Merge branch 'experimental' into ow_test_cect

c302/CompareMain.py

@@ -256,10 +256,11 @@ def matchLists(cols1, cols2, indexName1, indexName2):
 # 'R', 'Rp', 'S', 'Sp' map to 'Send'.
 # 'NMJ' does not map.
 def typeMapping(cols1, cols2, indexName1, indexName2):
-    list1 = ["GapJunction", "Send"]
-    list2 = ["EJ", "NMJ", "R", "Rp", "S", "Sp"]
-    type1 = cols1[indexName1[2]]
-    type2 = cols2[indexName2[2]]
+    # list1 = ["GapJunction", "Send"]
+    # list2 = ["EJ", "NMJ", "R", "Rp", "S", "Sp"]
+    # type1 = cols1[indexName1[2]]
+    # type2 = cols2[indexName2[2]]
+    pass
 
 
 if __name__ == "__main__":

c302/OpenWormReader.py

@@ -41,7 +41,7 @@ def read_data(self, include_nonconnected_cells=False):
 
         try:
             cell_names, pre, post, conns = self._read_connections("neuron")
-        except:
+        except Exception:
             print(
                 "\nProblem loading connections via owmeta! The package is installed however. You may need to try running:"
                 + "\n\n    owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'\n"

c302/SpreadsheetDataReader.py

@@ -10,9 +10,9 @@
 ############################################################
 
 
-from c302 import print_
 from c302.ConnectomeReader import ConnectionInfo
 from c302.ConnectomeReader import analyse_connections
+from c302 import print_
 
 from xlrd import open_workbook
 import os

c302/White_A.py

@@ -3,7 +3,7 @@
 
 from c302.WhiteDataReader import White_A
 
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 read_data = White_A.read_data
 read_muscle_data = White_A.read_muscle_data

c302/White_L4.py

@@ -3,7 +3,7 @@
 
 from c302.WhiteDataReader import White_L4
 
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 read_data = White_L4.read_data
 read_muscle_data = White_L4.read_muscle_data

c302/White_whole.py

@@ -3,7 +3,7 @@
 
 from c302.WhiteDataReader import White_whole
 
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 read_data = White_whole.read_data
 read_muscle_data = White_whole.read_muscle_data

c302/WitvlietDataReader1.py

@@ -2,7 +2,7 @@
 # Should be tidied up.
 
 from c302.W_SpreadsheetDataReader import WitvlietDataReader
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 wdr = WitvlietDataReader("witvliet_2020_7.xlsx")
 

c302/WitvlietDataReader2.py

@@ -2,7 +2,7 @@
 # Should be tidied up.
 
 from c302.W_SpreadsheetDataReader import WitvlietDataReader
-from c302.NeuroMLUtilities import analyse_connections
+from c302.ConnectomeReader import analyse_connections
 
 wdr = WitvlietDataReader("witvliet_2020_8.xlsx")
 

c302/__init__.py

@@ -23,7 +23,7 @@
 import neuroml.writers as writers
 import neuroml.loaders as loaders
 
-import c302.bioparameters
+# import c302.bioparameters
 
 import airspeed
 
@@ -39,6 +39,7 @@
 
 import json
 
+
 import collections
 
 
@@ -1710,10 +1711,15 @@ def parse_dict_arg(dict_arg):
 
 
 def main():
+    import importlib
+
     print("Starting c302 v%s..." % __version__)
     args = process_args()
 
-    exec("from c302.%s import ParameterisedModel" % args.parameters, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % args.parameters),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
     generate(
         args.reference,

c302/analyse.py

@@ -0,0 +1,28 @@
+import sys
+import matplotlib.pyplot as plt
+
+
+fig = plt.figure(facecolor="#FFFFFF", edgecolor="#FFFFFF")
+p = fig.add_subplot(111)
+
+
+dat_file = sys.argv[1]
+
+traces = open(dat_file, "r")
+volts = {}
+
+# Very inefficient...
+for line in traces:
+    if not line.strip().startswith("#"):
+        points = line.split()
+        for i in range(len(points)):
+            if not volts.has_key(i):
+                volts[i] = []
+            volts[i].append(float(points[i]) + 0.0020 * i)
+
+for cell_index in volts.keys():
+    if cell_index <= 302:
+        if cell_index > 0:
+            p.plot(volts[0], volts[cell_index])
+
+plt.show()

c302/c302_FW.py

@@ -1,5 +1,6 @@
 import sys
 import os
+import importlib
 
 sys.path.insert(0, os.path.abspath("."))
 
@@ -21,7 +22,10 @@ def setup(
     verbose=True,
     config_param_overrides={},
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter(
@@ -34,13 +38,14 @@ def setup(
         "unphysiological_offset_current_dur", "2000 ms", "Testing TapWithdrawal", "0"
     )
 
+    """
     VA_motors = ["VA%s" % c for c in range_incl(1, 12)]
-    VB_motors = ["VB%s" % c for c in range_incl(1, 11)]
     DA_motors = ["DA%s" % c for c in range_incl(1, 9)]
+    AS_motors = ["AS%s" % c for c in range_incl(1, 11)]"""
+    VB_motors = ["VB%s" % c for c in range_incl(1, 11)]
     DB_motors = ["DB%s" % c for c in range_incl(1, 7)]
     DD_motors = ["DD%s" % c for c in range_incl(1, 6)]
     VD_motors = ["VD%s" % c for c in range_incl(1, 13)]
-    AS_motors = ["AS%s" % c for c in range_incl(1, 11)]
 
     cells = list(["AVBL", "AVBR"] + DB_motors + VD_motors + VB_motors + DD_motors)
 

c302/c302_Full.py

@@ -1,6 +1,8 @@
 import c302
 import sys
 
+import importlib
+
 
 def setup(
     parameter_set,
@@ -14,7 +16,10 @@ def setup(
     config_param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     # Some random set of neurons

c302/c302_IClamp.py

@@ -2,6 +2,8 @@
 import sys
 import neuroml.writers as writers
 
+import importlib
+
 
 def setup(
     parameter_set,
@@ -17,11 +19,14 @@ def setup(
     reference = "c302_%s_IClamp" % parameter_set
     c302.print_("Setting up %s" % reference)
 
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     stim_amplitudes = ["1pA", "2pA", "3pA", "4pA", "5pA", "6pA"]
-    if duration == None:
+    if duration is None:
         duration = (len(stim_amplitudes)) * 1000
 
     my_cells = ["ADAL", "PVCL"]

c302/c302_IClampMuscle.py

@@ -1,6 +1,8 @@
 import c302
 import sys
 
+import importlib
+
 
 def setup(
     parameter_set,
@@ -12,7 +14,10 @@ def setup(
     param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     my_cells = []

c302/c302_MultiSyns.py

@@ -1,14 +1,18 @@
-from c302 import generate, add_new_input
+from c302 import generate, add_new_input, print_
 
 import neuroml.writers as writers
 
+import importlib
 import sys
 
 
 if __name__ == "__main__":
     parameter_set = sys.argv[1] if len(sys.argv) == 2 else "A"
 
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     cells = ["URYDL", "SMDDR", "ADAL", "RIML", "IL2VL", "RIPL"]
@@ -26,7 +30,7 @@
         duration=1000,
         dt=0.1,
         target_directory=target_directory,
-        verbose=verbose,
+        verbose=True,
     )
 
     stim_amplitude = "0.35nA"
@@ -39,4 +43,4 @@
         nml_doc, nml_file
     )  # Write over network file written above...
 
-    c302.print_("(Re)written network file to: " + nml_file)
+    print_("(Re)written network file to: " + nml_file)

c302/c302_MuscleTest.py

@@ -1,5 +1,6 @@
 import sys
 import os
+import importlib
 
 sys.path.insert(0, os.path.abspath("."))
 
@@ -21,7 +22,10 @@ def setup(
     verbose=True,
     config_param_overrides={},
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter(
@@ -34,13 +38,14 @@ def setup(
         "unphysiological_offset_current_dur", "2000 ms", "Testing TapWithdrawal", "0"
     )
 
+    """
     VA_motors = ["VA%s" % c for c in range_incl(1, 12)]
     VB_motors = ["VB%s" % c for c in range_incl(1, 11)]
     DA_motors = ["DA%s" % c for c in range_incl(1, 9)]
     DB_motors = ["DB%s" % c for c in range_incl(1, 7)]
     DD_motors = ["DD%s" % c for c in range_incl(1, 6)]
     VD_motors = ["VD%s" % c for c in range_incl(1, 13)]
-    AS_motors = ["AS%s" % c for c in range_incl(1, 11)]
+    AS_motors = ["AS%s" % c for c in range_incl(1, 11)]"""
 
     cells = []
 
@@ -75,7 +80,7 @@ def setup(
         "ca_conc_rho_muscle": "0.002138919 mol_per_m_per_A_per_s",
     }
 
-    end = "%sms" % (int(duration) - 100)
+    # end = "%sms" % (int(duration) - 100)
 
     input_list = []
 
@@ -174,4 +179,4 @@ def setup(
     if len(sys.argv) == 3:
         setup_kwargs["data_reader"] = sys.argv[2]
 
-    setup(parameter_set, generate=True, data_reader=data_reader)
+    # setup(parameter_set, generate=True, data_reader=data_reader)

c302/c302_Muscles.py

@@ -1,6 +1,8 @@
 import c302
 import sys
 
+import importlib
+
 
 def setup(
     parameter_set,
@@ -13,7 +15,10 @@ def setup(
     config_param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter(

c302/c302_MusclesSine.py

@@ -1,5 +1,6 @@
 import c302
 import sys
+import importlib
 
 
 def setup(
@@ -13,7 +14,10 @@ def setup(
     config_param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter(

c302/c302_Oscillator.py

@@ -1,5 +1,6 @@
 import c302
 import sys
+import importlib
 
 
 def setup(
@@ -13,7 +14,10 @@ def setup(
     config_param_overrides={},
     verbose=True,
 ):
-    exec("from c302.parameters_%s import ParameterisedModel" % parameter_set, globals())
+    ParameterisedModel = getattr(
+        importlib.import_module("c302.parameters_%s" % parameter_set),
+        "ParameterisedModel",
+    )
     params = ParameterisedModel()
 
     params.set_bioparameter("unphysiological_offset_current", "4pA", "Testing Osc", "0")