Index: /trunk/MagicSoft/TDAS-Extractor/Calibration.tex
===================================================================
--- /trunk/MagicSoft/TDAS-Extractor/Calibration.tex	(revision 6438)
+++ /trunk/MagicSoft/TDAS-Extractor/Calibration.tex	(revision 6439)
@@ -400,5 +400,5 @@
 
 \begin{equation}
-c_{phe} =\  <Phe> / <\widehat{S}>
+c_{phe} =\  <N_{phe}> / <\widehat{S}>
 \end{equation}
 
@@ -406,11 +406,12 @@
 optical transmission devices~\cite{david} is a linear device over a 
 wide dynamic range, the number of photo-electrons per charge has to remain constant over the tested 
-linearity region. We will show here only examples of extractors which were not already excluded in the 
-previous section.
+linearity region. 
 \par
 A first test concerns the stability of the conversion factor: mean number of averaged photo-electrons 
-per FADC counts over the 
-tested intensity region. A much more detailed investigation on the linearity will be shown in a 
-separate TDAS~\cite{tdas-calibration}.
+per FADC counts over the tested intensity region. This test includes all systematic uncertainties 
+in the calculation of the number of photo-electrons and the computation of the mean signal. 
+A more detailed investigation on the linearity will be shown in a 
+separate TDAS~\cite{tdas-calibration}, although there, the number of photo-electrons will be calculated 
+in a more direct way.
 
 \par
@@ -418,13 +419,26 @@
 obtained for different light intensities 
 and colours for three exemplary inner and three exemplary outer pixels using a fixed window on 
-8 FADC slices. Some of the pixels show a difference 
+8 FADC slices. The conversion factor seem to be linear to a good approximation, 
+except for two cases:
+\begin{itemize}
+\item The green pulses yield systematically low conversion factors
+\item Some of the pixels show a difference 
 between the high-gain ($<$100\ phes for the inner, $<$300\ phes for the outer pixels) and the low-gain 
 ($>$100\ phes for the inner, $>$300\ phes for the outer pixels) region and 
 a rather good stability of $c_{phe}$ for each region separately.
-We conclude that the fixed window extractor \#4 is a linear extractor 
-for both high-gain and low-gain regions, separately.
-\par
-
-\begin{figure}[htp]
+\end{itemize}
+
+We conclude that, apart from the two reasons above, 
+the fixed window extractor \#4 is a linear extractor for both high-gain 
+and low-gain regions, separately.
+\par
+
+Figures~\ref{fig:linear:phevscharge9} and~\ref{fig:linear:phevscharge15} show the conversion factors 
+using an integrated spline and a fixed window with global peak search, respectively, over 
+an extraction window of 8 FADC slices. The same behaviour is obtained as before. These extractors are 
+linear to a good approximation, except for the two cases mentionned above.
+\par
+
+\begin{figure}[h!]
 \centering
 \includegraphics[width=0.99\linewidth]{PheVsCharge-9.eps}
@@ -436,11 +450,5 @@
 \end{figure}
 
-Figures~\ref{fig:linear:phevscharge9} and~\ref{fig:linear:phevscharge15} shows the conversion factors 
-using an integrated spline and a fixed window with global peak search, respectively, over 
-an extraction window of 8 FADC slices. The same behaviour as before is obtained. These extractors are 
-thus linear to good approximation, for the two amplification regions, separately.
-\par
-
-\begin{figure}[htp]
+\begin{figure}[h!]
 \centering
 \includegraphics[width=0.99\linewidth]{PheVsCharge-15.eps}
@@ -452,5 +460,10 @@
 \end{figure}
 
-\begin{figure}[htp]
+Figure~\ref{fig:linear:phevscharge20} shows the conversion factors using a sliding window of 6 FADC slices. 
+The linearity is maintained like in the previous examples, except for the smallest signals the effect
+of the bias is already visible.
+\par
+
+\begin{figure}[h!]
 \centering
 \includegraphics[width=0.99\linewidth]{PheVsCharge-20.eps}
@@ -462,10 +475,15 @@
 \end{figure}
 
-Figure~\ref{fig:linear:phevscharge20} shows the conversion factors using a sliding window of 6 FADC slices. 
-The linearity is maintained like in the previous examples, except for the smallest signals where the effect
-of the bias is already visible.
-\par
-
-\begin{figure}[htp]
+Figure~\ref{fig:linear:phevscharge23} shows the conversion factors using the amplitude-extracting spline 
+(extractor \#23).
+Here, the linearity is worse than in the previous samples. 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 
+that extractor \#23 is still unstable against the linearity tests.
+\par
+
+\begin{figure}[h!]
 \centering
 \includegraphics[width=0.99\linewidth]{PheVsCharge-23.eps}
@@ -482,5 +500,15 @@
 \end{figure}
 
-\begin{figure}[htp]
+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).
+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 
+in conversion factors is smaller. 
+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 not too stable, but 
+preferable to amplitude extractor.
+\par
+
+\begin{figure}[h!]
 \centering
 \includegraphics[width=0.99\linewidth]{PheVsCharge-24.eps}
@@ -499,4 +527,13 @@
 \end{figure}
 
+Looking at figure~\ref{fig:linear:phevscharge25}, one can see that raising the integration window by 
+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 that 
+there seems to be a small systematic increase of the conversion factor in the low-gain range. This effect 
+is not significant in figure~\ref{fig:linear:phevschargearea25}, however it can be seen in five out of the 
+six tested channels of figure~\ref{fig:linear:phevscharge25}. We conclude that extractor \#25 is 
+almost as stable as the fixed window extractors. 
+\par
+
 \begin{figure}[htp]
 \centering
@@ -516,16 +553,15 @@
 \end{figure}
 
-Figure~\ref{fig:linear:phevscharge25} shows the conversion factors using a spline 
-extractor with an integration window of 2 FADC slices in the high-gain and 3 FADC slices in the 
-low-gain. There seems to be a systematic 
-increase in the conversion factor in the low-gain range. In order to see if this effect is systematic, 
-we calculated the average of all conversion factors over the camera, separated for inner and outer 
-pixels (figure~\ref{fig:linear:phevschargearea25}).
-
-
-If one uses this extractor, probably this effect will have to be corrected for.
-
-\par
-
+Figure~\ref{fig:linear:phevscharge30} shows the conversion factors using a digital filter, 
+applied on 6 FADC slices with weights calculated from the UV-calibration pulse.
+One can see that many blue and green calibration pulses at low and intermediate intensity fall
+out of the linear region, moreover there is also a systematic offset between high-gain and low-gain region. 
+It seems that the digital filter does not pass this test if the pulse form changes slightly from the 
+expected one. The effect is not as problematic as it may appear here, because the actual calibration 
+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.
+
+\par
 
 \begin{figure}[htp]
@@ -546,12 +582,4 @@
 \end{figure}
 
-Figure~\ref{fig:linear:phevscharge30} shows the conversion factors using a digital filter applied on 6 FADC slices with weights calculated from 
-the UV-calibration pulse.
-One can see that all calibration blue and green calibration pulses at low and intermediate intensity fall
- out of the linear region, moreover there seems to be 
-a systematic offset between high-gain and low-gain. These offsets have to corrected for in any way, however the loss of stability against the 
-exact pulse form in the high-gain is more problematic.
-
-\par
 
 \begin{figure}[htp]
@@ -576,6 +604,6 @@
 \subsection{Time Resolution}
 
-The extractors \#17--32 are able to extract also the arrival time of each pulse. The calibration
-delivers a fast-rising pulse, uniform over the camera in signal size and time. 
+The extractors \#17--39 are able to compute the arrival time of each pulse. 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
@@ -588,10 +616,10 @@
 
 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). For one calibration run, one can then fill 
-histograms of $\delta t_i$ for each pixel and fit them to the expected Gaussian distribution. The fits 
+arrival time of the reference pixel nr. 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 
-systematic offsets in the signal delay, and a sigma $\sigma(\delta t_i)$, a measure of the 
+systematic delays in the signal travel time, and a sigma $\sigma(\delta t_i)$, a measure of the 
 combined time resolutions of pixel $i$ and pixel 1. Assuming that the PMTs and readout channels are 
-of a same kind, we obtain an approximate absolute time resolution of pixel $i$ by:
+of a same kind, we obtain an approximate time resolution of pixel $i$:
 
 \begin{equation}
