Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
FemlabMeshReader.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 "FemlabMeshReader.hpp"
37#include "Exception.hpp"
38
39#include <sstream>
40
42// Implementation
44
45template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
47 const std::string& rNodeFileName,
48 const std::string& rElementFileName,
49 const std::string& rEdgeFileName)
50{
51
52 // Open node file and store the lines as a vector of strings (minus the comments)
53 std::string node_file_name = rPathBaseName + rNodeFileName;
54 this->mNodeRawData = this->GetRawDataFromFile(node_file_name);
55
56 // Read the node data using TokenizeStringsToDoubles method
57 this->mNodeData = TokenizeStringsToDoubles(this->mNodeRawData);
58
59 // Initialise iterator for public GetNextNode method
60 this->mpNodeIterator = this->mNodeData.begin();
61
62
63 // Open element file and store the lines as a vector of strings (minus the comments)
64 std::string element_file_name = rPathBaseName + rElementFileName;
65 this->mElementRawData = this->GetRawDataFromFile(element_file_name);
66
67 // Read the rest of the element data using TokenizeStringsToInts method
68 this->mElementData = TokenizeStringsToInts(this->mElementRawData, SPACE_DIM + 1);
69 this->mpElementIterator = this->mElementData.begin();
70
71 /*
72 * Open edge file and store the lines as a vector of strings (minus the comments)
73 * We store edges as "faces" but the superclass
74 * provides a GetNextEdgeData method which queries this data.
75 */
76
77 std::string edge_file_name = rPathBaseName + rEdgeFileName;
78 this->mFaceRawData = this->GetRawDataFromFile(edge_file_name);
79
80 // Read the rest of the face/edge data using TokenizeStringsToInts method
81 this->mFaceData = TokenizeStringsToInts(this->mFaceRawData, SPACE_DIM);
82 this->mpFaceIterator = this->mFaceData.begin();
83}
84
85template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
88
89template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
90std::vector < std::vector<double> >
92{
93 std::vector < std::vector < double > >tokenized_data; // Output
94
95 // Iterate over the lines of input
96 unsigned dimension_count = 0;
97 std::vector < std::string >::const_iterator the_iterator;
98 for (the_iterator = rRawData.begin(); the_iterator != rRawData.end();
99 the_iterator++)
100 {
101 const std::string& r_line_of_data = *the_iterator;
102 std::stringstream line_stream (r_line_of_data);
103
104 if (dimension_count == 0)
105 {
106 // First iteration, build the tokenized_data vector and push in x coordinates
107 while (!line_stream.eof())
108 {
109 double item_coord;
110
111 std::vector < double >x_coord;
112 line_stream >> item_coord;
113 x_coord.push_back (item_coord);
114 tokenized_data.push_back (x_coord);
115 }
116 }
117 else
118 {
119 unsigned current_node = 0;
120
121 // Other iterations, push in coordinates other than x
122 while (!line_stream.eof())
123 {
124 double item_coord;
125 line_stream >> item_coord;
126 tokenized_data[current_node].push_back (item_coord);
127 current_node++;
128 }
129 }
130 // Dimension of mesh is the same as the line of rawData
131 dimension_count++;
132 }
133
134 if (SPACE_DIM != dimension_count)
135 {
136 EXCEPTION("SPACE_DIM != dimension read from file");
137 }
138 return (tokenized_data);
139}
140
141template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
142std::vector < std::vector < unsigned > >
143 FemlabMeshReader<ELEMENT_DIM, SPACE_DIM>::TokenizeStringsToInts(const std::vector<std::string>& rRawData, unsigned dimensionOfObject)
144{
145 std::vector < std::vector < unsigned > >tokenized_data;
146
147 // There are dimensionOfObject lines to be read
148 for (unsigned i = 0; i < dimensionOfObject; i++)
149 {
150 const std::string& r_line_of_data = rRawData[i];
151 std::stringstream line_stream (r_line_of_data);
152
153 if (i == 0)
154 {
155 // First iteration, build the tokenized_data vector and push in x coordinates
156 while (!line_stream.eof())
157 {
158 double item_index;
159
160 std::vector < unsigned >first_index;
161 line_stream >> item_index;
162 first_index.push_back ((unsigned) (item_index - 0.5)); // item indices should be minus 1
163 tokenized_data.push_back (first_index);
164 }
165 }
166 else
167 {
168 unsigned current_node = 0;
169
170 // Other iterations, push in coordinates other than x.
171 while (!line_stream.eof())
172 {
173 double item_index;
174 line_stream >> item_index;
175 tokenized_data[current_node].
176 push_back ((unsigned) (item_index - 0.5));
177 current_node++;
178 }
179 }
180 }
181 return (tokenized_data);
182}
183
184
185// Explicit instantiation
186template class FemlabMeshReader<1,1>;
187template class FemlabMeshReader<1,2>;
188template class FemlabMeshReader<1,3>;
189template class FemlabMeshReader<2,2>;
190template class FemlabMeshReader<2,3>;
191template class FemlabMeshReader<3,3>;
#define EXCEPTION(message)
std::vector< std::vector< unsigned > > TokenizeStringsToInts(const std::vector< std::string > &rRawData, unsigned dimensionOfObject)
FemlabMeshReader(const std::string &rPathBaseName, const std::string &rNodeFileName, const std::string &rElementFileName, const std::string &rEdgeFileName)
std::vector< std::vector< double > > TokenizeStringsToDoubles(const std::vector< std::string > &rRawData)