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thesis/chapters/chap5_alcap_setup.tex

@@ -19,7 +19,7 @@ provide veto signals for the silicon and germanium detectors. Two liquid
 scintillators for neutron measurements were also tested in this run.  
 \begin{figure}[btp] 
 	\centering
-	\includegraphics[width=0.55\textwidth]{figs/alcap_setup_detailed} 
+	\includegraphics[width=0.65\textwidth]{figs/alcap_setup_detailed} 
 	\caption{AlCap detectors: two silicon packages inside the vacuum vessel, 
     muon beam detectors including plastic scintillators and a wire chamber, 
     germanium detector and veto plastic scintillators.}
@@ -28,22 +28,22 @@ scintillators for neutron measurements were also tested in this run.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Muon beam and vacuum chamber}
 Muons in the $\pi$E1 beam line are decay products of pions created
-as a \SI{590}{\mega\electronvolt} proton beam hits a thick carbon target
+as a \SI{590}{\mega\electronvolt} proton beam hits a thick carbon target. The
-(E-target in \cref{fig:psi_exp_hall_all}). The beam line was designed to
+beam line was designed to deliver muons with momenta ranging from
-deliver muons with momenta ranging from
+\SIrange{10}{500}{\mega\electronvolt\per\cc} and momentum spread from
-\SIrange{10}{500}{\mega\electronvolt\per\cc} and
+\SIrange{0.26}{8.0}{\percent}~\cite{Foroughli.1997}. These parameters can be
-momentum spread from \SIrange{0.26}{8.0}{\percent}. These parameters can be
 selected by changing various magnets and slits shown in
-\cref{fig:psi_piE1_elements}~\cite{Foroughli.1997}.
+\cref{fig:psi_piE1_elements}.
 
-\begin{figure}[p]
+%(E-target in \cref{fig:psi_exp_hall_all}). 
-  \centering
+%\begin{figure}[p]
-    \includegraphics[height=0.85\textheight]{figs/psi_exp_hall_all}
+  %\centering
-  \caption{Layout of the PSI experimental hall, $\pi$E1 experimental area is
+    %\includegraphics[height=0.85\textheight]{figs/psi_exp_hall_all}
-	marked with the red circle. \\Image taken from
+  %\caption{Layout of the PSI experimental hall, $\pi$E1 experimental area is
-	\url{http://www.psi.ch/num/FacilitiesEN/HallenplanPSI.png}}
+	%marked with the red circle. \\Image taken from
-  \label{fig:psi_exp_hall_all}
+	%\url{http://www.psi.ch/num/FacilitiesEN/HallenplanPSI.png}}
-\end{figure}
+  %\label{fig:psi_exp_hall_all}
+%\end{figure}
 
 \begin{figure}[btp]
   \centering
@@ -402,8 +402,8 @@ correlation between detectors would be established in the analysis stage.
 
 At the beginning of each block, the time counter in each digitiser is reset to
 ensure time alignment across all modules. The period of 110~ms was chosen to be:
-{\em i} long enough compared to the time scale of several \si{\micro\second}\
+{\em i}) long enough compared to the time scale of several \si{\micro\second}\
-of the physics of interest, {\em ii} short enough so that there is no timer
+of the physics of interest, {\em ii}) short enough so that there is no timer
 rollover on any digitiser (a FADC runs at its maximum speed of
 \SI{170}{\mega\hertz} could handle up to about \SI{1.5}{\second} with its
 28-bit time counter).
@@ -430,8 +430,8 @@ The energy calibration for the silicon detectors were done routinely during the
 run, by:
 \begin{itemize}
   \item a \SI{79.5}{\becquerel} $^{241}\textrm{Am}$ alpha source.  The most
-    prominent alpha particles have energies of \SI{5.484}{\si{\MeV}} (85.2\%)
+    prominent alpha particles have energies of \SI{5.484}{\MeV} (85.2\%)
-    and \SI{5.442}{\si{\MeV}} (12.5\%).  The alpha particles from the source
+    and \SI{5.442}{\MeV} (12.5\%).  The alpha particles from the source
     would lose about \SI{66}{\kilo\eV} in the \SI{0.5}{\um}-thick dead layer,
     and the peak would appear at \SI{5418}{\kilo\eV} (\cref{fig:toyMC_alpha}); 
   
@@ -753,12 +753,12 @@ sets are shown in \cref{tb:stat}.
       Al 	100 \si{\micro\meter}& 1.09& 14.37&$2.94 \times 10^8$\\
       & 1.07&  2.56& $4.99 \times 10^7$\\
       \midrule
-      Al 	50 \si{\micro\meter} m						& 1.07& 51.94& $8.81 \times 10^8$\\
+      Al 	50 \si{\micro\meter} & 1.07& 51.94& $8.81 \times 10^8$\\
       \bottomrule
     \end{tabular}
   \end{center}
-  \caption{Run statistics. Momentum scaling
+  \caption{Run statistics. Momentum scaling factors are normalised to
-    normalized to 28 MeV/c.}
+    \SI{28}{\MeV\per\cc}.}
   \label{tb:stat} 
 \end{table}
 
@@ -913,12 +913,126 @@ example, the X-ray spectrum analysis was done to confirm that we could observe
 the muon capture process and to help in choosing optimal momenta which
 maximised the number of stopped muons.  
 
-Although the offline analyser is still not fully developed yet, several modules
+Although the offline analyser is still not fully available yet, several modules
-are ready. They are described in detailed in the next chapter.
+are ready(\cref{tab:offline_modules}). An initial analysis is possible using
+the existing modules thanks to the modularity of the analysis framework. 
+
+\begin{table}[htb]
+  \begin{center}
+    \begin{tabular}{l p{8cm}}
+      \toprule
+      \textbf{Module name} & \textbf{Functions}\\
+      \midrule
+      MakeAnalysedPulses  & make a pulse with parameters extracted from
+      a waveform\\
+      MaxBinAPGenerator   & simplest algorithm to get pulse information\\
+      TSimpleMuonEvent    & sort pulses occur in a fixed time window around the
+      muon hits\\
+      ExportPulse \& PulseViewer & plot waveforms for diagnostics\\
+      PlotAmplitude       & plot pulse height spectra\\
+      PlotAmpVsTdiff      & plot pulse correlations in timing and amplitude\\
+      EvdE                & plot \sdEdx histograms\\
+      \bottomrule
+    \end{tabular}
+  \end{center}
+  \caption{Available offline analysis modules.}
+  \label{tab:offline_modules}
+\end{table}
+
+The MakeAnalysedPulses module takes a raw waveform, calculates the pedestal
+from a predefined number of first samples, subtracts this pedestal taking
+pulse polarity into account, then calls another module to extract pulse
+parameters. At the moment, the simplest module, so-called MaxBinAPGenerator,
+for pulse information calculation is in use. The module looks for the
+sample that has the maximal deviation from the baseline, takes the deviation as
+pulse amplitude and the time stamp of the sample as pulse time. The procedure
+is illustrated on \cref{fig:tap_maxbin_algo}. This module could not handle
+pile-up or double pulses in one \tpulseisland{} in \cref{fig:tap_maxbin_bad}.
+\begin{figure}[htb]
+  \centering
+    \includegraphics[width=0.85\textwidth]{figs/tap_maxbin_algo}
+  \caption{Pulse parameters extraction with MaxBinAPGenerator.}
+  \label{fig:tap_maxbin_algo}
+\end{figure}
+\begin{figure}[htb]
+  \centering
+    \includegraphics[width=0.47\textwidth]{figs/tap_maxbin_bad}
+    \includegraphics[width=0.47\textwidth]{figs/tap_maxbin_bad2}
+  \caption{Double pulse and pile up are taken as one single pulse by the
+    MaxBinAPGenerator}
+  \label{fig:tap_maxbin_bad}
+\end{figure}
+
+The TSimpleMuonEvent first picks a muon candidate, then loops through all
+pulses on all detector channels, and picks all pulses occur in
+a time window of \SI{\pm 10}{\si{\us}} around each candidate to build
+a muon event. A muon candidates is a hit on the upstream plastic scintillator
+with an amplitude higher than a threshold which was chosen to reject MIPs. The
+period of \SI{10}{\si{\us}} is long enough compared to the mean life time of
+muons in the target materials
+(\SI{0.758}{\si{\us}} for silicon, and \SI{0.864}{\si{\us}}
+for aluminium~\cite{SuzukiMeasday.etal.1987}) so practically all of emitted
+charged particles would be recorded in this time window.
+%\begin{figure}[htb]
+  %\centering
+    %\includegraphics[width=0.85\textwidth]{figs/tme_musc_threshold}
+  %\caption{Pulse height spectrum of the $\mu$Sc scintillator}
+  %\label{fig:tme_musc_threshold}
+%\end{figure}
+
+A pile-up protection mechanism is employed to reject multiple muons events: if
+there exists another muon hit in less than \SI{15}{\us} from the
+candidate then both the candidate and the other muon are discarded. This
+pile-up protection would cut out less than 11\% total number of events because
+the beam rate was generally less than \SI{8}{\kilo\hertz}.
+
+%In runs with active silicon targets, another requirement is applied for the
+%candidate: a prompt hit on the target in $\pm 200$ \si{\ns}\ around the
+%time of the $\mu$Sc pulse. The number comes from the observation of the
+%time correlation between hits on the target and the $\mu$Sc
+%(\cref{fig:tme_sir_prompt_rational}).
+%\begin{figure}[htb]
+  %\centering
+    %\includegraphics[width=0.85\textwidth]{figs/tme_sir_prompt_rational}
+  %\caption{Correlation in time between SiR2 hit and muon hit}
+  %\label{fig:tme_sir_prompt_rational}
+%\end{figure}
+
+To make sure that we will analyse good data, a low level data quality checking
+was done on the whole data sets. The idea is plotting the variations of basic
+parameters, such as noise level, length of raw waveforms, pulse rate, time
+correlation to hits on the muon counter on each channel during the data
+collecting period. Runs with significant difference from the averaging 
+values were further checked for possible causes, and would be discarded if such
+discrepancy was too large or unaccounted for. Examples of such trend plots are
+shown in \cref{fig:lldq}.
+\begin{figure}[htb]
+  \centering
+    \includegraphics[width=0.47\textwidth]{figs/lldq_noise}
+    \includegraphics[width=0.47\textwidth]{figs/lldq_tdiff}
+  \caption{Example trend plots used in the low level data quality checking:
+    noise level in FWHM (left) and time correlation with muon hits (right). The
+    noise level was basically stable in in this data set, except for one
+    channel. On the right hand side, this sanity check helped find out the
+    sampling frequency was wrongly applied in the first tranche of the data
+    set.}
+  \label{fig:lldq}
+\end{figure}
 % subsection offline_analyser (end)
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% section analysis_strategy (end)
+\section{Monte Carlo simulation}
+\label{sec:monte_carlo_simulation}
 
+A full Monte Carlo (MC) simulation of the experimental set up has been developed
+based on Geant4~\cite{Agostinelli.etal.2003}. The geometrical implementation
+was as detailed as possible and could be modified via configuration script at
+run time. Descriptions of the muon beam came from the beam line optic
+calculation provided by the accelerator experts at PSI.
+
+The MC model greatly assisted the design of the experiment, such as alignment
+of the detectors with respect to the target, and shielding of scattered muons.
+It also helps make sense of observed results during the run and data
+analysing. 
 
 % chapter the_alcap_run_2013 (end)
 

thesis/chapters/chap6_analysis.tex

@@ -1,116 +1,14 @@
 \chapter{Data analysis}
 \label{cha:data_analysis}
-
+This chapter presents initial analysis on subsets of the collected data.
-\section{Analysis modules}
+Purposes of the analysis include:
-\label{sec:analysis_modules}
+\begin{itemize}
-A full analysis has not been completed yet, but initial analysis
+  \item testing the analysis chain;
-based on the existing modules (\cref{tab:offline_modules}) is possible
+  \item verification of the experimental method, specifically the
-thanks to the modularity of the analysis framework. 
+    normalisation of number of stopped muons, and particle identification
-
+    using specific energy loss;
-\begin{table}[htb]
+  \item extracting a preliminary rate of proton emission from aluminium.
-  \begin{center}
+\end{itemize}
-    \begin{tabular}{l p{8cm}}
-      \toprule
-      \textbf{Module name} & \textbf{Functions}\\
-      \midrule
-      MakeAnalysedPulses  & make a pulse with parameters extracted from
-      a waveform\\
-      MaxBinAPGenerator   & simplest algorithm to get pulse information\\
-      TSimpleMuonEvent    & sort pulses occur in a fixed time window around the
-      muon hits\\
-      ExportPulse \& PulseViewer & plot waveforms for diagnostics\\
-      PlotAmplitude       & plot pulse height spectra\\
-      PlotAmpVsTdiff      & plot pulse correlations in timing and amplitude\\
-      EvdE                & identify charged particles using dE/dx\\
-      \bottomrule
-    \end{tabular}
-  \end{center}
-  \caption{Available offline analysis modules.}
-  \label{tab:offline_modules}
-\end{table}
-
-The MakeAnalysedPulses module takes a raw waveform, calculates the pedestal
-from a predefined number of first samples, subtracts this pedestal taking
-pulse polarity into account, then calls another module to extract pulse
-parameters. At the moment, the simplest module, so-called MaxBinAPGenerator,
-for pulse information calculation is in use. The module looks for the
-sample that
-has the maximal deviation from the baseline, takes the deviation as pulse
-amplitude and the time stamp of the sample as pulse time. The procedure is
-illustrated on \cref{fig:tap_maxbin_algo}. This module could not account for
-pile-up or double pulses in one \tpulseisland{} in \cref{fig:tap_maxbin_bad}.
-\begin{figure}[htb]
-  \centering
-    \includegraphics[width=0.85\textwidth]{figs/tap_maxbin_algo}
-  \caption{Pulse parameters extraction with MaxBinAPGenerator.}
-  \label{fig:tap_maxbin_algo}
-\end{figure}
-\begin{figure}[htb]
-  \centering
-    \includegraphics[width=0.47\textwidth]{figs/tap_maxbin_bad}
-    \includegraphics[width=0.47\textwidth]{figs/tap_maxbin_bad2}
-  \caption{Double pulse and pile up are taken as one single pulse by the
-    MaxBinAPGenerator}
-  \label{fig:tap_maxbin_bad}
-\end{figure}
-
-The TSimpleMuonEvent first picks a muon candidate, then loops through all
-pulses on all detector channels, and picks all pulses occur in
-a time window of \SI{\pm 10}{\si{\us}} around each candidate to build
-a muon event. A muon candidates is a hit on the upstream plastic scintillator
-with an amplitude higher than a threshold which was chosen to reject MIPs. The
-period of \SI{10}{\si{\us}} is long enough compared to the mean life time of
-muons in the target materials
-(\SI{0.758}{\si{\us}} for silicon, and \SI{0.864}{\si{\us}}
-for aluminium~\cite{SuzukiMeasday.etal.1987}) so practically all of emitted
-charged particles would be recorded in this time window.
-%\begin{figure}[htb]
-  %\centering
-    %\includegraphics[width=0.85\textwidth]{figs/tme_musc_threshold}
-  %\caption{Pulse height spectrum of the $\mu$Sc scintillator}
-  %\label{fig:tme_musc_threshold}
-%\end{figure}
-
-A pile-up protection mechanism is employed to reject multiple muons events: if
-there exists another muon hit in less than \SI{15}{\si{\us}} from the
-candidate then both the candidate and the other muon are discarded. This
-pile-up protection would cut out less than 11\% total number of events because
-the beam rate was generally less than \SI{8}{\kilo\hertz}.
-
-%In runs with active silicon targets, another requirement is applied for the
-%candidate: a prompt hit on the target in $\pm 200$ \si{\ns}\ around the
-%time of the $\mu$Sc pulse. The number comes from the observation of the
-%time correlation between hits on the target and the $\mu$Sc
-%(\cref{fig:tme_sir_prompt_rational}).
-%\begin{figure}[htb]
-  %\centering
-    %\includegraphics[width=0.85\textwidth]{figs/tme_sir_prompt_rational}
-  %\caption{Correlation in time between SiR2 hit and muon hit}
-  %\label{fig:tme_sir_prompt_rational}
-%\end{figure}
-
-To make sure that we will analyse good data, a low level data quality checking
-was done on the whole data sets. The idea is plotting the variations of basic
-parameters, such as noise level, length of raw waveforms, pulse rate, time
-correlation to hits on the muon counter on each channel during the data
-collecting period. Runs with significant difference from the averaging 
-values were further checked for possible causes, and would be discarded if such
-discrepancy was too large or unaccounted for. Examples of such trend plots are
-shown in \cref{fig:lldq}.
-\begin{figure}[htb]
-  \centering
-    \includegraphics[width=0.47\textwidth]{figs/lldq_noise}
-    \includegraphics[width=0.47\textwidth]{figs/lldq_tdiff}
-  \caption{Example trend plots used in the low level data quality checking:
-    noise level in FWHM (left) and time correlation with muon hits (right). The
-    noise level was basically stable in in this data set, except for one
-    channel. On the right hand side, this sanity check helped find out the
-    sampling frequency was wrongly applied in the first tranche of the data
-    set.}
-  \label{fig:lldq}
-\end{figure}
-% section analysis_modules (end)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Charged particles following muon capture on a thick silicon target}
 \label{sec:charged_particles_from_muon_capture_on_silicon_thick_silicon}
 This analysis was done on a subset of the active target runs

thesis/thesis.bib

@@ -112,6 +112,23 @@
   Timestamp                = {2014-04-09}
 }
 
+@Article{Agostinelli.etal.2003,
+  Title                    = {{GEANT4: A Simulation toolkit}},
+  Author                   = {Agostinelli, S. and others},
+  Journal                  = {Nucl.Instrum.Meth.},
+  Year                     = {2003},
+  Pages                    = {250-303},
+  Volume                   = {A506},
+
+  __markedentry            = {[NT:6]},
+  Collaboration            = {GEANT4},
+  Doi                      = {10.1016/S0168-9002(03)01368-8},
+  Owner                    = {NT},
+  Reportnumber             = {SLAC-PUB-9350, FERMILAB-PUB-03-339},
+  Slaccitation             = {%%CITATION = NUIMA,A506,250;%%},
+  Timestamp                = {2014-10-11}
+}
+
 @Article{AhmadAzuelos.etal.1988,
   Title                    = {Search for muon-electron and muon-positron conversion},
   Author                   = {Ahmad, S and Azuelos, G and Blecher, M and Bryman, DA and Burnham, RA and Clifford, ETH and Depommier, P and Dixit, MS and Gotow, K and Hargrove, CK and others},
@@ -471,7 +488,7 @@
   Pages                    = {154--197},
   Volume                   = {562},
 
-  __markedentry            = {[NT:6]},
+  __markedentry            = {[NT:]},
   Doi                      = {10.1016/j.nima.2006.03.009},
   File                     = {Published version:Bichsel.2006.pdf:PDF},
   Owner                    = {NT},
@@ -1065,6 +1082,7 @@
   Month                    = {Aug},
   Pages                    = {741--757},
   Volume                   = {36},
+
   Doi                      = {10.1103/PhysRevC.36.741},
   File                     = {Published version:GadioliGadioli.1987.pdf:PDF},
   Issue                    = {2},
@@ -1872,7 +1890,7 @@
 @Article{MeasdayStocki.etal.2007,
   Title                    = {$\gamma$ rays from muon capture in Al 27 and natural Si},
   Author                   = {Measday, David F and Stocki, Trevor J and Moftah, Belal A and Tam, Heywood},
-  Journal                  = {Physical Review C},
+  Journal                  = {Phys. Rev. C},
   Year                     = {2007},
   Number                   = {3},
   Pages                    = {035504},
@@ -2299,6 +2317,7 @@
   Month                    = {Jan},
   Pages                    = {135--141},
   Volume                   = {19},
+
   Doi                      = {10.1103/PhysRevC.19.135},
   File                     = {Published version:SchlepuetzComiso.etal.1979.pdf:PDF},
   Issue                    = {1},
@@ -2484,8 +2503,6 @@
   Year                     = {2003},
   Pages                    = {MOLT007},
   Volume                   = {C0303241},
-
-  __markedentry            = {[NT:]},
   Archiveprefix            = {arXiv},
   Eprint                   = {physics/0306116},
   File                     = {arXiv v1:VerkerkeKirkby.2003-eprintv1.pdf:PDF},