gillespy2/core/liveGraphing.py
# GillesPy2 is a modeling toolkit for biochemical simulation.
# Copyright (C) 2019-2023 GillesPy2 developers.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import sys
import json
import threading
from math import floor
from gillespy2.core.results import common_rgb_values
from gillespy2.core.gillespyError import SimulationError
from gillespy2.core import log
class CRepeatTimer(threading.Timer):
"""
Threading timer which repeatedly calls the given function instead of simply ending.
Used for C solver live graphing support
"""
pause = False
def run(self):
_ = str.join('', [*self.args[1]])
while not self.finished.wait(self.interval):
args = self.args[0].get()
self.function(*args, **self.kwargs)
if not self.pause:
args = self.args[0].get()
self.kwargs['finished'] = True
self.function(*args, **self.kwargs)
class RepeatTimer(threading.Timer):
"""
Threading timer which repeatedly calls the given function instead of simply ending
"""
pause = False
def run(self):
_ = str.join('', [*self.args[3]])
self.args = self.args[:3]
while not self.finished.wait(self.interval):
self.function(*self.args, **self.kwargs)
if not self.pause:
self.kwargs['finished'] = True
self.function(*self.args, **self.kwargs)
def display_types():
'''
Get the list of supported display types.
:returns: Supported display types.
:rtype: list
'''
return ["graph", "text", "progress"]
def valid_graph_params(live_output_options):
'''
Validated the live output options.
:param live_output_options: Options to be validated.
:type live_output_options: dict
:raises SimulationError: If the display type is invalid.
'''
if live_output_options['type'] not in ['progress', 'graph', 'text']:
raise SimulationError("Invalid input to 'live_output', please check spelling and ensure input is"
" lower case.")
if 'interval' not in live_output_options:
live_output_options['interval'] = 1
elif live_output_options['interval'] < 0:
message = f"In LiveGraphing live_output_options, got 'interval' = '{live_output_options['interval']}'."
message += " setting interval = 1"
log.warning(message)
live_output_options['interval'] = 1
if live_output_options['type'] == "graph" and live_output_options['interval'] < 1:
message = f"In LiveGraphing live_output_options, got 'interval' = '{live_output_options['interval']}'."
message += "Consider using an interval >= 1 when displaying graphs."
log.warning(message)
if 'clear_output' not in live_output_options:
if live_output_options['type'] == "graph" or live_output_options['type'] == "progress":
live_output_options['clear_output'] = True
else:
live_output_options['clear_output'] = False
if 'file_path' not in live_output_options:
live_output_options['file_path'] = None
elif live_output_options['type'] == "graph" and live_output_options['file_path'] is not None:
live_output_options['type'] = "figure"
class LiveDisplayer():
"""
holds information required for displaying information when live_output = True
"""
def __init__(self, model=None, timeline=None, number_of_trajectories=1, live_output_options={}, resume=False):
self.display_type = live_output_options['type']
self.display_interval = live_output_options['interval']
self.file_path = live_output_options['file_path']
self.model = model
self.resume = resume
self.timeline = timeline
self.timeline_len = timeline.size
self.x_shift = int(timeline[0])
self.number_of_trajectories = number_of_trajectories
self.clear_output = live_output_options['clear_output']
species_mappings = model._listOfSpecies
self.species = list(species_mappings.keys())
self.number_species = len(self.species)
self.current_trajectory = 1
self.header_printed = False
def trajectory_header(self):
'''
Create the trajectory header for the output.
'''
return "Trajectory (" + str(self.current_trajectory) + "/" + str(self.number_of_trajectories) + ")"
def increment_trajectory(self, trajectory_num):
'''
Increment the trejectory counter.
'''
self.current_trajectory = trajectory_num + 1
self.header_printed = False
def print_text_header(self, file_obj):
'''
Print the header for text display type.
:param file_obj: File object to write text output.
:type file_obj: file object
'''
self.header_printed = True
if self.number_of_trajectories > 1:
print(self.trajectory_header(), file=file_obj)
print("Time |", end="", file=file_obj)
for species in self.model.listOfSpecies:
print(species[:10].ljust(10), end="|", file=file_obj)
print("", file=file_obj)
def display(self, curr_state, curr_time, trajectory_base, finished=False):
'''
Display the output for the live grapher.
:param curr_state: Current state of the simulation. Should be a list of len 1 to get reference.
:type curr_state: list
:param curr_time: Current time of the simulation. Should be a list of len 1 to get reference.
:type curr_time: list
:param trajectory_base: Current results of the simulation.
:type trajectory_base: list
:param finished: Indicates whether or not the simulation has finished.
:type finished: bool
'''
from IPython.display import clear_output # pylint: disable=import-outside-toplevel
curr_time = curr_time[0]
curr_state = curr_state[0]
# necessary for __f function in hybrid solver
if 't' in curr_state:
if curr_state['t'] > curr_time:
curr_time = curr_state['t']
elif 'time' in curr_state:
if curr_state['time'] > curr_time:
curr_time = curr_state['time']
if self.file_path is None or self.display_type == "graph":
if self.clear_output:
clear_output(wait=True)
file_obj = sys.stdout
else:
mode = "w" if self.clear_output else "a"
file_obj = open(self.file_path, mode, encoding="utf-8")
if self.display_type == "text":
if not self.header_printed:
self.print_text_header(file_obj)
print(str(round(curr_time, 2))[:10].ljust(10), end="|", file=file_obj)
for i in range(self.number_species):
print(str(curr_state[self.species[i]])[:10].ljust(10), end="|", file=file_obj)
print("", file=file_obj)
elif finished and self.display_type == "progress":
print("progress = 100 %", file=file_obj)
elif self.display_type == "progress":
if self.number_of_trajectories > 1:
print(self.trajectory_header(), file=file_obj)
if self.resume is True:
print(f"progress = {round(((curr_time-self.x_shift)/self.timeline_len)*100, 2)} %\n", file=file_obj)
else:
print(
f"progress = {round((curr_time / (self.timeline_len + self.x_shift)) * 100, 2) }%\n", file=file_obj
)
elif self.display_type == "graph":
if finished:
return
import matplotlib.pyplot as plt # pylint: disable=import-outside-toplevel
entry_count = floor(curr_time) - self.x_shift
plt.figure(figsize=(18, 10))
plt.xlim(right=self.timeline[-1])
plt.xlim(left=self.timeline[0])
plt.title(self.trajectory_header())
for i in range(self.number_species):
line_color = common_rgb_values()[(i) % len(common_rgb_values())]
plt.plot(trajectory_base[0][:, 0][:entry_count].tolist(),
trajectory_base[0][:, i + 1][:entry_count].tolist(), color=line_color,
label=self.species[i])
plt.plot([entry_count - 1, curr_time - self.timeline[0]], [trajectory_base[0][:, i + 1][entry_count - 1]
, curr_state[self.species[i]]], linewidth=3,
color=line_color)
plt.legend(loc='upper right')
plt.show()
elif self.display_type == "figure":
import plotly # pylint: disable=import-outside-toplevel
import plotly.graph_objs as go # pylint: disable=import-outside-toplevel
entry_count = floor(curr_time) - self.x_shift
trace_list = []
for i, species in enumerate(self.species):
line_dict = {"color": common_rgb_values()[(i) % len(common_rgb_values())]}
trace_list.append(
go.Scatter(
x=trajectory_base[0][:, 0][:entry_count].tolist(),
y=trajectory_base[0][:, i + 1][:entry_count].tolist(),
mode="lines", name=species, line=line_dict, legendgroup=species
)
)
layout = go.Layout(
showlegend=True, title=self.trajectory_header(),
xaxis={"range": [self.timeline[0], self.timeline[-1]]}
)
fig = dict(data=trace_list, layout=layout)
json.dump(fig, file_obj, cls=plotly.utils.PlotlyJSONEncoder)
if self.file_path is not None and self.display_type != "graph":
file_obj.close()