2018-04-21 22:05

10 files changed, 148 insertions, 58 deletions

diff --git a/literature/SinghAkshay2014a.pdf b/literature/SinghAkshay2014a.pdf
new file mode 100644
index 0000000..138e65d
--- /dev/null
+++ b/literature/SinghAkshay2014a.pdf
diff --git a/literature/SinghAkshay2014a_2.png b/literature/SinghAkshay2014a_2.png
new file mode 100644
index 0000000..805bb84
--- /dev/null
+++ b/literature/SinghAkshay2014a_2.png
diff --git a/presentation.pdf b/presentation.pdf
index e496166..28118b1 100644
--- a/presentation.pdf
+++ b/presentation.pdf
diff --git a/presentation.tex b/presentation.tex
index 47ae640..874fdea 100644
--- a/presentation.tex
+++ b/presentation.tex
@@ -1,6 +1,6 @@
 \documentclass{presentation}

 

-\title{Development of \\ Frequency Domain Multidimensional Spectroscopy}

+\title{Development of \\ Frequency-Domain Multidimensional Spectroscopy}

 \subtitle{---Beyond Two Dimensions---}

 \author{Blaise Thompson}

 

@@ -10,22 +10,27 @@
 \begin{document}

 \maketitle

 

-\begin{frame}{Brown et al. (1999)}

+\begin{frame}{Introduction to CMDS}

   \begin{columns}

-    \begin{column}{0.5\textwidth}

-      \fbox{\adjincludegraphics[width=\textwidth]{"literature/BrownEmilyJ1999a"}}

+    \begin{column}{0.6\textwidth}

+      \includegraphics[width=\textwidth]{presentation/SK_PhDThesis_fsTable-Overview}

     \end{column}

-    \begin{column}{0.5\textwidth}

+    \begin{column}{0.4\textwidth}

       \includegraphics[width=\textwidth]{"literature/BrownEmilyJ1999a_1"}

       \centering

       \\

       \vspace{2\baselineskip}

       $\vec{k_{\text{sig}}} = \vec{k_a} - \vec{k_b} + \vec{k_c}$

+      \vspace{2\baselineskip} \\

+      \tiny \raggedright

+      Figure: \\

+      Brown, E., Zhang, Q. and Dantus, M. (1999). \\

+      The Journal of Chemical Physics, 110(12), pp.5772-5788.

     \end{column}

   \end{columns}

 \end{frame}

 

-\begin{frame}{Overview}

+\begin{frame}{Introduction to CMDS}

   \adjincludegraphics[width=\textwidth]{"mixed_domain/simulation overview"}

 \end{frame}

 

@@ -88,15 +93,28 @@
   \end{columns}

 \end{frame}

 

-\begin{frame}{Postage stamp}

-  [FIGURE FROM LIT]

-\end{frame}

-

-\begin{frame}{Czech}

-  [FIGURE FROM CZECH]

+\begin{frame}{Two strategies for CMDS}

+  \begin{columns}

+    \begin{column}{0.5\textwidth}

+      Time Domain

+      \includegraphics[width=\textwidth]{"literature/SinghAkshay2014a_2"}

+      \tiny

+      Figure: \\

+      Singh, A., Moody, G., Wu, S., Wu, Y., Ghimire, N., Yan, J., Mandrus, D., Xu, X. and Li, X.

+      (2014).

+      Coherent Electronic Coupling in Atomically Thin MoSe$_2$. Physical Review Letters, 112(21).

+    \end{column}

+    \begin{column}{0.5\textwidth}

+      Frequency Domain

+      \adjincludegraphics[width=\textwidth]{presentation/singh_czech}

+      More \hl{bandwidth}.

+      Crucial for electronic states, band structure.

+    \end{column}

+  \end{columns}

 \end{frame}

 

 \begin{frame}{Bandwidth}

+  A lot more bandwidth... through the usage of OPAs

   \adjincludegraphics[width=\textwidth]{opa/OPA_ranges}

 \end{frame}

 

@@ -105,24 +123,6 @@
   Two ``stages'', each with two motorized optics.

 \end{frame}

 

-\begin{frame}{Tuning}

-  % TODO: curve plot?

-  Tuning curves---recorded correspondence between motor positions and output color.

-  \vspace{\baselineskip} \\

-  Exquisite sensitivity to alignment and lab conditions---tuning required roughly once a week.

-  \vspace{\baselineskip} \\

-  Manual tuning is difficult...

-  \begin{itemize}

-    \item high dimensional motor space

-    \item difficult to asses overall quality

-    \item several hours of work per OPA (sometimes, an entire day for one OPA)

-  \end{itemize}

-\end{frame}

-

-\begin{frame}{Preamp}

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

-\end{frame}

-

 \begin{frame}{Automation}

   \begin{columns}

     \begin{column}{0.5\textwidth}

@@ -178,24 +178,33 @@
   \end{itemize}

 \end{frame}

 

-\begin{frame}{Extensibility}

-\end{frame}

-  

-\subsection{Hardware}  % --------------------------------------------------------------------------

-

-\begin{frame}{Modular Hardware Model}

-  [DARIEN ADDED AEROTECH IN ONE DAY]

-  [I ADDED NEW OPA IN TWO DAYS]

-\end{frame}

-

-\subsection{Acquisitions}  % ----------------------------------------------------------------------

+\subsection{Extensibility}  % ---------------------------------------------------------------------

 

-\begin{frame}{Acquisition Modules}

-  [SUNDEN ADDED POYNTING TUNE IN SEVERAL DAYS]

+\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{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.

+      \end{itemize}

+      just need to copy a script and modify...

+      % PoyntinTune

+      \vfill

+    \end{column}

+  \end{columns}

 \end{frame}

-  

+ 

 \subsection{Queue}  % -----------------------------------------------------------------------------

 

+% TODO: consider cropping, making into one slide

+

 \begin{frame}{Queue}

   \adjincludegraphics[width=\textwidth]{acquisition/screenshots/004}

 \end{frame}

@@ -243,6 +252,19 @@
   % mention: including expressions

 \end{frame}

 

+\begin{frame}{Universal format}

+  WrightTools defines a \emph{universal file format} for CMDS.

+  \begin{itemize}

+    \item store multiple multidimensional arrays

+    \item metadata

+  \end{itemize}

+  Import data from a variety of sources.

+  \begin{itemize}

+    \item previous Wright Group acquisition software

+    \item commercial instruments (JASCO, Shimadzu, Ocean Optics)

+  \end{itemize}

+\end{frame}

+

 \section{Conclusion}  % ===========================================================================

 

 \begin{frame}{Conclusion}

@@ -255,6 +277,7 @@
       Wright Group

       \begin{itemize}

         \item Kyle Sunden

+        \item Natalia Spitha

         \item Darien Morrow

         \item Jonathan Handali

         \item Nathan Neff-Mallon

@@ -290,7 +313,25 @@
 \end{frame}

   

 \section{Supplement}  % ===========================================================================

- 

+

+\begin{frame}{Tuning}

+  % TODO: curve plot?

+  Tuning curves---recorded correspondence between motor positions and output color.

+  \vspace{\baselineskip} \\

+  Exquisite sensitivity to alignment and lab conditions---tuning required roughly once a week.

+  \vspace{\baselineskip} \\

+  Manual tuning is difficult...

+  \begin{itemize}

+    \item high dimensional motor space

+    \item difficult to asses overall quality

+    \item several hours of work per OPA (sometimes, an entire day for one OPA)

+  \end{itemize}

+\end{frame}

+

+\begin{frame}{Preamp}

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

+\end{frame}

+

 \begin{frame}{Modular hardware model}

   \adjincludegraphics[scale=0.25]{acquisition/hardware_inheritance}

 \end{frame}

@@ -303,19 +344,6 @@
   Sensors with size contribute new variables (dimensions).

 \end{frame}

 

-\begin{frame}{Universal format}

-  WrightTools defines a \emph{universal file format} for CMDS.

-  \begin{itemize}

-    \item store multiple multidimensional arrays

-    \item metadata

-  \end{itemize}

-  Import data from a variety of sources.

-  \begin{itemize}

-    \item previous Wright Group acquisition software

-    \item commercial instruments (JASCO, Shimadzu, Ocean Optics)

-  \end{itemize}

-\end{frame}

-

 \begin{frame}{Domains of CMDS}

   CMDS can be collected in two domains:

   \begin{itemize}

diff --git a/presentation/SK_PhDThesis_fsTable-Overview.png b/presentation/SK_PhDThesis_fsTable-Overview.png
new file mode 100644
index 0000000..dd3bb88
--- /dev/null
+++ b/presentation/SK_PhDThesis_fsTable-Overview.png
diff --git a/presentation/SK_PhDThesis_fsTable-Overview_ORIGINAL.pdf b/presentation/SK_PhDThesis_fsTable-Overview_ORIGINAL.pdf
new file mode 100644
index 0000000..78f3cd0
--- /dev/null
+++ b/presentation/SK_PhDThesis_fsTable-Overview_ORIGINAL.pdf
diff --git a/presentation/hardware.PNG b/presentation/hardware.PNG
new file mode 100644
index 0000000..4f7a5f9
--- /dev/null
+++ b/presentation/hardware.PNG
diff --git a/presentation/module.PNG b/presentation/module.PNG
new file mode 100644
index 0000000..5a7ce05
--- /dev/null
+++ b/presentation/module.PNG
diff --git a/presentation/singh_czech.png b/presentation/singh_czech.png
new file mode 100644
index 0000000..f231346
--- /dev/null
+++ b/presentation/singh_czech.png
diff --git a/presentation/singh_czech.py b/presentation/singh_czech.py
new file mode 100644
index 0000000..398e22e
--- /dev/null
+++ b/presentation/singh_czech.py
@@ -0,0 +1,62 @@
+"""Bandwidth comparison between Singh & Czech."""
+
+
+# --- import --------------------------------------------------------------------------------------
+
+
+import os
+
+import numpy as np
+
+import matplotlib.pyplot as plt
+import matplotlib.patches as patches
+
+import WrightTools as wt
+from WrightTools import datasets
+
+
+# --- define --------------------------------------------------------------------------------------
+
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+
+# --- workspace -----------------------------------------------------------------------------------
+
+
+fig, gs = wt.artists.create_figure(cols=[1, 'cbar'])
+ax = plt.subplot(gs[0, 0])
+
+# get data
+ps = datasets.COLORS.v2p1_MoS2_TrEE_movie
+data = wt.data.from_COLORS(ps)
+data.convert('eV', convert_variables=True)
+data.ai0.signed = False
+data.ai0.clip(min=0, replace='value')
+data = data.chop('w1=wm', 'w2', at={'d2': [-80, 'fs']})[0]
+
+# czech
+ax.pcolor(data)
+
+# singh
+edges = np.array([1660, 1610], dtype=np.float64)  # meV
+edges = wt.units.converter(edges, 'meV', 'eV')
+corner = min(edges)
+width = abs(edges[1] - edges[0])
+rectangle = patches.Rectangle((corner, corner), width, width, fc='m')
+ax.add_patch(rectangle)
+
+# decoration
+ax.set_xlim(corner, data.w1.max())
+ax.set_ylim(corner, data.w2.max())
+wt.artists.set_ax_labels(ax=ax, xlabel=data.w1__e__wm.label, ylabel=data.w2.label)
+ax.grid()
+wt.artists.diagonal_line()
+
+# colorbar
+cax = plt.subplot(gs[0, -1])
+wt.artists.plot_colorbar(cax=cax, label='intensity')
+
+# save
+p = os.path.join(here, 'singh_czech.png')
+plt.savefig(p, bbox_inches='tight')