static igtl::TransformMessage::Pointer createIGTLTransformMessage(Image::pointer image) {
// Create transform message from the scene graph information of image
igtl::Matrix4x4 matrix;
AffineTransformation::pointer T = image->getSceneGraphNode()->getTransformation();
for(int i = 0; i < 4; i++) {
for(int j = 0; j < 4; j++) {
matrix[i][j] = T->getTransform().matrix()(i,j);
}}
igtl::TransformMessage::Pointer message = igtl::TransformMessage::New();
message->SetDeviceName("DummyTransform");
message->SetMatrix(matrix);
return message;
}
void MetaImageImporter::execute() {
if(mFilename == "")
throw Exception("Filename was not set in MetaImageImporter");
// Open and parse mhd file
std::fstream mhdFile;
mhdFile.open(mFilename.c_str(), std::fstream::in);
if(!mhdFile.is_open())
throw FileNotFoundException(mFilename);
std::string line;
std::string rawFilename;
bool sizeFound = false,
rawFilenameFound = false,
typeFound = false,
dimensionsFound = false;
std::string typeName;
// Find NDims first
bool imageIs3D = false;
do {
std::getline(mhdFile, line);
if(line.substr(0, 5) == "NDims") {
if(line.substr(5+3, 1) == "3") {
imageIs3D = true;
} else if(line.substr(5+3, 1) == "2") {
imageIs3D = false;
}
dimensionsFound = true;
}
} while(!mhdFile.eof() && !dimensionsFound);
if(!dimensionsFound)
throw Exception("NDims not found in metaimage file.");
// Reset and start reading file from beginning
mhdFile.seekg(0);
unsigned int width, height, depth = 1;
unsigned int nrOfComponents = 1;
Image::pointer output = getOutputData<Image>(0);
Vector3f spacing(1,1,1), offset(0,0,0), centerOfRotation(0,0,0);
Matrix3f transformMatrix = Matrix3f::Identity();
bool isCompressed = false;
std::size_t compressedDataSize = 0;
do{
std::getline(mhdFile, line);
boost::trim(line);
if(line.size() == 0) // line is empty
continue;
int firstSpace = line.find(" ");
std::string key = line.substr(0, firstSpace);
boost::trim(key);
int equalSignPos = line.find("=");
std::string value = line.substr(equalSignPos+1);
boost::trim(value);
if(key == "DimSize") {
std::vector<std::string> values;
boost::split(values, value, boost::is_any_of(" "));
// Remove any empty values:
values.erase(std::remove(values.begin(), values.end(), ""), values.end());
if(imageIs3D) {
if(values.size() != 3)
throw Exception("DimSize in MetaImage file did not contain 3 numbers");
depth = boost::lexical_cast<int>(values[2]);
} else {
if(values.size() != 2)
throw Exception("DimSize in MetaImage file did not contain 2 numbers");
}
width = boost::lexical_cast<int>(values[0]);
height = boost::lexical_cast<int>(values[1]);
sizeFound = true;
} else if(key == "CompressedData" && value == "True") {
isCompressed = true;
} else if(key == "CompressedDataSize") {
compressedDataSize = boost::lexical_cast<int>(value);
} else if(key == "ElementDataFile") {
rawFilename = value;
rawFilenameFound = true;
// Remove any trailing spaces
int pos = rawFilename.find(" ");
if(pos > 0)
rawFilename = rawFilename.substr(0,pos);
// Get path name
pos = mFilename.rfind('/');
if(pos > 0)
rawFilename = mFilename.substr(0,pos+1) + rawFilename;
} else if(key == "ElementType") {
typeFound = true;
typeName = value;
// Remove any trailing spaces
int pos = typeName.find(" ");
if(pos > 0)
typeName = typeName.substr(0,pos);
if(typeName == "MET_SHORT") {
} else if(typeName == "MET_USHORT") {
} else if(typeName == "MET_CHAR") {
} else if(typeName == "MET_UCHAR") {
} else if(typeName == "MET_INT") {
} else if(typeName == "MET_UINT") {
} else if(typeName == "MET_FLOAT") {
} else {
throw Exception("Trying to read volume of unsupported data type", __LINE__, __FILE__);
}
} else if(key == "ElementNumberOfChannels") {
nrOfComponents = boost::lexical_cast<int>(value.c_str());
if(nrOfComponents <= 0)
throw Exception("Error in reading the number of components in the MetaImageImporter");
} else if(key == "ElementSpacing") {
std::vector<std::string> values;
boost::split(values, value, boost::is_any_of(" "));
// Remove any empty values:
values.erase(std::remove(values.begin(), values.end(), ""), values.end());
if(imageIs3D) {
if(values.size() != 3)
throw Exception("ElementSpacing in MetaImage file did not contain 3 numbers");
spacing[0] = boost::lexical_cast<float>(values[0]);
spacing[1] = boost::lexical_cast<float>(values[1]);
spacing[2] = boost::lexical_cast<float>(values[2]);
} else {
if(values.size() != 2 && values.size() != 3)
throw Exception("ElementSpacing in MetaImage file did not contain 2 or 3 numbers");
spacing[0] = boost::lexical_cast<float>(values[0]);
spacing[1] = boost::lexical_cast<float>(values[1]);
if(values.size() == 2) {
spacing[2] = 1;
} else {
spacing[2] = boost::lexical_cast<float>(values[2]);
}
}
} else if(key == "CenterOfRotation") {
//reportInfo() << "WARNING: CenterOfRotation in Metaimage file ignored" << Reporter::end;
std::vector<std::string> values;
boost::split(values, value, boost::is_any_of(" "));
// Remove any empty values:
values.erase(std::remove(values.begin(), values.end(), ""), values.end());
if(imageIs3D) {
if(values.size() != 3)
throw Exception("CenterOfRotation in MetaImage file did not contain 3 numbers");
centerOfRotation[0] = boost::lexical_cast<float>(values[0]);
centerOfRotation[1] = boost::lexical_cast<float>(values[1]);
centerOfRotation[2] = boost::lexical_cast<float>(values[2]);
} else {
if(values.size() != 2 && values.size() != 3)
throw Exception("CenterOfRotation in MetaImage file did not contain 2 or 3 numbers");
centerOfRotation[0] = boost::lexical_cast<float>(values[0]);
centerOfRotation[1] = boost::lexical_cast<float>(values[1]);
if(values.size() == 2) {
centerOfRotation[2] = 0;
} else {
centerOfRotation[2] = boost::lexical_cast<float>(values[2]);
}
}
} else if(key == "Offset" || key == "Origin" || key == "Position") {
std::vector<std::string> values;
boost::split(values, value, boost::is_any_of(" "));
// Remove any empty values:
values.erase(std::remove(values.begin(), values.end(), ""), values.end());
if(values.size() != 3)
throw Exception("Offset/Origin/Position in MetaImage file did not contain 3 numbers");
offset[0] = boost::lexical_cast<float>(values[0].c_str());
offset[1] = boost::lexical_cast<float>(values[1].c_str());
offset[2] = boost::lexical_cast<float>(values[2].c_str());
} else if(key == "TransformMatrix" || key == "Rotation" || key == "Orientation") {
std::vector<std::string> values;
boost::split(values, value, boost::is_any_of(" "));
// Remove any empty values:
values.erase(std::remove(values.begin(), values.end(), ""), values.end());
if(values.size() != 9)
throw Exception("Encountered a transform/orientation/rotation matrix with incorrect number of elements in the MetaImageImporter");
for(unsigned int i = 0; i < 3; i++) {
for(unsigned int j = 0; j < 3; j++) {
transformMatrix(j,i) = boost::lexical_cast<float>(values[j+i*3].c_str());
}}
}
} while(!mhdFile.eof());
mhdFile.close();
if(!sizeFound || !rawFilenameFound || !typeFound || !dimensionsFound)
throw Exception("Error reading the mhd file", __LINE__, __FILE__);
void * data;
DataType type;
if(typeName == "MET_SHORT") {
type = TYPE_INT16;
data = readRawData<short>(rawFilename, width, height, depth, nrOfComponents, isCompressed, compressedDataSize);
} else if(typeName == "MET_USHORT") {
type = TYPE_UINT16;
data = readRawData<unsigned short>(rawFilename, width, height, depth, nrOfComponents, isCompressed, compressedDataSize);
} else if(typeName == "MET_CHAR") {
type = TYPE_INT8;
data = readRawData<char>(rawFilename, width, height, depth, nrOfComponents, isCompressed, compressedDataSize);
} else if(typeName == "MET_UCHAR") {
type = TYPE_UINT8;
data = readRawData<unsigned char>(rawFilename, width, height, depth, nrOfComponents, isCompressed, compressedDataSize);
} else if(typeName == "MET_FLOAT") {
type = TYPE_FLOAT;
data = readRawData<float>(rawFilename, width, height, depth, nrOfComponents, isCompressed, compressedDataSize);
}
if(imageIs3D) {
output->create(width,height,depth,type,nrOfComponents,getMainDevice(),data);
} else {
output->create(width,height,type,nrOfComponents,getMainDevice(),data);
}
output->setSpacing(spacing);
// Create transformation
AffineTransformation::pointer T = AffineTransformation::New();
T->translation() = offset;
T->linear() = transformMatrix;
output->getSceneGraphNode()->setTransformation(T);
// Clean up
deleteArray(data, type);
}