Index: /trunk/MagicSoft/TDAS-Extractor/Calibration.tex
===================================================================
--- /trunk/MagicSoft/TDAS-Extractor/Calibration.tex	(revision 6628)
+++ /trunk/MagicSoft/TDAS-Extractor/Calibration.tex	(revision 6629)
@@ -370,5 +370,5 @@
 
 As the photo-multiplier and the subsequent 
-optical transmission devices~\cite{david} is a linear device over a 
+optical transmission devices~\cite{david} is a relatively linear device over a 
 wide dynamic range, the number of photo-electrons per charge has to remain constant over the tested 
 linearity region. 
@@ -427,16 +427,21 @@
 \begin{figure}[h!]
 \centering
-\includegraphics[width=0.99\linewidth]{PheVsCharge-11.eps}
+\includegraphics[width=0.99\linewidth]{PheVsCharge-14.eps}
 \caption{Example of a the development of the conversion factor FADC counts to photo-electrons for three 
 exemplary inner pixels (upper plots) and three exemplary outer ones (lower plots) obtained with the extractor 
 {\textit{MExtractFixedWindowPeakSearch}} 
-on a window size of 2 high-gain and 2 low-gain slices (extractor \#11). }
+on a window size of 6 high-gain and 6 low-gain slices (extractor \#11). }
 \label{fig:linear:phevscharge11}
 \end{figure}
 
 Figure~\ref{fig:linear:phevscharge11} shows the conversion factors using a fixed window with global peak search 
-integrating a window of 2 FADC slices. One can see that the linearity is completely lost! Especially in the low-gain, 
-the reconstructed number of photo-electrons is much too low and the conversion factors bend down. A similiar behaviour can 
-be found for all extractors with window sizes smaller than 6 FADC slices, especially in the low-gain region. (This behaviour 
+integrating a window of 6 FADC slices. One can see that the linearity is completely lost above 300 photo-electrons in the 
+outer pixels. Especially in the low-gain, 
+the reconstructed mean charge is too low and the conversion factors bend down. We show this extractor especially because it has 
+been used in the analysis and to derive a Crab spectrum with the consequence that the spectrum bends down at high energies. We 
+suppose that the loss of linearity due to usage of this extractor is responsible for the encountered problems.
+A similiar behaviour can be found for all extractors with window sizes smaller than 6 FADC slices, especially in the low-gain region. 
+This is understandable since the low-gain pulse covers at least 6 FADC slices.
+(This behaviour 
 was already visible in the investigations on the number of photo-electrons in the previous section~\ref{sec:photo-electrons}).
 \par
@@ -458,9 +463,9 @@
 Figure~\ref{fig:linear:phevscharge23} shows the conversion factors using the amplitude-extracting spline 
 (extractor \#23).
-Here, the linearity worse than in the previous sample. A very clear difference between high-gain and 
+Here, the linearity is worse than in the previous sample. A very clear difference between high-gain and 
 low-gain regions can be seen as well as a bigger general spread in conversion factors. In order to investigate
 if there is a common, systematic effect of the extractor, we show the averaged conversion factors over all 
 inner and outer pixels in figure~\ref{fig:linear:phevschargearea23}. Both characteristics are maintained 
-there. Although the differences between high-gain and low-gain can be easily corrected for, we conclude 
+there. Although the differences between high-gain and low-gain could be easily corrected for, we conclude 
 that extractor \#23 is still unstable against the linearity tests.
 \par
@@ -482,5 +487,5 @@
 
 Figure~\ref{fig:linear:phevscharge24} shows the conversion factors using a spline integrating over 
-one effective FADC slice in the high-gain and 1.5 effective FADC slices in the low-gain (extractor \#24).
+one effective FADC slice in the high-gain and 1.5 effective FADC slices in the low-gain region (extractor \#24).
 The same problems are found as with extractor \#23, however to a much lower extent. 
 The difference between high-gain and low-gain regions is less pronounced and the spread 
@@ -488,5 +493,5 @@
 Figure~\ref{fig:linear:phevschargearea24} shows already rather good stability except for the two 
 lowest intensity pulses in green and blue. We conclude that extractor \#24 is still un-stable, but 
-preferable to amplitude extractor.
+preferable to the amplitude extractor.
 \par
 
@@ -511,7 +516,6 @@
 to two  effective FADC slices in the high-gain and three effective FADC slices in the low-gain 
 (extractor \#25), the stability is completely resumed, except for 
-a small systematic increase of the conversion factor in the low-gain range. This effect 
-is not very significant, however it can be seen in five out of the 
-six tested channels. We conclude that extractor \#25 is almost as stable as the fixed window extractors. 
+a systematic increase of the conversion factor above 200 photo-electrons. 
+We conclude that extractor \#25 is almost as stable as the fixed window extractors. 
 \par
 
@@ -534,5 +538,6 @@
 
 Figure~\ref{fig:linear:phevscharge30} and~\ref{fig:linear:phevscharge31} show the conversion factors using a digital filter, 
-applied on 6 FADC slices and respectively 4 FADC slices with weights calculated from the UV-calibration pulse.
+applied on 6 FADC slices and respectively 4 FADC slices with weights calculated from the UV-calibration pulse in the 
+high-gain region and from the blue calibration pulse in the low-gain region.
 One can see that one or two blue  calibration pulses at low and intermediate intensity fall
 out of the linear region, moreover there is a small systematic offset between the high-gain and low-gain region. 
@@ -541,5 +546,5 @@
 will not calculate the number of photo-electrons (with the F-Factor method) for every signal intensity. 
 Thus, one possible reason for the instability falls away in the cosmics analysis. However, the limits 
-of this extraction are clearly visible here and have to be monitored further.
+of this extraction are visible here and should  be monitored further.
 
 \par
@@ -584,10 +589,13 @@
 \subsection{Relative Arrival Time Calibration}
 
-The extractors \#17--33 are able to compute the arrival time of each pulse. The calibration LEDs
+The calibration LEDs
 deliver a fast-rising pulses, uniform over the camera in signal size and time. 
 We estimate the time-uniformity to better 
 than 300\,ps, a limit due to the different travel times of the light between inner and outer parts of the
-camera. Since the calibration does not permit a precise measurement of the absolute arrival time, we measure 
-the relative arrival time for every channel with respect to a reference channel (usually pixel Nr.\,1):
+camera. 
+
+The extractors \#17--33 are able to compute the arrival time of each pulse. 
+Since the calibration does not permit a precise measurement of the absolute arrival time, we measure 
+the relative arrival time for every channel with respect to a reference channel (usually pixel no.\,1):
 
 \begin{equation}
@@ -596,5 +604,5 @@
 
 where $t_i$ denotes the reconstructed arrival time of pixel number $i$ and $t_1$ the reconstructed 
-arrival time of the reference pixel nr. 1 (software numbering). In one calibration run, one can then fill 
+arrival time of the reference pixel no. 1 (software numbering). In one calibration run, one can then fill 
 histograms of $\delta t_i$ and fit them to the expected Gaussian distribution. The fits 
 yield a mean $\mu(\delta t_i)$, comparable to 
@@ -604,5 +612,5 @@
 
 \begin{equation}
-t^{res}_i \approx \sigma(\delta t_i)/\sqrt(2)
+t^{res}_i \approx \sigma(\delta t_i)/\sqrt{2}
 \end{equation}
 
@@ -622,5 +630,5 @@
 \includegraphics[width=0.45\linewidth]{RelTime_100_Extractor30.eps}
 \includegraphics[width=0.45\linewidth]{RelTime_100_Extractor31.eps}
-\caption{Examples of a distributions of relative arrival times $\delta t_i$ of an inner pixel (Nr. 100) \protect\\
+\caption{Examples of a distributions of relative arrival times $\delta t_i$ of an inner pixel (no. 100) \protect\\
 Top: {\textit{\bf MExtractTimeAndChargeSlidingWindow}} over 2  slices (\#17) and 4  slices (\#18) \protect\\
 Center: {\textit{\bf MExtractTimeAndChargeSpline}} with maximum (\#23) and half-maximum pos. (\#24) \protect\\
@@ -632,5 +640,5 @@
 Figures~\ref{fig:reltimesinnerledblue1} and~\ref{fig:reltimesinnerledblue2} show 
 the distributions of $\delta t_i$ for a typical inner pixel and an intense, high-gain-saturating calibration 
-pulse of blue light. 
+pulse of blue light, obtained from the low-gain readout channel.
 One can see that the sliding window extractors yield double Gaussian structures, except for the 
 largest window sizes of 8 and 10 FADC slices. Even then, the distributions are not exactly Gaussian.
@@ -651,5 +659,5 @@
 \includegraphics[width=0.45\linewidth]{RelTime_100_Extractor23_logain.eps}
 \includegraphics[width=0.45\linewidth]{RelTime_100_Extractor24_logain.eps}
-\caption{Examples of a distributions of relative arrival times $\delta t_i$ of an inner pixel (Nr. 100) \protect\\
+\caption{Examples of a distributions of relative arrival times $\delta t_i$ of an inner pixel (no. 100) \protect\\
 Top: {\textit{\bf MExtractTimeAndChargeSlidingWindow}} over 4  slices (\#18) and 6  slices (\#19) \protect\\
 Center: {\textit{\bf MExtractTimeAndChargeSlidingWindow}} over 8  slices (\#20) and 10  slices (\#21)\protect\\
@@ -665,5 +673,5 @@
 \includegraphics[width=0.45\linewidth]{RelTime_100_Extractor32_logain.eps}
 \includegraphics[width=0.45\linewidth]{RelTime_100_Extractor33_logain.eps}
-\caption{Examples of a distributions of relative arrival times $\delta t_i$ of an inner pixel (Nr. 100) \protect\\
+\caption{Examples of a distributions of relative arrival times $\delta t_i$ of an inner pixel (no. 100) \protect\\
 Top: {\textit{\bf MExtractTimeAndChargeDigitalFilter}} 
 fitted to cosmics pulses over 6 slices (\#30) and 4  slices (\#31) \protect\\
@@ -679,5 +687,5 @@
 %\includegraphics[width=0.31\linewidth]{RelArrTime_Pixel400_10LedUV_Extractor17.eps}
 %\caption{Example of a two distributions of relative arrival times of an outer pixel with respect to 
-%the arrival time of the reference pixel Nr. 1. The left plot shows the result using the digital filter
+%the arrival time of the reference pixel no. 1. The left plot shows the result using the digital filter
 % (extractor \#32), the central plot shows the result obtained with the half-maximum of the spline and the 
 %right plot the result of the sliding window with a window size of 2  slices (extractor \#17). A 
@@ -691,5 +699,5 @@
 %\includegraphics[width=0.31\linewidth]{RelArrTime_Pixel97_10LedBlue_Extractor32.eps}
 %\caption{Example of a two distributions of relative arrival times of an inner pixel with respect to 
-%the arrival time of the reference pixel Nr. 1. The left plot shows the result using the half-maximum of the spline (extractor \#23), the right plot shows the result obtained with the digital filter
+%the arrival time of the reference pixel no. 1. The left plot shows the result using the half-maximum of the spline (extractor \#23), the right plot shows the result obtained with the digital filter
 %(extractor \#32). A 
 %medium sized Blue-pulse (10Leds Blue) has been used which saturates the high-gain readout channel.}
@@ -704,5 +712,5 @@
 %\includegraphics[width=0.31\linewidth]{RelArrTime_Pixel400_10LedBlue_Extractor32.eps}
 %\caption{Example of a two distributions of relative arrival times of an outer pixel with respect to 
-%the arrival time of the reference pixel Nr. 1. The left plot shows the result using the half-maximum of the spline (extractor \#23), the right plot shows the result obtained with the digital filter
+%the arrival time of the reference pixel no. 1. The left plot shows the result using the half-maximum of the spline (extractor \#23), the right plot shows the result obtained with the digital filter
 %(extractor \#32). A 
 %medium sized Blue-pulse (10Leds Blue) has been used which saturates the high-gain readout channel.}
@@ -710,4 +718,6 @@
 %\end{figure}
 
+\clearpage
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -716,8 +726,30 @@
 As in section~\ref{sec:uncalibrated}, we tested the number of outliers from the Gaussian distribution
 in order to count how many times the extractor has failed to reconstruct the correct arrival time.
-
-\begin{figure}[htp]
-\centering
-\includegraphics[width=0.95\linewidth]{UnsuitTimeVsExtractor-5LedsUV-Colour-12.eps}
+\par
+Figure~\ref{fig:time:5ledsuv} shows the number of outliers for the different time extractors, obtained with 
+a UV pulse of about 20 photo-electrons. One can see that all time extractors yield an acceptable mis-reconstruction 
+rate of about 0.5\%, except for the maximum searching spline yields three times more mis-reconstructions. 
+\par
+If one goes to very low-intensity pulses, as shown in figure~\ref{fig:time:1leduv}, obtained with on average 4 photo-electrons, 
+the number of mis-reconstructions increases considerably up to 20\% for some extractors. We interpret this high mis-reconstruction 
+rate to the increase possibility to mis-reconstruct a pulse from the night sky background noise instead of the signal pulse from the 
+calibration LEDs. One can see that the digital filter using weights on 4 FADC slices is clear inferior to the one using 6 FADC slices 
+in that respect. 
+\par
+The same conclusion seems to hold for the green pulse of about 20 photo-electrons (figure~\ref{fig:time:2ledsgreen}) 
+where the digital filter over 6 FADC slices seems to 
+yield more stable results than the one over 4 FADC slices. The half-maximum searching spline seems to be superior to the maximum-searching 
+one. 
+\par
+In figure~\ref{fig:time:23ledsblue}, one can see the number of outliers from an intense calibration pulse of blue light yielding about 
+600 photo-electrons per inner pixel. All extractors seem to be stable, except for the digital filter with weigths over 4 FADC slices. This
+is expected, since the low-gain pulse is wider than 4 FADC slices.
+\par 
+In all previous plots, the sliding window yielded the most stable results, however later we will see that this stability is only due to 
+an increased time spread. 
+
+\begin{figure}[htp]
+\centering
+\includegraphics[height=0.35\textheight]{UnsuitTimeVsExtractor-5LedsUV-Colour-12.eps}
 \caption{Reconstructed arrival time resolutions from a typical, not saturating calibration pulse 
 of colour UV, reconstructed with each of the tested arrival time extractors. 
@@ -730,5 +762,5 @@
 \begin{figure}[htp]
 \centering
-\includegraphics[width=0.95\linewidth]{UnsuitTimeVsExtractor-1LedUV-Colour-04.eps}
+\includegraphics[height=0.35\textheight]{UnsuitTimeVsExtractor-1LedUV-Colour-04.eps}
 \caption{Reconstructed arrival time resolutions from the lowest intensity calibration pulse 
 of colour UV (carrying a mean number of 4 photo-electrons), 
@@ -742,5 +774,5 @@
 \begin{figure}[htp]
 \centering
-\includegraphics[width=0.95\linewidth]{UnsuitTimeVsExtractor-2LedsGreen-Colour-02.eps}
+\includegraphics[height=0.35\textheight]{UnsuitTimeVsExtractor-2LedsGreen-Colour-02.eps}
 \caption{Reconstructed arrival time resolutions from a typical, not saturating calibration pulse 
 of colour Green, reconstructed with each of the tested arrival time extractors. 
@@ -753,5 +785,5 @@
 \begin{figure}[htp]
 \centering
-\includegraphics[width=0.95\linewidth]{UnsuitTimeVsExtractor-23LedsBlue-Colour-00.eps}
+\includegraphics[height=0.35\textheight]{UnsuitTimeVsExtractor-23LedsBlue-Colour-00.eps}
 \caption{Reconstructed arrival time resolutions from the highest intensity calibration pulse 
 of colour blue, reconstructed with each of the tested arrival time extractors. 
@@ -762,7 +794,39 @@
 \end{figure}
 
+\clearpage
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 \subsection{Time Resolution}
+
+There are three intrinsic contributions to the timing accuracy of the signal:
+
+\begin{enumerate}
+\item Intrinsic transit time spread TTS of the PMT. It can be in the order 
+of a few hundreds of ps per single photo electron. When we reconstruct 
+the mean pulse arrival time the error of the mean is given by the time 
+spread per single photo electron dividid by the square root of number of 
+photo electrons.
+\item Intrinsic arrival time spread of the photons on the PMT. For our 
+calibration LEDs this can be up to about 2 ns, for muons it is about a 
+few hundreds of ps and for hadrons a few ns. The error of the mean 
+arrival time of the total pulse is again the arrival time spread of the 
+photons divided by the number of photo electrons.
+\item reconstruction error due to noise and error of the numeric fit in 
+case of the digital filter. In case of the digital filter the error for 
+the standard noise level in the MC is about 2.7 ns divided by the signal 
+in photo electrons.
+\end{enumerate}
+
+All this seems to quite agree with the results obtained with the MC 
+TestPulses. As 1) and 2) are proportional to one over the square root of 
+the signal and 3 is proportional to one over the signal, for small 
+pulses the noise determins the resolution, but for larger pulses the 
+intrinsic fluctuations limit the timing resolution.
+
+When we get a time resolution of about 300 ps for calibration LED pulses 
+we can not distinquish 1) and 2). Thus we have to wait for the exact 
+measurement.
+
 
 \begin{figure}[htp]
