Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
Hdf5ToCmguiConverter.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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12Redistribution and use in source and binary forms, with or without
13modification, 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.
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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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32OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33
34*/
35
36#include "Hdf5ToCmguiConverter.hpp"
37#include "CmguiMeshWriter.hpp"
39#include "HeartConfig.hpp"
40#include "PetscTools.hpp"
41#include "Exception.hpp"
42#include "ReplicatableVector.hpp"
43#include "DistributedVector.hpp"
44#include "DistributedVectorFactory.hpp"
45#include "Version.hpp"
46#include "GenericMeshReader.hpp"
47
48template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
50{
51 out_stream p_file = out_stream(NULL);
52
53 unsigned num_nodes = this->mpReader->GetNumberOfRows();
54 unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();
55
56 DistributedVectorFactory factory(num_nodes);
57
58 Vec data = factory.CreateVec();//for V
59 Vec data_phie = factory.CreateVec();//for phi_e
60 Vec data_second_cell = factory.CreateVec();//for the V of the second cell, used in extended bidomain problems.
61
62 for (unsigned time_step=0; time_step<num_timesteps; time_step++)
63 {
64 // Create the file for this time step
65 std::stringstream time_step_string;
66
67 // unsigned to string
68 time_step_string << time_step;
70 {
71 p_file = this->mpOutputFileHandler->OpenOutputFile(this->mFileBaseName + "_" + time_step_string.str() + ".exnode");
72
73 // Check how many digits are to be output in the solution (0 goes to default value of digits)
74 if (this->mPrecision != 0)
75 {
76 p_file->precision(this->mPrecision);
77 }
78 }
79
80 std::vector<ReplicatableVector*> all_data;
81 unsigned num_vars = this->mpReader->GetVariableNames().size();
82 for (unsigned var=0; var<num_vars; var++)
83 {
84 // Read the data for this time step
85 this->mpReader->GetVariableOverNodes(data, this->mpReader->GetVariableNames()[var], time_step);
86 ReplicatableVector* p_repl_data = new ReplicatableVector(data);
87 assert(p_repl_data->GetSize()==num_nodes);
88 all_data.push_back(p_repl_data);
89 }
90
92 {
93 // Write provenance info
94 std::string comment = "! " + ChasteBuildInfo::GetProvenanceString();
95 *p_file << comment;
96 // The header first
97 *p_file << "Group name: " << this->mFileBaseName << "\n";
98 *p_file << "#Fields=" << num_vars << "\n";
99 for (unsigned var=0; var<num_vars; var++)
100 {
101 *p_file << " " << var+1 << ") " <<this->mpReader->GetVariableNames()[var]<< " , field, rectangular cartesian, #Components=1" << "\n" << "x. Value index=1, #Derivatives=0, #Versions=1"<<"\n";
102 if (var != num_vars-1)
103 {
104 *p_file << "\n";
105 }
106 }
107
108 // Write the data
109 for (unsigned i=0; i<num_nodes; i++)
110 {
111 // cmgui counts nodes from 1
112 *p_file << "Node: "<< i+1 << "\n";
113 for (unsigned var=0; var<num_vars; var++)
114 {
115 *p_file << (*(all_data[var]))[i] << "\n";
116 }
117 }
118 }
119
120 for (unsigned var=0; var<num_vars; var++)
121 {
122 delete all_data[var];
123 }
124 }
126 PetscTools::Destroy(data_phie);
127 PetscTools::Destroy(data_second_cell);
128
130 {
131 p_file->close();
132 }
133}
134
135template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
137 const std::string& rFileBaseName,
139 bool hasBath,
140 unsigned precision)
141 : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory, rFileBaseName, pMesh, "cmgui_output", precision)
142{
144 while (this->mDatasetNames[this->mOpenDatasetIndex] != "Data")
145 {
146 bool next_open = this->MoveOntoNextDataset();
147 UNUSED_OPT(next_open);
148 assert(next_open);
149 }
150
151 // Write the node data out
152 Write("");
153
154 // Write mesh in a suitable form for cmgui
155 std::string output_directory = HeartConfig::Instance()->GetOutputDirectory() + "/cmgui_output";
156
157 CmguiMeshWriter<ELEMENT_DIM,SPACE_DIM> cmgui_mesh_writer(output_directory, HeartConfig::Instance()->GetOutputFilenamePrefix(), false);
158
159 // Used to inform the mesh of the data names
160 std::vector<std::string> field_names = this->mpReader->GetVariableNames();
161 cmgui_mesh_writer.SetAdditionalFieldNames(field_names);
162 if (hasBath)
163 {
164 std::vector<std::string> names;
165 names.push_back("tissue");
166 names.push_back("bath");
167 cmgui_mesh_writer.SetRegionNames(names);
168 }
169
170 // Normally the in-memory mesh is converted:
171 if (HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering() == false || !this->mpMesh->IsMeshOnDisk())
172 {
173 cmgui_mesh_writer.WriteFilesUsingMesh(*(this->mpMesh), false);
174 }
175 else
176 {
177 // In this case we expect the mesh to have been read in from file
179 // Note that the next line will throw if the mesh has not been read from file
180 std::string original_file=this->mpMesh->GetMeshFileBaseName();
181 std::shared_ptr<AbstractMeshReader<ELEMENT_DIM, SPACE_DIM> > p_original_mesh_reader
182 = GenericMeshReader<ELEMENT_DIM, SPACE_DIM>(original_file);
183 cmgui_mesh_writer.WriteFilesUsingMeshReader(*p_original_mesh_reader);
184 }
185
187 PetscTools::Barrier("Hdf5ToCmguiConverter");
188}
189
190template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
192{
193 unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();
194 assert(this->mpReader->GetVariableNames().size() > 0); // seg fault guard
195 std::string variable_name = this->mpReader->GetVariableNames()[0];
196
198 {
199 out_stream p_script_file = this->mpOutputFileHandler->OpenOutputFile("LoadSolutions.com");
200
201 // Write provenance info, note the # instead of ! because this is - essentially - a PERL script that Cmgui interprets
202 std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
203 *p_script_file << comment;
204
205 *p_script_file << "# Read the mesh \n"
206 << "gfx read node "<<HeartConfig::Instance()->GetOutputFilenamePrefix()<<".exnode \n"
207 << "gfx read elem "<<HeartConfig::Instance()->GetOutputFilenamePrefix()<<".exelem \n" // note the mesh file name is taken from HeartConfig...
208 << "gfx define faces egroup "<<HeartConfig::Instance()->GetOutputFilenamePrefix()<<"\n"
209 << "# Create a window \n"
210 << "gfx cre win 1 \n"
211 << "# Modify the scene (obtained by gfx list g_element XXXX commands) to visualize first var on lines and nodes \n"
212 << "gfx modify g_element "<< HeartConfig::Instance()->GetOutputFilenamePrefix()<<" general clear circle_discretization 6 default_coordinate coordinates element_discretization \"4*4*4\" native_discretization none; \n"
213 << "gfx modify g_element "<< HeartConfig::Instance()->GetOutputFilenamePrefix()<<" lines select_on material default data "<<variable_name<<" spectrum default selected_material default_selected; \n"
214 << "gfx modify g_element "<< HeartConfig::Instance()->GetOutputFilenamePrefix()<<" node_points glyph point general size \"1*1*1\" centre 0,0,0 font default select_on material default data "<<variable_name<<" spectrum default selected_material default_selected; \n"
215 << "# Load the data \n"
216 << "for ($i=0; $i<" << num_timesteps << "; $i++) { \n"
217 << " gfx read node " << this->mFileBaseName << "_$i.exnode time $i\n" // ...while the data file from mFileBaseName...
218 << "}\n";
219 p_script_file->close();
220 }
221}
222
223// Explicit instantiation
224template class Hdf5ToCmguiConverter<1,1>;
225template class Hdf5ToCmguiConverter<1,2>;
226template class Hdf5ToCmguiConverter<2,2>;
227template class Hdf5ToCmguiConverter<1,3>;
228template class Hdf5ToCmguiConverter<2,3>;
229template class Hdf5ToCmguiConverter<3,3>;
#define UNUSED_OPT(var)
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpMesh
std::vector< std::string > mDatasetNames
boost::shared_ptr< Hdf5DataReader > mpReader
void WriteFilesUsingMeshReader(AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)
virtual void WriteFilesUsingMesh(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, bool keepOriginalElementIndexing=true)
static std::string GetProvenanceString()
void SetAdditionalFieldNames(std::vector< std::string > &rFieldNames)
void SetRegionNames(std::vector< std::string > &rRegionNames)
Hdf5ToCmguiConverter(const FileFinder &rInputDirectory, const std::string &rFileBaseName, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, bool hasBath=false, unsigned precision=0u)
void Write(std::string type)
std::string GetOutputFilenamePrefix() const
std::string GetOutputDirectory() const
static HeartConfig * Instance()
static void Destroy(Vec &rVec)
static bool AmMaster()
static void Barrier(const std::string callerId="")