1 /*****************************************************************************
4 ** Name: projections.cpp Projection data classes
5 ** Programmer: Kevin Rosenberg
6 ** Date Started: Aug 84
8 ** This is part of the CTSim program
9 ** Copyright (C) 1983-2000 Kevin Rosenberg
11 ** $Id: projections.cpp,v 1.41 2001/01/07 23:18:13 kevin Exp $
13 ** This program is free software; you can redistribute it and/or modify
14 ** it under the terms of the GNU General Public License (version 2) as
15 ** published by the Free Software Foundation.
17 ** This program is distributed in the hope that it will be useful,
18 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
19 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20 ** GNU General Public License for more details.
22 ** You should have received a copy of the GNU General Public License
23 ** along with this program; if not, write to the Free Software
24 ** Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
25 ******************************************************************************/
29 const kuint16 Projections::m_signature = ('P'*256 + 'J');
31 const int Projections::POLAR_INTERP_INVALID = -1;
32 const int Projections::POLAR_INTERP_NEAREST = 0;
33 const int Projections::POLAR_INTERP_BILINEAR = 1;
34 const int Projections::POLAR_INTERP_BICUBIC = 2;
36 const char* Projections::s_aszInterpName[] =
43 const char* Projections::s_aszInterpTitle[] =
50 const int Projections::s_iInterpCount = sizeof(s_aszInterpName) / sizeof(char*);
54 * Projections Constructor for projections matrix storage
57 * proj = projections_create (filename, nView, nDet)
58 * Projections& proj Allocated projections structure & matrix
59 * int nView Number of rotated view
60 * int nDet Number of detectors
64 Projections::Projections (const Scanner& scanner)
67 initFromScanner (scanner);
71 Projections::Projections (const int nView, const int nDet)
77 Projections::Projections (void)
83 Projections::~Projections (void)
89 Projections::convertInterpNameToID (const char* const interpName)
91 int interpID = POLAR_INTERP_INVALID;
93 for (int i = 0; i < s_iInterpCount; i++)
94 if (strcasecmp (interpName, s_aszInterpName[i]) == 0) {
103 Projections::convertInterpIDToName (const int interpID)
105 static const char *interpName = "";
107 if (interpID >= 0 && interpID < s_iInterpCount)
108 return (s_aszInterpName[interpID]);
114 Projections::convertInterpIDToTitle (const int interpID)
116 static const char *interpTitle = "";
118 if (interpID >= 0 && interpID < s_iInterpCount)
119 return (s_aszInterpTitle[interpID]);
121 return (interpTitle);
127 Projections::init (const int nView, const int nDet)
129 m_label.setLabelType (Array2dFileLabel::L_HISTORY);
134 time_t t = time (NULL);
135 tm* lt = localtime (&t);
136 m_year = lt->tm_year;
137 m_month = lt->tm_mon;
139 m_hour = lt->tm_hour;
140 m_minute = lt->tm_min;
141 m_second = lt->tm_sec;
145 Projections::initFromScanner (const Scanner& scanner)
147 m_label.setLabelType (Array2dFileLabel::L_HISTORY);
149 init (scanner.nView(), scanner.nDet());
151 m_phmLen = scanner.phmLen();
152 m_rotInc = scanner.rotInc();
153 m_detInc = scanner.detInc();
154 m_geometry = scanner.geometry();
155 m_focalLength = scanner.focalLength();
156 m_fieldOfView = scanner.fieldOfView();
158 m_detStart = -(scanner.detLen() / 2);
162 Projections::setNView (int nView) // used by MPI to reduce # of views
165 init (nView, m_nDet);
172 Projections::newProjData (void)
175 sys_error(ERR_WARNING, "m_projData != NULL [newProjData]");
177 if (m_nView > 0 && m_nDet) {
178 m_projData = new DetectorArray* [m_nView];
180 for (int i = 0; i < m_nView; i++)
181 m_projData[i] = new DetectorArray (m_nDet);
187 * projections_free Free memory allocated to projections
190 * projections_free(proj)
191 * Projections& proj Projectionss to be deallocated
195 Projections::deleteProjData (void)
197 if (m_projData != NULL) {
198 for (int i = 0; i < m_nView; i++)
199 delete m_projData[i];
208 * Projections::headerWwrite Write data header for projections file
213 Projections::headerWrite (fnetorderstream& fs)
215 kuint16 _hsize = m_headerSize;
216 kuint16 _signature = m_signature;
217 kuint32 _nView = m_nView;
218 kuint32 _nDet = m_nDet;
219 kuint32 _geom = m_geometry;
220 kuint16 _remarksize = m_remark.length();
221 kuint16 _year = m_year;
222 kuint16 _month = m_month;
223 kuint16 _day = m_day;
224 kuint16 _hour = m_hour;
225 kuint16 _minute = m_minute;
226 kuint16 _second = m_second;
228 kfloat64 _calcTime = m_calcTime;
229 kfloat64 _rotStart = m_rotStart;
230 kfloat64 _rotInc = m_rotInc;
231 kfloat64 _detStart = m_detStart;
232 kfloat64 _detInc = m_detInc;
233 kfloat64 _phmLen = m_phmLen;
234 kfloat64 _fieldOfView = m_fieldOfView;
235 kfloat64 _focalLength = m_focalLength;
241 fs.writeInt16 (_hsize);
242 fs.writeInt16 (_signature);
243 fs.writeInt32 (_nView);
244 fs.writeInt32 (_nDet);
245 fs.writeInt32 (_geom);
246 fs.writeFloat64 (_calcTime);
247 fs.writeFloat64 (_rotStart);
248 fs.writeFloat64 (_rotInc);
249 fs.writeFloat64 (_detStart);
250 fs.writeFloat64 (_detInc);
251 fs.writeFloat64 (_phmLen);
252 fs.writeFloat64 (_focalLength);
253 fs.writeFloat64 (_fieldOfView);
254 fs.writeInt16 (_year);
255 fs.writeInt16 (_month);
256 fs.writeInt16 (_day);
257 fs.writeInt16 (_hour);
258 fs.writeInt16 (_minute);
259 fs.writeInt16 (_second);
260 fs.writeInt16 (_remarksize);
261 fs.write (m_remark.c_str(), _remarksize);
263 m_headerSize = fs.tellp();
264 _hsize = m_headerSize;
266 fs.writeInt16 (_hsize);
274 * projections_read_header Read data header for projections file
278 Projections::headerRead (fnetorderstream& fs)
280 kuint16 _hsize, _signature, _year, _month, _day, _hour, _minute, _second, _remarksize = 0;
281 kuint32 _nView, _nDet, _geom;
282 kfloat64 _calcTime, _rotStart, _rotInc, _detStart, _detInc, _phmLen, _focalLength, _fieldOfView;
288 fs.readInt16 (_hsize);
289 fs.readInt16 (_signature);
290 fs.readInt32 (_nView);
291 fs.readInt32 (_nDet);
292 fs.readInt32 (_geom);
293 fs.readFloat64 (_calcTime);
294 fs.readFloat64 (_rotStart);
295 fs.readFloat64 (_rotInc);
296 fs.readFloat64 (_detStart);
297 fs.readFloat64 (_detInc);
298 fs.readFloat64 (_phmLen);
299 fs.readFloat64 (_focalLength);
300 fs.readFloat64 (_fieldOfView);
301 fs.readInt16 (_year);
302 fs.readInt16 (_month);
304 fs.readInt16 (_hour);
305 fs.readInt16 (_minute);
306 fs.readInt16 (_second);
307 fs.readInt16 (_remarksize);
310 sys_error (ERR_SEVERE, "Error reading header information , _remarksize=%d [projections_read_header]", _remarksize);
314 if (_signature != m_signature) {
315 sys_error (ERR_SEVERE, "File %s does not have a valid projection file signature", m_filename.c_str());
319 char* pszRemarkStorage = new char [_remarksize+1];
320 fs.read (pszRemarkStorage, _remarksize);
322 sys_error (ERR_SEVERE, "Error reading remark, _remarksize = %d", _remarksize);
325 pszRemarkStorage[_remarksize] = 0;
326 m_remark = pszRemarkStorage;
327 delete pszRemarkStorage;
329 off_t _hsizeread = fs.tellg();
330 if (!fs || _hsizeread != _hsize) {
331 sys_error (ERR_WARNING, "File header size read %ld != file header size stored %ld [read_projections_header]\n_remarksize=%ld", (long int) _hsizeread, _hsize, _remarksize);
335 m_headerSize = _hsize;
339 m_calcTime = _calcTime;
340 m_rotStart = _rotStart;
342 m_detStart = _detStart;
345 m_focalLength = _focalLength;
346 m_fieldOfView = _fieldOfView;
354 m_label.setLabelType (Array2dFileLabel::L_HISTORY);
355 m_label.setLabelString (m_remark);
356 m_label.setCalcTime (m_calcTime);
357 m_label.setDateTime (m_year, m_month, m_day, m_hour, m_minute, m_second);
363 Projections::read (const std::string& filename)
365 return read (filename.c_str());
370 Projections::read (const char* filename)
372 m_filename = filename;
374 frnetorderstream fileRead (m_filename.c_str(), std::ios::in | std::ios::binary);
376 frnetorderstream fileRead (m_filename.c_str(), std::ios::in | std::ios::binary | std::ios::nocreate);
382 if (! headerRead (fileRead))
388 for (int i = 0; i < m_nView; i++) {
389 if (! detarrayRead (fileRead, *m_projData[i], i))
399 Projections::copyViewData (const std::string& filename, std::ostream& os, int startView, int endView)
401 return copyViewData (filename.c_str(), os, startView, endView);
405 Projections::copyViewData (const char* const filename, std::ostream& os, int startView, int endView)
407 frnetorderstream is (filename, ios::in | ios::binary);
408 kuint16 sizeHeader, signature;
409 kuint32 _nView, _nDet;
411 is.readInt16 (sizeHeader);
412 is.readInt16 (signature);
413 is.readInt32 (_nView);
414 is.readInt32 (_nDet);
418 if (signature != m_signature) {
419 sys_error (ERR_FATAL, "Illegal signature in projection file %s", filename);
425 if (startView > nView - 1)
427 if (endView < 0 || endView > nView - 1)
430 if (startView > endView) { // swap if start > end
431 int tempView = endView;
433 startView = tempView;
436 int sizeView = 8 /* view_angle */ + 4 /* nDet */ + (4 * nDet);
437 unsigned char* pViewData = new unsigned char [sizeView];
439 for (int i = startView; i <= endView; i++) {
440 is.seekg (sizeHeader + i * sizeView);
441 is.read (reinterpret_cast<char*>(pViewData), sizeView);
442 os.write (reinterpret_cast<char*>(pViewData), sizeView);
443 if (is.fail() || os.fail())
449 sys_error (ERR_FATAL, "Error reading projection file");
451 sys_error (ERR_FATAL, "Error writing projection file");
453 return (! (is.fail() | os.fail()));
457 Projections::copyHeader (const std::string& filename, std::ostream& os)
459 return copyHeader (filename.c_str(), os);
463 Projections::copyHeader (const char* const filename, std::ostream& os)
465 frnetorderstream is (filename, std::ios::in | std::ios::binary);
466 kuint16 sizeHeader, signature;
467 is.readInt16 (sizeHeader);
468 is.readInt16 (signature);
470 if (signature != m_signature) {
471 sys_error (ERR_FATAL, "Illegal signature in projection file %s", filename);
475 unsigned char* pHdrData = new unsigned char [sizeHeader];
476 is.read (reinterpret_cast<char*>(pHdrData), sizeHeader);
478 sys_error (ERR_FATAL, "Error reading header");
482 os.write (reinterpret_cast<char*>(pHdrData), sizeHeader);
484 sys_error (ERR_FATAL, "Error writing header");
492 Projections::write (const std::string& filename)
494 return write (filename.c_str());
498 Projections::write (const char* filename)
500 frnetorderstream fs (filename, std::ios::out | std::ios::binary | std::ios::trunc | std::ios::ate);
501 m_filename = filename;
503 sys_error (ERR_SEVERE, "Error opening file %s for output [projections_create]", filename);
507 if (! headerWrite (fs))
510 if (m_projData != NULL) {
511 for (int i = 0; i < m_nView; i++) {
512 if (! detarrayWrite (fs, *m_projData[i], i))
525 * detarrayRead Read a Detector Array structure from the disk
528 * detarrayRead (proj, darray, view_num)
529 * DETARRAY *darray Detector array storage location to be filled
530 * int view_num View number to read
534 Projections::detarrayRead (fnetorderstream& fs, DetectorArray& darray, const int iview)
536 const int detval_bytes = darray.nDet() * sizeof(kfloat32);
537 const int detheader_bytes = sizeof(kfloat64) /* view_angle */ + sizeof(kint32) /* nDet */;
538 const int view_bytes = detheader_bytes + detval_bytes;
539 const off_t start_data = m_headerSize + (iview * view_bytes);
540 DetectorValue* detval_ptr = darray.detValues();
544 fs.seekg (start_data);
546 fs.readFloat64 (view_angle);
548 darray.setViewAngle (view_angle);
549 // darray.setNDet ( nDet);
551 for (unsigned int i = 0; i < nDet; i++) {
553 fs.readFloat32 (detval);
554 detval_ptr[i] = detval;
564 * detarrayWrite Write detector array data to the disk
567 * detarrayWrite (darray, view_num)
568 * DETARRAY *darray Detector array data to be written
569 * int view_num View number to write
572 * This routine writes the detarray data from the disk sequentially to
573 * the file that was opened with open_projections(). Data is written in
578 Projections::detarrayWrite (fnetorderstream& fs, const DetectorArray& darray, const int iview)
580 const int detval_bytes = darray.nDet() * sizeof(float);
581 const int detheader_bytes = sizeof(kfloat64) /* view_angle */ + sizeof(kint32) /* nDet */;
582 const int view_bytes = detheader_bytes + detval_bytes;
583 const off_t start_data = m_headerSize + (iview * view_bytes);
584 const DetectorValue* const detval_ptr = darray.detValues();
585 kfloat64 view_angle = darray.viewAngle();
586 kuint32 nDet = darray.nDet();
588 fs.seekp (start_data);
590 sys_error (ERR_SEVERE, "Error seeking detectory array [detarrayWrite]");
594 fs.writeFloat64 (view_angle);
595 fs.writeInt32 (nDet);
597 for (unsigned int i = 0; i < nDet; i++) {
598 kfloat32 detval = detval_ptr[i];
599 fs.writeFloat32 (detval);
609 * printProjectionData Print projections data
612 * printProjectionData ()
616 Projections::printProjectionData ()
618 printProjectionData (0, nView() - 1);
622 Projections::printProjectionData (int startView, int endView)
624 printf("Projections Data\n\n");
625 printf("Description: %s\n", m_remark.c_str());
626 printf("Geometry: %s\n", Scanner::convertGeometryIDToName (m_geometry));
627 printf("nView = %8d nDet = %8d\n", m_nView, m_nDet);
628 printf("focalLength = %8.4f fieldOfView = %8.4f\n", m_focalLength, m_fieldOfView);
629 printf("rotStart = %8.4f rotInc = %8.4f\n", m_rotStart, m_rotInc);
630 printf("detStart = %8.4f detInc = %8.4f\n", m_detStart, m_detInc);
631 if (m_projData != NULL) {
634 if (startView > m_nView - 1)
635 startView = m_nView - 1;
636 if (endView > m_nView - 1)
637 endView = m_nView - 1;
638 for (int ir = startView; ir <= endView - 1; ir++) {
639 printf("View %d: angle %f\n", ir, m_projData[ir]->viewAngle());
640 DetectorValue* detval = m_projData[ir]->detValues();
641 for (int id = 0; id < m_projData[ir]->nDet(); id++)
642 printf("%8.4f ", detval[id]);
649 Projections::printScanInfo (std::ostringstream& os) const
651 os << "Number of detectors: " << m_nDet << "\n";
652 os << " Number of views: " << m_nView<< "\n";
653 os << " Remark: " << m_remark.c_str()<< "\n";
654 os << " Geometry: " << Scanner::convertGeometryIDToName (m_geometry)<< "\n";
655 os << " Focal Length: " << m_focalLength<< "\n";
656 os << " Field Of View: " << m_fieldOfView<< "\n";
657 os << " phmLen: " << m_phmLen<< "\n";
658 os << " detStart: " << m_detStart<< "\n";
659 os << " detInc: " << m_detInc<< "\n";
660 os << " rotStart: " << m_rotStart<< "\n";
661 os << " rotInc: " << m_rotInc<< "\n";
666 Projections::convertPolar (ImageFile& rIF, int iInterpolationID)
668 unsigned int nx = rIF.nx();
669 unsigned int ny = rIF.ny();
670 ImageFileArray v = rIF.getArray();
671 ImageFileArray vImag = rIF.getImaginaryArray();
673 if (! v || nx == 0 || ny == 0)
676 Array2d<double> adView (nx, ny);
677 Array2d<double> adDet (nx, ny);
678 double** ppdView = adView.getArray();
679 double** ppdDet = adDet.getArray();
681 calcArrayPolarCoordinates (nx, ny, ppdView, ppdDet);
683 std::complex<double>** ppcDetValue = new std::complex<double>* [m_nView];
684 for (unsigned int iView = 0; iView < m_nView; iView++) {
685 ppcDetValue[iView] = new std::complex<double> [m_nDet];
686 for (unsigned int iDet = 0; iDet < m_nDet; iDet++)
687 ppcDetValue[iView][iDet] = std::complex<double>(getDetectorArray (iView).detValues()[iDet], 0);
690 interpolatePolar (v, vImag, nx, ny, ppcDetValue, ppdView, ppdDet, m_nView, m_nDet, iInterpolationID);
692 for (iView = 0; iView < m_nView; iView++)
693 delete [] ppcDetValue[iView];
694 delete [] ppcDetValue;
701 Projections::convertFFTPolar (ImageFile& rIF, int iInterpolationID, int iZeropad)
703 unsigned int nx = rIF.nx();
704 unsigned int ny = rIF.ny();
705 ImageFileArray v = rIF.getArray();
706 if (! rIF.isComplex())
707 rIF.convertRealToComplex();
708 ImageFileArray vImag = rIF.getImaginaryArray();
710 if (! v || nx == 0 || ny == 0)
716 Array2d<double> adView (nx, ny);
717 Array2d<double> adDet (nx, ny);
718 double** ppdView = adView.getArray();
719 double** ppdDet = adDet.getArray();
721 std::complex<double>** ppcDetValue = new std::complex<double>* [m_nView];
723 double* pdDet = new double [m_nDet];
724 fftw_complex* pcIn = new fftw_complex [m_nDet];
725 fftw_plan plan = fftw_create_plan (m_nDet, FFTW_FORWARD, FFTW_IN_PLACE);
727 for (iView = 0; iView < m_nView; iView++) {
729 for (iDet = 0; iDet < m_nDet; iDet++) {
730 pcIn[iDet].re = getDetectorArray(iView).detValues()[iDet];
733 fftw_one (plan, pcIn, NULL);
734 ppcDetValue[iView] = new std::complex<double> [m_nDet];
735 for (iDet = 0; iDet < m_nDet; iDet++)
736 ppcDetValue[iView][iDet] = std::complex<double> (pcIn[iDet].re, pcIn[iDet].im);
737 Fourier::shuffleFourierToNaturalOrder (ppcDetValue[iView], m_nDet);
740 fftw_destroy_plan (plan);
743 calcArrayPolarCoordinates (nx, ny, ppdView, ppdDet);
745 interpolatePolar (v, vImag, nx, ny, ppcDetValue, ppdView, ppdDet, m_nView, m_nDet, iInterpolationID);
747 for (iView = 0; iView < m_nView; iView++)
748 delete [] ppcDetValue[iView];
749 delete [] ppcDetValue;
757 Projections::calcArrayPolarCoordinates (unsigned int nx, unsigned int ny, double** ppdView, double** ppdDet)
759 double xMin = -m_phmLen / 2;
760 double xMax = xMin + m_phmLen;
761 double yMin = -m_phmLen / 2;
762 double yMax = yMin + m_phmLen;
764 double xInc = (xMax - xMin) / nx; // size of cells
765 double yInc = (yMax - yMin) / ny;
767 int iDetCenter = (m_nDet - 1) / 2; // index refering to L=0 projection
769 if (m_geometry != Scanner::GEOMETRY_PARALLEL) {
770 sys_error (ERR_WARNING, "convertPolar supports Parallel only");
774 // Calculates polar coordinates (view#, det#) for each point on phantom grid
775 double x = xMin + xInc / 2; // Rectang coords of center of pixel
776 for (unsigned int ix = 0; ix < nx; x += xInc, ix++) {
777 double y = yMin + yInc / 2;
778 for (unsigned int iy = 0; iy < ny; y += yInc, iy++) {
779 double r = ::sqrt (x * x + y * y);
780 double phi = atan2 (y, x);
784 } else if (phi < 0) {
789 ppdView[ix][iy] = (phi - m_rotStart) / m_rotInc;
790 ppdDet[ix][iy] = (r / m_detInc) + iDetCenter;
796 Projections::interpolatePolar (ImageFileArray& v, ImageFileArray& vImag,
797 unsigned int nx, unsigned int ny, std::complex<double>** ppcDetValue,
798 double** ppdView, double** ppdDet, unsigned int nView, unsigned int nDet, int iInterpolationID)
800 for (unsigned int ix = 0; ix < ny; ix++) {
801 for (unsigned int iy = 0; iy < ny; iy++) {
802 if (iInterpolationID == POLAR_INTERP_NEAREST) {
803 int iView = nearest<int> (ppdView[ix][iy]);
804 int iDet = nearest<int> (ppdDet[ix][iy]);
805 if (iView == nView) {
807 // iDet = m_nDet - iDet;
809 if (iDet >= 0 && iDet < nDet && iView >= 0 && iView < nView) {
810 v[ix][iy] = ppcDetValue[iView][iDet].real();
812 vImag[ix][iy] = ppcDetValue[iView][iDet].imag();
814 sys_error (ERR_SEVERE, "Can't find projection data for ix=%d,iy=%d with radView=%f and radDet=%f",
815 ix, iy, ppdView[ix][iy], ppdDet[ix][iy]);
818 } else if (iInterpolationID == POLAR_INTERP_BILINEAR) {
819 int iFloorView = static_cast<int>(ppdView[ix][iy]);
820 double dFracView = ppdView[ix][iy] - iFloorView;
821 int iFloorDet = static_cast<int>(ppdDet[ix][iy]);
822 double dFracDet = ppdDet[ix][iy] - iFloorDet;
824 if (iFloorDet >= 0 && iFloorView >= 0) {
825 std::complex<double> v1 = ppcDetValue[iFloorView][iFloorDet];
826 std::complex<double> v2, v3, v4;
827 if (iFloorView < nView - 1)
828 v2 = ppcDetValue[iFloorView + 1][iFloorDet];
830 v2 = ppcDetValue[0][iFloorDet];
831 if (iFloorDet < nDet - 1)
832 v4 = ppcDetValue[iFloorView][iFloorDet+1];
835 if (iFloorView < nView - 1 && iFloorDet < nDet - 1)
836 v3 = ppcDetValue [iFloorView+1][iFloorDet+1];
837 else if (iFloorView < nView - 1)
840 v3 = ppcDetValue[0][iFloorDet+1];
841 std::complex<double> vInterp = (1 - dFracView) * (1 - dFracDet) * v1 +
842 dFracView * (1 - dFracDet) * v2 + dFracView * dFracDet * v3 +
843 dFracDet * (1 - dFracView) * v4;
844 v[ix][iy] = vInterp.real();
846 vImag[ix][iy] = vInterp.imag();
848 sys_error (ERR_SEVERE, "Can't find projection data for ix=%d,iy=%d with radView=%f and radDet=%f",
849 ix, iy, ppdView[ix][iy], ppdDet[ix][iy]);
854 } else if (iInterpolationID == POLAR_INTERP_BICUBIC) {