ENH: Add string array type

Add tests for I/O of strings (to hdf5 and xml).
Fix bug in XdmfExodusReader when reading grid centered data.
Add string I/O in python and add tests.

core/XdmfArray.cpp

@@ -167,6 +167,12 @@ public:
     return XdmfArrayType::UInt32();
   }
 
+  shared_ptr<const XdmfArrayType>
+  getArrayType(const std::string * const) const
+  {
+    return XdmfArrayType::String();
+  }
+
   shared_ptr<const XdmfArrayType>
   operator()(const boost::blank & array) const
   {
@@ -685,6 +691,9 @@ XdmfArray::initialize(const shared_ptr<const XdmfArrayType> arrayType,
   else if(arrayType == XdmfArrayType::UInt32()) {
     this->initialize<unsigned int>(size);
   }
+  else if(arrayType == XdmfArrayType::String()) {
+    this->initialize<std::string>(size);
+  }
   else if(arrayType == XdmfArrayType::Uninitialized()) {
     this->release();
   }
@@ -833,11 +842,21 @@ XdmfArray::populateItem(const std::map<std::string, std::string> & itemPropertie
     unsigned int index = 0;
     boost::char_separator<char> sep(" \t\n");
     boost::tokenizer<boost::char_separator<char> > tokens(contentVal, sep);
-    for(boost::tokenizer<boost::char_separator<char> >::const_iterator
-          iter = tokens.begin();
-        iter != tokens.end();
-        ++iter, ++index) {
-      this->insert(index, atof((*iter).c_str()));
+    if(arrayType == XdmfArrayType::String()) {
+      for(boost::tokenizer<boost::char_separator<char> >::const_iterator
+            iter = tokens.begin();
+          iter != tokens.end();
+          ++iter, ++index) {
+        this->insert(index, *iter);
+      }
+    }
+    else {
+      for(boost::tokenizer<boost::char_separator<char> >::const_iterator
+            iter = tokens.begin();
+          iter != tokens.end();
+          ++iter, ++index) {
+        this->insert(index, atof((*iter).c_str()));
+      }
     }
   }
   else {

core/XdmfArray.hpp

@@ -89,6 +89,7 @@ class XdmfHeavyDataController;
  *   UInt8
  *   UInt16
  *   UInt32
+ *   String
  */
 class XDMFCORE_EXPORT XdmfArray : public XdmfItem {
 
@@ -527,6 +528,7 @@ private:
     shared_ptr<std::vector<unsigned char> >,
     shared_ptr<std::vector<unsigned short> >,
     shared_ptr<std::vector<unsigned int> >,
+    shared_ptr<std::vector<std::string> >,
     boost::shared_array<const char>,
     boost::shared_array<const short>,
     boost::shared_array<const int>,

core/XdmfArrayType.cpp

@@ -97,6 +97,13 @@ XdmfArrayType::UInt32()
   return p;
 }
 
+shared_ptr<const XdmfArrayType>
+XdmfArrayType::String()
+{
+  static shared_ptr<const XdmfArrayType> p(new XdmfArrayType("String", 0));
+  return p;
+}
+
 XdmfArrayType::XdmfArrayType(const std::string & name,
                              const unsigned int precision) :
   mName(name),
@@ -141,6 +148,9 @@ XdmfArrayType::New(const std::map<std::string, std::string> & itemProperties)
     }
     return Int32();
   }
+  else if(typeVal.compare("String") == 0) {
+    return String();
+  }
   else if(typeVal.compare("Char") == 0) {
     return Int8();
   }

core/XdmfArrayType.hpp

@@ -47,6 +47,7 @@
  *   UInt8
  *   UInt16
  *   UInt32
+ *   String
  */
 class XDMFCORE_EXPORT XdmfArrayType : public XdmfItemProperty {
 
@@ -67,6 +68,7 @@ public:
   static shared_ptr<const XdmfArrayType> UInt8();
   static shared_ptr<const XdmfArrayType> UInt16();
   static shared_ptr<const XdmfArrayType> UInt32();
+  static shared_ptr<const XdmfArrayType> String();
 
   /**
    * Get the data size, in bytes, of the value associated with this

core/XdmfCore.i

@@ -245,6 +245,13 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
         }
     }
 
+    void insertAsString(int startIndex, PyObject * list) {
+        Py_ssize_t size = PyList_Size(list);
+        for(Py_ssize_t i = 0; i < size; ++i) {
+            $self->insert<std::string>(i+startIndex, PyString_AsString(PyList_GetItem(list, i)));
+        }
+    }
+
 };
 
 %extend XdmfArrayType {
@@ -340,6 +347,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 %template(getValueAsUInt8) XdmfArray::getValue<unsigned char>;
 %template(getValueAsUInt16) XdmfArray::getValue<unsigned short>;
 %template(getValueAsUInt32) XdmfArray::getValue<unsigned int>;
+%template(getValueAsString) XdmfArray::getValue<std::string>;
 
 %template(initializeAsInt8) XdmfArray::initialize<char>;
 %template(initializeAsInt16) XdmfArray::initialize<short>;
@@ -350,6 +358,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 %template(initializeAsUInt8) XdmfArray::initialize<unsigned char>;
 %template(initializeAsUInt16) XdmfArray::initialize<unsigned short>;
 %template(initializeAsUInt32) XdmfArray::initialize<unsigned int>;
+%template(initializeAsString) XdmfArray::initialize<std::string>;
 
 %template(insertValueAsInt8) XdmfArray::insert<char>;
 %template(insertValueAsInt16) XdmfArray::insert<short>;
@@ -360,6 +369,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 %template(insertValueAsUInt8) XdmfArray::insert<unsigned char>;
 %template(insertValueAsUInt16) XdmfArray::insert<unsigned short>;
 %template(insertValueAsUInt32) XdmfArray::insert<unsigned int>;
+%template(insertValueAsString) XdmfArray::insert<std::string>;
 
 %template(pushBackAsInt8) XdmfArray::pushBack<char>;
 %template(pushBackAsInt16) XdmfArray::pushBack<short>;
@@ -370,6 +380,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 %template(pushBackAsUInt8) XdmfArray::pushBack<unsigned char>;
 %template(pushBackAsUInt16) XdmfArray::pushBack<unsigned short>;
 %template(pushBackAsUInt32) XdmfArray::pushBack<unsigned int>;
+%template(pushBackAsString) XdmfArray::pushBack<std::string>;
 
 %template(resizeAsInt8) XdmfArray::resize<char>;
 %template(resizeAsInt16) XdmfArray::resize<short>;
@@ -380,6 +391,7 @@ swig -v -c++ -python -o XdmfCorePython.cpp XdmfCore.i
 %template(resizeAsUInt8) XdmfArray::resize<unsigned char>;
 %template(resizeAsUInt16) XdmfArray::resize<unsigned short>;
 %template(resizeAsUInt32) XdmfArray::resize<unsigned int>;
+%template(resizeAsString) XdmfArray::resize<std::string>;
 
 %template(UIntVector) std::vector<unsigned int>;
 %template(ItemVector) std::vector<boost::shared_ptr<XdmfItem> >;

core/XdmfHDF5Controller.cpp

@@ -115,6 +115,7 @@ XdmfHDF5Controller::read(XdmfArray * const array, const int fapl)
      NULL);*/
 
   hid_t datatype;
+  bool closeDatatype = false;
   if(mType == XdmfArrayType::Int8()) {
     datatype = H5T_NATIVE_CHAR;
   }
@@ -142,6 +143,11 @@ XdmfHDF5Controller::read(XdmfArray * const array, const int fapl)
   else if(mType == XdmfArrayType::UInt32()) {
     datatype = H5T_NATIVE_UINT;
   }
+  else if(mType == XdmfArrayType::String()) {
+    datatype = H5Tcopy(H5T_C_S1);
+    H5Tset_size(datatype, H5T_VARIABLE);
+    closeDatatype = true;
+  }
   else {
     XdmfError::message(XdmfError::FATAL,
                        "Unknown XdmfArrayType encountered in hdf5 "
@@ -156,15 +162,37 @@ XdmfHDF5Controller::read(XdmfArray * const array, const int fapl)
                        "allocated size in XdmfArray.");
   }
 
-  status = H5Dread(dataset,
-                   datatype,
-                   memspace,
-                   dataspace,
-                   H5P_DEFAULT,
-                   array->getValuesInternal());
+  if(closeDatatype) {
+    char ** data = new char*[numVals];
+    status = H5Dread(dataset, 
+                     datatype, 
+                     memspace,
+                     dataspace,
+                     H5P_DEFAULT, 
+                     data);
+    for(hssize_t i=0; i<numVals; ++i) {
+      array->insert<std::string>(i, data[i]);
+    }
+    status = H5Dvlen_reclaim(datatype, 
+                             dataspace, 
+                             H5P_DEFAULT, 
+                             data);
+    delete [] data;
+  }
+  else {
+    status = H5Dread(dataset,
+                     datatype,
+                     memspace,
+                     dataspace,
+                     H5P_DEFAULT,
+                     array->getValuesInternal());
+  }
 
   status = H5Sclose(dataspace);
   status = H5Sclose(memspace);
   status = H5Dclose(dataset);
+  if(closeDatatype) {
+    status = H5Tclose(datatype);
+  }
   status = H5Fclose(hdf5Handle);
 }

core/XdmfHDF5Writer.cpp

@@ -171,6 +171,7 @@ XdmfHDF5Writer::write(XdmfArray & array,
                       const int fapl)
 {
   hid_t datatype = -1;
+  bool closeDatatype = false;
 
   if(array.isInitialized()) {
     if(array.getArrayType() == XdmfArrayType::Int8()) {
@@ -200,6 +201,11 @@ XdmfHDF5Writer::write(XdmfArray & array,
     else if(array.getArrayType() == XdmfArrayType::UInt32()) {
       datatype = H5T_NATIVE_UINT;
     }
+    else if(array.getArrayType() == XdmfArrayType::String()) {
+      datatype = H5Tcopy(H5T_C_S1);
+      H5Tset_size(datatype, H5T_VARIABLE);
+      closeDatatype = true;
+    }
     else {
       XdmfError::message(XdmfError::FATAL,
                          "Array of unsupported type in "
@@ -395,6 +401,9 @@ XdmfHDF5Writer::write(XdmfArray & array,
       status = H5Sclose(memspace);
     }
     status = H5Dclose(dataset);
+    if(closeDatatype) {
+      status = H5Tclose(datatype);
+    }
     if(closeFile) {
       mImpl->closeFile();
     }

core/tests/Cxx/TestXdmfArray.cpp

@@ -303,5 +303,25 @@ int main(int, char **)
   array9->insert<double>(9, 1.0);
   assert(array9->getDimensionsString() == "10");
 
+  //
+  // STRINGS
+  //
+  shared_ptr<XdmfArray> stringArray = XdmfArray::New();
+  stringArray->resize<std::string>(3, "");
+  std::string firstValue = stringArray->getValue<std::string>(0);
+  assert(firstValue.compare("") == 0);
+  stringArray->insert<std::string>(0, "foo");
+  stringArray->insert<std::string>(1, "bar");
+  stringArray->insert<std::string>(2, "cat");
+  firstValue = stringArray->getValue<std::string>(0);
+  assert(firstValue.compare("foo") == 0);
+  std::string allValues = stringArray->getValuesString();
+  assert(allValues.compare("foo bar cat") == 0);
+  stringArray->insert<int>(3, 1);
+  allValues = stringArray->getValuesString();
+  assert(allValues.compare("foo bar cat 1") == 0);
+  int num = stringArray->getValue<int>(3);
+  assert(num == 1);
+
   return 0;
 }

core/tests/Cxx/TestXdmfArrayWriteRead.cpp

@@ -22,4 +22,36 @@ int main(int, char **)
 
   array->read();
   assert(array->getValuesString().compare("1 2 3 4") == 0);
+
+  shared_ptr<XdmfArray> stringArray = XdmfArray::New();
+  stringArray->pushBack<std::string>("foo");
+  stringArray->pushBack<std::string>("bar");
+  stringArray->pushBack<std::string>("cat");
+  stringArray->pushBack<std::string>("dog");
+  stringArray->pushBack<std::string>("blah");
+  assert(stringArray->getSize() == 5);
+  assert(stringArray->getValuesString().compare("foo bar cat dog blah") == 0);
+
+  shared_ptr<XdmfHDF5Writer> stringWriter = 
+    XdmfHDF5Writer::New("testString.h5");
+  stringArray->accept(stringWriter);
+
+  stringArray->release();
+  stringArray->read();
+  assert(stringArray->getSize() == 5);
+  assert(stringArray->getValuesString().compare("foo bar cat dog blah") == 0);
+  assert(stringArray->getValue<std::string>(0).compare("foo") == 0);
+  
+  /*
+  assert(array->getSize() == 4);
+  assert(array->getValuesString().compare("1 2 3 4") == 0);
+
+  array->release();
+  assert(array->getValuesString() == "");
+  assert(array->getSize() == 4);
+
+  array->read();
+  assert(array->getValuesString().compare("1 2 3 4") == 0);
+  */
+
 }

core/tests/Python/TestXdmfArray.py

@@ -49,3 +49,18 @@ if __name__ == "__main__":
     array9.insertAsUInt32(0, values1)
     print array9.getValuesString()
     assert array9.getArrayType() == XdmfArrayType.UInt32()
+
+    stringArray = XdmfArray.New()
+    stringArray.insertValueAsString(0, "foo")
+    strings = ["bar", "car", "cellar"]
+    assert stringArray.getArrayType() == XdmfArrayType.String()
+    stringArray.insertAsString(0, strings)
+    assert stringArray.getSize() == 3
+    assert stringArray.getValueAsString(0) == "bar"
+    stringArray.pushBackAsString("dog")
+    assert stringArray.getSize() == 4
+    assert stringArray.getValueAsString(3) == "dog"
+    stringArray.resizeAsString(5, "")
+    assert stringArray.getSize() == 5
+    assert stringArray.getValueAsString(4) == ""
+    print stringArray.getValuesString()

tests/Cxx/TestXdmfReader.cpp

@@ -40,11 +40,10 @@ int main(int, char **)
 
   std::vector<shared_ptr<XdmfItem> > readItems2 =
     reader->read("TestXdmfReader1.xmf", "//Attribute");
-  assert(readItems2.size() == 4);
+  assert(readItems2.size() == 6);
   shared_ptr<XdmfAttribute> readAttribute =
     shared_dynamic_cast<XdmfAttribute>(readItems2[0]);
-  assert(readAttribute->getName().compare("Nodal Attribute") == 0 ||
-         readAttribute->getName().compare("Cell Attribute"));
+  assert(readAttribute->getName().compare("Nodal Attribute") == 0);
 
   return 0;
 }

tests/Cxx/TestXdmfVisitorValueCounter.cpp

@@ -56,7 +56,7 @@ int main(int, char **)
 
   grid->accept(visitor);
 
-  assert(visitor->getCount() == 69);
+  assert(visitor->getCount() == 71);
 
   return 0;
 }

tests/Cxx/XdmfTestDataGenerator.hpp

@@ -20,10 +20,11 @@ public:
    * Number of Attributes = 2
    *   Cell Attributes = 1
    *   Nodal Attributes = 1
+   *   Grid Attributes = 1
    * Number of Sets = 1
    *   Nodal Set = 1
    * Time = 100
-   * Total Number of Values = 69
+   * Total Number of Values = 71
    */
   static shared_ptr<XdmfUnstructuredGrid> createHexahedron()
   {
@@ -61,6 +62,16 @@ public:
     cellAttribute->setCenter(XdmfAttributeCenter::Cell());
     cellAttribute->insert(0, &cellValues[0], 2);
 
+    // Add Grid Attribute
+    shared_ptr<XdmfAttribute> gridAttribute = XdmfAttribute::New();
+    std::string gridValues[] = {"foo", "bar"};
+    //int gridValues[] = {1, 2};
+    gridAttribute->setName("Grid Attribute");
+    gridAttribute->setType(XdmfAttributeType::Vector());
+    gridAttribute->setCenter(XdmfAttributeCenter::Grid());
+    gridAttribute->insert(0, &gridValues[0], 2);
+
+
     // Add Node Set
     shared_ptr<XdmfSet> nodeSet = XdmfSet::New();
     int nodeIds[] = {0, 1, 2};
@@ -74,6 +85,7 @@ public:
 
     grid->insert(nodalAttribute);
     grid->insert(cellAttribute);
+    grid->insert(gridAttribute);
     grid->insert(nodeSet);
     return grid;
   }

utils/XdmfExodusReader.cpp

@@ -561,7 +561,7 @@ XdmfExodusReader::read(const std::string & fileName,
 
   // Global variable data
   double * global_var_vals = new double[num_global_vars];
-  ex_get_glob_vars(exodusHandle, 1, num_global_vars, &global_var_vals);
+  ex_get_glob_vars(exodusHandle, 1, num_global_vars, global_var_vals);
   for (int i=0; i<num_global_vars; ++i) {
     // Write global attribute to xdmf
     shared_ptr<XdmfAttribute> attribute = XdmfAttribute::New();

utils/tests/Cxx/TestXdmfExodusIO.cpp

@@ -33,17 +33,19 @@ int main(int, char *)
     assert(grid->getTopology()->getValue<double>(i) ==
            hexahedron->getTopology()->getValue<double>(i));
   }
-  assert(hexahedron->getNumberAttributes() + 1 == grid->getNumberAttributes());
+  assert(hexahedron->getNumberAttributes() + 2 == grid->getNumberAttributes());
   for(unsigned int i=0; i<hexahedron->getNumberAttributes(); ++i) {
     shared_ptr<XdmfAttribute> attribute1 = hexahedron->getAttribute(i);
-    shared_ptr<XdmfAttribute> attribute2 =
-      grid->getAttribute(attribute1->getName());
-    assert(attribute1->getCenter() == attribute2->getCenter());
-    assert(attribute1->getType() == attribute2->getType());
-    assert(attribute1->getSize() == attribute2->getSize());
-    for(unsigned int j=0; j<attribute1->getSize(); ++j) {
-      assert(attribute1->getValue<double>(i) ==
-             attribute2->getValue<double>(i));
+    if(attribute1->getCenter() != XdmfAttributeCenter::Grid()) {
+      shared_ptr<XdmfAttribute> attribute2 =
+        grid->getAttribute(attribute1->getName());
+      assert(attribute1->getCenter() == attribute2->getCenter());
+      assert(attribute1->getType() == attribute2->getType());
+      assert(attribute1->getSize() == attribute2->getSize());
+      for(unsigned int j=0; j<attribute1->getSize(); ++j) {
+        assert(attribute1->getValue<double>(i) ==
+               attribute2->getValue<double>(i));
+      }
     }
   }
 }