Merge branch 'jcw'

7 files changed, 19 insertions, 16 deletions

diff --git a/abstract.tex b/abstract.tex
index dd08aa0..2c9b4ed 100644
--- a/abstract.tex
+++ b/abstract.tex
@@ -5,9 +5,10 @@
 
 Coherent multidimensional spectroscopy (CMDS) encompasses a family of experimental strategies
 involving the nonlinear interaction between electric fields and a material under investigation.  %
-This approach has several unique capabilities: 1. resolving congested states [CITE KLUG], 2.
-extracting spectra that would otherwise be selection-rule disslowed [CITE BOYLE], 3. resolving
-fully coherent dyanmics [CITE], 4. measuring coupling [CITE], and 5. resolving ultrafast dynamics
+This approach has several unique capabilities: 1. resolving congested states [CITE KLUG and % JCW Zhao and Wright-JACS], 
+2. extracting spectra that would otherwise be selection-rule disslowed [CITE BOYLE], 3. resolving
+fully coherent dyanmics [CITE % JCW Pakoulev and Wright], 
+4. measuring coupling [CITE], and 5. resolving ultrafast dynamics
 [CITE].  %
 
 CMDS can be collected in the frequency or the time domain, and each approach has advantages and
diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex
index 0d3d1c5..0436028 100644
--- a/acquisition/chapter.tex
+++ b/acquisition/chapter.tex
@@ -36,7 +36,7 @@ for w2 in w2_points:
             set_d2(d2)

             measure_signal()

 \end{codefragment}

-In this simple example, there are 5 \python{w1} destinations, 7 \phon{w2} destinations, and 12

+In this simple example, there are 5 \python{w1} destinations, 7 \python{w2} destinations, and 12

 \python{d2} destinations, so there are a total of $5\times7\times12=420$ pixels in the

 three-dimensional scan.  %

 The acquisition software must set the hardware to each of these points and acquire data at each of

@@ -732,7 +732,7 @@ We can write the conjugate equation to \ref{eq:simple_exponential_decay}, asking
 need to get a cerain signal level?'':

 \begin{eqnarray}

 \log{(S)} &=& -\frac{t}{\tau} \\

-t &=& -\taulog{(S)}.

+t &=& -\tau\log{(S)}.

 \end{eqnarray}

 So to step linearly in $t$, my step size has to go as $-\tau\log{(S)}$.

 

diff --git a/dissertation.cls b/dissertation.cls
index afb2dc9..aecaaad 100644
--- a/dissertation.cls
+++ b/dissertation.cls
@@ -118,17 +118,17 @@
   colback=bg,
   boxrule=1pt,
   colframe=bg,
-  arc=0,
+  arc=0pt,
   shadow=false,
-  use counter=equation,
+  new/use counter=equation,
   boxsep=1ex, top=0pt, left=0pt, right=0pt, bottom=0pt,
   comment={\hfill(\arabic{chapter}.\arabic{equation})},
   listing outside comment,
-  righthand width=2.5em,
+  righthand width=3em,
   sidebyside gap=0pt,
   minted language=#1,
-  before skip =-0.5\baselinestretch,
-  after skip=2\baselinestretch,
+  %before skip =-0.5\baselinestretch,
+  %after skip=2\baselinestretch,
 }
 
 \BeforeBeginEnvironment{codefragment}{\begin{singlespace}\stepcounter{equation}}
diff --git a/introduction/chapter.tex b/introduction/chapter.tex
index be4572d..b8877e6 100644
--- a/introduction/chapter.tex
+++ b/introduction/chapter.tex
@@ -52,7 +52,7 @@ flexable in the kinds of experiments that they can perform.  %
 This dissertation contains several projects undertaken to improve the reliability and accessibility

 of MR-CMDS.  %

 While MR-CMDS will never be a single-shot experiment, there are many improvements that can improve

-data collection speed.  %

+data collection speed.  % JCW- NOT SO SURE IT CAN'T BE SINGLE SHOT

 Necessary calibration, especially OPA calibration, can be made robust and fully automatic.  %

 Common artifacts can be addressed through relatively simple modifications in hardware and

 software.  %

@@ -64,11 +64,12 @@ frequency-domain coherent multidimensional spectroscopy.  %
 Due to its diversity and dimensionality, MR-CMDS data is challenging to process and represent.  %

 The data processing tools that a scientist develops to process one experiment may not work when she

 attempts to process an experiment where different experimental variables are explored.  %

-Historically, this has meant that MR-CMDS practitioners have used custom, one-off data processing

+Historically, this % JCW- "THIS" SHOULDN'T BE A NOUN STANDING ALONE AS THE SUBJECT OF THE SENTENCE

+has meant that MR-CMDS practitioners have used custom, one-off data processing

 workflows that need to be changed for each particular experiment.  %

 These changes take time to implement, and can become stumbling blocks or opportunities for

 error.  %

-Even worse, the challenge of designing a new processing workflow may make dissuade scientist from

+Even worse, the challenge of designing a new processing workflow may dissuade A scientist from

 creatively modifying their experimental strategy, or comparing their data with data taken from

 another group.  %

 This limit to creativity and flexibility defeats one of the main advantages of the MR-CMDS

diff --git a/opa/chapter.tex b/opa/chapter.tex
index 75459b5..a57847a 100644
--- a/opa/chapter.tex
+++ b/opa/chapter.tex
@@ -129,7 +129,7 @@ are shown.  %
 \end{figure}

 

 \begin{figure}

-  \includegraphics[width=\textwidth]{opa/c2}}

+  \includegraphics[width=\textwidth]{opa/c2}

   \caption{

     CAPTION TODO

   }

diff --git a/processing/chapter.tex b/processing/chapter.tex
index 81886c2..baca84c 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -128,7 +128,7 @@ It contains a central data ``container'' that is capable of storing all of the i
 each multidimensional (or one-dimensional) spectra: the \python{Data} class.  %

 It also defines a \python{Collection} class that contains data objects, collection

 objects, and other pieces of metadata in a hierarchical structure.  %

-Let's first discuss \mitinline{python}{Data}.

+Let's first discuss \mintinline{python}{Data}.

 

 All spectra are stored within WrightTools as multidimensional arrays.  %

 Arrays are containers that store many instances of the same data type, typically numerical

diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex
index 3bde7b4..030edd5 100644
--- a/spectroscopy/chapter.tex
+++ b/spectroscopy/chapter.tex
@@ -67,6 +67,7 @@ For simplicity, we consider a single transition dipole, $\mu$.  %
 

 The Hamiltonian which controls the coupling of or simple system to the electric field described in

 ...:

+% jcw- ISN'T IT JUST MU DOT E WHERE E IS A VECTOR THAT IS TIME DEPENDENT, NOT A TIME DERIVATIVE 

 \begin{equation}

   H = H_{\circ} - \mu \dot E

 \end{equation}

@@ -90,7 +91,7 @@ In Dirac notation \cite{DiracPaulAdrienMaurice1939a}., an observable (such as $\
 \end{equation}

 The complex wavefunction is called a \emph{ket}, represented $|b>$.  %

 The complex conjugate is called a \emph{bra}, represented $<a|$.  %

-When expanded,

+When expanded,  % JCW- MU IS NOT THE OPERATOR. THE OPERATOR IS THE TIME DEPENDENT HAMILTONIAN. MU MULIPLIES ca and cb

 \begin{equation}

   \mu(t) = c_a^2\mu_a + c_b^2\mu_b + \left< c_aa \left| \hat{mu} \right| c_bb \right> +

   \left<c_bb \left| \hat{mu} \right| c_aa \right>