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FieldIO.h
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1 ///////////////////////////////////////////////////////////////////////////////
2 //
3 // File FieldIO.h
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7 // The MIT License
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9 // Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
10 // Department of Aeronautics, Imperial College London (UK), and Scientific
11 // Computing and Imaging Institute, University of Utah (USA).
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31 //
32 // Description: Field IO prototype definitions
33 //
34 ///////////////////////////////////////////////////////////////////////////////
35 
36 #ifndef NEKTAR_LIB_UTILITIES_BASIC_UTILS_FIELDIO_H
37 #define NEKTAR_LIB_UTILITIES_BASIC_UTILS_FIELDIO_H
38 
39 #include <LibUtilities/BasicUtils/SessionReader.h>
40 #include <LibUtilities/Communication/Comm.h>
41 #include <LibUtilities/BasicUtils/ParseUtils.hpp>
42 #include <LibUtilities/BasicUtils/ShapeType.hpp>
43 #include <LibUtilities/Foundations/Basis.h>
44 #include <LibUtilities/Foundations/Points.h>
45 #include <tinyxml.h>
46 
47 // These are required for the Write(...) and Import(...) functions.
48 #include <boost/archive/iterators/base64_from_binary.hpp>
49 #include <boost/archive/iterators/binary_from_base64.hpp>
50 #include <boost/archive/iterators/transform_width.hpp>
51 #include <boost/iostreams/copy.hpp>
52 #include <boost/iostreams/filter/zlib.hpp>
53 #include <boost/iostreams/filtering_stream.hpp>
54 #include <boost/assign/list_of.hpp>
55 
56 namespace Nektar
57 {
58  namespace LibUtilities
59  {
60 
61  static std::vector<NekDouble> NullNekDoubleVector;
62  static std::vector<LibUtilities::PointsType> NullPointsTypeVector;
63  static std::vector<unsigned int> NullUnsignedIntVector;
64 
65  typedef std::map<std::string, std::string> FieldMetaDataMap;
66  static FieldMetaDataMap NullFieldMetaDataMap;
67  static std::vector<std::vector< NekDouble> > NullVectorNekDoubleVector = boost::assign::list_of(NullNekDoubleVector);
68 
69  struct FieldDefinitions
70  {
71  FieldDefinitions(ShapeType shapeType,
72  const std::vector<unsigned int> &elementIDs,// vector[2]
73  const std::vector<LibUtilities::BasisType> &basis,
74  bool uniOrder,
75  // UniOrder = vector[dimension] - MixOrder
76  // = vector[element*dimension]
77  const std::vector<unsigned int> &numModes,
78  const std::vector<std::string> &fields,
79  int NumHomoDir = 0,
80  const std::vector<NekDouble> &HomoLengths =
81  NullNekDoubleVector,
82  const std::vector<unsigned int> &HomoZIDs =
83  NullUnsignedIntVector,
84  const std::vector<unsigned int> &HomoYIDs =
85  NullUnsignedIntVector,
86  const std::vector<LibUtilities::PointsType> &points =
87  NullPointsTypeVector,
88  bool pointsDef = false,
89  const std::vector<unsigned int> &numPoints =
90  NullUnsignedIntVector,
91  bool numPointsDef = false):
92  m_shapeType(shapeType),
93  m_elementIDs(elementIDs),
94  m_basis(basis),
95  m_numHomogeneousDir(NumHomoDir),
96  m_homogeneousLengths(HomoLengths),
97  m_homogeneousZIDs(HomoZIDs),
98  m_homogeneousYIDs(HomoYIDs),
99  m_points(points),
100  m_pointsDef(pointsDef),
101  m_uniOrder(uniOrder),
102  m_numModes(numModes),
103  m_numPoints(numPoints),
104  m_numPointsDef(numPointsDef),
105  m_fields(fields)
106  {
107  }
108 
109  ShapeType m_shapeType;
110  std::vector<unsigned int> m_elementIDs;
111  std::vector<LibUtilities::BasisType> m_basis;
112  int m_numHomogeneousDir;
113  std::vector<NekDouble> m_homogeneousLengths;
114  std::vector<unsigned int> m_homogeneousZIDs;
115  std::vector<unsigned int> m_homogeneousYIDs;
116 
117  /// Define the type of points per direction.
118  std::vector<LibUtilities::PointsType> m_points;
119  bool m_pointsDef;
120  /// Define order of the element group.
121  /// * UniOrder: same order for each element
122  /// * MixOrder: definition of a different order for each element.
123  bool m_uniOrder;
124  /// Define number of modes per direction.
125  std::vector<unsigned int> m_numModes;
126  std::vector<unsigned int> m_numPoints;
127  bool m_numPointsDef;
128  std::vector<std::string> m_fields;
129  };
130 
131  typedef boost::shared_ptr<FieldDefinitions> FieldDefinitionsSharedPtr;
132 
133 
134  /// Write a field file in serial only
135  LIB_UTILITIES_EXPORT void Write(
136  const std::string &outFile,
137  std::vector<FieldDefinitionsSharedPtr> &fielddefs,
138  std::vector<std::vector<NekDouble> > &fielddata,
139  const FieldMetaDataMap &fieldinfomap = NullFieldMetaDataMap);
140 
141  /// Imports an FLD file
142  LIB_UTILITIES_EXPORT void Import(
143  const std::string& infilename,
144  std::vector<FieldDefinitionsSharedPtr> &fielddefs,
145  std::vector<std::vector<NekDouble> > &fielddata = NullVectorNekDoubleVector,
146  FieldMetaDataMap &fieldinfomap = NullFieldMetaDataMap,
147  const Array<OneD, int> ElementiDs = NullInt1DArray);
148 
149 
150  /// Class for operating on FLD files
151  class FieldIO
152  {
153  public:
154  /// Constructor
155  LIB_UTILITIES_EXPORT FieldIO(
156  LibUtilities::CommSharedPtr pComm);
157 
158  /// Write data in FLD format
159  LIB_UTILITIES_EXPORT void Write(
160  const std::string &outFile,
161  std::vector<FieldDefinitionsSharedPtr> &fielddefs,
162  std::vector<std::vector<NekDouble> > &fielddata,
163  const FieldMetaDataMap &fieldinfomap = NullFieldMetaDataMap);
164 
165  /// Imports an FLD file.
166  LIB_UTILITIES_EXPORT void Import(
167  const std::string& infilename,
168  std::vector<FieldDefinitionsSharedPtr> &fielddefs,
169  std::vector<std::vector<NekDouble> > &fielddata = NullVectorNekDoubleVector,
170  FieldMetaDataMap &fieldinfomap = NullFieldMetaDataMap,
171  const Array<OneD, int> ElementiDs = NullInt1DArray);
172 
173  /// Imports the definition of the meta data
174  LIB_UTILITIES_EXPORT void ImportFieldMetaData(
175  std::string filename,
176  FieldMetaDataMap &fieldmetadatamap);
177 
178  /// Imports the definition of the meta data
179  LIB_UTILITIES_EXPORT void ImportFieldMetaData(
180  TiXmlDocument &doc,
181  FieldMetaDataMap &fieldmetadatamap);
182 
183  /// Imports the definition of the fields.
184  LIB_UTILITIES_EXPORT void ImportFieldDefs(
185  TiXmlDocument &doc,
186  std::vector<FieldDefinitionsSharedPtr> &fielddefs,
187  bool expChild);
188 
189  /// Imports the data fileds.
190  LIB_UTILITIES_EXPORT void ImportFieldData(
191  TiXmlDocument &doc,
192  const std::vector<FieldDefinitionsSharedPtr> &fielddefs,
193  std::vector<std::vector<NekDouble> > &fielddata);
194 
195  LIB_UTILITIES_EXPORT void WriteMultiFldFileIDs(
196  const std::string &outfile,
197  const std::vector<std::string> fileNames,
198  std::vector<std::vector<unsigned int> > &elementList,
199  const FieldMetaDataMap &fieldinfomap = NullFieldMetaDataMap);
200 
201 
202  private:
203  /// Communicator to use when writing parallel format
204  LibUtilities::CommSharedPtr m_comm;
205 
206  LIB_UTILITIES_EXPORT void AddInfoTag(
207  TiXmlElement * root,
208  const FieldMetaDataMap &fieldmetadatamap);
209 
210  LIB_UTILITIES_EXPORT void GenerateSeqString(
211  const std::vector<unsigned int> &elmtids,
212  std::string &idString);
213 
214  LIB_UTILITIES_EXPORT std::string SetUpOutput(
215  const std::string outname,
216  const std::vector<FieldDefinitionsSharedPtr> &fielddefs,
217  const FieldMetaDataMap &fieldmetadatamap);
218 
219  LIB_UTILITIES_EXPORT void ImportMultiFldFileIDs(
220  const std::string &inFile,
221  std::vector<std::string> &fileNames,
222  std::vector<std::vector<unsigned int> > &elementList,
223  FieldMetaDataMap &fieldmetadatamap);
224 
225  LIB_UTILITIES_EXPORT int CheckFieldDefinition(
226  const FieldDefinitionsSharedPtr &fielddefs);
227 
228  LIB_UTILITIES_EXPORT int Deflate(
229  std::vector<NekDouble>& in,
230  string& out);
231 
232  LIB_UTILITIES_EXPORT int Inflate(string& in,
233  std::vector<NekDouble>& out);
234  };
235 
236  typedef boost::shared_ptr<FieldIO> FieldIOSharedPtr;
237  }
238 }
239 #endif
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