add missing files from secop_psi
- all of them have to be checked! Change-Id: I89d55ca683d0b2710222f14c2c3cd42f8fbf3a1f
This commit is contained in:
261
frappy_psi/ultrasound.py
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261
frappy_psi/ultrasound.py
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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# *****************************************************************************
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# This program is free software; you can redistribute it and/or modify it under
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# the terms of the GNU General Public License as published by the Free Software
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# Foundation; either version 2 of the License, or (at your option) any later
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# version.
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#
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# This program is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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# details.
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#
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# You should have received a copy of the GNU General Public License along with
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# this program; if not, write to the Free Software Foundation, Inc.,
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# 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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#
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# Module authors:
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# Markus Zolliker <markus.zolliker@psi.ch>
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# *****************************************************************************
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"""frappy support for ultrasound"""
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import math
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#import serial
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import os
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import time
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import numpy as np
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import frappy_psi.iqplot as iqplot
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from frappy_psi.adq_mr import Adq
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from frappy.core import Attached, BoolType, Done, FloatRange, HasIO, \
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IntRange, Module, Parameter, Readable, StringIO, StringType
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from frappy.properties import Property
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def fname_from_time(t, extension):
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tm = time.localtime(t)
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dirname = os.path.join('..', 'data', time.strftime("%Y-%m-%d_%H", tm))
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filename = time.strftime("%Y-%m-%d_%H-%M-%S_", tm)
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filename = filename + ("%.1f" % t)[-1]
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if not os.path.isdir(dirname):
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os.makedirs(dirname)
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return os.path.join(dirname, filename)
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class Roi(Readable):
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main = Attached()
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value = Parameter('amplitude', FloatRange(), default=0)
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phase = Parameter('phase', FloatRange(unit='deg'), default=0)
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i = Parameter('in phase', FloatRange(), default=0)
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q = Parameter('out of phase', FloatRange(), default=0)
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time = Parameter('start time', FloatRange(unit='nsec'), readonly=False)
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size = Parameter('interval (symmetric around time)', FloatRange(unit='nsec'), readonly=False)
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enable = Parameter('calculate this roi', BoolType(), readonly=False, default=True)
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#status = Parameter(export=False)
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pollinterval = Parameter(export=False)
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interval = (0,0)
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def initModule(self):
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super().initModule()
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self.main.register_roi(self)
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self.calc_interval()
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def calc_interval(self):
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self.interval = (self.time - 0.5 * self.size, self.time + 0.5 * self.size)
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def write_time(self, value):
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self.time = value
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self.calc_interval()
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return Done
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def write_size(self, value):
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self.size = value
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self.calc_interval()
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return Done
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class Pars(Module):
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description = 'relevant parameters from SEA'
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timestamp = Parameter('unix timestamp', StringType(), default='0', readonly=False)
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temperature = Parameter('T', FloatRange(unit='K'), default=0, readonly=False)
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mf = Parameter('field', FloatRange(unit='T'), default=0, readonly=False)
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sr = Parameter('rotaion angle', FloatRange(unit='deg'), default=0, readonly=False)
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class FreqStringIO(StringIO):
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end_of_line = '\r'
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class Frequency(HasIO, Readable):
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pars = Attached()
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sr = Property('samples per record', datatype=IntRange(), default=16384)
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maxy = Property('plot y scale', datatype=FloatRange(), default=0.5)
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value = Parameter('frequency@I,q', datatype=FloatRange(unit='Hz'), default=0)
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basefreq = Parameter('base frequency', FloatRange(unit='Hz'), readonly=False)
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nr = Parameter('number of records', datatype=IntRange(1,10000), default=500)
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freq = Parameter('target frequency', FloatRange(unit='Hz'), readonly=False)
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bw = Parameter('bandwidth lowpassfilter', datatype=FloatRange(unit='Hz'),default=10E6)
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amp = Parameter('amplitude', FloatRange(unit='dBm'), readonly=False)
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control = Parameter('control loop on?', BoolType(), readonly=False, default=True)
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time = Parameter('pulse start time', FloatRange(unit='nsec'),
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readonly=False)
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size = Parameter('pulse length (starting from time)', FloatRange(unit='nsec'),
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readonly=False)
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pulselen = Parameter('adjusted pulse length (integer number of periods)', FloatRange(unit='nsec'), default=1)
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maxstep = Parameter('max frequency step', FloatRange(unit='Hz'), readonly=False,
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default=10000)
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minstep = Parameter('min frequency step for slope calculation', FloatRange(unit='Hz'),
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readonly=False, default=4000)
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slope = Parameter('inphase/frequency slope', FloatRange(), readonly=False,
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default=1e6)
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plot = Parameter('create plot images', BoolType(), readonly=False, default=True)
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save = Parameter('save data', BoolType(), readonly=False, default=True)
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pollinterval = Parameter(datatype=FloatRange(0,120))
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ioClass = FreqStringIO
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lastfreq = None
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old = None
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starttime = None
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interval = (0,0)
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def earlyInit(self):
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super().earlyInit()
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self.adq = Adq(self.nr, self.sr, self.bw)
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self.roilist = []
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self.write_nr(self.nr)
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self.skipctrl = 0
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self.plotter = iqplot.Plot(self.maxy)
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self.calc_interval()
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def calc_interval(self):
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self.interval = (self.time, self.time + self.size)
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def write_time(self, value):
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self.time = value
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self.calc_interval()
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return Done
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def write_size(self, value):
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self.size = value
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self.calc_interval()
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return Done
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def write_nr(self, value):
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# self.pollinterval = value * 0.0001
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return value
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def register_roi(self, roi):
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self.roilist.append(roi)
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def set_freq(self):
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freq = self.freq + self.basefreq
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self.communicate('FREQ %.15g;FREQ?' % freq)
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#self._iodev.readline().decode('ascii')
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return freq
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def write_amp(self, amp):
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reply = self.communicate('AMPR %g;AMPR?' % amp)
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return float(reply)
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def read_amp(self):
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reply = self.communicate('AMPR?')
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return float(reply)
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def write_freq(self, value):
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self.skipctrl = 2 # suppress control for the 2 next steps
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return value
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def doPoll(self):
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"""main poll loop body"""
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if self.lastfreq is None:
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self.lastfreq = self.set_freq()
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self.adq.start()
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if self.starttime is None:
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self.starttime = time.time()
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times = []
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times.append(('init', time.time()))
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seadata = {p: float(getattr(self.pars, p)) for p in self.pars.parameters}
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data = self.adq.getdata() # this will wait, if not yet finished
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#save sample
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#np.save('sample.dat',data)
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times.append(('wait',time.time()))
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if self.control:
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freq = self.lastfreq # data was acquired at this freq
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else:
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freq = self.set_freq()
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seadata['frequency'] = freq
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if self.control:
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self.lastfreq = self.set_freq()
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times.append(('setf',time.time()))
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self.adq.start() # start next acq
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times.append(('start',time.time()))
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roilist = [r for r in self.roilist if r.enable]
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gates = self.adq.gates_and_curves(data, freq, self.interval,
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[r.interval for r in roilist])
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if self.save:
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times.append(('save',time.time()))
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tdata, idata, qdata, pdata = self.adq.curves
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seadata['timestep'] = tdata[1] - tdata[0]
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iqdata = np.array((idata, qdata, pdata), dtype='f4')
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ts = seadata['timestamp']
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if ts:
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filename = fname_from_time(ts, '.npz')
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seanp = np.array(list(seadata.items()), dtype=[('name', 'U16'), ('value', 'f8')])
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np.savez(filename, seadata=seanp, iqdata=iqdata)
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# can be load back via
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# content = np.load(filename)
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# content['seadata'], content['iqdata']
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self.pulselen = self.adq.pulselen
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times.append(('ana',time.time()))
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if self.plot:
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# get reduced interval from adq.sinW
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pulseint = (self.interval[0], self.interval[0] + self.pulselen)
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try:
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self.plotter.plot(
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self.adq.curves,
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rois=[pulseint] + [r.interval for r in roilist],
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average=([r.time for r in roilist],
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[r.i for r in roilist],
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[r.q for r in roilist]))
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except Exception as e:
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self.log.warning('can not plot %r' % e)
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else:
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self.plotter.close()
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now = time.time()
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times.append(('plot',now))
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# print(' '.join('%s %5.3f' % (label, t - self.starttime) for label, t in times))
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self.starttime = now
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self.value = freq - self.basefreq
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for i, roi in enumerate(roilist):
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roi.i = a = gates[i][0]
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roi.q = b = gates[i][1]
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roi.value = math.sqrt(a ** 2 + b ** 2)
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roi.phase = math.atan2(a,b) * 180 / math.pi
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inphase = self.roilist[0].i
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if self.control:
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newfreq = freq + inphase * self.slope - self.basefreq
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# step = sorted((-self.maxstep, inphase * self.slope, self.maxstep))[1]
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if self.old:
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fdif = freq - self.old[0]
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idif = inphase - self.old[1]
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if abs(fdif) >= self.minstep:
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self.slope = - fdif / idif
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else:
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fdif = 0
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idif = 0
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newfreq = freq + self.minstep
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self.old = (freq, inphase)
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if self.skipctrl > 0: # do no control for some time after changing frequency
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self.skipctrl -= 1
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elif self.control:
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self.freq = sorted((self.freq - self.maxstep, newfreq, self.freq + self.maxstep))[1]
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#print(times)
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return Done
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