/*!
\brief Modify input tractogram: fiber resampling, compression, pruning and transformation.
*/
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Fiber Processing");
parser.setCategory("Fiber Tracking and Processing Methods");
parser.setDescription("Modify input tractogram: fiber resampling, compression, pruning and transformation.");
parser.setContributor("MIC");
parser.setArgumentPrefix("--", "-");
parser.beginGroup("1. Mandatory arguments:");
parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "Input fiber bundle (.fib, .trk, .tck)", us::Any(), false, false, false, mitkCommandLineParser::Input);
parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "Output fiber bundle (.fib, .trk)", us::Any(), false, false, false, mitkCommandLineParser::Output);
parser.endGroup();
parser.beginGroup("2. Resampling:");
parser.addArgument("spline_resampling", "", mitkCommandLineParser::Float, "Spline resampling:", "Resample fiber using splines with the given point distance (in mm)");
parser.addArgument("linear_resampling", "", mitkCommandLineParser::Float, "Linear resampling:", "Resample fiber linearly with the given point distance (in mm)");
parser.addArgument("num_resampling", "", mitkCommandLineParser::Int, "Num. fiber points resampling:", "Resample all fibers to the given number of points");
parser.addArgument("compress", "", mitkCommandLineParser::Float, "Compress:", "Compress fiber using the given error threshold (in mm)");
parser.endGroup();
parser.beginGroup("3. Filtering:");
parser.addArgument("min_length", "", mitkCommandLineParser::Float, "Minimum length:", "Minimum fiber length (in mm)");
parser.addArgument("max_length", "", mitkCommandLineParser::Float, "Maximum length:", "Maximum fiber length (in mm)");
parser.addArgument("max_angle", "", mitkCommandLineParser::Float, "Maximum angle:", "Maximum angular STDEV (in degree) over given distance");
parser.addArgument("max_angle_dist", "", mitkCommandLineParser::Float, "Distance:", "Distance in mm", 10);
parser.addArgument("remove", "", mitkCommandLineParser::Bool, "Remove fibers exceeding curvature threshold:", "If false, only the high curvature parts are removed");
parser.addArgument("subsample", "", mitkCommandLineParser::Float, "Randomly select fraction of streamlines:", "Randomly select the specified fraction of streamlines from the input tractogram");
parser.addArgument("random_subsample", "", mitkCommandLineParser::Bool, "Randomly seed subsampling:", "Randomly seed subsampling. Else, use seed 0.");
parser.endGroup();
parser.beginGroup("4. Transformation:");
parser.addArgument("mirror", "", mitkCommandLineParser::Int, "Invert coordinates:", "Invert fiber coordinates XYZ (e.g. 010 to invert y-coordinate of each fiber point)");
parser.addArgument("rotate_x", "", mitkCommandLineParser::Float, "Rotate x-axis:", "Rotate around x-axis (in deg)");
parser.addArgument("rotate_y", "", mitkCommandLineParser::Float, "Rotate y-axis:", "Rotate around y-axis (in deg)");
parser.addArgument("rotate_z", "", mitkCommandLineParser::Float, "Rotate z-axis:", "Rotate around z-axis (in deg)");
parser.addArgument("scale_x", "", mitkCommandLineParser::Float, "Scale x-axis:", "Scale in direction of x-axis");
parser.addArgument("scale_y", "", mitkCommandLineParser::Float, "Scale y-axis:", "Scale in direction of y-axis");
parser.addArgument("scale_z", "", mitkCommandLineParser::Float, "Scale z-axis", "Scale in direction of z-axis");
parser.addArgument("translate_x", "", mitkCommandLineParser::Float, "Translate x-axis:", "Translate in direction of x-axis (in mm)");
parser.addArgument("translate_y", "", mitkCommandLineParser::Float, "Translate y-axis:", "Translate in direction of y-axis (in mm)");
parser.addArgument("translate_z", "", mitkCommandLineParser::Float, "Translate z-axis:", "Translate in direction of z-axis (in mm)");
parser.endGroup();
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
bool remove = false;
if (parsedArgs.count("remove"))
remove = us::any_cast<bool>(parsedArgs["remove"]);
bool random_subsample = false;
if (parsedArgs.count("random_subsample"))
random_subsample = us::any_cast<bool>(parsedArgs["random_subsample"]);
float spline_resampling = -1;
if (parsedArgs.count("spline_resampling"))
spline_resampling = us::any_cast<float>(parsedArgs["spline_resampling"]);
float linear_resampling = -1;
if (parsedArgs.count("linear_resampling"))
linear_resampling = us::any_cast<float>(parsedArgs["linear_resampling"]);
int num_resampling = -1;
if (parsedArgs.count("num_resampling"))
num_resampling = us::any_cast<int>(parsedArgs["num_resampling"]);
float subsample = -1;
if (parsedArgs.count("subsample"))
subsample = us::any_cast<float>(parsedArgs["subsample"]);
float compress = -1;
if (parsedArgs.count("compress"))
compress = us::any_cast<float>(parsedArgs["compress"]);
float minFiberLength = -1;
if (parsedArgs.count("min_length"))
minFiberLength = us::any_cast<float>(parsedArgs["min_length"]);
float maxFiberLength = -1;
if (parsedArgs.count("max_length"))
maxFiberLength = us::any_cast<float>(parsedArgs["max_length"]);
float max_angle_dist = 10;
if (parsedArgs.count("max_angle_dist"))
max_angle_dist = us::any_cast<float>(parsedArgs["max_angle_dist"]);
float maxAngularDev = -1;
if (parsedArgs.count("max_angle"))
maxAngularDev = us::any_cast<float>(parsedArgs["max_angle"]);
int axis = 0;
if (parsedArgs.count("mirror"))
axis = us::any_cast<int>(parsedArgs["mirror"]);
float rotateX = 0;
if (parsedArgs.count("rotate_x"))
rotateX = us::any_cast<float>(parsedArgs["rotate_x"]);
float rotateY = 0;
if (parsedArgs.count("rotate_y"))
rotateY = us::any_cast<float>(parsedArgs["rotate_y"]);
float rotateZ = 0;
if (parsedArgs.count("rotate_z"))
rotateZ = us::any_cast<float>(parsedArgs["rotate_z"]);
float scaleX = 0;
if (parsedArgs.count("scale_x"))
scaleX = us::any_cast<float>(parsedArgs["scale_x"]);
float scaleY = 0;
if (parsedArgs.count("scale_y"))
scaleY = us::any_cast<float>(parsedArgs["scale_y"]);
float scaleZ = 0;
if (parsedArgs.count("scale_z"))
scaleZ = us::any_cast<float>(parsedArgs["scale_z"]);
float translateX = 0;
if (parsedArgs.count("translate_x"))
translateX = us::any_cast<float>(parsedArgs["translate_x"]);
float translateY = 0;
if (parsedArgs.count("translate_y"))
translateY = us::any_cast<float>(parsedArgs["translate_y"]);
float translateZ = 0;
if (parsedArgs.count("translate_z"))
translateZ = us::any_cast<float>(parsedArgs["translate_z"]);
std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
std::string outFileName = us::any_cast<std::string>(parsedArgs["o"]);
try
{
mitk::FiberBundle::Pointer fib = LoadFib(inFileName);
if (subsample>0)
fib = fib->SubsampleFibers(subsample, random_subsample);
if (maxAngularDev>0)
{
auto filter = itk::FiberCurvatureFilter::New();
filter->SetInputFiberBundle(fib);
filter->SetAngularDeviation(maxAngularDev);
filter->SetDistance(max_angle_dist);
filter->SetRemoveFibers(remove);
filter->Update();
fib = filter->GetOutputFiberBundle();
}
if (minFiberLength>0)
fib->RemoveShortFibers(minFiberLength);
if (maxFiberLength>0)
fib->RemoveLongFibers(maxFiberLength);
if (spline_resampling>0)
fib->ResampleSpline(spline_resampling);
if (linear_resampling>0)
fib->ResampleLinear(linear_resampling);
if (num_resampling>0)
fib->ResampleToNumPoints(num_resampling);
if (compress>0)
fib->Compress(compress);
if (axis/100==1)
fib->MirrorFibers(0);
if ((axis%100)/10==1)
fib->MirrorFibers(1);
if (axis%10==1)
fib->MirrorFibers(2);
if (rotateX > 0 || rotateY > 0 || rotateZ > 0){
std::cout << "Rotate " << rotateX << " " << rotateY << " " << rotateZ;
fib->RotateAroundAxis(rotateX, rotateY, rotateZ);
}
if (translateX > 0 || translateY > 0 || translateZ > 0){
fib->TranslateFibers(translateX, translateY, translateZ);
}
if (scaleX > 0 || scaleY > 0 || scaleZ > 0)
fib->ScaleFibers(scaleX, scaleY, scaleZ);
mitk::IOUtil::Save(fib.GetPointer(), outFileName );
}
catch (itk::ExceptionObject e)
{
std::cout << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
/*!
\brief Modify input tractogram: fiber resampling, compression, pruning and transformation.
*/
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Fiber Processing");
parser.setCategory("Fiber Tracking and Processing Methods");
parser.setDescription("Modify input tractogram: fiber resampling, compression, pruning and transformation.");
parser.setContributor("MBI");
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", mitkCommandLineParser::InputFile, "Input:", "input fiber bundle (.fib)", us::Any(), false);
parser.addArgument("outFile", "o", mitkCommandLineParser::OutputFile, "Output:", "output fiber bundle (.fib)", us::Any(), false);
parser.addArgument("smooth", "s", mitkCommandLineParser::Float, "Spline resampling:", "Resample fiber using splines with the given point distance (in mm)");
parser.addArgument("compress", "c", mitkCommandLineParser::Float, "Compress:", "Compress fiber using the given error threshold (in mm)");
parser.addArgument("minLength", "l", mitkCommandLineParser::Float, "Minimum length:", "Minimum fiber length (in mm)");
parser.addArgument("maxLength", "m", mitkCommandLineParser::Float, "Maximum length:", "Maximum fiber length (in mm)");
parser.addArgument("maxAngle", "a", mitkCommandLineParser::Float, "Maximum angle:", "Maximum angular STDEV over 1cm (in degree)");
parser.addArgument("mirror", "p", mitkCommandLineParser::Int, "Invert coordinates:", "Invert fiber coordinates XYZ (e.g. 010 to invert y-coordinate of each fiber point)");
parser.addArgument("rotate-x", "rx", mitkCommandLineParser::Float, "Rotate x-axis:", "Rotate around x-axis (if copy is given the copy is rotated, in deg)");
parser.addArgument("rotate-y", "ry", mitkCommandLineParser::Float, "Rotate y-axis:", "Rotate around y-axis (if copy is given the copy is rotated, in deg)");
parser.addArgument("rotate-z", "rz", mitkCommandLineParser::Float, "Rotate z-axis:", "Rotate around z-axis (if copy is given the copy is rotated, in deg)");
parser.addArgument("scale-x", "sx", mitkCommandLineParser::Float, "Scale x-axis:", "Scale in direction of x-axis (if copy is given the copy is scaled)");
parser.addArgument("scale-y", "sy", mitkCommandLineParser::Float, "Scale y-axis:", "Scale in direction of y-axis (if copy is given the copy is scaled)");
parser.addArgument("scale-z", "sz", mitkCommandLineParser::Float, "Scale z-axis", "Scale in direction of z-axis (if copy is given the copy is scaled)");
parser.addArgument("translate-x", "tx", mitkCommandLineParser::Float, "Translate x-axis:", "Translate in direction of x-axis (if copy is given the copy is translated, in mm)");
parser.addArgument("translate-y", "ty", mitkCommandLineParser::Float, "Translate y-axis:", "Translate in direction of y-axis (if copy is given the copy is translated, in mm)");
parser.addArgument("translate-z", "tz", mitkCommandLineParser::Float, "Translate z-axis:", "Translate in direction of z-axis (if copy is given the copy is translated, in mm)");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
float smoothDist = -1;
if (parsedArgs.count("smooth"))
smoothDist = us::any_cast<float>(parsedArgs["smooth"]);
float compress = -1;
if (parsedArgs.count("compress"))
compress = us::any_cast<float>(parsedArgs["compress"]);
float minFiberLength = -1;
if (parsedArgs.count("minLength"))
minFiberLength = us::any_cast<float>(parsedArgs["minLength"]);
float maxFiberLength = -1;
if (parsedArgs.count("maxLength"))
maxFiberLength = us::any_cast<float>(parsedArgs["maxLength"]);
float maxAngularDev = -1;
if (parsedArgs.count("maxAngle"))
maxAngularDev = us::any_cast<float>(parsedArgs["maxAngle"]);
int axis = 0;
if (parsedArgs.count("mirror"))
axis = us::any_cast<int>(parsedArgs["mirror"]);
float rotateX = 0;
if (parsedArgs.count("rotate-x"))
rotateX = us::any_cast<float>(parsedArgs["rotate-x"]);
float rotateY = 0;
if (parsedArgs.count("rotate-y"))
rotateY = us::any_cast<float>(parsedArgs["rotate-y"]);
float rotateZ = 0;
if (parsedArgs.count("rotate-z"))
rotateZ = us::any_cast<float>(parsedArgs["rotate-z"]);
float scaleX = 0;
if (parsedArgs.count("scale-x"))
scaleX = us::any_cast<float>(parsedArgs["scale-x"]);
float scaleY = 0;
if (parsedArgs.count("scale-y"))
scaleY = us::any_cast<float>(parsedArgs["scale-y"]);
float scaleZ = 0;
if (parsedArgs.count("scale-z"))
scaleZ = us::any_cast<float>(parsedArgs["scale-z"]);
float translateX = 0;
if (parsedArgs.count("translate-x"))
translateX = us::any_cast<float>(parsedArgs["translate-x"]);
float translateY = 0;
if (parsedArgs.count("translate-y"))
translateY = us::any_cast<float>(parsedArgs["translate-y"]);
float translateZ = 0;
if (parsedArgs.count("translate-z"))
translateZ = us::any_cast<float>(parsedArgs["translate-z"]);
string inFileName = us::any_cast<string>(parsedArgs["input"]);
string outFileName = us::any_cast<string>(parsedArgs["outFile"]);
try
{
mitk::FiberBundle::Pointer fib = LoadFib(inFileName);
if (minFiberLength>0)
fib->RemoveShortFibers(minFiberLength);
if (maxFiberLength>0)
fib->RemoveLongFibers(maxFiberLength);
if (maxAngularDev>0)
{
auto filter = itk::FiberCurvatureFilter::New();
filter->SetInputFiberBundle(fib);
filter->SetAngularDeviation(maxAngularDev);
filter->SetDistance(10);
filter->SetRemoveFibers(true);
filter->Update();
fib = filter->GetOutputFiberBundle();
}
if (smoothDist>0)
fib->ResampleSpline(smoothDist);
if (compress>0)
fib->Compress(compress);
if (axis/100==1)
fib->MirrorFibers(0);
if ((axis%100)/10==1)
fib->MirrorFibers(1);
if (axis%10==1)
fib->MirrorFibers(2);
if (rotateX > 0 || rotateY > 0 || rotateZ > 0){
std::cout << "Rotate " << rotateX << " " << rotateY << " " << rotateZ;
fib->RotateAroundAxis(rotateX, rotateY, rotateZ);
}
if (translateX > 0 || translateY > 0 || translateZ > 0){
fib->TranslateFibers(translateX, translateY, translateZ);
}
if (scaleX > 0 || scaleY > 0 || scaleZ > 0)
fib->ScaleFibers(scaleX, scaleY, scaleZ);
mitk::IOUtil::SaveBaseData(fib.GetPointer(), outFileName );
}
catch (itk::ExceptionObject e)
{
std::cout << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
