def __init__(self,
dims1,
dims2,
F,
C,
r=1,
update=False,
corr=False,
save=False,
numpoints=None):
"""F: R^a --> R^b
Note: I did not assign b automatically (although I could - it would just be b = p*q) since
you may not want to use all of the entries of S. Some bordering methods are not
minimally augmented systems and thus only require certain entries of S."""
(n, m) = dims2
TestFunc.__init__(self, dims1, F, C, save=save, numpoints=numpoints)
self.update = update
self.corr = corr
s = max(n, m)
if self.data is None:
self.data = args()
self.data.n, self.data.m = n, m
self.data.p = s - m + r
self.data.q = s - n + r
def __init__(self, dims, F, C, save=False, numpoints=None):
(n,m) = dims
TestFunc.__init__(self, dims, F, C, save=save, numpoints=numpoints)
if self.data is None:
self.data = args()
n = len(self.F.coords)
self.data.P = zeros((n*(n-1)/2, n*(n-1)/2), float)
def get_pysces_model(filename, target='Vode'):
path, fname = os.path.split(filename)
m = pysces.model(fname, dir=path)
max_t = np.Inf
parlist = m.__fixed_species__ + m.__parameters__
pardict = dict([(pname, p['initial']) for pname, p in m.__pDict__.items()])
varlist = m.__species__ # list ['s0', 's1', 's2']
icdict = dict([(vname, v['initial']) for vname, v in m.__sDict__.items()
if not v['fixed']])
fixed_species = dict([(pname, p['initial'])
for pname, p in m.__sDict__.items() if p['fixed']])
pardict.update(fixed_species)
fnspecs = {}
for R in m.__reactions__: # list ['R1', 'R2', 'R3', 'R4']
R_info = m.__nDict__[R]
#assert R_info['Modifiers'] == []
assert R_info['Type'] == 'Rever'
arglist = []
for reagent in R_info['Reagents']:
r = reagent.replace('self.', '')
if r in varlist:
arglist.append(r)
arglist.sort()
fnspecs[R] = (arglist, R_info['RateEq'].replace('self.', ''))
varspecs = make_varspecs(m, fnspecs)
for fname, fspec in m.__userfuncs__.items():
# Don't know how these are implemented yet
fnspec[fname] = fspec
dsargs = args(name=fname[:-3],
varspecs=varspecs,
fnspecs=fnspecs,
pars=pardict,
ics=icdict,
tdata=[0, max_t])
genclassname = target + '_ODEsystem'
try:
genclass = getattr(Generator, genclassname)
except AttributeError:
raise TypeError("Invalid ODE solver type")
return genclass(dsargs)
def __init__(self, testfuncs, flagfuncs, label='Bifurcation', stop=False):
self.testfuncs = []
self.flagfuncs = []
self.found = []
self.label = label
self.stop = stop
self.data = args()
if not isinstance(testfuncs, list):
testfuncs = [testfuncs]
if not isinstance(flagfuncs, list):
flagfuncs = [flagfuncs]
self.testfuncs.extend(testfuncs)
self.flagfuncs.extend(flagfuncs)
self.tflen = len(self.testfuncs)
def __init__(self, testfuncs, flagfuncs, label='Bifurcation', stop=False):
self.testfuncs = []
self.flagfuncs = []
self.found = []
self.label = label
self.stop = stop
self.data = args()
if not isinstance(testfuncs, list):
testfuncs = [testfuncs]
if not isinstance(flagfuncs, list):
flagfuncs = [flagfuncs]
self.testfuncs.extend(testfuncs)
self.flagfuncs.extend(flagfuncs)
self.tflen = len(self.testfuncs)
def get_pysces_model(filename, target='Vode'):
path, fname = os.path.split(filename)
m = pysces.model(fname, dir=path)
max_t = np.Inf
parlist = m.__fixed_species__ + m.__parameters__
pardict = dict([(pname, p['initial']) for pname, p in m.__pDict__.items()])
varlist = m.__species__ # list ['s0', 's1', 's2']
icdict = dict([(vname, v['initial']) for vname, v in m.__sDict__.items() if not v['fixed']])
fixed_species = dict([(pname, p['initial']) for pname, p in m.__sDict__.items() if p['fixed']])
pardict.update(fixed_species)
fnspecs = {}
for R in m.__reactions__: # list ['R1', 'R2', 'R3', 'R4']
R_info = m.__nDict__[R]
#assert R_info['Modifiers'] == []
assert R_info['Type'] == 'Rever'
arglist = []
for reagent in R_info['Reagents']:
r = reagent.replace('self.','')
if r in varlist:
arglist.append(r)
arglist.sort()
fnspecs[R] = (arglist, R_info['RateEq'].replace('self.',''))
varspecs = make_varspecs(m, fnspecs)
for fname, fspec in m.__userfuncs__.items():
# Don't know how these are implemented yet
fnspec[fname] = fspec
dsargs = args(name=fname[:-3],
varspecs=varspecs,
fnspecs=fnspecs,
pars=pardict,
ics=icdict,
tdata=[0, max_t])
genclassname = target + '_ODEsystem'
try:
genclass = getattr(Generator, genclassname)
except AttributeError:
raise TypeError("Invalid ODE solver type")
return genclass(dsargs)
def __init__(self, dims1, dims2, F, C, r=1, update=False, corr=False, save=False, numpoints=None):
"""F: R^a --> R^b
Note: I did not assign b automatically (although I could - it would just be b = p*q) since
you may not want to use all of the entries of S. Some bordering methods are not
minimally augmented systems and thus only require certain entries of S."""
(n,m) = dims2
TestFunc.__init__(self, dims1, F, C, save=save, numpoints=numpoints)
self.update = update
self.corr = corr
s = max(n,m)
if self.data is None:
self.data = args()
self.data.n, self.data.m = n, m
self.data.p = s-m+r
self.data.q = s-n+r
def defineSystem():
# Create an object of args class from common module
DSargs = cmn.args(name='Genetic Toggle Switch with SA')
# Initialize the DSargs object with parameters
#DSargs.pars = aux.parameter_set_1()
#DSargs.pars = aux.parameter_set_2()
DSargs.pars = aux.parameter_set_3()
# obtain the differential equations:
DSargs.varspecs = aux.equations()
# obtain the auxiliary functions:
DSargs.fnspecs = aux.functions()
# Set initial conditions:
DSargs.ics = {'X': 1, 'Y': 1}
DSargs.xdomain = {'X': [0, 1.0e+4], 'Y': [0, 1.0e+4]}
# Set the range of integration:
DSargs.tdomain = [0, 100]
return DSargs
def defineSystem():
'''
Create an object that defines the desired ODE system.
'''
# Create an object of args class from common module
DSargs = cmn.args(name='Toggle switch of two genes X and Y')
# Set the parameters:
DSargs.pars = aux.parameter_set_4()
# Set the variables:
DSargs.varspecs = aux.equations()
# Set the auxiliary functions:
DSargs.fnspecs = aux.functions()
# Set initial conditions:
DSargs.ics = {'X': 10, 'Y': 10}
DSargs.xdomain = {'X': [0, 1.0e+4], 'Y':[0, 1.0e+4]}
# Set the range of integration:
DSargs.tdomain = [0,100]
return DSargs
def setup_module(PyDSTool):
# Tests with dummy epoch stubs
namemap = parseUtils.symbolMapClass({'w': 'w', 'x': 'x', 'y': 'y', 'z': 'z'})
ep1 = common.args(actives=['x','y'],modulatory=['z','w'],sigma=2,relative_ratios=True,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res1 = transition_psi(ep1, Point({'x': 1, 'y': 0.499, 'z': 0.2, 'w': 0.1}), 0.01)
res2 = transition_psi(ep1, Point({'x': 1, 'y': 0.601, 'z': 0.3, 'w': 0.1}), 0.01)
ep2 = common.args(actives=['x'],modulatory=['z','w'],sigma=2,relative_ratios=True,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res3 = transition_psi(ep2, Point({'x': 1, 'z': 0.1, 'w': 0.501}), 0.01)
ep3 = common.args(actives=['x','y'],modulatory=['z','w'],sigma=2,relative_ratios=False,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res5 = transition_psi(ep3, Point({'x': 1, 'y': 0.499, 'z': 0.2, 'w': 0.1}), 0.01)
res6 = transition_psi(ep3, Point({'x': 1, 'y': 0.601, 'z': 0.499, 'w': 0.1}), 0.01)
ep4 = common.args(actives=['x'],modulatory=['z','w'],sigma=2,relative_ratios=False,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res7 = transition_psi(ep4, Point({'x': 1, 'z': 0.1, 'w': 0.501}), 0.01)
ep5 = common.args(actives=['x','y'],modulatory=[],sigma=2,relative_ratios=False,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res9 = transition_psi(ep5, Point({'x': 1, 'y': 0.501}), 0.01)
ep6 = common.args(fast=['x','y'],slow=['w','z'],order1=['v'],gamma=2,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res10 = transition_tau(ep6, Point({'x': 0.3, 'y': 0.2, 'v':1, 'w': 2.005, 'z': 3}), 0.01)
PyDSTool.TestDSSRT.ep1 = ep1
PyDSTool.TestDSSRT.ep2 = ep2
PyDSTool.TestDSSRT.ep3 = ep3
PyDSTool.TestDSSRT.ep4 = ep4
PyDSTool.TestDSSRT.ep5 = ep5
PyDSTool.TestDSSRT.ep6 = ep6
PyDSTool.TestDSSRT.res1 = res1
PyDSTool.TestDSSRT.res2 = res2
PyDSTool.TestDSSRT.res3 = res3
# no 4
PyDSTool.TestDSSRT.res5 = res5
PyDSTool.TestDSSRT.res6 = res6
PyDSTool.TestDSSRT.res7 = res7
# no 8
PyDSTool.TestDSSRT.res9 = res9
PyDSTool.TestDSSRT.res10 = res10
def setup_module(PyDSTool):
# Tests with dummy epoch stubs
namemap = parseUtils.symbolMapClass({'w': 'w', 'x': 'x', 'y': 'y', 'z': 'z'})
ep1 = common.args(actives=['x','y'],modulatory=['z','w'],sigma=2,relative_ratios=True,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res1 = transition_psi(ep1, Point({'x': 1, 'y': 0.499, 'z': 0.2, 'w': 0.1}), 0.01)
res2 = transition_psi(ep1, Point({'x': 1, 'y': 0.601, 'z': 0.3, 'w': 0.1}), 0.01)
ep2 = common.args(actives=['x'],modulatory=['z','w'],sigma=2,relative_ratios=True,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res3 = transition_psi(ep2, Point({'x': 1, 'z': 0.1, 'w': 0.501}), 0.01)
ep3 = common.args(actives=['x','y'],modulatory=['z','w'],sigma=2,relative_ratios=False,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res5 = transition_psi(ep3, Point({'x': 1, 'y': 0.499, 'z': 0.2, 'w': 0.1}), 0.01)
res6 = transition_psi(ep3, Point({'x': 1, 'y': 0.601, 'z': 0.499, 'w': 0.1}), 0.01)
ep4 = common.args(actives=['x'],modulatory=['z','w'],sigma=2,relative_ratios=False,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res7 = transition_psi(ep4, Point({'x': 1, 'z': 0.1, 'w': 0.501}), 0.01)
ep5 = common.args(actives=['x','y'],modulatory=[],sigma=2,relative_ratios=False,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res9 = transition_psi(ep5, Point({'x': 1, 'y': 0.501}), 0.01)
ep6 = common.args(fast=['x','y'],slow=['w','z'],order1=['v'],gamma=2,
inv_psi_namemap=namemap, inv_tau_namemap=namemap)
res10 = transition_tau(ep6, Point({'x': 0.3, 'y': 0.2, 'v':1, 'w': 2.005, 'z': 3}), 0.01)
PyDSTool.TestDSSRT.ep1 = ep1
PyDSTool.TestDSSRT.ep2 = ep2
PyDSTool.TestDSSRT.ep3 = ep3
PyDSTool.TestDSSRT.ep4 = ep4
PyDSTool.TestDSSRT.ep5 = ep5
PyDSTool.TestDSSRT.ep6 = ep6
PyDSTool.TestDSSRT.res1 = res1
PyDSTool.TestDSSRT.res2 = res2
PyDSTool.TestDSSRT.res3 = res3
# no 4
PyDSTool.TestDSSRT.res5 = res5
PyDSTool.TestDSSRT.res6 = res6
PyDSTool.TestDSSRT.res7 = res7
# no 8
PyDSTool.TestDSSRT.res9 = res9
PyDSTool.TestDSSRT.res10 = res10
def __init__(self, (a,b), (n,m), F, C, r=1, update=False, corr=False, save=False, numpoints=None):
"""F: R^a --> R^b
Note: I did not assign b automatically (although I could - it would just be b = p*q) since
you may not want to use all of the entries of S. Some bordering methods are not
minimally augmented systems and thus only require certain entries of S."""
TestFunc.__init__(self, (a,b), F, C, save=save, numpoints=numpoints)
self.update = update
self.corr = corr
s = max(n,m)
if self.data is None:
self.data = args()
self.data.n, self.data.m = n, m
self.data.p = s-m+r
self.data.q = s-n+r
def setdata(self, A):
"""Note: p, q <= min(n,m)"""
self.data.Brand = 2*(random((A.shape[0],self.data.p))-0.5)
self.data.Crand = 2*(random((A.shape[1],self.data.q))-0.5)
self.data.D = zeros((self.data.q,self.data.p), Float)
if self.update:
U, S, Vh = linalg.svd(A)
self.data.B = U[:,-1*self.data.p:]
self.data.C = num_transpose(Vh)[:,-1*self.data.q:]
else:
def process(self, X, V, C):
data = args()
data.X = todict(C, X)
data.V = todict(C, V)
self.found.append(data)
def find_recurrences(data, refix, r, times=None, ignore_small=0,
which_norm=2):
"""Find recurrences of a trajectory in a ball of radius r centred at the
reference point given by refix in data.
If recurrence times are desired, pass an associated time array corresponding
to the points in the data.
If ignore_small > 0, recurrences of fewer than this number of data points
will be treated as anomalous and ignored completely.
Returns a structure (class common.args) having attributes:
partitions -- pairs of entry and exit indices for each recurrence in
the ball
ball_ixs -- all consecutive indices into data for each recurrence
partitions_lengths -- number of indices in each partition
rec_times -- times to next recurrence in the set from previous
"""
if times is not None:
assert len(times) == len(data), "Times must have same length as data"
# ball_ixs is already sorted
ball_ixs = find_nearby_ball(data, refix, r, which_norm, include_ref=True)
result = args(ball_ixs=[], partitions=[], partition_lengths=[],
rec_times=None)
if len(ball_ixs) == 0:
# No points found in ball
return result
# find boundaries of each partition between contiguous indices
partition_bds = out_of_seq(ball_ixs)
if len(partition_bds) == 0:
result.ball_ixs = ball_ixs
result.partitions = [(ball_ixs[0], ball_ixs[-1])]
result.partition_lengths = [ball_ixs[-1] - ball_ixs[0] + 1]
if times is not None:
# only update this if times present to be consistent with other
# changes of rec_times from default None
result.rec_times = [Inf]
return result
else:
plen = ball_ixs[partition_bds[0]-1] - ball_ixs[0] + 1
if plen > ignore_small:
partitions = [(ball_ixs[0], ball_ixs[partition_bds[0]-1])]
else:
partitions = []
# find contiguous indices (and corresponding times)
for i in range(len(partition_bds)-1):
plo = ball_ixs[partition_bds[i]]
phi = ball_ixs[partition_bds[i+1]-1]
plen = phi - plo + 1
if plen > ignore_small:
partitions.append((plo, phi))
plo = ball_ixs[partition_bds[-1]]
phi = ball_ixs[-1]
plen = phi - plo + 1
if plen > ignore_small:
partitions.append((plo, phi))
result.ball_ixs = ball_ixs
result.partitions = partitions
result.partition_lengths = [p[1]-p[0]+1 for p in partitions]
if times is None:
return result
else:
result.rec_times = recurrence_times(times, partitions)
return result
def newCurve(self, initargs):
"""Create new curve with arguments specified in the dictionary initargs."""
curvetype = initargs['type'].upper()
if curvetype not in self.curve_list:
raise PyDSTool_TypeError(str(curvetype) + ' not an allowable curve type')
# Check name
cname = initargs['name']
if 'force' in initargs:
if initargs['force'] and cname in self.curves:
del self.curves[cname]
if cname in self.curves:
raise ValueError('Ambiguous name field: ' + cname \
+ ' already exists (use force=True to override)')
# Check parameters
if (curvetype != 'UD-C' and self.model.pars == {}) or \
(curvetype == 'UD-C' and 'userpars' not in initargs):
raise ValueError('No parameters defined for this system!')
# Process initial point
initargs = initargs.copy() # ensures no side-effects outside
if 'initpoint' not in initargs or initargs['initpoint'] is None:
# Default to initial conditions for model
if self.model.icdict == {}:
raise ValueError('No initial point defined for this system!')
elif 'uservars' in initargs:
if remain(initargs['uservars'], self.model.icdict.keys()) == []:
# uservars just used to select a subset of system's regular state vars
initargs['initpoint'] = filteredDict(self.model.icdict,
initargs['uservars'])
else:
raise ValueError('No initial point defined for this system!')
else:
initargs['initpoint'] = self.model.icdict.copy()
#for p in initargs['freepars']:
# initargs['initpoint'][p] = self.model.pars[p]
else:
if isinstance(initargs['initpoint'], dict):
initargs['initpoint'] = initargs['initpoint'].copy()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
elif isinstance(initargs['initpoint'], str):
curvename, pointname = initargs['initpoint'].split(':')
pointtype = pointname.strip('0123456789')
if curvename not in self.curves:
raise KeyError('No curve of name ' + curvename + ' exists.')
else:
point = self.curves[curvename].getSpecialPoint(pointtype, pointname)
if point is None:
raise KeyError('No point of name ' + pointname + ' exists.')
else:
initargs['initpoint'] = point
# Separate from if-else above since 'str' clause returns type Point
if isinstance(initargs['initpoint'], Point):
# Check to see if point contains a cycle. If it does, assume
# we are starting at a cycle and save it in initcycle
for v in initargs['initpoint'].labels.values():
if 'cycle' in v:
initargs['initcycle'] = v # Dictionary w/ cycle, name, and tangent information
# Save initial point information
initPoint = {}
if 'curvename' in locals() and curvename in self.curves:
initPoint = self.curves[curvename].parsdict.copy()
initPoint.update(initargs['initpoint'].copy().todict())
initargs['initpoint'] = initPoint
# initargs['initpoint'] = initargs['initpoint'].copy().todict()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
# Process cycle
if 'initcycle' in initargs:
if isinstance(initargs['initcycle'], ndarray):
c0 = {}
c0['data'] = args(V = {'udotps': None, 'rldot': None})
c0['cycle'] = Pointset({'coordnames': self.gensys.funcspec.vars,
'coordarray': initargs['initcycle'][1:,:].copy(),
'indepvarname': 't',
'indepvararray': initargs['initcycle'][0,:].copy()
})
initargs['initcycle'] = c0
elif isinstance(initargs['initcycle'], Pointset):
c0 = {}
c0['data'] = args(V = {'udotps': None, 'rldot': None})
c0['cycle'] = initargs['initcycle']
initargs['initcycle'] = c0
# Load auto module if required
automod = None
if curvetype in auto_list:
if self._autoMod is None:
self.loadAutoMod()
automod = self._autoMod
self.curves[cname] = self.curve_list[curvetype](self.model, self.gensys, automod, self.plot, initargs)
def process(self, X, V, C):
data = args()
data.X = todict(C, X)
data.V = todict(C, V)
self.found.append(data)
def newCurve(self, initargs):
"""Create new curve with arguments specified in the dictionary initargs."""
curvetype = initargs['type']
curvetype = curvetype.upper()
if curvetype not in curve_list:
raise TypeError(curvetype + ' not an allowable curve type')
# Check name
if initargs['name'] in self.curves.keys():
raise AttributeError('Ambiguous name field: ' + initargs['name'] + ' already exists')
# Check parameters
if self.model.pars == {}:
raise ValueError('No parameters defined for this system!')
# Process initial point
if 'initpoint' not in initargs:
# Default to initial conditions for model
if self.model.icdict == {}:
raise ValueError('No initial point defined for this system!')
initargs['initpoint'] = self.model.icdict.copy()
#for p in initargs['freepars']:
# initargs['initpoint'][p] = self.model.pars[p]
else:
if isinstance(initargs['initpoint'], dict):
initargs['initpoint'] = initargs['initpoint'].copy()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
elif isinstance(initargs['initpoint'], str):
curvename, pointname = initargs['initpoint'].split(':')
pointtype = pointname.strip('0123456789')
if not self.curves.has_key(curvename):
raise KeyError('No curve of name ' + curvename + ' exists.')
else:
point = self.curves[curvename].getSpecialPoint(pointtype, pointname)
if point is None:
raise KeyError('No point of name ' + pointname + ' exists.')
else:
initargs['initpoint'] = point
# Separate from if-else above since 'str' clause returns type Point
if isinstance(initargs['initpoint'], Point):
# Check to see if point contains a cycle. If it does, assume
# we are starting at a cycle and save it in initcycle
for v in initargs['initpoint'].labels.itervalues():
if v.has_key('cycle'):
initargs['initcycle'] = v # Dictionary w/ cycle, name, and tangent information
# Save initial point information
initargs['initpoint'] = initargs['initpoint'].todict()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
# Process cycle
if 'initcycle' in initargs:
if isinstance(initargs['initcycle'], NumArray):
c0 = {}
c0['data'] = args(V = {'udotps': None, 'rldot': None})
c0['cycle'] = Pointset({'coordnames': self.gensys.funcspec.vars,
'coordarray': num_transpose(initargs['initcycle'][:,1:]).copy(),
'indepvarname': 't',
'indepvararray': num_transpose(initargs['initcycle'][:,0]).copy()
})
initargs['initcycle'] = c0
elif isinstance(initargs['initcycle'], Pointset):
c0 = {}
c0['data'] = args(V = {'udotps': None, 'rldot': None})
c0['cycle'] = initargs['initcycle']
initargs['initcycle'] = c0
# Load auto module if required
automod = None
if curvetype in auto_list:
if self._autoMod is None:
self.loadAutoMod()
automod = self._autoMod
self.curves[initargs['name']] = curve_list[curvetype](self.model, self.gensys, automod, self.plot, initargs)
def newCurve(self, initargs):
"""Create new curve with arguments specified in the dictionary initargs."""
curvetype = initargs['type'].upper()
if curvetype not in self.curve_list:
raise PyDSTool_TypeError(
str(curvetype) + ' not an allowable curve type')
# Check name
cname = initargs['name']
if 'force' in initargs:
if initargs['force'] and cname in self.curves:
del self.curves[cname]
if cname in self.curves:
raise ValueError('Ambiguous name field: ' + cname \
+ ' already exists (use force=True to override)')
# Check parameters
if (curvetype != 'UD-C' and self.model.pars == {}) or \
(curvetype == 'UD-C' and 'userpars' not in initargs):
raise ValueError('No parameters defined for this system!')
# Process initial point
initargs = initargs.copy() # ensures no side-effects outside
if 'initpoint' not in initargs or initargs['initpoint'] is None:
# Default to initial conditions for model
if self.model.icdict == {}:
raise ValueError('No initial point defined for this system!')
elif 'uservars' in initargs:
if remain(initargs['uservars'],
self.model.icdict.keys()) == []:
# uservars just used to select a subset of system's regular state vars
initargs['initpoint'] = filteredDict(
self.model.icdict, initargs['uservars'])
else:
raise ValueError(
'No initial point defined for this system!')
else:
initargs['initpoint'] = self.model.icdict.copy()
#for p in initargs['freepars']:
# initargs['initpoint'][p] = self.model.pars[p]
else:
if isinstance(initargs['initpoint'], dict):
initargs['initpoint'] = initargs['initpoint'].copy()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
elif isinstance(initargs['initpoint'], str):
curvename, pointname = initargs['initpoint'].split(':')
pointtype = pointname.strip('0123456789')
if curvename not in self.curves:
raise KeyError('No curve of name ' + curvename +
' exists.')
else:
point = self.curves[curvename].getSpecialPoint(
pointtype, pointname)
if point is None:
raise KeyError('No point of name ' + pointname +
' exists.')
else:
initargs['initpoint'] = point
# Separate from if-else above since 'str' clause returns type Point
if isinstance(initargs['initpoint'], Point):
# Check to see if point contains a cycle. If it does, assume
# we are starting at a cycle and save it in initcycle
for v in initargs['initpoint'].labels.values():
if 'cycle' in v:
initargs[
'initcycle'] = v # Dictionary w/ cycle, name, and tangent information
# Save initial point information
initPoint = {}
if 'curvename' in locals() and curvename in self.curves:
initPoint = self.curves[curvename].parsdict.copy()
initPoint.update(initargs['initpoint'].copy().todict())
initargs['initpoint'] = initPoint
# initargs['initpoint'] = initargs['initpoint'].copy().todict()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
# Process cycle
if 'initcycle' in initargs:
if isinstance(initargs['initcycle'], ndarray):
c0 = {}
c0['data'] = args(V={'udotps': None, 'rldot': None})
c0['cycle'] = Pointset({
'coordnames':
self.gensys.funcspec.vars,
'coordarray':
initargs['initcycle'][1:, :].copy(),
'indepvarname':
't',
'indepvararray':
initargs['initcycle'][0, :].copy()
})
initargs['initcycle'] = c0
elif isinstance(initargs['initcycle'], Pointset):
c0 = {}
c0['data'] = args(V={'udotps': None, 'rldot': None})
c0['cycle'] = initargs['initcycle']
initargs['initcycle'] = c0
# Load auto module if required
automod = None
if curvetype in auto_list:
if self._autoMod is None:
self.loadAutoMod()
automod = self._autoMod
self.curves[cname] = self.curve_list[curvetype](self.model,
self.gensys, automod,
self.plot, initargs)
def newCurve(self, initargs):
"""Create new curve with arguments specified in the dictionary initargs."""
curvetype = initargs['type']
curvetype = curvetype.upper()
if curvetype not in curve_list:
raise TypeError(curvetype + ' not an allowable curve type')
# Check name
if initargs['name'] in self.curves.keys():
raise AttributeError('Ambiguous name field: ' + initargs['name'] +
' already exists')
# Check parameters
if self.model.pars == {}:
raise ValueError('No parameters defined for this system!')
# Process initial point
if 'initpoint' not in initargs:
# Default to initial conditions for model
if self.model.icdict == {}:
raise ValueError('No initial point defined for this system!')
initargs['initpoint'] = self.model.icdict.copy()
#for p in initargs['freepars']:
# initargs['initpoint'][p] = self.model.pars[p]
else:
if isinstance(initargs['initpoint'], dict):
initargs['initpoint'] = initargs['initpoint'].copy()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
elif isinstance(initargs['initpoint'], str):
curvename, pointname = initargs['initpoint'].split(':')
pointtype = pointname.strip('0123456789')
if not self.curves.has_key(curvename):
raise KeyError('No curve of name ' + curvename +
' exists.')
else:
point = self.curves[curvename].getSpecialPoint(
pointtype, pointname)
if point is None:
raise KeyError('No point of name ' + pointname +
' exists.')
else:
initargs['initpoint'] = point
# Separate from if-else above since 'str' clause returns type Point
if isinstance(initargs['initpoint'], Point):
# Check to see if point contains a cycle. If it does, assume
# we are starting at a cycle and save it in initcycle
for v in initargs['initpoint'].labels.itervalues():
if v.has_key('cycle'):
initargs[
'initcycle'] = v # Dictionary w/ cycle, name, and tangent information
# Save initial point information
initargs['initpoint'] = initargs['initpoint'].todict()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
# Process cycle
if 'initcycle' in initargs:
if isinstance(initargs['initcycle'], NumArray):
c0 = {}
c0['data'] = args(V={'udotps': None, 'rldot': None})
c0['cycle'] = Pointset({
'coordnames':
self.gensys.funcspec.vars,
'coordarray':
num_transpose(initargs['initcycle'][:, 1:]).copy(),
'indepvarname':
't',
'indepvararray':
num_transpose(initargs['initcycle'][:, 0]).copy()
})
initargs['initcycle'] = c0
elif isinstance(initargs['initcycle'], Pointset):
c0 = {}
c0['data'] = args(V={'udotps': None, 'rldot': None})
c0['cycle'] = initargs['initcycle']
initargs['initcycle'] = c0
# Load auto module if required
automod = None
if curvetype in auto_list:
if self._autoMod is None:
self.loadAutoMod()
automod = self._autoMod
self.curves[initargs['name']] = curve_list[curvetype](self.model,
self.gensys,
automod,
self.plot,
initargs)