+bool
+Projections::convertPolar (ImageFile& rIF, int iInterpolationID)
+{
+ unsigned int nx = rIF.nx();
+ unsigned int ny = rIF.ny();
+ ImageFileArray v = rIF.getArray();
+ ImageFileArray vImag = rIF.getImaginaryArray();
+
+ if (! v || nx == 0 || ny == 0)
+ return false;
+
+ if (m_geometry != Scanner::GEOMETRY_PARALLEL) {
+ sys_error (ERR_WARNING, "convertPolar supports Parallel only");
+ return false;
+ }
+
+ Array2d<double> adView (nx, ny);
+ Array2d<double> adDet (nx, ny);
+ double** ppdView = adView.getArray();
+ double** ppdDet = adDet.getArray();
+
+ if (! calcArrayPolarCoordinates (nx, ny, ppdView, ppdDet))
+ return false;
+
+ std::complex<double>** ppcDetValue = new std::complex<double>* [m_nView];
+ unsigned int iView;
+ for (iView = 0; iView < m_nView; iView++) {
+ ppcDetValue[iView] = new std::complex<double> [m_nDet];
+ for (unsigned int iDet = 0; iDet < m_nDet; iDet++)
+ ppcDetValue[iView][iDet] = std::complex<double>(getDetectorArray (iView).detValues()[iDet], 0);
+ }
+
+ interpolatePolar (v, vImag, nx, ny, ppcDetValue, ppdView, ppdDet, m_nView, m_nDet, iInterpolationID);
+
+ for (iView = 0; iView < m_nView; iView++)
+ delete [] ppcDetValue[iView];
+ delete [] ppcDetValue;
+
+ return true;
+}
+
+
+bool
+Projections::convertFFTPolar (ImageFile& rIF, int iInterpolationID, int iZeropad)
+{
+ unsigned int nx = rIF.nx();
+ unsigned int ny = rIF.ny();
+ ImageFileArray v = rIF.getArray();
+ if (! rIF.isComplex())
+ rIF.convertRealToComplex();
+ ImageFileArray vImag = rIF.getImaginaryArray();
+
+ if (! v || nx == 0 || ny == 0)
+ return false;
+
+ if (m_geometry != Scanner::GEOMETRY_PARALLEL) {
+ sys_error (ERR_WARNING, "convertFFTPolar supports Parallel only");
+ return false;
+ }
+
+#ifndef HAVE_FFT
+ return false;
+#else
+ Array2d<double> adView (nx, ny);
+ Array2d<double> adDet (nx, ny);
+ double** ppdView = adView.getArray();
+ double** ppdDet = adDet.getArray();
+
+ std::complex<double>** ppcDetValue = new std::complex<double>* [m_nView];
+ unsigned int iView;
+ double* pdDet = new double [m_nDet];
+ fftw_complex* pcIn = new fftw_complex [m_nDet];
+ fftw_plan plan = fftw_create_plan (m_nDet, FFTW_FORWARD, FFTW_IN_PLACE);
+
+ for (iView = 0; iView < m_nView; iView++) {
+ unsigned int iDet;
+ for (iDet = 0; iDet < m_nDet; iDet++) {
+ pcIn[iDet].re = getDetectorArray(iView).detValues()[iDet];
+ pcIn[iDet].im = 0;
+ }
+ fftw_one (plan, pcIn, NULL);
+ ppcDetValue[iView] = new std::complex<double> [m_nDet];
+ for (iDet = 0; iDet < m_nDet; iDet++)
+ ppcDetValue[iView][iDet] = std::complex<double> (pcIn[iDet].re, pcIn[iDet].im);
+ Fourier::shuffleFourierToNaturalOrder (ppcDetValue[iView], m_nDet);
+ }
+
+ fftw_destroy_plan (plan);
+ delete [] pcIn;
+
+ bool bError = calcArrayPolarCoordinates (nx, ny, ppdView, ppdDet);
+
+ if (! bError)
+ interpolatePolar (v, vImag, nx, ny, ppcDetValue, ppdView, ppdDet, m_nView, m_nDet, iInterpolationID);
+
+ for (iView = 0; iView < m_nView; iView++)
+ delete [] ppcDetValue[iView];
+ delete [] ppcDetValue;
+
+ return bError;
+#endif
+}
+
+
+bool
+Projections::calcArrayPolarCoordinates (unsigned int nx, unsigned int ny, double** ppdView, double** ppdDet)
+{
+ double xMin = -phmLen() / 2;
+ double xMax = xMin + phmLen();
+ double yMin = -phmLen() / 2;
+ double yMax = yMin + phmLen();
+
+ double xInc = (xMax - xMin) / nx; // size of cells
+ double yInc = (yMax - yMin) / ny;
+
+ int iDetCenter = (m_nDet - 1) / 2; // index refering to L=0 projection
+
+ // Calculates polar coordinates (view#, det#) for each point on phantom grid
+ double x = xMin + xInc / 2; // Rectang coords of center of pixel
+ for (unsigned int ix = 0; ix < nx; x += xInc, ix++) {
+ double y = yMin + yInc / 2;
+ for (unsigned int iy = 0; iy < ny; y += yInc, iy++) {
+ double r = ::sqrt (x * x + y * y);
+ double phi = atan2 (y, x);
+
+ if (phi >= PI) {
+ phi -= PI;
+ } else if (phi < 0) {
+ phi += PI;
+ } else
+ r = -r;
+
+ ppdView[ix][iy] = (phi - m_rotStart) / m_rotInc;
+ ppdDet[ix][iy] = (r / m_detInc) + iDetCenter;
+ }
+ }
+
+ return true;
+}
+
+void
+Projections::interpolatePolar (ImageFileArray& v, ImageFileArray& vImag,
+ unsigned int nx, unsigned int ny, std::complex<double>** ppcDetValue,
+ double** ppdView, double** ppdDet, unsigned int nView, unsigned int nDet, int iInterpolationID)
+{
+ for (unsigned int ix = 0; ix < ny; ix++) {
+ for (unsigned int iy = 0; iy < ny; iy++) {
+ if (iInterpolationID == POLAR_INTERP_NEAREST) {
+ unsigned int iView = nearest<int> (ppdView[ix][iy]);
+ unsigned int iDet = nearest<int> (ppdDet[ix][iy]);
+ if (iView == nView) {
+ iView = 0;
+ // iDet = m_nDet - iDet;
+ }
+ if (iDet >= 0 && iDet < nDet && iView >= 0 && iView < nView) {
+ v[ix][iy] = ppcDetValue[iView][iDet].real();
+ if (vImag)
+ vImag[ix][iy] = ppcDetValue[iView][iDet].imag();
+ } else {
+ sys_error (ERR_SEVERE, "Can't find projection data for ix=%d,iy=%d with radView=%f and radDet=%f",
+ ix, iy, ppdView[ix][iy], ppdDet[ix][iy]);
+ v[ix][iy] = 0;
+ }
+ } else if (iInterpolationID == POLAR_INTERP_BILINEAR) {
+ unsigned int iFloorView = static_cast<int>(ppdView[ix][iy]);
+ double dFracView = ppdView[ix][iy] - iFloorView;
+ unsigned int iFloorDet = static_cast<int>(ppdDet[ix][iy]);
+ double dFracDet = ppdDet[ix][iy] - iFloorDet;
+
+ if (iFloorDet >= 0 && iFloorView >= 0) {
+ std::complex<double> v1 = ppcDetValue[iFloorView][iFloorDet];
+ std::complex<double> v2, v3, v4;
+ if (iFloorView < nView - 1)
+ v2 = ppcDetValue[iFloorView + 1][iFloorDet];
+ else
+ v2 = ppcDetValue[0][iFloorDet];
+ if (iFloorDet < nDet - 1)
+ v4 = ppcDetValue[iFloorView][iFloorDet+1];
+ else
+ v4 = v1;
+ if (iFloorView < nView - 1 && iFloorDet < nDet - 1)
+ v3 = ppcDetValue [iFloorView+1][iFloorDet+1];
+ else if (iFloorView < nView - 1)
+ v3 = v2;
+ else
+ v3 = ppcDetValue[0][iFloorDet+1];
+ std::complex<double> vInterp = (1 - dFracView) * (1 - dFracDet) * v1 +
+ dFracView * (1 - dFracDet) * v2 + dFracView * dFracDet * v3 +
+ dFracDet * (1 - dFracView) * v4;
+ v[ix][iy] = vInterp.real();
+ if (vImag)
+ vImag[ix][iy] = vInterp.imag();
+ } else {
+ sys_error (ERR_SEVERE, "Can't find projection data for ix=%d,iy=%d with radView=%f and radDet=%f",
+ ix, iy, ppdView[ix][iy], ppdDet[ix][iy]);
+ v[ix][iy] = 0;
+ if (vImag)
+ vImag[ix][iy] = 0;
+ }
+ } else if (iInterpolationID == POLAR_INTERP_BICUBIC) {
+ v[ix][iy] =0;
+ if (vImag)
+ vImag[ix][iy] = 0;
+ }
+ }
+ }
+}
+
+
+bool
+Projections::initFromSomatomAR_STAR (int iNViews, int iNDets, unsigned char* pData, unsigned long lDataLength)
+{
+ init (iNViews, iNDets);
+ m_geometry = Scanner::GEOMETRY_EQUIANGULAR;
+ m_dFanBeamAngle = iNDets * convertDegreesToRadians (3.06976 / 60);
+ m_dFocalLength = 51;
+ m_dSourceDetectorLength = 89;
+ m_detInc = convertDegreesToRadians (3.06976 / 60);
+ m_detStart = -m_dFanBeamAngle / 2;
+ m_rotInc = TWOPI / static_cast<double>(iNViews);
+ m_rotStart = HALFPI;
+ m_dViewDiameter = sin (m_dFanBeamAngle / 2) * m_dFocalLength * 2;
+
+ if (iNDets != 1024)
+ return false;
+ bool bValid = (iNViews == 750 && lDataLength == 1560000L) || (iNViews == 950 && lDataLength == 1976000L) || (iNViews == 1500 && lDataLength == 3120000);
+ if (! bValid)
+ return false;
+
+ long lDataPos = 0;
+ for (int iv = 0; iv < iNViews; iv++) {
+ unsigned char* pArgBase = pData + lDataPos;
+ unsigned char* p = pArgBase+0;
+#ifndef WORDS_BIGENDIAN
+ SwapBytes4 (p);
+#endif
+ long lProjNumber = *reinterpret_cast<long*>(p);
+
+ p = pArgBase+20;
+#ifndef WORDS_BIGENDIAN
+ SwapBytes4 (p);
+#endif
+ long lEscale = *reinterpret_cast<long*>(p);
+
+ p = pArgBase+28;
+#ifndef WORDS_BIGENDIAN
+ SwapBytes4 (p);
+#endif
+ long lTime = *reinterpret_cast<long*>(p);
+
+ p = pArgBase + 4;
+#ifndef WORDS_BIGENDIAN
+ SwapBytes4 (p);
+#endif
+ double dAlpha = *reinterpret_cast<float*>(p) + HALFPI;
+
+ p = pArgBase+12;
+#ifndef WORDS_BIGENDIAN
+ SwapBytes4 (p);
+#endif
+ double dAlign = *reinterpret_cast<float*>(p);
+
+ p = pArgBase + 16;
+#ifndef WORDS_BIGENDIAN
+ SwapBytes4 (p);
+#endif
+ double dMaxValue = *reinterpret_cast<float*>(p);
+
+ lDataPos += 32;
+ double dEScale = pow (2.0, -lEscale);
+ double dBetaInc = convertDegreesToRadians (3.06976 / 60);
+ int iCenter = (iNDets + 1) / 2;
+
+ DetectorArray& detArray = getDetectorArray( iv );
+ detArray.setViewAngle (dAlpha);
+ DetectorValue* detval = detArray.detValues();
+
+ double dTempScale = 2294.4871 * dEScale;
+ for (int id = 0; id < iNDets; id++) {
+ int iV = pData[lDataPos+1] + 256 * pData[lDataPos];
+ if (iV > 32767) // two's complement signed conversion
+ iV = iV - 65536;
+ double dCosScale = cos ((id + 1 - iCenter) * dBetaInc);
+ detval[id] = iV / (dTempScale * dCosScale);
+ lDataPos += 2;
+ }
+ }
+
+ return true;
+}
+
+Projections*
+Projections::interpolateToParallel ()
+{
+ if (m_geometry == Scanner::GEOMETRY_PARALLEL)
+ return this;
+
+ int nDet = m_nDet;
+ int nView = m_nView;
+ Projections* pProjNew = new Projections (nView, nDet);
+ pProjNew->m_geometry = Scanner::GEOMETRY_PARALLEL;
+ pProjNew->m_dFocalLength = m_dFocalLength;
+ pProjNew->m_dSourceDetectorLength = m_dSourceDetectorLength;
+ pProjNew->m_dViewDiameter = m_dViewDiameter;
+ pProjNew->m_dFanBeamAngle = m_dFanBeamAngle;
+ pProjNew->m_calcTime = 0;
+ pProjNew->m_remark = m_remark;
+ pProjNew->m_remark += "; Interpolate to Parallel";
+ pProjNew->m_label.setLabelType (Array2dFileLabel::L_HISTORY);
+ pProjNew->m_label.setLabelString (pProjNew->m_remark);
+ pProjNew->m_label.setCalcTime (pProjNew->m_calcTime);
+ pProjNew->m_label.setDateTime (pProjNew->m_year, pProjNew->m_month, pProjNew->m_day, pProjNew->m_hour, pProjNew->m_minute, pProjNew->m_second);
+
+ pProjNew->m_rotStart = 0;
+ pProjNew->m_rotInc = PI / nView;;
+ pProjNew->m_detStart = -m_dViewDiameter / 2;
+ pProjNew->m_detInc = m_dViewDiameter / nDet;
+ if (nDet % 2 == 0) // even
+ pProjNew->m_detInc = m_dViewDiameter / (nDet - 1);
+
+ ParallelRaysums parallel (this);
+
+ double* pdThetaValuesForT = new double [pProjNew->nView()];
+ double* pdRaysumsForT = new double [pProjNew->nView()];
+
+ // interpolate to evenly spaced theta (views)
+ double dDetPos = pProjNew->m_detStart;
+ for (int iD = 0; iD < pProjNew->nDet(); iD++, dDetPos += pProjNew->m_detInc) {
+ parallel.getThetaAndRaysumsForT (iD, pdThetaValuesForT, pdRaysumsForT);
+
+ double dViewAngle = m_rotStart;
+ for (int iV = 0; iV < pProjNew->nView(); iV++, dViewAngle += pProjNew->m_rotInc) {
+ DetectorValue* detValues = pProjNew->getDetectorArray (iV).detValues();
+
+ detValues[iD] = parallel.interpolate (pdThetaValuesForT, pdRaysumsForT, pProjNew->nView(), dViewAngle);
+ }
+ }
+ delete pdThetaValuesForT;
+ delete pdRaysumsForT;
+
+ // interpolate to evenly space t (detectors)
+ double* pdOriginalDetPositions = new double [pProjNew->nDet()];
+ parallel.getDetPositions (pdOriginalDetPositions);
+
+ double* pdDetValueCopy = new double [pProjNew->nDet()];
+ double dViewAngle = m_rotStart;
+ for (int iV = 0; iV < pProjNew->nView(); iV++, dViewAngle += pProjNew->m_rotInc) {
+ DetectorArray& detArray = pProjNew->getDetectorArray (iV);
+ DetectorValue* detValues = detArray.detValues();
+ detArray.setViewAngle (dViewAngle);
+
+ for (int i = 0; i < pProjNew->nDet(); i++)
+ pdDetValueCopy[i] = detValues[i];
+
+ double dDetPos = pProjNew->m_detStart;
+ for (int iD = 0; iD < pProjNew->nDet(); iD++, dDetPos += pProjNew->m_detInc) {
+ detValues[iD] = parallel.interpolate (pdOriginalDetPositions, pdDetValueCopy, pProjNew->nDet(), dDetPos);
+ }
+ }
+ delete pdDetValueCopy;
+ delete pdOriginalDetPositions;
+
+ return pProjNew;
+}
+
+
+///////////////////////////////////////////////////////////////////////////////
+//
+// Class ParallelRaysums
+//
+// Used for converting divergent beam raysums into Parallel raysums
+//
+///////////////////////////////////////////////////////////////////////////////
+
+ParallelRaysums::ParallelRaysums (Projections* pProjections)
+: m_iNumCoordinates(0), m_iNumView(pProjections->nView()), m_iNumDet(pProjections->nDet())
+{
+ int iGeometry = pProjections->geometry();
+ double dDetInc = pProjections->detInc();
+ double dDetStart = pProjections->detStart();
+ double dFocalLength = pProjections->focalLength();
+
+ m_iNumCoordinates = m_iNumView * m_iNumDet;
+ m_vecpCoordinates.reserve (m_iNumCoordinates);
+ for (int i = 0; i < m_iNumCoordinates; i++)
+ m_vecpCoordinates[i] = new ParallelRaysumCoordinate;
+
+ int iCoordinate = 0;
+ for (int iV = 0; iV < m_iNumView; iV++) {
+ double dViewAngle = pProjections->getDetectorArray(iV).viewAngle();
+ const DetectorValue* detValues = pProjections->getDetectorArray(iV).detValues();
+
+ double dDetPos = dDetStart;
+ for (int iD = 0; iD < m_iNumDet; iD++) {
+ ParallelRaysumCoordinate* pC = m_vecpCoordinates[iCoordinate++];
+
+ if (iGeometry == Scanner::GEOMETRY_PARALLEL) {
+ pC->m_dTheta = normalizeAngle (dViewAngle);
+ pC->m_dT = dDetPos;
+ } else if (iGeometry == Scanner::GEOMETRY_EQUILINEAR) {
+ double dFanAngle = atan (dDetPos / pProjections->sourceDetectorLength());
+ pC->m_dTheta = normalizeAngle (dViewAngle + dFanAngle);
+ pC->m_dT = dFocalLength * sin(dFanAngle);
+
+ } else if (iGeometry == Scanner::GEOMETRY_EQUIANGULAR) {
+ // fan angle is same as dDetPos
+ pC->m_dTheta = normalizeAngle (dViewAngle + dDetPos);
+ pC->m_dT = dFocalLength * sin (dDetPos);
+ }
+ if (pC->m_dTheta >= PI) { // convert T/Theta to 0-PI interval
+ pC->m_dTheta -= PI;
+ pC->m_dT = -pC->m_dT - pProjections->detInc();
+ }
+ pC->m_dRaysum = detValues[iD];
+ dDetPos += dDetInc;
+ }
+ }
+}
+
+ParallelRaysums::~ParallelRaysums()
+{
+ for (int i = 0; i < m_iNumCoordinates; i++)
+ delete m_vecpCoordinates[i];
+}
+
+ParallelRaysums::CoordinateContainer&
+ParallelRaysums::getSortedByTheta()
+{
+ if (m_vecpSortedByTheta.size() == 0) {
+ m_vecpSortedByTheta.resize (m_iNumCoordinates);
+ for (int i = 0; i < m_iNumCoordinates; i++)
+ m_vecpSortedByTheta[i] = m_vecpCoordinates[i];
+ std::sort (m_vecpSortedByTheta.begin(), m_vecpSortedByTheta.end(), ParallelRaysumCoordinate::compareByTheta);
+ }
+
+ return m_vecpSortedByTheta;
+}
+
+ParallelRaysums::CoordinateContainer&
+ParallelRaysums::getSortedByT()
+{
+ if (m_vecpSortedByT.size() == 0) {
+ m_vecpSortedByT.resize (m_iNumCoordinates);
+ for (int i = 0; i < m_iNumCoordinates; i++)
+ m_vecpSortedByT[i] = m_vecpCoordinates[i];
+ std::sort (m_vecpSortedByT.begin(), m_vecpSortedByT.end(), ParallelRaysumCoordinate::compareByT);
+ }
+
+ return m_vecpSortedByT;
+}
+
+
+void
+ParallelRaysums::getLimits (double* dMinT, double* dMaxT, double* dMinTheta, double* dMaxTheta) const
+{
+ if (m_iNumCoordinates <= 0)
+ return;
+
+ *dMinT = *dMaxT = m_vecpCoordinates[0]->m_dT;
+ *dMinTheta = *dMaxTheta = m_vecpCoordinates[0]->m_dTheta;
+
+ for (int i = 0; i < m_iNumCoordinates; i++) {
+ double dT = m_vecpCoordinates[i]->m_dT;
+ double dTheta = m_vecpCoordinates[i]->m_dTheta;
+
+ if (dT < *dMinT)
+ *dMinT = dT;
+ else if (dT > *dMaxT)
+ *dMaxT = dT;
+
+ if (dTheta < *dMinTheta)
+ *dMinTheta = dTheta;
+ else if (dTheta > *dMaxTheta)
+ *dMaxTheta = dTheta;
+ }
+}
+
+void
+ParallelRaysums::getThetaAndRaysumsForT (int iTheta, double* pTheta, double* pRaysum)
+{
+ const CoordinateContainer& coordsT = getSortedByT();
+
+ int iBase = iTheta * m_iNumView;
+ for (int i = 0; i < m_iNumView; i++) {
+ int iPos = iBase + i;
+ pTheta[i] = coordsT[iPos]->m_dTheta;
+ pRaysum[i] = coordsT[iPos]->m_dRaysum;
+ }
+}
+
+void
+ParallelRaysums::getDetPositions (double* pdDetPos)
+{
+ const CoordinateContainer& coordsT = getSortedByT();
+
+ int iPos = 0;
+ for (int i = 0; i < m_iNumDet; i++) {
+ pdDetPos[i] = coordsT[iPos]->m_dT;
+ iPos += m_iNumView;
+ }
+}
+
+// locate by bisection, O(log2(n))
+double
+ParallelRaysums::interpolate (double* pdX, double* pdY, int n, double dX)
+{
+ int iLower = -1;
+ int iUpper = n;
+
+ while (iUpper - iLower > 1) {
+ int iMiddle = (iUpper + iLower) >> 1;
+ if (dX >= pdX[iMiddle])
+ iLower = iMiddle;
+ else
+ iUpper = iMiddle;
+ }
+ if (dX <= pdX[0])
+ return pdY[0];
+ else if (dX >= pdX[n-1])
+ return pdY[1];
+
+ if (iLower < 0 || iLower >= n) {
+ sys_error (ERR_SEVERE, "Coordinate out of range [locateThetaBase]");
+ return 0;
+ }
+
+ return pdY[iLower] + (pdY[iUpper] - pdY[iLower]) * ((dX - pdX[iLower]) / (pdX[iUpper] - pdX[iLower]));
+}
+