VolumeCollection* AnalyzeVolumeReader::readAnalyze(const std::string &fileName)
throw (tgt::FileException, std::bad_alloc)
{
LWARNING("Loading analyze file " << fileName);
LWARNING("Related img file: " << getRelatedImgFileName(fileName));
std::ifstream file(fileName.c_str(), std::ios::in | std::ios::binary);
if(!file) {
throw tgt::FileNotFoundException("Failed to open file: ", fileName);
}
file.seekg(0, std::ios::end);
std::streamoff fileSize = file.tellg();
file.seekg(0, std::ios::beg);
if(fileSize != 348)
LWARNING("Filesize != 348");
header_key header;
if (!file.read((char*)&header, sizeof(header))) {
throw tgt::CorruptedFileException("Failed to read header!", fileName);
}
image_dimension dimension;
if (!file.read((char*)&dimension, sizeof(dimension))) {
throw tgt::CorruptedFileException("Failed to read dimensions!", fileName);
}
data_history history;
if (!file.read((char*)&history, sizeof(history))) {
throw tgt::CorruptedFileException("Failed to read history!", fileName);
}
bool bigEndian = false;
//check if swap is necessary:
if((dimension.dim[0] < 0) || (dimension.dim[0] > 15)) {
bigEndian = true;
header.swapEndianess();
dimension.swapEndianess();
history.swapEndianess();
}
RawVolumeReader::ReadHints h;
h.dimensions_.x = dimension.dim[1];
h.dimensions_.y = dimension.dim[2];
h.dimensions_.z = dimension.dim[3];
LINFO("Resolution: " << h.dimensions_);
if (hor(lessThanEqual(h.dimensions_, ivec3(0)))) {
LERROR("Invalid resolution or resolution not specified: " << h.dimensions_);
throw tgt::CorruptedFileException("error while reading data", fileName);
}
h.spacing_.x = dimension.pixdim[1];
h.spacing_.y = dimension.pixdim[2];
h.spacing_.z = dimension.pixdim[3];
LINFO("Spacing: " << h.spacing_);
LINFO("Datatype: " << dimension.datatype);
switch(dimension.datatype) {
case DT_UNSIGNED_CHAR:
h.format_ = "UCHAR";
h.objectModel_ = "I";
break;
case DT_SIGNED_SHORT:
h.format_ = "SHORT";
h.objectModel_ = "I";
break;
case DT_SIGNED_INT:
h.format_ = "INT";
h.objectModel_ = "I";
break;
case DT_FLOAT:
h.format_ = "FLOAT";
h.objectModel_ = "I";
break;
case DT_DOUBLE:
h.format_ = "DOUBLE";
h.objectModel_ = "I";
break;
case DT_RGB:
h.format_ = "UCHAR";
h.objectModel_ = "RGB";
break;
case DT_ALL:
case DT_COMPLEX:
case 0: //DT_NONE/DT_UNKNOWN
case DT_BINARY:
default:
throw tgt::UnsupportedFormatException("Unsupported datatype!");
}
h.bigEndianByteOrder_ = bigEndian;
std::string objectType;
std::string gridType;
RawVolumeReader rawReader(getProgressBar());
rawReader.setReadHints(h);
VolumeCollection* volumeCollection = rawReader.read(getRelatedImgFileName(fileName));
if (!volumeCollection->empty()) {
static_cast<VolumeHandle*>(volumeCollection->first())->setOrigin(VolumeOrigin(fileName));
oldVolumePosition(static_cast<VolumeHandle*>(volumeCollection->first()));
}
return volumeCollection;
}
VolumeCollection* AnalyzeVolumeReader::readAnalyze(const std::string &fileName, int volId)
throw (tgt::FileException, std::bad_alloc)
{
LINFO("Loading analyze file " << fileName);
LINFO("Related img file: " << getRelatedImgFileName(fileName));
std::ifstream file(fileName.c_str(), std::ios::in | std::ios::binary);
if(!file) {
throw tgt::FileNotFoundException("Failed to open file: ", fileName);
}
file.seekg(0, std::ios::end);
std::streamoff fileSize = file.tellg();
file.seekg(0, std::ios::beg);
if(fileSize != 348)
LWARNING("Filesize != 348");
header_key header;
if (!file.read((char*)&header, sizeof(header))) {
throw tgt::CorruptedFileException("Failed to read header!", fileName);
}
image_dimension dimension;
if (!file.read((char*)&dimension, sizeof(dimension))) {
throw tgt::CorruptedFileException("Failed to read dimensions!", fileName);
}
data_history history;
if (!file.read((char*)&history, sizeof(history))) {
throw tgt::CorruptedFileException("Failed to read history!", fileName);
}
bool bigEndian = false;
//check if swap is necessary:
if((dimension.dim[0] < 0) || (dimension.dim[0] > 15)) {
bigEndian = true;
header.swapEndianess();
dimension.swapEndianess();
history.swapEndianess();
}
ivec3 dimensions;
dimensions.x = dimension.dim[1];
dimensions.y = dimension.dim[2];
dimensions.z = dimension.dim[3];
LINFO("Resolution: " << dimensions);
int numVolumes = dimension.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 = dimension.pixdim[1];
spacing.y = dimension.pixdim[2];
spacing.z = dimension.pixdim[3];
LINFO("Spacing: " << spacing);
LINFO("Datatype: " << dimension.datatype);
std::string voreenVoxelType;
switch(dimension.datatype) {
case DT_UNSIGNED_CHAR:
voreenVoxelType = "uint8";
break;
case DT_SIGNED_SHORT:
voreenVoxelType = "int16";
break;
case DT_SIGNED_INT:
voreenVoxelType = "int32";
break;
case DT_FLOAT:
voreenVoxelType = "float";
break;
case DT_DOUBLE:
voreenVoxelType = "double";
break;
case DT_RGB:
voreenVoxelType = "Vector3(uint8)";
break;
case DT_ALL:
case DT_COMPLEX:
case 0: //DT_NONE/DT_UNKNOWN
case DT_BINARY:
default:
throw tgt::UnsupportedFormatException("Unsupported datatype!");
}
std::string objectType;
std::string gridType;
int start = 0;
int stop = numVolumes;
if(volId != -1) {
//we want to load a single volume:
start = volId;
stop = start + 1;
}
// Nifti transformations give us the center of the first voxel, we translate to correct:
mat4 pToW = mat4::createTranslation(-spacing * 0.5f);
VolumeCollection* vc = new VolumeCollection();
size_t volSize = hmul(tgt::svec3(dimensions)) * (dimension.bitpix / 8);
for(int i=start; i<stop; i++) {
VolumeRepresentation* volume = new VolumeDisk(getRelatedImgFileName(fileName), voreenVoxelType, dimensions, i * volSize, bigEndian);
Volume* vh = new Volume(volume, spacing, vec3(0.0f));
vh->setOrigin(VolumeURL(fileName));
vh->setPhysicalToWorldMatrix(pToW);
VolumeURL origin(fileName);
origin.addSearchParameter("volumeId", itos(i));
vh->setOrigin(origin);
vc->add(vh);
}
return vc;
}
VolumeCollection* AnalyzeVolumeReader::readNifti(const std::string &fileName, bool standalone)
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);
}
//file.seekg(0, std::ios::end);
//int fileSize = file.tellg();
//file.seekg(0, std::ios::beg);
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 hdr+img Nifti as standalone!");
standalone = false;
}
else
throw tgt::CorruptedFileException("Not a Nifti header!", fileName);
RawVolumeReader::ReadHints h;
h.dimensions_.x = header.dim[1];
h.dimensions_.y = header.dim[2];
h.dimensions_.z = header.dim[3];
LINFO("Resolution: " << h.dimensions_);
if (hor(lessThanEqual(h.dimensions_, ivec3(0)))) {
LERROR("Invalid resolution or resolution not specified: " << h.dimensions_);
throw tgt::CorruptedFileException("error while reading data", fileName);
}
h.spacing_.x = header.pixdim[1];
h.spacing_.y = header.pixdim[2];
h.spacing_.z = header.pixdim[3];
LINFO("Spacing: " << h.spacing_);
LINFO("Datatype: " << header.datatype);
//TODO: support more datatypes
if(header.datatype > 128) {
header.datatype -= 128;
h.objectModel_ = "RGB";
}
else
h.objectModel_ = "I";
switch(header.datatype) {
case DT_UNSIGNED_CHAR:
h.format_ = "UCHAR";
h.objectModel_ = "I";
break;
case DT_SIGNED_SHORT:
h.format_ = "SHORT";
h.objectModel_ = "I";
break;
case DT_SIGNED_INT:
h.format_ = "INT";
h.objectModel_ = "I";
break;
case DT_FLOAT:
h.format_ = "FLOAT";
h.objectModel_ = "I";
break;
case DT_DOUBLE:
h.format_ = "DOUBLE";
h.objectModel_ = "I";
break;
case DT_RGB:
h.format_ = "UCHAR";
h.objectModel_ = "RGB";
break;
case DT_RGBA32: /* 4 byte RGBA (32 bits/voxel) */
h.format_ = "UCHAR";
h.objectModel_ = "RGBA";
break;
case DT_INT8: /* signed char (8 bits) */
h.format_ = "CHAR";
h.objectModel_ = "I";
break;
case DT_UINT16: /* unsigned short (16 bits) */
h.format_ = "USHORT";
h.objectModel_ = "I";
break;
case DT_UINT32: /* unsigned int (32 bits) */
h.format_ = "UINT";
h.objectModel_ = "I";
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!");
}
if (header.intent_code == IC_INTENT_SYMMATRIX) {
h.objectModel_ = "TENSOR_FUSION_LOW";
}
h.bigEndianByteOrder_ = bigEndian;
//std::string objectType;
//std::string gridType;
//} else if (type == "ObjectType:") {
//args >> objectType;
//LDEBUG(type << " " << objectType);
//} else if (type == "GridType:") {
//args >> gridType;
//LDEBUG(type << " " << gridType);
//} else if (type == "BitsStored:") {
//args >> h.bitsStored_;
//LDEBUG(type << " " << h.bitsStored_);
//} else if (type == "Unit:") {
//args >> h.unit_;
//LDEBUG(type << " " << h.unit_);
if (standalone)
h.headerskip_ = static_cast<uint16_t>(header.vox_offset);
RawVolumeReader rawReader(getProgressBar());
rawReader.setReadHints(h);
VolumeCollection* volumeCollection = 0;
if(standalone)
volumeCollection = rawReader.read(fileName);
else
volumeCollection = rawReader.read(getRelatedImgFileName(fileName));
if (!volumeCollection->empty()) {
static_cast<VolumeHandle*>(volumeCollection->first())->setOrigin(VolumeOrigin(fileName));
oldVolumePosition(static_cast<VolumeHandle*>(volumeCollection->first()));
}
return volumeCollection;
}
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;
}
