2018-03-25 18:57

2 files changed, 143 insertions, 58 deletions

diff --git a/bibliography.bib b/bibliography.bib
index 02c8475..86bd315 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -1054,6 +1054,12 @@ year = {1998}
   month =        {jun},

 }

 

+@misc{Mayavi,

+  note =         {Accessed: 2018-03-25},

+  title =        {Mayavi: 3D scientific data visualization and plotting in Python},

+  url =          {http://docs.enthought.com/mayavi/mayavi/},

+}

+

 @article{McCamantDavidW2005a,

   author =       {McCamant, David W. and Kukura, Philipp and Mathies, Richard A},

   title =        {{Femtosecond Stimulated Raman Study of Excited-State Evolution in

@@ -1609,7 +1615,7 @@ year = {1998}
   month =        {oct},

 }

 

-@article{tVardenyZ1981ta,

+@article{VardenyZ1981ta,

   author =       {Vardeny, Z. and Tauc, J.},

   title =        {{Picosecond coherence coupling in the pump and probe technique}},

   journal =      {Optics Communications},

@@ -1886,6 +1892,7 @@ year = {1998}
   year =         2000,

 }

 

+

 @article{ZhuBairen2014a,

   author =       {Bairen Zhu and Hualing Zeng and Junfeng Dai and Xiaodong Cui},

   title =        {The Study of Spin-Valley Coupling in Atomically Thin Group {VI} Transition Metal

@@ -1899,3 +1906,9 @@ year = {1998}
   month =        {apr},

   publisher =    {Wiley-Blackwell},

 }

+

+@misc{h5py.Group,

+  note =         {Accessed: 2018-03-25},

+  title =        {h5py Groups documentation.},

+  url =          {http://docs.h5py.org/en/latest/high/group.html#groups},

+}

diff --git a/processing/chapter.tex b/processing/chapter.tex
index 40055c4..94ef12e 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -36,6 +36,8 @@ WrightTools is a software package at the heart of all work in the Wright Group.
 

 % TODO: more intro

 

+\section{Introduction to WrightTools}  % ==========================================================

+

 WrightTools is written in Python, and endeavors to have a ``pythonic'', explicit and ``natural''

 application programming interface (API).  %

 To use WrightTools, simply import:

@@ -88,8 +90,6 @@ Within the public API are two classes, \python{Collection} \&
 \python{Collection} stores \textit{groups} of data objects (and other collection

 objects) in a hierarchical way for internal organization purposes.  %

 

-\section{Data object model}  % ====================================================================

-

 WrightTools uses a programming strategy called object oriented programming (OOP).  %

 % TODO: introduce HDF5

 % TODO: elaborate on the concept of OOP and how it relates to WrightTools

@@ -214,9 +214,9 @@ A lexicographical list of axis attributes and methods follows.
   \item method \python{max}

 \end{ditemize}  % TODO: actually lexicographical

 

-\subsection{Creating a data object}  % ------------------------------------------------------------

+\section{Creating a data object}  % ===============================================================

 

-WrightTools data objects are capable of storing arbitrary multidimensional spectra, but how can we

+WrightTools data objects are capable of storing arbitrary multidimensional spectra, but how can w

 actually get data into WrightTools?  %

 If you start with a wt5 file, the answer is easy: \python{wt.open(<filepath>)}.  %

 But what if you have data that was written using some other software?  %

@@ -299,7 +299,64 @@ library Qhull.  %
 This strategy can be copied in the future if other non-self-describing data sources are added into

 WrightTools.  %

 

-\subsubsection{From directory}

+\section{Collections}  % ==========================================================================

+

+The WrightTools \python{Collection} class is a container class meant to organize the contents of

+the wt5 file.  %

+It can contain other collection instances and data objects.  %

+Conceptually, it behaves like a folder in a traditional file-system.  %

+\python{wt.Collection} is a child of \python{h5py.Group} \cite{h5py.Group}.

+

+The primary attributes and methods of \python{Collection} are

+\begin{ditemize}

+  \item attribute item_names

+  \item attribute \python{fullpath}

+\end{ditemize}

+% TODO: finish adding attributes and methodsd  

+

+Collections are useful because they allow WrightTools users to ``carry around'' several associated

+data objects in the same file.  %

+For example, a publication might contain several experiments on the same sample.  %

+Collections allow such experiments to be organized in a hierarchical way.  %

+The hierarchy of contents that a collection contains can be easily visualized using the

+\python{print_tree} method.  %

+As an example, consider the following collection instance which contains some experiments

+accomplished on neat carbon tetrachloride.  %

+\begin{codefragment}{bash}

+>>> import WrightTools as wt

+>>> root = wt.open('CCl4.wt5')

+>>> root.print_tree()

+CCl4 (/tmp/0tze7b8a.wt5)

+├── 0: delay (111,)

+│   ├── axes: d1 (fs)

+│   └── channels: ai0, ai1, ai2, ai3

+└── 1: frequency

+    ├── 0: delay_0 (51, 51)

+    │   ├── axes: w2 (eV), w1=wm (eV)

+    │   └── channels: ai0, ai1, ai2, ai3, ai4, mc

+    └── 1: delay_200 (18, 20)

+        ├── axes: w1=wm (eV), w2 (eV)

+        └── channels: ai0, ai1, ai2, ai3

+\end{codefragment}

+Looking at the output of \python{print_tree}, we can see that this collection (named \python{CCl4})

+contains the following:

+\begin{denumerate}

+  \item A data object ``\python{delay}'', shape \python{(111,)}.

+  \item A collection object ``\python{frequency}'', containing two 2D data objects.

+    \begin{denumerate}

+      \item A data object ``\python{delay_0}'', shape \python{(51, 51)}.

+      \item A data object ``\python{delay_200}'', shape \python{18, 20}.

+    \end{denumerate}

+\end{denumerate}

+Since this is all contained in one file, a user of WrightTools can easily manage all three

+associated datasets.  %

+Upon simple inspection it is obvious that two of the datasets are 2D frequency-frequency scans

+while one is a 1D delay slice.  %

+

+Like \python{Channel}, \python{Data} and \python{Variable}, \python{Collection} supports adding

+arbitrary metadata through the \python{attrs} dictionary.  % TODO: cite

+

+\subsection{From directory}  % --------------------------------------------------------------------

 

 The \python{wt.collection.from_directory} function can be used to automatically import all of the

 data sources in an entire directory tree.  %

@@ -309,7 +366,51 @@ Users can configure which files are routed to which from-function.  %
 

 % TODO (also document on wright.tools)

 

-\subsection{Variables and channels}  % ------------------------------------------------------------

+\section{Visualizing a data object}  % ============================================================

+

+After importing and manipulating data, one typically wants to create a plot.  %

+The artists sub-package contains everything users need to plot their data objects.  %

+This includes both ``quick'' artists, which generate simple plots as quickly as possible, and a

+full figure layout toolkit that allows users to generate full publication quality figures.  %

+It also includes ``specialty'' artists which are made to perform certain popular plotting

+operations, as I will describe below.  %

+

+Currently the artists sub-package is built on-top of the wonderful matplotlib library.  %

+In the future, other libraries (e.g. Mayavi \cite{Mayavi}), may be incorporated.  %

+

+\subsection{Colormaps}  % -------------------------------------------------------------------------

+

+% TODO: figure like made by visualize_colormap_components

+

+% TODO: figure like one on wall

+

+% TODO: mention isoluminant

+

+\subsection{Interpolation}  % ---------------------------------------------------------------------

+

+% TODO: fill types figure from wright.tools

+

+\subsection{Quick}  % -----------------------------------------------------------------------------

+

+\subsubsection{1D}

+

+\begin{figure}

+  \includegraphics[width=0.5\textwidth]{"processing/quick1D 000"}

+  \includepython{"processing/quick1D.py"}

+  \caption[CAPTION TODO]

+    {CAPTION TODO}

+\end{figure}

+

+\subsubsection{2D}

+

+\begin{figure}

+  \includegraphics[width=0.5\textwidth]{"processing/quick2D 000"}

+  \includepython{"processing/quick2D.py"}

+  \caption[CAPTION TODO]

+    {CAPTION TODO}

+\end{figure}

+

+\section{Variables and channels}  % ===============================================================

 

 Data objects are made up of many component channels and variables, each array having the same

 dimensionality of its parent data.  %

@@ -352,6 +453,11 @@ From a quick inspection, one can see that \python{w1} and \python{wm} were scann
 \python{w2} and \python{d2} were the other two dimensions.  %

 \python{w3}, \python{d0}, and \python{d1} were not moved at all, yet their coordinates are still

 propagated.  %

+

+

+\section{Axes}  % =================================================================================

+

+

 The axes have the joint shape of their component variables.  %

 Although not shown in this example, channels also may have axes with length 1.

 

@@ -367,13 +473,13 @@ squeezed and broadcasted array, respectively.  %
 \end{figure}

 

 

-\subsection{Math}  % ------------------------------------------------------------------------------

+\section{Math}  % =================================================================================

 

 Now that we know the basics of how the WrightTools \python{Data} class stores data, it's time to do

 some data manipulation.  %

 Let's start with some elementary algebra.  %

 

-\subsubsection{In-place operators}

+\subsection{In-place operators}

 

 In Python, operators are symbols that carry out some computation.  %

 Consider the following:

@@ -432,30 +538,30 @@ data.created at /tmp/tdyvfxu8.wt5::/
 \end{codefragment}

 Variables also support in-place operators.  %

 

-\subsubsection{Clip}

+\subsection{Clip}

 

 % TODO

 

-\subsubsection{Symmetric root}

+\subsection{Symmetric root}

 

 % TODO

 

-\subsubsection{Log}

+\subsection{Log}

 

 % TODO

 

-\subsection{Dimensionality manipulation}  % -------------------------------------------------------

+\section{Dimensionality manipulation}  % ==========================================================

 

 WrightTools offers several strategies for reducing the dimensionality of a data object.  %

 Also consider using the fit sub-package.  % TODO: more info, link to section

 

-\subsubsection{Chop}

+\subsection{Chop}  % ------------------------------------------------------------------------------

 

 Chop is one of the most important methods of data, although it is typically not called directly by

 users of WrightTools.  %

 Chop takes n-dimensional data and ``chops'' it into all of it's lower dimensional components.  %

-Consider a 3D dataset in \python{('wm', 'w2', 'w1')}.  %

-This dataset can be chopped to it's component 2D \python{('wm', 'w1')} spectra.  %

+Consider a 3D dataset in \python{('wm', 'w2', 'w1''''')}.  %

+This dataset can be chopped to it's component 2D \python{('wm'', 'w1')} spectra.  %

 \begin{codefragment}{python, label=test_label}

 >>> import WrightTools as wt; from WrightTools import datasets

 >>> data = wt.data.from_PyCMDS(datasets.PyCMDS.wm_w2_w1_000)

@@ -499,47 +605,13 @@ array([1580.0])
 Note the [0]...  % TODO

 This same syntax used in artists...  % TODO

 

-\subsubsection{Collapse}

-

-\subsubsection{Split}

-

-\subsubsection{Join}

+\subsection{Collapse}  % --------------------------------------------------------------------------

 

-\subsection{The wt5 file format}  % ---------------------------------------------------------------

+\subsection{Split}  % -----------------------------------------------------------------------------

 

-Since WrightTools is based on the hdf5 file format...  % TODO

+\subsection{Join}  % ------------------------------------------------------------------------------

 

-\section{Artists}  % ==============================================================================

-

-After importing and manipulating data, one typically wants to create a plot.  %

-The artists sub-package contains everything users need to plot their data objects.  %

-This includes both ``quick'' artists, which generate simple plots as quickly as possible, and a

-full figure layout toolkit that allows users to generate full publication quality figures.  %

-It also includes ``specialty'' artists which are made to perform certain popular plotting

-operations, as I will describe below.  %

-

-Currently the artists sub-package is built on-top of the wonderful matplotlib library.  %

-In the future, other libraries (e.g. mayavi), may be incorporated.  %

-

-\subsection{Quick}  % -----------------------------------------------------------------------------

-

-\subsubsection{1D}

-

-\begin{figure}

-  \includegraphics[width=0.5\textwidth]{"processing/quick1D 000"}

-  \includepython{"processing/quick1D.py"}

-  \caption[CAPTION TODO]

-    {CAPTION TODO}

-\end{figure}

-

-\subsubsection{2D}

-

-\begin{figure}

-  \includegraphics[width=0.5\textwidth]{"processing/quick2D 000"}

-  \includepython{"processing/quick2D.py"}

-  \caption[CAPTION TODO]

-    {CAPTION TODO}

-\end{figure}

+\section{Specialty visualizations}  % =============================================================

 

 \subsection{Specialty}  % -------------------------------------------------------------------------

 

@@ -558,13 +630,13 @@ introduces the unique strategy that the WrightTools wrapper takes.  %
 

 % TODO: finish discussion

 

-\subsection{Colormaps}  % -------------------------------------------------------------------------

+\section{Fitting}  % ==============================================================================

 

-\subsection{Interpolation}  % ---------------------------------------------------------------------

+\section{Construction and maintenance}  % =========================================================

 

-\section{Fitting}  % ==============================================================================

+\subsection{Unit tests}  % ------------------------------------------------------------------------

 

-\section{Distribution and licensing} \label{sec:processing_disbribution}  % =======================

+\section{Distribution and licensing} \label{pro:sec:disbribution}  % ==============================

 

 WrightTools is MIT licensed.  %