2018-04-08 10:27

3 files changed, 102 insertions, 95 deletions

diff --git a/dissertation.tex b/dissertation.tex
index b2aa572..2a7a6d9 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -72,12 +72,12 @@ This dissertation is approved by the following members of the Final Oral Committ
 \include{acquisition/chapter}

 \include{active_correction/chapter}

 \include{opa/chapter}

-\include{mixed_domain/chapter}

+%\include{mixed_domain/chapter}

 

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

-\include{PbSe/chapter}

-\include{MX2/chapter}

-\include{PEDOT_PSS/chapter}

+%\include{PbSe/chapter}

+%\include{MX2/chapter}

+%\include{PEDOT_PSS/chapter}

 

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

 

@@ -85,15 +85,15 @@ This dissertation is approved by the following members of the Final Oral Committ
 

 \part{Appendix} \label{prt:appendix}

 \begin{appendix}

-\include{public/chapter}

-\include{procedures/chapter}

-\include{hardware/chapter}

+%\include{public/chapter}

+%\include{procedures/chapter}

+%\include{hardware/chapter}

 % TODO: consider inserting WrightTools documentation as PDF

-\include{irf/chapter}

-\include{quantitative_ta/chapter}

-\include{tg/chapter}

-\include{errata/chapter}

-\include{colophon/chapter}

+%\include{irf/chapter}

+%\include{quantitative_ta/chapter}

+%\include{tg/chapter}

+%\include{errata/chapter}

+%\include{colophon/chapter}

 \end{appendix}

 

 % post --------------------------------------------------------------------------------------------

diff --git a/processing/chapter.tex b/processing/chapter.tex
index c1e46f4..2feec22 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -44,21 +44,24 @@ The biggest challenge is to find a really good definition for what constitutes a
 Once understood, this common denominator can be enshrined into software and built upon.  %

 

 WrightTools is a software package written in Python, built using the excellent tools provided by

-the scientific Python collection of packages, especially Scipy and Numpy. [CITE?]  %

+the scientific Python collection of packages, especially Scipy \cite{SciPy} and Numpy

+\cite{OliphantTravisE2006a}.  %

 WrightTools defines a universal file-format that is flexible enough to encompass the diversity of

 CMDS while still being entirely self-describing.  %

-This file format is based on the popular binary format ``HDF5''. \cite{h5py}  %

+This file format is based on the popular binary format ``HDF5'' \cite{FolkMike2011a}, as

+interfaced by the h5py python library \cite{h5py}.  %

 This format allows for computers to interact with the arrays piece-by-piece in a very fast and

 reliable way, without loading the entire array in and out of memory.  %

-WrightTools piggybacks on this, allowing users to interact with legitimately large CMDS datasets

-without worrying about memory overflow.  %

+Using object oriented programming, the main classes in WrightTools are children of h5py classes,

+allowing users to interact with legitimately large CMDS datasets without worrying about memory

+overflow.  %

 WrightTools takes a unique approach to representing CMDS data in array format, nick-named

 ``semi-structure'', that allows for greater flexibility in representing CMDS in different

 coordinate spaces.  %

 

 WrightTools is written to be used in scripts and in the command line.  %

 It does not have any graphical components built in, except for the ability to generate plots using

-matplotlib. [CITE?]  %

+matplotlib \cite{HunterJohnD2007a}.  %

 Being built in this way gives WrightTools users maximum flexibility, and allows for rapid

 collaborative development.  %

 It also allows other software packages to use WrightTools as a ``back-end'' foundational software,

@@ -78,6 +81,8 @@ To use WrightTools, simply import:
 I'll discuss more about how exactly WrightTools packaging, distribution, and instillation works in

 \autoref{pro:sec:distribution}.

 

+% TODO: consider making the following into a table

+

 We can use the builtin Python function \python{dir} to interrogate the contents of the

 WrightTools package.  %

 \begin{codefragment}{python}

@@ -149,38 +154,38 @@ Typical variables might be \python{[w1, w2, w3, d1, d2]}, and typical channels
 \begin{table}

   \begin{tabular}{c | c | l}

     & type & description \\ \hline

-    \python{collapse} & method & Collapse along one dimension in a well-defined way. \\ \hline

-    \python{convert} & method & Convert all axes of a certain kind. \\ \hline

-    \python{create_channel} & method & Create a new channel. \\ \hline

-    \python{create_variable} & method & Create a new variable. \\ \hline

-    \python{fullpath} & attribute & \\ \hline

-    \python{get_nadir} & & \\ \hline

-    \python{get_zenith} & & \\ \hline

-    \python{heal} & & \\ \hline

-    \python{kind} & & \\ \hline

-    \python{level} & & \\ \hline

-    \python{map_variable} & & \\ \hline

-    \python{natural_name} & & \\ \hline

-    \python{ndim} & & \\ \hline

-    \python{offset} & & \\ \hline

-    \python{print_tree} & & \\ \hline

-    \python{remove_channel} & & \\ \hline

-    \python{remove_variable} & & \\ \hline

-    \python{rename_channels} & & \\ \hline

-    \python{shape} & & \\ \hline

-    \python{share_nans} & & \\ \hline

-    \python{size} & & \\ \hline

-    \python{smooth} & & \\ \hline

-    \python{source} & & \\ \hline

-    \python{split} & & \\ \hline

-    \python{transform} & & \\ \hline

-    \python{units} & & \\ \hline

-    \python{variable_names} & & \\ \hline

-    \python{variables} & & \\ \hline

-    \python{zoom} & & \\ \hline

+    \texttt{collapse} & method & Collapse along one dimension in a well-defined way. \\ \hline

+    \texttt{convert} & method & Convert all axes of a certain kind. \\ \hline

+    \texttt{create\_channel} & method & Create a new channel. \\ \hline

+    \texttt{create\_variable} & method & Create a new variable. \\ \hline

+    \texttt{fullpath} & attribute & \\ \hline

+    \texttt{get\_nadir} & method & Get the coordinates, in units, of the minimum of a channel. \\ \hline

+    \texttt{get\_zenith} & method & Get the coordinates, in units, of the maximum of a channel \\ \hline

+    \texttt{heal} & method & Remove nans from channel using interpolation. \\ \hline

+    \texttt{kind} & attribute & \\ \hline

+    \texttt{level} & method & Subtract the average value of npts at the edge of a given axis. \\ \hline

+    \texttt{map\_variable} & method & Map points of a variable to new points using linear interpolation. \\ \hline

+    \texttt{natural\_name} & attribute & \\ \hline

+    \texttt{ndim} & attribute & \\ \hline

+    \texttt{offset} & method & Offset one variable based on another variables' values. \\ \hline

+    \texttt{print\_tree} & method & \\ \hline

+    \texttt{remove\_channel} & method & \\ \hline

+    \texttt{remove\_variable} & method & \\ \hline

+    \texttt{rename\_channels} & method & \\ \hline

+    \texttt{shape} & attribute & \\ \hline

+    \texttt{share\_nans} & method & Share not-a-numbers between all channels. \\ \hline

+    \texttt{size} & attribute & \\ \hline

+    \texttt{smooth} & method & Smooth a channel using an n-dimensional Kaiser window. \\ \hline

+    \texttt{source} & attribute & \\ \hline

+    \texttt{split} & method & Split the data along a given axis, in units. \\ \hline

+    \texttt{transform} & method & Transform the data. \\ \hline

+    \texttt{units} & attribute & \\ \hline

+    \texttt{variable\_names} & attribute & \\ \hline

+    \texttt{variables} & attribute & \\ \hline

+    \texttt{zoom} & method & Zoom the data using spline interpolation of the requested order. \\ \hline

   \end{tabular}

-  \caption[Attributes and methods of Data]{

-    Key attributes and methods of data, lexicographically listed

+  \caption[Attributes and methods of Data.]{

+    Key attributes and methods of data, lexicographically listed.

   }

 \end{table}

 

@@ -195,31 +200,31 @@ discussed more in...  % TODO: where is it discussed more?
 \begin{table}

   \begin{tabular}{c | c | c | l}

     & type & of & description \\ \hline

-    \python{argmax} & method & both & \\ \hline

-    \python{argmin} & & & \\ \hline

-    \python{chunkwise} & & & \\ \hline

-    \python{clip} & & & \\ \hline

-    \python{convert} & & & \\ \hline

-    \python{full} & & & \\ \hline

-    \python{fullpath} & & & \\ \hline

-    \python{label} & attribute & variable & \\ \hline

-    \python{log} & & & \\ \hline

-    \python{log10} & & & \\ \hline

-    \python{log2} & & & \\ \hline

-    \python{mag} & & & \\ \hline

-    \python{major_extent} & attribute & channel & \\ \hline

-    \python{max} & & & \\ \hline

-    \python{min} & & & \\ \hline

-    \python{minor_extent} & attribute & channel & \\ \hline

-    \python{natural_name} & & & \\ \hline

-    \python{normalize} & & channel & \\ \hline

-    \python{null} & & channel & \\ \hline

-    \python{parent} & & & \\ \hline

-    \python{points} & & & \\ \hline

-    \python{signed} & & channel & \\ \hline

-    \python{slices} & & & \\ \hline

-    \python{symmetric_root}

-    \python{trim} & & channel & \\ \hline

+    \texttt{argmax} & method & both & Index of maximum, ignoring nans. \\ \hline

+    \texttt{argmin} & method & both & Index of minimum, ignoring nans. \\ \hline

+    \texttt{chunkwise} & method & both & Execute a function for each chunk in the dataset. \\ \hline

+    \texttt{clip} & method & both & Clip values outside of a desired range. \\ \hline

+    \texttt{convert} & method & both & Convert units, writing to disk. \\ \hline

+    \texttt{full} & attribute & both & \\ \hline

+    \texttt{fullpath} & attribute & both & \\ \hline

+    \texttt{label} & attribute & variable & \\ \hline

+    \texttt{log} & method & both & Take the log of the entire dataset, with choice of base. \\ \hline

+    \texttt{log10} & method & both & Take the base 10 log of the entire dataset. \\ \hline

+    \texttt{log2} & method & both & Take the base 2 log of the entire dataset. \\ \hline

+    \texttt{mag} & method & channel & \\ \hline

+    \texttt{major\_extent} & attribute & channel & \\ \hline

+    \texttt{max} & method & both & Maximum, ignoring nans. \\ \hline

+    \texttt{min} & method & both & Minimum, ignoring nans. \\ \hline

+    \texttt{minor\_extent} & attribute & channel & \\ \hline

+    \texttt{natural\_name} & attribute & both & \\ \hline

+    \texttt{normalize} & method & channel & \\ \hline

+    \texttt{null} & attribute & channel & \\ \hline

+    \texttt{parent} & attribute & both & \\ \hline

+    \texttt{points} & attribute & both & \\ \hline

+    \texttt{signed} & attribute & channel & \\ \hline

+    \texttt{slices} & method & both & Returns a generator yielding tuple of slice objects. \\ \hline

+    \texttt{symmetric\_root} & method & both & \\ \hline

+    \texttt{trim} & method & channel & \\ \hline

   \end{tabular}

   \caption[Attributes and methods of Channel and Variable.]{

     Key attributes and methods of channel and variable, lexicographically listed

@@ -240,22 +245,21 @@ Axes can be directly indexed / sliced into using \python{__getitem__}, and they
 ``numpy-like'' attributes.  %

 A lexicographical list of axis attributes and methods follows.

 

-

 \begin{table}

   \begin{tabular}{c | c | l}

     & type & description \\ \hline

-    \python{full} & & \\ \hline

-    \python{label} & & \\ \hline

-    \python{natural_name} & & \\ \hline

-    \python{ndim} & & \\ \hline

-    \python{points} & & \\ \hline

-    \python{shape} & & \\ \hline

-    \python{size} & & \\ \hline

-    \python{units_kind} & & \\ \hline

-    \python{variables} & & \\ \hline

-    \python{convert} & & \\ \hline

-    \python{min} & & \\ \hline

-    \python{max} & & \\ \hline

+    \texttt{full} & & \\ \hline

+    \texttt{label} & & \\ \hline

+    \texttt{natural\_name} & & \\ \hline

+    \texttt{ndim} & & \\ \hline

+    \texttt{points} & & \\ \hline

+    \texttt{shape} & & \\ \hline

+    \texttt{size} & & \\ \hline

+    \texttt{units\_kind} & & \\ \hline

+    \texttt{variables} & & \\ \hline

+    \texttt{convert} & & \\ \hline

+    \texttt{min} & & \\ \hline

+    \texttt{max} & & \\ \hline

   \end{tabular}

   \caption[Attributes and methods of Axis.]{

     Key attributes and methods of axis, lexicographically listed

diff --git a/todo.org b/todo.org
index 8dcbfac..324b062 100644
--- a/todo.org
+++ b/todo.org
@@ -8,26 +8,29 @@
   CLOSED: [2018-04-07 Sat 16:47]
 * DONE citations                                               :introduction:
   CLOSED: [2018-04-07 Sat 18:19]
-* TODO finish intro to oop content                                 :software:
-* TODO incorporate "most software is not peer reviewed"            :software:
+* 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
-* TODO incorporate idea "most people over-trust software"          :software:
-* TODO incorporate all references                                  :software:
-* TODO incorporate StoddenVictoria2016a                            :software:
+* DONE incorporate all references                                  :software:
+  CLOSED: [2018-04-07 Sat 23:19]
 * TODO more references for object oriented programming             :software:
+* TODO tables                                                    :processing:
+* TODO distribution section                                      :processing:
+* TODO development history from github                           :processing:
+* TODO development section                                       :processing:
 * TODO describe spectroscopic instrument                       :spectroscopy:
 * TODO "quadrants of complexity" idea                           :acquisition:
 ** TODO figure
 ** TODO arguments
-* TODO tables                                                    :processing:
-* TODO distribution section                                      :processing:
-* TODO development section                                       :processing:
-* TODO development history from github                           :processing:
 * TODO insert content                                                  :PbSe:
 * TODO summarize PbSe chapter                                  :introduction:
 * TODO summarize MX2 chapter                                   :introduction:
 * TODO summarize PEDOT:PSS chapter                             :introduction:
 * TODO insert content from SI                                  :mixed_domain:
+* 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: