def make_jac_pydstool(ode):
jac, new_fnspecs = dst.prepJacobian(ode.funcspec._initargs['varspecs'],
['X', 'Y', 'A', 'B'],
ode.funcspec._initargs['fnspecs'])
scope = dst.copy(ode.pars)
scope.update(new_fnspecs)
jac_fn = dst.expr2fun(jac, ensure_args=['t'], **scope)
return jac_fn
def make_measure(fn_name, fn_spec, **defs):
"""Dynamically create a python function for use with calculation
context.
"""
all_defs = defs.copy()
q = dst.QuantSpec('_dummy_', fn_spec, treatMultiRefs=False)
import PyDSTool.parseUtils as pu
mapping = pu.symbolMapClass()
assumed_modules = []
tokens = q.parser.tokenized
for sym in q.freeSymbols:
# Hack, for now: if first (therefore, assumed all)
# occurrences of symbol are in quotes, then don't convert.
# Better solution would be to make parser create "x" as a single
# symbol, at least with a detect quote option
first_ix = tokens.index(sym)
if first_ix == 0 or (first_ix > 0 and tokens[first_ix-1] not in ['"', "'"]):
if pu.isHierarchicalName(sym):
parts = sym.split('.')
if parts[0] == 'sim':
mapping[sym] = 'con.'+sym
## elif parts[0] == 'bombardier':
## # special case as this factory function is defined in that
## # module so that reference will fail at runtime: remove
## # 'bombardier' prefix
## rest_sym = '.'.join(parts[1:])
## mapping[sym] = rest_sym
## scope = globals()
## # locals override
## scope.update(locals())
## if parts[1] in scope:
## all_defs[parts[1]] = scope[parts[1]]
## else:
## raise ValueError("Cannot resolve scope of symbol '%s'"%sym)
else:
# assume module reference
assumed_modules.append(parts[0])
# record here to ensure inclusion in dyn_dummy
mapping[sym] = 'self.'+sym
else:
mapping[sym] = 'con.workspace.'+sym
elif first_ix > 0 and tokens[first_ix-1] in ['"', "'"]:
# put this symbol in the mapping values to ensure not included
# as an argument to the function
mapping[sym] = sym
q.mapNames(mapping)
import types
for module_name in assumed_modules:
global_scope = globals()
# test if module name in scope
if module_name in global_scope:
_mod = global_scope[module_name]
if isinstance(_mod, types.ModuleType):
all_defs[module_name] = _mod
# dyn_dummy contains dummy mappings but declares symbols to leave
# evaluating until runtime
dyn_dummy = dict(zip(mapping.values(), ['']*len(mapping)))
funq = dst.expr2fun(q, ensure_args=['con'], ensure_dynamic=dyn_dummy,
for_funcspec=False, fn_name=fn_name,
**all_defs)
# decorate output
funq.attr_name = fn_name
return funq
# find dixed points of the model
fp_coord = pp.find_fixedpoints(dmModel, n=4, eps=1e-8)
# plot the null-clines
nulls_x, nulls_y = pp.find_nullclines(dmModel, 's1', 's2', n=3, \
eps=1e-8, max_step=0.01, fps=fp_coord)
plot(nulls_x[:,0], nulls_x[:,1], 'b')
plot(nulls_y[:,0], nulls_y[:,1], 'g')
# compute the jacobian matrix
jac, new_fnspecs = dst.prepJacobian(dmModel.funcspec._initargs['varspecs'],
['s1','s2'],dmModel.funcspec._initargs['fnspecs'])
scope = dst.copy(dmModel.pars)
scope.update(new_fnspecs)
jac_fn = dst.expr2fun(jac, ensure_args=['t'],**scope)
# add fixed points to the phase portrait
for i in range(0,len(fp_coord)):
fp = pp.fixedpoint_2D(dmModel, dst.Point(fp_coord[i]),
jac = jac_fn, eps=1e-8)
pp.plot_PP_fps(fp)
# compute and plot projectories
traj = dmModel.compute('trajectory1')
pts = traj.sample()
plot(pts['s1'], pts['s2'], 'r-o')
xlabel('s_1')
ylabel('s_2')
title('Phase plane I1=0.035 nA, I2=0.035 nA')
def make_measure(fn_name, fn_spec, **defs):
"""Dynamically create a python function for use with calculation
context.
"""
all_defs = defs.copy()
q = dst.QuantSpec('_dummy_', fn_spec, treatMultiRefs=False)
import PyDSTool.parseUtils as pu
mapping = pu.symbolMapClass()
assumed_modules = []
tokens = q.parser.tokenized
for sym in q.freeSymbols:
# Hack, for now: if first (therefore, assumed all)
# occurrences of symbol are in quotes, then don't convert.
# Better solution would be to make parser create "x" as a single
# symbol, at least with a detect quote option
first_ix = tokens.index(sym)
if first_ix == 0 or (first_ix > 0 and tokens[first_ix-1] not in ['"', "'"]):
if pu.isHierarchicalName(sym):
parts = sym.split('.')
if parts[0] == 'sim':
mapping[sym] = 'con.'+sym
## elif parts[0] == 'bombardier':
## # special case as this factory function is defined in that
## # module so that reference will fail at runtime: remove
## # 'bombardier' prefix
## rest_sym = '.'.join(parts[1:])
## mapping[sym] = rest_sym
## scope = globals()
## # locals override
## scope.update(locals())
## if parts[1] in scope:
## all_defs[parts[1]] = scope[parts[1]]
## else:
## raise ValueError("Cannot resolve scope of symbol '%s'"%sym)
else:
# assume module reference
assumed_modules.append(parts[0])
# record here to ensure inclusion in dyn_dummy
mapping[sym] = 'self.'+sym
else:
mapping[sym] = 'con.workspace.'+sym
elif first_ix > 0 and tokens[first_ix-1] in ['"', "'"]:
# put this symbol in the mapping values to ensure not included
# as an argument to the function
mapping[sym] = sym
q.mapNames(mapping)
import types
for module_name in assumed_modules:
global_scope = globals()
# test if module name in scope
if module_name in global_scope:
_mod = global_scope[module_name]
if isinstance(_mod, types.ModuleType):
all_defs[module_name] = _mod
# dyn_dummy contains dummy mappings but declares symbols to leave
# evaluating until runtime
dyn_dummy = dict(zip(mapping.values(), ['']*len(mapping)))
funq = dst.expr2fun(q, ensure_args=['con'], ensure_dynamic=dyn_dummy,
for_funcspec=False, fn_name=fn_name,
**all_defs)
# decorate output
funq.attr_name = fn_name
return funq
