Visualisation Output Files

If the parameter visualisation_recording_on is set to yes, various kinds of data are written to files for subsequent playback as `movies' of the run. Each file contains data about the spatial distribution of a particular aspect of the system, at a number of times during the run.

There are seven different aspects of the system that can be recorded in this way. These are:

1.

The ages of the cells in the population, expressed as the number of time slices that have elapsed since their birth (recorded in the file v_age.dat).

2.

The number of energy tokens that each cell has in its Energy Token Store (recorded in the file v_cell_energy.dat).

3.

A flag to indicate whether each cell has executed any foreign code from its Received Message Store during its lifetime (recorded in the file v_comms.dat).

4.

The number of energy tokens stored at each square in the environment (recorded in the file v_env_energy.dat).

5.

The SpeciesID of each cell, which also indicates the length of each cell's genome (recorded in the file v_id.dat).

6.

The size of each organism, in terms of number of cells (recorded in the file v_orgsize.dat).

7.

The direction of movement (if any) of each organism in the previous time slice (recorded in the file v_move.dat).

Normally, if visualisation_recording_on is set to yes, then all of these files get written. However, if visualisation_record_energy_only is additionally set to yes rather than no, then only the files v_cell_energy.dat and v_env_energy.dat are written.

The files are updated during the run at intervals determined by the system parameters visualisation_intersample_period, visualisation_intrasample_period and visualisation_sample_size. Specifically, data is recorded for a number of sample periods during the run. The number of time slices between successive samples is determined by visualisation_intersample_period. Each sample consists of data for a number of time slices, determined by visualisation_sample_size. The number of time slices between successive records within a sample is determined by the parameter visualisation_intrasample_period.

At each time slice when a record is to be made, a batch of data is written to each file. This data is written in grid_size+1 rows of grid_size+1columns. The elements of the final row, and of the final column, are all -1. This extra row and column is added purely to easy the process of producing a graphical display from the data using the MATLAB visualisation software package. The remaining elements of the data correspond to individual squares of the environment. For the file v_env_energy.dat, each element represents the number of energy tokens available at the corresponding square. For the other files, the element represents data associated with any cell(s) that are present at the corresponding square. If no cells are present, the element is given the value -1. If a single cell is present, the element is given the appropriate value (according to which file is being written) for that cell. If multiple cells are present, the element contains the appropriate values for each cell, separated by colons (:s).

An extra file, v_idx.dat, is also written along with these other visualisation files. At each time slice when data is written to the other files, the corresponding time slice number is written to v_idx.dat.