README.md

The FieldCoordinate Package

This package is intended to create a class for point lists with local coordinate systems.

The coord.data.frame

The coord.data.frame is a data.frame with the following mandatory columns:

• id - point identifying variable.

• x - X-coordinate.

• y - Y-coordinate.

A coord.data.frame additionally can contain point-attribute variables.

Construct a coord.data.frame with the as.coord.data.frame function.

df %>% as.coord.data.frame(id=id,x=x,y=y,diameter,species)

Implemented Methods

filter_radius Filter coordinate points by maximum radius (inclusive). Filter origin can be set.

coords.df %>% filter_radius(x=2, y=3, radius=10)

plot Plot a coord.data.frame by calling ggplot2. This is a very preliminary function that assumes that your coord.data.frame has the variables 'diameter' and 'species'.

Convenience functions

Transform to and from Polar Coordinates.

cartesian_to_polar_coordinate

polar_to_cartesian_coordinate

Transform between degree and radian

degree_to_radian

radian_to_degree

Point Manipulations

coordinate_rotation Rotate a coord.data.frame by an angle of rotation (radian).

translate_coordinates Translate points in a coord.data.frame coordinate system by x, y.

coordinate_reflect Reflect points in a coord.data.frame around an axis of the coordinate system.

Image registration

produce_gauss_matrix Represent a number of coordinate points in a coord.data.frame as a gaussian process, where the amplitude is equivalent to an attribute of the point, the standard deviation is the positional error, and a certain resolution (number of cells per radius). To distinguish between the data structures, the coord.data.frame is transformed into a gauss.coord.data.frame .

This can be plotted with plot .

Image creation and saving is handled by save_gauss which takes an gauss.coord.data.frame and saves it as an .png without any borders.

Read PNG images into R with the png::readPNG() function. To outline a number of euclidean geometric transformations, we use the image registration software interface RNiftyReg.

#Image registration.
affine_transformation <- niftyreg.linear(gauss1_img,gauss2_img)

#the transformation matrix
forward(affine_transformation)

The Affine matrix can be handed to fieldcoordinate::coordinate_transform to apply the transformations on the coord.data.frame rather than the gaussian representation. OBSERVE this only handles translation and rotation so far.