2018-04-11 14:49

4 files changed, 103 insertions, 54 deletions

diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex
index d997e44..86c5c8c 100644
--- a/acquisition/chapter.tex
+++ b/acquisition/chapter.tex
@@ -11,7 +11,6 @@
 

 \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.  %

@@ -25,7 +24,7 @@ An automated monchromator is typically used to spectrally resolve or isolate out
 Each of these features is an optomechanical device: a piece of hardware that must be controlled in

 the context of an MR-CMDS experiment.  %

 

-A scan in MR-CMDS typically means going to a whole series of different positions.  %

+A scan in MR-CMDS typically means sending hardware 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

@@ -59,21 +58,35 @@ software must be built in an extendable way to accommodate the ever-changing har
 configurations.  %

 In this chapter I describe how I built such an acquisition software, PyCMDS.  %

 

+For context, some description of the acquisition software that PyCMDS replaced is warranted.  %

+

+On the ``ps table'' (focus on mixed vibrational-electronic spectroscopy of molecular systems),

+PyCMDS replaces `ps\_control', an older acquisition software first developed in [YEAR] by Kent

+Meyer [CITE].  %

+ps\_control was very-much not modular, designed by generations of graduate students to get to

+``minimum viable'' as quickly as possible.  %

+When I joined the group, ps\_control had become unsustainable.  %

+The ps table was being revamped with new hardware, and the old motherboard finally died, so new

+software was desperately needed.  %

+

+On the ``fs table'' (focus on semiconductor photophysics), PyCMDS replaces `Control for Lots of

+Research in Spectroscopy' (COLORS), developed by Schuyler Kain [CITE].  %

+PyCMDS is, in many ways, inspired by COLORS.  %

+Kain's design was modular in many ways.  %

+Still, there were fundamental problems that COLORS could not address.  %

+Chief among them was Kain's approach to the National Instruments DAQ card, which did not allow for

+the flexibility required to introduce more interesting chopping schemes [SECTION].  %

+

 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.

-[CITE]  %

+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.  %

-% 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:

+Today PyCMDS is used to drive both the ps and fs tables.   %

+

+PyCMDS is best thought of as a core program with three kinds of modular ``plugins'' that can be

+extended as needed.  %

+The three plugin kinds are

 \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}).

@@ -92,9 +105,13 @@ Besides the extendable modular pieces, the rest of PyCMDS is a mostly-static cod
 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

-

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

+PyCMDS offers many ways to interact with component hardwares.  %

+Hardware can be set directly, or it can be moved in the context of a scan.  %

+Less obviously, hardware must also move in the context of ``active correction'', such as spectral

+delay correction.  %

+I love to use the analogy of the nervous system when thinking of these two kinds of

+instructions.  %

+I have borrowed the terms ``autonomic'' and ``somatic'':

 

 \begin{dquote}

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

@@ -114,6 +131,13 @@ In designing PyCMDS, I was inspired by the nervous system...
   \dsignature{W. J\"{a}nig, Autonomic Nervous System (1989) \cite{JanigW1989a}}

 \end{dquote}

 

+Within PyCMDS, the autonomic system [SECTION] handles the ``reflex'' motion that is part of active

+correction.  %

+The somatic system [SECTION], on the other hand, handles the ``voluntary'' motion in the context of

+acquiring a multidimensional scan.  %

+

+% BJT: consider a layout preview paragraph or two

+

 \clearpage

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

 

diff --git a/dissertation.tex b/dissertation.tex
index a38db68..798d378 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -64,21 +64,21 @@ This dissertation is approved by the following members of the Final Oral Committ
 \include{introduction/chapter}

 

 \part{Background} \label{prt:background}

-\include{spectroscopy/chapter}

-\include{software/chapter}  % sof

+%\include{spectroscopy/chapter}

+%\include{software/chapter}  % sof

 

 \part{Development} \label{prt:development}

-\include{processing/chapter}  % pro

+%\include{processing/chapter}  % pro

 \include{acquisition/chapter}  % acq

-\include{active_correction/chapter}  % act

-\include{opa/chapter}  % opa

-\include{mixed_domain/chapter}

+%\include{active_correction/chapter}  % act

+%\include{opa/chapter}  % opa

+%\include{mixed_domain/chapter}

 

 \part{Applications} \label{prt:applications}

-\include{PbSe_susceptibility/chapter}

-\include{PbSe_global_analysis/chapter}

-\include{MX2/chapter}

-\include{PEDOT_PSS/chapter}

+%\include{PbSe_susceptibility/chapter}

+%\include{PbSe_global_analysis/chapter}

+%\include{MX2/chapter}

+%\include{PEDOT_PSS/chapter}

 

 % appendix -----------------------------------------------------------------------------------------

 

diff --git a/todo.org b/todo.org
index 0f0687c..24fa962 100644
--- a/todo.org
+++ b/todo.org
@@ -1,9 +1,3 @@
-* DONE distribution section                                      :processing:
-  CLOSED: [2018-04-11 Wed 11:28]
-* DONE development history from github                           :processing:
-  CLOSED: [2018-04-11 Wed 11:29]
-* DONE development section                                       :processing:
-  CLOSED: [2018-04-11 Wed 11:30]
 * TODO headers                                                 :introduction:
 * TODO cite important CMDS discoveries, reviews                :introduction:
 * TODO incorporate Nancy's comments                            :introduction:
@@ -14,26 +8,29 @@
 * TODO verify light-matter interaction content                 :spectroscopy:
 * TODO finish instrumentation section (darien)                 :spectroscopy:
 * IDEA linear vs multidimensional figure                       :spectroscopy:
-* IDEA see Paul's dissertation re: loss of resonance advantage with very fast pulses :spectroscopy:
-* TODO more references for object oriented programming             :software:
-* IDEA incorporate StoddenVictoria2016a                            :software:
-* IDEA incorporate idea "most people over-trust software"          :software:
-* IDEA consider refactoring or expanding OOP section               :software:
-* TODO summary paragraphs in introduction                        :processing:
-* TODO finish discussing interpolation types                     :processing:
+* IDEA see Paul's dissertation                                 :spectroscopy:
+** re: loss of resonance advantage with very fast pulses
+* TODO more references for object oriented programming                  :sof:
+** in inbox
+* IDEA incorporate StoddenVictoria2016a                                 :sof:
+* IDEA incorporate idea "most people over-trust software"               :sof:
+* IDEA consider refactoring or expanding OOP section                    :sof:
+* TODO summary paragraphs in introduction                               :pro:
+* TODO finish discussing interpolation types                            :pro:
 ** TODO describe figure
-* TODO specialty artists                                         :processing:
-* TODO artist API                                                :processing:
-* TODO gotchas (figures from czech...)                           :processing:
-* TODO axes content                                              :processing:
-* TODO level                                                     :processing:
-* TODO tables                                                    :processing:
-* TODO finish describing function objects                        :processing:
-* TODO describe continuous integration                           :processing:
-* TODO describe readthedocs documentation                        :processing:
-* TODO future directions                                         :processing:
-* TODO figure captions                                           :processing:
-* TODO flesh out introduction                                           :acq:
+* TODO specialty artists                                                :pro:
+* TODO artist API                                                       :pro:
+* TODO gotchas (figures from czech...)                                  :pro:
+* TODO axes content                                                     :pro:
+* TODO level                                                            :pro:
+* TODO tables                                                           :pro:
+* TODO finish describing function objects                               :pro:
+* TODO describe continuous integration                                  :pro:
+* TODO describe readthedocs documentation                               :pro:
+* TODO future directions                                                :pro:
+* TODO figure captions                                                  :pro:
+* DONE flesh out introduction                                           :acq:
+  CLOSED: [2018-04-11 Wed 14:48]
 * TODO show queue figure in GUI section                                 :acq:
 * TODO parents _are_ virtual hardware                                   :acq:
 * TODO hardware advanced panel descriptions                             :acq:
@@ -47,12 +44,13 @@
 * TODO introduction paragraphs                                          :act:
 * TODO spectral delay correction                                        :act:
 * TODO poynting correction                                              :act:
-* IDEA excitation power correction                                      :act:
 * TODO chopping (minimal)                                               :act:
 * TODO fibrillation (minimal)                                           :act:
 * TODO conclusions                                                      :act:
 * TODO figure captions                                                  :act:
+* IDEA excitation power correction                                      :act:
+* IDEA 2D delay example from ps system                                  :act:
 * TODO insert content                                                  :PbSe:
 * TODO insert content from SI                                  :mixed_domain:
-* IDEA 2D delay example from ps system                               :active:
 * TODO verify all references                                         :polish:
+* TODO read through and make links where appropriate                 :polish:
diff --git a/todo.org_archive b/todo.org_archive
index 2949981..324681b 100644
--- a/todo.org_archive
+++ b/todo.org_archive
@@ -76,3 +76,30 @@ Archived entries from file /home/blaise/source/dissertation/todo.org
   :ARCHIVE_CATEGORY: todo
   :ARCHIVE_TODO: DONE
   :END:
+
+* DONE distribution section                                      :processing:
+  CLOSED: [2018-04-11 Wed 11:28]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 14:04
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+
+* DONE development history from github                           :processing:
+  CLOSED: [2018-04-11 Wed 11:29]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 14:04
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+
+* DONE development section                                       :processing:
+  CLOSED: [2018-04-11 Wed 11:30]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 14:04
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END: