overloading template function is not so straight-forward when

typecasting can happen by itslf e.g. int and unsigned int.

Author: Dilawar Singh

pybind11/MooseVec.cpp

@@ -94,15 +94,34 @@ ObjId MooseVec::getFieldItem(const size_t i) const
     return ObjId(oid_.path(), oid_.dataIndex, i);
 }
 
-vector<py::object> MooseVec::getAttribute(const string& name)
-{
+py::object MooseVec::getAttribute(const string& name)
+{
+    // If type if double, int, bool etc, then return the numpy array. else
+    // return the list of python object.
+    auto cinfo = oid_.element()->cinfo();
+    auto finfo = cinfo->findFinfo(name);
+    auto rttType = finfo->rttiType();
+
+    if(rttType == "double")
+        return getAttributeNumpy<double>(name);
+    if(rttType == "unsigned int")
+        return getAttributeNumpy<unsigned int>(name);
+    if(rttType == "int")
+        return getAttributeNumpy<unsigned int>(name);
+
+    // FIXME: bool type is not working. Need to raise the ticket on pybind11
+    // after creating and MWE.
+    //if(rttType == "bool")
+    //    return getAttributeNumpy<bool>(name);
+
     vector<py::object> res(size());
     for (unsigned int i = 0; i < size(); i++)
         res[i] = getFieldGeneric(getItem(i), name);
-    return res;
+    return py::cast(res);
 }
 
 
+
 // // FIXME: Only double is supported here. Not sure if this is enough. This
 // // should be the API function.
 // py::array_t<double> MooseVec::getAttributeNumpy(const string &name)

pybind11/MooseVec.h

@@ -76,10 +76,11 @@ class MooseVec
 
 
     // Get attributes.
-    vector<py::object> getAttribute(const string& name);
+    py::object getAttribute(const string& name);
 
-    // TODO: May be buffer https://pybind11.readthedocs.io/en/stable/advanced/pycpp/numpy.html#buffer-protocol
-    template<typename T=double>
+    vector<ObjId> objs() const;
+
+    template<typename T>
     py::array_t<T> getAttributeNumpy(const string& name)
     {
         vector<T> res(size());
@@ -88,9 +89,6 @@ class MooseVec
         return py::array_t<T>(res.size(), res.data());
     }
 
-    vector<ObjId> objs() const;
-
-
     ObjId connectToSingle(const string& srcfield, const ObjId& tgt, const string& tgtfield, const string& msgtype);
 
     ObjId connectToVec(const string& srcfield, const MooseVec& tgt, const string& tgtfield, const string& msgtype);

pybind11/helper.h

@@ -56,10 +56,9 @@ inline ObjId mooseObjIdPath(const string& p)
     string path(p);
 
     // If path is a relative path.
-    if (p[0] != '/') 
-    {
+    if (p[0] != '/') {
         string cwepath(mooseGetCweId().path());
-        if(cwepath.back() != '/')
+        if (cwepath.back() != '/')
             cwepath.push_back('/');
         path = cwepath + p;
     }

pybind11/pymoose.cpp

@@ -309,12 +309,9 @@ PYBIND11_MODULE(_moose, m)
         .def("__setattr__", &MooseVec::setAttrOneToAll<double>)
         .def("__setattr__", &MooseVec::setAttrOneToAll<string>)
         .def("__setattr__", &MooseVec::setAttrOneToAll<bool>)
-        .def("__getattr__", &MooseVec::getAttributeNumpy<double>)
-        .def("__getattr__", &MooseVec::getAttributeNumpy<float>)
-        // These three are probably never needed.
-        .def("__getattr__", &MooseVec::getAttributeNumpy<unsigned int>)
-        .def("__getattr__", &MooseVec::getAttributeNumpy<unsigned long>)
-        // For the rest non-POD types.
+        // Beware of pybind11 overload resolution order:
+        // https://pybind11.readthedocs.io/en/stable/advanced/functions.html#overload-resolution-order
+        // Templated function won't work here. The first one is always called.
         .def("__getattr__", &MooseVec::getAttribute)
         .def("__repr__", [](const MooseVec & v)->string {
              return "<moose.vec class=" + v.dtype() + " path=" + v.path() +

pybind11/pymoose.h

@@ -36,7 +36,7 @@ inline T getField(const ObjId& id, const string& fname)
 
 // FIXME: Is it most efficient?
 // See discussion here: https://github.com/pybind/pybind11/issues/1042
-template <typename T = double>
+template <typename T>
 inline py::array_t<T> getFieldNumpy(const ObjId& id, const string& fname)
 {
     auto v = Field<vector<T>>::get(id, fname);

tests/py_moose/test_connectionLists.py

@@ -45,16 +45,11 @@
 
 def makeGlobalBalanceNetwork():
     stim = moose.RandSpike( '/model/stim', params['numInputs'] )
-
     inhib = moose.LIF( '/model/inhib', params['numInhib'] )
-
     insyn = moose.SimpleSynHandler(inhib.path + '/syns', params['numInhib'])
-
     moose.connect( insyn, 'activationOut', inhib, 'activation', 'OneToOne' )
     output = moose.LIF( '/model/output', params['numOutput'] )
-
     outsyn = moose.SimpleSynHandler(output.path+'/syns',params['numOutput'])
-
     moose.connect(outsyn, 'activationOut', output, 'activation', 'OneToOne')
     outInhSyn = moose.SimpleSynHandler(output.path+'/inhsyns',params['numOutput'])
     moose.connect(outInhSyn, 'activationOut', output, 'activation', 'OneToOne')
@@ -63,41 +58,47 @@ def makeGlobalBalanceNetwork():
     ov = moose.vec( outsyn.path + '/synapse' )
     oiv = moose.vec( outInhSyn.path + '/synapse' )
 
-    inhibMatrix = moose.connect( stim, 'spikeOut', iv, 'addSpike', 'Sparse' )
-    #  inhibMatrix = moose.element(temp)
+    assert len(iv) == 0
+    assert len(ov) == 0
+    assert len(oiv) == 0
 
-    inhibMatrix.setRandomConnectivity(params['stimToInhProb'], params['stimToInhSeed'])
+    temp = moose.connect( stim, 'spikeOut', iv, 'addSpike', 'Sparse' )
+    inhibMatrix = moose.element( temp )
+    inhibMatrix.setRandomConnectivity( 
+            params['stimToInhProb'], params['stimToInhSeed'] )
     cl = inhibMatrix.connectionList
 
     # This can change when random-number generator changes.
+    # This was before we used c++11 <random> to generate random numbers. This
+    # test has changes on Tuesday 31 July 2018 11:12:35 AM IST
     #  expectedCl = [ 1,4,13,13,26,42,52,56,80,82,95,97,4,9,0,9,4,8,0,6,1,6,6,7]
     expectedCl=[0,6,47,50,56,67,98,2,0,3,5,4,8,3]
 
-    #  print('CL', cl)
     assert list(cl) == expectedCl, "Expected %s, got %s" % (expectedCl, cl)
-    assert inhibMatrix.numEntries == 7, inhibMatrix.numEntries
 
-    excMatrix = moose.connect( stim, 'spikeOut', ov, 'addSpike', 'Sparse' )
-    #  excMatrix = moose.element(temp)
-    print('111',  excMatrix)
-    excMatrix.setRandomConnectivity(params['stimToOutProb'], params['stimToOutSeed'])
-    assert excMatrix.numEntries == 62, excMatrix.numEntries
+    temp = moose.connect( stim, 'spikeOut', ov, 'addSpike', 'Sparse' )
+    excMatrix = moose.element( temp )
+    excMatrix.setRandomConnectivity( 
+            params['stimToOutProb'], params['stimToOutSeed'] )
 
-    negFFMatrix = moose.connect(inhib, 'spikeOut', oiv, 'addSpike', 'Sparse')
-    #  negFFMatrix = moose.element( temp )
-    negFFMatrix.setRandomConnectivity(params['inhToOutProb'], params['inhToOutSeed'] )
-    assert negFFMatrix.numEntries == 55, negFFMatrix.numEntries
+    temp = moose.connect( inhib, 'spikeOut', oiv, 'addSpike', 'Sparse' )
+    negFFMatrix = moose.element( temp )
+    negFFMatrix.setRandomConnectivity( 
+            params['inhToOutProb'], params['inhToOutSeed'] )
+
+    # print("ConnMtxEntries: ", inhibMatrix.numEntries, excMatrix.numEntries, negFFMatrix.numEntries)
+    got = (inhibMatrix.numEntries, excMatrix.numEntries, negFFMatrix.numEntries)
+    expected = (7, 62, 55)
+    assert expected == got, "Expected %s, Got %s" % (expected,got)
 
     cl = negFFMatrix.connectionList
     numInhSyns = [ ]
     niv = 0
     nov = 0
     noiv = 0
-
-    insyn = moose.vec(insyn)
-    for i in insyn:
+    for i in moose.vec( insyn ):
         niv += i.synapse.num
-        numInhSyns.append( i.synapse.num)
+        numInhSyns.append( i.synapse.num )
         if i.synapse.num > 0:
             i.synapse.weight = params['wtStimToInh']
 
@@ -106,28 +107,30 @@ def makeGlobalBalanceNetwork():
     assert numInhSyns == expected, "Expected %s, got %s" % (expected,numInhSyns)
 
     for i in moose.vec( outsyn ):
+        print('111', i)
         nov += i.synapse.num
         if i.synapse.num > 0:
             i.synapse.weight = params['wtStimToOut']
     for i in moose.vec( outInhSyn ):
         noiv += i.synapse.num
+        #print i.synapse.num
         if i.synapse.num > 0:
             i.synapse.weight = params['wtInhToOut']
-     
-    print(iv.numField, ov.numField, oiv.numField)
+
     print("SUMS: ", sum( iv.numField ), sum( ov.numField ), sum( oiv.numField ))
-    #  assert [1, 64, 25] == [sum( iv.numField ), sum( ov.numField ), sum( oiv.numField )]
-    assert [1, 50, 27] == [sum( iv.numField ), sum( ov.numField ), sum( oiv.numField )]
+    assert [1, 64, 25] == [sum( iv.numField ), sum( ov.numField ), sum( oiv.numField )]
     print("SUMS2: ", niv, nov, noiv)
-    #  assert [7, 62, 55] ==  [ niv, nov, noiv ]
     assert [7, 62, 55] ==  [ niv, nov, noiv ]
-
-    print(insyn.vec)
-    print(outsyn.vec)
-    print(outInhSyn)
     print("SUMS3: ", sum( insyn.vec.numSynapses ), sum( outsyn.vec.numSynapses ), sum( outInhSyn.vec.numSynapses ))
     assert [7,62,55] == [ sum( insyn.vec.numSynapses ), sum( outsyn.vec.numSynapses ), sum( outInhSyn.vec.numSynapses ) ]
 
+    # print(oiv.numField)
+    # print(insyn.vec[1].synapse.num)
+    # print(insyn.vec.numSynapses)
+    # print(sum( insyn.vec.numSynapses ))
+    # niv = iv.numSynapses
+    # ov = iv.numSynapses
+
     sv = moose.vec( stim )
     sv.rate = params['randInputRate']
     sv.refractT = params['randRefractTime']