# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2007,2008, William Trevor King
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# 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 file is part of calibcant.
#
-# 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.
+# calibcant is free software: you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-# 02111-1307, USA.
+# 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 Lesser General Public License for more details.
#
-# The author may be contacted at <wking@drexel.edu> on the Internet, or
-# write to Trevor King, Drexel University, Physics Dept., 3141 Chestnut St.,
-# Philadelphia PA 19104, USA.
+# You should have received a copy of the GNU Lesser General Public
+# License along with calibcant. If not, see
+# <http://www.gnu.org/licenses/>.
"""Define some variables to configure the package for a particular lab
and workflow."""
-import z_piezo
-
-DEFAULT_TEMP = 22 # assume 22 deg C
-LOG_DATA = True # quietly grab all real-world data and log to LOG_DIR
-LOG_DIR = '$DEFAULT$/calibrate_cantilever'
-GNUFIT_DATA_BASE='./calibrate_cantilever_fitdata'
-TEXT_VERBOSE = True # for debugging
-GNUPLOT_VERBOSE = True # turn on fit check plotting
-PYLAB_VERBOSE = True # turn on plotting
-PYLAB_INTERACTIVE = True # select between draw() and show() for flushing plots
-BASE_FIGNUM = 20 # to avoid writing to already existing figures
-
-
-# HACK
-# make sure you make a system note (add_system_note) if you change
-# these in case you don't have access to a z_piezo for conversion
-# functions
-
-# zpGain zpiezo applied voltage per output Volt
-zpGain = z_piezo.DEFAULT_GAIN
-# zpSensitivity nm zpiezo response per applied Volt
-zpSensitivity = z_piezo.DEFAULT_SENSITIVITY
-# Vzp_out2V function that converts output DAC bits to Volts
-Vzp_out2V = z_piezo.DEFAULT_VZP_OUT_2_VOLTS
-# Vphoto_in2V function that converts input ADC bits to Volts
-Vphoto_in2V = z_piezo.DEFAULT_VPHOTO_IN_2_VOLTS
-# zeroVphoto_bits ADC bit output for a 0V input
-zeroVphoto_bits = z_piezo.DEFAULT_ZERO_PHOTODIODE_BITS
+import sys as _sys
+
+from FFT_tools import window_hann as _window_hann
+import h5config.config as _config
+import h5config.tools as _h5config_tools
+
+
+class PackageConfig (_h5config_tools.PackageConfig):
+ "Configure `calibcant` module operation"
+ settings = _h5config_tools.PackageConfig.settings + [
+ _config.BooleanSetting(
+ name='matplotlib',
+ help='Plot piezo motion using `matplotlib`.',
+ default=False),
+ _config.FloatSetting(
+ name='temperature',
+ help=('Default temperature for thermal calibration in degrees '
+ 'Celsius.'),
+ default=22),
+ ]
+
+class _TemperatureUnit (object):
+ pass
+class Celsius (_TemperatureUnit):
+ pass
+class Kelvin (_TemperatureUnit):
+ pass
+
+class TemperatureConfig (_config.Config):
+ "Configure `calibcant` temperature operation"
+ settings = [
+ _config.ChoiceSetting(
+ name='units',
+ help='Units of raw temperature measurements.',
+ default=Celsius,
+ choices=[
+ ('Celsius', Celsius),
+ ('Kelvin', Kelvin),
+ ]),
+ _config.BooleanSetting(
+ name='default',
+ help=('The temperature values are defaults (vs. real '
+ 'measurements).'),
+ default=True),
+ ]
+
+class _BumpModel (object):
+ pass
+class Linear (_BumpModel):
+ pass
+class Quadratic (_BumpModel):
+ pass
+
+class BumpConfig (_config.Config):
+ "Configure `calibcant` bump operation"
+ settings = [
+ _config.FloatSetting(
+ name='initial-position',
+ help=('Position relative to surface for start of bump in meters. '
+ 'Should be less than zero to ensure non-contact region '
+ 'before you hit the surface.'),
+ default=-50e-9),
+ _config.FloatSetting(
+ name='setpoint',
+ help=('Maximum deflection in volts in case of stepper positioning '
+ 'to achieve the initial position.'),
+ default=2.0),
+ _config.IntegerSetting(
+ name='far-steps',
+ help=('Number of stepper steps to move "far" away from the '
+ 'surface. For possible stepper adjustments while initially '
+ 'locating the surface.'),
+ default=200),
+ _config.FloatSetting(
+ name='push-depth',
+ help='Distance to approach in meters.',
+ default=200e-9),
+ _config.FloatSetting(
+ name='push-speed',
+ help='Approach/retract speed in meters/second.',
+ default=1e-6),
+ _config.FloatSetting(
+ name='samples',
+ help='Number of samples during approach and during retreat.',
+ default=1024),
+ _config.ChoiceSetting(
+ name='model',
+ help='Bump deflection model.',
+ default=Quadratic,
+ choices=[
+ ('linear', Linear),
+ ('quadratic', Quadratic),
+ ]),
+ ]
+
+class _VibrationModel (object):
+ pass
+class Variance (_VibrationModel):
+ pass
+class BreitWigner (_VibrationModel):
+ pass
+class OffsetBreitWigner (_VibrationModel):
+ pass
+
+class VibrationConfig (_config.Config):
+ "Configure `calibcant` vibration operation"
+ settings = [
+ _config.FloatSetting(
+ name='frequency',
+ help='Sampling frequency in Hz.',
+ default=50e3),
+ _config.FloatSetting(
+ name='sample-time',
+ help=('Aquisition time in seconds. This is rounded up as required '
+ 'so the number of samples will be an integer power of two.'),
+ default=1),
+ _config.ChoiceSetting(
+ name='model',
+ help='Vibration model.',
+ default=BreitWigner,
+ choices=[
+ ('variance', Variance),
+ ('Breit-Wigner', BreitWigner),
+ ('offset Breit-Wigner', OffsetBreitWigner),
+ ]),
+ _config.IntegerSetting(
+ name='chunk-size',
+ help='FFT chunk size (for PSD fits).',
+ default=2048),
+ _config.BooleanSetting(
+ name='overlap',
+ help='Overlap FFT chunks (for PSD fits).'),
+ _config.ChoiceSetting(
+ name='window',
+ help='FFT chunk window (for PSD fits).',
+ default=_window_hann,
+ choices=[
+ ('Hann', _window_hann),
+ ]),
+ _config.FloatSetting(
+ name='minimum-fit-frequency',
+ help='Lower bound of Lorentzian fitting region.',
+ default=500.),
+ _config.FloatSetting(
+ name='maximum-fit-frequency',
+ help='Upper bound of Lorentzian fitting region.',
+ default=25e3),
+ ]
+
+
+class CalibrationConfig (_config.Config):
+ "Configure a full `calibcant` calibration run"
+ settings = [
+ _config.IntegerSetting(
+ name='num-bumps',
+ help='Number of surface bumps.',
+ default=10),
+ _config.IntegerSetting(
+ name='num-temperatures',
+ help='Number of temperature measurements.',
+ default=10),
+ _config.IntegerSetting(
+ name='num-vibrations',
+ help='Number of thermal vibration measurements.',
+ default=20),
+ _config.FloatSetting(
+ name='temperature-sleep',
+ help=('Time between temperature measurements (in seconds) to get '
+ 'independent measurements when reading from slow sensors.'),
+ default=1),
+ _config.FloatSetting(
+ name='vibration-spacing',
+ help=('Approximate distance from the surface in meters for the '
+ 'vibration measurements. This should be large enough that '
+ 'surface effects are negligable.'),
+ default=50e-6),
+ ]
projects / calibcant.git / blobdiff