Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
MemfemMeshReader.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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34*/
35
36#include "MemfemMeshReader.hpp"
37#include "Exception.hpp"
38
39#include <sstream>
40
42// Implementation
44
45template<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// LCOV_EXCL_START
75 EXCEPTION("Number of nodes does not match expected number declared in header");
76// LCOV_EXCL_STOP
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// LCOV_EXCL_START
98 EXCEPTION("Number of elements does not match expected number declared in header");
99// LCOV_EXCL_STOP
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
113template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
116
117template<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
150template <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
184// Explicit instantiation
185template class MemfemMeshReader<1,1>;
186template class MemfemMeshReader<1,2>;
187template class MemfemMeshReader<1,3>;
188template class MemfemMeshReader<2,2>;
189template class MemfemMeshReader<2,3>;
190template class MemfemMeshReader<3,3>;
#define EXCEPTION(message)
std::vector< std::vector< double > > TokenizeStringsToDoubles(const std::vector< std::string > &rRawData)
std::vector< std::vector< unsigned > > TokenizeStringsToInts(const std::vector< std::string > &rRawData, unsigned dimensionOfObject, bool readHeader)
MemfemMeshReader(const std::string &rPathBaseName)