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fix bug where some 2D arrays are not accepted instead lists of 1D arrays #11

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fix bug where some 2D arrays are not accepted instead lists of 1D arrays #11

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4774c34
fix bug where some 2D arrays are not accepted instead lists of 1D arrays
regislachaume Nov 29, 2019
43b65b7
start may be a 2D array instead of an array list
regislachaume Nov 29, 2019
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10 changes: 5 additions & 5 deletions pydream/Dream.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@ def __init__(self, model, variables=None, nseedchains=None, nCR=3, adapt_crossov
self.last_logp = None

#Set the number of seedchains to 10*dimensions to fit
if self.nseedchains == None:
if self.nseedchains is None:
self.nseedchains = self.total_var_dimension*10

#Set array of gamma values (decreasing step size with increasing level)
Expand Down Expand Up @@ -228,7 +228,7 @@ def astep(self, q0, T=1., last_loglike=None, last_logprior=None):

try:

if last_loglike != None:
if last_loglike is not None:
self.last_like = last_loglike
self.last_prior = last_logprior
self.last_logp = T*self.last_like + self.last_prior
Expand All @@ -254,7 +254,7 @@ def astep(self, q0, T=1., last_loglike=None, last_logprior=None):
else:
proposed_pts, snooker_logp_prop, z = self.generate_proposal_points(self.multitry, q0, CR, DEpair_choice, gamma_level, snooker=True)

if self.last_logp == None:
if self.last_logp is None:
self.last_prior, self.last_like = self.logp(q0)
self.last_logp = T*self.last_like + self.last_prior

Expand Down Expand Up @@ -424,11 +424,11 @@ def set_current_position_arr(self, ndimensions, q_new):
accepted point in parameter space
"""

if self.nchains == None:
if self.nchains is None:
current_positions = np.frombuffer(Dream_shared_vars.current_positions.get_obj())
self.nchains = len(current_positions)//ndimensions

if self.chain_n == None:
if self.chain_n is None:
with Dream_shared_vars.nchains.get_lock():
self.chain_n = Dream_shared_vars.nchains.value-1
Dream_shared_vars.nchains.value -= 1
Expand Down
11 changes: 6 additions & 5 deletions pydream/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def run_dream(parameters, likelihood, nchains=5, niterations=50000, start=None,
"""

if restart:
if start == None:
if start is None:
raise Exception('Restart run specified but no start positions given.')
if 'model_name' not in kwargs:
raise Exception('Restart run specified but no model name to load history and crossover value files from given.')
Expand All @@ -63,7 +63,8 @@ def run_dream(parameters, likelihood, nchains=5, niterations=50000, start=None,

else:

if type(start) is list:
if (type(start) is list
or isinstance(start, np.ndarray) and start.ndim == 2):
args = zip([step_instance]*nchains, [niterations]*nchains, start, [verbose]*nchains, [nverbose]*nchains)

else:
Expand Down Expand Up @@ -215,7 +216,7 @@ def _sample_dream_pt(nchains, niterations, step_instance, start, pool, verbose):
naccepts[i] += 1
naccepts100win[i] += 1
except TypeError:
#On first iteration without starting points this will fail because q0 == None
#On first iteration without starting points this will fail because q0 is None
pass

args = list(zip(dream_instances, qnews, T, loglikenews, logprinews))
Expand Down Expand Up @@ -280,10 +281,10 @@ def _setup_mp_dream_pool(nchains, niterations, step_instance, start_pt=None):
n = mp.Value('i', 0)
tf = mp.Value('c', b'F')

if step_instance.crossover_burnin == None:
if step_instance.crossover_burnin is None:
step_instance.crossover_burnin = int(np.floor(niterations/10))

if start_pt != None:
if start_pt is not None:
if step_instance.start_random:
print('Warning: start position provided but random_start set to True. Overrode random_start value and starting walk at provided start position.')
step_instance.start_random = False
Expand Down