From c14b98d9386263a2dca4cdd95d8b2551c23b1584 Mon Sep 17 00:00:00 2001
From: bergamaschi <bergamaschi@951219d9-93cf-4727-9268-0efd64621fa3>
Date: Fri, 25 May 2012 15:23:32 +0000
Subject: [PATCH] impplemented the possibility of setting the bad channels on a
 module basis

git-svn-id: file:///afs/psi.ch/project/sls_det_software/svn/slsDetectorSoftware@183 951219d9-93cf-4727-9268-0efd64621fa3
---
 .../multiSlsDetector/multiSlsDetector.cpp     | 18 +++--
 .../slsDetector/slsDetector.cpp               | 46 +++++++++---
 slsDetectorSoftware/slsDetector/slsDetector.h |  2 +-
 .../slsDetector/slsDetectorUtils.cpp          | 75 +++++++++++++++++++
 .../slsDetector/slsDetectorUtils.h            |  4 +-
 .../slsDetectorAnalysis/postProcessing.cpp    | 70 +++++++++--------
 .../slsDetectorAnalysis/postProcessing.h      |  8 +-
 7 files changed, 166 insertions(+), 57 deletions(-)

diff --git a/slsDetectorSoftware/multiSlsDetector/multiSlsDetector.cpp b/slsDetectorSoftware/multiSlsDetector/multiSlsDetector.cpp
index 69265f3c6..d5e8fc8be 100644
--- a/slsDetectorSoftware/multiSlsDetector/multiSlsDetector.cpp
+++ b/slsDetectorSoftware/multiSlsDetector/multiSlsDetector.cpp
@@ -1969,13 +1969,19 @@ int multiSlsDetector::setBadChannelCorrection(string fname){
 
   int badlist[MAX_BADCHANS];// badlistdet[MAX_BADCHANS];
   int nbad=0;//, nbaddet=0, choff=0, idet=0;
+  int ret=0;
+
 
   if (fname=="default")
     fname=string(thisMultiDetector->badChanFile);
+  
+  
+  
 
-  int ret=setBadChannelCorrection(fname, nbad, badlist);
+
+  ret=setBadChannelCorrection(fname, nbad, badlist);
 #ifdef VERBOSE
-  cout << "file contained " << ret << " badcahns" << endl; 
+  cout << "file contained " << ret << " badchans" << endl; 
 #endif
   if (ret==0) {
     thisMultiDetector->correctionMask&=~(1<<DISCARD_BAD_CHANNELS);
@@ -2021,7 +2027,7 @@ int multiSlsDetector::setBadChannelCorrection(int nbad, int *badlist, int ff) {
       }
     }
     if (nbaddet>0) {
-
+      
       if (detectors[idet]) {
 #ifdef VERBOSE
 	cout << "setting " << nbaddet << " badchans to detector " << idet << endl;
@@ -2035,7 +2041,7 @@ int multiSlsDetector::setBadChannelCorrection(int nbad, int *badlist, int ff) {
     nbaddet=0;
     for (int i=idet; i<thisMultiDetector->numberOfDetectors; i++) {
 #ifdef VERBOSE
-	  cout << "setting " << 0 << " badchans to detector " << i << endl;
+      cout << "setting " << 0 << " badchans to detector " << i << endl;
 #endif
       if (detectors[i]) {
 	detectors[i]->setBadChannelCorrection(nbaddet,badlist,0);
@@ -2047,9 +2053,9 @@ int multiSlsDetector::setBadChannelCorrection(int nbad, int *badlist, int ff) {
     for (int i=0; i<thisMultiDetector->numberOfDetectors; i++) {
       if (detectors[idet]) {
 #ifdef VERBOSE
-	  cout << "setting " << 0 << " badchans to detector " << idet << endl;
+	cout << "setting " << 0 << " badchans to detector " << idet << endl;
 #endif
-	detectors[idet]->setBadChannelCorrection(nbaddet,badlist,0);
+	  detectors[idet]->setBadChannelCorrection(nbaddet,badlist,0);
       }
     }
     thisMultiDetector->correctionMask&=~(1<<DISCARD_BAD_CHANNELS);
diff --git a/slsDetectorSoftware/slsDetector/slsDetector.cpp b/slsDetectorSoftware/slsDetector/slsDetector.cpp
index 144da6461..e45979657 100644
--- a/slsDetectorSoftware/slsDetector/slsDetector.cpp
+++ b/slsDetectorSoftware/slsDetector/slsDetector.cpp
@@ -4239,23 +4239,44 @@ int slsDetector::rateCorrect(float* datain, float *errin, float* dataout, float
   
   return 0;
 };
-int slsDetector::setBadChannelCorrection(string fname){
 
+
+
+
+
+
+
+int slsDetector::setBadChannelCorrection(string fname){
+  
+
+  int nbadmod,ret=0;
+  int badchanlist[MAX_BADCHANS];
+  int off;
+
+  string fn=fname;
+  
   if (fname=="default")
-    fname=string(thisDetector->badChanFile);
-  int ret=setBadChannelCorrection(fname, thisDetector->nBadChans, thisDetector->badChansList);
+    fname=string(badChanFile);
+
+  if (nBadChans && badChansList)
+    ret=setBadChannelCorrection(fname, *nBadChans, badChansList);
 
   if (ret) {
-    thisDetector->correctionMask|=(1<<DISCARD_BAD_CHANNELS);
-    strcpy(thisDetector->badChanFile,fname.c_str());
+    *correctionMask|=(1<<DISCARD_BAD_CHANNELS);
+    strcpy(badChanFile,fname.c_str());
   } else
-    thisDetector->correctionMask&=~(1<<DISCARD_BAD_CHANNELS);
+    *correctionMask&=~(1<<DISCARD_BAD_CHANNELS);
 
   fillBadChannelMask();
-  return  thisDetector->correctionMask&(1<<DISCARD_BAD_CHANNELS);
+  return  (*correctionMask)&(1<<DISCARD_BAD_CHANNELS);
 }
 
 
+
+
+
+
+
 int slsDetector::setBadChannelCorrection(int nch, int *chs, int ff) {
 #ifdef VERBOSE
   cout << "setting " << nch << " bad chans " << endl;
@@ -4263,9 +4284,12 @@ int slsDetector::setBadChannelCorrection(int nch, int *chs, int ff) {
   if (ff==0) {
     if (nch<MAX_BADCHANS && nch>0) {
       thisDetector->correctionMask|=(1<<DISCARD_BAD_CHANNELS);
-      thisDetector->nBadChans=nch;
+      thisDetector->nBadChans=0;
       for (int ich=0 ;ich<nch; ich++) {
-	thisDetector->badChansList[ich]=chs[ich];
+	if (chs[ich]<getMaxNumberOfChannels()) {
+	  thisDetector->badChansList[ich]=chs[ich];
+	  thisDetector->nBadChans++;
+	}
       }
     } else
       thisDetector->correctionMask&=~(1<<DISCARD_BAD_CHANNELS);
@@ -5316,7 +5340,7 @@ int slsDetector::writeSettingsFile(string fname, int imod){
 int slsDetector::loadSettingsFile(string fname, int imod) {
 
   sls_detector_module  *myMod=NULL;
-  string fn;
+  string fn=fname;
   fn=fname;
   int mmin=0, mmax=setNumberOfModules();
   if (imod>=0) {
@@ -5324,7 +5348,7 @@ int slsDetector::loadSettingsFile(string fname, int imod) {
     mmax=imod+1;
   }
   for (int im=mmin; im<mmax; im++) {
-    if (fname.find(".sn")==string::npos) {
+    if (fname.find(".sn")==string::npos && fname.find(".trim")) {
       ostringstream ostfn;
       ostfn << fname << ".sn"  << setfill('0') << setw(3) << hex << getId(MODULE_SERIAL_NUMBER, im); 
       fn=ostfn.str();
diff --git a/slsDetectorSoftware/slsDetector/slsDetector.h b/slsDetectorSoftware/slsDetector/slsDetector.h
index 15611adb8..88aed66b0 100644
--- a/slsDetectorSoftware/slsDetector/slsDetector.h
+++ b/slsDetectorSoftware/slsDetector/slsDetector.h
@@ -1108,7 +1108,7 @@ typedef  struct sharedSlsDetector {
       \returns 0 if bad channel disabled, >0 otherwise
   */
   int setBadChannelCorrection(string fname="");
-  
+
   /** 
       set bad channels correction
       \param nch number of bad channels
diff --git a/slsDetectorSoftware/slsDetector/slsDetectorUtils.cpp b/slsDetectorSoftware/slsDetector/slsDetectorUtils.cpp
index 2b08b7b3d..a726ef6ac 100644
--- a/slsDetectorSoftware/slsDetector/slsDetectorUtils.cpp
+++ b/slsDetectorSoftware/slsDetector/slsDetectorUtils.cpp
@@ -313,6 +313,81 @@ int slsDetectorUtils::setTotalProgress() {
 
 
 
+int slsDetectorUtils::setBadChannelCorrection(string fname, int &nbadtot, int *badchanlist, int off){
+
+  int nbad;
+  int badlist[MAX_BADCHANS];
+
+  ifstream infile;
+  string str;
+  int interrupt=0;
+  int ich;
+  int chmin,chmax;
+#ifdef VERBOSE
+  std::cout << "Setting bad channel correction to " << fname << std::endl;
+#endif
+  int modmi=0, modma=1;
+  int singlefile=0;
+
+  string fn;
+  int offset=off;
+
+
+  nbadtot=0;
+
+  if (fname=="" || fname=="none") {
+    ;
+  } else { 
+
+    if (fname.find(".sn")==string::npos && fname.find(".chans")==string::npos) {
+      modma=setNumberOfModules();
+      singlefile=1;
+    }
+
+    for (int im=0; im<modma; im++) {
+      
+
+      if (singlefile) {
+
+	ostringstream ostfn;
+	ostfn << fname << ".sn"  << setfill('0') << setw(3) << hex << getId(MODULE_SERIAL_NUMBER, im); 
+	fn=ostfn.str();
+  
+      } else
+	fn=fname;
+      
+
+
+    infile.open(fn.c_str(), ios_base::in);
+    if (infile.is_open()==0) {
+      std::cout << "could not open file " << fname <<std::endl;
+      return -1;
+    }
+
+
+    nbad=setBadChannelCorrection(infile, nbad, badlist, offset);
+    infile.close();
+    
+    for (int ich=0; ich<nbad; ich++) {
+      if (nbadtot<MAX_BADCHANS) {
+	badchanlist[nbadtot]=badlist[ich];
+	nbadtot++;
+      }
+    }
+    
+    offset+=getChansPerMod(im); 
+    
+  }
+  
+  }
+  if (nbadtot>0 && nbadtot<MAX_BADCHANS) {
+    return nbadtot;
+  } else
+    return 0;
+
+}
+
+
 
 
 float slsDetectorUtils::getCurrentProgress() {
diff --git a/slsDetectorSoftware/slsDetector/slsDetectorUtils.h b/slsDetectorSoftware/slsDetector/slsDetectorUtils.h
index e870cc88d..32527e75d 100644
--- a/slsDetectorSoftware/slsDetector/slsDetectorUtils.h
+++ b/slsDetectorSoftware/slsDetector/slsDetectorUtils.h
@@ -69,7 +69,8 @@ class slsDetectorUtils :  public slsDetectorActions, public postProcessing {
   // int getPositions(float *pos=NULL){return angularConversion::getPositions(pos);};
   
   using slsDetectorBase::setFlatFieldCorrection;
-  
+  using postProcessing::setBadChannelCorrection;
+
   // string getFilePath(){return fileIO::getFilePath();};
   // string setFilePath(string s){return fileIO::setFilePath(s);};
   
@@ -269,6 +270,7 @@ class slsDetectorUtils :  public slsDetectorActions, public postProcessing {
 
 
 
+  int setBadChannelCorrection(string fname, int &nbadtot, int *badchanlist, int off=0);
 
 
 
diff --git a/slsDetectorSoftware/slsDetectorAnalysis/postProcessing.cpp b/slsDetectorSoftware/slsDetectorAnalysis/postProcessing.cpp
index 7c7a7d2fd..2b82d5c22 100644
--- a/slsDetectorSoftware/slsDetectorAnalysis/postProcessing.cpp
+++ b/slsDetectorSoftware/slsDetectorAnalysis/postProcessing.cpp
@@ -55,33 +55,26 @@ int postProcessing::flatFieldCorrect(float datain, float errin, float &dataout,
 };
 
 
-int postProcessing::setBadChannelCorrection(string fname, int &nbad, int *badlist){
-  ifstream infile;
-  string str;
+
+
+
+int postProcessing::setBadChannelCorrection(ifstream &infile, int &nbad, int *badlist, int moff){
+  
   int interrupt=0;
   int ich;
   int chmin,chmax;
-#ifdef VERBOSE
-  std::cout << "Setting bad channel correction to " << fname << std::endl;
-#endif
+  string str;
 
-  if (fname=="" || fname=="none") {
-    nbad=0;
-    return 0;
-  } else { 
-    infile.open(fname.c_str(), ios_base::in);
-    if (infile.is_open()==0) {
-      std::cout << "could not open file " << fname <<std::endl;
-      return -1;
-    }
-    nbad=0;
-    while (infile.good() and interrupt==0) {
-      getline(infile,str);
+
+  
+  nbad=0;
+  while (infile.good() and interrupt==0) {
+    getline(infile,str);
 #ifdef VERBOSE
-      std::cout << str << std::endl;
+    std::cout << str << std::endl;
 #endif
-      istringstream ssstr;
-      ssstr.str(str);
+    istringstream ssstr;
+    ssstr.str(str);
       if (ssstr.bad() || ssstr.fail() || infile.eof()) {
 	interrupt=1;
 	break;
@@ -117,16 +110,26 @@ int postProcessing::setBadChannelCorrection(string fname, int &nbad, int *badlis
 	} else
 	  interrupt=1;
       }
-    }
   }
-  infile.close();
-  if (nbad>0 && nbad<MAX_BADCHANS) {
-    return nbad;
-  } else
-  return 0;
+
+  for (int ich=0; ich<nbad; ich++) {
+    badlist[ich]=badlist[ich]+moff;
+  }
+  return nbad;
 }
 
 
+
+
+
+
+
+
+
+
+
+
+
 void postProcessing::processFrame(int *myData, int delflag) {
 
   string fname;
@@ -401,12 +404,12 @@ int postProcessing::fillBadChannelMask() {
 #ifdef VERBOSE
       cout << "deleting bad channel mask beacuse number of bad channels is 0" << endl;
 #endif
-	
-	delete [] badChannelMask;
-	badChannelMask=NULL;
+      
+      delete [] badChannelMask;
+      badChannelMask=NULL;
       }
     }
-
+    
   } else {
 #ifdef VERBOSE
     cout << "bad channel correction is disabled " << nbad << endl;
@@ -419,11 +422,12 @@ int postProcessing::fillBadChannelMask() {
       badChannelMask=NULL;
     }
   }
-
+  
 #ifdef VERBOSE
-    cout << "number of bad channels is " << nbad << endl;
+  cout << "number of bad channels is " << nbad << endl;
 #endif
   return  nbad;
+
 }
 
 
diff --git a/slsDetectorSoftware/slsDetectorAnalysis/postProcessing.h b/slsDetectorSoftware/slsDetectorAnalysis/postProcessing.h
index b300055a5..1905b5cc4 100644
--- a/slsDetectorSoftware/slsDetectorAnalysis/postProcessing.h
+++ b/slsDetectorSoftware/slsDetectorAnalysis/postProcessing.h
@@ -74,10 +74,8 @@ class postProcessing : public angularConversion, public fileIO
       \returns 0 if bad channel disabled, >0 otherwise
   */
   virtual int setBadChannelCorrection(string fname="")=0;
-
-
-
-
+  
+  static int setBadChannelCorrection(ifstream &infile, int &nbad, int *badlist, int moff=0);
   /** 
       set bad channels correction
       \param fname file with bad channel list ("" disable)
@@ -85,7 +83,7 @@ class postProcessing : public angularConversion, public fileIO
       \param badlist array of badchannels
       \returns 0 if bad channel disabled, >0 otherwise
   */
-   static int setBadChannelCorrection(string fname, int &nbad, int *badlist);
+  virtual int setBadChannelCorrection(string fname, int &nbad, int *badlist, int off=0)=0;
 
   
   /**