diff options
| -rw-r--r-- | acquisition/chapter.tex | 116 |
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. %
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