Merge pull request #41 from genn-team/small_fixes

Small fixes
genn-team · Sep 18, 2019 · 0774e22 · 0774e22
2 parents eee732f + c10903f
commit 0774e22
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Showing 2 changed files with 30 additions and 21 deletions.
diff --git a/pynn_genn/model.py b/pynn_genn/model.py
@@ -79,7 +79,7 @@ def build_genn_model(self, defs, native_params, init_vals,
             # and, without the prefix, it is in parameters
             if not param.is_homogeneous and field_name.startswith(prefix) and field_name_no_prefix in param_name_types:
                 # Add it to variables
-                var_name_types.append((field_name,
+                var_name_types.append((field_name_no_prefix,
                                        param_name_types[field_name_no_prefix]))
 
                 # Remove from parameters
@@ -110,10 +110,10 @@ def build_genn_model(self, defs, native_params, init_vals,
                 if not ini.is_homogeneous:
                     # Add it to variables
                     var_name_types.append(
-                        (param_name, param_name_types[param_name_no_prefix]))
+                        (param_name_no_prefix, param_name_types[param_name_no_prefix]))
 
                     # Remove from parameters
-                    del param_name_types[field_name_no_prefix]
+                    del param_name_types[param_name_no_prefix]
 
         # Set parameter names in defs
         genn_defs["param_names"] = list(param_name_types.keys())
@@ -259,13 +259,22 @@ def build_genn_wum(self, conn_params, init_vals):
         wum_params = {n: conn_params[n][0]
                       for n in genn_defs["param_names"]}
 
-        # Convert variables to arrays with correct data type
-        wum_init = {n: conn_params[n].astype(genn_to_numpy_types[t]
-                                             if t in genn_to_numpy_types
-                                             else np.float32,
-                                             copy=False)
-                    for n, t in iteritems(vars)}
-
+        # Loop through GeNN variables
+        wum_init = {}
+        for n, t in iteritems(vars):
+            # Get type to use for variable
+            var_type = (genn_to_numpy_types[t] if t in genn_to_numpy_types
+                        else np.float32)
+
+            # If this variable is set by connection parameters, use these as initial values
+            if n in conn_params:
+                wum_init[n] = conn_params[n].astype(var_type, copy=False)
+            # Otherwise, if there is a default in the model, use that
+            elif n in self.default_initial_values:
+                wum_init[n] = self.default_initial_values[n]
+            else:
+                raise Exception("Variable '{}' not "
+                                "correctly initialised".format(n))
         # Zero all presynaptic variables
         # **TODO** other means of initialisation
         wum_pre_init = (None

diff --git a/pynn_genn/standardmodels/synapses.py b/pynn_genn/standardmodels/synapses.py
@@ -55,22 +55,22 @@ class TsodyksMarkramSynapse(synapses.TsodyksMarkramSynapse, GeNNStandardSynapseT
         "z" : 0.0
     })
 
+    mutable_vars = set(["x", "y", "z", "u"])
+
     wum_defs = {
         "sim_code" : """
-            scalar deltaST = $(t) - $(sT_pre);
-            $(z) *= exp( -deltaST / $(tauRec) );
-            $(z) += $(y) * ( exp( -deltaST / $(tauPsc) ) -
-            exp( -deltaST / $(tauRec) ) ) / ( ( $(tauPsc) / $(tauRec) ) - 1 );
-            $(y) *= exp( -deltaST / $(tauPsc) );
-            $(x) = 1 - $(y) - $(z);
-            $(u) *= exp( -deltaST / $(tauFacil) );
-            $(u) += $(U) * ( 1 - $(u) );
-            if ( $(u) > $(U) ) {
-            $(u) = $(U);
+            const scalar deltaST = $(t) - $(sT_pre);
+            $(z) *= exp(-deltaST / $(tauRec));
+            $(z) += $(y) * (exp(-deltaST / $(tauPsc)) - exp(-deltaST / $(tauRec))) / (($(tauPsc) / $(tauRec)) - 1.0);
+            $(y) *= exp(-deltaST / $(tauPsc));
+            $(x) = 1.0 - $(y) - $(z);
+            $(u) *= exp(-deltaST / $(tauFacil));
+            $(u) += $(U) * (1.0 - $(u));
+            if ($(u) > $(U)) {
+                $(u) = $(U);
             }
             $(y) += $(x) * $(u);
             $(addToInSyn, $(g) * $(x) * $(u));
-            $(updatelinsyn);
         """,
         "vars" : {
             "U": "scalar",        # asymptotic value of probability of release