Updated spreadsheet with latest readers

.gitignore

@@ -91,3 +91,7 @@ arm64
 /c302/.ipynb_checkpoints
 .ipynb_checkpoints
 /c302/data/~$*.xlsx
+/examples/test/images/cell_C.xml
+/examples/test/images/c302_C1_Oscillator.net.nml
+/examples/test/images/LEMS_c302_C1_Oscillator.xml
+/c302/VarshneyDataReader2.py

c302/ConnectomeReader.py

@@ -0,0 +1,180 @@
+# -*- coding: utf-8 -*-
+
+############################################################
+
+#    Utilities for reading/writing/parsing NeuroML 2 files
+
+############################################################
+
+from c302 import print_
+
+PREFERRED_NEURON_NAMES = ['ADAL', 'ADAR', 'ADEL', 'ADER', 'ADFL', 'ADFR', 'ADLL', 'ADLR', 'AFDL', 'AFDR', 'AIAL', 'AIAR', 'AIBL', 'AIBR', 'AIML', 'AIMR', 'AINL', 'AINR', 'AIYL', 'AIYR', 'AIZL', 'AIZR', 'ALA', 'ALML', 'ALMR', 'ALNL', 'ALNR', 'AQR', 'AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'ASEL', 'ASER', 'ASGL', 'ASGR', 'ASHL', 'ASHR', 'ASIL', 'ASIR', 'ASJL', 'ASJR', 'ASKL', 'ASKR', 'AUAL', 'AUAR', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'AVEL', 'AVER', 'AVFL', 'AVFR', 'AVG', 'AVHL', 'AVHR', 'AVJL', 'AVJR', 'AVKL', 'AVKR', 'AVL', 'AVM', 'AWAL', 'AWAR', 'AWBL', 'AWBR', 'AWCL', 'AWCR', 'BAGL', 'BAGR', 'BDUL', 'BDUR', 'CANL', 'CANR', 'CEPDL', 'CEPDR', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVA', 'DVB', 'DVC', 'FLPL', 'FLPR', 'HSNL', 'HSNR', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'IL2DL', 'IL2DR', 'IL2L', 'IL2R', 'IL2VL', 'IL2VR', 'LUAL', 'LUAR', 'M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'MCL', 'MCR', 'MI', 'NSML', 'NSMR', 'OLLL', 'OLLR', 'OLQDL', 'OLQDR', 'OLQVL', 'OLQVR', 'PDA', 'PDB', 'PDEL', 'PDER', 'PHAL', 'PHAR', 'PHBL', 'PHBR', 'PHCL', 'PHCR', 'PLML', 'PLMR', 'PLNL', 'PLNR', 'PQR', 'PVCL', 'PVCR', 'PVDL', 'PVDR', 'PVM', 'PVNL', 'PVNR', 'PVPL', 'PVPR', 'PVQL', 'PVQR', 'PVR', 'PVT', 'PVWL', 'PVWR', 'RIAL', 'RIAR', 'RIBL', 'RIBR', 'RICL', 'RICR', 'RID', 'RIFL', 'RIFR', 'RIGL', 'RIGR', 'RIH', 'RIML', 'RIMR', 'RIPL', 'RIPR', 'RIR', 'RIS', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMFR', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SAADL', 'SAADR', 'SAAVL', 'SAAVR', 'SABD', 'SABVL', 'SABVR', 'SDQL', 'SDQR', 'SIADL', 'SIADR', 'SIAVL', 'SIAVR', 'SIBDL', 'SIBDR', 'SIBVL', 'SIBVR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'URBL', 'URBR', 'URXL', 'URXR', 'URYDL', 'URYDR', 'URYVL', 'URYVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9']
+PREFERRED_MUSCLE_NAMES = ['MANAL', 'MDL01', 'MDL02', 'MDL03', 'MDL04', 'MDL05', 'MDL06', 'MDL07', 'MDL08', 'MDL09', 'MDL10', 'MDL11', 'MDL12', 'MDL13', 'MDL14', 'MDL15', 'MDL16', 'MDL17', 'MDL18', 'MDL19', 'MDL20', 'MDL21', 'MDL22', 'MDL23', 'MDL24', 'MDR01', 'MDR02', 'MDR03', 'MDR04', 'MDR05', 'MDR06', 'MDR07', 'MDR08', 'MDR09', 'MDR10', 'MDR11', 'MDR12', 'MDR13', 'MDR14', 'MDR15', 'MDR16', 'MDR17', 'MDR18', 'MDR19', 'MDR20', 'MDR21', 'MDR22', 'MDR23', 'MDR24', 'MVL01', 'MVL02', 'MVL03', 'MVL04', 'MVL05', 'MVL06', 'MVL07', 'MVL08', 'MVL09', 'MVL10', 'MVL11', 'MVL12', 'MVL13', 'MVL14', 'MVL15', 'MVL16', 'MVL17', 'MVL18', 'MVL19', 'MVL20', 'MVL21', 'MVL22', 'MVL23', 'MVR01', 'MVR02', 'MVR03', 'MVR04', 'MVR05', 'MVR06', 'MVR07', 'MVR08', 'MVR09', 'MVR10', 'MVR11', 'MVR12', 'MVR13', 'MVR14', 'MVR15', 'MVR16', 'MVR17', 'MVR18', 'MVR19', 'MVR20', 'MVR21', 'MVR22', 'MVR23', 'MVR24', 'MVULVA']
+
+
+def convert_to_preferred_muscle_name(muscle):
+
+    if muscle.startswith("BWM-VL"):
+        return "MVL%s" %muscle[6:]
+    elif muscle.startswith("BWM-VR"):
+        return "MVR%s" %muscle[6:]
+    elif muscle.startswith("BWM-DL"):
+        return "MDL%s" %muscle[6:]
+    elif muscle.startswith("BWM-DR"):
+        return "MDR%s" %muscle[6:]
+    elif muscle=='LegacyBodyWallMuscles':
+        return 'BWM'
+    else:
+        return muscle + "???"
+
+def get_all_muscle_prefixes():
+    return ["pm", "vm", "um", "BWM-D", "BWM-V", "LegacyBodyWallMuscles"]
+
+
+def get_body_wall_muscle_prefixes():
+    return ["BWM-D", "BWM-V", "LegacyBodyWallMuscles"]
+
+
+def is_muscle(cell):
+    known_muscle_prefixes = get_all_muscle_prefixes()
+    return cell.startswith(tuple(known_muscle_prefixes))
+
+
+def is_body_wall_muscle(cell):
+    known_muscle_prefixes = get_body_wall_muscle_prefixes()
+    return cell.startswith(tuple(known_muscle_prefixes))
+
+
+def is_neuron(cell):
+    return not is_body_wall_muscle(cell)
+
+class ConnectionInfo:
+
+    def __init__(self,
+                 pre_cell,
+                 post_cell,
+                 number,
+                 syntype,
+                 synclass):
+
+        self.pre_cell = pre_cell
+        self.post_cell = post_cell
+        self.number = number
+        self.syntype = syntype
+        self.synclass = synclass
+
+
+    def __str__(self):
+        return "Connection from %s to %s (%i times, type: %s, neurotransmitter: %s)"%(self.pre_cell, self.post_cell, self.number, self.syntype, self.synclass)
+
+    def short(self):
+        return "Connection from %s to %s (%s)"%(self.pre_cell, self.post_cell, self.syntype)
+
+    def __eq__(self, other):
+        return other.pre_cell == self.pre_cell and other.post_cell == self.post_cell and  other.number == self.number and other.syntype == self.syntype and other.synclass == self.synclass 
+
+    def __lt__(self, other):
+        if other.pre_cell+other.post_cell > self.pre_cell+self.post_cell:
+            return True
+        else: 
+            return False
+
+    def __repr__(self):
+        return self.__str__()
+
+
+def check_neurons(cells):
+
+    preferred = []
+    not_in_preferred = []
+    missing_preferred = [n for n in PREFERRED_NEURON_NAMES]
+    for c in cells:
+        if not c in PREFERRED_NEURON_NAMES:
+            not_in_preferred.append(c)
+        else:
+            preferred.append(c)
+        if c in missing_preferred:
+            missing_preferred.remove(c)
+
+    return preferred, not_in_preferred, missing_preferred
+
+def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns):
+
+    print_("Found %s cells: %s\n"%(len(cells),sorted(cells)))
+    #assert(len(cells) == 302)
+    #print_("Expected number of cells correct if include_nonconnected_cells=True")
+
+    preferred, not_in_preferred, missing_preferred = check_neurons(cells)
+
+    print_("Found %s non-neuron(s) here: %s\n"%(len(not_in_preferred),sorted(not_in_preferred)))
+    print_("Known neurons not present: %s\n"%(sorted(missing_preferred)))
+
+    print_("Found %s connections..."%(len(neuron_conns)))
+    for c in neuron_conns[:5]: print_("   %s"%c)
+
+    print_("   ...\n")
+    nts = {}
+    nts_tot = {}
+    for c in neuron_conns:
+        nt = c.synclass
+        if not nt in nts:
+            nts[nt] = 0
+            nts_tot[nt] = 0
+        nts[nt]+=1
+        nts_tot[nt]+=c.number
+
+    for nt in sorted(nts.keys()):
+        print_("   %s present in %s connections, %s synapses total (avg %.3f syns per conn)"%(nt, nts[nt], nts_tot[nt], nts_tot[nt]/nts[nt]))
+
+    print_("")
+    print_("   ---  Muscles  ---")
+    print_("")
+
+    print_("Found %s muscles: %s\n"%(len(muscles),sorted(muscles)))
+    not_in_preferred = []
+    for m in muscles:
+        if not m in PREFERRED_MUSCLE_NAMES:
+            not_in_preferred.append(m)
+
+    print_("Found %s unidentified muscles: %s\n"%(len(not_in_preferred),sorted(not_in_preferred)))
+
+    print_("Found %i neurons connected to muscles: %s\n"%(len(neurons2muscles), sorted(neurons2muscles)))
+    print_("Found %i muscles connected to neurons: %s\n"%(len(muscles), sorted(muscles)))
+
+    print_("Found %i connections between neurons and muscles%s\n"%(len(muscle_conns), (', e.g. %s'%muscle_conns[0]) if len(muscle_conns)>0 else ''))
+
+    nts = {}
+    nts_tot = {}
+    for c in muscle_conns:
+        nt = c.synclass
+        if not nt in nts:
+            nts[nt] = 0
+            nts_tot[nt] = 0
+        nts[nt]+=1
+        nts_tot[nt]+=c.number
+
+    for nt in nts:
+        print_("  %s present in %s connections, %s synapses total (avg %.3f syns per conn)"%(nt, nts[nt], nts_tot[nt], nts_tot[nt]/nts[nt]))
+
+
+    core_set = ['AVBL','PVCL','VA6', 'VB6', 'VD6', 'DB4', 'DD4']
+    #core_set = ['VA6', 'VD6']
+    print_("\n\nConnections between cells in the subset %s:\n"%(core_set))
+
+
+    for c in neuron_conns:
+        if c.pre_cell in core_set and c.post_cell in core_set:
+            print_(str(c))
+
+
+    print_("")
+
+
+if __name__ == "__main__":
+
+    from SpreadsheetDataReader import read_data, read_muscle_data
+
+    cells, neuron_conns = read_data(include_nonconnected_cells=True)
+    neurons2muscles, muscles, muscle_conns = read_muscle_data()
+
+    analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)

c302/NeuroMLUtilities.py

@@ -8,44 +8,11 @@
 
 from c302 import print_
 
-PREFERRED_NEURON_NAMES = ['ADAL', 'ADAR', 'ADEL', 'ADER', 'ADFL', 'ADFR', 'ADLL', 'ADLR', 'AFDL', 'AFDR', 'AIAL', 'AIAR', 'AIBL', 'AIBR', 'AIML', 'AIMR', 'AINL', 'AINR', 'AIYL', 'AIYR', 'AIZL', 'AIZR', 'ALA', 'ALML', 'ALMR', 'ALNL', 'ALNR', 'AQR', 'AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'ASEL', 'ASER', 'ASGL', 'ASGR', 'ASHL', 'ASHR', 'ASIL', 'ASIR', 'ASJL', 'ASJR', 'ASKL', 'ASKR', 'AUAL', 'AUAR', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'AVEL', 'AVER', 'AVFL', 'AVFR', 'AVG', 'AVHL', 'AVHR', 'AVJL', 'AVJR', 'AVKL', 'AVKR', 'AVL', 'AVM', 'AWAL', 'AWAR', 'AWBL', 'AWBR', 'AWCL', 'AWCR', 'BAGL', 'BAGR', 'BDUL', 'BDUR', 'CANL', 'CANR', 'CEPDL', 'CEPDR', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVA', 'DVB', 'DVC', 'FLPL', 'FLPR', 'HSNL', 'HSNR', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'IL2DL', 'IL2DR', 'IL2L', 'IL2R', 'IL2VL', 'IL2VR', 'LUAL', 'LUAR', 'M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'MCL', 'MCR', 'MI', 'NSML', 'NSMR', 'OLLL', 'OLLR', 'OLQDL', 'OLQDR', 'OLQVL', 'OLQVR', 'PDA', 'PDB', 'PDEL', 'PDER', 'PHAL', 'PHAR', 'PHBL', 'PHBR', 'PHCL', 'PHCR', 'PLML', 'PLMR', 'PLNL', 'PLNR', 'PQR', 'PVCL', 'PVCR', 'PVDL', 'PVDR', 'PVM', 'PVNL', 'PVNR', 'PVPL', 'PVPR', 'PVQL', 'PVQR', 'PVR', 'PVT', 'PVWL', 'PVWR', 'RIAL', 'RIAR', 'RIBL', 'RIBR', 'RICL', 'RICR', 'RID', 'RIFL', 'RIFR', 'RIGL', 'RIGR', 'RIH', 'RIML', 'RIMR', 'RIPL', 'RIPR', 'RIR', 'RIS', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMFR', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SAADL', 'SAADR', 'SAAVL', 'SAAVR', 'SABD', 'SABVL', 'SABVR', 'SDQL', 'SDQR', 'SIADL', 'SIADR', 'SIAVL', 'SIAVR', 'SIBDL', 'SIBDR', 'SIBVL', 'SIBVR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'URBL', 'URBR', 'URXL', 'URXR', 'URYDL', 'URYDR', 'URYVL', 'URYVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9']
-PREFERRED_MUSCLE_NAMES = ['MANAL', 'MDL01', 'MDL02', 'MDL03', 'MDL04', 'MDL05', 'MDL06', 'MDL07', 'MDL08', 'MDL09', 'MDL10', 'MDL11', 'MDL12', 'MDL13', 'MDL14', 'MDL15', 'MDL16', 'MDL17', 'MDL18', 'MDL19', 'MDL20', 'MDL21', 'MDL22', 'MDL23', 'MDL24', 'MDR01', 'MDR02', 'MDR03', 'MDR04', 'MDR05', 'MDR06', 'MDR07', 'MDR08', 'MDR09', 'MDR10', 'MDR11', 'MDR12', 'MDR13', 'MDR14', 'MDR15', 'MDR16', 'MDR17', 'MDR18', 'MDR19', 'MDR20', 'MDR21', 'MDR22', 'MDR23', 'MDR24', 'MVL01', 'MVL02', 'MVL03', 'MVL04', 'MVL05', 'MVL06', 'MVL07', 'MVL08', 'MVL09', 'MVL10', 'MVL11', 'MVL12', 'MVL13', 'MVL14', 'MVL15', 'MVL16', 'MVL17', 'MVL18', 'MVL19', 'MVL20', 'MVL21', 'MVL22', 'MVL23', 'MVR01', 'MVR02', 'MVR03', 'MVR04', 'MVR05', 'MVR06', 'MVR07', 'MVR08', 'MVR09', 'MVR10', 'MVR11', 'MVR12', 'MVR13', 'MVR14', 'MVR15', 'MVR16', 'MVR17', 'MVR18', 'MVR19', 'MVR20', 'MVR21', 'MVR22', 'MVR23', 'MVR24', 'MVULVA']
-
-
-class ConnectionInfo:
-
-    def __init__(self,
-                 pre_cell,
-                 post_cell,
-                 number,
-                 syntype,
-                 synclass):
-
-        self.pre_cell = pre_cell
-        self.post_cell = post_cell
-        self.number = number
-        self.syntype = syntype
-        self.synclass = synclass
-
-
-    def __str__(self):
-        return "Connection from %s to %s (%i times, type: %s, neurotransmitter: %s)"%(self.pre_cell, self.post_cell, self.number, self.syntype, self.synclass)
-
-    def short(self):
-        return "Connection from %s to %s (%s)"%(self.pre_cell, self.post_cell, self.syntype)
-
-    def __eq__(self, other):
-        return other.pre_cell == self.pre_cell and other.post_cell == self.post_cell and  other.number == self.number and other.syntype == self.syntype and other.synclass == self.synclass 
-
-    def __lt__(self, other):
-        if other.pre_cell+other.post_cell > self.pre_cell+self.post_cell:
-            return True
-        else: 
-            return False
-
-    def __repr__(self):
-        return self.__str__()
+from c302.ConnectomeReader import PREFERRED_NEURON_NAMES
+from c302.ConnectomeReader import PREFERRED_MUSCLE_NAMES
 
+from c302.ConnectomeReader import ConnectionInfo
+from c302.ConnectomeReader import analyse_connections
 
 
 def getSegmentIds(cell):
@@ -78,63 +45,12 @@ def fract(a, b, f):
     return a+(b-a)*f
 
 
-def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns):
-
-    print_("Found %s cells: %s\n"%(len(cells),sorted(cells)))
-    #assert(len(cells) == 302)
-    #print_("Expected number of cells correct if include_nonconnected_cells=True")
-    not_in_preferred = []
-    for c in cells:
-        if not c in PREFERRED_NEURON_NAMES:
-            not_in_preferred.append(c)
+if __name__ == "__main__":
 
-    print_("Found %s non-neuron(s): %s\n"%(len(not_in_preferred),sorted(not_in_preferred)))
-
-    print_("Found %s connections..."%(len(neuron_conns)))
-    for c in neuron_conns[:5]: print_("   %s"%c)
-
-    print_("   ...\n")
-    nts = {}
-    nts_tot = {}
-    for c in neuron_conns:
-        nt = c.synclass
-        if not nt in nts:
-            nts[nt] = 0
-            nts_tot[nt] = 0
-        nts[nt]+=1
-        nts_tot[nt]+=c.number
-
-    for nt in sorted(nts.keys()):
-        print_("   %s present in %s connections, %s synapses total (avg %.3f syns per conn)"%(nt, nts[nt], nts_tot[nt], nts_tot[nt]/nts[nt]))
-
-    print_("")
-    print_("   ---  Muscles  ---")
-    print_("")
-
-    print_("Found %s muscles: %s\n"%(len(muscles),sorted(muscles)))
-    not_in_preferred = []
-    for m in muscles:
-        if not m in PREFERRED_MUSCLE_NAMES:
-            not_in_preferred.append(m)
-
-    print_("Found %s unidentified muscles: %s\n"%(len(not_in_preferred),sorted(not_in_preferred)))
-
-    print_("Found %i neurons connected to muscles: %s\n"%(len(neurons2muscles), sorted(neurons2muscles)))
-    print_("Found %i muscles connected to neurons: %s\n"%(len(muscles), sorted(muscles)))
-
-    print_("Found %i connections between neurons and muscles%s\n"%(len(muscle_conns), (', e.g. %s'%muscle_conns[0]) if len(muscle_conns)>0 else ''))
-
-    nts = {}
-    nts_tot = {}
-    for c in muscle_conns:
-        nt = c.synclass
-        if not nt in nts:
-            nts[nt] = 0
-            nts_tot[nt] = 0
-        nts[nt]+=1
-        nts_tot[nt]+=c.number
+    from SpreadsheetDataReader import read_data, read_muscle_data
+    from WormNeuroAtlasReader import read_data, read_muscle_data
 
-    for nt in nts:
-        print_("  %s present in %s connections, %s synapses total (avg %.3f syns per conn)"%(nt, nts[nt], nts_tot[nt], nts_tot[nt]/nts[nt]))
+    cells, neuron_conns = read_data(include_nonconnected_cells=True)
+    neurons2muscles, muscles, muscle_conns = read_muscle_data()
 
-    print_("")
+    analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)

c302/VarshneyDataReader.py

@@ -30,7 +30,7 @@ def read_data(include_nonconnected_cells=False, neuron_connect=True):
             if not post==NMJ_ENDPOINT:        
                 syntype = str(row[2])
                 num = int(row[3])
-                synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse'
+                synclass = 'Generic_GJ' if 'EJ' in syntype else 'Generic_CS'
 
                 conns.append(ConnectionInfo(pre, post, num, syntype, synclass))
                 if pre not in cells:
@@ -60,7 +60,7 @@ def read_muscle_data():
         if post==NMJ_ENDPOINT:        
             syntype = str(row[2])
             num = int(row[3])
-            synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse'
+            synclass = 'Generic_GJ' if 'EJ' in syntype else 'Generic_CS'
 
             conns.append(ConnectionInfo(pre, post, num, syntype, synclass))
             if pre not in neurons: