diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rwxr-xr-x | build.sh | 2 | ||||
| -rw-r--r-- | dissertation.cls | 37 | ||||
| -rw-r--r-- | dissertation.pdf | bin | 34267376 -> 34299047 bytes | |||
| -rw-r--r-- | processing/chapter.tex | 87 |
5 files changed, 84 insertions, 43 deletions
@@ -10,6 +10,7 @@ *.fot *.cb *.cb2 +*.listing ## Intermediate documents: *.dvi @@ -27,7 +27,7 @@ if [[ "$1" = "all" ]] || [[ "$1" = "data" ]] ; then #printThenPython "data/TA A.py" #printThenPython "data/TA B.py" #printThenPython "data/TG A.py" - #printThenPython "data/TG B.py" + #printThenPython "data/TG B.py" fi # make figures diff --git a/dissertation.cls b/dissertation.cls index 74cd49b..452057b 100644 --- a/dissertation.cls +++ b/dissertation.cls @@ -10,7 +10,7 @@ \RequirePackage[letterpaper, margin=1in]{geometry} % 1 inch margins required \RequirePackage{setspace} \RequirePackage{afterpage} -\RequirePackage{color} +\RequirePackage{xcolor} \RequirePackage{array} % --- headers ------------------------------------------------------------------------------------- @@ -49,9 +49,6 @@ \newcommand{\dsignature}[1]{\hfill \normalfont{-- #1}} -% THE FOLLOWING IS DARK MAGIC THAT I DON'T UNDERSTAND -% I'M SURE I COULD DO BETTER... -% - Blaise 2018-03-06 \RequirePackage[shortlabels]{enumitem} \setlist[enumerate, 1]{nosep} \setlist[enumerate, 2]{nosep, topsep=-5ex} @@ -78,11 +75,35 @@ % --- code environment ---------------------------------------------------------------------------- \RequirePackage{etoolbox} -\RequirePackage[chapter]{minted} +\RequirePackage[section]{minted} \usemintedstyle{colorfuli} -\BeforeBeginEnvironment{minted}{\begin{singlespace}} -\AfterEndEnvironment{minted}{\end{singlespace}} -\setminted[python]{linenos=false, frame=lines} +\setminted[python]{linenos=false, frame=none} + +\definecolor{bg}{rgb}{0.95,0.95,0.95} + +\setmintedinline[python]{bgcolor=bg} + +\RequirePackage[many]{tcolorbox} +\tcbuselibrary{minted} + +\NewTCBListing{codefragment}{mo}{% + colback=bg, + boxrule=1pt, + colframe=bg, + arc=0, + shadow=false, + boxsep=1ex, top=0pt, left=0pt, right=0pt, bottom=0pt, + comment={\hfill(\arabic{chapter}.\arabic{equation})}, + listing outside comment, + righthand width=2.5em, + sidebyside gap=0pt, + minted language=#1, + before skip =-0.5\baselinestretch, + after skip=2\baselinestretch, +} + +\BeforeBeginEnvironment{codefragment}{\begin{singlespace}\stepcounter{equation}} +\AfterEndEnvironment{codefragment}{\end{singlespace}} % --- tables -------------------------------------------------------------------------------------- diff --git a/dissertation.pdf b/dissertation.pdf Binary files differindex 228593d..3efe0c6 100644 --- a/dissertation.pdf +++ b/dissertation.pdf diff --git a/processing/chapter.tex b/processing/chapter.tex index 9d50bac..a1967c9 100644 --- a/processing/chapter.tex +++ b/processing/chapter.tex @@ -2,6 +2,8 @@ % TODO: cool quote, if I can think of one
+\clearpage
+
From a data science perspective, CMDS has several unique challenges:
\begin{ditemize}
\item Dimensionality of datasets can typically be greater than two, complicating
@@ -27,52 +29,69 @@ each multidimensional (or one-dimensional) spectra. % WrightTools is written in Python, and endeavors to have a ``pythonic'', explicit and ``natural''
application programming interface (API). %
To use WrightTools, simply import:
-
-\begin{minted}{python}
-import numpy as np
-
-def incmatrix(genl1,genl2):
- m = len(genl1)
- n = len(genl2)
- M = None #to become the incidence matrix
- VT = np.zeros((n*m,1), int) #dummy variable
-
- #compute the bitwise xor matrix
- M1 = bitxormatrix(genl1)
- M2 = np.triu(bitxormatrix(genl2),1)
-
- for i in range(m-1):
- for j in range(i+1, m):
- [r,c] = np.where(M2 == M1[i,j])
- for k in range(len(r)):
- VT[(i)*n + r[k]] = 1;
- VT[(i)*n + c[k]] = 1;
- VT[(j)*n + r[k]] = 1;
- VT[(j)*n + c[k]] = 1;
-
- if M is None:
- M = np.copy(VT)
- else:
- M = np.concatenate((M, VT), 1)
-
- VT = np.zeros((n*m,1), int)
-
- return M
-\end{minted}
+\begin{codefragment}{python}
+>>> import WrightTools as wt
+>>> wt.__version__
+3.0.0
+\end{codefragment}
+I'll discuss more about how exactly WrightTools packaging, distribution, and instillation works in
+\autoref{sec:processing_distbribution}.
+
+We can use the builtin Python function \mintinline{python}{dir} to interrogate the contents of the
+WrightTools package. %
+\begin{codefragment}{python}
+>>> dir(wt)
+['Collection',
+ 'Data',
+ '__branch__',
+ '__builtins__',
+ '__cached__',
+ '__doc__',
+ '__file__',
+ '__loader__',
+ '__name__',
+ '__package__',
+ '__path__',
+ '__spec__',
+ '__version__',
+ '__wt5_version__',
+ '_dataset',
+ '_group',
+ '_open',
+ '_sys',
+ 'artists',
+ 'collection',
+ 'data',
+ 'diagrams',
+ 'exceptions',
+ 'kit',
+ 'open',
+ 'units']
+\end{codefragment}
+Many of these are dunder (double underscore) attributes---Python internals that are not normally
+used directly. %
+The ten attributes that do not start with underscore are the public API that users of WrightTools
+typically use. %
+Within the public API are two classes, \mintinline{python}{Collection} \&
+\mintinline{python}{Data}, which are the two main classes in the WrightTools object model. %
+\mintinline{python}{Data} stores spectra directly as multidimensional arrays, and
+\mintinline{python}{Collection} stores \textit{groups} of data objects (and other collection
+objects) in a hierarchical way for internal organization purposes. %
\subsubsection{wt5 file format} % ----------------------------------------------------------------
\section{Artists} % ==============================================================================
+\subsection{Colormaps} % -------------------------------------------------------------------------
+\subsection{Interpolation} % ---------------------------------------------------------------------
\section{Fitting} % ==============================================================================
-\section{Distribution and licensing} % ===========================================================
-
+\section{Distribution and licensing} \label{sec:processing_disbribution} % =======================
\section{Future directions} % ====================================================================
\ No newline at end of file |