Index: trunk/MagicSoft/TDAS-Extractor/Conclusions.tex
===================================================================
--- trunk/MagicSoft/TDAS-Extractor/Conclusions.tex	(revision 6744)
+++ trunk/MagicSoft/TDAS-Extractor/Conclusions.tex	(revision 6745)
@@ -1,3 +1,3 @@
-\section{Conclusions}
+\section{Conclusions \label{sec:conclusion}}
 
 In the past, many MAGIC analyses have been conducted using different signal extractors. 
@@ -60,3 +60,4 @@
 %%% mode: latex
 %%% TeX-master: "MAGIC_signal_reco"
+%%% TeX-master: "MAGIC_signal_reco"
 %%% End: 
Index: trunk/MagicSoft/TDAS-Extractor/Criteria.tex
===================================================================
--- trunk/MagicSoft/TDAS-Extractor/Criteria.tex	(revision 6744)
+++ trunk/MagicSoft/TDAS-Extractor/Criteria.tex	(revision 6745)
@@ -1,3 +1,3 @@
-\section{Criteria for the Optimal Signal Extraction}
+\section{Criteria for the Optimal Signal Extraction \label{sec:criteria}}
 
 The goal for the optimal signal reconstruction algorithm is to compute an unbiased estimate of the strength and arrival time of the 
Index: trunk/MagicSoft/TDAS-Extractor/Introduction.tex
===================================================================
--- trunk/MagicSoft/TDAS-Extractor/Introduction.tex	(revision 6744)
+++ trunk/MagicSoft/TDAS-Extractor/Introduction.tex	(revision 6745)
@@ -2,12 +2,15 @@
 
 
-The MAGIC telescope aims to study the gamma ray emission from high energy phenomena and the violent physics processes in the universe 
+The MAGIC telescope aims to study the gamma ray emission from high energy phenomena and the violent physics 
+processes in the universe 
 at the lowest energy threshold possible \cite{low_energy}. 
 
-Figure~\ref{fig:MAGIC_read-out_scheme} shows a sketch of the MAGIC read-out scheme, including the PMT camera, 
-the analog-optical link, the majority trigger logic and 
-FADCs. The used PMTs provide a very fast 
+Figure~\ref{fig:MAGIC_read-out_scheme} shows a sketch of the MAGIC read-out scheme, including the 
+photomultiplier tubes (PMT) camera, 
+the analog-optical link, the majority trigger logic and flash analog-to-digital converters (FADCs). 
+The used PMTs provide a very fast 
 response to the input light signal. The response of the PMTs to sub-ns input light pulses shows a FWHM of 
-1.0 - 1.2 ns and rise and fall times of 600 and 700 ps correspondingly \cite{Magic-PMT}. By modulating VCSEL 
+1.0 - 1.2 ns and rise and fall times of 600 and 700\,ps correspondingly~\cite{Magic-PMT}. By modulating 
+vertical-cavity surface-emitting laser (VCSEL)
 type laser diodes in amplitude, the fast analogue signals from the PMTs are transferred via 162\,m long, 
 50/125\,$\mu$m diameter optical fibers to the counting house \cite{MAGIC-analog-link-2}. After transforming the 
@@ -25,5 +28,5 @@
 \caption[Current MAGIC read-out scheme.]{Current MAGIC read-out scheme: the analog PMT signals are 
 transferred via an analog optical link to the counting house -- where after the trigger decision -- the signals 
-are digitized by a 300 MHz FADCs system and written to the hard disk of a DAQ PC.} 
+are digitized by a 300\,MHz FADCs system and written to the hard disk of a data acquisition PC.} 
 \label{fig:MAGIC_read-out_scheme}
 \end{figure}
@@ -37,19 +40,38 @@
 resolution of 8 bit only, the signals are split into two branches with gains differing by a factor 10. 
 One branch is delayed by 55\,ns and then both branches are multiplexed and consecutively read-out by one FADC.
-Figure~\ref{fig:pulpo_shape_high} shows a typical average of identical signals. A more detailed overview about the MAGIC read-out and DAQ system is given in \cite{Magic-DAQ}.
+Figure~\ref{fig:pulpo_shape_high} shows a typical average of identical signals. 
+A more detailed overview about the MAGIC read-out and DAQ system is given in \cite{Magic-DAQ}.
 % The maximum sustained trigger rate could be 1 kHz. The FADCs feature a FIFO memory which allows a significantly higher short-time rate.
 % Obviously by doing this, more LONS is integrated and thus the performance of the telescope on the analysis level is degraded. 
 
 
-To reach the highest sensitivity and the lowest possible analysis energy threshold the recorded signals from Cherenkov light have to be accurately reconstructed. Therefore the highest possible signal to noise ratio, signal reconstruction resolution and a small bias are important.
+To reach the highest sensitivity and the lowest possible analysis energy threshold the recorded signals from 
+Cherenkov light have to be accurately reconstructed. Therefore the highest possible signal to noise ratio, 
+signal reconstruction resolution and a small bias are important.
 
-Monte Carlo (MC) based simulations predict different time structures for gamma and hadron induced shower images as well as for images of single muons. An accurate arrival time determination may therefore improve the separation power of gamma events from the background events. Moreover, the timing information may be used in the image cleaning to discriminate between pixels which signal belongs to the shower and pixels which are affected by randomly timed background noise.
+Monte Carlo (MC) based simulations predict different time structures for gamma and hadron induced shower 
+images as well as for images of single muons. An accurate arrival time determination may therefore improve 
+the separation power of gamma events from the background events. Moreover, the timing information may be 
+used in the image cleaning to discriminate between pixels which signal belongs to the shower and pixels 
+which are affected by randomly timed background noise.
 
 
-This note is structured as follows: In section 2 the average pulse shapes are reconstructed from the recorded FADC samples for calibration and cosmics pulses. These pulse shapes are compared with the pulse shape implemented in the MC. In section 3 different signal reconstruction algorithms and their implementation in the common MAGIC software framework MARS are reviewed. In section 4 criteria for an optimal signal reconstruction are developed. Thereafter the signal extraction algorithms under study are applied to pedestal, calibration and MC events in sections 5 to 7. The CPU requirements of the different algorithms are compared in section 8. Finally in section 9 the results are summarized and in section 10 a standard signal extraction algorithm for MAGIC is proposed.
+This note is structured as follows: In section~\ref{sec:reco} the average pulse shapes are reconstructed 
+from the recorded
+ FADC samples for calibration and cosmics pulses. These pulse shapes are compared with the pulse shape 
+implemented in the Monte-Carlo (MC) simulation. 
+In section~\ref{sec:algorithms} different signal reconstruction algorithms and their implementation in 
+the common MAGIC software framework MARS are reviewed. In section~\ref{sec:criteria} criteria for an optimal 
+signal 
+reconstruction are developed. Thereafter the signal extraction algorithms under study are applied to 
+pedestal, calibration and MC events in sections~\ref{sec:pedestals} to~\ref{sec:mc}. 
+The CPU requirements of the different algorithms 
+are compared in section~\ref{sec:speed}. Finally in section~\ref{sec:results} the results are summarized 
+and in section~\ref{sec:conclusion} a standard signal extraction algorithm for MAGIC is proposed.
 
 \subsection{Characteristics of the current read-out system}
 
-The following intrinsic characteristics of the current read-out system affect especially the signal reconstruction:
+The following intrinsic characteristics of the current read-out system affect especially the signal 
+reconstruction:
 
 \begin{description}
@@ -77,4 +99,5 @@
 %%% mode: latex
 %%% TeX-master: "MAGIC_signal_reco"
+%%% TeX-master: "Introduction"
 %%% End: 
 
Index: trunk/MagicSoft/TDAS-Extractor/Reconstruction.tex
===================================================================
--- trunk/MagicSoft/TDAS-Extractor/Reconstruction.tex	(revision 6744)
+++ trunk/MagicSoft/TDAS-Extractor/Reconstruction.tex	(revision 6745)
@@ -1,3 +1,3 @@
-\section{Pulse Shape Reconstruction}
+\section{Pulse Shape Reconstruction \label{sec:reco}}
 
 The FADC clock is not synchronized with the trigger. Therefore, the relative position of the recorded 
Index: trunk/MagicSoft/TDAS-Extractor/Results.tex
===================================================================
--- trunk/MagicSoft/TDAS-Extractor/Results.tex	(revision 6744)
+++ trunk/MagicSoft/TDAS-Extractor/Results.tex	(revision 6745)
@@ -1,3 +1,3 @@
-\section{Results}
+\section{Results \label{sec:results}}
 
 Based on the previous investigations, we summarize the obtained results in table~\ref{tab:result}. The following criteria 
@@ -61,5 +61,5 @@
 4   & Fix Win. (8,8)     & \no & \ok & \ok &\best& \no & \ok & --  & n/a & n/a & \ok \\   
 5   & Fix W. (14,10)     & \no & \ok & \ok &\best& \no & \ok & --  & n/a & n/a & \ok \\   
-\hline                                                              		  
+\hline                                                                            
 6   & FW. Spl. (4,4)     & \ok & \no & \no & \no & \ok & \no & --  & n/a & n/a & \ok \\   
 7   & FW. Spl. (4,6)     & \ok & \no & \no & \no & \ok & \no & --  & n/a & n/a & \ok \\   
@@ -67,5 +67,5 @@
 9   & FW. Spl. (8,8)     & \no & \ok & \ok & \ok & \no & \ok & --  & n/a & n/a & \ok \\   
 10  & FW. Spl (14,10)    & \no & \ok & \ok & \ok & \no & \ok &  -- & n/a & n/a & \ok \\   
-\hline                                                       	          	  
+\hline                                                                            
 11  & FW. Pk S. (2,2)    & \no & \no & \no & \no & \no & \no & --  & n/a & n/a & \ok \\   
 12  & FW. Pk S. (4,4)    & \ok & \no & \no & \no & \no & \no & --  & n/a & n/a & \ok \\   
@@ -74,5 +74,5 @@
 15  & FW. Pk S. (8,8)    & \no & \ok & \ok & \ok & \no & \ok & --  & n/a & n/a & \ok \\   
 16  & FW Pk S (14,10)    & \no & \ok & \ok & \ok & \no & \ok & --  & n/a & n/a & \ok \\   
-\hline                                                        	    	  
+\hline                                                                    
 17  & Slid. W. (2,2)     & \ok & \no & \no & \no & \ok & \no & \ok & \no & \no & \ok \\   
 18  & Slid. W. (4,4)     & \ok & \ok & \ok & \no & \ok & \ok & \ok & \no & \no & \ok \\   
@@ -81,5 +81,5 @@
 21  & Slid. W. (8,8)     & \ok & \ok & \ok & \ok & \no & \ok & \ok & \ok & \ok &\best\\   
 22  & Slid. W. (14,10)   & \no & \ok & \ok & \ok & \no & \no & \ok & \no & \ok &\best\\   
-\hline                                                        	    	  
+\hline                                                                    
 23  & Spline Ampl.       & \no &\nt  & \ok & \no & \no & \no & \no &\ok  & \no & \ok \\
     &                    &     &\test&     &     &     &     &     &     &     &     \\
@@ -110,3 +110,4 @@
 %%% mode: latex
 %%% TeX-master: "MAGIC_signal_reco"
+%%% TeX-master: "MAGIC_signal_reco"
 %%% End: 
Index: trunk/MagicSoft/TDAS-Extractor/Speed.tex
===================================================================
--- trunk/MagicSoft/TDAS-Extractor/Speed.tex	(revision 6744)
+++ trunk/MagicSoft/TDAS-Extractor/Speed.tex	(revision 6745)
@@ -1,3 +1,3 @@
-\section{CPU Requirements}
+\section{CPU Requirements \label{sec:speed}}
 
 We tested the speed of the extractors by running them on an Intel\ Pentium\ IV, 
@@ -68,2 +68,7 @@
 \end{table}
 
+
+%%% Local Variables: 
+%%% mode: latex
+%%% TeX-master: "MAGIC_signal_reco"
+%%% End: 
