SynapseTest is also passing.

Author: Dilawar Singh

pybind11/Finfo.cpp

@@ -29,23 +29,24 @@ __Finfo__::__Finfo__(const ObjId& oid, const Finfo* f, const string& finfoType)
 {
     // cout << " __Finfo__ type " << finfoType << endl;
 
-    if(finfoType == "DestFinfo")
+    if (finfoType == "DestFinfo")
         func_ = [oid, f, this](const py::object& key) {
             return getLookupValueFinfoItem(oid, f, key);
         };
-    else if(finfoType == "FieldElementFinfo")
+    else if (finfoType == "FieldElementFinfo")
         func_ = [oid, f, this](const py::object& index) {
             // this is essential of make this function static.
             return getElementFinfoItem(oid, f, py::cast<unsigned int>(index));
         };
-    else if(finfoType == "LookupValueFinfo")
+    else if (finfoType == "LookupValueFinfo")
         func_ = [oid, f, this](const py::object& key) {
             // Assigning is essential or make these functions static.
             return this->getLookupValueFinfoItem(oid, f, key);
         };
     else
         func_ = [this](const py::object& key) {
-            throw runtime_error("Not supported for Finfo type '"+finfoType_+"'");
+            throw runtime_error("Not supported for Finfo type '" + finfoType_ +
+                                "'");
             return py::none();
         };
 }
@@ -84,7 +85,8 @@ bool __Finfo__::setLookupValueFinfoItem(const ObjId& oid, const py::object& key,
     return true;
 }
 
-py::object __Finfo__::getLookupValueFinfoItem(const ObjId& oid, const Finfo* f, const py::object& key)
+py::object __Finfo__::getLookupValueFinfoItem(const ObjId& oid, const Finfo* f,
+                                              const py::object& key)
 {
     auto rttType = f->rttiType();
     auto fname = f->name();
@@ -130,8 +132,7 @@ py::cpp_function __Finfo__::getDestFinfoSetterFunc(const ObjId& oid,
     vector<string> types;
     moose::tokenize(rttType, ",", types);
 
-    if (types.size() == 1)
-        return getDestFinfoSetterFunc1(oid, finfo, types[0]);
+    if (types.size() == 1) return getDestFinfoSetterFunc1(oid, finfo, types[0]);
 
     assert(types.size() == 2);
     return getDestFinfoSetterFunc2(oid, finfo, types[0], types[1]);
@@ -147,11 +148,18 @@ py::cpp_function __Finfo__::getDestFinfoSetterFunc2(const ObjId& oid,
     if (ftype1 == "double") {
         if (ftype2 == "unsigned int") {
             std::function<bool(double, unsigned int)> func = [oid, fname](
-                const double a, const long b) {
+                const double a, const unsigned int b) {
                 return SetGet2<double, unsigned int>::set(oid, fname, a, b);
             };
             return func;
         }
+        if (ftype2 == "long") {
+            std::function<bool(double, long)> func = [oid, fname](
+                const double a, const long b) {
+                return SetGet2<double, long>::set(oid, fname, a, b);
+            };
+            return func;
+        }
     }
     throw runtime_error("getFieldPropertyDestFinfo2::NotImplemented " + fname +
                         " for rttType " + finfo->rttiType() + " for oid " +
@@ -251,10 +259,11 @@ py::list __Finfo__::getElementFinfo(const ObjId& objid, const Finfo* f)
     return py::cast(res);
 }
 
-py::object __Finfo__::getElementFinfoItem(const ObjId& oid, const Finfo* f, unsigned int index)
+py::object __Finfo__::getElementFinfoItem(const ObjId& oid, const Finfo* f,
+                                          unsigned int index)
 {
     // cout << "Fetching at index " << index << " " << getNumField() << endl ;
-    if(index >= getNumFieldStatic(oid, f)) {
+    if (index >= getNumFieldStatic(oid, f)) {
         throw py::index_error("Index " + to_string(index) + " out of range.");
     }
     auto o = ObjId(oid.path() + '/' + f->name());
@@ -268,18 +277,17 @@ string __Finfo__::type() const
 
 // py::object __Finfo__::getAttr(const string& key)
 // {
-    // std::cout << "Accessing " << key << std::endl;
+// std::cout << "Accessing " << key << std::endl;
 // }
 
-unsigned int __Finfo__::getNumField() 
+unsigned int __Finfo__::getNumField()
 {
     return __Finfo__::getNumFieldStatic(oid_, f_);
 }
 
-unsigned int __Finfo__::getNumFieldStatic(const ObjId& oid, const Finfo* f) 
+unsigned int __Finfo__::getNumFieldStatic(const ObjId& oid, const Finfo* f)
 {
     auto o = ObjId(oid.path() + '/' + f->name());
     return Field<unsigned int>::get(o, "numField");
 }
 
-

pybind11/MooseVec.cpp

@@ -64,7 +64,8 @@ ObjId MooseVec::getItem(const size_t i) const
 
 void MooseVec::setAttrOneToAll(const string& name, const py::object& val)
 {
-    setFieldGeneric(oid_, name, val);
+    for(size_t i = 0; i < size(); i++)
+        setFieldGeneric(getItem(i), name, val);
 }
 
 void MooseVec::setAttrOneToOne(const string& name, const py::sequence& val)

shell/Shell.cpp

@@ -284,7 +284,6 @@ ObjId Shell::doAddMsg(const string& msgType, ObjId src, const string& srcField,
     }
 
     const Msg* m = innerAddMsg(msgType, src, srcField, dest, destField, 0);
-    cout << "Msg " << m << " mid:" << m->mid() << endl;
 
     SetGet6<string, ObjId, string, ObjId, string, unsigned int>::set(
         ObjId(),   // Apply command to Shell
@@ -387,9 +386,7 @@ void Shell::doMove(Id orig, ObjId newParent)
         warning(ss.str());
         return;
     }
-
     SetGet2<Id, ObjId>::set(ObjId(), "move", orig, newParent);
-    // innerMove( orig, newParent );
 }
 
 bool extractIndex(const string& s, unsigned int& index)

tests/py_moose/test_GraupnerBrunel2012_STDPfromCaPlasticity.py

@@ -39,17 +39,17 @@ def test_GB2012_STDP():
     # ###########################################
 
     ## two neurons: index 0 will be presynaptic, 1 will be postsynaptic
-    network = moose.vec(moose.LIF( 'network', 2 ))
+    network = moose.LIF( 'network', 2 );
     moose.le( '/network' )
-    print(network)
-    network.Em = Vrest
-    network.thresh = Vt_base
-    network.refractoryPeriod = refrT
-    network.Rm = R
-    network.vReset = Vreset
-    network.Cm = tau/R
-    network.inject = 0.
-    network.initVm = Vrest
+    network.vec.Em = Vrest
+    assert np.allclose(network.vec.Em, Vrest), (network.vec.Em, Vrest)
+    network.vec.thresh = Vt_base
+    network.vec.refractoryPeriod = refrT
+    network.vec.Rm = R
+    network.vec.vReset = Vreset
+    network.vec.Cm = tau/R
+    network.vec.inject = 0.
+    network.vec.initVm = Vrest
 
     tauCa = 20e-3     
     tauSyn = 150.0    
@@ -65,13 +65,11 @@ def test_GB2012_STDP():
     bistable = True   
 
     syn = moose.GraupnerBrunel2012CaPlasticitySynHandler( '/network/syn' )
-    print(dir(syn))
     syn.numSynapses = 1   
-    assert syn.numSynapses == 1, syn.numSynapses
     moose.connect( syn, 'activationOut', network.vec[1], 'activation' )
 
     # synapse from presynaptic neuron
-    moose.connect( network.vec[0], 'spikeOut', syn.synapse[0], 'addSpike')
+    moose.connect( network.vec[0],'spikeOut', syn.synapse[0], 'addSpike')
 
     # post-synaptic spikes also needed for STDP
     moose.connect( network.vec[1], 'spikeOut', syn, 'addPostSpike')
@@ -100,9 +98,9 @@ def test_GB2012_STDP():
     # Setting up tables
     # ###########################################
 
-    Vms = moose.vec(moose.Table( '/plotVms', 2))
+    Vms = moose.Table( '/plotVms', 2 )
     moose.connect( network, 'VmOut', Vms, 'input', 'OneToOne')
-    spikes = moose.vec(moose.Table( '/plotSpikes', 2))
+    spikes = moose.Table( '/plotSpikes', 2 )
     moose.connect( network, 'spikeOut', spikes, 'input', 'OneToOne')
     CaTable = moose.Table( '/plotCa', 1 )
     moose.connect( CaTable, 'requestOut', syn, 'getCa')
@@ -190,15 +188,15 @@ def make_neuron_spike(nrnidx,I=1e-7,duration=1e-3):
         print(('pre before post, dt = %1.3f s, dw/w = %1.3f'%(deltat,dw)))
         dwlist_pos.append(dw)
 
-    Vmseries0 = Vms[0].vector
+    Vmseries0 = Vms.vec[0].vector
     numsteps = len(Vmseries0)
 
-    for t in spikes[0].vector:
+    for t in spikes.vec[0].vector:
         Vmseries0[int(t/dt)-1] = 30e-3 # V
 
-    Vmseries1 = Vms[1].vector
+    Vmseries1 = Vms.vec[1].vector
 
-    for t in spikes[1].vector:
+    for t in spikes.vec[1].vector:
         Vmseries1[int(t/dt)-1] = 30e-3 # V
 
     timeseries = np.linspace(0.,200*numsteps*dt,numsteps)

tests/py_moose/test_vec.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import moose
+import numpy as np
 
 def test_vec():
     foo = moose.Pool('/foo1', 500)
@@ -20,7 +21,16 @@ def test_vec2():
     assert iaf[5].Vm == 5, iaf[5].Vm
     print(iaf.Vm)
 
+def test_vec3():
+    print("test vec3")
+    foo = moose.Pool('/foo1', 500)
+    foo.vec.concInit = 0.123
+    print(foo.vec)
+    assert foo.concInit == 0.123, foo.concInit
+    assert np.allclose(foo.vec.concInit, [0.123]*500)
+
 
 if __name__ == '__main__':
     test_vec()
     test_vec2()
+    test_vec3()