2018-04-11 11:51

6 files changed, 137 insertions, 54 deletions

diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex
index df1c887..d997e44 100644
--- a/acquisition/chapter.tex
+++ b/acquisition/chapter.tex
@@ -891,13 +891,7 @@ 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}

-

+\clearpage

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

 

 [GOOGLE DRIVE]

diff --git a/dissertation.tex b/dissertation.tex
index 29b092a..a38db68 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -68,17 +68,17 @@ This dissertation is approved by the following members of the Final Oral Committ
 \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/spectroscopy/auto/chapter.el b/spectroscopy/auto/chapter.el
index 6fd7dd7..4966739 100644
--- a/spectroscopy/auto/chapter.el
+++ b/spectroscopy/auto/chapter.el
@@ -3,7 +3,6 @@
  (lambda ()
    (LaTeX-add-labels
     "cha:spc"
-    "spc:fig:decongestion"
     "spc:fig:power_curves"))
  :latex)
 
diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex
index eb41d10..cdd3955 100644
--- a/spectroscopy/chapter.tex
+++ b/spectroscopy/chapter.tex
@@ -172,14 +172,6 @@ The most obvious advantage of multidimensional spectroscopy comes directly from
 itself.  %

 Multidimensional spectroscopy can \emph{decongest} spectra with overlapping peaks by isolating

 peaks in a multidimensional resonance landscape.  %

-Figure \ref{spc:fig:decongestion} shows...

-

-\begin{figure}

-  \caption[Dimensionality and decongestion.]{

-    CAPTION TODO.

-  }

-  \label{spc:fig:decongestion}

-\end{figure}

 

 \subsection{Frequency vs time domain}  % ----------------------------------------------------------

 

diff --git a/todo.org b/todo.org
index 15fb378..0f0687c 100644
--- a/todo.org
+++ b/todo.org
@@ -1,38 +1,58 @@
-* DONE draft challenges section                                    :software:
-  CLOSED: [2018-04-05 Thu 09:12]
-* DONE quote from RC                                           :introduction:
-  CLOSED: [2018-04-07 Sat 11:20]
-* DONE dichotomies                                             :spectroscopy:
-  CLOSED: [2018-04-07 Sat 15:57]
-* DONE citations                                                   :abstract:
-  CLOSED: [2018-04-07 Sat 16:47]
-* DONE citations                                               :introduction:
-  CLOSED: [2018-04-07 Sat 18:19]
-* DONE finish intro to oop content                                 :software:
-  CLOSED: [2018-04-07 Sat 23:19]
-* DONE incorporate "most software is not peer reviewed"            :software:
-  CLOSED: [2018-04-07 Sat 23:19]
-** see Joppa reference 6
-* DONE incorporate all references                                  :software:
-  CLOSED: [2018-04-07 Sat 23:19]
-* TODO tables                                                    :processing:
-* TODO distribution section                                      :processing:
-* TODO development history from github                           :processing:
-* TODO development section                                       :processing:
-* TODO describe spectroscopic instrument                       :spectroscopy:
-* TODO more references for object oriented programming             :software:
-* TODO "quadrants of complexity" idea                           :acquisition:
-** TODO figure
-** TODO arguments
-* TODO insert content                                                  :PbSe:
+* 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:
+* TODO incorporate Claire's comments                           :introduction:
 * TODO summarize PbSe chapter                                  :introduction:
 * TODO summarize MX2 chapter                                   :introduction:
 * TODO summarize PEDOT:PSS chapter                             :introduction:
-* TODO insert content from SI                                  :mixed_domain:
+* 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 2D delay example from ps system                               :active:
 * IDEA consider refactoring or expanding OOP section               :software:
-* IDEA see Paul's dissertation re: loss of resonance advantage with very fast pulses :spectroscopy:
+* TODO summary paragraphs in introduction                        :processing:
+* TODO finish discussing interpolation types                     :processing:
+** 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 show queue figure in GUI section                                 :acq:
+* TODO parents _are_ virtual hardware                                   :acq:
+* TODO hardware advanced panel descriptions                             :acq:
+* TODO sensors section                                                  :acq:
+* TODO autonomic SDC screenshot                                         :acq:
+* TODO acquisition modules                                              :acq:
+* TODO conditional validity                                             :acq:
+* TODO integrations                                                     :acq:
+* TODO future directions cleanup                                        :acq:
+* TODO figure captions                                                  :acq:
+* 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:
+* TODO insert content                                                  :PbSe:
+* TODO insert content from SI                                  :mixed_domain:
+* IDEA 2D delay example from ps system                               :active:
+* TODO verify all references                                         :polish:
diff --git a/todo.org_archive b/todo.org_archive
new file mode 100644
index 0000000..2949981
--- /dev/null
+++ b/todo.org_archive
@@ -0,0 +1,78 @@
+#    -*- mode: org -*-
+
+
+Archived entries from file /home/blaise/source/dissertation/todo.org
+
+
+* DONE draft challenges section                                    :software:
+  CLOSED: [2018-04-05 Thu 09:12]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 11:18
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+
+* DONE quote from RC                                           :introduction:
+  CLOSED: [2018-04-07 Sat 11:20]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 11:18
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+
+* DONE dichotomies                                             :spectroscopy:
+  CLOSED: [2018-04-07 Sat 15:57]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 11:18
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+
+* DONE citations                                                   :abstract:
+  CLOSED: [2018-04-07 Sat 16:47]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 11:18
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+
+* DONE citations                                               :introduction:
+  CLOSED: [2018-04-07 Sat 18:19]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 11:18
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+
+* DONE finish intro to oop content                                 :software:
+  CLOSED: [2018-04-07 Sat 23:19]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 11:18
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+
+* DONE incorporate "most software is not peer reviewed"            :software:
+  CLOSED: [2018-04-07 Sat 23:19]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 11:18
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END:
+** see Joppa reference 6
+
+* DONE incorporate all references                                  :software:
+  CLOSED: [2018-04-07 Sat 23:19]
+  :PROPERTIES:
+  :ARCHIVE_TIME: 2018-04-11 Wed 11:18
+  :ARCHIVE_FILE: ~/source/dissertation/todo.org
+  :ARCHIVE_CATEGORY: todo
+  :ARCHIVE_TODO: DONE
+  :END: