The project simulates life at the imaginary island of Rossumøya, given several initial parameters.
As a user and initializer you have the possibility to create an island of your choice with
pre-defined values for the different parameters. Another option is to run simulations with the
default set of parameters.
In the examples folder you are presented with some examples of different
types of simulations. What varies is the size of the island, the distribution of landscape types,
and the distribution and initialization of animals.
Defining the geography of the island:
geogr = """\
WWWW
WLHW
WWWW"""Border can only be water, everything else can be either Highland(H), Lowland(L), or Desert(D).
Initiating the population of the island:
ini_herbs = [{'loc': (2, 2),
'pop': [{'species': 'Herbivore',
'age': 5,
'weight': 20}
for _ in range(50)]}]
ini_carns = [{'loc': (2, 3),
'pop': [{'species': 'Carnivore',
'age': 5,
'weight': 20}
for _ in range(20)]}]Choose the location, species and their age and weight. The rest of the parameters are taken from the default values, but can be changed and specified by the user (see example 3).
Initializing the simulation:
for seed in range(100, 103):
sim = BioSim(geogr, [ini_herbs and/or ini_herbs], seed=seed,
log_file=f'data/simulation_hc_{seed:05d}',
img_dir='data', img_base=f'simulation_hc_{seed:05d}', img_years=300)The different parameters and what type of values that can be used is documented
here in biosim/simulation.py.
One can add animals and change parameters once a simulation is completed for a set of years. It is then possible to restart simulation for another set of years with the new parameters. e.g.
sim = BioSim(...)
sim.simulate(<some number of years>)
sim.add_population(<some extra population>)
sim.set_animal_parameters(<changed animal parameters>)
sim.set_landscape_parameters(<changed landscape parameters>)
sim.simulate(<a few more years>)For further documentation and
information about the different classes, parameters and possible restrictions is documented in each
file and package in the folder biosim, here.
In this folder you have various python files, all containing code to run different types of simulations.
Python file here.
If you want to analyze previously saved logs, this file can be used to get this data visualized
in a plot.
Python file here.
Same as the file in reference_examples, but in this file we have added the make_movie()-
method.
Python file here.
Sample simulation with bigger island.
Note: make two inner folders inside examples called data
and results. This is where the logs and results will be saved.
Python file here.
Simulation of island with Herbivores for 50 years, then adding Carnivores and simulation goes
on for 251 years (260 in total).
Python file here.
Simulation of 10 years with only Herbivores, then Carnivores are added and the simulation goes on
for 251 more years (260 years in total).
Python file here.
Simulation of a small island with only Herbivores. Logs the population count and statistics are
visualized in plots in a separate window.
Python file here.
Simulation of 7 years with both Herbivores and Carnivores initialized from year 0. Parameters have
been changed to ensure that only migration happens and nothing else. This is so that we can verify
that the migration works correctly. Map and distribution of animals is shown in the console.
Python file here.
Simulation of 10 years with only Herbivores, then Carnivores are added and the simulation goes on
for 50 more years. Weight and age of animals are initialized, and the number of each fauna type.
Default parameters used. Map and distribution of animals is only shown in the console.
Python file here.
We simulate a period of 400 years.
The initialized animals in year 0 are 200 Herbivores and 50 Carnivores. The movie found
here is the changes visualized per year from this simulation.
In biosim/simulation.py, an extra parameter has been added to the BioSim-instance parameters:
console_output_island. Setting this to True enables print-out of island map in the console.
Running examples/simulation_migration.py (here) gives us the
following output in the console for year 3:
{width=600 height=500px}
The parameters in the mentioned file is set in a way so that we can observe that the migration
for each animal in each cell works properly (following the set restrictions).
The image below presents how the statistics from the simulation are visualized. In the two windows
showing the distribution of Herbivore and Carnivores, we have chosen to make the part of the map
that is set to geography type Water, blue.
The distribution is set by getting the details of the animals in each cell, and we then set the
count of the animals = -1 where its water. While refreshing the heatmaps we set a mask on the cells
where the number of animals is equal to -1 (which is done where there is geo type water on the map).
In visuals.py, here, the color of this mask is set to blue.
This ensures that the water areas are masked, and therefore blue, making the visualization better.
{width=600 height=500px}
We have added __str__ to all of our objects. This can be observed during debugging,
as shown in the image below.
{width=300 height=50}
The letters indicate the following:
- C = Carnivore
- H = Herbivore
- A followed by number = Represents the age
- W followed by number = Represents the weight
- F followed by number = Represents the fitness
- M followed by 0 or 1 = Boolean value, telling us if the animal has moved or not
While in root file, run the following command in the terminal:
python -m build
pip install .Then, all simulations in the examples folder will be runnable.
The saved videos from examples/check_sim.py and examples/simulation_visual.py can be found and
viewed from folder Exam. In the same folder you can view saved images of plots that were made
during the process of the project (folder Exam/pics).
- Code optimization done with Sourcery: https://sourcery.ai/
- Sougata Bhattacharya, [email protected]
- Tonje Martine Lorgen Kirkholt, [email protected]