def plot_results(self, results, agent, obs_name, thresh=50):
plt.figure()
plt.ion()
max_val_lim = max(
max((numpy.max(results[0][1][obs_name]) +
0.25 * numpy.max(results[0][1][obs_name])), 101.0), thresh)
max_time = max([result[0][-1] for result in results])
lr = matplotlib.patches.Rectangle((0, 0),
max_time,
thresh,
color='red',
alpha=0.1)
hr = matplotlib.patches.Rectangle((0, thresh),
max_time,
max_val_lim - thresh,
color='green',
alpha=0.1)
ax = plt.gca()
ax.add_patch(lr)
ax.add_patch(hr)
if thresh + 0.05 * max_val_lim < max_val_lim:
plt.text(10, thresh + 0.05 * max_val_lim, 'High', fontsize=10)
plt.text(10, thresh - 0.05 * max_val_lim, 'Low')
for tspan, yobs in results:
plt.plot(tspan, yobs[obs_name])
plt.ylim(-5, max_val_lim)
plt.xlim(-100, 10100)
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent).agent_str
plt.title('Simulation results for %s' % agent_str)
fig_path = get_img_path(obs_name + '.png')
plt.savefig(fig_path)
return fig_path
def plot_results(self, results, agent, obs_name, thresh=50):
plt.figure()
plt.ion()
max_val_lim = max(max(numpy.max(results[0][1][obs_name]), 101.0),
thresh)
max_time = max([result[0][-1] for result in results])
lr = matplotlib.patches.Rectangle((0, 0), max_time, thresh, color='red',
alpha=0.1)
hr = matplotlib.patches.Rectangle((0, thresh), max_time,
max_val_lim-thresh,
color='green', alpha=0.1)
ax = plt.gca()
ax.add_patch(lr)
ax.add_patch(hr)
if thresh + 5 < max_val_lim:
plt.text(10, thresh + 5, 'High', fontsize=10)
plt.text(10, thresh - 5, 'Low')
for tspan, yobs in results:
plt.plot(tspan, yobs[obs_name])
plt.ylim(-1, max_val_lim)
plt.xlim(-100, 10100)
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent)
plt.title('Simulation results for %s' % agent_str)
fig_path = get_img_path(obs_name + '.png')
plt.savefig(fig_path)
return fig_path
def report_paths_graph(self, paths_list):
from indra.assemblers.graph import GraphAssembler
from indra.util import flatten
path_stmts = [stmts_from_json(l) for l in paths_list]
all_stmts = flatten(path_stmts)
ga = GraphAssembler(all_stmts)
ga.make_model()
resource = get_img_path('qca_paths.png')
ga.save_pdf(resource)
content = KQMLList('display-image')
content.set('type', 'simulation')
content.sets('path', resource)
self.tell(content)
def plot_compare_conditions(self, ts, results, agent, obs_name):
plt.figure()
plt.ion()
plt.plot(ts, results[0][:len(ts)], label='Without condition')
plt.plot(ts, results[-1][:len(ts)], label='With condition')
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent).agent_str
plt.title('Simulation results for %s' % agent_str)
plt.legend()
fig_path = get_img_path(obs_name + '.png')
plt.savefig(fig_path)
return fig_path
def plot_compare_conditions(self, ts, results, agent, obs_name):
plt.figure()
plt.ion()
plt.plot(ts, results[0][:len(ts)], label='Without condition')
plt.plot(ts, results[-1][:len(ts)], label='With condition')
plt.xlabel('Time (s)')
plt.ylabel('Amount (molecules)')
agent_str = english_assembler._assemble_agent_str(agent)
plt.title('Simulation results for %s' % agent_str)
plt.legend()
fig_path = get_img_path(obs_name + '.png')
plt.savefig(fig_path)
return fig_path
def report_paths_graph(self, paths_list):
from indra.assemblers.graph import GraphAssembler
from indra.util import flatten
path_stmts = [stmts_from_json(l) for l in paths_list]
all_stmts = flatten(path_stmts)
ga = GraphAssembler(all_stmts)
ga.make_model()
resource = get_img_path('qca_paths.png')
ga.save_pdf(resource)
content = KQMLList('display-image')
content.set('type', 'simulation')
content.sets('path', resource)
self.tell(content)
def make_pic_name(model_id, token):
"""Create a standardized picture name."""
s = 'model%d_%s' % (model_id, token)
return get_img_path(s)
def make_pic_name(model_id, token):
"""Create a standardized picture name."""
s = 'model%d_%s' % (model_id, token)
return get_img_path(s)