Array indexing

Multidimensional data is most of the time stored as unidimensional arrays. There are usually dedicated functions helping to access elements by coordinates, however, it may still be of interest to understand how data are stored in the first place. This is what this section will do, by explaining how to compute the unidimensional array index from coordinates.

Let N, w, h and d be respectively the number of species in a system, and the system width, height and depth in cells.

Space cell index

The index i of a cell in a grid space is given by

\[i = z * w*h + y*w + x\]

where x, y and z are the grid dimensions.

System state and system chemostats

The index i is, for a given species at a given position is given by

\[i = species_index * space_size + space_index\]

State trajectory data

Trajectory data are stored in the RDTrajectory.data property. The index i is, for a given species, in a given sample at a given position is given by

\[i = sample_index * n_samples*n_species*space_size + species_index*space_size + space_index\]