def test_stochastic_variable():
'''
Test that a NeuronGroup with a stochastic variable can be simulated. Only
makes sure no error occurs.
'''
tau = 10 * ms
G = NeuronGroup(1, 'dv/dt = -v/tau + xi*tau**-0.5: 1')
net = Network(G)
net.run(defaultclock.dt)
def test_stochastic_variable_multiplicative():
'''
Test that a NeuronGroup with multiplicative noise can be simulated. Only
makes sure no error occurs.
'''
mu = 0.5/second # drift
sigma = 0.1/second #diffusion
G = NeuronGroup(1, 'dX/dt = (mu - 0.5*second*sigma**2)*X + X*sigma*xi*second**.5: 1')
net = Network(G)
net.run(defaultclock.dt)
def test_custom_events():
G = NeuronGroup(2, '''event_time1 : second
event_time2 : second''',
events={'event1': 't>=i*ms and t<i*ms+dt',
'event2': 't>=(i+1)*ms and t<(i+1)*ms+dt'})
G.run_on_event('event1', 'event_time1 = t')
G.run_on_event('event2', 'event_time2 = t')
net = Network(G)
net.run(2.1*ms)
assert_allclose(G.event_time1[:], [0, 1]*ms)
assert_allclose(G.event_time2[:], [1, 2]*ms)
def test_threshold_reset():
'''
Test that threshold and reset work in the expected way.
'''
# Membrane potential does not change by itself
G = NeuronGroup(3, 'dv/dt = 0 / second : 1',
threshold='v > 1', reset='v=0.5')
G.v = np.array([0, 1, 2])
net = Network(G)
net.run(defaultclock.dt)
assert_equal(G.v[:], np.array([0, 1, 0.5]))
def test_custom_events():
G = NeuronGroup(2, '''event_time1 : second
event_time2 : second''',
events={'event1': 't>=i*ms and t<i*ms+dt',
'event2': 't>=(i+1)*ms and t<(i+1)*ms+dt'})
G.run_on_event('event1', 'event_time1 = t')
G.run_on_event('event2', 'event_time2 = t')
net = Network(G)
net.run(2.1*ms)
assert_allclose(G.event_time1[:], [0, 1]*ms)
assert_allclose(G.event_time2[:], [1, 2]*ms)
def test_stochastic_variable():
'''
Test that a NeuronGroup with a stochastic variable can be simulated. Only
makes sure no error occurs.
'''
tau = 10 * ms
for codeobj_class in codeobj_classes:
G = NeuronGroup(1, 'dv/dt = -v/tau + xi*tau**-0.5: 1',
codeobj_class=codeobj_class)
net = Network(G)
net.run(defaultclock.dt)
def test_linked_var_in_reset_size_1():
G1 = NeuronGroup(1, 'x:1')
G2 = NeuronGroup(1, '''x_linked : 1 (linked)
y:1''',
threshold='y>1', reset='y=0; x_linked += 1')
G2.x_linked = linked_var(G1, 'x')
G2.y = 1.1
net = Network(G1, G2)
# In this context, x_linked should not be considered as a scalar variable
# and therefore the reset statement should be allowed
net.run(3*defaultclock.dt)
assert_equal(G1.x[:], 1)
def test_threshold_reset():
'''
Test that threshold and reset work in the expected way.
'''
for codeobj_class in codeobj_classes:
# Membrane potential does not change by itself
G = NeuronGroup(3, 'dv/dt = 0 / second : 1',
threshold='v > 1', reset='v=0.5', codeobj_class=codeobj_class)
G.v = np.array([0, 1, 2])
net = Network(G)
net.run(defaultclock.dt)
assert_equal(G.v[:], np.array([0, 1, 0.5]))
def test_random_vector_values():
# Make sure that the new "loop-invariant optimisation" does not pull out
# the random number generation and therefore makes all neurons receiving
# the same values
tau = 10*ms
G = NeuronGroup(100, 'dv/dt = -v / tau + xi*tau**-0.5: 1')
G.v[:] = 'rand()'
assert np.var(G.v[:]) > 0
G.v[:] = 0
net = Network(G)
net.run(defaultclock.dt)
assert np.var(G.v[:]) > 0
def test_stochastic_variable_multiplicative():
'''
Test that a NeuronGroup with multiplicative noise can be simulated. Only
makes sure no error occurs.
'''
for codeobj_class in codeobj_classes:
mu = 0.5/second # drift
sigma = 0.1/second #diffusion
G = NeuronGroup(1, 'dX/dt = (mu - 0.5*second*sigma**2)*X + X*sigma*xi*second**.5: 1',
codeobj_class=codeobj_class)
net = Network(G)
net.run(defaultclock.dt)
def test_random_vector_values():
# Make sure that the new "loop-invariant optimisation" does not pull out
# the random number generation and therefore makes all neurons receiving
# the same values
tau = 10*ms
G = NeuronGroup(100, 'dv/dt = -v / tau + xi*tau**-0.5: 1')
G.v[:] = 'rand()'
assert np.var(G.v[:]) > 0
G.v[:] = 0
net = Network(G)
net.run(defaultclock.dt)
assert np.var(G.v[:]) > 0
def test_linked_variable_scalar():
'''
Test linked variable from a size 1 group.
'''
G1 = NeuronGroup(1, 'dx/dt = -x / (10*ms) : 1')
G2 = NeuronGroup(10, '''dy/dt = (-y + x) / (20*ms) : 1
x : 1 (linked)''')
G1.x = 1
G2.y = np.linspace(0, 1, 10)
G2.x = linked_var(G1.x)
mon = StateMonitor(G2, 'y', record=True)
net = Network(G1, G2, mon)
net.run(10*ms)
def test_aliasing_in_statements():
'''
Test an issue around variables aliasing other variables (#259)
'''
runner_code = '''x_1 = x_0
x_0 = -1'''
g = NeuronGroup(1, model='''x_0 : 1
x_1 : 1 ''', codeobj_class=NumpyCodeObject)
custom_code_obj = g.custom_operation(runner_code)
net = Network(g, custom_code_obj)
net.run(defaultclock.dt)
assert_equal(g.x_0_[:], np.array([-1]))
assert_equal(g.x_1_[:], np.array([0]))
def test_linked_var_in_reset_incorrect():
# Raise an error if a scalar variable (linked variable from a group of size
# 1 is set in a reset statement of a group with size > 1)
G1 = NeuronGroup(1, 'x:1')
G2 = NeuronGroup(2, '''x_linked : 1 (linked)
y:1''',
threshold='y>1', reset='y=0; x_linked += 1')
G2.x_linked = linked_var(G1, 'x')
G2.y = 1.1
net = Network(G1, G2)
# It is not well-defined what x_linked +=1 means in this context
# (as for any other shared variable)
assert_raises(SyntaxError, lambda: net.run(0*ms))
def test_linked_var_in_reset_incorrect():
# Raise an error if a scalar variable (linked variable from a group of size
# 1 is set in a reset statement of a group with size > 1)
G1 = NeuronGroup(1, 'x:1')
G2 = NeuronGroup(2, '''x_linked : 1 (linked)
y:1''',
threshold='y>1', reset='y=0; x_linked += 1')
G2.x_linked = linked_var(G1, 'x')
G2.y = 1.1
net = Network(G1, G2)
# It is not well-defined what x_linked +=1 means in this context
# (as for any other shared variable)
assert_raises(SyntaxError, lambda: net.run(0*ms))
def test_unit_errors_threshold_reset():
'''
Test that unit errors in thresholds and resets are detected.
'''
# Unit error in threshold
group = NeuronGroup(1, 'dv/dt = -v/(10*ms) : 1', threshold='v > -20*mV')
assert_raises(DimensionMismatchError,
lambda: Network(group).run(0*ms))
# Unit error in reset
group = NeuronGroup(1, 'dv/dt = -v/(10*ms) : 1',
threshold='True',
reset='v = -65*mV')
assert_raises(DimensionMismatchError,
lambda: Network(group).run(0*ms))
# More complicated unit reset with an intermediate variable
# This should pass
group = NeuronGroup(1, 'dv/dt = -v/(10*ms) : 1',
threshold='False',
reset='''temp_var = -65
v = temp_var''')
run(0*ms)
# throw in an empty line (should still pass)
group = NeuronGroup(1, 'dv/dt = -v/(10*ms) : 1',
threshold='False',
reset='''temp_var = -65
v = temp_var''')
run(0*ms)
# This should fail
group = NeuronGroup(1, 'dv/dt = -v/(10*ms) : 1',
threshold='False',
reset='''temp_var = -65*mV
v = temp_var''')
assert_raises(DimensionMismatchError,
lambda: Network(group).run(0*ms))
# Resets with an in-place modification
# This should work
group = NeuronGroup(1, 'dv/dt = -v/(10*ms) : 1',
threshold='False',
reset='''v /= 2''')
run(0*ms)
# This should fail
group = NeuronGroup(1, 'dv/dt = -v/(10*ms) : 1',
threshold='False',
reset='''v -= 60*mV''')
assert_raises(DimensionMismatchError,
lambda: Network(group).run(0*ms))
def test_referred_scalar_variable():
'''
Test the correct handling of referred scalar variables in subexpressions
'''
G = NeuronGroup(10, '''out = sin(2*pi*t*freq) + x: 1
x : 1
freq : Hz (shared)''')
G.freq = 1*Hz
G.x = np.arange(10)
G2 = NeuronGroup(10, '')
G2.variables.add_reference('out', G)
net = Network(G, G2)
net.run(.25*second)
assert_allclose(G2.out[:], np.arange(10)+1)
def test_linked_variable_correct():
'''
Test correct uses of linked variables.
'''
tau = 10*ms
G1 = NeuronGroup(10, 'dv/dt = -v / tau : volt')
G1.v = np.linspace(0*mV, 20*mV, 10)
G2 = NeuronGroup(10, 'v : volt (linked)')
G2.v = linked_var(G1.v)
mon1 = StateMonitor(G1, 'v', record=True)
mon2 = StateMonitor(G2, 'v', record=True)
net = Network(G1, G2, mon1, mon2)
net.run(10*ms)
assert_equal(mon1.v[:, :], mon2.v[:, :])
def test_custom_events_schedule():
# In the same time step: event2 will be checked and its code executed
# before event1 is checked and its code executed
G = NeuronGroup(2, '''x : 1
event_time : second''',
events={'event1': 'x>0',
'event2': 't>=(i+1)*ms and t<(i+1)*ms+dt'})
G.set_event_schedule('event1', when='after_resets')
G.run_on_event('event2', 'x = 1', when='resets')
G.run_on_event('event1',
'''event_time = t
x = 0''', when='after_resets', order=1)
net = Network(G)
net.run(2.1*ms)
assert_allclose(G.event_time[:], [1, 2]*ms)
def test_custom_events_schedule():
# In the same time step: event2 will be checked and its code executed
# before event1 is checked and its code executed
G = NeuronGroup(2, '''x : 1
event_time : second''',
events={'event1': 'x>0',
'event2': 't>=(i+1)*ms and t<(i+1)*ms+dt'})
G.set_event_schedule('event1', when='after_resets')
G.run_on_event('event2', 'x = 1', when='resets')
G.run_on_event('event1',
'''event_time = t
x = 0''', when='after_resets', order=1)
net = Network(G)
net.run(2.1*ms)
assert_allclose(G.event_time[:], [1, 2]*ms)
def find_synapses(self):
# Write the global objects
networks = [
net() for net in Network.__instances__()
if net().name != '_fake_network'
]
synapses = []
for net in networks:
net_synapses = [s for s in net.objects if isinstance(s, Synapses)]
synapses.extend(net_synapses)
# We don't currently support pathways with scalar delays
for synapse_obj in net_synapses:
for pathway in synapse_obj._pathways:
if not isinstance(pathway.variables['delay'],
DynamicArrayVariable):
error_msg = (
'The "%s" pathway uses a scalar '
'delay (instead of a delay per synapse). '
'This is not yet supported. Do not '
'specify a delay in the Synapses(...) '
'call but instead set its delay attribute '
'afterwards.') % (pathway.name)
raise NotImplementedError(error_msg)
self.networks = networks
self.net_synapses = synapses
def test_aliasing_in_statements():
'''
Test an issue around variables aliasing other variables (#259)
'''
if prefs.codegen.target != 'numpy':
raise SkipTest('numpy-only test')
runner_code = '''x_1 = x_0
x_0 = -1'''
g = NeuronGroup(1, model='''x_0 : 1
x_1 : 1 ''')
g.run_regularly(runner_code)
net = Network(g)
net.run(defaultclock.dt)
assert_equal(g.x_0_[:], np.array([-1]))
assert_equal(g.x_1_[:], np.array([0]))
def test_aliasing_in_statements():
'''
Test an issue around variables aliasing other variables (#259)
'''
if prefs.codegen.target != 'numpy':
raise SkipTest('numpy-only test')
runner_code = '''x_1 = x_0
x_0 = -1'''
g = NeuronGroup(1, model='''x_0 : 1
x_1 : 1 ''')
g.run_regularly(runner_code)
net = Network(g)
net.run(defaultclock.dt)
assert_equal(g.x_0_[:], np.array([-1]))
assert_equal(g.x_1_[:], np.array([0]))
def test_referred_scalar_variable():
'''
Test the correct handling of referred scalar variables in subexpressions
'''
for codeobj_class in codeobj_classes:
G = NeuronGroup(10, '''out = sin(2*pi*t*freq) + x: 1
x : 1
freq : Hz (shared)''',
codeobj_class=codeobj_class)
G.freq = 1*Hz
G.x = np.arange(10)
G2 = NeuronGroup(10, '', codeobj_class=codeobj_class)
G2.variables.add_reference('out', G)
net = Network(G, G2)
net.run(.25*second)
assert_allclose(G2.out[:], np.arange(10)+1)
def find_synapses(self):
# Write the global objects
networks = [net() for net in Network.__instances__() if net().name != "_fake_network"]
synapses = []
for net in networks:
net_synapses = [s for s in net.objects if isinstance(s, Synapses)]
synapses.extend(net_synapses)
self.networks = networks
self.net_synapses = synapses
def test_syntax_errors():
'''
Test that syntax errors are already caught at initialization time.
For equations this is already tested in test_equations
'''
# We do not specify the exact type of exception here: Python throws a
# SyntaxError while C++ results in a ValueError
# Syntax error in threshold
group = NeuronGroup(1, 'dv/dt = 5*Hz : 1',
threshold='>1')
assert_raises(Exception, lambda: Network(group).run(0*ms))
# Syntax error in reset
group = NeuronGroup(1, 'dv/dt = 5*Hz : 1',
threshold='True',
reset='0')
assert_raises(Exception, lambda: Network(group).run(0*ms))
def test_linked_subexpression_2():
'''
Test a linked variable referring to a subexpression without indices
'''
G = NeuronGroup(2, '''dv/dt = 100*Hz : 1
I = clip(v, 0, inf) : 1''',
threshold='v>1', reset='v=0')
G.v = [0, .5]
G2 = NeuronGroup(2, '''I_l : 1 (linked) ''')
G2.I_l = linked_var(G.I)
mon1 = StateMonitor(G, 'I', record=True)
mon = StateMonitor(G2, 'I_l', record=True)
net = Network(G, G2, mon, mon1)
net.run(5*ms)
assert all(mon[0].I_l == mon1[0].I)
assert all(mon[1].I_l == mon1[1].I)
def test_scalar_variable():
'''
Test the correct handling of scalar variables
'''
tau = 10*ms
G = NeuronGroup(10, '''E_L : volt (shared)
s2 : 1 (shared)
dv/dt = (E_L - v) / tau : volt''')
# Setting should work in these ways
G.E_L = -70*mV
assert_allclose(G.E_L[:], -70*mV)
G.E_L[:] = -60*mV
assert_allclose(G.E_L[:], -60*mV)
G.E_L = 'E_L + s2*mV - 10*mV'
assert_allclose(G.E_L[:], -70*mV)
G.E_L[:] = '-75*mV'
assert_allclose(G.E_L[:], -75*mV)
net = Network(G)
net.run(defaultclock.dt)
def test_scalar_variable():
'''
Test the correct handling of scalar variables
'''
tau = 10*ms
G = NeuronGroup(10, '''E_L : volt (shared)
s2 : 1 (shared)
dv/dt = (E_L - v) / tau : volt''')
# Setting should work in these ways
G.E_L = -70*mV
assert_allclose(G.E_L[:], -70*mV)
G.E_L[:] = -60*mV
assert_allclose(G.E_L[:], -60*mV)
G.E_L = 'E_L + s2*mV - 10*mV'
assert_allclose(G.E_L[:], -70*mV)
G.E_L[:] = '-75*mV'
assert_allclose(G.E_L[:], -75*mV)
net = Network(G)
net.run(defaultclock.dt)
def test_namespace_errors():
# model equations use unknown identifier
G = NeuronGroup(1, 'dv/dt = -v/tau : 1')
net = Network(G)
assert_raises(KeyError, lambda: net.run(1*ms))
# reset uses unknown identifier
G = NeuronGroup(1, 'dv/dt = -v/tau : 1', threshold='False', reset='v = v_r')
net = Network(G)
assert_raises(KeyError, lambda: net.run(1*ms))
# threshold uses unknown identifier
G = NeuronGroup(1, 'dv/dt = -v/tau : 1', threshold='v > v_th')
net = Network(G)
assert_raises(KeyError, lambda: net.run(1*ms))
def test_linked_subexpression():
'''
Test a subexpression referring to a linked variable.
'''
G = NeuronGroup(2, 'dv/dt = 100*Hz : 1',
threshold='v>1', reset='v=0')
G.v = [0, .5]
G2 = NeuronGroup(10, '''I = clip(x, 0, inf) : 1
x : 1 (linked) ''')
G2.x = linked_var(G.v, index=np.array([0, 1]).repeat(5))
mon = StateMonitor(G2, 'I', record=True)
net = Network(G, G2, mon)
net.run(5*ms)
# Due to the linking, the first 5 and the second 5 recorded I vectors should
# be identical
assert all((all(mon[i].I == mon[0].I) for i in xrange(5)))
assert all((all(mon[i+5].I == mon[5].I) for i in xrange(5)))
def test_linked_variable_scalar():
'''
Test linked variable from a size 1 group.
'''
G1 = NeuronGroup(1, 'dx/dt = -x / (10*ms) : 1')
G2 = NeuronGroup(10, '''dy/dt = (-y + x) / (20*ms) : 1
x : 1 (linked)''')
G1.x = 1
G2.y = np.linspace(0, 1, 10)
G2.x = linked_var(G1.x)
mon = StateMonitor(G2, 'y', record=True)
net = Network(G1, G2, mon)
# We don't test anything for now, except that it runs without raising an
# error
net.run(10*ms)
# Make sure that printing the variable values works
assert len(str(G2.x)) > 0
assert len(repr(G2.x)) > 0
assert len(str(G2.x[:])) > 0
assert len(repr(G2.x[:])) > 0
def test_linked_subexpression_3():
'''
Test a linked variable referring to a subexpression with indices
'''
G = NeuronGroup(2, '''dv/dt = 100*Hz : 1
I = clip(v, 0, inf) : 1''',
threshold='v>1', reset='v=0')
G.v = [0, .5]
G2 = NeuronGroup(10, '''I_l : 1 (linked) ''')
G2.I_l = linked_var(G.I, index=np.array([0, 1]).repeat(5))
mon1 = StateMonitor(G, 'I', record=True)
mon = StateMonitor(G2, 'I_l', record=True)
net = Network(G, G2, mon, mon1)
net.run(5*ms)
# Due to the linking, the first 5 and the second 5 recorded I vectors should
# refer to the
assert all((all(mon[i].I_l == mon1[0].I) for i in xrange(5)))
assert all((all(mon[i+5].I_l == mon1[1].I) for i in xrange(5)))
def find_synapses(self):
# Write the global objects
networks = [
net() for net in Network.__instances__()
if net().name != '_fake_network'
]
synapses = []
for net in networks:
net_synapses = [s for s in net.objects if isinstance(s, Synapses)]
synapses.extend(net_synapses)
self.networks = networks
self.net_synapses = synapses
def test_incomplete_namespace():
'''
Test that the namespace does not have to be complete at creation time.
'''
# This uses tau which is not defined yet (explicit namespace)
G = NeuronGroup(1, 'dv/dt = -v/tau : 1', namespace={})
G.namespace['tau'] = 10*ms
net = Network(G)
net.run(0*ms)
# This uses tau which is not defined yet (implicit namespace)
G = NeuronGroup(1, 'dv/dt = -v/tau : 1')
tau = 10*ms
net = Network(G)
net.run(0*ms)
def test_incorrect_custom_event_definition():
# Incorrect event name
assert_raises(TypeError, lambda: NeuronGroup(1, '', events={'1event': 'True'}))
# duplicate definition of 'spike' event
assert_raises(ValueError, lambda: NeuronGroup(1, '', threshold='True',
events={'spike': 'False'}))
# not a threshold
G = NeuronGroup(1, '', events={'my_event': 10*mV})
assert_raises(TypeError, lambda: Network(G).run(0*ms))
# schedule for a non-existing event
G = NeuronGroup(1, '', threshold='False', events={'my_event': 'True'})
assert_raises(ValueError, lambda: G.set_event_schedule('another_event'))
# code for a non-existing event
assert_raises(ValueError, lambda: G.run_on_event('another_event', ''))
def test_incomplete_namespace():
'''
Test that the namespace does not have to be complete at creation time.
'''
# This uses tau which is not defined yet (explicit namespace)
G = NeuronGroup(1, 'dv/dt = -v/tau : 1', namespace={})
G.namespace['tau'] = 10*ms
net = Network(G)
net.run(0*ms)
# This uses tau which is not defined yet (implicit namespace)
G = NeuronGroup(1, 'dv/dt = -v/tau : 1')
tau = 10*ms
net = Network(G)
net.run(0*ms)
def test_namespace_errors():
# model equations use unknown identifier
G = NeuronGroup(1, 'dv/dt = -v/tau : 1')
net = Network(G)
assert_raises(KeyError, lambda: net.run(1*ms))
# reset uses unknown identifier
G = NeuronGroup(1, 'dv/dt = -v/tau : 1', threshold='False', reset='v = v_r')
net = Network(G)
assert_raises(KeyError, lambda: net.run(1*ms))
# threshold uses unknown identifier
G = NeuronGroup(1, 'dv/dt = -v/tau : 1', threshold='v > v_th')
net = Network(G)
assert_raises(KeyError, lambda: net.run(1*ms))
def find_synapses(self):
# Write the global objects
networks = [net() for net in Network.__instances__()
if net().name != '_fake_network']
synapses = []
for net in networks:
net_synapses = [s for s in net.objects if isinstance(s, Synapses)]
synapses.extend(net_synapses)
# We don't currently support pathways with scalar delays
for synapse_obj in net_synapses:
for pathway in synapse_obj._pathways:
if not isinstance(pathway.variables['delay'],
DynamicArrayVariable):
error_msg = ('The "%s" pathway uses a scalar '
'delay (instead of a delay per synapse). '
'This is not yet supported. Do not '
'specify a delay in the Synapses(...) '
'call but instead set its delay attribute '
'afterwards.') % (pathway.name)
raise NotImplementedError(error_msg)
self.networks = networks
self.net_synapses = synapses
def create_lems_model(self, network=None, namespace={}, initializers={},
constants_file=None, includes=[],
recordingsname='recording'):
"""
From given *network* returns LEMS model object.
Parameters
----------
network : str, optional
all brian objects collected into netowrk or None. In the
second case brian2 objects are collected autmatically from
the above scope.
namespace : dict
namespace variables defining extra model parameters
initializers : dict
all values which need to be initialized before simulation
running
constants_file : str, optional
file with units as constants definitions, if None an
LEMS_CONSTANTS_XML is added automatically
includes : list of str
all additional XML files added in preamble
recordingsname : str, optional
output of LEMS simulation recordings, values with extension
.dat and spikes with .spikes, default 'recording'
"""
if network is None:
net = Network(collect(level=1))
else:
net = network
if not constants_file:
self._model.add(lems.Include(LEMS_CONSTANTS_XML))
else:
self._model.add(lems.Include(constants_file))
includes = set(includes)
for incl in INCLUDES:
includes.add(incl)
neuron_groups = [o for o in net.objects if type(o) is NeuronGroup]
state_monitors = [o for o in net.objects if type(o) is StateMonitor]
spike_monitors = [o for o in net.objects if type(o) is SpikeMonitor]
for o in net.objects:
if type(o) not in [NeuronGroup, StateMonitor, SpikeMonitor,
Thresholder, Resetter, StateUpdater]:
logger.warn("""{} export functionality
is not implemented yet.""".format(type(o).__name__))
# --- not fully implemented
synapses = [o for o in net.objects if type(o) is Synapses]
netinputs = [o for o in net.objects if type(o) is PoissonInput]
# ---
#if len(synapses) > 0:
# logger.warn("Synpases export functionality is not implemented yet.")
#if len(netinputs) > 0:
# logger.warn("Network Input export functionality is not implemented yet.")
if len(netinputs) > 0:
includes.add(LEMS_INPUTS)
for incl in includes:
self.add_include(incl)
# First step is to add individual neuron deifinitions and initialize
# them by MultiInstantiate
for e, obj in enumerate(neuron_groups):
self.add_neurongroup(obj, e, namespace, initializers)
# DOM structure of the whole model is constructed below
self._dommodel = self._model.export_to_dom()
# input support - currently only Poisson Inputs
for e, obj in enumerate(netinputs):
self.add_input(obj, counter=e)
# A population should be created in *make_multiinstantiate*
# so we can add it to our DOM structure.
if self._population:
self._extend_dommodel(self._population)
# if some State or Spike Monitors occur we support them by
# Simulation tag
self._model_namespace['simulname'] = "sim1"
self._simulation = NeuroMLSimulation(self._model_namespace['simulname'],
self._model_namespace['networkname'])
for e, obj in enumerate(state_monitors):
self.add_statemonitor(obj, filename=recordingsname, outputfile=True)
for e, obj in enumerate(spike_monitors):
self.add_spikemonitor(obj, filename=recordingsname)
simulation = self._simulation.build()
self._extend_dommodel(simulation)
target = NeuroMLTarget(self._model_namespace['simulname'])
target = target.build()
self._extend_dommodel(target)
def build(self, directory='output',
compile=True, run=True, debug=False, clean=True,
with_output=True, native=True,
additional_source_files=None, additional_header_files=None,
main_includes=None, run_includes=None,
run_args=None, **kwds):
'''
Build the project
TODO: more details
Parameters
----------
directory : str
The output directory to write the project to, any existing files will be overwritten.
compile : bool
Whether or not to attempt to compile the project
run : bool
Whether or not to attempt to run the built project if it successfully builds.
debug : bool
Whether to compile in debug mode.
with_output : bool
Whether or not to show the ``stdout`` of the built program when run.
native : bool
Whether or not to compile for the current machine's architecture (best for speed, but not portable)
clean : bool
Whether or not to clean the project before building
additional_source_files : list of str
A list of additional ``.cpp`` files to include in the build.
additional_header_files : list of str
A list of additional ``.h`` files to include in the build.
main_includes : list of str
A list of additional header files to include in ``main.cpp``.
run_includes : list of str
A list of additional header files to include in ``run.cpp``.
'''
renames = {'project_dir': 'directory',
'compile_project': 'compile',
'run_project': 'run'}
if len(kwds):
msg = ''
for kwd in kwds:
if kwd in renames:
msg += ("Keyword argument '%s' has been renamed to "
"'%s'. ") % (kwd, renames[kwd])
else:
msg += "Unknown keyword argument '%s'. " % kwd
raise TypeError(msg)
if additional_source_files is None:
additional_source_files = []
if additional_header_files is None:
additional_header_files = []
if main_includes is None:
main_includes = []
if run_includes is None:
run_includes = []
if run_args is None:
run_args = []
self.project_dir = directory
ensure_directory(directory)
compiler, extra_compile_args = get_compiler_and_args()
compiler_flags = ' '.join(extra_compile_args)
for d in ['code_objects', 'results', 'static_arrays']:
ensure_directory(os.path.join(directory, d))
writer = CPPWriter(directory)
# Get the number of threads if specified in an openmp context
nb_threads = prefs.devices.cpp_standalone.openmp_threads
# If the number is negative, we need to throw an error
if (nb_threads < 0):
raise ValueError('The number of OpenMP threads can not be negative !')
logger.debug("Writing C++ standalone project to directory "+os.path.normpath(directory))
if nb_threads > 0:
logger.warn("OpenMP code is not yet well tested, and may be inaccurate.", "openmp", once=True)
logger.debug("Using OpenMP with %d threads " % nb_threads)
for codeobj in self.code_objects.itervalues():
if not 'IS_OPENMP_COMPATIBLE' in codeobj.template_source:
raise RuntimeError(("Code object '%s' uses the template %s "
"which is not compatible with "
"OpenMP.") % (codeobj.name,
codeobj.template_name))
arange_arrays = sorted([(var, start)
for var, start in self.arange_arrays.iteritems()],
key=lambda (var, start): var.name)
# # Find np arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, np.ndarray):
self.static_arrays[name] = value
# write the static arrays
logger.debug("static arrays: "+str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in sorted(self.static_arrays.items()):
arr.tofile(os.path.join(directory, 'static_arrays', name))
static_array_specs.append((name, c_data_type(arr.dtype), arr.size, name))
# Write the global objects
networks = [net() for net in Network.__instances__()
if net().name != '_fake_network']
synapses = []
for net in networks:
net_synapses = [s for s in net.objects if isinstance(s, Synapses)]
synapses.extend(net_synapses)
# We don't currently support pathways with scalar delays
for synapse_obj in net_synapses:
for pathway in synapse_obj._pathways:
if not isinstance(pathway.variables['delay'],
DynamicArrayVariable):
error_msg = ('The "%s" pathway uses a scalar '
'delay (instead of a delay per synapse). '
'This is not yet supported. Do not '
'specify a delay in the Synapses(...) '
'call but instead set its delay attribute '
'afterwards.') % (pathway.name)
raise NotImplementedError(error_msg)
# Not sure what the best place is to call Network.after_run -- at the
# moment the only important thing it does is to clear the objects stored
# in magic_network. If this is not done, this might lead to problems
# for repeated runs of standalone (e.g. in the test suite).
for net in networks:
net.after_run()
arr_tmp = CPPStandaloneCodeObject.templater.objects(
None, None,
array_specs=self.arrays,
dynamic_array_specs=self.dynamic_arrays,
dynamic_array_2d_specs=self.dynamic_arrays_2d,
zero_arrays=self.zero_arrays,
arange_arrays=arange_arrays,
synapses=synapses,
clocks=self.clocks,
static_array_specs=static_array_specs,
networks=networks)
writer.write('objects.*', arr_tmp)
main_lines = []
procedures = [('', main_lines)]
runfuncs = {}
for func, args in self.main_queue:
if func=='run_code_object':
codeobj, = args
main_lines.append('_run_%s();' % codeobj.name)
elif func=='run_network':
net, netcode = args
main_lines.extend(netcode)
elif func=='set_by_array':
arrayname, staticarrayname = args
code = '''
{pragma}
for(int i=0; i<_num_{staticarrayname}; i++)
{{
{arrayname}[i] = {staticarrayname}[i];
}}
'''.format(arrayname=arrayname, staticarrayname=staticarrayname, pragma=openmp_pragma('static'))
main_lines.extend(code.split('\n'))
elif func=='set_by_single_value':
arrayname, item, value = args
code = '{arrayname}[{item}] = {value};'.format(arrayname=arrayname,
item=item,
value=value)
main_lines.extend([code])
elif func=='set_array_by_array':
arrayname, staticarrayname_index, staticarrayname_value = args
code = '''
{pragma}
for(int i=0; i<_num_{staticarrayname_index}; i++)
{{
{arrayname}[{staticarrayname_index}[i]] = {staticarrayname_value}[i];
}}
'''.format(arrayname=arrayname, staticarrayname_index=staticarrayname_index,
staticarrayname_value=staticarrayname_value, pragma=openmp_pragma('static'))
main_lines.extend(code.split('\n'))
elif func=='insert_code':
main_lines.append(args)
elif func=='start_run_func':
name, include_in_parent = args
if include_in_parent:
main_lines.append('%s();' % name)
main_lines = []
procedures.append((name, main_lines))
elif func=='end_run_func':
name, include_in_parent = args
name, main_lines = procedures.pop(-1)
runfuncs[name] = main_lines
name, main_lines = procedures[-1]
else:
raise NotImplementedError("Unknown main queue function type "+func)
# generate the finalisations
for codeobj in self.code_objects.itervalues():
if hasattr(codeobj.code, 'main_finalise'):
main_lines.append(codeobj.code.main_finalise)
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, AttributeVariable):
# We assume all attributes are implemented as property-like methods
line = 'const {c_type} {varname} = {objname}.{attrname}();'
lines.append(line.format(c_type=c_data_type(v.dtype), varname=k, objname=v.obj.name,
attrname=v.attribute))
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = &{dyn_array_name}[0];'
line = line.format(c_type=c_data_type(v.dtype), array_name=array_name,
dyn_array_name=dyn_array_name)
lines.append(line)
line = 'const int _num{k} = {dyn_array_name}.size();'
line = line.format(k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append('const int _num%s = %s;' % (k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%', '\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n'+code
writer.write('code_objects/'+codeobj.name+'.cpp', code)
writer.write('code_objects/'+codeobj.name+'.h', codeobj.code.h_file)
# The code_objects are passed in the right order to run them because they were
# sorted by the Network object. To support multiple clocks we'll need to be
# smarter about that.
main_tmp = CPPStandaloneCodeObject.templater.main(None, None,
main_lines=main_lines,
code_objects=self.code_objects.values(),
report_func=self.report_func,
dt=float(defaultclock.dt),
additional_headers=main_includes,
)
writer.write('main.cpp', main_tmp)
if compiler=='msvc':
std_move = 'std::move'
else:
std_move = ''
network_tmp = CPPStandaloneCodeObject.templater.network(None, None,
std_move=std_move)
writer.write('network.*', network_tmp)
synapses_classes_tmp = CPPStandaloneCodeObject.templater.synapses_classes(None, None)
writer.write('synapses_classes.*', synapses_classes_tmp)
# Generate the run functions
run_tmp = CPPStandaloneCodeObject.templater.run(None, None, run_funcs=runfuncs,
code_objects=self.code_objects.values(),
additional_headers=run_includes,
)
writer.write('run.*', run_tmp)
# Copy the brianlibdirectory
brianlib_dir = os.path.join(os.path.split(inspect.getsourcefile(CPPStandaloneCodeObject))[0],
'brianlib')
brianlib_files = copy_directory(brianlib_dir, os.path.join(directory, 'brianlib'))
for file in brianlib_files:
if file.lower().endswith('.cpp'):
writer.source_files.append('brianlib/'+file)
elif file.lower().endswith('.h'):
writer.header_files.append('brianlib/'+file)
# Copy the CSpikeQueue implementation
shutil.copy2(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0], 'cspikequeue.cpp'),
os.path.join(directory, 'brianlib', 'spikequeue.h'))
shutil.copy2(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0], 'stdint_compat.h'),
os.path.join(directory, 'brianlib', 'stdint_compat.h'))
writer.source_files.extend(additional_source_files)
writer.header_files.extend(additional_header_files)
if compiler=='msvc':
if native:
arch_flag = ''
try:
from cpuinfo import cpuinfo
res = cpuinfo.get_cpu_info()
if 'sse' in res['flags']:
arch_flag = '/arch:SSE'
if 'sse2' in res['flags']:
arch_flag = '/arch:SSE2'
except ImportError:
logger.warn('Native flag for MSVC compiler requires installation of the py-cpuinfo module')
compiler_flags += ' '+arch_flag
if nb_threads>1:
openmp_flag = '/openmp'
else:
openmp_flag = ''
# Generate the visual studio makefile
source_bases = [fname.replace('.cpp', '').replace('/', '\\') for fname in writer.source_files]
win_makefile_tmp = CPPStandaloneCodeObject.templater.win_makefile(
None, None,
source_bases=source_bases,
compiler_flags=compiler_flags,
openmp_flag=openmp_flag,
)
writer.write('win_makefile', win_makefile_tmp)
else:
# Generate the makefile
if os.name=='nt':
rm_cmd = 'del *.o /s\n\tdel main.exe $(DEPS)'
else:
rm_cmd = 'rm $(OBJS) $(PROGRAM) $(DEPS)'
makefile_tmp = CPPStandaloneCodeObject.templater.makefile(None, None,
source_files=' '.join(writer.source_files),
header_files=' '.join(writer.header_files),
compiler_flags=compiler_flags,
rm_cmd=rm_cmd)
writer.write('makefile', makefile_tmp)
# build the project
if compile:
with in_directory(directory):
if compiler=='msvc':
# TODO: handle debug
if debug:
logger.warn('Debug flag currently ignored for MSVC')
vcvars_search_paths = [
# futureproofing!
r'c:\Program Files\Microsoft Visual Studio 15.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 15.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 14.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 13.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 13.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 12.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 11.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 11.0\VC\vcvarsall.bat',
r'c:\Program Files\Microsoft Visual Studio 10.0\VC\vcvarsall.bat',
r'c:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\vcvarsall.bat',
]
vcvars_loc = prefs['codegen.cpp.msvc_vars_location']
if vcvars_loc=='':
for fname in vcvars_search_paths:
if os.path.exists(fname):
vcvars_loc = fname
break
if vcvars_loc=='':
raise IOError("Cannot find vcvarsall.bat on standard search path.")
# TODO: copy vcvars and make replacements for 64 bit automatically
arch_name = prefs['codegen.cpp.msvc_architecture']
if arch_name=='':
mach = platform.machine()
if mach=='AMD64':
arch_name = 'x86_amd64'
else:
arch_name = 'x86'
vcvars_cmd = '"{vcvars_loc}" {arch_name}'.format(
vcvars_loc=vcvars_loc, arch_name=arch_name)
make_cmd = 'nmake /f win_makefile'
if os.path.exists('winmake.log'):
os.remove('winmake.log')
with std_silent(debug):
if clean:
os.system('%s >>winmake.log 2>&1 && %s clean >>winmake.log 2>&1' % (vcvars_cmd, make_cmd))
x = os.system('%s >>winmake.log 2>&1 && %s >>winmake.log 2>&1' % (vcvars_cmd, make_cmd))
if x!=0:
raise RuntimeError("Project compilation failed")
else:
with std_silent(debug):
if clean:
os.system('make clean')
if debug:
x = os.system('make debug')
elif native:
x = os.system('make native')
else:
x = os.system('make')
if x!=0:
raise RuntimeError("Project compilation failed")
if run:
if not with_output:
stdout = open(os.devnull, 'w')
else:
stdout = None
if os.name=='nt':
x = subprocess.call(['main'] + run_args, stdout=stdout)
else:
x = subprocess.call(['./main'] + run_args, stdout=stdout)
if x:
raise RuntimeError("Project run failed")
self.has_been_run = True
def test_namespace_warnings():
G = NeuronGroup(1, '''x : 1
y : 1''',
# unique names to get warnings every time:
name='neurongroup_'+str(uuid.uuid4()).replace('-', '_'))
# conflicting variable in namespace
y = 5
with catch_logs() as l:
G.x = 'y'
assert len(l) == 1, 'got %s as warnings' % str(l)
assert l[0][1].endswith('.resolution_conflict')
del y
# conflicting variables with special meaning
i = 5
N = 3
with catch_logs() as l:
G.x = 'i / N'
assert len(l) == 2, 'got %s as warnings' % str(l)
assert l[0][1].endswith('.resolution_conflict')
assert l[1][1].endswith('.resolution_conflict')
del i
del N
# conflicting variables in equations
y = 5*Hz
G = NeuronGroup(1, '''y : Hz
dx/dt = y : 1''',
# unique names to get warnings every time:
name='neurongroup_'+str(uuid.uuid4()).replace('-', '_'))
net = Network(G)
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 1, 'got %s as warnings' % str(l)
assert l[0][1].endswith('.resolution_conflict')
del y
i = 5
# i is referring to the neuron number:
G = NeuronGroup(1, '''dx/dt = i*Hz : 1''',
# unique names to get warnings every time:
name='neurongroup_'+str(uuid.uuid4()).replace('-', '_'))
net = Network(G)
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 1, 'got %s as warnings' % str(l)
assert l[0][1].endswith('.resolution_conflict')
del i
# Variables that are used internally but not in equations should not raise
# a warning
N = 3
i = 5
dt = 1*ms
G = NeuronGroup(1, '''dx/dt = x/(10*ms) : 1''',
# unique names to get warnings every time:
name='neurongroup_'+str(uuid.uuid4()).replace('-', '_'))
net = Network(G)
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 0, 'got %s as warnings' % str(l)
def build(self, project_dir='output', compile_project=True, run_project=False, debug=True,
with_output=True):
ensure_directory(project_dir)
for d in ['code_objects', 'results', 'static_arrays']:
ensure_directory(os.path.join(project_dir, d))
logger.debug("Writing C++ standalone project to directory "+os.path.normpath(project_dir))
# # Find numpy arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, numpy.ndarray):
self.static_arrays[name] = value
# write the static arrays
logger.debug("static arrays: "+str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in self.static_arrays.iteritems():
arr.tofile(os.path.join(project_dir, 'static_arrays', name))
static_array_specs.append((name, c_data_type(arr.dtype), arr.size, name))
# Write the global objects
networks = [net() for net in Network.__instances__() if net().name!='_fake_network']
synapses = [S() for S in Synapses.__instances__()]
arr_tmp = CPPStandaloneCodeObject.templater.objects(None,
array_specs=self.arrays,
dynamic_array_specs=self.dynamic_arrays,
dynamic_array_2d_specs=self.dynamic_arrays_2d,
zero_arrays=self.zero_arrays,
arange_arrays=self.arange_arrays,
synapses=synapses,
clocks=self.clocks,
static_array_specs=static_array_specs,
networks=networks,
)
logger.debug("objects: "+str(arr_tmp))
open(os.path.join(project_dir, 'objects.cpp'), 'w').write(arr_tmp.cpp_file)
open(os.path.join(project_dir, 'objects.h'), 'w').write(arr_tmp.h_file)
main_lines = []
for func, args in self.main_queue:
if func=='run_code_object':
codeobj, = args
main_lines.append('_run_%s(t);' % codeobj.name)
elif func=='run_network':
net, netcode = args
main_lines.extend(netcode)
elif func=='set_by_array':
arrayname, staticarrayname = args
code = '''
for(int i=0; i<_num_{staticarrayname}; i++)
{{
{arrayname}[i] = {staticarrayname}[i];
}}
'''.format(arrayname=arrayname, staticarrayname=staticarrayname)
main_lines.extend(code.split('\n'))
elif func=='set_array_by_array':
arrayname, staticarrayname_index, staticarrayname_value = args
code = '''
for(int i=0; i<_num_{staticarrayname_index}; i++)
{{
{arrayname}[{staticarrayname_index}[i]] = {staticarrayname_value}[i];
}}
'''.format(arrayname=arrayname, staticarrayname_index=staticarrayname_index,
staticarrayname_value=staticarrayname_value)
main_lines.extend(code.split('\n'))
elif func=='insert_code':
main_lines.append(args)
else:
raise NotImplementedError("Unknown main queue function type "+func)
# generate the finalisations
for codeobj in self.code_objects.itervalues():
if hasattr(codeobj.code, 'main_finalise'):
main_lines.append(codeobj.code.main_finalise)
# Generate data for non-constant values
handled_arrays = defaultdict(set)
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
for k, v in codeobj.variables.iteritems():
if k=='t':
pass
elif isinstance(v, Subexpression):
pass
elif isinstance(v, AttributeVariable):
c_type = c_data_type(v.dtype)
# TODO: Handle dt in the correct way
if v.attribute == 'dt_':
code = ('const {c_type} {k} = '
'{value};').format(c_type=c_type,
k=k,
value=v.get_value())
else:
code = ('const {c_type} {k} = '
'{name}.{attribute};').format(c_type=c_type,
k=k,
name=v.obj.name,
attribute=v.attribute)
code_object_defs[codeobj.name].append(code)
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
code_object_defs[codeobj.name].append('{c_type}* const {array_name} = &{dyn_array_name}[0];'.format(c_type=c_data_type(v.dtype),
array_name=array_name,
dyn_array_name=dyn_array_name))
code_object_defs[codeobj.name].append('const int _num{k} = {dyn_array_name}.size();'.format(k=k,
dyn_array_name=dyn_array_name))
else:
code_object_defs[codeobj.name].append('const int _num%s = %s;' % (k, v.size))
except TypeError:
pass
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%', '\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n'+code
open(os.path.join(project_dir, 'code_objects', codeobj.name+'.cpp'), 'w').write(code)
open(os.path.join(project_dir, 'code_objects', codeobj.name+'.h'), 'w').write(codeobj.code.h_file)
# The code_objects are passed in the right order to run them because they were
# sorted by the Network object. To support multiple clocks we'll need to be
# smarter about that.
main_tmp = CPPStandaloneCodeObject.templater.main(None,
main_lines=main_lines,
code_objects=self.code_objects.values(),
dt=float(defaultclock.dt),
)
logger.debug("main: "+str(main_tmp))
open(os.path.join(project_dir, 'main.cpp'), 'w').write(main_tmp)
# Copy the brianlibdirectory
brianlib_dir = os.path.join(os.path.split(inspect.getsourcefile(CPPStandaloneCodeObject))[0],
'brianlib')
copy_directory(brianlib_dir, os.path.join(project_dir, 'brianlib'))
# Copy the CSpikeQueue implementation
shutil.copy(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0],
'cspikequeue.cpp'),
os.path.join(project_dir, 'brianlib', 'spikequeue.h'))
# build the project
if compile_project:
with in_directory(project_dir):
if debug:
x = os.system('g++ -I. -g *.cpp code_objects/*.cpp brianlib/*.cpp -o main')
else:
x = os.system('g++ -I. -O3 -ffast-math -march=native *.cpp code_objects/*.cpp brianlib/*.cpp -o main')
if x==0:
if run_project:
if not with_output:
stdout = open(os.devnull, 'w')
else:
stdout = None
if os.name=='nt':
x = subprocess.call('main', stdout=stdout)
else:
x = subprocess.call('./main', stdout=stdout)
if x:
raise RuntimeError("Project run failed")
else:
raise RuntimeError("Project compilation failed")
def build(self, project_dir='output', compile_project=True, run_project=False, debug=True,
with_output=True, native=True,
additional_source_files=None, additional_header_files=None,
main_includes=None, run_includes=None,
run_args=None,
):
'''
Build the project
TODO: more details
Parameters
----------
project_dir : str
The output directory to write the project to, any existing files will be overwritten.
compile_project : bool
Whether or not to attempt to compile the project using GNU make.
run_project : bool
Whether or not to attempt to run the built project if it successfully builds.
debug : bool
Whether to compile in debug mode.
with_output : bool
Whether or not to show the ``stdout`` of the built program when run.
native : bool
Whether or not to compile natively using the ``--march=native`` gcc option.
additional_source_files : list of str
A list of additional ``.cpp`` files to include in the build.
additional_header_files : list of str
A list of additional ``.h`` files to include in the build.
main_includes : list of str
A list of additional header files to include in ``main.cpp``.
run_includes : list of str
A list of additional header files to include in ``run.cpp``.
'''
if additional_source_files is None:
additional_source_files = []
if additional_header_files is None:
additional_header_files = []
if main_includes is None:
main_includes = []
if run_includes is None:
run_includes = []
if run_args is None:
run_args = []
self.project_dir = project_dir
ensure_directory(project_dir)
for d in ['code_objects', 'results', 'static_arrays']:
ensure_directory(os.path.join(project_dir, d))
writer = CPPWriter(project_dir)
logger.debug("Writing C++ standalone project to directory "+os.path.normpath(project_dir))
arange_arrays = sorted([(var, start)
for var, start in self.arange_arrays.iteritems()],
key=lambda (var, start): var.name)
# # Find np arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, np.ndarray):
self.static_arrays[name] = value
# write the static arrays
logger.debug("static arrays: "+str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in sorted(self.static_arrays.items()):
arr.tofile(os.path.join(project_dir, 'static_arrays', name))
static_array_specs.append((name, c_data_type(arr.dtype), arr.size, name))
# Write the global objects
networks = [net() for net in Network.__instances__() if net().name!='_fake_network']
synapses = [S() for S in Synapses.__instances__()]
arr_tmp = CPPStandaloneCodeObject.templater.objects(
None, None,
array_specs=self.arrays,
dynamic_array_specs=self.dynamic_arrays,
dynamic_array_2d_specs=self.dynamic_arrays_2d,
zero_arrays=self.zero_arrays,
arange_arrays=arange_arrays,
synapses=synapses,
clocks=self.clocks,
static_array_specs=static_array_specs,
networks=networks,
)
writer.write('objects.*', arr_tmp)
main_lines = []
procedures = [('', main_lines)]
runfuncs = {}
for func, args in self.main_queue:
if func=='run_code_object':
codeobj, = args
main_lines.append('_run_%s();' % codeobj.name)
elif func=='run_network':
net, netcode = args
main_lines.extend(netcode)
elif func=='set_by_array':
arrayname, staticarrayname = args
code = '''
for(int i=0; i<_num_{staticarrayname}; i++)
{{
{arrayname}[i] = {staticarrayname}[i];
}}
'''.format(arrayname=arrayname, staticarrayname=staticarrayname)
main_lines.extend(code.split('\n'))
elif func=='set_array_by_array':
arrayname, staticarrayname_index, staticarrayname_value = args
code = '''
for(int i=0; i<_num_{staticarrayname_index}; i++)
{{
{arrayname}[{staticarrayname_index}[i]] = {staticarrayname_value}[i];
}}
'''.format(arrayname=arrayname, staticarrayname_index=staticarrayname_index,
staticarrayname_value=staticarrayname_value)
main_lines.extend(code.split('\n'))
elif func=='insert_code':
main_lines.append(args)
elif func=='start_run_func':
name, include_in_parent = args
if include_in_parent:
main_lines.append('%s();' % name)
main_lines = []
procedures.append((name, main_lines))
elif func=='end_run_func':
name, include_in_parent = args
name, main_lines = procedures.pop(-1)
runfuncs[name] = main_lines
name, main_lines = procedures[-1]
else:
raise NotImplementedError("Unknown main queue function type "+func)
# generate the finalisations
for codeobj in self.code_objects.itervalues():
if hasattr(codeobj.code, 'main_finalise'):
main_lines.append(codeobj.code.main_finalise)
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, AttributeVariable):
# We assume all attributes are implemented as property-like methods
line = 'const {c_type} {varname} = {objname}.{attrname}();'
lines.append(line.format(c_type=c_data_type(v.dtype), varname=k, objname=v.obj.name,
attrname=v.attribute))
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = &{dyn_array_name}[0];'
line = line.format(c_type=c_data_type(v.dtype), array_name=array_name,
dyn_array_name=dyn_array_name)
lines.append(line)
line = 'const int _num{k} = {dyn_array_name}.size();'
line = line.format(k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append('const int _num%s = %s;' % (k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%', '\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n'+code
writer.write('code_objects/'+codeobj.name+'.cpp', code)
writer.write('code_objects/'+codeobj.name+'.h', codeobj.code.h_file)
# The code_objects are passed in the right order to run them because they were
# sorted by the Network object. To support multiple clocks we'll need to be
# smarter about that.
main_tmp = CPPStandaloneCodeObject.templater.main(None, None,
main_lines=main_lines,
code_objects=self.code_objects.values(),
report_func=self.report_func,
dt=float(defaultclock.dt),
additional_headers=main_includes,
)
writer.write('main.cpp', main_tmp)
# Generate the run functions
run_tmp = CPPStandaloneCodeObject.templater.run(None, None, run_funcs=runfuncs,
code_objects=self.code_objects.values(),
additional_headers=run_includes,
)
writer.write('run.*', run_tmp)
# Copy the brianlibdirectory
brianlib_dir = os.path.join(os.path.split(inspect.getsourcefile(CPPStandaloneCodeObject))[0],
'brianlib')
brianlib_files = copy_directory(brianlib_dir, os.path.join(project_dir, 'brianlib'))
for file in brianlib_files:
if file.lower().endswith('.cpp'):
writer.source_files.append('brianlib/'+file)
elif file.lower().endswith('.h'):
writer.header_files.append('brianlib/'+file)
# Copy the CSpikeQueue implementation
spikequeue_h = os.path.join(project_dir, 'brianlib', 'spikequeue.h')
shutil.copy2(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0], 'cspikequeue.cpp'),
spikequeue_h)
#writer.header_files.append(spikequeue_h)
writer.source_files.extend(additional_source_files)
writer.header_files.extend(additional_header_files)
# Generate the makefile
if os.name=='nt':
rm_cmd = 'del'
else:
rm_cmd = 'rm'
makefile_tmp = CPPStandaloneCodeObject.templater.makefile(None, None,
source_files=' '.join(writer.source_files),
header_files=' '.join(writer.header_files),
rm_cmd=rm_cmd)
writer.write('makefile', makefile_tmp)
# build the project
if compile_project:
with in_directory(project_dir):
if debug:
x = os.system('make debug')
elif native:
x = os.system('make native')
else:
x = os.system('make')
if x==0:
if run_project:
if not with_output:
stdout = open(os.devnull, 'w')
else:
stdout = None
if os.name=='nt':
x = subprocess.call(['main'] + run_args, stdout=stdout)
else:
x = subprocess.call(['./main'] + run_args, stdout=stdout)
if x:
raise RuntimeError("Project run failed")
self.has_been_run = True
else:
raise RuntimeError("Project compilation failed")
def test_namespace_warnings():
G = NeuronGroup(1, '''x : 1
y : 1''',
# unique names to get warnings every time:
name='neurongroup_'+str(uuid.uuid4()).replace('-', '_'))
# conflicting variable in namespace
y = 5
with catch_logs() as l:
G.x = 'y'
assert len(l) == 1, 'got %s as warnings' % str(l)
assert l[0][1].endswith('.resolution_conflict')
del y
# conflicting variables with special meaning
i = 5
N = 3
with catch_logs() as l:
G.x = 'i / N'
assert len(l) == 2, 'got %s as warnings' % str(l)
assert l[0][1].endswith('.resolution_conflict')
assert l[1][1].endswith('.resolution_conflict')
del i
del N
# conflicting variables in equations
y = 5*Hz
G = NeuronGroup(1, '''y : Hz
dx/dt = y : 1''',
# unique names to get warnings every time:
name='neurongroup_'+str(uuid.uuid4()).replace('-', '_'))
net = Network(G)
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 1, 'got %s as warnings' % str(l)
assert l[0][1].endswith('.resolution_conflict')
del y
i = 5
# i is referring to the neuron number:
G = NeuronGroup(1, '''dx/dt = i*Hz : 1''',
# unique names to get warnings every time:
name='neurongroup_'+str(uuid.uuid4()).replace('-', '_'))
net = Network(G)
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 1, 'got %s as warnings' % str(l)
assert l[0][1].endswith('.resolution_conflict')
del i
# Variables that are used internally but not in equations should not raise
# a warning
N = 3
i = 5
dt = 1*ms
G = NeuronGroup(1, '''dx/dt = x/(10*ms) : 1''',
# unique names to get warnings every time:
name='neurongroup_'+str(uuid.uuid4()).replace('-', '_'))
net = Network(G)
with catch_logs() as l:
net.run(0*ms)
assert len(l) == 0, 'got %s as warnings' % str(l)
def before_run(self, run_namespace=None, level=0):
self._update_magic_objects(level=level+1)
Network.before_run(self, run_namespace, level=level+1)
def build(
self,
project_dir='output',
compile_project=True,
run_project=False,
debug=True,
with_output=True,
native=True,
additional_source_files=None,
additional_header_files=None,
main_includes=None,
run_includes=None,
run_args=None,
):
'''
Build the project
TODO: more details
Parameters
----------
project_dir : str
The output directory to write the project to, any existing files will be overwritten.
compile_project : bool
Whether or not to attempt to compile the project using GNU make.
run_project : bool
Whether or not to attempt to run the built project if it successfully builds.
debug : bool
Whether to compile in debug mode.
with_output : bool
Whether or not to show the ``stdout`` of the built program when run.
native : bool
Whether or not to compile natively using the ``--march=native`` gcc option.
additional_source_files : list of str
A list of additional ``.cpp`` files to include in the build.
additional_header_files : list of str
A list of additional ``.h`` files to include in the build.
main_includes : list of str
A list of additional header files to include in ``main.cpp``.
run_includes : list of str
A list of additional header files to include in ``run.cpp``.
'''
if additional_source_files is None:
additional_source_files = []
if additional_header_files is None:
additional_header_files = []
if main_includes is None:
main_includes = []
if run_includes is None:
run_includes = []
if run_args is None:
run_args = []
self.project_dir = project_dir
ensure_directory(project_dir)
for d in ['code_objects', 'results', 'static_arrays']:
ensure_directory(os.path.join(project_dir, d))
writer = CPPWriter(project_dir)
logger.debug("Writing C++ standalone project to directory " +
os.path.normpath(project_dir))
arange_arrays = sorted(
[(var, start) for var, start in self.arange_arrays.iteritems()],
key=lambda (var, start): var.name)
# # Find np arrays in the namespaces and convert them into static
# # arrays. Hopefully they are correctly used in the code: For example,
# # this works for the namespaces for functions with C++ (e.g. TimedArray
# # treats it as a C array) but does not work in places that are
# # implicitly vectorized (state updaters, resets, etc.). But arrays
# # shouldn't be used there anyway.
for code_object in self.code_objects.itervalues():
for name, value in code_object.variables.iteritems():
if isinstance(value, np.ndarray):
self.static_arrays[name] = value
# write the static arrays
logger.debug("static arrays: " +
str(sorted(self.static_arrays.keys())))
static_array_specs = []
for name, arr in sorted(self.static_arrays.items()):
arr.tofile(os.path.join(project_dir, 'static_arrays', name))
static_array_specs.append(
(name, c_data_type(arr.dtype), arr.size, name))
# Write the global objects
networks = [
net() for net in Network.__instances__()
if net().name != '_fake_network'
]
synapses = [S() for S in Synapses.__instances__()]
arr_tmp = CPPStandaloneCodeObject.templater.objects(
None,
None,
array_specs=self.arrays,
dynamic_array_specs=self.dynamic_arrays,
dynamic_array_2d_specs=self.dynamic_arrays_2d,
zero_arrays=self.zero_arrays,
arange_arrays=arange_arrays,
synapses=synapses,
clocks=self.clocks,
static_array_specs=static_array_specs,
networks=networks,
)
writer.write('objects.*', arr_tmp)
main_lines = []
procedures = [('', main_lines)]
runfuncs = {}
for func, args in self.main_queue:
if func == 'run_code_object':
codeobj, = args
main_lines.append('_run_%s();' % codeobj.name)
elif func == 'run_network':
net, netcode = args
main_lines.extend(netcode)
elif func == 'set_by_array':
arrayname, staticarrayname = args
code = '''
for(int i=0; i<_num_{staticarrayname}; i++)
{{
{arrayname}[i] = {staticarrayname}[i];
}}
'''.format(arrayname=arrayname,
staticarrayname=staticarrayname)
main_lines.extend(code.split('\n'))
elif func == 'set_array_by_array':
arrayname, staticarrayname_index, staticarrayname_value = args
code = '''
for(int i=0; i<_num_{staticarrayname_index}; i++)
{{
{arrayname}[{staticarrayname_index}[i]] = {staticarrayname_value}[i];
}}
'''.format(arrayname=arrayname,
staticarrayname_index=staticarrayname_index,
staticarrayname_value=staticarrayname_value)
main_lines.extend(code.split('\n'))
elif func == 'insert_code':
main_lines.append(args)
elif func == 'start_run_func':
name, include_in_parent = args
if include_in_parent:
main_lines.append('%s();' % name)
main_lines = []
procedures.append((name, main_lines))
elif func == 'end_run_func':
name, include_in_parent = args
name, main_lines = procedures.pop(-1)
runfuncs[name] = main_lines
name, main_lines = procedures[-1]
else:
raise NotImplementedError("Unknown main queue function type " +
func)
# generate the finalisations
for codeobj in self.code_objects.itervalues():
if hasattr(codeobj.code, 'main_finalise'):
main_lines.append(codeobj.code.main_finalise)
# Generate data for non-constant values
code_object_defs = defaultdict(list)
for codeobj in self.code_objects.itervalues():
lines = []
for k, v in codeobj.variables.iteritems():
if isinstance(v, AttributeVariable):
# We assume all attributes are implemented as property-like methods
line = 'const {c_type} {varname} = {objname}.{attrname}();'
lines.append(
line.format(c_type=c_data_type(v.dtype),
varname=k,
objname=v.obj.name,
attrname=v.attribute))
elif isinstance(v, ArrayVariable):
try:
if isinstance(v, DynamicArrayVariable):
if v.dimensions == 1:
dyn_array_name = self.dynamic_arrays[v]
array_name = self.arrays[v]
line = '{c_type}* const {array_name} = &{dyn_array_name}[0];'
line = line.format(
c_type=c_data_type(v.dtype),
array_name=array_name,
dyn_array_name=dyn_array_name)
lines.append(line)
line = 'const int _num{k} = {dyn_array_name}.size();'
line = line.format(
k=k, dyn_array_name=dyn_array_name)
lines.append(line)
else:
lines.append('const int _num%s = %s;' %
(k, v.size))
except TypeError:
pass
for line in lines:
# Sometimes an array is referred to by to different keys in our
# dictionary -- make sure to never add a line twice
if not line in code_object_defs[codeobj.name]:
code_object_defs[codeobj.name].append(line)
# Generate the code objects
for codeobj in self.code_objects.itervalues():
ns = codeobj.variables
# TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant.
code = freeze(codeobj.code.cpp_file, ns)
code = code.replace('%CONSTANTS%',
'\n'.join(code_object_defs[codeobj.name]))
code = '#include "objects.h"\n' + code
writer.write('code_objects/' + codeobj.name + '.cpp', code)
writer.write('code_objects/' + codeobj.name + '.h',
codeobj.code.h_file)
# The code_objects are passed in the right order to run them because they were
# sorted by the Network object. To support multiple clocks we'll need to be
# smarter about that.
main_tmp = CPPStandaloneCodeObject.templater.main(
None,
None,
main_lines=main_lines,
code_objects=self.code_objects.values(),
report_func=self.report_func,
dt=float(defaultclock.dt),
additional_headers=main_includes,
)
writer.write('main.cpp', main_tmp)
# Generate the run functions
run_tmp = CPPStandaloneCodeObject.templater.run(
None,
None,
run_funcs=runfuncs,
code_objects=self.code_objects.values(),
additional_headers=run_includes,
)
writer.write('run.*', run_tmp)
# Copy the brianlibdirectory
brianlib_dir = os.path.join(
os.path.split(inspect.getsourcefile(CPPStandaloneCodeObject))[0],
'brianlib')
brianlib_files = copy_directory(brianlib_dir,
os.path.join(project_dir, 'brianlib'))
for file in brianlib_files:
if file.lower().endswith('.cpp'):
writer.source_files.append('brianlib/' + file)
elif file.lower().endswith('.h'):
writer.header_files.append('brianlib/' + file)
# Copy the CSpikeQueue implementation
spikequeue_h = os.path.join(project_dir, 'brianlib', 'spikequeue.h')
shutil.copy2(
os.path.join(
os.path.split(inspect.getsourcefile(Synapses))[0],
'cspikequeue.cpp'), spikequeue_h)
#writer.header_files.append(spikequeue_h)
writer.source_files.extend(additional_source_files)
writer.header_files.extend(additional_header_files)
# Generate the makefile
if os.name == 'nt':
rm_cmd = 'del'
else:
rm_cmd = 'rm'
makefile_tmp = CPPStandaloneCodeObject.templater.makefile(
None,
None,
source_files=' '.join(writer.source_files),
header_files=' '.join(writer.header_files),
rm_cmd=rm_cmd)
writer.write('makefile', makefile_tmp)
# build the project
if compile_project:
with in_directory(project_dir):
if debug:
x = os.system('make debug')
elif native:
x = os.system('make native')
else:
x = os.system('make')
if x == 0:
if run_project:
if not with_output:
stdout = open(os.devnull, 'w')
else:
stdout = None
if os.name == 'nt':
x = subprocess.call(['main'] + run_args,
stdout=stdout)
else:
x = subprocess.call(['./main'] + run_args,
stdout=stdout)
if x:
raise RuntimeError("Project run failed")
self.has_been_run = True
else:
raise RuntimeError("Project compilation failed")
inputParsName)
if os.path.isdir(opDir):
ch = input('Results already exist at {}. Delete?(y/n):'.format(opDir))
if ch == 'y':
shutil.rmtree(opDir)
os.makedirs(opDir)
period265 = (1 / 265)
inputPars = getattr(inputParsList, inputParsName)
JO = JOSpikes265(nOutputs=1, simSettleTime=simSettleTime, **inputPars)
dlint2.addExp2Synapses(name='JO',
nSyn=1,
sourceNG=JO.JOSGG,
sourceInd=0,
**getattr(synapsePropsList, NeuronSynapseProps))
net = Network()
net.add(JO.JOSGG)
dlint2.addToNetwork(net)
defaultclock.dt = simStepSize
totalSimDur = simDuration + simSettleTime
net.run(totalSimDur, report='text')
simT, memV = dlint2.getMemVTrace()
spikeTimes = dlint2.getSpikes()
fig, axs = plt.subplots(nrows=2, figsize=(10, 6.25), sharex='col')
axs[0].plot(simT / units.ms, memV / units.mV)
spikesY = memV.min() + 1.05 * (memV.max() - memV.min())
axs[0].plot(spikeTimes / units.ms, [spikesY / units.mV] * spikeTimes.shape[0],
'k^')
axs[0].set_ylabel('DLInt1 \nmemV (mV)')
axs[0].set_xlim([simSettleTime / units.ms - 50, totalSimDur / units.ms + 50])
def before_run(self, namespace):
self._update_magic_objects()
Network.before_run(self, namespace)
ch = input('Results already exist at {}. Delete?(y/n):'.format(OPNixFile))
if ch == 'y':
os.remove(OPNixFile)
if os.path.isfile(opFileDLInt1):
os.remove(opFileDLInt1)
if os.path.isfile(opFileDLInt2):
os.remove(opFileDLInt2)
else:
sys.exit('User Abort!')
elif not os.path.isdir(opDir):
os.makedirs(opDir)
inputPars = getattr(inputParsList, inputParsName)
net = Network()
JO = JOSpikes265(nOutputs=1, simSettleTime=simSettleTime, **inputPars)
net.add(JO.JOSGG)
DLInt1PropsDict = getattr(AdExpPars, DLInt1ModelProps)
dlint1 = VSNeuron(**AdExp, inits=DLInt1PropsDict, name='dlint1')
dlint1.recordSpikes()
dlint1.recordMembraneV()
if DLInt1SynapsePropsE:
synPropsEDLInt1 = getattr(synapsePropsList, DLInt1SynapsePropsE)
dlint1.addSynapse(synName="ExiJO",
sourceNG=JO.JOSGG,
**exp2Syn,
synParsInits=synPropsEDLInt1,
synStateInits=exp2SynStateInits,