compare-unfold.py: add bit-level comparison between my and Marisa's programs.

Marisa was using Prof. Yang's LabVIEW unfolder, while I use my
pyafm-based unfolder.  The `compare-unfold.py` script allows bit-level
comparison between the two approaches, reading the native data saved
by each approach.  Here's an example using local data on my system:

  $ ./compare-unfold.py \
    ~/rsrch/analysis/labview-comparison/gyang/2012-10-01-unfold/ \
    ~/rsrch/analysis/labview-comparison/wking/unfold/

diff --git a/posts/Comparing_velocity_clamp_experiments/compare-unfold.py b/posts/Comparing_velocity_clamp_experiments/compare-unfold.py
new file mode 100755 (executable)
index 0000000..9ffd53a
--- /dev/null
+++ b/posts/Comparing_velocity_clamp_experiments/compare-unfold.py
@@ -0,0 +1,92 @@
+#!/usr/bin/env python2
+#
+# Copyright (C) 2012  W. Trevor King <wking@tremily.us>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""Compare unfolding pulls between Prof. Yang's software and my own.
+"""
+
+import os as _os
+
+import crunch as _crunch
+import gyang_curve as _gyang_curve
+from matplotlib import pylab as _pylab
+from pypiezo import surface as _pypiezo_surface
+
+
+def load_yang_curves(basedir):
+    for series in sorted(_os.listdir(basedir)):
+        if series.endswith('.ibw'):
+            path = _os.path.join(basedir, series)
+            for curve in _gyang_curve.load_all_traces(path):
+                yield curve
+
+def load_king_curves(basedir):
+    for path in sorted(_os.listdir(basedir)):
+        if path.endswith('.h5'):
+            curve = _os.path.join(basedir, path)
+            yield _crunch.load_pull(filename=curve)
+
+
+def plot_comparison(yang_dir, king_dir):
+    yang = load_yang_curves(yang_dir)
+    king = load_king_curves(king_dir)
+    figure = _pylab.figure()
+    axes = figure.add_subplot(1, 1, 1)
+    axes.set_title('velocity clamp unfolding')
+    axes.set_xlabel('z piezo (bits)')
+    axes.set_ylabel('deflection (bits)')
+    axes.hold(True)
+    xyc = []
+    for curve in yang:
+        xyc.append(
+            (curve.piezo_expanded + 2**15, curve.deflection + 2**15, 'b'))
+    for curve in king:
+        xyc.append((curve['alpha_v'], curve['alpha_f'], 'r'))
+    for x, y, c in xyc:
+        ddict = {
+            'approach': {  # for _analyze_surface_position_data
+                'z': x[::-1],
+                'deflection': y[::-1],
+                }
+            }
+        (non_contact_offset,non_contact_slope,kink,alpha_dp
+         ) = _pypiezo_surface.analyze_surface_position_data(
+            ddict, return_all_parameters=True)
+        y0 = non_contact_offset + non_contact_slope*(kink-x.min())
+        x0 = x.max() - (y.max()-y0)/alpha_dp
+        axes.plot(
+            x - x0, y - y0,
+            linestyle='none', marker=',', color=c, markeredgecolor=c)
+    return figure
+
+
+if __name__ == '__main__':
+    import argparse
+
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument(
+        'yang', metavar='DIR',
+        help="directory for data taken with Prof. Yang's LabVIEW program")
+    parser.add_argument(
+        'king', metavar='DIR',
+        help='directory for data taken with my pyafm-based unfolder')
+
+    args = parser.parse_args()
+
+    plot_comparison(
+        yang_dir=_os.path.expanduser(args.yang),
+        king_dir=_os.path.expanduser(args.king))
+    _pylab.show()