void hsMatrix44::MakeCameraMatrices(const hsPoint3& from, const hsPoint3& at, const hsVector3& up, hsMatrix44& worldToCamera, hsMatrix44& cameraToWorld) { hsVector3 dirZ(&at, &from); hsVector3 dirX(dirZ % up); dirX.Normalize(); hsVector3 dirY(dirX % dirZ); dirY.Normalize(); worldToCamera.Reset(false); cameraToWorld.Reset(false); int i; for( i = 0; i < 3; i++ ) { worldToCamera.fMap[0][i] = dirX[i]; worldToCamera.fMap[1][i] = dirY[i]; worldToCamera.fMap[2][i] = dirZ[i]; cameraToWorld.fMap[i][0] = dirX[i]; cameraToWorld.fMap[i][1] = dirY[i]; cameraToWorld.fMap[i][2] = dirZ[i]; } hsPoint3 trans = -from; worldToCamera.fMap[0][3] = dirX.InnerProduct(trans); worldToCamera.fMap[1][3] = dirY.InnerProduct(trans); worldToCamera.fMap[2][3] = dirZ.InnerProduct(trans); cameraToWorld.fMap[0][3] = from.fX; cameraToWorld.fMap[1][3] = from.fY; cameraToWorld.fMap[2][3] = from.fZ; }
bool ContactDistanceCalc<BasicTraits,BVOL,Metric>::InitDouble (GroupType* g0, const TransformType& m0, const TransformType& f0, GroupType* g1, const TransformType& m1, const TransformType& f1) { // transformation matrix model1 to model0 // m0^(-1) * m1 if (!m_M1ToM0.invertFrom(m0)) { return false; } m_M1ToM0.mult(m1); // m1^(-1) * m0 m_M0ToM1.invertFrom(m_M1ToM0); m_M0 = m0; u32 k, kk; VectorClass trans(m_M1ToM0[3][0], m_M1ToM0[3][1], m_M1ToM0[3][2]); VectorClass dirX(m_M1ToM0[0][0], m_M1ToM0[0][1], m_M1ToM0[0][2]); VectorClass dirY(m_M1ToM0[1][0], m_M1ToM0[1][1], m_M1ToM0[1][2]); VectorClass dirZ(m_M1ToM0[2][0], m_M1ToM0[2][1], m_M1ToM0[2][2]); for (k=0; k<BVOL::Size; ++k) { m_proj[k][0] = BVOL::getDirection()[k].dot(dirX); m_proj[k][1] = BVOL::getDirection()[k].dot(dirY); m_proj[k][2] = BVOL::getDirection()[k].dot(dirZ); m_M1Offset[k] = BVOL::getDirection()[k].dot(trans); } #if 0 for (k=0, kk=BVOL::Size; k<BVOL::Size; ++k, ++kk) { m_M1ToM0.mult(BVOL::getDirection()[k], m_M1Direction[k]); m_M1Direction[kk] = -m_M1Direction[k]; } #endif m_scale = m_proj[0].length(); u32 i; Real value, maxValue, sx, sy; for (k=0, kk=BVOL::Size; k<BVOL::Size; ++k, ++kk) { // calc remapping m_perm m_perm[k] = 0; maxValue = m_proj[k].dot(BVOL::getDirection()[0]); for (i=1; i<2*BVOL::Size; ++i) { if ((value=m_proj[k].dot(BVOL::getDirection()[i])) > maxValue) { maxValue = value; m_perm[k] = i; } } if (m_perm[k] < BVOL::Size) { m_perm[kk] = m_perm[k]+BVOL::Size; } else { m_perm[kk] = m_perm[k]-BVOL::Size; } maxValue /= m_scale; // mask for (m_mask[k]=0; m_mask[k]<OccTableHighestBit; ++m_mask[k]) { if (maxValue >= BVOL::unitDopAngleTable()[m_mask[k]]) { break; } } m_mask[kk] = m_mask[k]; #ifdef GV_WITH_SUBCONES // calc ring section index m_submask[k],m_submask[kk] dirZ = BVOL::getDirection()[m_perm[k]]-(maxValue*m_scale)*m_proj[k]; m_M1ToM0.mult(BVOL::BVolGeometry::getFrameX()[m_perm[k]], dirX); //dirX -= dirX.dot(BVOL::getDirection()[k])*M1Direction[m_perm[k]]; //dirX = BVOL::BVolGeometry::getFrameX()[k]; m_M1ToM0.mult(BVOL::BVolGeometry::getFrameY()[m_perm[k]], dirY); //dirY -= dirY.dot(BVOL::getDirection()[k])*M1Direction[m_perm[k]]; //dirY = BVOL::BVolGeometry::getFrameY()[k]; sx = dirZ.dot(dirX)/(dirZ.length()*dirX.length()); sy = dirZ.dot(dirY)/(dirZ.length()*dirY.length()); //std::cout << "k=" << k << ": (" << sx << ", " << sy << ")" << std::endl; m_submask[k] = (sx < 0 ? 2 : 0) + (sx < 0 && sy >= 0 ? 1 : 0) + (sx >= 0 && sy < 0 ? 1 : 0); assert(m_submask[k] < 4); if (m_submask[k] < 2) { m_submask[kk] = m_submask[k]+2; } else { m_submask[kk] = m_submask[k]-2; } assert(m_submask[kk] < 4); #endif } m_intersect = false; return true; }
virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const { notice()<<"Reading DICOM file "<<file<<" using DCMTK"<<std::endl; std::string ext = osgDB::getLowerCaseFileExtension(file); if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED; std::string fileName = file; if (ext=="dicom") { fileName = osgDB::getNameLessExtension(file); } fileName = osgDB::findDataFile( fileName, options ); if (fileName.empty()) return ReadResult::FILE_NOT_FOUND; Files files; osgDB::FileType fileType = osgDB::fileType(fileName); if (fileType==osgDB::DIRECTORY) { getDicomFilesInDirectory(fileName, files); } else { #if 1 files.push_back(fileName); #else if (!getDicomFilesInDirectory(osgDB::getFilePath(fileName), files)) { files.push_back(fileName); } #endif } if (files.empty()) { return ReadResult::FILE_NOT_FOUND; } osg::ref_ptr<osg::RefMatrix> matrix = new osg::RefMatrix; osg::ref_ptr<osg::Image> image; unsigned int imageNum = 0; EP_Representation pixelRep = EPR_Uint8; int numPlanes = 0; GLenum pixelFormat = 0; GLenum dataType = 0; unsigned int pixelSize = 0; typedef std::list<FileInfo> FileInfoList; FileInfoList fileInfoList; typedef std::map<double, FileInfo> DistanceFileInfoMap; typedef std::map<osg::Vec3d, DistanceFileInfoMap> OrientationFileInfoMap; OrientationFileInfoMap orientationFileInfoMap; unsigned int totalNumSlices = 0; for(Files::iterator itr = files.begin(); itr != files.end(); ++itr) { DcmFileFormat fileformat; OFCondition status = fileformat.loadFile((*itr).c_str()); if(!status.good()) return ReadResult::ERROR_IN_READING_FILE; FileInfo fileInfo; fileInfo.filename = *itr; double pixelSize_y = 1.0; double pixelSize_x = 1.0; double sliceThickness = 1.0; double imagePositionPatient[3] = {0, 0, 0}; double imageOrientationPatient[6] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0 }; Uint16 numOfSlices = 1; double value = 0.0; if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, value,0).good()) { pixelSize_y = value; fileInfo.matrix(1,1) = pixelSize_y; } if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, value,1).good()) { pixelSize_x = value; fileInfo.matrix(0,0) = pixelSize_x; } // Get slice thickness if (fileformat.getDataset()->findAndGetFloat64(DCM_SliceThickness, value).good()) { sliceThickness = value; notice()<<"sliceThickness = "<<sliceThickness<<std::endl; fileInfo.sliceThickness = sliceThickness; } notice()<<"tagExistsWithValue(DCM_NumberOfFrames)="<<fileformat.getDataset()->tagExistsWithValue(DCM_NumberOfFrames)<<std::endl; notice()<<"tagExistsWithValue(DCM_NumberOfSlices)="<<fileformat.getDataset()->tagExistsWithValue(DCM_NumberOfSlices)<<std::endl; Uint32 numFrames; if (fileformat.getDataset()->findAndGetUint32(DCM_NumberOfFrames, numFrames).good()) { fileInfo.numSlices = numFrames; notice()<<"Read number of frames = "<<numFrames<<std::endl; } OFString numFramesStr; if (fileformat.getDataset()->findAndGetOFString(DCM_NumberOfFrames, numFramesStr).good()) { fileInfo.numSlices = atoi(numFramesStr.c_str()); notice()<<"Read number of frames = "<<numFramesStr<<std::endl; } if (fileformat.getDataset()->findAndGetUint16(DCM_NumberOfFrames, numOfSlices).good()) { fileInfo.numSlices = numOfSlices; notice()<<"Read number of frames = "<<numOfSlices<<std::endl; } if (fileformat.getDataset()->findAndGetUint16(DCM_NumberOfSlices, numOfSlices).good()) { fileInfo.numSlices = numOfSlices; notice()<<"Read number of slices = "<<numOfSlices<<std::endl; } // patient position for(int i=0; i<3; ++i) { if (fileformat.getDataset()->findAndGetFloat64(DCM_ImagePositionPatient, imagePositionPatient[i],i).good()) { notice()<<"Read DCM_ImagePositionPatient["<<i<<"], "<<imagePositionPatient[i]<<std::endl; } else { notice()<<"Have not read DCM_ImagePositionPatient["<<i<<"]"<<std::endl; } } //notice()<<"imagePositionPatient[2]="<<imagePositionPatient[2]<<std::endl; fileInfo.matrix.setTrans(imagePositionPatient[0],imagePositionPatient[1],imagePositionPatient[2]); for(int i=0; i<6; ++i) { double value = 0.0; if (fileformat.getDataset()->findAndGetFloat64(DCM_ImageOrientationPatient, value,i).good()) { imageOrientationPatient[i] = value; notice()<<"Read imageOrientationPatient["<<i<<"], "<<imageOrientationPatient[i]<<std::endl; } else { notice()<<"Have not read imageOrientationPatient["<<i<<"]"<<std::endl; } } osg::Vec3d dirX(imageOrientationPatient[0],imageOrientationPatient[1],imageOrientationPatient[2]); osg::Vec3d dirY(imageOrientationPatient[3],imageOrientationPatient[4],imageOrientationPatient[5]); osg::Vec3d dirZ = dirX ^ dirY; dirZ.normalize(); dirX *= pixelSize_x; dirY *= pixelSize_y; fileInfo.matrix(0,0) = dirX[0]; fileInfo.matrix(1,0) = dirX[1]; fileInfo.matrix(2,0) = dirX[2]; fileInfo.matrix(0,1) = dirY[0]; fileInfo.matrix(1,1) = dirY[1]; fileInfo.matrix(2,1) = dirY[2]; fileInfo.matrix(0,2) = dirZ[0]; fileInfo.matrix(1,2) = dirZ[1]; fileInfo.matrix(2,2) = dirZ[2]; fileInfo.distance = dirZ * (osg::Vec3d(0.0,0.0,0.0)*fileInfo.matrix); notice()<<"dirX = "<<dirX<<std::endl; notice()<<"dirY = "<<dirY<<std::endl; notice()<<"dirZ = "<<dirZ<<std::endl; notice()<<"matrix = "<<fileInfo.matrix<<std::endl; notice()<<"pos = "<<osg::Vec3d(0.0,0.0,0.0)*fileInfo.matrix<<std::endl; notice()<<"dist = "<<fileInfo.distance<<std::endl; notice()<<std::endl; (orientationFileInfoMap[dirZ])[fileInfo.distance] = fileInfo; totalNumSlices += fileInfo.numSlices; } if (orientationFileInfoMap.empty()) return 0; typedef std::map<double, FileInfo> DistanceFileInfoMap; typedef std::map<osg::Vec3d, DistanceFileInfoMap> OrientationFileInfoMap; for(OrientationFileInfoMap::iterator itr = orientationFileInfoMap.begin(); itr != orientationFileInfoMap.end(); ++itr) { notice()<<"Orientation = "<<itr->first<<std::endl; DistanceFileInfoMap& dfim = itr->second; for(DistanceFileInfoMap::iterator ditr = dfim.begin(); ditr != dfim.end(); ++ditr) { FileInfo& fileInfo = ditr->second; notice()<<" d = "<<fileInfo.distance<<" "<<fileInfo.filename<<std::endl; } } DistanceFileInfoMap& dfim = orientationFileInfoMap.begin()->second; if (dfim.empty()) return 0; double totalDistance = 0.0; if (dfim.size()>1) { totalDistance = fabs(dfim.rbegin()->first - dfim.begin()->first); } else { totalDistance = dfim.begin()->second.sliceThickness * double(dfim.begin()->second.numSlices); } notice()<<"Total Distance including ends "<<totalDistance<<std::endl; double averageThickness = totalNumSlices<=1 ? 1.0 : totalDistance / double(totalNumSlices-1); notice()<<"Average thickness "<<averageThickness<<std::endl; for(DistanceFileInfoMap::iterator ditr = dfim.begin(); ditr != dfim.end(); ++ditr) { FileInfo& fileInfo = ditr->second; std::auto_ptr<DicomImage> dcmImage(new DicomImage(fileInfo.filename.c_str())); if (dcmImage.get()) { if (dcmImage->getStatus()==EIS_Normal) { // get the pixel data const DiPixel* pixelData = dcmImage->getInterData(); if(!pixelData) { warning()<<"Error: no data in DicomImage object."<<std::endl; return ReadResult::ERROR_IN_READING_FILE; } osg::ref_ptr<osg::Image> imageAdapter = new osg::Image; EP_Representation curr_pixelRep; int curr_numPlanes; GLenum curr_pixelFormat; GLenum curr_dataType; unsigned int curr_pixelSize; // create the new image convertPixelTypes(pixelData, curr_pixelRep, curr_numPlanes, curr_dataType, curr_pixelFormat, curr_pixelSize); imageAdapter->setImage(dcmImage->getWidth(), dcmImage->getHeight(), dcmImage->getFrameCount(), curr_pixelFormat, curr_pixelFormat, curr_dataType, (unsigned char*)(pixelData->getData()), osg::Image::NO_DELETE); if (!image) { pixelRep = curr_pixelRep; numPlanes = curr_numPlanes; dataType = curr_dataType; pixelFormat = curr_pixelFormat; pixelSize = curr_pixelSize; (*matrix)(0,0) = fileInfo.matrix(0,0); (*matrix)(1,0) = fileInfo.matrix(1,0); (*matrix)(2,0) = fileInfo.matrix(2,0); (*matrix)(0,1) = fileInfo.matrix(0,1); (*matrix)(1,1) = fileInfo.matrix(1,1); (*matrix)(2,1) = fileInfo.matrix(2,1); (*matrix)(0,2) = fileInfo.matrix(0,2) * averageThickness; (*matrix)(1,2) = fileInfo.matrix(1,2) * averageThickness; (*matrix)(2,2) = fileInfo.matrix(2,2) * averageThickness; image = new osg::Image; image->setUserData(matrix.get()); image->setFileName(fileName.c_str()); image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), totalNumSlices, pixelFormat, dataType); matrix->preMult(osg::Matrix::scale(double(image->s()), double(image->t()), double(image->r()))); notice()<<"Image dimensions = "<<image->s()<<", "<<image->t()<<", "<<image->r()<<" pixelFormat=0x"<<std::hex<<pixelFormat<<" dataType=0x"<<std::hex<<dataType<<std::dec<<std::endl; } else if (pixelData->getPlanes()>numPlanes || pixelData->getRepresentation()>pixelRep) { notice()<<"Need to reallocated "<<image->s()<<", "<<image->t()<<", "<<image->r()<<std::endl; // record the previous image settings to use when we copy back the content. osg::ref_ptr<osg::Image> previous_image = image; // create the new image convertPixelTypes(pixelData, pixelRep, numPlanes, dataType, pixelFormat, pixelSize); image = new osg::Image; image->setUserData(previous_image->getUserData()); image->setFileName(fileName.c_str()); image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), totalNumSlices, pixelFormat, dataType); osg::copyImage(previous_image.get(), 0,0,0, previous_image->s(), previous_image->t(), imageNum, image.get(), 0, 0, 0, false); } osg::copyImage(imageAdapter.get(), 0,0,0, imageAdapter->s(), imageAdapter->t(), imageAdapter->r(), image.get(), 0, 0, imageNum, false); imageNum += dcmImage->getFrameCount(); } else { warning()<<"Error in reading dicom file "<<fileName.c_str()<<", error = "<<DicomImage::getString(dcmImage->getStatus())<<std::endl; } } } if (!image) { return ReadResult::ERROR_IN_READING_FILE; } notice()<<"Spacing = "<<*matrix<<std::endl; return image.get(); }