void MPVMVolumeReader::printMetaInfo(MetaDataOwner* metaDataOwner, std::string key) {
StringMetaData* metaData = metaDataOwner->getMetaData<StringMetaData>(key);
if (metaData) {
std::string metaStr = metaData->get();
replaceInString(metaStr, "\n", ", ");
key[0] = static_cast<char>(toupper(key[0]));
LogInfo(key << ": " << metaStr);
}
}
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;
}
void PVMVolumeWriter::writeData(const Volume *data, const std::string filePath) const {
if (filesystem::fileExists(filePath) && !overwrite_)
throw DataWriterException("Error: Output file: " + filePath + " already exists",
IvwContext);
const DataFormatBase *format = data->getDataFormat();
int components = 0;
#include <warn/push>
#include <warn/ignore/switch-enum>
switch (format->getId()) {
case inviwo::DataFormatId::UInt8:
components = 1;
break;
case inviwo::DataFormatId::UInt16:
components = 2;
break;
default:
break;
}
#include <warn/pop>
if (components == 0)
throw DataWriterException("Error: Output format " + std::string(format->getString()) +
" not support by PVM writer",
IvwContext);
const VolumeRAM *vr = data->getRepresentation<VolumeRAM>();
const unsigned char *dataPtr = (const unsigned char *)vr->getData();
size3_t dim = vr->getDimensions();
vec3 spacing(1.f);
mat3 basis = data->getBasis();
spacing.x = basis[0][0] / dim.x;
spacing.y = basis[1][1] / dim.y;
spacing.z = basis[2][2] / dim.z;
unsigned char *data2Ptr = nullptr;
if (components == 2) {
size_t size = dim.x * dim.y * dim.z;
data2Ptr = new unsigned char[size * components];
size_t bytes = format->getSize();
memcpy(data2Ptr, dataPtr, size * bytes);
swapbytes(data2Ptr, static_cast<unsigned int>(size * bytes));
dataPtr = (const unsigned char *)data2Ptr;
}
unsigned char *description = nullptr;
StringMetaData *descMetaData = data->getMetaData<StringMetaData>("description");
if (descMetaData) {
description = new unsigned char[descMetaData->get().size() + 1];
strncpy((char *)description, descMetaData->get().c_str(), descMetaData->get().size());
description[descMetaData->get().size()] = '\0';
}
unsigned char *courtesy = nullptr;
StringMetaData *courMetaData = data->getMetaData<StringMetaData>("courtesy");
if (courMetaData) {
courtesy = new unsigned char[courMetaData->get().size() + 1];
strncpy((char *)courtesy, courMetaData->get().c_str(), courMetaData->get().size());
courtesy[courMetaData->get().size()] = '\0';
}
unsigned char *parameter = nullptr;
StringMetaData *paraMetaData = data->getMetaData<StringMetaData>("parameter");
if (paraMetaData) {
parameter = new unsigned char[paraMetaData->get().size() + 1];
strncpy((char *)parameter, paraMetaData->get().c_str(), paraMetaData->get().size());
parameter[paraMetaData->get().size()] = '\0';
}
unsigned char *comment = nullptr;
StringMetaData *commMetaData = data->getMetaData<StringMetaData>("comment");
if (commMetaData) {
comment = new unsigned char[commMetaData->get().size() + 1];
strncpy((char *)comment, commMetaData->get().c_str(), commMetaData->get().size());
comment[commMetaData->get().size()] = '\0';
}
writePVMvolume(filePath.c_str(), dataPtr, static_cast<unsigned int>(dim.x),
static_cast<unsigned int>(dim.y), static_cast<unsigned int>(dim.z), components,
spacing.x, spacing.y, spacing.z, description, courtesy, parameter, comment);
delete[] data2Ptr;
delete[] description;
delete[] courtesy;
delete[] parameter;
delete[] comment;
}
