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) 1983-2000 Kevin Rosenberg
12 ** $Id: phm2if.cpp,v 1.24 2001/04/02 03:49:52 kevin Exp $
14 ** This program is free software; you can redistribute it and/or modify
15 ** it under the terms of the GNU General Public License (version 2) as
16 ** published by the Free Software Foundation.
18 ** This program is distributed in the hope that it will be useful,
19 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
20 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 ** GNU General Public License for more details.
23 ** You should have received a copy of the GNU General Public License
24 ** along with this program; if not, write to the Free Software
25 ** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
26 ******************************************************************************/
32 enum { O_PHANTOM, O_DESC, O_NSAMPLE, O_FILTER, O_VIEW_RATIO, O_TRACE, O_VERBOSE, O_HELP,
33 O_PHMFILE, O_FILTER_DOMAIN, O_FILTER_BW, O_FILTER_PARAM, O_DEBUG, O_VERSION };
35 static struct option my_options[] =
37 {"phantom", 1, 0, O_PHANTOM},
38 {"phmfile", 1, 0, O_PHMFILE},
39 {"desc", 1, 0, O_DESC},
40 {"nsample", 1, 0, O_NSAMPLE},
41 {"filter", 1, 0, O_FILTER},
42 {"filter-domain", 1, 0, O_FILTER_DOMAIN},
43 {"filter-bw", 1, 0, O_FILTER_BW},
44 {"filter-param", 1, 0, O_FILTER_PARAM},
45 {"trace", 1, 0, O_TRACE},
46 {"view-ratio", 1, 0, O_VIEW_RATIO},
47 {"verbose", 0, 0, O_VERBOSE},
48 {"debug", 0, 0, O_DEBUG},
49 {"help", 0, 0, O_HELP},
50 {"version", 0, 0, O_VERSION},
54 static const char* g_szIdStr = "$Id: phm2if.cpp,v 1.24 2001/04/02 03:49:52 kevin Exp $";
57 phm2if_usage (const char *program)
59 std::cout << "phm2if_usage: " << fileBasename(program) << " outfile nx ny [--phantom phantom-name] [--phmfile filename] [--filter filter-name] [OPTIONS]\n";
60 std::cout << "Generate phantom image from a predefined --phantom or a --phmfile\n";
61 std::cout << std::endl;
62 std::cout << " outfile Name of output file for image\n";
63 std::cout << " nx Number of pixels X-axis\n";
64 std::cout << " ny Number of pixels Y-axis\n";
65 std::cout << " --view-ratio View diameter to phantom diameter ratio (default = 1)\n";
66 std::cout << " --phantom Phantom to use for projection\n";
67 std::cout << " herman Herman head phantom\n";
68 std::cout << " shepp-logan Shepp-Logan head phantom\n";
69 std::cout << " unit-pulse Unit pulse phantom\n";
70 std::cout << " --phmfile Generate Phantom from phantom file\n";
71 std::cout << " --filter Generate Phantom from a filter function\n";
72 std::cout << " abs_bandlimit Abs * Bandlimiting\n";
73 std::cout << " abs_sinc Abs * Sinc\n";
74 std::cout << " abs_cos Abs * Cosine\n";
75 std::cout << " abs_hamming Abs * Hamming\n";
76 std::cout << " shepp Shepp-Logan\n";
77 std::cout << " bandlimit Bandlimiting\n";
78 std::cout << " sinc Sinc\n";
79 std::cout << " cos Cosine\n";
80 std::cout << " triangle Triangle\n";
81 std::cout << " hamming Hamming\n";
82 std::cout << " --filter-param Alpha level for Hamming filter\n";
83 std::cout << " --filter-domain Set domain of filter\n";
84 std::cout << " spatial Spatial domain (default)\n";
85 std::cout << " freq Frequency domain\n";
86 std::cout << " --filter-bw Filter bandwidth (default = 1)\n";
87 std::cout << " --desc Description of raysum\n";
88 std::cout << " --nsample Number of samples per axis per pixel (default = 1)\n";
89 std::cout << " --trace Trace level to use\n";
90 std::cout << " none No tracing (default)\n";
91 std::cout << " console Trace text level\n";
92 std::cout << " phantom Trace phantom\n";
93 std::cout << " proj Trace projections\n";
94 std::cout << " plot Trace plot\n";
95 std::cout << " clipping Trace clipping\n";
96 std::cout << " --debug Debug mode\n";
97 std::cout << " --verbose Verbose mode\n";
98 std::cout << " --version Print version\n";
99 std::cout << " --help Print this help message\n";
103 void mpi_gather_image (MPIWorld& mpiWorld, ImageFile* pImGlobal, ImageFile* pImLocal, const int optDebug);
107 phm2if_main (int argc, char* const argv[])
109 ImageFile* pImGlobal = NULL;
111 std::string optPhmName;
112 std::string optFilterName;
113 std::string optDomainName (SignalFilter::convertDomainIDToName (SignalFilter::DOMAIN_SPATIAL));
114 std::string optOutFilename;
116 std::string optPhmFilename;
120 double optViewRatio = 1.;
121 double optFilterParam = 1.;
122 double optFilterBW = 1.;
123 int optTrace = Trace::TRACE_NONE;
124 bool optVerbose = false;
125 bool optDebug = false;
131 ImageFile* pImLocal = NULL;
132 MPIWorld mpiWorld (argc, argv);
133 if (mpiWorld.getRank() == 0) {
136 int c = getopt_long(argc, argv, "", my_options, NULL);
145 optPhmFilename = optarg;
154 if ((optTrace = Trace::convertTraceNameToID(optarg)) == Trace::TRACE_INVALID) {
155 phm2if_usage(argv[0]);
160 optFilterName = optarg;
162 case O_FILTER_DOMAIN:
163 optDomainName = optarg;
169 optFilterBW = strtod(optarg, &endptr);
170 endstr = optarg + strlen(optarg);
171 if (endptr != endstr) {
172 sys_error(ERR_SEVERE,"Error setting --filter-bw to %s\n", optarg);
173 phm2if_usage(argv[0]);
178 optViewRatio = strtod(optarg, &endptr);
179 endstr = optarg + strlen(optarg);
180 if (endptr != endstr) {
181 sys_error(ERR_SEVERE,"Error setting --view-ratio to %s\n", optarg);
182 phm2if_usage(argv[0]);
187 optFilterParam = strtod(optarg, &endptr);
188 endstr = optarg + strlen(optarg);
189 if (endptr != endstr) {
190 sys_error(ERR_SEVERE,"Error setting --filter-param to %s\n", optarg);
191 phm2if_usage(argv[0]);
196 opt_nsample = strtol(optarg, &endptr, 10);
197 endstr = optarg + strlen(optarg);
198 if (endptr != endstr) {
199 sys_error(ERR_SEVERE,"Error setting --nsample to %s\n", optarg);
200 phm2if_usage(argv[0]);
206 std::cout << "Version " << VERSION << std::endl << g_szIdStr << std::endl;
208 std::cerr << "Unknown version number\n";
212 phm2if_usage(argv[0]);
215 phm2if_usage(argv[0]);
220 if (optPhmName == "" && optFilterName == "" && optPhmFilename == "") {
221 std::cerr << "No phantom defined\n" << std::endl;
222 phm2if_usage(argv[0]);
226 if (optind + 3 != argc) {
227 phm2if_usage(argv[0]);
230 optOutFilename = argv[optind];
231 opt_nx = strtol(argv[optind+1], &endptr, 10);
232 endstr = argv[optind+1] + strlen(argv[optind+1]);
233 if (endptr != endstr) {
234 sys_error(ERR_SEVERE,"Error setting nx to %s\n", argv[optind+1]);
235 phm2if_usage(argv[0]);
238 opt_ny = strtol(argv[optind+2], &endptr, 10);
239 endstr = argv[optind+2] + strlen(argv[optind+2]);
240 if (endptr != endstr) {
241 sys_error(ERR_SEVERE,"Error setting ny to %s\n", argv[optind+2]);
242 phm2if_usage(argv[0]);
246 std::ostringstream oss;
247 oss << "phm2if: nx=" << opt_nx << ", ny=" << opt_ny << ", viewRatio=" << optViewRatio << ", nsample=" << opt_nsample << ", ";
248 if (optPhmFilename != "")
249 oss << "phantomFile=" << optPhmFilename;
250 else if (optPhmName != "")
251 oss << "phantom=" << optPhmName;
252 else if (optFilterName != "") {
253 oss << "filter=" << optFilterName << " - " << optDomainName;
256 oss << ": " << optDesc;
259 if (optPhmName != "") {
260 phm.createFromPhantom (optPhmName.c_str());
262 std::cout << phm.failMessage() << std::endl << std::endl;
263 phm2if_usage(argv[0]);
268 if (optPhmFilename != "") {
269 phm.createFromFile(optPhmFilename.c_str());
271 if (mpiWorld.getRank() == 0)
272 std::cerr << "Can't use phantom from file in MPI mode\n";
278 std::cout << "Rasterize Phantom to Image\n" << std::endl;
284 TimerCollectiveMPI timerBcast (mpiWorld.getComm());
285 mpiWorld.BcastString (optPhmName);
286 mpiWorld.getComm().Bcast (&optVerbose, 1, MPI::INT, 0);
287 mpiWorld.getComm().Bcast (&optDebug, 1, MPI::INT, 0);
288 mpiWorld.getComm().Bcast (&optTrace, 1, MPI::INT, 0);
289 mpiWorld.getComm().Bcast (&opt_nx, 1, MPI::INT, 0);
290 mpiWorld.getComm().Bcast (&opt_ny, 1, MPI::INT, 0);
291 mpiWorld.getComm().Bcast (&opt_nsample, 1, MPI::INT, 0);
292 mpiWorld.getComm().Bcast (&optViewRatio, 1, MPI::DOUBLE, 0);
293 mpiWorld.getComm().Bcast (&optFilterParam, 1, MPI::DOUBLE, 0);
294 mpiWorld.getComm().Bcast (&optFilterBW, 1, MPI::DOUBLE, 0);
296 mpiWorld.BcastString (optFilterName);
297 mpiWorld.BcastString (optDomainName);
300 timerBcast.timerEndAndReport ("Time to broadcast variables");
302 mpiWorld.setTotalWorkUnits (opt_nx);
304 if (mpiWorld.getRank() > 0 && optPhmName != "")
305 phm.createFromPhantom (optPhmName.c_str());
307 if (mpiWorld.getRank() == 0) {
308 pImGlobal = new ImageFile (opt_nx, opt_ny);
310 pImLocal = new ImageFile (opt_nx, opt_ny);
312 pImGlobal = new ImageFile (opt_nx, opt_ny);
315 ImageFileArray v = NULL;
317 if (mpiWorld.getRank() == 0)
318 v = pImGlobal->getArray ();
320 if (phm.getComposition() == P_UNIT_PULSE) {
321 if (mpiWorld.getRank() == 0) {
322 v[opt_nx/2][opt_ny/2] = 1.;
324 } else if (optFilterName != "") {
325 if (mpiWorld.getRank() == 0) {
326 pImGlobal->filterResponse (optDomainName.c_str(), optFilterBW, optFilterName.c_str(), optFilterParam);
329 TimerCollectiveMPI timerRasterize (mpiWorld.getComm());
330 phm.convertToImagefile (*pImLocal, optViewRatio, opt_nsample, optTrace, mpiWorld.getMyStartWorkUnit(), mpiWorld.getMyLocalWorkUnits(), false);
332 timerRasterize.timerEndAndReport ("Time to rasterize phantom");
334 TimerCollectiveMPI timerGather (mpiWorld.getComm());
335 mpi_gather_image (mpiWorld, pImGlobal, pImLocal, optDebug);
337 timerGather.timerEndAndReport ("Time to gather image");
340 v = pImGlobal->getArray ();
341 if (phm.getComposition() == P_UNIT_PULSE) {
342 v[opt_nx/2][opt_ny/2] = 1.;
343 } else if (optFilterName != "") {
344 pImGlobal->filterResponse (optDomainName.c_str(), optFilterBW, optFilterName.c_str(), optFilterParam);
346 phm.convertToImagefile (*pImGlobal, optViewRatio, opt_nsample, optTrace);
351 if (mpiWorld.getRank() == 0)
354 double calctime = timerProgram.timerEnd ();
355 pImGlobal->labelAdd (Array2dFileLabel::L_HISTORY, optDesc.c_str(), calctime);
356 pImGlobal->fileWrite (optOutFilename.c_str());
358 std::cout << "Time to rasterize phantom: " << calctime << " seconds\n";
372 void mpi_gather_image (MPIWorld& mpiWorld, ImageFile* pImGlobal, ImageFile* pImLocal, const int optDebug)
374 ImageFileArray vLocal = pImLocal->getArray();
375 ImageFileArray vGlobal = NULL;
376 int nyLocal = pImLocal->ny();
378 if (mpiWorld.getRank() == 0)
379 vGlobal = pImGlobal->getArray();
381 for (int iw = 0; iw < mpiWorld.getMyLocalWorkUnits(); iw++)
382 mpiWorld.getComm().Send(vLocal[iw], nyLocal, pImLocal->getMPIDataType(), 0, 0);
384 if (mpiWorld.getRank() == 0) {
385 for (int iProc = 0; iProc < mpiWorld.getNumProcessors(); iProc++) {
386 for (int iw = mpiWorld.getStartWorkUnit(iProc); iw <= mpiWorld.getEndWorkUnit(iProc); iw++) {
388 mpiWorld.getComm().Recv(vGlobal[iw], nyLocal, pImLocal->getMPIDataType(), iProc, 0, status);
398 main (int argc, char* argv[])
403 retval = phm2if_main(argc, argv);
404 } catch (exception e) {
405 std::cerr << "Exception: " << e.what() << std::endl;
407 std::cerr << "Unknown exception\n";