Rather than using R's save and load functions directly for reference objects, TractoR uses the SerialisableObject class and these functions to save and load objects. The main difference is that this approach stores only the data in the object, and not the functions which operate on them. This helps backward compatibility when new member functions are added.
The empty matrix is a standard matrix of dimensions 0 x 0. It is intended to be used as a placeholder where a matrix is required but no information is stored.
This class represents an array with any number of dimensions, in which a significant proportion of entries are zero. The coordinates of nonzero entries are stored along with their values, with all remaining entries assumed to be zero. Methods are provided to index into the array in the standard way, using matrix or vector indices; and for coercing between SparseArray objects and standard (dense) arrays.
The execute function is a wrapper around the system2 function in base, which additionally echoes the command being run (including the full path to the executable) if the reportr output level is Debug. locateExecutable simply returns the path to an executable file on the system PATH.
This class represents an MRI image. An object of this class is made up of some voxel data, stored as a sparse or dense numeric array, and some metadata, such as the file it was read from, the voxel dimensions, and so on. The group generic functions Math, Ops and Summary are defined for this class, as are methods for coercing to and from a standard array.
The nil object is an empty object of class SerialisableObject. It can be used as a placeholder where such an object of this class, or one of its subclasses, is required. It serialises to the empty list.
This function returns its arguments, after concatenating them using c and then removing elements with duplicate names. The first element with each name will remain. Unnamed elements are retained.
Visualise MriImage objects noninteractively using an R graphics device. See viewImages for an interactive alternative. These functions create 2D visualisations of 3D images by slicing or maximum intensity projection.
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