From: W. Trevor King <wking@drexel.edu>
Date: Sat, 14 May 2011 17:41:27 +0000 (-0400)
Subject: Transition from \asyfig to the stock \asyinclude.
X-Git-Tag: v1.0~359
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=814ad84078a6ee0dbc07fd9654e47dde302e29a1;p=thesis.git

Transition from \asyfig to the stock \asyinclude.
---

diff --git a/tex/site_cons/site_tools/asymptote.py b/tex/site_cons/site_tools/asymptote.py
index 1ad5466..f954bd1 100644
--- a/tex/site_cons/site_tools/asymptote.py
+++ b/tex/site_cons/site_tools/asymptote.py
@@ -9,8 +9,8 @@ import doctest
 
 double_quoted_string_re = re.compile(r'"([^"]*)"', re.M)
 
-# SCons' LaTeX scanner doesn't understand \asyfig{}, so keep track of
-# all Asymptote graphics for phony target creation.
+# SCons' LaTeX scanner doesn't understand \asyinclude{}, so keep track
+# of all Asymptote graphics for phony target creation.
 asyfigs = []
 
 def asymptote_scan(node, env, path, arg=None):
@@ -58,10 +58,8 @@ def asymptote_scan(node, env, path, arg=None):
 def asymptote_emitter(target, source, env):
     assert str(source[0]).endswith('.asy'), str(source[0])
     filebase = str(source[0])[:-len('.asy')]
-    target.extend(['%s_%s' % (filebase, ext)
-                   for ext in ['.tex', '.pre', '0.pdf']])
-    target.extend(['%s-comp.%s' % (filebase, ext)
-                   for ext in ['idx', 'log', 'nlo', 'pdf']])
+    target.extend(['%s%s' % (filebase, ext)
+                   for ext in ['.tex', '.pre', '_0.pdf']])
     source.append(SCons.Script.Alias('asytools'))
     # side effect, keep track of all asymptote graphics.
     asyfigs.append(target[0])
@@ -79,13 +77,12 @@ def generate(env):
     #pdf.generate(env)
 
     env['BUILDERS']['Asymptote'] = SCons.Script.Builder(
-        action=AsymptoteAction, suffix='_.tex', src_suffix = '.asy',
+        action=AsymptoteAction, suffix='.tex', src_suffix = '.asy',
         emitter=asymptote_emitter)
-    env['ASYMPTOTE'] = '../asy/asyprocess'
+
+    env['ASYMPTOTE'] = 'asy'
     env['ASYMPTOTEFLAGS'] = SCons.Util.CLVar(
-        "--texinputs=../..: "
-        "--pretex='\documentclass{drexel-thesis} \input{packages}' "
-        "--")
+        '-tex pdflatex -inlineimage -inlinetex')
     env['ASYMPTOTECOM']  = 'cd ${TARGET.dir} && $ASYMPTOTE $ASYMPTOTEFLAGS ${SOURCE.filebase}'
     env.Append(SCANNERS=SCons.Scanner.Base(
             function=asymptote_scan,
diff --git a/tex/src/apparatus/afm.tex b/tex/src/apparatus/afm.tex
index 1fb8b56..65b358e 100644
--- a/tex/src/apparatus/afm.tex
+++ b/tex/src/apparatus/afm.tex
@@ -16,7 +16,7 @@ bending force constant of the cantilever is known\citep{levy02}, the
 force applied to the sample can be calculated.
 
 \begin{figure}
-  \asyfig{figures/schematic/afm}%
+  \asyinclude{figures/schematic/afm}%
   \caption{Operating principle for an Atomic Force
     Microscope\index{AFM}.  A sharp tip integrated at the end of a
     cantilever interacts with the sample.  Cantilever bending is
diff --git a/tex/src/apparatus/procedure.tex b/tex/src/apparatus/procedure.tex
index 1c3e186..e1927f3 100644
--- a/tex/src/apparatus/procedure.tex
+++ b/tex/src/apparatus/procedure.tex
@@ -33,10 +33,10 @@ multi-domain test proteins.
 
 \begin{figure}
   \begin{center}
-  \subfloat[][]{\asyfig{figures/schematic/unfolding}%
+  \subfloat[][]{\asyinclude{figures/schematic/unfolding}%
     \label{fig:unfolding-schematic}}
   % \hspace{.25in}%
-  \subfloat[][]{\asyfig{figures/expt-sawtooth/expt-sawtooth}%
+  \subfloat[][]{\asyinclude{figures/expt-sawtooth/expt-sawtooth}%
     \label{fig:expt-sawtooth}}
   \caption{(a) Schematic of the experimental setup for mechanical
     unfolding of proteins using an AFM (not to scale).  An experiment
diff --git a/tex/src/blurb/acknowledgments.tex b/tex/src/blurb/acknowledgments.tex
index ea72b96..fd02ef2 100644
--- a/tex/src/blurb/acknowledgments.tex
+++ b/tex/src/blurb/acknowledgments.tex
@@ -5,8 +5,7 @@ This work was produced using the following open source software projects:
       \href{http://www.ctan.org/}{CTAN}]
   Typesetting.
 \item[\href{http://sourceforge.net/projects/pgf/}{PGF}/%
-      \href{http://asymptote.sourceforge.net/}{Asymptote}/%
-      \href{http://github.com/wspr/asyfig/}{Asyfig}]
+      \href{http://asymptote.sourceforge.net/}{Asymptote}]
   Graphical programming.
 \item[\href{http://www.python.org/}{Python}]
   General purpose scripting.
diff --git a/tex/src/cantilever-calib/contour_integration.tex b/tex/src/cantilever-calib/contour_integration.tex
index 0f05d25..6bae7e6 100644
--- a/tex/src/cantilever-calib/contour_integration.tex
+++ b/tex/src/cantilever-calib/contour_integration.tex
@@ -5,7 +5,7 @@ As a brief review, some definite integrals from $-\infty$ to $\infty$%
 along the contour \C\ shown in \cref{fig:UHP-contour}.
 
 \begin{figure}
-  \asyfig{figures/contour/contour}
+  \asyinclude{figures/contour/contour}
   \caption{Integral contour \C\ enclosing the upper half of the
     complex plane.  If the integrand $f(z)$ goes to zero ``quickly
     enough'' as the radius of \C\ approaches infinity, then the only
diff --git a/tex/src/cantilever/methods.tex b/tex/src/cantilever/methods.tex
index 373f045..83f100b 100644
--- a/tex/src/cantilever/methods.tex
+++ b/tex/src/cantilever/methods.tex
@@ -36,7 +36,7 @@ averaged across each cantilever-stiffness/pulling-speed group to
 produce \cref{fig:cant:v-dep}.
 
 \begin{figure}
-  \asyfig{figures/cantilever-data/v-dep}
+  \asyinclude{figures/cantilever-data/v-dep}
   \caption{Pulling speed dependence of I27 for different cantilever
     stiffnesses.  The listed stiffnesses are averages across several
     individual cantilevers and calibrations.  Each box is the average
@@ -55,6 +55,6 @@ loading rates were extracted from the data by taking the slope of the
 fit WLC\index{WLC} at unfolding.
 
 \begin{figure}
-  \asyfig{figures/cantilever-data/loading-rate}
+  \asyinclude{figures/cantilever-data/loading-rate}
   \caption{Loading rate.\label{fig:cant:load-dep}}
 \end{figure}
diff --git a/tex/src/cantilever/simulations.tex b/tex/src/cantilever/simulations.tex
index fd9ff15..db4744c 100644
--- a/tex/src/cantilever/simulations.tex
+++ b/tex/src/cantilever/simulations.tex
@@ -9,19 +9,19 @@ following results
 (\cref{fig:cant:sim:v-dep,fig:cant:sim:load-dep,fig:cant:sim:i-dep}).
 
 \begin{figure}
-  \asyfig{figures/cantilever-sim/v-dep}
+  \asyinclude{figures/cantilever-sim/v-dep}
   \caption{Unfolding force velocity dependence for different
     cantilevers.\label{fig:cant:sim:v-dep}}
 \end{figure}
 
 \begin{figure}
-  \asyfig{figures/cantilever-sim/loading-rate}
+  \asyinclude{figures/cantilever-sim/loading-rate}
   \caption{Unfolding force loading rate dependence simulations for
     different cantilevers.\label{fig:cant:sim:load-dep}}
 \end{figure}
 
 \begin{figure}
-  \asyfig{figures/cantilever-sim/i-dep}
+  \asyinclude{figures/cantilever-sim/i-dep}
   \caption{Unfolding force peak index dependence simulations for
     different cantilevers.\label{fig:cant:sim:i-dep}}
 \end{figure}
diff --git a/tex/src/cantilever/theory.tex b/tex/src/cantilever/theory.tex
index ae30cd9..0daf5fe 100644
--- a/tex/src/cantilever/theory.tex
+++ b/tex/src/cantilever/theory.tex
@@ -1,7 +1,7 @@
 \section{Theory}
 
 \begin{figure}
-  \asyfig{figures/schematic/landscape-cant}
+  \asyinclude{figures/schematic/landscape-cant}
   \caption{Energy landscape schematic.\label{fig:landscape}}
 \end{figure}
 
diff --git a/tex/src/packages.tex b/tex/src/packages.tex
index f6d62f2..ce6e2e7 100644
--- a/tex/src/packages.tex
+++ b/tex/src/packages.tex
@@ -61,7 +61,7 @@
 \usetikzlibrary{automata} % graph-theory library
 \usetikzlibrary{calc}     % coordinate-calculation library
 
-\usepackage{asyfig}       % more fancy graphics ;).
+\usepackage[inline]{asymptote}    % more fancy graphics ;).
 
 \usepackage{epsdice}      % dice-face font
 
diff --git a/tex/src/root.tex b/tex/src/root.tex
index 785af80..c8c908e 100644
--- a/tex/src/root.tex
+++ b/tex/src/root.tex
@@ -33,6 +33,16 @@
 \input{packages}
 
 \begin{document}
+
+% Work-directory for Asymptote files (no spaces):
+\def\asydir{figures/scratch}
+\begin{asydef}
+// Global Asymptote definitions go here.
+//texpreamble("\documentclass{drexel-thesis}");
+//usepackage("packages");
+\end{asydef}
+
+
 \begin{preamble}
 
 \include{blurb/dedications}
diff --git a/tex/src/sawsim/discussion.tex b/tex/src/sawsim/discussion.tex
index ec63d63..777e50c 100644
--- a/tex/src/sawsim/discussion.tex
+++ b/tex/src/sawsim/discussion.tex
@@ -23,10 +23,10 @@ deviation of $25\U{pN}$.
 \begin{figure}
 \vspace{-1in}
 \begin{center}
-\subfloat[][]{\asyfig{figures/sim-sawtooth/sim-sawtooth}%
+\subfloat[][]{\asyinclude{figures/sim-sawtooth/sim-sawtooth}%
   \label{fig:sawsim:sim-sawtooth}%
 }\\
-\subfloat[][]{\asyfig{figures/sim-hist/sim-hist}%
+\subfloat[][]{\asyinclude{figures/sim-hist/sim-hist}%
   \label{fig:sawsim:sim-hist}%
 }
 \caption{(a) Three simulated force curves from pulling a polymer of
@@ -157,7 +157,7 @@ unfolding order and polymer length.
 
 \begin{figure}
   \begin{center}
-  \asyfig{figures/order-dep/order-dep}
+  \asyinclude{figures/order-dep/order-dep}
   \caption{The dependence of the unfolding force on the temporal
     unfolding order for four polymers with $4$, $8$, $12$, and $16$
     identical protein domains.  Each point in the figure is the
@@ -217,7 +217,7 @@ to WLC\index{WLC} or other polymer models (\cref{fig:expt-sawtooth}).
 
 \begin{figure}
 \begin{center}
-\asyfig{figures/kappa-sawteeth/kappa-sawteeth}
+\asyinclude{figures/kappa-sawteeth/kappa-sawteeth}
 \caption{Simulated force curves obtained from pulling a polymer with
   eight protein molecules using cantilevers with different force
   constants $\kappa_c$.  Parameters used in generating these curves
@@ -302,10 +302,10 @@ about the protein from other sources.
 
 \begin{figure}
   \begin{center}
-  \subfloat[][]{\asyfig{figures/v-dep/v-dep}%
+  \subfloat[][]{\asyinclude{figures/v-dep/v-dep}%
     \label{fig:sawsim:v-dep}%
   } \\
-  \subfloat[][]{\asyfig{figures/v-dep/v-dep-sd}%
+  \subfloat[][]{\asyinclude{figures/v-dep/v-dep-sd}%
     \label{fig:sawsim:width-v-dep}%
   }
   \caption{(a) The dependence of the unfolding forces on the pulling
@@ -324,7 +324,7 @@ about the protein from other sources.
 
 \begin{figure}
   \begin{center}
-  \asyfig{figures/fit-space/fit-valley}
+  \asyinclude{figures/fit-space/fit-valley}
   \caption{Fit quality between an experimental data set and simulated
     data sets obtained using various values of unfolding rate
     parameters $k_{u0}$ and $\Delta x_u$.  The experimental data are
diff --git a/tex/src/sawsim/methods.tex b/tex/src/sawsim/methods.tex
index 69d9082..ec8de7e 100644
--- a/tex/src/sawsim/methods.tex
+++ b/tex/src/sawsim/methods.tex
@@ -174,7 +174,7 @@ group of $N_f$ identical domains to unfold in a given time step is
 where the approximation is valid when $N_fP_1 \ll 1$.
 
 \begin{figure}
-  \asyfig{figures/schematic/monte-carlo}
+  \asyinclude{figures/schematic/monte-carlo}
   \caption{Once the unfolding probability has been caculated, we need
     to determine whether or not a domain should unfold.  We do this by
     generating a random number, and comparing that number to the