tools/phm2helix.cpp

   1 /*****************************************************************************
   2 ** FILE IDENTIFICATION
   3 **
   4 **   Name:          phm2helix.cpp
   5 **   Purpose:       Take projections of a phantom object
   6 **   Programmers:   Ian Kay and Kevin Rosenberg
   7 **   Date Started:  Aug 2001
   8 **
   9 **  This is part of the CTSim program
  10 **  Copyright (C) 1983-2009 Kevin Rosenberg
  11 **
  12 **  This program is free software; you can redistribute it and/or modify
  13 **  it under the terms of the GNU General Public License (version 2) as
  14 **  published by the Free Software Foundation.
  15 **
  16 **  This program is distributed in the hope that it will be useful,
  17 **  but WITHOUT ANY WARRANTY; without even the implied warranty of
  18 **  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  19 **  GNU General Public License for more details.
  20 **
  21 **  You should have received a copy of the GNU General Public License
  22 **  along with this program; if not, write to the Free Software
  23 **  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
  24 ******************************************************************************/
  25
  26 #include "ct.h"
  27 #include "timer.h"
  28
  29
  30 enum { O_PHANTOMPROG, O_PHMFILE,  O_DESC, O_NRAY, O_ROTANGLE, O_GEOMETRY, O_FOCAL_LENGTH, O_CENTER_DETECTOR_LENGTH,
  31   O_VIEW_RATIO, O_SCAN_RATIO, O_OFFSETVIEW,  O_TRACE, O_VERBOSE, O_HELP, O_DEBUG, O_VERSION };
  32
  33 static struct option phm2helix_options[] =
  34 {
  35   {"phantom", 1, 0, O_PHANTOMPROG},
  36   {"desc", 1, 0, O_DESC},
  37   {"nray", 1, 0, O_NRAY},
  38   {"rotangle", 1, 0, O_ROTANGLE},
  39   {"geometry", 1, 0, O_GEOMETRY},
  40   {"focal-length", 1, 0, O_FOCAL_LENGTH},
  41   {"center-detector-length", 1, 0, O_CENTER_DETECTOR_LENGTH},
  42   {"view-ratio", 1, 0, O_VIEW_RATIO},
  43   {"scan-ratio", 1, 0, O_SCAN_RATIO},
  44   {"offsetview", 1, 0, O_OFFSETVIEW},
  45   {"trace", 1, 0, O_TRACE},
  46   {"verbose", 0, 0, O_VERBOSE},
  47   {"help", 0, 0, O_HELP},
  48   {"debug", 0, 0, O_DEBUG},
  49   {"version", 0, 0, O_VERSION},
  50   {"phmfile", 1, 0, O_PHMFILE},
  51   {0, 0, 0, 0}
  52 };
  53
  54 static const char* g_szIdStr = "$Id$";
  55
  56
  57 void
  58 phm2helix_usage (const char *program)
  59 {
  60           std::cout << "usage: " << fileBasename(program) << " outfile ndet nview phmprog [OPTIONS]\n";
  61           std::cout << "Calculate (projections) through time varying phantom object  \n\n";
  62           std::cout << "     outfile          Name of output file for projectsions\n";
  63           std::cout << "     ndet             Number of detectors\n";
  64           std::cout << "     nview            Number of rotated views\n";
  65           std::cout << "     phmprog          Name of phm generation executable\n";
  66           std::cout << "     --phmfile        Temp phantom file name \n";
  67           std::cout << "     --desc           Description of raysum\n";
  68           std::cout << "     --nray           Number of rays per detector (default = 1)\n";
  69           std::cout << "     --rotangle       Angle to rotate view through (fraction of a circle)\n";
  70           std::cout << "                      (default = select appropriate for geometry)\n";
  71           std::cout << "     --geometry       Geometry of scanning\n";
  72           std::cout << "        parallel      Parallel scan beams (default)\n";
  73           std::cout << "        equilinear    Equilinear divergent scan beams\n";
  74           std::cout << "        equiangular   Equiangular divergent scan beams\n";
  75           std::cout << "     --focal-length   Focal length ratio (ratio to radius of phantom)\n";
  76           std::cout << "                      (default = 1)\n";
  77           std::cout << "     --view-ratio     Length to view (view diameter to phantom diameter)\n";
  78           std::cout << "                      (default = 1)\n";
  79           std::cout << "     --scan-ratio     Length to scan (scan diameter to view diameter)\n";
  80           std::cout << "                      (default = 1)\n";
  81           std::cout << "     --offsetview     Initial gantry offset in 'views' (default = 0)\n";
  82           std::cout << "     --trace          Trace level to use\n";
  83           std::cout << "        none          No tracing (default)\n";
  84           std::cout << "        console       Trace text level\n";
  85           std::cout << "     --verbose        Verbose mode\n";
  86           std::cout << "     --debug          Debug mode\n";
  87           std::cout << "     --version        Print version\n";
  88           std::cout << "     --help           Print this help message\n";
  89 }
  90
  91
  92 int
  93 phm2helix_main (int argc, char* const argv[])
  94 {
  95         Phantom phm;
  96         std::string optGeometryName = Scanner::convertGeometryIDToName(Scanner::GEOMETRY_PARALLEL);
  97         char *opt_outfile = NULL;
  98         std::string opt_desc;
  99         std::string opt_PhmProg;
 100         std::string opt_PhmFileName = "tmpphmfile";
 101         int opt_ndet;
 102         int opt_nview;
 103         int opt_offsetview = 0;
 104         int opt_nray = 1;
 105         double dOptFocalLength = 2.;
 106         double dOptCenterDetectorLength = 2;
 107         double dOptViewRatio = 1.;
 108         double dOptScanRatio = 1.;
 109         int opt_trace = Trace::TRACE_NONE;
 110         int opt_verbose = 0;
 111         int opt_debug = 0;
 112         double opt_rotangle = -1;
 113         char* endptr = NULL;
 114         char* endstr;
 115
 116         Timer timerProgram;
 117
 118         while (1) {
 119                 int c = getopt_long(argc, argv, "", phm2helix_options, NULL);
 120
 121                 if (c == -1)
 122                 break;
 123
 124         switch (c) {
 125         case O_VERBOSE:
 126                 opt_verbose = 1;
 127                 break;
 128         case O_DEBUG:
 129                 opt_debug = 1;
 130                 break;
 131         case O_TRACE:
 132                 if ((opt_trace = Trace::convertTraceNameToID(optarg))
 133                                                                 == Trace::TRACE_INVALID) {
 134                         phm2helix_usage(argv[0]);
 135                         return (1);
 136                 }
 137                 break;
 138                           case O_PHMFILE:
 139                                 opt_PhmFileName = optarg;
 140                                 break;
 141                           case O_DESC:
 142                                 opt_desc = optarg;
 143                                 break;
 144                           case O_ROTANGLE:
 145                                 opt_rotangle = strtod(optarg, &endptr);
 146                                 endstr = optarg + strlen(optarg);
 147                                 if (endptr != endstr) {
 148                                         std::cerr << "Error setting --rotangle to " << optarg << std::endl;
 149                                         phm2helix_usage(argv[0]);
 150                                         return (1);
 151                                 }
 152                                 break;
 153                           case O_GEOMETRY:
 154                                 optGeometryName = optarg;
 155                                 break;
 156                           case O_FOCAL_LENGTH:
 157                                 dOptFocalLength = strtod(optarg, &endptr);
 158                                 endstr = optarg + strlen(optarg);
 159                                 if (endptr != endstr) {
 160                                         std::cerr << "Error setting --focal-length to " << optarg << std::endl;
 161                                         phm2helix_usage(argv[0]);
 162                                         return (1);
 163                                 }
 164                                 break;
 165                           case  O_CENTER_DETECTOR_LENGTH:
 166                                 dOptCenterDetectorLength = strtod(optarg, &endptr);
 167                                 endstr = optarg + strlen(optarg);
 168                                 if (endptr != endstr) {
 169                                         std::cerr << "Error setting --center-detector-length to " << optarg << std::endl;
 170                                         phm2helix_usage(argv[0]);
 171                                         return (1);
 172                                 }
 173                           break;
 174                           case O_VIEW_RATIO:
 175                                 dOptViewRatio = strtod(optarg, &endptr);
 176                                 endstr = optarg + strlen(optarg);
 177                                 if (endptr != endstr) {
 178                                         std::cerr << "Error setting --view-ratio to " << optarg << std::endl;
 179                                         phm2helix_usage(argv[0]);
 180                                         return (1);
 181                                 }
 182                                 break;
 183                           case O_SCAN_RATIO:
 184                                 dOptScanRatio = strtod(optarg, &endptr);
 185                                 endstr = optarg + strlen(optarg);
 186                                 if (endptr != endstr) {
 187                                         std::cerr << "Error setting --scan-ratio to " << optarg << std::endl;
 188                                         phm2helix_usage(argv[0]);
 189                                         return (1);
 190                                 }
 191                                 break;
 192                           case O_NRAY:
 193                                 opt_nray = strtol(optarg, &endptr, 10);
 194                                 endstr = optarg + strlen(optarg);
 195                                 if (endptr != endstr) {
 196                                   std::cerr << "Error setting --nray to %s" << optarg << std::endl;
 197                                   phm2helix_usage(argv[0]);
 198                                   return (1);
 199                                 }
 200                                 break;
 201                           case O_OFFSETVIEW:
 202                                 opt_offsetview = strtol(optarg, &endptr, 10);
 203                                 endstr = optarg + strlen(optarg);
 204                                 if (endptr != endstr) {
 205                                   std::cerr << "Error setting --offsetview to %s" << optarg << std::endl;
 206                                   phm2helix_usage(argv[0]);
 207                                   return (1);
 208                                 }
 209                                 break;
 210                           case O_VERSION:
 211 #ifdef VERSION
 212                                   std::cout << "Version: " << VERSION << std::endl << g_szIdStr << std::endl;
 213 #else
 214                                           std::cout << "Unknown version number\n";
 215 #endif
 216                                   return (0);
 217                           case O_HELP:
 218                           case '?':
 219                                 phm2helix_usage(argv[0]);
 220                                 return (0);
 221                           default:
 222                                 phm2helix_usage(argv[0]);
 223                                 return (1);
 224                         } // end of switch
 225           } // end of while loop
 226
 227           if (optind + 4 != argc) {
 228                 phm2helix_usage(argv[0]);
 229                 return (1);
 230           }
 231
 232           opt_outfile = argv[optind];
 233           opt_ndet = strtol(argv[optind+1], &endptr, 10);
 234           endstr = argv[optind+1] + strlen(argv[optind+1]);
 235           if (endptr != endstr) {
 236                 std::cerr << "Error setting --ndet to " << argv[optind+1] << std::endl;
 237                 phm2helix_usage(argv[0]);
 238                 return (1);
 239           }
 240           opt_nview = strtol(argv[optind+2], &endptr, 10);
 241           endstr = argv[optind+2] + strlen(argv[optind+2]);
 242           if (endptr != endstr) {
 243                 std::cerr << "Error setting --nview to " << argv[optind+2] << std::endl;
 244                 phm2helix_usage(argv[0]);
 245                 return (1);
 246           }
 247           opt_PhmProg = argv[optind+3];
 248
 249           if (opt_rotangle < 0) {
 250                 if (optGeometryName.compare ("parallel") == 0)
 251                   opt_rotangle = 0.5;
 252                 else
 253                   opt_rotangle = 1.0;
 254           }
 255
 256           std::ostringstream desc;
 257           desc << "phm2helix: NDet=" << opt_ndet
 258                    << ", Nview=" << opt_nview
 259                    << ", NRay=" << opt_nray
 260                    << ", RotAngle=" << opt_rotangle
 261                    << ", OffsetView =" << opt_offsetview
 262                    << ", Geometry=" << optGeometryName
 263                    << ", PhantomProg=" << opt_PhmProg
 264                    << ", PhmFileName=" << opt_PhmFileName;
 265           if (opt_desc.length()) {
 266                 desc << ": " << opt_desc;
 267           }
 268           opt_desc = desc.str();
 269
 270           opt_rotangle *= TWOPI;
 271
 272           int stat;
 273           char extcommand[100];
 274           if(opt_debug != 0)
 275                         std::cout  <<  opt_PhmProg  <<  " " << 0 << " " <<  opt_nview << " " << opt_PhmFileName  << std::endl;
 276            //extcommand <<  opt_PhmProg  <<  " " << 0 << " " <<  opt_nview << " " << opt_PhmFileName ;
 277
 278           sprintf(extcommand, "%s %d %d %s",    opt_PhmProg.c_str(), 0, opt_nview, opt_PhmFileName.c_str() );
 279
 280            stat = system( extcommand );
 281           if (stat != 0 )
 282                         std::cerr << "Error executing external phantom program " << opt_PhmProg << " with command " << extcommand << std::endl;
 283
 284           phm.createFromPhmFile (opt_PhmFileName.c_str());
 285           remove(opt_PhmFileName.c_str());
 286
 287           Scanner scanner (phm, optGeometryName.c_str(), opt_ndet, opt_nview,
 288                                 opt_offsetview, opt_nray, opt_rotangle, dOptFocalLength,
 289                                 dOptCenterDetectorLength, dOptViewRatio, dOptScanRatio);
 290           if (scanner.fail()) {
 291                  std::cout << "Scanner Creation Error: " << scanner.failMessage()
 292                                                         << std::endl;
 293                  return (1);
 294           }
 295
 296           Projections pjGlobal(scanner);
 297
 298
 299           for( int iView = 0; iView < opt_nview; iView++ ){
 300                 if(opt_debug != 0)
 301                         std::cout  <<  opt_PhmProg  <<  " " << iView << " " <<  opt_nview << " " << opt_PhmFileName  << std::endl;
 302            //extcommand <<  opt_PhmProg  <<  " " << iView << " " <<  opt_nview << " " << opt_PhmFileName ;
 303
 304                 sprintf(extcommand, "%s %d %d %s",
 305                         opt_PhmProg.c_str(), iView, opt_nview,
 306                         opt_PhmFileName.c_str() );
 307                 stat = system( extcommand );
 308
 309                 if (stat != 0 )
 310                         std::cerr << "Error executing external phantom program " << opt_PhmProg << " with command " << extcommand << std::endl;
 311                 Phantom phmtmp;
 312                 phmtmp.createFromPhmFile (opt_PhmFileName.c_str());
 313
 314                 scanner.collectProjections (pjGlobal, phmtmp, iView,
 315                           1, scanner.offsetView(), true, opt_trace);
 316                 remove(opt_PhmFileName.c_str());
 317           }
 318
 319
 320           pjGlobal.setCalcTime (timerProgram.timerEnd());
 321           pjGlobal.setRemark (opt_desc);
 322           pjGlobal.write (opt_outfile);
 323           if (opt_verbose) {
 324             phm.print (std::cout);
 325             std::cout << std::endl;
 326             std::ostringstream os;
 327             pjGlobal.printScanInfo (os);
 328             std::cout << os.str() << std::endl;
 329             std::cout << "  Remark: " << pjGlobal.remark() << std::endl;
 330             std::cout << "Run time: " << pjGlobal.calcTime() << " seconds\n";
 331           }
 332
 333           return (0);
 334 }
 335
 336
 337 #ifndef NO_MAIN
 338 int
 339 main (int argc, char* argv[])
 340 {
 341   int retval = 1;
 342
 343   try {
 344     retval = phm2helix_main(argc, argv);
 345 #if HAVE_DMALLOC
 346     //    dmalloc_shutdown();
 347 #endif
 348   } catch (exception e) {
 349     std::cerr << "Exception: " << e.what() << std::endl;
 350   } catch (...) {
 351     std::cerr << "Unknown exception\n";
 352   }
 353
 354   return (retval);
 355 }
 356 #endif
 357