get/set are on ObjId .

Author: Dilawar Singh

pybind11/pymoose.cpp

@@ -46,13 +46,13 @@ Id initModule(py::module& m)
     return initShell();
 }
 
-template <typename T>
+template <typename T=double>
 void setProp(const ObjId& id, const string& fname, T val)
 {
     Field<T>::set(id, fname, val);
 }
 
-template <typename T>
+template <typename T=double>
 T getProp(const ObjId& id, const string& fname)
 {
     return Field<T>::get(id, fname);
@@ -114,11 +114,30 @@ PYBIND11_MODULE(_cmoose, m)
         .def_property_readonly("id", [](ObjId& oid) { return oid.id; })
         .def_property_readonly(
              "type", [](ObjId& oid) { return oid.element()->cinfo()->name(); })
+
+        // Add set and get
+        // Overload of Field::set
+        .def("set", &setProp<double>)
+        .def("set", &setProp<double>)
+        .def("set", &setProp<vector<double>>)
+        .def("set", &setProp<string>)
+        .def("set", &setProp<bool>)
+        // Overload for Field::get
+        .def("get", &getProp<double>)
+        .def("get", &getProp<string>)
+        .def("get", &getProp<unsigned int>)
+        .def("get", &getProp<bool>)
+        .def("getVec", &getPropVec<double>)
+        .def("getNumpy", &getPropNumpy<double>)
+
+        // Representation.
         .def("__repr__", [](const ObjId& oid) {
              return "<" + oid.element()->cinfo()->name() + " id=" +
                     std::to_string(oid.id.value()) + " path=" + oid.path() +
                     ">";
-         });
+                    }
+                )
+        ;
 
     py::class_<FinfoWrapper>(m, "_FinfoWrapper")
         .def(py::init<const Finfo*>())
@@ -182,25 +201,6 @@ PYBIND11_MODULE(_cmoose, m)
 
     m.def("loadModelInternal", &loadModelInternal);
 
-    // Overload for Field::get
-    m.def("get", &getProp<double>);
-    m.def("get", &getProp<string>);
-    m.def("get", &getProp<unsigned int>);
-    m.def("get", &getProp<bool>);
-
-    m.def("getVec", &getPropVec<double>);
-    m.def("getNumpy", &getPropNumpy<double>);
-
-    // Overload of Field::set
-    m.def("set", &setProp<double>);
-    m.def("set", &setProp<vector<double>>);
-    m.def("set", &setProp<string>);
-    m.def("set", &setProp<unsigned int>);
-    m.def("set", &setProp<bool>);
-
-    // m.def("setVec", &setPropVec<double>);
-    // m.def("getVec", &getPropVec<double>);
-
     m.def("getShell",
           []() { return reinterpret_cast<Shell*>(Id().eref().data()); },
           py::return_value_policy::reference);

tests/pybind11/test_shell.py

@@ -1,4 +1,5 @@
 import moose._cmoose as M
+import numpy as np
 import math
 
 def makereac():
@@ -38,7 +39,7 @@ def makereac():
     s.addMsg("Single", r1, "prd", B, "reac");
 
     #  Field<unsigned int>::set(sum, "numVars", 2);
-    M.set(sum, "numVars", 2)
+    sum.set("numVars", 2)
 
     s.addMsg("Single", A, "nOut", M._ObjId(sumInput, 0, 0), "input");
     s.addMsg("Single", B, "nOut", M._ObjId(sumInput, 0, 1), "input");
@@ -58,32 +59,38 @@ def makereac():
     s.addMsg("Single", e2, "prd", E, "reac");
 
     # Set parameters.
-    M.set(A, "concInit", 2);
-    M.set(e1Pool, "concInit", 1);
-    M.set(e2Pool, "concInit", 1);
-    M.set(sum, "expr", "x0+x1");
-    M.set(r1, "Kf", 0.2);
-    M.set(r1, "Kb", 0.1);
-    M.set(r2, "Kf", 0.1);
-    M.set(r2, "Kb", 0.0);
-    M.set(e1, "Km", 5);
-    M.set(e1, "kcat", 1);
-    M.set(e1, "ratio", 4);
-    M.set(e2, "Km", 5);
-    M.set(e2, "kcat", 1);
-
-    vol = M.get(kin, "volume");
+    A.set("concInit", 2);
+    assert A.get("concInit") == 2, A.get("concInit")
+
+    e1Pool.set("concInit", 1);
+    e1Pool.set("concInit", 1)
+
+    e2Pool.set("concInit", 1);
+    sum.set("expr", "x0+x1");
+    r1.set("Kf", 0.2);
+    assert r1.get("Kf") == 0.2
+    r1.set("Kb", 0.1);
+    r2.set("Kf", 0.1);
+    r2.set("Kb", 0.0);
+    e1.set("Km", 5);
+    assert e1.get("Km") ==  5
+    e1.set("kcat", 1);
+    e1.set("ratio", 4);
+    e2.set("Km", 5);
+    e2.set("kcat", 1);
+
+    vol = kin.get("volume");
     print("Volume", vol)
 
     stim = []
     for i in range(100):
         stim.append(vol * M.NA * (1.0 + math.sin(i * 2.0 * M.PI / 100.0)))
 
-    M.set(tab, "vector", stim);
-    M.set(tab, "stepSize", 0.0);
-    M.set(tab, "stopTime", 10.0);
-    M.set(tab, "loopTime", 10.0);
-    M.set(tab, "doLoop", True);
+    tab.set("vector", stim);
+    tab.set("stepSize", 0.0);
+    tab.set("stopTime", 10.0);
+    tab.set("loopTime", 10.0);
+    tab.set("doLoop", True);
 
     #  Connect outputs
     for i in range(7):
@@ -95,17 +102,20 @@ def makereac():
     s.setClock(18, plotDt);
     return kin, tab 
 
-
-def test_shell():
+def test_ksolve():
     rec, tab = makereac()
     s = M.getShell()
     s.reinit()
     s.start(20.0)
     print(tab)
-    data = M.getNumpy(tab, "vector")
-    print(data)
+    dataN = tab.getNumpy("vector")
+    data = np.array(tab.getVec("vector"))
+    assert np.allclose(dataN, data)
     # get data.
     print("Done ksolve")
 
+def main():
+    test_ksolve()
+
 if __name__ == '__main__':
-    test_shell()
+    main()