Refs #4315. Add first UnitCell function for numpy pass throughs

Allows the test to do something moderately useful and this allows me to
check it works on all platforms

Code/Mantid/Framework/PythonInterface/CMakeLists.txt

@@ -86,6 +86,7 @@ set ( TEST_PY_FILES
   test/python/SimpleAPITest.py
   test/python/QuatTest.py
   test/python/V3DTest.py
+  test/python/UnitCellTest.py
   test/python/WorkspaceTest.py
 )
 

Code/Mantid/Framework/PythonInterface/inc/MantidPythonInterface/kernel/NumpyConverters.h

@@ -32,15 +32,23 @@ namespace Mantid
   {
     namespace Numpy
     {
+      /** @name Create Numpy arrays */
+      //@{
       /// Create a numpy array wrapper around existing vector. This is only possible for contiguous data
       DLLExport PyObject *wrapWithNumpy(const std::vector<double> & data);
       /// Create a read-only numpy array wrapper around existing data.
       DLLExport PyObject *wrapWithReadOnlyNumpy(const std::vector<double> & data);
-
       /// Create a read-only array wrapper around a double Matrix
       DLLExport PyObject *wrapWithNumpy(const Kernel::DblMatrix & data);
       /// Create a read-only array wrapper around a double Matrix
       DLLExport PyObject *wrapWithReadOnlyNumpy(const Kernel::DblMatrix & data);
+      //@}
+
+      /** @name Create Mantid objects from python sequences */
+      //@{
+      DLLExport Kernel::DblMatrix createMatrixFromNumpyArray(PyObject* data);
+      //@}
+
     }
   }
 }

Code/Mantid/Framework/PythonInterface/mantid/api/src/api.cpp.in

@@ -4,6 +4,7 @@
 // See http://docs.scipy.org/doc/numpy/reference/c-api.array.html#PY_ARRAY_UNIQUE_SYMBOL
 #define PY_ARRAY_UNIQUE_SYMBOL API_ARRAY_API
 #include <numpy/arrayobject.h>
+#include <boost/python/numeric.hpp>
 
 // Forward declare
 @EXPORT_DECLARE@
@@ -14,6 +15,7 @@ BOOST_PYTHON_MODULE(_api)
   boost::python::docstring_options docstrings(true, true, false);
   // Import numpy
   _import_array();
+  boost::python::numeric::array::set_module_and_type("numpy", "ndarray");
 
 @EXPORT_FUNCTIONS@
 }

Code/Mantid/Framework/PythonInterface/mantid/geometry/src/UnitCell.cpp

@@ -1,4 +1,5 @@
 #include "MantidGeometry/Crystal/UnitCell.h"
+#include "MantidPythonInterface/kernel/NumpyConverters.h"
 #include <boost/python/class.hpp>
 #include <boost/python/enum.hpp>
 #include <boost/python/scope.hpp>
@@ -7,8 +8,19 @@ using Mantid::Geometry::UnitCell;
 using Mantid::Geometry::AngleUnits;
 using Mantid::Geometry::angRadians;
 using Mantid::Geometry::angDegrees;
+using Mantid::Kernel::DblMatrix;
 using namespace boost::python;
 
+// Functions purely to aid with wrapping
+namespace //<unnamed>
+{
+  void recalculateFromGstar(UnitCell & self, PyObject* values)
+  {
+    // Create a double matrix and put this in to the unit cell
+    self.recalculateFromGstar(Mantid::PythonInterface::Numpy::createMatrixFromNumpyArray(values));
+  }
+}
+
 void export_UnitCell()
 {
   enum_<AngleUnits>("AngleUnits")
@@ -58,8 +70,8 @@ void export_UnitCell()
     .def( "volume", (double ( UnitCell::* )() const) &UnitCell::volume)
     // .def( "getG", &UnitCellWrapper::getG)
     // .def( "getGstar", &UnitCellWrapper::getGstar)
-    // .def( "getB", &UnitCellWrapper::getB )
-    // .def( "recalculateFromGstar", &UnitCellWrapper::recalculateFromGStar) ;
+    //.def( "getB", &getB )
+    .def( "recalculateFromGstar", &recalculateFromGstar)
     ;
 
     scope().attr("deg2rad") = Mantid::Geometry::deg2rad;

Code/Mantid/Framework/PythonInterface/mantid/geometry/src/geometry.cpp.in

@@ -5,6 +5,7 @@
 // See http://docs.scipy.org/doc/numpy/reference/c-api.array.html#PY_ARRAY_UNIQUE_SYMBOL
 #define PY_ARRAY_UNIQUE_SYMBOL GEOMETRY_ARRAY_API
 #include <numpy/arrayobject.h>
+#include <boost/python/numeric.hpp>
 
 using boost::python::def;
 
@@ -17,6 +18,7 @@ BOOST_PYTHON_MODULE(_geometry)
   boost::python::docstring_options docstrings(true, true, false);
   // Import numpy
   _import_array();
+  boost::python::numeric::array::set_module_and_type("numpy", "ndarray");
 
 @EXPORT_FUNCTIONS@
 }

Code/Mantid/Framework/PythonInterface/mantid/kernel/src/NumpyConverters.cpp

@@ -5,6 +5,10 @@
 #define NO_IMPORT_ARRAY
 #include <numpy/ndarrayobject.h>
 
+#include <boost/python/tuple.hpp>
+#include <boost/python/numeric.hpp>
+#include <boost/python/extract.hpp>
+
 namespace Mantid
 {
   namespace PythonInterface
@@ -61,6 +65,43 @@ namespace Mantid
         return (PyObject*)nparray;
       }
 
-    }
+      /**
+       * Create a Matrix of doubles from a 2D numpy array
+       * @param data A python object that points to a 2D numpy array
+       * @return A Matrix<double> created from the input array
+       */
+      Kernel::DblMatrix createMatrixFromNumpyArray(PyObject *data)
+      {
+        using namespace boost::python;
+        if( PyArray_Check(data) )
+        {
+          numeric::array numarray = extract<numeric::array>(data);
+          numarray = (boost::python::numeric::array) numarray.astype('d'); // Force the array to be of double type (in case it was int)
+          boost::python::tuple shape( numarray.attr("shape") );
+          if( boost::python::len(shape) != 2 )
+          {
+            std::ostringstream msg;
+            msg << "createMatrixFromNumpyArray - Expected an array with 2 dimensions but was given array with " << boost::python::len(shape) << " dimensions.";
+            throw std::invalid_argument(msg.str());
+          }
+          size_t nx = boost::python::extract<size_t>(shape[0]);
+          size_t ny = boost::python::extract<size_t>(shape[1]);
+          Kernel::Matrix<double> matrix(nx,ny);
+          for( size_t i = 0; i < nx; i++ )
+          {
+            for( size_t j = 0; j < ny; j++ )
+            {
+              matrix[i][j] = extract<double>( numarray[boost::python::make_tuple( i, j )]);
+            }
+          }
+          return matrix;
+        }
+        else
+        {
+          throw std::invalid_argument(std::string("createMatrixFromNumpyArray - Expected numpy array as input, found ") + data->ob_type->tp_name);
+        }
+      }
+
+    } // Numpy
   }
 }

Code/Mantid/Framework/PythonInterface/mantid/kernel/src/kernel.cpp.in

@@ -10,6 +10,7 @@
 // See http://docs.scipy.org/doc/numpy/reference/c-api.array.html#PY_ARRAY_UNIQUE_SYMBOL
 #define PY_ARRAY_UNIQUE_SYMBOL KERNEL_ARRAY_API
 #include <numpy/arrayobject.h>
+#include <boost/python/numeric.hpp>
 
 using namespace Mantid::PythonInterface;
 using PropertyMarshal::SingleValueTypeHandler;
@@ -25,6 +26,7 @@ BOOST_PYTHON_MODULE(_kernel)
   boost::python::docstring_options docstrings(true, true, false);
   // Import numpy
   _import_array();
+  boost::python::numeric::array::set_module_and_type("numpy", "ndarray");
 
   def("version_str", &Mantid::Kernel::MantidVersion::version, 
       "Returns the Mantid version string in the form \"major.minor.patch\"");