def __init__(self, pipeline, fixed_params, variable_param_options,
eval_metrics, n_repeat, working_directory):
self.pipeline = pipeline
self.fixed_params = OrderedDict(fixed_params)
self.variable_param_options = OrderedDict(variable_param_options)
self.eval_metrics = eval_metrics
self.working_directory = working_directory
self.n_repeat = n_repeat
mkpath(working_directory)
# Handle repetitions as a variable parameter
self.variable_param_options['i_repeat'] = list(range(n_repeat))
def animate_walk(simulation, alpha=0.3, anim_folder=ANIM_FOLDER):
mkpath(anim_folder)
walk = simulation.get_location_history()
n = walk.shape[0]
n_steps, n_sites, n_dim = walk.shape
assert n_sites == simulation.n_sites
assert n_dim == 2
x_min, y_min, x_max, y_max = bounding_box(walk.reshape(-1, 2), margin=0.05)
fig = plt.figure()
ax = fig.add_axes([0, 0, 1, 1])
plt.tight_layout(pad=0)
ax.set_xlim(x_min, x_max), ax.set_xticks([])
ax.set_ylim(y_min, y_max), ax.set_yticks([])
w, h = fig.get_size_inches()
h *= 15 / w
w = 15
fig.set_size_inches(w, h)
paths = []
for i in range(simulation.n_sites):
p, = ax.plot([], [], color=COLOR_PATH, lw=PATH_WIDTH, zorder=0)
paths.append(p)
root = ax.scatter(*walk[0, :, :].T, marker='*', c=COLOR_ROOT_TRUE, s=500, zorder=5)
scat = ax.scatter(*walk[0, :, :].T, color=COLOR_SCATTER, s=30, lw=0, zorder=4)
def update(frame):
if frame > n+1:
return
scat.set_offsets(walk[frame-2:frame+3, :, :].mean(axis=0))
for i, p in enumerate(paths):
p.set_data(walk[:frame, i, 0], walk[:frame, i, 1])
# plt.savefig(anim_folder + 'step_%i.png' % frame)
anim = animation.FuncAnimation(fig, update, frames=n_steps-1 + 20,
interval=60)
anim.save('results/animation.gif', dpi=100, writer='imagemagick')
plt.show()
ADAPT_HEIGHT = False
FIX_ROOT = False
# SUFFIX = '_missingClades'
WORKING_DIR = 'data/bantu_{model}_outgroup_{og}_adapttree_{at}_' + \
'adaptheight_{ah}_hpd_{hpd}{fixroot}{suffix}/'
WORKING_DIR = WORKING_DIR.format(
model=MODEL, og=USE_OUTGROUP, at=ADAPT_TREE, ah=ADAPT_HEIGHT, hpd=HPD,
fixroot='_fixroot' if FIX_ROOT else '', suffix=SUFFIX
)
BANTU_XML_PATH = WORKING_DIR + 'nowhere.xml'
GEOJSON_PATH = 'africa.geojson'
GEO_TREE_PATH = WORKING_DIR + 'nowhere.tree'
GEO_TREES_PATH = WORKING_DIR + 'nowhere.trees'
mkpath(WORKING_DIR)
HOMELAND = np.array([10.5, 6.5])
ax.scatter(*HOMELAND, marker='*', c=TURQUOISE, s=200, zorder=3)
write_bantu_xml(BANTU_XML_PATH, CHAIN_LENGTH,
root=HOMELAND if FIX_ROOT else None,
exclude_outgroup=not USE_OUTGROUP,
adapt_tree=ADAPT_TREE,
adapt_height=ADAPT_HEIGHT,
movement_model=MODEL)
# Run the BEAST analysis
run_beast(WORKING_DIR)
run_treeannotator(HPD, BURNIN, WORKING_DIR)
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import os
import subprocess
import logging
import time
from src.beast_xml_templates import *
from src.tree import Tree
from src.util import str_concat_array, extract_newick_from_nexus, SubprocessException, mkpath
BEAST_LOGGER_PATH = 'logs/beast.log'
mkpath(BEAST_LOGGER_PATH)
EXPERIMENT_LOGGER = logging.getLogger('experiment')
BEAST_LOGGER = logging.getLogger('beast')
BEAST_LOGGER.setLevel(logging.DEBUG)
BEAST_LOGGER.addHandler(logging.FileHandler(BEAST_LOGGER_PATH))
BEAST_LOGGER.info('=' * 100)
BEAST_LOGGER.info('New Run')
BEAST_LOGGER.info('=' * 100)
def write_nexus(simulation, path, fossils=None):
data_str = ''
for i, state in enumerate(simulation.societies):
name = state.name
fs = state.featureState.features.astype(int)