// Function for retreiving all the files in the given path including sub directories
Files Receiver::showFiles(const Path1& path, Patterns& patts)
{
Files *files = new Files();
Path *p=new Path();
string fullpath = p->getFullFileSpec(path);
if (!FileSystem::Directory::exists(path))
{
std::ostringstream out;
out << "path " << path << "does not exist";
throw std::exception(out.str().c_str());
}
std::vector<std::string> directories;
directories.push_back(fullpath);
showAllDirectories((fullpath), directories);
for (auto direc : directories){
FileSystem::Directory::setCurrentDirectory(direc);
for (auto patt : patts)
{
std::string fp = FileSystem::Directory::getCurrentDirectory();
std::vector<std::string> temp = FileSystem::Directory::getFiles(FileSystem::Directory::getCurrentDirectory(), patt);
for (size_t i = 0; i < temp.size(); i++){
temp[i] = fp + "\\" + temp[i];
}
files->insert(files->end(), temp.begin(), temp.end());
}
}
return *files;
}
void DirView::forEachFile(FileEnumCallback f, void *user, bool /*ignored*/)
{
Files flist; // TODO: optimize allocation
for(ViewList::reverse_iterator it = _view.rbegin(); it != _view.rend(); ++it)
(*it)->forEachFile(_addFileCallback, &flist);
for(Files::iterator it = flist.begin(); it != flist.end(); ++it)
f(it->second, user);
}
int App::run()
{
_options.parse();
#ifdef DEBUG
_options.dump(cerr);
cerr << "\n";
#endif
Files f = _options.files();
for (Files::iterator it = f.begin(); it != f.end(); it++)
{
char cmd[255] = {0};
sprintf(cmd, "deltree /y %s", it->c_str());
system(cmd); // temporary solution
}
return 0;
}
bool open(osg::Group* group)
{
Files files;
readMasterFile(files);
for(Files::iterator itr = files.begin();
itr != files.end();
++itr)
{
osg::ref_ptr<osg::Node> model = osgDB::readRefNodeFile(*itr);
if (model)
{
osg::notify(osg::NOTICE)<<"open: Loaded file "<<*itr<<std::endl;
group->addChild(model);
_existingFilenameNodeMap[*itr] = model;
}
}
return true;
}
BOOL __stdcall APIHook_WriteFile(
LPVOID hFile,
LPVOID lpBuffer,
unsigned long int nNumberOfBytesToWrite,
unsigned long int * lpNumberOfBytesWritten,
LPOVERLAPPED lpOverlapped)
{
BOOL result = WriteFile (
hFile,
lpBuffer,
nNumberOfBytesToWrite,
lpNumberOfBytesWritten,
lpOverlapped);
Files::iterator it = files.find(hFile);
if(it != files.end())
{
logger.write(it->second, result == TRUE ? "WriteFile OK" : "WriteFile ERROR", lpBuffer, nNumberOfBytesToWrite);
}
return result;
}
BOOL __stdcall APIHook_ReadFile(
LPVOID hFile,
LPVOID lpBuffer,
unsigned long int nNumberOfBytesToRead,
unsigned long int * lpNumberOfBytesRead,
LPOVERLAPPED lpOverlapped)
{
BOOL result = ReadFile (
hFile,
lpBuffer,
nNumberOfBytesToRead,
lpNumberOfBytesRead,
lpOverlapped);
Files::iterator it = files.find(hFile);
if(result == TRUE && it != files.end())
{
logger.write(it->second, "ReadFile", lpBuffer, *lpNumberOfBytesRead);
}
return result;
}
void DumpFiles( const Files& files, BOOL bOnlyFileName )
{
if(files.empty())
{
_tprintf(_T("Empty Files\r\n"));
}
else
{
int i=0;
for(Files::const_iterator it=files.begin(); it!=files.end(); ++it)
{
++i;
LPCTSTR szFile = *it;
if(bOnlyFileName)
{
LPCTSTR szName = _tcsrchr(szFile, _T('\\'));
if(szName)
szFile = ++szName;
}
_tprintf(_T("%d/%d %s\r\n"), i, files.size(), szFile);
}
}
}
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();
}
int main(int argc, char** argv)
{
if(argc < 3){
cout << "Prague metadata tool" << endl;
cout << "Usage: " << argv[0] <<" [-s] [-c] [-o <output file>] <metadata filename1>...<metadata filenameN>" << endl;
cout << "\t-s\t\t" << "change byteorder of metadata from little-endian to big-endian" << endl;
cout << "\t-c\t\t" << "save in metacache format" << endl;
cout << "\t-m\t\t" << "save in multimeta format" << endl;
cout << "\t-o <filename>\t" << "name of output file [default is out.meta]" << endl;
return -1;
}
bool swap = false;
bool cache = false;
bool multi = false;
Files files;
int i = 1;
string outfile("out.meta");
while(i < argc){
if(argv[i][0] == '-'){
switch(argv[i++][1]){
case 's': swap = true; break;
case 'c': cache = true; break;
case 'm': multi = true; break;
case 'o':
if(i < argc)
outfile = argv[i++];
else
cerr << "an output file is not specified" << endl;
break;
default: cerr << "unknown option '" << argv[i][1] << "'" << endl;
}
}
else
files.push_back(argv[i++]);
}
PragueMetadata metadata;
MetaLoader<GetLEValue> loader;
for(Files::const_iterator i = files.begin(); i != files.end(); ++i)
if(!loader.load(i->c_str(), metadata)){
cerr << "Can't load metadata from " << *i << endl;
continue;
}
bool result = false;
if(swap){
MetaSaver<SaveBEValue> saver;
if(!saver.open(outfile.c_str())){
cerr << "can't open " << outfile << endl;
return -1;
}
if(cache)
result = saver.saveCache(metadata);
else if(multi || (metadata.count() > 1))
result = saver.saveMulti(metadata);
else
result = saver.saveOne(metadata);
}
else{
MetaSaver<SaveValue> saver;
if(!saver.open(outfile.c_str())){
cerr << "can't open " << outfile << endl;
return -1;
}
if(cache)
result = saver.saveCache(metadata);
else if(multi || (metadata.count() > 1))
result = saver.saveMulti(metadata);
else
result = saver.saveOne(metadata);
}
if(!result){
cerr << "Can't save metadata to " << outfile << endl;
return -1;
}
return 0;
}
static void _iterFiles(Files &m, FileEnumCallback f, void *user)
{
for(Files::iterator it = m.begin(); it != m.end(); ++it)
f(it->second.content(), user);
}
void load()
{
//osg::notify(osg::NOTICE)<<"void load(Object)"<<std::endl;
Files filesA;
Files filesB;
readMasterFile(filesB);
// osg::notify(osg::NOTICE)<<"First read "<<filesA.size()<<std::endl;
// itererate until the master file is stable
do
{
OpenThreads::Thread::microSleep(100000);
filesB.swap(filesA);
filesB.clear();
readMasterFile(filesB);
// osg::notify(osg::NOTICE)<<"second read "<<filesB.size()<<std::endl;
} while (filesA!=filesB);
Files files;
files.swap(filesB);
// osg::notify(osg::NOTICE)<<"Now equal "<<files.size()<<std::endl;
Files newFiles;
Files removedFiles;
// find out which files are new, and which ones have been removed.
{
OpenThreads::ScopedLock<OpenThreads::Mutex> lock(_mutex);
for(Files::iterator fitr = files.begin();
fitr != files.end();
++fitr)
{
if (_existingFilenameNodeMap.count(*fitr)==0) newFiles.insert(*fitr);
}
for(FilenameNodeMap::iterator litr = _existingFilenameNodeMap.begin();
litr != _existingFilenameNodeMap.end();
++litr)
{
if (files.count(litr->first)==0)
{
removedFiles.insert(litr->first);
}
}
}
#if 0
if (!newFiles.empty() || !removedFiles.empty())
{
osg::notify(osg::NOTICE)<<std::endl<<std::endl<<"void operator () files.size()="<<files.size()<<std::endl;
}
#endif
// first load the new files.
FilenameNodeMap nodesToAdd;
if (!newFiles.empty())
{
typedef std::vector< osg::ref_ptr<osg::GraphicsThread> > GraphicsThreads;
GraphicsThreads threads;
for(unsigned int i=0; i<= osg::GraphicsContext::getMaxContextID(); ++i)
{
osg::GraphicsContext* gc = osg::GraphicsContext::getCompileContext(i);
osg::GraphicsThread* gt = gc ? gc->getGraphicsThread() : 0;
if (gt) threads.push_back(gt);
}
if (_operationQueue.valid())
{
// osg::notify(osg::NOTICE)<<"Using OperationQueue"<<std::endl;
_endOfLoadBlock = new osg::RefBlockCount(newFiles.size());
_endOfLoadBlock->reset();
typedef std::list< osg::ref_ptr<LoadAndCompileOperation> > LoadAndCompileList;
LoadAndCompileList loadAndCompileList;
for(Files::iterator nitr = newFiles.begin();
nitr != newFiles.end();
++nitr)
{
// osg::notify(osg::NOTICE)<<"Adding LoadAndCompileOperation "<<*nitr<<std::endl;
osg::ref_ptr<LoadAndCompileOperation> loadAndCompile = new LoadAndCompileOperation( *nitr, _incrementalCompileOperation.get(), _endOfLoadBlock.get() );
loadAndCompileList.push_back(loadAndCompile);
_operationQueue->add( loadAndCompile.get() );
}
#if 1
osg::ref_ptr<osg::Operation> operation;
while ((operation=_operationQueue->getNextOperation()).valid())
{
// osg::notify(osg::NOTICE)<<"Local running of operation"<<std::endl;
(*operation)(0);
}
#endif
// osg::notify(osg::NOTICE)<<"Waiting for completion of LoadAndCompile operations"<<std::endl;
_endOfLoadBlock->block();
// osg::notify(osg::NOTICE)<<"done ... Waiting for completion of LoadAndCompile operations"<<std::endl;
for(LoadAndCompileList::iterator litr = loadAndCompileList.begin();
litr != loadAndCompileList.end();
++litr)
{
if ((*litr)->_loadedModel.valid())
{
nodesToAdd[(*litr)->_filename] = (*litr)->_loadedModel;
}
}
}
else
{
_endOfLoadBlock = new osg::RefBlockCount(newFiles.size());
_endOfLoadBlock->reset();
for(Files::iterator nitr = newFiles.begin();
nitr != newFiles.end();
++nitr)
{
osg::ref_ptr<osg::Node> loadedModel = osgDB::readRefNodeFile(*nitr);
if (loadedModel.get())
{
nodesToAdd[*nitr] = loadedModel;
if (_incrementalCompileOperation.valid())
{
osg::ref_ptr<osgUtil::IncrementalCompileOperation::CompileSet> compileSet =
new osgUtil::IncrementalCompileOperation::CompileSet(loadedModel.get());
compileSet->_compileCompletedCallback = new ReleaseBlockOnCompileCompleted(_endOfLoadBlock.get());
_incrementalCompileOperation->add(compileSet.get());
}
else
{
_endOfLoadBlock->completed();
}
}
else
{
_endOfLoadBlock->completed();
}
}
_endOfLoadBlock->block();
}
}
bool requiresBlock = false;
// pass the locally peppared data to MasterOperations shared data
// so that updated thread can merge these changes with the main scene
// graph. This merge is carried out via the update(..) method.
if (!removedFiles.empty() || !nodesToAdd.empty())
{
OpenThreads::ScopedLock<OpenThreads::Mutex> lock(_mutex);
_nodesToRemove.swap(removedFiles);
_nodesToAdd.swap(nodesToAdd);
requiresBlock = true;
}
// now block so we don't try to load anything till the new data has been merged
// otherwise _existingFilenameNodeMap will get out of sync.
if (requiresBlock)
{
_updatesMergedBlock.block();
}
else
{
OpenThreads::Thread::YieldCurrentThread();
}
}
// Remove the files in the given list of files
void RemoveFiles(const Files &files)
{
std::for_each(files.begin(), files.end(), [](const std::string &file) { remove(file.c_str()); });
}