Sampler
- class orbitize.sampler.MCMC(system, num_temps=20, num_walkers=1000, num_threads=1, chi2_type='standard', like='chi2_lnlike', custom_lnlike=None, prev_result_filename=None)[source]
MCMC sampler. Supports either parallel tempering or just regular MCMC. Parallel tempering will be run if
num_temps
> 1 Parallel-Tempered MCMC Sampler uses ptemcee, a fork of the emcee Affine-infariant sampler Affine-Invariant Ensemble MCMC Sampler uses emcee.Warning
may not work well for multi-modal distributions
- Parameters
system (system.System) – system.System object
num_temps (int) – number of temperatures to run the sampler at. Parallel tempering will be used if num_temps > 1 (default=20)
num_walkers (int) – number of walkers at each temperature (default=1000)
num_threads (int) – number of threads to use for parallelization (default=1)
chi2_type (str, optional) – either “standard”, or “log”
like (str) – name of likelihood function in
lnlike.py
custom_lnlike (func) – ability to include an addition custom likelihood function in the fit. The function looks like
clnlikes = custon_lnlike(params)
whereparams
is a RxM array of fitting parameters, where R is the number of orbital paramters (can be passed in system.compute_model()), and M is the number of orbits we need model predictions for. It returnsclnlikes
which is an array of length M, or it can be a single float if M = 1.prev_result_filename (str) – if passed a filename to an HDF5 file containing a orbitize.Result data, MCMC will restart from where it left off.
Written: Jason Wang, Henry Ngo, 2018
- check_prior_support()[source]
Review the positions of all MCMC walkers, to verify that they are supported by the prior space. This function will raise a descriptive ValueError if any positions lie outside prior support. Otherwise, it will return nothing.
(written): Adam Smith, 2021
- chop_chains(burn, trim=0)[source]
Permanently removes steps from beginning (and/or end) of chains from the Results object. Also updates curr_pos if steps are removed from the end of the chain.
- Parameters
burn (int) – The number of steps to remove from the beginning of the chains
trim (int) – The number of steps to remove from the end of the chians (optional)
Warning
Does not update bookkeeping arrays within MCMC sampler object.
(written): Henry Ngo, 2019
- examine_chains(param_list=None, walker_list=None, n_walkers=None, step_range=None, transparency=1)[source]
Plots position of walkers at each step from Results object. Returns list of figures, one per parameter :param param_list: List of strings of parameters to plot (e.g. “sma1”)
If None (default), all parameters are plotted
- Parameters
walker_list – List or array of walker numbers to plot If None (default), all walkers are plotted
n_walkers (int) – Randomly select n_walkers to plot Overrides walker_list if this is set If None (default), walkers selected as per walker_list
step_range (array or tuple) – Start and end values of step numbers to plot If None (default), all the steps are plotted
transparency (int or float) – Determines visibility of the plotted function If 1 (default) results plot at 100% opacity
- Returns
Walker position plot for each parameter selected
- Return type
List of
matplotlib.pyplot.Figure
objects
(written): Henry Ngo, 2019
- run_sampler(total_orbits, burn_steps=0, thin=1, examine_chains=False, output_filename=None, periodic_save_freq=None)[source]
Runs PT MCMC sampler. Results are stored in
self.chain
andself.lnlikes
. Results also added toorbitize.results.Results
object (self.results
)Note
Can be run multiple times if you want to pause and inspect things. Each call will continue from the end state of the last execution.
- Parameters
total_orbits (int) – total number of accepted possible orbits that are desired. This equals
num_steps_per_walker
xnum_walkers
burn_steps (int) – optional paramter to tell sampler to discard certain number of steps at the beginning
thin (int) – factor to thin the steps of each walker by to remove correlations in the walker steps
examine_chains (boolean) – Displays plots of walkers at each step by running examine_chains after total_orbits sampled.
output_filename (str) – Optional filepath for where results file can be saved.
periodic_save_freq (int) – Optionally, save the current results into
output_filename
every nth step while running, where n is value passed into this variable.
- Returns
the sampler used to run the MCMC
- Return type
emcee.sampler
object
- class orbitize.sampler.NestedSampler(system)[source]
Implements nested sampling using Dynesty package.
Thea McKenna, Sarah Blunt, & Lea Hirsch 2024
- ptform(u)[source]
Prior transform function.
- Parameters
u (array of floats) – list of samples with values 0 < u < 1.
- Returns
- 1D u samples transformed to a chosen Prior
Class distribution.
- Return type
numpy array of floats
- run_sampler(static=False, bound='multi', pfrac=1.0, num_threads=1, start_method='fork', run_nested_kwargs={})[source]
Runs the nested sampler from the Dynesty package.
- Parameters
static (bool) – True if using static nested sampling, False if using dynamic.
bound (str) – Method used to approximately bound the prior using the current set of live points. Conditions the sampling methods used to propose new live points. See https://dynesty.readthedocs.io/en/latest/quickstart.html#bounding-options for complete list of options.
pfrac (float) – posterior weight, between 0 and 1. Can only be altered for the Dynamic nested sampler, otherwise this keyword is unused.
num_threads (int) – number of threads to use for parallelization (default=1)
start_method (str) – multiprocessing start method. Default “fork,” which won’t work on all OS. Change to “spawn” if you get an error, and make sure you run your orbitize! script inside an if __name__==’__main__’ condition to protect entry points.
run_nested_kwargs (dict) – dictionary of keywords to be passed into dynesty.Sampler.run_nested()
- Returns
numpy.array of float: posterior samples
int: number of iterations it took to converge
- Return type
tuple
- class orbitize.sampler.OFTI(system, like='chi2_lnlike', custom_lnlike=None, chi2_type='standard')[source]
OFTI Sampler
- Parameters
system (system.System) –
system.System
objectlike (string) – name of likelihood function in
lnlike.py
custom_lnlike (func) – ability to include an addition custom likelihood function in the fit. The function looks like
clnlikes = custon_lnlike(params)
whereparams
is a RxM array of fitting parameters, where R is the number of orbital paramters (can be passed in system.compute_model()), and M is the number of orbits we need model predictions for. It returnsclnlikes
which is an array of length M, or it can be a single float if M = 1.
Written: Isabel Angelo, Sarah Blunt, Logan Pearce, 2018
- prepare_samples(num_samples)[source]
Prepare some orbits for rejection sampling. This draws random orbits from priors, and performs scale & rotate.
- Parameters
num_samples (int) – number of orbits to draw and scale & rotate for OFTI to run rejection sampling on
- Returns
array of prepared samples. The first dimension has size of num_samples. This should be passed into
OFTI.reject()
- Return type
np.array
- reject(samples)[source]
Runs rejection sampling on some prepared samples.
- Parameters
samples (np.array) – array of prepared samples. The first dimension has size
num_samples
. This should be the output ofprepare_samples()
.- Returns
np.array: a subset of
samples
that are accepted based on the data.np.array: the log likelihood values of the accepted orbits.
- Return type
tuple
- run_sampler(total_orbits, num_samples=10000, num_cores=None, OFTI_warning=60.0)[source]
Runs OFTI in parallel on multiple cores until we get the number of total accepted orbits we want.
- Parameters
total_orbits (int) – total number of accepted orbits desired by user
num_samples (int) – number of orbits to prepare for OFTI to run rejection sampling on. Defaults to 10000.
num_cores (int) – the number of cores to run OFTI on. Defaults to number of cores availabe.
OFTI_warning (float) – if OFTI doesn’t accept a single orbit before this amount of time (in seconds), print a warning suggesting to try MCMC. If None, don’t print a warning.
- Returns
array of accepted orbits. Size: total_orbits.
- Return type
np.array
Written by: Vighnesh Nagpal(2019)