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larsrolliklarsrollik
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initial code from original github.com/sanworks/pulsepal repo [develop branch] added for integration with pybpod-api com arcom implementation
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‎templatepy/__init__.py ‎pypulsepal/__init__.py

File renamed without changes.

‎pypulsepal/pulsepal.py

+244
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,244 @@
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from ArCOM import ArCOMObject
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import math
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class PulsePalObject(object):
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def __init__(self, PortName):
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self.OpMenuByte = 213
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self.model = 0
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self.dac_bitMax = 0;
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self.Port = ArCOMObject(PortName, 115200)
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# Handshake to confirm connectivity
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self.Port.write((self.OpMenuByte,72), 'uint8')
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Handshake = self.Port.read(1, 'uint8')
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if Handshake != 75:
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raise PulsePalError('Error: incorrect handshake returned.')
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FirmwareVersion = self.Port.read(1, 'uint32')
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if FirmwareVersion < 20:
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self.model = 1;
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self.dac_bitMax = 255;
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else:
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self.model = 2;
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self.dac_bitMax = 65535;
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self.firmwareVersion = FirmwareVersion
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if self.firmwareVersion == 20:
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print("Notice: NOTE: A firmware update is available. It fixes a bug in Pulse Gated trigger mode when used with multiple inputs.")
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print("To update, follow the instructions at https://sites.google.com/site/pulsepalwiki/updating-firmware")
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self.Port.write((self.OpMenuByte,89,80,89,84,72,79,78), 'uint8') # Client name op + 'PYTHON' in ASCII
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self.cycleFrequency = 20000;
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self.isBiphasic = [float('nan'),0, 0, 0, 0];
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self.phase1Voltage = [float('nan'),5, 5, 5, 5];
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self.phase2Voltage = [float('nan'),-5, -5, -5, -5];
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self.restingVoltage = [float('nan'),0, 0, 0, 0];
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self.phase1Duration = [float('nan'),0.001, 0.001, 0.001, 0.001];
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self.interPhaseInterval = [float('nan'),0.001, 0.001, 0.001, 0.001];
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self.phase2Duration = [float('nan'),0.001, 0.001, 0.001, 0.001];
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self.interPulseInterval = [float('nan'),0.01, 0.01, 0.01, 0.01];
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self.burstDuration = [float('nan'),0, 0, 0, 0];
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self.interBurstInterval = [float('nan'),0, 0, 0, 0];
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self.pulseTrainDuration = [float('nan'),1, 1, 1, 1];
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self.pulseTrainDelay = [float('nan'),0, 0, 0, 0];
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self.linkTriggerChannel1 = [float('nan'),1, 1, 1, 1];
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self.linkTriggerChannel2 = [float('nan'),0, 0, 0, 0];
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self.customTrainID = [float('nan'),0, 0, 0, 0];
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self.customTrainTarget = [float('nan'),0, 0, 0, 0];
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self.customTrainLoop = [float('nan'),0, 0, 0, 0];
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self.triggerMode = [float('nan'),0, 0];
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self.outputParameterNames = ['isBiphasic', 'phase1Voltage','phase2Voltage', 'phase1Duration', 'interPhaseInterval',
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'phase2Duration','interPulseInterval', 'burstDuration', 'interBurstInterval', 'pulseTrainDuration',
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'pulseTrainDelay', 'linkTriggerChannel1', 'linkTriggerChannel2', 'customTrainID',
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'customTrainTarget', 'customTrainLoop', 'restingVoltage']
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self.triggerParameterNames = ['triggerMode']
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def setFixedVoltage(self, channel, voltage):
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voltage = math.ceil(((voltage+10)/float(20))*self.dac_bitMax) # Convert volts to bytes
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if self.model == 1:
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self.Port.write((self.OpMenuByte, 79, channel, voltage), 'uint8')
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else:
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self.Port.write((self.OpMenuByte, 79, channel), 'uint8', voltage, 'uint16')
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# Receive acknowledgement
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ok = self.Port.read(1, 'uint8')
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if len(ok) == 0:
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raise PulsePalError('Error: Pulse Pal did not return an acknowledgement byte after a call to setFixedVoltage.')
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def programOutputChannelParam(self, paramName, channel, value):
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originalValue = value
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if isinstance(paramName, str):
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paramCode = self.outputParameterNames.index(paramName)+1
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else:
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paramCode = paramName
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if 2 <= paramCode <= 3 or paramCode == 17:
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value = math.ceil(((value+10)/float(20))*self.dac_bitMax) # Convert volts to bits
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if self.model == 1:
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self.Port.write((self.OpMenuByte,74,paramCode,channel,value),'uint8')
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else:
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self.Port.write((self.OpMenuByte,74,paramCode,channel),'uint8',value,'uint16')
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elif 4 <= paramCode <= 11:
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self.Port.write((self.OpMenuByte,74,paramCode,channel),'uint8',value*self.cycleFrequency,'uint32')
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else:
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self.Port.write((self.OpMenuByte,74,paramCode,channel,value),'uint8')
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# Receive acknowledgement
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ok = self.Port.read(1, 'uint8')
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if len(ok) == 0:
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raise PulsePalError('Error: Pulse Pal did not return an acknowledgement byte after a call to programOutputChannelParam.')
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# Update the PulsePal object's parameter fields
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if paramCode == 1:
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self.isBiphasic[channel] = originalValue
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elif paramCode == 2:
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self.phase1Voltage[channel] = originalValue
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elif paramCode == 3:
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self.phase2Voltage[channel] = originalValue
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elif paramCode == 4:
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self.phase1Duration[channel] = originalValue
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elif paramCode == 5:
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self.interPhaseInterval[channel] = originalValue
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elif paramCode == 6:
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self.phase2Duration[channel] = originalValue
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elif paramCode == 7:
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self.interPulseInterval[channel] = originalValue
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elif paramCode == 8:
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self.burstDuration[channel] = originalValue
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elif paramCode == 9:
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self.interBurstInterval[channel] = originalValue
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elif paramCode == 10:
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self.pulseTrainDuration[channel] = originalValue
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elif paramCode == 11:
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self.pulseTrainDelay[channel] = originalValue
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elif paramCode == 12:
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self.linkTriggerChannel1[channel] = originalValue
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elif paramCode == 13:
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self.linkTriggerChannel2[channel] = originalValue
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elif paramCode == 14:
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self.customTrainID[channel] = originalValue
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elif paramCode == 15:
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self.customTrainTarget[channel] = originalValue
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elif paramCode == 16:
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self.customTrainLoop[channel] = originalValue
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elif paramCode == 17:
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self.restingVoltage[channel] = originalValue
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def programTriggerChannelParam(self, paramName, channel, value):
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originalValue = value
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if isinstance(paramName, str):
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paramCode = self.triggerParameterNames.index(paramName)+128
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else:
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paramCode = paramName
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self.Port.write((self.OpMenuByte,74,paramCode,channel,value),'uint8')
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# Receive acknowledgement
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ok = self.Port.read(1, 'uint8')
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if len(ok) == 0:
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raise PulsePalError('Error: Pulse Pal did not return an acknowledgement byte after a call to programTriggerChannelParam.')
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if paramCode == 1:
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self.triggerMode[channel] = originalValue
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def syncAllParams(self):
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# Prepare 32-bit time params
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programValues32 = [0]*32; pos = 0
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for i in range(1,5):
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programValues32[pos] = self.phase1Duration[i]*self.cycleFrequency; pos+=1
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programValues32[pos] = self.interPhaseInterval[i]*self.cycleFrequency; pos+=1
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programValues32[pos] = self.phase2Duration[i]*self.cycleFrequency; pos+=1
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programValues32[pos] = self.interPulseInterval[i]*self.cycleFrequency; pos+=1
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programValues32[pos] = self.burstDuration[i]*self.cycleFrequency; pos+=1
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programValues32[pos] = self.interBurstInterval[i]*self.cycleFrequency; pos+=1
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programValues32[pos] = self.pulseTrainDuration[i]*self.cycleFrequency; pos+=1
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programValues32[pos] = self.pulseTrainDelay[i]*self.cycleFrequency; pos+=1
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# Prepare 16-bit voltages
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if self.model == 2:
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programValues16 = [0]*12;
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pos = 0
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for i in range(1,5):
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value = math.ceil(((self.phase1Voltage[i]+10)/float(20))*self.dac_bitMax) # Convert volts to bits
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programValues16[pos] = value; pos+=1
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value = math.ceil(((self.phase2Voltage[i]+10)/float(20))*self.dac_bitMax) # Convert volts to bits
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programValues16[pos] = value; pos+=1
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value = math.ceil(((self.restingVoltage[i]+10)/float(20))*self.dac_bitMax) # Convert volts to bits
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programValues16[pos] = value; pos+=1
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# Prepare 8-bit params
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if self.model == 1:
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programValues8 = [0]*28;
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else:
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programValues8 = [0]*16;
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pos = 0
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for i in range(1,5):
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programValues8[pos] = self.isBiphasic[i]; pos+=1
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if self.model == 1:
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value = math.ceil(((self.phase1Voltage[i]+10)/float(20))*self.dac_bitMax) # Convert volts to bits
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programValues8[pos] = value; pos+=1
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value = math.ceil(((self.phase2Voltage[i]+10)/float(20))*self.dac_bitMax) # Convert volts to bits
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programValues8[pos] = value; pos+=1
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programValues8[pos] = self.customTrainID[i]; pos+=1
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programValues8[pos] = self.customTrainTarget[i]; pos+=1
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programValues8[pos] = self.customTrainLoop[i]; pos+=1
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if self.model == 1:
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value = math.ceil(((self.restingVoltage[i]+10)/float(20))*self.dac_bitMax) # Convert volts to bits
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programValues8[pos] = value; pos+=1
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# Prepare trigger channel link params
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programValuesTL = [0]*8; pos = 0
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for i in range(1,5):
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programValuesTL[pos] = self.linkTriggerChannel1[i]; pos+=1
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for i in range(1,5):
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programValuesTL[pos] = self.linkTriggerChannel2[i]; pos+=1
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# Send all params to device
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if self.model == 1:
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self.Port.write(
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(self.OpMenuByte, 73), 'uint8',
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programValues32, 'uint32',
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programValues8, 'uint8',
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programValuesTL, 'uint8',
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self.triggerMode[1:3], 'uint8')
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if self.model == 2:
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self.Port.write(
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(self.OpMenuByte, 73), 'uint8',
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programValues32, 'uint32',
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programValues16, 'uint16',
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programValues8, 'uint8',
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programValuesTL, 'uint8',
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self.triggerMode[1:3], 'uint8')
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# Receive acknowledgement
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ok = self.Port.read(1, 'uint8')
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if len(ok) == 0:
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raise PulsePalError('Error: Pulse Pal did not return an acknowledgement byte after a call to syncAllParams.')
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def sendCustomPulseTrain(self, customTrainID, pulseTimes, pulseVoltages):
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nPulses = len(pulseTimes)
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for i in range(0,nPulses):
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pulseTimes[i] = pulseTimes[i]*self.cycleFrequency # Convert seconds to multiples of minimum cycle (100us)
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pulseVoltages[i] = math.ceil(((pulseVoltages[i]+10)/float(20))*self.dac_bitMax) # Convert volts to bytes
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opCode = customTrainID + 74 # 75 if custom train 1, 76 if 2
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if self.model == 1:
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self.Port.write((self.OpMenuByte , opCode, 0), 'uint8', nPulses, 'uint32', pulseTimes, 'uint32', pulseVoltages, 'uint8')
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else:
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self.Port.write((self.OpMenuByte , opCode), 'uint8', nPulses, 'uint32', pulseTimes, 'uint32', pulseVoltages, 'uint16')
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# Receive acknowledgement
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ok = self.Port.read(1, 'uint8')
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if len(ok) == 0:
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raise PulsePalError('Error: Pulse Pal did not return an acknowledgement byte after a call to sendCustomPulseTrain.')
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def sendCustomWaveform(self, customTrainID, pulseWidth, pulseVoltages): # For custom pulse trains with pulse times = pulse width
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nPulses = len(pulseVoltages)
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pulseTimes = [0]*nPulses
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pulseWidth = pulseWidth*self.cycleFrequency # Convert seconds to to multiples of minimum cycle (100us)
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for i in range(0,nPulses):
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pulseTimes[i] = pulseWidth*i # Add consecutive pulse
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pulseVoltages[i] = math.ceil(((pulseVoltages[i]+10)/float(20))*self.dac_bitMax) # Convert volts to bytes
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opCode = customTrainID + 74 # 75 if custom train 1, 76 if 2
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if self.model == 1:
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self.Port.write((self.OpMenuByte , opCode, 0), 'uint8', nPulses, 'uint32', pulseTimes, 'uint32', pulseVoltages, 'uint8')
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else:
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self.Port.write((self.OpMenuByte , opCode), 'uint8', nPulses, 'uint32', pulseTimes, 'uint32', pulseVoltages, 'uint16')
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# Receive acknowledgement
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ok = self.Port.read(1, 'uint8')
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if len(ok) == 0:
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raise PulsePalError('Error: Pulse Pal did not return an acknowledgement byte after a call to sendCustomWaveform.')
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def setContinuousLoop(self, channel, state):
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self.Port.write((self.OpMenuByte, 82, channel, state), 'uint8')
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def triggerOutputChannels(self, channel1, channel2, channel3, channel4):
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triggerByte = (1*channel1) + (2*channel2) + (4*channel3) + (8*channel4)
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self.Port.write((self.OpMenuByte, 77, triggerByte), 'uint8')
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def abortPulseTrains(self):
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self.Port.write((self.OpMenuByte, 80), 'uint8')
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def __del__(self):
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self.Port.write((self.OpMenuByte, 81), 'uint8')
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self.Port.close()
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class PulsePalError(Exception):
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pass

‎setup.py

+6-9
Original file line numberDiff line numberDiff line change
@@ -13,18 +13,20 @@
1313

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setup(
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name="templatepy",
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name="pypulsepal",
1717
version="0.0.1.dev0",
18-
description="templatepy",
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description="pypulsepal",
1919
long_description=long_description,
2020
long_description_content_type="text/markdown",
2121
python_requires=">=3.6",
2222
packages=find_packages(),
23-
url="https://github.com/larsrollik/templatepy",
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url="https://github.com/larsrollik/pypulsepal",
2424
author="Lars B. Rollik",
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author_email="L.B.Rollik@protonmail.com",
2626
license=license_text,
27-
install_requires=[],
27+
install_requires=[
28+
"pybpod-api", # for Arcom
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],
2830
extras_require={
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"dev": [
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"black",
@@ -39,9 +41,4 @@
3941
},
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zip_safe=False,
4143
include_package_data=True,
42-
entry_points={
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"console_scripts": [
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"console_script_name = module.path.to.function:function_name",
45-
],
46-
},
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)

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