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+ GNU GENERAL PUBLIC LICENSE
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+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ 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/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
TEXT_VERBOSE = False
-PYLAB_INTERACTIVE_VERBOSE = False
+PYLAB_INTERACTIVE = True
+PYLAB_VERBOSE = True
BASE_FIG_NUM = 60
LOG_DATA = True
LOG_DIR = '$DEFAULT$/z_piezo_utils'
from numpy import array, arange, ones, zeros, linspace, uint16, float, sin, cos, pi
from scipy.stats import linregress
import curses_check_for_keypress
-import fit
+import scipy.optimize
import data_logger
import time
-if PYLAB_INTERACTIVE_VERBOSE :
- from pylab import figure, plot, title, legend, hold, subplot
-
+_flush_plot = None
+_final_flush_plot = None
+_pylab = None
+def _dummy_fn(): pass
+
+def _import_pylab():
+ """Import pylab plotting functions for when we need to plot. This
+ function can be called multiple times, and ensures that the pylab
+ setup is only imported once. It defines the functions
+ _flush_plot() to be called after incremental changes,
+ _final_flush_plot(), to be called at the end of any graphical processing, and
+ _pylab, a reference to the pylab module."""
+ global _pylab
+ global _flush_plot
+ global _final_flush_plot
+ if _pylab == None :
+ import pylab as _pylab
+ if _flush_plot == None :
+ if PYLAB_INTERACTIVE :
+ _flush_plot = _pylab.draw
+ else :
+ _flush_plot = _pylab.show
+ if _final_flush_plot == None :
+ if PYLAB_INTERACTIVE :
+ _final_flush_plot = _pylab.draw
+ else :
+ _final_flush_plot = _dummy_fn
+
class error (Exception) :
pass
class poorFit (error) :
pass
def moveToPosOrDef(zpiezo, pos, defl, step, return_data=False) :
- if return_data or LOG_DATA or PYLAB_INTERACTIVE_VERBOSE :
+ if return_data or LOG_DATA or PYLAB_VERBOSE :
aquire_data = True
else :
aquire_data = False
if zpiezo.setExternalZPiezo != None :
zpiezo.setExternalZPiezo(zpiezo.pos_out2nm(zpiezo.curPos()))
- if PYLAB_INTERACTIVE_VERBOSE :
- figure(BASE_FIG_NUM)
+ if PYLAB_VERBOSE :
+ _import_pylab()
+ _pylab.figure(BASE_FIG_NUM)
timestamp = time.strftime('%H%M%S')
- plot(pos_array, def_array, '.', label=timestamp)
- title('step approach')
- legend(loc='best')
+ _pylab.plot(pos_array, def_array, '.', label=timestamp)
+ _pylab.title('step approach')
+ _pylab.legend(loc='best')
+ _flush_plot()
if LOG_DATA :
log = data_logger.data_log(LOG_DIR, noclobber_logsubdir=False,
log_name="moveToPosOrDef")
def wiggleForInterferenceMin(zpiezo, wig_amp=20000, wig_freq=100,
plotVerbose=True) :
"Output sin to measure interference"
- if PYLAB_INTERACTIVE_VERBOSE or plotVerbose:
- from pylab import figure, plot, title, hold, ion, ioff, draw, axes
+ if PYLAB_VERBOSE or plotVerbose:
+ _import_pylab()
npoints = 1000
scanfreq = wig_freq*npoints
out = zeros((npoints,), dtype=uint16)
for i in range(npoints) :
out[i] = int(sin(4*pi*i/npoints)*wig_amp+32000)
# 4 for 2 periods
- if PYLAB_INTERACTIVE_VERBOSE or plotVerbose:
- figure(BASE_FIG_NUM+1)
- a = axes()
- title('wiggle for interference')
- hold(False)
- p = plot(out, out, 'b.-')
+ if PYLAB_VERBOSE or plotVerbose:
+ _pylab.figure(BASE_FIG_NUM+1)
+ a = _pylab.axes()
+ _pylab.title('wiggle for interference')
+ _pylab.hold(False)
+ p = _pylab.plot(out, out, 'b.-')
if LOG_DATA :
log = data_logger.data_log(LOG_DIR, noclobber_logsubdir=False,
log_name="wiggle")
data = zpiezo.ramp(out, scanfreq)
dmin = data["Deflection input"].min()
dmax = data["Deflection input"].max()
- if PYLAB_INTERACTIVE_VERBOSE or plotVerbose:
+ if PYLAB_VERBOSE or plotVerbose:
p[0].set_ydata(data["Deflection input"])
a.set_ylim([dmin,dmax])
- draw()
+ _flush_plot()
if LOG_DATA :
log.write_dict_of_arrays(data)
- if PYLAB_INTERACTIVE_VERBOSE or plotVerbose:
- hold(True)
+ if PYLAB_VERBOSE or plotVerbose:
+ _pylab.hold(True)
def getSurfPosData(zpiezo, maxDefl, textVerbose=False, plotVerbose=False) :
"Measure the distance to the surface"
- if plotVerbose and not PYLAB_INTERACTIVE_VERBOSE :
- from pylab import figure, plot, title, legend, hold, subplot
+ if plotVerbose and not PYLAB_VERBOSE :
+ _import_pylab()
origPos = zpiezo.curPos()
# fully retract the piezo
if TEXT_VERBOSE or textVerbose :
ret3=zpiezo.ramp(out, 10e3)
del(out)
zpiezo.updateInputs()
- if PYLAB_INTERACTIVE_VERBOSE or plotVerbose :
- figure(BASE_FIG_NUM+2)
+ if PYLAB_VERBOSE or plotVerbose :
+ _pylab.figure(BASE_FIG_NUM+2)
def plot_dict(d, label) :
print d.keys()
- plot(d["Z piezo output"], d["Deflection input"], '.',label=label)
+ _pylab.plot(d["Z piezo output"], d["Deflection input"], '.',label=label)
plot_dict(ret1, 'First retract')
plot_dict(mtpod, 'Single step in')
plot_dict(ret3, 'Return to start')
- legend(loc='best')
- title('Too close')
+ _pylab.legend(loc='best')
+ _pylab.title('Too close')
raise tooClose, "Way too close!\n(highContactPos %d <= origPos %d)" % (highContactPos, origPos)
zpiezo.updateInputs()
# fully retract the piezo again
if TEXT_VERBOSE or textVerbose :
print "start Def %d, final def %d, start pos %d, final pos %d" % (startDef, finalDef, startPos, finalPos)
print "Guessed params ", pstart
- params = fit.fit(data=[data["Z piezo output"][dump_before_index:], data["Deflection input"][dump_before_index:]],
- model='bilinear', start=pstart, scale=scale)
+ def bilinear(x, params):
+ left_offset,left_slope,kink_position,right_slope = params
+ if x < kink_position:
+ y = left_offset + left_slope*x
+ else:
+ y = left_offset + left_slope*kink_position \
+ + right_slope*(x-kink_position)
+ def residual(p, y, x):
+ Y = bilinear(x, p)
+ return Y-y
+ leastsq = scipy.optimize.leastsq
+ params,cov,info,mesg,ier = leastsq(
+ residual, pstart,
+ args=(data["Deflection input"][dump_before_index:],
+ data["Z piezo output"][dump_before_index:]),
+ full_output=True, maxfev=10000)
if TEXT_VERBOSE or textVerbose :
print "Best fit parameters: ", params
- if PYLAB_INTERACTIVE_VERBOSE or plotVerbose :
- if plotVerbose and not PYLAB_INTERACTIVE_VERBOSE :
- from pylab import figure, plot, title, legend, hold, subplot
- figure(BASE_FIG_NUM+3)
+ if PYLAB_VERBOSE or plotVerbose :
+ _import_pylab()
+ _pylab.figure(BASE_FIG_NUM+3)
def plot_dict(d, label) :
- plot(d["Z piezo output"], d["Deflection input"], '.',label=label)
+ _pylab.plot(d["Z piezo output"], d["Deflection input"], '.',label=label)
try :
plot_dict(ddict['ret1'], 'First retract')
plot_dict(ddict['mtpod'], 'Single step in')
return params[0] + params[1]*x
else :
return params[0] + params[1]*params[2] + params[3]*(x-params[2])
- plot([startPos, params[2], finalPos],
- [fit_fn(startPos, params), fit_fn(params[2], params), fit_fn(finalPos, params)],
- '-',label='fit')
- title('surf_pos %5g %5g %5g %5g' % (params[0], params[1], params[2], params[3]))
- legend(loc='best')
-
+ _pylab.plot([startPos, params[2], finalPos],
+ [fit_fn(startPos, params), fit_fn(params[2], params), fit_fn(finalPos, params)],
+ '-',label='fit')
+ _pylab.title('surf_pos %5g %5g %5g %5g' % (params[0], params[1], params[2], params[3]))
+ _pylab.legend(loc='best')
+ _flush_plot()
+
# check that the fit is reasonable
# params[1] is slope in non-contact region
# params[3] is slope in contact region
outdata.append(out)
if plotVerbose :
from pylab import figure, plot, title, legend, hold, subplot
- if PYLAB_INTERACTIVE_VERBOSE or plotVerbose :
- figure(BASE_FIG_NUM+4)
+ if PYLAB_VERBOSE or plotVerbose :
+ _import_pylab()
+ _pylab.figure(BASE_FIG_NUM+4)
for i in range(10) :
- plot(indata[i]['Z piezo output'],
- indata[i]['Deflection input'], '+--', label='in')
- plot(outdata[i]['Z piezo output'],
- outdata[i]['Deflection input'], '.-', label='out')
- title('test smoothness (step in, ramp out)')
- #legend(loc='best')
+ _pylab.plot(indata[i]['Z piezo output'],
+ indata[i]['Deflection input'], '+--', label='in')
+ _pylab.plot(outdata[i]['Z piezo output'],
+ outdata[i]['Deflection input'], '.-', label='out')
+ _pylab.title('test smoothness (step in, ramp out)')
+ #_pylab.legend(loc='best')
def test() :
import z_piezo
if TEXT_VERBOSE :
print "Surface at %g nm", pos
print "success"
+ if PYLAB_VERBOSE and _final_flush_plot != None:
+ _final_flush_plot()
projects / pypiezo.git / commitdiff