_matplotlib = None
_matplotlib_import_error = e
-try:
- import h5py as _h5py
- import h5config as _h5config
- from h5config.storage.hdf5 import HDF5_Storage as _HDF5_Storage
- from h5config.storage.hdf5 import h5_create_group as _h5_create_group
-except ImportError, e:
- _h5py = None
- _h5py_import_error = e
-
-from curses_check_for_keypress import CheckForKeypress as _CheckForKeypress
-
from . import LOG as _LOG
from . import base as _base
from . import package_config as _package_config
from . import surface as _surface
+from . import wiggle as _wiggle
class AFMPiezo (_base.Piezo):
}
return data
- def wiggle_for_interference(
- self, config, plot=True, filename=None, group='/',
- keypress_test_mode=False):
- """Output a sine wave and measure interference.
-
- With a poorly focused or aligned laser, leaked laser light
- reflecting off the surface may interfere with the light
- reflected off the cantilever, causing distance-dependent
- interference with a period roughly half the laser's
- wavelength. This method wiggles the cantilever near the
- surface and monitors the magnitude of deflection oscillation,
- allowing the operator to adjust the laser alignment in order
- to minimize the interference.
-
- Modern commercial AFMs with computer-aligned lasers must do
- something like this automatically.
- """
- if _package_config['matplotlib']:
- plot = True
- if config['wavelength'] and config['amplitude']:
- log_string = \
- 'use either laser_wavelength or amplitude, but not both'
- _LOG.warn(log_string)
-
- if None in (config['amplitude'], config['offset']):
- output_axis = self.axis_by_name(config['axis'])
- maxdata = output_axis.axis_channel.get_maxdata()
- midpoint = int(maxdata/2)
- if config['offset'] is None:
- offset = midpoint
- _LOG.debug(('generated offset for interference wiggle: {}'
- ).format(config['offset']))
- if config['amplitude'] is None:
- if config['offset'] <= midpoint:
- max_amplitude = int(config['offset'])
- else:
- max_amplitude = int(maxdata-config['offset'])
- offset_meters = _base.convert_bits_to_meters(
- output_axis.config, config['offset'])
- if config['wavelength'] is None:
- config['amplitude'] = 0.5*max_amplitude
- else:
- bit_wavelength = _base.convert_meters_to_bits(
- output_axis.config,
- offset_meters + config['wavelength']
- ) - config['offset']
- config['amplitude'] = 2*bit_wavelength
- _LOG.debug(('generated amplitude for interference wiggle: {}'
- ).format(config['amplitude']))
- if config['amplitude'] > max_amplitude:
- raise ValueError(
- 'no room for a two wavelength wiggle ({} > {})'.format(
- config['amplitude'], max_amplitude))
-
- n = config['samples'] # samples in a single oscillation
- scan_frequency = config['frequency'] * n
- out = (config['amplitude']
- * _numpy.sin(_numpy.arange(2*n)*2*_numpy.pi/n)
- + config['offset'])
- # 2*n for 2 periods, so you can judge precision
- out = out.reshape((len(out), 1)).astype(
- self.channel_dtype(config['axis'], direction='output'))
-
- _LOG.debug('oscillate for interference wiggle ({})'.format(config))
-
- if filename:
- if not _h5py:
- raise _h5py_import_error
- if not output_axis: # from amplitude/offset setup
- output_axis = afm.piezo.axis_by_name(config['axis'])
- input_channel = afm.piezo.input_channel_by_name(config['input'])
- with _h5py.File(filename, 'w') as f:
- cwg = _h5_create_group(f, group)
- storage = _HDF5_Storage()
- for config_,key in [
- (config, 'config/wiggle'),
- (output.axis.config,
- 'config/{}/axis'.format(config['axis'])),
- (input_channel.config,
- 'config/{}/channel'.format(config['input']))]:
- if config_ is None:
- continue
- config_cwg = _h5_create_group(cwg, key)
- storage.save(config=config, group=config_cwg)
- if plot:
- if not _matplotlib:
- raise _matplotlib_import_error
- interactive = _matplotlib.is_interactive()
- _matplotlib.interactive(True)
- figure = _matplotlib_pyplot.figure()
- axes = figure.add_subplot(1, 1, 1)
- axes.hold(False)
- timestamp = _time.strftime('%H%M%S')
- axes.set_title('wiggle for interference %s' % timestamp)
- plot_p = axes.plot(out, out, 'b.-')
- figure.show()
- _matplotlib_pyplot.draw()
- _matplotlib_pyplot.show()
- cycle = 0
- c = _CheckForKeypress(test_mode=keypress_test_mode)
- while c.input() == None:
- # input will need processing for multi-segment AFMs...
- data = self.ramp(
- out, scan_frequency, output_names=[config['axis']],
- input_names=[config['input']])
- _LOG.debug('completed a wiggle round')
- if filename:
- timestamp = ('{0}-{1:02d}-{2:02d}T{3:02d}-{4:02d}-{5:02d}'
- ).format(*_time.localtime())
- with _h5py.File(filename, 'a') as f:
- wiggle_group = _h5_create_group(f, group)
- cwg = _h5_create_group(
- wiggle_group, 'wiggle/{}'.format(cycle))
- cwg['time'] = timestamp
- cwg['raw/{}'.format(config['axis'])] = out
- cwg['raw/{}'.format(config['input'])] = data
- if plot:
- plot_p[0].set_ydata(data[:,0])
- axes.set_ylim([data.min(), data.max()])
- _matplotlib_pyplot.draw()
- cycle += 1
- if plot:
- _matplotlib.interactive(interactive)
- self.last_output[config['axis']] = out[-1,0]
- _LOG.debug('interference wiggle complete')
-
+ wiggle_for_interference = _wiggle.wiggle_for_interference
get_surface_position = _surface.get_surface_position
--- /dev/null
+# Copyright (C) 2011-2012 W. Trevor King <wking@drexel.edu>
+#
+# This file is part of pypiezo.
+#
+# pypiezo 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.
+#
+# pypiezo 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
+# pypiezo. If not, see <http://www.gnu.org/licenses/>.
+
+"""Utilities for wiggling a the piezo near the surface.
+
+This helps you detect interference between the laser bouncing off the
+tip and the surface. The wiggling continues until you stop it, which
+gives you feedback while you reposition the laser to minimize the
+interference. One day we'll all have fancy AFMs with software control
+over the laser alignment, but until then, we've got this module
+helping you with your thumbscrews.
+"""
+
+import time as _time
+
+try:
+ import h5py as _h5py
+ import h5config as _h5config
+ from h5config.storage.hdf5 import HDF5_Storage as _HDF5_Storage
+ from h5config.storage.hdf5 import h5_create_group as _h5_create_group
+except ImportError, e:
+ _h5py = None
+ _h5py_import_error = e
+
+try:
+ import matplotlib as _matplotlib
+ import matplotlib.pyplot as _matplotlib_pyplot
+except (ImportError, RuntimeError), e:
+ _matplotlib = None
+ _matplotlib_import_error = e
+
+from curses_check_for_keypress import CheckForKeypress as _CheckForKeypress
+
+from . import LOG as _LOG
+
+
+def _setup_config(peizo, config):
+ if config['wavelength'] and config['amplitude']:
+ log_string = \
+ 'use either laser_wavelength or amplitude, but not both'
+ _LOG.warn(log_string)
+
+ if None in (config['amplitude'], config['offset']):
+ output_axis = piezo.axis_by_name(config['axis'])
+ maxdata = output_axis.axis_channel.get_maxdata()
+ midpoint = int(maxdata/2)
+ if config['offset'] is None:
+ offset = midpoint
+ _LOG.debug(('generated offset for interference wiggle: {}'
+ ).format(config['offset']))
+ if config['amplitude'] is None:
+ if config['offset'] <= midpoint:
+ max_amplitude = int(config['offset'])
+ else:
+ max_amplitude = int(maxdata-config['offset'])
+ offset_meters = _base.convert_bits_to_meters(
+ output_axis.config, config['offset'])
+ if config['wavelength'] is None:
+ config['amplitude'] = 0.5*max_amplitude
+ else:
+ bit_wavelength = _base.convert_meters_to_bits(
+ output_axis.config,
+ offset_meters + config['wavelength']
+ ) - config['offset']
+ config['amplitude'] = 2*bit_wavelength
+ _LOG.debug(('generated amplitude for interference wiggle: {}'
+ ).format(config['amplitude']))
+ if config['amplitude'] > max_amplitude:
+ raise ValueError(
+ 'no room for a two wavelength wiggle ({} > {})'.format(
+ config['amplitude'], max_amplitude))
+
+def _construct_output(piezo, config):
+ n = config['samples'] # samples in a single oscillation
+ out = (config['amplitude']
+ * _numpy.sin(_numpy.arange(2*n)*2*_numpy.pi/n)
+ + config['offset'])
+ # 2*n for 2 periods, so you can judge precision
+ out = out.reshape((len(out), 1)).astype(
+ piezo.channel_dtype(config['axis'], direction='output'))
+ return out
+
+def _setup_datafile(filename, group, piezo, config, output):
+ if not _h5py:
+ raise _h5py_import_error
+ output_axis = afm.piezo.axis_by_name(config['axis'])
+ input_channel = afm.piezo.input_channel_by_name(config['input'])
+ with _h5py.File(filename, 'w') as f:
+ cwg = _h5_create_group(f, group)
+ storage = _HDF5_Storage()
+ for config_,key in [
+ (config, 'config/wiggle'),
+ (output.axis.config,
+ 'config/{}/axis'.format(config['axis'])),
+ (input_channel.config,
+ 'config/{}/channel'.format(config['input']))]:
+ if config_ is None:
+ continue
+ config_cwg = _h5_create_group(cwg, key)
+ storage.save(config=config, group=config_cwg)
+ cwg['wiggle/raw/{}'.format(config['axis'])] = output
+
+def _update_datafile(filename, group, config, cycle, data):
+ timestamp = ('{0}-{1:02d}-{2:02d}T{3:02d}-{4:02d}-{5:02d}'
+ ).format(*_time.localtime())
+ with _h5py.File(filename, 'a') as f:
+ wiggle_group = _h5_create_group(f, group)
+ cwg = _h5_create_group(
+ wiggle_group, 'wiggle/{}'.format(cycle))
+ cwg['time'] = timestamp
+ cwg['raw/{}'.format(config['input'])] = data
+
+def _setup_plot(piezo, config):
+ if not _matplotlib:
+ raise _matplotlib_import_error
+ _matplotlib.interactive(True)
+ figure = _matplotlib_pyplot.figure()
+ axes = figure.add_subplot(1, 1, 1)
+ axes.hold(False)
+ timestamp = _time.strftime('%H%M%S')
+ axes.set_title('wiggle for interference %s' % timestamp)
+ plot = axes.plot(out, out, 'b.-')
+ figure.show()
+ _matplotlib_pyplot.draw()
+ _matplotlib_pyplot.show()
+ return plot
+
+def _update_plot(plot, cycle, data):
+ plot[0].set_ydata(data[:,0])
+ axes.set_ylim([data.min(), data.max()])
+ _matplotlib_pyplot.draw()
+
+def _run_wiggles(piezo, config, plot, output, filename=None, group='/',
+ keypress_test_mode=False):
+ scan_frequency = config['frequency'] * n
+ cycle = 0
+ c = _CheckForKeypress(test_mode=keypress_test_mode)
+ while c.input() == None:
+ # input will need processing for multi-segment AFMs...
+ data = piezo.ramp(
+ output, scan_frequency, output_names=[config['axis']],
+ input_names=[config['input']])
+ _LOG.debug('completed a wiggle round')
+ if filename:
+ _update_datafile(
+ filename=filename, group=group, config=config,
+ cycle=cycle, data=data)
+ if plot:
+ _update_plot(plot=plot, cycle=cycle, data=data)
+ cycle += 1
+
+def wiggle_for_interference(
+ piezo, config, plot=True, filename=None, group='/',
+ keypress_test_mode=False):
+ """Output a sine wave and measure interference.
+
+ With a poorly focused or aligned laser, leaked laser light
+ reflecting off the surface may interfere with the light
+ reflected off the cantilever, causing distance-dependent
+ interference with a period roughly half the laser's
+ wavelength. This method wiggles the cantilever near the
+ surface and monitors the magnitude of deflection oscillation,
+ allowing the operator to adjust the laser alignment in order
+ to minimize the interference.
+
+ Modern commercial AFMs with computer-aligned lasers must do
+ something like this automatically.
+ """
+ if _package_config['matplotlib']:
+ plot = True
+ _setup_config(piezo=piezo, config=config)
+ _LOG.debug('oscillate for interference wiggle ({})'.format(config))
+ output = _construct_output(piezo=piezo, config=config)
+
+ if filename:
+ _setup_datafile(
+ filename=filename, group=group, piezo=piezo, config=config,
+ output=output)
+ if plot:
+ interactive = _matplotlib.is_interactive()
+ plot_ = _setup_plot(piezo=piezo, config=config, output=output)
+ _run_wiggles(piezo=piezo, config=config, plot=plot_)
+ if plot:
+ _matplotlib.interactive(interactive)
+ piezo.last_output[config['axis']] = out[-1,0]
+ _LOG.debug('interference wiggle complete')
projects / pypiezo.git / commitdiff