def sample_chains_arviz(self,
n_sample,
init_states,
chain_var_funcs=None,
n_process=1):
"""Sample one or more Markov chains from given initial states.
Performs a specified number of chain iterations (each of which may
be composed of multiple individual Markov transitions), recording
the outputs of functions of the sampled chain state after each
iteration. The chains may be run in parallel across multiple
independent processes or sequentially. Chain data is returned in an
`arviz.InferenceData` container object.
Args:
n_sample (int): Number of samples to draw per chain.
init_states (Iterable[HamiltonianState] or Iterable[array]):
Initial chain states. Each state can be either an array
specifying the state position component or a
`HamiltonianState` instance. If an array is passed or the
`mom` attribute of the state is not set, a momentum
component will be independently sampled from its conditional
distribution. One chain will be run for each state in the
iterable sequence.
chain_var_funcs (dict[str, callable]): Dictionary of functions
which compute the chain variables to be recorded at each
iteration, with each function being passed the current state
and returning an array corresponding to the variable(s) to
be stored. By default (or if set to `None`) a single
function which returns the position component of the state
is used. The keys to the functions are used to index the
chain variable arrays in the returned data.
n_process (int or None): Number of parallel processes to run
chains over. If set to one then chains will be run
sequentially in otherwise a `multiprocessing.Pool` object
will be used to dynamically assign the chains across
multiple processes. If set to `None` then the number of
processes will default to the output of `os.cpu_count()`.
Returns:
arvix.InferenceData:
An arviz data container with groups `posterior` and
'sample_stats', both of instances of `xarray.Dataset`.
The `posterior` group corresponds to the chain variable
samples computed using the `chain_var_funcs` entries (with
the data variable keys corresponding to the keys there).
The `sample_stats` group corresponds to the statistics of
the integration transition such as the acceptance
probabilities and number of integrator steps.
"""
chains, chain_stats = self.sample_chains(n_sample, init_states,
chain_var_funcs,
n_process)
return arviz.InferenceData(
posterior=arviz.dict_to_dataset(chains, library=hmc),
sample_stats=arviz.dict_to_dataset(chain_stats, library=hmc))
def convert_to_arviz_inference_data(
traces, chain_stats, sample_stats_key=None):
"""Wrap chain outputs in an `arviz.InferenceData` container object.
The `traces` and `chain_stats` arguments should correspond to a
multiple-chain sampler output i.e. the returned values from a
`sample_chains` call.
Args:
traces (Dict[str, List[array]]): Trace arrays, with one entry per
function in `trace_funcs` passed to sampler method. Each entry
consists of a list of arrays, one per chain, with the first
axes of the arrays corresponding to the sampling (draw) index.
chain_stats (Dict[str, List[array]]): Chain integration transition
statistics as a dictionary with string keys describing the
statistics recorded and values corresponding to a list of
arrays with one array per chain and the first axis of the
arrays corresponding to the sampling index.
sample_stats_key (str): Optional. Key of transition in
`chain_stats` to use the recorded statistics of to populate the
`sampling_stats` group in the returned `InferenceData` object.
Returns:
arviz.InferenceData:
An arviz data container with groups `posterior` and
'sample_stats', both of instances of `xarray.Dataset`. The
`posterior` group corresponds to the chain variable traces
provides in the `traces` argument and the `sample_stats`
group corresponds to the chain transitions statistics passed
in the `chain_stats` argument (if multiple transition
statistics dictionaries are present the `sample_stats_key`
argument should be specified to indicate which to use).
"""
if (sample_stats_key is not None and
sample_stats_key not in chain_stats):
raise ValueError(
f'Specified `sample_stats_key` ({sample_stats_key}) does '
f'not match any transition in `chain_stats`.')
if sample_stats_key is not None:
return arviz.InferenceData(
posterior=arviz.dict_to_dataset(traces, library=mici),
sample_stats=arviz.dict_to_dataset(
chain_stats[sample_stats_key], library=mici))
elif not isinstance(next(iter(chain_stats.values())), dict):
# chain_stats dictionary value not another dictionary therefore
# assume corresponds to statistics for a single transition
return arviz.InferenceData(
posterior=arviz.dict_to_dataset(traces, library=mici),
sample_stats=arviz.dict_to_dataset(chain_stats, library=mici))
elif len(chain_stats) == 1:
# single transtition statistics dictionary in chain_stats therefore
# unambiguous to set sample_stats
return arviz.InferenceData(
posterior=arviz.dict_to_dataset(traces, library=mici),
sample_stats=arviz.dict_to_dataset(
chain_stats.popitem()[1], library=mici))
else:
raise ValueError(
'`sample_stats_key` must be specified as `chain_stats` '
'contains multiple transtitiion statistics dictionaries.')
def to_arviz(self, burn_in=0, thin=0):
'''Exports posterior samples as Arviz object for visualisation.'''
import arviz as az
samples = self.get_results(burn_in=burn_in, thin=thin)
nchains = len(set(samples['chain']))
nsteps = len(set(samples['iter']))
npars = len(self.par_names)
par_dict = {}
for k in self.par_names:
X = samples.pivot_table(values=k, columns='iter', index='chain').values
par_dict[k] = X
posterior = az.dict_to_dataset(par_dict)
return posterior
def sample_chains_arviz(self,
n_sample,
init_states,
chain_var_funcs=None,
sample_stats_key=None,
**kwargs):
"""Sample one or more Markov chains from given initial states.
Performs a specified number of chain iterations (each of which may
be composed of multiple individual Markov transitions), recording
the outputs of functions of the sampled chain state after each
iteration. The chains may be run in parallel across multiple
independent processes or sequentially. Chain data is returned in an
`arviz.InferenceData` container object.
Args:
n_sample (int): Number of samples to draw per chain.
init_states (Iterable[ChainState] or Iterable[array]):
Initial chain states. Each entry can be either an array
specifying the state or a `ChainState` instance. One chain
will be run for each state in the iterable sequence.
chain_var_funcs (dict[str, callable]): Dictionary of functions
which compute the chain variables to be recorded at each
iteration, with each function being passed the current
state and returning an array corresponding to the
variable(s) to be stored. The keys to the functions are
used to index the chain variable arrays in the returned
data.
sample_stats_key (str): Key of transition to use the
recorded statistics of to populate the `sampling_stats`
group in the returned `InferenceData` object.
Kwargs:
n_process (int or None): Number of parallel processes to run
chains over. If set to one then chains will be run
sequentially in otherwise a `multiprocessing.Pool` object
will be used to dynamically assign the chains across
multiple processes. If set to `None` then the number of
processes will default to the output of `os.cpu_count()`.
memmap_enabled (bool): Whether to memory-map arrays used to
store chain data to files on disk to avoid excessive system
memory usage for long chains and/or high memory chain
states. The chain data is written to `.npy` files in the
directory specified by `memmap_path` (or a temporary
directory if not provided). These files persist after the
termination of the function so should be manually deleted
when no longer required.
memmap_path (str): Path to directory to write memory-mapped
chain data to. If not provided, a temporary directory will
be created and the chain data written to files there.
Returns:
arvix.InferenceData:
An arviz data container with groups `posterior` and
'sample_stats', both of instances of `xarray.Dataset`.
The `posterior` group corresponds to the chain variable
samples computed using the `chain_var_funcs` entries (with
the data variable keys corresponding to the keys there).
The `sample_stats` group corresponds to the statistics of
the transition indicated by the `sample_stats_key`
argument.
"""
if (sample_stats_key is not None
and sample_stats_key not in self.transitions):
raise ValueError(
f'Specified `sample_stats_key` ({sample_stats_key}) does '
f'not match any transition.')
chains, chain_stats = self.sample_chains(n_sample, init_states,
chain_var_funcs, **kwargs)
if sample_stats_key is None:
return arviz.InferenceData(
posterior=arviz.dict_to_dataset(chains, library=hmc))
else:
return arviz.InferenceData(posterior=arviz.dict_to_dataset(
chains, library=hmc),
sample_stats=arviz.dict_to_dataset(
chain_stats[sample_stats_key],
library=hmc))
def sample_chains_arviz(self, n_sample, init_states,
chain_var_funcs=None, **kwargs):
"""Sample one or more Markov chains from given initial states.
Performs a specified number of chain iterations (each of which may
be composed of multiple individual Markov transitions), recording
the outputs of functions of the sampled chain state after each
iteration. The chains may be run in parallel across multiple
independent processes or sequentially. Chain data is returned in an
`arviz.InferenceData` container object.
Args:
n_sample (int): Number of samples to draw per chain.
init_states (Iterable[HamiltonianState] or Iterable[array]):
Initial chain states. Each state can be either an array
specifying the state position component or a
`HamiltonianState` instance. If an array is passed or the
`mom` attribute of the state is not set, a momentum
component will be independently sampled from its conditional
distribution. One chain will be run for each state in the
iterable sequence.
chain_var_funcs (dict[str, callable]): Dictionary of functions
which compute the chain variables to be recorded at each
iteration, with each function being passed the current state
and returning an array corresponding to the variable(s) to
be stored. By default (or if set to `None`) a single
function which returns the position component of the state
is used. The keys to the functions are used to index the
chain variable arrays in the returned data.
Kwargs:
n_process (int or None): Number of parallel processes to run
chains over. If set to one then chains will be run
sequentially in otherwise a `multiprocessing.Pool` object
will be used to dynamically assign the chains across
multiple processes. If set to `None` then the number of
processes will default to the output of `os.cpu_count()`.
memmap_enabled (bool): Whether to memory-map arrays used to
store chain data to files on disk to avoid excessive system
memory usage for long chains and/or high memory chain
states. The chain data is written to `.npy` files in the
directory specified by `memmap_path` (or a temporary
directory if not provided). These files persist after the
termination of the function so should be manually deleted
when no longer required.
memmap_path (str): Path to directory to write memory-mapped
chain data to. If not provided, a temporary directory will
be created and the chain data written to files there.
Returns:
arvix.InferenceData:
An arviz data container with groups `posterior` and
'sample_stats', both of instances of `xarray.Dataset`.
The `posterior` group corresponds to the chain variable
samples computed using the `chain_var_funcs` entries (with
the data variable keys corresponding to the keys there).
The `sample_stats` group corresponds to the statistics of
the integration transition such as the acceptance
probabilities and number of integrator steps.
"""
chains, chain_stats = self.sample_chains(
n_sample, init_states, chain_var_funcs, **kwargs)
return arviz.InferenceData(
posterior=arviz.dict_to_dataset(chains, library=hmc),
sample_stats=arviz.dict_to_dataset(chain_stats, library=hmc))