def test_unit_checking():
# dummy Variable class
class S(object):
def __init__(self, unit):
self.unit = unit
# inconsistent unit for a differential equation
eqs = Equations('dv/dt = -v : volt')
group = SimpleGroup({'v': S(volt)})
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(group))
eqs = Equations('dv/dt = -v / tau: volt')
group = SimpleGroup(namespace={'tau': 5*mV}, variables={'v': S(volt)})
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(group))
group = SimpleGroup(namespace={'I': 3*second}, variables={'v': S(volt)})
eqs = Equations('dv/dt = -(v + I) / (5 * ms): volt')
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(group))
eqs = Equations('''dv/dt = -(v + I) / (5 * ms): volt
I : second''')
group = SimpleGroup(variables={'v': S(volt),
'I': S(second)}, namespace={})
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(group))
# inconsistent unit for a subexpression
eqs = Equations('''dv/dt = -v / (5 * ms) : volt
I = 2 * v : amp''')
group = SimpleGroup(variables={'v': S(volt),
'I': S(second)}, namespace={})
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(group))
def test_unit_checking():
# dummy Variable class
class S(object):
def __init__(self, unit):
self.unit = unit
# Let's create a namespace with a user-defined namespace that we can
# updater later on
namespace = create_namespace({})
# inconsistent unit for a differential equation
eqs = Equations('dv/dt = -v : volt')
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(namespace, {'v': S(volt)}))
eqs = Equations('dv/dt = -v / tau: volt')
namespace['tau'] = 5*mV
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(namespace, {'v': S(volt)}))
namespace['I'] = 3*second
eqs = Equations('dv/dt = -(v + I) / (5 * ms): volt')
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(namespace, {'v': S(volt)}))
eqs = Equations('''dv/dt = -(v + I) / (5 * ms): volt
I : second''')
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(namespace, {'v': S(volt),
'I': S(second)}))
# inconsistent unit for a static equation
eqs = Equations('''dv/dt = -v / (5 * ms) : volt
I = 2 * v : amp''')
assert_raises(DimensionMismatchError,
lambda: eqs.check_units(namespace, {'v': S(volt),
'I': S(amp)}))
def test_repeated_construction():
eqs1 = Equations('dx/dt = x : 1')
eqs2 = Equations('dx/dt = x : 1', x='y')
assert len(eqs1) == 1
assert 'x' in eqs1
assert eqs1['x'].expr == Expression('x')
assert len(eqs2) == 1
assert 'y' in eqs2
assert eqs2['y'].expr == Expression('y')
def test_substitute():
# Check that Equations.substitute returns an independent copy
eqs = Equations('dx/dt = x : 1')
eqs2 = eqs.substitute(x='y')
# First equation should be unaffected
assert len(eqs) == 1 and 'x' in eqs
assert eqs['x'].expr == Expression('x')
# Second equation should have x substituted by y
assert len(eqs2) == 1 and 'y' in eqs2
assert eqs2['y'].expr == Expression('y')
def test_substitute():
# Check that Equations.substitute returns an independent copy
eqs = Equations('dx/dt = x : 1')
eqs2 = eqs.substitute(x='y')
# First equation should be unaffected
assert len(eqs) == 1 and 'x' in eqs
assert eqs['x'].expr == Expression('x')
# Second equation should have x substituted by y
assert len(eqs2) == 1 and 'y' in eqs2
assert eqs2['y'].expr == Expression('y')
def test_correct_replacements():
''' Test replacing variables via keyword arguments '''
# replace a variable name with a new name
eqs = Equations('dv/dt = -v / tau : 1', v='V')
# Correct left hand side
assert ('V' in eqs) and not ('v' in eqs)
# Correct right hand side
assert ('V' in eqs['V'].identifiers) and not ('v' in eqs['V'].identifiers)
# replace a variable name with a value
eqs = Equations('dv/dt = -v / tau : 1', tau=10 * ms)
assert not 'tau' in eqs['v'].identifiers
def test_identifier_checks():
legal_identifiers = ['v', 'Vm', 'V', 'x', 'ge', 'g_i', 'a2', 'gaba_123']
illegal_identifiers = ['_v', '1v', 'ü', 'ge!', 'v.x', 'for', 'else', 'if']
for identifier in legal_identifiers:
try:
check_identifier_basic(identifier)
check_identifier_reserved(identifier)
except ValueError as ex:
raise AssertionError(
f'check complained about identifier "{identifier}": {ex}')
for identifier in illegal_identifiers:
with pytest.raises(SyntaxError):
check_identifier_basic(identifier)
for identifier in ('t', 'dt', 'xi', 'i', 'N'):
with pytest.raises(SyntaxError):
check_identifier_reserved(identifier)
for identifier in ('not_refractory', 'refractory', 'refractory_until'):
with pytest.raises(SyntaxError):
check_identifier_refractory(identifier)
for identifier in ('exp', 'sin', 'sqrt'):
with pytest.raises(SyntaxError):
check_identifier_functions(identifier)
for identifier in ('e', 'pi', 'inf'):
with pytest.raises(SyntaxError):
check_identifier_constants(identifier)
for identifier in ('volt', 'second', 'mV', 'nA'):
with pytest.raises(SyntaxError):
check_identifier_units(identifier)
# Check identifier registry
assert check_identifier_basic in Equations.identifier_checks
assert check_identifier_reserved in Equations.identifier_checks
assert check_identifier_refractory in Equations.identifier_checks
assert check_identifier_functions in Equations.identifier_checks
assert check_identifier_constants in Equations.identifier_checks
assert check_identifier_units in Equations.identifier_checks
# Set up a dummy identifier check that disallows the variable name
# gaba_123 (that is otherwise valid)
def disallow_gaba_123(identifier):
if identifier == 'gaba_123':
raise SyntaxError("I do not like this name")
Equations.check_identifier('gaba_123')
old_checks = set(Equations.identifier_checks)
Equations.register_identifier_check(disallow_gaba_123)
with pytest.raises(SyntaxError):
Equations.check_identifier('gaba_123')
Equations.identifier_checks = old_checks
# registering a non-function should not work
with pytest.raises(ValueError):
Equations.register_identifier_check('no function')
def brian2(self) -> BrianObject:
model = Equations('''
w1 : 1
w2 : 1
w3 : 1
w4 : 1
''')
on_pre = f'''
{self.post_variable_name[0]} += w1
{self.post_variable_name[1]} += w2
{self.post_variable_name[2]} += w3
{self.post_variable_name[3]} += w4
'''
syn = Synapses(
source=self.origin.brian2,
target=self.target.brian2,
method='euler',
model=model,
on_pre=on_pre,
name=self.ref,
)
syn.connect(j='i')
syn.w1[:] = 1
syn.w2[:] = 1
syn.w3[:] = 1
syn.w4[:] = 1
return syn
def plot_inf(ax, parameters):
"""Plot gating variable steady-state values as function of membrane potential.
ax -- matplotlib axes to be plotted on
parameters -- dictionary of parameters for gating variable steady-state equations
"""
inf_group = NeuronGroup(100,
Equations('v : volt') +
reduce(operator.add, [
construct_gating_variable_inf_equation(gv)
for gv in ['m', 'n', 'h']
]),
method='euler',
namespace=parameters)
inf_group.v = np.linspace(-100, 100, len(inf_group)) * mV
ax.plot(inf_group.v / mV, inf_group.m_inf, label=r'$m_\infty$')
ax.plot(inf_group.v / mV, inf_group.n_inf, label=r'$n_\infty$')
ax.plot(inf_group.v / mV, inf_group.h_inf, label=r'$h_\infty$')
ax.set_xlabel('$v$ (mV)')
ax.set_ylabel('steady-state activation')
ax.yaxis.set_label_position("right")
ax.yaxis.tick_right()
ax.legend()
def test_dependency_calculation():
eqs = Equations('''dv/dt = I_m / C_m : volt
I_m = I_ext + I_pas : amp
I_ext = 1*nA + sin(2*pi*100*Hz*t)*nA : amp
I_pas = g_L*(E_L - v) : amp''')
deps = eqs.dependencies
assert set(deps.keys()) == {'v', 'I_m', 'I_ext', 'I_pas'}
# v depends directly on I_m, on I_ext and I_pas via I_m, and on v via I_m -> I_pas
assert len(deps['v']) == 4
assert set(d.equation.varname
for d in deps['v']) == {'I_m', 'I_ext', 'I_pas', 'v'}
expected_via = {
'I_m': (),
'I_pas': ('I_m', ),
'I_ext': ('I_m', ),
'v': ('I_m', 'I_pas')
}
assert all([d.via == expected_via[d.equation.varname] for d in deps['v']])
# I_m depends directly on I_ext and I_pas, and on v via I_pas
assert len(deps['I_m']) == 3
assert set(d.equation.varname
for d in deps['I_m']) == {'I_ext', 'I_pas', 'v'}
expected_via = {'I_ext': (), 'I_pas': (), 'v': ('I_pas', )}
assert all(
[d.via == expected_via[d.equation.varname] for d in deps['I_m']])
# I_ext does not depend on anything
assert len(deps['I_ext']) == 0
# I_pas depends on v directly
assert len(deps['I_pas']) == 1
assert deps['I_pas'][0].equation.varname == 'v'
assert deps['I_pas'][0].via == ()
def brian2(self) -> BrianObject:
model = Equations(
'''
w : 1
s_post = w * s : 1 (summed)
ds / dt = - s / tau + alpha * x * (1 - s) : 1 (clock-driven)
dx / dt = - x / tau_rise : 1 (clock-driven)
''',
s_post=f'{self.post_variable_name_tot}_post',
s=self.post_variable_name,
x=self.post_nonlinear_name,
tau=self[IP.TAU],
tau_rise=self[IP.TAU_NMDA_RISE],
alpha=self[IP.ALPHA],
)
eqs_pre = f'''
{self.post_nonlinear_name} += 1
'''
C = Synapses(
self.origin.brian2,
self.target.brian2,
method='euler',
model=model,
on_pre=eqs_pre,
name=self.ref,
)
C.connect()
C.w[:] = 1
return C
def test_str_repr():
'''
Test the string representation (only that it does not throw errors).
'''
tau = 10 * ms
eqs = Equations('''dv/dt = -(v + I)/ tau : volt (unless refractory)
I = sin(2 * 22/7. * f * t)* volt : volt
f : Hz''')
assert len(str(eqs)) > 0
assert len(repr(eqs)) > 0
# Test str and repr of SingleEquations explicitly (might already have been
# called by Equations
for eq in eqs.itervalues():
assert (len(str(eq))) > 0
assert (len(repr(eq))) > 0
def test_str_repr():
'''
Test the string representation (only that it does not throw errors).
'''
tau = 10 * ms
eqs = Equations('''dv/dt = -(v + I)/ tau : volt (unless refractory)
I = sin(2 * 22/7. * f * t)* volt : volt
f : Hz''')
assert len(str(eqs)) > 0
assert len(repr(eqs)) > 0
# Test str and repr of SingleEquations explicitly (might already have been
# called by Equations
for eq in eqs.itervalues():
assert(len(str(eq))) > 0
assert(len(repr(eq))) > 0
def setup_spikes(request):
def fin():
reinit_devices()
request.addfinalizer(fin)
EL = -70 * mV
VT = -50 * mV
DeltaT = 2 * mV
C = 1 * nF
gL = 30 * nS
I = TimedArray(input_current, dt=0.01 * ms)
model = Equations('''
dv/dt = (gL*(EL-v)+gL*DeltaT*exp((v-VT)/DeltaT) + I(t))/C : volt
''')
group = NeuronGroup(1,
model,
threshold='v > -50*mV',
reset='v = -70*mV',
method='exponential_euler')
group.v = -70 * mV
spike_mon = SpikeMonitor(group)
run(60 * ms)
spikes = getattr(spike_mon, 't_')
return spike_mon, spikes
def test_fitter_fit_methods(method):
dt = 0.01 * ms
model = Equations('''
I = g*(v-E) : amp
g : siemens (constant)
E : volt (constant)
''')
tf = TraceFitter(dt=dt,
model=model,
input_var='v',
output_var='I',
input=input_traces,
output=output_traces,
n_samples=30)
# Skip all BO methods for now (TODO: check what is going on)
if 'BO' in method:
pytest.skip(f'Skipping method {method}')
optimizer = NevergradOptimizer(method)
# Just make sure that it can run at all
tf.fit(n_rounds=2,
optimizer=optimizer,
metric=metric,
g=[1 * nS, 30 * nS],
E=[-60 * mV, -20 * mV],
callback=None)
def brian2(self) -> BrianObject:
model = Equations('''
x : 1
u : 1
w : 1
''')
U = self[IP.U]
tauf = self[IP.TAU_F]
taud = self[IP.TAU_D]
on_pre = f'''
u = {U} + (u - {U}) * exp(- (t - lastupdate) / ({tauf / units.ms} * ms))
x = 1 + (x - 1) * exp(- (t - lastupdate) / ({taud / units.ms} * ms))
{self.post_variable_name} += w * u * x
x *= (1 - u)
u += {U} * (1 - u)
'''
syn = Synapses(source=self.origin.brian2,
target=self.target.brian2,
method='euler',
model=model,
on_pre=on_pre,
name=self.ref)
self.connection.simulation(syn)
syn.w[:] = self[IP.W]
syn.x[:] = 1
syn.u[:] = 1
return syn
def plot_tau(ax, parameters):
"""Plot gating variable time constants as function of membrane potential.
ax -- matplotlib axes to be plotted on
parameters -- dictionary of parameters for gating variable time constant equations
"""
tau_group = NeuronGroup(100,
Equations('v : volt') +
reduce(operator.add, [
construct_gating_variable_tau_equation(gv)
for gv in ['m', 'n', 'h']
]),
method='euler',
namespace=parameters)
min_v = -100
max_v = 100
tau_group.v = np.linspace(min_v, max_v, len(tau_group)) * mV
ax.plot(tau_group.v / mV, tau_group.tau_m / ms, label=r'$\tau_m$')
ax.plot(tau_group.v / mV, tau_group.tau_n / ms, label=r'$\tau_n$')
ax.plot(tau_group.v / mV, tau_group.tau_h / ms, label=r'$\tau_h$')
ax.set_xlabel('$v$ (mV)')
ax.set_ylabel(r'$\tau$ (ms)')
ax.yaxis.set_label_position("right")
ax.yaxis.tick_right()
ax.legend()
def introspect_population(pop):
if False:
print(pop.thresholder)
print(pop.resetter)
print(pop.events['spike'])
print(pop.event_codes.get('spike'))
print('{} [{}] n: {}'.format(pop.__class__.__name__, pop.name, pop.N))
print(Equations(str(pop.user_equations), **globals))
def test_resolve():
'''
Test resolving identifiers in equations.
'''
def foo(x):
return 5 * x
tau = 10 * ms
tau2 = 20
eqs = '''dv/dt = -v / tau : volt
du/dt = -foo(u) * param / (tau_long * ms): volt
param : 1
'''
eq = Equations(eqs, namespace={'tau_long': tau2}, exhaustive=False)
namespace = eq.resolve()
assert namespace['tau'] is tau
assert namespace['tau_long'] is tau2
assert namespace['foo'] is foo
assert namespace['ms'] is ms
assert set(namespace.keys()) == set(('tau', 'tau_long', 'foo', 'ms'))
def construct_gating_variable_ode(gating_variable):
"""Construct the ordinary differential equation of the gating variable.
gating_variable -- gating variable, typically one of "m", "n" and "h"
"""
return Equations('dx/dt = (xinf - x)/tau : 1',
x=gating_variable,
xinf=f'{gating_variable}_inf',
tau=f'tau_{gating_variable}')
def test_extract_subexpressions():
eqs = Equations("""dv/dt = -v / (10*ms) : 1
s1 = 2*v : 1
s2 = -v : 1 (constant over dt)
""")
variable, constant = extract_constant_subexpressions(eqs)
assert [var in variable for var in ['v', 's1', 's2']]
assert variable['s1'].type == SUBEXPRESSION
assert variable['s2'].type == PARAMETER
assert constant['s2'].type == SUBEXPRESSION
def test_construction_errors():
'''
Test that the Equations constructor raises errors correctly
'''
# parse error
assert_raises(EquationError, lambda: Equations('dv/dt = -v / tau volt'))
# Only a single string or a list of SingleEquation objects is allowed
assert_raises(TypeError, lambda: Equations(None))
assert_raises(TypeError, lambda: Equations(42))
assert_raises(TypeError, lambda: Equations(['dv/dt = -v / tau : volt']))
# duplicate variable names
assert_raises(EquationError, lambda: Equations('''dv/dt = -v / tau : volt
v = 2 * t/second * volt : volt'''))
eqs = [SingleEquation(DIFFERENTIAL_EQUATION, 'v', volt,
expr=Expression('-v / tau')),
SingleEquation(SUBEXPRESSION, 'v', volt,
expr=Expression('2 * t/second * volt'))
]
assert_raises(EquationError, lambda: Equations(eqs))
# illegal variable names
assert_raises(ValueError, lambda: Equations('ddt/dt = -dt / tau : volt'))
assert_raises(ValueError, lambda: Equations('dt/dt = -t / tau : volt'))
assert_raises(ValueError, lambda: Equations('dxi/dt = -xi / tau : volt'))
assert_raises(ValueError, lambda: Equations('for : volt'))
assert_raises((EquationError, ValueError),
lambda: Equations('d1a/dt = -1a / tau : volt'))
assert_raises(ValueError, lambda: Equations('d_x/dt = -_x / tau : volt'))
# xi in a subexpression
assert_raises(EquationError,
lambda: Equations('''dv/dt = -(v + I) / (5 * ms) : volt
I = second**-1*xi**-2*volt : volt'''))
# more than one xi
assert_raises(EquationError,
lambda: Equations('''dv/dt = -v / tau + xi/tau**.5 : volt
dx/dt = -x / tau + 2*xi/tau : volt
tau : second'''))
# using not-allowed flags
eqs = Equations('dv/dt = -v / (5 * ms) : volt (flag)')
eqs.check_flags({DIFFERENTIAL_EQUATION: ['flag']}) # allow this flag
assert_raises(ValueError, lambda: eqs.check_flags({DIFFERENTIAL_EQUATION: []}))
assert_raises(ValueError, lambda: eqs.check_flags({}))
assert_raises(ValueError, lambda: eqs.check_flags({SUBEXPRESSION: ['flag']}))
assert_raises(ValueError, lambda: eqs.check_flags({DIFFERENTIAL_EQUATION: ['otherflag']}))
# Circular subexpression
assert_raises(ValueError, lambda: Equations('''dv/dt = -(v + w) / (10 * ms) : 1
w = 2 * x : 1
x = 3 * w : 1'''))
# Boolean/integer differential equations
assert_raises(TypeError, lambda: Equations('dv/dt = -v / (10*ms) : boolean'))
assert_raises(TypeError, lambda: Equations('dv/dt = -v / (10*ms) : integer'))
def brian2(self) -> BrianObject:
model = Equations('w : 1')
on_pre = f'{self.post_variable_name} += w'
syn = Synapses(source=self.origin.brian2,
target=self.target.brian2,
method='euler',
model=model,
on_pre=on_pre,
name=self.ref)
self.connection.simulation(syn)
syn.w[:] = self[IP.W]
return syn
def test_ipython_pprint():
from io import StringIO
eqs = Equations("""dv/dt = -(v + I)/ tau : volt (unless refractory)
I = sin(2 * 22/7. * f * t)* volt : volt
f : Hz""")
# Test ipython's pretty printing
old_stdout = sys.stdout
string_output = StringIO()
sys.stdout = string_output
pprint(eqs)
assert len(string_output.getvalue()) > 0
sys.stdout = old_stdout
def construct_gating_variable_inf_equation(gating_variable):
"""Construct the voltage-dependent steady-state gating variable equation.
Approximated by Boltzmann function.
gating_variable -- gating variable, typically one of "m", "n" and "h"
"""
return Equations('xinf = 1/(1+exp((v_half-v)/k)) : 1',
xinf=f'{gating_variable}_inf',
v_half=f'v_{gating_variable}_half',
k=f'k_{gating_variable}')
def test_identifier_checks():
legal_identifiers = ['v', 'Vm', 'V', 'x', 'ge', 'g_i', 'a2', 'gaba_123']
illegal_identifiers = ['_v', '1v', u'ü', 'ge!', 'v.x', 'for', 'else', 'if']
for identifier in legal_identifiers:
try:
check_identifier_basic(identifier)
check_identifier_reserved(identifier)
except ValueError as ex:
raise AssertionError('check complained about '
'identifier "%s": %s' % (identifier, ex))
for identifier in illegal_identifiers:
assert_raises(ValueError, lambda: check_identifier_basic(identifier))
for identifier in ('t', 'dt', 'xi'):
assert_raises(ValueError, lambda: check_identifier_reserved(identifier))
for identifier in ('is_active', 'refractory', 'refractory_until'):
assert_raises(ValueError, lambda: check_identifier_refractory(identifier))
# Check identifier registry
assert check_identifier_basic in Equations.identifier_checks
assert check_identifier_reserved in Equations.identifier_checks
assert check_identifier_refractory in Equations.identifier_checks
# Set up a dummy identifier check that disallows the variable name
# gaba_123 (that is otherwise valid)
def disallow_gaba_123(identifier):
if identifier == 'gaba_123':
raise ValueError('I do not like this name')
check_identifier('gaba_123')
old_checks = Equations.identifier_checks
Equations.register_identifier_check(disallow_gaba_123)
assert_raises(ValueError, lambda: check_identifier('gaba_123'))
Equations.identifier_checks = old_checks
# registering a non-function should now work
assert_raises(ValueError, lambda: Equations.register_identifier_check('no function'))
def test_wrong_replacements():
'''Tests for replacements that should not work'''
# Replacing a variable name with an illegal new name
assert_raises(SyntaxError,
lambda: Equations('dv/dt = -v / tau : 1', v='illegal name'))
assert_raises(SyntaxError,
lambda: Equations('dv/dt = -v / tau : 1', v='_reserved'))
assert_raises(SyntaxError,
lambda: Equations('dv/dt = -v / tau : 1', v='t'))
# Replacing a variable name with a value that already exists
assert_raises(
EquationError, lambda: Equations('''
dv/dt = -v / tau : 1
dx/dt = -x / tau : 1
''',
v='x'))
# Replacing a model variable name with a value
assert_raises(ValueError,
lambda: Equations('dv/dt = -v / tau : 1', v=3 * mV))
# Replacing with an illegal value
assert_raises(SyntaxError,
lambda: Equations('dv/dt = -v/tau : 1', tau=np.arange(5)))
def test_concatenation():
eqs1 = Equations('''dv/dt = -(v + I) / tau : volt
I = sin(2*pi*freq*t) : volt
freq : Hz''')
# Concatenate two equation objects
eqs2 = (Equations('dv/dt = -(v + I) / tau : volt') +
Equations('''I = sin(2*pi*freq*t) : volt
freq : Hz'''))
# Concatenate using "in-place" addition (which is not actually in-place)
eqs3 = Equations('dv/dt = -(v + I) / tau : volt')
eqs3 += Equations('''I = sin(2*pi*freq*t) : volt
freq : Hz''')
# Concatenate with a string (will be parsed first)
eqs4 = Equations('dv/dt = -(v + I) / tau : volt')
eqs4 += '''I = sin(2*pi*freq*t) : volt
freq : Hz'''
# Concatenating with something that is not a string should not work
assert_raises(TypeError, lambda: eqs4 + 5)
# The string representation is canonical, therefore it should be identical
# in all cases
assert str(eqs1) == str(eqs2)
assert str(eqs2) == str(eqs3)
assert str(eqs3) == str(eqs4)
def test_properties():
'''
Test accessing the various properties of equation objects
'''
tau = 10 * ms
eqs = Equations('''dv/dt = -(v + I)/ tau : volt
I = sin(2 * 22/7. * f * t)* volt : volt
f = freq * Hz: Hz
freq : 1''')
assert (len(eqs.diff_eq_expressions) == 1 and
eqs.diff_eq_expressions[0][0] == 'v' and
isinstance(eqs.diff_eq_expressions[0][1], Expression))
assert eqs.diff_eq_names == {'v'}
assert (len(eqs.eq_expressions) == 3 and
set([name for name, _ in eqs.eq_expressions]) == {'v', 'I', 'f'} and
all((isinstance(expr, Expression) for _, expr in eqs.eq_expressions)))
assert len(eqs.eq_names) == 3 and eqs.eq_names == {'v', 'I', 'f'}
assert set(eqs.keys()) == {'v', 'I', 'f', 'freq'}
# test that the equations object is iterable itself
assert all((isinstance(eq, SingleEquation) for eq in eqs.itervalues()))
assert all((isinstance(eq, basestring) for eq in eqs))
assert (len(eqs.ordered) == 4 and
all((isinstance(eq, SingleEquation) for eq in eqs.ordered)) and
[eq.varname for eq in eqs.ordered] == ['f', 'I', 'v', 'freq'])
assert [eq.unit for eq in eqs.ordered] == [Hz, volt, volt, 1]
assert eqs.names == {'v', 'I', 'f', 'freq'}
assert eqs.parameter_names == {'freq'}
assert eqs.subexpr_names == {'I', 'f'}
dimensions = eqs.dimensions
assert set(dimensions.keys()) == {'v', 'I', 'f', 'freq'}
assert dimensions['v'] is volt.dim
assert dimensions['I'] is volt.dim
assert dimensions['f'] is Hz.dim
assert dimensions['freq'] is DIMENSIONLESS
assert eqs.names == set(eqs.dimensions.keys())
assert eqs.identifiers == {'tau', 'volt', 'Hz', 'sin', 't'}
# stochastic equations
assert len(eqs.stochastic_variables) == 0
assert eqs.stochastic_type is None
eqs = Equations('''dv/dt = -v / tau + 0.1*second**-.5*xi : 1''')
assert eqs.stochastic_variables == {'xi'}
assert eqs.stochastic_type == 'additive'
eqs = Equations('''dv/dt = -v / tau + 0.1*second**-.5*xi_1 + 0.1*second**-.5*xi_2: 1''')
assert eqs.stochastic_variables == {'xi_1', 'xi_2'}
assert eqs.stochastic_type == 'additive'
eqs = Equations('''dv/dt = -v / tau + 0.1*second**-1.5*xi*t : 1''')
assert eqs.stochastic_type == 'multiplicative'
eqs = Equations('''dv/dt = -v / tau + 0.1*second**-1.5*xi*v : 1''')
assert eqs.stochastic_type == 'multiplicative'
def brian2_model(self) -> Equations:
"""Returns Brian2 dynamic (Equations) affecting specified populations."""
return Equations(
'''
I = g * (v - vrev) * s : amp
ds / dt = - s / tau : 1
''',
I=self.current_name,
g=self[IP.GM],
s=self.post_variable_name,
vrev=self[IP.VREV],
tau=self[IP.TAU],
)
def test_ipython_pprint():
if pprint is None:
raise SkipTest('ipython is not available')
eqs = Equations('''dv/dt = -(v + I)/ tau : volt (unless refractory)
I = sin(2 * 22/7. * f * t)* volt : volt
f : Hz''')
# Test ipython's pretty printing
old_stdout = sys.stdout
string_output = StringIO()
sys.stdout = string_output
pprint(eqs)
assert len(string_output.getvalue()) > 0
sys.stdout = old_stdout
def brian2_model(self) -> Equations:
return Equations(
'''
I = g * (v - vrev) / (1 + mg * gamma * exp(- beta * v / mV) ) * s : amp
s: 1
''',
s=self.post_variable_name_tot,
I=self.current_name,
g=self[IP.GM],
vrev=self[IP.VREV],
beta=self[IP.BETA],
gamma=self[IP.GAMMA],
mg=self[IP.MG],
)
def brian2_model(self) -> Equations:
return Equations(
'''
I = g * (v - vrev ) / (1 + gamma * exp(- beta * v)) * s : amp
ds / dt = - s / tau_decay : 1
''',
I=self.current_name,
g=self[IP.GM],
s=self.post_variable_name,
s_post=self.post_variable_name + '_post',
vrev=self[IP.VREV],
tau_decay=self[IP.TAU],
gamma=self[IP.GAMMA],
beta=self[IP.BETA] / units.mV,
)
def test_str_repr():
'''
Test the string representation (only that it does not throw errors).
'''
tau = 10 * ms
eqs = Equations('''dv/dt = -(v + I)/ tau : volt (unless-refractory)
I = sin(2 * 22/7. * f * t)* volt : volt
f : Hz''')
assert len(str(eqs)) > 0
assert len(repr(eqs)) > 0
# Test str and repr of SingleEquations explicitly (might already have been
# called by Equations
for eq in eqs.itervalues():
assert (len(str(eq))) > 0
assert (len(repr(eq))) > 0
# Test ipython's pretty printing
old_stdout = sys.stdout
string_output = StringIO()
sys.stdout = string_output
pprint(eqs)
assert len(string_output.getvalue()) > 0
sys.stdout = old_stdout
def test_str_repr():
'''
Test the string representation (only that it does not throw errors).
'''
tau = 10 * ms
eqs = Equations('''dv/dt = -(v + I)/ tau : volt (unless-refractory)
I = sin(2 * 22/7. * f * t)* volt : volt
f : Hz''')
assert len(str(eqs)) > 0
assert len(repr(eqs)) > 0
# Test str and repr of SingleEquations explicitly (might already have been
# called by Equations
for eq in eqs.itervalues():
assert(len(str(eq))) > 0
assert(len(repr(eq))) > 0
# Test ipython's pretty printing
old_stdout = sys.stdout
string_output = StringIO()
sys.stdout = string_output
pprint(eqs)
assert len(string_output.getvalue()) > 0
sys.stdout = old_stdout
def construct_gating_variable_tau_equation(gating_variable):
"""Construct the voltage-dependent gating variable time constant equation.
Approximated by Gaussian function.
gating_variable -- gating variable, typically one of "m", "n" and "h"
"""
return Equations(
'tau = c_base + c_amp*exp(-(v_max - v)**2/sigma**2) : second',
tau=f'tau_{gating_variable}',
c_base=f'c_{gating_variable}_base',
c_amp=f'c_{gating_variable}_amp',
v_max=f'v_{gating_variable}_max',
sigma=f'sigma_{gating_variable}')
def test_ipython_pprint():
try:
from cStringIO import StringIO # Python 2
except ImportError:
from io import StringIO # Python 3
eqs = Equations('''dv/dt = -(v + I)/ tau : volt (unless refractory)
I = sin(2 * 22/7. * f * t)* volt : volt
f : Hz''')
# Test ipython's pretty printing
old_stdout = sys.stdout
string_output = StringIO()
sys.stdout = string_output
pprint(eqs)
assert len(string_output.getvalue()) > 0
sys.stdout = old_stdout
def test_identifier_checks():
legal_identifiers = ['v', 'Vm', 'V', 'x', 'ge', 'g_i', 'a2', 'gaba_123']
illegal_identifiers = ['_v', '1v', u'ü', 'ge!', 'v.x', 'for', 'else', 'if']
for identifier in legal_identifiers:
try:
check_identifier_basic(identifier)
check_identifier_reserved(identifier)
except ValueError as ex:
raise AssertionError('check complained about '
'identifier "%s": %s' % (identifier, ex))
for identifier in illegal_identifiers:
assert_raises(ValueError, lambda: check_identifier_basic(identifier))
for identifier in ('t', 'dt', 'xi'):
assert_raises(ValueError,
lambda: check_identifier_reserved(identifier))
for identifier in ('not_refractory', 'refractory', 'refractory_until'):
assert_raises(ValueError,
lambda: check_identifier_refractory(identifier))
for identifier in ('exp', 'sin', 'sqrt'):
assert_raises(ValueError,
lambda: check_identifier_functions(identifier))
for identifier in ('volt', 'second', 'mV', 'nA'):
assert_raises(ValueError, lambda: check_identifier_units(identifier))
# Check identifier registry
assert check_identifier_basic in Equations.identifier_checks
assert check_identifier_reserved in Equations.identifier_checks
assert check_identifier_refractory in Equations.identifier_checks
assert check_identifier_functions in Equations.identifier_checks
assert check_identifier_units in Equations.identifier_checks
# Set up a dummy identifier check that disallows the variable name
# gaba_123 (that is otherwise valid)
def disallow_gaba_123(identifier):
if identifier == 'gaba_123':
raise ValueError('I do not like this name')
Equations.check_identifier('gaba_123')
old_checks = set(Equations.identifier_checks)
Equations.register_identifier_check(disallow_gaba_123)
assert_raises(ValueError, lambda: Equations.check_identifier('gaba_123'))
Equations.identifier_checks = old_checks
# registering a non-function should now work
assert_raises(ValueError,
lambda: Equations.register_identifier_check('no function'))
def brian2_model(self) -> Optional[Equations]:
eqs = Equations(
'dv / dt = (- g * (v - vl) - I) / cm : volt',
g=self[PP.GM],
vl=self[PP.VL],
cm=self[PP.CM]
)
all_currents = []
for s in self.inputs + self.noises:
eqs += s.brian2_model
all_currents.append(s.current_name)
if len(all_currents):
sum_currents = ' + '.join(all_currents)
eqs += f'I = {sum_currents} : amp'
else:
eqs += 'I = 0 : amp'
return eqs
def test_construction_errors():
'''
Test that the Equations constructor raises errors correctly
'''
# parse error
assert_raises(SyntaxError, lambda: Equations('dv/dt = -v / tau volt'))
# Only a single string or a list of SingleEquation objects is allowed
assert_raises(TypeError, lambda: Equations(None))
assert_raises(TypeError, lambda: Equations(42))
assert_raises(TypeError, lambda: Equations(['dv/dt = -v / tau : volt']))
# duplicate variable names
assert_raises(SyntaxError, lambda: Equations('''dv/dt = -v / tau : volt
v = 2 * t/second * volt : volt'''))
# illegal variable names
assert_raises(ValueError, lambda: Equations('ddt/dt = -dt / tau : volt'))
assert_raises(ValueError, lambda: Equations('dt/dt = -t / tau : volt'))
assert_raises(ValueError, lambda: Equations('dxi/dt = -xi / tau : volt'))
assert_raises(ValueError, lambda: Equations('for : volt'))
assert_raises((SyntaxError, ValueError),
lambda: Equations('d1a/dt = -1a / tau : volt'))
assert_raises(ValueError, lambda: Equations('d_x/dt = -_x / tau : volt'))
# inconsistent unit for a differential equation
assert_raises(DimensionMismatchError,
lambda: Equations('dv/dt = -v : volt'))
assert_raises(DimensionMismatchError,
lambda: Equations('dv/dt = -v / tau: volt',
namespace={'tau': 5 * mV}))
assert_raises(DimensionMismatchError,
lambda: Equations('dv/dt = -(v + I) / (5 * ms): volt',
namespace={'I': 3 * second}))
# inconsistent unit for a static equation
assert_raises(DimensionMismatchError,
lambda: Equations('''dv/dt = -v / (5 * ms) : volt
I = 2 * v : amp'''))
# xi in a static equation
assert_raises(SyntaxError,
lambda: Equations('''dv/dt = -(v + I) / (5 * ms) : volt
I = second**-1*xi**-2*volt : volt''' ))
# more than one xi
assert_raises(SyntaxError,
lambda: Equations('''dv/dt = -v / tau + xi/tau**.5 : volt
dx/dt = -x / tau + 2*xi/tau : volt
tau : second'''))
# using not-allowed flags
eqs = Equations('dv/dt = -v / (5 * ms) : volt (flag)')
eqs.check_flags({DIFFERENTIAL_EQUATION: ['flag']}) # allow this flag
assert_raises(ValueError, lambda: eqs.check_flags({DIFFERENTIAL_EQUATION: []}))
assert_raises(ValueError, lambda: eqs.check_flags({}))
assert_raises(ValueError, lambda: eqs.check_flags({STATIC_EQUATION: ['flag']}))
assert_raises(ValueError, lambda: eqs.check_flags({DIFFERENTIAL_EQUATION: ['otherflag']}))
# Circular static equations
assert_raises(ValueError, lambda: Equations('''dv/dt = -(v + w) / (10 * ms) : 1
w = 2 * x : 1
x = 3 * w : 1'''))
