update model for python3 and modeldb-ci support (#4)

* update model for python3 and modeldb-ci support

* izhi2007.mod: `t0` as RANGE in the NEURON block

Co-authored-by: Alexandru Săvulescu <[email protected]>

Author: kotsaloscv

analysis.py

@@ -1,68 +1,68 @@
 # dummyArm.py -- Python code for interfacing the sim with a virtual arm
-# 
+#
 # Last update: 07/21/14 ([email protected])
 
-import matplotlib 
+import matplotlib
 matplotlib.use('TkAgg') # for visualization
-from socket import *  
-import select	# for socket reading
-import struct	# to pack messages for socket comms	
+from socket import *
+import select   # for socket reading
+import struct   # to pack messages for socket comms
 import numpy
 from pylab import figure, show, ion, pause
 
 
-# Initialize and setup the sockets and data format 
+# Initialize and setup the sockets and data format
 def setup():
-	sendMsgFormat = "dd"  # messages contain 2 doubles = joint angles of shoulder and elbow 
-	receiveMsgFormat = "dd"  # messages contain 2 doubles =  velocities
-	receiveMsgSize = struct.calcsize(receiveMsgFormat)
-	localHostIP =  "127.0.0.1"#"localhost"#"192.168.1.2"# # set IP for local connection 
-
-	print "Setting up connection..." # setup connection to model
-	sockReceive = socket(AF_INET, SOCK_DGRAM) # create sockets
-	hostPortReceive = 31000 # set port for receiving packets
-	sockReceive.bind(('', hostPortReceive)) # bind to port
-	sockReceive.setblocking(1) # Set blocking/non-blocking mode
-	print ("Created UDP socket to receive packets from NEURON model; binded to port %d"%hostPortReceive)
-		
-	sockSend = socket(AF_INET, SOCK_DGRAM) 	# connect to socket for sending packets	
-	hostPortSend = 32000 # set port for sending packets
-	sockSend.connect((localHostIP, hostPortSend))
-	sockSend.setblocking(1) # Set blocking/non-blocking mode
-	print ("Created UDP socket to send packets to NEURON model; socket connected to IP %s, port %d" % (localHostIP, hostPortSend))
-
-	return sendMsgFormat, receiveMsgFormat,  sockReceive, sockSend
+    sendMsgFormat = "dd"  # messages contain 2 doubles = joint angles of shoulder and elbow
+    receiveMsgFormat = "dd"  # messages contain 2 doubles =  velocities
+    receiveMsgSize = struct.calcsize(receiveMsgFormat)
+    localHostIP =  "127.0.0.1"#"localhost"#"192.168.1.2"# # set IP for local connection
+
+    print("Setting up connection...") # setup connection to model
+    sockReceive = socket(AF_INET, SOCK_DGRAM) # create sockets
+    hostPortReceive = 31000 # set port for receiving packets
+    sockReceive.bind(('', hostPortReceive)) # bind to port
+    sockReceive.setblocking(1) # Set blocking/non-blocking mode
+    print(("Created UDP socket to receive packets from NEURON model; binded to port %d"%hostPortReceive))
+
+    sockSend = socket(AF_INET, SOCK_DGRAM)  # connect to socket for sending packets
+    hostPortSend = 32000 # set port for sending packets
+    sockSend.connect((localHostIP, hostPortSend))
+    sockSend.setblocking(1) # Set blocking/non-blocking mode
+    print(("Created UDP socket to send packets to NEURON model; socket connected to IP %s, port %d" % (localHostIP, hostPortSend)))
+
+    return sendMsgFormat, receiveMsgFormat,  sockReceive, sockSend
 
 # Send and receive packets to/from virtual arm
 def sendAndReceivePackets(dataSend, sendMsgFormat, receiveMsgFormat,  sockReceive, sockSend):
-	dataReceived = [0,0]
-	try:
-		receiveMsgSize = struct.calcsize(receiveMsgFormat)
-		dataReceivedPacked = sockReceive.recv(receiveMsgSize) # read packet from socket	
-		if len(dataReceivedPacked) == receiveMsgSize:
-			dataReceived = struct.unpack(receiveMsgFormat, dataReceivedPacked)
-			print "Received packet from model: (%.2f,%.2f)" % (dataReceived[0],dataReceived[1])
-	except:
-		print "Error receiving packet"
-
-	inputready, outputready, e = select.select([] ,[sockSend],[], 0.0) 	# check if other side ready to receive
-	if len(outputready)>0:
-		try: 
-			sent = sockSend.send(struct.pack(sendMsgFormat, dataSend[0], dataSend[1])) # send packet
-			print "Sent packet to virtual arm: (%.2f, %.2f)" % (dataSend[0], dataSend[1])
-		except:
-			print "Sending socket ready but error sending packet"
-	else:
-		print "Sending socket not ready"	
-	return dataReceived	  
+    dataReceived = [0,0]
+    try:
+        receiveMsgSize = struct.calcsize(receiveMsgFormat)
+        dataReceivedPacked = sockReceive.recv(receiveMsgSize) # read packet from socket
+        if len(dataReceivedPacked) == receiveMsgSize:
+            dataReceived = struct.unpack(receiveMsgFormat, dataReceivedPacked)
+            print("Received packet from model: (%.2f,%.2f)" % (dataReceived[0],dataReceived[1]))
+    except:
+        print("Error receiving packet")
+
+    inputready, outputready, e = select.select([] ,[sockSend],[], 0.0)      # check if other side ready to receive
+    if len(outputready)>0:
+        try:
+            sent = sockSend.send(struct.pack(sendMsgFormat, dataSend[0], dataSend[1])) # send packet
+            print("Sent packet to virtual arm: (%.2f, %.2f)" % (dataSend[0], dataSend[1]))
+        except:
+            print("Sending socket ready but error sending packet")
+    else:
+        print("Sending socket not ready")
+    return dataReceived
 
 # Main code for simple virtual arm
 duration = 4 # sec
 interval = 0.010 # time between packets (sec)
-L1 = 1.0 # arm segment 1 length 
+L1 = 1.0 # arm segment 1 length
 L2 = 0.8 # arm segment 2 length
-shang = numpy.pi/2 # shoulder angle (rad) 
-elang = numpy.pi/2 # elbow angle (rad) 
+shang = numpy.pi/2 # shoulder angle (rad)
+elang = numpy.pi/2 # elbow angle (rad)
 shvel = 0 # shoulder velocity (rad/s)
 elvel = 0 # elbow velocity (rad/s)
 friction = 0.1 # friction coefficient
@@ -75,29 +75,21 @@ def sendAndReceivePackets(dataSend, sendMsgFormat, receiveMsgFormat,  sockReceiv
 ax.grid()
 line, = ax.plot([], [], 'o-', lw=2)
 
-raw_input("Press Enter to continue...")
+input("Press Enter to continue...")
 for i in numpy.arange(0, duration, interval):
-	shang = (shang + shvel * interval) % (2*numpy.pi) # update shoulder angle
-	elang = (elang + elvel * interval) % (2*numpy.pi)# update elbow angle
-	if shang<0: shang = 2*numpy.pi + shang
-	if elang<0: elang = 2*numpy.pi + shang
-	shpos = [L1*numpy.sin(shang), L1*numpy.cos(shang)] # calculate shoulder x-y pos
-	elpos = [L2*numpy.sin(shang+elang) + shpos[0], L2*numpy.cos(shang+elang) + shpos[1]] # calculate elbow x-y pos
-
-	dataSend = [shang, elang] # set data to send
-	dataReceived = sendAndReceivePackets(dataSend, sendMsgFormat, receiveMsgFormat,  sockReceive, sockSend) # send and receive data
-	shvel = shvel+dataReceived[0] - (friction * shvel)# update velocities based on incoming commands (accelerations) and friction
-	elvel = elvel+dataReceived[1] - (friction * elvel)
-
-	line.set_data([0, shpos[0], elpos[0]], [0, shpos[1], elpos[1]]) # update line in figure
-	ax.set_title('Time = %.1f ms, shoulder: pos=%.2f rad, vel=%.2f, acc=%.2f ; elbow: pos = %.2f rad, vel = %.2f, acc=%.2f' % (float(i)*1000, shang, shvel, dataReceived[0] - (friction * shvel), elang, elvel, dataReceived[1] - (friction * elvel) ), fontsize=10)
-	show()
-	pause(0.0001) # pause so that the figure refreshes at every time step
-
-
-
-
-
-
-
-
+    shang = (shang + shvel * interval) % (2*numpy.pi) # update shoulder angle
+    elang = (elang + elvel * interval) % (2*numpy.pi)# update elbow angle
+    if shang<0: shang = 2*numpy.pi + shang
+    if elang<0: elang = 2*numpy.pi + shang
+    shpos = [L1*numpy.sin(shang), L1*numpy.cos(shang)] # calculate shoulder x-y pos
+    elpos = [L2*numpy.sin(shang+elang) + shpos[0], L2*numpy.cos(shang+elang) + shpos[1]] # calculate elbow x-y pos
+
+    dataSend = [shang, elang] # set data to send
+    dataReceived = sendAndReceivePackets(dataSend, sendMsgFormat, receiveMsgFormat,  sockReceive, sockSend) # send and receive data
+    shvel = shvel+dataReceived[0] - (friction * shvel)# update velocities based on incoming commands (accelerations) and friction
+    elvel = elvel+dataReceived[1] - (friction * elvel)
+
+    line.set_data([0, shpos[0], elpos[0]], [0, shpos[1], elpos[1]]) # update line in figure
+    ax.set_title('Time = %.1f ms, shoulder: pos=%.2f rad, vel=%.2f, acc=%.2f ; elbow: pos = %.2f rad, vel = %.2f, acc=%.2f' % (float(i)*1000, shang, shvel, dataReceived[0] - (friction * shvel), elang, elvel, dataReceived[1] - (friction * elvel) ), fontsize=10)
+    show()
+    pause(0.0001) # pause so that the figure refreshes at every time step

arm.py

@@ -4,77 +4,77 @@
 
 
 def getTarget0err(f):
-  stdin,stdout = os.popen2("tail -n 4 "+f)
-  stdin.close()
-  lines = stdout.readlines(); stdout.close()
-  line = lines[0].split()
-  return float(line[5])
+    stdin,stdout = os.popen2("tail -n 4 "+f)
+    stdin.close()
+    lines = stdout.readlines(); stdout.close()
+    line = lines[0].split()
+    return float(line[5])
 
 def errorFromShell(filestem, readTarget0ErrFromRunFile, maxGens, maxCands, maxTargets):
 
     minVal = 1
     minValtarg0 = 1
     for igen in range(maxGens):
-            for icand in range(maxCands):
-                    error = []
-                    for itarget in range(maxTargets):
-                            try:
-                                    errfilename = '%s/gen_%s_cand_%d_target_%d_error' % (filestem,igen,icand,itarget)
-                                    runfilename = '%s/gen_%s_cand_%d.run' % (filestem,igen,icand)
-                                    with open(errfilename, 'r') as f:
-                                            error.append(pickle.load(f))
-                                            print 'gen=%d, cand=%d, target=%d: error = %f' % (igen, icand, itarget, error[-1])
-                            except:
-                                    print('not found file: stem=%s, gen=%d, cand=%d, targ=%d' % (filestem,igen,icand,itarget))
-                    avgErr = pylab.mean(error)
-                    if readTarget0ErrFromRunFile:
-                            try:
-                                    target0err = getTarget0err(runfilename)
-                                    print "error target 0: %.2f \n" % (target0err)  
-                                    if target0err < minValtarg0:
-                                            minValtarg0 = target0err
-                                            minCandtarg0 = icand
-                                            minGentarg0 = igen     
-                            except:       
-                                    print "error reading file:", runfilename        
+        for icand in range(maxCands):
+            error = []
+            for itarget in range(maxTargets):
+                try:
+                    errfilename = '%s/gen_%s_cand_%d_target_%d_error' % (filestem,igen,icand,itarget)
+                    runfilename = '%s/gen_%s_cand_%d.run' % (filestem,igen,icand)
+                    with open(errfilename, 'r') as f:
+                        error.append(pickle.load(f))
+                        print('gen=%d, cand=%d, target=%d: error = %f' % (igen, icand, itarget, error[-1]))
+                except:
+                    print(('not found file: stem=%s, gen=%d, cand=%d, targ=%d' % (filestem,igen,icand,itarget)))
+            avgErr = pylab.mean(error)
+            if readTarget0ErrFromRunFile:
+                try:
+                    target0err = getTarget0err(runfilename)
+                    print("error target 0: %.2f \n" % (target0err))
+                    if target0err < minValtarg0:
+                        minValtarg0 = target0err
+                        minCandtarg0 = icand
+                        minGentarg0 = igen
+                except:
+                    print("error reading file:", runfilename)
 
-                    print "avg error: %.2f \n" % (avgErr)
-                    if avgErr < minVal:
-                            minVal = avgErr
-                            minCand = icand
-                            minGen = igen
+            print("avg error: %.2f \n" % (avgErr))
+            if avgErr < minVal:
+                minVal = avgErr
+                minCand = icand
+                minGen = igen
 
-    print "Min error = %f ; gen = %d ; cand = %d \n" % (minVal, minGen, minCand)
-    if readTarget0ErrFromRunFile: 
-            print "Min error (target 0) = %f ; gen = %d ; cand = %d \n" % (minValtarg0, minGentarg0, minCandtarg0)
+    print("Min error = %f ; gen = %d ; cand = %d \n" % (minVal, minGen, minCand))
+    if readTarget0ErrFromRunFile:
+        print("Min error (target 0) = %f ; gen = %d ; cand = %d \n" % (minValtarg0, minGentarg0, minCandtarg0))
 
 def errorFromPickle(filestem, maxGens, maxCands):
     from collections import OrderedDict
     minVals = OrderedDict
     minVals = {'error0_pre': [1,0,0], 'error1_pre': [1,0,0], 'error_pre': [1,0,0], 'errord_pre': [1,0,0], \
         'error0_post': [1,0,0], 'error1_post': [1,0,0], 'error_post': [1,0,0], 'errord_post': [1,0,0], \
         'error0_lesion': [1,0,0], 'error1_lesion': [1,0,0], 'error_pre': [1,0,0], 'errord_tot': [1,0,0], 'error_fitness': [1,0,0]}
-    
+
     for igen in range(maxGens):
         for icand in range(maxCands):
             error = []
             try:
                 errfilename = '%s/gen_%d_cand_%d_target_0_error' % (filestem,igen,icand)
                 with open(errfilename, 'r') as f:
-                        error = pickle.load(f)
-                        #print 'gen=%d, cand=%d, errord_tot = %f, error_fitness = %f' % (igen, icand, error['errord_tot'], error['error_fitness'])
-                for key,val in error.iteritems():
-                    if val < minVals[key][0]: 
+                    error = pickle.load(f)
+                    #print 'gen=%d, cand=%d, errord_tot = %f, error_fitness = %f' % (igen, icand, error['errord_tot'], error['error_fitness'])
+                for key,val in error.items():
+                    if val < minVals[key][0]:
                         minVals[key][0] = val
                         minVals[key][1] = igen
                         minVals[key][2] = icand
             except:
-                    print('not found file: stem=%s, gen=%d, cand=%d' % (filestem,igen,icand))
+                print(('not found file: stem=%s, gen=%d, cand=%d' % (filestem,igen,icand)))
+
+    for key,val in minVals.items():
+        print("%s = %f ; gen = %d ; cand = %d \n" % (key, val[0], val[1], val[2]))
+
 
-    for key,val in minVals.iteritems():
-        print "%s = %f ; gen = %d ; cand = %d \n" % (key, val[0], val[1], val[2])
-   
-   
 
 # set params
 filestem = '../data/15aug29_evolutionStrategy'
@@ -88,5 +88,3 @@ def errorFromPickle(filestem, maxGens, maxCands):
 
 # call function to obtain errors from pickle file
 errorFromPickle(filestem, maxGens, maxCands)
-
-