2018-03-24 21:59

8 files changed, 180 insertions, 123 deletions

diff --git a/MX2/chapter.tex b/MX2/chapter.tex
index 60aa0eb..88b496e 100644
--- a/MX2/chapter.tex
+++ b/MX2/chapter.tex
@@ -1,4 +1,4 @@
-\chapter{Transition metal dichalcogenide thin films}
+\chapter{Transition metal dichalcogenide thin films} \label{cha:mx2}
 
 \textit{This Chapter borrows extensively from \textcite{CzechKyleJonathan2015a}.}
 
diff --git a/bibliography.bib b/bibliography.bib
index 30ea418..02c8475 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -63,20 +63,6 @@
   pages =        2337,

   year =         2012,

   doi =          {10.1364/OL.37.002337},

-  issn =         {0146--9592},

-  month =        {jun},

-}

-

-@article{AubockGerald2012a,

-  author =       {Aub{\"{o}}ck, Gerald and Consani, Cristina and van Mourik, Frank and Chergui,

-                  Majed},

-  title =        {{Ultrabroadband femtosecond two-dimensional ultraviolet transient absorption}},

-  journal =      {Optics Letters},

-  volume =       37,

-  number =       12,

-  pages =        2337,

-  year =         2012,

-  doi =          {10.1364/OL.37.002337},

   issn =         {0146-9592},

   month =        {jun},

 }

@@ -208,17 +194,6 @@
   pmid =         15332970,

 }

 

-@article{BrixnerTobias2004a,

-	author = {Brixner, Tobias and Mancal, Tomas and Stiopkin, Igor V. and Fleming, Graham R.},

-	title = {Phase-stabilized two-dimensional electronic spectroscopy},

-	year = {2004},

-	volume = {121},

-	number = {9},

-	pages = {4221},

-	journal = {The Journal of Chemical Physics},

-	doi = {10.1063/1.1776112},

-}

-

 @article{CarlsonRogerJ1990a,

   author =       {Carlson, Roger J. and Wright, John C.},

   title =        {{Line narrowing in multiresonant third order molecular spectroscopies}},

@@ -456,7 +431,6 @@ year = {1998}
   month =        {sep},

 }

 

-

 @article{DonaldsonPaulMurray2008a,

   author =       {Donaldson, Paul M and Guo, Rui and Fournier, Frederic and Gardner, Elizabeth M

                   and Gould, Ian R and Klug, David R},

@@ -475,6 +449,7 @@ year = {1998}
   month =        {jun},

 }

 

+

 @article{DonaldsonPaulMurray2010a,

   author =       {Donaldson, Paul M and Willison, Keith R and Klug, David R},

   title =        {{Generation of Simplified Protein Raman Spectra Using Three-Color Picosecond

@@ -710,6 +685,7 @@ year = {1998}
   issn =         {0027-8424},

   month =        {mar},

 }

+

 @article{HammPeter2000a,

   author =       {Hamm, Peter and Lim, Manho and DeGrado, William F. and Hochstrasser, Robin M},

   title =        {{Pump/probe self heterodyned 2D spectroscopy of vibrational transitions of a

@@ -723,7 +699,6 @@ year = {1998}
   issn =         {0021-9606},

   month =        {jan},

 }

-

 @inproceedings{HannayJoErskine2009a,

   author =       {Jo Erskine Hannay and Carolyn MacLeod and Janice Singer and Hans Petter

                   Langtangen and Dietmar Pfahl and Greg Wilson},

@@ -1242,22 +1217,6 @@ year = {1998}
   pmid =         16526612,

 }

 

-@article{PakoulevAndreiV2006a,

-  author =       {Andrei V. Pakoulev and Mark A. Rickard and Kent A. Meyer and

-                  Kathryn Kornau and Nathan A. Mathew and David E. Thompson and

-                  John C. Wright},

-  title =        {Mixed Frequency/Time Domain Optical Analogues of Heteronuclear

-                  Multidimensional {NMR}},

-  journal =      {The Journal of Physical Chemistry A},

-  volume =       110,

-  number =       10,

-  pages =        {3352--3355},

-  year =         2006,

-  doi =          {10.1021/jp057339y},

-  month =        {mar},

-  publisher =    {American Chemical Society ({ACS})},

-}

-

 @article{PakoulevAndreiV2007a,

   author =       {Pakoulev, Andrei V. and Rickard, Mark A and Mathew, Nathan A and Kornau, Kathryn

                   M. and Wright, John C.},

@@ -1581,29 +1540,17 @@ year = {1998}
   month =        {oct},

 }

 

-@article{SteehlerJK1985a,

-  author =       {Steehler, J. K. and Wright, J. C.},

-  title =        {{Parametric and nonparametric four‐wave mixing in pentacene: p ‐terphenyl}},

-  journal =      {The Journal of Chemical Physics},

-  volume =       83,

-  number =       7,

-  pages =        {3200--3208},

-  year =         1985,

-  doi =          {10.1063/1.449177},

-  issn =         {0021-9606},

-  month =        {oct},

-}

-

 @article{StoddenVictoria2016a,

-	author = {Stodden, V. and McNutt, M. and Bailey, D. H. and Deelman, E. and Gil, Y. and Hanson, B. and Heroux, M. A. and Ioannidis, J. P. A. and Taufer, M.},

-	title = {Enhancing reproducibility for computational methods},

-	year = {2016},

-	month = {dec},

-	volume = {354},

-	number = {6317},

-	pages = {1240--1241},

-	journal = {Science},

-	doi = {10.1126/science.aah6168},

+  author =       {Stodden, V. and McNutt, M. and Bailey, D. H. and Deelman, E. and Gil, Y. and

+                  Hanson, B. and Heroux, M. A. and Ioannidis, J. P. A. and Taufer, M.},

+  title =        {Enhancing reproducibility for computational methods},

+  journal =      {Science},

+  volume =       354,

+  number =       6317,

+  pages =        {1240--1241},

+  year =         2016,

+  doi =          {10.1126/science.aah6168},

+  month =        {dec},

 }

 

 @article{SunDezheng2014a,

@@ -1662,7 +1609,7 @@ year = {1998}
   month =        {oct},

 }

 

-@article{VardenyZ1981a,

+@article{tVardenyZ1981ta,

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

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

   journal =      {Optics Communications},

@@ -1675,6 +1622,12 @@ year = {1998}
   month =        {nov},

 }

 

+@misc{VingeVernor2012a,

+  note =         {Accessed: 2018-03-24},

+  title =        {A Singularity Sensation},

+  url =          {http://sm.stanford.edu/archive/stanmed/2012summer/article4.html},

+}

+

 @article{VolkmerAndreas2001a,

   author =       {Andreas Volkmer and Ji-Xin Cheng and X. Sunney Xie},

   title =        {Vibrational Imaging with High Sensitivity via Epidetected Coherent Anti-Stokes

@@ -1883,20 +1836,6 @@ year = {1998}
   month =        {nov},

 }

 

-@article{YursLenaA2011a,

-  author =       {Yurs, Lena A and Block, Stephen B. and Pakoulev, Andrei V and

-                  Selinsky, Rachel S. and Jin, Song and Wright, John},

-  title =        {Multiresonant Coherent Multidimensional Electronic

-                  Spectroscopy of Colloidal PbSe Quantum Dots},

-  journal =      {The Journal of Physical Chemistry C},

-  volume =       115,

-  number =       46,

-  pages =        {22833--22844},

-  year =         2011,

-  doi =          {10.1021/jp207273x},

-  month =        {nov},

-}

-

 @article{ZanniMartinT2001a,

   author =       {Zanni, Martin T and Asplund, Matthew C and Hochstrasser, Robin M},

   title =        {{Two-dimensional heterodyned and stimulated infrared photon echoes of

@@ -1913,29 +1852,6 @@ year = {1998}
 @article{ZengHualing2012a,

   author =       {Hualing Zeng and Junfeng Dai and Wang Yao and Di Xiao and Xiaodong Cui},

   title =        {Valley polarization in {MoS}2 monolayers by optical pumping},

-  journal =      {Nature Nanotechnology},

-  volume =       7,

-  number =       8,

-  pages =        {490--493},

-  year =         2012,

-  doi =          {10.1038/nnano.2012.95},

-  month =        {jun},

-  publisher =    {Springer Nature},

-}

-

-@article{ZhaoWei1999a,

-  author =       {Zhao, Wei and Wright, John C.},

-  title =        {{Measurement of {\textless}math display="inline"{\textgreater}

-                  {\textless}mrow{\textgreater} {\textless}msup{\textgreater}

-                  {\textless}mrow{\textgreater} {\textless}mi

-                  mathvariant="italic"{\textgreater}$\chi${\textless}/mi{\textgreater}

-                  {\textless}/mrow{\textgreater} {\textless}mrow{\textgreater}

-                  {\textless}mo{\textgreater}({\textless}/mo{\textgreater}

-                  {\textless}mn{\textgreater}3{\textless}/mn{\textgreater}

-                  {\textless}mo{\textgreater}){\textless}/mo{\textgreater}

-                  {\textless}/mrow{\textgreater} {\textless}/msup{\textgreater}

-                  {\textless}/mrow{\textgreater} {\textless}/math{\textgreater} for Doubly

-                  Vibrationally Enhanced Four Wave Mixing Spectroscopy}},

   journal =      {Physical Review Letters},

   volume =       83,

   number =       10,

diff --git a/dissertation.cls b/dissertation.cls
index bf2e6f6..6d2364c 100644
--- a/dissertation.cls
+++ b/dissertation.cls
@@ -91,8 +91,9 @@
 % --- code environment ----------------------------------------------------------------------------
 
 \RequirePackage{etoolbox}
+\RequirePackage{pmboxdraw}  % for box drawing charachters
 \RequirePackage[section]{minted}
-\usemintedstyle{colorfuli}
+\usemintedstyle{default}
 \setminted[python]{linenos=false, frame=none}
 
 \definecolor{bg}{rgb}{0.95, 0.95, 0.95}
diff --git a/dissertation.tex b/dissertation.tex
index c5c1a1a..f80af7e 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -75,8 +75,8 @@ This dissertation is approved by the following members of the Final Oral Committ
 %\include{software/chapter}

 

 \part{Development}

-%\include{processing/chapter}

-%\include{acquisition/chapter}

+\include{processing/chapter}

+\include{acquisition/chapter}

 %\include{active_correction/chapter}

 %\include{opa/chapter}

 %\include{mixed_domain/chapter}

diff --git a/outline.org b/outline.org
index 0d66e26..47368ae 100644
--- a/outline.org
+++ b/outline.org
@@ -1,12 +1,21 @@
-* abstract
-* introduction
+* META
+** labeling convention
+*** chapter:kind:identifier, where kind is one of the following:
+**** cha: chapter
+**** sec: section (including subsections)
+**** eqn: equation
+**** fig: figure
+**** tab: table
+**** lst: code listing
+* abs: abstract
+* int: introduction
 ** TODO cite:MaimanTheodoreHarold1960a
-* spectroscopy
+* spe: spectroscopy
 ** TODO paul has a great discussion of the drawbacks of homodyne detection docview:HebertPaulC2016a.pdf::150
 ** TODO cite:AubockGerald2012a
-* materials
-* software
-* processing
+* mat: materials
+* sof: software
+* pro: processing
 ** data object model
 *** creating a data object
 *** dimensionality manipulation
diff --git a/processing/chapter.tex b/processing/chapter.tex
index 28d1858..40055c4 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -1,6 +1,25 @@
-\chapter{Processing}

-

-% TODO: cool quote, if I can think of one

+\chapter{Processing} \label{cha:pro}

+

+\begin{dquote}

+  What we have is data glut.

+  What we really want is the ability to manipulate the information and to reach conclusions from

+  it.

+  I think we are at the point where that is slipping beyond unaided humans’ abilities.

+  So the real thing to be looking for is processing schemes.

+  One way is automatic processing: for instance, the sort of analysis that we saw with the IBM

+  Watson on Jeopardy.

+  Putting that in service to humankind in fields that are suffering from data glut at least gives

+  people who are in charge the ability to keep some sort of track of what is going on.

+

+  The other great thing that we have going for us is that we have billions of very intelligent

+  people out there in the world.

+  :With the networking that we have now, we’re beginning to see that those large populations,

+  coordinating amongst themselves, are an intellectual resource that trumps all institutional

+  intellectual resources and has a real possibility, if it’s supported by the proper automation, of

+  creating solutions to problems, including the problem of the data glut.

+

+  \dsignature{Vernor Vinge \cite{VingeVernor2012a}}

+\end{dquote}

 

 \clearpage

 

@@ -290,6 +309,64 @@ Users can configure which files are routed to which from-function.  %
 

 % TODO (also document on wright.tools)

 

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

+

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

+dimensionality of its parent data.  %

+This strategy allows for maximal flexibility in data representation, but it can be overly expensive

+if certain arrays do not actually change against all of the dimensions.  %

+This is often especially true with variables, which typically correspond to scannable hardware that

+may not have even moved across some (or any) dimensions.  %

+To avoid unnecessarily large arrays, WrightTools allows Channels and Variables to have different

+sizes than the parent data.  %

+As an example, consider the following object.

+\begin{codefragment}{bash}  % TODO: need to use bash here because of box charachters :-(

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

+>>> data = wt.data.from_COLORS(datasets.COLORS.v2p1_MoS2_TrEE_movie)

+>>> data.print_tree()

+MoS2 (/tmp/qhg_1b3l.wt5)

+├── axes

+│   ├── 0: w2 (nm) (41, 1, 1)

+│   ├── 1: w1=wm (nm) (1, 41, 1)

+│   └── 2: d2 (fs) (1, 1, 23)

+├── variables

+│   ├── 0: w2 (nm) (41, 1, 1)

+│   ├── 1: w1 (nm) (1, 41, 1)

+│   ├── 2: wm (nm) (1, 41, 1)

+│   ├── 3: d2 (fs) (1, 1, 23)

+│   ├── 4: w3 (nm) (1, 1, 1)

+│   ├── 5: d0 (fs) (1, 1, 1)

+│   └── 6: d1 (fs) (1, 1, 1)

+└── channels

+    ├── 0: ai0 (41, 41, 23)

+    ├── 1: ai1 (41, 41, 23)

+    ├── 2: ai2 (41, 41, 23)

+    ├── 3: ai3 (41, 41, 23)

+    ├── 4: ai4 (41, 41, 23)

+    └── 5: mc (41, 41, 23)

+\end{codefragment}

+Note that this is the primary dataset discussed in \autoref{cha:mx2}.  %

+The shape of this data object is \python{(41, 41, 23)}, but none of the variables have that full

+shape.  %

+From a quick inspection, one can see that \python{w1} and \python{wm} were scanned together, while

+\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.  %

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

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

+

+Axes, variables, and channels are array-likes, so they support slicing operations.  %

+In addition, all three classes have \python{points} and \python{full} attributes that return the

+squeezed and broadcasted array, respectively.  %

+

+\begin{figure}

+  \includegraphics[width=\textwidth]{"processing/fringes_transform"}

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

+  \caption[CAPTION TODO]{

+    CAPTION TODO}

+\end{figure}

+

+

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

 

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

@@ -300,7 +377,7 @@ Let's start with some elementary algebra.  %
 

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

 Consider the following:

-\begin{codefragment}{python, label=abcdefg}

+\begin{codefragment}{python, label=pro:lst:array_addition}

 >>> import numpy as np

 >>> a = np.array([4, 5, 6])

 >>> b = np.array([-1, -2, -3])

@@ -312,7 +389,7 @@ Here, \python{a} and \python{b} are operands and \python{+} is an operator.  %
 When used in this simple way, operators typically create and return a \emph{new} object in the

 computers memory.  %

 We can verify this by using Python's built-in \python{id} function on the objects created in

-\ref{abcdefg}.  %

+\ref{pro:lst:array_addition}.  %

 \begin{codefragment}{python}

 >>> id(a), id(b), id(c)

 (139712529580400, 139712333712320, 139712333713040)

@@ -321,12 +398,39 @@ This is usually fine, but sometimes the operands are unwieldy large objects that
 memory to store.  %

 In other cases operators are used millions of times such that, used as above, millions of new

 arrays will be created.  %

-One way to avoid these problems is to use \emph{in-place} operators

-

-Because the \python{Data} object is mostly stored outside of memory, it is better to do

-in-place... % TODO

 

-Broadcasting... % TODO

+One way to avoid these problems is to use \emph{in-place} operators.  %

+Using a slightly different syntax, one can tell Python to overwrite one of the operands with the

+new value. %

+Continuing from \ref{pro:lst:array_addition}:

+\begin{codefragment}{python, label=pro:lst:in_place_addition}

+>>> a += b

+>>> a

+array([3, 3, 3])

+\end{codefragment}

+No output \python{c} array was created, so no additional memory footprint is needed in

+\ref{pro:lst:in_place_addition}.  %

+Since WrightTools channels and variables are typically large arrays, and since these arrays are

+stored on disk inside of a larger file, WrightTools requires the use of in-place operators for all

+normal math.  %

+Currently WrightTools supports addition (\python{+=}), multiplication(\python{*=}),

+power (\python{**=}), subtraction (\python{-=}), and division (\python{/=}).  %

+As an example, consider dividing a channel by a specific factor:

+\begin{codefragment}{python}

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

+>>> data = wt.data.from_JASCO(datasets.JASCO.PbSe_batch_1)

+data.created at /tmp/tdyvfxu8.wt5::/

+  range: 2500.0 to 700.0 (nm)

+  size: 1801

+>>> data.signal

+<WrightTools.Channel 'signal' at /tmp/tdyvfxu8.wt5::/signal>

+>>> data.signal.min(), data.signal.max()

+(0.10755, 1.58144)

+>>> data.signal /= 2

+>>> data.signal.max(), data.signal.min()

+(0.053775, 0.79072)

+\end{codefragment}

+Variables also support in-place operators.  %

 

 \subsubsection{Clip}

 

diff --git a/processing/fringes_transform.png b/processing/fringes_transform.png
new file mode 100644
index 0000000..4d400d2
--- /dev/null
+++ b/processing/fringes_transform.png
diff --git a/processing/fringes_transform.py b/processing/fringes_transform.py
new file mode 100644
index 0000000..1f80a86
--- /dev/null
+++ b/processing/fringes_transform.py
@@ -0,0 +1,27 @@
+import os
+import matplotlib.pyplot as plt
+import WrightTools as wt; from WrightTools import datasets
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+data = wt.data.from_PyCMDS(datasets.PyCMDS.w2_w1_000)
+data.signal_mean.symmetric_root(0.5)  # to amplitude level
+data.convert('wn')
+
+fig, gs = wt.artists.create_figure(width='double', cols=[1, 1, 'cbar'])
+# as taken
+ax = plt.subplot(gs[0, 0])
+ax.pcolor(data)
+wt.artists.set_ax_labels(xlabel=data.w2.label, ylabel=data.w1.label)
+ax.grid(); ax.set_title('as taken', fontsize=20)
+# transformed
+ax = plt.subplot(gs[0, 1])
+data.transform('wm', 'w1')
+data.convert('wn')
+ax.pcolor(data)
+wt.artists.set_ax_labels(xlabel=data.wm.label, yticks=False)
+ax.grid(); ax.set_title('transformed', fontsize=20)
+# colorbar
+wt.artists.plot_colorbar(plt.subplot(gs[0, -1]), label='amplitude')
+# save
+wt.artists.savefig(os.path.join(here, 'fringes_transform.png'))