def create_individual(self):
"""Hacky function to do the bare minimum needed to create some individuals. The initial population is generated and we yield from that. Useful for debugging, to just playing with a single dataset/individual.
"""
if self.multi_config:
raise ValueError(f"Not available in multi_config mdoe - Need a single config to generate an individual from")
# Create the RandomState instance
self.set_global_rng(self.seed_num)
# Create the Dataset instance
dataset_obj = Dataset(**self.full_config["dataset"])
# Setup some attributes for the Cluster class
Cluster.setup_variables(dataset_obj, self.full_config["ga"])
# Setup the GA
objective_dict, pop = self.setup_ga(dataset_obj, self.full_config)
# Take from the initial population
yield from pop
def generate_indiv(icls, dataset_obj):
# Create the individual
# Uses the DEAP wrapper around Genotype()
indiv = icls([Cluster(size) for size in dataset_obj.cluster_sizes])
# Create the views (each cluster.values is a view into genotype.all_values)
indiv.create_views()
# And sample some initial values
indiv.resample_values()
return indiv
def setUp(self):
# Whatever setup is needed
rng = np.random.RandomState(42)
Genotype.global_rng = rng
Cluster.global_rng = rng
sizes = [190, 20, 30, 110]
self.indiv = Genotype([Cluster(size) for size in sizes])
self.indiv.create_views()
self.indiv.resample_values()
hawks.objectives.Silhouette.setup_indiv(self.indiv)
def test_eigenratio_eccentric(self):
clust1 = Cluster(50)
clust1.mean = np.array([0, 0])
clust1.cov = np.array([[10, 0], [0, 1]])
clust2 = Cluster(80)
clust2.mean = np.array([0, 0])
clust2.cov = np.array([[9.9, 0], [0, 1]])
indiv = Genotype([clust1, clust2])
eigen_ratio = hawks.constraints.eigenval_ratio(indiv)
self.assertEqual(eigen_ratio, 10)
def setUp(self):
# Whatever setup is needed
rng = np.random.RandomState(42)
Genotype.global_rng = rng
Cluster.global_rng = rng
sizes = [190, 20, 30, 110]
setattr(Cluster, "num_dims", 2)
setattr(Cluster, "initial_mean_upper", 1.0)
setattr(Cluster, "initial_cov_upper", 0.5)
self.indiv = Genotype([Cluster(size) for size in sizes])
self.indiv.create_views()
self.indiv.resample_values()
hawks.objectives.Silhouette.setup_indiv(self.indiv)
def test_overlap_same(self):
clust1 = Cluster(4000)
clust1.mean = np.array([0, 0])
clust1.cov = np.array([[1, 0], [0, 1]])
clust2 = Cluster(4000)
clust2.mean = np.array([0, 0])
clust2.cov = np.array([[1, 0], [0, 1]])
indiv = Genotype([clust1, clust2])
indiv.create_views()
indiv.resample_values()
overlap = hawks.constraints.overlap(indiv)
self.assertAlmostEqual(overlap, 0.5, places=1)
def test_overlap_separated(self):
clust1 = Cluster(50)
clust1.mean = np.array([0, 0])
clust1.cov = np.array([[1, 0], [0, 1]])
clust2 = Cluster(80)
clust2.mean = np.array([10, 10])
clust2.cov = np.array([[1, 0], [0, 1]])
indiv = Genotype([clust1, clust2])
indiv.create_views()
indiv.resample_values()
overlap = hawks.constraints.overlap(indiv)
self.assertEqual(overlap, 0)
def test_silhouette_singleton_cluster(self):
rng = np.random.RandomState(42)
Genotype.global_rng = rng
Cluster.global_rng = rng
sizes = [1, 20, 30, 110]
self.indiv = Genotype([Cluster(size) for size in sizes])
self.indiv.create_views()
self.indiv.resample_values()
hawks.objectives.Silhouette.setup_indiv(self.indiv)
hawks.objectives.Silhouette.eval_objective(self.indiv)
close_to_sk = np.isclose(
silhouette_score(self.indiv.all_values,
self.indiv.labels,
metric="sqeuclidean"), self.indiv.silhouette)
self.assertTrue(close_to_sk)
def setUp(self):
rng = np.random.RandomState(42)
Cluster.global_rng = rng
Genotype.global_rng = rng
setattr(Cluster, "num_dims", 2)
clust1 = Cluster(50)
clust1.mean = np.array([0, 0])
clust1.cov = np.array([[1, 0], [0, 1]])
clust2 = Cluster(30)
clust2.mean = np.array([5, 5])
clust2.cov = np.array([[5, 0], [0, 10]])
self.indiv1 = Genotype([clust1, clust2])
self.indiv1.create_views()
self.indiv1.resample_values()
clust3 = Cluster(50)
clust3.mean = np.array([2, 2])
clust3.cov = np.array([[2, 0], [0, 2]])
clust4 = Cluster(30)
clust4.mean = np.array([10, 10])
clust4.cov = np.array([[4, 0], [0, 2]])
self.indiv2 = Genotype([clust3, clust4])
self.indiv2.create_views()
self.indiv2.resample_values()
def animate(self, record_stats=False, plot_pop=True, **kwargs):
"""Function to animate a run of HAWKS (showing how the datasets evolve). An example of this can be found in the README. Produces a series of PNGs, and creates a gif using `ImageMagick <https://imagemagick.org/index.php>`_.
Args:
record_stats (bool, optional): Whether the results of the run should be recorded (and therefore can be saved, depending on the config). Defaults to False.
plot_pop (bool, optional): Whether to plot the whole population. If False, just plots the best individual. Defaults to True.
Raises:
ValueError: Animation cannot be run for a multi_config; only a single set of parameters is permitted.
"""
# Raise error if multi-config specified
if self.multi_config:
raise ValueError(f"Animation is not implemented for multi-config")
# Perform initial setup
total_configs, key_paths, param_lists = self._setup()
# Setup the containers for storing results
if record_stats:
num_rows = self.full_config["ga"]["num_indivs"]
results_dict = defaultdict(list)
# Setup the plot folder
plot_folder = self._plot_save_setup()
# Loop over each run
for num_run in tqdm(range(self.num_runs), desc="Runs", leave=False):
animate_folder = plot_folder / f"animate_run{num_run}"
animate_folder.mkdir(exist_ok=True, parents=True)
# Super special seed selection
global_seed = self.increment_seed(num_run)
# Create the RandomState instance
self.set_global_rng(global_seed)
# Create the Dataset instance
dataset_obj = Dataset(**self.full_config["dataset"])
# Setup some attributes for the Cluster class
Cluster.setup_variables(dataset_obj, self.full_config["ga"])
# Setup the GA
objective_dict, pop = self.setup_ga(dataset_obj, self.full_config)
# Plot the initial population
if plot_pop:
plotting.plot_pop(
pop,
fpath=animate_folder / "pop_gen-0",
fig_format="png",
save=True,
remove_axis=True,
fig_title="Generation 0",
show=False,
**kwargs
)
# Plot the best indiv
else:
best_indiv, best_index = self._best_in_pop(pop)
plotting.plot_indiv(
best_indiv,
fpath=animate_folder / "indiv_gen-0",
remove_axis=True,
save=True,
show=False,
**kwargs
)
if record_stats:
# Store results from the initial population
results_dict = self._store_results(
results_dict, pop, num_run, 0, num_rows, objective_dict
)
# Go through each generation
for gen in tqdm(
range(1, self.full_config["ga"]["num_gens"]),
desc="Generations", leave=False
):
pop = ga.generation(
pop,
self.deap_toolbox,
self.full_config["constraints"],
cxpb=self.full_config["ga"]["mate_prob"]
)
# Plot the initial population
if plot_pop:
plotting.plot_pop(
pop,
fpath=animate_folder / f"gen-{gen}",
fig_format="png",
save=True,
remove_axis=True,
fig_title=f"Generation {gen}",
show=False,
**kwargs
)
# Plot the best indiv
else:
best_indiv, best_index = self._best_in_pop(pop)
plotting.plot_indiv(
best_indiv,
fpath=animate_folder / f"indiv_gen-{gen}",
remove_axis=True,
save=True,
show=False,
**kwargs
)
if record_stats:
# Store results from each generation
results_dict = self._store_results(
results_dict, pop, num_run, gen, num_rows, objective_dict
)
# Keep a reference to the most recent population
self.population = pop
if record_stats:
self.stats = self.stats.append(
pd.DataFrame.from_dict(results_dict), ignore_index=True
)
if self.save_stats:
# Save to CSV
utils.df_to_csv(
df=self.stats,
path=self.base_folder,
filename="hawks_stats"
)
# Create the gif if convert is available
which_convert = shutil.which("convert")
if which_convert is not None:
subprocess.run(
"convert -resize 50% -delay 30 -loop 0 `ls -v | grep 'gen-'` hawks_animation.gif",
shell=True,
check=True,
cwd=animate_folder
)
def run_step(self):
"""Run function that contains the actual code, yielding after each run, if desired.
Yields:
:class:`~hawks.generator.SingleObjective`: The generator instance at the time, allowing inspection of the process.
"""
total_configs, key_paths, param_lists = self._setup()
# Initialize the config_id
config_id = 0
# Loop over each config
for params, config in tqdm(self._get_configs(key_paths, param_lists), desc="Configs", total=total_configs):
# Add the config to the list
self.config_list.append(config)
# Add a list as container for new runs
self.best_each_run.append([])
# Local ref to best for each config
best_indiv_run = None
# Setup the containers for storing results
num_rows = config["ga"]["num_indivs"]
results_dict = defaultdict(list)
# Add the config_id, which is also used for the filename when saving the config
results_dict["config_id"] = [config_id]*(num_rows*config["ga"]["num_gens"]*self.num_runs)
# Add the specific parameters for this config
if self.multi_config:
for key, param in zip(key_paths, params):
name = "_".join(key[1:])
results_dict[name] += [param]*(num_rows*config["ga"]["num_gens"]*self.num_runs)
# Loop over each run
for num_run in tqdm(range(self.num_runs), desc="Runs", leave=False):
# Increment the seed for this run
global_seed = self.increment_seed(num_run)
# Create the RandomState instance
self.set_global_rng(global_seed)
# Create the Dataset instance
dataset_obj = Dataset(**config["dataset"])
# Setup some attributes for the Cluster class
Cluster.setup_variables(dataset_obj, config["ga"])
# Setup the GA
objective_dict, pop = self.setup_ga(dataset_obj, config)
# Store results from the initial population
results_dict = self._store_results(
results_dict, pop, num_run, 0, num_rows, objective_dict
)
# Go through each generation
for gen in tqdm(
range(1, config["ga"]["num_gens"]),
desc="Generations", leave=False
):
pop = ga.generation(
pop,
self.deap_toolbox,
config["constraints"],
cxpb=config["ga"]["mate_prob"]
)
# Store results from each generation
results_dict = self._store_results(
results_dict, pop, num_run, gen, num_rows, objective_dict
)
best_indiv_run, best_index = self._best_in_pop(pop)
# Store the best indiv from each run
self.best_each_run[-1].append(best_indiv_run)
# Add column to show best dataset from run
results_dict = self._store_best_indiv(
results_dict, best_index, config["ga"]["num_gens"], num_rows
)
# Keep a reference to the most recent population
self.population = pop
# YIELDIT
yield self
# Iterate the config_id
config_id += 1
# Append the results of this config to the overall results
self.stats = self.stats.append(
pd.DataFrame.from_dict(results_dict), ignore_index=True
)
# Save the stats for this run if specified
if self.save_stats:
# Save to CSV
utils.df_to_csv(
df=self.stats,
path=self.base_folder,
filename="hawks_stats"
)
# Save the best individual(s) and their associated config(s)
if self.save_best_data:
# Loop over each indiv in each config
for config_num, indiv_list in enumerate(self.best_each_run):
for run_num, indiv in enumerate(indiv_list):
# Save the best data
indiv.save_clusters(
folder=self.base_folder / "datasets",
fname=f"config-{config_num}_run-{run_num}_best_data"
)