some updates to the moench data processing

libs/pybind11

@@ -1 +1 @@
-Subproject commit 914c06fb252b6cc3727d0eedab6736e88a3fcb01
+Subproject commit 8de7772cc72daca8e947b79b83fea46214931604

slsDetectorCalibration/moench03CommonMode.h

@@ -21,9 +21,9 @@ class commonModeSubtractionColumn : public commonModeSubtraction {
                 nCm[iroi]++;
                 if (nCm[iroi] > rows)
                     std::cout << "Too many pixels added " << nCm[iroi] << std::endl;
-                /* if (ix==10 && iy<20) */
+                /* if (ix==10 && iy==20) */
-                /*   cout << " ** "<<val << " " << mean[iroi] << " " <<
+		/*   std::cout << " ** "<<val << " " << mean[iroi] << " " << */
-                 * nCm[iroi] << " " << getCommonMode(ix, iy) << endl; */
+		/*     nCm[iroi] << " " << getCommonMode(ix, iy) << std::endl; */
             }
         }
     };
@@ -36,6 +36,40 @@ class commonModeSubtractionColumn : public commonModeSubtraction {
     int rows;
 };
 
+class commonModeSubtractionRow : public commonModeSubtraction {
+  public:
+    commonModeSubtractionRow(int nc = 400)
+        : commonModeSubtraction(200), cols(nc){};
+  virtual int getROI(int ix, int iy) { 
+    if (iy/200<1) return 199-iy%200; 
+    else return iy%200;
+  } 
+
+    virtual void addToCommonMode(double val, int ix = 0, int iy = 0) {
+        if (ix < cols || ix > 399 - cols) {
+            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] > 4*cols)
+		std::cout << "Too many pixels added " << nCm[iroi] << std::endl;
+                /* if (ix==10 && iy==20) */
+		/*   std::cout << " ** "<<val << " " << mean[iroi] << " " << */
+		/*     nCm[iroi] << " " << getCommonMode(ix, iy) << std::endl; */
+            }
+        }
+    };
+
+    virtual commonModeSubtractionRow *Clone() {
+        return new commonModeSubtractionRow(this->cols);
+    };
+
+  private:
+    int cols;
+};
+
 class commonModeSubtractionSuperColumn : public commonModeSubtraction {
   public:
     commonModeSubtractionSuperColumn() : commonModeSubtraction(32){};
@@ -51,14 +85,15 @@ class commonModeSubtractionHalf : public commonModeSubtraction {
     };
 };
 
-class moench03CommonMode : public commonModeSubtractionColumn {
+class moench03CommonMode : public commonModeSubtractionRow {
     /** @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 nr = 20) : commonModeSubtractionColumn(nr){};
+    //moench03CommonMode(int nr = 20) : commonModeSubtractionColumn(nr){};
+    moench03CommonMode(int nr = 20) : commonModeSubtractionRow(nr){};
 };
 
 #endif

slsDetectorCalibration/moenchExecutables/moenchRawDataProcess.cpp

@@ -2,11 +2,12 @@
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 //#include "sls/ansi.h"
 #include <iostream>
+//#define CORR
 #undef CORR
 
-#define C_GHOST 0.0004
+#define C_GHOST 0 //0.0004
 
-#define CM_ROWS 50
+#define CM_ROWS 20
 
 #define RAWDATA
 
@@ -164,8 +165,8 @@ int main(int argc, char *argv[]) {
     cout << "Applying common mode  " << ncol_cm << endl;
     cm = new moench03CommonMode(ncol_cm);
 
-    cout << "Applying ghost corrections " << xt_ghost << endl;
+    // cout << "Applying ghost corrections " << xt_ghost << endl;
-    gs = new moench03GhostSummation(decoder, xt_ghost);
+    // gs = new moench03GhostSummation(decoder, xt_ghost);
 #endif
 
     singlePhotonDetector *filter = new singlePhotonDetector(
@@ -222,15 +223,20 @@ int main(int argc, char *argv[]) {
     //  cout << "mt " << endl;
 
     int ifr = 0;
-
+    char froot[1000];
     double *ped=new double[nx * ny];//, *ped1;
-
+    int pos,pos1;
+    
     if (pedfile) {
+      if (string(pedfile).find(".raw") != std::string::npos) {
+	pos1=string(pedfile).rfind("/");
+	strcpy(froot,pedfile+pos1);
+	pos=string(froot).find(".raw");
+	froot[pos]='\0';
+      }
 
-        cout << "PEDESTAL " << endl;
+      cout << "PEDESTAL " << endl;
-        sprintf(imgfname, "%s/pedestals.tiff", outdir);
+      if (string(pedfile).find(".tif") == std::string::npos) {
-
-        if (string(pedfile).find(".tif") == std::string::npos) {
             sprintf(fname, "%s", pedfile);
             cout << fname << endl;
             std::time(&end_time);
@@ -259,6 +265,10 @@ int main(int argc, char *argv[]) {
                     ;
                 }
 
+		sprintf(imgfname, "%s/%s_ped.tiff", outdir,froot);
+		mt->writePedestal(imgfname);
+		sprintf(imgfname, "%s/%s_var.tiff", outdir,froot);
+		mt->writePedestalRMS(imgfname);
             } else
                 cout << "Could not open pedestal file " << fname
                      << " for reading " << endl;
@@ -276,7 +286,6 @@ int main(int argc, char *argv[]) {
                      << " for reading " << endl;
             }
         }
-        mt->writePedestal(imgfname);
         std::time(&end_time);
         cout << std::ctime(&end_time) << endl;
     }

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

@@ -88,7 +88,7 @@ int main(int argc, char *argv[]) {
     char *socketip2 = 0;
     uint32_t portnum2 = 0;
 
-    zmqHeader zHeader, outHeader;
+    sls::zmqHeader zHeader, outHeader;
     zHeader.jsonversion = SLS_DETECTOR_JSON_HEADER_VERSION;
     outHeader.jsonversion = SLS_DETECTOR_JSON_HEADER_VERSION;
 
@@ -219,14 +219,14 @@ int main(int argc, char *argv[]) {
     mt->StartThreads();
     mt->popFree(buff);
 
-    ZmqSocket *zmqsocket = NULL;
+    sls::ZmqSocket *zmqsocket = NULL;
 
 #ifdef NEWZMQ
     // receive socket
     try {
 #endif
 
-        zmqsocket = new ZmqSocket(socketip, portnum);
+      zmqsocket = new sls::ZmqSocket(socketip, portnum);
 
 #ifdef NEWZMQ
     } catch (...) {
@@ -256,14 +256,14 @@ int main(int argc, char *argv[]) {
         printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress().c_str());
 
     // send socket
-    ZmqSocket *zmqsocket2 = 0;
+    sls::ZmqSocket *zmqsocket2 = 0;
     // cout << "zmq2 " << endl;
     if (send) {
 #ifdef NEWZMQ
         // receive socket
         try {
 #endif
-            zmqsocket2 = new ZmqSocket(portnum2, socketip2);
+	  zmqsocket2 = new sls::ZmqSocket(portnum2, socketip2);
 
 #ifdef NEWZMQ
         } catch (...) {

slsDetectorCalibration/singlePhotonDetector.h

@@ -229,7 +229,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
                 double *rest = new double[ny * nx];
                 newFrame(data);
                 if (cmSub) {
-                    cout << "add to common mode?" << endl;
+		  //cout << "add to common mode?" << endl;
                     addToCommonMode(data);
                 }
                 for (iy = ymin; iy < ymax; ++iy) {
@@ -386,7 +386,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         // double quadTot;
         // quadrant quad;
         double rms;
-        // if (cmSub) cm=1;
+
         if (ph == NULL)
             ph = image;