-       hiy[0]=hy[0];
-       for (int ib=1; ib<nbeta; ib++) {
-	 hix[ib]=hix[ib-1]+hx[ib];
-	 hiy[ib]=hiy[ib-1]+hy[ib];
+       
+       for (ipy=0; ipy<nSubPixels; ipy++) {
+	 hix[ipy][0]=hx[ipy][0];
+	 hiy[ipy][0]=hy[ipy][0];
+	 for (int ib=1; ib<nbeta; ib++) {
+	   hix[ipy][ib]=hix[ipy][ib-1]+hx[ipy][ib];
+	   hiy[ipy][ib]=hiy[ipy][ib-1]+hy[ipy][ib];
+	 }
+	 tot_eta_x[ipy]=hix[ipy][nbeta-1]+1;
+	 tot_eta_y[ipy]=hiy[ipy][nbeta-1]+1;
+	 // cout << ipy << " " << tot_eta_x[ipy] << " " << tot_eta_y[ipy] << endl;
+	 
        }
-       // tot_eta_x=hix[nbeta-1];
-       // tot_eta_y=hiy[nbeta-1];
-       /* cout << "ipx " << ipy << " x: " << tot_eta_x << " " << hix[10]<< " " << hix[nbeta-1] << endl; */
-       /* cout << "ipy " << ipy << " y: " << tot_eta_y << " " << hiy[10]<< " " << hiy[nbeta-1] << endl; */
-  
-  // for (int ipy=0; ipy<nSubPixels; ipy++) {
+       // for (int ipy=0; ipy<nSubPixels; ipy++) {
        
        for (int ibx=0; ibx<nbeta; ibx++) {
 	 for (int iby=0; iby<nbeta; iby++) {
 	   
-	   if ( hhy[ibx+iby*nbeta]>=((ipy)*bsize) && hhy[ibx+iby*nbeta]<=((ipy+1)*bsize)) {
-	     newhhx[ibx+iby*nbeta]=hix[ibx]/((double)tot_eta_x);
-	     if (newhhx[ibx+iby*nbeta]>1) cout << "***"<< ibx << " " << iby << newhhx[ibx+iby*nbeta] << endl;
+	   //   if ( hhy[ibx+iby*nbeta]>=((ipy)*bsize) && hhy[ibx+iby*nbeta]<=((ipy+1)*bsize)) {
+	   ipy=hhy[ibx+iby*nbeta]*nSubPixels;
+
+	   if (ipy<0) ipy=0;
+	   if (ipy>=nSubPixels) ipy=nSubPixels-1;
+
+	   if (ipy>=0 && ipy<nSubPixels)
+	     if (tot_eta_x[ipy]>0)
+	       newhhx[ibx+iby*nbeta]=hix[ipy][ibx]/(tot_eta_x[ipy]);
+	     else
+	       cout << "Bad tot_etax " << ipy << " " << tot_eta_x[ipy] << endl;
+	   else
+	     cout << "** Bad value ipy " << ibx << " " << iby << " "<< ipy << " " << hhy[ibx+iby*nbeta]*nSubPixels << endl;
+	   // if (newhhx[ibx+iby*nbeta]>=1 || newhhx[ibx+iby*nbeta]<0 ) cout << "***"<< ibx << " " << iby << newhhx[ibx+iby*nbeta] << endl;
 	     // if (ipy==3 && ibx==10) cout << newhhx[ibx+iby*nbeta] << " " << hix[ibx] << " " << ibx+iby*nbeta << endl;
-	   }
-	   if (hhx[ibx+iby*nbeta]>=((ipy)*bsize) && hhx[ibx+iby*nbeta]<=((ipy+1)*bsize)) {
-	     newhhy[ibx+iby*nbeta]=hiy[iby]/((double)tot_eta_y);
-	     if (newhhy[ibx+iby*nbeta]>1) cout << "***"<< ibx << " " << iby << newhhy[ibx+iby*nbeta] << endl;
+	   // }
+	   ipy=hhx[ibx+iby*nbeta]*nSubPixels;
+	   //if (hhx[ibx+iby*nbeta]>=((ipy)*bsize) && hhx[ibx+iby*nbeta]<=((ipy+1)*bsize)) {
+	   if (ipy<0) ipy=0;
+	   if (ipy>=nSubPixels) ipy=nSubPixels-1;
+
+	   if (ipy>=0 && ipy<nSubPixels)
+	     if (tot_eta_y[ipy]>0)
+	       newhhy[ibx+iby*nbeta]=hiy[ipy][iby]/(tot_eta_y[ipy]);
+	     else
+	       cout << "Bad tot_etay " << ipy << " " << tot_eta_y[ipy] << endl;
+	   else
+	     cout << "** Bad value ipx " << ibx << " " << iby << " "<< ipy << " " << hhx[ibx+iby*nbeta]*nSubPixels << endl;
+	   // if (newhhy[ibx+iby*nbeta]>=1 || newhhy[ibx+iby*nbeta]<0 ) cout << "***"<< ibx << " " << iby << newhhy[ibx+iby*nbeta] << endl;
 	     //  if (ipy==3 && iby==10) cout << newhhy[ibx+iby*nbeta] << " " << hiy[iby] << " " << ibx+iby*nbeta << endl;
-	   }
+	   //   }
 	 }
        }
-  }
+       // }
     
     
   }
   
 
  public:
- etaInterpolationAdaptiveBins(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationPosXY(nx,ny,ns, nb, emin,emax){};
+ etaInterpolationAdaptiveBins(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationPosXY(nx,ny,ns, nb, emin,emax){
+    //   flat=new double[nSubPixels*nSubPixels]; flat_x=new double[nSubPixels]; flat_y=new double[nSubPixels];
+    //    flat=new double[nSubPixels*nSubPixels];
+};
 
- etaInterpolationAdaptiveBins(etaInterpolationAdaptiveBins *orig): etaInterpolationPosXY(orig){};
+ etaInterpolationAdaptiveBins(etaInterpolationAdaptiveBins *orig): etaInterpolationPosXY(orig){hintcorr=new int[nPixelsX*nPixelsY*nSubPixels];}; 
 
-  virtual etaInterpolationAdaptiveBins* Clone() {
+  virtual etaInterpolationAdaptiveBins* Clone()=0;
 
-    return new etaInterpolationAdaptiveBins(this);
+  /*   return new etaInterpolationAdaptiveBins(this); */
 
-  };
+  /* }; */
 
 
 
-  virtual void prepareInterpolation(int &ok)
+  virtual void prepareInterpolation(int &ok) {
+    prepareInterpolation(ok, 1000);
+  }
+
+  virtual void prepareInterpolation(int &ok, int nint)
   {
    ok=1;  
-   cout << "Adaptive bins" << endl;
 
    ///*Eta Distribution Rebinning*///
    double bsize=1./nSubPixels; //precision
@@ -153,65 +159,36 @@ class etaInterpolationAdaptiveBins : public etaInterpolationPosXY {
    //  }
    // }
    
-       etaInterpolationPosXY::prepareInterpolation(ok);
+   etaInterpolationPosXY::prepareInterpolation(ok);
 
-#ifdef SAVE_ALL
-   
-   char tit[10000];
-   float *etah=new float[nbeta*nbeta];
-  int etabins=nbeta;
-
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    
-    etah[ii]=hhx[ii];
-  }
-  sprintf(tit,"/scratch/start_hhx.tiff");
-  WriteToTiff(etah, tit, etabins, etabins);
-	  
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    etah[ii]=hhy[ii];
-  }
-  sprintf(tit,"/scratch/start_hhy.tiff");
-  WriteToTiff(etah, tit, etabins, etabins);
-	  
-#endif
-   int nint=1000;
 
    double thr=1./((double)nSubPixels);
    double avg=tot_eta/((double)(nSubPixels*nSubPixels));
-   cout << "total eta entries is :"<< tot_eta << " avg: "<< avg << endl;   
-   cout << "Start " << endl;
+   double rms=sqrt(tot_eta);
+   cout << "total eta entries is :"<< tot_eta << " avg: "<< avg << " rms: " << sqrt(tot_eta) << endl;   
    double old_diff=calcDiff(avg, hhx, hhy), new_diff=old_diff+1, best_diff=old_diff;
-   cout << " diff= " << old_diff << endl;
-   
-
+   // cout << " chi2= " << old_diff << " (rms= " << sqrt(tot_eta) << ")" << endl;
+   cout << endl;
+   cout << endl;
+   debugSaveAll(0);
    int iint=0;
    float *newhhx=new float[nbeta*nbeta]; //profile x
    float *newhhy=new float[nbeta*nbeta]; //profile y
    float *besthhx=hhx; //profile x
    float *besthhy=hhy; //profile y
-   while (iint<nint) {
-     
-     cout << "Iteration " << iint << endl;
+
+   cout << "Iteration "<< iint << " Chi2: " << old_diff <<  endl; //" Best: "<< best_diff << " RMS: "<< rms<< endl;
+   while (iint<nint && best_diff > rms) {
+
+/* #ifdef SAVE_ALL */
+/*      if (iint%10==0) */
+/*        debugSaveAll(iint); */
+/* #endif */
+     //  cout << "Iteration " << iint << endl;
      iterate(newhhx,newhhy);
      new_diff=calcDiff(avg, newhhx, newhhy);
-     cout << " diff= " << new_diff << endl;
-/* #ifdef SAVE_ALL */
-/*   for (int ii=0; ii<etabins*etabins; ii++) { */
-/*     etah[ii]=newhhx[ii]; */
-/*     if (etah[ii]>1 || etah[ii]<0  ) cout << "***"<< ii << etah[ii] << endl; */
-   
-/*   } */
-/*   sprintf(tit,"/scratch/neweta_hhx_%d.tiff",iint); */
-/*   WriteToTiff(etah, tit, etabins, etabins); */
-	  
-/*   for (int ii=0; ii<etabins*etabins; ii++) { */
-/*     etah[ii]=newhhy[ii]; */
-/*     if (etah[ii]>1 || etah[ii]<0  ) cout << "***"<< ii << etah[ii] << endl; */
-/*   } */
-/*   sprintf(tit,"/scratch/neweta_hhy_%d.tiff",iint); */
-/*   WriteToTiff(etah, tit, etabins, etabins); */
-/* #endif */
+     //   cout << " chi2= " << new_diff << " (rms= " << sqrt(tot_eta) << ")"<<endl;
+
   if (new_diff<best_diff) {
     best_diff=new_diff;
     besthhx=newhhx;
@@ -225,19 +202,33 @@ class etaInterpolationAdaptiveBins : public etaInterpolationPosXY {
   
   hhx=newhhx;
   hhy=newhhy;
+
+  
+#ifdef SAVE_ALL
+  if (new_diff<=best_diff) {
+       debugSaveAll(iint);
+  }
+#endif
+
+
   newhhx=new float[nbeta*nbeta]; //profile x
   newhhy=new float[nbeta*nbeta]; //profile y
 
-  old_diff=new_diff;
-  //} /* else { */
-     /*   cout << "Difference not decreasing after "<< iint << " iterations (" << old_diff << " < " << new_diff << ")"<< endl; */
-     /*   break; */
-     /* } */
   
-  iint++;
+    /* if (new_diff<old_diff){ */
+    /*   cout << "best difference at iteration "<< iint << " (" << new_diff << " < " << old_diff << ")"<< "Best: "<< best_diff << " RMS: "<< sqrt(tot_eta) << endl; */
+    /*   ; */
+    /* } else {  */
+     // break;
+     // }
+  
+    old_diff=new_diff;
+
+    iint++;
+    cout << "Iteration "<< iint << " Chi2: " << new_diff <<  endl; //" Best: "<< best_diff << " RMS: "<< rms<< endl;
    }
-     delete [] newhhx;
-     delete [] newhhy;
+   delete [] newhhx;
+   delete [] newhhy;
      
   if (hhx!=besthhx)
     delete [] hhx;
@@ -247,35 +238,48 @@ class etaInterpolationAdaptiveBins : public etaInterpolationPosXY {
   hhx=besthhx;
   hhy=besthhy;
 
-   
-
-
-
+  
+    cout << "Iteration "<< iint << " Chi2: " << best_diff <<  endl; //" Best: "<< best_diff << " RMS: "<< rms<< endl;
 #ifdef SAVE_ALL
-   
-
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    etah[ii]=hhx[ii];
-  }
-  sprintf(tit,"/scratch/eta_hhx_%d.tiff",id);
-  WriteToTiff(etah, tit, etabins, etabins);
-	  
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    etah[ii]=hhy[ii];
-  }
-  sprintf(tit,"/scratch/eta_hhy_%d.tiff",id);
-  WriteToTiff(etah, tit, etabins, etabins);
-	  
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    etah[ii]=heta[ii];
-  }
-  sprintf(tit,"/scratch/eta_%d.tiff",id);
-  WriteToTiff(etah, tit, etabins, etabins);
-  delete [] etah;
+  debugSaveAll(iint);
 #endif
+
   return ;
   }
 
+
+
+
+
+};
+
+class eta2InterpolationAdaptiveBins : public virtual eta2InterpolationBase, public virtual etaInterpolationAdaptiveBins {
+ public:
+ eta2InterpolationAdaptiveBins(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta2InterpolationBase(nx,ny,ns, nb, emin,emax),etaInterpolationAdaptiveBins(nx,ny,ns, nb, emin,emax){
+    cout << "NSUBPIX is " <<  ns << " " << nSubPixels << endl;
+    //  cout << "e2pxy " << nb << " " << emin << " " << emax << endl; 
+  };
+ 
+ eta2InterpolationAdaptiveBins(eta2InterpolationAdaptiveBins *orig): etaInterpolationBase(orig), etaInterpolationAdaptiveBins(orig)  {};
+
+  virtual eta2InterpolationAdaptiveBins* Clone() { return new eta2InterpolationAdaptiveBins(this);};
+
+
+
+
+};
+
+
+
+class eta3InterpolationAdaptiveBins : public virtual eta3InterpolationBase, public virtual etaInterpolationAdaptiveBins {
+ public:
+ eta3InterpolationAdaptiveBins(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta3InterpolationBase(nx,ny,ns, nb, emin,emax), etaInterpolationAdaptiveBins(nx,ny,ns, nb, emin,emax){
+      cout << "e3pxy " << nbeta << " " << etamin << " " << etamax << " " << nSubPixels<< endl;  
+  };
+
+ eta3InterpolationAdaptiveBins(eta3InterpolationAdaptiveBins *orig): etaInterpolationBase(orig), etaInterpolationAdaptiveBins(orig)  {};
+
+  virtual eta3InterpolationAdaptiveBins* Clone() { return new eta3InterpolationAdaptiveBins(this);};
 };
 
 #endif

slsDetectorCalibration/interpolations/etaInterpolationCleverAdaptiveBins.h

@@ -0,0 +1,263 @@
+#ifndef ETA_INTERPOLATION_CLEVER_ADAPTIVEBINS_H
+#define ETA_INTERPOLATION_CLEVER_ADAPTIVEBINS_H
+
+#include <cmath>
+#include "tiffIO.h"
+//#include "etaInterpolationBase.h"
+#include "etaInterpolationAdaptiveBins.h"
+
+
+//#define HSIZE 1
+
+
+class etaInterpolationCleverAdaptiveBins : public etaInterpolationAdaptiveBins {
+
+ private:
+
+
+  //  double *gradientX, *gradientY, *gradientXY;
+
+
+  virtual void iterate(float *newhhx, float *newhhy) {
+
+    double bsize=1./nSubPixels;
+    
+    /* double hy[nSubPixels*HSIZE][nbeta]; //profile y */
+    /* double hx[nSubPixels*HSIZE][nbeta]; //profile x */
+    //  double hix[nSubPixels*HSIZE][nbeta]; //integral of projection x
+    // double hiy[nSubPixels*HSIZE][nbeta]; //integral of projection y
+    int ipy, ipx, ippx, ippy;
+    // double tot_eta_x[nSubPixels*HSIZE];
+    //double tot_eta_y[nSubPixels*HSIZE];
+
+    double mean=0;
+    double maxflat=0, minflat=0, maxgradX=0, mingradX=0, maxgradY=0, mingradY=0, maxgr=0, mingr=0;
+
+    int ix_maxflat, iy_maxflat, ix_minflat, iy_minflat, ix_maxgrX, iy_maxgrX, ix_mingrX, iy_mingrX,ix_maxgrY, iy_maxgrY, ix_mingrY, iy_mingrY, ix_mingr, iy_mingr, ix_maxgr, iy_maxgr; 
+    int maskMin[nSubPixels*nSubPixels], maskMax[nSubPixels*nSubPixels];
+
+
+    //for (int ipy=0; ipy<nSubPixels; ipy++) {
+     
+    for (ipy=0; ipy<nSubPixels; ipy++) {
+      for (ipx=0; ipx<nSubPixels; ipx++) {
+	//	cout << ipx << " " << ipy << endl;
+	mean+=flat[ipx+nSubPixels*ipy]/((double)(nSubPixels*nSubPixels));
+      }
+    }
+
+    //  cout << "Mean is " << mean << endl;
+
+    /*** Find local minima and maxima within the staistical uncertainty **/
+    for (ipy=0; ipy<nSubPixels; ipy++) {
+      for (ipx=0; ipx<nSubPixels; ipx++) {
+	if (flat[ipx+nSubPixels*ipy]<mean-3.*sqrt(mean))maskMin[ipx+nSubPixels*ipy]=1; else maskMin[ipx+nSubPixels*ipy]=0;
+	if (flat[ipx+nSubPixels*ipy]>mean+3.*sqrt(mean)) maskMax[ipx+nSubPixels*ipy]=1; else maskMax[ipx+nSubPixels*ipy]=0;
+	if (ipx>0 && ipy>0) {
+	  if (flat[ipx+nSubPixels*ipy]<flat[ipx-1+nSubPixels*(ipy-1)]) 	maskMax[ipx+nSubPixels*ipy]=0;
+	  if (flat[ipx+nSubPixels*ipy]>flat[ipx-1+nSubPixels*(ipy-1)]) 	maskMin[ipx+nSubPixels*ipy]=0;
+	}
+	if (ipx>0 && ipy<nSubPixels-1) {
+	  if (flat[ipx+nSubPixels*ipy]<flat[ipx-1+nSubPixels*(ipy+1)]) 	maskMax[ipx+nSubPixels*ipy]=0;
+	  if (flat[ipx+nSubPixels*ipy]>flat[ipx-1+nSubPixels*(ipy+1)]) 	maskMin[ipx+nSubPixels*ipy]=0;
+	}
+	if (ipy>0 && ipx<nSubPixels-1) {
+	  if (flat[ipx+nSubPixels*ipy]<flat[ipx+1+nSubPixels*(ipy-1)]) 	maskMax[ipx+nSubPixels*ipy]=0;
+	  if (flat[ipx+nSubPixels*ipy]>flat[ipx+1+nSubPixels*(ipy-1)]) 	maskMin[ipx+nSubPixels*ipy]=0;
+	}
+	if (ipy<nSubPixels-1 && ipx<nSubPixels-1) {
+	  if (flat[ipx+nSubPixels*ipy]<flat[ipx+1+nSubPixels*(ipy+1)]) 	maskMax[ipx+nSubPixels*ipy]=0;
+	  if (flat[ipx+nSubPixels*ipy]>flat[ipx+1+nSubPixels*(ipy+1)]) 	maskMin[ipx+nSubPixels*ipy]=0;
+	}
+	if (ipy<nSubPixels-1 ) {
+	  if (flat[ipx+nSubPixels*ipy]<flat[ipx+nSubPixels*(ipy+1)]) 	maskMax[ipx+nSubPixels*ipy]=0;
+	  if (flat[ipx+nSubPixels*ipy]>flat[ipx+nSubPixels*(ipy+1)]) 	maskMin[ipx+nSubPixels*ipy]=0;
+	}
+	if (ipx<nSubPixels-1) {
+	  if (flat[ipx+nSubPixels*ipy]<flat[ipx+1+nSubPixels*(ipy)]) 	maskMax[ipx+nSubPixels*ipy]=0;
+	  if (flat[ipx+nSubPixels*ipy]>flat[ipx+1+nSubPixels*(ipy)]) 	maskMin[ipx+nSubPixels*ipy]=0;
+	}
+	
+	if (ipy>0 ) {
+	  if (flat[ipx+nSubPixels*ipy]<flat[ipx+nSubPixels*(ipy-1)]) 	maskMax[ipx+nSubPixels*ipy]=0;
+	  if (flat[ipx+nSubPixels*ipy]>flat[ipx+nSubPixels*(ipy-1)]) 	maskMin[ipx+nSubPixels*ipy]=0;
+	}
+
+	if (ipx>0 ) {
+	  if (flat[ipx+nSubPixels*ipy]<flat[ipx-1+nSubPixels*(ipy)]) 	maskMax[ipx+nSubPixels*ipy]=0;
+	  if (flat[ipx+nSubPixels*ipy]>flat[ipx-1+nSubPixels*(ipy)]) 	maskMin[ipx+nSubPixels*ipy]=0;
+	}
+
+	//	if (maskMin[ipx+nSubPixels*ipy]) cout << ipx << " " << ipy << " is a local minimum " << flat[ipx+nSubPixels*ipy] << endl;
+	//	if (maskMax[ipx+nSubPixels*ipy]) cout << ipx << " " << ipy << " is a local maximum "<< flat[ipx+nSubPixels*ipy] << endl;
+
+      }
+    }
+    int is_a_border=0;
+
+    //initialize the new partition to the previous one
+    // int ibx_p, iby_p, ibx_n, iby_n;
+    int ibbx, ibby;
+
+  
+    memcpy(newhhx,hhx,nbeta*nbeta*sizeof(float));
+    memcpy(newhhy,hhy,nbeta*nbeta*sizeof(float));
+
+    for (int ibx=0; ibx<nbeta; ibx++) {
+      for (int iby=0; iby<nbeta; iby++) { 
+ 
+	ippy=hhy[ibx+iby*nbeta]*nSubPixels;
+	ippx=hhx[ibx+iby*nbeta]*nSubPixels;
+	
+	
+	is_a_border=0;
+	
+	if (maskMin[ippx+nSubPixels*ippy] || maskMax[ippx+nSubPixels*ippy]) {
+	  
+
+	  for (int ix=-1; ix<2; ix++) {
+	    ibbx=ibx+ix;
+	    if (ibbx<0) ibbx=0;
+	    if (ibbx>nbeta-1) ibbx=nbeta-1;
+	    for (int iy=-1; iy<2; iy++) {
+	      ibby=iby+iy;
+	      if (ibby<0) ibby=0;
+	      if (ibby>nbeta-1) ibby=nbeta-1;
+	      
+	      
+	      ipy=hhy[ibbx+ibby*nbeta]*nSubPixels;
+	      ipx=hhx[ibbx+ibby*nbeta]*nSubPixels;
+
+	      
+	      if (ipx!=ippx || ipy!=ippy) {
+		is_a_border=1;
+		if (maskMin[ippx+nSubPixels*ippy]) {
+		  //increase the region
+		  newhhx[ibbx+ibby*nbeta]=((double)ippx+0.5)/((double)nSubPixels);
+		  newhhy[ibbx+ibby*nbeta]=((double)ippy+0.5)/((double)nSubPixels);
+		}
+		if (maskMax[ippx+nSubPixels*ippy]) {
+		  //reduce the region
+		  newhhx[ibx+iby*nbeta]=((double)ipx+0.5)/((double)nSubPixels);
+		  newhhy[ibx+iby*nbeta]=((double)ipy+0.5)/((double)nSubPixels);
+		}
+
+		//	cout << ippx << " " << ippy << " " << ibx << " " << iby << " * " << ipx << " " << ipy << " " << ibbx << " " << ibby << endl;
+	      }
+
+
+	    }
+	  }
+	} 	
+
+
+
+      }
+
+    }
+  
+
+    //Check that the resulting histograms are monotonic and they don't have holes!
+  
+    for (int ibx=0; ibx<nbeta-1; ibx++) {
+      for (int iby=0; iby<nbeta-1; iby++) {
+	
+    	ippy=newhhy[ibx+iby*nbeta]*nSubPixels;
+    	ippx=newhhx[ibx+iby*nbeta]*nSubPixels;
+	
+    	ipy=newhhy[ibx+(iby+1)*nbeta]*nSubPixels;
+    	ipx=newhhx[ibx+1+iby*nbeta]*nSubPixels;
+
+    	if ( ippx>ipx)
+    	  newhhx[ibx+1+iby*nbeta]=newhhx[ibx+iby*nbeta];
+    	else if (ipx >ippx+1)
+    	  newhhx[ibx+1+iby*nbeta]=((double)(ippx+1+0.5))/((double)nSubPixels);
+	  
+    	if ( ippy>ipy)
+    	  newhhy[ibx+(iby+1)*nbeta]=newhhy[ibx+iby*nbeta];
+    	else if (ipy >ippy+1)
+    	  newhhy[ibx+(iby+1)*nbeta]=((double)(ippy+1+0.5))/((double)nSubPixels);
+	  
+      }
+    }
+
+    
+  }
+  
+
+ public:
+ etaInterpolationCleverAdaptiveBins(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationAdaptiveBins(nx,ny,ns, nb, emin,emax){
+  
+    
+  };
+
+ etaInterpolationCleverAdaptiveBins(etaInterpolationCleverAdaptiveBins *orig): etaInterpolationAdaptiveBins(orig){}; 
+
+  virtual etaInterpolationCleverAdaptiveBins* Clone()=0;
+
+  /*   return new etaInterpolationCleverAdaptiveBins(this); */
+
+  /* }; */
+
+
+};
+
+class eta2InterpolationCleverAdaptiveBins : public virtual eta2InterpolationBase, public virtual etaInterpolationCleverAdaptiveBins {
+ public:
+ eta2InterpolationCleverAdaptiveBins(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta2InterpolationBase(nx,ny,ns, nb, emin,emax),etaInterpolationCleverAdaptiveBins(nx,ny,ns, nb, emin,emax){
+  };
+ 
+ eta2InterpolationCleverAdaptiveBins(eta2InterpolationCleverAdaptiveBins *orig): etaInterpolationBase(orig), etaInterpolationCleverAdaptiveBins(orig)  {};
+
+  virtual eta2InterpolationCleverAdaptiveBins* Clone() { return new eta2InterpolationCleverAdaptiveBins(this);};
+
+  // virtual int *getInterpolatedImage(){return eta2InterpolationBase::getInterpolatedImage();};
+
+  /* virtual int *getInterpolatedImage(){ */
+  /*   int ipx, ipy; */
+  /*   cout << "ff" << endl; */
+  /*   calcDiff(1, hhx, hhy); //get flat */
+  /*   double avg=0; */
+  /*  for (ipx=0; ipx<nSubPixels; ipx++) */
+  /*    for (ipy=0; ipy<nSubPixels; ipy++) */
+  /*      avg+=flat[ipx+ipy*nSubPixels]; */
+  /*  avg/=nSubPixels*nSubPixels; */
+   
+  /*  for (int ibx=0 ; ibx<nSubPixels*nPixelsX; ibx++) { */
+  /*    ipx=ibx%nSubPixels-nSubPixels; */
+  /*    if (ipx<0) ipx=nSubPixels+ipx; */
+  /*    for (int iby=0 ; iby<nSubPixels*nPixelsY; iby++) { */
+  /*    ipy=iby%nSubPixels-nSubPixels; */
+  /*    if (ipy<0) ipy=nSubPixels+ipy; */
+     
+  /*    if (flat[ipx+ipy*nSubPixels]>0) */
+  /*      hintcorr[ibx+iby*nSubPixels*nPixelsX]=hint[ibx+iby*nSubPixels*nPixelsX]*(avg/flat[ipx+ipy*nSubPixels]); */
+  /*    else */
+  /*      hintcorr[ibx+iby*nSubPixels*nPixelsX]=hint[ibx+iby*nSubPixels*nPixelsX]; */
+
+
+  /*    } */
+  /*  } */
+
+
+
+  /*   return hintcorr; */
+  /* }; */
+
+
+};
+
+
+
+class eta3InterpolationCleverAdaptiveBins : public virtual eta3InterpolationBase, public virtual etaInterpolationCleverAdaptiveBins {
+ public:
+ eta3InterpolationCleverAdaptiveBins(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta3InterpolationBase(nx,ny,ns, nb, emin,emax), etaInterpolationCleverAdaptiveBins(nx,ny,ns, nb, emin,emax){
+     
+  };
+
+ eta3InterpolationCleverAdaptiveBins(eta3InterpolationCleverAdaptiveBins *orig): etaInterpolationBase(orig), etaInterpolationCleverAdaptiveBins(orig)  {};
+
+  virtual eta3InterpolationCleverAdaptiveBins* Clone() { return new eta3InterpolationCleverAdaptiveBins(this);};
+};
+
+#endif

slsDetectorCalibration/interpolations/etaInterpolationGlobal.h

@@ -4,11 +4,11 @@
 
 #include "etaInterpolationBase.h"
 
-class etaInterpolationGlobal : public etaInterpolationBase{
+class etaInterpolationGlobal : public virtual etaInterpolationBase {
  public:
- globalEtaInterpolation(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax){};
+ etaInterpolationGlobal(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns,nsy, nb, nby,emin,emax){};
+  
   
-
 
   virtual void prepareInterpolation(int &ok)
   {
@@ -24,62 +24,106 @@ class etaInterpolationGlobal : public etaInterpolationBase{
 
 
    ///*Eta Distribution Rebinning*///
-   double bsize=1./nSubPixels; //precision
+   // double bsizeX=1./nSubPixelsX; //precision
    // cout<<"nPixelsX = "<<nPixelsX<<" nPixelsY = "<<nPixelsY<<" nSubPixels = "<<nSubPixels<<endl;
    double tot_eta=0;
-   for (int ip=0; ip<nbeta*nbeta; ip++)
+   for (int ip=0; ip<nbetaX*nbetaY; ip++)
      tot_eta+=heta[ip];
    cout << "total eta entries is :"<< tot_eta << endl;   
    if (tot_eta<=0) {ok=0; return;};
 
 
-   double hx[nbeta]; //projection x
-   double hy[nbeta]; //projection y
+   double hx[nbetaX]; //projection x
+   double hy[nbetaY]; //projection y
 
-   for (int ibx=0; ibx<nbeta; ibx++) {
-     for (int iby=0; iby<nbeta; iby++) {
-       hx[ibx]=hx[ibx]+heta[ibx+iby*nbeta];
-       hy[iby]=hx[iby]+heta[ibx+iby*nbeta];
+   for (int ibx=0; ibx<nbetaX; ibx++) { hx[ibx]=0;}
+
+     for (int iby=0; iby<nbetaY; iby++) { hy[iby]=0;}
+
+   for (int ibx=0; ibx<nbetaX; ibx++) {
+     for (int iby=0; iby<nbetaY; iby++) {
+       hx[ibx]=hx[ibx]+heta[ibx+iby*nbetaX];
+       hy[iby]=hy[iby]+heta[ibx+iby*nbetaX];
      }
    }
-  double hix[nbeta]; //integral of projection x
-  double hiy[nbeta]; //integral of projection y
+  double hix[nbetaX]; //integral of projection x
+  double hiy[nbetaY]; //integral of projection y
   hix[0]=hx[0];
   hiy[0]=hy[0];
   
-  for (int ib=1; ib<nbeta; ib++) {
+  for (int ib=1; ib<nbetaX; ib++) {
     hix[ib]=hix[ib-1]+hx[ib];
-    hiy[ib]=hiy[ib-1]+hx[ib];
   }
 
+  for (int ib=1; ib<nbetaY; ib++) {
+    hiy[ib]=hiy[ib-1]+hy[ib];
+  }
+  double tot_x=hix[nbetaX-1]+1;
+  double tot_y=hiy[nbetaY-1]+1;
   int ib=0;
-   for (int ibx=0; ibx<nbeta; ibx++) {
-     if (hix[ibx]>(ib+1)*tot_eta*bsize) ib++;
-     for (int iby=0; iby<nbeta; iby++) {
-#ifdef MYROOT1  
-       hhx->SetBinContent(ibx+1,iby+1,ib);
-#endif
-#ifndef MYROOT1  
-       hhx[ibx+iby*nbeta]=ib; 
-#endif
-     }
-   }
-   ib=0;
-   for (int iby=0; iby<nbeta; iby++) {
-     if (hiy[iby]>(ib+1)*tot_eta*bsize) ib++;
-     for (int ibx=0; ibx<nbeta; ibx++) {
-#ifdef MYROOT1 
-       hhy->SetBinContent(ibx+1,iby+1,ib); 
-#endif
-#ifndef MYROOT1  
-       hhy[ibx+iby*nbeta]=ib; 
-#endif
+
+  for (int ibx=0; ibx<nbetaX; ibx++) {
+    //     if (hix[ibx]>(ib+1)*tot_eta*bsize) ib++;
+    for (int iby=0; iby<nbetaY; iby++) {
+
+      if (tot_x>0)
+	hhx[ibx+iby*nbetaX]=hix[ibx]/tot_x; 
+      else
+	hhx[ibx+iby*nbetaX]=-1; 
+      
+      if (tot_y>0)
+       hhy[ibx+iby*nbetaX]=hiy[iby]/tot_y;  
+      else
+	hhy[ibx+iby*nbetaX]=-1; 
      }
    }
+/*    ib=0; */
+/*    for (int iby=0; iby<nbeta; iby++) { */
+/*      if (hiy[iby]>(ib+1)*tot_eta*bsize) ib++; */
+/*      for (int ibx=0; ibx<nbeta; ibx++) { */
+/* #ifdef MYROOT1  */
+/*        hhy->SetBinContent(ibx+1,iby+1,ib);  */
+/* #endif */
+/* #ifndef MYROOT1   */
+/*        hhy[ibx+iby*nbeta]=ib;  */
+/* #endif */
+/*      } */
+/*    } */
 
    return ;
   };
+  
+ etaInterpolationGlobal(etaInterpolationGlobal *orig): etaInterpolationBase(orig)  {};
 
 };
 
+
+//etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),
+
+class eta2InterpolationGlobal : public virtual eta2InterpolationBase, public virtual etaInterpolationGlobal {
+  
+ public:
+ eta2InterpolationGlobal(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : eta2InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax), etaInterpolationGlobal(nx,ny, ns, nsy, nb, nby, emin, emax){
+    cout << "e2pxy " << nbetaX << " " << nbetaY << etamin << " " << etamax << " " << nSubPixelsX<< " " << nSubPixelsY << endl;  
+  };
+ 
+ eta2InterpolationGlobal(eta2InterpolationGlobal *orig): etaInterpolationBase(orig), etaInterpolationGlobal(orig)  {};
+
+  virtual eta2InterpolationGlobal* Clone() { return new eta2InterpolationGlobal(this);};
+
+};
+
+//etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),
+
+class eta3InterpolationGlobal : public virtual eta3InterpolationBase, public virtual etaInterpolationGlobal {
+ public:
+ eta3InterpolationGlobal(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) :  eta3InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax), etaInterpolationGlobal(nx,ny, ns, nsy, nb, nby, emin, emax){
+    cout << "e3pxy " << nbetaX << " " << nbetaY << etamin << " " << etamax << " " << nSubPixelsX<< " " << nSubPixelsY << endl;  
+  };
+
+ eta3InterpolationGlobal(eta3InterpolationGlobal *orig): etaInterpolationBase(orig), etaInterpolationGlobal(orig)  {};
+
+  virtual eta3InterpolationGlobal* Clone() {return new eta3InterpolationGlobal(this);};
+};
+
 #endif

slsDetectorCalibration/interpolations/etaInterpolationPosXY.h

@@ -4,12 +4,10 @@
 
 //#include "tiffIO.h"
 #include "etaInterpolationBase.h"
-#include "eta2InterpolationBase.h"
-#include "eta3InterpolationBase.h"
 
 class etaInterpolationPosXY : public virtual etaInterpolationBase{
  public:
- etaInterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax){
+ etaInterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax){
     //  cout << "epxy " << nb << " " << emin << " " << emax << endl; cout << nbeta << " " << etamin << " " << etamax << endl; 
   };
 
@@ -24,135 +22,171 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
   virtual void prepareInterpolation(int &ok)
   {
    ok=1;  
-#ifdef MYROOT1   
-   if (hhx) delete hhx;
-   if (hhy) delete hhy;
-
-   hhx=new TH2D("hhx","hhx",heta->GetNbinsX(),heta->GetXaxis()->GetXmin(),heta->GetXaxis()->GetXmax(), heta->GetNbinsY(),heta->GetYaxis()->GetXmin(),heta->GetYaxis()->GetXmax()); 
-   hhy=new TH2D("hhy","hhy",heta->GetNbinsX(),heta->GetXaxis()->GetXmin(),heta->GetXaxis()->GetXmax(), heta->GetNbinsY(),heta->GetYaxis()->GetXmin(),heta->GetYaxis()->GetXmax()); 
-   
-#endif
 
 
    ///*Eta Distribution Rebinning*///
-   double bsize=1./nSubPixels; //precision
+   // double bsize=1./nSubPixels; //precision
    // cout<<"nPixelsX = "<<nPixelsX<<" nPixelsY = "<<nPixelsY<<" nSubPixels = "<<nSubPixels<<endl;
    double tot_eta=0;
    double tot_eta_x=0;
    double tot_eta_y=0;
-   for (int ip=0; ip<nbeta*nbeta; ip++)
+   for (int ip=0; ip<nbetaX*nbetaY; ip++)
      tot_eta+=heta[ip];
    cout << "total eta entries is :"<< tot_eta << endl;   
    if (tot_eta<=0) {ok=0; return;};
 
 
-   double hx[nbeta]; //profile x
-   double hy[nbeta]; //profile y
-   double hix[nbeta]; //integral of projection x
-   double hiy[nbeta]; //integral of projection y
-   int ii=0;
-   for (int ib=0; ib<nbeta; ib++) {
+   double hx[nbetaX]; //profile x
+   double hy[nbetaY]; //profile y
+   double hix[nbetaX]; //integral of projection x
+   double hiy[nbetaY]; //integral of projection y
+   //  int ii=0;
+   double etax, etay;
+   
+   for (int ib=0; ib<nbetaX; ib++) {
+     //tot_eta_y=0;
 
-     tot_eta_x=0;
-     tot_eta_y=0;
-
-     for (int iby=0; iby<nbeta; iby++) {
-       hx[iby]=heta[iby+ib*nbeta];
-       tot_eta_x+=hx[iby];
-       hy[iby]=heta[ib+iby*nbeta];
-       tot_eta_y+=hy[iby];
+     for (int iby=0; iby<nbetaY; iby++) {
+       etay=etamin+iby*etastepY;
+       //cout << etax << endl;
+     
+       // tot_eta_x+=hx[iby];
+       //  if (etay>=0 && etay<=1)
+	 hy[iby]=heta[ib+iby*nbetaX];
+	 // else
+	 //	 hy[iby]=0;
+       // tot_eta_y+=hy[iby];
      }
 
-     hix[0]=hx[0];
+   
      hiy[0]=hy[0];
 
-     for (int iby=1; iby<nbeta; iby++) {
-       hix[iby]=hix[iby-1]+hx[iby];
+     for (int iby=1; iby<nbetaY; iby++) {
        hiy[iby]=hiy[iby-1]+hy[iby];
      }
 
-     ii=0;
+     tot_eta_y=hiy[nbetaY-1]+1;
      
-     for (int ibx=0; ibx<nbeta; ibx++) {
-       if (tot_eta_x==0) {
-	 hhx[ibx+ib*nbeta]=((float)ibx)/((float)nbeta);
-	 ii=(ibx)/nbeta;
-       } else //if (hix[ibx]>(ii+1)*tot_eta_x*bsize) 
-	 {
-	 //ii++;
-	 // cout << ib << " x " << ibx << " " << tot_eta_x << " " << (ii)*tot_eta_x*bsize << " " << ii << endl;
-	 // }
-#ifdef MYROOT1  
-       hhx->SetBinContent(ibx+1,ib+1,ii);
-#endif
-#ifndef MYROOT1  
-       hhx[ibx+ib*nbeta]=hix[ibx]/((float)tot_eta_x);//ii; 
-#endif
-	 }
+     for (int iby=0; iby<nbetaY; iby++) {
+       if (tot_eta_y<=1) {
+	 hhy[ib+iby*nbetaX]=-1;
+	 //ii=(ibx*nSubPixels)/nbeta;
+       } else {   
+	 //if (hiy[ibx]>tot_eta_y*(ii+1)/nSubPixels) ii++;
+	 hhy[ib+iby*nbetaX]=hiy[iby]/tot_eta_y;
+       }
      }
-     /* if (ii!=(nSubPixels-1)) */
-     /*   cout << ib << " x " <<  tot_eta_x << " " << (ii+1)*tot_eta_x*bsize << " " << ii << " " << hix[nbeta-1]<< endl; */
-     
-     ii=0;
-     
-     for (int ibx=0; ibx<nbeta; ibx++) {
-       if (tot_eta_y==0) {
-	 hhx[ibx+ib*nbeta]=((float)ibx)/((float)nbeta);
-	 ii=(ibx*nSubPixels)/nbeta;
-       } else //if (hiy[ibx]>(ii+1)*tot_eta_y*bsize) 
-	 {
-	   //ii++;
-	 //cout << ib << " y " << ibx << " " << tot_eta_y << " "<< (ii)*tot_eta_y*bsize << " " << ii << endl;
-	   //}
-#ifdef MYROOT1  
-       hhy->SetBinContent(ib+1,ibx+1,ii);
-#endif
-#ifndef MYROOT1  
-       hhy[ib+ibx*nbeta]=hiy[ibx]/((float)tot_eta_y);//ii; 
-#endif
-	 }
-     }
-     /* if (ii!=(nSubPixels-1)) */
-     /*   cout << ib << " y " <<  tot_eta_y << " " << (ii+1)*tot_eta_y*bsize << " " << ii << " " << hiy[nbeta-1]<< endl; */
-     
-     //	 cout << "y " << nbeta << " " << (ii+1)*tot_eta_x*bsize << " " << ii << endl;
-     
    }
+   cout << "hhy filled " << endl;
+
+
+   for (int ib=0; ib<nbetaY; ib++) {
+
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       etax=etamin+ibx*etastepX;
+       //cout << etax << endl;
+       //   if (etax>=0 && etax<=1)
+	 hx[ibx]=heta[ibx+ib*nbetaX];
+	 //  else {
+	 //	 hx[ibx]=0;
+	 // }
+     }
+     hix[0]=hx[0];
+       
+     for (int ibx=1; ibx<nbetaX; ibx++) {
+       hix[ibx]=hix[ibx-1]+hx[ibx];
+     }
+
+  
+     tot_eta_x=hix[nbetaX-1]+1;
+     
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       if (tot_eta_x<=1) {
+	 hhx[ibx+ib*nbetaX]=-1;
+       } 
+       else { 
+	 hhx[ibx+ib*nbetaX]=hix[ibx]/tot_eta_x;
+       }
+     }
+     
+
+     
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       if (tot_eta_x<=0) {
+	 hhx[ibx+ib*nbetaX]=-1;
+       } else	 { 
+	 //if (hix[ibx]>tot_eta_x*(ii+1)/nSubPixels) ii++;
+	 hhx[ibx+ib*nbetaX]=hix[ibx]/tot_eta_x;
+       }
+     }
+  }
+
+     
+   /* cout << "hhx filled " << endl; */
+   /* int ibx, iby, ib; */
+   
+   /* iby=0; */
+   /* while (hhx[iby*nbetaY+nbetaY/2]<0 && iby<nbetaY/2) iby++; */
+   /* for (ib=0; ib<iby;ib++) { */
+   /*   for (ibx=0; ibx<nbetaX;ibx++) */
+   /*     hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby]; */
+   /* } */
+   
+   /* cout << "hhx  low optimized" << endl; */
+
+   /* iby=nbetaY-1; */
+   /* while (hhx[iby*nbetaY+nbetaY/2]<0 && iby>0) iby--; */
+   
+   /* for (ib=iby+1; ib<nbetaY;ib++) { */
+   /*   for (ibx=0; ibx<nbetaX;ibx++){ */
+   /*     cout << iby << " " << ib << " " << ibx << " " << ibx+nbetaX*ib << " " << ibx+nbetaX*iby << " " << nbetaX*nbetaY << endl; */
+   /*     hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby]; */
+   /* 	 } */
+   /* } */
+   
+   /* cout << "hhx  high optimized" << endl; */
+
+   /* iby=0; */
+   /* while (hhy[nbetaX/2*nbetaX+iby]<0 && iby<nbetaX) iby++; */
+   /* for (ib=0; ib<iby;ib++) { */
+   /*   for (ibx=0; ibx<nbetaY;ibx++) */
+   /*     hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx]; */
+   /* } */
+   /* cout << "hhy  low optimized" << endl; */
+
+   /* iby=nbetaX-1; */
+   /* while (hhy[nbetaX/2*nbetaX+iby]<0 && iby>) iby--; */
+   /* for (ib=iby+1; ib<nbetaX;ib++) { */
+   /*   for (ibx=0; ibx<nbetaY;ibx++) */
+   /*     hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx]; */
+   /* } */
+
+   /* cout << "hhy  high optimized" << endl; */
+
+
+     
+   
+
 
 #ifdef SAVE_ALL
-   char tit[10000];
-   
-  float *etah=new float[nbeta*nbeta];
-  int etabins=nbeta;
-
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    etah[ii]=hhx[ii];
-  }
-  sprintf(tit,"/scratch/eta_hhx_%d.tiff",id);
-  WriteToTiff(etah, tit, etabins, etabins);
-	  
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    etah[ii]=hhy[ii];
-  }
-  sprintf(tit,"/scratch/eta_hhy_%d.tiff",id);
-  WriteToTiff(etah, tit, etabins, etabins);
-	  
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    etah[ii]=heta[ii];
-  }
-  sprintf(tit,"/scratch/eta_%d.tiff",id);
-  WriteToTiff(etah, tit, etabins, etabins);
-  delete [] etah;
+   debugSaveAll();
 #endif	  
   return ;
   }
 
 };
 
+
+
+
+
+
+
+
 class eta2InterpolationPosXY : public virtual eta2InterpolationBase, public virtual etaInterpolationPosXY {
  public:
- eta2InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta2InterpolationBase(nx,ny,ns, nb, emin,emax),etaInterpolationPosXY(nx,ny,ns, nb, emin,emax){
-    //  cout << "e2pxy " << nb << " " << emin << " " << emax << endl; 
+ eta2InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),eta2InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),etaInterpolationPosXY(nx,ny, ns, nsy, nb, nby, emin, emax){
+    cout << "e2pxy " << nbetaX << " " << nbetaY << etamin << " " << etamax << " " << nSubPixelsX<< " " << nSubPixelsY << endl;  
   };
  
  eta2InterpolationPosXY(eta2InterpolationPosXY *orig): etaInterpolationBase(orig), etaInterpolationPosXY(orig)  {};
@@ -161,12 +195,12 @@ class eta2InterpolationPosXY : public virtual eta2InterpolationBase, public virt
 
 };
 
-
+//
 
 class eta3InterpolationPosXY : public virtual eta3InterpolationBase, public virtual etaInterpolationPosXY {
  public:
- eta3InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta3InterpolationBase(nx,ny,ns, nb, emin,emax), etaInterpolationPosXY(nx,ny,ns, nb, emin,emax){
-      cout << "e3pxy " << nbeta << " " << etamin << " " << etamax << " " << nSubPixels<< endl;  
+ eta3InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax), eta3InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax), etaInterpolationPosXY(nx,ny, ns, nsy, nb, nby, emin, emax){
+    cout << "e3pxy " << nbetaX << " " << nbetaY << etamin << " " << etamax << " " << nSubPixelsX<< " " << nSubPixelsY << endl;  
   };
 
  eta3InterpolationPosXY(eta3InterpolationPosXY *orig): etaInterpolationBase(orig), etaInterpolationPosXY(orig)  {};

slsDetectorCalibration/interpolations/etaVEL/etaVELInterpolation.h~

@@ -0,0 +1,52 @@
+#ifndef INTERPOLATION_ETAVEL_H
+#define INTERPOLATION_ETAVEL_H
+
+#include <slsInterpolation.h>
+#include "EtaVEL.h"
+#include "TH2F.h"
+//#include "EtaVEL.cpp"
+//class EtaVEL;
+
+class  interpolation_EtaVEL: public slsInterpolation {
+
+ public:
+  interpolation_EtaVEL(int nx=40, int ny=160, int ns=25, double etamin=-0.02, double etamax=1.02, int p=0);
+  ~interpolation_EtaVEL();
+ 
+ 
+  //create eta distribution, eta rebinnining etc.
+  //returns flat field image
+  void prepareInterpolation(int &ok){prepareInterpolation(ok,10000);};
+  void prepareInterpolation(int &ok, int maxit);
+
+  //create interpolated image
+  //returns interpolated image
+  
+  //return position inside the pixel for the given photon
+  void getInterpolatedPosition(Int_t x, Int_t y, Double_t *data, Double_t &int_x, Double_t &int_y);
+  void getInterpolatedBin(Double_t *cluster, Int_t &int_x, Int_t &int_y);
+ 
+
+
+  int addToFlatField(Double_t *cluster, Double_t &etax, Double_t &etay);
+  int addToFlatField(Double_t etax, Double_t etay);
+  int setPlot(int p=-1) {if (p>=0) plot=p; return plot;};
+  int WriteH(){newEta->Write("newEta"); heta->Write("heta");};
+  EtaVEL *setEta(EtaVEL *ev){if (ev) {delete newEta; newEta=ev;} return newEta;};
+  TH2F *setEta(TH2F *ev){if (ev) {delete heta; heta=ev;} return heta;};
+  void iterate();
+  void DrawH();
+  double getChiSq(){return newEta->getChiSq();};
+ 
+
+
+ protected:
+  EtaVEL *newEta;
+  TH2F *heta;
+  int plot;
+
+  //  ClassDefNV(interpolation_EtaVEL,1);
+  // #pragma link C++ class interpolation_EtaVEL-;
+};
+
+#endif

slsDetectorCalibration/interpolations/slsInterpolation.h

@@ -1,12 +1,6 @@
 #ifndef SLS_INTERPOLATION_H
 #define SLS_INTERPOLATION_H
 
-#ifdef MYROOT1
-#include <TObject.h>
-#include <TTree.h>
-#include <TH2F.h>
-#endif
-
 #include <cstdlib> 
 #ifndef MY_TIFF_IO_H
 #include "tiffIO.h"
@@ -35,30 +29,21 @@ class slsInterpolation
 {
 
  public:
- slsInterpolation(int nx=400, int ny=400, int ns=25) :nPixelsX(nx), nPixelsY(ny),  nSubPixels(ns), id(0) {
+ slsInterpolation(int nx=400, int ny=400, int ns=25, int nsy=-1) :nPixelsX(nx), nPixelsY(ny),  nSubPixelsX(ns), nSubPixelsY(nsy),id(0) {
    
-#ifdef MYROOT1
-hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
-#endif
-   
-#ifndef MYROOT1
- hint=new int[ns*nx*ns*ny];
-#endif
+    if (nSubPixelsY<=0) nSubPixelsY=nSubPixelsX;
+    hint=new int[nSubPixelsX*nx*nSubPixelsY*ny];
 
 };
   
  slsInterpolation(slsInterpolation *orig){
    nPixelsX=orig->nPixelsX;
    nPixelsY=orig->nPixelsY;
-   nSubPixels=orig->nSubPixels;
-#ifdef MYROOT1
-   hint=(TH2F*)(orig->hint)->Clone("hint");
-#endif
+   nSubPixelsX=orig->nSubPixelsX;
+   nSubPixelsY=orig->nSubPixelsY;
    
-#ifndef MYROOT1
-   hint=new int[nSubPixels*nPixelsX*nSubPixels*nPixelsY];
-   memcpy(hint, orig->hint,nSubPixels*nPixelsX*nSubPixels*nPixelsY*sizeof(int));
-#endif
+   hint=new int[nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY];
+   memcpy(hint, orig->hint,nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY*sizeof(int));
  
  };
 
@@ -68,23 +53,37 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
    return new slsInterpolation(this);
    }*/
 
-  int getNSubPixels() {return nSubPixels;};
+  int getNSubPixelsX() {return nSubPixelsX;};
+  int getNSubPixelsY() {return nSubPixelsY;};
+  int getNSubPixels() {if (nSubPixelsX==nSubPixelsY) return nSubPixelsX; else return 0;};
+  void getNSubPixels(int &nsx, int &nsy) {nsx=nSubPixelsX; nsy=nsx=nSubPixelsY;}
 
-
-  int setNSubPixels(int ns)   {
-    if (ns>0 && ns!=nSubPixels) {
+  void setNSubPixels(int ns, int nsy=-1)   {
+   
       delete [] hint;
-      nSubPixels=ns;
-      hint=new int[nSubPixels*nPixelsX*nSubPixels*nPixelsY];
-    }
-    return nSubPixels;
+      nSubPixelsX=ns;
+      if (nsy>0)  nSubPixelsY=nsy;
+      else nSubPixelsY=ns;
+      
+      hint=new int[nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY];
+      
+      //return nSubPixels;
   }
 
-  int getImageSize(int &nnx, int &nny, int &ns) {
-    nnx=nSubPixels*nPixelsX;
-    nny=nSubPixels*nPixelsY;
-    ns=nSubPixels;
-    return nSubPixels*nSubPixels*nPixelsX*nPixelsY;
+  
+
+
+  int getImageSize(int &nnx, int &nny, int &nsx, int &nsy) {
+    nnx=nSubPixelsX*nPixelsX;
+    nny=nSubPixelsY*nPixelsY;
+    nsx=nSubPixelsX;
+    nsy=nSubPixelsY;
+    return nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY;
+  };
+  
+
+  int getImageSize() {
+    return nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY;
   };
   
   
@@ -94,34 +93,30 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
 
   //create interpolated image
   //returns interpolated image
-#ifdef MYROOT1
-  virtual TH2F *getInterpolatedImage(){return hint;};
-#endif
-
-#ifndef MYROOT1
   virtual int *getInterpolatedImage(){
-    //  cout << "return interpolated image " << endl;
-    /* for (int i=0; i<nSubPixels*  nSubPixels* nPixelsX*nPixelsY; i++) { */
-    /*   cout << i << " " << hint[i] << endl; */
-    /* } */
+    //cout << "?" <<endl;
     return hint;
   };
-#endif
 
 
 
     
   void *writeInterpolatedImage(const char * imgname) {
-    //cout << "!" <<endl;
     float *gm=NULL;
-    gm=new float[ nSubPixels*  nSubPixels* nPixelsX*nPixelsY];
+    //cout << "!" <<endl;
+    int *dummy=getInterpolatedImage();
+    cout << "got interpolated image " << endl;
+    gm=new float[ nSubPixelsX*  nSubPixelsY* nPixelsX*nPixelsY];
+    cout << "created dummy " << endl;
     if (gm) {
-      for (int ix=0; ix<nPixelsX*nSubPixels; ix++) {
-	for (int iy=0; iy<nPixelsY*nSubPixels; iy++) {
-	  gm[iy*nPixelsX*nSubPixels+ix]=hint[iy*nPixelsX*nSubPixels+ix];
+      for (int ix=0; ix<nPixelsX*nSubPixelsX; ix++) {
+	for (int iy=0; iy<nPixelsY*nSubPixelsY; iy++) {
+	  gm[iy*nPixelsX*nSubPixelsX+ix]=dummy[iy*nPixelsX*nSubPixelsX+ix];
+	  //  cout << "++" << ix << " " << iy << " " << iy*nPixelsX*nSubPixelsX+ix << endl;
 	}
       }
-      WriteToTiff(gm, imgname,nSubPixels* nPixelsX ,nSubPixels* nPixelsY); 
+      WriteToTiff(gm, imgname,nSubPixelsX* nPixelsX ,nSubPixelsY* nPixelsY); 
+      // cout << "wrote to tiff " << endl;
       delete [] gm;
     } else cout << "Could not allocate float image " << endl;
     return NULL;    
@@ -142,16 +137,11 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
   virtual void clearInterpolatedImage() {
 
 
-#ifdef MYROOT1
-    hint->Reset();
-#endif
-#ifndef MYROOT1
-      for (int ix=0; ix<nPixelsX*nSubPixels; ix++) {
-	for (int iy=0; iy<nPixelsY*nSubPixels; iy++) {
-	  hint[iy*nPixelsX*nSubPixels+ix]=0;
+      for (int ix=0; ix<nPixelsX*nSubPixelsX; ix++) {
+	for (int iy=0; iy<nPixelsY*nSubPixelsY; iy++) {
+	  hint[iy*nPixelsX*nSubPixelsX+ix]=0;
 	}
       }
-#endif
 
 
   };
@@ -159,24 +149,18 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
 
 
 
-#ifdef MYROOT1
-  TH2F *addToImage(double int_x, double int_y){hint->Fill(int_x, int_y); return hint;};
-#endif
-
-#ifndef MYROOT1
   virtual int *addToImage(double int_x, double int_y){ 
-    int iy=((double)nSubPixels)*int_y; 
-    int ix=((double)nSubPixels)*int_x; 
-     if (ix>=0 && ix<(nPixelsX*nSubPixels) && iy<(nSubPixels*nPixelsY) && iy>=0 ){
+    int iy=((double)nSubPixelsY)*int_y; 
+    int ix=((double)nSubPixelsX)*int_x; 
+     if (ix>=0 && ix<(nPixelsX*nSubPixelsX) && iy<(nSubPixelsY*nPixelsY) && iy>=0 ){
        // cout << int_x << " " << int_y << " " << "  " << ix << " " << iy << " " << ix+iy*nPixelsX*nSubPixels << " " << hint[ix+iy*nPixelsX*nSubPixels];
-       (*(hint+ix+iy*nPixelsX*nSubPixels))+=1; 
+       (*(hint+ix+iy*nPixelsX*nSubPixelsX))+=1; 
        // cout << " " << hint[ix+iy*nPixelsX*nSubPixels] << endl;
      }// else
       // cout << "bad! "<< int_x << " " << int_y << " " << "  " << ix << " " << iy << " " << ix+iy*nPixelsX*nSubPixels << endl;
        
     return hint;
   };
-#endif
 
 
   virtual int addToFlatField(double *cluster, double &etax, double &etay)=0;
@@ -185,19 +169,11 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
   virtual int  addToFlatField(double totquad,int quad,double *cluster,double &etax, double &etay)=0;
   virtual int addToFlatField(double etax, double etay)=0;
 
-#ifdef MYROOT1
-  virtual TH2D *getFlatField(){return NULL;};
-  virtual TH2D *setFlatField(TH2D *h, int nb=-1, double emin=-1, double emax=-1){return NULL;};
- virtual TH2D *getFlatField(int &nb, double &emin, double &emax){nb=0; emin=0; emax=0; return getFlatField();}; 
-#endif
-  
-#ifndef MYROOT1
   virtual int *getFlatField(){return NULL;};
   virtual int *setFlatField(int *h, int nb=-1, double emin=-1, double emax=-1){return NULL;}; 
   virtual void *writeFlatField(const char * imgname){return NULL;};
   virtual void *readFlatField(const char * imgname, int nb=-1, double emin=1, double emax=0){return NULL;};
  virtual int *getFlatField(int &nb, double &emin, double &emax){nb=0; emin=0; emax=0; return getFlatField();}; 
-#endif
 
  virtual void resetFlatField()=0;
 
@@ -213,12 +189,13 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
     
 
   static int calcQuad(double *cl, double &sum, double &totquad, double sDum[2][2]){
+    //cout << "2";
     
     int corner = UNDEFINED_QUADRANT;
-    double *cluster[3];
-    cluster[0]=cl;
-    cluster[1]=cl+3;
-    cluster[2]=cl+6;
+    /* double *cluster[3]; */
+    /* cluster[0]=cl; */
+    /* cluster[1]=cl+3; */
+    /* cluster[2]=cl+6; */
     
     sum=0;
     double sumBL=0;
@@ -228,11 +205,11 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
     int xoff=0, yoff=0;
     for (int ix=0; ix<3; ix++) {
       for (int iy=0; iy<3; iy++) {
-	sum+=cluster[iy][ix];
-	 if (ix<=1 && iy<=1) sumBL+=cluster[iy][ix];
-	 if (ix<=1 && iy>=1) sumTL+=cluster[iy][ix];
-	 if (ix>=1 && iy<=1) sumBR+=cluster[iy][ix];
-	 if (ix>=1 && iy>=1) sumTR+=cluster[iy][ix];
+	sum+=cl[ix+3*iy];
+	 if (ix<=1 && iy<=1) sumBL+=cl[ix+iy*3];
+	 if (ix<=1 && iy>=1) sumTL+=cl[ix+iy*3];
+	 if (ix>=1 && iy<=1) sumBR+=cl[ix+iy*3];
+	 if (ix>=1 && iy>=1) sumTR+=cl[ix+iy*3];
       }
     }
 
@@ -240,6 +217,8 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
     /* sDum[0][1] = cluster[0][1]; sDum[1][1] = cluster[1][1]; */
     corner = BOTTOM_LEFT;
     totquad=sumBL;
+    xoff=0;
+    yoff=0;
 
     
     if(sumTL  >= totquad){
@@ -274,7 +253,7 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
 
     for (int ix=0; ix<2; ix++) {
       for (int iy=0; iy<2; iy++) {
-	sDum[iy][ix] = cluster[iy+yoff][ix+xoff]; 
+	sDum[iy][ix] = cl[ix+xoff+(iy+yoff)*3]; 
       }
     }
   
@@ -391,17 +370,18 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
 
 
   static int calcEta3(double *cl, double &etax, double &etay, double &sum) {
+    // cout << "3";
     double l=0,r=0,t=0,b=0, val;
     sum=0;
     //  int quad;
     for (int ix=0; ix<3; ix++) {
       for (int iy=0; iy<3; iy++) {
-	val=cl[iy+3*ix];
+	val=cl[ix+3*iy];
 	sum+=val;
-	if (iy==0) l+=val;
-	if (iy==2) r+=val;
-	if (ix==0) b+=val;
-	if (ix==2) t+=val;
+	if (ix==0) l+=val;
+	if (ix==2) r+=val;
+	if (iy==0) b+=val;
+	if (iy==2) t+=val;
       }
     }
     if (sum>0) {
@@ -440,92 +420,92 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
   }
 
 
-  static int calcMyEta(double totquad, int quad, double *cl, double &etax, double &etay) {
-    double l,r,t,b, sum;
-    int yoff;
-    switch (quad) {
-     case BOTTOM_LEFT:
-     case BOTTOM_RIGHT:
-       yoff=0;
-       break;
-     case TOP_LEFT:
-     case TOP_RIGHT:
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-      l=cl[0+yoff*3]+cl[0+yoff*3+3];
-      r=cl[2+yoff*3]+cl[2+yoff*3+3];
-      b=cl[0+yoff*3]+cl[1+yoff*3]*cl[2+yoff*3];
-      t=cl[0+yoff*3+3]+cl[1+yoff*3+3]*cl[0+yoff*3+3];
-      sum=t+b;
-    if (sum>0) {
-      etax=(-l+r)/sum;
-      etay=(+t)/sum;
-    }
+  /* static int calcMyEta(double totquad, int quad, double *cl, double &etax, double &etay) { */
+  /*   double l,r,t,b, sum; */
+  /*   int yoff; */
+  /*   switch (quad) { */
+  /*    case BOTTOM_LEFT: */
+  /*    case BOTTOM_RIGHT: */
+  /*      yoff=0; */
+  /*      break; */
+  /*    case TOP_LEFT: */
+  /*    case TOP_RIGHT: */
+  /*      yoff=1; */
+  /*      break; */
+  /*    default: */
+  /*      ; */
+  /*    }  */
+  /*     l=cl[0+yoff*3]+cl[0+yoff*3+3]; */
+  /*     r=cl[2+yoff*3]+cl[2+yoff*3+3]; */
+  /*     b=cl[0+yoff*3]+cl[1+yoff*3]*cl[2+yoff*3]; */
+  /*     t=cl[0+yoff*3+3]+cl[1+yoff*3+3]*cl[0+yoff*3+3]; */
+  /*     sum=t+b; */
+  /*   if (sum>0) { */
+  /*     etax=(-l+r)/sum; */
+  /*     etay=(+t)/sum; */
+  /*   } */
     
-    return -1;
-  }
+  /*   return -1; */
+  /* } */
 
-  static int calcMyEta(double totquad, int quad, int *cl, double &etax, double &etay) {
-    double l,r,t,b, sum;
-    int yoff;
-    switch (quad) {
-     case BOTTOM_LEFT:
-     case BOTTOM_RIGHT:
-       yoff=0;
-       break;
-     case TOP_LEFT:
-     case TOP_RIGHT:
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-      l=cl[0+yoff*3]+cl[0+yoff*3+3];
-      r=cl[2+yoff*3]+cl[2+yoff*3+3];
-      b=cl[0+yoff*3]+cl[1+yoff*3]*cl[2+yoff*3];
-      t=cl[0+yoff*3+3]+cl[1+yoff*3+3]*cl[0+yoff*3+3];
-      sum=t+b;
-    if (sum>0) {
-      etax=(-l+r)/sum;
-      etay=(+t)/sum;
-    }
+  /* static int calcMyEta(double totquad, int quad, int *cl, double &etax, double &etay) { */
+  /*   double l,r,t,b, sum; */
+  /*   int yoff; */
+  /*   switch (quad) { */
+  /*    case BOTTOM_LEFT: */
+  /*    case BOTTOM_RIGHT: */
+  /*      yoff=0; */
+  /*      break; */
+  /*    case TOP_LEFT: */
+  /*    case TOP_RIGHT: */
+  /*      yoff=1; */
+  /*      break; */
+  /*    default: */
+  /*      ; */
+  /*    }  */
+  /*     l=cl[0+yoff*3]+cl[0+yoff*3+3]; */
+  /*     r=cl[2+yoff*3]+cl[2+yoff*3+3]; */
+  /*     b=cl[0+yoff*3]+cl[1+yoff*3]*cl[2+yoff*3]; */
+  /*     t=cl[0+yoff*3+3]+cl[1+yoff*3+3]*cl[0+yoff*3+3]; */
+  /*     sum=t+b; */
+  /*   if (sum>0) { */
+  /*     etax=(-l+r)/sum; */
+  /*     etay=(+t)/sum; */
+  /*   } */
     
-    return -1;
-  }
+  /*   return -1; */
+  /* } */
 
 
 
-  static int calcEta3X(double *cl, double &etax, double &etay, double &sum) {
-    double l,r,t,b;
-    sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8];
-    if (sum>0) {
-      l=cl[3];
-      r=cl[5];
-      b=cl[1];
-      t=cl[7];
-      etax=(-l+r)/sum;
-      etay=(-b+t)/sum;
-    }
-    return -1;
-  }
+  /* static int calcEta3X(double *cl, double &etax, double &etay, double &sum) { */
+  /*   double l,r,t,b; */
+  /*   sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8]; */
+  /*   if (sum>0) { */
+  /*     l=cl[3]; */
+  /*     r=cl[5]; */
+  /*     b=cl[1]; */
+  /*     t=cl[7]; */
+  /*     etax=(-l+r)/sum; */
+  /*     etay=(-b+t)/sum; */
+  /*   } */
+  /*   return -1; */
+  /* } */
 
 
-  static int calcEta3X(int *cl, double &etax, double &etay, double &sum) {
-    double l,r,t,b;
-    sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8];
-    if (sum>0) {
-      l=cl[3];
-      r=cl[5];
-      b=cl[1];
-      t=cl[7];
-      etax=(-l+r)/sum;
-      etay=(-b+t)/sum;
-    }
-    return -1;
-  }
+  /* static int calcEta3X(int *cl, double &etax, double &etay, double &sum) { */
+  /*   double l,r,t,b; */
+  /*   sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8]; */
+  /*   if (sum>0) { */
+  /*     l=cl[3]; */
+  /*     r=cl[5]; */
+  /*     b=cl[1]; */
+  /*     t=cl[7]; */
+  /*     etax=(-l+r)/sum; */
+  /*     etay=(-b+t)/sum; */
+  /*   } */
+  /*   return -1; */
+  /* } */
 
 
 
@@ -534,15 +514,9 @@ hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);
 
  protected:
   int nPixelsX, nPixelsY;
-  int nSubPixels; 
-#ifdef MYROOT1
-  TH2F *hint;
-#endif
-#ifndef MYROOT1
-  int *hint;
-#endif
+  int nSubPixelsX, nSubPixelsY;
   int id;
-
+  int *hint;
 };
 
 #endif

slsDetectorCalibration/moench03CommonMode.h

@@ -1,44 +1,60 @@
 #ifndef MOENCH03COMMONMODE_H
 #define MOENCH03COMMONMODE_H
 
-#include "commonModeSubtraction.h"
+#include "commonModeSubtractionNew.h"
 
-class moench03CommonMode : public commonModeSubtraction {
+class commonModeSubtractionColumn:  public commonModeSubtraction{
+public:
+ commonModeSubtractionColumn(int nr=200) : commonModeSubtraction(800), rows(nr) {};
+  virtual int getROI(int ix, int iy){return ix+(iy/200)*400;};
+  
+   virtual void addToCommonMode(double val, int ix=0, int iy=0) {
+     if (iy<rows || iy>399-rows) {
+       int iroi=getROI(ix,iy);
+       // cout << iy << " " << ix << " " << iroi ;
+       if (iroi>=0 && iroi<nROI) {
+	 mean[iroi]+=val; 
+	 mean2[iroi]+=val*val; 
+	 nCm[iroi]++;
+	 if (nCm[iroi]>rows) cout << "Too many pixels added " << nCm[iroi] << endl;
+	 /* if (ix==10 && iy<20) */
+	 /*   cout << " ** "<<val << " " << mean[iroi] << " " << nCm[iroi] << " " << getCommonMode(ix, iy) << endl; */
+       }
+     }
+    };
+
+  virtual  commonModeSubtractionColumn *Clone() {
+      return new  commonModeSubtractionColumn(this->rows);
+    }
+
+ private:
+  int rows;
+};
+
+
+class commonModeSubtractionSuperColumn:  public commonModeSubtraction{
+public:
+commonModeSubtractionSuperColumn() : commonModeSubtraction(32) {};
+  virtual int getROI(int ix, int iy){  return ix/25+(iy/200)*16;};
+};
+
+
+class commonModeSubtractionHalf:  public commonModeSubtraction{
+public:
+commonModeSubtractionHalf() : commonModeSubtraction(2) {};
+  virtual int getROI(int ix, int iy){  (void) ix; return iy/200;};
+};
+
+
+class moench03CommonMode : public commonModeSubtractionColumn {
   /** @short class to calculate the common mode noise for moench02 i.e. on 4 supercolumns separately */
  public:
   /** constructor -  initalizes a commonModeSubtraction with 4 different regions of interest 
       \param nn number of samples for the moving average
   */
-  moench03CommonMode(int nn=1000) : commonModeSubtraction(nn,32){} ;
+  moench03CommonMode(int nr=20) : commonModeSubtractionColumn(nr){} ;
     
 
-    /** add value to common mode as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each;
-	\param val value to add to the common mode
-	\param ix pixel coordinate in the x direction
-	\param iy pixel coordinate in the y direction
-    */
-    virtual void addToCommonMode(double val, int ix=0, int iy=0) {
-      // (void) iy;  
-      int isc=ix/25+(iy/200)*16;
-      if (isc>=0 && isc<nROI) {
-	cmPed[isc]+=val; 
-	nCm[isc]++;
-      }
-    };
-     /**returns common mode value as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each;
-	\param ix pixel coordinate in the x direction
-	\param iy pixel coordinate in the y direction
-	\returns common mode value
-    */
-    virtual double getCommonMode(int ix=0, int iy=0) {
-      (void) iy;
-      int isc=ix/25+(iy/200)*16;
-      if (isc>=0 && isc<nROI) { 
-	if (nCm[isc]>0) return cmPed[isc]/nCm[isc]-cmStat[isc].Mean(); 
-      }
-      return 0;
-    };
-
 };
 
 

slsDetectorCalibration/moench03GhostSummation.h

@@ -0,0 +1,64 @@
+#ifndef MOENCH03GHOSTSUMMATION_H
+#define MOENCH03GHOSTSUMMATION_H
+
+#include "ghostSummation.h"
+
+class moench03GhostSummation : public ghostSummation<uint16_t> {
+
+  /** @short virtual calss to handle ghosting*/ 
+
+ public:
+  
+  /** constructor
+      \param xt crosstalk
+  */
+ moench03GhostSummation(slsDetectorData<uint16_t> *d, double xt=0.0004) : ghostSummation<uint16_t>(d, xt)  {}
+  
+  virtual void calcGhost(char *data){
+    for (int iy=0; iy<200; iy++){
+      for (int ix=0; ix<25; ix++){
+	calcGhost(data,ix,iy);
+      }
+    }
+  };
+
+ moench03GhostSummation(moench03GhostSummation *orig) : ghostSummation(orig) {
+  }
+
+  virtual  moench03GhostSummation *Clone() {
+    return new  moench03GhostSummation(this);
+  }
+
+  virtual double calcGhost(char *data, int x, int y=0){
+    int ix=x%25;
+    int iy=y;
+    if (y>=200) iy=399-y;
+    if (iy<0 || ix<0) return 0;
+    double val=0;
+    val=0;
+    for (int isc=0; isc<16; isc++) {
+      val+=det->getChannel(data,ix+25*isc,iy);
+      //  cout << val << " " ;
+      val+=det->getChannel(data,ix+25*isc,399-iy);
+      //  cout << val << " " ;
+    }
+    ghost[iy*nx+ix]=xtalk*val;
+    // if (ix==15 && iy==15) cout << ":" << ghost[iy*nx+ix] << " " << val << endl; 
+    return ghost[iy*nx+ix];
+  };
+
+
+  virtual double getGhost(int ix, int iy) {
+    if (iy >=0 && iy<200) return ghost[iy*nx+(ix%25)]; 
+    if (iy<400) return ghost[(399-iy)*nx+(ix%25)];
+    return 0;
+  };
+
+
+};
+
+
+
+
+
+#endif

slsDetectorCalibration/moenchCommonMode.h

@@ -1,7 +1,7 @@
 #ifndef MOENCHCOMMONMODE_H
 #define MOENCHCOMMONMODE_H
 
-#include "commonModeSubtraction.h"
+#include "commonModeSubtractionNew.h"
 
 class moenchCommonMode : public commonModeSubtraction {
   /** @short class to calculate the common mode noise for moench02 i.e. on 4 supercolumns separately */
@@ -9,35 +9,36 @@ class moenchCommonMode : public commonModeSubtraction {
   /** constructor -  initalizes a commonModeSubtraction with 4 different regions of interest 
       \param nn number of samples for the moving average
   */
-  moenchCommonMode(int nn=1000) : commonModeSubtraction(nn,4){} ;
+
+  moenchCommonMode(int nn=0) : commonModeSubtraction(0){} ;
     
 
-    /** add value to common mode as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each;
-	\param val value to add to the common mode
-	\param ix pixel coordinate in the x direction
-	\param iy pixel coordinate in the y direction
-    */
-    virtual void addToCommonMode(double val, int ix=0, int iy=0) {
-      (void) iy;  
-      int isc=ix/40;
-      if (isc>=0 && isc<nROI) {
-	cmPed[isc]+=val; 
-	nCm[isc]++;
-      }
-    };
-     /**returns common mode value as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each;
-	\param ix pixel coordinate in the x direction
-	\param iy pixel coordinate in the y direction
-	\returns common mode value
-    */
-    virtual double getCommonMode(int ix=0, int iy=0) {
-      (void) iy;
-      int isc=ix/40;
-      if (isc>=0 && isc<nROI) { 
-	if (nCm[isc]>0) return cmPed[isc]/nCm[isc]-cmStat[isc].Mean(); 
-      }
-      return 0;
-    };
+    /* /\** add value to common mode as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each; */
+    /* 	\param val value to add to the common mode */
+    /* 	\param ix pixel coordinate in the x direction */
+    /* 	\param iy pixel coordinate in the y direction */
+    /* *\/ */
+    /* virtual void addToCommonMode(double val, int ix=0, int iy=0) { */
+    /*   (void) iy;   */
+    /*   int isc=ix/40; */
+    /*   if (isc>=0 && isc<nROI) { */
+    /* 	cmPed[isc]+=val;  */
+    /* 	nCm[isc]++; */
+    /*   } */
+    /* }; */
+    /*  /\**returns common mode value as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each; */
+    /* 	\param ix pixel coordinate in the x direction */
+    /* 	\param iy pixel coordinate in the y direction */
+    /* 	\returns common mode value */
+    /* *\/ */
+    /* virtual double getCommonMode(int ix=0, int iy=0) { */
+    /*   (void) iy; */
+    /*   int isc=ix/40; */
+    /*   if (isc>=0 && isc<nROI) {  */
+    /* 	if (nCm[isc]>0) return cmPed[isc]/nCm[isc]-cmStat[isc].Mean();  */
+    /*   } */
+    /*   return 0; */
+    /* }; */
 
 };
 

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder

@@ -1,39 +1,47 @@
+#module add CBFlib/0.9.5
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures  -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/
+
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff -O3  -std=c++11
 
-CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ 
-#LIBHDF5=
-LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt -L$(CBFLIBDIR)/lib/   -ltiff 
-#-L$(ZMQLIB) -lzmq
-#-L../../bin 
 MAIN=moench03ClusterFinder.cpp
-#-lhdf5
-#DESTDIR?=../bin
+
 
 all: moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog
 
 
 
-moenchClusterFinder:  $(MAIN)  $(INCS) clean
-			 g++ -o moenchClusterFinder  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DOLDDATA #-DNEWRECEIVER 
+moenchClusterFinder:  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinder  moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DNEWRECEIVER 
 
-moenchMakeEta:  moench03MakeEta.cpp  $(INCS) clean
-			 g++ -o moenchMakeEta moench03MakeEta.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL
+
+moenchClusterFinderHighZ:  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinderHighZ  moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DNEWRECEIVER -DHIGHZ 
+
+
+
+
+moenchMakeEta:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchMakeEta moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF
 
 moenchInterpolation:  moench03Interpolation.cpp  $(INCS) clean
-			 g++ -o moenchInterpolation moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL 
+			 g++ -o moenchInterpolation moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  
 
 moenchNoInterpolation:  moench03NoInterpolation.cpp  $(INCS) clean
-			 g++ -o moenchNoInterpolation moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL
+			 g++ -o moenchNoInterpolation moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
 
 moenchPhotonCounter: moenchPhotonCounter.cpp   $(INCS) clean
-			 g++ -o moenchPhotonCounter  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DNEWRECEIVER
+			 g++ -o moenchPhotonCounter  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER
 
 moenchAnalog: moenchPhotonCounter.cpp  $(INCS) clean
-			 g++ -o moenchAnalog  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DNEWRECEIVER -DANALOG
+			 g++ -o moenchAnalog  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG
+
+moenchPhotonCounterHighZ: moenchPhotonCounter.cpp   $(INCS) clean
+			 g++ -o moenchPhotonCounterHighZ  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DHIGHZ
+
+moenchAnalogHighZ: moenchPhotonCounter.cpp  $(INCS) clean
+			 g++ -o moenchAnalogHighZ  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG -DHIGHZ
 
 clean: 	
-	rm -f  moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter
+	rm -f  moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog
 
 

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder_rect_rh7

@@ -0,0 +1,40 @@
+
+#CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
+#ZMQLIB=../slsReceiverSoftware/include
+#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include 
+#-I$(CBFLIBDIR)/include/ 
+#LIBHDF5=
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt   -ltiff 
+#-L$(ZMQLIB) -lzmq -L$(CBFLIBDIR)/lib/ 
+#-L../../bin 
+MAIN=moench03ClusterFinder.cpp
+#-lhdf5
+#DESTDIR?=../bin
+
+all: moenchClusterFinderRect moenchMakeEtaRect moenchInterpolationRect moenchNoInterpolationRect moenchPhotonCounterRect moenchAnalogRect
+
+
+
+moenchClusterFinderRect:  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinderRect  moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) -DSAVE_ALL  -DNEWRECEIVER -DRECT
+
+moenchMakeEtaRect:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchMakeEtaRect moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF -DRECT
+
+moenchInterpolationRect:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchInterpolationRect moench03Interpolation.cpp    $(LDFLAG) $(INCDIR)   -DRECT
+
+moenchNoInterpolationRect:  moench03NoInterpolation.cpp  $(INCS) clean
+			 g++ -o moenchNoInterpolationRect moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR)  -DRECT
+
+moenchPhotonCounterRect: moenchPhotonCounter.cpp   $(INCS) clean
+			 g++ -o moenchPhotonCounterRect  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $  -DNEWRECEIVER -DRECT
+
+moenchAnalogRect: moenchPhotonCounter.cpp  $(INCS) clean
+			 g++ -o moenchAnalogRect  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER -DANALOG -DRECT
+
+clean: 	
+	rm -f  moenchClusterFinderRect moenchMakeEtaRect moenchInterpolationRect moenchNoInterpolationRect moenchPhotonCounterRect moenchAnalogRect
+
+

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder_rh7

@@ -0,0 +1,40 @@
+
+#CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
+#ZMQLIB=../slsReceiverSoftware/include
+#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include 
+#-I$(CBFLIBDIR)/include/ 
+#LIBHDF5=
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt   -ltiff 
+#-L$(ZMQLIB) -lzmq -L$(CBFLIBDIR)/lib/ 
+#-L../../bin 
+MAIN=moench03ClusterFinder.cpp
+#-lhdf5
+#DESTDIR?=../bin
+
+all: moenchClusterFinder moenchMakeEta  moenchInterpolation  moenchNoInterpolation  moenchPhotonCounter  moenchAnalog 
+
+
+
+moenchClusterFinder :  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinder   moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) -DSAVE_ALL  -DNEWRECEIVER -DWRITE_QUAD
+
+moenchMakeEta :  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchMakeEta  moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF -DWRITE_QUAD
+
+moenchInterpolation :  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchInterpolation  moench03Interpolation.cpp    $(LDFLAG) $(INCDIR)  -DWRITE_QUAD
+
+moenchNoInterpolation :  moench03NoInterpolation.cpp  $(INCS) clean
+			 g++ -o moenchNoInterpolation  moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR)  -DWRITE_QUAD
+
+moenchPhotonCounter : moenchPhotonCounter.cpp   $(INCS) clean
+			 g++ -o moenchPhotonCounter   moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $  -DNEWRECEIVER -DWRITE_QUAD
+
+moenchAnalog : moenchPhotonCounter.cpp  $(INCS) clean
+			 g++ -o moenchAnalog   moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER -DANALOG -DWRITE_QUAD
+
+clean: 	
+	rm -f  moenchClusterFinder  moenchMakeEta  moenchInterpolation  moenchNoInterpolation  moenchPhotonCounter  moenchAnalog 
+
+

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder_sl6

@@ -1,10 +1,15 @@
-#module add CBFlib/0.9.5
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include 
-
-LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff -O3
 
+CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
+#ZMQLIB=../slsReceiverSoftware/include
+#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ 
+#LIBHDF5=
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt -L$(CBFLIBDIR)/lib/   -ltiff 
+#-L$(ZMQLIB) -lzmq
+#-L../../bin 
 MAIN=moench03ClusterFinder.cpp
-
+#-lhdf5
+#DESTDIR?=../bin
 
 all: moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog
 

slsDetectorCalibration/moenchExecutables/Makefile.moench

@@ -1,20 +0,0 @@
-
-CBFLIBDIR=/afs/psi.ch/project/sls_det_software/CBFlib-0.9.5
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-IslsDetectorCalibration -I../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ -I. -IetaVEL
-LIBHDF5=-L$(CBFLIBDIR)/lib/ -lhdf5
-LDFLAG= -L/usr/lib64/ -lpthread
-#-L../../bin 
-MAIN=moench03OnTheFlyAnalysis.C
-
-#DESTDIR?=../bin
-
-all: moench03OnTheFlyAnalysis
-
-
-
-moench03OnTheFlyAnalysis:  $(MAIN)  $(INCS) clean
-			   g++ -o moench03OnTheFlyAnalysis  $(MAIN)  -lm -ltiff -lstdc++ $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL
-
-clean:
-	rm -f moench03OnTheFlyAnalysis

slsDetectorCalibration/moenchExecutables/Makefile.moench_eta

@@ -1,23 +0,0 @@
-
-CBFLIBDIR= /home/l_msdetect/CBFlib-0.9.5
-ZMQLIB=../slsReceiverSoftware/include
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-IslsDetectorCalibration -I../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ -I. 
-#-IetaVEL
-LIBHDF5=
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++ -L. -lzmq -pthread -lrt -L$(CBFLIBDIR)/lib/ -lhdf5 -ltiff -L$(ZMQLIB)
-#-L../../bin 
-MAIN=moench03ClusterFinder.cpp
-
-#DESTDIR?=../bin
-
-all: moench03ClusterFinder
-
-
-
-moench03ClusterFinder:  $(MAIN)  $(INCS) clean
-			 g++ -o moenchClusterFinder  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) tiffIO.cpp -DSAVE_ALL
-
-clean: 	
-	rm -f  moench03ClusterFinder
-

slsDetectorCalibration/moenchExecutables/Makefile.moench_zmq_rh7

@@ -1,17 +0,0 @@
-
-ZMQLIB=../../slsReceiverSoftware/include
-INCDIR= -I$(ZMQLIB)  -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff -L$(ZMQLIB)  -O3 
-#-L../../bin -lhdf5  -L.
-
-#DESTDIR?=../bin
-
-all:  moenchZmqProcess
-
-moenchZmqProcess:  moenchZmqProcess.cpp   clean
-		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP
-
-clean: 	
-	rm -f  moenchZmqProcess  
-
-

slsDetectorCalibration/moenchExecutables/Makefile.moench_zmq_sl6

@@ -1,12 +1,8 @@
-
-CBFLIBDIR=/afs/psi.ch/project/sls_det_software/CBFlib-0.9.5
+CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
 ZMQLIB=../../slsReceiverSoftware/include
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/
-LIBHDF5=
-#-I../interpolations/etaVEL 
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++ -L. -lzmq -pthread -lrt -lhdf5 -ltiff -L$(ZMQLIB) -L$(CBFLIBDIR)/lib/ -O3 
-#-L../../bin 
+INCDIR= -I$(ZMQLIB)  -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/  -I$(CBFLIBDIR)/include/
+LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt  -lrt -L$(CBFLIBDIR)/lib/ -ltiff -L$(ZMQLIB)  -O3 
+#-L../../bin -lhdf5  -L.
 
 #DESTDIR?=../bin
 
@@ -14,7 +10,7 @@ aaa: moenchZmqProcess
 
 all: moenchZmqClusterFinder moenchZmqInterpolating moenchZmqAnalog
 
-moenchZmqProcess:  moenchZmqProcess.cpp  $(INCS) clean
+moenchZmqProcess:  moenchZmqProcess.cpp   clean
 		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ
 
 moenchZmqInterpolating:  $(MAIN)  $(INCS) clean

slsDetectorCalibration/moenchExecutables/Makefile.phoenix

@@ -1,24 +0,0 @@
-
-CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I..  -I. -I../interpolations -I../interpolations/etaVEL -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/  ../tiffIO.cpp -I../dataStructures
-#LIBHDF5=
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt -L$(CBFLIBDIR)/lib/   -ltiff -lhdf5
-#-L$(ZMQLIB) -lzmq
-#-L../../bin 
-MAIN=moench03ClusterFinderPhoenix.cpp
-#
-#DESTDIR?=../bin
-
-all: moenchClusterFinderPhoenix 
-#moenchMakeEtaPhoenix moenchInterpolationPhoenix
-
-
-
-moenchClusterFinderPhoenix:  $(MAIN)  $(INCS) clean
-			 g++ -o moenchClusterFinderPhoenix  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)
-
-clean: 	
-	rm -f  moenchClusterFinderPhoenix 
-

slsDetectorCalibration/moenchExecutables/Makefile.reoder_image

@@ -1,22 +0,0 @@
-
-CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ 
-LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt -L$(CBFLIBDIR)/lib/   -ltiff 
-MAIN=moench03ReorderImage.cpp
-
-all: moenchReorderImage moenchClusterFinder
-
-
-
-moenchReorderImage:  $(MAIN)  $(INCS) clean
-			 g++ -o moenchReorderImage  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DNEWRECEIVER 
-
-moenchClusterFinder: moench03ClusterFinder.cpp
-			 g++ -o moenchClusterFinder  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DNEWRECEIVER 
-
-
-clean: 	
-	rm -f  moenchReorderImage moenchClusterFinder
-
-

slsDetectorCalibration/moenchExecutables/Makefile.tiff_to_th2f

@@ -1,27 +0,0 @@
-#INCSROOT= receiverGui.h 
-#INCS= $(INCSROOT) moench03_receiver.h 
-#LINKDEF=receiverGuiLinkDef.h 
-
-#CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include -I$(ROOTSYS)/include
-#-I$(CBFLIBDIR)/include/ 
-#LIBHDF5=
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt  -ltiff 
-#-L$(CBFLIBDIR)/lib/ -lhdf5 
-
-MAIN=tiff_to_th2f.cpp 
-
-
-all: tiff_to_th2f 
-
-
-
-tiff_to_th2f: $(MAIN)  $(INCS) 
-	      	
-	   g++ -o tiff_to_th2f  $(MAIN) `root-config --cflags --glibs` -lMinuit -lm -ltiff -lstdc++ $(LDFLAG) $(INCDIR)  ../tiffIO.cpp 
-#$(LIBRARYCBF)  $(LIBHDF5)
-clean: 	
-	rm -f tiff_to_th2f
-

slsDetectorCalibration/moenchExecutables/Makefile.zmq

@@ -0,0 +1,24 @@
+
+INCDIR=   -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/ -I../../slsDetectorSoftware/commonFiles/ -I../../slsReceiverSoftware/include/
+LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3 -g -std=c++11 -Wall
+#-L../../bin -lhdf5  -L.
+
+#DESTDIR?=../bin
+
+all:  moenchZmqProcess moenchZmqProcessHighZ moenchZmqProcessRect
+
+moenchZmqProcess:  moenchZmqProcess.cpp   clean
+		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP
+moenchZmqProcessRect:  moenchZmqProcess.cpp   clean
+		      g++ -o moenchZmqProcessRect  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DRECT
+		      
+moenchZmqProcessHighZ:  moenchZmqProcess.cpp   clean
+		      g++ -o moenchZmqProcessHighZ  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DHIGHZ
+
+
+
+clean: 	
+	rm -f  moenchZmqProcess  moenchZmqProcessHighZ
+
+
+

slsDetectorCalibration/moenchExecutables/moench03ClusterFinder.cpp

@@ -22,6 +22,10 @@
 #include "moench03Ctb10GbT1Data.h"
 #endif 
 
+#ifdef REORDERED
+#include "moench03T1ReorderedData.h"
+#endif
+
 // #include "interpolatingDetector.h"
 //#include "etaInterpolationPosXY.h"
 // #include "linearInterpolation.h"
@@ -55,7 +59,7 @@ int main(int argc, char *argv[]) {
   int csize=3;
   int nx=400, ny=400;
   int save=1;
-  int nsigma=5;
+  int nsigma=1;
   int nped=1000;
   int ndark=100;
   int ok;
@@ -83,6 +87,14 @@ int main(int argc, char *argv[]) {
   cout << "OLD RECEIVER DATA!"<<endl;
 #endif
 
+#ifdef REORDERED
+  moench03T1ReorderedData *decoder=new  moench03T1ReorderedData();
+  cout << "REORDERED DATA!"<<endl;
+#endif
+
+
+  decoder->getDetectorSize(nx,ny);
+  cout << "nx " << nx << " ny " << ny << endl;
 
   //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
   singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
@@ -183,13 +195,21 @@ int main(int argc, char *argv[]) {
 	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
 	//	cout << ff << " " << np << endl;
   	//         //push
-	mt->pushData(buff);
-  // 	//         //pop
-	mt->nextThread();
-  // // 		//	cout << " " << (void*)buff;
-	mt->popFree(buff);
-	ifr++;
-	if (ifr%10000==0) cout << ifr << " " << ff << endl;
+	// for (int ix=0; ix<400; ix++)
+	//   for (int iy=0; iy<400; iy++) {
+	//     if (decoder->getChannel(buff, ix, iy)<3000 || decoder->getChannel(buff, ix, iy)>8000) {
+	//       cout <<  ifr << " " << ff << " " << ix << " " << iy << " " << decoder->getChannel(buff, ix, iy) << endl ;
+	//     }
+	//   }
+	if (np==40) {
+	  mt->pushData(buff);
+	  // 	//         //pop
+	  mt->nextThread();
+	  // // 		//	cout << " " << (void*)buff;
+	  mt->popFree(buff);
+	  ifr++;
+	  if (ifr%10000==0) cout << ifr << " " << ff << endl;
+	}
 	ff=-1;
       }
         cout << "--" << endl;

slsDetectorCalibration/moenchExecutables/moench03ClusterFinderPhoenix.cpp

@@ -1,201 +0,0 @@
-//#include "ansi.h"
-#include <iostream>
-
-//#include "moench03T1ZmqData.h"
-//#include "moench03T1ReceiverData.h"
-
-#include "moench03Ctb10GbT1Data.h"
-
-// #include "interpolatingDetector.h"
-//#include "etaInterpolationPosXY.h"
-// #include "linearInterpolation.h"
-// #include "noInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-#include "singlePhotonDetector.h"
-//#include "interpolatingDetector.h"
-
-#include <stdio.h>
-#include <map>
-#include <fstream>
-#include <sys/stat.h>
-
-#include <ctime>
-using namespace std;
-
-
-int main(int argc, char *argv[]) {
-
-
-  if (argc<6) {
-    cout << "Usage is " << argv[0] << "indir outdir fname runmin runmax " << endl;
-    return 0;
-  }
-  int ii=0;
-  int p=10000;
-  int fifosize=1000;
-  int nthreads=5;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
-  int csize=3;
-  int nx=400, ny=400;
-  int save=1;
-  int nsigma=5;
-  int nped=1000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
-  moench03Ctb10GbT1Data *decoder=new  moench03Ctb10GbT1Data();
-  cout << "decoder" << endl;
-  //moench03T1ReceiverData *decoder=new  moench03T1ReceiverData();
-  //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
-  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 100);
-  //  char tit[10000];
-  cout << "filter" << endl;
-
-
-
-
-  // filter->readPedestals("/scratch/ped_100.tiff");
-  // interp->readFlatField("/scratch/eta_100.tiff",etamin,etamax);
-  // cout << "filter "<< endl;
-  
-
-  int size = 327680;////atoi(argv[3]);
-  
-  int* image;
-	//int* image =new int[327680/sizeof(int)];
-  filter->newDataSet();
-
-  cout << "dataset" << endl;
-
-  int ff, np;
-  int dsize=decoder->getDataSize();
-  cout << " data size is " << dsize << endl;
-  
-
-  char data[dsize];
-
-  ifstream filebin;
-  char *indir=argv[1];
-  cout << "input directory is " << indir << endl;
-  char *outdir=argv[2];
-  cout << "output directory is " << outdir << endl;
-  char *fformat=argv[3];
-  cout << "fileformat is " << fformat << endl;
-  int runmin=atoi(argv[4]);
-  cout << "runmin : " << runmin << endl;
-  int runmax=atoi(argv[5]);
-  cout << "runmax : " << runmax << endl;
-  
-  char fname[10000];
-  char outfname[10000];
-  char imgfname[10000];
-  char pedfname[10000];
-  char fn[10000];
-  
-  std::time_t end_time;
-
-  FILE *of=NULL;
-  
-  
-  cout << "time " << endl;
-  std::time(&end_time);
-  cout << std::ctime(&end_time) <<   endl;
-  filter->setFrameMode(eFrame);
-	//  mt->setFrameMode(ePedestal);
- 
-
-  // for (int ix=0; ix<400; ix++)
-  //   for (int iy=0; iy<400; iy++)
-  //     cout << ix << " " << iy << " " << filter->getPedestal(ix,iy) << " " << filter->getPedestalRMS(ix,iy) << endl;
-
-
-  char* buff;
-  cout << "aa " << endl;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-  cout << "mt " << endl;
-  
-  // mt->setFrameMode(eFrame); //need to find a way to switch between flat and frames!
-  // mt->prepareInterpolation(ok);
-  mt->setFrameMode(eFrame);
-  mt->StartThreads();
-  mt->popFree(buff);
-  
-
-  
-  int ifr=0;
-  // //loop on files
-  // mt->setFrameMode(eFrame);
-  //mt->setFrameMode(eFlat);
-  
-  
-  
-  
-  
-  for (int irun=runmin; irun<runmax; irun++) {
-    sprintf(fn,fformat,irun);
-    sprintf(fname,"%s/%s.raw",indir,fn);
-    sprintf(outfname,"%s/%s.clust",outdir,fn);
-    sprintf(imgfname,"%s/%s.tiff",outdir,fn);
-    std::time(&end_time);
-    cout << std::ctime(&end_time) <<    endl;
-    cout <<  fname << " " << outfname << " " << imgfname <<  endl;
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    if (filebin.is_open()){
-      of=fopen(outfname,"w");
-      if (of) {
-  	mt->setFilePointer(of);
-	//	cout << "file pointer set " << endl;
-      } else {
-  	cout << "Could not open "<< outfname << " for writing " << endl;
-  	mt->setFilePointer(NULL);
-  	return 1;
-      }
-      //     //while read frame 
-      ff=-1;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	//cout << "*"<<ifr++<<"*"<<ff<< endl;
-	//cout << ff << " " << np << endl;
-  	//         //push
-  		mt->pushData(buff);
-  // 	//         //pop
-  		mt->nextThread();
-  // // 		//	cout << " " << (void*)buff;
-   		mt->popFree(buff);
-	
-		ff=-1;
-		ii++;
-		if (ii%10000==0) {
-
-		  cout << ii << endl;
-
-		  while (mt->isBusy()) {;}//wait until all data are processed from the queues
-		  mt->writeImage("/scratch/tmp.tiff");
-      		}
-      }
-      //  cout << "--" << endl;
-      filebin.close();	 
-      //      //close file 
-      //     //join threads
-      while (mt->isBusy()) {;}//wait until all data are processed from the queues
-      if (of)
-  	fclose(of);
-      
-      mt->writeImage(imgfname);
-      mt->clearImage();
-   
-      std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
-
-    } else 
-     cout << "Could not open "<< fname << " for reading " << endl;
-      
-    
-  }
-    
-
-  return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moench03CodedApertureColor.cpp

@@ -0,0 +1,245 @@
+
+#include "ansi.h"
+#include <iostream>
+#include <math.h>
+
+//#include "moench03T1ZmqData.h"
+//#define DOUBLE_SPH
+//#define MANYFILES
+
+#ifdef DOUBLE_SPH
+#include "single_photon_hit_double.h"
+#endif
+
+#ifndef DOUBLE_SPH
+#include "single_photon_hit.h"
+#endif
+
+//#include "etaInterpolationPosXY.h"
+#include "slsInterpolation.h"
+#include "Stat.h"
+//#include "etaInterpolationRandomBins.h"
+using namespace std;
+#define NC 400
+#define NR 400
+#define MAX_EBINS 100
+
+int main(int argc, char *argv[]) {
+
+  if (argc<7) {
+    cout << "Wrong usage! Should be: "<< argv[0] << " infile  outfile runmin runmax cmin cmax nb" << endl;
+    return 1;
+  }
+  
+  int iarg=4;
+  char infname[10000];
+  char fname[10000];
+  char outfname[10000];
+
+  float img[NC*NR];
+  iarg=3;
+
+  int runmin=atoi(argv[iarg++]);
+  int runmax=atoi(argv[iarg++]); 
+  cout << "Run min: " << runmin << endl;
+  cout << "Run max: " << runmax << endl;
+  
+
+  float cmin=atof(argv[iarg++]);
+  float cmax=atof(argv[iarg++]);
+  cout << "Energy min: " << cmin << endl;
+  cout << "Energy max: " << cmax << endl;
+  int n_ebins=1;
+  if (argc>iarg)
+    n_ebins=atoi(argv[iarg++]);
+  //int etabins=500;
+  int etabins=1000;//nsubpix*2*100;
+  double etamin=-1, etamax=2;
+  //double etamin=-0.1, etamax=1.1;
+  double eta3min=-2, eta3max=2;
+  int quad;
+  double sum, totquad;
+  double sDum[2][2];
+  double etax, etay, int_x, int_y;
+  double eta3x, eta3y, int3_x, int3_y, noint_x, noint_y;
+  int ok;
+  int f0=-1;
+  int ix, iy, isx, isy;
+  int nframes=0, lastframe=-1;
+  double d_x, d_y, res=5, xx, yy;
+  int nph=0, badph=0, totph=0;
+    FILE *f=NULL;
+
+    single_photon_hit cl(3,3);
+
+
+    int iebin=0;
+    double eb_size=(cmax-cmin)/n_ebins;
+
+    Stat *statsX=new Stat[(n_ebins+1)*NC*NR];
+    Stat *statsY=new Stat[(n_ebins+1)*NC*NR];
+    
+
+    int irun;
+    for (irun=runmin; irun<runmax; irun++) {
+      sprintf(infname,argv[1],irun);
+ 
+      f=fopen(infname,"r");
+      if (f) {
+	cout << infname << endl;
+	nframes=0;
+	f0=-1;
+
+	while (cl.read(f)) {
+	  totph++;
+	  if (lastframe!=cl.iframe) {
+	    lastframe=cl.iframe;
+	    // cout << cl.iframe << endl;
+	    // f0=cl.iframe;
+	    if (nframes==0) f0=lastframe;
+	    nframes++;
+	  }
+	  slsInterpolation::calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
+	  if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
+	    nph++;
+	    iebin=(sum-cmin)/eb_size;
+	    if (iebin>=0 && iebin<n_ebins && cl.x>=0 && cl.x<NC && cl.y>=0 && cl.y<NR) {
+	      statsX[iebin+cl.x*(n_ebins+1)+cl.y*(NC*(n_ebins+1))].Push(etax);
+	      statsY[iebin+cl.x*(n_ebins+1)+cl.y*(NC*(n_ebins+1))].Push(etay);  
+	      statsX[n_ebins+cl.x*(n_ebins+1)+cl.y*(NC*(n_ebins+1))].Push(etax);
+	      statsY[n_ebins+cl.x*(n_ebins+1)+cl.y*(NC*(n_ebins+1))].Push(etay);  
+	    }
+	    
+	    if (nph%1000000==0) cout << nph << endl;
+	   
+	  }
+	} 
+	fclose(f);
+      } else
+	  cout << "could not open file " << infname << endl;
+    
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_abs_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].NumDataValues();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etameanX_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].Mean();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etarmsX_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].StandardDeviation();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etameanY_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsY[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].Mean();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etarmsY_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsY[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].StandardDeviation();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+
+
+      
+
+    }
+
+
+
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_abs_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].NumDataValues();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etameanX_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].Mean();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etarmsX_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].StandardDeviation();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etameanY_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsY[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].Mean();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etarmsY_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsY[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].StandardDeviation();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+
+
+    cout << "Filled " << nph << " (/"<< totph <<") " << endl; 
+    return 0;
+}
+

slsDetectorCalibration/moenchExecutables/moench03Interpolation.cpp

@@ -14,20 +14,34 @@
 #include "single_photon_hit.h"
 #endif
 
+#ifdef RECT
+#include "etaInterpolationGlobal.h"
+#endif
+#ifndef RECT
 #include "etaInterpolationPosXY.h"
+#endif
 #include "noInterpolation.h"
-//#include "etaInterpolationAdaptiveBins.h"
+//#include "etaInterpolationCleverAdaptiveBins.h"
 //#include "etaInterpolationRandomBins.h"
 using namespace std;
+#ifndef RECT
 #define NC 400
 #define NR 400
+#endif
+#ifdef RECT
+#define NC 200
+#define NR 800
+#endif
 
 
+#define MAX_ITERATIONS (nSubPixels*100)
+
 #define XTALK
 
 int main(int argc, char *argv[]) {
 
 #ifndef FF
+  cout << "INTERPOLATING" << endl;
   if (argc<9) {
     cout << "Wrong usage! Should be: "<< argv[0] << " infile  etafile outfile runmin runmax ns cmin cmax" << endl;
     return 1;
@@ -35,6 +49,7 @@ int main(int argc, char *argv[]) {
 #endif
   
 #ifdef FF
+  cout << "CALC ETA" << endl;
   if (argc<7) {
     cout << "Wrong usage! Should be: "<< argv[0] << " infile  etafile runmin runmax cmin cmax" << endl;
     return 1;
@@ -65,10 +80,12 @@ int main(int argc, char *argv[]) {
   float cmax=atof(argv[iarg++]);
   cout << "Energy min: " << cmin << endl;
   cout << "Energy max: " << cmax << endl;
-  
-  int etabins=1000;//nsubpix*2*100;
-  double etamin=-1, etamax=2;
-  double eta3min=-2, eta3max=2;
+  //int etabins=500;
+  int etabins=999;//nsubpix*2*100;
+  int etabinsY=etabins;//nsubpix*2*100;
+  double etamin=0, etamax=1;
+  //double etamin=-0.1, etamax=1.1;
+  double eta3min=-1, eta3max=1;
   int quad;
   double sum, totquad;
   double sDum[2][2];
@@ -82,6 +99,9 @@ int main(int argc, char *argv[]) {
   int nph=0, badph=0, totph=0;
     FILE *f=NULL;
 
+
+    char fff[10000];
+
 #ifdef DOUBLE_SPH
     single_photon_hit_double cl(3,3);
 #endif
@@ -89,28 +109,66 @@ int main(int argc, char *argv[]) {
 #ifndef DOUBLE_SPH
     single_photon_hit cl(3,3);
 #endif
+    int nSubPixels=nsubpix;
+    int nSubPixelsY=nsubpix;
+#ifdef RECT
+    nSubPixels=5; //might make more sense using 2?
+    // etabins=5;
+#endif
+#ifndef NOINTERPOLATION
+    etaInterpolationBase *interp;
+#ifndef RECT
+    interp=new eta2InterpolationPosXY(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, etamin, etamax);
+   //eta2InterpolationCleverAdaptiveBins *interp=new eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin, etamax);  
+#endif
+#ifdef RECT
+    interp=new eta2InterpolationGlobal(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, eta3min, eta3max);
+ 
+    //  eta3InterpolationPosXY *interpOdd=new eta3InterpolationPosXY(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, eta3min, eta3max);
+   //eta2InterpolationCleverAdaptiveBins *interp=new eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin, etamax);  
+ 
+#endif
+
+#endif
+#ifdef NOINTERPOLATION
+    noInterpolation *interp=new noInterpolation(NC, NR, nsubpix, nSubPixelsY);  
+#endif
 
 
-    eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(NC, NR, nsubpix, etabins, etamin, etamax);
-   
+ 
 #ifndef FF
+#ifndef NOINTERPOLATION
     cout << "read ff " << argv[2] << endl;
     sprintf(fname,"%s",argv[2]);
-    interp->readFlatField(fname);
-    interp->prepareInterpolation(ok);
-
+    //#ifndef RECT
+    interp->readFlatField(fname, etamin, etamax);
+    interp->prepareInterpolation(ok);//, MAX_ITERATIONS);
+    interp->debugSaveAll(0);
+    //#endif
+// #ifdef RECT
+//     sprintf(fff,"%s.even",fname);
+//     interpEven->readFlatField(fff, etamin, etamax);
+//     interpEven->prepareInterpolation(ok);, MAX_ITERATIONS);
+//     interpEven->debugSaveAll(1);
+//     sprintf(fff,"%s.odd",fname);
+//     interpOdd->readFlatField(fff, etamin, etamax);
+//     interpOdd->prepareInterpolation(ok);, MAX_ITERATIONS);
+//     interpOdd->debugSaveAll(2);
+// #endif
+#endif
+    // return 0;
 #endif
 #ifdef FF
     cout << "Will write eta file " << argv[2] << endl;
 #endif
 
     int *img;
-    float *totimg=new float[NC*NR*nsubpix*nsubpix];
+    float *totimg=new float[NC*NR*nSubPixels*nSubPixelsY];
     for (ix=0; ix<NC; ix++) {
       for (iy=0; iy<NR; iy++) {
-	for (isx=0; isx<nsubpix; isx++) {
-	  for (isy=0; isy<nsubpix; isy++) {
-	    totimg[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)]=0;
+	for (isx=0; isx<nSubPixels; isx++) {
+	  for (isy=0; isy<nSubPixelsY; isy++) {
+	    totimg[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)]=0;
 	      }
 	}
       }
@@ -119,6 +177,9 @@ int main(int argc, char *argv[]) {
 #ifdef FF
       sprintf(outfname,argv[2]);
 #endif     
+ 
+
+      int tl=0, tr=0, bl=0, br=0;
 
     int irun;
     for (irun=runmin; irun<runmax; irun++) {
@@ -137,65 +198,151 @@ int main(int argc, char *argv[]) {
 	  totph++;
 	  if (lastframe!=cl.iframe) {
 	    lastframe=cl.iframe;
-	    // cout << cl.iframe << endl;
-	    // f0=cl.iframe;
 	    if (nframes==0) f0=lastframe;
 	    nframes++;
 	  }
-	  quad=interp->calcQuad(cl.get_cluster(), sum, totquad, sDum);
-	  if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
-	    nph++;
-	    //  if (sum>200 && sum<580) {
-	    //  interp->getInterpolatedPosition(cl.x,cl.y, totquad,quad,cl.get_cluster(),int_x, int_y);
-#ifdef SOLEIL
-	    if (cl.x>210 && cl.x<240 && cl.y>210 && cl.y<240) {
+#ifdef RECT
+	  //	  quad=interp->calcEta3(cl.get_cluster(), etax, etay, sum);  
+	  quad=interp->calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
+	  // if (cl.y%2==0)
+	  //   if (etay>0)
+	  //     interp=interpEven;
+	  //   else
+	  //     interp=interpOdd;
+	  // else
+	  //   if (etay>0)
+	  //     interp=interpOdd;
+	  //   else
+	  //     interp=interpEven;
+	  
 #endif
-#ifndef FF
-	    interp->getInterpolatedPosition(cl.x,cl.y, cl.get_cluster(),int_x, int_y);
+
+#ifndef RECT
+	  quad=interp->calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
+
+	
+#endif
+	  switch(quad) {
+	  case TOP_LEFT:
+	    tl++;
+	    break;
+	  case TOP_RIGHT:
+	    tr++;
+	    break;
+	  case BOTTOM_LEFT:
+	    bl++;
+	    break;
+	  case BOTTOM_RIGHT:
+	    br++;
+	    break;
+	  }
+	  //  if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
+	  if (sum>cmin &&  sum<cmax ) {
+	      nph++;
+#ifndef FF 
+	      interp->getInterpolatedPosition(cl.x,cl.y, etax, etay, quad,int_x, int_y);
 	    interp->addToImage(int_x, int_y);
 #endif
 #ifdef FF
-	    interp->addToFlatField(cl.get_cluster(), etax, etay);
-#endif
-#ifdef SOLEIL
-	    }
+	      interp->addToFlatField(etax, etay);
 #endif
 	    
 	    if (nph%1000000==0) cout << nph << endl;
-	    if (nph%100000000==0) { 
+	    if (nph%10000000==0) { 
 #ifndef FF
-		interp->writeInterpolatedImage(outfname);
+	      
+	      cout << "writing interpolated iamge" << endl;
+	      //#ifndef RECT
+	interp->writeInterpolatedImage(outfname); 
+	//#endif
+// #ifdef RECT
+// 	sprintf(fff,"%s.even",outfname);
+// 	interpEven->writeInterpolatedImage(fff); 
+// 	sprintf(fff,"%s.odd",outfname);
+// 	interpOdd->writeInterpolatedImage(fff); 
+// #endif
+		cout << "done" << endl;
 #endif
 #ifdef FF 
-		interp->writeFlatField(outfname);
+		cout << "writing eta" << endl;
+		//#ifndef RECT
+	interp->writeFlatField(outfname);
+	//#endif
+// #ifdef RECT
+// 	sprintf(fff,"%s.even",outfname);
+// 	interpEven->writeFlatField(fff);
+// 	sprintf(fff,"%s.odd",outfname);
+// 	interpOdd->writeFlatField(fff);
+// #endif
+		cout << "done" << endl;
 #endif
 		
-	    }
+		}
+	  }
 	    
-	  } 
+	} 
 	  
 	  
-	}
 	fclose(f);
 #ifdef FF
+	//#ifndef RECT
 	interp->writeFlatField(outfname);
+// #endif
+// #ifdef RECT
+// 	sprintf(fff,"%s.even",outfname);
+// 	interpEven->writeFlatField(outfname);
+// 	sprintf(fff,"%s.odd",outfname);
+// 	interpOdd->writeFlatField(outfname);
+// #endif
 #endif
 	
 #ifndef FF
+	  //#ifndef RECT
 	interp->writeInterpolatedImage(outfname); 
+// #endif
+// #ifdef RECT
+// 	sprintf(fff,"%s.even",outfname);
+// 	interpEven->writeInterpolatedImage(fff); 
+// 	sprintf(fff,"%s.odd",outfname);
+// 	interpOdd->writeInterpolatedImage(fff); 
+// #endif
 
+//#ifdef RECT
+	  //interp=interpEven;
+	//#endif
 	img=interp->getInterpolatedImage();
 	for (ix=0; ix<NC; ix++) {
 	  for (iy=0; iy<NR; iy++) {
-	    for (isx=0; isx<nsubpix; isx++) {
-	      for (isy=0; isy<nsubpix; isy++) {
-		totimg[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)]+=img[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)];
+	    for (isx=0; isx<nSubPixels; isx++) {
+	      for (isy=0; isy<nSubPixelsY; isy++) {
+		totimg[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)]+=img[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)];
+		//	cout << "--" << ix << " " << iy <<" " << ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels) << endl;
 		}
 	    }
 	  }
 	}
-	cout << "Read " << nframes << " frames (first frame: " << f0 << " last frame: " << lastframe << " delta:" << lastframe-f0 << ")"<<endl;
+	cout << "Read " << nframes << " frames (first frame: " << f0 << " last frame: " << lastframe << " delta:" << lastframe-f0 << ") nph="<< nph <<endl;
+	cout << "Top-Left=" << tl << " " << " Top-Right=" << tr << " Bottom-Left="<< bl << " Bottom-Right=" << br << endl;
 	interp->clearInterpolatedImage();
+// #ifdef RECT
+
+// 	interp=interpOdd;
+// 	img=interp->getInterpolatedImage();
+// 	for (ix=0; ix<NC; ix++) {
+// 	  for (iy=0; iy<NR; iy++) {
+// 	    for (isx=0; isx<nSubPixels; isx++) {
+// 	      for (isy=0; isy<nSubPixelsY; isy++) {
+// 		totimg[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)]+=img[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)];
+// 		//	cout << "--" << ix << " " << iy <<" " << ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels) << endl;
+// 		}
+// 	    }
+// 	  }
+// 	}
+
+// 	interp->clearInterpolatedImage();
+// #endif
+
+
 #endif
 	
       } else
@@ -203,11 +350,19 @@ int main(int argc, char *argv[]) {
     }
 #ifndef FF
     sprintf(outfname,argv[3],11111);
-    WriteToTiff(totimg, outfname,NC*nsubpix,NR*nsubpix);
+    WriteToTiff(totimg, outfname,NC*nSubPixels,NR*nSubPixelsY);
 #endif 
     
 #ifdef FF
+    //#ifndef RECT
 	interp->writeFlatField(outfname);
+	//#endif
+// #ifdef RECT
+// 	sprintf(fff,"%s.even",outfname);
+// 	interpEven->writeFlatField(fff);
+// 	sprintf(fff,"%s.odd",outfname);
+// 	interpOdd->writeFlatField(fff);
+// #endif
 #endif
 
     cout << "Filled " << nph << " (/"<< totph <<") " << endl; 

slsDetectorCalibration/moenchExecutables/moench03MakeEta.cpp

@@ -1,114 +0,0 @@
-
-#include "ansi.h"
-#include <iostream>
-
-#include "moench03T1ZmqData.h"
-#include "single_photon_hit.h"
-
- #include "etaInterpolationPosXY.h"
-
-using namespace std;
-#define NC 400
-#define NR 400
-
-#define XTALK
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [outfname]
- *
- */
-  int nsubpix=10;
-  int etabins=nsubpix*100;
-  double etamin=-1, etamax=2;
-  double eta3min=-2, eta3max=2;
-  int quad;
-  double sum, totquad;
-  double sDum[2][2];
-  char fname[10000];
-  double etax, etay;
-  int runmin, runmax;
-    single_photon_hit cl(3,3);
-int iph=0;
- 
-  if (argc<7) {
-    cout << "Wrong usage! Should be: "<< argv[0] << " infile " << " outfile runmin runmax cmin cmax" << endl;
-    return 1;
-  }
-
-  eta2InterpolationPosXY *interp2=new eta2InterpolationPosXY(NR, NC, nsubpix, etabins, etamin, etamax);
-  cout << "###########"<< endl;
-  eta3InterpolationPosXY *interp3=new eta3InterpolationPosXY(NR, NC, nsubpix, etabins, eta3min, eta3max);
-  // cout << eta3min << " " << eta3max << endl;
-  runmin=atoi(argv[3]);
-  runmax=atoi(argv[4]);
-  double cmin=atof(argv[5]); //200
-  double cmax=atof(argv[6]); //3000
-  
-#ifdef XTALK
-  int old_val[3][3];
-  int new_val[3][3];
-  double xcorr=0.04;
-  
-  // int ix=0;
-#endif
-
-    FILE *f;
-    for (int i=runmin; i<runmax; i++) {
-	sprintf(fname,argv[1],i);
-      f=fopen(fname,"r");
-      if (f) {
-	cout << "*" << endl;
-	while (cl.read(f)) {
-#ifdef XTALK
-	  if ((cl.x+1)%25!=0) {
-	  for (int ix=-1; ix<2; ix++) {
-	    for (int iy=-1; iy<2; iy++) {
-	      old_val[iy+1][ix+1]=cl.get_data(ix,iy);
-	      if (ix>=0) {
-		new_val[iy+1][ix+1]=old_val[iy+1][ix+1]-old_val[iy+1][ix]*xcorr;
-		cl.set_data(new_val[iy+1][ix+1],ix,iy);
-	      }
-	    }
-	  }
-	  }
-#endif
-	   quad=interp2->calcQuad(cl.get_cluster(), sum, totquad, sDum);
-	   
-	    if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && totquad<cmax && quad<cmax) {
-	      /* Cross talk corrections !!! */
-	      //	for (int ix=0; ix<2; ix++) {
-	  
-
-	      interp2->addToFlatField(cl.get_cluster(),etax, etay);
-	      // if (etax>0.49 && etax<0.51 && etay>0.49 && etay<0.51 ) {
-	      // 	cout << cl.y << " " << cl.x << " " << quad << " "<< totquad << " " <<sum << endl;
-
-	      // } 
-	      interp3->addToFlatField(cl.get_cluster(),etax, etay);
-	      iph++;
-	      if (iph%1000000==0) cout << iph << endl;
-	      if (iph%100000000==0) { 
-		sprintf(fname,"%s_eta2.tiff",argv[2]);
-		interp2->writeFlatField(fname);
-		sprintf(fname,"%s_eta3.tiff",argv[2]);
-		interp3->writeFlatField(fname);
-	      }
-	      // if (iph>1E8) break;
-	    }
-	    //	  }
-	  
-	}
-	fclose(f);
-	
-      }
-      else cout << "could not open file " << fname << endl;
-    }
-    
-    sprintf(fname,"%s_eta2.tiff",argv[2]);
-	interp2->writeFlatField(fname);
-    sprintf(fname,"%s_eta3.tiff",argv[2]);
-	interp3->writeFlatField(fname);
-    return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moench03NoInterpolation.cpp

@@ -2,7 +2,6 @@
 #include "ansi.h"
 #include <iostream>
 
-#include "moench03T1ZmqData.h"
 #include "single_photon_hit.h"
 
 #include "noInterpolation.h"

slsDetectorCalibration/moenchExecutables/moench03ReorderImage.cpp

@@ -1,163 +0,0 @@
-//#include "ansi.h"
-#include <iostream>
-
-
-
-//#include "moench03T1ZmqData.h"
-
-#include "moench03T1ReceiverDataNew.h"
-
-// #include "interpolatingDetector.h"
-//#include "etaInterpolationPosXY.h"
-// #include "linearInterpolation.h"
-// #include "noInterpolation.h"
-//#include "interpolatingDetector.h"
-
-#include <stdio.h>
-#include <map>
-#include <fstream>
-#include <sys/stat.h>
-
-#include <cstdlib>
-
-#include <ctime>
-using namespace std;
-
-#define NX 400 //number of x pixels
-#define NY 400 //number of y pixels
-
-int main(int argc, char *argv[]) {
-
-
-  if (argc<6) {
-    cout << "Usage is " << argv[0] << "indir outdir fname runmin runmax " << endl;
-    return 1;
-  }
-  int p=10000;
-  int fifosize=1000;
-  int nthreads=8;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
-  int csize=3;
-  int nx=400, ny=400;
-  int save=1;
-  int nsigma=5;
-  int nped=1000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
-
-
-
-
-  moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
-
-
-  uint16_t data[NY*NX];
-
-
-  int size = 327680;////atoi(argv[3]);
-  
-  int* image;
-
-  int ff, np;
-  int dsize=decoder->getDataSize();
-  
-
-  //char data[dsize];
-
-  ifstream filebin;
-  char *indir=argv[1];
-  char *outdir=argv[2];
-  char *fformat=argv[3];
-  int runmin=atoi(argv[4]);
-  int runmax=atoi(argv[5]);
-  
-  char fname[10000];
-  char outfname[10000];
-  char imgfname[10000];
-  char pedfname[10000];
-  //  strcpy(pedfname,argv[6]);
-  char fn[10000];
-  
-  std::time_t end_time;
-
-  FILE *of=NULL;
-  cout << "input directory is " << indir << endl;
-  cout << "output directory is " << outdir << endl;
-  cout << "fileformat is " << fformat << endl;
-  
-
-  std::time(&end_time);
-  cout << std::ctime(&end_time) <<   endl;
- 
-
-
-
-
-
-
-  char* buff;
-
- 
-
-
-  int ifr=0;
- 
-
-  for (int irun=runmin; irun<runmax; irun++) {
-    sprintf(fn,fformat,irun);
-    sprintf(fname,"%s/%s.raw",indir,fn);
-    sprintf(outfname,"%s/%s_image.raw",outdir,fn);
-    std::time(&end_time);
-    cout << std::ctime(&end_time) <<    endl;
-    cout <<  fname << " " << outfname << " " << imgfname <<  endl;
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    if (filebin.is_open()){
-      of=fopen(outfname,"w");
-      if (of) {
-	;
-      } else {
-  	cout << "Could not open "<< outfname << " for writing " << endl;
-  	return 1;
-      }
-      //     //while read frame 
-      ff=-1;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	for (int ix=0; ix<400; ix++)
-	  for (int iy=0; iy<400; iy++)
-	    data[iy*NX+ix]=decoder->getChannel(buff,ix,iy);
-	
-	ifr++;
-
-	fwrite(&ff, 8, 1,of);//write detector frame number
-	fwrite(&ifr, 8, 1,of);//write datset frame number
-	fwrite(data,2,NX*NY,of);//write reordered data
-
-	if (ifr%10000==0) cout << ifr << " " << ff << endl;
-	ff=-1;
-
-      }
-        cout << "--" << endl;
-      filebin.close();	 
-      //      //close file 
-      //     //join threads
-  
-      if (of)
-  	fclose(of);
-      
-      std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
-
-    } else 
-     cout << "Could not open "<< fname << " for reading " << endl;
-      
-    
-  }
-    
-
-  return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchAnalog.cpp

@@ -1,242 +0,0 @@
-//#include "ansi.h"
-#include <iostream>
-
-
-
-//#include "moench03T1ZmqData.h"
-#ifdef NEWRECEIVER
-#include "moench03T1ReceiverDataNew.h"
-#endif
-#ifdef CSAXS_FP
-#include "moench03T1ReceiverData.h"
-#endif 
-#ifdef OLDDATA
-#include "moench03Ctb10GbT1Data.h"
-#endif 
-
-// #include "interpolatingDetector.h"
-//#include "etaInterpolationPosXY.h"
-// #include "linearInterpolation.h"
-// #include "noInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-#include "singlePhotonDetector.h"
-//#include "interpolatingDetector.h"
-
-#include <stdio.h>
-#include <map>
-#include <fstream>
-#include <sys/stat.h>
-
-#include <ctime>
-using namespace std;
-
-
-int main(int argc, char *argv[]) {
-
-
-  if (argc<4) {
-    cout << "Usage is " << argv[0] << "indir outdir fname [pedfile] [threshold]" << endl;
-    return 1;
-  }
-  int p=10000;
-  int fifosize=1000;
-  int nthreads=8;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
-  int csize=3;
-  int nx=400, ny=400;
-  int save=1;
-  int nsigma=5;
-  int nped=1000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
-
-
-
-#ifdef NEWRECEIVER
-  moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
-  cout << "RECEIVER DATA WITH ONE HEADER!"<<endl;
-#endif
-
-#ifdef CSAXS_FP
-  moench03T1ReceiverData *decoder=new  moench03T1ReceiverData();
-  cout << "RECEIVER DATA WITH ALL HEADERS!"<<endl;
-#endif
-
-#ifdef OLDDATA
-  moench03Ctb10GbT1Data *decoder=new  moench03Ctb10GbT1Data();
-  cout << "OLD RECEIVER DATA!"<<endl;
-#endif
-
-#ifndef ANALOG
-  //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
-  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
-  //  char tit[10000];
-  cout << "filter " << endl;
-#endif
-
-#ifdef ANALOG
-  //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
-  analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(decoder, 1, 0, nped);
-  //  char tit[10000];
-  cout << "filter " << endl;
-#endif
-
-
-
-  // filter->readPedestals("/scratch/ped_100.tiff");
-  // interp->readFlatField("/scratch/eta_100.tiff",etamin,etamax);
-  // cout << "filter "<< endl;
-  
-
-  int size = 327680;////atoi(argv[3]);
-  
-  int* image;
-	//int* image =new int[327680/sizeof(int)];
-  filter->newDataSet();
-
-
-  int ff, np;
-  int dsize=decoder->getDataSize();
-  cout << " data size is " << dsize;
-  
-
-  char data[dsize];
-
-  ifstream filebin;
-  char *indir=argv[1];
-  char *outdir=argv[2];
-  char *fformat=argv[3];
-  char *pedfile=NULL;
-  if (argc>=5) {
-    pedfile=argv[4];
-  }
-  double thr=0;
-  if (argc>=6) {
-    thr=atoi(argv[5]);
-  }
-  
-
-  char fname[10000];
-  char imgfname[10000];
-  //  strcpy(pedfname,argv[6]);
-  char fn[10000];
-  
-  std::time_t end_time;
-
-  FILE *of=NULL;
-  cout << "input directory is " << indir << endl;
-  cout << "output directory is " << outdir << endl;
-  cout << "input file is " << fformat << endl;
-  if (pedfile)
-    cout << "pedestal file is " << pedfile << endl;
-  if (thr>0) {
-    cout << "threshold is " << thr << endl;
-    filter->setThreshold(thr);
-  }
-
-  filter->setROI(0,150,0,150);
-
-  std::time(&end_time);
-  cout << std::ctime(&end_time) <<   endl;
- 
-
-
-
-
-
-
-
-  char* buff;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-
- 
-  mt->StartThreads();
-  mt->popFree(buff);
-
-
-  cout << "mt " << endl;
-
-  int ifr=0;
- 
-
-
-
-
-
-
-
-
-
-  for (int irun=0; irun<2; irun++) {
-    if (irun>0) {
-      mt->setFrameMode(eFrame);
-      // sprintf(fn,fformat,irun);
-      sprintf(fname,"%s/%s.raw",indir,fformat);
-    //  sprintf(outfname,"%s/%s.clust",outdir,fn);
-      sprintf(imgfname,"%s/%s.tiff",outdir,fformat);
-    } else {
-      mt->setFrameMode(ePedestal);
-      // sprintf(fn,fformat,irun);
-      sprintf(fname,"%s/%s.raw",indir,pedfile);
-    //  sprintf(outfname,"%s/%s.clust",outdir,fn);
-      // sprintf(imgfname,"%s/%s.tiff",outdir,fn);
-    }
-    cout << fname << endl;
-    std::time(&end_time);
-    cout << std::ctime(&end_time) <<    endl;
-    //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    if (filebin.is_open()){
-      // of=fopen(outfname,"w");
-      // if (of) {
-      // 	mt->setFilePointer(of);
-      // 	//	cout << "file pointer set " << endl;
-      // } else {
-      // 	cout << "Could not open "<< outfname << " for writing " << endl;
-      // 	mt->setFilePointer(NULL);
-      // 	return 1;
-      // }
-      //     //while read frame 
-      ff=-1;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
-	//	cout << ff << " " << np << endl;
-  	//         //push
-	mt->pushData(buff);
-  // 	//         //pop
-	mt->nextThread();
-  // // 		//	cout << " " << (void*)buff;
-	mt->popFree(buff);
-	ifr++;
-	if (ifr%10000==0) cout << ifr << " " << ff << endl;
-	ff=-1;
-      }
-      cout << "--" << endl;
-      filebin.close();	 
-      //      //close file 
-      //     //join threads
-      while (mt->isBusy()) {;}//wait until all data are processed from the queues
-      // if (of)
-      // 	fclose(of);
-      if (irun>0) {
-	cout << "Writing tiff to " << imgfname << endl;
-	mt->writeImage(imgfname);
-	//	mt->clearImage();
-      }
-      std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
-
-    } else 
-     cout << "Could not open "<< fname << " for reading " << endl;
-      
-    
-   }
-    
-
-  return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchPhotonCounter.cpp

@@ -1,7 +1,12 @@
 //#include "ansi.h"
 #include <iostream>
+#define CORR
 
+#define C_GHOST 0.0004
 
+#define CM_ROWS 50
+
+//#define VERSION_V1
 
 //#include "moench03T1ZmqData.h"
 #ifdef NEWRECEIVER
@@ -27,8 +32,11 @@
 //#include "etaInterpolationPosXY.h"
 // #include "linearInterpolation.h"
 // #include "noInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
+#include "multiThreadedCountingDetector.h"
+//#include "multiThreadedAnalogDetector.h"
 #include "singlePhotonDetector.h"
+#include "moench03GhostSummation.h"
+#include "moench03CommonMode.h"
 //#include "interpolatingDetector.h"
 
 #include <stdio.h>
@@ -44,7 +52,7 @@ int main(int argc, char *argv[]) {
 
 
   if (argc<4) {
-    cout << "Usage is " << argv[0] << "indir outdir fname [runmin] [runmax] [pedfile] [threshold] [nframes] [xmin xmax ymin ymax]" << endl;
+    cout << "Usage is " << argv[0] << "indir outdir fname [runmin] [runmax] [pedfile] [threshold] [nframes] [xmin xmax ymin ymax] [gainmap]" << endl;
     cout << "threshold <0 means analog; threshold=0 means cluster finder; threshold>0 means photon counting" << endl;
     cout << "nframes <0 means sum everything; nframes=0 means one file per run; nframes>0 means one file every nframes" << endl;
     return 1;
@@ -52,14 +60,14 @@ int main(int argc, char *argv[]) {
 
   int p=10000;
   int fifosize=1000;
-  int nthreads=8;
+  int nthreads=10;
   int nsubpix=25;
   int etabins=nsubpix*10;
   double etamin=-1, etamax=2;
   int csize=3;
   int save=1;
   int nsigma=5;
-  int nped=1000;
+  int nped=10000;
   int ndark=100;
   int ok;
   int iprog=0;
@@ -88,21 +96,24 @@ int main(int argc, char *argv[]) {
 
   decoder->getDetectorSize(nx,ny);
 
-  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
+  int ncol_cm=CM_ROWS;
+  double xt_ghost=C_GHOST;
+  moench03CommonMode *cm=NULL;
+  moench03GhostSummation *gs;
+  double *gainmap=NULL;
+  float *gm;
+
+
 
   int size = 327680;////atoi(argv[3]);
   
   int* image;
 	//int* image =new int[327680/sizeof(int)];
-  filter->newDataSet();
-
 
   int ff, np;
-  int dsize=decoder->getDataSize();
   //cout << " data size is " << dsize;
   
 
-  char data[dsize];
 
   ifstream filebin;
   char *indir=argv[1];
@@ -129,7 +140,7 @@ int main(int argc, char *argv[]) {
   double thr1=1;
 
   if (argc>=8) {
-    thr=atoi(argv[7]);
+    thr=atof(argv[7]);
   }
   
 
@@ -147,6 +158,12 @@ int main(int argc, char *argv[]) {
   }
 
   
+  char *gainfname=NULL;
+  if (argc>13) {
+    gainfname=argv[13];
+    cout << "Gain map file name is: " << gainfname << endl;
+  }
+
   
 
 
@@ -166,25 +183,74 @@ int main(int argc, char *argv[]) {
   cout << "runmax is " << runmax << endl;
   if (pedfile)
     cout << "pedestal file is " << pedfile << endl;
+ if (thr>0) 
+    cout << "threshold is " << thr << endl;
+ 
+ uint32 nnx, nny;
+ double *gmap;
+
+  // if (gainfname) {
+  //   gm=ReadFromTiff(gainfname, nny, nnx);
+  //   if (gm && nnx==nx && nny==ny) {
+  //     gmap=new double[nx*ny];
+  //     for (int i=0; i<nx*ny; i++) {
+  // 	gmap[i]=gm[i];
+  //     }
+  //     delete gm;
+  //   } else
+  //     cout << "Could not open gain map " << gainfname << endl;
+  // }
+
+#ifdef CORR
+ cout << "Applying common mode  " << ncol_cm << endl;
+  cm=new moench03CommonMode(ncol_cm);
+  
+
+  cout << "Applying ghost corrections " << xt_ghost << endl;
+  gs=new moench03GhostSummation(decoder, xt_ghost);
+#endif
+
+  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, cm, nped, 200, -1, -1, gainmap, gs);
+
+  if (gainfname) {
+
+    if (filter->readGainMap(gainfname))
+      cout << "using gain map " << gainfname << endl;
+    else
+      cout << "Could not open gain map " << gainfname << endl;
+  } else
+    thr=0.15*thr;
+  filter->newDataSet();
+  int dsize=decoder->getDataSize();
+
+
+  char data[dsize];
+
+
+
+
+
   //#ifndef ANALOG
   if (thr>0) {
     cout << "threshold is " << thr << endl;
+    //#ifndef ANALOG
     filter->setThreshold(thr);
+    //#endif
+      cf=0;
+
   } else
     cf=1;
   //#endif
 
 
   filter->setROI(xmin,xmax,ymin,ymax);
-#ifdef SOLEIL
-  filter->setROI(150,210,170,230);
-  nframes=-1;
-#endif
   std::time(&end_time);
   cout << std::ctime(&end_time) <<   endl;
 
   char* buff;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
+
+  // multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
+ multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
 #ifndef ANALOG
     mt->setDetectorMode(ePhotonCounting);
     cout << "Counting!" << endl;
@@ -197,8 +263,7 @@ int main(int argc, char *argv[]) {
       mt->setDetectorMode(eAnalog);
       cout << "Analog!" << endl;
       cf=0;
-// #ifdef ANALOG
-//       thr1=thr;
+      //thr1=thr;
 #endif  
       //  }
   
@@ -209,51 +274,78 @@ int main(int argc, char *argv[]) {
   //  cout << "mt " << endl;
 
   int ifr=0;
- 
 
+  double ped[nx*ny], *ped1;
 
 
   if (pedfile) {
-    cout << "PEDESTAL " ;
-    sprintf(fname,"%s.raw",pedfile);
-    cout << fname << endl ;
-    sprintf(imgfname,"%s/pedestals.tiff",outdir,fformat);
-    std::time(&end_time);
-    cout << "aaa" << std::ctime(&end_time) <<   endl;
 
+    cout << "PEDESTAL " << endl;
+    sprintf(imgfname,"%s/pedestals.tiff",outdir);
 
-    mt->setFrameMode(ePedestal);
-      // sprintf(fn,fformat,irun);
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    if (filebin.is_open()){
-      ff=-1;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	mt->pushData(buff);
-	mt->nextThread();
-	mt->popFree(buff);
-	ifr++;
-	if (ifr%10000==0) 
-	  cout << ifr << " " << ff << " " << np << endl;
-	ff=-1;
-      }
-      filebin.close();	 
-      while (mt->isBusy()) {;}
-      mt->writePedestal(imgfname);
+    if (string(pedfile).find(".tif")==std::string::npos){
+      sprintf(fname,"%s.raw",pedfile);
+      cout << fname << endl ;
       std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
+      cout << "aaa" << std::ctime(&end_time) <<   endl;
       
+      
+      mt->setFrameMode(ePedestal);
+      // sprintf(fn,fformat,irun);
+      filebin.open((const char *)(fname), ios::in | ios::binary);
+      //      //open file
+      if (filebin.is_open()){
+	ff=-1;
+	while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	  if (np==40) {
+	    mt->pushData(buff);
+	    mt->nextThread();
+	    mt->popFree(buff);
+	    ifr++;
+	    if (ifr%100==0) 
+	      cout << ifr << " " << ff << " " << np << endl;
+	  } else
+	    cout << ifr << " " << ff << " " << np << endl;
+	  ff=-1;
+	}
+	filebin.close();	 
+	while (mt->isBusy()) {;}
+	
       } else 
-	cout << "Could not open "<< fname << " for reading " << endl;
+	cout << "Could not open pedestal file "<< fname << " for reading " << endl;
+    } else {
+      float *pp=ReadFromTiff(pedfile, nny, nnx);
+      if (pp && nnx==nx && nny==ny) {
+	for (int i=0; i<nx*ny; i++) {
+	  ped[i]=pp[i];
+	}
+	delete [] pp;
+	mt->setPedestal(ped);
+	// ped1=mt->getPedestal();
+	
+	// for (int i=0; i<nx*ny; i++) {
+
+	//   cout << ped[i]<<"/"<<ped1[i] << " " ;
+	// }
+	cout << "Pedestal set from tiff file " << pedfile << endl;
+      } else {
+	cout << "Could not open pedestal tiff file "<< pedfile << " for reading " << endl;
+      }
+    }
+    mt->writePedestal(imgfname);
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<   endl;
   }
   
 
+
   ifr=0;
   int ifile=0;
   
+  mt->setFrameMode(eFrame);
+
   for (int irun=runmin; irun<=runmax; irun++) {
     cout << "DATA " ;
-    mt->setFrameMode(eFrame);
     // sprintf(fn,fformat,irun);
     sprintf(ffname,"%s/%s.raw",indir,fformat);
     sprintf(fname,ffname,irun);
@@ -270,8 +362,7 @@ int main(int argc, char *argv[]) {
     //      //open file
     ifile=0;
     if (filebin.is_open()){
-      if (thr<=0) {
-	if (cf) {
+      if (thr<=0 && cf!=0) { //cluster finder
 	  if (of==NULL) {
 	    of=fopen(cfname,"w");
 	    if (of) {
@@ -283,35 +374,40 @@ int main(int argc, char *argv[]) {
 	      return 1;
 	    }
 	  }
-	}
       }
       //     //while read frame 
       ff=-1;
       ifr=0;
       while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	if (np==40) {
 	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
 	//	cout << ff << " " << np << endl;
   	//         //push
-	mt->pushData(buff);
-  // 	//         //pop
-	mt->nextThread();
-  // // 		//	cout << " " << (void*)buff;
-	mt->popFree(buff);
-	ifr++;
-	if (ifr%1000==0) cout << ifr << " " << ff << endl;
-	if (nframes>0) {
-	  if (ifr%nframes==0) {
-	    //The name has an additional "_fXXXXX" at the end, where "XXXXX" is the initial frame number of the image (0,1000,2000...)
-	    
-	    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
-	    sprintf(imgfname,ffname,irun);
-	    //cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
-	    mt->writeImage(imgfname, thr1);
-	    mt->clearImage();
-	    ifile++;
-	  }
-	}
+	  mt->pushData(buff);
+	  // 	//         //pop
+	  mt->nextThread();
+	  // // 		//	cout << " " << (void*)buff;
+	  mt->popFree(buff);
 
+
+
+
+	  ifr++;
+	  if (ifr%100==0) cout << ifr << " " << ff << endl;
+	  if (nframes>0) {
+	    if (ifr%nframes==0) {
+	      //The name has an additional "_fXXXXX" at the end, where "XXXXX" is the initial frame number of the image (0,1000,2000...)
+	      
+	      sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
+	      sprintf(imgfname,ffname,irun);
+	      //cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+	      mt->writeImage(imgfname, thr1);
+	      mt->clearImage();
+	      ifile++;
+	    }
+	  }
+	} else
+	  cout << ifr << " " << ff << " " << np << endl;
 	ff=-1;
       }
       cout << "--" << endl;
@@ -323,9 +419,10 @@ int main(int argc, char *argv[]) {
 	if (nframes>0) {
 	    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
 	    sprintf(imgfname,ffname,irun);
+	} else {
+	  sprintf(ffname,"%s/%s.tiff",outdir,fformat);
+	  sprintf(imgfname,ffname,irun);
 	}
-	sprintf(ffname,"%s/%s.tiff",outdir,fformat);
-	sprintf(imgfname,ffname,irun);
 	cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
 	mt->writeImage(imgfname, thr1);
 	mt->clearImage();
@@ -340,6 +437,13 @@ int main(int argc, char *argv[]) {
     } else 
       cout << "Could not open "<< fname << " for reading " << endl;
   }
+  if (nframes<0){
+    sprintf(ffname,"%s/%s.tiff",outdir,fformat);
+    strcpy(imgfname,ffname);
+    cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
+    mt->writeImage(imgfname, thr1);
+  }
+    
 
 
   return 0;

slsDetectorCalibration/moenchExecutables/moenchZmqAnalog.cpp

@@ -1,394 +0,0 @@
-//#define ROOTSPECTRUM
-
-#include "multiThreadedAnalogDetector.h"
-
-#include "sls_receiver_defs.h"
-#include "ZmqSocket.h"
-#include "moench03T1ZmqDataNew.h"
-
-#ifdef ROOTSPECTRUM
-#include <TPaveText.h> 
-#include <TLegend.h> 
-#include <TF1.h> 
-#include <TGraphErrors.h> 
-#include <TH2F.h> 
-#include <TASImage.h> 
-#include <TImage.h> 
-#include <TFile.h> 
-#endif
-
-#include <vector> 
-#include <string> 
-#include <sstream> 
-#include <iomanip> 
-#include <fstream> 
-#include "tiffIO.h"
-
-#include<iostream>
-
-//#include "analogDetector.h"
-#include "singlePhotonDetector.h"
-#include "ansi.h"
-#include <iostream>
-using namespace std;
-
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
-
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [send_socket ip] [send port number]
- *
- */
-  int fifosize=1000;
-  int nthreads=20;
-  char* buff;
-  char tit[10000];
-	// help
-	if (argc < 3 ) {
-		cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number]\n");
-		return EXIT_FAILURE;
-	}
-
-	// receive parameters
-	bool send = false;
-	  char* socketip=argv[1];
-	uint32_t portnum = atoi(argv[2]);
-	int size = 32*2*5000;//atoi(argv[3]);
-
-	// send parameters if any
-	char* socketip2 = 0;
-	uint32_t portnum2 = 0;
-	if (argc > 3) {
-		send = true;
-		socketip2 = argv[3];
-		portnum2 = atoi(argv[4]);
-	}
-	cout << "\nrx socket ip : " << socketip <<
-			"\nrx port num  : " <<  portnum ;
-	if (send) {
-		cout << "\nsd socket ip : " << socketip2 <<
-				"\nsd port num  : " <<  portnum2;
-	}
-	cout << endl;
-
-	//slsDetectorData *det=new moench03T1ZmqDataNew(); 
-	 moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
-	 analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det,1,NULL,1000);
-	 //singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, 0, 1000, 10);
-	 //filter->setROI(250, 400, 30, 150);
-	 float threshold=1;
-	if (argc > 5) {
-	  threshold=atof(argv[5]);
-	 filter->setThreshold(threshold);
-	  cout << "Threshold set to " << threshold << endl;
-	}
-
-	int nnx, nny, nns;
-	int imsize=filter->getImageSize(nnx,nny,nns);
-
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-
-
-
-  // mt->prepareInterpolation(ok);
-  mt->StartThreads();
-  mt->popFree(buff);
-
-
-
-	  cout << "det " << endl;
-	int16_t dout[400*400];
-	double ddark[400*400];
-	  cout << "dout " << endl;
-
-	// receive socket
-	  ZmqSocket* zmqsocket = new ZmqSocket(socketip,portnum); 
-#ifdef ROOTSPECTRUM
-	  TH2F *h2=NULL;
-	  TH2F *hmap=NULL;
-	  TFile *froot=NULL;
-
-	  h2=new TH2F("hs","hs",500,-500,500,400*400,-0.5,400*400-0.5);
-	  hmap=new TH2F("hmap","hmap",400,-0.5,400-0.5,400,-0.5,400-0.5);
-#endif
-	  cout << "zmq1 " << endl;
-	  
-	if (zmqsocket->IsError()) {
-		cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-		delete zmqsocket;
-		return EXIT_FAILURE;
-	}
-	zmqsocket->Connect();
-	printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress());
-
-	// send socket
-	ZmqSocket* zmqsocket2 = 0;
-	  cout << "zmq2 " << endl;
-	if (send) {
-		zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-		if (zmqsocket2->IsError()) {
-			bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-			delete zmqsocket2;
-			delete zmqsocket;
-			return EXIT_FAILURE;
-		}
-		zmqsocket2->Connect();
-		printf("Zmq Server started at %s\n", zmqsocket2->GetZmqServerAddress());
-		//	zmqsocket2->Disconnect();
-	}
-
-
-	// header variables
-	uint64_t acqIndex = -1;
-	uint64_t frameIndex = -1;
-	uint32_t subframeIndex = -1;
-	uint64_t fileindex = -1;
-	string filename = "";
-	//char* image = new char[size];
-	//int* image = new int[(size/sizeof(int))]();
-
-	int *nph;//[400*400];
-	int iframe=0;
-	char rootfname[10000];
-		    
-	char fname[10000];
-	char ff[10000];
-	int fi;
-	int length;
-	char newped=-1, ped=-1, dat=-1, isdark=-1;
-	
-	double *peds;
-	int *im;
-	int fnumber;
-	float *gm=new float[400*400];
-	// infinite loop
-	while(1) {
-	  
-
-	  //	  cout << "+++++++++++++++++++++++++++++++LOOP" << endl;
-		// get header, (if dummy, fail is on parse error or end of acquisition)
-	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)){
-	    //	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)) {
-			cprintf(RED, "Got Dummy\n");
-			while (mt->isBusy()) {;}//wait until all data are processed from the queues
-			if (dat==1) {
-			  
-			  sprintf(tit,"%s_%lld.tiff",filename.c_str(),fi);
-			  cout << tit << endl;
-			  im=mt->getImage(nnx,nny,nns);
-			  if (isdark) cout << "getting dark "<< endl;
-			  else cout << "subtracting dark"<< endl;
-			  if (gm) {
-			    for (int ii=0; ii<400*400; ii++) {
-			      //      if (image[ix]>0) cout << ix << " " << image[ix]<< endl;
-			      if (isdark) {
-				ddark[ii]=(double)im[ii]/((double)iframe);
-				if (ddark[ii]>0) cout << "*" ;
-				gm[ii]=im[ii];
-				if (send) dout[ii]=im[ii];
-			      } else {
-				gm[ii]=im[ii];//-ddark[ii]*iframe;
-				if (gm[ii]<0) gm[ii]=0;
-				if (send) dout[ii]=gm[ii];
-			      }
-			      //cout << endl;
-			      
-			    }
-			    cout << endl;
-			    //cout << "image " << nnx << " " << nny << endl;
-			    WriteToTiff(gm,tit ,nnx, nny); 
-			    // delete [] gm;
-			  } else cout << "Could not allocate float image " << endl;
-     
-
-
-			} else {
-
-			  sprintf(tit,"%s_%lld.tiff",filename.c_str(),fi);
-			  cout << tit << endl;
-			  mt->writePedestal(tit);
-
-			}
-
-			// mt->writeImage(tit);
-			//  cout << "wrote" << endl;
-	
-	 
-	 
-
-
-
-
-	 
-			  if (send) {
-			  if (dat==1) {
-			    //im=mt->getImage(nnx,nny,nns);
-			    
-			    //if (im)
-			    //  cout << "got image" << endl;
-			    //else
-			    //  cout << "could not get image" << endl;
-			    
-
-			    //for (int ii=0; ii<400*400; ii++) {
-			      //if (im[ii]>0)
-			      //cout << im[ii] << endl;
-			      //  if (im[ii]>=0)
-			      
-			    // if (isdark) {
-				//ddark[ii]=im[ii];
-			    //	dout[ii]=im[ii];
-			    // } else {
-			    //	dout[ii]=im[ii]-ddark[ii];
-			    //	if (dout[ii]<0) dout[ii]=0;
-			    // }
-			      // else
-			      //	dout[ii]=0;
-				//else
-				//dout[ii]=0;
-			      // cout << im[ii] << " " << dout[ii] << endl;
-			    //  }
-			    //for (int iiy=49; iiy<52; iiy++)
-			    //  for (int iix=80; iix<83; iix++)
-			    //	dout[iiy*400+iix]=0;
-			    ;
-			  } else {
-			    peds=mt->getPedestal();
-			    //  sprintf(tit,"%s_%lld.tiff",filename.c_str(),fi);
-			    //cout << tit << endl;
-			    //mt->writePedestal(tit);
-			    if (peds)
-			      cout << "got peds" << endl;
-			    else
-			      cout << "could not get peds" << endl;
-			    for (int ii=0; ii<400*400; ii++) {
-			      dout[ii]=peds[ii];
-			      // if (ii%400==10 && ii/400==10)
-			      // 	cout << ii/400 << " " << ii%400 << " " << peds[ii] << " " << dout[ii] << endl; 
-			      // if (ii%400==100 && ii/400==100)
-			      // 	cout << ii/400 << " " << ii%400 << " " << peds[ii] << " " << dout[ii] << endl; 
-			    }
-
-			  }
-
-			    
-		// zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-		// if (zmqsocket2->IsError()) {
-		// 	bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-		// 	delete zmqsocket2;
-		// 	delete zmqsocket;
-		// 	return EXIT_FAILURE;
-		// }
-		// zmqsocket2->Connect();
-		// printf("Zmq Server started at %s\n", zmqsocket2->GetZmqServerAddress());
-			  //zmqsocket2->Connect();
-
-	
-			  zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,ff, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-			  
-			  
-			  zmqsocket2->SendData((char*)dout,length);
-			  cprintf(GREEN, "Sent Data %d \n",length);
-			  
-			  zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-			  cprintf(RED, "Sent Dummy\n");
-			  //	zmqsocket2->Disconnect();
-
-			  // delete zmqsocket2;
-			  }
-			  cout << "Acquired "<< iframe << " frames " << endl;
-			  iframe=0;
-			  newped=-1;
-			  ped=-1;
-			  dat=-1;
-			  mt->clearImage();
-			  isdark=0;
-			  continue; //continue to not get out
-	  }
-	  //	cprintf(GREEN, "Got Header \n");
-
-	  strcpy(ff,filename.c_str());
-	  fi=fileindex;
-	  //isdark=0;
-	  if (newped<0) {
-	    if (filename.find("newped")!=std::string::npos) {
-	      cout << "NEWPED" << endl;
-	      if (newped<=0) {
-		newped=1;
-		ped=1;
-		while (mt->isBusy()) {;}
-		mt->newDataSet(); //resets pedestal
-		mt->setFrameMode(ePedestal);
-		cout << "New data set"<< endl;
-	      }
-	    } else {
-	      newped=0;
-	    }
-	  }
-	  if (ped<0) { 
-	    if (filename.find("ped")!=std::string::npos) {
-	      ped=1;
-	      dat=0;
-	      while (mt->isBusy()) {;}
-	      mt->setFrameMode(ePedestal);
-	      cout << "pedestal!"<< endl;
-	    } else {
-	      ped=0;
-	      dat=1;	
-	      while (mt->isBusy()) {;}
-	      mt->setFrameMode(eFrame);
-	      cout << "data!"<< endl;
-	      if (filename.find("dark")!=std::string::npos) {
-		isdark=1;
-		cout << "this is a dark image" << endl;
-	      }
-	      
-	    }
-	  }
-	  
-		// get data
-	  length = zmqsocket->ReceiveData(0, buff, size);
-		//	cprintf(GREEN, "Got Data\n");
-
-		//processing with image
-		//...
-		//	if (iframe<10) {
-		// filter->addToPedestal(image);
-		//} else {
-		//SLOW!!!
-		//***
-		//filter->getNPhotons(image);
-		//nph=filter->getImage();
-		//filter->addToPedestal(image);
-		//*****
-	 
-		//	cprintf(BLUE, "Data processed\n");
-	  
-
-		mt->pushData(buff);
-		mt->nextThread();
-		//	cout << " " << (void*)buff;
-		mt->popFree(buff);
-		
-	  
-	  
-		//stream data from socket 2
-		  
-	  iframe++;
-	}
-	
-	//	}// exiting infinite loop
-	
-
-	
-	delete zmqsocket;
-	if (send)
-	  delete zmqsocket2;
-	
-
-	cout<<"Goodbye"<<  endl;
-	return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchZmqClusterFinder.cpp

@@ -1,402 +0,0 @@
-#include "sls_receiver_defs.h"
-#include "ZmqSocket.h"
-#include "moench03T1ZmqDataNew.h"
-#include <vector> 
-#include <string> 
-#include <sstream> 
-#include <iomanip> 
-#include <fstream> 
-#include "tiffIO.h"
-
-
-//#define NEWZMQ
-#ifdef NEWZMQ
-#include <rapidjson/document.h> //json header in zmq stream
-#endif
-
-#include<iostream>
-
-//#include "analogDetector.h"
-#include "singlePhotonDetector.h"
-#include "multiThreadedAnalogDetector.h"
-#include "ansi.h"
-#include <iostream>
-using namespace std;
-
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
-
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [send_socket ip] [send port number]
- *
- */
-  FILE *of=NULL;
-  int fifosize=1000;
-  int nthreads=20;
-	// help
-  if (argc < 3 ) {
-    cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number]\n");
-    return EXIT_FAILURE;
-  }
-  
-  // receive parameters
-  bool send = false;
-  char* socketip=argv[1];
-  uint32_t portnum = atoi(argv[2]);
-  int maxSize = 32*2*8192;//5000;//atoi(argv[3]);
-  int size= 32*2*5000;
-  int multisize=size;
-  // send parameters if any
-  char* socketip2 = 0;
-  uint32_t portnum2 = 0;
-  if (argc > 3) {
-	  send = true;
-	  socketip2 = argv[3];
-	  portnum2 = atoi(argv[4]);
-  }
-  cout << "\nrx socket ip : " << socketip <<
-    "\nrx port num  : " <<  portnum ;
-  if (send) {
-    cout << "\nsd socket ip : " << socketip2 <<
-      "\nsd port num  : " <<  portnum2;
-  }
-  cout << endl;
-  
-  //slsDetectorData *det=new moench03T1ZmqDataNew(); 
-  moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
-  //analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det,1,NULL,1000);
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, 0, 1000, 10);
-  
-
-  char* buff;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-  mt->setFrameMode(eFrame);
-  mt->StartThreads();
-  mt->popFree(buff);
-  
-  
-  ZmqSocket* zmqsocket=NULL;
-
-#ifdef NEWZMQ
-  // receive socket
-  try{
-#endif
-    
-    zmqsocket = new ZmqSocket(socketip,portnum); 
-    
-
-#ifdef NEWZMQ
-	  }  catch (...) {
-		cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-		delete zmqsocket;
-		return EXIT_FAILURE;
-        }
-#endif
-
-#ifndef NEWZMQ	  
-	if (zmqsocket->IsError()) {
-		cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-		delete zmqsocket;
-		return EXIT_FAILURE;
-	}
-#endif
-	if (zmqsocket->Connect()) {
-	  cprintf(RED, "Error: Could not connect to socket  %s\n",
-		  zmqsocket->GetZmqServerAddress());
-	  delete zmqsocket;
-	  return EXIT_FAILURE;
-	} else 
-	  printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress());
-	
-	// send socket
-	ZmqSocket* zmqsocket2 = 0;
-	  cout << "zmq2 " << endl;
-	if (send) {
-#ifdef NEWZMQ
-	// receive socket
-	  try{
-#endif
-		zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-
-
-
-#ifdef NEWZMQ
-	  }  catch (...) {
-			cprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-			delete zmqsocket2;
-			delete zmqsocket;
-			return EXIT_FAILURE;
-	  }
-#endif
-
-#ifndef NEWZMQ	  
-		if (zmqsocket2->IsError()) {
-			cprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-			delete zmqsocket2;
-			delete zmqsocket;
-			return EXIT_FAILURE;
-		}
-#endif	
-		if (zmqsocket2->Connect()) {
-		  cprintf(RED, "Error: Could not connect to socket  %s\n",
-					zmqsocket2->GetZmqServerAddress());
-		delete zmqsocket2;
-		return EXIT_FAILURE;
-	} else 
-		  printf("Zmq Client at %s\n", zmqsocket2->GetZmqServerAddress());
-
-	}
-
-
-	// header variables
-	uint64_t acqIndex = -1;
-	uint64_t frameIndex = -1;
-	uint32_t subFrameIndex = -1;
-	uint64_t fileindex = -1;
-	string filename = "";
-	//	char* image = new char[size];
-	//int* image = new int[(size/sizeof(int))]();
-	uint32_t flippedDataX = -1;
-	int *nph;
-	int iframe=0;
-	char ofname[10000];
-		    
-	char fname[10000];
-	int length;
-	int *detimage;
-	int nnx, nny,nns;
-	uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0, dynamicRange = 0;
-	filter->getImageSize(nnx, nny,nns);
-	int16_t *dout=new int16_t [nnx*nny];
-	// infinite loop
-	uint32_t packetNumber = 0;
-	uint64_t bunchId = 0;
-	uint64_t timestamp = 0;
-	int16_t modId = 0;
-	uint16_t xCoord = 0;
-	uint16_t yCoord = 0;
-	uint16_t zCoord = 0;
-	uint32_t debug = 0;
-	uint32_t dr = 16;
-	uint16_t roundRNumber = 0;
-	uint8_t detType = 0;
-	uint8_t version = 0;
-	int* flippedData = 0;
-	char* additionalJsonHeader = 0;
-
-	uint32_t threshold=0;
-	
-	uint32_t xmin=0, xmax=400, ymin=0, ymax=400;
-	
-	string frameMode_s, detectorMode_s;
-
-	int emin, emax;
-
-
-	int newFrame=1;
-
-	while(1) {
-
-
-	  //  cout << "+++++++++++++++++++++++++++++++LOOP" << endl;
-		// get header, (if dummy, fail is on parse error or end of acquisition)
-#ifndef NEWZMQ	
-	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)){
-#endif
-
-#ifdef NEWZMQ	
-	    rapidjson::Document doc;
-	    if (!zmqsocket->ReceiveHeader(0, doc, SLS_DETECTOR_JSON_HEADER_VERSION)) {
-	      zmqsocket->CloseHeaderMessage();
-
-#endif
-	    //	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)) {
-	    cprintf(RED, "Got Dummy\n");
-
-
-
-
-	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
-			
-	    
-	    detimage=mt->getImage(nnx,nny,nns);
-	    for (int ix=0; ix<nnx; ix++) {
-	      for (int iy=0; iy<nny; iy++) {
-		dout[iy*nnx+ix]=detimage[iy*nnx+ix];
-	      }
-	    }
-
-	    if (send) {
-	      strcpy(fname,filename.c_str());
-#ifdef NEWZMQ	
-	      //zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dynamicRange, fileindex,
-	      //			  nnx, nny, nns*dynamicRange/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
-	
-	      zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex,
-					  nnx, nny, nns*dr/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
-					   				   
-#endif
-
-#ifndef NEWZMQ
-	        zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-#endif
-	     
-	      zmqsocket2->SendData((char*)dout,length);
-	      cprintf(GREEN, "Sent Data\n");
-	    }
-	    
-	    
-	    // stream dummy  to socket2 to signal end of acquisition
-	    if (send) {
-	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	      cprintf(RED, "Sent Dummy\n");
-	    }
-	    mt->clearImage();
-	    if (of) {
-	      fclose(of);
-	      of=NULL;
-	    }
-	    
-	    newFrame=1;
-	    continue; //continue to not get out
-	  }
-
-#ifdef NEWZMQ
-	    if (newFrame) {
-	      //  acqIndex, frameIndex, subframeIndex, filename, fileindex
-	      size       = doc["size"].GetUint();
-	      multisize  = size;// * zmqsocket->size();
-	      dynamicRange  = doc["bitmode"].GetUint();
-	      nPixelsX = doc["shape"][0].GetUint();
-	      nPixelsY = doc["shape"][1].GetUint();
-	      filename        = doc["fname"].GetString();
-	      acqIndex = doc["acqIndex"].GetUint64();
-	      frameIndex       = doc["fIndex"].GetUint64();
-	      fileindex        = doc["fileIndex"].GetUint64();
-	      subFrameIndex    = doc["expLength"].GetUint();
-	      xCoord                  = doc["xCoord"].GetUint();
-	      yCoord                  = doc["yCoord"].GetUint();
-	      zCoord                  = doc["zCoord"].GetUint();
-	      flippedDataX=doc["flippedDataX"].GetUint();
-	      packetNumber=doc["packetNumber"].GetUint();
-	      bunchId=doc["bunchId"].GetUint();
-	      timestamp=doc["timestamp"].GetUint();
-	      modId=doc["modId"].GetUint();
-	      debug=doc["debug"].GetUint();
-	      roundRNumber=doc["roundRNumber"].GetUint();
-	      detType=doc["detType"].GetUint();
-	      version=doc["version"].GetUint();
-
-
-
-	      cprintf(BLUE, "Header Info:\n"
-		      "size: %u\n"
-		      "multisize: %u\n"
-		      "dynamicRange: %u\n"
-		      "nPixelsX: %u\n"
-		      "nPixelsY: %u\n"
-		      "currentFileName: %s\n"
-		      "currentAcquisitionIndex: %lu\n"
-		      "currentFrameIndex: %lu\n"
-		      "currentFileIndex: %lu\n"
-		      "currentSubFrameIndex: %u\n"
-		      "xCoordX: %u\n"
-		      "yCoordY: %u\n"
-		      "zCoordZ: %u\n"
-		      "flippedDataX: %u\n"
-		      "packetNumber: %u\n"
-		      "bunchId: %u\n"
-		      "timestamp: %u\n"
-		      "modId: %u\n"
-		      "debug: %u\n"
-		      "roundRNumber: %u\n"
-		      "detType: %u\n"
-		      "version: %u\n",
-		      size, multisize, dynamicRange, nPixelsX, nPixelsY,
-		      filename.c_str(), acqIndex,
-		      frameIndex, fileindex, subFrameIndex,
-		      xCoord, yCoord,zCoord,
-		      flippedDataX, packetNumber, bunchId, timestamp, modId, debug, roundRNumber, detType, version);
-
-
-	      if (doc.HasMember("threshold")) {
-		version=doc["threshold"].GetUint();
-	
-	      }
-
-	      if (doc.HasMember("roi")) {
-		xmin=doc["roi"][0].GetUint();
-		xmax=doc["roi"][1].GetUint();
-		ymin=doc["roi"][2].GetUint();
-		ymax=doc["roi"][3].GetUint();	
-
-	      }
-	      
-	      if (doc.HasMember("frameMode")) {
-		frameMode_s=doc["frameMode"].GetString();
-
-	      }
-	      
-	      if (doc.HasMember("detectorMode")) {
-		detectorMode_s=doc["detectorMode"].GetString();
-
-	      }
-	      
-	      if (doc.HasMember("energyRange")) {
-		emin=doc["energyRange"][0].GetUint();
-		emax=doc["energyRange"][0].GetUint();
-
-	      }
-	      
-	      
-	      if (doc.HasMember("dynamicRange")) {
-		dr=doc["dynamicRange"].GetUint();
-	      }
-	      
-	      if (doc.HasMember("nSubPixels")) {
-		nsubPixels=doc["nSubPixels"].GetUint();
-	      }
-	      
-	      
-
-	      newFrame=0;
-	      zmqsocket->CloseHeaderMessage();
-	    }
-#endif
-
-	  if (of==NULL) {
-	    sprintf(ofname,"%s_%d.clust",filename.c_str(),fileindex);
-	    of=fopen(ofname,"w");
-	    if (of) {
-	      mt->setFilePointer(of);
-	    }else {
-	      cout << "Could not open "<< ofname << " for writing " << endl;
-	      mt->setFilePointer(NULL);
-	    }
-	  }
-	  
-	  // get data
-	  length = zmqsocket->ReceiveData(0, buff, size);
-	  mt->pushData(buff);
-	  mt->nextThread();
-	  mt->popFree(buff);
-	  
-	
-	  
-	  
-	  iframe++;
-	}	// exiting infinite loop
-
-
-
-	delete zmqsocket;
-	if (send)
-	  delete zmqsocket2;
-
-	
-	cout<<"Goodbye"<<  endl;
-	return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchZmqInterpolating.cpp

@@ -1,292 +0,0 @@
-#include "sls_receiver_defs.h"
-#include "ZmqSocket.h"
-#include "moench03T1ZmqDataNew.h"
-#include <vector> 
-#include <string> 
-#include <sstream> 
-#include <iomanip> 
-#include <fstream> 
-#include "tiffIO.h"
-
-#include<iostream>
-
-//#include "analogDetector.h"
-#include "interpolatingDetector.h"
-#include "linearInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-#include "ansi.h"
-#include <iostream>
-using namespace std;
-
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
-
-
-
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [send_socket ip] [send port number]
- *
- */
-
-  int nthreads=20;
-  int nsigma=5;
-  int xmin=0;
-  int xmax=400;
-  int ymin=0;
-  int ymax=400;
-  int nsubpixels=2;
-
-
-  FILE *of=NULL;
-  int fifosize=1000;
-  int int_ready=0;
-  int ok;
-  // help
-  if (argc < 3 ) {
-    cprintf(RED, "Help: %s [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number] [nsubpixels] [nthreads] [nsigma] [xmin xmax ymin ymax]\n", argv[0]);
-    return EXIT_FAILURE;
-  }
-
-  char* socketip2 = 0;
-  uint32_t portnum2 = 0;
-	// receive parameters
-  int size = 32*2*5000;//atoi(argv[3]);
-  bool send = false;
-
-
-
-  char* socketip=argv[1];
-  uint32_t portnum = atoi(argv[2]);
-  if (argc > 3) {
-    send = true;
-    socketip2 = argv[3];
-    portnum2 = atoi(argv[4]);
-  }
-  if (argc > 5) {
-    nsubpixels=atoi(argv[5]);
-  }
-  if (argc>6) {
-    nthreads=atoi(argv[6]);
-  }
-  if (argc>7) {
-    nsigma=atoi(argv[7]);
-  }
-  if (argc>11) {
-    xmin=atoi(argv[8]);
-    xmax=atoi(argv[8]);
-    ymin=atoi(argv[10]);
-    ymax=atoi(argv[11]);
-  }
-
-  cout << "\nrx socket ip : " << socketip <<
-    "\nrx port num  : " <<  portnum ;
-  if (send) {
-    cout << "\nsd socket ip : " << socketip2 <<
-      "\nsd port num  : " <<  portnum2;
-	}
-  cout << endl;
-
-  //slsDetectorData *det=new moench03T1ZmqDataNew(); 
-  int npx, npy;
-  moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
-  det->getDetectorSize(npx, npy);
-  linearInterpolation *interp=new linearInterpolation(npx,npy,nsubpixels);
-  interpolatingDetector *filter=new interpolatingDetector(det,interp, nsigma, 1, 0, 1000, 100,npx,npy);
-  cout << "Setting noise cut to " << nsigma << " sigma"<< endl;
-  filter->setROI(xmin,xmax,ymin,ymax);
-  cout << "Setting ROI to "<< xmin << " " << xmax << " " << ymin << " " << ymax << endl;
-  
-  char* buff;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-	  int frameMode=eFrame;
-	  mt->setFrameMode(frameMode);
-	  mt->StartThreads();
-	  mt->popFree(buff);
-
-
-	  
-
-
-	// receive socket
-	  ZmqSocket* zmqsocket = new ZmqSocket(socketip,portnum); 
-	if (zmqsocket->IsError()) {
-		cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-		delete zmqsocket;
-		return EXIT_FAILURE;
-	}
-	zmqsocket->Connect();
-	printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress());
-
-	// send socket
-	ZmqSocket* zmqsocket2 = 0;
-	if (send) {
-		zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-		if (zmqsocket2->IsError()) {
-			bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-			delete zmqsocket2;
-			delete zmqsocket;
-			return EXIT_FAILURE;
-		}
-		zmqsocket2->Connect();
-		printf("Zmq Server started at %s\n", zmqsocket2->GetZmqServerAddress());
-	}
-
-
-	// header variables
-	uint64_t acqIndex = -1;
-	uint64_t frameIndex = -1;
-	uint32_t subframeIndex = -1;
-	uint64_t fileindex = -1;
-	string filename = "";
-	char ffname[10000];
-	int ffindex;
-
-	char* image = new char[size];
-	//int* image = new int[(size/sizeof(int))]();
-
-	int *nph;
-	int iframe=0;
-	char ofname[10000];
-		    
-	char fname[10000];
-	int length;
-	int *detimage;
-	int nnx, nny,nns;
-	int nix, niy,nis;
-	filter->getImageSize(nnx, nny,nns);
-	int16_t *dout=new int16_t [nnx*nny];
-	// infinite loop
-	int ix, iy, isx, isy;
-	while(1) {
-
-
-	  //  cout << "+++++++++++++++++++++++++++++++LOOP" << endl;
-		// get header, (if dummy, fail is on parse error or end of acquisition)
-	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)){
-	    //	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)) {
-	    // cprintf(RED, "Got Dummy\n");
-	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
-	    if (frameMode==ePedestal) {	
-	      detped=mt->getPedestal();
- 	      if (detped) {
-		
- 		for (ix=0; ix<400; ix++) {
- 		  for (iy=0; iy<400; iy++) {
- 		    dout[iy*400+ix]+=detped[iy*400+ix];
-		  }
-		}
-	      }
-
-	    } else {	      
- 	      detimage=mt->getImage(nix,niy,nis);
- 	      if (detimage) {
- 		for (ix=0; ix<nix/nis; ix++) {
-                   for (iy=0; iy<niy/nis; iy++) {
-                     dout[iy*(nix/nis)+ix]=0;
- 		  }
- 		}
- 		for (ix=0; ix<nix; ix++) {
- 		  for (iy=0; iy<niy; iy++) {
- 		    dout[(iy/nis)*(nix/nis)+(ix/nis)]+=detimage[iy*nix+ix];
-		  }
-		}
-	      }
-	    }
-	  	    
-	     
-	   
-	   
-	    if (send) {
-	      strcpy(fname,filename.c_str());
-	      //  zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,16,fileindex,400,400,400*400, acqIndex,frameIndex,fname, acqIndex, 0,0,0,0,0,0,0,0,0,0,0,1);
-	      zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-	      
-	      zmqsocket2->SendData((char*)dout,length);
-	      cprintf(GREEN, "Sent Data\n");
-	    }
-	    
-	    sprintf(ofname,"%s_%d.tiff",ffname,ffindex);
-	    if (frameMode==eFlat)
-	      mt->writeFlatField(ofname); 
-	    else if (frameMode==ePedestal)
-	      mt->writePedestal(ofname);
-	    else
-	      mt->writeImage(ofname); 
-	    
-	  
-	    // stream dummy  to socket2 to signal end of acquisition
-	    if (send) {
-	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	      // cprintf(RED, "Sent Dummy\n");
-	      cprintf(RED, "Received %d frames\n", iframe);
-	    }
-	    mt->clearImage();
-	    if (of) {
-	      fclose(of);
-	      of=NULL;
-	    }
-	    iframe=0;
-	    continue; //continue to not get out
-	  }
-
-
-	  if (of==NULL) {  
-	    while (mt->isBusy()) {;}
-	    sprintf(ofname,"%s_%d.clust",filename.c_str(),fileindex);
-	    of=fopen(ofname,"w");
-	    if (of) {
-	      mt->setFilePointer(of);
-	    }else {
-	      cout << "Could not open "<< ofname << " for writing " << endl;
-	      mt->setFilePointer(NULL);
-	    }
-	    ffindex=fileindex;
-	    strcpy(ffname,filename.c_str());
-	    if (filename.find("flat")!=std::string::npos) {
-	      cout << "add to ff" << endl;
-	      frameMode=eFlat;//ePedestal;
-	      int_ready=0;
-	      
-	    } else if  (filename.find("newped")!=std::string::npos) {
-	      frameMode=ePedestal;
-	      cout << "new pedestal" << endl;
-	      
-	      mt->newDataSet();
-	    } else if  (filename.find("ped")!=std::string::npos){ 
-	      frameMode=ePedestal;
-	      cout << "pedestal" << endl;
-	    } else { 
-	      frameMode=eFrame;
-	      cout << "data" << endl;
-	      if (int_ready==0) {
-		mt->prepareInterpolation(ok);
-		cout << "prepare interpolation " << endl;
-		int_ready=1;
-	      }
-	    }
-	   
-	    mt->setFrameMode(frameMode);
-	  }
-	  
-	  // get data
-	  length = zmqsocket->ReceiveData(0, buff, size);
-	  mt->pushData(buff);
-	  mt->nextThread();
-	  mt->popFree(buff);
-	  
-	  iframe++;
-	}	// exiting infinite loop
-
-
-
-	delete zmqsocket;
-	if (send)
-	  delete zmqsocket2;
-
-	
-	//	cout<<"Goodbye"<<  endl;
-	return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

@@ -1,6 +1,20 @@
-#include "sls_receiver_defs.h"
+#define WRITE_QUAD
+#define MOENCH_BRANCH
+
+#define C_GHOST 0.0004
+
+#define CM_ROWS 20
+
+#include "sls_detector_defs.h"
 #include "ZmqSocket.h"
+#ifndef RECT
 #include "moench03T1ZmqDataNew.h"
+#endif
+#ifdef RECT
+#include "moench03T1ZmqDataNewRect.h"
+#endif
+#include "moench03GhostSummation.h"
+#include "moench03CommonMode.h"
 #include <vector> 
 #include <string> 
 #include <sstream> 
@@ -8,11 +22,7 @@
 #include <fstream> 
 #include "tiffIO.h"
 
-
-//#define NEWZMQ
-#ifdef NEWZMQ
 #include <rapidjson/document.h> //json header in zmq stream
-#endif
 
 #include<iostream>
 
@@ -25,10 +35,15 @@
 #include "etaInterpolationPosXY.h"
 #include "ansi.h"
 #include <iostream>
+
+//#include <chrono>
+#include <ctime> // time_t
+#include <cstdio>
+
 using namespace std;
+//using namespace std::chrono;
 
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
+//#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
 
 	//	myDet->setNetworkParameter(ADDITIONAL_JSON_HEADER, " \"what\":\"nothing\" ");
 
@@ -38,12 +53,14 @@ int main(int argc, char *argv[]) {
  *
  */
   FILE *of=NULL;
-  int fifosize=1000;
+  int fifosize=5000;
   int etabins=1000;//nsubpix*2*100;
   double etamin=-1, etamax=2;
+  int nSubPixels=2;
+  //	int emin, emax;
 	// help
   if (argc < 3 ) {
-    cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number] [nthreads] [nsubpix] [etafile]\n");
+    cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number] [nthreads] [nsubpix] [gainmap]  [etafile]\n");
     return EXIT_FAILURE;  
   }
   
@@ -55,11 +72,13 @@ int main(int argc, char *argv[]) {
   char* socketip2 = 0;
   uint32_t portnum2 = 0;
 
+  uint32_t nSigma=5;
 
   int ok;
 
-
-
+  // high_resolution_clock::time_point t1;
+  // high_resolution_clock::time_point t2 ;
+  time_t begin,end,finished;
 
 
   if (argc > 4) {
@@ -79,17 +98,22 @@ int main(int argc, char *argv[]) {
     nthreads=atoi(argv[5]);
 
   cout << "Number of threads is: " << nthreads << endl;
-  int nSubPixels=2;
   if (argc>6)
     nSubPixels=atoi(argv[6]);
   cout << "Number of subpixels is: " << nSubPixels << endl;
   
-  char *etafname=NULL;
+
+  char *gainfname=NULL;
   if (argc>7) {
-    etafname=argv[7];
-    cout << "Eta file name is: " << etafname << endl;
+    gainfname=argv[7];
+    cout << "Gain map file name is: " << gainfname << endl;
   }
 
+  char *etafname=NULL;
+  if (argc>8) {
+    etafname=argv[8];
+    cout << "Eta file name is: " << etafname << endl;
+  }
 
   //slsDetectorData *det=new moench03T1ZmqDataNew(); 
   moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
@@ -97,20 +121,49 @@ int main(int argc, char *argv[]) {
   int npx, npy;
   det->getDetectorSize(npx, npy);
 
-
+  int send_something=0;
 
 
   int maxSize = npx*npy*2;//32*2*8192;//5000;//atoi(argv[3]);
   int size= maxSize;//32*2*5000;
-  int multisize=size;
-  int dataSize=size;
+  //int multisize=size;
+  //int dataSize=size;
+
+  char dummybuff[size];
+  
+
+  int ncol_cm=CM_ROWS;
+  double xt_ghost=C_GHOST;
+  moench03CommonMode *cm=new moench03CommonMode(ncol_cm);
+  moench03GhostSummation *gs=new moench03GhostSummation(det, xt_ghost);
+  double *gainmap=NULL;
+  float *gm;
+  double *gmap=NULL;
+
+  uint32_t nnnx, nnny;
+  if (gainfname) {
+    gm=ReadFromTiff(gainfname, nnny, nnnx);
+    if (gm && nnnx==(uint)npx && nnny==(uint)npy) {
+      gmap=new double[npx*npy];
+      for (int i=0; i<npx*npy; i++) {
+	gmap[i]=gm[i];
+      }
+      delete [] gm;
+    } else
+      cout << "Could not open gain map " << gainfname << endl;
+  }
+
+
+
+
+
 
 
 
 
   //analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det,1,NULL,1000);
 #ifndef INTERP
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, 0, 1000, 10);
+  singlePhotonDetector *filter=new singlePhotonDetector(det,3, nSigma, 1, cm, 1000, 10, -1, -1, gainmap, gs);
 
     multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
 
@@ -121,7 +174,7 @@ int main(int argc, char *argv[]) {
 
   if (etafname) interp->readFlatField(etafname);
 
-  interpolatingDetector *filter=new interpolatingDetector(det,interp, 5, 1, 0, 1000, 10);
+  interpolatingDetector *filter=new interpolatingDetector(det,interp, nSigma, 1, cm,  1000, 10, -1, -1, gainmap, gs);
   multiThreadedInterpolatingDetector *mt=new multiThreadedInterpolatingDetector(filter,nthreads,fifosize);
 #endif
 
@@ -212,21 +265,32 @@ int main(int argc, char *argv[]) {
 	// header variables
 	uint64_t acqIndex = -1;
 	uint64_t frameIndex = -1;
-	uint32_t subFrameIndex = -1;
+#ifdef MOENCH_BRANCH
+ 	uint32_t subFrameIndex = -1;
+	int* flippedData = 0;
+#endif
+	
+	uint64_t subframes=0;
+	//uint64_t  isubframe=0;
+	uint64_t  insubframe=0;
+	double subnorm=1;
+	uint64_t  f0=-1, nsubframes=0, nnsubframe=0;
+
 	uint64_t fileindex = -1;
 	string filename = "";
 	//	char* image = new char[size];
 	//int* image = new int[(size/sizeof(int))]();
-	uint32_t flippedDataX = -1;
-	int *nph;
+	//uint32_t flippedDataX = -1;
+	//int *nph;
 	int iframe=0;
 	char ofname[10000];
 		    
 	char fname[10000];
-	int length;
-	int *detimage;
+	//	int length;
+	int *detimage=NULL;
 	int nnx, nny,nns;
-	uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0, dynamicRange = 0;
+	//uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0, 
+	//uint32_t  dynamicRange = 0;
 	// infinite loop
 	uint32_t packetNumber = 0;
 	uint64_t bunchId = 0;
@@ -240,11 +304,10 @@ int main(int argc, char *argv[]) {
 	//int16_t *dout;//=new int16_t [nnx*nny];
 	uint32_t dr = 32;
 	int32_t *dout=NULL;//=new int32_t [nnx*nny];
-	uint32_t nSigma=5;
+	float *doutf=NULL;//=new int32_t [nnx*nny];
 	uint16_t roundRNumber = 0;
 	uint8_t detType = 0;
 	uint8_t version = 0;
-	int* flippedData = 0;
 	char* additionalJsonHeader = 0;
 
 	int32_t threshold=0;
@@ -253,15 +316,14 @@ int main(int argc, char *argv[]) {
 	
 	string frameMode_s, detectorMode_s, intMode_s;
 
-	int emin, emax;
-	int resetFlat=0;
-	int resetPed=0;
-	int nsubPixels=1;
-	int isPedestal;
-	int isFlat=0;
+	//	int resetFlat=0;
+	//int resetPed=0;
+	//	int nsubPixels=1;
+	//int isPedestal=0;
+	//int isFlat=0;
 	int newFrame=1;
-	detectorMode dMode;
-	frameMode fMode;
+	detectorMode dMode=eAnalog;
+	frameMode fMode=eFrame;
 	double *ped;
 
 	filter->getImageSize(nnx, nny,nns);
@@ -283,13 +345,13 @@ int main(int argc, char *argv[]) {
 #ifdef NEWZMQ	
 	    rapidjson::Document doc;
 	    if (!zmqsocket->ReceiveHeader(0, doc, SLS_DETECTOR_JSON_HEADER_VERSION)) {
-	      zmqsocket->CloseHeaderMessage();
+	      /* zmqsocket->CloseHeaderMessage();*/
 
 #endif
 	    //	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)) {
-	    cprintf(RED, "Got Dummy\n");
-
-
+	      //  cprintf(RED, "Got Dummy\n");
+	      //   t1=high_resolution_clock::now();
+	      time(&end);
 
 
 	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
@@ -305,28 +367,61 @@ int main(int argc, char *argv[]) {
 	      cprintf(RED, "Sent Dummy\n");
 	    }
 	    } else {
-	    if (fMode==ePedestal) {
-	      sprintf(ofname,"%s_%d_ped.tiff",fname,fileindex);
-	      mt->writePedestal(ofname);
-	       cout << "Writing pedestal to " << ofname << endl;
-	    }
+	      send_something=0;
+	      if (fMode==ePedestal) {
+		sprintf(ofname,"%s_%ld_ped.tiff",fname,fileindex);
+		mt->writePedestal(ofname);
+		cout << "Writing pedestal to " << ofname << endl;
+		send_something=1;
+	      }
 #ifdef INTERP
-	    else if  (fMode==eFlat) {
-	      mt->prepareInterpolation(ok);
-	      sprintf(ofname,"%s_%d_eta.tiff",fname,fileindex);
-	      mt->writeFlatField(ofname);
-	       cout << "Writing eta to " << ofname << endl;
-	    }
+	      else if  (fMode==eFlat) {
+		mt->prepareInterpolation(ok);
+		sprintf(ofname,"%s_%ld_eta.tiff",fname,fileindex);
+		mt->writeFlatField(ofname);
+		cout << "Writing eta to " << ofname << endl;
+		send_something=1;
+	      }
 #endif
-	    else {
-	      sprintf(ofname,"%s_%d.tiff",fname,fileindex);
-	      mt->writeImage(ofname);
-	       cout << "Writing image to " << ofname << endl;
-	    }
-	    //  cout << nns*nnx*nny*nns*dr/8 << " " << length << endl;
+	      else {
+		if (subframes>0 ) { 
+		  if (insubframe>0) {
+		    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname,nnsubframe,fileindex);
+		    //		  mt->writeImage(ofname);
+		    doutf= new float[nnx*nny];
+		    if (subframes>0 && insubframe!=subframes && insubframe>0)
+		      subnorm=((double)subframes)/((double)insubframe);
+		    else
+		      subnorm=1.;
+		    for (int ix=0; ix<nnx*nny; ix++) {
+		    doutf[ix]=detimage[ix]*subnorm;
+		    if (doutf[ix]<0) doutf[ix]=0;
+		    }
+	    
+		    cout << "Writing image to " << ofname << endl;
+		    
+		    WriteToTiff(doutf,ofname ,nnx, nny); 
+		    
+		    if (doutf)
+		      delete [] doutf;
+		    doutf=NULL;
+		    
+		    nsubframes++;
+		    insubframe=0;
+		    send_something=1;
+		  }
+		} else {
+		  sprintf(ofname,"%s_%ld.tiff",fname,fileindex);
+		  mt->writeImage(ofname);
+		  send_something=1;
+		}
+		
+		cout << "Writing image to " << ofname << endl;
+	      }
+	      //  cout << nns*nnx*nny*nns*dr/8 << " " << length << endl;
 
 	    if (send) {
-
+	      
 	    if (fMode==ePedestal) {   
 	      cprintf(MAGENTA,"Get pedestal!\n");
 	      nns=1;
@@ -348,7 +443,7 @@ int main(int argc, char *argv[]) {
 #ifdef INTERP
 	    else if  (fMode==eFlat) {
 	       int nb;
-	      double emi, ema;
+	       double emi=0, ema=1;
 	       int *ff=mt->getFlatField(nb, emi, ema);
 	       nnx=nb;
 	       nny=nb;
@@ -368,6 +463,10 @@ int main(int argc, char *argv[]) {
 	      // nnx=nnx*nns;
 	      //nny=nny*nns;
 	      dout= new int32_t[nnx*nny];
+	      if (subframes>0 && insubframe!=subframes && insubframe>0)
+		subnorm=((double)subframes)/((double)insubframe);
+	      else
+		subnorm=1.;
 	      for (int ix=0; ix<nnx*nny; ix++) {
 		// for (int iy=0; iy<nny*nns; iy++) {
 		 //  for (int isx=0; isx<nns; isx++) {
@@ -379,40 +478,55 @@ int main(int argc, char *argv[]) {
 		    
 		//   }
 		// }
-		  dout[ix]=detimage[ix];
+		  dout[ix]=detimage[ix]*subnorm;
 		  if (dout[ix]<0) dout[ix]=0;
 		  //   cout << ix << " " << dout[ix] << endl;
 		  // }
 	      }
 	    }
+	    //if ((insubframe>0 && subframes>0) || (subframes<=0) ){
 
-
-
-#ifdef NEWZMQ	
-	    cout << "Sending image size " << nnx << " " << nny << endl;
+	    if(send_something) {
+#ifndef DEVELOPER
+#ifndef MOENCH_BRANCH
+	      zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, 0,0, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname, acqIndex,0 , packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, additionalJsonHeader);
+#endif
+#endif
+	      
+#ifdef DEVELOPER
+	      zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 0,0,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,additionalJsonHeader);
+#endif	
+#ifdef MOENCH_BRANCH
+	   
 	      zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
-					   				   
-#endif
-
-#ifndef NEWZMQ
-	        zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-#endif
-		
-		zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
-		cprintf(GREEN, "Sent Data\n");
-		
-		zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-		cprintf(RED, "Sent Dummy\n");
-		if (dout)
-		  delete [] dout;
-		dout=NULL;
-
+#endif		
+	      
+			
+	      
+	      zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
+	      cprintf(GREEN, "Sent Data\n");
+	    }
+	    
+	    zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+	    cprintf(RED, "Sent Dummy\n");
+	    if (dout)
+	      delete [] dout;
+	    dout=NULL;
+	    
 	    }
 	    }
 
 	    mt->clearImage();
 	    
 	    newFrame=1;
+	    //t2 = high_resolution_clock::now();
+	    
+	      time(&finished);
+	      //   auto meas_duration = duration_cast<microseconds>( t2 - t0 ).count();
+	      //   auto real_duration = duration_cast<microseconds>( t2 - t1 ).count();
+	    
+	    cout << "Measurement lasted " << difftime(end,begin) << endl;
+	    cout << "Processing lasted " << difftime(finished,begin) << endl;
 	    continue; //continue to not get out
 
 
@@ -420,33 +534,31 @@ int main(int argc, char *argv[]) {
 
 #ifdef NEWZMQ
 	    if (newFrame) {
-
+	      time(&begin);
+	      // t0 = high_resolution_clock::now();
+	      //cout <<"new frame" << endl;
 
 	      //  acqIndex, frameIndex, subframeIndex, filename, fileindex
 	      size       = doc["size"].GetUint();
-	      multisize  = size;// * zmqsocket->size();
-	      dynamicRange  = doc["bitmode"].GetUint();
-	      nPixelsX = doc["shape"][0].GetUint();
-	      nPixelsY = doc["shape"][1].GetUint();
+	      // multisize  = size;// * zmqsocket->size();
+	      // dynamicRange  = doc["bitmode"].GetUint();
+	      //  nPixelsX = doc["shape"][0].GetUint();
+	      // nPixelsY = doc["shape"][1].GetUint();
 	      filename        = doc["fname"].GetString();
-	      acqIndex = doc["acqIndex"].GetUint64();
-	      frameIndex       = doc["fIndex"].GetUint64();
+	      //acqIndex = doc["acqIndex"].GetUint64();
+	      //frameIndex       = doc["fIndex"].GetUint64();
 	      fileindex        = doc["fileIndex"].GetUint64();
-	      subFrameIndex    = doc["expLength"].GetUint();
-	      xCoord                  = doc["xCoord"].GetUint();
-	      yCoord                  = doc["yCoord"].GetUint();
-	      zCoord                  = doc["zCoord"].GetUint();
-	      flippedDataX=doc["flippedDataX"].GetUint();
-	      packetNumber=doc["packetNumber"].GetUint();
-	      bunchId=doc["bunchId"].GetUint();
-	      timestamp=doc["timestamp"].GetUint();
-	      modId=doc["modId"].GetUint();
-	      debug=doc["debug"].GetUint();
-	      roundRNumber=doc["roundRNumber"].GetUint();
-	      detType=doc["detType"].GetUint();
-	      version=doc["version"].GetUint();
+	      //subFrameIndex    = doc["expLength"].GetUint();
+	      //packetNumber=doc["packetNumber"].GetUint();
+	      //bunchId=doc["bunchId"].GetUint();
+	      //timestamp=doc["timestamp"].GetUint();
+	      //modId=doc["modId"].GetUint();
+	      //debug=doc["debug"].GetUint();
+	      //roundRNumber=doc["roundRNumber"].GetUint();
+	      //detType=doc["detType"].GetUint();
+	      //version=doc["version"].GetUint();
 
-	      dataSize=size;
+	      //dataSize=size;
 
 	      strcpy(fname,filename.c_str());
 
@@ -480,8 +592,8 @@ int main(int argc, char *argv[]) {
 	      // 	      flippedDataX, packetNumber, bunchId, timestamp, modId, debug, roundRNumber, detType, version);
 	      
 	      /* Analog detector commands */
-	      isPedestal=0;
-	      isFlat=0;
+	      //isPedestal=0;
+	      //isFlat=0;
 	      fMode=eFrame;
 	      frameMode_s="frame";
 	      cprintf(MAGENTA, "Frame mode: ");
@@ -490,28 +602,28 @@ int main(int argc, char *argv[]) {
 		  frameMode_s=doc["frameMode"].GetString();
 		  if (frameMode_s == "pedestal"){
 		    fMode=ePedestal;
-		    isPedestal=1;
+		    //isPedestal=1;
 		  } else if (frameMode_s == "newPedestal"){
 		    mt->newDataSet(); //resets pedestal  
 		    // cprintf(MAGENTA, "Resetting pedestal\n");
 		    fMode=ePedestal;
-		    isPedestal=1;
+		    //isPedestal=1;
 		  }
 #ifdef INTERP 
 		  else if (frameMode_s == "flatfield") {
 		     fMode=eFlat;
-		     isFlat=1;
+		     //isFlat=1;
 		   } else if (frameMode_s == "newFlatfield") {
 		     mt->resetFlatField();
-		     isFlat=1;
+		     //isFlat=1;
 		     cprintf(MAGENTA, "Resetting flatfield\n");
 		     fMode=eFlat;
 		   }
 #endif
 		  else {
 		    fMode=eFrame;
-		    isPedestal=0;
-		    isFlat=0;
+		    //isPedestal=0;
+		    //isFlat=0;
 		    fMode=eFrame;
 		    frameMode_s="frame";
 		  }
@@ -634,16 +746,36 @@ int main(int argc, char *argv[]) {
 	      // 	mt->setNSubPixels(nSubPixels);
 	      // }
 	      
+	      // threshold=0;
+	      cprintf(MAGENTA, "Subframes: ");
+	      subframes=0;
+	      //isubframe=0;
+	      insubframe=0;
+	      subnorm=1;
+	      f0=0;
+	      nnsubframe=0;
+	      if (doc.HasMember("subframes")) {	
+		if (doc["subframes"].IsInt()) {
+		  subframes=doc["subframes"].GetInt();
+		}
+	      }	
+	      cprintf(MAGENTA, "%ld\n", subframes);
+
 	      
 	      newFrame=0;
-	      zmqsocket->CloseHeaderMessage();
+	      /* zmqsocket->CloseHeaderMessage();*/
 	    }
 #endif
 
 	    // cout << "file" << endl;
 	    //  cout << "data " << endl;
 	  if (of==NULL) {
-	    sprintf(ofname,"%s_%d.clust",filename.c_str(),fileindex);
+#ifdef WRITE_QUAD
+	    sprintf(ofname,"%s_%ld.clust2",filename.c_str(),fileindex);
+#endif
+#ifndef WRITE_QUAD
+	    sprintf(ofname,"%s_%ld.clust",filename.c_str(),fileindex);
+#endif
 	    of=fopen(ofname,"w");
 	    if (of) {
 	      mt->setFilePointer(of);
@@ -652,16 +784,109 @@ int main(int argc, char *argv[]) {
 	      mt->setFilePointer(NULL);
 	    }
 	  }
+
 	  
 
 	  // cout << "data" << endl;
 	  // get data
-	  length = zmqsocket->ReceiveData(0, buff, size);
-	  mt->pushData(buff);
-	  mt->nextThread();
-	  mt->popFree(buff);
+	  // acqIndex = doc["acqIndex"].GetUint64();
+
+	  frameIndex       = doc["fIndex"].GetUint64();
+
+	  // subFrameIndex    = doc["expLength"].GetUint();
+
+	  //  bunchId=doc["bunchId"].GetUint();
+	  //  timestamp=doc["timestamp"].GetUint();
+	  packetNumber=doc["packetNumber"].GetUint();
+	  // cout << acqIndex << " " << frameIndex << " " << subFrameIndex << " "<< bunchId << " " << timestamp << " " << packetNumber << endl;
+	  if (packetNumber>=40) {
+	    //*((int*)buff)=frameIndex;
+	    if (insubframe==0) f0=frameIndex;
+	    memcpy(buff,&frameIndex,sizeof(int));
+	    //length = 
+	    zmqsocket->ReceiveData(0, buff+sizeof(int), size);
+	    mt->pushData(buff);
+	    mt->nextThread();
+	    mt->popFree(buff);
+	    insubframe++;
+	    nsubframes=frameIndex+1-f0;
+	  } else {
+	    cprintf(RED, "Incomplete frame: received only %d packet\n", packetNumber);
+	    //length = 
+	    zmqsocket->ReceiveData(0, dummybuff, size);
+	  }
 	  
+
+
+
+	  if (subframes>0 && insubframe>=subframes && fMode==eFrame) {
+	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
+	    detimage=mt->getImage(nnx,nny,nns);
+	    cprintf(MAGENTA,"Get image!\n");
+	    dout= new int32_t[nnx*nny];
+	    doutf= new float[nnx*nny];
+	    if (subframes>0 && insubframe!=subframes && insubframe>0)
+	      subnorm=((double)subframes)/((double)insubframe);
+	    else
+	      subnorm=1.;
+	    for (int ix=0; ix<nnx*nny; ix++) {
+	      dout[ix]=detimage[ix]*subnorm;
+	      if (dout[ix]<0) dout[ix]=0;
+	      doutf[ix]=dout[ix];
+	    }
+	    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname,nnsubframe,fileindex);
+	    
+	    cout << "Writing image to " << ofname << endl;
+
+	    WriteToTiff(doutf,ofname ,nnx, nny); 
+	    nsubframes++;
+	    insubframe=0;
+	    nnsubframe++;
+
+
+#ifndef DEVELOPER
+#ifndef MOENCH_BRANCH
+	    zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, 0,0, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname, acqIndex,0 , packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, additionalJsonHeader);
+#endif
+#endif
+
+#ifdef DEVELOPER
+	    zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 0,0,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,additionalJsonHeader);
+#endif	
+#ifdef MOENCH_BRANCH
+	   
+	    zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
+#endif		
+	       
+	    
+
+	    zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
+	    cprintf(GREEN, "Sent subdata\n");
+		
+
+	    if (dout)
+	      delete [] dout;
+	    dout=NULL;
+
+	    if (doutf)
+	      delete [] doutf;
+	    doutf=NULL;
+	    
+	    mt->clearImage();
+	    
+	  }
+
+		 
+
+
+
+
+
+
 	
+	      
+
+
 	  
 	  
 	  iframe++;

slsDetectorCalibration/moenchExecutables/tiff_to_th2f.cpp

@@ -1,57 +0,0 @@
-#include <TPaveText.h> 
-#include <TLegend.h> 
-#include <TF1.h> 
-#include <TGraphErrors.h> 
-#include <TH2F.h> 
-#include <TASImage.h> 
-#include <TImage.h> 
-#include <TFile.h> 
-#include <vector> 
-#include <string> 
-#include <sstream> 
-#include <iomanip> 
-#include <fstream> 
-#include "tiffIO.h"
-
-#include<iostream>
-
-using namespace std;
-
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [outfname]
- *
- */
-
-  if (argc<3) {
-    cout << "Wrong usage! Should be: "<< argv[0] << " infile " << " outfile " << endl;
-    return 1;
-  }
-
-  uint32  nx, ny;
-  
-  float *data=ReadFromTiff(argv[1],nx, ny);
-
-  TH2F *h2=NULL;
-  if (data) {
-    TFile *fout=new TFile(argv[2],"RECREATE");
-    if (fout) {
-      h2=new TH2F("h2",argv[1],nx,0,nx,ny,0, ny);
-      for (int ix=0; ix<nx ; ix++) {
-	for (int iy=0; iy<ny ; iy++) {
-	  
-	  h2->SetBinContent(ix+1, iy+1, data[ix+iy*nx]);
-	}
-      }
-      h2->Write();
-      fout->Close();
-    }
-    delete [] data;
-  }
-    
-
- 
-  return 0;
-}
-

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -27,26 +27,42 @@
 using namespace std;
 
 
+
 class threadedAnalogDetector
 {
 public:
   threadedAnalogDetector(analogDetector<uint16_t> *d, int fs=10000) {
-    char *mem, *mm;
+    char *mm;//*mem, 
     det=d;
     fifoFree=new CircularFifo<char>(fs);
     fifoData=new CircularFifo<char>(fs);
-    mem=(char*)malloc(fs*det->getDataSize());
-    // cout << "data size is " << det->getDataSize()*fs << endl;
-    for (int i=0; i<fs; i++) {
-      mm=mem+i*det->getDataSize();
-      fifoFree->push(mm);
+    // mem==NULL;
+    /* mem=(char*)calloc(fs, det->getDataSize()); */
+    /* if (mem) */
+    /*   memset(mem,0, fs*det->getDataSize()); */
+    int i;
+    for (i=0; i<fs; i++) { 
+      //
+      //  mm=mem+i*det->getDataSize();
+      // cout << i << endl;
+      mm=(char*)calloc(1, det->getDataSize());
+     
+      if (mm) { 
+	//memset(mm,0, det->getDataSize());
+	fifoFree->push(mm);
+      } else
+	break;
     }  
+    if (i<fs) cout << "Could allocate only "<< i <<" frames";
+    
+
     busy=0;
     stop=1;
     fMode=eFrame;
     ff=NULL;
   }
-  
+
+
 
   virtual int setFrameMode(int fm) {
     if (fm>=0) {
@@ -82,11 +98,14 @@ public:
   virtual int getImageSize(int &nnx, int &nny, int &ns) {return det->getImageSize(nnx, nny, ns);};
   virtual int getDetectorSize(int &nnx, int &nny) {return det->getDetectorSize(nnx, nny);};
 
-  ~threadedAnalogDetector() {StopThread(); free(mem); delete fifoFree; delete fifoData;}
+  virtual ~threadedAnalogDetector() {StopThread();  delete fifoFree; delete fifoData;}
 
    /** Returns true if the thread was successfully started, false if there was an error starting the thread */
    virtual bool StartThread()
-   { stop=0; 
+   { stop=0;  
+     cout << "Detector number " << det->getId() << endl; 
+     cout << "common mode is " << det->getCommonModeSubtraction()<< endl;
+     cout << "ghost summation is " << det->getGhostSummation()<< endl;
      return (pthread_create(&_thread, NULL, processData, this) == 0);
    }
 
@@ -97,14 +116,20 @@ public:
    
 
    virtual bool pushData(char* &ptr) {
-     fifoData->push(ptr);
+     return fifoData->push(ptr);
    }
 
    virtual bool popFree(char* &ptr) {
-     fifoFree->pop(ptr);
+     return fifoFree->pop(ptr);
    }
 
-   virtual int isBusy() {return busy;}
+   virtual int isBusy() {
+     if (fifoData->isEmpty()) 
+       busy=0; 
+     else 
+       busy=1; 
+     return busy;
+   }
    
    //protected:
    /** Implement this method in your subclass with the code you want your thread to run. */
@@ -168,16 +193,19 @@ FILE *getFilePointer(){return det->getFilePointer();};
 
    void *writeFlatField(const char * imgname) {
      slsInterpolation *interp=(det)->getInterpolation();
-     cout << "interp " << interp << endl;
+     //cout << "interp " << interp << endl;
      if (interp)  {
        cout << imgname << endl;
-       interp->writeFlatField(imgname);
+       return interp->writeFlatField(imgname);
      }
+     return NULL;
    }
+
    void *readFlatField(const char * imgname, int nb=-1, double emin=1, double emax=0){
      slsInterpolation *interp=(det)->getInterpolation();
      if (interp)  
-       interp->readFlatField(imgname, nb, emin, emax);
+       return interp->readFlatField(imgname, nb, emin, emax);
+     return NULL;
    }
 
    virtual int *getFlatField(int &nb, double emi, double ema){
@@ -199,10 +227,11 @@ FILE *getFilePointer(){return det->getFilePointer();};
    }
 
 
-   virtual int setNSubPixels(int ns)  { 
+   virtual void setNSubPixels(int ns, int nsy=-1) {
      slsInterpolation *interp=(det)->getInterpolation();
-     if (interp)  return interp->setNSubPixels(ns);
-     else return 1;};
+     if (interp) interp->setNSubPixels(ns, nsy);
+     //else return 1;
+   };
 
 
    virtual slsInterpolation *setInterpolation(slsInterpolation *f){
@@ -214,7 +243,6 @@ protected:
    int dMode;
    int *dataSize;
    pthread_t _thread;
-   char *mem;
    CircularFifo<char> *fifoFree;
    CircularFifo<char> *fifoData;
    int stop;
@@ -228,13 +256,13 @@ protected:
    }
 
    void * processData() {
-     busy=1;
+     // busy=1;
      while (!stop) {
        if (fifoData->isEmpty()) {
-	 busy=0;
+	 // busy=0;
 	 usleep(100);
        } else {
-	 busy=1;
+	 // busy=1;
 	 fifoData->pop(data); //blocking!
 	 det->processData(data);
 	 fifoFree->push(data); 
@@ -264,6 +292,7 @@ public:
     }
     
     for (int i=0; i<nThreads; i++) {
+      cout << "**" << i << endl;
       dets[i]=new threadedAnalogDetector(dd[i], fs);
     }
     
@@ -277,15 +306,15 @@ public:
     StopThreads();
     for (int i=0; i<nThreads; i++) 
       delete dets[i]; 
-    for (int i=1; i<nThreads; i++) 
-      delete dd[i];
+    /* for (int i=1; i<nThreads; i++)  */
+    /*   delete dd[i]; */
     //delete [] image;
   }
 
 
-  virtual int setFrameMode(int fm) { int ret; for (int i=0; i<nThreads; i++) {  ret=dets[i]->setFrameMode(fm);} return ret;};
-  virtual double setThreshold(int fm) { double ret; for (int i=0; i<nThreads; i++) ret=dets[i]->setThreshold(fm); return ret;};
-  virtual int setDetectorMode(int dm) { int ret; for (int i=0; i<nThreads; i++) ret=dets[i]->setDetectorMode(dm); return ret;};
+  virtual int setFrameMode(int fm) { int ret=dets[0]->setFrameMode(fm); for (int i=1; i<nThreads; i++) { dets[i]->setFrameMode(fm);} return ret;};
+  virtual double setThreshold(int fm) { double ret=dets[0]->setThreshold(fm); for (int i=1; i<nThreads; i++) dets[i]->setThreshold(fm); return ret;};
+  virtual int setDetectorMode(int dm) { int ret=dets[0]->setDetectorMode(dm);; for (int i=1; i<nThreads; i++) dets[i]->setDetectorMode(dm); return ret;};
   virtual void setROI(int xmin, int xmax, int ymin, int ymax) { for (int i=0; i<nThreads; i++) dets[i]->setROI(xmin, xmax,ymin,ymax);};
   
    
@@ -309,8 +338,11 @@ public:
       img=dets[ii]->getImage();
       for (int i=0; i<nn; i++) {
 	if (ii==0)
-	  image[i]=img[i];
-	else
+	  //	  if (img[i]>0)
+	    image[i]=img[i];
+	// else
+	//  image[i]=0;
+	else	//if (img[i]>0)
 	  image[i]+=img[i];
 	//if (img[i])	  cout << "det " << ii << " pix " << i << " val " <<  img[i] << " " << image[i] << endl;
       }
@@ -344,11 +376,14 @@ public:
      float *gm=new float[nn];
      if (gm) {
        for (int ix=0; ix<nn; ix++) {
-	 if (t)
-	   gm[ix]=(image[ix])/t;
-	 else
+	 if (t) {
+	   if (image[ix]<0) 
+	     gm[ix]=0;
+	   else
+	     gm[ix]=(image[ix])/t;
+	 } else
 	   gm[ix]=image[ix];
-	   
+
 	 //if (image[ix]>0 && ix/nnx<350) cout << ix/nnx << " " << ix%nnx << " " << image[ix]<< " " << gm[ix] << endl;
        }
        //cout << "image " << nnx << " " << nny << endl;
@@ -387,12 +422,12 @@ public:
   
    
    virtual bool pushData(char* &ptr) {
-     dets[ithread]->pushData(ptr);
+     return dets[ithread]->pushData(ptr);
    }
 
    virtual bool popFree(char* &ptr) {
      //  cout << ithread << endl;
-     dets[ithread]->popFree(ptr);
+     return dets[ithread]->popFree(ptr);
    }
    
    virtual int nextThread() {
@@ -472,20 +507,21 @@ public:
 
   virtual void *readPedestal(const char * imgname, int nb=-1, double emin=1, double emax=0){
     
-     int nx, ny;
-     dets[0]->getDetectorSize(nx,ny);
+    int nx, ny;
+    dets[0]->getDetectorSize(nx,ny);
     uint32 nnx;
     uint32 nny;
     float *gm=ReadFromTiff(imgname, nnx, nny);
     if (ped) delete [] ped;
-    if (nnx>nx) nx=nnx;
-    if (nny>ny) ny=nny;
+    if (nnx>(uint)nx) nx=nnx;
+    if (nny>(uint)ny) ny=nny;
     ped=new double[nx*ny];
     
     for (int ix=0; ix<nx*ny; ix++) {
       ped[ix]=gm[ix];
     }
     delete [] gm;
+    
     return setPedestal();
     
   };

slsDetectorCalibration/multiThreadedCountingDetector.h

@@ -25,7 +25,7 @@ class multiThreadedCountingDetector : public multiThreadedAnalogDetector
 public:
  multiThreadedCountingDetector(singlePhotonDetector *d, int n, int fs=1000) : multiThreadedAnalogDetector(d,n,fs) { };
 
-  virtual double setNSigma(double n) {double ret; for (int i=0; i<nThreads; i++) ret=(dets[i])->setNSigma(n); return ret;};
+  virtual double setNSigma(double n) {double ret=(dets[0])->setNSigma(n); for (int i=1; i<nThreads; i++) (dets[i])->setNSigma(n); return ret;};
   virtual void setEnergyRange(double emi, double ema) {for (int i=0; i<nThreads; i++) (dets[i])->setEnergyRange(emi,ema);};
   
 };

slsDetectorCalibration/multiThreadedInterpolatingDetector.h

@@ -37,12 +37,12 @@ public:
    }; 
 
    void *writeFlatField(const char * imgname){
-     dets[0]->writeFlatField(imgname);
+     return dets[0]->writeFlatField(imgname);
    };
 
 
   void *readFlatField(const char * imgname, int nb=-1, double emin=1, double emax=0){
-    (dets[0])->readFlatField(imgname, nb, emin, emax);
+    return (dets[0])->readFlatField(imgname, nb, emin, emax);
   };
   
 
@@ -56,7 +56,7 @@ public:
     \returns current file pointer
 */
    virtual slsInterpolation *setInterpolation(slsInterpolation *f){
-     int ok;
+     //int ok;
      for (int i=0; i<nThreads; i++)  
        (dets[i])->setInterpolation(f);
      return  (dets[0])->getInterpolation();

slsDetectorCalibration/singlePhotonDetector.h

@@ -58,7 +58,7 @@ public analogDetector<uint16_t> {
 		      int sign=1,
 		      commonModeSubtraction *cm=NULL,
 		      int nped=1000,
-		      int nd=100, int nnx=-1, int nny=-1, double *gm=NULL) : analogDetector<uint16_t>(d, sign, cm, nped, nnx, nny, gm),   nDark(nd), eventMask(NULL),nSigma (nsigma), clusterSize(csize), clusterSizeY(csize), clusters(NULL),   quad(UNDEFINED_QUADRANT), tot(0), quadTot(0), eMin(-1), eMax(-1) {
+		      int nd=100, int nnx=-1, int nny=-1, double *gm=NULL, ghostSummation<uint16_t> *gs=NULL) : analogDetector<uint16_t>(d, sign, cm, nped, nnx, nny, gm, gs),   nDark(nd), eventMask(NULL),nSigma (nsigma), eMin(-1), eMax(-1), clusterSize(csize), clusterSizeY(csize), clusters(NULL),   quad(UNDEFINED_QUADRANT), tot(0), quadTot(0)  {
     
     
     
@@ -183,13 +183,13 @@ public analogDetector<uint16_t> {
       //nph=new int[nx*ny];
       
       double rest[ny][nx];
-      int cy=(clusterSizeY+1)/2; //quad size
-      int cs=(clusterSize+1)/2; //quad size
+      //int cy=(clusterSizeY+1)/2; //quad size
+      //int cs=(clusterSize+1)/2; //quad size
       
-      int ccs=clusterSize; //cluster size
-      int ccy=clusterSizeY; //cluster size
+      //int ccs=clusterSize; //cluster size
+      //int ccy=clusterSizeY; //cluster size
       
-      double g=1.;
+      //double g=1.;
 
       
       double tthr=thr, tthr1, tthr2;
@@ -201,10 +201,10 @@ public analogDetector<uint16_t> {
       if (cmSub) cm=1;
 
       if (thr>0) {
-	cy=1;
-	cs=1;
-	ccs=1;
-	ccy=1;
+	//cy=1;
+	//cs=1;
+	//ccs=1;
+	//ccy=1;
       }
       if (iframe<nDark) { 
 	//	cout << "ped " << iframe << endl;
@@ -213,13 +213,13 @@ public analogDetector<uint16_t> {
 	return nph;
       }	else {
 	if (thr>0) {
-	  newFrame();
+	  newFrame(data);
 	  if (cmSub) {
 	    cout << "add to common mode?"<< endl;
 	    addToCommonMode(data);
 	  }
-	  for (int ix=xmin; ix<xmax; ix++) {
 	    for (int iy=ymin; iy<ymax; iy++) {
+	  for (int ix=xmin; ix<xmax; ix++) {
 	      if (det->isGood(ix,iy)) {
 		val=subtractPedestal(data,ix,iy, cm);
 		
@@ -236,8 +236,8 @@ public analogDetector<uint16_t> {
 	    }
 	  }
 	  
-	for (int ix=xmin; ix<xmax; ix++) {
 	  for (int iy=ymin; iy<ymax; iy++) {
+	for (int ix=xmin; ix<xmax; ix++) {
 	    
 	    if (det->isGood(ix,iy)) {
 	      eventMask[iy][ix]=PEDESTAL;
@@ -276,7 +276,6 @@ public analogDetector<uint16_t> {
 		      //}
 		    }
 		  }
-		}
 		
 		if (rest[iy][ix]>=max) { 
 		  if (bl>=br && bl>=tl && bl>=tr) {
@@ -324,6 +323,7 @@ public analogDetector<uint16_t> {
 	      }
 	    }
 	  }
+		}
 	}
 	} else return getClusters(data, nph);
       }
@@ -331,113 +331,6 @@ public analogDetector<uint16_t> {
     };
 
 
-  /*   /\** finds event type for pixel and fills cluster structure. The algorithm loops only if the evenMask for this pixel is still undefined. */
-  /* 	if pixel or cluster around it are above threshold (nsigma*pedestalRMS) cluster is filled and pixel mask is PHOTON_MAX (if maximum in cluster) or NEIGHBOUR; If PHOTON_MAX, the elements of the cluster are also set as NEIGHBOURs in order to speed up the looping */
-  /* 	if below threshold the pixel is either marked as PEDESTAL (and added to the pedestal calculator) or NEGATIVE_PEDESTAL is case it's lower than -threshold, otherwise the pedestal average would drift to negative values while it should be 0. */
-
-  /* 	/param data pointer to the data */
-  /* 	/param ix pixel x coordinate */
-  /* 	/param iy pixel y coordinate */
-  /* 	/param cm enable(1)/disable(0) common mode subtraction (if defined). */
-  /* 	/returns event type for the given pixel */
-  /*   *\/ */
-  /*   eventType getEventType(char *data, int ix, int iy, int cm=0) { */
-
-  /*     // eventType ret=PEDESTAL; */
-  /*     double max=0, tl=0, tr=0, bl=0,br=0, v; */
-  /*     //  cout << iframe << endl; */
-    
-  /*     int cy=(clusterSizeY+1)/2; */
-  /*     int cs=(clusterSize+1)/2; */
-  /*     double val; */
-  /*     tot=0; */
-  /*     quadTot=0; */
-  /*     quad=UNDEFINED_QUADRANT; */
-
-  /*     if (iframe<nDark) { */
-  /* 	addToPedestal(data, ix,iy); */
-  /* 	return UNDEFINED_EVENT; */
-  /*     } */
-
-
-     
-      
-
-  /*     //   if (eventMask[iy][ix]==UNDEFINED) { */
-	
-  /*     eventMask[iy][ix]=PEDESTAL; */
-	
-	
-  /*     clusters->x=ix; */
-  /*     clusters->y=iy; */
-  /*     clusters->rms=getPedestalRMS(ix,iy); */
-  /*     clusters->ped=getPedestal(ix,iy, cm); */
-	
-
-  /*     for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) { */
-  /* 	for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) { */
-  /* 	    if ((iy+ir)>=0 && (iy+ir)<ny && (ix+ic)>=0 && (ix+ic)<nx) { */
-	      
-  /* 	      v=subtractPedestal(data, ix+ic, iy+ir); */
-	      
-  /* 	      clusters->set_data(v, ic, ir); */
-  /* 	      //  v=clusters->get_data(ic,ir); */
-  /* 	      tot+=v; */
-  /* 	      if (ir<=0 && ic<=0) */
-  /* 		bl+=v; */
-  /* 	      if (ir<=0 && ic>=0) */
-  /* 		br+=v; */
-  /* 	      if (ir>=0 && ic<=0) */
-  /* 		tl+=v; */
-  /* 	      if (ir>=0 && ic>=0) */
-  /* 		tr+=v; */
-	      
-  /* 	      if (v>max) { */
-  /* 		max=v; */
-  /* 	      } */
-  /* 	      if (ir==0 && ic==0) { */
-  /* 		if (v<-nSigma*clusters->rms) */
-  /* 		  eventMask[iy][ix]=NEGATIVE_PEDESTAL; */
-  /* 	      } */
-  /* 	    } */
-  /* 	  } */
-  /* 	} */
-	
-  /* 	if (bl>=br && bl>=tl && bl>=tr) { */
-  /* 	  quad=BOTTOM_LEFT; */
-  /* 	  quadTot=bl; */
-  /* 	} else if (br>=bl && br>=tl && br>=tr) { */
-  /* 	  quad=BOTTOM_RIGHT; */
-  /* 	  quadTot=br; */
-  /* 	} else if (tl>=br && tl>=bl && tl>=tr) { */
-  /* 	  quad=TOP_LEFT; */
-  /* 	  quadTot=tl; */
-  /*    	} else if   (tr>=bl && tr>=tl && tr>=br) { */
-  /* 	  quad=TOP_RIGHT; */
-  /* 	  quadTot=tr; */
-  /* 	} */
-	
-  /* 	if (max>nSigma*clusters->rms || tot>sqrt(clusterSizeY*clusterSize)*nSigma*clusters->rms || quadTot>cy*cs*nSigma*clusters->rms) { */
-  /* 	  if (clusters->get_data(0,0)>=max) { */
-  /* 	    eventMask[iy][ix]=PHOTON_MAX; */
-  /* 	  } else { */
-  /* 	    eventMask[iy][ix]=PHOTON; */
-  /* 	  } */
-  /* 	} else if (eventMask[iy][ix]==PEDESTAL) { */
-  /* 	  if (cm==0) { */
-  /* 	    if (det) */
-  /* 	      val=dataSign*det->getValue(data, ix, iy); */
-  /* 	    else */
-  /* 	      val=((double**)data)[iy][ix]; */
-  /* 	    addToPedestal(val,ix,iy); */
-  /* 	  } */
-  /* 	} */
-      
-
-
-  /*     return  eventMask[iy][ix]; */
-
-  /* }; */
 
 
 
@@ -456,9 +349,9 @@ int *getClusters(char *data,  int *ph=NULL) {
   double val[ny][nx];
   int cy=(clusterSizeY+1)/2;
   int cs=(clusterSize+1)/2;
-  int ir, ic;
+  //int ir, ic;
   
-  double max=0, tl=0, tr=0, bl=0,br=0, *v, vv;
+  double max=0, tl=0, tr=0, bl=0,br=0, *v;
   int cm=0;
   int good=1;
   if (cmSub) cm=1;
@@ -469,7 +362,7 @@ int *getClusters(char *data,  int *ph=NULL) {
     addToPedestal(data);
     return 0;
   }
-  newFrame();
+  newFrame(data);
 
 
   
@@ -477,8 +370,8 @@ int *getClusters(char *data,  int *ph=NULL) {
     addToCommonMode(data);
 
 
-  for (int ix=xmin; ix<xmax; ix++) {
     for (int iy=ymin; iy<ymax; iy++) {
+  for (int ix=xmin; ix<xmax; ix++) {
       if (det->isGood(ix,iy)) {
 	max=0;
 	tl=0;
@@ -523,10 +416,14 @@ int *getClusters(char *data,  int *ph=NULL) {
 	    if (ir==0 && ic==0) {
 	      if (*v<-nSigma*(clusters+nph)->rms)
 		eventMask[iy][ix]=NEGATIVE_PEDESTAL;
+	      else if (*v>nSigma*(clusters+nph)->rms)
+		eventMask[iy][ix]=PHOTON;
 	    }
 	    
+	  }
 	}
-	}
+	if (eventMask[iy][ix]==PHOTON && val[iy][ix]<max) 
+	  continue;
 	
 	if (bl>=br && bl>=tl && bl>=tr) {
 	  (clusters+nph)->quad=BOTTOM_LEFT;
@@ -548,7 +445,8 @@ int *getClusters(char *data,  int *ph=NULL) {
 	  (clusters+nph)->tot=tot;
 	  (clusters+nph)->x=ix;
 	  (clusters+nph)->y=iy;
-	  (clusters+nph)->iframe=det->getFrameNumber(data);
+	  //	  (clusters+nph)->iframe=det->getFrameNumber(data);
+	  // cout << det->getFrameNumber(data) << " " << (clusters+nph)->iframe << endl;
 	  (clusters+nph)->ped=getPedestal(ix,iy,0);
 	  for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
 	    for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
@@ -576,8 +474,8 @@ int *getClusters(char *data,  int *ph=NULL) {
   nphFrame=nph;
   nphTot+=nph;
   //cout << nphFrame << endl;
-  // cout <<"**********************************"<< endl;
-  writeClusters();
+  //  cout <<"**********************************"<< det->getFrameNumber(data) << " " << nphFrame << endl;
+  writeClusters(det->getFrameNumber(data));
   return  image;
   
 };
@@ -662,13 +560,27 @@ int *getClusters(char *data,  int *ph=NULL) {
 
 */
 
-static void writeClusters(FILE *f, single_photon_hit *clusters, int nph){for (int i=0; i<nph; i++) (clusters+i)->write(f);};
-void writeClusters(FILE *f){for (int i=0; i<nphFrame; i++) (clusters+i)->write(f);};
- void writeClusters(){if (myFile) {  
+    static void writeClusters(FILE *f, single_photon_hit *cl, int nph, int fn=0){
+  
+/* #ifndef OLDFORMAT   */
+/*       if (fwrite((void*)&fn, 1,  sizeof(int), f))  */
+/* 	if (fwrite((void*)&nph, 1,  sizeof(int), f))  */
+/* #endif    */
+	  for (int i=0; i<nph; i++) (cl+i)->write(f);
+};
+ void writeClusters(FILE *f, int fn=0){
+   writeClusters(f,clusters,nphFrame, fn);
+  //for (int i=0; i<nphFrame; i++) 
+  //(clusters+i)->write(f);
+};
+ void writeClusters(int fn){
+   if (myFile) {  
      //cout << "++" << endl;  
      pthread_mutex_lock(fm);
-     for (int i=0; i<nphFrame; i++) 
-       (clusters+i)->write(myFile);
+     //   cout <<"**********************************"<< fn << " " << nphFrame << endl;
+     writeClusters(myFile,clusters,nphFrame, fn);
+     // for (int i=0; i<nphFrame; i++) 
+     //  (clusters+i)->write(myFile);
      pthread_mutex_unlock(fm); 
      //cout << "--" << endl; 
    } 
@@ -680,7 +592,7 @@ void writeClusters(FILE *f){for (int i=0; i<nphFrame; i++) (clusters+i)->write(f
       switch(fMode) {
       case ePedestal:
 	//cout <<"spc add to ped " << endl;
-	addToPedestal(data);
+	addToPedestal(data,1);
 	break;
       default:
 	switch (dMode) {

slsDetectorCalibration/single_photon_hit.h

@@ -38,8 +38,62 @@ class single_photon_hit {
   size_t write(FILE *myFile) {
     //fwrite((void*)this, 1, 3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
     
-    if (fwrite((void*)this, 1, sizeof(int)+2*sizeof(int16_t), myFile)) 
+    // if (fwrite((void*)this, 1, sizeof(int)+2*sizeof(int16_t), myFile))
+    //#ifdef OLDFORMAT 
+    if (fwrite((void*)&iframe, 1,  sizeof(int), myFile)) {};
+      //#endif  
+#ifndef WRITE_QUAD
+      //printf("no quad ");
+    if (fwrite((void*)&x, 2,  sizeof(int16_t), myFile)) 
       return fwrite((void*)data, 1, dx*dy*sizeof(int), myFile);
+#endif 
+#ifdef WRITE_QUAD
+    // printf("quad ");
+    int qq[4];
+    switch(quad) {
+    case TOP_LEFT:
+      qq[0]=data[3];
+      qq[1]=data[4];
+      qq[2]=data[6];
+      qq[3]=data[7];
+      x=x-1;
+      y=y;
+      break;
+      
+    case TOP_RIGHT:
+      qq[0]=data[4];
+      qq[1]=data[5];
+      qq[2]=data[7];
+      qq[3]=data[8];
+      x=x;
+      y=y;
+      break;
+
+
+    case BOTTOM_LEFT:
+      qq[0]=data[0];
+      qq[1]=data[1];
+      qq[2]=data[3];
+      qq[3]=data[4];
+      x=x-1;
+      y=y-1;
+      break;
+    case BOTTOM_RIGHT:
+      qq[0]=data[1];
+      qq[1]=data[2];
+      qq[2]=data[4];
+      qq[3]=data[5];
+      x=x;
+      y=y-1;
+      break;
+
+
+    default:
+      ;
+    }
+    if (fwrite((void*)&x, 2,  sizeof(int16_t), myFile)) 
+      return fwrite((void*)qq, 1, 4*sizeof(int), myFile);
+#endif
     return 0;
   };   
   
@@ -50,11 +104,126 @@ class single_photon_hit {
   size_t read(FILE *myFile) {
     //fread((void*)this, 1,  3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
     
-    if (fread((void*)this, 1,  sizeof(int)+2*sizeof(int16_t), myFile))  
+    //#ifdef OLDFORMAT 
+    if (fread((void*)&iframe, 1,  sizeof(int), myFile))  {}
+      //#endif   
+#ifndef WRITE_QUAD
+      // printf( "no quad \n");
+    if (fread((void*)&x, 2,  sizeof(int16_t), myFile))  
       return fread((void*)data, 1, dx*dy*sizeof(int), myFile);
+#endif 
+#ifdef WRITE_QUAD
+    int qq[4];
+    // printf( "quad \n");
+    if (fread((void*)&x, 2,  sizeof(int16_t), myFile))  
+      if (fread((void*)qq, 1, 4*sizeof(int), myFile)) {
+
+	quad=TOP_RIGHT;
+	/*	int mm=qq[0]; */
+	/* for (int i=1; i<4; i++) { */
+	/*   if (qq[i]>mm) { */
+	/*     switch (i) { */
+	/*     case 1:  */
+	/*       quad=TOP_LEFT; */
+	/*       break; */
+	/*     case 2: */
+	/*       quad=BOTTOM_RIGHT; */
+	/*       break; */
+	/*     case 3: */
+	/*       quad=BOTTOM_LEFT; */
+	/*       break; */
+	/*     default: */
+	/*       ; */
+	/*     } */
+
+	/*   } */
+
+	/* } */
+
+
+    /* switch(quad) { */
+    /* case TOP_LEFT: */
+    /*   data[0]=0; */
+    /*   data[1]=0; */
+    /*   data[2]=0; */
+    /*   data[3]=qq[0]; */
+    /*   data[4]=qq[1]; */
+    /*   data[5]=0; */
+    /*   data[6]=qq[2]; */
+    /*   data[7]=qq[3]; */
+    /*   data[8]=0; */
+    /*   x=x+1; */
+    /*   y=y; */
+    /*   break; */
+      
+    /* case TOP_RIGHT: */
+      data[0]=0;
+      data[1]=0;
+      data[2]=0;
+      data[3]=0;
+      data[4]=qq[0];
+      data[5]=qq[1];
+      data[6]=0;
+      data[7]=qq[2];
+      data[8]=qq[3];
+      x=x;
+      y=y;
+     /*  break; */
+
+
+    /* case BOTTOM_LEFT: */
+    /*   data[0]=qq[0]; */
+    /*   data[1]=qq[1]; */
+    /*   data[2]=0; */
+    /*   data[3]=qq[2]; */
+    /*   data[4]=qq[3]; */
+    /*   data[5]=0; */
+    /*   data[6]=0; */
+    /*   data[7]=0; */
+    /*   data[8]=0; */
+    /*   x=x+1; */
+    /*   y=y+1; */
+    /*   break; */
+    /* case BOTTOM_RIGHT: */
+    /*   data[0]=0; */
+    /*   data[1]=qq[0]; */
+    /*   data[2]=qq[1]; */
+    /*   data[3]=0; */
+    /*   data[4]=qq[2]; */
+    /*   data[5]=qq[3]; */
+    /*   data[6]=0; */
+    /*   data[7]=0; */
+    /*   data[8]=0; */
+    /*   x=x; */
+    /*   y=y+1; */
+    /*   break; */
+
+
+    /* default: */
+    /*   ; */
+    /* } */
+    return 1;
+      }
+#endif
+
     return 0;
   };
 
+  void print() {
+
+   // int ix, iy;
+    printf("*** %d %d %d\n",iframe, x, y);
+    for (int iy=0; iy<dy; iy++) {
+      for (int ix=0; ix<dx; ix++) {
+	printf("%d \t",data[ix+iy*dx]);
+
+      }
+    printf("\n");
+    }
+    printf("***\n");
+  }
+
+
     /** 
 	assign the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
 	\param v value to be set

slsDetectorCalibration/single_photon_hit_double.h

@@ -1,98 +0,0 @@
-#ifndef SINGLE_PHOTON_HIT_H
-#define SINGLE_PHOTON_HIT_H
-#include <stdio.h>
-#include <stdint.h>
-
-typedef  double double32_t;
-typedef  float float32_t;
-typedef  int int32_t;
-
-#ifndef DEF_QUAD
-#define DEF_QUAD
-  enum quadrant {
-    TOP_LEFT=0,
-    TOP_RIGHT=1,
-    BOTTOM_LEFT=2,
-    BOTTOM_RIGHT=3,
-    UNDEFINED_QUADRANT=-1
-  };
-#endif
-
-
-class single_photon_hit_double {
-
-  /** @short Structure for a single photon hit */
-
- public: 
-  /** constructor, instantiates the data array  -- all class elements are public!
-      \param nx cluster size in x direction
-      \param ny cluster size in y direction (defaults to 1 for 1D detectors)
-  */
-  single_photon_hit_double(int nx=3, int ny=3): dx(nx), dy(ny) {
-    data=new double[dx*dy];
-  };
-
-  ~single_photon_hit_double(){delete [] data;};  /**< destructor, deletes the data array */
-
-  /** binary write to file of all elements of the structure, except size of the cluster
-      \param myFile file descriptor
-  */
-  size_t write(FILE *myFile) {
-    //fwrite((void*)this, 1, 3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    if (fwrite((void*)this, 1, sizeof(int)+2*sizeof(int), myFile)) 
-      return fwrite((void*)data, 1, dx*dy*sizeof(double), myFile);
-    return 0;
-  };   
-  
-  /** 
-      binary read from file of all elements of the structure, except size of the cluster. The structure is then filled with those args
-      \param myFile file descriptor
-  */
-  size_t read(FILE *myFile) {
-    //fread((void*)this, 1,  3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    
-    if (fread((void*)this, 1,  sizeof(int)+2*sizeof(int), myFile))  
-      return fread((void*)data, 1, dx*dy*sizeof(double), myFile);
-    return 0;
-  };
-
-    /** 
-	assign the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
-	\param v value to be set
-	\param ix coordinate x within the cluster (center is (0,0))
-	\param iy coordinate y within the cluster (center is (0,0))
-  */
-  void set_data(double v, int ix, int iy=0){data[(iy+dy/2)*dx+ix+dx/2]=v;};
-
-  void set_cluster_size(int nx, int ny) {
-  
-  if (nx>0) dx=nx; if (ny>0) dy=ny; delete [] data; data=new double[dx*dy];
-  };
-  void get_cluster_size(int &nx, int &ny) {nx=dx; ny=dy;};
-  void get_pixel(int &x1, int &y1) {x1=x; y1=y;};
-
-    /** 
-	gets the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
-	\param ix coordinate x within the cluster (center is (0,0))
-	\param iy coordinate y within the cluster (center is (0,0))
-	\returns value of the cluster element
-  */
-  double get_data(int ix, int iy=0){return data[(iy+dy/2)*dx+ix+dx/2];};
-  double *get_cluster() {return data;};
-
-  int	iframe; 	        /**< frame number */
-  int 	x; 			/**< x-coordinate of the center of hit */
-  int	y; 			/**< x-coordinate of the center of hit */
-  double	rms; 		/**< noise of central pixel l -- at some point it can be removed*/
-  double 	ped; 		/**< pedestal of the central pixel -- at some point it can be removed*/
-   double tot; /**< sum of the 3x3 cluster */
-   quadrant quad; /**< quadrant where the photon is located */
-   double quadTot; /**< sum of the maximum 2x2cluster */ 
-  int dx;	                /**< size of data cluster in x */
-  int dy;                 /**< size of data cluster in y */  
-  double *data;		        /**< pointer to data */
-};
-
-
-
-#endif

slsDetectorCalibration/single_photon_hit_old.h

@@ -1,93 +0,0 @@
-#ifndef SINGLE_PHOTON_HIT_H
-#define SINGLE_PHOTON_HIT_H
-#include <stdio.h>
-#include <stdint.h>
-
-typedef  double double32_t;
-typedef  float float32_t;
-typedef  int int32_t;
-
-#ifndef DEF_QUAD
-#define DEF_QUAD
-  enum quadrant {
-    TOP_LEFT=0,
-    TOP_RIGHT=1,
-    BOTTOM_LEFT=2,
-    BOTTOM_RIGHT=3,
-    UNDEFINED_QUADRANT=-1
-  };
-#endif
-
-
-class single_photon_hit {
-
-  /** @short Structure for a single photon hit */
-
- public: 
-  /** constructor, instantiates the data array  -- all class elements are public!
-      \param nx cluster size in x direction
-      \param ny cluster size in y direction (defaults to 1 for 1D detectors)
-  */
-  single_photon_hit(int nx=3, int ny=3): dx(nx), dy(ny) {data=new int[dx*dy];};
-
-  ~single_photon_hit(){delete [] data;};  /**< destructor, deletes the data array */
-
-  /** binary write to file of all elements of the structure, except size of the cluster
-      \param myFile file descriptor
-  */
-  size_t write(FILE *myFile) {
-    //fwrite((void*)this, 1, 3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    if (fwrite((void*)this, 1, sizeof(int)+2*sizeof(int16_t), myFile)) 
-      return fwrite((void*)data, 1, dx*dy*sizeof(int), myFile);
-    return 0;
-  };   
-  
-  /** 
-      binary read from file of all elements of the structure, except size of the cluster. The structure is then filled with those args
-      \param myFile file descriptor
-  */
-  size_t read(FILE *myFile) {
-    //fread((void*)this, 1,  3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    
-    if (fread((void*)this, 1,  sizeof(int)+2*sizeof(int16_t), myFile))  
-      return fread((void*)data, 1, dx*dy*sizeof(int), myFile);
-    return 0;
-  };
-
-    /** 
-	assign the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
-	\param v value to be set
-	\param ix coordinate x within the cluster (center is (0,0))
-	\param iy coordinate y within the cluster (center is (0,0))
-  */
-  void set_data(double v, int ix, int iy=0){data[(iy+dy/2)*dx+ix+dx/2]=v;};
-
-  void set_cluster_size(int nx, int ny) {if (nx>0) dx=nx; if (ny>0) dy=ny; delete [] data; data=new int[dx*dy];};
-  void get_cluster_size(int &nx, int &ny) {nx=dx; ny=dy;};
-  void get_pixel(int &x1, int &y1) {x1=x; y1=y;};
-
-    /** 
-	gets the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
-	\param ix coordinate x within the cluster (center is (0,0))
-	\param iy coordinate y within the cluster (center is (0,0))
-	\returns value of the cluster element
-  */
-  double get_data(int ix, int iy=0){return data[(iy+dy/2)*dx+ix+dx/2];};
-  int *get_cluster() {return data;};
-
-  int	iframe; 	        /**< frame number */
-  int16_t 	x; 			/**< x-coordinate of the center of hit */
-  int16_t	y; 			/**< x-coordinate of the center of hit */
-  double	rms; 		/**< noise of central pixel l -- at some point it can be removed*/
-  double 	ped; 		/**< pedestal of the central pixel -- at some point it can be removed*/
-   double tot; /**< sum of the 3x3 cluster */
-   quadrant quad; /**< quadrant where the photon is located */
-   double quadTot; /**< sum of the maximum 2x2cluster */ 
-  int dx;	                /**< size of data cluster in x */
-  int dy;                 /**< size of data cluster in y */  
-  int *data;		        /**< pointer to data */
-};
-
-
-
-#endif

slsDetectorCalibration/slsDetectorCalibration.doxy

@@ -1,103 +0,0 @@
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
-# documentation are documented, even if no documentation was available. 
-# Private class members and static file members will be hidden unless 
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL            = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
-# will be included in the documentation.
-
-EXTRACT_PRIVATE        = NO
-
-
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file 
-# will be included in the documentation.
-
-EXTRACT_STATIC         = YES
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES  = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS  = YES
-
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespace are hidden.
-
-EXTRACT_ANON_NSPACES   = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS     = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES     = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS  = NO
-
-INTERNAL_DOCS = NO
-
-SHOW_INCLUDE_FILES = NO
-
-SHOW_FILES = NO
-
-SHOW_NAMESPACES = NO
-
-COMPACT_LATEX = YES
-
-PAPER_TYPE = a4
-
-PDF_HYPERLINKS = YES
-
-USE_PDFLATEX = YES
-
-LATEX_HIDE_INDICES = YES
-
-PREDEFINED           = __cplusplus
-
-INPUT		= analogDetector.h \
-		pedestalSubtraction.h \ 
-		MovingStat.h  \
-		singlePhotonDetector.h  \
-		interpolatingDetector.h tiffIO.h \
-		single_photon_hit.h \
-		dataStructures/slsDetectorData.h \
-		commonModeSubtraction.h \			 
-		RunningStat.h \
-		interpolations/etaInterpolationBase.h \
-		interpolations/slsInterpolation.h \
-		interpolations/etaInterpolationPosXY.h \
-		interpolations/linearInterpolation.h \
-		interpolations/noInterpolation.h \
-		interpolations/etaInterpolationGlobal.h \
-		multiThreadedAnalogDetector.h 
-				
-			
-OUTPUT_DIRECTORY = slsDetectorCalibrationDocs
-
-#moench03Ctb10GbT1Data.h moench03TCtbData.h moench03T1CtbData.h moench03CtbData.h moench03Ctb10GbData.h moench03TCtb10GbData.h Mythen3_01_jctbData.h adcSar2_jctbData.h eigerHalfModuleData.h energyCalibration.h slsReceiverData.h gotthardModuleData.h gotthardShortModuleData.h jungfrau02Data.h jungfrau10ModuleData.h moench02Ctb10GbData.h moench02CtbData.h moench02ModuleData.h moench03CommonMode.h moenchCommonMode.h chiptestBoardData.h interpolation/etaVEL/interpolation_EtaVEL.h interpolation/etaVEL/EtaVEL.h etaVEL/iterativeEtaInterpolation.h dataStructures/moench03T1ZmqData.h	

slsDetectorCalibration/tiffIO.cpp

@@ -4,21 +4,21 @@
 #include<iostream>
 using namespace std;
 // #undef cbf_failnez 
-// #define cbf_failnez(x)				\
-//   {						\
-//   int err;	        			\
-//   err = (x);					\
-//   if (err) {						\
-//   fprintf(stderr,"\nCBFlib fatal error %x \n",err);	\
-//   exit(-1);						\
-//   }							\
+// #define cbf_failnez(x)				
+//   {						
+//   int err;	        			
+//   err = (x);					
+//   if (err) {						
+//   fprintf(stderr,"\nCBFlib fatal error %x \n",err);	
+//   exit(-1);						
+//   }							
 //   }
 
-void *WriteToTiff(float * imgData, const char * imgname, int nrow, int ncol){
+void *WriteToTiff(float * imgData, const char * imgname, int ncol, int nrow){
   int sampleperpixel=1;
   // unsigned char * buff=NULL;
-  tsize_t linebytes;
- cout << "--" <<endl;
+  //tsize_t linebytes;
+  // cout << "--" <<endl;
   TIFF * tif = TIFFOpen(imgname,"w");
   if (tif) {
     TIFFSetField(tif,TIFFTAG_IMAGEWIDTH,ncol);
@@ -30,7 +30,7 @@ void *WriteToTiff(float * imgData, const char * imgname, int nrow, int ncol){
     TIFFSetField(tif, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
     TIFFSetField(tif, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_IEEEFP);
     
-    linebytes = sampleperpixel*ncol;
+    //linebytes = sampleperpixel*ncol;
     TIFFSetField(tif, TIFFTAG_ROWSPERSTRIP, TIFFDefaultStripSize(tif, ncol*sampleperpixel));
     for(int irow=0; irow<nrow; irow++){
       TIFFWriteScanline(tif,&imgData[irow*ncol],irow,0);
@@ -43,14 +43,14 @@ void *WriteToTiff(float * imgData, const char * imgname, int nrow, int ncol){
   return NULL;
 };
 
-float *ReadFromTiff( const char * imgname, uint32 &nrow, uint32 &ncol){
+float *ReadFromTiff( const char * imgname, uint32 &ncol, uint32 &nrow){
   // unsigned char * buff=NULL;
 
   TIFF * tif = TIFFOpen(imgname,"r");
   if (tif){
         uint32 bps;
 	uint32 sampleperpixel=1;
-  tsize_t linebytes;
+  //tsize_t linebytes;
 
  uint32 imagelength;
 
@@ -61,9 +61,9 @@ float *ReadFromTiff( const char * imgname, uint32 &nrow, uint32 &ncol){
     TIFFGetField(tif, TIFFTAG_IMAGELENGTH, &imagelength);
 
     float * imgData=new float[ncol*nrow];
-    linebytes = sampleperpixel*ncol;
+    //linebytes = sampleperpixel*ncol;
     //  TIFFSetField(tif, TIFFTAG_ROWSPERSTRIP, TIFFDefaultStripSize(tif, ncol*sampleperpixel));
-    for(int irow=0; irow<nrow; irow++){
+    for(uint32 irow=0; irow<nrow; irow++){
       //tiffreadscanline(tif, buf, row);
       TIFFReadScanline(tif,&imgData[irow*ncol],irow);
     }

slsDetectorSoftware/commonFiles/communication_funcs.c

@@ -31,6 +31,9 @@ int myport=-1;
 //struct sockaddr_in address;
 //#define VERBOSE
 
+#define BLACKFIN_DRVR_SND_LMT	(30000) // rough limit
+#define BLACKFIN_RSND_PCKT_LOOP	(10)
+#define BLACKFIN_RSND_WAIT_US	(1)
 
 int bindSocket(unsigned short int port_number) {
   int i;
@@ -314,13 +317,46 @@ int receiveData(int file_des, void* buf,int length, intType itype){
 	return ret;
 }
 
-
- int sendDataOnly(int file_des, void* buf,int length) {
+int sendDataOnly(int file_des, void* buf,int length) {
      if (!length)
          return 0;
-	 int ret =  write(file_des, buf, length); //value of -1 is other end socket crash as sigpipe is ignored
-	 if (ret < 0) cprintf(BG_RED, "Error writing to socket. Possible socket crash\n");
-	 return ret;
+
+
+	  int bytesSent = 0;
+	  int retry = 0; // retry index when buffer is blocked (write returns 0)
+	  while (bytesSent < length) {
+
+		  // setting a max packet size for blackfin driver (and network driver does not do a check if packets sent)
+		  int bytesToSend = length - bytesSent;
+		  if (bytesToSend > BLACKFIN_DRVR_SND_LMT)
+			  bytesToSend = BLACKFIN_DRVR_SND_LMT;
+
+		  // send
+		  int rc = write(file_des, (char*)((char*)buf + bytesSent), bytesToSend);
+		  // error
+		  if (rc < 0) {
+		    cprintf(BG_RED, "Error writing to socket. Possible socket crash: left=%d rc=%d length=%d sent=%d\n", bytesToSend, rc, length, bytesSent);
+			  return bytesSent;
+		  }
+		  // also error, wrote nothing, buffer blocked up, too fast sending for client
+		  if (rc == 0) {
+			  cprintf(RED, "Error writing to socket. Buffer full. Retry: %d\n", retry);
+			  ++retry;
+			  // wrote nothing for many loops
+			  if (retry >= BLACKFIN_RSND_PCKT_LOOP) {
+				  cprintf(BG_RED, "Error writing to socket. Buffer full! Too fast! No more.\n");
+				  return bytesSent;
+			  }
+			  usleep(BLACKFIN_RSND_WAIT_US);
+		  }
+		  // wrote something, reset retry
+		  else  {
+			  retry = 0;
+		  }
+		  bytesSent += rc;
+	  }
+
+	  return bytesSent;
 }
 
 

slsDetectorSoftware/commonFiles/sls_detector_defs.h

@@ -195,7 +195,7 @@ enum networkParameter {
 /**
     type of action performed (for text client)
 */
-enum {GET_ACTION, PUT_ACTION, READOUT_ACTION, HELP_ACTION};
+ enum {GET_ACTION, PUT_ACTION, READOUT_ACTION, HELP_ACTION, PROCESS_ACTION};
 
 /** online flags enum \sa setOnline*/
 enum {GET_ONLINE_FLAG=-1, /**< returns wether the detector is in online or offline state */

slsDetectorSoftware/jctbDetectorServer/firmware_funcs.c

@@ -75,7 +75,8 @@ typedef struct ip_header_struct {
 
 struct timeval tss,tse,tsss; //for timing
 
-
+#define MAXDAC 32
+u_int32_t dac[MAXDAC];
 
 FILE *debugfp, *datafp;
 
@@ -890,107 +891,33 @@ int setTiming(int ti) {
 
 
   int ret=GET_EXTERNAL_COMMUNICATION_MODE;
-
+  int val;
   int g=-1, t=-1, rot=-1;
 
   int i;
 
+  val=bus_r(EXT_SIGNAL_REG); 
   switch (ti) {
   case AUTO_TIMING:
-    timingMode=ti;
-    // disable all gates/triggers in except if used for master/slave synchronization
-    for (i=0; i<4; i++) {
-      if (getFPGASignal(i)>0 && getFPGASignal(i)<GATE_OUT_ACTIVE_HIGH && signals[i]!=MASTER_SLAVE_SYNCHRONIZATION)
-	setFPGASignal(i,SIGNAL_OFF);
-    }
+    bus_w(EXT_SIGNAL_REG,val&~(0x1));
     break;
 
   case   TRIGGER_EXPOSURE:
-    timingMode=ti;
-    // if one of the signals is configured to be trigger, set it and unset possible gates
-    for (i=0; i<4; i++) {
-      if (signals[i]==TRIGGER_IN_RISING_EDGE ||  signals[i]==TRIGGER_IN_FALLING_EDGE)
-	setFPGASignal(i,signals[i]);
-      else if (signals[i]==GATE_IN_ACTIVE_HIGH || signals[i]==GATE_IN_ACTIVE_LOW)
-	setFPGASignal(i,SIGNAL_OFF);
-      else if (signals[i]==RO_TRIGGER_IN_RISING_EDGE ||  signals[i]==RO_TRIGGER_IN_FALLING_EDGE)
-	setFPGASignal(i,SIGNAL_OFF);
-
-    }
+    bus_w(EXT_SIGNAL_REG,val|(0x1));
     break;
 
 
-
-  case  TRIGGER_READOUT:
-    timingMode=ti;
-    // if one of the signals is configured to be trigger, set it and unset possible gates
-    for (i=0; i<4; i++) {
-      if (signals[i]==RO_TRIGGER_IN_RISING_EDGE ||  signals[i]==RO_TRIGGER_IN_FALLING_EDGE)
-	setFPGASignal(i,signals[i]);
-      else if (signals[i]==GATE_IN_ACTIVE_HIGH || signals[i]==GATE_IN_ACTIVE_LOW)
-	setFPGASignal(i,SIGNAL_OFF);
-      else if (signals[i]==TRIGGER_IN_RISING_EDGE ||  signals[i]==TRIGGER_IN_FALLING_EDGE)
-	setFPGASignal(i,SIGNAL_OFF);
-    }
-    break;
-
-  case GATE_FIX_NUMBER:
-    timingMode=ti;
-    // if one of the signals is configured to be trigger, set it and unset possible gates
-    for (i=0; i<4; i++) {
-      if (signals[i]==RO_TRIGGER_IN_RISING_EDGE ||  signals[i]==RO_TRIGGER_IN_FALLING_EDGE)
-	setFPGASignal(i,SIGNAL_OFF);
-      else if (signals[i]==GATE_IN_ACTIVE_HIGH || signals[i]==GATE_IN_ACTIVE_LOW)
-	setFPGASignal(i,signals[i]);
-      else if (signals[i]==TRIGGER_IN_RISING_EDGE ||  signals[i]==TRIGGER_IN_FALLING_EDGE)
-	setFPGASignal(i,SIGNAL_OFF);
-    }
-    break;
-
-
-
-  case GATE_WITH_START_TRIGGER:
-    timingMode=ti;
-    for (i=0; i<4; i++) {
-      if (signals[i]==RO_TRIGGER_IN_RISING_EDGE ||  signals[i]==RO_TRIGGER_IN_FALLING_EDGE)
-	setFPGASignal(i,SIGNAL_OFF);
-      else if (signals[i]==GATE_IN_ACTIVE_HIGH || signals[i]==GATE_IN_ACTIVE_LOW)
-	setFPGASignal(i,signals[i]);
-      else if (signals[i]==TRIGGER_IN_RISING_EDGE ||  signals[i]==TRIGGER_IN_FALLING_EDGE)
-	setFPGASignal(i,signals[i]);
-    }
-    break;
-
   default:
 	  break;
 
   }
 
-
-
-  for (i=0; i<4; i++) {
-    if (signals[i]!=MASTER_SLAVE_SYNCHRONIZATION) {
-      if (getFPGASignal(i)==RO_TRIGGER_IN_RISING_EDGE ||  getFPGASignal(i)==RO_TRIGGER_IN_FALLING_EDGE)
-	rot=i;
-      else if (getFPGASignal(i)==GATE_IN_ACTIVE_HIGH || getFPGASignal(i)==GATE_IN_ACTIVE_LOW)
-	g=i;
-      else if (getFPGASignal(i)==TRIGGER_IN_RISING_EDGE ||  getFPGASignal(i)==TRIGGER_IN_FALLING_EDGE)
-	t=i;
-    }
-  }
-
-
-  if (g>=0 && t>=0 && rot<0) {
-    ret=GATE_WITH_START_TRIGGER;
-  } else if (g<0 && t>=0 && rot<0) {
+  if (bus_r(EXT_SIGNAL_REG)&0x1)
     ret=TRIGGER_EXPOSURE;
-  } else if (g>=0 && t<0 && rot<0) {
-    ret=GATE_FIX_NUMBER;
-  } else if (g<0 && t<0 && rot>0) {
-    ret=TRIGGER_READOUT;
-  } else if (g<0 && t<0 && rot<0) {
+  else
     ret=AUTO_TIMING;
-  }
+
+
 
   // timingMode=ret;
 
@@ -1671,22 +1598,28 @@ int initHighVoltage(int val, int imod){
        codata=((dacvalue)&0xff);
      
     
-       valw=bus_r(offw)&0x7fff; //switch off HV 
+       valw=(bus_r(offw) & 0x7fff) | 0x00ff;
+
        bus_w(offw,(valw)); // start point
        valw=((valw&(~(0x1<<csdx))));bus_w(offw,valw); //chip sel bar down
+       
        for (i=0;i<8;i++) {
-	valw=(valw&(~(0x1<<cdx)));bus_w(offw,valw); //cldwn
-	valw=((valw&(~(0x1<<ddx)))+(((codata>>(7-i))&0x1)<<ddx));bus_w(offw,valw);//write data (i)
-	valw=((valw&(~(0x1<<cdx)))+(0x1<<cdx));bus_w(offw,valw);//clkup
+	 valw=(valw&(~(0x1<<cdx)));bus_w(offw,valw); //cldwn
+	 valw=((valw&(~(0x1<<ddx)))+(((codata>>(7-i))&0x1)<<ddx));bus_w(offw,valw);//write data (i)
+	 valw=((valw&(~(0x1<<cdx)))+(0x1<<cdx));bus_w(offw,valw);//clkup
        }
        valw=((valw&(~(0x1<<csdx)))+(0x1<<csdx));bus_w(offw,valw); //csup
        
        valw=(valw&(~(0x1<<cdx)));bus_w(offw,valw); //cldwn
+
+
        
-       if (dacvalue>=0) {
-	 valw=bus_r(offw)|0xff00;; //switch on HV
+       if (val>=0) {
+	 valw=bus_r(offw) | 0x8000;; //switch on HV
+	 printf("switch on HV in CTB4 %x\n");
        } else {
-	 valw=bus_r(offw)&0x7fff;//switch off HV
+	 valw=bus_r(offw) & 0x7fff;//switch off HV
+	 printf("switch off HV in CTB4\n");
        }
 
 
@@ -1695,6 +1628,22 @@ int initHighVoltage(int val, int imod){
        
        bus_w(HV_REG,val);
        
+
+       //added for CTB5!
+
+       // valw=bus_r(POWER_ON_REG);
+       if (val>=0) {
+	 i=bus_r(POWER_ON_REG) | 0x80000000;; //switch on HV
+	 printf("switch on HV in CTB5 %08x\n", i);
+       } else {
+	 i=bus_r(POWER_ON_REG)  & 0x7fffffff;//switch off HV
+	 printf("switch off HV in CTB5 %08x\n", i);
+       }
+       
+       bus_w(POWER_ON_REG,i);
+
+
+
 	 // } 
   }
 
@@ -3212,12 +3161,22 @@ int setDacRegister(int dacnum,int dacvalue) {
 /*   printf("Dac register %x wrote %08x\n",(DAC_REG_OFF+dacnum/2)<<11,val); */
 /*     bus_w((DAC_REG_OFF+dacnum/2)<<11, val); */
     
-
+#ifdef CTB4
   bus_w(DAC_NUM_REG, dacnum);
   bus_w(DAC_VAL_REG, dacvalue);
   bus_w(DAC_NUM_REG, dacnum | (1<<16));
   bus_w(DAC_NUM_REG, dacnum);
   printf("Wrote dac register value %d address %d\n",bus_r(DAC_VAL_REG),bus_r(DAC_NUM_REG)) ;
+#endif
+  
+#ifndef CTB4
+  
+  if (dacnum<MAXDAC) {
+    printf("dac variable %d set to  value %d\n",dacnum, dacvalue) ;
+    dac[dacnum]=dacvalue;
+  } else
+    printf("Bad dac index %d\n", dacnum);
+#endif
   return getDacRegister(dacnum);
   
 
@@ -3225,9 +3184,22 @@ int setDacRegister(int dacnum,int dacvalue) {
 int getDacRegister(int dacnum) {
 
   
+#ifdef CTB4
   bus_w(DAC_NUM_REG, dacnum);
   printf("READ dac register value %d address %d\n",(int16_t)bus_r(DAC_VAL_OUT_REG),bus_r(DAC_NUM_REG)) ;
   return (int16_t)bus_r(DAC_VAL_OUT_REG);
+#endif
+
+#ifndef CTB4
+  if (dacnum<MAXDAC) {
+    printf("dac variable %d is %d\n",dacnum,dac[dacnum]) ;
+    return dac[dacnum];
+  }else
+    printf("Bad dac index %d\n", dacnum);
+#endif
+
+  return -1;
+
 /* #define DAC_VAL_REG 121<<11 */
 /* #define DAC_NUM_REG 122<<11 */
 /* #define DAC_VAL_OUT_REG 42<<11 */
@@ -3533,6 +3505,7 @@ int powerChip(int arg) {
   
   u_int32_t preg=bus_r(POWER_ON_REG); 
   if (myDetectorType!=JUNGFRAUCTB) {
+    printf("This is not a JCTB!\n");
     if (arg>=0) {
       if (arg)
 	bus_w(POWER_ON_REG,preg|0xffff0000);

slsDetectorSoftware/jctbDetectorServer/gitInfo.txt

@@ -1,9 +1,9 @@
 Path: slsDetectorsPackage/slsDetectorSoftware/jctbDetectorServer 
 URL: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
 Repository Root: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
-Repsitory UUID: 83600fcb15c8261173ab15a8ba8d1009693f2d23 
-Revision: 27 
-Branch: anna 
-Last Changed Author: Anna_Bergamaschi 
-Last Changed Rev: 3962 
-Last Changed Date: 2018-09-04 11:59:37.000000002 +0200 ./firmware_funcs.c
+Repsitory UUID: 9e5ec6a57bf206fe9384260fc4040867a9bbd71c 
+Revision: 33 
+Branch: developer 
+Last Changed Author: Erik_Frojdh 
+Last Changed Rev: 4065 
+Last Changed Date: 2019-01-30 17:38:35.000000002 +0100 ./firmware_funcs.c

slsDetectorSoftware/jctbDetectorServer/gitInfoMoench.h

@@ -1,6 +1,6 @@
 #define GITURL "git@github.com:slsdetectorgroup/slsDetectorPackage.git"
-#define GITREPUUID "83600fcb15c8261173ab15a8ba8d1009693f2d23"
-#define GITAUTH "Anna_Bergamaschi"
-#define GITREV 0x3962
-#define GITDATE 0x20180904
-#define GITBRANCH "anna"
+#define GITREPUUID "9e5ec6a57bf206fe9384260fc4040867a9bbd71c"
+#define GITAUTH "Erik_Frojdh"
+#define GITREV 0x4065
+#define GITDATE 0x20190130
+#define GITBRANCH "developer"