2to3

CElegans/pythonScripts/c302/UpdatedSpreadsheetDataReader.py

@@ -98,9 +98,9 @@ def readDataFromSpreadsheet(include_nonconnected_cells=False):
     conns = []
     cells = []
 
-    with open(filename, 'rb') as f:
+    with open(filename, 'r') as f:
         reader = csv.DictReader(f)
-        print "Opened file: " + filename
+        print("Opened file: " + filename)
 
         known_nonconnected_cells = ['CANL', 'CANR']
 
@@ -140,9 +140,9 @@ def readMuscleDataFromSpreadsheet():
     muscles = []
     conns = []
 
-    with open(filename, 'rb') as f:
+    with open(filename, 'r') as f:
         reader = csv.DictReader(f)
-        print "Opened file: " + filename
+        print("Opened file: " + filename)
 
         for row in reader:
             pre, post, num, syntype, synclass = parse_row(row)

CElegans/pythonScripts/c302/bioparameters.py

@@ -136,7 +136,7 @@ def get_syn(self, pre_cell, post_cell, type, pol):
 
 
     def create_n_connection_synapse(self, prototype_syn, n, nml_doc, existing_synapses):
-        if existing_synapses.has_key(prototype_syn.id):
+        if prototype_syn.id in existing_synapses:
             return existing_synapses[prototype_syn.id]
 
         existing_synapses[prototype_syn.id] = prototype_syn

CElegans/pythonScripts/c302/c302.py

@@ -46,7 +46,7 @@
 try:
     from urllib2 import URLError  # Python 2
 except:
-    from urllib import URLError  # Python 3
+    from urllib.error import URLError  # Python 3
 
 import sys
 sys.path.append("..")
@@ -249,7 +249,7 @@ def add_new_sinusoidal_input(nml_doc, cell, delay, duration, amplitude, period,
         phase = DB_soma_pos[cell]
     #phase = get_cell_position(cell).x
     phase = phase * -0.886
-    print "### CELL %s PHASE: %s" % (cell, phase)
+    print("### CELL %s PHASE: %s" % (cell, phase))
 
     if cell.startswith("VB"):
         if amplitude.startswith("-"):
@@ -356,7 +356,7 @@ def get_random_colour_hex():
 
 def get_file_name_relative_to_c302(file_name):
 
-    if os.environ.has_key('C302_HOME'):
+    if 'C302_HOME' in os.environ:
         return os.path.relpath(os.environ['C302_HOME'],file_name)
 
 
@@ -477,13 +477,14 @@ def generate(net_id,
 
     regex_param_overrides = {'mirrored_elec_conn_params':{}}
     if param_overrides:
-        for k, v in param_overrides.iteritems():
+        for k, v in param_overrides.items():
             if k == 'mirrored_elec_conn_params':
-                for mk, mv in v.iteritems():
+                for mk, mv in v.items():
                     if is_regex_string(mk):
                         regex_param_overrides['mirrored_elec_conn_params'][mk] = mv
                         continue
-                    mirror_param(params, mk, mv)
+                    else:
+                        mirror_param(params, mk, mv)
 
 
             elif k == 'custom_component_type_gate_overrides':
@@ -559,7 +560,10 @@ def generate(net_id,
     nml_doc.pulse_generators.append(params.offset_current)
 
     if is_cond_based_cell(params):
-        nml_doc.fixed_factor_concentration_models.append(params.concentration_model)
+        if isinstance(params.concentration_model, list):
+            nml_doc.fixed_factor_concentration_models.extend(params.concentration_model)
+        else:
+            nml_doc.fixed_factor_concentration_models.append(params.concentration_model)
 
     cell_names, conns = get_cell_names_and_connection(data_reader)
 
@@ -596,11 +600,11 @@ def generate(net_id,
                 # def_file = './%s' % ctd
                 def_file = "%s/%s" % (os.path.dirname(os.path.abspath(__file__)), ctd)
 
-                if param_overrides.has_key('custom_component_type_gate_overrides') and param_overrides[
+                if param_overrides and 'custom_component_type_gate_overrides' in param_overrides and param_overrides[
                     'custom_component_type_gate_overrides']:
                     root = etree.parse(def_file).getroot()
 
-                    for k, v in param_overrides['custom_component_type_gate_overrides'].iteritems():
+                    for k, v in param_overrides['custom_component_type_gate_overrides'].items():
                         channel_id = k.split('__')[0]
                         gate_id = k.split('__')[1]
                         gate_attr = k.split('__')[2]
@@ -653,7 +657,7 @@ def generate(net_id,
             # put that Population into the Network data structure from above
             net.populations.append(pop0)
 
-            if cells_vs_name.has_key(cell):
+            if cell in cells_vs_name:
                 p = Property(tag="OpenWormBackerAssignedName", value=cells_vs_name[cell])
                 pop0.properties.append(p)
 
@@ -784,7 +788,7 @@ def generate(net_id,
             # put that Population into the Network data structure from above
             net.populations.append(pop0)
 
-            if cells_vs_name.has_key(muscle):
+            if muscle in cells_vs_name:
                 # No muscles adopted yet, but just in case they are in future...
                 p = Property(tag="OpenWormBackerAssignedName", value=cells_vs_name[muscle])
                 pop0.properties.append(p)
@@ -897,19 +901,27 @@ def generate(net_id,
                     new_param = new_param.replace('_GJ', '')
                     new_param_v = regex_param_overrides[key]
 
+
+                    if new_param in param_overrides:
+                        continue
+                    # add regex param unless there is a specific param
                     set_param(params, new_param, new_param_v)
 
-            if regex_param_overrides.has_key('mirrored_elec_conn_params'):
-                for k, v in regex_param_overrides['mirrored_elec_conn_params'].iteritems():
+            if 'mirrored_elec_conn_params' in regex_param_overrides:
+                for k, v in regex_param_overrides['mirrored_elec_conn_params'].items():
 
                     pattern = k.split('$')[0] + '$'
                     pattern = pattern.replace('_to_', '-')
 
                     if re.match(pattern, conn_shorthand):
                         new_param = conn_shorthand.replace('-', '_to_') + k.split('$')[1]
                         new_param = new_param.replace('_GJ', '')
+                        new_param_mirrored = conn.post_cell + '_' + new_param.split('_')[1] + '_' + conn.pre_cell + '_' + '_'.join(new_param.split('_')[3:])
                         new_param_v = v
 
+                        if new_param in param_overrides['mirrored_elec_conn_params'] or new_param_mirrored in param_overrides['mirrored_elec_conn_params']:
+                            continue
+                        # add regex param unless there is a specific param
                         mirror_param(params, new_param, new_param_v)
 
             if conns_to_include and conn_shorthand not in conns_to_include:
@@ -926,7 +938,7 @@ def generate(net_id,
             syn0 = params.get_syn(conn.pre_cell, conn.post_cell, conn_type, conn_pol)
 
             if print_connections:
-                print conn_shorthand + " " + str(conn.number) + " " + orig_pol + " " + conn.synclass + " " + syn0.id
+                print(conn_shorthand + " " + str(conn.number) + " " + orig_pol + " " + conn.synclass + " " + syn0.id)
 
 
             polarity = None
@@ -980,9 +992,9 @@ def generate(net_id,
                         break
             '''
             else:
-                print conn_shorthand
-                print conn_number_override
-                print conn_number_scaling'''
+                print(conn_shorthand)
+                print(conn_number_override)
+                print(conn_number_scaling)'''
             """if polarity:
                 print "%s %s num:%s" % (conn_shorthand, polarity, number_syns)
             elif elect_conn:
@@ -1076,11 +1088,13 @@ def generate(net_id,
 
     if len(muscles_to_include)>0:
         for conn in muscle_conns:
-            if not conn.post_cell in muscles_to_include:
-                continue
+            if not conn.post_cell in muscles_to_include:#
+                continue#
             if not conn.pre_cell in lems_info["cells"] and not conn.pre_cell in muscles_to_include:
                 continue
 
+
+
             # take information about each connection and package it into a
             # NeuroML Projection data structure
             proj_id = get_projection_id(conn.pre_cell, conn.post_cell, conn.synclass, conn.syntype)
@@ -1092,6 +1106,8 @@ def generate(net_id,
             conn_type = "neuron_to_muscle"
             if conn.pre_cell in muscles_to_include:
                 conn_type = "muscle_to_muscle"
+            #if conn.post_cell in lems_info['cells']:
+            #    conn_type = "muscle_to_neuron"
             conn_pol = "exc"
             orig_pol = "exc"
 
@@ -1118,19 +1134,27 @@ def generate(net_id,
                     new_param = new_param.replace('_GJ', '')
                     new_param_v = regex_param_overrides[key]
 
+
+                    if new_param in param_overrides:
+                        continue
+                    # add regex param unless there is a specific param
                     set_param(params, new_param, new_param_v)
 
-            if regex_param_overrides.has_key('mirrored_elec_conn_params'):
-                for k, v in regex_param_overrides['mirrored_elec_conn_params'].iteritems():
+            if 'mirrored_elec_conn_params' in regex_param_overrides:
+                for k, v in regex_param_overrides['mirrored_elec_conn_params'].items():
 
                     pattern = k.split('$')[0] + '$'
                     pattern = pattern.replace('_to_', '-')
 
                     if re.match(pattern, conn_shorthand):
                         new_param = conn_shorthand.replace('-', '_to_') + k.split('$')[1]
                         new_param = new_param.replace('_GJ', '')
+                        new_param_mirrored = conn.post_cell + '_' + new_param.split('_')[1] + '_' + conn.pre_cell + '_' + '_'.join(new_param.split('_')[3:])
                         new_param_v = v
 
+                        if new_param in param_overrides['mirrored_elec_conn_params'] or new_param_mirrored in param_overrides['mirrored_elec_conn_params']:
+                            continue
+                        # add regex param unless there is a specific param
                         mirror_param(params, new_param, new_param_v)
 
             if conns_to_include and conn_shorthand not in conns_to_include:
@@ -1147,7 +1171,7 @@ def generate(net_id,
             syn0 = params.get_syn(conn.pre_cell, conn.post_cell, conn_type, conn_pol)
 
             if print_connections:
-                print conn_shorthand + " " + str(conn.number) + " " + orig_pol + " " + conn.synclass
+                print(conn_shorthand + " " + str(conn.number) + " " + orig_pol + " " + conn.synclass)
 
 
             polarity = None
@@ -1195,9 +1219,9 @@ def generate(net_id,
                         break
             '''
             else:
-                print conn_shorthand
-                print conn_number_override
-                print conn_number_scaling'''
+                print(conn_shorthand)
+                print(conn_number_override)
+                print(conn_number_scaling)'''
             """if polarity:
                 print "%s %s num:%s" % (conn_shorthand, polarity, number_syns)
             elif elect_conn: