2018-04-10 20:13

1 files changed, 90 insertions, 26 deletions

diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex
index 02be26a..803049e 100644
--- a/acquisition/chapter.tex
+++ b/acquisition/chapter.tex
@@ -94,6 +94,26 @@ between them.  %
 

 % TODO: describe each of the sections of this chapter

 

+In designing PyCMDS, I was inspired by the nervous system...

+

+\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}

+

 \clearpage

 \section{Graphical user interface}  % =============================================================

 

@@ -385,6 +405,8 @@ which point \python{Driver.dequeue} will be called in the worker thread.  %
 There is no way for the driver to command hardware to do something in the main thread, but the

 driver can trigger signals like \python{update_ui} and modify Mutexes.  % 

 

+[PARENTS ARE VIRTUAL HARDWARE]

+

 \begin{figure}

 	\includepython{"acquisition/parent_hardware.py"}

   \caption[Parent to hardware and sensors.]{

@@ -409,8 +431,8 @@ The PyCMDS GUI must change depending on which exact hardware, sensors, and acqui
 being used on a given instrument and given day.  %

 Internally, the GUI components are made to be modular and flexable to accommodate this

 requirement.  %

-

-[programmatically defined GUI]

+Rather than having each piece placed ``by hand'', the PyCMDS GUI is defined programmatically and,

+as such, the full power of abstraction and inheritance is available to the GUI-defining code.  %

 

 To keep things simple and easy to extend, PyCMDS is made up of only a few minimalist GUI

 elements.  %

@@ -460,6 +482,8 @@ delay stage.  %
 

 PyCMDS uses pyqtgraph \cite{pyqtgraph} for interactive plotting.  %

 pyqtgraph is great because it is optimized for speed and interactivity.  %

+Currently only line plots are supported (through the \python{PyCMDS.project.widgets.Plot1D} class),

+but 2D plots are supported by pyqtgraph and could be added in future versions.  %

 

 For those wanting to learn more, all graphical components are defined in

 \bash{PyCMDS/project/widgets.py}.  %

@@ -639,39 +663,83 @@ Old boxcar: 300 ns window, ~10 micosecond delay. Onset of saturation ~2 V.
 

 \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 system is used to define ``reflexes'' for PyCMDS---operations that are automatically

+applied when certain conditions are met.  %

+Currently the autonomic system has only functionality: \emph{offset} certain hardware as functional

+of other hardware's positions.  %

 

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

+The classic example of autonomic offsets comes from spectral delay correction (see section

+[ACT]).  %

+Spectral delay refers to the small delay changes that occur when OPAs change output frequency.  %

+To correct for spectral delay, the appropriate delay stages can simply be \emph{offset}.  %

 

-  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).  %

+In PyCMDS, the autonomic system is fully general---that is to say, any hardware can be offset

+according to any other hardware.  %

+This means that spectral delay correction is possible for arbitrarily complex laser setups, and it

+means that PyCMDS is prepared for corrections that have not yet been fully implemented, such as

+automated power correction.  %

 

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

-\end{dquote}

+Simple plain-text \bash{.coset} files define the offset arrays.  %

+They are automatically generated using processing scripts in \python{attune} [CITE].  %

+Their headers prevent them from being loaded in the wrong spot.  %

+These files are internally represented as instances of the \python{CoSet} class, which is capable

+of linear interpolation and extrapolation at the edges.  %

 

-% TODO: concept of additive offsets

+A single hardware can be offset by multiple other hardwares.  %

+In such cases, \emph{offsets always add}.  %

 

 \begin{figure}

-  \caption[Representative spectral delay correction]{

-    CAPTION TODO

-  }

-  \label{aqn:fig:sdc}

+  \caption{AUTONOMIC SDC SCREENSHOT}

 \end{figure}

-  

+

+\clearpage

 \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!

 

+PyCMDS uses the words ``scan'' and ``acquisition'' in very careful ways.  %

+\begin{ditemize}

+  \item An acquisition is a single user-defined, enqueable, instruction.

+  \item A scan is a single traversal in the multidimensional hardware space.  %

+\end{ditemize}

+Each scan corresponds to one \bash{.data} file, and one WrightTools \python{Data} instance (see

+section ...)  %

+There can be many scans within a single acquisition.  %

+And there can be many acquisitions in a queue.  %

+

+PyCMDS saves the data that it is collecting within a nested folder structure

+queue/acquisition/scan.  %

+A \bash{.queue} file holds everything needed to recreate the queue, \python{.aqn} files define each

+acquisition in plain text and \python{.data} files hold the multidimensional data itself.  %

+

+In this section I describe each component of the somatic system in greater detail.  %

+

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

+

+The queue manager keeps track of all enqueued acquisitions, and tells each acquisition when to

+begin.  %

+A singleton \python{Queue} class lives in the main thread and handles interfacing to the

+\bash{.queue} plain-text file.  %

+When a user appends new acquisitions, or changes their order, the \python{queue} instance makes

+sure that those changes are reflected in the GUI and the file.  %

+

+A special singleton \python{QueueStatus} keeps track of, well, the queue status: a series of

+booleans \python{go}, \python{going}, \python{pause}, \python{paused}, \python{stop}, and

+\python{stopped}.  %

+The verb booleans (\python{go}, \python{pause}, \python{paused}), are control flags, to be

+written by the main thread.  %

+The present particple booleans (\python{going}, \python{paused}, \python{stopped}) are flags to be

+written by the worker thread to indicate status of the current acquisition.  %

+

+A singleton \python{Worker} class lives in the acquisition worker thread and carries out the actual

+operation.  %

+The \python{queue} instance pushes operations to the \python{worker}, and the \python{worker} sends

+a signal that causes \python{queue.on_action_complete} to be called.  %

+If there are more enqueued acquisitions, and \python{queue_status.go} is true, the \python{queue}

+instance pushes the next operation to the \python{worker} and the process starts over again.  %

+

 \subsection{Scans}  % -----------------------------------------------------------------------------

 

 The central loop of scans in PyCMDS.  %

@@ -731,10 +799,6 @@ Automatically do appropriate scans and process as in chapter...
 

 Dedicated to poynting (get content from Kyle S)...

 

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

-

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

-

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

 

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