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();
}
