1.1 --- a/thesis/cortex.org	Sun Mar 30 01:22:23 2014 -0400
     1.2 +++ b/thesis/cortex.org	Sun Mar 30 01:34:43 2014 -0400
     1.3 @@ -1134,7 +1134,7 @@
     1.4      #+caption: pixels is denser in the middle and falls off at the 
     1.5      #+caption: edges and is inspired by the human retina.
     1.6      #+name: retina
     1.7 -    #+ATTR_LaTeX: :width 10cm
     1.8 +    #+ATTR_LaTeX: :width 7cm
     1.9      [[./images/retina-small.png]]
    1.10  
    1.11      Together, the number 0xFF0000 and the image image above describe

     2.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     2.2 +++ b/thesis/extraplaceins.sty	Sun Mar 30 01:34:43 2014 -0400
     2.3 @@ -0,0 +1,120 @@
     2.4 +%  P L A C E I N S . S T Y          ver 2.2  April 18, 2005
     2.5 +%  Donald Arseneau                  asnd@triumf.ca
     2.6 +%
     2.7 +%  Modified on March 6, 2011
     2.8 +%  Lex Fridman                      lexfridman@gmail.com
     2.9 +%  See: http://bit.ly/h2Se0u
    2.10 +%
    2.11 +%  Keep floats `in their place'; don't let them float into another section.
    2.12 +%  Instructions are below.
    2.13 +%
    2.14 +%  placeins.sty is freely released to the public domain.
    2.15 +
    2.16 +
    2.17 +\def\@fb@botlist{\@botlist}
    2.18 +\def\@fb@topbarrier{\suppressfloats[t]}
    2.19 +
    2.20 +\catcode`\V=14 % `V' is a comment character unless [verbose]
    2.21 +
    2.22 +\@ifundefined{DeclareOption}{}%
    2.23 +{\DeclareOption{below}{\def\@fb@botlist{}}
    2.24 + \DeclareOption{above}{\def\@fb@topbarrier{}}
    2.25 + \DeclareOption{section}{\AtBeginDocument{%
    2.26 +     \expandafter\renewcommand\expandafter\section\expandafter
    2.27 +       {\expandafter\@fb@secFB\section}%
    2.28 +     \newcommand\@fb@secFB{\FloatBarrier
    2.29 +     \gdef\@fb@afterHHook{\@fb@topbarrier \gdef\@fb@afterHHook{}}}
    2.30 +     \g@addto@macro\@afterheading{\@fb@afterHHook}
    2.31 +     \gdef\@fb@afterHHook{}
    2.32 +  }}
    2.33 + \DeclareOption{subsection}{\AtBeginDocument{%
    2.34 +     \expandafter\renewcommand\expandafter\subsection\expandafter
    2.35 +       {\expandafter\@fb@subsecFB\subsection}%
    2.36 +     \newcommand\@fb@subsecFB{\FloatBarrier
    2.37 +     \gdef\@fb@afterHHook{\@fb@topbarrier \gdef\@fb@afterHHook{}}}
    2.38 +     \g@addto@macro\@afterheading{\@fb@afterHHook}
    2.39 +     \gdef\@fb@afterHHook{}
    2.40 +  }}
    2.41 + \DeclareOption{subsubsection}{\AtBeginDocument{%
    2.42 +     \expandafter\renewcommand\expandafter\subsubsection\expandafter
    2.43 +       {\expandafter\@fb@subsubsecFB\subsubsection}%
    2.44 +     \newcommand\@fb@subsubsecFB{\FloatBarrier
    2.45 +     \gdef\@fb@afterHHook{\@fb@topbarrier \gdef\@fb@afterHHook{}}}
    2.46 +     \g@addto@macro\@afterheading{\@fb@afterHHook}
    2.47 +     \gdef\@fb@afterHHook{}
    2.48 +  }}
    2.49 + \DeclareOption{verbose}{\catcode`\V=9 }% Activate things after `V'
    2.50 + \ProvidesPackage{placeins}[2005/04/18 \space  v 2.2]
    2.51 + \ProcessOptions 
    2.52 +} % end of \@ifundefined
    2.53 +
    2.54 +\def\FloatBarrier{\par\begingroup \let\@elt\relax
    2.55 +V\edef\@tempa{\write\m@ne{Package placeins Info: Float barrier, from
    2.56 +V  input line \the\inputlineno, processed on page \thepage, lands on
    2.57 +V  page \noexpand\thepage. }}\@tempa
    2.58 + \edef\@tempa{\@fb@botlist\@deferlist\@dbldeferlist}%
    2.59 + \ifx\@tempa\@empty V\PackageInfo{placeins}{No floats held,}%
    2.60 + \else
    2.61 +    \ifx\@fltovf\relax % my indicator of recursion
    2.62 +       \if@firstcolumn V\PackageWarning{placeins}{Some floats are stuck,}%
    2.63 +         \clearpage 
    2.64 +       \else V\PackageInfo{placeins}{Eject a column and check again:}%
    2.65 +         \null\newpage\FloatBarrier 
    2.66 +       \fi
    2.67 +    \else V\PackageInfo{placeins}{Must dump some floats}%
    2.68 +       \newpage \let\@fltovf\relax V\PackageInfo{placeins}{Check again:}%
    2.69 +       \FloatBarrier % recurse once only
    2.70 + \fi\fi \endgroup
    2.71 + \@fb@topbarrier }
    2.72 +
    2.73 +\catcode`\V=11
    2.74 +\endinput
    2.75 +
    2.76 +%====================== BEGIN INSTRUCTIONS ===========================
    2.77 +
    2.78 +  p l a c e i n s . s t y          ver 2.2  April 18, 2005
    2.79 +  Donald Arseneau                  asnd@triumf.ca
    2.80 +
    2.81 +
    2.82 +Placeins.sty keeps floats `in their place', preventing them from floating
    2.83 +past a "\FloatBarrier" command into another section.  To use it, declare
    2.84 +"\usepackage{placeins}" and insert "\FloatBarrier" at places that floats 
    2.85 +should not move past, perhaps at every "\section".  
    2.86 +
    2.87 +Option:  [section]
    2.88 +
    2.89 +A more convenient way to stop floats at section boundaries is to change 
    2.90 +the definition of "\section" to include "\FloatBarrier", either at the
    2.91 +beginning, before "\@startsection", or in the `style' specification (see 
    2.92 +The LaTeX Companion, section 2.2.2; or 2.3 in the 1st ed).  If you specify 
    2.93 +"\usepackage[section]{placeins}", then the "\section" command will be 
    2.94 +redefined with "\FloatBarrier" inserted at the beginning.
    2.95 +
    2.96 +Options:  [above]  [below]
    2.97 +
    2.98 +Something you may not like is that, by default, "\FloatBarrier" is very 
    2.99 +strict, and will (try to) prevent a float from appearing above the start 
   2.100 +of the current section or below the start of the next section, even 
   2.101 +though the float is still on the same page as its intended section.  
   2.102 +Each restriction can be relaxed separately by using the "[above]" and 
   2.103 +"[below]" package options: "[above]" allows floats to appear above their 
   2.104 +section, if on the same page; "[below]" allows below.
   2.105 +
   2.106 +NOTE!  The original version of placeins.sty acted like it was loaded
   2.107 +with the option "[above]" specified.
   2.108 +
   2.109 +There is a problem with LaTeX's "\suppressfloats" being out of step with 
   2.110 +the page breaking (see usenet msg <yfi656pbsn0.fsf@triumf.ca> and thread)
   2.111 +which sometimes allows a float to go above a "\FloatBarrier" placed near
   2.112 +the top of a page. Maybe placeins will fix it sometime later.
   2.113 +
   2.114 +Option: [verbose]
   2.115 +
   2.116 +There is a package option "[verbose]" that causes many messages to be
   2.117 +written in the log file.  It might be used to answer the question:
   2.118 +`How did *that* get *there*?!?'
   2.119 +
   2.120 +%====================== END INSTRUCTIONS ========================
   2.121 +
   2.122 +Test file integrity:  ASCII 32-57, 58-126:  !"#$%&'()*+,-./0123456789
   2.123 +:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~

     3.1 Binary file thesis/images/diagram_rendermanager2.png has changed

     4.1 --- a/thesis/rlm-cortex-meng.tex	Sun Mar 30 01:22:23 2014 -0400
     4.2 +++ b/thesis/rlm-cortex-meng.tex	Sun Mar 30 01:34:43 2014 -0400
     4.3 @@ -52,6 +52,8 @@
     4.4  \usepackage{xcolor}
     4.5  \usepackage{minted}    
     4.6  \usepackage[backend=bibtex,style=alphabetic]{biblatex}
     4.7 +%\usepackage[section]{placeins}
     4.8 +\usepackage[section,subsection,subsubsection]{extraplaceins}
     4.9  %\floatsetup[listing]{style=Plaintop}    
    4.10  
    4.11