Add fit lines to cantilever-sim/v-dep

Also tab-separate (vs space separate) cantilever-sim/v-dep.d/*
with:

  for f in v_dep_*; do
    awk 'BEGIN{OFS="\t"}{print $1, $2}' "$f" > tmp && mv -f tmp "$f";
  done

diff --git a/tex/src/figures/cantilever-sim/SConscript b/tex/src/figures/cantilever-sim/SConscript
index 19e66cb1bfddad2fded21c66c1a2fa30e923aad7..545c9f4c4a09bfd5b56dc4239337d725b58c56de 100644 (file)
--- a/tex/src/figures/cantilever-sim/SConscript
+++ b/tex/src/figures/cantilever-sim/SConscript
@@ -1,14 +1,45 @@
-from site_cons.site_init import link_wtk_graph
+import os.path
+
+from site_cons.site_init import link_wtk_graph, link_pyfit
+
 
 FIGURES = ['v-dep', 'loading-rate', 'i-dep']
 
 # Get the passed in environment.
 Import('env')
 
+v_dep_data_dir = env.Dir('v-dep.d')
+v_dep_data_files = [
+    f for f in env.Glob(os.path.join(str(v_dep_data_dir), '*'))
+    if 'fit' not in str(f)]
+
+pyfit = link_pyfit(env)
+
+v_dep_fit_files = []
+for f in v_dep_data_files:
+    fit = env.Command(
+        str(f)+'.fit',
+        [f, pyfit],
+        "python %s -m math:log -f 'A*log(x,10)+B' -v $SOURCE > $TARGET"
+        % pyfit[0].get_abspath())
+    fit_dat = env.Command(
+        str(fit[0])+'.dat',
+        fit,
+        "sed -n 's/^[A-Z]: //p' $SOURCE > $TARGET")
+    v_dep_fit_files.append(fit_dat)
+
+v_dep_data = v_dep_data_files + v_dep_fit_files
+
 wtk_graph = link_wtk_graph(env)
 
 for fig in FIGURES:
-    env.Asymptote(['%s.asy' % fig, wtk_graph])
+    asyfile = '%s.asy' % fig  # static .asy file
+    pyfig = fig.replace('-', '_')
+    data = '%s_data' % (pyfig)
+    asydata = []
+    if data in globals():     # generated data dependencies
+        asydata = globals()[data]
+    env.Asymptote([asyfile, wtk_graph] + asydata)
 
 # Pass back the modified environment.
 Return('env')

diff --git a/tex/src/figures/cantilever-sim/v-dep.asy b/tex/src/figures/cantilever-sim/v-dep.asy
index 056e477a47b9604dd21cec500eb601f302c91d49..5b34d4e9f3ef116bf55ea6182befba3a872d6a08 100644 (file)
--- a/tex/src/figures/cantilever-sim/v-dep.asy
+++ b/tex/src/figures/cantilever-sim/v-dep.asy
@@ -1,21 +1,48 @@
 import wtk_graph;
 
 size(15cm,10cm,IgnoreAspect);
+
 scale(Log, Linear);
-real xscale=1e6;
-real yscale=1e12;
-graphFile("v-dep.d/v_dep_127_8", xscale, yscale, p=phard, mpath=m8, t=units("127","pN/nm")+", 8 domains");
-graphFile("v-dep.d/v_dep_27_8", xscale, yscale, p=pmed, mpath=m8, t=units("27","pN/nm")+", 8 domains");
-graphFile("v-dep.d/v_dep_127_30", xscale, yscale, p=phard, mpath=m30, t=units("127","pN/nm")+", 30 domains");
-graphFile("v-dep.d/v_dep_27_30", xscale, yscale, p=pmed, mpath=m30, t=units("27","pN/nm")+", 30 domains");
-graphFile("v-dep.d/v_dep_0.1_1", xscale, yscale, p=psoft, mpath=m1, t=units("0.1","pN/nm")+", 1 domain");
-graphFile("v-dep.d/v_dep_0.1_30", xscale, yscale, p=psoft, mpath=m30, t=units("0.1","pN/nm")+", 30 domains");
-
-//xlimits(1,10);
-ylimits(150,340);
-
-label(sLabel("Pulling speed dependence"), point(N),N);
-xaxis(sLabel("Pulling speed ($\mu$m/s)"),BottomTop,LeftTicks);
-yaxis(sLabel("Unfolding force (pN)"),LeftRight,RightTicks);
-
-add(legend(),point(E),20E,UnFill);
+real vscale = 1e9;
+real fscale = 1e12;
+
+real vmin = 0.2e-6;
+real vmax = 5e-6;
+
+/* f(x) = A + log10(x) + B */
+real fn_logxliny(real x, real[] params) {
+  return params[0] * log10(x) + params[1];
+}
+
+graphFile("v-dep.d/v_dep_127_8", vscale, fscale, p=phard, mpath=m8,
+         t=units("127","pN/nm")+", 8 domains", dots=true);
+graphFile("v-dep.d/v_dep_27_8", vscale, fscale, p=pmed, mpath=m8,
+         t=units("27","pN/nm")+", 8 domains", dots=true);
+graphFile("v-dep.d/v_dep_127_30", vscale, fscale, p=phard, mpath=m30,
+         t=units("127","pN/nm")+", 30 domains", dots=true);
+graphFile("v-dep.d/v_dep_27_30", vscale, fscale, p=pmed, mpath=m30,
+         t=units("27","pN/nm")+", 30 domains", dots=true);
+graphFile("v-dep.d/v_dep_0.1_1", vscale, fscale, p=psoft, mpath=m1,
+         t=units("0.1","pN/nm")+", 1 domain", dots=true);
+graphFile("v-dep.d/v_dep_0.1_30", vscale, fscale, p=psoft, mpath=m30,
+         t=units("0.1","pN/nm")+", 30 domains", dots=true);
+fitFile("v-dep.d/v_dep_127_8.fit.dat", f=fn_logxliny,
+       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=phard);
+fitFile("v-dep.d/v_dep_27_8.fit.dat", f=fn_logxliny,
+       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=pmed);
+fitFile("v-dep.d/v_dep_127_30.fit.dat", f=fn_logxliny,
+       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=phard);
+fitFile("v-dep.d/v_dep_27_30.fit.dat", f=fn_logxliny,
+       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=pmed);
+fitFile("v-dep.d/v_dep_0.1_1.fit.dat", f=fn_logxliny,
+       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=psoft);
+fitFile("v-dep.d/v_dep_0.1_30.fit.dat", f=fn_logxliny,
+       xmin=1e-9, xmax=1e-5, xscale=vscale, yscale=fscale, p=psoft);
+
+ylimits(150, 340, crop=true);
+
+label(sLabel("Pulling speed dependence"), point(N), N);
+xaxis(sLabel("Pulling speed (nm/s)"), BottomTop, LeftTicks);
+yaxis(sLabel("Unfolding force (pN)"), LeftRight, RightTicks);
+
+add(legend(), point(E), 20E, UnFill);

diff --git a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_0.1_1 b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_0.1_1
index 12cb97b055b371471dd97c1ad2b9b4db90bb968e..ef544ba74d7fe1e6f3279659d09e4388c8199029 100644 (file)
--- a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_0.1_1
+++ b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_0.1_1
@@ -1,5 +1,5 @@
-.2e-6 1.73195e-10
-.5e-6 1.90315e-10
-1e-6 2.03703e-10
-2e-6 2.15506e-10
-5e-6 2.3314e-10
+.2e-6  1.73195e-10
+.5e-6  1.90315e-10
+1e-6   2.03703e-10
+2e-6   2.15506e-10
+5e-6   2.3314e-10

diff --git a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_0.1_30 b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_0.1_30
index 30557358235536aa38ee631e5582cbd7ab1ea3bb..b3a3ddbbf5fb69c543016e99b3f578961cbda660 100644 (file)
--- a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_0.1_30
+++ b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_0.1_30
@@ -1,5 +1,5 @@
-.2e-6 1.62618e-10
-.5e-6 1.79418e-10
-1e-6 1.922e-10
-2e-6 2.05009e-10
-5e-6 2.21851e-10
+.2e-6  1.62618e-10
+.5e-6  1.79418e-10
+1e-6   1.922e-10
+2e-6   2.05009e-10
+5e-6   2.21851e-10

diff --git a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_127_30 b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_127_30
index 3474b921ea77351712f803d20a0971488739a16a..91d0fa599aeec4c0308e24927afef3437430b6c9 100644 (file)
--- a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_127_30
+++ b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_127_30
@@ -1,5 +1,5 @@
-.2e-6 2.155e-10
-.5e-6 2.35401e-10
-1e-6 2.5027e-10
-2e-6 2.64939e-10
-5e-6 2.8421e-10
+.2e-6  2.155e-10
+.5e-6  2.35401e-10
+1e-6   2.5027e-10
+2e-6   2.64939e-10
+5e-6   2.8421e-10

diff --git a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_127_8 b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_127_8
index 7744c31fd0e14dddc0a2196ea530bfb9171fe54a..01c774c6b37e2e2b88218f81eca83dac02c96c92 100644 (file)
--- a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_127_8
+++ b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_127_8
@@ -1,5 +1,5 @@
-.2e-6 2.68946e-10
-.5e-6 2.88158e-10
-1e-6 3.01288e-10
-2e-6 3.14864e-10
-5e-6 3.33625e-10
+.2e-6  2.68946e-10
+.5e-6  2.88158e-10
+1e-6   3.01288e-10
+2e-6   3.14864e-10
+5e-6   3.33625e-10

diff --git a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_27_30 b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_27_30
index e112b51379d1590cb2f8f3c86bb13c25edcc758b..a46215b4d0e48a2005b3eae6d95ea010e48cc8a2 100644 (file)
--- a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_27_30
+++ b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_27_30
@@ -1,5 +1,5 @@
-.2e-6 2.07085e-10
-.5e-6 2.25884e-10
-1e-6 2.40152e-10
-2e-6 2.54356e-10
-5e-6 2.72657e-10
+.2e-6  2.07085e-10
+.5e-6  2.25884e-10
+1e-6   2.40152e-10
+2e-6   2.54356e-10
+5e-6   2.72657e-10

diff --git a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_27_8 b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_27_8
index bb767a47484c7213106682e9bccfa530238b2859..e9f1200fe84324e69e36ce37d383cf5fba701ca7 100644 (file)
--- a/tex/src/figures/cantilever-sim/v-dep.d/v_dep_27_8
+++ b/tex/src/figures/cantilever-sim/v-dep.d/v_dep_27_8
@@ -1,5 +1,5 @@
-.2e-6 2.46117e-10
-.5e-6 2.63033e-10
-1e-6 2.77235e-10
-2e-6 2.90754e-10
-5e-6 3.07902e-10
+.2e-6  2.46117e-10
+.5e-6  2.63033e-10
+1e-6   2.77235e-10
+2e-6   2.90754e-10
+5e-6   3.07902e-10