314 lines
13 KiB
Python
314 lines
13 KiB
Python
# *****************************************************************************
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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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# Damaris Tartarotti Maimone
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# Markus Zolliker <markus.zolliker@psi.ch>
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# *****************************************************************************
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"""Wrapper for the ADQ data acquisition card for ultrasound"""
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import sys
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import atexit
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import signal
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import time
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import numpy as np
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import ctypes as ct
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from scipy.signal import butter, filtfilt
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# For different trigger modes
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SW_TRIG = 1
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# The following external trigger does not work if the level of the trigger is very close to 0.5V.
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# Now we have it close to 3V, and it works
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EXT_TRIG_1 = 2
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EXT_TRIG_2 = 7
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EXT_TRIG_3 = 8
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LVL_TRIG = 3
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INT_TRIG = 4
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LVL_FALLING = 0
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LVL_RISING = 1
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ADQ_CLOCK_INT_INTREF = 0 # internal clock source
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ADQ_CLOCK_EXT_REF = 1 # internal clock source, external reference
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ADQ_CLOCK_EXT_CLOCK = 2 # External clock source
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ADQ_TRANSFER_MODE_NORMAL = 0x00
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ADQ_CHANNELS_MASK = 0x3
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GHz = 1e9
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class Adq:
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sample_rate = 2 * GHz
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max_number_of_channels = 2
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ndecimate = 50 # decimation ratio (2GHz / 40 MHz)
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number_of_records = 1
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samples_per_record = 16384
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bw_cutoff = 10E6
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trigger = EXT_TRIG_1
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adq_num = 1
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UNDEFINED = -1
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IDLE = 0
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BUSY = 1
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READY = 2
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status = UNDEFINED
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data = None
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def __init__(self):
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global ADQAPI
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ADQAPI = ct.cdll.LoadLibrary("libadq.so.0")
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ADQAPI.ADQAPI_GetRevision()
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# Manually set return type from some ADQAPI functions
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ADQAPI.CreateADQControlUnit.restype = ct.c_void_p
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ADQAPI.ADQ_GetRevision.restype = ct.c_void_p
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ADQAPI.ADQ_GetPtrStream.restype = ct.POINTER(ct.c_int16)
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ADQAPI.ADQControlUnit_FindDevices.argtypes = [ct.c_void_p]
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# Create ADQControlUnit
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self.adq_cu = ct.c_void_p(ADQAPI.CreateADQControlUnit())
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ADQAPI.ADQControlUnit_EnableErrorTrace(self.adq_cu, 3, '.')
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# Find ADQ devices
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ADQAPI.ADQControlUnit_FindDevices(self.adq_cu)
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n_of_adq = ADQAPI.ADQControlUnit_NofADQ(self.adq_cu)
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if n_of_adq != 1:
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raise RuntimeError('number of ADQs must be 1, not %d' % n_of_adq)
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rev = ADQAPI.ADQ_GetRevision(self.adq_cu, self.adq_num)
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revision = ct.cast(rev, ct.POINTER(ct.c_int))
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print('\nConnected to ADQ #1')
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# Print revision information
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print('FPGA Revision: {}'.format(revision[0]))
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if revision[1]:
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print('Local copy')
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else:
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print('SVN Managed')
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if revision[2]:
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print('Mixed Revision')
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else:
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print('SVN Updated')
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print('')
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ADQAPI.ADQ_SetClockSource(self.adq_cu, self.adq_num, ADQ_CLOCK_EXT_REF)
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##########################
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# Test pattern
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# ADQAPI.ADQ_SetTestPatternMode(self.adq_cu, self.adq_num, 4)
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##########################
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# Sample skip
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# ADQAPI.ADQ_SetSampleSkip(self.adq_cu, self.adq_num, 1)
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##########################
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# set trigger mode
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if not ADQAPI.ADQ_SetTriggerMode(self.adq_cu, self.adq_num, self.trigger):
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raise RuntimeError('ADQ_SetTriggerMode failed.')
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if self.trigger == LVL_TRIG:
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if not ADQAPI.ADQ_SetLvlTrigLevel(self.adq_cu, self.adq_num, -100):
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raise RuntimeError('ADQ_SetLvlTrigLevel failed.')
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if not ADQAPI.ADQ_SetTrigLevelResetValue(self.adq_cu, self.adq_num, 1000):
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raise RuntimeError('ADQ_SetTrigLevelResetValue failed.')
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if not ADQAPI.ADQ_SetLvlTrigChannel(self.adq_cu, self.adq_num, 1):
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raise RuntimeError('ADQ_SetLvlTrigChannel failed.')
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if not ADQAPI.ADQ_SetLvlTrigEdge(self.adq_cu, self.adq_num, LVL_RISING):
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raise RuntimeError('ADQ_SetLvlTrigEdge failed.')
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elif self.trigger == EXT_TRIG_1:
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if not ADQAPI.ADQ_SetExternTrigEdge(self.adq_cu, self.adq_num, 2):
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raise RuntimeError('ADQ_SetLvlTrigEdge failed.')
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# if not ADQAPI.ADQ_SetTriggerThresholdVoltage(self.adq_cu, self.adq_num, trigger, ct.c_double(0.2)):
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# raise RuntimeError('SetTriggerThresholdVoltage failed.')
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print("CHANNEL:"+str(ct.c_int(ADQAPI.ADQ_GetLvlTrigChannel(self.adq_cu, self.adq_num))))
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atexit.register(self.deletecu)
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signal.signal(signal.SIGTERM, lambda *_: sys.exit(0))
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def init(self, samples_per_record=None, number_of_records=None):
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"""initialize dimensions"""
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if samples_per_record:
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self.samples_per_record = samples_per_record
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if number_of_records:
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self.number_of_records = number_of_records
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# Setup target buffers for data
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self.target_buffers = (ct.POINTER(ct.c_int16 * self.samples_per_record * self.number_of_records)
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* self.max_number_of_channels)()
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for bufp in self.target_buffers:
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bufp.contents = (ct.c_int16 * self.samples_per_record * self.number_of_records)()
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def deletecu(self):
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# Only disarm trigger after data is collected
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ADQAPI.ADQ_DisarmTrigger(self.adq_cu, self.adq_num)
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ADQAPI.ADQ_MultiRecordClose(self.adq_cu, self.adq_num)
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# Delete ADQControlunit
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ADQAPI.DeleteADQControlUnit(self.adq_cu)
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def start(self):
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# Start acquisition
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ADQAPI.ADQ_MultiRecordSetup(self.adq_cu, self.adq_num,
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self.number_of_records,
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self.samples_per_record)
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ADQAPI.ADQ_DisarmTrigger(self.adq_cu, self.adq_num)
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ADQAPI.ADQ_ArmTrigger(self.adq_cu, self.adq_num)
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self.status = self.BUSY
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def get_status(self):
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"""check if ADQ card is busy"""
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if self.status == self.BUSY:
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if ADQAPI.ADQ_GetAcquiredAll(self.adq_cu, self.adq_num):
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self.status = self.READY
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else:
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if self.trigger == SW_TRIG:
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ADQAPI.ADQ_SWTrig(self.adq_cu, self.adq_num)
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return self.status
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def get_data(self, dataclass, **kwds):
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"""when ready, get raw data from card, else return cached data
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return
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"""
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if self.get_status() == self.READY:
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# Get data from ADQ
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if not ADQAPI.ADQ_GetData(self.adq_cu, self.adq_num, self.target_buffers,
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self.samples_per_record * self.number_of_records, 2,
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0, self.number_of_records, ADQ_CHANNELS_MASK,
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0, self.samples_per_record, ADQ_TRANSFER_MODE_NORMAL):
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raise RuntimeError('no success from ADQ_GetDATA')
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self.data = dataclass(self, **kwds)
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self.status = self.IDLE
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if self.status == self.UNDEFINED:
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raise RuntimeError('no data available yet')
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return self.data
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class PEdata:
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def __init__(self, adq):
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self.sample_rate = adq.sample_rate
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self.samp_freq = self.sample_rate / GHz
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self.number_of_records = adq.number_of_records
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data = []
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for ch in range(2):
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onedim = np.frombuffer(adq.target_buffers[ch].contents, dtype=np.int16)
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data.append(onedim.reshape(adq.number_of_records, adq.samples_per_record) / float(2**14)) # 14 bits ADC
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# Now this is an array with all records, but the time is artificial
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self.data = data
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def sinW(self, sig, freq, ti, tf):
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# sig: signal array
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# freq
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# ti, tf: initial and end time
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si = int(ti * self.samp_freq)
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nperiods = freq * (tf - ti)
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n = int(round(max(2, int(nperiods)) / nperiods * (tf-ti) * self.samp_freq))
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self.nperiods = n
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t = np.arange(si, len(sig)) / self.samp_freq
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t = t[:n]
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self.pulselen = n / self.samp_freq
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sig = sig[si:si+n]
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a = 2*np.sum(sig*np.cos(2*np.pi*freq*t))/len(sig)
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b = 2*np.sum(sig*np.sin(2*np.pi*freq*t))/len(sig)
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return a, b
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def mix(self, sigin, sigout, freq, ti, tf):
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# sigin, sigout: signal array, incomping, output
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# freq
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# ti, tf: initial and end time of sigin
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a, b = self.sinW(sigin, freq, ti, tf)
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amp = np.sqrt(a**2 + b**2)
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a, b = a/amp, b/amp
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# si = int(ti * self.samp_freq)
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t = np.arange(len(sigout)) / self.samp_freq
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wave1 = sigout * (a * np.cos(2*np.pi*freq*t) + b * np.sin(2*np.pi*freq*t))
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wave2 = sigout * (a * np.sin(2*np.pi*freq*t) - b * np.cos(2*np.pi*freq*t))
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return wave1, wave2
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def averageiq(self, data, freq, ti, tf):
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"""Average over records"""
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iorq = np.array([self.mix(data[0][i], data[1][i], freq, ti, tf) for i in range(self.number_of_records)])
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return iorq.sum(axis=0) / self.number_of_records
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def filtro(self, iorq, cutoff):
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# butter lowpass
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nyq = 0.5 * self.sample_rate
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normal_cutoff = cutoff / nyq
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order = 5
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b, a = butter(order, normal_cutoff, btype='low', analog=False)
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iqf = [filtfilt(b, a, iorq[i]) for i in np.arange(len(iorq))]
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return iqf
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def box(self, iorq, ti, tf):
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si = int(self.samp_freq * ti)
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sf = int(self.samp_freq * tf)
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bxa = [sum(iorq[i][si:sf])/(sf-si) for i in np.arange(len(iorq))]
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return bxa
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def gates_and_curves(self, freq, pulse, roi, bw_cutoff):
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"""return iq values of rois and prepare plottable curves for iq"""
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self.ndecimate = int(round(self.sample_rate / freq))
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# times = []
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# times.append(('aviq', time.time()))
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iq = self.averageiq(self.data, freq / GHz, *pulse)
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# times.append(('filtro', time.time()))
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iqf = self.filtro(iq, bw_cutoff)
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m = len(iqf[0]) // self.ndecimate
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ll = m * self.ndecimate
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iqf = [iqfx[0:ll] for iqfx in iqf]
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# times.append(('iqdec', time.time()))
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iqd = np.average(np.resize(iqf, (2, m, self.ndecimate)), axis=2)
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t_axis = np.arange(m) * self.ndecimate / self.samp_freq
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pulsig = np.abs(self.data[0][0])
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# times.append(('pulsig', time.time()))
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pulsig = np.average(np.resize(pulsig, (m, self.ndecimate)), axis=1)
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self.curves = (t_axis, iqd[0], iqd[1], pulsig)
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# print(times)
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return [self.box(iqf, *r) for r in roi]
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class RUSdata:
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def __init__(self, adq, freq, periods):
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self.sample_rate = adq.sample_rate
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self.freq = freq
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self.periods = periods
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self.samples_per_record = adq.samples_per_record
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input_signal = np.frombuffer(adq.target_buffers[0].contents, dtype=np.int16)
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output_signal = np.frombuffer(adq.target_buffers[1].contents, dtype=np.int16)
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complex_sinusoid = np.exp(1j * 2 * np.pi * self.freq / self.sample_rate * np.arange(len(input_signal)))
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self.input_mixed = input_signal * complex_sinusoid
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self.output_mixed = output_signal * complex_sinusoid
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self.input_mean = self.input_mixed.mean()
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self.output_mean = self.output_mixed.mean()
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self.iq = self.output_mean / self.input_mean
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def get_reduced(self, mixed):
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"""get reduced array and normalize"""
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nper = self.samples_per_record // self.periods
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mean = mixed.mean()
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return mixed[:self.period * nper].reshape((-1, nper)).mean(axis=0) / mean
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def calc_quality(self):
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"""get signal quality info
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quality info (small values indicate good quality):
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- input_std and output_std:
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the imaginary part indicates deviations in phase
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the real part indicates deviations in amplitude
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- input_slope and output_slope:
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the imaginary part indicates a turning phase (rad/sec)
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the real part indicates changes in amplitude (0.01 ~= 1%/sec)
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"""
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reduced = self.get_reduced(self.input_mixed)
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self.input_stdev = reduced.std()
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reduced = self.get_reduced(self.output_mixed)
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timeaxis = np.arange(len(reduced)) * self.sample_rate / self.freq
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self.output_slope = np.polyfit(timeaxis, reduced, 1)[0]
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