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::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;
}
VolumeList* AmiraMeshReader::readMetaFile(const std::string &fileName, size_t firstSlice, size_t lastSlice, int timeframe)
throw (tgt::FileException, std::bad_alloc)
{
bool error = false;
const char* FileName = fileName.c_str();
FILE* fp = fopen(FileName, "rb");
if (!fp)
{
LERROR("Could not find :" << FileName);
error = true;
goto K;
}
char buffer[2048];
fread(buffer, sizeof(char), 2047, fp);
buffer[2047] = '\0'; //The following string routines prefer null-terminated strings
if (!strstr(buffer, "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1") && !strstr(buffer, "# AmiraMesh 3D BINARY 2.0"))
{
LERROR("Not a proper AmiraMesh file.");
fclose(fp);
error = true;
goto K;
}
//Find the Lattice definition, i.e., the dimensions of the uniform grid
int xDim(0), yDim(0), zDim(0);
sscanf(FindAndJump(buffer, "define Lattice"), "%d %d %d", &xDim, &yDim, &zDim);
LDEBUG("Grid Dimensions: " << xDim << " " << yDim << " " << zDim);
//Find the BoundingBox
float xmin(1.0f), ymin(1.0f), zmin(1.0f);
float xmax(-1.0f), ymax(-1.0f), zmax(-1.0f);
sscanf(FindAndJump(buffer, "BoundingBox"), "%g %g %g %g %g %g", &xmin, &xmax, &ymin, &ymax, &zmin, &zmax);
LDEBUG("BoundingBox in x-Direction: [" << xmin << " " << xmax << "]");
LDEBUG("BoundingBox in x-Direction: [" << ymin << " " << ymax << "]");
LDEBUG("BoundingBox in x-Direction: [" << zmin << " " << zmax << "]");
//Is it a uniform grid? We need this only for the sanity check below.
const bool bIsUniform = (strstr(buffer, "CoordType \"uniform\"") != NULL);
LDEBUG("GridType: " << bIsUniform ? "uniform" : "UNKNOWN");
//Type of the field: scalar, vector
int NumComponents(0);
if (strstr(buffer, "Lattice { float Data }"))
{
//Scalar field
NumComponents = 1;
}
else
{
//A field with more than one component, i.e., a vector field
sscanf(FindAndJump(buffer, "Lattice { float["), "%d", &NumComponents);
}
LDEBUG("Number of Components: " << NumComponents);
//Sanity check
if (xDim <= 0 || yDim <= 0 || zDim <= 0
|| xmin > xmax || ymin > ymax || zmin > zmax
|| !bIsUniform || NumComponents <= 0)
{
printf("Something went wrong\n");
fclose(fp);
error = true;
goto K;
}
K : RawVolumeReader::ReadHints h;
std::string objectFilename = fileName;
h.headerskip_ = strstr(buffer, "# Data section follows") - buffer;
//Set the file pointer to the beginning of "# Data section follows"
fseek(fp, h.headerskip_, SEEK_SET);
//Consume this line, which is "# Data section follows"
char buf1[2048];
fgets(buf1, 2047, fp);
int l1 = strlen(buf1);
//Consume the next line, which is "@1"
char buf2[2048];
fgets(buf2, 2047, fp);
int l2 = strlen(buf2);
vec3 sliceThickness = vec3(1.f, 1.f, 1.f);
int numFrames = NumComponents;
h.dimensions_.x = xDim;
h.dimensions_.y = yDim;
h.dimensions_.z = zDim;
h.format_ = "FLOAT";
h.objectModel_ = "I";
h.bigEndianByteOrder_ = false;
h.headerskip_ += (l1 + l2);
LDEBUG("Header size : " << h.headerskip_);
if (hor(lessThanEqual(h.dimensions_, ivec3(0)))) {
LERROR("Invalid resolution or resolution not specified: " << h.dimensions_);
error = true;
}
h.spacing_ = sliceThickness;
h.timeStep_ = 0;
if (!error) {
RawVolumeReader rawReader(getProgressBar());
// do we have a relative path?
if ((objectFilename.substr(0, 1) != "/") && (objectFilename.substr(0, 1) != "\\") &&
(objectFilename.substr(1, 2) != ":/") && (objectFilename.substr(1, 2) != ":\\"))
{
size_t p = fileName.find_last_of("\\/");
// construct path relative to dat file
objectFilename = fileName.substr(0, p + 1) + objectFilename;
}
int start = 0;
int end = numFrames;
if (timeframe != -1) {
if (timeframe >= numFrames)
throw tgt::FileException("Specified time frame not in volume", fileName);
start = timeframe;
end = timeframe+1;
}
VolumeList* toReturn = new VolumeList();
for (int frame = start; frame < end; ++frame) {
h.timeframe_ = frame;
rawReader.setReadHints(h);
VolumeList* volumeList = rawReader.readSlices(objectFilename, firstSlice, lastSlice);
if (!volumeList->empty()) {
VolumeURL origin(fileName);
origin.addSearchParameter("timeframe", itos(frame));
Volume* vh = static_cast<Volume*>(volumeList->first());
vh->setOrigin(origin);
vh->setTimestep(static_cast<float>(frame));
oldVolumePosition(vh);
if(!h.hash_.empty())
vh->setHash(h.hash_);
toReturn->add(volumeList->first());
}
delete volumeList;
}
return toReturn;
}
else {
throw tgt::CorruptedFileException("error while reading data", fileName);
}
}
