VolumeList* ECAT7VolumeReader::read(const std::string &url, int volumeId)
throw(tgt::CorruptedFileException, tgt::IOException, std::bad_alloc)
{
LINFO("Loading dataset " << url << " vid: " << volumeId);
VolumeURL origin(url);
std::string fileName = origin.getPath();
FILE* fin = fopen(fileName.c_str(), "rb");
if(!fin) {
throw tgt::FileNotFoundException("ECAT7: File not found", fileName);
}
ECAT7VolumeReader::ECAT7Structure s = readStructure(fileName);
VolumeList* vc = new VolumeList();
for(size_t i=0; i<s.subVolumes_.size(); i++) {
fseek(fin, s.subVolumes_[i].de_.startBlock_ * 512, SEEK_SET);
fseek(fin, 512, SEEK_CUR); //skip past header (already read)
tgt::svec3 dimensions = s.subVolumes_[i].getDimensions();
//tgt::mat4 m = s.subVolumes_[i].getTransformation();
tgt::vec3 spacing = s.subVolumes_[i].getSpacing();
tgt::vec3 offset = s.subVolumes_[i].getOffset();
if(volumeId != -1) {
if(volumeId != s.subVolumes_[i].getId())
continue;
}
if(s.subVolumes_[i].ih_.num_dimensions != 3)
continue;
if (getProgressBar()) {
getProgressBar()->setTitle("Loading Volume");
getProgressBar()->setProgressMessage("Loading volume: " + fileName);
}
VolumeRAM* vol;
RealWorldMapping denormalize;
if(s.h_.file_type == 6) {
vol = new VolumeRAM_UInt8(dimensions);
denormalize = RealWorldMapping::createDenormalizingMapping<uint8_t>();
}
else if(s.h_.file_type == 7) {
vol = new VolumeRAM_UInt16(dimensions);
denormalize = RealWorldMapping::createDenormalizingMapping<uint16_t>();
}
else {
LERROR("Unknown file format detected.");
return 0;
}
float scale = s.subVolumes_[i].ih_.scale_factor * s.h_.ecat_calibration_factor;
RealWorldMapping rwm(scale, 0.0f, s.h_.data_units);
VolumeReader::read(vol, fin);
// Assume that the pixel size values given in the ecat header are in cm. Multiply spacing and offset
// with 0.1 to convert to mm.
Volume* vh = new Volume(vol, spacing * 0.1f, offset * 0.1f);
vh->setRealWorldMapping(RealWorldMapping::combine(denormalize, rwm));
if(s.swapEndianness_)
VolumeOperatorSwapEndianness::APPLY_OP(vh);
// TODO: This must depend on some parameter in the headers, figure out which and how
bool mirrorZ = true;
if(mirrorZ)
{
Volume* mirrored = VolumeOperatorMirrorZ::APPLY_OP(vh);
delete vh;
vh = mirrored;
}
VolumeURL o("ecat7", fileName);
o.addSearchParameter("volumeId", itos(s.subVolumes_[i].de_.id_));
vh->setOrigin(o);
s.transformMetaData(vh->getMetaDataContainer(), static_cast<int>(i));
if(length(offset) == 0.f)
centerVolume(vh);
vc->add(vh);
if (getProgressBar())
getProgressBar()->hide();
}
fclose(fin);
return vc;
}
VolumeCollection* AnalyzeVolumeReader::readNifti(const std::string &fileName, bool standalone, int volId)
throw (tgt::FileException, std::bad_alloc)
{
LINFO("Loading nifti file " << fileName);
std::ifstream file(fileName.c_str(), std::ios::in | std::ios::binary);
if(!file) {
throw tgt::FileNotFoundException("Failed to open file: ", fileName);
}
nifti_1_header header;
if (!file.read((char*)&header, sizeof(header))) {
throw tgt::CorruptedFileException("Failed to read header!", fileName);
}
file.close();
bool bigEndian = false;
//check if swap is necessary:
if((header.dim[0] < 0) || (header.dim[0] > 15)) {
bigEndian = true;
header.swapEndianess();
}
if(header.sizeof_hdr != 348) {
throw tgt::CorruptedFileException("Invalid header.sizeof_hdr", fileName);
}
if(!( (header.magic[0] == 'n') && (header.magic[2] == '1') && (header.magic[3] == 0) ))
throw tgt::CorruptedFileException("Not a Nifti header!", fileName);
if(header.magic[1] == '+') {
if(!standalone)
LWARNING("Tried to read standalone Nifti as hdr+img!");
standalone = true;
}
else if(header.magic[1] == 'i') {
if(!standalone)
LWARNING("Tried to read hdr+img Nifti as standalone!");
standalone = false;
}
else
throw tgt::CorruptedFileException("Not a Nifti header!", fileName);
ivec3 dimensions;
dimensions.x = header.dim[1];
dimensions.y = header.dim[2];
dimensions.z = header.dim[3];
LINFO("Resolution: " << dimensions);
int numVolumes = header.dim[4];
LINFO("Number of volumes: " << numVolumes);
if (hor(lessThanEqual(dimensions, ivec3(0)))) {
LERROR("Invalid resolution or resolution not specified: " << dimensions);
throw tgt::CorruptedFileException("error while reading data", fileName);
}
vec3 spacing;
spacing.x = header.pixdim[1];
spacing.y = header.pixdim[2];
spacing.z = header.pixdim[3];
LINFO("Spacing: " << spacing);
int timeunit = XYZT_TO_TIME(header.xyzt_units);
int spaceunit = XYZT_TO_SPACE(header.xyzt_units);
LINFO("timeunit: " << timeunit << " spaceunit: " << spaceunit);
float dt = header.pixdim[4];
float toffset = header.toffset;
switch(timeunit) {
case NIFTI_UNITS_SEC:
dt *= 1000.0f;
toffset *= 1000.0f;
break;
case NIFTI_UNITS_MSEC:
//nothing to do
break;
case NIFTI_UNITS_USEC:
dt /= 1000.0f;
toffset /= 1000.0f;
break;
}
switch(spaceunit) {
case NIFTI_UNITS_MM:
//nothing to do
break;
case NIFTI_UNITS_METER:
spacing *= 1000.0f;
LWARNING("Units: meter");
break;
case NIFTI_UNITS_MICRON:
spacing /= 1000.0f;
LWARNING("Units: micron");
break;
case NIFTI_UNITS_UNKNOWN:
default:
LWARNING("Unknown space unit!");
break;
}
LINFO("Datatype: " << header.datatype);
std::string voreenVoxelType = "";
RealWorldMapping denormalize;
bool applyRWM = header.scl_slope != 0.0f;
switch(header.intent_code) {
case IC_INTENT_SYMMATRIX: /* parameter at each voxel is symmetrical matrix */
//TODO: should be relatively easy (=> tensors)
case IC_INTENT_DISPVECT: /* parameter at each voxel is displacement vector */
case IC_INTENT_VECTOR: /* parameter at each voxel is vector */
//TODO: should be relatively easy
case IC_INTENT_GENMATRIX: /* parameter at each voxel is matrix */
//TODO: should be relatively easy
case IC_INTENT_POINTSET: /* value at each voxel is spatial coordinate (vertices/nodes of surface mesh) */
case IC_INTENT_TRIANGLE: /* value at each voxel is spatial coordinate (vertices/nodes of surface mesh) */
case IC_INTENT_QUATERNION:
throw tgt::UnsupportedFormatException("Unsupported intent code!");
break;
case IC_INTENT_ESTIMATE: /* parameter for estimate in intent_name */
case IC_INTENT_LABEL: /* parameter at each voxel is index to label defined in aux_file */
case IC_INTENT_NEURONAME: /* parameter at each voxel is index to label in NeuroNames label set */
case IC_INTENT_DIMLESS: /* dimensionless value */
case IC_INTENT_NONE:
break;
default:
LWARNING("Unhandled intent code");
break;
}
//if (header.intent_code == IC_INTENT_SYMMATRIX) {
//h.objectModel_ = "TENSOR_FUSION_LOW";
//}
if(voreenVoxelType == "") {
switch(header.datatype) {
case DT_UNSIGNED_CHAR:
voreenVoxelType = "uint8";
denormalize = RealWorldMapping::createDenormalizingMapping<uint8_t>();
break;
case DT_SIGNED_SHORT:
voreenVoxelType = "int16";
denormalize = RealWorldMapping::createDenormalizingMapping<int16_t>();
break;
case DT_SIGNED_INT:
voreenVoxelType = "int32";
denormalize = RealWorldMapping::createDenormalizingMapping<int32_t>();
break;
case DT_FLOAT:
voreenVoxelType = "float";
break;
case DT_DOUBLE:
voreenVoxelType = "double";
break;
case DT_RGB:
voreenVoxelType = "Vector3(uint8)";
applyRWM = false;
break;
case DT_RGBA32: /* 4 byte RGBA (32 bits/voxel) */
voreenVoxelType = "Vector4(uint8)";
applyRWM = false;
break;
case DT_INT8: /* signed char (8 bits) */
voreenVoxelType = "int8";
break;
case DT_UINT16: /* unsigned short (16 bits) */
voreenVoxelType = "uint16";
denormalize = RealWorldMapping::createDenormalizingMapping<uint16_t>();
break;
case DT_UINT32: /* unsigned int (32 bits) */
voreenVoxelType = "uint32";
denormalize = RealWorldMapping::createDenormalizingMapping<uint32_t>();
break;
case DT_INT64: /* long long (64 bits) */
case DT_UINT64: /* unsigned long long (64 bits) */
case DT_FLOAT128: /* long double (128 bits) */
case DT_COMPLEX128: /* double pair (128 bits) */
case DT_COMPLEX256: /* long double pair (256 bits) */
case DT_ALL:
case DT_COMPLEX:
case 0: //DT_NONE/DT_UNKNOWN
case DT_BINARY:
default:
throw tgt::UnsupportedFormatException("Unsupported datatype!");
}
}
RealWorldMapping rwm(header.scl_slope, header.scl_inter, "");
int headerskip = static_cast<uint16_t>(header.vox_offset);
std::string rawFilename = fileName;
if(!standalone)
rawFilename = getRelatedImgFileName(fileName);
mat4 pToW = mat4::identity;
//Calculate transformation:
if(header.sform_code > 0) {
mat4 vToW(header.srow_x[0], header.srow_x[1], header.srow_x[2], header.srow_x[3],
header.srow_y[0], header.srow_y[1], header.srow_y[2], header.srow_y[3],
header.srow_z[0], header.srow_z[1], header.srow_z[2], header.srow_z[3],
0.0f, 0.0f, 0.0f, 1.0f);
mat4 wToV = mat4::identity;
if(!vToW.invert(wToV)) {
LERROR("Failed to invert voxel to world matrix!");
}
mat4 vToP = mat4::createScale(spacing); //no offset
pToW = vToP * wToV;
}
else if(header.qform_code > 0) {
float b = header.quatern_b;
float c = header.quatern_c;
float d = header.quatern_d;
float a = static_cast<float>(sqrt(1.0-(b*b+c*c+d*d)));
mat4 rot2(a*a+b*b-c*c-d*d, 2*b*c-2*a*d, 2*b*d+2*a*c, 0.0f,
2*b*c+2*a*d, a*a+c*c-b*b-d*d, 2*c*d-2*a*b, 0.0f,
2*b*d-2*a*c, 2*c*d+2*a*b, a*a+d*d-c*c-b*b, 0.0f,
0.0f, 0.0f, 0.0f, 1.0f);
float qfac = header.pixdim[0];
if(fabs(qfac) < 0.1f)
qfac = 1.0f;
mat4 sc = mat4::createScale(vec3(1.0f, 1.0f, qfac));
mat4 os = mat4::createTranslation(vec3(header.qoffset_x, header.qoffset_y, header.qoffset_z));
pToW = os * rot2 * sc;
}
// Nifti transformations give us the center of the first voxel, we translate to correct:
pToW = pToW * mat4::createTranslation(-spacing * 0.5f);
VolumeCollection* vc = new VolumeCollection();
size_t volSize = hmul(tgt::svec3(dimensions)) * (header.bitpix / 8);
int start = 0;
int stop = numVolumes;
if(volId != -1) {
//we want to load a single volume:
start = volId;
stop = start + 1;
}
for(int i=start; i<stop; i++) {
VolumeRepresentation* volume = new VolumeDisk(rawFilename, voreenVoxelType, dimensions, headerskip + (i * volSize), bigEndian);
Volume* vh = new Volume(volume, spacing, vec3(0.0f));
VolumeURL origin(fileName);
origin.addSearchParameter("volumeId", itos(i));
vh->setOrigin(origin);
vh->setPhysicalToWorldMatrix(pToW);
vh->setMetaDataValue<StringMetaData>("Description", std::string(header.descrip));
//vh->addMetaData("ActualFrameDuration", new IntMetaData(ih_.frame_duration));
//vh->addMetaData("FrameTime", new IntMetaData(ih_.frame_start_time));
vh->setMetaDataValue<IntMetaData>("FrameTime", static_cast<int>(toffset + (i * dt)));
if(applyRWM)
vh->setRealWorldMapping(RealWorldMapping::combine(denormalize, rwm));
vc->add(vh);
}
return vc;
}
