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/XdmfArray.tpp

 /*****************************************************************************/
-/*                                    XDMF                                   */
-/*                       eXtensible Data Model and Format                    */
+/*                                    Xdmf                                   */
+/*                       Extensible Data Model and Format                    */
 /*                                                                           */
 /*  Id : XdmfArray.tpp                                                       */
 /*                                                                           */
@@ -23,6 +23,7 @@
 
 #include <functional>
 #include <numeric>
+#include <sstream>
 #include "XdmfArray.hpp"
 
 template <typename T>
@@ -40,6 +41,12 @@ public:
     return 0;
   }
 
+  T
+  operator()(const shared_ptr<std::vector<std::string> > & array) const
+  {
+    return (T)atof(array->operator[](mIndex).c_str());
+  }
+
   template<typename U>
   T
   operator()(const shared_ptr<std::vector<U> > & array) const
@@ -59,6 +66,57 @@ private:
   const unsigned int mIndex;
 };
 
+template <>
+class XdmfArray::GetValue<std::string> : 
+  public boost::static_visitor<std::string> {
+public:
+
+  GetValue(const unsigned int index) :
+    mIndex(index)
+  {
+  }
+
+  std::string
+  operator()(const boost::blank & array) const
+  {
+    return "";
+  }
+
+  std::string
+  operator()(const shared_ptr<std::vector<std::string> > & array) const
+  {
+    return array->operator[](mIndex);
+  }
+
+  template<typename U>
+  std::string
+  operator()(const shared_ptr<std::vector<U> > & array) const
+  {
+    std::stringstream value;
+    value << array->operator[](mIndex);
+    return value.str();
+  }
+
+  std::string
+  operator()(const boost::shared_array<const std::string> & array) const
+  {
+    return array[mIndex];
+  }
+
+  template<typename U>
+  std::string
+  operator()(const boost::shared_array<const U> & array) const
+  {
+    std::stringstream value;
+    value << array[mIndex];
+    return value.str();
+  }
+
+private:
+
+  const unsigned int mIndex;
+};
+
 template <typename T>
 class XdmfArray::GetValues : public boost::static_visitor<void> {
 public:
@@ -82,6 +140,15 @@ public:
     return;
   }
 
+  void
+  operator()(const shared_ptr<std::vector<std::string> > & array) const
+  {
+    for(unsigned int i=0; i<mNumValues; ++i) {
+      mValuesPointer[i*mValuesStride] =
+        (T)atof(array->operator[](mStartIndex + i*mArrayStride).c_str());
+    }
+  }
+
   template<typename U>
   void
   operator()(const shared_ptr<std::vector<U> > & array) const
@@ -110,6 +177,60 @@ private:
   const unsigned int mValuesStride;
 };
 
+template <>
+class XdmfArray::GetValues<std::string> : public boost::static_visitor<void> {
+public:
+
+  GetValues(const unsigned int startIndex,
+            std::string * valuesPointer,
+            const unsigned int numValues,
+            const unsigned int arrayStride,
+            const unsigned int valuesStride) :
+    mStartIndex(startIndex),
+    mValuesPointer(valuesPointer),
+    mNumValues(numValues),
+    mArrayStride(arrayStride),
+    mValuesStride(valuesStride)
+  {
+  }
+
+  void
+  operator()(const boost::blank & array) const
+  {
+    return;
+  }
+
+  template<typename U>
+  void
+  operator()(const shared_ptr<std::vector<U> > & array) const
+  {
+    for(unsigned int i=0; i<mNumValues; ++i) {
+      std::stringstream value;
+      value << array->operator[](mStartIndex + i*mArrayStride);
+      mValuesPointer[i*mValuesStride] = value.str();
+    }
+  }
+
+  template<typename U>
+  void
+  operator()(const boost::shared_array<const U> & array) const
+  {
+    for(unsigned int i=0; i<mNumValues; ++i) {
+      std::stringstream value;
+      value << array[mStartIndex + i*mArrayStride];
+      mValuesPointer[i*mValuesStride] = value.str();
+    }
+  }
+
+private:
+
+  const unsigned int mStartIndex;
+  std::string * mValuesPointer;
+  const unsigned int mNumValues;
+  const unsigned int mArrayStride;
+  const unsigned int mValuesStride;
+};
+
 template <typename T>
 class XdmfArray::Insert : public boost::static_visitor<void> {
 public:
@@ -139,6 +260,24 @@ public:
                          mArray->mArray);
   }
 
+  void
+  operator()(shared_ptr<std::vector<std::string> > & array) const
+  {
+    unsigned int size = mStartIndex + mNumValues;
+    if(mArrayStride > 1) {
+      size = mStartIndex + mNumValues * mArrayStride - 1;
+    }
+    if(array->size() < size) {
+      array->resize(size);
+      mDimensions.clear();
+    }
+    for(unsigned int i=0; i<mNumValues; ++i) {
+      std::stringstream value;
+      value << mValuesPointer[i*mValuesStride];
+      array->operator[](mStartIndex + i*mArrayStride) = value.str();
+    }
+  }
+
   template<typename U>
   void
   operator()(shared_ptr<std::vector<U> > & array) const
@@ -177,6 +316,90 @@ private:
   std::vector<unsigned int> & mDimensions;
 };
 
+template <>
+class XdmfArray::Insert<std::string> : public boost::static_visitor<void> {
+public:
+
+  Insert(XdmfArray * const array,
+         const unsigned int startIndex,
+         const std::string * const valuesPointer,
+         const unsigned int numValues,
+         const unsigned int arrayStride,
+         const unsigned int valuesStride,
+         std::vector<unsigned int> & dimensions) :
+    mArray(array),
+    mStartIndex(startIndex),
+    mValuesPointer(valuesPointer),
+    mNumValues(numValues),
+    mArrayStride(arrayStride),
+    mValuesStride(valuesStride),
+    mDimensions(dimensions)
+  {
+  }
+
+  void
+  operator()(const boost::blank & array) const
+  {
+    mArray->initialize<std::string>();
+    boost::apply_visitor(*this,
+                         mArray->mArray);
+  }
+
+  void
+  operator()(shared_ptr<std::vector<std::string> > & array) const
+  {
+    unsigned int size = mStartIndex + mNumValues;
+    if(mArrayStride > 1) {
+      size = mStartIndex + mNumValues * mArrayStride - 1;
+    }
+    if(array->size() < size) {
+      array->resize(size);
+      mDimensions.clear();
+    }
+    for(unsigned int i=0; i<mNumValues; ++i) {
+      array->operator[](mStartIndex + i*mArrayStride) =
+        mValuesPointer[i*mValuesStride].c_str();
+    }
+  }
+
+  template<typename U>
+  void
+  operator()(shared_ptr<std::vector<U> > & array) const
+  {
+    unsigned int size = mStartIndex + mNumValues;
+    if(mArrayStride > 1) {
+      size = mStartIndex + mNumValues * mArrayStride - 1;
+    }
+    if(array->size() < size) {
+      array->resize(size);
+      mDimensions.clear();
+    }
+    for(unsigned int i=0; i<mNumValues; ++i) {
+      array->operator[](mStartIndex + i*mArrayStride) =
+        (U)atof(mValuesPointer[i*mValuesStride].c_str());
+    }
+  }
+
+  template<typename U>
+  void
+  operator()(boost::shared_array<const U> & array) const
+  {
+    mArray->internalizeArrayPointer();
+    boost::apply_visitor(*this,
+                         mArray->mArray);
+  }
+
+private:
+
+  XdmfArray * const mArray;
+  const unsigned int mStartIndex;
+  const std::string * const mValuesPointer;
+  const unsigned int mNumValues;
+  const unsigned int mArrayStride;
+  const unsigned int mValuesStride;
+  std::vector<unsigned int> & mDimensions;
+};
+
 template <typename T>
 class XdmfArray::PushBack : public boost::static_visitor<void> {
 public:
@@ -196,6 +419,15 @@ public:
                          mArray->mArray);
   }
 
+  void
+  operator()(shared_ptr<std::vector<std::string> > & array) const
+  {
+    std::stringstream value;
+    value << mVal;
+    array->push_back(value.str());
+    mArray->mDimensions.clear();
+  }
+
   template<typename U>
   void
   operator()(shared_ptr<std::vector<U> > & array) const
@@ -219,6 +451,55 @@ private:
   XdmfArray * const mArray;
 };
 
+template <>
+class XdmfArray::PushBack<std::string> : public boost::static_visitor<void> {
+public:
+
+  PushBack(const std::string & val,
+           XdmfArray * const array) :
+    mVal(val),
+    mArray(array)
+  {
+  }
+
+  void
+  operator()(const boost::blank & array) const
+  {
+    mArray->initialize<std::string>();
+    boost::apply_visitor(*this,
+                         mArray->mArray);
+  }
+
+  void
+  operator()(shared_ptr<std::vector<std::string> > & array) const
+  {
+    array->push_back(mVal);
+    mArray->mDimensions.clear();
+  }
+
+  template<typename U>
+  void
+  operator()(shared_ptr<std::vector<U> > & array) const
+  {
+    array->push_back((U)atof(mVal.c_str()));
+    mArray->mDimensions.clear();
+  }
+
+  template<typename U>
+  void
+  operator()(const boost::shared_array<const U> & array) const
+  {
+    mArray->internalizeArrayPointer();
+    boost::apply_visitor(*this,
+                         mArray->mArray);
+  }
+
+private:
+
+  const std::string & mVal;
+  XdmfArray * const mArray;
+};
+
 template <typename T>
 class XdmfArray::Resize : public boost::static_visitor<void> {
 public:
@@ -240,6 +521,15 @@ public:
                          mArray->mArray);
   }
 
+  void
+  operator()(shared_ptr<std::vector<std::string> > & array) const
+  {
+    std::stringstream value;
+    value << mVal;
+    array->resize(mNumValues, value.str());
+    mArray->mDimensions.clear();
+  }
+
   template<typename U>
   void
   operator()(shared_ptr<std::vector<U> > & array) const
@@ -264,6 +554,58 @@ private:
   const T & mVal;
 };
 
+template <>
+class XdmfArray::Resize<std::string> : public boost::static_visitor<void> {
+public:
+
+  Resize(XdmfArray * const array,
+         const unsigned int numValues,
+         const std::string & val) :
+    mArray(array),
+    mNumValues(numValues),
+    mVal(val)
+  {
+  }
+
+  void
+  operator()(const boost::blank & array) const
+  {
+    mArray->initialize<std::string>();
+    boost::apply_visitor(*this,
+                         mArray->mArray);
+  }
+
+  void
+  operator()(shared_ptr<std::vector<std::string> > & array) const
+  {
+    array->resize(mNumValues, mVal);
+    mArray->mDimensions.clear();
+  }
+
+  template<typename U>
+  void
+  operator()(shared_ptr<std::vector<U> > & array) const
+  {
+    array->resize(mNumValues, (U)atof(mVal.c_str()));
+    mArray->mDimensions.clear();
+  }
+
+  template<typename U>
+  void
+  operator()(const boost::shared_array<const U> & array) const
+  {
+    mArray->internalizeArrayPointer();
+    boost::apply_visitor(*this,
+                         mArray->mArray);
+  }
+
+private:
+
+  XdmfArray * mArray;
+  const unsigned int mNumValues;
+  const std::string & mVal;
+};
+
 struct XdmfArray::NullDeleter
 {
   void

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) {