Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
TrianglesMeshReader.hpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
16 * Redistributions in binary form must reproduce the above copyright notice,
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19 * Neither the name of the University of Oxford nor the names of its
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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34*/
35
36
37#ifndef _TRIANGLESMESHREADER_HPP_
38#define _TRIANGLESMESHREADER_HPP_
39
40#include <vector>
41#include <string>
42#include <fstream>
43#include "AbstractMeshReader.hpp"
44
51template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
52class TrianglesMeshReader : public AbstractMeshReader<ELEMENT_DIM,SPACE_DIM>
53{
54
55 friend class TestTrianglesMeshReader;//for testing
56
57private:
58
61 std::string mFilesBaseName;
63 std::ifstream mNodesFile;
64 std::ifstream mElementsFile;
65 std::ifstream mFacesFile;
66 std::ifstream mNclFile;
67 std::ifstream mCableElementsFile;
69 std::streampos mNodeFileDataStart;
70 std::streamoff mNodeItemWidth;
71 std::streampos mElementFileDataStart;
72 std::streamoff mElementItemWidth;
73 std::streampos mFaceFileDataStart;
74 std::streamoff mFaceItemWidth;
75 std::streampos mNclFileDataStart;
76 std::streamoff mNclItemWidth;
78 unsigned mNumNodes;
79 unsigned mNumElements;
80 unsigned mNumFaces;
83 unsigned mNodesRead;
84 unsigned mElementsRead;
86 unsigned mFacesRead;
88 unsigned mNclItemsRead;
89 std::vector<unsigned> mOneDimBoundary;
92 std::vector<double> mNodeAttributes;
118 std::vector<unsigned> mPermutationVector;
119 std::vector<unsigned> mInversePermutationVector;
121// /** The containing element for each boundary element (obtaining by doing tetgen with the -nn flag).
122// * In a std::vector rather than the struct to save space if not read.
123// */
124// std::vector<unsigned> mContainingElementsOfBoundaryElement;
125//
126// unsigned mIndexIntoContainingElementsVector; /**< Which index to use when GetNextContainingElementOfBoundaryElement() is called */
127
128public:
129
142 TrianglesMeshReader(std::string pathBaseName,
143 unsigned orderOfElements=1,
144 unsigned orderOfBoundaryElements=1,
145 bool readContainingElementsForBoundaryElements=false);
146
151
153 unsigned GetNumElements() const;
154
156 unsigned GetNumNodes() const;
157
159 unsigned GetNumFaces() const;
160
162 unsigned GetNumCableElements() const;
163
165 unsigned GetNumElementAttributes() const;
166
168 unsigned GetNumFaceAttributes() const;
169
171 unsigned GetNumCableElementAttributes() const;
172
174 void Reset();
175
177 std::vector<double> GetNextNode();
178
181
184
187
188
193 {
194 return mOrderOfElements;
195 }
200 {
202 }
203
211
215 std::vector<double> GetNodeAttributes();
216
223 std::vector<double> GetNode(unsigned index);
224
231 ElementData GetElementData(unsigned index);
232
239 ElementData GetFaceData(unsigned index);
240
248 std::vector<unsigned> GetContainingElementIndices(unsigned index);
249
250
251 /*** @return true if reading binary files, false if reading ascii files */
252 bool IsFileFormatBinary();
253
259 bool HasNclFile();
260
266 void SetReadBufferSize(unsigned bufferSize);
267
275 void SetNodePermutation(std::vector<unsigned>& rPermutationVector);
276
280 bool HasNodePermutation();
281
285 const std::vector<unsigned>& rGetNodePermutation();
286
287
288private:
289
291 void OpenFiles();
292
294 void OpenNodeFile();
295
297 void OpenElementsFile();
298
300 void OpenFacesFile();
301
303 void OpenNclFile();
304
307
309 void ReadHeaders();
310
312 void CloseFiles();
313
320 void GetNextLineFromStream(std::ifstream& rFileStream, std::string& rRawLine);
321
332 template<class T_DATA>
333 void GetNextItemFromStream(std::ifstream& rFileStream, unsigned expectedItemNumber,
334 std::vector<T_DATA>& rDataPacket, const unsigned& rNumAttributes,
335 std::vector<double>& rAttributes);
336
338 std::string GetMeshFileBaseName();
339
341 void GetOneDimBoundary();
342
350 void EnsureIndexingFromZero(std::vector<unsigned>& rNodeIndices);
351};
352
353#endif //_TRIANGLESMESHREADER_HPP_
ElementData GetFaceData(unsigned index)
std::vector< double > mNodeAttributes
unsigned GetNumElementAttributes() const
std::vector< double > GetNextNode()
unsigned GetNumFaceAttributes() const
ElementData GetNextCableElementData()
std::streamoff mElementItemWidth
std::vector< double > GetNodeAttributes()
std::streampos mNodeFileDataStart
std::vector< unsigned > GetContainingElementIndices(unsigned index)
std::vector< double > GetNode(unsigned index)
unsigned GetNumElements() const
unsigned GetNumCableElements() const
std::streampos mFaceFileDataStart
void GetNextItemFromStream(std::ifstream &rFileStream, unsigned expectedItemNumber, std::vector< T_DATA > &rDataPacket, const unsigned &rNumAttributes, std::vector< double > &rAttributes)
void EnsureIndexingFromZero(std::vector< unsigned > &rNodeIndices)
std::vector< unsigned > mPermutationVector
unsigned GetNumCableElementAttributes() const
std::vector< unsigned > mInversePermutationVector
std::vector< unsigned > mOneDimBoundary
void SetNodePermutation(std::vector< unsigned > &rPermutationVector)
const std::vector< unsigned > & rGetNodePermutation()
std::streampos mElementFileDataStart
void GetNextLineFromStream(std::ifstream &rFileStream, std::string &rRawLine)
void SetReadBufferSize(unsigned bufferSize)
ElementData GetElementData(unsigned index)
std::streampos mNclFileDataStart