def __init__(self, command_line, path):
"""
The Data class holds the cosmological information, the parameters from
the MCMC run, the information coming from the likelihoods. It is a wide
collections of information, with in particular two main dictionaries:
cosmo_arguments and mcmc_parameters.
It defines several useful **methods**. The following ones are called
just once, at initialization:
* :func:`fill_mcmc_parameters`
* :func:`read_file`
* :func:`read_version`
* :func:`group_parameters_in_blocks`
On the other hand, these two following functions are called every step.
* :func:`check_for_slow_step`
* :func:`update_cosmo_arguments`
Finally, the convenient method :func:`get_mcmc_parameters` will be
called in many places, to return the proper list of desired parameters.
It has a number of different **attributes**, and the more important
ones are listed here:
* :attr:`boundary_loglike`
* :attr:`cosmo_arguments`
* :attr:`mcmc_parameters`
* :attr:`need_cosmo_update`
* :attr:`log_flag`
.. note::
The `experiments` attribute is extracted from the parameter file,
and contains the list of likelihoods to use
.. note::
The path argument will be used in case it is a first run, and hence
a new folder is created. If starting from an existing folder, this
dictionary will be compared with the one extracted from the
log.param, and will use the latter while warning the user.
.. warning::
New in version 2.0.0, you can now specify an oversampling of the
nuisance parameters, to hasten the execution of a run with
likelihoods that have many of them. You should specify a new field
in the parameter file, `data.over_sampling = [1, ...]`, that
contains a 1 on the first element, and then the over sampling of
the desired likelihoods. This array must have the same size as the
number of blocks (1 for the cosmo + 1 for each likelihood with
varying nuisance parameters). You need to call the code with the
flag `-j jast` for it to be used.
To create an instance of this class, one must feed the following
parameters and keyword arguments:
Parameters
----------
command_line : NameSpace
NameSpace containing the input from the :mod:`parser_mp`. It
stores the input parameter file, the jumping methods, the output
folder, etc... Most of the information extracted from the
command_file will be transformed into :class:`Data` attributes,
whenever it felt meaningful to do so.
path : dict
Contains a dictionary of important local paths. It is used here to
find the cosmological module location.
"""
# Initialisation of the random seed
rd.seed()
# Store the parameter file
self.param = command_line.param
# Recover jumping method from command_line
self.jumping = command_line.jumping
self.jumping_factor = command_line.jumping_factor
# Store the rest of the command line
self.command_line = command_line
# Initialise the path dictionnary.
self.path = {}
self.boundary_loglike = -1e30
"""
Define the boundary loglike, the value used to defined a loglike
that is out of bounds. If a point in the parameter space is affected to
this value, it will be automatically rejected, hence increasing the
multiplicity of the last accepted point.
"""
# Creation of the two main dictionnaries:
self.cosmo_arguments = {}
"""
Simple dictionary that will serve as a communication interface with the
cosmological code. It contains all the parameters for the code that
will not be set to their default values. It is updated from
:attr:`mcmc_parameters`.
:rtype: dict
"""
self.mcmc_parameters = od()
"""
Ordered dictionary of dictionaries, it contains everything needed by
the :mod:`mcmc` module for the MCMC procedure. Every parameter name
will be the key of a dictionary, containing the initial configuration,
role, status, last accepted point and current point.
:rtype: ordereddict
"""
# Arguments for PyMultiNest
self.NS_param_names = []
self.NS_arguments = {}
"""
Dictionary containing the parameters needed by the PyMultiNest sampler.
It is filled just before the run of the sampler. Those parameters not
defined will be set to the default value of PyMultiNest.
:rtype: dict
"""
# Initialise the experiments attribute
self.experiments = []
# Initialise the oversampling setting
self.over_sampling = []
"""
List storing the respective over sampling of the parameters. The first
entry, applied to the cosmological parameters, will always be 1.
Setting it to anything else would simply rescale the whole process. If
not specified otherwise in the parameter file, all other numbers will
be set to 1 as well.
:rtype: list
"""
# Default value for the number of steps
self.N = 10
# Create the variable out, and out_name, which will be initialised
# later by the :mod:`io_mp` module
self.out = None
self.out_name = ''
# If the parameter file is not a log.param, the path will be read
# before reading the parameter file.
if self.param.find('log.param') == -1:
self.path.update(path)
# Read from the parameter file to fill properly the mcmc_parameters
# dictionary.
self.fill_mcmc_parameters()
# Test if the recovered path agrees with the one extracted from
# the configuration file.
if self.path != {}:
if not self.path.has_key('root'):
self.path.update({'root': path['root']})
if self.path != path:
warnings.warn("Your code location in the log.param file is "
"in contradiction with your .conf file. "
"I will use the one from log.param.")
# Determine which cosmological code is in use
if self.path['cosmo'].find('class') != -1:
self.cosmological_module_name = 'CLASS'
else:
self.cosmological_module_name = None
# check for MPI
try:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
except ImportError:
# set all chains to master if no MPI
rank = 0
# Recover the cosmological code version (and git hash if relevant).
# To implement a new cosmological code, please add another case to the
# test below.
if self.cosmological_module_name == 'CLASS':
# Official version number
common_file_path = os.path.join(self.path['cosmo'], 'include',
'common.h')
with open(common_file_path, 'r') as common_file:
for line in common_file:
if line.find('_VERSION_') != -1:
self.version = line.split()[-1].replace('"', '')
break
if not command_line.silent and not rank:
print 'with CLASS %s' % self.version
# Git version number and branch
try:
# This nul_file helps to get read of a potential useless error
# message
with open(os.devnull, "w") as nul_file:
self.git_version = sp.Popen(
["git", "rev-parse", "HEAD"],
cwd=self.path['cosmo'],
stdout=sp.PIPE,
stderr=nul_file).communicate()[0].strip()
self.git_branch = sp.Popen(
["git", "rev-parse", "--abbrev-ref", "HEAD"],
cwd=self.path['cosmo'],
stdout=sp.PIPE,
stderr=nul_file).communicate()[0].strip()
except (sp.CalledProcessError, OSError):
# Note, OSError seems to be raised on some systems, instead of
# sp.CalledProcessError - which seems to be linked to the
# existence of os.devnull, so now both error are caught.
warnings.warn(
"Running CLASS from a non version-controlled repository")
self.git_version, self.git_branch = '', ''
# If using an existing log.param, read in and compare this number
# to the already stored one
if self.param.find('log.param') != -1:
try:
version, git_version, git_branch = self.read_version(
self.param_file)
if version != self.version:
warnings.warn(
"Your version of CLASS: %s" % self.version +
" does not match the one used previously" +
" in this folder (%s)." % version +
" Proceed with caution")
else:
if self.git_branch != git_branch:
warnings.warn(
"CLASS set to branch %s" % self.git_branch +
", wrt. the one used in the log.param:" +
" %s." % git_branch)
if self.git_version != git_version:
warnings.warn(
"CLASS set to version %s" % self.git_version +
", wrt. the one used in the log.param:" +
" %s." % git_version)
except AttributeError:
# This error is raised when the regular expression match
# failed - due to comparing to an old log.param that did
# not have this feature properly implemented. Ignore this.
pass
else:
raise io_mp.CosmologicalModuleError(
"If you want to check for another cosmological module version"
" please add an elif clause to this part")
# End of initialisation with the parameter file
self.param_file.close()
self.log_flag = False
"""
Stores the information whether or not the likelihood data files need to
be written down in the log.param file. Initially at False.
:rtype: bool
"""
self.need_cosmo_update = True
"""
`added in version 1.1.1`. It stores the truth value of whether the
cosmological block of parameters was changed from one step to another.
See :meth:`group_parameters_in_blocks`
:rtype: bool
"""
# logging the parameter file (only if folder does not exist !)
## temporary variable for readability
log_param = os.path.join(command_line.folder, 'log.param')
if (os.path.exists(command_line.folder)
and not os.path.exists(log_param)):
if command_line.param is not None:
warnings.warn(
"Detecting empty folder, logging the parameter file")
io_mp.log_parameters(self, command_line)
self.log_flag = True
if not os.path.exists(command_line.folder):
os.makedirs(command_line.folder)
# Logging of parameters
io_mp.log_parameters(self, command_line)
self.log_flag = True
if not command_line.silent and not rank:
print '\nTesting likelihoods for:\n ->',
print ', '.join(self.experiments) + '\n'
self.initialise_likelihoods(self.experiments)
# Storing parameters by blocks of speed
self.group_parameters_in_blocks()
# Finally, log the cosmo_arguments used. This comes in the end, because
# it can be modified inside the likelihoods init functions
if self.log_flag:
io_mp.log_cosmo_arguments(self, command_line)
io_mp.log_default_configuration(self, command_line)
# Log plotting parameter names file for compatibility with GetDist
io_mp.log_parameter_names(self, command_line)
def compute_lkl(cosmo, data):
"""
Compute the likelihood, given the current point in parameter space.
This function now performs a test before calling the cosmological model
(**new in version 1.2**). If any cosmological parameter changed, the flag
:code:`data.need_cosmo_update` will be set to :code:`True`, from the
routine :func:`check_for_slow_step <data.Data.check_for_slow_step>`.
Returns
-------
loglike : float
The log of the likelihood (:math:`\\frac{-\chi^2}2`) computed from the
sum of the likelihoods of the experiments specified in the input
parameter file.
This function returns :attr:`data.boundary_loglkie
<data.data.boundary_loglike>`, defined in the module :mod:`data` if
*i)* the current point in the parameter space has hit a prior edge, or
*ii)* the cosmological module failed to compute the model. This value
is chosen to be extremly small (large negative value), so that the step
will always be rejected.
"""
from classy import CosmoSevereError, CosmoComputationError
# If the cosmological module has already been called once, and if the
# cosmological parameters have changed, then clean up, and compute.
if cosmo.state and data.need_cosmo_update is True:
cosmo.struct_cleanup()
# If the data needs to change, then do a normal call to the cosmological
# compute function. Note that, even if need_cosmo update is True, this
# function must be called if the jumping factor is set to zero. Indeed,
# this means the code is called for only one point, to set the fiducial
# model.
if ((data.need_cosmo_update) or (not cosmo.state)
or (data.jumping_factor == 0)):
# Prepare the cosmological module with the new set of parameters
cosmo.set(data.cosmo_arguments)
# Compute the model, keeping track of the errors
# In classy.pyx, we made use of two type of python errors, to handle
# two different situations.
# - CosmoSevereError is returned if a parameter was not properly set
# during the initialisation (for instance, you entered Ommega_cdm
# instead of Omega_cdm). Then, the code exits, to prevent running with
# imaginary parameters. This behaviour is also used in case you want to
# kill the process.
# - CosmoComputationError is returned if Class fails to compute the
# output given the parameter values. This will be considered as a valid
# point, but with minimum likelihood, so will be rejected, resulting in
# the choice of a new point.
try:
cosmo.compute(["lensing"])
except CosmoComputationError as failure_message:
sys.stderr.write(str(failure_message) + '\n')
sys.stderr.flush()
return data.boundary_loglike
except CosmoSevereError as critical_message:
raise io_mp.CosmologicalModuleError(
"Something went wrong when calling CLASS" +
str(critical_message))
except KeyboardInterrupt:
raise io_mp.CosmologicalModuleError("You interrupted execution")
# For each desired likelihood, compute its value against the theoretical
# model
loglike = 0
# This flag holds the information whether a fiducial model was written. In
# this case, the log likelihood returned will be '1j', meaning the
# imaginary number i.
flag_wrote_fiducial = 0
for likelihood in data.lkl.itervalues():
if likelihood.need_update is True:
value = likelihood.loglkl(cosmo, data)
# Storing the result
likelihood.backup_value = value
# Otherwise, take the existing value
else:
value = likelihood.backup_value
loglike += value
# In case the fiducial file was written, store this information
if value == 1j:
flag_wrote_fiducial += 1
# Compute the derived parameters if relevant
if data.get_mcmc_parameters(['derived']) != []:
try:
derived = cosmo.get_current_derived_parameters(
data.get_mcmc_parameters(['derived']))
for name, value in derived.iteritems():
data.mcmc_parameters[name]['current'] = value
except AttributeError:
# This happens if the classy wrapper is still using the old
# convention, expecting data as the input parameter
cosmo.get_current_derived_parameters(data)
except CosmoSevereError:
raise io_mp.CosmologicalModuleError(
"Could not write the current derived parameters")
for elem in data.get_mcmc_parameters(['derived']):
data.mcmc_parameters[elem]['current'] /= \
data.mcmc_parameters[elem]['scale']
# If fiducial files were created, inform the user, and exit
if flag_wrote_fiducial > 0:
if flag_wrote_fiducial == len(data.lkl):
raise io_mp.FiducialModelWritten(
"Fiducial file(s) was(were) created, please start a new chain")
else:
raise io_mp.FiducialModelWritten(
"Some previously non-existing fiducial files were created, " +
"but potentially not all of them. Please check now manually" +
" on the headers, of the corresponding that all parameters " +
"are coherent for your tested models")
return loglike