def model_transform(model):
# check integrals
if isinstance(model, NumDSWrapper):
return model
elif isinstance(model, ODEIntegrator): #
model = [model]
if isinstance(model, (list, tuple)):
if len(model) == 0:
raise errors.AnalyzerError(f'Found no integrators: {model}')
model = tuple(model)
for intg in model:
if not isinstance(intg, ODEIntegrator):
raise errors.AnalyzerError(
f'Must be the instance of {ODEIntegrator}, but got {intg}.'
)
elif isinstance(model, dict):
if len(model) == 0:
raise errors.AnalyzerError(f'Found no integrators: {model}')
model = tuple(model.values())
for intg in model:
if not isinstance(intg, ODEIntegrator):
raise errors.AnalyzerError(
f'Must be the instance of {ODEIntegrator}, but got {intg}')
elif isinstance(model, DynamicalSystem):
model = tuple(model.ints().subset(ODEIntegrator).unique().values())
else:
raise errors.UnsupportedError(
f'Dynamics analysis by symbolic approach only supports '
f'list/tuple/dict of {ODEIntegrator} or {DynamicalSystem}, '
f'but we got: {type(model)}: {str(model)}')
# pars to update
pars_update = set()
for intg in model:
pars_update.update(intg.parameters[1:])
all_variables = set()
all_parameters = set()
for integral in model:
if len(integral.variables) != 1:
raise errors.AnalyzerError(
f'Only supports one {ODEIntegrator.__name__} one variable, '
f'but we got {len(integral.variables)} variables in {integral}.'
)
var = integral.variables[0]
if var in all_variables:
raise errors.AnalyzerError(
f'Variable name {var} has been defined before. '
f'Please change another name.')
all_variables.add(var)
# parameters
all_parameters.update(integral.parameters[1:])
# form a dynamic model
return NumDSWrapper(integrals=model,
variables=list(all_variables),
parameters=list(all_parameters),
pars_update=pars_update)
def __init__(self, var_name, variables, expressions, derivative_expr, scope, func_name):
self.func_name = func_name
# function scope
self.func_scope = scope
# differential variable name and time name
self.var_name = var_name
self.t_name = 't'
# analyse function code
self.expressions = [Expression(v, expr) for v, expr in zip(variables, expressions)]
self.f_expr = Expression('_f_res_', derivative_expr)
for k, num in Counter(variables).items():
if num > 1:
raise errors.AnalyzerError(
f'Found "{k}" {num} times. Please assign each expression '
f'in differential function with a unique name. ')
def __init__(self,
model,
target_vars,
fixed_vars=None,
target_pars=None,
pars_update=None,
resolutions=None,
**kwargs):
if (target_pars is not None) and len(target_pars) > 0:
raise errors.AnalyzerError(
f'Phase plane analysis does not support "target_pars". '
f'While we detect "target_pars={target_pars}".')
super(PhasePlane1D, self).__init__(model=model,
target_vars=target_vars,
fixed_vars=fixed_vars,
target_pars=target_pars,
pars_update=pars_update,
resolutions=resolutions,
**kwargs)
def separate_variables(func_or_code):
"""Separate the expressions in a differential equation for each variable.
For example, take the HH neuron model as an example:
>>> eq_code = '''
>>> def derivative(V, m, h, n, t, C, gNa, ENa, gK, EK, gL, EL, Iext):
>>> alpha = 0.1 * (V + 40) / (1 - bp.math.exp(-(V + 40) / 10))
>>> beta = 4.0 * bp.math.exp(-(V + 65) / 18)
>>> dmdt = alpha * (1 - m) - beta * m
>>>
>>> alpha = 0.07 * bp.math.exp(-(V + 65) / 20.)
>>> beta = 1 / (1 + bp.math.exp(-(V + 35) / 10))
>>> dhdt = alpha * (1 - h) - beta * h
>>>
>>> alpha = 0.01 * (V + 55) / (1 - bp.math.exp(-(V + 55) / 10))
>>> beta = 0.125 * bp.math.exp(-(V + 65) / 80)
>>> dndt = alpha * (1 - n) - beta * n
>>>
>>> I_Na = (gNa * m ** 3.0 * h) * (V - ENa)
>>> I_K = (gK * n ** 4.0) * (V - EK)
>>> I_leak = gL * (V - EL)
>>> dVdt = (- I_Na - I_K - I_leak + Iext) / C
>>>
>>> return dVdt, dmdt, dhdt, dndt
>>> '''
>>> separate_variables(eq_code)
{'code_lines_for_returns': {'dVdt': ['I_Na = gNa * m ** 3.0 * h * (V - ENa)\n',
'I_K = gK * n ** 4.0 * (V - EK)\n',
'I_leak = gL * (V - EL)\n',
'dVdt = (-I_Na - I_K - I_leak + Iext) / C\n'],
'dhdt': ['alpha = 0.07 * bp.math.exp(-(V + 65) / 20.0)\n',
'beta = 1 / (1 + bp.math.exp(-(V + 35) / 10))\n',
'dhdt = alpha * (1 - h) - beta * h\n'],
'dmdt': ['alpha = 0.1 * (V + 40) / (1 - '
'bp.math.exp(-(V + 40) / 10))\n',
'beta = 4.0 * bp.math.exp(-(V + 65) / 18)\n',
'dmdt = alpha * (1 - m) - beta * m\n'],
'dndt': ['alpha = 0.01 * (V + 55) / (1 - '
'bp.math.exp(-(V + 55) / 10))\n',
'beta = 0.125 * bp.math.exp(-(V + 65) / 80)\n',
'dndt = alpha * (1 - n) - beta * n\n']},
'expressions_for_returns': {'dVdt': ['gNa * m ** 3.0 * h * (V - ENa)',
'gK * n ** 4.0 * (V - EK)',
'gL * (V - EL)',
'(-I_Na - I_K - I_leak + Iext) / C'],
'dhdt': ['0.07 * bp.math.exp(-(V + 65) / 20.0)',
'1 / (1 + bp.math.exp(-(V + 35) / 10))',
'alpha * (1 - h) - beta * h'],
'dmdt': ['0.1 * (V + 40) / (1 - '
'bp.math.exp(-(V + 40) / 10))',
'4.0 * bp.math.exp(-(V + 65) / 18)',
'alpha * (1 - m) - beta * m'],
'dndt': ['0.01 * (V + 55) / (1 - '
'bp.math.exp(-(V + 55) / 10))',
'0.125 * bp.math.exp(-(V + 65) / 80)',
'alpha * (1 - n) - beta * n']},
'variables_for_returns': {'dVdt': [['I_Na'], ['I_K'], ['I_leak'], ['dVdt']],
'dhdt': [['alpha'], ['beta'], ['dhdt']],
'dmdt': [['alpha'], ['beta'], ['dmdt']],
'dndt': [['alpha'], ['beta'], ['dndt']]}}
Parameters
----------
func_or_code : callable, str
The callable function or the function code.
Returns
-------
anlysis : dict
The expressions for each return variable.
"""
if callable(func_or_code):
if tools.is_lambda_function(func_or_code):
raise errors.AnalyzerError(
f'Cannot analyze lambda function: {func_or_code}.')
func_or_code = tools.deindent(inspect.getsource(func_or_code))
assert isinstance(func_or_code, str)
analyser = DiffEqReader()
analyser.visit(ast.parse(func_or_code))
returns = analyser.returns
variables = analyser.variables
right_exprs = analyser.rights
code_lines = analyser.code_lines
return_requires = OrderedDict([(r, set(tools.get_identifiers(r)))
for r in returns])
code_lines_for_returns = OrderedDict([(r, []) for r in returns])
variables_for_returns = OrderedDict([(r, []) for r in returns])
expressions_for_returns = OrderedDict([(r, []) for r in returns])
length = len(variables)
reverse_ids = list(reversed([i - length for i in range(length)]))
for r in code_lines_for_returns.keys():
for rid in reverse_ids:
dep = []
for v in variables[rid]:
if v in return_requires[r]:
dep.append(v)
if len(dep):
code_lines_for_returns[r].append(code_lines[rid])
variables_for_returns[r].append(variables[rid])
expr = right_exprs[rid]
expressions_for_returns[r].append(expr)
for d in dep:
return_requires[r].remove(d)
return_requires[r].update(tools.get_identifiers(expr))
for r in list(code_lines_for_returns.keys()):
code_lines_for_returns[r] = code_lines_for_returns[r][::-1]
variables_for_returns[r] = variables_for_returns[r][::-1]
expressions_for_returns[r] = expressions_for_returns[r][::-1]
analysis = tools.DictPlus(
code_lines_for_returns=code_lines_for_returns,
variables_for_returns=variables_for_returns,
expressions_for_returns=expressions_for_returns,
)
return analysis
def plot_trajectory(self,
initials,
duration,
plot_durations=None,
axes='v-v',
dt=None,
show=False,
with_plot=True,
with_return=False,
**kwargs):
"""Plot trajectories according to the settings.
Parameters
----------
initials : list, tuple, dict
The initial value setting of the targets. It can be a tuple/list of floats to specify
each value of dynamical variables (for example, ``(a, b)``). It can also be a
tuple/list of tuple to specify multiple initial values (for example,
``[(a1, b1), (a2, b2)]``).
duration : int, float, tuple, list
The running duration. Same with the ``duration`` in ``NeuGroup.run()``.
- It can be a int/float (``t_end``) to specify the same running end time,
- Or it can be a tuple/list of int/float (``(t_start, t_end)``) to specify
the start and end simulation time.
- Or, it can be a list of tuple (``[(t1_start, t1_end), (t2_start, t2_end)]``)
to specify the specific start and end simulation time for each initial value.
plot_durations : tuple, list, optional
The duration to plot. It can be a tuple with ``(start, end)``. It can
also be a list of tuple ``[(start1, end1), (start2, end2)]`` to specify
the plot duration for each initial value running.
axes : str
The axes to plot. It can be:
- 'v-v': Plot the trajectory in the 'x_var'-'y_var' axis.
- 't-v': Plot the trajectory in the 'time'-'var' axis.
show : bool
Whether show or not.
"""
utils.output('I am plotting the trajectory ...')
if axes not in ['v-v', 't-v']:
raise errors.AnalyzerError(
f'Unknown axes "{axes}", only support "v-v" and "t-v".')
# check the initial values
initials = utils.check_initials(initials, self.target_var_names)
# 2. format the running duration
assert isinstance(duration, (int, float))
# 3. format the plot duration
plot_durations = utils.check_plot_durations(plot_durations, duration,
initials)
# 5. run the network
dt = math.get_dt() if dt is None else dt
traject_model = utils.TrajectModel(initial_vars=initials,
integrals={
self.x_var: self.F_int_x,
self.y_var: self.F_int_y
},
dt=dt)
mon_res = traject_model.run(duration=duration)
if with_plot:
# plots
for i, initial in enumerate(zip(*list(initials.values()))):
# legend
legend = f'$traj_{i}$: '
for j, key in enumerate(self.target_var_names):
legend += f'{key}={round(float(initial[j]), 4)}, '
legend = legend[:-2]
# visualization
start = int(plot_durations[i][0] / dt)
end = int(plot_durations[i][1] / dt)
if axes == 'v-v':
lines = plt.plot(mon_res[self.x_var][start:end, i],
mon_res[self.y_var][start:end, i],
label=legend,
**kwargs)
utils.add_arrow(lines[0])
else:
plt.plot(mon_res.ts[start:end],
mon_res[self.x_var][start:end, i],
label=legend + f', {self.x_var}',
**kwargs)
plt.plot(mon_res.ts[start:end],
mon_res[self.y_var][start:end, i],
label=legend + f', {self.y_var}',
**kwargs)
# visualization of others
if axes == 'v-v':
plt.xlabel(self.x_var)
plt.ylabel(self.y_var)
scale = (self.lim_scale - 1.) / 2
plt.xlim(
*utils.rescale(self.target_vars[self.x_var], scale=scale))
plt.ylim(
*utils.rescale(self.target_vars[self.y_var], scale=scale))
plt.legend()
else:
plt.legend(title='Initial values')
if show:
plt.show()
if with_return:
return mon_res
def plot_fixed_point(
self,
with_plot=True,
with_return=False,
show=False,
tol_unique=1e-2,
tol_aux=1e-8,
tol_opt_screen=None,
select_candidates='fx-nullcline',
num_rank=100,
):
"""Plot the fixed point and analyze its stability.
"""
utils.output('I am searching fixed points ...')
if self._can_convert_to_one_eq():
if self.convert_type() == C.x_by_y:
candidates = self.resolutions[self.y_var].value
else:
candidates = self.resolutions[self.x_var].value
else:
if select_candidates == 'fx-nullcline':
candidates = [
self.analyzed_results[key][0]
for key in self.analyzed_results.keys()
if key.startswith(C.fx_nullcline_points)
]
if len(candidates) == 0:
raise errors.AnalyzerError(
f'No nullcline points are found, please call '
f'".{self.plot_nullcline.__name__}()" first.')
candidates = jnp.vstack(candidates)
elif select_candidates == 'fy-nullcline':
candidates = [
self.analyzed_results[key][0]
for key in self.analyzed_results.keys()
if key.startswith(C.fy_nullcline_points)
]
if len(candidates) == 0:
raise errors.AnalyzerError(
f'No nullcline points are found, please call '
f'".{self.plot_nullcline.__name__}()" first.')
candidates = jnp.vstack(candidates)
elif select_candidates == 'nullclines':
candidates = [
self.analyzed_results[key][0]
for key in self.analyzed_results.keys()
if key.startswith(C.fy_nullcline_points)
or key.startswith(C.fy_nullcline_points)
]
if len(candidates) == 0:
raise errors.AnalyzerError(
f'No nullcline points are found, please call '
f'".{self.plot_nullcline.__name__}()" first.')
candidates = jnp.vstack(candidates)
elif select_candidates == 'aux_rank':
candidates, _ = self._get_fp_candidates_by_aux_rank(
num_rank=num_rank)
else:
raise ValueError
# get fixed points
if len(candidates):
fixed_points, _, _ = self._get_fixed_points(
jnp.asarray(candidates),
tol_aux=tol_aux,
tol_unique=tol_unique,
tol_opt_candidate=tol_opt_screen)
utils.output(
'I am trying to filter out duplicate fixed points ...')
fixed_points = np.asarray(fixed_points)
fixed_points, _ = utils.keep_unique(fixed_points,
tolerance=tol_unique)
utils.output(f'{C.prefix}Found {len(fixed_points)} fixed points.')
else:
utils.output(f'{C.prefix}Found no fixed points.')
return
# stability analysis
# ------------------
container = {
a: {
'x': [],
'y': []
}
for a in stability.get_2d_stability_types()
}
for i in range(len(fixed_points)):
x = fixed_points[i, 0]
y = fixed_points[i, 1]
fp_type = stability.stability_analysis(self.F_jacobian(x, y))
utils.output(
f"{C.prefix}#{i + 1} {self.x_var}={x}, {self.y_var}={y} is a {fp_type}."
)
container[fp_type]['x'].append(x)
container[fp_type]['y'].append(y)
# visualization
# -------------
if with_plot:
for fp_type, points in container.items():
if len(points['x']):
plot_style = stability.plot_scheme[fp_type]
plt.plot(points['x'],
points['y'],
'.',
markersize=20,
**plot_style,
label=fp_type)
plt.legend()
if show:
plt.show()
if with_return:
return fixed_points
def plot_vector_field(self,
with_plot=True,
with_return=False,
plot_method='streamplot',
plot_style=None,
show=False):
"""Plot the vector field.
Parameters
----------
with_plot: bool
with_return : bool
show : bool
plot_method : str
The method to plot the vector filed. It can be "streamplot" or "quiver".
plot_style : dict, optional
The style for vector filed plotting.
- For ``plot_method="streamplot"``, it can set the keywords like "density",
"linewidth", "color", "arrowsize". More settings please check
https://matplotlib.org/api/_as_gen/matplotlib.pyplot.streamplot.html.
- For ``plot_method="quiver"``, it can set the keywords like "color",
"units", "angles", "scale". More settings please check
https://matplotlib.org/api/_as_gen/matplotlib.pyplot.quiver.html.
"""
utils.output('I am creating the vector field ...')
# get vector fields
xs = self.resolutions[self.x_var]
ys = self.resolutions[self.y_var]
X, Y = bm.meshgrid(xs, ys)
dx = self.F_fx(X, Y)
dy = self.F_fy(X, Y)
X, Y = np.asarray(X), np.asarray(Y)
dx, dy = np.asarray(dx), np.asarray(dy)
if with_plot: # plot vector fields
if plot_method == 'quiver':
if plot_style is None:
plot_style = dict(units='xy')
if (not np.isnan(dx).any()) and (not np.isnan(dy).any()):
speed = np.sqrt(dx**2 + dy**2)
dx = dx / speed
dy = dy / speed
plt.quiver(X, Y, dx, dy, **plot_style)
elif plot_method == 'streamplot':
if plot_style is None:
plot_style = dict(arrowsize=1.2,
density=1,
color='thistle')
linewidth = plot_style.get('linewidth', None)
if linewidth is None:
if (not np.isnan(dx).any()) and (not np.isnan(dy).any()):
min_width, max_width = 0.5, 5.5
speed = np.nan_to_num(np.sqrt(dx**2 + dy**2))
linewidth = min_width + max_width * (speed /
speed.max())
plt.streamplot(X, Y, dx, dy, linewidth=linewidth, **plot_style)
else:
raise errors.AnalyzerError(
f'Unknown plot_method "{plot_method}", '
f'only supports "quiver" and "streamplot".')
plt.xlabel(self.x_var)
plt.ylabel(self.y_var)
if show:
plt.show()
if with_return: # return vector fields
return dx, dy
def plot_trajectory(self,
initials,
duration,
plot_duration=None,
show=False):
"""Plot trajectories according to the settings.
Parameters
----------
initials : list, tuple
The initial value setting of the targets. It can be a tuple/list of floats to specify
each value of dynamical variables (for example, ``(a, b)``). It can also be a
tuple/list of tuple to specify multiple initial values (for example,
``[(a1, b1), (a2, b2)]``).
duration : int, float, tuple, list
The running duration. Same with the ``duration`` in ``NeuGroup.run()``.
It can be a int/float (``t_end``) to specify the same running end time,
or it can be a tuple/list of int/float (``(t_start, t_end)``) to specify
the start and end simulation time. Or, it can be a list of tuple
(``[(t1_start, t1_end), (t2_start, t2_end)]``) to specify the specific
start and end simulation time for each initial value.
plot_duration : tuple/list of tuple, optional
The duration to plot. It can be a tuple with ``(start, end)``. It can
also be a list of tuple ``[(start1, end1), (start2, end2)]`` to specify
the plot duration for each initial value running.
show : bool
Whether show or not.
"""
print('plot trajectory ...')
# 1. format the initial values
all_vars = self.fast_var_names + self.slow_var_names
if isinstance(initials, dict):
initials = [initials]
elif isinstance(initials, (list, tuple)):
if isinstance(initials[0], (int, float)):
initials = [{all_vars[i]: v for i, v in enumerate(initials)}]
elif isinstance(initials[0], dict):
initials = initials
elif isinstance(initials[0], (tuple, list)) and isinstance(
initials[0][0], (int, float)):
initials = [{all_vars[i]: v
for i, v in enumerate(init)} for init in initials]
else:
raise ValueError
else:
raise ValueError
for initial in initials:
if len(initial) != len(all_vars):
raise errors.AnalyzerError(
f'Should provide all fast-slow variables ({all_vars}) '
f' initial values, but we only get initial values for '
f'variables {list(initial.keys())}.')
# 2. format the running duration
if isinstance(duration, (int, float)):
duration = [(0, duration) for _ in range(len(initials))]
elif isinstance(duration[0], (int, float)):
duration = [duration for _ in range(len(initials))]
else:
assert len(duration) == len(initials)
# 3. format the plot duration
if plot_duration is None:
plot_duration = duration
if isinstance(plot_duration[0], (int, float)):
plot_duration = [plot_duration for _ in range(len(initials))]
else:
assert len(plot_duration) == len(initials)
# 5. run the network
for init_i, initial in enumerate(initials):
traj_group = Trajectory(size=1,
integrals=self.model.integrals,
target_vars=initial,
fixed_vars=self.fixed_vars,
pars_update=self.pars_update,
scope=self.model.scopes)
traj_group.run(duration=duration[init_i], report=False)
# 5.3 legend
legend = f'$traj_{init_i}$: '
for key in all_vars:
legend += f'{key}={initial[key]}, '
legend = legend[:-2]
# 5.4 trajectory
start = int(plot_duration[init_i][0] / backend.get_dt())
end = int(plot_duration[init_i][1] / backend.get_dt())
# 5.5 visualization
for var_name in self.fast_var_names:
s0 = traj_group.mon[self.slow_var_names[0]][start:end, 0]
fast = traj_group.mon[var_name][start:end, 0]
fig = plt.figure(var_name)
if len(self.slow_var_names) == 1:
lines = plt.plot(s0, fast, label=legend)
utils.add_arrow(lines[0])
# middle = int(s0.shape[0] / 2)
# plt.arrow(s0[middle], fast[middle],
# s0[middle + 1] - s0[middle], fast[middle + 1] - fast[middle],
# shape='full')
elif len(self.slow_var_names) == 2:
fig.gca(projection='3d')
s1 = traj_group.mon[self.slow_var_names[1]][start:end, 0]
plt.plot(s0, s1, fast, label=legend)
else:
raise errors.AnalyzerError
# 6. visualization
for var_name in self.fast_vars.keys():
fig = plt.figure(var_name)
# scale = (self.lim_scale - 1.) / 2
if len(self.slow_var_names) == 1:
# plt.xlim(*utils.rescale(self.slow_vars[self.slow_var_names[0]], scale=scale))
# plt.ylim(*utils.rescale(self.fast_vars[var_name], scale=scale))
plt.xlabel(self.slow_var_names[0])
plt.ylabel(var_name)
elif len(self.slow_var_names) == 2:
ax = fig.gca(projection='3d')
# ax.set_xlim(*utils.rescale(self.slow_vars[self.slow_var_names[0]], scale=scale))
# ax.set_ylim(*utils.rescale(self.slow_vars[self.slow_var_names[1]], scale=scale))
# ax.set_zlim(*utils.rescale(self.fast_vars[var_name], scale=scale))
ax.set_xlabel(self.slow_var_names[0])
ax.set_ylabel(self.slow_var_names[1])
ax.set_zlabel(var_name)
plt.legend()
if show:
plt.show()
def plot_limit_cycle_by_sim(self,
var,
duration=100,
inputs=(),
plot_style=None,
tol=0.001,
show=False):
print('plot limit cycle ...')
if self.fixed_points is None:
raise errors.AnalyzerError(
'Please call "plot_bifurcation()" before "plot_limit_cycle_by_sim()".'
)
if plot_style is None:
plot_style = dict()
fmt = plot_style.pop('fmt', '.')
if var not in [self.x_var, self.y_var]:
raise errors.AnalyzerError()
all_xs, all_ys, all_p0, all_p1 = [], [], [], []
# unstable node
unstable_node = self.fixed_points[stability.UNSTABLE_NODE_2D]
all_xs.extend(unstable_node[self.x_var])
all_ys.extend(unstable_node[self.y_var])
if len(self.dpar_names) == 1:
all_p0.extend(unstable_node['p'])
elif len(self.dpar_names) == 2:
all_p0.extend(unstable_node['p0'])
all_p1.extend(unstable_node['p1'])
else:
raise ValueError
# unstable focus
unstable_focus = self.fixed_points[stability.UNSTABLE_FOCUS_2D]
all_xs.extend(unstable_focus[self.x_var])
all_ys.extend(unstable_focus[self.y_var])
if len(self.dpar_names) == 1:
all_p0.extend(unstable_focus['p'])
elif len(self.dpar_names) == 2:
all_p0.extend(unstable_focus['p0'])
all_p1.extend(unstable_focus['p1'])
else:
raise ValueError
# format points
all_xs = np.array(all_xs)
all_ys = np.array(all_ys)
all_p0 = np.array(all_p0)
all_p1 = np.array(all_p1)
# fixed variables
fixed_vars = dict()
for key, val in self.fixed_vars.items():
fixed_vars[key] = val
fixed_vars[self.dpar_names[0]] = all_p0
if len(self.dpar_names) == 2:
fixed_vars[self.dpar_names[1]] = all_p1
# initialize neuron group
length = all_xs.shape[0]
traj_group = Trajectory(size=length,
integrals=self.model.integrals,
target_vars={
self.x_var: all_xs,
self.y_var: all_ys
},
fixed_vars=fixed_vars,
pars_update=self.pars_update,
scope=self.model.scopes)
traj_group.run(duration=duration)
# find limit cycles
limit_cycle_max = []
limit_cycle_min = []
# limit_cycle = []
p0_limit_cycle = []
p1_limit_cycle = []
for i in range(length):
data = traj_group.mon[var][:, i]
max_index = utils.find_indexes_of_limit_cycle_max(data, tol=tol)
if max_index[0] != -1:
x_cycle = data[max_index[0]:max_index[1]]
limit_cycle_max.append(data[max_index[1]])
limit_cycle_min.append(x_cycle.min())
# limit_cycle.append(x_cycle)
p0_limit_cycle.append(all_p0[i])
if len(self.dpar_names) == 2:
p1_limit_cycle.append(all_p1[i])
self.fixed_points['limit_cycle'] = {
var: {
'max': limit_cycle_max,
'min': limit_cycle_min,
# 'cycle': limit_cycle
}
}
p0_limit_cycle = np.array(p0_limit_cycle)
p1_limit_cycle = np.array(p1_limit_cycle)
# visualization
if len(self.dpar_names) == 2:
self.fixed_points['limit_cycle'] = {
'p0': p0_limit_cycle,
'p1': p1_limit_cycle
}
plt.figure(var)
plt.plot(p0_limit_cycle,
p1_limit_cycle,
limit_cycle_max,
**plot_style,
label='limit cycle (max)')
plt.plot(p0_limit_cycle,
p1_limit_cycle,
limit_cycle_min,
**plot_style,
label='limit cycle (min)')
plt.legend()
else:
self.fixed_points['limit_cycle'] = {'p': p0_limit_cycle}
if len(limit_cycle_max):
plt.figure(var)
plt.plot(p0_limit_cycle,
limit_cycle_max,
fmt,
**plot_style,
label='limit cycle (max)')
plt.plot(p0_limit_cycle,
limit_cycle_min,
fmt,
**plot_style,
label='limit cycle (min)')
plt.legend()
if show:
plt.show()
del traj_group
gc.collect()
