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authorBlaise Thompson <blaise@untzag.com>2018-03-26 22:34:02 -0500
committerBlaise Thompson <blaise@untzag.com>2018-03-26 22:34:02 -0500
commit5aa9d5e00d28c91190a2c07866bb0139275133e3 (patch)
treeefee9a2879b774cdcad22cffd9e6218f852e0604
parent8c899a01c80fdceab395e5c11389ca8334c67864 (diff)
2018-03-26 22:34
-rw-r--r--MoS2_TSF.wt5bin0 -> 800 bytes
-rw-r--r--acquisition/chapter.tex23
-rw-r--r--processing/MX2_TSF.wt5bin0 -> 4561160 bytes
-rw-r--r--processing/TSF_MoS2.wt5bin0 -> 874248 bytes
-rw-r--r--processing/chapter.tex7
-rw-r--r--processing/join.py49
-rw-r--r--processing/join_example.pngbin0 -> 116930 bytes
-rw-r--r--processing/join_example.py64
8 files changed, 134 insertions, 9 deletions
diff --git a/MoS2_TSF.wt5 b/MoS2_TSF.wt5
new file mode 100644
index 0000000..82daee0
--- /dev/null
+++ b/MoS2_TSF.wt5
Binary files differ
diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex
index e3035a0..8e75cc1 100644
--- a/acquisition/chapter.tex
+++ b/acquisition/chapter.tex
@@ -1,7 +1,14 @@
-\chapter{Acquistion}
+\chapter{Acquistion} \label{cha:acq}
% TODO: cool quote, if I can think of one
+\begin{dquote}
+ The question of software correctness ultimately boils down to, “Does it do what we have in our
+ minds, even the things we have not gotten around to thinking about yet?”
+
+ \dsignature{Alistair Cockburn}
+\end{dquote}
+
\clearpage
In the Wright Group, \gls{PyCMDS} replaces the old acquisition softwares `ps control', written by
@@ -13,15 +20,15 @@ PyCMDS directly addresses the hardware during experiments.
PyCMDS has, through software improvements alone, dramatically lessened scan times...
-\begin{itemize}[topsep=-1.5ex, itemsep=0ex, partopsep=0ex, parsep=0ex, label=$\rightarrow$]
- \item simultaneous motor motion
+\begin{ditemize}
+ \item simultaneous motor motion
\item digital signal processing % TODO: reference section when it exists
- \item ideal axis positions \ref{sec:ideal_axis_positions}
-\end{itemize}
+ \item ideal axis positions \ref{acq:sec:ideal_axis_positions}
+\end{ditemize}
\section{Future directions} % ====================================================================
-\subsection{Ideal Axis Positions}\label{sec:ideal_axis_positions} % ------------------------------
+\subsection{Ideal Axis Positions} \label{acq:sec:ideal_axis_positions} % -------------------------
Frequency domain multidimensional spectroscopy is a time-intensive process. %
A typical \gls{pixel} takes between one-half second and three seconds to acquire. %
@@ -85,7 +92,7 @@ will also ignore these. %
Derivations of the ideal pixel positions for each of these lineshapes appear below.
% TODO: cite Wright Group quantum beating paper, Kambempati breathing paper
-\subsection{Exponential}
+\subsubsection{Exponential}
Simple exponential decays are typically used to describe population and coherence-level dynamics in
CMDS. %
@@ -124,7 +131,7 @@ S_n &=& (1-c)\left(\frac{n}{N}\right)^{\frac{\tau_{\mathrm{step}}}{\tau_{\mathrm
\begin{figure}
\includegraphics[scale=0.5]{"processing/PyCMDS/ideal axis positions/exponential"}
\caption[TODO]{TODO}
- \label{fig:exponential_steps}
+ \label{aqn:fig:exponential_steps}
\end{figure}
\subsubsection{Gaussian}
diff --git a/processing/MX2_TSF.wt5 b/processing/MX2_TSF.wt5
new file mode 100644
index 0000000..f13c74b
--- /dev/null
+++ b/processing/MX2_TSF.wt5
Binary files differ
diff --git a/processing/TSF_MoS2.wt5 b/processing/TSF_MoS2.wt5
new file mode 100644
index 0000000..f905737
--- /dev/null
+++ b/processing/TSF_MoS2.wt5
Binary files differ
diff --git a/processing/chapter.tex b/processing/chapter.tex
index a32f170..db8da3b 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -795,7 +795,12 @@ It is also not a method of the \python{Data} class, it is a bare function. %
Join accepts multiple data objects and attempts to join them together. %
To do this, the variable and channel names must agree. %
-% TODO: join example (from Darien on slack)
+\begin{figure}
+ \includegraphics[width=\textwidth]{"processing/join_example"}
+ \caption[CAPTION TODO]{
+ CAPTION TODO}
+ \label{pro:fig:join_example}
+\end{figure}
\section{Fitting} % ==============================================================================
diff --git a/processing/join.py b/processing/join.py
new file mode 100644
index 0000000..f3a4203
--- /dev/null
+++ b/processing/join.py
@@ -0,0 +1,49 @@
+"""Join figure."""
+
+
+# --- import --------------------------------------------------------------------------------------
+
+
+import os
+
+import matplotlib.pyplot as plt
+
+import WrightTools as wt
+
+
+# --- define --------------------------------------------------------------------------------------
+
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+
+# --- workspace -----------------------------------------------------------------------------------
+
+
+wt.artists.apply_rcparams('publication')
+
+fig, gs = wt.artists.create_figure(width='double', cols=[1, 0, 1, 1, 1, 'cbar'], nrows=4)
+
+root = wt.open(os.path.join(here, 'MX2_TSF.wt5'))
+
+def plot(ax, d):
+ d.transform('w1', 'w2')
+ d.sig.clip(0, 4)
+ ax.pcolor(d)
+
+# II
+ax = plt.subplot(gs[0, 0])
+plot(ax, root.processed_tsf.divided_tsf.II)
+
+# IS
+ax = plt.subplot(gs[1, 0])
+plot(ax, root.processed_tsf.divided_tsf.IS)
+
+# SS
+ax = plt.subplot(gs[2, 0])
+plot(ax, root.processed_tsf.divided_tsf.SS)
+
+
+# savefig
+p = os.path.join(here, 'join.png')
+plt.show()
diff --git a/processing/join_example.png b/processing/join_example.png
new file mode 100644
index 0000000..a2c83f5
--- /dev/null
+++ b/processing/join_example.png
Binary files differ
diff --git a/processing/join_example.py b/processing/join_example.py
new file mode 100644
index 0000000..ce1e18e
--- /dev/null
+++ b/processing/join_example.py
@@ -0,0 +1,64 @@
+"""Join example."""
+
+
+# --- import --------------------------------------------------------------------------------------
+
+
+import os
+
+import WrightTools as wt
+
+import numpy as np
+
+import matplotlib.pyplot as plt
+
+
+# --- define and import ---------------------------------------------------------------------------
+
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+p = os.path.join(here, 'MX2_TSF.wt5')
+root = wt.open(p)
+divided = root.processed_tsf.divided_tsf
+
+def individual_plotter(gs, d, j):
+ ax = plt.subplot(gs[0,j])
+ ax.pcolor(d)
+ ax.grid()
+ wt.artists.set_ax_labels(ax=ax, xlabel=d.w1.label, ylabel=d.w2.label)
+
+ # join
+ds = [divided[0], divided[1], divided[2]]
+joined = wt.data.join(ds, parent=divided, )
+# pretty up indivudal
+for d in ds:
+ d.transform('w1', 'w2')
+ d.sig.clip(0,4)
+# pretty up joined
+joined.sig.clip(0,4)
+joined.transform('w1', 'w2')
+
+
+# --- workspace -----------------------------------------------------------------------------------
+
+
+# instantiate figure
+fig, gs = wt.artists.create_figure(width='double', nrows=3, cols=[1,'cbar',1,'cbar',1,'cbar'], hspace=.75, wspace=.35)
+# plot indiviudal data
+d = divided[0]
+individual_plotter(gs, d, 0)
+d = divided[1]
+individual_plotter(gs, d, 2)
+d = divided[2]
+individual_plotter(gs, d, 4)
+# plot joined data
+ax = plt.subplot(gs[1:,:-1])
+ax.pcolor(joined)
+ax.grid()
+wt.artists.set_ax_labels(ax=ax, xlabel=d.w1.label, ylabel=d.w2.label)
+# colorbar
+cax = plt.subplot(gs[:,-1])
+ticks = np.linspace(joined.sig.min(), joined.sig.max(), 11)
+label = 'TSF amplitude'
+wt.artists.plot_colorbar(cax=cax, ticks=ticks, label=label)