# HG changeset patch
# User Scott Morrison <scott@tqft.net>
# Date 1291658239 21600
# Node ID a9b9094e3b9cad09c652a0b92d03fa899d4363f5
# Parent  ccc2d7fe57b3f99eeb3462b66fa2558a08aef71d
moving everything into one directory for PNAS submission, and externalizing TikZ

diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/diagrams/deligne/mapping-cylinders.pdf
Binary file pnas/diagrams/deligne/mapping-cylinders.pdf has changed
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/diagrams/externalization-jobs.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pnas/diagrams/externalization-jobs.sh	Mon Dec 06 11:57:19 2010 -0600
@@ -0,0 +1,1 @@
+grep -o beginpgfgraphicnamed\{[0-9A-Za-z-]*\} < *.tex | sed -e 's/beginpgfgraphicnamed{//' | sed -e 's/}//'
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/diagrams/externalize-tikz.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pnas/diagrams/externalize-tikz.sh	Mon Dec 06 11:57:19 2010 -0600
@@ -0,0 +1,6 @@
+for job in `./externalization-jobs.sh`; do
+	pdflatex --jobname $job tikz-figures.tex;
+	rm $job.log;
+	rm $job.out;
+	rm $job.aux;
+done
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/diagrams/ncat/zz2.pdf
Binary file pnas/diagrams/ncat/zz2.pdf has changed
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/diagrams/tikz-figures.tex
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pnas/diagrams/tikz-figures.tex	Mon Dec 06 11:57:19 2010 -0600
@@ -0,0 +1,44 @@
+\documentclass{amsart}
+
+\usepackage{tikz}
+\pgfrealjobname{tikz-figures}
+
+\begin{document}
+
+\begin{figure}
+\centering
+\beginpgfgraphicnamed{figure1}%
+\begin{tikzpicture}[%every label/.style={green}
+]
+\node[fill=black, circle, label=below:$E$, inner sep=1.5pt](S) at (0,0) {};
+\node[fill=black, circle, label=above:$E$, inner sep=1.5pt](N) at (0,2) {};
+\draw (S) arc  (-90:90:1);
+\draw (N) arc  (90:270:1);
+\node[left] at (-1,1) {$B_1$};
+\node[right] at (1,1) {$B_2$};
+\end{tikzpicture}
+\endpgfgraphicnamed%
+\mbox{} % <-- weird, doesn't compile unless I put something here after the \endpgfgraphicnamed...? -S
+\caption{Combining two balls to get a full boundary.}\label{blah3}\end{figure}
+
+\begin{figure}
+\centering
+\beginpgfgraphicnamed{figure2}%
+\begin{tikzpicture}[%every label/.style={green},
+				x=1.5cm,y=1.5cm]
+\node[fill=black, circle, label=below:$E$, inner sep=2pt](S) at (0,0) {};
+\node[fill=black, circle, label=above:$E$, inner sep=2pt](N) at (0,2) {};
+\draw (S) arc  (-90:90:1);
+\draw (N) arc  (90:270:1);
+\draw (N) -- (S);
+\node[left] at (-1/4,1) {$B_1$};
+\node[right] at (1/4,1) {$B_2$};
+\node at (1/6,3/2)  {$Y$};
+\end{tikzpicture}
+\endpgfgraphicnamed%
+\mbox{} % <-- weird, doesn't compile unless I put something here after the \endpgfgraphicnamed...? -S
+\caption{From two balls to one ball.}\label{blah5}\end{figure}
+
+
+\end{document}
+
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/figure1.pdf
Binary file pnas/figure1.pdf has changed
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/figure2.pdf
Binary file pnas/figure2.pdf has changed
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/mapping-cylinders.pdf
Binary file pnas/mapping-cylinders.pdf has changed
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/pnas.tex
--- a/pnas/pnas.tex	Fri Dec 03 19:11:40 2010 -0600
+++ b/pnas/pnas.tex	Mon Dec 06 11:57:19 2010 -0600
@@ -249,17 +249,17 @@
 % figures
 
 \newcommand{\mathfig}[2]{\ensuremath{\hspace{-3pt}\begin{array}{c}%
-  \raisebox{-2.5pt}{\includegraphics[width=#1\textwidth]{diagrams/#2}}%
+  \raisebox{-2.5pt}{\includegraphics[width=#1\textwidth]{#2}}%
 \end{array}\hspace{-3pt}}}
 
 
 % packages
 
 \usepackage{tikz}
-\usetikzlibrary{shapes}
-\usetikzlibrary{backgrounds}
-\usetikzlibrary{decorations,decorations.pathreplacing}
-\usetikzlibrary{fit,calc,through}
+%\usetikzlibrary{shapes}
+%\usetikzlibrary{backgrounds}
+%\usetikzlibrary{decorations,decorations.pathreplacing}
+%\usetikzlibrary{fit,calc,through}
 
 \usepackage[all,color]{xy}
 \SelectTips{cm}{}
@@ -1356,36 +1356,20 @@
 
 
 \begin{figure}
-\centering
-\begin{tikzpicture}[%every label/.style={green}
-]
-\node[fill=black, circle, label=below:$E$, inner sep=1.5pt](S) at (0,0) {};
-\node[fill=black, circle, label=above:$E$, inner sep=1.5pt](N) at (0,2) {};
-\draw (S) arc  (-90:90:1);
-\draw (N) arc  (90:270:1);
-\node[left] at (-1,1) {$B_1$};
-\node[right] at (1,1) {$B_2$};
-\end{tikzpicture}
+\begin{equation*}
+\mathfig{0.18}{figure1}
+\end{equation*}
 \caption{Combining two balls to get a full boundary.}\label{blah3}\end{figure}
 
 \begin{figure}
-\centering
-\begin{tikzpicture}[%every label/.style={green},
-				x=1.5cm,y=1.5cm]
-\node[fill=black, circle, label=below:$E$, inner sep=2pt](S) at (0,0) {};
-\node[fill=black, circle, label=above:$E$, inner sep=2pt](N) at (0,2) {};
-\draw (S) arc  (-90:90:1);
-\draw (N) arc  (90:270:1);
-\draw (N) -- (S);
-\node[left] at (-1/4,1) {$B_1$};
-\node[right] at (1/4,1) {$B_2$};
-\node at (1/6,3/2)  {$Y$};
-\end{tikzpicture}
+\begin{equation*}
+\mathfig{0.14}{figure2}
+\end{equation*}
 \caption{From two balls to one ball.}\label{blah5}\end{figure}
 
 \begin{figure}
 \begin{equation*}
-\mathfig{.23}{ncat/zz2}
+\mathfig{.23}{zz2}
 \end{equation*}
 \caption{A small part of $\cell(W)$.}
 \label{partofJfig}
@@ -1393,7 +1377,7 @@
 
 \begin{figure}
 %$$\mathfig{.4}{deligne/manifolds}$$
-$$\mathfig{.4}{deligne/mapping-cylinders}$$
+$$\mathfig{.4}{mapping-cylinders}$$
 \caption{An $n$-dimensional surgery cylinder.}\label{delfig2}
 \end{figure}
 
diff -r ccc2d7fe57b3 -r a9b9094e3b9c pnas/zz2.pdf
Binary file pnas/zz2.pdf has changed