VolumeCollection* FlowReader::read(const std::string& url)
throw(tgt::FileException, std::bad_alloc)
{
VolumeOrigin origin(url);
std::string fileName = origin.getPath();
LINFO("reading flow file '" << fileName << "'...");
// try to open the file
//
std::fstream ifs(fileName.c_str(), std::ios_base::in | std::ios_base::binary);
if (ifs.good() == false)
throw tgt::IOException("Unable to open flow file for reading", fileName);
// read the magic number (string "VOREENFLOW")
//
char magicNumber[11] = {0};
ifs.read(magicNumber, 11);
std::string temp(magicNumber);
if (temp != "VOREENFLOW")
throw tgt::IOException("Missing magic number in flow file", fileName);
// read file version (must currently be 1 or 2)
//
unsigned int fileVersion = 0;
ifs.read(reinterpret_cast<char*>(&fileVersion), sizeof(unsigned int));
LINFO("file version: " << fileVersion);
if ((fileVersion < 1) || (fileVersion > 2))
throw tgt::IOException("Unsupported file version of flow file", fileName);
// read flow dimension (usually 3 for 3D flows)
//
unsigned int flowDimension = 0;
ifs.read(reinterpret_cast<char*>(&flowDimension), sizeof(unsigned int));
LINFO("flow dimension: " << flowDimension << "D");
if (flowDimension != 3)
throw tgt::IOException("Unsupported flow dimension in flow file", fileName);
unsigned char dataOrientation = 0;
unsigned char reverseSlicesMask = 0;
ifs.read(reinterpret_cast<char*>(&dataOrientation), sizeof(unsigned char));
if (fileVersion > 1) {
ifs.read(reinterpret_cast<char*>(&reverseSlicesMask), sizeof(unsigned char));
}
// read the dimension of the volume data containing the flow
//
tgt::ivec3 dimensions;
ifs.read(reinterpret_cast<char*>(&dimensions), sizeof(tgt::ivec3));
LINFO("volume dimensions: " << dimensions);
unsigned int byteSize = 0;
ifs.read(reinterpret_cast<char*>(&byteSize), sizeof(unsigned int));
LINFO("expected size of vector field: " << byteSize << " byte");
VolumeFlow3D* volume = readConvert(dimensions, dataOrientation, ifs);
ifs.close();
if (volume == 0) {
LERROR("an error occured during reading flow data! Proceeding impossible.");
return 0;
}
if (reverseSlicesMask != 0)
reverseSlices(volume, reverseSlicesMask);
// TODO: volume container merge
/*VolumeSet* volumeSet = new VolumeSet(fileName);
VolumeSeries* volumeSeries = new VolumeSeries(Modality::MODALITY_FLOW.getName(),
Modality::MODALITY_FLOW);
volumeSet->addSeries(volumeSeries);
VolumeHandle* volumeHandle = new VolumeHandle(volume, 0.0f);
volumeSeries->addVolumeHandle(volumeHandle); */
VolumeCollection* collection = new VolumeCollection();
VolumeHandle* volumeHandle = new VolumeHandle(volume, tgt::vec3(1.0f), tgt::vec3(0.0f));//FIXME: spacing?
oldVolumePosition(volumeHandle);
volumeHandle->setModality(Modality::MODALITY_FLOW);
collection->add(volumeHandle);
// TODO: origin does not save series and timestamp anymore
//volumeHandle->setOrigin(fileName, Modality::MODALITY_FLOW.getName(), 0.0f);
volumeHandle->setOrigin(fileName);
return collection;
}
VolumeCollection* PVMVolumeReader::read(const std::string &url)
throw (tgt::FileException, tgt::IOException, std::bad_alloc)
{
VolumeOrigin origin(url);
std::string fileName = origin.getPath();
uint8_t* data;
uint8_t* tmpData;
unsigned int width, height, depth, components;
float scalex, scaley, scalez;
unsigned char *description;
unsigned char *courtesy;
unsigned char *parameter;
unsigned char *comment;
LINFO("Reading PVM volume " << fileName);
/*
TODO This subroutine returns an array created with malloc but it should
be created with 'new[]' because this chunk of data will be deleted with 'delete[]'.
This can cause hard to find errors.
As a temporary workaround the data are copied over into a new array
and the c-array is deleted with 'free'.
Because of some c-pointer vodoo done in ddsbase.cpp free must be invoked
after the use of all other returned pointers. (roland)
*/
tmpData = readPVMvolume(const_cast<char*>(fileName.c_str()), getProgressBar(),
&width, &height, &depth, &components,
&scalex, &scaley, &scalez, &description, &courtesy,
¶meter, &comment);
if (!tmpData) {
LERROR("PVM Reading failed");
return 0;
}
data = new uint8_t[width * height * depth * components];
memcpy(data, tmpData, width * height * depth * components);
Volume* dataset = 0;
if (!data) {
throw tgt::IOException();
}
else {
LINFO("Size: " << width << " x " << height << " x " << depth);
LINFO("Spacing: " << scalex << " x " << scaley << " x " << scalez);
LINFO("Components: " << components);
if (description)
LINFO("Description: " << description);
if (courtesy)
LINFO("Courtesy: " << courtesy);
if (parameter)
LINFO("Parameter: " << parameter);
if (comment)
LINFO("Comment: " << comment);
if (components == 1) {
LINFO("Create 8 bit data set.");
dataset = new VolumeUInt8(data, tgt::ivec3(width, height, depth),
tgt::vec3(scalex, scaley, scalez));
}
else if (components == 2) {
// the endianness conversion in ddsbase.cpp seem to be broken,
// so we perform it here instead
uint16_t* data16 = reinterpret_cast<uint16_t*>(data);
int numElements = width * height * depth;
uint16_t maxValue = 0;
for (int i=0; i < numElements; i++) {
endian_swap(data16[i]);
if (data16[i] > maxValue)
maxValue = data16[i];
}
int bits;
if (maxValue < 4096) {
LINFO("Create 12 bit data set.");
bits = 12;
} else {
LINFO("Create 16 bit data set.");
bits = 16;
}
dataset = new VolumeUInt16((uint16_t*)data,
tgt::ivec3(width, height, depth),
tgt::vec3(scalex, scaley, scalez),
tgt::mat4::identity,
bits);
}
else LERROR("Bit depth not supported.");
}
// TODO now it is safe to free
free(tmpData);
VolumeCollection* volumeCollection = new VolumeCollection();
if (dataset) {
VolumeHandle* volumeHandle = new VolumeHandle(dataset, 0.0f);
volumeHandle->setOrigin(VolumeOrigin(fileName));
volumeCollection->add(volumeHandle);
}
return volumeCollection;
}
