Index: trunk/Mars/ceres.rc
===================================================================
--- trunk/Mars/ceres.rc	(revision 17991)
+++ trunk/Mars/ceres.rc	(revision 18009)
@@ -233,2 +233,7 @@
 # Does not trigger anyway
 ContEmpty3.Condition: MPhotonEvent.GetNumPhotons<10
+
+MFixTimeOffset.FileName: resmc/fact/pixel_delays_ALL_ZERO.csv
+# MFixTimeOffset.FileName: resmc/fact/AllPhidoFiles_delays.csv
+
+# last line comment
Index: trunk/Mars/mfileio/FileIOLinkDef.h
===================================================================
--- trunk/Mars/mfileio/FileIOLinkDef.h	(revision 17991)
+++ trunk/Mars/mfileio/FileIOLinkDef.h	(revision 18009)
@@ -19,4 +19,5 @@
 #pragma link C++ class MWriteRootFile+;
 #pragma link C++ class MWriteFitsFile+;
+#pragma link C++ class MMatrix+;
 
 #endif
Index: trunk/Mars/mfileio/MMatrix.cc
===================================================================
--- trunk/Mars/mfileio/MMatrix.cc	(revision 18009)
+++ trunk/Mars/mfileio/MMatrix.cc	(revision 18009)
@@ -0,0 +1,316 @@
+/* ======================================================================== *\
+!
+!   Author(s): Sebastian Mueller and Dominik Neise for the FACT Colaboration
+!              2014 Nov 05
+!
+!   Copyright: "THE BEER-WARE LICENSE" (Revision 42):
+!
+!   The FACT Colaboration wrote this file. As long as you retain this notice you
+!   can do whatever you want with this stuff. If we meet some day, and you think
+!   this stuff is worth it, you can buy us a beer in return.
+!
+\* ======================================================================== */
+
+//////////////////////////////////////////////////////////////////////////////
+//
+//  MMatrix
+//
+//  A generic container to store a matrix of floating point numbers.
+//  More precise it is a vector of vectors of floating numbers.
+//  The rows can have an individual number of columns.
+//  The data structure fM itself is public.
+// 
+//  A delimiter seperated value text file parser is used to obtain the data
+//  from a text file.
+//
+//////////////////////////////////////////////////////////////////////////////
+#include "MMatrix.h"
+
+ClassImp(MMatrix);
+//------------------------------------------------------------------------------
+MMatrix::MMatrix(const char *name, const char *title){
+    if( name == NULL ){
+        std::exception error;
+        *fLog << err; 
+    	*fLog << "In Source: "<< __FILE__ <<" in line: "<< __LINE__ <<" ";
+       	*fLog << "in function: "<< __func__ <<"\n";
+		*fLog << "The name string is pointing to NULL!\n";
+        throw error;	
+    }else{
+        fName  = name;          
+    }
+
+    fTitle = title ? title : 
+    "Parameter container storing a vector of vectors to hold floating numbers";
+}
+//------------------------------------------------------------------------------
+MMatrix::~MMatrix(){ clear(); }
+//------------------------------------------------------------------------------
+void MMatrix::ReadFile(const TString path_to_text_file){
+	// Here a text file is parsed into the internal data structure fM
+	// All errors which might occur during parsing result in exceptions.
+	// Right before the exception a info text is printed using the error logger.
+
+	// the delimiter symbol must not be a white space
+	if( std::isspace(fDelimiter) ){
+		std::exception error;
+		*fLog << err; 
+    	*fLog << "In Source: "<< __FILE__ <<" in line: "<< __LINE__ <<" ";
+       	*fLog << "in function: "<< __func__ <<"\n";
+		*fLog << "The delimiter symbol must not be a white space character!\n";
+        throw error;			
+	}
+
+	// the comment symbol must not be a white space
+	if( std::isspace(fComment) ){
+		std::exception error;
+		*fLog << err; 
+    	*fLog << "In Source: "<< __FILE__ <<" in line: "<< __LINE__ <<" ";
+       	*fLog << "in function: "<< __func__ <<"\n";
+		*fLog << "The comment symbol must not be a white space character!\n";
+        throw error;			
+	}
+
+	// make sure the data Matrix fM is wiped out before new data is read.
+	clear();
+
+	std::ifstream dsv_input_file( path_to_text_file, std::ifstream::in);
+
+	if( !dsv_input_file.is_open() ){
+
+		// a file which can not be opened must not pass silent!
+		*fLog << err; 
+    	*fLog << "In file: "<< __FILE__ <<" in line: "<< __LINE__ <<" ";
+       	*fLog << "in function: "<< __func__ <<"\n";
+		*fLog << "The file: "<< path_to_text_file <<" could no be opened!\n";
+		std::exception error;
+        throw error;	
+	}else{
+		// the file does exist and is now parsed
+
+		// only here the filename is set to ensure it is related to the actual 
+		// file being parsed.
+		fFileName = path_to_text_file;
+
+		// we set the line counter to 0 because we read a new file.
+		fLineNumber = 0;
+
+		//as long as there are lines in the file:
+		std::string line;
+        while ( getline(dsv_input_file, line ) ){
+
+        	fLineNumber++;
+
+        	// check if the line can be ignored
+        	if( !is_comment(line) && !is_empty_or_has_only_white_spaces(line)){
+
+	        	std::stringstream line_stream(line);
+	        	std::string token;
+				
+				// create an empty row to be filled with the data chunks of 
+				// a text file line
+				std::vector< double > row;
+
+	        	//as long as there are tokens in a line:
+				while( getline(line_stream, token, fDelimiter)){
+
+					// remove tailing and leading whitespaces
+					token = remove_leading_white_spaces(token);
+					token = remove_tailing_white_spaces(token);
+
+					// parse the text chunk to a floating number and push it
+					// back the data row
+					row.push_back(pedantic_strtod(token));
+				}
+
+				// Now that a whole text file line was parsed into a data row,
+				// the row is pushed back into the data matrix.
+				fM.push_back( row );
+		 	}
+        }
+	}
+
+	dsv_input_file.close();
+}
+//------------------------------------------------------------------------------
+double MMatrix::pedantic_strtod(std::string text)const{
+	// a pedantic string to float converter
+
+	// since std::strtod will return 0.0 in case the text string is empty we 
+	// check for this in advance.
+	if(text.empty() ){
+		std::exception error;
+		*fLog << err; 
+    	*fLog << "In Source: "<< __FILE__ <<" in line: "<< __LINE__ <<" ";
+       	*fLog << "in function: "<< __func__ <<"\n";
+		*fLog << "In file: "<< fFileName <<" in line: "<<fLineNumber<<"\n";		
+		*fLog << "The given text to be converted to a flot is empty! \n";
+		throw error;
+	}
+
+	// Ok the text string is not empty and might store a valid floating number.
+
+	// This pointer to character is used to verify if std::strtod has parsed
+	// the string to its end.
+	char * e;
+	double FloatingNumber = std::strtod(text.c_str(), &e);
+
+	// when std::strtod parsed until the last character in the input string,
+	// e is pointing to an empty string. 
+	// Otherwise e is pointing to the remaining string.
+	// Example:
+	// OK : '65.456456'          -> e = ''
+	// BAD: '65.456456   585.46' -> e = '   585.46'
+
+	if (*e != 0) {
+		std::exception error;
+		*fLog << err; 
+    	*fLog << "In Source: "<< __FILE__ <<" in line: "<< __LINE__ <<" ";
+       	*fLog << "in function: "<< __func__ <<"\n";
+		*fLog << "In file: "<< fFileName <<" in line: "<<fLineNumber<<"\n";	
+		*fLog << "The given text: '" << text <<"' can not be converted ";
+		*fLog << "to a floating point number!\n";
+		throw error;
+	}
+	return FloatingNumber;
+}
+//------------------------------------------------------------------------------
+void MMatrix::clear(){
+	// Not sure if this is neccessary but it shall enforce the correct erasing 
+	// of the data Matrix fM e.g. before a new text file is parsed in.
+	for(unsigned int row=0; row<fM.size(); row++)
+		fM[row].clear();
+
+	fM.clear();
+}
+//------------------------------------------------------------------------------
+void MMatrix::print()const{
+	// A info text is printed to std::cout showing the data, 
+	// the number of lines parsed in and the name of the text file parsed in.
+
+	std::stringstream info;
+	info << std::fixed << std::setprecision( 2 );
+	info << " ___MMatrix."<< __func__ <<"()____________________\n";
+	info << "| \n";
+	for(unsigned int row=0; row<fM.size(); row++){
+		info << "| "<< row <<" ";
+		for(unsigned int col=0; col<fM[row].size(); col++){
+			info << "[" << fM[row][col] << "] ";
+		}
+		info << "\n";
+	}
+	info << "| . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .\n";
+	info << "| file:  " << fFileName << "\n";
+	info << "| lines: " << fLineNumber << "\n";	
+	info << "|______________________________________________________________\n";
+
+	std::cout << info.str();
+}
+//------------------------------------------------------------------------------
+bool MMatrix::is_empty_or_has_only_white_spaces(std::string line)const{
+	// Shall return TRUE when the text line is empty or only holding white 
+	// spaces and FALSE otherwise.
+
+	if(line.size() == 0){
+		return true;
+	}else{
+
+		bool there_are_only_whitespaces = true;
+
+		int i = 0;
+		while ( line[i] ){
+
+		    if( !isspace(line[i]) ){
+				there_are_only_whitespaces = false;
+		    }
+		    i++;
+		}
+
+		return there_are_only_whitespaces;
+	}
+}
+//------------------------------------------------------------------------------
+bool MMatrix::is_comment(std::string line)const{
+	// TRUE -> the whole line is a comment
+	// FALSE -> the line is data or something else
+	// a comment line is a line of arbitrary number of white spaces followed 
+	// by the fComment symbol
+
+	if( line.empty() ){
+		// an empty line is not a comment line
+		return false;
+	}else{
+		// remove leading whitespaces
+		line = remove_leading_white_spaces(line);
+		if( line.empty() ){
+			// after the white spaces have been removed the line turns out to 
+			// be empty; so it is not a comment
+			return false;
+		}else if( line[0] == fComment ){
+			// this is a comment line
+			return true;
+		}else{
+			// there is some thing not comment like in this line
+			return false;
+		}
+	}
+}
+//------------------------------------------------------------------------------
+// Both string trimmers are taken from StackOverflow
+//http://stackoverflow.com/questions/216823/whats-the-best-way-to-trim-stdstring
+std::string MMatrix::remove_leading_white_spaces(std::string &s)const{
+	// trim from start
+    s.erase(
+    	s.begin(), 
+    	std::find_if(
+    		s.begin(), 
+    		s.end(), 
+    		std::not1(std::ptr_fun<int, int>(std::isspace))
+    	)
+    );
+    return s;
+}
+//------------------------------------------------------------------------------
+std::string MMatrix::remove_tailing_white_spaces(std::string &s)const{
+	// trim from end
+    s.erase(
+    	std::find_if(
+    		s.rbegin(),
+    		s.rend(),
+    		std::not1(std::ptr_fun<int, int>(std::isspace))
+    	).base(),
+    	s.end()
+    );
+    return s;
+}
+//------------------------------------------------------------------------------
+Int_t MMatrix::ReadEnv(const TEnv &env, TString prefix, Bool_t print){
+
+    if (IsEnvDefined(env, prefix, "FileName", print))
+    {
+        TString temp_file_name = 
+        GetEnvValue(env, prefix, "FileName", fFileName);
+
+		try{// to parse the text file
+			ReadFile(temp_file_name);
+		}
+		catch(std::exception error){
+			// Oh oh. There was some trouble when parsing the file. This must 
+			// not be accepted.
+			return kERROR;
+		}
+
+		// The text file was correctly parsed
+		return kTRUE;
+    }
+
+    /*
+    *fLog << err << "In Source: "<< __FILE__ <<" in line: "<< __LINE__;
+    *fLog << " in function: "<< __func__ <<"\n";
+    *fLog << "There is no:'"<< prefix<<".FileName' in the config file. ";
+    *fLog << "The filename is crucial because there are no default values ";
+    *fLog << "to be asigned in case the input file with name filename is not ";
+    *fLog << "found." << std::endl;
+    */
+    return kFALSE;
+}
Index: trunk/Mars/mfileio/MMatrix.h
===================================================================
--- trunk/Mars/mfileio/MMatrix.h	(revision 18009)
+++ trunk/Mars/mfileio/MMatrix.h	(revision 18009)
@@ -0,0 +1,68 @@
+#ifndef MARS_MMatrix
+#define MARS_MMatrix
+
+#ifndef MARS_MParContainer
+#include "MParContainer.h"
+#endif
+
+#include <iostream>     // std::cout
+#include <sstream>
+#include <fstream>      // std::ifstream
+#include <iomanip>
+#include <algorithm> 
+#include <cctype>
+#include <locale>
+#include "MLog.h"
+#include "MLogManip.h"
+      
+class MMatrix : public MParContainer
+{
+public:
+    MMatrix(const char *name, const char *title);
+    ~MMatrix();
+
+    Int_t ReadEnv(const TEnv &env, TString prefix, Bool_t print=kFALSE);
+    void print()const;
+
+    // The floating point data stored in this object has an arbitrary number of
+    // rows and each row can have a unique number of floating numbers.
+    // M[row i][column j]
+    std::vector< std::vector< double > > fM;
+private:
+    // The deilimiter symbol which seperates the data chunks in the file to be 
+    // parsed.
+    char fDelimiter = ',';
+
+    // The data text file to be parsed may have comment lines which are 
+    // indicated with the comment character.
+    // Leading whitespaces in front of the comment symbol are fine/ are ignored. 
+    char fComment = '#';
+
+    // The fFileName can only be set using ReadFile( filename ). This is to make
+    // sure that the fFileName is always the one of the actual file parsed in.
+    TString fFileName = "";
+
+    // the line number worked on is stored here by the ReadFile( fileneam ) 
+    // function so that other functions as the pedantic_strtod() can provide
+    // an additional information in case they have to throw exceptions.
+    unsigned int fLineNumber = 0;
+
+    // a more pedantic version of std::strtod()
+    double pedantic_strtod(std::string text)const;
+
+    // deleting all information stored in the Matrix fM
+    void clear();
+
+    // the text file parser
+    void ReadFile(const TString path_to_text_file );
+
+    // text parsing helpers
+    bool is_empty_or_has_only_white_spaces(std::string line)const;
+    bool is_comment(std::string line)const;
+    std::string remove_leading_white_spaces(std::string &s)const;
+    std::string remove_tailing_white_spaces(std::string &s)const;
+
+    ClassDef(MMatrix, 1) // generic parameter container with text file parser
+};
+    
+#endif //MMatrix
Index: trunk/Mars/mfileio/Makefile
===================================================================
--- trunk/Mars/mfileio/Makefile	(revision 17991)
+++ trunk/Mars/mfileio/Makefile	(revision 18009)
@@ -33,5 +33,6 @@
            MWriteFitsFile.cc \
            MTopFitsGroup.cc \
-           MFitsArray.cc
+           MFitsArray.cc \
+           MMatrix.cc
 
 ############################################################
Index: trunk/Mars/mjobs/MJSimulation.cc
===================================================================
--- trunk/Mars/mjobs/MJSimulation.cc	(revision 17991)
+++ trunk/Mars/mjobs/MJSimulation.cc	(revision 18009)
@@ -113,4 +113,5 @@
 #include "MParSpline.h"
 #include "MGeomCam.h"
+#include "MMatrix.h"
 
 #include "MPedestalCam.h"
@@ -718,4 +719,11 @@
     trigger.SetVal(0);
     plist.AddToList(&trigger);
+    
+    // -------------------------------------------------------------------
+    // Dominik and Sebastian on: fix time offsets
+    MMatrix fix_time_offsets_between_pixels_in_ns(
+        "MFixTimeOffset","titel"
+    );
+    plist.AddToList(&fix_time_offsets_between_pixels_in_ns);
 
     // -------------------------------------------------------------------
Index: trunk/Mars/msimcamera/MSimCamera.cc
===================================================================
--- trunk/Mars/msimcamera/MSimCamera.cc	(revision 17991)
+++ trunk/Mars/msimcamera/MSimCamera.cc	(revision 18009)
@@ -122,4 +122,54 @@
         return kFALSE;
     }
+    // -------------------------------------------------------------------
+    // Dominik Neise and Sebastian Mueller on fix time offsets:
+    // We obtain the fix temporal offsets for the FACT camera pixels out of 
+    // a text file. The textfile must be mentioned in the ceres.rc file.
+    // There are no default offsets on purporse. The filename must be specified
+    // in ceres.rc and the file must be parsed without errors and it must 
+    // provide exactly 1440 floating point numbers.   
+    fFixTimeOffsetsBetweenPixelsInNs = 
+    (MMatrix*)pList->FindObject("MFixTimeOffset");
+    if (!fFixTimeOffsetsBetweenPixelsInNs)
+    {
+        // the key value pair providing the text file is not present in the
+        // environment env.
+        *fLog << err << "In Source: "<< __FILE__ <<" in line: "<< __LINE__;
+        *fLog << " in function: "<< __func__ <<"\n";
+        *fLog << "MFixTimeOffset not found... aborting." << endl;
+        return kFALSE;
+
+    }
+    else if ( fFixTimeOffsetsBetweenPixelsInNs->fM.size() != 1440 )
+    {
+        // The number of time offsets must match the number of pixels in the
+        // FACT camera.
+        *fLog << err << "In Source: "<< __FILE__ <<" in line: "<< __LINE__;
+        *fLog << " in function: "<< __func__ <<"\n";
+        *fLog << "MFixTimeOffset has the wrong dimension! ";
+        *fLog << "There should be "<< 1440 <<" time offsets ";
+        *fLog << "(one for each pixel in FACT) but there are: ";
+        *fLog << fFixTimeOffsetsBetweenPixelsInNs->fM.size() << "! ";
+        *fLog << "... aborting." << endl;
+        return kFALSE;
+    }
+    // Check all entries for inf and nan. Those are not accepted here.
+    for( std::vector< double > row : fFixTimeOffsetsBetweenPixelsInNs->fM ){
+        for( double number : row){
+
+            if( std::isnan(number) || std::isinf(number) ){
+
+                *fLog << err << "In Source: "<< __FILE__ <<" in line: ";
+                *fLog << __LINE__;
+                *fLog << " in function: "<< __func__ <<"\n";
+                *fLog << "There is a non normal number in the fix temporal ";
+                *fLog << "pixel offsets. This is at least one number is ";
+                *fLog << "NaN or Inf. This here is >"<< number;
+                *fLog << "<... aborting." << endl;               
+                return kFALSE;
+            }
+        }
+    }
+    // -------------------------------------------------------------------
 /*
     fPulsePos = (MParameterD*)pList->FindObject("IntendedPulsePos", "MParameterD");
@@ -353,4 +403,6 @@
     }
 
+    //--------------------------------------------------------------------------
+
     // Simulate pulses
     for (Int_t i=0; i<num; i++)
@@ -359,5 +411,12 @@
 
         const UInt_t   idx = ph.GetTag();
-        const Double_t t   = (ph.GetTime()-fStat->GetTimeFirst())*freq+rndm;// - fSpline->GetXmin();
+        Double_t t   = (ph.GetTime()-fStat->GetTimeFirst())*freq+rndm;// - fSpline->GetXmin();
+
+        // Sebastian Mueller and Dominik Neise on fix time offsets:
+        // We add a fix temporal offset to the relative arrival time of the 
+        // individual pixel. The offsets are stored in the
+        // fFixTimeOffsetsBetweenPixelsInNs -> fM matrix. We identify the first
+        // column to hold the offsets in ns.
+        t = t + freq*fFixTimeOffsetsBetweenPixelsInNs->fM[idx][0];
 
         // FIXME: Time jitter?
Index: trunk/Mars/msimcamera/MSimCamera.h
===================================================================
--- trunk/Mars/msimcamera/MSimCamera.h	(revision 17991)
+++ trunk/Mars/msimcamera/MSimCamera.h	(revision 18009)
@@ -7,4 +7,5 @@
 
 #include "MArrayF.h"
+#include "MMatrix.h"
 
 class MMcEvt;
@@ -35,4 +36,7 @@
 
     MParameterD       *fCrosstalkCoeffParam;
+
+    MMatrix *fFixTimeOffsetsBetweenPixelsInNs; //! Container to store the fix temporal offsets for each pixel in ns
+
     MTruePhotonsPerPixelCont    *fTruePhotons;  //! Container to store the number of photons per pixel
 
Index: trunk/Mars/resmc/fact/AllPhidoFiles_delays.csv
===================================================================
--- trunk/Mars/resmc/fact/AllPhidoFiles_delays.csv	(revision 18009)
+++ trunk/Mars/resmc/fact/AllPhidoFiles_delays.csv	(revision 18009)
@@ -0,0 +1,1445 @@
+# These delays were measured by Max Noethe and Dominik using all data, that was available on phido around Nov.2014. Using methods you can find here https://bitbucket.org/dneise/time_mismatch/
+# Since pixel 873 was never hit by a ring, its delay was estimated by the mean of pixels 874:878, since those are on the same chip.
+# The delays were calculated with respect to pixel 992. 
+# The mean of all dealys was shifted to zero.
+# The unit slices
+-0.690774
+0.594751
+-0.254749
+-0.131914
+-0.169193
+-0.676826
+0.499615
+-0.045110
+0.173720
+-0.023879
+-0.468595
+-0.685972
+0.076943
+-0.746126
+0.209488
+0.374118
+-0.287650
+-0.331726
+0.069503
+0.006177
+0.226890
+-0.310991
+-0.165482
+-0.231287
+0.272004
+-0.090579
+0.371025
+-0.061777
+-0.118755
+-0.220815
+0.328442
+0.177198
+0.358897
+0.138307
+0.134305
+-0.100768
+-0.102954
+-0.727379
+-0.558005
+-0.106035
+-0.130041
+-0.336583
+-0.512592
+-0.622099
+-0.184195
+-0.121157
+0.539584
+0.065023
+-0.150077
+-0.613966
+-0.074330
+-0.279982
+-0.907991
+0.325417
+0.189585
+-0.022929
+-0.349525
+-0.622241
+0.225978
+0.196219
+-0.098989
+0.033872
+-0.094247
+-0.030276
+-0.405620
+-0.307164
+-0.582798
+-0.008446
+0.238100
+-0.171741
+0.477917
+-0.077567
+-0.606829
+-1.116597
+-0.528520
+-1.216409
+-0.115900
+-0.855728
+-1.321320
+-1.964978
+-0.732642
+-0.474807
+-0.089542
+-0.159770
+0.035138
+-0.412538
+-0.108199
+-0.533523
+0.141545
+-0.745074
+-0.293046
+-0.425487
+-0.345823
+-0.368095
+-0.064311
+-0.096285
+-0.275166
+-0.373298
+-0.252940
+-0.793023
+-0.131334
+-0.629890
+-0.797632
+-0.117605
+-0.647579
+-0.673269
+-0.383657
+-0.187279
+0.343992
+0.149857
+0.492708
+0.068072
+0.214271
+0.319134
+0.148953
+0.382146
+0.456074
+0.211042
+0.557078
+0.521536
+0.528947
+0.477310
+0.451999
+0.456908
+0.521020
+0.240466
+-0.086755
+0.302926
+0.066941
+0.154476
+0.235597
+0.280406
+0.661045
+0.182168
+0.784997
+0.338742
+0.400068
+0.010374
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Index: trunk/Mars/resmc/fact/pixel_delays_ALL_ZERO.csv
===================================================================
--- trunk/Mars/resmc/fact/pixel_delays_ALL_ZERO.csv	(revision 18009)
+++ trunk/Mars/resmc/fact/pixel_delays_ALL_ZERO.csv	(revision 18009)
@@ -0,0 +1,1450 @@
+# The FACT Colaboration November 2014
+#
+# Fix temporal offsets in between individual pixels in units of ns
+#
+# Our telescope seems to have fix temporal deleays in between the
+# individual pixels. To simulate this behaviour the telescope 
+# simulation will parse this CSV file and add the deleays listed here.
+# Only the first column is taken into account for the time offsets.
+# Each row referes to a pixel where the order of the rows adresses the
+# pixel's Continuous Hardware ID (CHID).
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