# -*- coding: utf-8 -*-
"""
Utilities for plotting with `bokeh <https://bokeh.pydata.org>`_.
"""
from __future__ import (absolute_import, division, print_function)
from collections import OrderedDict, defaultdict
from itertools import chain
from chempy.kinetics.ode import get_odesys
from chempy.units import to_unitless, linspace, logspace_from_lin
[docs]def integration_with_sliders(
rsys, tend, c0, parameters, fig_kwargs=None, unit_registry=None, output_conc_unit=None,
output_time_unit=None, slider_kwargs=None, x_axis_type="linear", y_axis_type="linear",
integrate_kwargs=None, substitutions=None):
import numpy as np
from bokeh.plotting import Figure
from bokeh.models import ColumnDataSource, HBox, VBoxForm
from bokeh.models.widgets import Slider
if slider_kwargs is None:
slider_kwargs = {}
odesys, state_keys, rarg_keys, p_units = get_odesys(
rsys, unit_registry=unit_registry, substitutions=substitutions,
output_conc_unit=output_conc_unit,
output_time_unit=output_time_unit)[:4]
if output_conc_unit is None:
output_conc_unit = 1
if output_time_unit is None:
output_conc_unit = 1
param_keys = list(chain(state_keys, rarg_keys))
if x_axis_type == 'linear':
tout = linspace(tend*0, tend)
elif x_axis_type == 'log':
tout = logspace_from_lin(tend*1e-9, tend)
else:
raise NotImplementedError("Unknown x_axis_type: %s" % x_axis_type)
tout, Cout, info = odesys.integrate(tout, c0, parameters, **(integrate_kwargs or {}))
sources = [ColumnDataSource(data={
'tout': to_unitless(tout, output_time_unit),
k: to_unitless(Cout[:, idx], output_conc_unit)
}) for idx, k in enumerate(rsys.substances)]
if fig_kwargs is None:
Cmax = np.max(Cout)
x_range = list(to_unitless([tend*0, tend], output_time_unit))
y_range = list(to_unitless([Cmax*0, Cmax*1.1], output_conc_unit))
fig_kwargs = dict(plot_height=400, plot_width=400, title="C vs t",
tools="crosshair,pan,reset,resize,save,wheel_zoom",
x_range=x_range, y_range=y_range, x_axis_type=x_axis_type,
y_axis_type=y_axis_type)
plot = Figure(**fig_kwargs)
colors = 'red green blue black cyan magenta'.split()
for idx, k in enumerate(rsys.substances):
plot.line('tout', k, source=sources[idx], line_width=3, line_alpha=0.6,
color=colors[idx % len(colors)])
def _C(k):
return to_unitless(c0[k], output_conc_unit)
p_ul = [to_unitless(parameters[k], _u) for k, _u in zip(param_keys, p_units)]
c0_widgets = OrderedDict([
(k, Slider(
title=k if output_conc_unit is 1 else k + ' / ' + output_conc_unit.dimensionality.unicode,
value=_C(k), **slider_kwargs.get(k, dict(start=_C(k)/2, end=_C(k)*2, step=_C(k)/10))))
for k in rsys.substances])
def _dict_to_unitless(d, u):
return {k: to_unitless(v, u) for k, v in d.items()}
param_widgets = OrderedDict([
(k, Slider(title=k if u is None else k + ' / ' + u.dimensionality.unicode,
value=v, **_dict_to_unitless(
slider_kwargs.get(k, dict(start=v/10, end=v*10, step=v/10)),
u)))
for k, v, u in zip(param_keys, p_ul, p_units)])
all_widgets = list(chain(param_widgets.values(), c0_widgets.values()))
def update_data(attrname, old, new):
_c0 = defaultdict(lambda: 0*output_conc_unit)
for k, w in c0_widgets.items():
_c0[k] = w.value * output_conc_unit
_params = {}
for (k, w), u in zip(param_widgets.items(), p_units):
_params[k] = w.value if u is None else w.value * u
_tout, _Cout, _info = odesys.integrate(tout, _c0, _params)
for idx, k in enumerate(rsys.substances):
sources[idx].data = {
'tout': to_unitless(_tout, output_time_unit),
k: to_unitless(_Cout[:, idx], output_conc_unit)
}
for w in all_widgets:
w.on_change('value', update_data)
inputs = VBoxForm(children=all_widgets)
return HBox(children=[inputs, plot], width=800)