2018-03-27 23:25

4 files changed, 126 insertions, 9 deletions

diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex
index 863bf96..832e698 100644
--- a/acquisition/chapter.tex
+++ b/acquisition/chapter.tex
@@ -1,7 +1,5 @@
 \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?”

@@ -259,7 +257,6 @@ from the global \python{Hardware} class shown in \autoref{aqn:lst:parent_hardwar
   \label{aqn:fig:hardware_class}

 \end{figure}

 

-

 \begin{figure}

 	\includebash{"acquisition/hardware_inheritance"}

   \caption[Hardware inheritance.]{

@@ -267,40 +264,152 @@ from the global \python{Hardware} class shown in \autoref{aqn:lst:parent_hardwar
   \label{aqn:fig:hardware_inheritance}

 \end{figure}

 

-

+So every hardware object must have the following...

 

 \subsection{Delays}  % ----------------------------------------------------------------------------

 

+Delays are the kind of thing that have a position in absolute units, a zero position, and a

+relative position measured in fs or ps.  %

+They also are the kind of thing that is most commonly subject to offset by the Autonomic

+system...  %

+

+In addition to the inherited methods, delay hardware objects require the following:

+\begin{ditemize}

+  \item \python{set_motor_position}

+\end{ditemize}

+

+Delay driver objects require the following:

+\begin{ditemize}

+  \item \python{set_motor_position}

+\end{ditemize}

+

+The delay GUI, by default, offers

+\begin{ditemize}

+  \item \python{on_home}

+  \item \python{on_set_motor}

+  \item \python{on_set_zero}

+\end{ditemize}

+  

 \subsection{Spectrometers}  % ---------------------------------------------------------------------

 

+Spectrometers are the kind of thing that can be set to a single color (typically native units are

+in nm).  %

+They often have turrets that allow for switching between gratings.  %

+Other features are not currently supported as PyCMDS has only been asked to drive one kind of

+monochromator so far.  %

+

+Hardware:

+

+Driver:

+

+GUI:

+

 \subsection{OPAs}  % ------------------------------------------------------------------------------

 

+Hardware:

+

+Driver:

+

+GUI:

+

+\subsubsection{Curves}

+

+Recursive

+

+United

+

+Interpolation

+

 \subsection{Filters}  % ---------------------------------------------------------------------------

 

+Hardware:

+

+Driver:

+

+GUI:

+

 \section{Sensors (devices)} \label{aqn:sec:sensors}  % ============================================

 

+Sensors are...

+

+For DAQ cards, shots and samples...

+

+Power of digital processing...

+

+% TODO: screenshots

+

 \subsection{Sensors as axes}  % -------------------------------------------------------------------

 

-\section{Autonomic}  % ============================================================================

+% TODO: equation from Skye

+

+% TODO: poweramp tune test  (see darien slack)

+

+\section{Autonomic} \label{aqn:sec:autonomic}  % ==================================================

+

+\begin{dquote}

+  The autonomic nervous system, which innervates primarily the smooth musculature of all organs,

+  the heart and the glands, mediates the neuronal regulation of the internal milieu.  %

+  The actions of this system, as its name implies, are in general not under direct voluntary

+  control.  %

+  These characteristics distinguish the autonomic nervous system from the somatic nervous system,

+  which mediates afferent and efferent communication with the enviornment and, for the most part,

+  is subject to voluntary control and accessible to consciousness.  %

+

+  The autonomic and somatic systems operate hand in hand...

+

+  The functions of the autnomic nervous system are to keep the internal milieu of the body constant

+  (homeostasis...) or adjust it as required by changing circumstances (e.g., mechanical work, food

+  intake, water deprivation, heat or cold).  %

+

+  \dsignature{W. J\"{a}nig, Autonomic Nervous System (1989) \cite{JanigW1989a}}

+\end{dquote}

 

 % TODO: concept of additive offsets

 

 \section{Somatic} \label{aqn:sec:somatic} % =======================================================

 

+In contrast with the autonomic system (\autoref{aqn:sec:autonomic}), the somatic system is all

+about voluntary, user specified motion.  %

+This is where the fun stuff happens---the acquisitions!

+

 \subsection{Acquisition modules}  % ---------------------------------------------------------------

 

-% TODO: the aqn file

+% TODO: the aqn file (show one!)

 

 % TODO: list of modules, descriptions thereof

 

+\subsubsection{Scan}

+

+\subsubsection{AutoTune}

+

+\subsubsection{MotorTune}

+

+\subsubsection{PoyntingTune}

+

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

 

 \subsection{The central loop of PyCMDS}  % --------------------------------------------------------

 

 \subsection{The data file}  % ---------------------------------------------------------------------

 

+Does not have the same dimensionality restrictions as prior acquisition software.  %

+

+Self describing (enabled by \python{tidy_headers}).

+

 \subsection{Automatic processing}  % --------------------------------------------------------------

 

+For scan module, just

+

+\section{Integrations}  % =========================================================================

+

+\begin{figure}

+	\frame{\includegraphics[width=\textwidth]{"acquisition/slack"}}

+	\caption[TODO]{

+    TODO

+  }

+  \label{aqn:fig:slack}

+\end{figure}

+

 \section{Future directions}  % ====================================================================

 

 \subsection{Spectral delay correction module}  % --------------------------------------------------

diff --git a/acquisition/slack.png b/acquisition/slack.png
new file mode 100644
index 0000000..91dd314
--- /dev/null
+++ b/acquisition/slack.png
diff --git a/acquisition/tune_test.png b/acquisition/tune_test.png
new file mode 100644
index 0000000..cb00346
--- /dev/null
+++ b/acquisition/tune_test.png
diff --git a/bibliography.bib b/bibliography.bib
index ee2d58f..61c7013 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -790,6 +790,16 @@ year = {1998}
   month =        {may},

 }

 

+@incollection{JanigW1989a,

+  author =       {W. J\"{a}nig},

+  booktitle =    {Human Physiology},

+  doi =          {10.1007/978-3-642-73831-9_16},

+  pages =        {333--370},

+  publisher =    {Springer Berlin Heidelberg},

+  title =        {Autonomic Nervous System},

+  year =         1989,

+}

+

 @article{JoffreM1988a,

   author =       {Joffre, M and la Guillaume, C. Benoit {\`{a}} and Peyghambarian, N and Lindberg,

                   M and Hulin, D and Migus, A and Koch, S W and Antonetti, A},

@@ -1874,6 +1884,7 @@ year = {1998}
   month =        {sep},

 }

 

+

 @article{ZhaoWei1999b,

   author =       {Zhao, Wei and Wright, John C.},

   title =        {{Spectral Simplification in Vibrational Spectroscopy Using Doubly Vibrationally

@@ -1888,7 +1899,6 @@ year = {1998}
   month =        {dec},

 }

 

-

 @article{ZhaoWei2000a,

   author =       {Zhao, Wei and Urdoch, Keith M M and Besemann, Daniel M and Condon, Nicholas J.

                   and Meyer, Kent a. and Right, John C W},

@@ -1919,8 +1929,6 @@ year = {1998}
   url =          {http://docs.h5py.org/en/latest/high/group.html#groups},

 }

 

-

-

 @misc{pyqtgraph,

   note =         {Accessed: 2018-03-27},

   title =        {PyQtGraph: Scientific Graphics and GUI Library for Python},