From 3dc46ef66670d4e465d7d662e5dd7175fb8fae2c Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Mon, 9 Apr 2018 21:03:57 -0500
Subject: 2018-04-09 21:03
---
acquisition/chapter.tex | 287 +++++++++++++++++++++++++++++-------------------
dissertation.tex | 4 +-
2 files changed, 174 insertions(+), 117 deletions(-)
diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex
index 0436028..4446c0f 100644
--- a/acquisition/chapter.tex
+++ b/acquisition/chapter.tex
@@ -9,8 +9,10 @@
\clearpage
-MR-CMDS relies on a good number of instrumental capabilities. %
-Fundamentally, MR-CMDS is about delivering multiple pulses of light to a given sample. %
+\section{Introduction} % =========================================================================
+
+MR-CMDS instruments need to be capable of several different things. %
+At its core, MR-CMDS is about delivering multiple pulses of light to a sample. %
The frequency and relative arrival time (delay) of each pulse must be scanned in the context of a
basic multidimensional experiment. %
Scanning frequency requires using motors to change crystal angles and other optics within Optical
@@ -19,10 +21,11 @@ Scanning delay typically involves moving mirrors very small distances such that
length of certain beam-lines changes. %
In addition to these ``first-order'' controls, the power of MR-CMDS is enhanced with additional
control of pulse intensity and polarization. % TODO: citations to motivate this 'enhancement'
-Each of these is an optomechanical device. %
An automated monchromator is typically used to spectrally resolve or isolate output signal. %
+Each of these features is an optomechanical device: a piece of hardware that must be controlled in
+the context of an MR-CMDS experiment. %
-An acquisition in MR-CMDS typically means going to a whole series of different positions. %
+A scan in MR-CMDS typically means going to a whole series of different positions. %
As an example, a three-dimensional ``movie'' might be collected in the following way:
\begin{codefragment}{python, label=aqn:lst:psuedoaqn}
w1_points = [14300, 14400, 14500, 14600, 14700] # wn
@@ -47,31 +50,58 @@ In practice, real scans are composed of $\sim$100 to $\sim$100,000 pixels, and t
minute and one day to acquire. %
Because of the highly specialized nature of these experiments, MR-CMDS instruments typically
-require custom software to address all of simultaneous, repeated motor motion that a scan
+require custom software to address all of the simultaneous, repeated motor motion that a scan
requires. %
Because MR-CMDS is really a family of techniques which require different kinds of motor motion,
this acqusition software should be flexable enough to meet the creativity of its users. %
Furthermore, because MR-CMDS is a bleeding edge, rapidly evolving technique the instrumental
software must be built in an extendable way to accommodate the ever-changing hardware
configurations. %
-In this chapter I describe how I built such an acquisition software. %
-
-\section{Overview} % =============================================================================
+In this chapter I describe how I built such an acquisition software, PyCMDS. %
PyCMDS is a unified software for controlling hardware and collecting data in the Wright Group. %
-It is written almost entirely in Python, with a graphical user interface (GUI) made using Qt. %
-It is cross-platform, running on Linux, Windows and macOS. %
-It is open source, developed on GitHub. % TODO: cite PyCMDS on github
-PyCMDS is used to drive both of the MR-CMDS instruments maintained by the Wright Group: the ``fs
-table'', focused on semiconductor photophysics, and the ``ps table'', focused on molecular
+It is written almost entirely in Python, with a graphical user interface (GUI) made using Qt.
+[CITE] %
+It is cross-platform, with a core capable of running on Linux, Windows and macOS. %
+It is open source, developed on GitHub. [CITE (GITHUB, PyCMDS)] %
+In the Wright Group, PyCMDS replaces the old acquisition softwares `ps control', written by
+Kent Meyer, [CITE] and `Control for Lots of Research in Spectroscopy' (COLORS) written by Schuyler
+Kain [CITE]. %
+Today PyCMDS is used to drive both of the MR-CMDS instruments maintained by the Wright Group: the
+``fs table'', focused on semiconductor photophysics, and the ``ps table'', focused on molecular
systems. %
-In the Wright Group, PyCMDS replaces the old acquisition softwares `ps control', ritten by
-Kent Meyer and `Control for Lots of Research in Spectroscopy' written by Schuyler Kain.
+% BJT: consider giving more historical context re: COLORS, ps_control
+
+PyCMDS is best thought of as a central program with three kinds of modular ``plugins'' that can be
+extended indefinitely:
+\begin{ditemize}
+ \item Hardware: things that can be set to a position (\autoref{aqn:sec:hardware}).
+ \item Sensors: things that can be used to measure a signal (\autoref{aqn:sec:sensors}).
+ \item Acquisition modules: things that can be used to define and carry out an acquisition, and
+ associated post-processing (\autoref{aqn:sec:somatic}).
+\end{ditemize}
+The first design rule for PyCMDS is that these three things should be easy for the average
+(motivated) user to add by herself. %
+Modularity and extensibility is important for all scientific software projects (see
+\autoref{cha:sof}), but it is of paramount importance for acquisition software simply because the
+diversity of hardware and experimental configurations is so great. %
+It is conceivable to imagine 90\% overlap between the data processing and simulation needs of one
+spectroscopist to the next, but there is almost no overlap between hardware configurations even in
+the two primary instruments maintained by the Wright Group. %
+Besides the extendable modular pieces, the rest of PyCMDS is a mostly-static code-base that accepts
+modules and does the necessary things to handle display of information from, and communication
+between them. %
+
+% TODO: describe each of the sections of this chapter
+
+\clearpage
+\section{Graphical user interface} % =============================================================
When PyCMDS starts up, the GUI is constructed out of modules depending on which hardware and
sensors the user has instructed the program to address. %
A screenshot of the PyCMDS GUI, running on the fs table, is shown in
\autoref{aqn:fig:pycmds_screenshot}. %
+
On the left hand there is a single column displaying the current positions for all loaded
hardware. %
Users may enter new destinations and hit the ``SET'' button. %
@@ -79,68 +109,94 @@ Positions have units, which are changeable through the pull-down menu next to th
display. %
Each hardware knows its own limits, displayed in a tool tip when hovering over the control. %
Users cannot type values outside of hardware limits into the controls. %
-
-The large right-hand section is tabbed...
+Each hardware also has an ``ADVANCED'' button, which takes the user to a more extensive GUI to
+control lots more features (see section ....) %
+At the very top, on the left hand side, is the ``SHUT DOWN'' button. %
+
+On the right hand side there is a extensive set of nested tabs. %
+The top level tabs are ``Program'', ``Hardware'', ``Devices'', ``Autonomic'', ``Somatic'' and
+``Plot''. %
+Under each of these tabs is an entire separate set of display and control elements. %
+Some of these elements are themselves tabbed, like the ``Somatic'' tab (active in
+\autoref{aqn:fig:pycmds_screenshot}), which has ``Queue'' and ``Scan'' sub-tabs. %
+At the top of the right hand side there is a progress bar and queue status display, which I will
+discuss further in future sections. %
\begin{landscape}
\begin{figure}
\includegraphics[scale=0.5]{"acquisition/screenshots/005"}
- \caption{
- TODO (PyCMDS screenshot)
+ \caption[PyCMDS at startup.]{
+ PyCMDS at startup, on the fs system. %
}
\label{aqn:fig:pycmds_screenshot}
\end{figure}
\end{landscape}
-To perform an acquisition, a user goes to the SOMATIC tab and enters an item into the QUEUE...
-
-During the acquisition...
-Progress bar...
-Cannot hit SET...
-QUEUE states...
+When PyCMDS opens (\autoref{aqn:fig:pycmds_screenshot}), the user is first greeted with the
+``Somatic/Queue'' tab on the right hand side of the GUI. %
+This is where the tells PyCMDS to do acquisitions. %
+In PyCMDS, all acquisitions are done in a queue system. %
+A queue is just a list of acquisitions, where the acquisitions are carried out one by one in
+order. %
+
+To instruct PyCMDS to do an acquisition, the user must first create a queue by entering in a chosen
+name (default is ``queue''), and pressing the ``MAKE NEW QUEUE'' button. %
+Alternatively the user may open an existing queue using ``OPEN QUEUE''. %
+
+Next, the user must add the desired acquisition(s) to the queue. %
+There are several acquisition modules, each with a different purpose. %
+Choose an acquisition module using the drop down menu. %
+Enter a name for your acquisition, and any additional info that you might want to keep track of. %
+Finally, fill out any additional information that acquisition module might require, and press
+``APPEND TO QUEUE''. %
+
+Once there are acquisitions in the queue, the user can press ``RUN QUEUE''. %
+\autoref{aqn:fig:pycmds_screenshot_during_scan} is a screenshot of PyCMDS during a representative
+acquisition. %
+This time, thee ``Somatic/Scan'' tab is chosen. %
+On the left hand side, we can see that the ``SHUT DOWN'' and ``SET'' buttons are grayed out and
+unclickable, since the somatic system is in control of PyCMDS. %
+At the moment when this screen shot was taken, PyCMDS is waiting for w3 (OPA-800CG) to finish
+moving, as the ``BUSY'' indicator shows. %
+The progress bar, near the top of the GUI, is partially green to indicate the portion of the
+current scan that is finished. %
+On the left hand side of the progress bar the time elapsed (fifteen minutes, thirty-seven seconds)
+is shown, and on the right hand shows the time remaining (three hours, eight minutes, sixteen
+seconds). %
+In the center of the progress bar are the current scan parameters. %
+
+The ``Somatic/Scan'' tab is built as an active display of currently acquiring data. %
+A large graph and number show the current signal levels. %
+On the far right-hand side, the device and channel to display can be chosen via drop-down menu. %
+Under ``Status'', the loop time and scan index help users gauge the progress of their scan. %
+In this case, the displayed pixel (index 6, 40) took 2.448 seconds to acquire. %
\begin{landscape}
\begin{figure}
\includegraphics[width=9in]{"acquisition/screenshots/000"}
- \caption{
- TODO (PyCMDS screenshot while acquiring data)
+ \caption[PyCMDS while scanning.]{
+ PyCMDS while acquiring data, on the ps system. %
}
\label{aqn:fig:pycmds_screenshot_during_scan}
\end{figure}
\end{landscape}
-\section{Structure} % ============================================================================
+\section{Internal structure} % ===================================================================
-I think of PyCMDS as a central program with three kinds of modular ``plugins'' that can be extended
-indefinitely:
-\begin{ditemize}
- \item Hardware: things that can be set to a position (\autoref{aqn:sec:hardware}).
- \item Sensors: things that can be used to measure a signal (\autoref{aqn:sec:sensors}).
- \item Acquisition modules: things that can be used to define and carry out an acquisition, and
- associated post-processing (\autoref{aqn:sec:somatic}).
-\end{ditemize}
-The first design rule for PyCMDS is that these three things should be easy for the average
-(motivated) user to add by herself. %
-Modularity and extensibility is important for all software projects, but it is of paramount
-importance for acquisition software simply because the diversity of hardware and experimental
-configurations is so great. %
-It is conceivable to imagine 90\% overlap between the data processing and simulation needs of one
-spectroscopist to the next, but there is almost no overlap between hardware configurations even in
-the two primary instruments maintained by the Wright Group. %
-Besides the extendable modular pieces, the rest of PyCMDS is a mostly-static code-base that accepts
-modules and does the necessary things to handle display of information from, and communication
-between them. %
+In this section I discuss the internal structure of PyCMDS. %
+While there are a huge number of details not worthy of discussion (at time of writing, PyCMDS
+consists of 16,582 lines of source code), PyCMDS is made to be maintained and extended by future
+graduate students, so some insight into the internal structure is warranted. %
\subsection{Multithreading} % --------------------------------------------------------------------
-For the kinds of acquisitions that the Wright Group has done the acquisition software spends the
-vast majority of its run-time waiting---waiting for user input through mouse clicks or keyboard
-presses, waiting for hardware to finish moving or for sensors to finish reading and return
-signals. %
+PyCMDS spends the vast majority of its runtime waiting---waiting for user input through mouse
+clicks or keyboard presses, waiting for hardware to finish moving or for sensors to finish reading
+and return signals. %
Despite all of this downtime, it is crucial that the software respond very quickly when
-instructions or signals are recieved. %
-A multi-threaded implementation is necessary to achieve this. %
-The main thread handles the graphical user interface (GUI) and other top level things. %
+instructions or signals are received. %
+To achieve this, PyCMDS is designed using \emph{multithreading}. %
+The main thread handles the graphical user interface (GUI) and other ``top level'' things. %
Everything else happens in child threads. %
Each hardware instance (e.g. a delay stage) lives in its own thread, as does each sensor. %
Since only one scan happens at a time, all acquisition modules share a single thread that handles
@@ -303,67 +359,6 @@ Use of qt plots...
pyqtgraph \cite{pyqtgraph}
-\subsection{Scans} % -----------------------------------------------------------------------------
-
-The central loop of scans in PyCMDS. %
-\begin{codefragment}{python, label=aqn:lst:loop_simple}
-for coordinates in list_of_coordinates:
- for hardware, coordinate in zip(hardwares, coordinates):
- hardware.set(coordinate)
- for hardware in hardwares:
- hardware.wait_until_still()
- for sensor in sensors:
- sensor.read()
- for sensor in sensors:
- sensor.wait_until_done()
-\end{codefragment}
-
-\subsection{Conditional validity} % --------------------------------------------------------------
-
-The central conceit of the PyCMDS modular hardware abstraction is that experiments can be boiled
-down to a set of orthogonal axes that can be set separately from other hardware and sensor
-status. %
-This requirement is loosened by the autonomic and expression systems, such that any experiment
-could \emph{probably} be forced into PyCMDS, but still the conceit stands---PyCMDS is probably
-\emph{not} the correct framework if your experiment cannot be reduced in this way. %
-From this we can see that it is useful to talk about the conditional validity of the modular
-hardware abstraction. %
-
-The important axis is hardware complexity vs measurement complexity.
-
-For hardware-complex problems, the challenge is coordination. %
-MR-CMDS is the perfect example of a hardware-complex problem. %
-MR-CMDS is composed of a collection (typically 5 to 10 members) of relatively simple hardware
-components. %
-The challenge is that experiments involve complex ``dances'', including expressions, of the
-component hardwares. %
-
-For measurement-complex problems, the challenge is, well, the measurement. %
-These are experiments where every little piece of the instrument is tied together into a complex
-network of inseparable parts. %
-These are often time-domain or ``single shot'' measurements. %
-Consider work of (GRAPES INVENTOR). %
-Such instruments are typically much faster at data acquisition and more reliable. %
-This comes at a price of flexibility: often such instruments cannot be modified or enhanced without
-touching everything. %
-
-From an acquisition software perspective, measurement-complex problems are not amenable to general
-purpose modular software design. %
-The instrument is so custom that it certainly requires entirely custom software. %
-
-Measurements can be neither hardware-complex nor software-complex (simple) or both (expensive). %
-Conceptually, can imagine a 4 quadrant system. %
-
-Thus PyCMDS can be proud to try and generalize the hardware-complex part of acquisition software
-because indeed that is all that can be generalized. %
-
-\begin{figure}
- \caption{
- CAPTION TODO: 4 QUADRANTS OF COMPLEXITY
- }
- \label{aqn:fig:complexity_quandrants}
-\end{figure}
-
\section{Hardware} \label{aqn:sec:hardware} % ====================================================
Hardware are things that 1) have a position, 2) can be set to a destination. %
@@ -564,6 +559,21 @@ In contrast with the autonomic system (\autoref{aqn:sec:autonomic}), the somatic
about voluntary, user specified motion. %
This is where the fun stuff happens---the acquisitions!
+\subsection{Scans} % -----------------------------------------------------------------------------
+
+The central loop of scans in PyCMDS. %
+\begin{codefragment}{python, label=aqn:lst:loop_simple}
+for coordinates in list_of_coordinates:
+ for hardware, coordinate in zip(hardwares, coordinates):
+ hardware.set(coordinate)
+ for hardware in hardwares:
+ hardware.wait_until_still()
+ for sensor in sensors:
+ sensor.read()
+ for sensor in sensors:
+ sensor.wait_until_done()
+\end{codefragment}
+
\subsection{Acquisition modules} % ---------------------------------------------------------------
Acquisition modules are defined interfaces which know how to assemble a scan. %
@@ -622,6 +632,53 @@ Self describing (enabled by \python{tidy_headers}).
For scan module, just
+\clearpage
+\section{Conditional validity} % =================================================================
+
+The central conceit of the PyCMDS modular hardware abstraction is that experiments can be boiled
+down to a set of orthogonal axes that can be set separately from other hardware and sensor
+status. %
+This requirement is loosened by the autonomic and expression systems, such that any experiment
+could \emph{probably} be forced into PyCMDS, but still the conceit stands---PyCMDS is probably
+\emph{not} the correct framework if your experiment cannot be reduced in this way. %
+From this we can see that it is useful to talk about the conditional validity of the modular
+hardware abstraction. %
+
+The important axis is hardware complexity vs measurement complexity.
+
+For hardware-complex problems, the challenge is coordination. %
+MR-CMDS is the perfect example of a hardware-complex problem. %
+MR-CMDS is composed of a collection (typically 5 to 10 members) of relatively simple hardware
+components. %
+The challenge is that experiments involve complex ``dances'', including expressions, of the
+component hardwares. %
+
+For measurement-complex problems, the challenge is, well, the measurement. %
+These are experiments where every little piece of the instrument is tied together into a complex
+network of inseparable parts. %
+These are often time-domain or ``single shot'' measurements. %
+Consider work of (GRAPES INVENTOR). %
+Such instruments are typically much faster at data acquisition and more reliable. %
+This comes at a price of flexibility: often such instruments cannot be modified or enhanced without
+touching everything. %
+
+From an acquisition software perspective, measurement-complex problems are not amenable to general
+purpose modular software design. %
+The instrument is so custom that it certainly requires entirely custom software. %
+
+Measurements can be neither hardware-complex nor software-complex (simple) or both (expensive). %
+Conceptually, can imagine a 4 quadrant system. %
+
+Thus PyCMDS can be proud to try and generalize the hardware-complex part of acquisition software
+because indeed that is all that can be generalized. %
+
+\begin{figure}
+ \caption{
+ CAPTION TODO: 4 QUADRANTS OF COMPLEXITY
+ }
+ \label{aqn:fig:complexity_quandrants}
+\end{figure}
+
\section{Integrations} % =========================================================================
\begin{figure}
diff --git a/dissertation.tex b/dissertation.tex
index f3734bc..369e9a3 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -70,8 +70,8 @@ This dissertation is approved by the following members of the Final Oral Committ
\part{Development} \label{prt:development}
\include{processing/chapter} % pro
\include{acquisition/chapter} % acq
-\include{active_correction/chapter} % act
-\include{opa/chapter} % opa
+%\include{active_correction/chapter} % act
+%\include{opa/chapter} % opa
%\include{mixed_domain/chapter}
\part{Applications} \label{prt:applications}
--
cgit v1.2.3