Address comments and make the captions more verbose

chap2.tex

@@ -11,7 +11,7 @@
 
 \chapter{Neutrino interactions with atomic nuclei}
 \label{chap:NeutrinoInteractionsAtomicNuclei}
-The neutrino is a strictly weakly\Yoshi{-}{hyphen}interacting particle.  This has difficult implications for any experiment aiming to study neutrinos as particle detectors generally rely on the electromagnetic force.  In fact, the only proven method of neutrino detection is to utilise a high mass target in which the neutrinos can interact\Yoshi{}{was ` with'}.  Generally speaking, charged particles are produced by this interaction which can be detected by the usual means.  The collected information from these charged final states can then be used to infer information about the incident neutrino.  \Yoshi{All neutrino experiments}{no they don't! Tritium decay mass measurements and the helicity measurement, the Homestake experiment -- all these are neutrino experiments that use other methods!} rely on this method and so any attempted measurements (e.g. \Yoshi{$\delta$)}{this is not a ``measurement''} rely on our understanding \Yoshi{of}{ was `on'} neutrino interactions with atomic nuclei.  Our understanding of such processes is encompassed in the models we use to simulate the interactions.
+The neutrino is a strictly weakly\Yoshi{-}{ADDRESSED - hyphen}interacting particle.  This has difficult implications for any experiment aiming to study neutrinos as particle detectors generally rely on the electromagnetic force.  In fact, the only proven method of neutrino detection is to utilise a high mass target in which the neutrinos can interact\Yoshi{}{ADDRESSED - was ` with'}.  Generally speaking, charged particles are produced by this interaction which can be detected by the usual means.  The collected information from these charged final states can then be used to infer information about the incident neutrino.  \Yoshi{Many modern neutrino experiments}{ADDRESSED - no they don't! Tritium decay mass measurements and the helicity measurement, the Homestake experiment -- all these are neutrino experiments that use other methods!} rely on this method and so, generally speaking, attempted measurements (e.g. \Yoshi{a measurement of $\delta$)}{ADDRESSED - this is not a ``measurement''} rely on our understanding \Yoshi{of}{ADDRESSED -  was `on'} neutrino interactions with atomic nuclei.  Our understanding of such processes is encompassed in the models we use to simulate the interactions.
 
 \section{Neutrino interactions at the GeV-scale}
 \label{sec:NeutrinoInteractionsGeVScale}
@@ -29,7 +29,7 @@ \section{Neutrino interactions at the GeV-scale}
 \nu_\mu p \rightarrow \nu_\mu p.
 \label{eq:NCQEInteractionProtonTarget}
 \end{equation}
-The two kinds of QE interaction are shown in Fig.~\ref{fig:QEFD}\Yoshi{}{In the figure, the W isn't really a W$^+$; it could be going either way in time. You can only call it a W}.
+The two kinds of QE interaction are shown in Fig.~\ref{fig:QEFD}\Yoshi{}{ADDRESSED - In the figure, the W isn't really a W$^+$; it could be going either way in time. You can only call it a W}.
 \begin{figure}%
   \centering
   \subfloat[CCQE.]{\includegraphics[width=8cm]{images/neutrino_interactions/CCQE_FD.eps} \label{fig:CCQEFD}}
@@ -65,16 +65,16 @@ \section{Neutrino interactions at the GeV-scale}
 \begin{figure}%
   \centering
   \includegraphics[width=8cm]{images/neutrino_interactions/CCDIS_FD.eps}
-  \caption{A Charged Current Deep Inelastic Scattering (CCDIS) interaction of a $\nu_\mu$ with a neutron. $X$ \Yoshi{represents}{was `resembles'} the leftover nuclear remnant.}
+  \caption{A Charged Current Deep Inelastic Scattering (CCDIS) interaction of a $\nu_\mu$ with a neutron. $X$ \Yoshi{represents}{ADDRESSED - was `resembles'} the leftover nuclear remnant.}
   \label{fig:CCDISFG}
 \end{figure}
 \newline
 \newline
 While the value of a particular interaction cross-section should depend on the nuclear environment, it is possible to make comparisons of the measured cross-section per nucleon.  Fig.~\ref{fig:CrossSectionMeasurements}\Yoshi{}{Make this figure bigger. Say something about the data points as well as the curves, and how up-to-date it is etc} shows a comparison of $\nu_\mu$ CC cross-section measurements per nucleon from different experiments, all of which sample a different neutrino energy range.  There are large uncertainties for many of the cross-section measurements, particularly for the ones sampling the lower energy ranges.  The T2K beam energy is $\sim$700~MeV, which sits in the region of higher uncertainty.
 \begin{figure}[b]%
   \centering
-  \includegraphics[width=8cm]{images/neutrino_interactions/CrossSectionMeasurements.pdf}
-  \caption{$\nu_\mu$ CC cross-section measurements per nucleon for a range of energies, showing the QE, RES and DIS contributions~\cite{RevModPhys.84.1307}.}
+  \includegraphics[width=12cm]{images/neutrino_interactions/CrossSectionMeasurements.pdf}
+  \caption{$\nu_\mu$ CC cross-section measurements per nucleon and divided by neutrino energy for a range of energies, showing the QE, RES and DIS contributions~\cite{RevModPhys.84.1307}.  The data points are provided by a range of experiments (from 1979 to 2010) including BEBC~(1979)~\cite{Colley:1979rt}, NuTeV~(2006)~\cite{PhysRevD.74.012008}, MINOS~(2010)~\cite{PhysRevD.81.072002} and others.  The example predictions are provided by the NUANCE generator~\cite{Casper:2002sd}.  Many measurements have a large associated uncertainty, particularly in the lower energy (less than 1~GeV) regime.  The heaviest target nucleus probed in the region of interest, near 1~GeV, is carbon.}
   \label{fig:CrossSectionMeasurements}
 \end{figure}
 \newline
@@ -88,7 +88,7 @@ \section{Neutrino interactions at the GeV-scale}
 \begin{figure}%
   \centering
   \includegraphics[width=12cm]{images/neutrino_interactions/CCQECrossSectionMiniBooNENOMAD.pdf}
-  \caption{The CCQE cross-sections measured by the MiniBooNE and NOMAD experiments.  The solid and dashed lines represent models with different values of $M_A$~\cite{PhysRevD.81.092005}.}
+  \caption{The CCQE cross-sections measured by the MiniBooNE~(2010)~\cite{PhysRevD.81.092005}, LSND~(2002)~\cite{Auerbach:2002iy} and NOMAD~(2009)~\cite{Lyubushkin:2008pe} experiments.  The solid and dashed lines represent predictions from the NUANCE generator with different values of $M_A$~\cite{PhysRevD.81.092005}.}
   \label{fig:CCQECrossSectionMiniBooNENOMAD}
 \end{figure}
 A popular explanation for this discrepancy is a lack of understanding of the nuclear environment.  Because the neutrino is not scattering of a free nucleon, but rather a nucleon in a strongly contained system, experiments actually measure an effective $M_A$.  It is possible that the nuclear effects cause a modification to the effective $M_A$ that the experiments measure.  This possible explanation for the discrepancy has placed a heavier emphasis on nuclear modelling in neutrino interaction experiments. 
@@ -100,29 +100,21 @@ \section{Neutrino interactions with heavy nuclei}
 The RFG can only model the effect of the nucleus on the initial neutrino interaction which creates the final states.  However, these final states are created within the nucleus and so additional interactions of the final states with the nucleus can occur.  The Final-State Interactions (FSI) can significantly alter the momentum and direction of the final-state particles.  As the final-state particles are used to infer neutrino properties, the FSI effects can alter the interpretation of the reconstructed events.  In simulation, variations of the cascade model are typically used.  This involves pushing the final-state particles through the nucleus in discreet steps and, at each step, probabilistically updating the particle properties.  If at any point a final-state particles knocks out another nucleon, the additional nucleon is also pushed through the nucleus in parallel.  The discreet stepping occurs until all relevant particles have escaped the nucleus.
 \newline
 \newline
-To test such cross-section models, including nuclear effects, it is necessary to compare prediction with collected data.  However, collected cross-section data for heavy nuclei is relatively sparse.  In the case of lead, only two experiments have performed cross-section measurements.  The first measurement was performed by the CHORUS~\cite{CHORUS_XSEC} experiment.  The CHORUS detector, exposed to the CERN SPS beam with a wide-band $\nu_\mu$ beam of 27~GeV average energy, measured a cross-section for lead, iron, marble and polyethylene.  However, because the absolute flux was not measured in the experiment, all of the cross-section measurements were normalised to a common constant.  Their results are summarised in Fig.~\ref{fig:CHORUSXSec}\Yoshi{}{``data/prediction'' is confusing because it looks like the ratio of the two. Say which experiment is, and when the data was taken, in the caption, not just the body text}.
+To test such cross-section models, including nuclear effects, it is necessary to compare prediction with collected data.  However, collected cross-section data for heavy nuclei is relatively sparse.  In the case of lead, only two experiments have performed cross-section measurements.  The first measurement was performed by the CHORUS~\cite{CHORUS_XSEC} experiment in 2003.  The CHORUS detector, exposed to the CERN SPS beam with a wide-band $\nu_\mu$ beam of 27~GeV average energy, measured a cross-section for lead, iron, marble and polyethylene.  However, because the absolute flux was not measured in the experiment, all of the cross-section measurements were normalised to a common constant.  Their results are summarised in Fig.~\ref{fig:CHORUSXSec}\Yoshi{}{ADDRESSED - ``data/prediction'' is confusing because it looks like the ratio of the two. Say which experiment is, and when the data was taken, in the caption, not just the body text}.
 \begin{figure}%
   \centering
   \includegraphics[width=8cm]{images/neutrino_interactions/CHORUS_XSec.pdf}
-  \caption{Measured values of the $\nu_\mu$ CC relative cross-section for several elements.  The black and white points are the collected data and prediction respectively.  The solid and dashed lines are the linear best fit lines to the data and prediction respectively.  Going from left to right, the points represent data/prediction for lead, iron marble and polyethylene.}
+  \caption{Measured values of the $\nu_\mu$ CC relative cross-section for several elements, as measured by the CHORUS experiment~(2003)~\cite{CHORUS_XSEC}.  The black and white points are the collected data and prediction respectively.  The solid and dashed lines are the linear best fit lines to the data and prediction respectively.  Going from left to right, the points represent data and prediction for lead, iron marble and polyethylene.  The prediction is taken from a set of quark distribution functions~\cite{Gluck:1998xa} provided by PDFLIB.}
   \label{fig:CHORUSXSec}
 \end{figure}
-The second measurement was made by the MINER$\nu$A experiment~\cite{PhysRevLett.112.231801}, which used the Fermilab NuMI beam with a 8~GeV average energy, to measure the relative $\nu_\mu$ CC cross-section on lead to that of plastic scintillator as a function of neutrino energy.  Their results, shown in Fig.~\ref{fig:MINERvAXSec}, largely agreed with the prediction.
+The second measurement was made by the MINER$\nu$A experiment~(2014)~\cite{PhysRevLett.112.231801}, which used the Fermilab NuMI beam with a 8~GeV average energy, to measure the relative $\nu_\mu$ CC cross-section on lead to that of plastic scintillator as a function of neutrino energy.  Their results, shown in Fig.~\ref{fig:MINERvAXSec}, largely agreed with the prediction.  The energy sampled is above the 1~GeV region of interest.
 \begin{figure}%
   \centering
-  \includegraphics[width=8cm]{images/neutrino_interactions/MINERvA_XSec.pdf}
-  \caption{Ratio of the measured $\nu_\mu$ CC inclusive cross-section on lead to plastic scintillator as a function of neutrino energy.  The error bars on the simulation (data) are statistical (systematic) uncertainties~\cite{PhysRevLett.112.231801}.\Yoshi{}{WHAT EXPERIMENT IS THIS? Your captions are generally lacking---they need to stand on their own, without the need for the reader to find the corresponding body text to figure out what a plot is about.}}
+  \includegraphics[width=10cm]{images/neutrino_interactions/MINERvA_XSec.pdf}
+  \caption{Ratio of the measured $\nu_\mu$ CC inclusive cross-section on lead to plastic scintillator as a function of neutrino energy, as measured by the MINER$\nu$A experiment~(2014)~\cite{PhysRevLett.112.231801}.  The simulation is based on the GENIE generator~\cite{Andreopoulos201087}.  The error bars on the simulation (data) are statistical (systematic) uncertainties.\Yoshi{}{ADDRESSED - WHAT EXPERIMENT IS THIS? Your captions are generally lacking---they need to stand on their own, without the need for the reader to find the corresponding body text to figure out what a plot is about.}}
   \label{fig:MINERvAXSec}
 \end{figure}
 \newline
 \newline
-As neutrino oscillation physics enters the precision era\Yoshi{}{We entered the precision era quite a while ago---see KamLAND's mixing angle error!}, it is becoming increasingly important that our understanding of neutrino cross-sections is improved.  To achieve this goal, more cross-section measurements across a range of nuclear targets are needed.  This thesis presents a measurement of the $\nu_\mu$ CC inclusive cross-section on lead using the electromagnetic calorimeters contained in the near detector of the T2K experiment.  
-
-
-
-
-
-
-
-
+As neutrino oscillation physics has entered the precision era\Yoshi{}{ADDRESSED - We entered the precision era quite a while ago---see KamLAND's mixing angle error!}, it has become very important that our understanding of neutrino cross-sections improves.  To achieve this goal, more cross-section measurements across a range of nuclear targets are needed.  This thesis presents a measurement of the $\nu_\mu$ CC inclusive cross-section on lead using the electromagnetic calorimeters contained in the near detector of the T2K experiment.  
 

chap3.tex

@@ -179,7 +179,7 @@ \subsubsection{Data acquisition system}
 The data is initially stored at KEK in Japan but is then replicated to TRIUMF in Canada and RAL in the UK for maximum redundancy and ease of access.
 
 \subsection{The far detector}
-The T2K experiment's far detector is Super-Kamiokande~\cite{Fukuda2003418}, which is a very large water Cherenkov detector containing 50~kton of ultra-pure water.  Positioned 295~km away from the J-PARC neutrino beam, SK is located under Mt.~Ikenoyama with an overburden of 1~km\Yoshi{}{also put water equivalent}.  SK consists of two detectors; the inner detector consists of 11,146 inward facing 20\Yoshi{$''$}{was ''} PMTs which surround 35,000~ton of water while the outer detector consists of 1,885 outward facing 8\Yoshi{$''$}{was ''} PMTs and acts as a veto for entering backgrounds.
+The T2K experiment's far detector is Super-Kamiokande~\cite{Fukuda2003418}, which is a very large water Cherenkov detector containing 50~kton of ultra-pure water.  Positioned 295~km away from the J-PARC neutrino beam, SK is located under Mt.~Ikenoyama with an overburden of 1~km\Yoshi{}{also put water equivalent}.  SK consists of two detectors; the inner detector consists of 11,146 inward facing 20\Yoshi{$''$}{ADDRESSED - was ''} PMTs which surround 35,000~ton of water while the outer detector consists of 1,885 outward facing 8\Yoshi{$''$}{ADDRESSED - was ''} PMTs and acts as a veto for entering backgrounds.
 \newline
 \newline
 SK detects particles via Cherenkov radiation which is produced as a result of charged particles travelling in excess of the speed of light in the local medium.  This radiation is emitted at an angle of $\cos \theta = c/nv$, where $n$ is the refractive index of the material and $v$ is the speed of the particle.  For water this equates to an angle of 42$^\circ$.  The medium imposes a damping effect on the velocity of the particle, which results in energy loss and there comes a point where the Cherenkov emission condition is no longer met.  So, SK detects a ring of light emitted by the particles propagating through it.

chap4.tex

@@ -12,7 +12,7 @@
 \chapter{ND280 software and existing ECal event reconstruction}
 \label{chap:ND280Software}
 The T2K experiment uses a bespoke software suite for simulation and analysis of ND280 data, which is based on the ROOT framework~\cite{Brun199781}.  The vast majority of the ND280 software suite utilises the oaEvent library which provides a unified framework for information manipulation and was specifically designed for this purpose.
-As ND280 consists of many detector\Yoshi{}{check your apstrophes}s each providing a specific function, the ND280 software suite is designed to reflect this.  Not only are there specific software modules for individual subdetectors, there are specific modules for each phase of the subdetector information processing e.g. \Yoshi{Trip-T}{was trip-T. Be consistent with Chap 3} calibration, TPC reconstruction etc.  
+As ND280 consists of many detector\Yoshi{}{ADDRESSED - check your apstrophes}s each providing a specific function, the ND280 software suite is designed to reflect this.  Not only are there specific software modules for individual subdetectors, there are specific modules for each phase of the subdetector information processing e.g. \Yoshi{Trip-T}{ADDRESSED - was trip-T. Be consistent with Chap 3} calibration, TPC reconstruction etc.  
 \newline
 \newline
 As the software suite handles both production of simulated data and the processing of collected data, there are sections of the software chain which are specific to type of data being processed.  While the Monte Carlo simulation and real data do see different areas of the software chain, the general philosophy is to manipulate the Monte Carlo or the real data to a point where they can be treated as equals and them process them as such.  So, the description of the software will follow the same path: the Monte Carlo and real data specifics will be discussed first and then the unified treatment will follow. 

images/neutrino_interactions/CCDIS.xml

@@ -434,7 +434,7 @@
       <object idref="PointArray10"/> 
      </void> 
      <void property="textString"> 
-      <string>W^+</string> 
+      <string>W</string> 
      </void> 
     </object> 
    </void>