2018-04-22 21:14

8 files changed, 147 insertions, 65 deletions

diff --git a/literature/MukamelShaul2009a_1.jpeg b/literature/MukamelShaul2009a_1.jpeg
new file mode 100644
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diff --git a/presentation.pdf b/presentation.pdf
index 28118b1..21127c0 100644
--- a/presentation.pdf
+++ b/presentation.pdf
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}
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