From: W. Trevor King <wking@drexel.edu>
Date: Sat, 1 May 2010 02:36:20 +0000 (-0400)
Subject: Converted sim-sawtooth from Gnuplot to Asymptote.
X-Git-Tag: v1.0~383
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=bf3cbfefeb07c9d86dcb9d983d84ee2e9a0b21be;p=thesis.git

Converted sim-sawtooth from Gnuplot to Asymptote.
---

diff --git a/tex/src/figures/asy/wtk_graph.asy b/tex/src/figures/asy/wtk_graph.asy
index 778252b..072d292 100644
--- a/tex/src/figures/asy/wtk_graph.asy
+++ b/tex/src/figures/asy/wtk_graph.asy
@@ -14,31 +14,42 @@ Label sLabel(string s, align align=NoAlign, int extra_spaces=0) {
   return Label(s+spaces, s+spaces, fontsize(fsize), align=align);
 }
 
-void graphFile(picture pic=currentpicture, string file="datafile",
-	       int xcol=0, int ycol=1,
-               real xscale=1, real yscale=1, pen p=red,
+void graphData(picture pic=currentpicture, real[] x, real[] y,
+               real xscale=1, real yscale=1, real dx=0, real dy=0, pen p=red,
                path mpath=scale(0.8mm)*unitcircle,
 	       markroutine markroutine=marknodes,
 	       string t="Title",
                bool dots=false) {
   pen pline=p;
   marker mk = nomarker;
-  file fin=input(file).line();
-  real[][] a=fin.dimension(0,0);
-  a=transpose(a);
-  real[] x=a[xcol];
-  real[] y=a[ycol];
   if (dots == true) {
     pline = invisible;
     mk = marker(mpath, markroutine, p);
   }
   if (t != "Title") {
-    draw(pic=pic, graph(pic,xscale*x,yscale*y), p=pline, legend=sLabel(t,extra_spaces=1), marker=mk);
+    draw(pic=pic, graph(pic,xscale*(x+dx),yscale*(y+dy)), p=pline,
+	 legend=sLabel(t,extra_spaces=1), marker=mk);
   } else {
-    draw(pic=pic, graph(pic,xscale*x,yscale*y), p=pline, marker=mk);
+    draw(pic=pic, graph(pic,xscale*(x+dx),yscale*(y+dy)), p=pline, marker=mk);
   }
 }
 
+void graphFile(picture pic=currentpicture, string file="datafile",
+	       int xcol=0, int ycol=1,
+               real xscale=1, real yscale=1, real dx=0, real dy=0, pen p=red,
+               path mpath=scale(0.8mm)*unitcircle,
+	       markroutine markroutine=marknodes,
+	       string t="Title",
+               bool dots=false) {
+  file fin=input(file).line();
+  real[][] a=fin.dimension(0,0);
+  a=transpose(a);
+  real[] x=a[xcol];
+  real[] y=a[ycol];
+  graphData(pic=pic, x=x, y=y, xscale=xscale, yscale=yscale, dx=dx, dy=dy, p=p,
+	    mpath=mpath, markroutine=markroutine, t=t, dots=dots);
+}
+
 void fitFile(picture pic=currentpicture, string file="fitparamfile",
 	     int pcol=0, real f(real x, real[] params),
 	     real xmin=realMin, real xmax=realMax,
diff --git a/tex/src/figures/sim-sawtooth/SConscript b/tex/src/figures/sim-sawtooth/SConscript
index 8ecd2a1..1bff1dc 100644
--- a/tex/src/figures/sim-sawtooth/SConscript
+++ b/tex/src/figures/sim-sawtooth/SConscript
@@ -1,9 +1,16 @@
+from site_cons.site_init import link_wtk_graph
+
+
+FIGURES = ['sim-sawtooth']
+
 # Get the passed in environment.
 Import('env')
 
-for gp in Glob('*.gp'):
-    env.Gnuplot(gp)
+wtk_graph = link_wtk_graph(env)
+
+for fig in FIGURES:
+    asyfile = '%s.asy' % fig  # static .asy file
+    env.Asymptote([asyfile, wtk_graph])
 
 # Pass back the modified environment.
 Return('env')
-
diff --git a/tex/src/figures/sim-sawtooth/fig.gp b/tex/src/figures/sim-sawtooth/fig.gp
deleted file mode 100644
index 3b5a921..0000000
--- a/tex/src/figures/sim-sawtooth/fig.gp
+++ /dev/null
@@ -1,35 +0,0 @@
-set terminal pdf font 'Times,7' size 9cm, 6cm
-set output 'fig.pdf'
-unset key
-set style data lines
-set xrange [-5:250]
-set yrange [-10:400]
-set ytics 0,100
-set xtics nomirror
-set ytics nomirror
-# border 3 = bottom & left
-set border 3
-set lmargin 9
-
-set multiplot
-
-set size 1,0.42;
-set origin 0.0,0.0;
-set xlabel 'Extension (nm)'
-plot 'fig1.d' using (($1-$2/0.05)*1e9):($2*1e12)
-
-set size 1,0.29;
-set origin 0.0,0.42;
-set bmargin 0
-unset xlabel
-set xtics format "" 
-set ylabel 'Force (pN)'
-plot 'fig2.d' using (($1-$2/0.05)*1e9):($2*1e12)
-
-set origin 0.0,0.71;
-set bmargin 0
-set xtics format ""
-unset ylabel
-plot 'fig3.d' using (($1-$2/0.05)*1e9):($2*1e12)
-
-unset multiplot
diff --git a/tex/src/figures/sim-sawtooth/fig1.d b/tex/src/figures/sim-sawtooth/fig1.dat
similarity index 100%
rename from tex/src/figures/sim-sawtooth/fig1.d
rename to tex/src/figures/sim-sawtooth/fig1.dat
diff --git a/tex/src/figures/sim-sawtooth/fig2.d b/tex/src/figures/sim-sawtooth/fig2.dat
similarity index 100%
rename from tex/src/figures/sim-sawtooth/fig2.d
rename to tex/src/figures/sim-sawtooth/fig2.dat
diff --git a/tex/src/figures/sim-sawtooth/fig3.d b/tex/src/figures/sim-sawtooth/fig3.dat
similarity index 100%
rename from tex/src/figures/sim-sawtooth/fig3.d
rename to tex/src/figures/sim-sawtooth/fig3.dat
diff --git a/tex/src/figures/sim-sawtooth/sim-sawtooth.asy b/tex/src/figures/sim-sawtooth/sim-sawtooth.asy
new file mode 100644
index 0000000..2a8032d
--- /dev/null
+++ b/tex/src/figures/sim-sawtooth/sim-sawtooth.asy
@@ -0,0 +1,59 @@
+import wtk_graph;
+
+size(15cm,10cm,IgnoreAspect);
+
+scale(Linear, Linear);
+real k = 0.05; /* spring constant in N/m */
+real xscale=1e9;
+real fscale=1e12;
+
+void graphSawtooth(string file="datafile", real k,
+		   int xcol=0, int fcol=1,
+		   real xscale=1, real fscale=1, real dx=0, real df=0,
+		   pen p=red) {
+  file fin=input(file).line();
+  real[][] a=fin.dimension(0,0);
+  a=transpose(a);
+  real[] x=a[xcol];
+  real[] f=a[fcol];
+  x = x - f/k; /* Remove cantilever extension */
+  graphData(x=x, y=f, xscale=xscale, yscale=fscale,
+	    dx=dx, dy=df, p=p, dots=false);
+}
+
+graphSawtooth("fig1.dat", k=k, xscale=xscale, fscale=fscale, p=psoft);
+graphSawtooth("fig2.dat", k=k, xscale=xscale, fscale=fscale,
+	      df=200e-12, p=pmed);
+graphSawtooth("fig3.dat", k=k, xscale=xscale, fscale=fscale,
+	      df=400e-12, p=phard);
+
+//xlimits(xmin, xmax);
+//ylimits(ymin, ymax);
+xaxis(sLabel("Distance (nm)"), BottomTop, LeftTicks);
+yaxis(sLabel("Force (pN)"), LeftRight, RightTicks);
+/*
+set xrange [-5:250]
+set yrange [-10:400]
+set ytics 0,100
+
+set multiplot
+
+set size 1,0.42;
+set origin 0.0,0.0;
+set xlabel 'Extension (nm)'
+plot 'fig1.d' using (($1-$2/0.05)*1e9):($2*1e12)
+
+set size 1,0.29;
+set origin 0.0,0.42;
+set bmargin 0
+unset xlabel
+set xtics format "" 
+set ylabel 'Force (pN)'
+plot 'fig2.d' using (($1-$2/0.05)*1e9):($2*1e12)
+
+set origin 0.0,0.71;
+set bmargin 0
+set xtics format ""
+unset ylabel
+plot 'fig3.d' using (($1-$2/0.05)*1e9):($2*1e12)
+*/
diff --git a/tex/src/sawsim/discussion.tex b/tex/src/sawsim/discussion.tex
index 8420223..232dd21 100644
--- a/tex/src/sawsim/discussion.tex
+++ b/tex/src/sawsim/discussion.tex
@@ -23,7 +23,8 @@ deviation of $25\U{pN}$.
 \begin{figure}
 \vspace{-1in}
 \begin{center}
-\subfloat[][]{\includegraphics{figures/sim-sawtooth/fig}\label{fig:sawsim:sim-sawtooth}%
+\subfloat[][]{\asyfig{figures/sim-sawtooth/sim-sawtooth}%
+  \label{fig:sawsim:sim-sawtooth}%
 }\\
 \subfloat[][]{\includegraphics{figures/sim-hist/fig}\label{fig:sawsim:sim-hist}%
 }
@@ -39,12 +40,14 @@ deviation of $25\U{pN}$.
   connected through the N-C termini\citep{chyan04,carrion-vazquez03}.
   Detachment from the tip or substrate is assumed to occur at a force
   of $400\U{pN}$.  In experiments, detachments have been observed to
-  occur at a variety of forces.  (b) The distribution of the unfolding
-  forces from $400$ simulated force curves ($3200$ data points) such
-  as that shown in (a). The frequency is normalized by the total
-  number of points, \ie, the height of each bin is equal to the number
-  of data points in that bin divided by the total number of data
-  points ($3200$, for this histogram).\label{fig:sawsim:sim-all}}
+  occur at a variety of forces.  For clarity, the green and blue
+  curves are offset by $200$ and $400\U{pN}$ respectively.  (b) The
+  distribution of the unfolding forces from $400$ simulated force
+  curves ($3200$ data points) such as that shown in (a). The frequency
+  is normalized by the total number of points, \ie, the height of each
+  bin is equal to the number of data points in that bin divided by the
+  total number of data points ($3200$, for this
+  histogram).\label{fig:sawsim:sim-all}}
 \end{center}
 \end{figure}