1 /*****************************************************************************
5 ** Purpose: Convert an phantom object to an image file
6 ** Programmer: Kevin Rosenberg
9 ** This is part of the CTSim program
10 ** Copyright (C) 1983-2009 Kevin Rosenberg
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.
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.
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 ******************************************************************************/
30 enum { O_PHANTOM, O_DESC, O_NSAMPLE, O_FILTER, O_VIEW_RATIO, O_TRACE, O_VERBOSE, O_HELP,
31 O_PHMFILE, O_FILTER_DOMAIN, O_FILTER_BW, O_FILTER_PARAM, O_DEBUG, O_VERSION };
33 static struct option my_options[] =
35 {"phantom", 1, 0, O_PHANTOM},
36 {"phmfile", 1, 0, O_PHMFILE},
37 {"desc", 1, 0, O_DESC},
38 {"nsample", 1, 0, O_NSAMPLE},
39 {"filter", 1, 0, O_FILTER},
40 {"filter-domain", 1, 0, O_FILTER_DOMAIN},
41 {"filter-bw", 1, 0, O_FILTER_BW},
42 {"filter-param", 1, 0, O_FILTER_PARAM},
43 {"trace", 1, 0, O_TRACE},
44 {"view-ratio", 1, 0, O_VIEW_RATIO},
45 {"verbose", 0, 0, O_VERBOSE},
46 {"debug", 0, 0, O_DEBUG},
47 {"help", 0, 0, O_HELP},
48 {"version", 0, 0, O_VERSION},
52 static const char* g_szIdStr = "$Id$";
55 phm2if_usage (const char *program)
57 std::cout << "phm2if_usage: " << fileBasename(program) << " outfile nx ny [--phantom phantom-name] [--phmfile filename] [--filter filter-name] [OPTIONS]\n";
58 std::cout << "Generate phantom image from a predefined --phantom or a --phmfile\n";
59 std::cout << std::endl;
60 std::cout << " outfile Name of output file for image\n";
61 std::cout << " nx Number of pixels X-axis\n";
62 std::cout << " ny Number of pixels Y-axis\n";
63 std::cout << " --view-ratio View diameter to phantom diameter ratio (default = 1)\n";
64 std::cout << " --phantom Phantom to use for projection\n";
65 std::cout << " herman Herman head phantom\n";
66 std::cout << " shepp-logan Shepp-Logan head phantom\n";
67 std::cout << " unit-pulse Unit pulse phantom\n";
68 std::cout << " --phmfile Generate Phantom from phantom file\n";
69 std::cout << " --filter Generate Phantom from a filter function\n";
70 std::cout << " abs_bandlimit Abs * Bandlimiting\n";
71 std::cout << " abs_sinc Abs * Sinc\n";
72 std::cout << " abs_cos Abs * Cosine\n";
73 std::cout << " abs_hamming Abs * Hamming\n";
74 std::cout << " shepp Shepp-Logan\n";
75 std::cout << " bandlimit Bandlimiting\n";
76 std::cout << " sinc Sinc\n";
77 std::cout << " cos Cosine\n";
78 std::cout << " triangle Triangle\n";
79 std::cout << " hamming Hamming\n";
80 std::cout << " --filter-param Alpha level for Hamming filter\n";
81 std::cout << " --filter-domain Set domain of filter\n";
82 std::cout << " spatial Spatial domain (default)\n";
83 std::cout << " freq Frequency domain\n";
84 std::cout << " --filter-bw Filter bandwidth (default = 1)\n";
85 std::cout << " --desc Description of raysum\n";
86 std::cout << " --nsample Number of samples per axis per pixel (default = 1)\n";
87 std::cout << " --trace Trace level to use\n";
88 std::cout << " none No tracing (default)\n";
89 std::cout << " console Trace text level\n";
90 std::cout << " --debug Debug mode\n";
91 std::cout << " --verbose Verbose mode\n";
92 std::cout << " --version Print version\n";
93 std::cout << " --help Print this help message\n";
97 void mpi_gather_image (MPIWorld& mpiWorld, ImageFile* pImGlobal, ImageFile* pImLocal, const int optDebug);
101 phm2if_main (int argc, char* const argv[])
103 ImageFile* pImGlobal = NULL;
105 std::string optPhmName;
106 std::string optFilterName;
107 std::string optDomainName (SignalFilter::convertDomainIDToName (SignalFilter::DOMAIN_SPATIAL));
108 std::string optOutFilename;
110 std::string optPhmFilename;
114 double optViewRatio = 1.;
115 double optFilterParam = 1.;
116 double optFilterBW = 1.;
117 int optTrace = Trace::TRACE_NONE;
118 bool optVerbose = false;
119 bool optDebug = false;
125 ImageFile* pImLocal = NULL;
126 MPIWorld mpiWorld (argc, argv);
127 if (mpiWorld.getRank() == 0) {
130 int c = getopt_long(argc, argv, "", my_options, NULL);
139 optPhmFilename = optarg;
148 if ((optTrace = Trace::convertTraceNameToID(optarg)) == Trace::TRACE_INVALID) {
149 phm2if_usage(argv[0]);
154 optFilterName = optarg;
156 case O_FILTER_DOMAIN:
157 optDomainName = optarg;
163 optFilterBW = strtod(optarg, &endptr);
164 endstr = optarg + strlen(optarg);
165 if (endptr != endstr) {
166 sys_error(ERR_SEVERE,"Error setting --filter-bw to %s\n", optarg);
167 phm2if_usage(argv[0]);
172 optViewRatio = strtod(optarg, &endptr);
173 endstr = optarg + strlen(optarg);
174 if (endptr != endstr) {
175 sys_error(ERR_SEVERE,"Error setting --view-ratio to %s\n", optarg);
176 phm2if_usage(argv[0]);
181 optFilterParam = strtod(optarg, &endptr);
182 endstr = optarg + strlen(optarg);
183 if (endptr != endstr) {
184 sys_error(ERR_SEVERE,"Error setting --filter-param to %s\n", optarg);
185 phm2if_usage(argv[0]);
190 opt_nsample = strtol(optarg, &endptr, 10);
191 endstr = optarg + strlen(optarg);
192 if (endptr != endstr) {
193 sys_error(ERR_SEVERE,"Error setting --nsample to %s\n", optarg);
194 phm2if_usage(argv[0]);
200 std::cout << "Version " << VERSION << std::endl << g_szIdStr << std::endl;
202 std::cerr << "Unknown version number\n";
206 phm2if_usage(argv[0]);
209 phm2if_usage(argv[0]);
214 if (optPhmName == "" && optFilterName == "" && optPhmFilename == "") {
215 std::cerr << "No phantom defined\n" << std::endl;
216 phm2if_usage(argv[0]);
220 if (optind + 3 != argc) {
221 phm2if_usage(argv[0]);
224 optOutFilename = argv[optind];
225 opt_nx = strtol(argv[optind+1], &endptr, 10);
226 endstr = argv[optind+1] + strlen(argv[optind+1]);
227 if (endptr != endstr) {
228 sys_error(ERR_SEVERE,"Error setting nx to %s\n", argv[optind+1]);
229 phm2if_usage(argv[0]);
232 opt_ny = strtol(argv[optind+2], &endptr, 10);
233 endstr = argv[optind+2] + strlen(argv[optind+2]);
234 if (endptr != endstr) {
235 sys_error(ERR_SEVERE,"Error setting ny to %s\n", argv[optind+2]);
236 phm2if_usage(argv[0]);
240 std::ostringstream oss;
241 oss << "phm2if: nx=" << opt_nx << ", ny=" << opt_ny << ", viewRatio=" << optViewRatio << ", nsample=" << opt_nsample << ", ";
242 if (optPhmFilename != "")
243 oss << "phantomFile=" << optPhmFilename;
244 else if (optPhmName != "")
245 oss << "phantom=" << optPhmName;
246 else if (optFilterName != "") {
247 oss << "filter=" << optFilterName << " - " << optDomainName;
250 oss << ": " << optDesc;
253 if (optPhmName != "") {
254 phm.createFromPhantom (optPhmName.c_str());
256 std::cout << phm.failMessage() << std::endl << std::endl;
257 phm2if_usage(argv[0]);
262 if (optPhmFilename != "") {
263 phm.createFromFile(optPhmFilename.c_str());
265 if (mpiWorld.getRank() == 0)
266 std::cerr << "Can't use phantom from file in MPI mode\n";
272 std::cout << "Rasterize Phantom to Image\n" << std::endl;
278 TimerCollectiveMPI timerBcast (mpiWorld.getComm());
279 mpiWorld.BcastString (optPhmName);
280 mpiWorld.getComm().Bcast (&optVerbose, 1, MPI::INT, 0);
281 mpiWorld.getComm().Bcast (&optDebug, 1, MPI::INT, 0);
282 mpiWorld.getComm().Bcast (&optTrace, 1, MPI::INT, 0);
283 mpiWorld.getComm().Bcast (&opt_nx, 1, MPI::INT, 0);
284 mpiWorld.getComm().Bcast (&opt_ny, 1, MPI::INT, 0);
285 mpiWorld.getComm().Bcast (&opt_nsample, 1, MPI::INT, 0);
286 mpiWorld.getComm().Bcast (&optViewRatio, 1, MPI::DOUBLE, 0);
287 mpiWorld.getComm().Bcast (&optFilterParam, 1, MPI::DOUBLE, 0);
288 mpiWorld.getComm().Bcast (&optFilterBW, 1, MPI::DOUBLE, 0);
290 mpiWorld.BcastString (optFilterName);
291 mpiWorld.BcastString (optDomainName);
294 timerBcast.timerEndAndReport ("Time to broadcast variables");
296 mpiWorld.setTotalWorkUnits (opt_nx);
298 if (mpiWorld.getRank() > 0 && optPhmName != "")
299 phm.createFromPhantom (optPhmName.c_str());
301 if (mpiWorld.getRank() == 0) {
302 pImGlobal = new ImageFile (opt_nx, opt_ny);
304 pImLocal = new ImageFile (opt_nx, opt_ny);
306 pImGlobal = new ImageFile (opt_nx, opt_ny);
309 ImageFileArray v = NULL;
311 if (mpiWorld.getRank() == 0)
312 v = pImGlobal->getArray ();
314 if (phm.getComposition() == P_UNIT_PULSE) {
315 if (mpiWorld.getRank() == 0) {
316 v[opt_nx/2][opt_ny/2] = 1.;
318 } else if (optFilterName != "") {
319 if (mpiWorld.getRank() == 0) {
320 pImGlobal->filterResponse (optDomainName.c_str(), optFilterBW, optFilterName.c_str(), optFilterParam);
323 TimerCollectiveMPI timerRasterize (mpiWorld.getComm());
324 phm.convertToImagefile (*pImLocal, optViewRatio, opt_nsample, optTrace, mpiWorld.getMyStartWorkUnit(), mpiWorld.getMyLocalWorkUnits(), false);
326 timerRasterize.timerEndAndReport ("Time to rasterize phantom");
328 TimerCollectiveMPI timerGather (mpiWorld.getComm());
329 mpi_gather_image (mpiWorld, pImGlobal, pImLocal, optDebug);
331 timerGather.timerEndAndReport ("Time to gather image");
334 v = pImGlobal->getArray ();
335 if (phm.getComposition() == P_UNIT_PULSE) {
336 v[opt_nx/2][opt_ny/2] = 1.;
337 } else if (optFilterName != "") {
338 pImGlobal->filterResponse (optDomainName.c_str(), optFilterBW, optFilterName.c_str(), optFilterParam);
340 phm.convertToImagefile (*pImGlobal, optViewRatio, opt_nsample, optTrace);
345 if (mpiWorld.getRank() == 0)
348 double calctime = timerProgram.timerEnd ();
349 pImGlobal->labelAdd (Array2dFileLabel::L_HISTORY, optDesc.c_str(), calctime);
350 pImGlobal->fileWrite (optOutFilename.c_str());
352 std::cout << "Time to rasterize phantom: " << calctime << " seconds\n";
366 void mpi_gather_image (MPIWorld& mpiWorld, ImageFile* pImGlobal, ImageFile* pImLocal, const int optDebug)
368 ImageFileArray vLocal = pImLocal->getArray();
369 ImageFileArray vGlobal = NULL;
370 int nyLocal = pImLocal->ny();
372 if (mpiWorld.getRank() == 0)
373 vGlobal = pImGlobal->getArray();
375 for (int iw = 0; iw < mpiWorld.getMyLocalWorkUnits(); iw++)
376 mpiWorld.getComm().Send(vLocal[iw], nyLocal, pImLocal->getMPIDataType(), 0, 0);
378 if (mpiWorld.getRank() == 0) {
379 for (int iProc = 0; iProc < mpiWorld.getNumProcessors(); iProc++) {
380 for (int iw = mpiWorld.getStartWorkUnit(iProc); iw <= mpiWorld.getEndWorkUnit(iProc); iw++) {
382 mpiWorld.getComm().Recv(vGlobal[iw], nyLocal, pImLocal->getMPIDataType(), iProc, 0, status);
392 main (int argc, char* argv[])
397 retval = phm2if_main(argc, argv);
398 } catch (exception e) {
399 std::cerr << "Exception: " << e.what() << std::endl;
401 std::cerr << "Unknown exception\n";