WIP new version of ultrasound
Change-Id: Iadb83396a64e277f6f0a37f7a96d92105648c4fe
This commit is contained in:
parent
b7bc81710d
commit
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@ -1,256 +1,313 @@
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"""
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Created on Tue Nov 26 15:42:43 2019
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@author: tartarotti_d-adm
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"""
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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 numpy import sqrt, arctan2, sin, cos
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import scipy.signal
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#from pylab import *
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#ADQAPI = ct.cdll.LoadLibrary("ADQAPI.dll")
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ADQAPI = ct.cdll.LoadLibrary("libadq.so.0")
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#For different trigger modes
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SW_TRIG = 1
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EXT_TRIG_1 = 2 #This external trigger does not work if the level of the trigger is very close to 0.5V. Now we have it close to 3V, and it works
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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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#samples_per_record=16384
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ADQ_TRANSFER_MODE_NORMAL = 0x00
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ADQ_CHANNELS_MASK = 0x3
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#f_LO = 40
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def butter_lowpass(cutoff, sr, order=5):
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nyq = 0.5 * sr
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normal_cutoff = cutoff / nyq
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b, a = scipy.signal.butter(order, normal_cutoff, btype = 'low', analog = False)
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return b, a
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class Adq(object):
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max_number_of_channels = 2
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samp_freq = 2
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#ndecimate = 50 # decimation ratio (2GHz / 40 MHz)
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ndecimate = 50
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def __init__(self, number_of_records, samples_per_record, bw_cutoff):
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self.number_of_records = number_of_records
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self.samples_per_record = samples_per_record
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self.bw_cutoff = bw_cutoff
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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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self.adq_num = 1
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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 ValueError('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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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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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 trig mode
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self.trigger = EXT_TRIG_1
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#trigger = LVL_TRIG
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success = ADQAPI.ADQ_SetTriggerMode(self.adq_cu, self.adq_num, self.trigger)
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if (success == 0):
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print('ADQ_SetTriggerMode failed.')
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if (self.trigger == LVL_TRIG):
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success = ADQAPI.ADQ_SetLvlTrigLevel(self.adq_cu, self.adq_num, -100)
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if (success == 0):
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print('ADQ_SetLvlTrigLevel failed.')
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success = ADQAPI.ADQ_SetTrigLevelResetValue(self.adq_cu, self.adq_num, 1000)
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if (success == 0):
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print('ADQ_SetTrigLevelResetValue failed.')
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success = ADQAPI.ADQ_SetLvlTrigChannel(self.adq_cu, self.adq_num, 1)
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if (success == 0):
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print('ADQ_SetLvlTrigChannel failed.')
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success = ADQAPI.ADQ_SetLvlTrigEdge(self.adq_cu, self.adq_num, LVL_RISING)
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if (success == 0):
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print('ADQ_SetLvlTrigEdge failed.')
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elif (self.trigger == EXT_TRIG_1) :
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success = ADQAPI.ADQ_SetExternTrigEdge(self.adq_cu, self.adq_num,2)
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if (success == 0):
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print('ADQ_SetLvlTrigEdge failed.')
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# success = ADQAPI.ADQ_SetTriggerThresholdVoltage(self.adq_cu, self.adq_num, trigger, ct.c_double(0.2))
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# if (success == 0):
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# print('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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self.setup_target_buffers()
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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 setup_target_buffers(self):
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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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print('ADQ closed')
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def start(self):
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"""start data acquisition"""
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# samples_per_records = samples_per_record/number_of_records
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# Change number of pulses to be acquired acording to how many records are taken
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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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def getdata(self):
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"""wait for aquisition to be finished and get data"""
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#start = time.time()
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while(ADQAPI.ADQ_GetAcquiredAll(self.adq_cu,self.adq_num) == 0):
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time.sleep(0.001)
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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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#mid = time.time()
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status = 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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#print(time.time()-mid,mid-start)
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if not status:
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raise ValueError('no succesS from ADQ_GetDATA')
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# Now this is an array with all records, but the time is artificial
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data = []
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for ch in range(2):
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onedim = np.frombuffer(self.target_buffers[ch].contents, dtype=np.int16)
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data.append(onedim.reshape(self.number_of_records, self.samples_per_record) / float(2**14)) # 14 bits ADC
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return data
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def acquire(self):
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self.start()
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return self.getdata()
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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 if sigin
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a, b = self.sinW(sigin, freq, ti, tf)
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phase = arctan2(a,b) * 180 / np.pi
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amp = 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 * cos(2*np.pi*freq*t) + b * sin(2*np.pi*freq*t))
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wave2 = sigout * (a * sin(2*np.pi*freq*t) - b * 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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# iorq = np.array([self.mix(data[0][:], data[1][:], freq, ti, tf)])
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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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b, a = butter_lowpass(cutoff, self.samp_freq*1e9)
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#ifi = np.array(scipy.signal.filtfilt(b,a,iorq[0]))
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#qf = np.array(scipy.signal.filtfilt(b,a,iorq[1]))
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iqf = [scipy.signal.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, data, freq, pulse, roi):
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"""return iq values of rois and prepare plottable curves for iq"""
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self.ndecimate = int(round(2E9/freq))
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times = []
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times.append(('aviq', time.time()))
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iq = self.averageiq(data,freq*1e-9,*pulse)
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times.append(('filtro', time.time()))
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iqf = self.filtro(iq,self.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(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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# *****************************************************************************
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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):
|
||||
"""initialize dimensions"""
|
||||
if samples_per_record:
|
||||
self.samples_per_record = samples_per_record
|
||||
if number_of_records:
|
||||
self.number_of_records = number_of_records
|
||||
# Setup target buffers for data
|
||||
self.target_buffers = (ct.POINTER(ct.c_int16 * self.samples_per_record * self.number_of_records)
|
||||
* self.max_number_of_channels)()
|
||||
for bufp in self.target_buffers:
|
||||
bufp.contents = (ct.c_int16 * self.samples_per_record * self.number_of_records)()
|
||||
|
||||
def deletecu(self):
|
||||
# Only disarm trigger after data is collected
|
||||
ADQAPI.ADQ_DisarmTrigger(self.adq_cu, self.adq_num)
|
||||
ADQAPI.ADQ_MultiRecordClose(self.adq_cu, self.adq_num)
|
||||
# Delete ADQControlunit
|
||||
ADQAPI.DeleteADQControlUnit(self.adq_cu)
|
||||
|
||||
def start(self):
|
||||
# Start acquisition
|
||||
ADQAPI.ADQ_MultiRecordSetup(self.adq_cu, self.adq_num,
|
||||
self.number_of_records,
|
||||
self.samples_per_record)
|
||||
|
||||
ADQAPI.ADQ_DisarmTrigger(self.adq_cu, self.adq_num)
|
||||
ADQAPI.ADQ_ArmTrigger(self.adq_cu, self.adq_num)
|
||||
self.status = self.BUSY
|
||||
|
||||
def get_status(self):
|
||||
"""check if ADQ card is busy"""
|
||||
if self.status == self.BUSY:
|
||||
if ADQAPI.ADQ_GetAcquiredAll(self.adq_cu, self.adq_num):
|
||||
self.status = self.READY
|
||||
else:
|
||||
if self.trigger == SW_TRIG:
|
||||
ADQAPI.ADQ_SWTrig(self.adq_cu, self.adq_num)
|
||||
return self.status
|
||||
|
||||
def get_data(self, dataclass, **kwds):
|
||||
"""when ready, get raw data from card, else return cached data
|
||||
|
||||
return
|
||||
"""
|
||||
if self.get_status() == self.READY:
|
||||
# Get data from ADQ
|
||||
if not ADQAPI.ADQ_GetData(self.adq_cu, self.adq_num, self.target_buffers,
|
||||
self.samples_per_record * self.number_of_records, 2,
|
||||
0, self.number_of_records, ADQ_CHANNELS_MASK,
|
||||
0, self.samples_per_record, ADQ_TRANSFER_MODE_NORMAL):
|
||||
raise RuntimeError('no success from ADQ_GetDATA')
|
||||
self.data = dataclass(self, **kwds)
|
||||
self.status = self.IDLE
|
||||
if self.status == self.UNDEFINED:
|
||||
raise RuntimeError('no data available yet')
|
||||
return self.data
|
||||
|
||||
|
||||
class PEdata:
|
||||
def __init__(self, adq):
|
||||
self.sample_rate = adq.sample_rate
|
||||
self.samp_freq = self.sample_rate / GHz
|
||||
self.number_of_records = adq.number_of_records
|
||||
data = []
|
||||
for ch in range(2):
|
||||
onedim = np.frombuffer(adq.target_buffers[ch].contents, dtype=np.int16)
|
||||
data.append(onedim.reshape(adq.number_of_records, adq.samples_per_record) / float(2**14)) # 14 bits ADC
|
||||
# Now this is an array with all records, but the time is artificial
|
||||
self.data = data
|
||||
|
||||
def sinW(self, sig, freq, ti, tf):
|
||||
# sig: signal array
|
||||
# freq
|
||||
# ti, tf: initial and end time
|
||||
si = int(ti * self.samp_freq)
|
||||
nperiods = freq * (tf - ti)
|
||||
n = int(round(max(2, int(nperiods)) / nperiods * (tf-ti) * self.samp_freq))
|
||||
self.nperiods = n
|
||||
t = np.arange(si, len(sig)) / self.samp_freq
|
||||
t = t[:n]
|
||||
self.pulselen = n / self.samp_freq
|
||||
sig = sig[si:si+n]
|
||||
a = 2*np.sum(sig*np.cos(2*np.pi*freq*t))/len(sig)
|
||||
b = 2*np.sum(sig*np.sin(2*np.pi*freq*t))/len(sig)
|
||||
return a, b
|
||||
|
||||
def mix(self, sigin, sigout, freq, ti, tf):
|
||||
# sigin, sigout: signal array, incomping, output
|
||||
# freq
|
||||
# ti, tf: initial and end time of sigin
|
||||
a, b = self.sinW(sigin, freq, ti, tf)
|
||||
amp = np.sqrt(a**2 + b**2)
|
||||
a, b = a/amp, b/amp
|
||||
# si = int(ti * self.samp_freq)
|
||||
t = np.arange(len(sigout)) / self.samp_freq
|
||||
wave1 = sigout * (a * np.cos(2*np.pi*freq*t) + b * np.sin(2*np.pi*freq*t))
|
||||
wave2 = sigout * (a * np.sin(2*np.pi*freq*t) - b * np.cos(2*np.pi*freq*t))
|
||||
return wave1, wave2
|
||||
|
||||
def averageiq(self, data, freq, ti, tf):
|
||||
"""Average over records"""
|
||||
iorq = np.array([self.mix(data[0][i], data[1][i], freq, ti, tf) for i in range(self.number_of_records)])
|
||||
return iorq.sum(axis=0) / self.number_of_records
|
||||
|
||||
def filtro(self, iorq, cutoff):
|
||||
# butter lowpass
|
||||
nyq = 0.5 * self.sample_rate
|
||||
normal_cutoff = cutoff / nyq
|
||||
order = 5
|
||||
b, a = butter(order, normal_cutoff, btype='low', analog=False)
|
||||
iqf = [filtfilt(b, a, iorq[i]) for i in np.arange(len(iorq))]
|
||||
return iqf
|
||||
|
||||
def box(self, iorq, ti, tf):
|
||||
si = int(self.samp_freq * ti)
|
||||
sf = int(self.samp_freq * tf)
|
||||
bxa = [sum(iorq[i][si:sf])/(sf-si) for i in np.arange(len(iorq))]
|
||||
return bxa
|
||||
|
||||
def gates_and_curves(self, freq, pulse, roi, bw_cutoff):
|
||||
"""return iq values of rois and prepare plottable curves for iq"""
|
||||
self.ndecimate = int(round(self.sample_rate / freq))
|
||||
# times = []
|
||||
# times.append(('aviq', time.time()))
|
||||
iq = self.averageiq(self.data, freq / GHz, *pulse)
|
||||
# times.append(('filtro', time.time()))
|
||||
iqf = self.filtro(iq, bw_cutoff)
|
||||
m = len(iqf[0]) // self.ndecimate
|
||||
ll = m * self.ndecimate
|
||||
iqf = [iqfx[0:ll] for iqfx in iqf]
|
||||
# times.append(('iqdec', time.time()))
|
||||
iqd = np.average(np.resize(iqf, (2, m, self.ndecimate)), axis=2)
|
||||
t_axis = np.arange(m) * self.ndecimate / self.samp_freq
|
||||
pulsig = np.abs(self.data[0][0])
|
||||
# times.append(('pulsig', time.time()))
|
||||
pulsig = np.average(np.resize(pulsig, (m, self.ndecimate)), axis=1)
|
||||
self.curves = (t_axis, iqd[0], iqd[1], pulsig)
|
||||
# print(times)
|
||||
return [self.box(iqf, *r) for r in roi]
|
||||
|
||||
|
||||
class RUSdata:
|
||||
def __init__(self, adq, freq, periods):
|
||||
self.sample_rate = adq.sample_rate
|
||||
self.freq = freq
|
||||
self.periods = periods
|
||||
self.samples_per_record = adq.samples_per_record
|
||||
input_signal = np.frombuffer(adq.target_buffers[0].contents, dtype=np.int16)
|
||||
output_signal = np.frombuffer(adq.target_buffers[1].contents, dtype=np.int16)
|
||||
complex_sinusoid = np.exp(1j * 2 * np.pi * self.freq / self.sample_rate * np.arange(len(input_signal)))
|
||||
self.input_mixed = input_signal * complex_sinusoid
|
||||
self.output_mixed = output_signal * complex_sinusoid
|
||||
self.input_mean = self.input_mixed.mean()
|
||||
self.output_mean = self.output_mixed.mean()
|
||||
self.iq = self.output_mean / self.input_mean
|
||||
|
||||
def get_reduced(self, mixed):
|
||||
"""get reduced array and normalize"""
|
||||
nper = self.samples_per_record // self.periods
|
||||
mean = mixed.mean()
|
||||
return mixed[:self.period * nper].reshape((-1, nper)).mean(axis=0) / mean
|
||||
|
||||
def calc_quality(self):
|
||||
"""get signal quality info
|
||||
|
||||
quality info (small values indicate good quality):
|
||||
- input_std and output_std:
|
||||
the imaginary part indicates deviations in phase
|
||||
the real part indicates deviations in amplitude
|
||||
- input_slope and output_slope:
|
||||
the imaginary part indicates a turning phase (rad/sec)
|
||||
the real part indicates changes in amplitude (0.01 ~= 1%/sec)
|
||||
"""
|
||||
reduced = self.get_reduced(self.input_mixed)
|
||||
self.input_stdev = reduced.std()
|
||||
|
||||
reduced = self.get_reduced(self.output_mixed)
|
||||
timeaxis = np.arange(len(reduced)) * self.sample_rate / self.freq
|
||||
self.output_slope = np.polyfit(timeaxis, reduced, 1)[0]
|
||||
|
||||
@ -19,18 +19,19 @@
|
||||
"""frappy support for ultrasound"""
|
||||
|
||||
import math
|
||||
#import serial
|
||||
import os
|
||||
import time
|
||||
|
||||
import numpy as np
|
||||
|
||||
import frappy_psi.iqplot as iqplot
|
||||
from frappy_psi.adq_mr import Adq
|
||||
from frappy_psi.adq_mr import Adq, PEdata, RUSdata
|
||||
from frappy.core import Attached, BoolType, Done, FloatRange, HasIO, \
|
||||
IntRange, Module, Parameter, Readable, StringIO, StringType, \
|
||||
IDLE, DISABLED, TupleOf, ArrayOf
|
||||
IntRange, Module, Parameter, Readable, Writable, Drivable, StringIO, StringType, \
|
||||
IDLE, BUSY, DISABLED, ERROR, TupleOf, ArrayOf, Command
|
||||
from frappy.properties import Property
|
||||
#from frappy.modules import Collector
|
||||
|
||||
Collector = Readable
|
||||
|
||||
|
||||
def fname_from_time(t, extension):
|
||||
@ -55,7 +56,7 @@ class Roi(Readable):
|
||||
enable = Parameter('calculate this roi', BoolType(), readonly=False, default=True)
|
||||
pollinterval = Parameter(export=False)
|
||||
|
||||
interval = (0,0)
|
||||
interval = (0, 0)
|
||||
|
||||
def initModule(self):
|
||||
super().initModule()
|
||||
@ -92,80 +93,22 @@ class FreqStringIO(StringIO):
|
||||
end_of_line = '\r'
|
||||
|
||||
|
||||
class Frequency(HasIO, Readable):
|
||||
pars = Attached()
|
||||
curves = Attached(mandatory=False)
|
||||
maxy = Property('plot y scale', datatype=FloatRange(), default=0.5)
|
||||
|
||||
value = Parameter('frequency@I,q', datatype=FloatRange(unit='Hz'), default=0)
|
||||
basefreq = Parameter('base frequency', FloatRange(unit='Hz'), readonly=False)
|
||||
nr = Parameter('number of records', datatype=IntRange(1,10000), default=500)
|
||||
sr = Parameter('samples per record', datatype=IntRange(1,1E9), default=16384)
|
||||
freq = Parameter('target frequency', FloatRange(unit='Hz'), readonly=False)
|
||||
bw = Parameter('bandwidth lowpassfilter', datatype=FloatRange(unit='Hz'),default=10E6)
|
||||
class Frequency(HasIO, Writable):
|
||||
value = Parameter('frequency', unit='Hz')
|
||||
amp = Parameter('amplitude', FloatRange(unit='dBm'), readonly=False)
|
||||
control = Parameter('control loop on?', BoolType(), readonly=False, default=True)
|
||||
rusmode = Parameter('RUS mode on?', BoolType(), readonly=False, default=False)
|
||||
time = Parameter('pulse start time', FloatRange(unit='nsec'),
|
||||
readonly=False)
|
||||
size = Parameter('pulse length (starting from time)', FloatRange(unit='nsec'),
|
||||
readonly=False)
|
||||
pulselen = Parameter('adjusted pulse length (integer number of periods)', FloatRange(unit='nsec'), default=1)
|
||||
maxstep = Parameter('max frequency step', FloatRange(unit='Hz'), readonly=False,
|
||||
default=10000)
|
||||
minstep = Parameter('min frequency step for slope calculation', FloatRange(unit='Hz'),
|
||||
readonly=False, default=4000)
|
||||
slope = Parameter('inphase/frequency slope', FloatRange(), readonly=False,
|
||||
default=1e6)
|
||||
plot = Parameter('create plot images', BoolType(), readonly=False, default=True)
|
||||
save = Parameter('save data', BoolType(), readonly=False, default=True)
|
||||
pollinterval = Parameter(datatype=FloatRange(0,120))
|
||||
|
||||
last_change = 0
|
||||
ioClass = FreqStringIO
|
||||
dif = None
|
||||
|
||||
lastfreq = None
|
||||
old = None
|
||||
starttime = None
|
||||
interval = (0,0)
|
||||
def register_dif(self, dif):
|
||||
self.dif = dif
|
||||
|
||||
def earlyInit(self):
|
||||
super().earlyInit()
|
||||
self.adq = Adq(self.nr, self.sr, self.bw)
|
||||
self.roilist = []
|
||||
self.write_nr(self.nr)
|
||||
self.write_sr(self.sr)
|
||||
self.skipctrl = 0
|
||||
self.plotter = iqplot.Plot(self.maxy)
|
||||
self.calc_interval()
|
||||
|
||||
def calc_interval(self):
|
||||
self.interval = (self.time, self.time + self.size)
|
||||
|
||||
def write_time(self, value):
|
||||
self.time = value
|
||||
self.calc_interval()
|
||||
return Done
|
||||
|
||||
def write_size(self, value):
|
||||
self.size = value
|
||||
self.calc_interval()
|
||||
return Done
|
||||
|
||||
def write_nr(self, value):
|
||||
# self.pollinterval = value * 0.0001
|
||||
return value
|
||||
|
||||
def write_sr(self, value):
|
||||
return value
|
||||
|
||||
def register_roi(self, roi):
|
||||
self.roilist.append(roi)
|
||||
|
||||
def set_freq(self):
|
||||
freq = self.freq + self.basefreq
|
||||
self.communicate('FREQ %.15g;FREQ?' % freq)
|
||||
#self._iodev.readline().decode('ascii')
|
||||
return freq
|
||||
def write_target(self, value):
|
||||
self.communicate('FREQ %.15g;FREQ?' % value)
|
||||
self.last_change = time.time()
|
||||
if self.dif:
|
||||
self.dif.read_value()
|
||||
|
||||
def write_amp(self, amp):
|
||||
reply = self.communicate('AMPR %g;AMPR?' % amp)
|
||||
@ -175,105 +118,196 @@ class Frequency(HasIO, Readable):
|
||||
reply = self.communicate('AMPR?')
|
||||
return float(reply)
|
||||
|
||||
def write_freq(self, value):
|
||||
self.skipctrl = 2 # suppress control for the 2 next steps
|
||||
return value
|
||||
|
||||
def doPoll(self):
|
||||
"""main poll loop body"""
|
||||
if self.lastfreq is None:
|
||||
self.lastfreq = self.set_freq()
|
||||
if self.rusmode:
|
||||
self.sr = int(12e9/self.lastfreq) #picking up 12 period at the ith frequency in the time scale
|
||||
# self.adq.samples_per_record = self.sr
|
||||
self.adq.start()
|
||||
class FrequencyDif(Readable):
|
||||
freq = Attached(Frequency)
|
||||
base = Parameter('base frequency', FloatRange(unit='Hz'), default=0)
|
||||
value = Parameter('difference to base frequency', FloatRange(unit='Hz'), default=0)
|
||||
|
||||
if self.starttime is None:
|
||||
self.starttime = time.time()
|
||||
times = []
|
||||
times.append(('init', time.time()))
|
||||
seadata = {p: float(getattr(self.pars, p)) for p in self.pars.parameters}
|
||||
data = self.adq.getdata() # this will wait, if not yet finished
|
||||
#save sample
|
||||
#np.save('sample.dat',data)
|
||||
times.append(('wait',time.time()))
|
||||
if self.control:
|
||||
freq = self.lastfreq # data was acquired at this freq
|
||||
else:
|
||||
freq = self.set_freq()
|
||||
seadata['frequency'] = freq
|
||||
if self.control:
|
||||
self.lastfreq = self.set_freq()
|
||||
times.append(('setf',time.time()))
|
||||
self.adq.start() # start next acq
|
||||
times.append(('start',time.time()))
|
||||
roilist = [r for r in self.roilist if r.enable]
|
||||
def initModule(self):
|
||||
super().initModule()
|
||||
self.freq.register_dif(self)
|
||||
|
||||
gates = self.adq.gates_and_curves(data, freq, self.interval,
|
||||
[r.interval for r in roilist])
|
||||
if self.curves: # if attached Curves module is defined, update it
|
||||
self.curves.value = self.adq.curves
|
||||
if self.save:
|
||||
times.append(('save',time.time()))
|
||||
tdata, idata, qdata, pdata = self.adq.curves
|
||||
seadata['timestep'] = tdata[1] - tdata[0]
|
||||
iqdata = np.array((idata, qdata, pdata), dtype='f4')
|
||||
ts = seadata['timestamp']
|
||||
if ts:
|
||||
filename = fname_from_time(ts, '.npz')
|
||||
seanp = np.array(list(seadata.items()), dtype=[('name', 'U16'), ('value', 'f8')])
|
||||
np.savez(filename, seadata=seanp, iqdata=iqdata)
|
||||
# can be load back via
|
||||
# content = np.load(filename)
|
||||
# content['seadata'], content['iqdata']
|
||||
self.pulselen = self.adq.pulselen
|
||||
times.append(('ana',time.time()))
|
||||
if self.plot:
|
||||
# get reduced interval from adq.sinW
|
||||
pulseint = (self.interval[0], self.interval[0] + self.pulselen)
|
||||
try:
|
||||
self.plotter.plot(
|
||||
self.adq.curves,
|
||||
rois=[pulseint] + [r.interval for r in roilist],
|
||||
average=([r.time for r in roilist],
|
||||
[r.i for r in roilist],
|
||||
[r.q for r in roilist]))
|
||||
except Exception as e:
|
||||
self.log.warning('can not plot %r' % e)
|
||||
else:
|
||||
self.plotter.close()
|
||||
now = time.time()
|
||||
times.append(('plot',now))
|
||||
# print(' '.join('%s %5.3f' % (label, t - self.starttime) for label, t in times))
|
||||
self.starttime = now
|
||||
self.value = freq - self.basefreq
|
||||
for i, roi in enumerate(roilist):
|
||||
roi.i = a = gates[i][0]
|
||||
roi.q = b = gates[i][1]
|
||||
roi.value = math.sqrt(a ** 2 + b ** 2)
|
||||
roi.phase = math.atan2(a,b) * 180 / math.pi
|
||||
inphase = self.roilist[0].i
|
||||
if self.control:
|
||||
newfreq = freq + inphase * self.slope - self.basefreq
|
||||
# step = sorted((-self.maxstep, inphase * self.slope, self.maxstep))[1]
|
||||
if self.old:
|
||||
fdif = freq - self.old[0]
|
||||
idif = inphase - self.old[1]
|
||||
if abs(fdif) >= self.minstep:
|
||||
self.slope = - fdif / idif
|
||||
else:
|
||||
fdif = 0
|
||||
idif = 0
|
||||
newfreq = freq + self.minstep
|
||||
self.old = (freq, inphase)
|
||||
if self.skipctrl > 0: # do no control for some time after changing frequency
|
||||
self.skipctrl -= 1
|
||||
elif self.control:
|
||||
self.freq = sorted((self.freq - self.maxstep, newfreq, self.freq + self.maxstep))[1]
|
||||
#print(times)
|
||||
return Done
|
||||
def read_value(self):
|
||||
return self.freq - self.base
|
||||
|
||||
|
||||
class Curves(Readable):
|
||||
class Base(Collector):
|
||||
freq = Attached()
|
||||
adq = Attached(Adq)
|
||||
sr = Parameter('samples per record', datatype=IntRange(1, 1E9), default=16384)
|
||||
pollinterval = Parameter(datatype=FloatRange(0, 120)) # allow pollinterval = 0
|
||||
_data = None
|
||||
_data_args = None
|
||||
|
||||
def read_status(self):
|
||||
adqstate = self.adq.get_status()
|
||||
if adqstate == Adq.BUSY:
|
||||
return BUSY, 'acquiring'
|
||||
if adqstate == Adq.UNDEFINED:
|
||||
return ERROR, 'no data yet'
|
||||
if adqstate == Adq.READY:
|
||||
return IDLE, 'new data available'
|
||||
return IDLE, ''
|
||||
|
||||
def get_data(self):
|
||||
data = self.adq.get_data(*self._data_args)
|
||||
if id(data) != id(self._data):
|
||||
self._data = data
|
||||
return data
|
||||
return None
|
||||
|
||||
|
||||
class PulseEcho(Base):
|
||||
value = Parameter("t, i, q, pulse curves",
|
||||
TupleOf(*[ArrayOf(FloatRange(), 0, 16283) for _ in range(4)]), default=[[]] * 4)
|
||||
nr = Parameter('number of records', datatype=IntRange(1, 9999), default=500)
|
||||
bw = Parameter('bandwidth lowpassfilter', datatype=FloatRange(unit='Hz'), default=10E6)
|
||||
control = Parameter('control loop on?', BoolType(), readonly=False, default=True)
|
||||
time = Parameter('pulse start time', FloatRange(unit='nsec'),
|
||||
readonly=False)
|
||||
size = Parameter('pulse length (starting from time)', FloatRange(unit='nsec'),
|
||||
readonly=False)
|
||||
pulselen = Parameter('adjusted pulse length (integer number of periods)', FloatRange(unit='nsec'), default=1)
|
||||
|
||||
starttime = None
|
||||
|
||||
def initModule(self):
|
||||
super().initModule()
|
||||
self.adq = Adq()
|
||||
self.adq.init(self.sr, self.nr)
|
||||
self.roilist = []
|
||||
|
||||
def write_nr(self, value):
|
||||
self.adq.init(self.sr, value)
|
||||
|
||||
def write_sr(self, value):
|
||||
self.adq.init(value, self.nr)
|
||||
|
||||
def write_bw(self, value):
|
||||
self.adq.bw_cutoff = value
|
||||
|
||||
def register_roi(self, roi):
|
||||
self.roilist.append(roi)
|
||||
|
||||
def go(self):
|
||||
self.starttime = time.time()
|
||||
self.adq.start()
|
||||
|
||||
def read_value(self):
|
||||
if self.get_rawdata(): # new data available
|
||||
roilist = [r for r in self.roilist if r.enable]
|
||||
freq = self.freq.value
|
||||
gates = self.adq.gates_and_curves(self._data, freq,
|
||||
(self.time, self.time + self.size),
|
||||
[r.interval for r in roilist])
|
||||
for i, roi in enumerate(roilist):
|
||||
roi.i = a = gates[i][0]
|
||||
roi.q = b = gates[i][1]
|
||||
roi.value = math.sqrt(a ** 2 + b ** 2)
|
||||
roi.phase = math.atan2(a, b) * 180 / math.pi
|
||||
return self.adq.curves
|
||||
|
||||
# TODO: CONTROL
|
||||
# inphase = self.roilist[0].i
|
||||
# if self.control:
|
||||
# newfreq = freq + inphase * self.slope - self.basefreq
|
||||
# # step = sorted((-self.maxstep, inphase * self.slope, self.maxstep))[1]
|
||||
# if self.old:
|
||||
# fdif = freq - self.old[0]
|
||||
# idif = inphase - self.old[1]
|
||||
# if abs(fdif) >= self.minstep:
|
||||
# self.slope = - fdif / idif
|
||||
# else:
|
||||
# fdif = 0
|
||||
# idif = 0
|
||||
# newfreq = freq + self.minstep
|
||||
# self.old = (freq, inphase)
|
||||
# if self.skipctrl > 0: # do no control for some time after changing frequency
|
||||
# self.skipctrl -= 1
|
||||
# elif self.control:
|
||||
# self.freq = sorted((self.freq - self.maxstep, newfreq, self.freq + self.maxstep))[1]
|
||||
|
||||
|
||||
class RUS(Base):
|
||||
value = Parameter('averaged (I, Q) tuple', TupleOf(FloatRange(), FloatRange()))
|
||||
periods = Parameter('number of periods', IntRange(1, 9999), default=12)
|
||||
scale = Parameter('scale,taking into account input attenuation', FloatRange(), default=0.1)
|
||||
input_phase_stddev = Parameter('input signal quality', FloatRange(unit='rad'))
|
||||
output_phase_slope = Parameter('output signal phase slope', FloatRange(unit='rad/sec'))
|
||||
output_amp_slope = Parameter('output signal amplitude change', FloatRange(unit='1/sec'))
|
||||
phase = Parameter('phase', FloatRange(unit='deg'))
|
||||
amp = Parameter('amplitude', FloatRange())
|
||||
|
||||
starttime = None
|
||||
_data_args = None
|
||||
|
||||
def initModule(self):
|
||||
super().initModule()
|
||||
self.adq = Adq()
|
||||
# self.write_periods(self.periods)
|
||||
|
||||
def read_value(self):
|
||||
if self._data_args is None:
|
||||
return self.value # or may we raise as no value is defined yet?
|
||||
data = self.get_data(RUSdata, *self._data_args)
|
||||
if data:
|
||||
# data available
|
||||
data.calc_quality()
|
||||
self.input_phase_stddev = data.input_stddev.imag
|
||||
self.output_phase_slope = data.output_slope.imag
|
||||
self.output_amp_slope = data.output_slope.real
|
||||
|
||||
iq = data.iq * self.scale
|
||||
self.phase = np.arctan2(iq.imag, iq.real) * 180 / np.pi
|
||||
self.amp = np.abs(iq.imag, iq.real)
|
||||
return iq.real, iq.imag
|
||||
return self.value
|
||||
|
||||
def go(self):
|
||||
self.starttime = time.time()
|
||||
freq = self.freq.value
|
||||
self._data_args = (RUSdata, freq, self.periods)
|
||||
self.sr = round(self.periods * self.adq.sample_rate / freq)
|
||||
self.adq.init(self.sr, 1)
|
||||
self.adq.start()
|
||||
self.read_status()
|
||||
|
||||
|
||||
class ControlLoop:
|
||||
maxstep = Parameter('max frequency step', FloatRange(unit='Hz'), readonly=False,
|
||||
default=10000)
|
||||
minstep = Parameter('min frequency step for slope calculation', FloatRange(unit='Hz'),
|
||||
readonly=False, default=4000)
|
||||
slope = Parameter('inphase/frequency slope', FloatRange(), readonly=False,
|
||||
default=1e6)
|
||||
|
||||
|
||||
# class Frequency(HasIO, Readable):
|
||||
# pars = Attached()
|
||||
# curves = Attached(mandatory=False)
|
||||
# maxy = Property('plot y scale', datatype=FloatRange(), default=0.5)
|
||||
#
|
||||
# value = Parameter('frequency@I,q', datatype=FloatRange(unit='Hz'), default=0)
|
||||
# basefreq = Parameter('base frequency', FloatRange(unit='Hz'), readonly=False)
|
||||
# nr = Parameter('number of records', datatype=IntRange(1,10000), default=500)
|
||||
# sr = Parameter('samples per record', datatype=IntRange(1,1E9), default=16384)
|
||||
# freq = Parameter('target frequency', FloatRange(unit='Hz'), readonly=False)
|
||||
# bw = Parameter('bandwidth lowpassfilter', datatype=FloatRange(unit='Hz'),default=10E6)
|
||||
# amp = Parameter('amplitude', FloatRange(unit='dBm'), readonly=False)
|
||||
# control = Parameter('control loop on?', BoolType(), readonly=False, default=True)
|
||||
# rusmode = Parameter('RUS mode on?', BoolType(), readonly=False, default=False)
|
||||
# time = Parameter('pulse start time', FloatRange(unit='nsec'),
|
||||
# readonly=False)
|
||||
# size = Parameter('pulse length (starting from time)', FloatRange(unit='nsec'),
|
||||
# readonly=False)
|
||||
# pulselen = Parameter('adjusted pulse length (integer number of periods)', FloatRange(unit='nsec'), default=1)
|
||||
# maxstep = Parameter('max frequency step', FloatRange(unit='Hz'), readonly=False,
|
||||
# default=10000)
|
||||
# minstep = Parameter('min frequency step for slope calculation', FloatRange(unit='Hz'),
|
||||
# readonly=False, default=4000)
|
||||
# slope = Parameter('inphase/frequency slope', FloatRange(), readonly=False,
|
||||
# default=1e6)
|
||||
# plot = Parameter('create plot images', BoolType(), readonly=False, default=True)
|
||||
# save = Parameter('save data', BoolType(), readonly=False, default=True)
|
||||
# pollinterval = Parameter(datatype=FloatRange(0,120))
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user