VolumeCollection* RawVoxVolumeReader::read(const std::string &url)
throw (tgt::CorruptedFileException, tgt::IOException, std::bad_alloc)
{
VolumeURL origin(url);
std::string fileName = origin.getPath();
LINFO("Reading file " << fileName);
std::fstream fin(fileName.c_str(), std::ios::in | std::ios::binary);
if (!fin.good())
throw tgt::IOException();
RawVoxHeader header;
fin.read(reinterpret_cast<char*>(&header), sizeof(header));
svec3 dimensions = svec3(header.sizeX_, header.sizeY_, header.sizeZ_);
if(header.magic_ != 1381388120) {
throw tgt::CorruptedFileException("Wrong magic number.");
}
VolumeRAM* dataset;
switch(header.bitsPerVoxel_) {
case 8:
LINFO("Reading 8 bit dataset");
dataset = new VolumeRAM_UInt8(dimensions);
break;
case 16:
LINFO("Reading 16 bit dataset");
dataset = new VolumeRAM_UInt16(dimensions);
break;
case 32:
LINFO("Reading 32 bit (float) dataset");
dataset = new VolumeRAM_Float(dimensions);
break;
default:
LERROR("Unknown bpp!");
throw tgt::UnsupportedFormatException("Unexpected bpp.");
}
fin.read(reinterpret_cast<char*>(dataset->getData()), dataset->getNumBytes());
if ( fin.eof() ) {
delete dataset;
throw tgt::CorruptedFileException();
}
fin.close();
VolumeCollection* volumeCollection = new VolumeCollection();
Volume* volumeHandle = new Volume(dataset, vec3(1.0f), vec3(0.0f));
oldVolumePosition(volumeHandle);
volumeHandle->setOrigin(fileName);
volumeCollection->add(volumeHandle);
return volumeCollection;
}
void VolumeSeriesSource::loadStep() {
if(!volume_)
return;
VolumeRAM* v = volume_->getWritableRepresentation<VolumeRAM>();
if (!v)
return;
int step = step_.get();
std::string filename;
if (files_.size() > 0 && step < static_cast<int>(files_.size()))
filename = files_[step];
else
return;
std::ifstream f(filename.c_str(), std::ios_base::binary);
if (!f) {
LERROR("Could not open file: " << filename);
return;
}
// read the volume as a raw blob, should be fast
LINFO("Loading raw file " << filename);
f.read(reinterpret_cast<char*>(v->getData()), v->getNumBytes());
if (!f.good()) {
LERROR("Reading from file failed: " << filename);
return;
}
// Special handling for float volumes: normalize values to [0.0; 1.0]
VolumeRAM_Float* vf = dynamic_cast<VolumeRAM_Float*>(v);
if (vf && spreadMin_ != spreadMax_) {
const size_t n = vf->getNumVoxels();
// use spread values if available
if (spreadMin_ != spreadMax_) {
const float d = spreadMax_ - spreadMin_;
float* voxel = vf->voxel();
for (size_t i = 0; i < n; ++i)
voxel[i] = (voxel[i] - spreadMin_) / d;
} else {
LINFO("Normalizing float data to [0.0; 1.0]. "
<< "This might not be what you want, better define 'Spread: <min> <max>' in the .sdat file.");
const float d = vf->max() - vf->min();
const float p = vf->min();
float* voxel = vf->voxel();
for (size_t i = 0; i < n; ++i)
voxel[i] = (voxel[i] - p) / d;
}
vf->invalidate();
}
needUpload_ = true;
invalidate();
}
void VolumeGL2RAMConverter::update(const DataRepresentation* source, DataRepresentation* destination) {
const VolumeGL* volumeSrc = static_cast<const VolumeGL*>(source);
VolumeRAM* volumeDst = static_cast<VolumeRAM*>(destination);
if (volumeSrc->getDimensions() != volumeDst->getDimensions()) {
volumeDst->setDimensions(volumeSrc->getDimensions());
}
volumeSrc->getTexture()->download(volumeDst->getData());
if (volumeDst->hasHistograms())
volumeDst->getHistograms()->setValid(false);
}
DataRepresentation* VolumeGL2RAMConverter::createFrom(const DataRepresentation* source) {
const VolumeGL* volumeGL = static_cast<const VolumeGL*>(source);
VolumeRAM* volume = createVolumeRAM(volumeGL->getDimensions(), volumeGL->getDataFormat());
if (volume) {
volumeGL->getTexture()->download(volume->getData());
return volume;
} else {
LogError("Cannot convert format from GL to RAM:" << volumeGL->getDataFormat()->getString());
}
return nullptr;
}
DataRepresentation* VolumeCL2RAMConverter::createFrom(const DataRepresentation* source) {
DataRepresentation* destination = 0;
const VolumeCL* volumeCL = static_cast<const VolumeCL*>(source);
size3_t dimensions = volumeCL->getDimensions();
destination = createVolumeRAM(dimensions, volumeCL->getDataFormat());
if (destination) {
VolumeRAM* volumeRAM = static_cast<VolumeRAM*>(destination);
volumeCL->download(volumeRAM->getData());
//const cl::CommandQueue& queue = OpenCL::getInstance()->getQueue();
//queue.enqueueReadImage(volumeCL->getVolume(), true, glm::size3_t(0), glm::size3_t(dimension), 0, 0, volumeRAM->getData());
}
return destination;
}
Volume* MPVMVolumeReader::readMetaData(std::string filePath) {
if (!filesystem::fileExists(filePath)) {
std::string newPath = filesystem::addBasePath(filePath);
if (filesystem::fileExists(newPath)) {
filePath = newPath;
} else {
throw DataReaderException("Error could not find input file: " + filePath, IvwContext);
}
}
std::string fileDirectory = filesystem::getFileDirectory(filePath);
// Read the mpvm file content
std::istream* f = new std::ifstream(filePath.c_str());
std::string textLine;
std::vector<std::string> files;
while (!f->eof()) {
getline(*f, textLine);
textLine = trim(textLine);
files.push_back(textLine);
};
delete f;
if (files.empty()) throw DataReaderException("Error: No PVM files found in " + filePath, IvwContext);
if (files.size() > 4)
throw DataReaderException("Error: Maximum 4 pvm files are supported, file: " + filePath, IvwContext);
// Read all pvm volumes
std::vector<Volume*> volumes;
for (size_t i = 0; i < files.size(); i++) {
Volume* newVol = PVMVolumeReader::readPVMData(fileDirectory + files[i]);
if (newVol)
volumes.push_back(newVol);
else
LogWarn("Could not load " << fileDirectory << files[i]);
}
if (volumes.empty())
throw DataReaderException("No PVM volumes could be read from file: " + filePath, IvwContext);
if (volumes.size() == 1) {
printPVMMeta(volumes[0], fileDirectory + files[0]);
return volumes[0];
}
// Make sure dimension and format match
const DataFormatBase* format = volumes[0]->getDataFormat();
size3_t mdim = volumes[0]->getDimensions();
for (size_t i = 1; i < volumes.size(); i++) {
if (format != volumes[i]->getDataFormat() || mdim != volumes[i]->getDimensions()) {
LogWarn("PVM volumes did not have the same format or dimensions, using first volume.");
printPVMMeta(volumes[0], fileDirectory + files[0]);
return volumes[0];
}
}
// Create new format
const DataFormatBase* mformat =
DataFormatBase::get(format->getNumericType(), volumes.size(), format->getSize()*8);
// Create new volume
Volume* volume = new Volume();
glm::mat3 basis = volumes[0]->getBasis();
volume->setBasis(basis);
volume->setOffset(-0.5f * (basis[0] + basis[1] + basis[2]));
volume->setDimensions(mdim);
volume->dataMap_.initWithFormat(mformat);
volume->setDataFormat(mformat);
volume->copyMetaDataFrom(*volumes[0]);
// Merge descriptions but ignore the rest
StringMetaData* metaData = volume->getMetaData<StringMetaData>("description");
if (metaData) {
std::string descStr = metaData->get();
for (size_t i = 1; i < volumes.size(); i++) {
metaData = volumes[0]->getMetaData<StringMetaData>("description");
if (metaData) descStr = descStr + ", " + metaData->get();
}
volume->setMetaData<StringMetaData>("description", descStr);
}
// Create RAM volume
VolumeRAM* mvolRAM = createVolumeRAM(mdim, mformat);
unsigned char* dataPtr = static_cast<unsigned char*>(mvolRAM->getData());
std::vector<const unsigned char*> volumesDataPtr;
for (size_t i = 0; i < volumes.size(); i++) {
volumesDataPtr.push_back(static_cast<const unsigned char*>(
volumes[i]->getRepresentation<VolumeRAM>()->getData()));
}
// Copy the data from the other volumes to the new multichannel volume
size_t mbytes = mformat->getSize();
size_t bytes = format->getSize();
size_t dims = mdim.x * mdim.y * mdim.z;
size_t vsize = volumesDataPtr.size();
for (size_t i = 0; i < dims; i++) {
for (size_t j = 0; j < vsize; j++) {
for (size_t b = 0; b < bytes; b++) {
dataPtr[i * mbytes + (j * bytes) + b] = volumesDataPtr[j][i * bytes + b];
}
}
}
// Delete the single channel volumes
for (size_t i = 0; i < volumes.size(); i++) {
delete volumes[i];
}
volume->addRepresentation(mvolRAM);
printPVMMeta(volume, filePath);
return volume;
}
VolumeRAM* VolumeDiskRaw::loadBrick(const tgt::svec3& pOffset, const tgt::svec3& pDimensions) const
throw (tgt::Exception)
{
//check for wrong parameter
if(tgt::hmul(pDimensions) == 0)
throw std::invalid_argument("requested brick dimensions are zero!");
if(!tgt::hand(tgt::lessThanEqual(pOffset+pDimensions,getDimensions())))
throw std::invalid_argument("requested brick outside volume date!");
//create new VolumeRam
VolumeFactory vf;
VolumeRAM* vr = vf.create(getFormat(), pDimensions);
if (!vr)
throw VoreenException("Failed to create VolumeRAM");
//open file
FILE* fin;
fin = fopen(getFileName().c_str(),"rb");
if (!fin)
throw tgt::FileException("Failed to open file for reading: " + getFileName());
size_t bytesPerVoxel = static_cast<size_t>(vr->getBitsAllocated() / 8);
size_t numVoxels = pDimensions.x;
size_t numBytes = numVoxels * bytesPerVoxel;
int64_t offset = getOffset();
if(offset < 0) {
//Assume data is aligned to end of file.
// get file size:
fseek(fin, 0, SEEK_END);
int64_t fileSize = ftell(fin);
rewind(fin);
//calculate real offset:
offset = fileSize - hmul(getDimensions())*bytesPerVoxel;
}
//modify offset to start at first slice
offset += getDimensions().x*getDimensions().y*pOffset.z*bytesPerVoxel;
fseek(fin, static_cast<long>(offset), SEEK_SET);
//read into ram
size_t pointerOffset = 0;
for(size_t z = 0; z < pDimensions.z; z++){
for(size_t y = 0; y < pDimensions.y; y++) {
//read into ram
if(fread(reinterpret_cast<char*>(vr->getData())+pointerOffset, numBytes, 1, fin) != 1) {
fclose(fin);
delete vr;
throw tgt::FileException("Failed to read from file: " + getFileName());
}
//move offset
pointerOffset += numBytes;
//move to next read
if(y < pDimensions.y)
fseek(fin, static_cast<long>(getDimensions().x-pDimensions.x),SEEK_SET);
}
//move to next read
if(z < pDimensions.z)
fseek(fin,static_cast<long>((getDimensions().x*getDimensions().y)-(pDimensions.x*pDimensions.y)),SEEK_SET);
}
fclose(fin);
//swap endian
if(getSwapEndian()) {
Volume* tempHandle = new Volume(vr, vec3(1.0f), vec3(0.0f));
VolumeOperatorSwapEndianness::APPLY_OP(tempHandle);
tempHandle->releaseAllRepresentations();
delete tempHandle;
}
return vr;
}
VolumeRAM* VolumeDiskRaw::loadSlices(const size_t firstSlice, const size_t lastSlice) const
throw (tgt::Exception)
{
//check for wrong parameter
if(getDimensions().z <= lastSlice)
throw std::invalid_argument("lastSlice is out of volume dimension!!!");
if(firstSlice > lastSlice)
throw std::invalid_argument("firstSlice has to be less or equal lastSlice!!!");
//create new VolumeRam
VolumeFactory vf;
VolumeRAM* vr = vf.create(getFormat(), tgt::svec3(getDimensions().x,getDimensions().y, lastSlice-firstSlice+1));
if (!vr)
throw VoreenException("Failed to create VolumeRAM");
//open file
std::ifstream infile(getFileName().c_str(), std::ios::in | std::ios::binary);
if (infile.fail())
throw tgt::FileException("Failed to open file for reading: " + getFileName());
size_t bytesPerVoxel = static_cast<size_t>(vr->getBitsAllocated() / 8);
size_t numVoxels = getDimensions().x*getDimensions().y*(lastSlice-firstSlice+1);
size_t numBytes = numVoxels * bytesPerVoxel;
int64_t offset = getOffset();
if(offset < 0) {
//Assume data is aligned to end of file.
// get file size:
infile.seekg( 0, infile.end);
std::streampos fileSize = infile.tellg();
infile.seekg( 0, infile.beg);
//calculate real offset:
offset = static_cast<std::string::size_type>(fileSize) - hmul(getDimensions())*bytesPerVoxel;
}
//modify offset to start at first slice
offset += getDimensions().x*getDimensions().y*firstSlice*bytesPerVoxel;
infile.seekg(offset);
//read into ram
infile.read(reinterpret_cast<char*>(vr->getData()),numBytes);
if (infile.fail()) {
//LERRORC("voreen.RepresentationConverterLoadFromDisk", "read() failed");
infile.close();
delete vr;
throw tgt::FileException("Failed to read from file: " + getFileName());
}
infile.close();
//swap endian
if(getSwapEndian()) {
Volume* tempHandle = new Volume(vr, vec3(1.0f), vec3(0.0f));
VolumeOperatorSwapEndianness::APPLY_OP(tempHandle);
tempHandle->releaseAllRepresentations();
delete tempHandle;
}
return vr;
}
VolumeRAM* VolumeDiskRaw::loadVolume() const
throw (tgt::Exception)
{
VolumeRAM* volume = 0;
LDEBUG("Creating volume from diskrepr. " << getFileName() << " format: " << getFormat());
VolumeFactory vf;
try {
volume = vf.create(getFormat(), getDimensions());
}
catch (std::bad_alloc&) {
throw tgt::Exception("bad allocation");
}
if (!volume)
throw VoreenException("Failed to create VolumeRAM");
FILE* fin;
fin = fopen(getFileName().c_str(),"rb");
if (fin == 0) {
throw tgt::IOException("Unable to open raw file for reading", getFileName());
}
size_t bytesPerVoxel = static_cast<size_t>(volume->getBitsAllocated() / 8);
size_t numVoxels = hmul(getDimensions());
size_t numBytes = numVoxels * bytesPerVoxel;
int64_t offset = getOffset();
if(offset < 0) {
//Assume data is aligned to end of file.
// get file size:
fseek(fin, 0, SEEK_END);
int64_t fileSize = ftell(fin);
rewind(fin);
//calculate real offset:
offset = fileSize - numBytes;
}
#ifdef _MSC_VER
_fseeki64(fin, offset, SEEK_SET);
#else
fseek(fin, offset, SEEK_SET);
#endif
if(fread(reinterpret_cast<char*>(volume->getData()), numBytes, 1, fin) != 1) {
//LERRORC("voreen.RepresentationConverterLoadFromDisk", "fread() failed");
fclose(fin);
delete volume;
throw tgt::FileException("Failed to read from file: " + getFileName());
}
fclose(fin);
if (getSwapEndian()) {
Volume* tempHandle = new Volume(volume, vec3(1.0f), vec3(0.0f));
VolumeOperatorSwapEndianness::APPLY_OP(tempHandle);
tempHandle->releaseAllRepresentations();
delete tempHandle;
}
return volume;
}
VolumeRepresentation* RepresentationConverterLoadFromDisk::convert(const VolumeRepresentation* source) const {
const VolumeDisk* dr = dynamic_cast<const VolumeDisk*>(source);
if(dr) {
VolumeRAM* volume = 0;
LDEBUGC("voreen.RepresentationConverterLoadFromDisk", "creating volume from diskrepr. " << dr->getFileName() << " format: " << dr->getFormat());
VolumeFactory vf;
volume = vf.create(dr->getFormat(), dr->getDimensions());
if(!volume)
return 0;
FILE* fin;
fin = fopen(dr->getFileName().c_str(),"rb");
if (fin == 0)
throw tgt::IOException("Unable to open raw file for reading", dr->getFileName());
size_t bytesPerVoxel = static_cast<size_t>(volume->getBitsAllocated() / 8);
size_t numVoxels = hmul(dr->getDimensions());
size_t numBytes = numVoxels * bytesPerVoxel;
int64_t offset = dr->getOffset();
if(offset < 0) {
//Assume data is aligned to end of file.
// get file size:
fseek(fin, 0, SEEK_END);
int64_t fileSize = ftell(fin);
rewind(fin);
//calculate real offset:
offset = fileSize - numBytes;
}
#ifdef _MSC_VER
_fseeki64(fin, offset, SEEK_SET);
#else
fseek(fin, offset, SEEK_SET);
#endif
if(fread(reinterpret_cast<char*>(volume->getData()), numBytes, 1, fin) != 1) {
LERRORC("voreen.RepresentationConverterLoadFromDisk", "fread() failed");
fclose(fin);
delete volume;
return 0;
}
fclose(fin);
if(dr->getSwapEndian()) {
Volume* tempHandle = new Volume(volume, vec3(1.0f), vec3(0.0f));
VolumeOperatorSwapEndianness::APPLY_OP(tempHandle);
tempHandle->releaseAllRepresentations();
}
return volume;
}
else {
//should have checked before...
//LERROR("Failed to convert!");
return 0;
}
}