ImageMesh::ImageMesh(const std::string & name, InputParameters parameters) :
GeneratedMesh(name, parameters),
_scale_to_one(getParam<bool>("scale_to_one")),
_cells_per_pixel(getParam<Real>("cells_per_pixel"))
{
// Set up the parameters associated with file ranges
int status = parseFileRange(_pars);
// Failure is not an option
if (status != 0)
mooseError(getFileRangeErrorMessage(status));
}
ImageMesh::ImageMesh(const InputParameters & parameters) :
GeneratedMesh(parameters),
_scale_to_one(getParam<bool>("scale_to_one")),
_cells_per_pixel(getParam<Real>("cells_per_pixel"))
{
// Set up the parameters associated with file ranges (this needs to be moved to validParams, if possible)
int status = parseFileRange(_app.getInputParameterWarehouse().getInputParameters(name()));
// Failure is not an option
if (status != 0)
mooseError(getFileRangeErrorMessage(status));
}
void
ImageFunction::initialSetup()
{
#ifdef LIBMESH_HAVE_VTK
// Get access to the Mesh object
FEProblem * fe_problem = getParam<FEProblem *>("_fe_problem");
MooseMesh & mesh = fe_problem->mesh();
// Set the dimensions from the Mesh if not set by the User
if (isParamValid("dimensions"))
_physical_dims = getParam<Point>("dimensions");
else
{
_physical_dims(0) = mesh.getParam<Real>("xmax") - mesh.getParam<Real>("xmin");
#if LIBMESH_DIM > 1
_physical_dims(1) = mesh.getParam<Real>("ymax") - mesh.getParam<Real>("ymin");
#endif
#if LIBMESH_DIM > 2
_physical_dims(2) = mesh.getParam<Real>("zmax") - mesh.getParam<Real>("zmin");
#endif
}
// Set the origin from the Mesh if not set in the input file
if (isParamValid("origin"))
_origin = getParam<Point>("origin");
else
{
_origin(0) = mesh.getParam<Real>("xmin");
#if LIBMESH_DIM > 1
_origin(1) = mesh.getParam<Real>("ymin");
#endif
#if LIBMESH_DIM > 2
_origin(2) = mesh.getParam<Real>("zmin");
#endif
}
// An array of filenames, to be filled in
std::vector<std::string> filenames;
// The file suffix, to be determined
std::string file_suffix;
// Try to parse our own file range parameters. If that fails, then
// see if the associated Mesh is an ImageMesh and use its. If that
// also fails, then we have to throw an error...
//
// The parseFileRange method sets parameters, thus a writable reference to the InputParameters
// object must be obtained from the warehouse. Generally, this should be avoided, but
// this is a special case.
int status = parseFileRange(_app.getInputParameterWarehouse().getInputParameters(_name));
if (status != 0)
{
// We don't have parameters, so see if we can get them from ImageMesh
ImageMesh * image_mesh = dynamic_cast<ImageMesh*>(&mesh);
if (!image_mesh)
mooseError("No file range parameters were provided and the Mesh is not an ImageMesh.");
// Get the ImageMesh's parameters. This should work, otherwise
// errors would already have been thrown...
const InputParameters & im_params = image_mesh->parameters();
filenames = im_params.get<std::vector<std::string> >("filenames");
file_suffix = im_params.get<std::string>("file_suffix");
}
else
{
// Use our own parameters
filenames = getParam<std::vector<std::string> >("filenames");
file_suffix = getParam<std::string>("file_suffix");
}
// Storage for the file names
_files = vtkSmartPointer<vtkStringArray>::New();
for (unsigned i=0; i<filenames.size(); ++i)
_files->InsertNextValue(filenames[i]);
// Error if no files where located
if (_files->GetNumberOfValues() == 0)
mooseError("No image file(s) located");
// Read the image stack. Hurray for VTK not using polymorphism in a
// smart way... we actually have to explicitly create the type of
// reader based on the file extension, using an if-statement...
if (file_suffix == "png")
_image = vtkSmartPointer<vtkPNGReader>::New();
else if (file_suffix == "tiff" || file_suffix == "tif")
_image = vtkSmartPointer<vtkTIFFReader>::New();
else
mooseError("Un-supported file type '" << file_suffix << "'");
// Now that _image is set up, actually read the images
// Indicate that data read has started
_console << "Reading image(s)..." << std::endl;
// Extract the data
_image->SetFileNames(_files);
_image->Update();
_data = _image->GetOutput();
_algorithm = _image->GetOutputPort();
// Set the image dimensions and voxel size member variable
int * dims = _data->GetDimensions();
for (unsigned int i = 0; i < 3; ++i)
{
_dims.push_back(dims[i]);
_voxel.push_back(_physical_dims(i)/_dims[i]);
}
// Set the dimensions of the image and bounding box
_data->SetSpacing(_voxel[0], _voxel[1], _voxel[2]);
_data->SetOrigin(_origin(0), _origin(1), _origin(2));
_bounding_box.min() = _origin;
_bounding_box.max() = _origin + _physical_dims;
// Indicate data read is completed
_console << " ...image read finished" << std::endl;
// Set the component parameter
// If the parameter is not set then vtkMagnitude() will applied
if (isParamValid("component"))
{
unsigned int n = _data->GetNumberOfScalarComponents();
_component = getParam<unsigned int>("component");
if (_component >= n)
mooseError("'component' parameter must be empty or have a value of 0 to " << n-1);
}
else
_component = 0;
// Apply filters, the toggling on and off of each filter is handled internally
vtkMagnitude();
vtkShiftAndScale();
vtkThreshold();
vtkFlip();
#endif
}