doxygen configuration file added

git-svn-id: file:///afs/psi.ch/project/sls_det_software/svn/slsDetectorCalibration@14 113b152e-814d-439b-b186-022a431db7b5

slsDetectorCalibration/commonModeSubtraction.h

@@ -36,20 +36,23 @@ class commonModeSubtraction {
 	cmPed[i]=0;
       }};
     
-    /** adds the pixel to the sum of pedestals -- virtual func 
-	\param isc region of interest index
+    /** adds the pixel to the sum of pedestals -- virtual func must be overloaded to define the regions of interest
+	\param ix region of interest index
     */
-    virtual void addToCommonMode(double val, int isc=0) {
-      if (isc>=0 && isc<nROI) {
-	cmPed[isc]+=val; 
-	nCm[isc]++;}};
+    virtual void addToCommonMode(double val, int ix=0, int iy=0) {
+      (void) ix; (void) iy;
       
-    /** gets the common mode i.e. the difference between the current average sum of pedestals mode and the average pedestal -- virtual func 
+      //if (isc>=0 && isc<nROI) {
+      cmPed[0]+=val; 
+      nCm[0]++;//}
+    };
+
+    /** gets the common mode i.e. the difference between the current average sum of pedestals mode and the average pedestal -- virtual func must be overloaded to define the regions of interest
 	\param isc region of interest index
 	\return the difference  between the current average sum of pedestals and the average pedestal
     */
-    virtual double getCommonMode(int isc=0) {
-      if (isc>=0 && isc<nROI)
+    virtual double getCommonMode(int ix=0, int iy=0) {
+      (void) ix; (void) iy;
       if (nCm[0]>0) return cmPed[0]/nCm[0]-cmStat[0].Mean(); 
       return 0;};
     

slsDetectorCalibration/doxy.config

@@ -0,0 +1,85 @@
+# 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            = MovingStat.h slsDetectorData.h slsReceiverData.h moench02ModuleData.h pedestalSubtraction.h commonModeSubtraction.h  moenchCommonMode.h singlePhotonDetector.h energyCalibration.h moenchReadData.C
+OUTPUT_DIRECTORY = docs
+

slsDetectorCalibration/moenchCommonMode.h

@@ -19,7 +19,11 @@ class moenchCommonMode : public commonModeSubtraction {
     */
     virtual void addToCommonMode(double val, int ix=0, int iy=0) {
       (void) iy;  
-      commonModeSubtraction::addToCommonMode(val, ix/40);
+      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
@@ -28,7 +32,11 @@ class moenchCommonMode : public commonModeSubtraction {
     */
     virtual double getCommonMode(int ix=0, int iy=0) {
       (void) iy;
-      return commonModeSubtraction::getCommonMode(ix/40);
+      int isc=ix/40;
+      if (isc>=0 && isc<nROI) { 
+	if (nCm[isc]>0) return cmPed[isc]/nCm[isc]-cmStat[isc].Mean(); 
+      }
+      return 0;
     };
 
 };

slsDetectorCalibration/moenchReadData.C

@@ -33,23 +33,21 @@ using namespace std;
 
 /**
 
-  char *fformat, file name format
-  char *tit, title of the tree etc.
-  int runmin, minimum run number
-  int runmax, max run number
-  int nbins=1500, number of bins for spectrum hists
-  int hmin=-500, minimum for spectrum hists
-  int hmax=1000, maximum for spectrum hists
-  int sign=1, sign of the spectrum to find hits
-  double hc=0, readout correlation coefficient with previous pixel
-  double tc=0, time correlation coefficient with previous frame (case of bad reset)
-  int xmin=0, minimum x coordinate
-  int xmax=NC, maximum x coordinate
-  int ymin=0, minimum y coordinate
-  int ymax=NR, maximum y coordinate
-  int pedsub=1, enable pedestal subtraction
-  int cmsub=0  enable commonmode subtraction
-
+  \param fformat, file name format
+  \param tit, title of the tree etc.
+  \param runmin, minimum run number
+  \param runmax, max run number
+  \param nbins=1500, number of bins for spectrum hists
+  \param hmin=-500, minimum for spectrum hists
+  \param hmax=1000, maximum for spectrum hists
+  \param sign=1, sign of the spectrum to find hits
+  \param hc=0, readout correlation coefficient with previous pixel
+  \param xmin=0, minimum x coordinate
+  \param xmax=NC, maximum x coordinate
+  \param ymin=0, minimum y coordinate
+  \param ymax=NR, maximum y coordinate
+  \param cmsub=0  enable commonmode subtraction
+  \returns pointer to histo stack with cluster spectra
 */