1 /*****************************************************************************
5 ** Purpose: Reconstruct an image from projections
6 ** Programmer: Kevin Rosenberg
7 ** Date Started: Aug 1984
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 ******************************************************************************/
29 enum {O_INTERP, O_FILTER, O_FILTER_METHOD, O_ZEROPAD, O_FILTER_PARAM, O_FILTER_GENERATION, O_BACKPROJ, O_PREINTERPOLATION_FACTOR, O_VERBOSE, O_TRACE, O_HELP, O_DEBUG, O_VERSION};
31 static struct option my_options[] =
33 {"interp", 1, 0, O_INTERP},
34 {"preinterpolation-factor", 1, 0, O_PREINTERPOLATION_FACTOR},
35 {"filter", 1, 0, O_FILTER},
36 {"filter-method", 1, 0, O_FILTER_METHOD},
37 {"zeropad", 1, 0, O_ZEROPAD},
38 {"filter-generation", 1, 0, O_FILTER_GENERATION},
39 {"filter-param", 1, 0, O_FILTER_PARAM},
40 {"backproj", 1, 0, O_BACKPROJ},
41 {"trace", 1, 0, O_TRACE},
42 {"debug", 0, 0, O_DEBUG},
43 {"verbose", 0, 0, O_VERBOSE},
44 {"help", 0, 0, O_HELP},
45 {"version", 0, 0, O_VERSION},
49 static const char* g_szIdStr = "$Id$";
52 pjrec_usage (const char *program)
54 std::cout << "usage: " << fileBasename(program) << " raysum-file image-file nx-image ny-image [OPTIONS]" << std::endl;
55 std::cout << "Image reconstruction from raysum projections" << std::endl;
56 std::cout << std::endl;
57 std::cout << " raysum-file Input raysum file" << std::endl;
58 std::cout << " image-file Output image file in SDF2D format" << std::endl;
59 std::cout << " nx-image Number of columns in output image" << std::endl;
60 std::cout << " ny-image Number of rows in output image" << std::endl;
61 std::cout << " --interp Interpolation method during backprojection" << std::endl;
62 std::cout << " nearest Nearest neighbor interpolation" << std::endl;
63 std::cout << " linear Linear interpolation (default)" << std::endl;
64 std::cout << " cubic Cubic interpolation\n";
65 #if HAVE_BSPLINE_INTERP
66 std::cout << " bspline B-spline interpolation" << std::endl;
68 std::cout << " --preinterpolate Preinterpolation factor (default = 1)\n";
69 std::cout << " Used only with frequency-based filtering\n";
70 std::cout << " --filter Filter name" << std::endl;
71 std::cout << " abs_bandlimit Abs * Bandlimiting (default)" << std::endl;
72 std::cout << " abs_sinc Abs * Sinc" << std::endl;
73 std::cout << " abs_cosine Abs * Cosine" << std::endl;
74 std::cout << " abs_hamming Abs * Hamming" << std::endl;
75 std::cout << " abs_hanning Abs * Hanning" << std::endl;
76 std::cout << " shepp Shepp-Logan" << std::endl;
77 std::cout << " bandlimit Bandlimiting" << std::endl;
78 std::cout << " sinc Sinc" << std::endl;
79 std::cout << " cosine Cosine" << std::endl;
80 std::cout << " triangle Triangle" << std::endl;
81 std::cout << " hamming Hamming" << std::endl;
82 std::cout << " hanning Hanning" << std::endl;
83 std::cout << " --filter-method Filter method before backprojections\n";;
84 std::cout << " convolution Spatial filtering (default)\n";
85 std::cout << " fourier Frequency filtering with discete fourier\n";
86 std::cout << " fourier_table Frequency filtering with table lookup fourier\n";
87 std::cout << " fft Fast Fourier Transform\n";
89 std::cout << " fftw Fast Fourier Transform West library\n";
90 std::cout << " rfftw Fast Fourier Transform West (real-mode) library\n";
92 std::cout << " --zeropad n Set zeropad level (default = 0)\n";
93 std::cout << " set n to number of powers to two to pad\n";
94 std::cout << " --filter-generation Filter Generation mode\n";
95 std::cout << " direct Use direct filter in spatial or frequency domain (default)\n";
96 std::cout << " inverse_fourier Use inverse fourier transform of inverse filter\n";
97 std::cout << " --backproj Backprojection Method" << std::endl;
98 std::cout << " trig Trigometric functions at every point" << std::endl;
99 std::cout << " table Trigometric functions with precalculated table" << std::endl;
100 std::cout << " diff Difference method" << std::endl;
101 std::cout << " idiff Difference method with integer math [default]" << std::endl;
102 std::cout << " --filter-param Alpha level for Hamming filter" << std::endl;
103 std::cout << " --trace Set tracing to level" << std::endl;
104 std::cout << " none No tracing (default)" << std::endl;
105 std::cout << " console Text level tracing" << std::endl;
106 std::cout << " --verbose Turn on verbose mode" << std::endl;
107 std::cout << " --debug Turn on debug mode" << std::endl;
108 std::cout << " --version Print version" << std::endl;
109 std::cout << " --help Print this help message" << std::endl;
114 static void ScatterProjectionsMPI (MPIWorld& mpiWorld, Projections& projGlobal, Projections& projLocal, const bool bDebug);
115 static void ReduceImageMPI (MPIWorld& mpiWorld, ImageFile* imLocal, ImageFile* imGlobal);
120 pjrec_main (int argc, char * const argv[])
122 Projections projGlobal;
123 ImageFile* imGlobal = NULL;
124 char* pszFilenameProj = NULL;
125 char* pszFilenameImage = NULL;
127 bool bOptVerbose = false;
130 int optTrace = Trace::TRACE_NONE;
131 double dOptFilterParam = -1;
132 std::string sOptFilterName (SignalFilter::convertFilterIDToName (SignalFilter::FILTER_ABS_BANDLIMIT));
133 std::string sOptFilterMethodName (ProcessSignal::convertFilterMethodIDToName (ProcessSignal::FILTER_METHOD_CONVOLUTION));
134 std::string sOptFilterGenerationName (ProcessSignal::convertFilterGenerationIDToName (ProcessSignal::FILTER_GENERATION_DIRECT));
135 std::string sOptInterpName (Backprojector::convertInterpIDToName (Backprojector::INTERP_LINEAR));
136 std::string sOptBackprojectName (Backprojector::convertBackprojectIDToName (Backprojector::BPROJ_IDIFF));
137 int iOptPreinterpolationFactor = 1;
142 int mpi_nview, mpi_ndet;
143 double mpi_detinc, mpi_rotinc, mpi_phmlen;
144 MPIWorld mpiWorld (argc, argv);
150 if (mpiWorld.getRank() == 0) {
153 int c = getopt_long(argc, argv, "", my_options, NULL);
162 sOptInterpName = optarg;
164 case O_PREINTERPOLATION_FACTOR:
165 iOptPreinterpolationFactor = strtol(optarg, &endptr, 10);
166 if (endptr != optarg + strlen(optarg)) {
167 pjrec_usage(argv[0]);
172 sOptFilterName = optarg;
174 case O_FILTER_METHOD:
175 sOptFilterMethodName = optarg;
177 case O_FILTER_GENERATION:
178 sOptFilterGenerationName = optarg;
181 dOptFilterParam = strtod(optarg, &endptr);
182 if (endptr != optarg + strlen(optarg)) {
183 pjrec_usage(argv[0]);
188 iOptZeropad = strtol(optarg, &endptr, 10);
189 if (endptr != optarg + strlen(optarg)) {
190 pjrec_usage(argv[0]);
195 sOptBackprojectName = optarg;
204 if ((optTrace = Trace::convertTraceNameToID(optarg)) == Trace::TRACE_INVALID) {
205 pjrec_usage(argv[0]);
211 std::cout << "Version " << VERSION << std::endl << g_szIdStr << std::endl;
213 std::cout << "Unknown version number" << std::endl;
218 pjrec_usage(argv[0]);
221 pjrec_usage(argv[0]);
226 if (optind + 4 != argc) {
227 pjrec_usage(argv[0]);
231 pszFilenameProj = argv[optind];
233 pszFilenameImage = argv[optind + 1];
235 nx = strtol(argv[optind + 2], &endptr, 10);
236 ny = strtol(argv[optind + 3], &endptr, 10);
238 std::ostringstream filterDesc;
239 if (dOptFilterParam >= 0)
240 filterDesc << sOptFilterName << ": alpha=" << dOptFilterParam;
242 filterDesc << sOptFilterName;
244 std::ostringstream label;
245 label << "pjrec: " << nx << "x" << ny << ", " << filterDesc.str() << ", " << sOptInterpName << ", preinterpolationFactor=" << iOptPreinterpolationFactor << ", " << sOptBackprojectName;
246 sRemark = label.str();
249 std::cout << "SRemark: " << sRemark << std::endl;
255 if (mpiWorld.getRank() == 0) {
256 projGlobal.read (pszFilenameProj);
259 projGlobal.printScanInfo (os);
260 std::cout << os.str();
263 mpi_ndet = projGlobal.nDet();
264 mpi_nview = projGlobal.nView();
265 mpi_detinc = projGlobal.detInc();
266 mpi_phmlen = projGlobal.phmLen();
267 mpi_rotinc = projGlobal.rotInc();
270 TimerCollectiveMPI timerBcast (mpiWorld.getComm());
271 mpiWorld.BcastString (sOptBackprojectName);
272 mpiWorld.BcastString (sOptFilterName);
273 mpiWorld.BcastString (sOptFilterMethodName);
274 mpiWorld.BcastString (sOptInterpName);
275 mpiWorld.getComm().Bcast (&bOptVerbose, 1, MPI::INT, 0);
276 mpiWorld.getComm().Bcast (&bOptDebug, 1, MPI::INT, 0);
277 mpiWorld.getComm().Bcast (&optTrace, 1, MPI::INT, 0);
278 mpiWorld.getComm().Bcast (&dOptFilterParam, 1, MPI::DOUBLE, 0);
279 mpiWorld.getComm().Bcast (&iOptZeropad, 1, MPI::INT, 0);
280 mpiWorld.getComm().Bcast (&iOptPreinterpolationFactor, 1, MPI::INT, 0);
281 mpiWorld.getComm().Bcast (&mpi_ndet, 1, MPI::INT, 0);
282 mpiWorld.getComm().Bcast (&mpi_nview, 1, MPI::INT, 0);
283 mpiWorld.getComm().Bcast (&mpi_detinc, 1, MPI::DOUBLE, 0);
284 mpiWorld.getComm().Bcast (&mpi_phmlen, 1, MPI::DOUBLE, 0);
285 mpiWorld.getComm().Bcast (&mpi_rotinc, 1, MPI::DOUBLE, 0);
286 mpiWorld.getComm().Bcast (&nx, 1, MPI::INT, 0);
287 mpiWorld.getComm().Bcast (&ny, 1, MPI::INT, 0);
289 timerBcast.timerEndAndReport ("Time to broadcast variables");
291 mpiWorld.setTotalWorkUnits (mpi_nview);
293 Projections projLocal (mpiWorld.getMyLocalWorkUnits(), mpi_ndet);
294 projLocal.setDetInc (mpi_detinc);
295 projLocal.setPhmLen (mpi_phmlen);
296 projLocal.setRotInc (mpi_rotinc);
298 TimerCollectiveMPI timerScatter (mpiWorld.getComm());
299 ScatterProjectionsMPI (mpiWorld, projGlobal, projLocal, bOptDebug);
301 timerScatter.timerEndAndReport ("Time to scatter projections");
303 if (mpiWorld.getRank() == 0) {
304 imGlobal = new ImageFile (nx, ny);
307 imLocal = new ImageFile (nx, ny);
310 if (! projGlobal.read (pszFilenameProj)) {
311 fprintf(stderr, "Unable to read projectfile file %s\n", pszFilenameProj);
316 std::ostringstream os;
317 projGlobal.printScanInfo(os);
318 std::cout << os.str();
321 imGlobal = new ImageFile (nx, ny);
325 TimerCollectiveMPI timerReconstruct (mpiWorld.getComm());
327 Reconstructor reconstruct (projLocal, *imLocal, sOptFilterName.c_str(), dOptFilterParam, sOptFilterMethodName.c_str(), iOptZeropad, sOptFilterGenerationName.c_str(), sOptInterpName.c_str(), iOptPreinterpolationFactor, sOptBackprojectName.c_str(), optTrace);
328 if (reconstruct.fail()) {
329 std::cout << reconstruct.failMessage();
332 reconstruct.reconstructAllViews();
335 timerReconstruct.timerEndAndReport ("Time to reconstruct");
337 TimerCollectiveMPI timerReduce (mpiWorld.getComm());
338 ReduceImageMPI (mpiWorld, imLocal, imGlobal);
340 timerReduce.timerEndAndReport ("Time to reduce image");
342 Reconstructor reconstruct (projGlobal, *imGlobal, sOptFilterName.c_str(), dOptFilterParam, sOptFilterMethodName.c_str(), iOptZeropad, sOptFilterGenerationName.c_str(), sOptInterpName.c_str(), iOptPreinterpolationFactor, sOptBackprojectName.c_str(), optTrace);
343 if (reconstruct.fail()) {
344 std::cout << reconstruct.failMessage();
347 reconstruct.reconstructAllViews();
351 if (mpiWorld.getRank() == 0)
354 double dCalcTime = timerProgram.timerEnd();
355 imGlobal->labelAdd (projGlobal.getLabel());
356 imGlobal->labelAdd (Array2dFileLabel::L_HISTORY, sRemark.c_str(), dCalcTime);
357 imGlobal->fileWrite (pszFilenameImage);
359 std::cout << "Run time: " << dCalcTime << " seconds" << std::endl;
369 //////////////////////////////////////////////////////////////////////////////////////
370 // MPI Support Routines
372 //////////////////////////////////////////////////////////////////////////////////////
375 static void ScatterProjectionsMPI (MPIWorld& mpiWorld, Projections& projGlobal, Projections& projLocal, const bool bOptDebug)
377 if (mpiWorld.getRank() == 0) {
378 for (int iProc = 0; iProc < mpiWorld.getNumProcessors(); iProc++) {
379 for (int iw = mpiWorld.getStartWorkUnit(iProc); iw <= mpiWorld.getEndWorkUnit(iProc); iw++) {
380 DetectorArray& detarray = projGlobal.getDetectorArray( iw );
381 int nDet = detarray.nDet();
382 DetectorValue* detval = detarray.detValues();
384 double viewAngle = detarray.viewAngle();
385 mpiWorld.getComm().Send(&nDet, 1, MPI::INT, iProc, 0);
386 mpiWorld.getComm().Send(&viewAngle, 1, MPI::DOUBLE, iProc, 0);
387 mpiWorld.getComm().Send(detval, nDet, MPI::FLOAT, iProc, 0);
392 for (int iw = 0; iw < mpiWorld.getMyLocalWorkUnits(); iw++) {
396 DetectorValue* detval = projLocal.getDetectorArray(iw).detValues();
398 mpiWorld.getComm().Recv(&nDet, 1, MPI::INT, 0, 0, status);
399 mpiWorld.getComm().Recv(&viewAngle, 1, MPI::DOUBLE, 0, 0, status);
400 mpiWorld.getComm().Recv(detval, nDet, MPI::FLOAT, 0, 0, status);
401 projLocal.getDetectorArray(iw).setViewAngle( viewAngle );
406 ReduceImageMPI (MPIWorld& mpiWorld, ImageFile* imLocal, ImageFile* imGlobal)
408 ImageFileArray vLocal = imLocal->getArray();
410 for (unsigned int ix = 0; ix < imLocal->nx(); ix++) {
411 void *recvbuf = NULL;
412 if (mpiWorld.getRank() == 0) {
413 ImageFileArray vGlobal = imGlobal->getArray();
414 recvbuf = vGlobal[ix];
416 mpiWorld.getComm().Reduce (vLocal[ix], recvbuf, imLocal->ny(), imLocal->getMPIDataType(), MPI::SUM, 0);
425 main (int argc, char* argv[])
430 retval = pjrec_main(argc, argv);
431 } catch (exception e) {
432 std::cerr << "Exception: " << e.what() << std::endl;
434 std::cerr << "Unknown exception" << std::endl;