2018-03-26 22:34

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
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
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
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
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)