CmguiMeshWriter.hpp

00001 /*
00002 
00003 Copyright (c) 2005-2015, University of Oxford.
00004 All rights reserved.
00005 
00006 University of Oxford means the Chancellor, Masters and Scholars of the
00007 University of Oxford, having an administrative office at Wellington
00008 Square, Oxford OX1 2JD, UK.
00009 
00010 This file is part of Chaste.
00011 
00012 Redistribution and use in source and binary forms, with or without
00013 modification, are permitted provided that the following conditions are met:
00014  * Redistributions of source code must retain the above copyright notice,
00015    this list of conditions and the following disclaimer.
00016  * Redistributions in binary form must reproduce the above copyright notice,
00017    this list of conditions and the following disclaimer in the documentation
00018    and/or other materials provided with the distribution.
00019  * Neither the name of the University of Oxford nor the names of its
00020    contributors may be used to endorse or promote products derived from this
00021    software without specific prior written permission.
00022 
00023 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
00024 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
00025 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
00026 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
00027 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
00028 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
00029 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
00030 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
00031 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
00032 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
00033 
00034 */
00035 
00036 #ifndef CMGUIWRITER_HPP_
00037 #define CMGUIWRITER_HPP_
00038 
00039 #include "AbstractTetrahedralMeshWriter.hpp"
00040 #include "OutputFileHandler.hpp"
00041 
00045 static const char CmguiNodeFileHeader3D[] = " #Fields=1\n\
00046  1) coordinates, coordinate, rectangular cartesian, #Components=3\n\
00047    x.  Value index= 1, #Derivatives= 0\n\
00048    y.  Value index= 2, #Derivatives= 0\n\
00049    z.  Value index= 3, #Derivatives= 0\n";
00050 
00054 static const char CmguiNodeFileHeader2D[] = " #Fields=1\n\
00055  1) coordinates, coordinate, rectangular cartesian, #Components=2\n\
00056    x.  Value index= 1, #Derivatives= 0\n\
00057    y.  Value index= 2, #Derivatives= 0\n";
00058 
00059 
00063 static const char CmguiNodeFileHeader1D[] = " #Fields=1\n\
00064  1) coordinates, coordinate, rectangular cartesian, #Components=1\n\
00065    x.  Value index= 1, #Derivatives= 0\n";
00066 
00070 static const char CmguiElementFileHeader3D[] = "Shape.  Dimension=3, simplex(2;3)*simplex*simplex\n\
00071  #Scale factor sets= 0\n\
00072  #Nodes= 4\n";
00073 
00077 static const char CmguiElementFileHeader3DQuadratic[] = "Shape.  Dimension=3, simplex(2;3)*simplex*simplex\n\
00078  #Scale factor sets= 0\n\
00079  #Nodes= 10\n";
00080 
00081 
00085 static const char CmguiElementFileHeader2D[] = "Shape.  Dimension=2, simplex(2)*simplex\n\
00086  #Scale factor sets= 0\n\
00087  #Nodes= 3\n";
00088 
00092 static const char CmguiElementFileHeader2DQuadratic[] = "Shape.  Dimension=2, simplex(2)*simplex\n\
00093  #Scale factor sets= 0\n\
00094  #Nodes= 6\n";
00095 
00099 static const char CmguiElementFileHeader1D[] = "Shape.  Dimension=1, line\n\
00100  #Scale factor sets= 0\n\
00101  #Nodes= 2\n";
00102 
00106 static const char CmguiElementFileHeader1DQuadratic[] = "Shape.  Dimension=1, line\n\
00107  #Scale factor sets= 0\n\
00108  #Nodes= 3\n";
00109 
00110 
00114 static const char CmguiCoordinatesFileHeader3D[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=3\n\
00115    x.  l.simplex(2;3)*l.simplex*l.simplex, no modify, standard node based.\n\
00116      #Nodes= 4\n\
00117       1.  #Values=1\n\
00118        Value indices:     1\n\
00119        Scale factor indices:   1\n\
00120       2.  #Values=1\n\
00121        Value indices:     1\n\
00122        Scale factor indices:   2\n\
00123       3.  #Values=1\n\
00124        Value indices:     1\n\
00125        Scale factor indices:   3\n\
00126       4.  #Values=1\n\
00127        Value indices:     1\n\
00128        Scale factor indices:   4\n\
00129    y.  l.simplex(2;3)*l.simplex*l.simplex, no modify, standard node based.\n\
00130      #Nodes= 4\n\
00131       1.  #Values=1\n\
00132        Value indices:     1\n\
00133        Scale factor indices:   1\n\
00134       2.  #Values=1\n\
00135        Value indices:     1\n\
00136        Scale factor indices:   2\n\
00137       3.  #Values=1\n\
00138        Value indices:     1\n\
00139        Scale factor indices:   3\n\
00140       4.  #Values=1\n\
00141        Value indices:     1\n\
00142        Scale factor indices:   4\n\
00143    z.  l.simplex(2;3)*l.simplex*l.simplex, no modify, standard node based.\n\
00144      #Nodes= 4\n\
00145       1.  #Values=1\n\
00146        Value indices:     1\n\
00147        Scale factor indices:   1\n\
00148       2.  #Values=1\n\
00149        Value indices:     1\n\
00150        Scale factor indices:   2\n\
00151       3.  #Values=1\n\
00152        Value indices:     1\n\
00153        Scale factor indices:   3\n\
00154       4.  #Values=1\n\
00155        Value indices:     1\n\
00156        Scale factor indices:   4\n";
00157 
00158 
00162 static const char CmguiCoordinatesFileHeader3DQuadratic[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=3\n\
00163    x.  q.simplex(2;3)*q.simplex*q.simplex, no modify, standard node based.\n\
00164      #Nodes= 10\n\
00165       1.  #Values=1\n\
00166        Value indices:     1\n\
00167        Scale factor indices:   1\n\
00168       2.  #Values=1\n\
00169        Value indices:     1\n\
00170        Scale factor indices:   2\n\
00171       3.  #Values=1\n\
00172        Value indices:     1\n\
00173        Scale factor indices:   3\n\
00174       4.  #Values=1\n\
00175        Value indices:     1\n\
00176        Scale factor indices:   4\n\
00177       5.  #Values=1\n\
00178        Value indices:     1\n\
00179        Scale factor indices:   5\n\
00180       6.  #Values=1\n\
00181        Value indices:     1\n\
00182        Scale factor indices:   6\n\
00183       7.  #Values=1\n\
00184        Value indices:     1\n\
00185        Scale factor indices:   7\n\
00186       8.  #Values=1\n\
00187        Value indices:     1\n\
00188        Scale factor indices:   8\n\
00189       9.  #Values=1\n\
00190        Value indices:     1\n\
00191        Scale factor indices:   9\n\
00192       10.  #Values=1\n\
00193        Value indices:     1\n\
00194        Scale factor indices:   10\n\
00195    y.  q.simplex(2;3)*q.simplex*q.simplex, no modify, standard node based.\n\
00196      #Nodes= 10\n\
00197       1.  #Values=1\n\
00198        Value indices:     1\n\
00199        Scale factor indices:   1\n\
00200       2.  #Values=1\n\
00201        Value indices:     1\n\
00202        Scale factor indices:   2\n\
00203       3.  #Values=1\n\
00204        Value indices:     1\n\
00205        Scale factor indices:   3\n\
00206       4.  #Values=1\n\
00207        Value indices:     1\n\
00208        Scale factor indices:   4\n\
00209       5.  #Values=1\n\
00210        Value indices:     1\n\
00211        Scale factor indices:   5\n\
00212       6.  #Values=1\n\
00213        Value indices:     1\n\
00214        Scale factor indices:   6\n\
00215       7.  #Values=1\n\
00216        Value indices:     1\n\
00217        Scale factor indices:   7\n\
00218       8.  #Values=1\n\
00219        Value indices:     1\n\
00220        Scale factor indices:   8\n\
00221       9.  #Values=1\n\
00222        Value indices:     1\n\
00223        Scale factor indices:   9\n\
00224       10.  #Values=1\n\
00225        Value indices:     1\n\
00226        Scale factor indices:   10\n\
00227    z.  q.simplex(2;3)*q.simplex*q.simplex, no modify, standard node based.\n\
00228      #Nodes= 10\n\
00229       1.  #Values=1\n\
00230        Value indices:     1\n\
00231        Scale factor indices:   1\n\
00232       2.  #Values=1\n\
00233        Value indices:     1\n\
00234        Scale factor indices:   2\n\
00235       3.  #Values=1\n\
00236        Value indices:     1\n\
00237        Scale factor indices:   3\n\
00238       4.  #Values=1\n\
00239        Value indices:     1\n\
00240        Scale factor indices:   4\n\
00241       5.  #Values=1\n\
00242        Value indices:     1\n\
00243        Scale factor indices:   5\n\
00244       6.  #Values=1\n\
00245        Value indices:     1\n\
00246        Scale factor indices:   6\n\
00247       7.  #Values=1\n\
00248        Value indices:     1\n\
00249        Scale factor indices:   7\n\
00250       8.  #Values=1\n\
00251        Value indices:     1\n\
00252        Scale factor indices:   8\n\
00253       9.  #Values=1\n\
00254        Value indices:     1\n\
00255        Scale factor indices:   9\n\
00256       10.  #Values=1\n\
00257        Value indices:     1\n\
00258        Scale factor indices:   10\n";
00259 
00260 
00264 static const char CmguiCoordinatesFileHeader2D[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=2\n\
00265    x.  l.simplex(2)*l.simplex, no modify, standard node based.\n\
00266      #Nodes= 3\n\
00267       1.  #Values=1\n\
00268        Value indices:     1\n\
00269        Scale factor indices:   1\n\
00270       2.  #Values=1\n\
00271        Value indices:     1\n\
00272        Scale factor indices:   2\n\
00273       3.  #Values=1\n\
00274        Value indices:     1\n\
00275        Scale factor indices:   3\n\
00276    y.  l.simplex(2)*l.simplex, no modify, standard node based.\n\
00277      #Nodes= 3\n\
00278       1.  #Values=1\n\
00279        Value indices:     1\n\
00280        Scale factor indices:   1\n\
00281       2.  #Values=1\n\
00282        Value indices:     1\n\
00283        Scale factor indices:   2\n\
00284       3.  #Values=1\n\
00285        Value indices:     1\n\
00286        Scale factor indices:   3\n";
00287 
00288 
00293 static const char CmguiCoordinatesFileHeader2DQuadratic[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=2\n\
00294    x.  q.simplex(2)*q.simplex, no modify, standard node based.\n\
00295      #Nodes= 6\n\
00296       1.  #Values=1\n\
00297        Value indices:     1\n\
00298        Scale factor indices:   1\n\
00299       2.  #Values=1\n\
00300        Value indices:     1\n\
00301        Scale factor indices:   2\n\
00302       3.  #Values=1\n\
00303        Value indices:     1\n\
00304        Scale factor indices:   3\n\
00305       4.  #Values=1\n\
00306        Value indices:     1\n\
00307        Scale factor indices:   4\n\
00308       5.  #Values=1\n\
00309        Value indices:     1\n\
00310        Scale factor indices:   5\n\
00311       6.  #Values=1\n\
00312        Value indices:     1\n\
00313        Scale factor indices:   6\n\
00314    y.  q.simplex(2)*q.simplex, no modify, standard node based.\n\
00315      #Nodes= 6\n\
00316       1.  #Values=1\n\
00317        Value indices:     1\n\
00318        Scale factor indices:   1\n\
00319       2.  #Values=1\n\
00320        Value indices:     1\n\
00321        Scale factor indices:   2\n\
00322       3.  #Values=1\n\
00323        Value indices:     1\n\
00324        Scale factor indices:   3\n\
00325       4.  #Values=1\n\
00326        Value indices:     1\n\
00327        Scale factor indices:   4\n\
00328       5.  #Values=1\n\
00329        Value indices:     1\n\
00330        Scale factor indices:   5\n\
00331       6.  #Values=1\n\
00332        Value indices:     1\n\
00333        Scale factor indices:   6\n";
00334 
00335 
00336 
00341 static const char CmguiCoordinatesFileHeader1D[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=1\n\
00342    x.  l.Lagrange, no modify, standard node based.\n\
00343      #Nodes= 2\n\
00344       1.  #Values=1\n\
00345        Value indices:     1\n\
00346        Scale factor indices:   1\n\
00347       2.  #Values=1\n\
00348        Value indices:     1\n\
00349        Scale factor indices:   2\n";
00350 
00351 
00356 static const char CmguiCoordinatesFileHeader1DQuadratic[] = " 1) coordinates, coordinate, rectangular cartesian, #Components=1\n\
00357    x.  q.Lagrange, no modify, standard node based.\n\
00358      #Nodes= 3\n\
00359       1.  #Values=1\n\
00360        Value indices:     1\n\
00361        Scale factor indices:   1\n\
00362       2.  #Values=1\n\
00363        Value indices:     1\n\
00364        Scale factor indices:   2\n\
00365       3.  #Values=1\n\
00366        Value indices:     1\n\
00367        Scale factor indices:   3\n";
00368 
00373 static const char CmguiAdditionalFieldHeader3D[] = " field, rectangular cartesian, #Components=1\n\
00374    x.  l.simplex(2;3)*l.simplex*l.simplex, no modify, standard node based.\n\
00375      #Nodes= 4\n\
00376       1.  #Values=1\n\
00377        Value indices:     1\n\
00378        Scale factor indices:   1\n\
00379       2.  #Values=1\n\
00380        Value indices:     1\n\
00381        Scale factor indices:   2\n\
00382       3.  #Values=1\n\
00383        Value indices:     1\n\
00384        Scale factor indices:   3\n\
00385       4.  #Values=1\n\
00386        Value indices:     1\n\
00387        Scale factor indices:   4\n";
00388 
00389 
00395 static const char CmguiAdditionalFieldHeader3DQuadratic[] = " field, rectangular cartesian, #Components=1\n\
00396    x.  q.simplex(2;3)*q.simplex*q.simplex, no modify, standard node based.\n\
00397      #Nodes= 10\n\
00398       1.  #Values=1\n\
00399        Value indices:     1\n\
00400        Scale factor indices:   1\n\
00401       2.  #Values=1\n\
00402        Value indices:     1\n\
00403        Scale factor indices:   2\n\
00404       3.  #Values=1\n\
00405        Value indices:     1\n\
00406        Scale factor indices:   3\n\
00407       4.  #Values=1\n\
00408        Value indices:     1\n\
00409        Scale factor indices:   4\n\
00410       5.  #Values=1\n\
00411        Value indices:     1\n\
00412        Scale factor indices:   5\n\
00413       6.  #Values=1\n\
00414        Value indices:     1\n\
00415        Scale factor indices:   6\n\
00416       7.  #Values=1\n\
00417        Value indices:     1\n\
00418        Scale factor indices:   7\n\
00419       8.  #Values=1\n\
00420        Value indices:     1\n\
00421        Scale factor indices:   8\n\
00422       9.  #Values=1\n\
00423        Value indices:     1\n\
00424        Scale factor indices:   9\n\
00425       10.  #Values=1\n\
00426        Value indices:     1\n\
00427        Scale factor indices:   10\n";
00428 
00433 static const char CmguiAdditionalFieldHeader2D[] = " field, rectangular cartesian, #Components=1\n\
00434    x.  l.simplex(2)*l.simplex, no modify, standard node based.\n\
00435      #Nodes= 3\n\
00436       1.  #Values=1\n\
00437        Value indices:     1\n\
00438        Scale factor indices:   1\n\
00439       2.  #Values=1\n\
00440        Value indices:     1\n\
00441        Scale factor indices:   2\n\
00442       3.  #Values=1\n\
00443        Value indices:     1\n\
00444        Scale factor indices:   3\n";
00445 
00450 static const char CmguiAdditionalFieldHeader2DQuadratic[] = " field, rectangular cartesian, #Components=1\n\
00451    x.  q.simplex(2)*q.simplex, no modify, standard node based.\n\
00452      #Nodes= 6\n\
00453       1.  #Values=1\n\
00454        Value indices:     1\n\
00455        Scale factor indices:   1\n\
00456       2.  #Values=1\n\
00457        Value indices:     1\n\
00458        Scale factor indices:   2\n\
00459       3.  #Values=1\n\
00460        Value indices:     1\n\
00461        Scale factor indices:   3\n\
00462       4.  #Values=1\n\
00463        Value indices:     1\n\
00464        Scale factor indices:   4\n\
00465       5.  #Values=1\n\
00466        Value indices:     1\n\
00467        Scale factor indices:   5\n\
00468       6.  #Values=1\n\
00469        Value indices:     1\n\
00470        Scale factor indices:   6\n";
00471 
00472 
00477 static const char CmguiAdditionalFieldHeader1D[] = " field, rectangular cartesian, #Components=1\n\
00478    x.  l.Lagrange, no modify, standard node based.\n\
00479      #Nodes= 2\n\
00480       1.  #Values=1\n\
00481        Value indices:     1\n\
00482        Scale factor indices:   1\n\
00483       2.  #Values=1\n\
00484        Value indices:     1\n\
00485        Scale factor indices:   2\n";
00486 
00491 static const char CmguiAdditionalFieldHeader1DQuadratic[] = " field, rectangular cartesian, #Components=1\n\
00492    x.  q.Lagrange, no modify, standard node based.\n\
00493      #Nodes= 2\n\
00494       1.  #Values=1\n\
00495        Value indices:     1\n\
00496        Scale factor indices:   1\n\
00497       2.  #Values=1\n\
00498        Value indices:     1\n\
00499        Scale factor indices:   2\n\
00500       3.  #Values=1\n\
00501        Value indices:     1\n\
00502        Scale factor indices:   3\n";
00503 
00504 
00516 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00517 class CmguiMeshWriter : public AbstractTetrahedralMeshWriter<ELEMENT_DIM,SPACE_DIM>
00518 {
00519 protected:
00520 
00524     std::vector<std::string> mAdditionalFieldNames;
00525 
00526 
00531     std::vector<std::string> mRegionNames;// {tissue, bath, whatever}
00532 
00539     std::string mGroupName;
00540 
00545     std::string mElementFileHeader;
00546 
00552     std::string mCoordinatesFileHeader;
00553 
00558     std::string mAdditionalFieldHeader;
00559 
00564     unsigned mNumNodesPerElement;
00565 
00569     std::vector<unsigned> mReordering;
00570 
00576     std::ios_base::openmode GetOpenMode(bool append);
00577 
00584     out_stream OpenNodeFile(bool append = false);
00585 
00592     std::vector<boost::shared_ptr<std::ofstream> > OpenElementFiles(bool append = false);
00593 
00600     void WriteNodeFileHeader(out_stream& rpNodeFile);
00601 
00607     void WriteElementsFileHeader(std::vector<boost::shared_ptr<std::ofstream> >& rElemFiles);
00608 
00609 
00613     void CreateFilesWithHeaders();
00614 
00618     void AppendLocalDataToFiles();
00619 
00623     void WriteFilesFooter();
00624 
00625 public:
00626 
00634     CmguiMeshWriter(const std::string& rDirectory,
00635                     const std::string& rBaseName,
00636                     bool cleanDirectory=true);
00637 
00641     void WriteFiles();
00642 
00648     void SetAdditionalFieldNames(std::vector<std::string>& rFieldNames);
00649 
00655     void SetRegionNames(std::vector<std::string>& rRegionNames);
00656 
00660     virtual ~CmguiMeshWriter()
00661     {}
00662 
00663 
00664     // A method called CompareCmguiFiles() has been removed, please use FileComparison class instead.
00665 
00666 };
00667 
00668 #endif /*CMGUIWRITER_HPP_*/