Run update-copyright.py

[calibcant.git] / bin / calibcant-calibrate.py

diff --git a/bin/calibcant-calibrate.py b/bin/calibcant-calibrate.py
index 3d20ab3dd0127ce1b145fcd227d137a3982927b9..afcbba46642d1dc454ad77f570d7a9dd7b8fb9fb 100755 (executable)
--- a/bin/calibcant-calibrate.py
+++ b/bin/calibcant-calibrate.py
@@ -1,21 +1,52 @@
 #!/usr/bin/env python
 # calibcant - tools for thermally calibrating AFM cantilevers
 #
-# Copyright
+# Copyright (C) 2012-2013 W. Trevor King <wking@tremily.us>
+#
+# This file is part of calibcant.
+#
+# calibcant 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.
+#
+# calibcant 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
+# calibcant.  If not, see <http://www.gnu.org/licenses/>.
 
 """Run a cantilever calibration using the default AFM
 (``pyafm.storage.load_afm()``).
 """
 
-import os
+import argparse as _argparse
 import time as _time
 
-from calibcant.calibrate import Calibrator as _Calibrator
+import h5py as _h5py
 from pyafm.storage import load_afm as _load_afm
+
+from calibcant.calibrate import Calibrator as _Calibrator
 import calibcant.config as _config
 
 
+_module_doc = __doc__
+
 def main(args):
+    parser = _argparse.ArgumentParser(description=_module_doc)
+    parser.add_argument(
+        '--num-bumps', type=int,
+        help='Number of surface bumps')
+    parser.add_argument(
+        '--num-temperatures', type=int,
+        help='Number of temperature measurements')
+    parser.add_argument(
+        '--num-vibrations', type=int,
+        help='Number of thermal vibration measurements')
+
+    args = parser.parse_args(args)
+
     timestamp = '{0}-{1:02d}-{2:02d}T{3:02d}-{4:02d}-{5:02d}'.format(
         *_time.localtime())
     filename = '{}-calibcant-data.h5'.format(timestamp)
@@ -25,6 +56,20 @@ def main(args):
         {'model':_config.Linear, 'initial-position':-150e-9})
     config['temperature'] = _config.TemperatureConfig()
     config['vibration'] = _config.VibrationConfig()
+    if args.num_bumps is None:
+        args.num_bumps = config['num-bumps']
+    else:
+        config['num-bumps'] = args.num_bumps
+    if args.num_temperatures is None:
+        args.num_temperatures = config['num-temperatures']
+    else:
+        config['num-temperatures'] = args.num_temperatures
+    if args.num_vibrations is None:
+        args.num_vibrations = config['num-vibrations']
+    else:
+        config['num-vibrations'] = args.num_vibrations
+    insufficient_calibration_data = 0 in [
+        args.num_bumps, args.num_temperatures, args.num_vibrations]
     devices = []
     try:
         afm = _load_afm()
@@ -33,8 +78,15 @@ def main(args):
         calibrator.setup_config()
         deflection = afm.piezo.read_deflection()
         try:
-            afm.stepper_approach(target_deflection=deflection + 1e3)
-            k,k_s,data = calibrator.calibrate(filename=filename)
+            position,deflection = afm.stepper_approach(
+                target_deflection=deflection + 1e3, record_data=True)
+            with _h5py.File(filename) as f:
+                f['/approach/position'] = position
+                f['/approach/deflection'] = deflection
+            if insufficient_calibration_data:
+                data = calibrator.acquire(filename=filename)
+            else:
+                k,k_s,data = calibrator.calibrate(filename=filename)
         except:
             afm.move_away_from_surface()
             afm.piezo.zero()
@@ -42,7 +94,16 @@ def main(args):
     finally:
         for device in devices:
             device.close()
-    print 'k: {:g} +/- {:g}'.format(k, k_s)
+    if insufficient_calibration_data:
+        for count,field,label in [
+            (args.num_bumps, 'bump', 'photodiode sensitivity (V/m)'),
+            (args.num_temperatures, 'temperature', 'temperature (K)'),
+            (args.num_vibrations, 'vibration', 'variance (V**2)')]:
+            if count:
+                d = data[field]
+                print('{}: {:g} +/- {:g}'.format(label, d.mean(), d.std()))
+    else:
+        print('k: {:g} +/- {:g}'.format(k, k_s))
     return 0
 
 if __name__ == '__main__':