Chimera.py
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Created: Fri, May 10, 00:19

Chimera.py
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	import ChimeraSettings as C
	import ok
	import ChimeraControls
	import os
	import pickle
	from PyQt5 import QtGui
	import datetime
	import numpy as np
	import time
	import csv
	import matplotlib.pyplot as plt
	import functions


	from matplotlib.ticker import EngFormatter
	Amp = EngFormatter(unit='A', places=2)
	Time = EngFormatter(unit='s', places=2)
	Volt = EngFormatter(unit='V', places=2)
	Cond = EngFormatter(unit='S', places=2)


	# Main Chimera Launcher
	class Launcher:

	def __init__(self, loadedInstance=None):
	if loadedInstance is None:
	self.ChimeraSettings = C.ChimeraSettings()
	else:
	self.ChimeraSettings = loadedInstance

	# Initialize Chimera
	self.xem = ok.FrontPanel()
	ChimeraControls.InitializeChimera(self.ChimeraSettings,self.xem)

	# Set savingfolder
	self.SetSavingFolder(os.getcwd())

	# Variables
	self.lowpass = 2e3
	self.displaySamplerate = self.lowpass*2

	self.IVUseAlternatingV = True
	self.LowerIV = 0.0
	self.HigherIV = 0.0
	self.StepIV = 0.0
	self.timeIV = 2


	# if os.stat("store.pckl").st_size:
	# ChimeraSettings.setStoredValues()

	# Data variables
	# self.blockvalues = np.empty((1048576,), dtype=np.uint16)
	# self.readvalues = ChimeraControls.ConvertBlockvalues(self.ChimeraSettings, blockvalues)
	#self.displaybuffer
	#self.blockvalues

	# self.newbiasvalue = 0


	def Initialize(self):
	ChimeraControls.InitializeChimera(self.ChimeraSettings, self.xem)

	def SetSavingFolder(self, savingFolder, experimentName = 'Untitled'):
	self.DataFolder = savingFolder
	self.todaysfolder = str(datetime.date.today())

	self.experimentName = experimentName

	if not os.path.exists(self.DataFolder):
	os.makedirs(self.DataFolder)

	if not os.path.exists(os.path.join(self.DataFolder, self.todaysfolder)):
	os.makedirs(os.path.join(self.DataFolder, self.todaysfolder))

	print('Files are saved in ' + os.path.join(os.path.join(self.DataFolder, self.todaysfolder), self.experimentName))

	def SetExperimentName(self, experimentName):
	self.SetSavingFolder(self.DataFolder, experimentName=experimentName)

	def SetVoltage(self, sb, write=True):
	self.newbiasvalue = sb
	# self.ChimeraSettings.RestartBuffer = True
	if write:
	self.SaveVoltage()

	ChimeraControls.CHIMERA_updateDACvalues1(self.ChimeraSettings, self.xem, self.newbiasvalue)

	def RecordTraceRaw(self):
	blockvalues = ChimeraControls.CHIMERA_process_triggers(self.ChimeraSettings,self.xem)
	#self.blockvalues = blockvalues

	readvalues = ChimeraControls.ConvertBlockvalues(self.ChimeraSettings, blockvalues)
	#self.readvalues = readvalues
	return readvalues

	def RecordTrace(self):
	blockvalues = ChimeraControls.CHIMERA_process_triggers(self.ChimeraSettings,self.xem)
	#self.blockvalues = blockvalues

	readvalues = ChimeraControls.ConvertBlockvalues(self.ChimeraSettings, blockvalues)
	#self.readvalues = readvalues
	Samplerate = self.ChimeraSettings.ADCSAMPLERATE
	displaybuffer, self.displaySamplerate = functions.LowPass(readvalues, Samplerate, self.lowpass)

	#displaybuffer = ChimeraControls.lowpass(self.ChimeraSettings, readvalues, cutoff=self.lowpass)
	return displaybuffer

	#def SaveSettings(self, fileName):
	# if fileName is not None and not os.path.exists(fileName):
	# filePath = os.path.split(fileName)
	# if not os.path.isdir(filePath):
	# os.mkdir(filePath)
	# else:
	# fileName = QtGui.QFileDialog.getOpenFileName()
	# fileName = fileName[0]
	# print(fileName)
	#
	# f = open(fileName, 'rb')
	# ChimeraSettings = self.ChimeraSettings
	# pickle.dump(ChimeraSettings, f)
	# f.close()
	# print('Saved as ' + fileName)

	def LoadInstance(self, fileName):
	if fileName is None or os.path.exists(fileName):
	fileName = QtGui.QFileDialog.getOpenFileName()
	fileName = fileName[0]
	print(fileName)

	f = open(fileName, 'rb')
	ChimeraSettings = pickle.load(f)
	f.close()

	self.ChimeraSettings = ChimeraSettings
	print('Loaded from ' + fileName + '. Re-initializing...')

	ChimeraControls.InitializeChimera(self.ChimeraSettings, self.xem)

	def updateBW(self):
	out = ChimeraControls.CHIMERA_bandwidthtimer(self.ChimeraSettings, self.xem)
	text1 = "Time\n{0}\nUSB Read Rate\n{1:} kHz\nUSB Write Rate\n{2}".format(out['text_time'],
	out['USB_readrate'],
	out['USB_writerate'])
	print(text1)
	text2 = "Buffer\n{0} kB\nBuffer Size\n{1} %\nSeconds buffered\n{2:.3f} sec".format(out['buffer'],
	out['bufferPC'],
	out['bufferseconds'])
	print(text2)

	# def update(self):

	# def PlotData(self):

	def ResetBuffer(self):
	print("Buffer is resetting...")
	ans1 = self.xem.SetWireInValue(self.ChimeraSettings.EP_WIREIN_TEST1, self.ChimeraSettings.EPBIT_GLOBALRESET, self.ChimeraSettings.EPBIT_GLOBALRESET)
	self.xem.UpdateWireIns()
	time.sleep(0.1)
	ans2 = self.xem.SetWireInValue(self.ChimeraSettings.EP_WIREIN_TEST1, 0, self.ChimeraSettings.EPBIT_GLOBALRESET)
	self.xem.UpdateWireIns()
	#self.RestartBuffer = 1

	def ZeroVolt(self):
	Vdelta = 0.02
	print('Measuring at {} ...'.format(Volt.format_data(Vdelta)), end='')
	self.SetVoltage(Vdelta, write=False)
	self.ResetBuffer()
	time.sleep(1)
	measI1 = np.mean(self.RecordTrace())
	print('{}'.format(Amp.format_data(measI1)))

	print('Measuring at {} ...'.format(Volt.format_data(0)), end='')
	self.SetVoltage(0, write=False)
	self.ResetBuffer()
	time.sleep(1)
	measI2 = np.mean(self.RecordTrace())
	print('{}'.format(Amp.format_data(measI2)))

	deltaI = measI1-measI2
	if deltaI == 0:
	print('Error, cannot zero voltage: deltaI = 0')
	else:
	measR = Vdelta / deltaI
	self.ResetBuffer()
	self.ChimeraSettings.voltageOffset += -measI2 * measR
	print('New voltage offset: {}'.format(Volt.format_data(self.ChimeraSettings.voltageOffset)))
	ChimeraControls.CHIMERA_updateDACvalues1(self.ChimeraSettings, self.xem)
	self.SetVoltage(self.ChimeraSettings.voltageOffset)

	def SaveVoltage(self):
	savingFolder = os.path.join(self.DataFolder, self.todaysfolder)
	savingName = self.experimentName + 'Vdata.csv'

	fullpath = os.path.join(savingFolder, savingName)
	data = [datetime.datetime.now(), self.newbiasvalue]

	with open(fullpath, 'w') as csvfile:
	writeline = csv.writer(csvfile, delimiter=',')
	writeline.writerows(data)


	class ChimeraPlot:

	def __init__(self, Chimera):
	self.fig, self.ax = plt.subplots(1, 1)
	self.ax.set_xlabel('Time [s]')
	self.ax.set_ylabel('Current [nA]')

	self.samplerate = Chimera.displaySamplerate

	def Update(self, trace):

	x = np.arange(len(g.trace)) / self.samplerate

	currentIDC = np.mean(trace)
	currentRMS = np.std(trace)

	if self.ax.lines:
	for line in self.ax.lines:
	line.set_xdata(x)
	line.set_ydata(trace)
	else:
	self.ax.plot(x, trace)

	self.ax.set_ylim([currentIDC - 10 * currentRMS, currentIDC + 10 * currentRMS])
	self.fig.canvas.draw()

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