From 7611f3741b5d3dec996b2cc349c36787271671a7 Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Sun, 22 Apr 2018 21:14:39 -0500
Subject: 2018-04-22 21:14

---
 presentation.tex | 212 ++++++++++++++++++++++++++++++++++++++-----------------
 1 file changed, 147 insertions(+), 65 deletions(-)

(limited to 'presentation.tex')

diff --git a/presentation.tex b/presentation.tex
index 874fdea..2ba5308 100644
--- a/presentation.tex
+++ b/presentation.tex
@@ -13,9 +13,15 @@
 \begin{frame}{Introduction to CMDS}
   \begin{columns}
     \begin{column}{0.6\textwidth}
-      \includegraphics[width=\textwidth]{presentation/SK_PhDThesis_fsTable-Overview}
-    \end{column}
-    \begin{column}{0.4\textwidth}
+      \includegraphics[width=\textwidth]{literature/MukamelShaul2009a_1}
+      \vspace{2\baselineskip} \\
+      \tiny
+      Figure: \\
+      Mukamel, S., Tanimura, Y. and Hamm, P. (2009).
+      Coherent Multidimensional Optical Spectroscopy.
+      Accounts of Chemical Research, 42(9), pp.1207-1209.
+  \end{column}
+  \begin{column}{0.4\textwidth}
       \includegraphics[width=\textwidth]{"literature/BrownEmilyJ1999a_1"}
       \centering
       \\
@@ -30,21 +36,35 @@
   \end{columns}
 \end{frame}
 
-\begin{frame}{Introduction to CMDS}
+\begin{frame}{Introduction to CMDS: table layout}
+  \adjincludegraphics[scale=0.2]{presentation/SK_PhDThesis_fsTable-Overview} \\
+  \tiny
+  Figure courtesy of Schuyler Kain
+\end{frame}
+
+\begin{frame}{Introduction to CMDS: microscopic picture}
   \adjincludegraphics[width=\textwidth]{"mixed_domain/simulation overview"}
 \end{frame}
 
 \begin{frame}{Diversity}
-  Great diversity of experimental strategies.
+  Great diversity of experimental strategies under the ``umbrella'' of CMDS:
   \vspace{\baselineskip} \\
-  Different phase matching conditions...
+  Experimental geometry...
+  \begin{itemize}
+    \item $\vec{k_a} - \vec{k_b} + \vec{k_c}$
+    \item $\vec{k_a} + \vec{k_b} + \vec{k_c}$
+    \item $\vec{k_a} - \vec{k_a} + \vec{k_b} + \vec{k_c} + \vec{k_d}$
+  \end{itemize}
+  \vspace{\baselineskip}
+  Dimensions explored...
   \begin{itemize}
-    \item transient grating $\vec{k_a} - \vec{k_b} + \vec{k_c}$
-    \item transient absorption
-    \item DOVE
-    % TODO: darien's experiments
+    \item MIR \& visible: DOVE, TRSF
+    \item fully visible: TREE, CARS
+    \item frequency-frequency: 2DES/2DIR, ``Resonant-(Raman/IR)''
+    \item frequency-delay: TG, TA
+    \item delay-delay: 3PE, MUPPETS
   \end{itemize}
-  But also different color combinations and dimensions explored.
+  Or 3D.. or 4D: many possibilities not yet popular enough to name  
   % SAY: based on the same basic ability to scan pulses in frequency, delay etc
 \end{frame}
 
@@ -119,8 +139,10 @@
 \end{frame}
 
 \begin{frame}{TOPAS-C}
+  One of four models of OPAs used within the Wright Group.
   \includegraphics[width=\textwidth]{opa/TOPAS-C}
   Two ``stages'', each with two motorized optics.
+  % SAY: crystal angle, temporal and spatial overlap
 \end{frame}
 
 \begin{frame}{Automation}
@@ -159,7 +181,9 @@
     \item filters
     \item OPAs
   \end{itemize}
-  $\sim10$ settable devices, $\sim25$ motors, multiple detectors.
+  $\sim10$ settable devices, $\sim25$ motors, multiple detectors. \\
+  \vphantom{M} \\
+  \hl{Coordination} problem.
 \end{frame}
 
 \begin{frame}{Acquisition}
@@ -167,90 +191,130 @@
   \adjincludegraphics[width=\textwidth]{acquisition/screenshots/000}
 \end{frame}
 
-\begin{frame}{Central loop}
-  At its core, PyCMDS does something very simple...
-  \vspace{\baselineskip} \\ 
-  Set, wait, read, wait, repeat.  % TODO: better figure
-  \vspace{\baselineskip} \\
-  Everything is multi-threaded (simultaneous motion, simultaneous read).
+\begin{frame}{Acquisition}
+  Capabilities of PyCMDS:
   \begin{itemize}
-    \item decrease scan time by up to $\sim2\times$, more for complex experiments
+    \item reconfigures itself based on available hardware (modularity)
+    \item multithreaded (up to 2x speed enhancement)
+    \item queued acquisitions
+      \begin{itemize}
+        \item long scans, short window of calibration---large duty cycle needed
+        \item shortly after implementation, two weeks of data collection yielded as many pixels as
+          the previous three years
+      \end{itemize}
+    \item extensibility
+      \begin{itemize}
+        \item easy to add new hardware, new sensors, and new acquisition strategies
+        \item typical addition $\sim100$ lines of new Python code
+      \end{itemize}
   \end{itemize}
 \end{frame}
 
-\subsection{Extensibility}  % ---------------------------------------------------------------------
-
 \begin{frame}{Extensibility}
   \begin{columns}
     \begin{column}{0.25\textwidth}
       \adjincludegraphics[width=\textwidth]{presentation/hardware}
     \end{column}
-    \begin{column}{0.75\textwidth}
-      A modular hardware system that can be easily added to
+    \begin{column}{0.7\textwidth}
+      Easy to add new hardware to PyCMDS
       \begin{itemize}
-        \item When a new OPA was installed on the picosecond system, PyCMDS was back in action the
-          next day.
-        \item Darien inherited a new delay stage from the Crim Group, and added it to PyCMDS in
-          less than two days.
-        \item New \emph{kinds} of hardware also possible to add, although this is more difficult.
+        \item In 2016, a new OPA was added to the picosecond system in one day.
+        \item In 2017, we added multiple delay stages to the femtosecond system. Implementation
+          took between one and four hours.
       \end{itemize}
-      just need to copy a script and modify...
-      % PoyntinTune
-      \vfill
+      Once added, new hardware is immediately available for scanning in a multidimensional space
+      with other hardware---no additional programming needed!
     \end{column}
   \end{columns}
 \end{frame}
- 
-\subsection{Queue}  % -----------------------------------------------------------------------------
 
-% TODO: consider cropping, making into one slide
+\section{Measurement enhancements}  % =============================================================
 
-\begin{frame}{Queue}
-  \adjincludegraphics[width=\textwidth]{acquisition/screenshots/004}
+\begin{frame}{Artifacts}
+  \centering \huge
+  Measurement enhancements
 \end{frame}
 
-\begin{frame}{Queue}
-  This strategy can be incredibly productive!
+\begin{frame}{Digital processing}
+  \large
+  boxcar averager \hfill digitize immediately
+  \begin{columns}
+    \begin{column}{0.5\textwidth}
+      \adjincludegraphics[width=\textwidth]{presentation/IMG_20180422_145632}
+    \end{column}
+    \begin{column}{0.5\textwidth}
+      \adjincludegraphics[width=\textwidth]{presentation/measure_digitize}
+    \end{column}
+  \end{columns}
+  \vphantom{M} \\
+  More flexibility:
   \begin{itemize}
-    \item Soon after the queue was first implemented, we collected more pixels in two weeks than
-      had been collected over the previous three years.
+    \item shot-level statistics
+    \item more complex multi-pulse sequences allowed for
   \end{itemize}
+  plus... no need to wait for the boxcar averager to settle (speed up of $\sim3\times$)  
 \end{frame}
 
-\section{Artifacts}  % ============================================================================
-
-\begin{frame}{Acquisition}
-  \centering \huge
-  Artifact Rejection
+\begin{frame}{Dual chopping}
+  \begin{columns}
+    \begin{column}{0.5\textwidth}
+      \adjincludegraphics[width=\textwidth]{presentation/IMG_20180422_145757}
+    \end{column}
+    \begin{column}{0.5\textwidth}
+      \begin{tabular}{ r | c | c | c | c }
+        & A       & B          & C          & D                       \\
+        signal    &            &            & \checkmark &            \\
+        scatter 1 &            & \checkmark & \checkmark &            \\
+        scatter 2 &            &            & \checkmark & \checkmark \\
+        other     & \checkmark & \checkmark & \checkmark & \checkmark
+      \end{tabular}
+    \end{column}
+  \end{columns}
+  \centering
+  \vphantom{M}
+  $\mathsf{I_{signal} = A - B + C - D}$
+  \begin{itemize}
+    \item{no scatter}
+    \item{no two-beam processes}
+    \item{no voltage offset or room lights}
+  \end{itemize}
 \end{frame}
 
-\begin{frame}{Shots Processing}
-  [DIGITAL SHOTS PROCESSING---NO MORE BOXCARS]
+\begin{frame}{Digital processing}
+  \adjincludegraphics[height=3in]{MX2/11}
 \end{frame}
- 
+
 \section{Processing}  % ===========================================================================
 
 \begin{frame}{Processing}
   \centering \huge
-  Data Processing
+  Data processing
 \end{frame}
 
-\begin{frame}{Dimensionality}
+\begin{frame}{Processing}
   \begin{columns}
+    \begin{column}{0.6\textwidth}
+      Great! We have \emph{lots} of CMDS data. \\
+      Now what? \\
+      \vphantom{M} \\
+      Working with multidimensional data is hard...
+      \begin{itemize}
+        \item storage
+        \item visualization
+        \item post-processing
+        \item fitting, modeling
+      \end{itemize}
+      and the dimensions are always changing! \\
+      \vphantom{M} \\
+      WrightTools---software to process CMDS.
+    \end{column}
     \begin{column}{0.4\textwidth}
       \adjincludegraphics[width=\textwidth]{presentation/TOC}
     \end{column}
-    \begin{column}{0.6\textwidth}
-      TEST
-    \end{column}
   \end{columns}
 \end{frame}
 
-\begin{frame}{Flexible data model}
-  Flexibility to transform into any desired ``projection'' on component variables.
-  \adjincludegraphics[width=\textwidth]{processing/fringes_transform}
-  % mention: including expressions
-\end{frame}
+\subsection{Universal format}  % ------------------------------------------------------------------
 
 \begin{frame}{Universal format}
   WrightTools defines a \emph{universal file format} for CMDS.
@@ -265,6 +329,20 @@
   \end{itemize}
 \end{frame}
 
+\subsection{Flexible data model}  % ---------------------------------------------------------------
+
+\begin{frame}{Flexible data model}
+  Flexibility to transform into any desired ``projection'' on component variables.
+  \adjincludegraphics[width=\textwidth]{processing/fringes_transform}
+  % mention: including expressions
+\end{frame}
+
+\subsection{Integrations}  % -----------------------------------------------------------------------
+
+\begin{frame}{Integrations}
+  \adjincludegraphics[height=3in]{PbSe_global_analysis/movies_fitted}
+\end{frame}
+
 \section{Conclusion}  % ===========================================================================
 
 \begin{frame}{Conclusion}
@@ -297,7 +375,7 @@
         \item Randall Goldsmith
         \item Tim Bertram
       \end{itemize}
-      \vspace{\baselineskip}
+      \phantom{M}
       UW-Madison Chemistry Department
       \begin{itemize}
         \item Rob McClain
@@ -305,7 +383,7 @@
         \item Bill Goebel
         \item Steve Myers
       \end{itemize}
-      \vspace{\baselineskip}  
+      \phantom{M}
       You, the audience!
       \hl{Questions?}
     \end{column}
@@ -386,11 +464,15 @@
   This means... [BOYLE]
 \end{frame}
 
-\begin{frame}{MR-CMDS theory}
-\end{frame}
-
-\begin{frame}{Mixed domain}
-  [FIGURES FROM DAN'S PAPER]
+\begin{frame}{Central loop}
+  At its core, PyCMDS does something very simple...
+  \vspace{\baselineskip} \\ 
+  Set, wait, read, wait, repeat.  % TODO: better figure
+  \vspace{\baselineskip} \\
+  Everything is multi-threaded (simultaneous motion, simultaneous read).
+  \begin{itemize}
+    \item decrease scan time by up to $\sim2\times$, more for complex experiments
+  \end{itemize}
 \end{frame}
 
 \end{document}
\ No newline at end of file
-- 
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