Chaste  Release::3.4
MemfemMeshReader.cpp
1 /*
2 
3 Copyright (c) 2005-2016, University of Oxford.
4 All rights reserved.
5 
6 University of Oxford means the Chancellor, Masters and Scholars of the
7 University of Oxford, having an administrative office at Wellington
8 Square, Oxford OX1 2JD, UK.
9 
10 This file is part of Chaste.
11 
12 Redistribution and use in source and binary forms, with or without
13 modification, are permitted provided that the following conditions are met:
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,
17  this list of conditions and the following disclaimer in the documentation
18  and/or other materials provided with the distribution.
19  * Neither the name of the University of Oxford nor the names of its
20  contributors may be used to endorse or promote products derived from this
21  software without specific prior written permission.
22 
23 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33 
34 */
35 
36 #include "MemfemMeshReader.hpp"
37 #include "Exception.hpp"
38 
39 #include <sstream>
40 
42 // Implementation
44 
45 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
47 {
48  // Open node file and store the lines as a vector of strings (minus the comments)
49  std::string node_file_name = rPathBaseName + ".pts";
50  this->mNodeRawData = this->GetRawDataFromFile(node_file_name);
51 
52  // Read single line header which is the number of nodes */
53  std::stringstream node_header_stream(this->mNodeRawData[0]);
54  unsigned num_nodes;
55  node_header_stream >> num_nodes;
56 
57  // All Memfem data is in 3D
58  if (SPACE_DIM != 3 || ELEMENT_DIM != 3)
59  {
60  EXCEPTION("You have asked to read non-3D data. All Memfem data is in 3D.");
61  }
62 
63  // Read the rest of the node data using TokenizeStringsToDoubles method
64  this->mNodeData = TokenizeStringsToDoubles(this->mNodeRawData);
65 
66  // Initialise iterator for public GetNextNode method
67  this->mpNodeIterator = this->mNodeData.begin();
68 
69  // Check that the size of the data matches the information in the header
70  if (num_nodes != this->mNodeData.size())
71  {
72  // ignored from coverage because otherwise would have to create files
73  // for a bad mesh just to test this line
74 #define COVERAGE_IGNORE
75  EXCEPTION("Number of nodes does not match expected number declared in header");
76 #undef COVERAGE_IGNORE
77  }
78 
79  // Open element file and store the lines as a vector of strings (minus the comments)
80  std::string element_file_name = rPathBaseName + ".tetras";
81  this->mElementRawData = this->GetRawDataFromFile(element_file_name);
82 
83  // Read single line header which is the number of elements
84  std::stringstream element_header_stream(this->mElementRawData[0]);
85  unsigned num_elements;
86  element_header_stream >> num_elements;
87 
88  // Read the rest of the element data using TokenizeStringsToInts method
89  this->mElementData = TokenizeStringsToInts(this->mElementRawData, SPACE_DIM+1, true);
90  this->mpElementIterator = this->mElementData.begin();
91 
92  // Check that the size of the data matches the information in the header
93  if (num_elements != this->mElementData.size())
94  {
95  // Ignored from coverage because otherwise we would have to create files
96  // for a bad mesh just to test this line
97 #define COVERAGE_IGNORE
98  EXCEPTION("Number of elements does not match expected number declared in header");
99 #undef COVERAGE_IGNORE
100  }
101 
102  // Open boundary face file and store the lines as a vector of strings (minus the comments)
103  std::string face_file_name = rPathBaseName + ".tri";
104  this->mFaceRawData = this->GetRawDataFromFile(face_file_name);
105 
106  // There is no header
107 
108  // Read the face/edge data using TokenizeStringsToInts method
109  this->mFaceData = TokenizeStringsToInts(this->mFaceRawData, SPACE_DIM, false);
110  this->mpFaceIterator = this->mFaceData.begin();
111 }
112 
113 template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
115 {}
116 
117 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
119  const std::vector<std::string>& rRawData)
120 {
121  std::vector<std::vector<double> > tokenized_data; // Output
122 
123  // Iterate over the lines of input
124  std::vector<std::string>::const_iterator the_iterator;
125  for (the_iterator = rRawData.begin(); the_iterator != rRawData.end(); the_iterator++ )
126  {
127  const std::string& r_line_of_data = *the_iterator;
128  std::stringstream line_stream(r_line_of_data);
129 
130  if (the_iterator != rRawData.begin()) // Ignore the header string
131  {
132  std::vector<double> current_coords;
133 
134  // Form the vector which represents the position of this item
135  for (unsigned i=0; i<SPACE_DIM; i++)
136  {
137  double item_coord;
138  line_stream >> item_coord;
139  current_coords.push_back(item_coord);
140  }
141 
142  // Put item onto main output vector
143  tokenized_data.push_back(current_coords);
144  }
145  }
146 
147  return tokenized_data;
148 }
149 
150 template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
152  const std::vector<std::string>& rRawData,
153  unsigned dimensionOfObject,
154  bool readHeader)
155 {
156  std::vector<std::vector<unsigned> > tokenized_data;
157 
158  std::vector<std::string>::const_iterator the_iterator;
159  for (the_iterator = rRawData.begin(); the_iterator != rRawData.end(); the_iterator++ )
160  {
161  const std::string& r_line_of_data = *the_iterator;
162  std::stringstream line_stream(r_line_of_data);
163 
164  if ( readHeader == false || the_iterator != rRawData.begin() )
165  {
166  std::vector<unsigned> current_indices;
167 
168  for (unsigned i=0; i<dimensionOfObject; i++)
169  {
170  unsigned item_index;
171  line_stream >> item_index;
172  // The nodes have been indexed from one so we need to shift the indices
173  item_index -= 1;
174  current_indices.push_back(item_index);
175  }
176 
177  tokenized_data.push_back(current_indices);
178  }
179  }
180 
181  return tokenized_data;
182 }
183 
185 // Explicit instantiation
187 
188 template class MemfemMeshReader<1,1>;
189 template class MemfemMeshReader<1,2>;
190 template class MemfemMeshReader<1,3>;
191 template class MemfemMeshReader<2,2>;
192 template class MemfemMeshReader<2,3>;
193 template class MemfemMeshReader<3,3>;
std::vector< std::vector< unsigned > > TokenizeStringsToInts(const std::vector< std::string > &rRawData, unsigned dimensionOfObject, bool readHeader)
#define EXCEPTION(message)
Definition: Exception.hpp:143
std::vector< std::vector< double > > TokenizeStringsToDoubles(const std::vector< std::string > &rRawData)
MemfemMeshReader(const std::string &rPathBaseName)