class KineticsSubcommands(WESTSubcommand):
'''Base class for common options for both kinetics schemes'''
def __init__(self, parent):
super(KineticsSubcommands, self).__init__(parent)
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_file = None
self.assignments_file = None
self.do_compression = True
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument(
'-a',
'--assignments',
default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
# default_kinetics_file will be picked up as a class attribute from the appropriate
# subclass
iogroup.add_argument(
'-o',
'--output',
dest='output',
default=self.default_kinetics_file,
help='''Store results in OUTPUT (default: %(default)s).''')
iogroup.add_argument(
'--no-compression',
dest='compression',
action='store_false',
help=
'''Do not store kinetics results compressed. This can increase disk
use about 100-fold, but can dramatically speed up subsequent analysis
for "w_kinavg matrix". Default: compress kinetics results.'''
)
self.progress.add_args(parser)
parser.set_defaults(compression=True)
def process_args(self, args):
self.progress.process_args(args)
self.assignments_file = h5io.WESTPAH5File(args.assignments, 'r')
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
self.output_file = h5io.WESTPAH5File(args.output,
'w',
creating_program=True)
h5io.stamp_creator_data(self.output_file)
if not self.iter_range.check_data_iter_range_least(
self.assignments_file):
raise ValueError(
'assignments do not span the requested iterations')
self.do_compression = args.compression
def __init__(self):
super(WNetworker, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.tm_filename = None
self.postprocess_function = None
def __init__(self, parent):
super(KineticsSubcommands, self).__init__(parent)
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_file = None
self.assignments_file = None
self.do_compression = True
def __init__(self):
super(WCrawl,self).__init__()
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection(self.data_reader)
self.crawler = None
self.task_callable = None
class WESTKineticsBase(WESTSubcommand):
'''
Common argument processing for w_direct/w_reweight subcommands.
Mostly limited to handling input and output from w_assign.
'''
def __init__(self, parent):
super(WESTKineticsBase,self).__init__(parent)
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
# This is actually applicable to both.
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
# Now we're adding in things that come from the old w_kinetics
self.do_compression = True
def add_args(self, parser):
self.progress.add_args(parser)
self.data_reader.add_args(parser)
self.iter_range.include_args['iter_step'] = True
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument('-a', '--assignments', default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
iogroup.add_argument('-o', '--output', dest='output', default=self.default_output_file,
help='''Store results in OUTPUT (default: %(default)s).''')
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(1, (self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
class WESTKineticsBase(WESTSubcommand):
'''
Common argument processing for w_direct/w_reweight subcommands.
Mostly limited to handling input and output from w_assign.
'''
def __init__(self, parent):
super(WESTKineticsBase,self).__init__(parent)
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
# This is actually applicable to both.
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
# Now we're adding in things that come from the old w_kinetics
self.do_compression = True
def add_args(self, parser):
self.progress.add_args(parser)
self.data_reader.add_args(parser)
self.iter_range.include_args['iter_step'] = True
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument('-a', '--assignments', default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
iogroup.add_argument('-o', '--output', dest='output', default=self.default_output_file,
help='''Store results in OUTPUT (default: %(default)s).''')
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(1, (self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
def __init__(self):
super(WSelectTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.output_filename = None
self.predicate = None
self.invert = False
self.include_ancestors = False
def __init__(self):
super(WNTopTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.assignments_filename = None
self.output_filename = None
self.what = None
self.timepoint = None
self.count = None
def __init__(self):
super(WFluxanlTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_h5file = None
self.output_group = None
self.target_groups = {}
self.fluxdata = {}
self.alpha = None
self.autocorrel_alpha = None
self.n_sets = None
self.do_evol = False
self.evol_step = 1
def __init__(self):
super(WPDist,self).__init__()
# Parallel processing by default (this is not actually necessary, but it is
# informative!)
self.wm_env.default_work_manager = self.wm_env.default_parallel_work_manager
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.input_dssynth = WESTDSSynthesizer(default_dsname='pcoord')
self.iter_range = IterRangeSelection(self.data_reader)
self.iter_range.include_args['iter_step'] = False
self.binspec = None
self.output_filename = None
self.output_file = None
self.dsspec = None
self.wt_dsspec = None # dsspec for weights
# These are used during histogram generation only
self.iter_start = None
self.iter_stop = None
self.ndim = None
self.ntimepoints = None
self.dset_dtype = None
self.binbounds = None # bin boundaries for each dimension
self.midpoints = None # bin midpoints for each dimension
self.data_range = None # data range for each dimension, as the pairs (min,max)
self.ignore_out_of_range = False
self.compress_output = False
def __init__(self):
super(WPostAnalysisReweightTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.kinetics_file = None
self.evolution_mode = None
def __init__(self):
super(StateProbTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
def __init__(self, parent):
super(KineticsSubcommands,self).__init__(parent)
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_file = None
self.assignments_file = None
self.do_compression = True
def __init__(self):
super(WCrawl,self).__init__()
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection(self.data_reader)
self.crawler = None
self.task_callable = None
class KineticsSubcommands(WESTSubcommand):
'''Base class for common options for both kinetics schemes'''
def __init__(self, parent):
super(KineticsSubcommands,self).__init__(parent)
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_file = None
self.assignments_file = None
self.do_compression = True
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument('-a', '--assignments', default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
# default_kinetics_file will be picked up as a class attribute from the appropriate
# subclass
iogroup.add_argument('-o', '--output', dest='output', default=self.default_kinetics_file,
help='''Store results in OUTPUT (default: %(default)s).''')
iogroup.add_argument('--no-compression', dest='compression', action='store_false',
help='''Do not store kinetics results compressed. This can increase disk
use about 100-fold, but can dramatically speed up subsequent analysis
for "w_kinavg matrix". Default: compress kinetics results.''')
self.progress.add_args(parser)
parser.set_defaults(compression=True)
def process_args(self, args):
self.progress.process_args(args)
self.assignments_file = h5io.WESTPAH5File(args.assignments, 'r')
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
self.output_file = h5io.WESTPAH5File(args.output, 'w', creating_program=True)
h5io.stamp_creator_data(self.output_file)
if not self.iter_range.check_data_iter_range_least(self.assignments_file):
raise ValueError('assignments do not span the requested iterations')
self.do_compression = args.compression
def __init__(self):
super(WSelectTool,self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.output_filename = None
self.predicate = None
self.invert = False
self.include_ancestors = False
def __init__(self):
super(WNTopTool,self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.assignments_filename = None
self.output_filename = None
self.what = None
self.timepoint = None
self.count = None
def __init__(self, parent):
super(WESTKineticsBase,self).__init__(parent)
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
# This is actually applicable to both.
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
# Now we're adding in things that come from the old w_kinetics
self.do_compression = True
def __init__(self):
super(WFluxanlTool,self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_h5file = None
self.output_group = None
self.target_groups = {}
self.fluxdata = {}
self.alpha = None
self.autocorrel_alpha = None
self.n_sets = None
self.do_evol = False
self.evol_step = 1
def __init__(self):
super(WPostAnalysisReweightTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.kinetics_file = None
self.evolution_mode = None
def __init__(self):
super(StateProbTool,self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
def __init__(self, parent):
super(WESTKineticsBase,self).__init__(parent)
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
# This is actually applicable to both.
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
# Now we're adding in things that come from the old w_kinetics
self.do_compression = True
class WPostAnalysisReweightTool(WESTTool):
prog = 'w_postanalysis_reweight'
description = '''\
Calculate average rates from weighted ensemble data using the postanalysis
reweighting scheme. Bin assignments (usually "assignments.h5") and pre-calculated
iteration flux matrices (usually "flux_matrices.h5") data files must have been
previously generated using w_postanalysis_matrix.py (see "w_assign --help" and
"w_kinetics --help" for information on generating these files).
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, usually "kinrw.h5") contains the following
dataset:
/state_prob_evolution [window,state]
The reweighted state populations based on windows
/color_prob_evolution [window,state]
The reweighted populations last assigned to each state based on windows
/bin_prob_evolution [window, bin]
The reweighted populations of each bin based on windows. Bins contain
one color each, so to recover the original un-colored spatial bins,
one must sum over all states.
/conditional_flux_evolution [window,state,state]
(Structured -- see below). State-to-state fluxes based on windows of
varying width
The structure of the final dataset is as follows:
iter_start
(Integer) Iteration at which the averaging window begins (inclusive).
iter_stop
(Integer) Iteration at which the averaging window ends (exclusive).
expected
(Floating-point) Expected (mean) value of the rate as evaluated within
this window, in units of inverse tau.
-----------------------------------------------------------------------------
Command-line options
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WPostAnalysisReweightTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.kinetics_file = None
self.evolution_mode = None
def add_args(self, parser):
self.progress.add_args(parser)
self.data_reader.add_args(parser)
self.iter_range.include_args['iter_step'] = True
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument(
'-a',
'--assignments',
default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
iogroup.add_argument(
'-k',
'--kinetics',
default='flux_matrices.h5',
help=
'''Per-iteration flux matrices calculated by w_postanalysis_matrix
(default: %(default)s).''')
iogroup.add_argument(
'-o',
'--output',
dest='output',
default='kinrw.h5',
help='''Store results in OUTPUT (default: %(default)s).''')
cogroup = parser.add_argument_group('calculation options')
cogroup.add_argument(
'-e',
'--evolution-mode',
choices=['cumulative', 'blocked'],
default='cumulative',
help='''How to calculate time evolution of rate estimates.
``cumulative`` evaluates rates over windows starting with --start-iter and getting progressively
wider to --stop-iter by steps of --step-iter.
``blocked`` evaluates rates over windows of width --step-iter, the first of which begins at
--start-iter.''')
cogroup.add_argument(
'--window-frac',
type=float,
default=1.0,
help=
'''Fraction of iterations to use in each window when running in ``cumulative`` mode.
The (1 - frac) fraction of iterations will be discarded from the start of each window.'''
)
cogroup.add_argument(
'--obs-threshold',
type=int,
default=1,
help=
'''The minimum number of observed transitions between two states i and j necessary to include
fluxes in the reweighting estimate''')
def open_files(self):
self.output_file = h5io.WESTPAH5File(self.output_filename,
'w',
creating_program=True)
h5io.stamp_creator_data(self.output_file)
self.assignments_file = h5io.WESTPAH5File(
self.assignments_filename,
'r') #, driver='core', backing_store=False)
self.kinetics_file = h5io.WESTPAH5File(
self.kinetics_filename,
'r') #, driver='core', backing_store=False)
if not self.iter_range.check_data_iter_range_least(
self.assignments_file):
raise ValueError(
'assignments data do not span the requested iterations')
if not self.iter_range.check_data_iter_range_least(self.kinetics_file):
raise ValueError(
'kinetics data do not span the requested iterations')
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(
1,
(self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.kinetics_filename = args.kinetics
self.evolution_mode = args.evolution_mode
self.evol_window_frac = args.window_frac
if self.evol_window_frac <= 0 or self.evol_window_frac > 1:
raise ValueError(
'Parameter error -- fractional window defined by --window-frac must be in (0,1]'
)
self.obs_threshold = args.obs_threshold
def go(self):
pi = self.progress.indicator
with pi:
pi.new_operation('Initializing')
self.open_files()
nstates = self.assignments_file.attrs['nstates']
nbins = self.assignments_file.attrs['nbins']
state_labels = self.assignments_file['state_labels'][...]
state_map = self.assignments_file['state_map'][...]
nfbins = self.kinetics_file.attrs['nrows']
npts = self.kinetics_file.attrs['npts']
assert nstates == len(state_labels)
assert nfbins == nbins * nstates
start_iter, stop_iter, step_iter = self.iter_range.iter_start, self.iter_range.iter_stop, self.iter_range.iter_step
start_pts = range(start_iter, stop_iter, step_iter)
flux_evol = np.zeros((len(start_pts), nstates, nstates),
dtype=ci_dtype)
color_prob_evol = np.zeros((len(start_pts), nstates))
state_prob_evol = np.zeros((len(start_pts), nstates))
bin_prob_evol = np.zeros((len(start_pts), nfbins))
pi.new_operation('Calculating flux evolution', len(start_pts))
if self.evolution_mode == 'cumulative' and self.evol_window_frac == 1.0:
print('Using fast streaming accumulation')
total_fluxes = np.zeros((nfbins, nfbins), weight_dtype)
total_obs = np.zeros((nfbins, nfbins), np.int64)
for iblock, start in enumerate(start_pts):
pi.progress += 1
stop = min(start + step_iter, stop_iter)
params = dict(start=start,
stop=stop,
nstates=nstates,
nbins=nbins,
state_labels=state_labels,
state_map=state_map,
nfbins=nfbins,
total_fluxes=total_fluxes,
total_obs=total_obs,
h5file=self.kinetics_file,
obs_threshold=self.obs_threshold)
rw_state_flux, rw_color_probs, rw_state_probs, rw_bin_probs, rw_bin_flux = reweight(
**params)
for k in xrange(nstates):
for j in xrange(nstates):
# Normalize such that we report the flux per tau (tau being the weighted ensemble iteration)
# npts always includes a 0th time point
flux_evol[iblock]['expected'][
k, j] = rw_state_flux[k, j] * (npts - 1)
flux_evol[iblock]['iter_start'][k, j] = start
flux_evol[iblock]['iter_stop'][k, j] = stop
color_prob_evol[iblock] = rw_color_probs
state_prob_evol[iblock] = rw_state_probs[:-1]
bin_prob_evol[iblock] = rw_bin_probs
else:
for iblock, start in enumerate(start_pts):
pi.progress += 1
stop = min(start + step_iter, stop_iter)
if self.evolution_mode == 'cumulative':
windowsize = max(
1,
int(self.evol_window_frac * (stop - start_iter)))
block_start = max(start_iter, stop - windowsize)
else: # self.evolution_mode == 'blocked'
block_start = start
params = dict(start=block_start,
stop=stop,
nstates=nstates,
nbins=nbins,
state_labels=state_labels,
state_map=state_map,
nfbins=nfbins,
total_fluxes=None,
total_obs=None,
h5file=self.kinetics_file)
rw_state_flux, rw_color_probs, rw_state_probs, rw_bin_probs, rw_bin_flux = reweight(
**params)
for k in xrange(nstates):
for j in xrange(nstates):
# Normalize such that we report the flux per tau (tau being the weighted ensemble iteration)
# npts always includes a 0th time point
flux_evol[iblock]['expected'][
k, j] = rw_state_flux[k, j] * (npts - 1)
flux_evol[iblock]['iter_start'][k, j] = start
flux_evol[iblock]['iter_stop'][k, j] = stop
color_prob_evol[iblock] = rw_color_probs
state_prob_evol[iblock] = rw_state_probs[:-1]
bin_prob_evol[iblock] = rw_bin_probs
ds_flux_evol = self.output_file.create_dataset(
'conditional_flux_evolution',
data=flux_evol,
shuffle=True,
compression=9)
ds_state_prob_evol = self.output_file.create_dataset(
'state_prob_evolution', data=state_prob_evol, compression=9)
ds_color_prob_evol = self.output_file.create_dataset(
'color_prob_evolution', data=color_prob_evol, compression=9)
ds_bin_prob_evol = self.output_file.create_dataset(
'bin_prob_evolution', data=bin_prob_evol, compression=9)
ds_state_labels = self.output_file.create_dataset(
'state_labels', data=state_labels)
class WFluxanlTool(WESTTool):
prog = 'w_fluxanl'
description = '''\
Extract fluxes into pre-defined target states from WEST data,
average, and construct confidence intervals. Monte Carlo bootstrapping
is used to account for the correlated and possibly non-Gaussian statistical
error in flux measurements.
All non-graphical output (including that to the terminal and HDF5) assumes that
the propagation/resampling period ``tau`` is equal to unity; to obtain results
in familiar units, divide all fluxes and multiply all correlation lengths by
the true value of ``tau``.
'''
output_format_version = 2
def __init__(self):
super(WFluxanlTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_h5file = None
self.output_group = None
self.target_groups = {}
self.fluxdata = {}
self.alpha = None
self.autocorrel_alpha = None
self.n_sets = None
self.do_evol = False
self.evol_step = 1
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
ogroup = parser.add_argument_group('output options')
ogroup.add_argument(
'-o',
'--output',
default='fluxanl.h5',
help=
'Store intermediate data and analysis results to OUTPUT (default: %(default)s).'
)
cgroup = parser.add_argument_group('calculation options')
cgroup.add_argument(
'--disable-bootstrap',
'-db',
dest='bootstrap',
action='store_const',
const=False,
help='''Enable the use of Monte Carlo Block Bootstrapping.''')
cgroup.add_argument('--disable-correl',
'-dc',
dest='correl',
action='store_const',
const=False,
help='''Disable the correlation analysis.''')
cgroup.add_argument(
'-a',
'--alpha',
type=float,
default=0.05,
help=
'''Calculate a (1-ALPHA) confidence interval on the average flux'
(default: %(default)s)''')
cgroup.add_argument(
'--autocorrel-alpha',
type=float,
dest='acalpha',
metavar='ACALPHA',
help='''Evaluate autocorrelation of flux to (1-ACALPHA) significance.
Note that too small an ACALPHA will result in failure to detect autocorrelation
in a noisy flux signal. (Default: same as ALPHA.)'''
)
cgroup.add_argument(
'-N',
'--nsets',
type=int,
help=
'''Use NSETS samples for bootstrapping (default: chosen based on ALPHA)'''
)
cgroup.add_argument(
'--evol',
action='store_true',
dest='do_evol',
help=
'''Calculate time evolution of flux confidence intervals (expensive).'''
)
cgroup.add_argument(
'--evol-step',
type=int,
default=1,
metavar='ESTEP',
help=
'''Calculate time evolution of flux confidence intervals every ESTEP
iterations (default: %(default)s)''')
def process_args(self, args):
self.data_reader.process_args(args)
self.data_reader.open()
self.iter_range.data_manager = self.data_reader
self.iter_range.process_args(args)
self.output_h5file = h5py.File(args.output, 'w')
self.alpha = args.alpha
# Disable the bootstrap or the correlation analysis.
self.mcbs_enable = args.bootstrap if args.bootstrap is not None else True
self.do_correl = args.correl if args.correl is not None else True
self.autocorrel_alpha = args.acalpha or self.alpha
self.n_sets = args.nsets or mclib.get_bssize(self.alpha)
self.do_evol = args.do_evol
self.evol_step = args.evol_step or 1
def calc_store_flux_data(self):
westpa.rc.pstatus(
'Calculating mean flux and confidence intervals for iterations [{},{})'
.format(self.iter_range.iter_start, self.iter_range.iter_stop))
fluxdata = extract_fluxes(self.iter_range.iter_start,
self.iter_range.iter_stop, self.data_reader)
# Create a group to store data in
output_group = h5io.create_hdf5_group(self.output_h5file,
'target_flux',
replace=False,
creating_program=self.prog)
self.output_group = output_group
output_group.attrs['version_code'] = self.output_format_version
self.iter_range.record_data_iter_range(output_group)
n_targets = len(fluxdata)
index = numpy.empty((len(fluxdata), ), dtype=target_index_dtype)
avg_fluxdata = numpy.empty((n_targets, ), dtype=ci_dtype)
for itarget, (target_label,
target_fluxdata) in enumerate(fluxdata.items()):
# Create group and index entry
index[itarget]['target_label'] = str(target_label)
target_group = output_group.create_group(
'target_{}'.format(itarget))
self.target_groups[target_label] = target_group
# Store per-iteration values
target_group['n_iter'] = target_fluxdata['n_iter']
target_group['count'] = target_fluxdata['count']
target_group['flux'] = target_fluxdata['flux']
h5io.label_axes(target_group['flux'], ['n_iter'], units=['tau^-1'])
# Calculate flux autocorrelation
fluxes = target_fluxdata['flux']
mean_flux = fluxes.mean()
fmm = fluxes - mean_flux
acorr = fftconvolve(fmm, fmm[::-1])
acorr = acorr[len(acorr) // 2:]
acorr /= acorr[0]
acorr_ds = target_group.create_dataset('flux_autocorrel',
data=acorr)
h5io.label_axes(acorr_ds, ['lag'], ['tau'])
# Calculate overall averages and CIs
#avg, lb_ci, ub_ci, correl_len = mclib.mcbs_ci_correl(fluxes, numpy.mean, self.alpha, self.n_sets,
# autocorrel_alpha=self.autocorrel_alpha, subsample=numpy.mean)
avg, lb_ci, ub_ci, sterr, correl_len = mclib.mcbs_ci_correl(
{'dataset': fluxes},
estimator=(lambda stride, dataset: numpy.mean(dataset)),
alpha=self.alpha,
n_sets=self.n_sets,
autocorrel_alpha=self.autocorrel_alpha,
subsample=numpy.mean,
do_correl=self.do_correl,
mcbs_enable=self.mcbs_enable)
avg_fluxdata[itarget] = (self.iter_range.iter_start,
self.iter_range.iter_stop, avg, lb_ci,
ub_ci, sterr, correl_len)
westpa.rc.pstatus('target {!r}:'.format(target_label))
westpa.rc.pstatus(
' correlation length = {} tau'.format(correl_len))
westpa.rc.pstatus(
' mean flux and CI = {:e} ({:e},{:e}) tau^(-1)'.format(
avg, lb_ci, ub_ci))
index[itarget]['mean_flux'] = avg
index[itarget]['mean_flux_ci_lb'] = lb_ci
index[itarget]['mean_flux_ci_ub'] = ub_ci
index[itarget]['mean_flux_correl_len'] = correl_len
# Write index and summary
index_ds = output_group.create_dataset('index', data=index)
index_ds.attrs['mcbs_alpha'] = self.alpha
index_ds.attrs['mcbs_autocorrel_alpha'] = self.autocorrel_alpha
index_ds.attrs['mcbs_n_sets'] = self.n_sets
self.fluxdata = fluxdata
self.output_h5file['avg_flux'] = avg_fluxdata
def calc_evol_flux(self):
westpa.rc.pstatus(
'Calculating cumulative evolution of flux confidence intervals every {} iteration(s)'
.format(self.evol_step))
for itarget, (target_label,
target_fluxdata) in enumerate(self.fluxdata.items()):
fluxes = target_fluxdata['flux']
target_group = self.target_groups[target_label]
iter_start = target_group['n_iter'][0]
iter_stop = target_group['n_iter'][-1]
iter_count = iter_stop - iter_start
n_blocks = iter_count // self.evol_step
if iter_count % self.evol_step > 0: n_blocks += 1
cis = numpy.empty((n_blocks, ), dtype=ci_dtype)
for iblock in range(n_blocks):
block_iter_stop = min(
iter_start + (iblock + 1) * self.evol_step, iter_stop)
istop = min((iblock + 1) * self.evol_step,
len(target_fluxdata['flux']))
fluxes = target_fluxdata['flux'][:istop]
#avg, ci_lb, ci_ub, correl_len = mclib.mcbs_ci_correl(fluxes, numpy.mean, self.alpha, self.n_sets,
# autocorrel_alpha = self.autocorrel_alpha,
# subsample=numpy.mean)
avg, ci_lb, ci_ub, sterr, correl_len = mclib.mcbs_ci_correl(
{'dataset': fluxes},
estimator=(lambda stride, dataset: numpy.mean(dataset)),
alpha=self.alpha,
n_sets=self.n_sets,
autocorrel_alpha=self.autocorrel_alpha,
subsample=numpy.mean,
do_correl=self.do_correl,
mcbs_enable=self.mcbs_enable)
cis[iblock]['iter_start'] = iter_start
cis[iblock]['iter_stop'] = block_iter_stop
cis[iblock]['expected'], cis[iblock]['ci_lbound'], cis[iblock][
'ci_ubound'] = avg, ci_lb, ci_ub
cis[iblock]['corr_len'] = correl_len
cis[iblock]['sterr'] = sterr
del fluxes
cis_ds = target_group.create_dataset('flux_evolution', data=cis)
cis_ds.attrs['iter_step'] = self.evol_step
cis_ds.attrs['mcbs_alpha'] = self.alpha
cis_ds.attrs['mcbs_autocorrel_alpha'] = self.autocorrel_alpha
cis_ds.attrs['mcbs_n_sets'] = self.n_sets
def go(self):
self.calc_store_flux_data()
if self.do_evol:
self.calc_evol_flux()
class StateProbTool(WESTParallelTool):
prog='w_stateprobs'
description = '''\
Calculate average populations and associated errors in state populations from
weighted ensemble data. Bin assignments, including macrostate definitions,
are required. (See "w_assign --help" for more information).
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, usually "stateprobs.h5") contains the following
dataset:
/avg_state_pops [state]
(Structured -- see below) Population of each state across entire
range specified.
If --evolution-mode is specified, then the following additional dataset is
available:
/state_pop_evolution [window][state]
(Structured -- see below). State populations based on windows of
iterations of varying width. If --evolution-mode=cumulative, then
these windows all begin at the iteration specified with
--start-iter and grow in length by --step-iter for each successive
element. If --evolution-mode=blocked, then these windows are all of
width --step-iter (excluding the last, which may be shorter), the first
of which begins at iteration --start-iter.
The structure of these datasets is as follows:
iter_start
(Integer) Iteration at which the averaging window begins (inclusive).
iter_stop
(Integer) Iteration at which the averaging window ends (exclusive).
expected
(Floating-point) Expected (mean) value of the rate as evaluated within
this window, in units of inverse tau.
ci_lbound
(Floating-point) Lower bound of the confidence interval on the rate
within this window, in units of inverse tau.
ci_ubound
(Floating-point) Upper bound of the confidence interval on the rate
within this window, in units of inverse tau.
corr_len
(Integer) Correlation length of the rate within this window, in units
of tau.
Each of these datasets is also stamped with a number of attributes:
mcbs_alpha
(Floating-point) Alpha value of confidence intervals. (For example,
*alpha=0.05* corresponds to a 95% confidence interval.)
mcbs_nsets
(Integer) Number of bootstrap data sets used in generating confidence
intervals.
mcbs_acalpha
(Floating-point) Alpha value for determining correlation lengths.
-----------------------------------------------------------------------------
Command-line options
-----------------------------------------------------------------------------
'''
def __init__(self):
super(StateProbTool,self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
def stamp_mcbs_info(self, dataset):
dataset.attrs['mcbs_alpha'] = self.mcbs_alpha
dataset.attrs['mcbs_acalpha'] = self.mcbs_acalpha
dataset.attrs['mcbs_nsets'] = self.mcbs_nsets
def add_args(self, parser):
self.progress.add_args(parser)
self.data_reader.add_args(parser)
self.iter_range.include_args['iter_step'] = True
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument('-a', '--assignments', default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
iogroup.add_argument('-o', '--output', dest='output', default='stateprobs.h5',
help='''Store results in OUTPUT (default: %(default)s).''')
cgroup = parser.add_argument_group('confidence interval calculation options')
cgroup.add_argument('--alpha', type=float, default=0.05,
help='''Calculate a (1-ALPHA) confidence interval'
(default: %(default)s)''')
cgroup.add_argument('--autocorrel-alpha', type=float, dest='acalpha', metavar='ACALPHA',
help='''Evaluate autocorrelation to (1-ACALPHA) significance.
Note that too small an ACALPHA will result in failure to detect autocorrelation
in a noisy flux signal. (Default: same as ALPHA.)''')
cgroup.add_argument('--nsets', type=int,
help='''Use NSETS samples for bootstrapping (default: chosen based on ALPHA)''')
cogroup = parser.add_argument_group('calculation options')
cogroup.add_argument('-e', '--evolution-mode', choices=['cumulative', 'blocked', 'none'], default='none',
help='''How to calculate time evolution of rate estimates.
``cumulative`` evaluates rates over windows starting with --start-iter and getting progressively
wider to --stop-iter by steps of --step-iter.
``blocked`` evaluates rates over windows of width --step-iter, the first of which begins at
--start-iter.
``none`` (the default) disables calculation of the time evolution of rate estimates.''')
def open_files(self):
self.output_file = h5io.WESTPAH5File(self.output_filename, 'w', creating_program=True)
h5io.stamp_creator_data(self.output_file)
self.assignments_file = h5io.WESTPAH5File(self.assignments_filename, 'r')#, driver='core', backing_store=False)
if not self.iter_range.check_data_iter_range_least(self.assignments_file):
raise ValueError('assignments data do not span the requested iterations')
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(1, (self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(self.mcbs_alpha)
self.evolution_mode = args.evolution_mode
def calc_state_pops(self):
start_iter, stop_iter = self.iter_range.iter_start, self.iter_range.iter_stop
nstates = self.nstates
state_map = self.state_map
iter_count = stop_iter-start_iter
pi = self.progress.indicator
pi.new_operation('Calculating state populations')
pops = h5io.IterBlockedDataset(self.assignments_file['labeled_populations'])
iter_state_pops = numpy.empty((nstates+1,), weight_dtype)
all_state_pops = numpy.empty((iter_count,nstates+1), weight_dtype)
avg_state_pops = numpy.zeros((nstates+1,), weight_dtype)
pops.cache_data(max_size='available')
try:
for iiter,n_iter in enumerate(xrange(start_iter,stop_iter)):
iter_state_pops.fill(0)
labeled_pops = pops.iter_entry(n_iter)
accumulate_state_populations_from_labeled(labeled_pops, state_map, iter_state_pops, check_state_map=False)
all_state_pops[iiter] = iter_state_pops
avg_state_pops += iter_state_pops
del labeled_pops
pi.progress += 1
finally:
pops.drop_cache()
self.output_file.create_dataset('state_pops', data=all_state_pops, compression=9, shuffle=True)
h5io.stamp_iter_range(self.output_file['state_pops'], start_iter, stop_iter)
self.all_state_pops = all_state_pops
avg_state_pops = numpy.zeros((nstates+1,), ci_dtype)
pi.new_operation('Calculating overall average populations and CIs', nstates)
# futures = []
# for istate in xrange(nstates):
# futures.append(self.work_manager.submit(_eval_block,kwargs=dict(iblock=None,istate=istate,
# start=start_iter,stop=stop_iter,
# state_pops=all_state_pops[:,istate],
# mcbs_alpha=self.mcbs_alpha, mcbs_nsets=self.mcbs_nsets,
# mcbs_acalpha = self.mcbs_acalpha)))
# for future in self.work_manager.as_completed(futures):
def taskgen():
for istate in xrange(nstates):
yield (_eval_block, (), dict(iblock=None,istate=istate,
start=start_iter,stop=stop_iter,
state_pops=all_state_pops[:,istate],
mcbs_alpha=self.mcbs_alpha, mcbs_nsets=self.mcbs_nsets,
mcbs_acalpha = self.mcbs_acalpha))
for future in self.work_manager.submit_as_completed(taskgen(), self.max_queue_len):
(_iblock,istate,ci_res) = future.get_result(discard=True)
avg_state_pops[istate] = ci_res
pi.progress += 1
self.output_file['avg_state_pops'] = avg_state_pops
self.stamp_mcbs_info(self.output_file['avg_state_pops'])
pi.clear()
maxlabellen = max(map(len,self.state_labels))
print('average state populations:')
for istate in xrange(nstates):
print('{:{maxlabellen}s}: mean={:21.15e} CI=({:21.15e}, {:21.15e})'
.format(self.state_labels[istate],
avg_state_pops['expected'][istate],
avg_state_pops['ci_lbound'][istate],
avg_state_pops['ci_ubound'][istate],
maxlabellen=maxlabellen))
def calc_evolution(self):
nstates = self.nstates
start_iter, stop_iter, step_iter = self.iter_range.iter_start, self.iter_range.iter_stop, self.iter_range.iter_step
start_pts = range(start_iter, stop_iter, step_iter)
pop_evol = numpy.zeros((len(start_pts), nstates), dtype=ci_dtype)
pi = self.progress.indicator
pi.new_operation('Calculating population evolution', len(start_pts)*nstates)
# futures = []
# for iblock, start in enumerate(start_pts):
# if self.evolution_mode == 'cumulative':
# block_start = start_iter
# else: # self.evolution_mode == 'blocked'
# block_start = start
# stop = min(start+step_iter, stop_iter)
#
# for istate in xrange(nstates):
# future = self.work_manager.submit(_eval_block,kwargs=dict(iblock=iblock,istate=istate,
# start=block_start,stop=stop,
# state_pops=self.all_state_pops[block_start-start_iter:stop-start_iter,istate],
# mcbs_alpha=self.mcbs_alpha, mcbs_nsets=self.mcbs_nsets,
# mcbs_acalpha = self.mcbs_acalpha))
# futures.append(future)
def taskgen():
for iblock, start in enumerate(start_pts):
if self.evolution_mode == 'cumulative':
block_start = start_iter
else: # self.evolution_mode == 'blocked'
block_start = start
stop = min(start+step_iter, stop_iter)
for istate in xrange(nstates):
yield (_eval_block,(),dict(iblock=iblock,istate=istate,
start=block_start,stop=stop,
state_pops=self.all_state_pops[block_start-start_iter:stop-start_iter,istate],
mcbs_alpha=self.mcbs_alpha, mcbs_nsets=self.mcbs_nsets,
mcbs_acalpha = self.mcbs_acalpha))
#for future in self.work_manager.as_completed(futures):
for future in self.work_manager.submit_as_completed(taskgen(), self.max_queue_len):
(iblock,istate,ci_res) = future.get_result(discard=True)
pop_evol[iblock,istate] = ci_res
pi.progress += 1
self.output_file.create_dataset('state_pop_evolution', data=pop_evol, shuffle=True, compression=9)
pi.clear()
def go(self):
pi = self.progress.indicator
with pi:
pi.new_operation('Initializing')
self.open_files()
nstates = self.nstates = self.assignments_file.attrs['nstates']
state_labels = self.state_labels = self.assignments_file['state_labels'][...]
state_map = self.state_map = self.assignments_file['state_map'][...]
if (state_map > nstates).any():
raise ValueError('invalid state mapping')
# copy metadata to output
self.output_file.attrs['nstates'] = nstates
self.output_file['state_labels'] = state_labels
# calculate overall averages
self.calc_state_pops()
# calculate evolution, if requested
if self.evolution_mode != 'none' and self.iter_range.iter_step:
self.calc_evolution()
class WCrawl(WESTParallelTool):
prog='w_crawl'
description = '''\
Crawl a weighted ensemble dataset, executing a function for each iteration.
This can be used for postprocessing of trajectories, cleanup of datasets,
or anything else that can be expressed as "do X for iteration N, then do
something with the result". Tasks are parallelized by iteration, and
no guarantees are made about evaluation order.
-----------------------------------------------------------------------------
Command-line options
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WCrawl,self).__init__()
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection(self.data_reader)
self.crawler = None
self.task_callable = None
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
tgroup = parser.add_argument_group('task options')
tgroup.add_argument('-c', '--crawler-instance',
help='''Use CRAWLER_INSTANCE (specified as module.instance) as an instance of
WESTPACrawler to coordinate the calculation. Required only if initialization,
finalization, or task result processing is required.''')
tgroup.add_argument('task_callable',
help='''Run TASK_CALLABLE (specified as module.function) on each iteration.
Required.''')
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
self.task_callable = get_object(args.task_callable, path=['.'])
if args.crawler_instance is not None:
self.crawler = get_object(args.crawler_instance, path=['.'])
else:
self.crawler = WESTPACrawler()
def go(self):
iter_start = self.iter_range.iter_start
iter_stop = self.iter_range.iter_stop
iter_count = iter_stop - iter_start
self.data_reader.open('r')
pi = self.progress.indicator
with pi:
pi.operation = 'Initializing'
self.crawler.initialize(iter_start, iter_stop)
try:
pi.new_operation('Dispatching tasks & processing results', iter_count)
task_gen = ((_remote_task, (n_iter, self.task_callable), {}) for n_iter in xrange(iter_start,iter_stop))
for future in self.work_manager.submit_as_completed(task_gen, self.max_queue_len):
n_iter, result = future.get_result(discard=True)
if self.crawler is not None:
self.crawler.process_iter_result(n_iter,result)
pi.progress += 1
finally:
pi.new_operation('Finalizing')
self.crawler.finalize()
class WPDist(WESTParallelTool):
prog = 'w_pdist'
description = '''\
Calculate time-resolved, multi-dimensional probability distributions of WE
datasets.
-----------------------------------------------------------------------------
Source data
-----------------------------------------------------------------------------
Source data is provided either by a user-specified function
(--construct-dataset) or a list of "data set specifications" (--dsspecs).
If neither is provided, the progress coordinate dataset ''pcoord'' is used.
To use a custom function to extract or calculate data whose probability
distribution will be calculated, specify the function in standard Python
MODULE.FUNCTION syntax as the argument to --construct-dataset. This function
will be called as function(n_iter,iter_group), where n_iter is the iteration
whose data are being considered and iter_group is the corresponding group
in the main WEST HDF5 file (west.h5). The function must return data which can
be indexed as [segment][timepoint][dimension].
To use a list of data set specifications, specify --dsspecs and then list the
desired datasets one-by-one (space-separated in most shells). These data set
specifications are formatted as NAME[,file=FILENAME,slice=SLICE], which will
use the dataset called NAME in the HDF5 file FILENAME (defaulting to the main
WEST HDF5 file west.h5), and slice it with the Python slice expression SLICE
(as in [0:2] to select the first two elements of the first axis of the
dataset). The ``slice`` option is most useful for selecting one column (or
more) from a multi-column dataset, such as arises when using a progress
coordinate of multiple dimensions.
-----------------------------------------------------------------------------
Histogram binning
-----------------------------------------------------------------------------
By default, histograms are constructed with 100 bins in each dimension. This
can be overridden by specifying -b/--bins, which accepts a number of different
kinds of arguments:
a single integer N
N uniformly spaced bins will be used in each dimension.
a sequence of integers N1,N2,... (comma-separated)
N1 uniformly spaced bins will be used for the first dimension, N2 for the
second, and so on.
a list of lists [[B11, B12, B13, ...], [B21, B22, B23, ...], ...]
The bin boundaries B11, B12, B13, ... will be used for the first dimension,
B21, B22, B23, ... for the second dimension, and so on. These bin
boundaries need not be uniformly spaced. These expressions will be
evaluated with Python's ``eval`` construct, with ``numpy`` available for
use [e.g. to specify bins using numpy.arange()].
The first two forms (integer, list of integers) will trigger a scan of all
data in each dimension in order to determine the minimum and maximum values,
which may be very expensive for large datasets. This can be avoided by
explicitly providing bin boundaries using the list-of-lists form.
Note that these bins are *NOT* at all related to the bins used to drive WE
sampling.
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file produced (specified by -o/--output, defaulting to "pdist.h5")
may be fed to plothist to generate plots (or appropriately processed text or
HDF5 files) from this data. In short, the following datasets are created:
``histograms``
Normalized histograms. The first axis corresponds to iteration, and
remaining axes correspond to dimensions of the input dataset.
``/binbounds_0``
Vector of bin boundaries for the first (index 0) dimension. Additional
datasets similarly named (/binbounds_1, /binbounds_2, ...) are created
for additional dimensions.
``/midpoints_0``
Vector of bin midpoints for the first (index 0) dimension. Additional
datasets similarly named are created for additional dimensions.
``n_iter``
Vector of iteration numbers corresponding to the stored histograms (i.e.
the first axis of the ``histograms`` dataset).
-----------------------------------------------------------------------------
Subsequent processing
-----------------------------------------------------------------------------
The output generated by this program (-o/--output, default "pdist.h5") may be
plotted by the ``plothist`` program. See ``plothist --help`` for more
information.
-----------------------------------------------------------------------------
Parallelization
-----------------------------------------------------------------------------
This tool supports parallelized binning, including reading of input data.
Parallel processing is the default. For simple cases (reading pre-computed
input data, modest numbers of segments), serial processing (--serial) may be
more efficient.
-----------------------------------------------------------------------------
Command-line options
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WPDist, self).__init__()
# Parallel processing by default (this is not actually necessary, but it is
# informative!)
self.wm_env.default_work_manager = self.wm_env.default_parallel_work_manager
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.input_dssynth = WESTDSSynthesizer(default_dsname='pcoord')
self.iter_range = IterRangeSelection(self.data_reader)
self.iter_range.include_args['iter_step'] = False
self.binspec = None
self.output_filename = None
self.output_file = None
self.dsspec = None
self.wt_dsspec = None # dsspec for weights
# These are used during histogram generation only
self.iter_start = None
self.iter_stop = None
self.ndim = None
self.ntimepoints = None
self.dset_dtype = None
self.binbounds = None # bin boundaries for each dimension
self.midpoints = None # bin midpoints for each dimension
self.data_range = None # data range for each dimension, as the pairs (min,max)
self.ignore_out_of_range = False
self.compress_output = False
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
parser.add_argument(
'-b',
'--bins',
dest='bins',
metavar='BINEXPR',
default='100',
help=
'''Use BINEXPR for bins. This may be an integer, which will be used for each
dimension of the progress coordinate; a list of integers (formatted as [n1,n2,...])
which will use n1 bins for the first dimension, n2 for the second dimension, and so on;
or a list of lists of boundaries (formatted as [[a1, a2, ...], [b1, b2, ...], ... ]), which
will use [a1, a2, ...] as bin boundaries for the first dimension, [b1, b2, ...] as bin boundaries
for the second dimension, and so on. (Default: 100 bins in each dimension.)'''
)
parser.add_argument(
'-o',
'--output',
dest='output',
default='pdist.h5',
help='''Store results in OUTPUT (default: %(default)s).''')
parser.add_argument(
'-C',
'--compress',
action='store_true',
help=
'''Compress histograms. May make storage of higher-dimensional histograms
more tractable, at the (possible extreme) expense of increased analysis time.
(Default: no compression.)''')
parser.add_argument(
'--loose',
dest='ignore_out_of_range',
action='store_true',
help=
'''Ignore values that do not fall within bins. (Risky, as this can make buggy bin
boundaries appear as reasonable data. Only use if you are
sure of your bin boundary specification.)''')
igroup = parser.add_argument_group(
'input dataset options').add_mutually_exclusive_group(
required=False)
igroup.add_argument(
'--construct-dataset',
help=
'''Use the given function (as in module.function) to extract source data.
This function will be called once per iteration as function(n_iter, iter_group)
to construct data for one iteration. Data returned must be indexable as
[seg_id][timepoint][dimension]''')
igroup.add_argument(
'--dsspecs',
nargs='+',
metavar='DSSPEC',
help=
'''Construct probability distribution from one or more DSSPECs.''')
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
self.input_dssynth.h5filename = self.data_reader.we_h5filename
self.input_dssynth.process_args(args)
self.dsspec = self.input_dssynth.dsspec
# Carrying an open HDF5 file across a fork() seems to corrupt the entire HDF5 library
# Open the WEST HDF5 file just long enough to process our iteration range, then close
# and reopen in go() [which executes after the fork]
with self.data_reader:
self.iter_range.process_args(args)
self.wt_dsspec = SingleIterDSSpec(self.data_reader.we_h5filename,
'seg_index',
slice=numpy.index_exp['weight'])
self.binspec = args.bins
self.output_filename = args.output
self.ignore_out_of_range = bool(args.ignore_out_of_range)
self.compress_output = args.compress or False
def go(self):
self.data_reader.open('r')
pi = self.progress.indicator
pi.operation = 'Initializing'
with pi:
self.output_file = h5py.File(self.output_filename, 'w')
h5io.stamp_creator_data(self.output_file)
self.iter_start = self.iter_range.iter_start
self.iter_stop = self.iter_range.iter_stop
# Construct bin boundaries
self.construct_bins(self.parse_binspec(self.binspec))
for idim, (binbounds, midpoints) in enumerate(
zip(self.binbounds, self.midpoints)):
self.output_file['binbounds_{}'.format(idim)] = binbounds
self.output_file['midpoints_{}'.format(idim)] = midpoints
# construct histogram
self.construct_histogram()
# Record iteration range
iter_range = self.iter_range.iter_range()
self.output_file['n_iter'] = iter_range
self.iter_range.record_data_iter_range(
self.output_file['histograms'])
self.output_file.close()
@staticmethod
def parse_binspec(binspec):
namespace = {'numpy': numpy, 'inf': float('inf')}
try:
binspec_compiled = eval(binspec, namespace)
except Exception as e:
raise ValueError('invalid bin specification: {!r}'.format(e))
else:
if log.isEnabledFor(logging.DEBUG):
log.debug('bin specs: {!r}'.format(binspec_compiled))
return binspec_compiled
def construct_bins(self, bins):
'''
Construct bins according to ``bins``, which may be:
1) A scalar integer (for that number of bins in each dimension)
2) A sequence of integers (specifying number of bins for each dimension)
3) A sequence of sequences of bin boundaries (specifying boundaries for each dimension)
Sets ``self.binbounds`` to a list of arrays of bin boundaries appropriate for passing to
fasthist.histnd, along with ``self.midpoints`` to the midpoints of the bins.
'''
if not isiterable(bins):
self._construct_bins_from_scalar(bins)
elif not isiterable(bins[0]):
self._construct_bins_from_int_seq(bins)
else:
self._construct_bins_from_bound_seqs(bins)
if log.isEnabledFor(logging.DEBUG):
log.debug('binbounds: {!r}'.format(self.binbounds))
def scan_data_shape(self):
if self.ndim is None:
dset = self.dsspec.get_iter_data(self.iter_start)
self.ntimepoints = dset.shape[1]
self.ndim = dset.shape[2]
self.dset_dtype = dset.dtype
def scan_data_range(self):
'''Scan input data for range in each dimension. The number of dimensions is determined
from the shape of the progress coordinate as of self.iter_start.'''
self.progress.indicator.new_operation('Scanning for data range',
self.iter_stop - self.iter_start)
self.scan_data_shape()
dset_dtype = self.dset_dtype
ndim = self.ndim
dsspec = self.dsspec
try:
minval = numpy.finfo(dset_dtype).min
maxval = numpy.finfo(dset_dtype).max
except ValueError:
minval = numpy.iinfo(dset_dtype).min
maxval = numpy.iinfo(dset_dtype).max
data_range = self.data_range = [(maxval, minval)
for _i in range(self.ndim)]
#futures = []
#for n_iter in xrange(self.iter_start, self.iter_stop):
#_remote_min_max(ndim, dset_dtype, n_iter, dsspec)
# futures.append(self.work_manager.submit(_remote_min_max, args=(ndim, dset_dtype, n_iter, dsspec)))
#for future in self.work_manager.as_completed(futures):
for future in self.work_manager.submit_as_completed(
((_remote_min_max, (ndim, dset_dtype, n_iter, dsspec), {})
for n_iter in range(self.iter_start, self.iter_stop)),
self.max_queue_len):
bounds = future.get_result(discard=True)
for idim in range(ndim):
current_min, current_max = data_range[idim]
current_min = min(current_min, bounds[idim][0])
current_max = max(current_max, bounds[idim][1])
data_range[idim] = (current_min, current_max)
self.progress.indicator.progress += 1
def _construct_bins_from_scalar(self, bins):
if self.data_range is None:
self.scan_data_range()
self.binbounds = []
self.midpoints = []
for idim in range(self.ndim):
lb, ub = self.data_range[idim]
# Advance just beyond the upper bound of the range, so that we catch
# the maximum in the histogram
ub *= 1.01
boundset = numpy.linspace(lb, ub, bins + 1)
midpoints = (boundset[:-1] + boundset[1:]) / 2.0
self.binbounds.append(boundset)
self.midpoints.append(midpoints)
def _construct_bins_from_int_seq(self, bins):
if self.data_range is None:
self.scan_data_range()
self.binbounds = []
self.midpoints = []
for idim in range(self.ndim):
lb, ub = self.data_range[idim]
# Advance just beyond the upper bound of the range, so that we catch
# the maximum in the histogram
ub *= 1.01
boundset = numpy.linspace(lb, ub, bins[idim] + 1)
midpoints = (boundset[:-1] + boundset[1:]) / 2.0
self.binbounds.append(boundset)
self.midpoints.append(midpoints)
def _construct_bins_from_bound_seqs(self, bins):
self.binbounds = []
self.midpoints = []
for boundset in bins:
boundset = numpy.asarray(boundset)
if (numpy.diff(boundset) <= 0).any():
raise ValueError(
'boundary set {!r} is not strictly monotonically increasing'
.format(boundset))
self.binbounds.append(boundset)
self.midpoints.append((boundset[:-1] + boundset[1:]) / 2.0)
def construct_histogram(self):
'''Construct a histogram using bins previously constructed with ``construct_bins()``.
The time series of histogram values is stored in ``histograms``.
Each histogram in the time series is normalized.'''
self.scan_data_shape()
iter_count = self.iter_stop - self.iter_start
histograms_ds = self.output_file.create_dataset(
'histograms',
dtype=numpy.float64,
shape=((iter_count, ) +
tuple(len(bounds) - 1 for bounds in self.binbounds)),
compression=9 if self.compress_output else None)
binbounds = [
numpy.require(boundset, self.dset_dtype, 'C')
for boundset in self.binbounds
]
self.progress.indicator.new_operation('Constructing histograms',
self.iter_stop - self.iter_start)
task_gen = (
(_remote_bin_iter,
(iiter, n_iter, self.dsspec, self.wt_dsspec,
1 if iiter > 0 else 0, binbounds, self.ignore_out_of_range), {})
for (iiter,
n_iter) in enumerate(range(self.iter_start, self.iter_stop)))
#futures = set()
#for iiter, n_iter in enumerate(xrange(self.iter_start, self.iter_stop)):
# initpoint = 1 if iiter > 0 else 0
# futures.add(self.work_manager.submit(_remote_bin_iter,
# args=(iiter, n_iter, self.dsspec, self.wt_dsspec, initpoint, binbounds)))
#for future in self.work_manager.as_completed(futures):
#future = self.work_manager.wait_any(futures)
#for future in self.work_manager.submit_as_completed(task_gen, self.queue_size):
log.debug('max queue length: {!r}'.format(self.max_queue_len))
for future in self.work_manager.submit_as_completed(
task_gen, self.max_queue_len):
iiter, n_iter, iter_hist = future.get_result(discard=True)
self.progress.indicator.progress += 1
# store histogram
histograms_ds[iiter] = iter_hist
del iter_hist, future
class WNTopTool(WESTTool):
prog = 'w_ntop'
description = '''\
Select walkers from bins . An assignment file mapping walkers to
bins at each timepoint is required (see``w_assign --help`` for further
information on generating this file). By default, high-weight walkers are
selected (hence the name ``w_ntop``: select the N top-weighted walkers from
each bin); however, minimum weight walkers and randomly-selected walkers
may be selected instead.
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, by default "ntop.h5") contains the following
datasets:
``/n_iter`` [iteration]
*(Integer)* Iteration numbers for each entry in other datasets.
``/n_segs`` [iteration][bin]
*(Integer)* Number of segments in each bin/state in the given iteration.
This will generally be the same as the number requested with
``--n/--count`` but may be smaller if the requested number of walkers
does not exist.
``/seg_ids`` [iteration][bin][segment]
*(Integer)* Matching segments in each iteration for each bin.
For an iteration ``n_iter``, only the first ``n_iter`` entries are
valid. For example, the full list of matching seg_ids in bin 0 in the
first stored iteration is ``seg_ids[0][0][:n_segs[0]]``.
``/weights`` [iteration][bin][segment]
*(Floating-point)* Weights for each matching segment in ``/seg_ids``.
-----------------------------------------------------------------------------
Command-line arguments
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WNTopTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.assignments_filename = None
self.output_filename = None
self.what = None
self.timepoint = None
self.count = None
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
igroup = parser.add_argument_group('input options')
igroup.add_argument(
'-a',
'--assignments',
default='assign.h5',
help=
'''Use assignments from the given ASSIGNMENTS file (default: %(default)s).'''
)
sgroup = parser.add_argument_group('selection options')
sgroup.add_argument(
'-n',
'--count',
type=int,
default=1,
help=
'''Select COUNT walkers from each iteration for each bin (default: %(default)s).'''
)
sgroup.add_argument(
'-t',
'--timepoint',
type=int,
default=-1,
help=
'''Base selection on the given TIMEPOINT within each iteration. Default (-1)
corresponds to the last timepoint.''')
cgroup = parser.add_mutually_exclusive_group()
cgroup.add_argument(
'--highweight',
dest='select_what',
action='store_const',
const='highweight',
help='''Select COUNT highest-weight walkers from each bin.''')
cgroup.add_argument(
'--lowweight',
dest='select_what',
action='store_const',
const='lowweight',
help='''Select COUNT lowest-weight walkers from each bin.''')
cgroup.add_argument(
'--random',
dest='select_what',
action='store_const',
const='random',
help='''Select COUNT walkers randomly from each bin.''')
parser.set_defaults(select_what='highweight')
ogroup = parser.add_argument_group('output options')
ogroup.add_argument(
'-o',
'--output',
default='ntop.h5',
help='''Write output to OUTPUT (default: %(default)s).''')
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
self.what = args.select_what
self.output_filename = args.output
self.assignments_filename = args.assignments
self.count = args.count
self.timepoint = args.timepoint
def go(self):
self.data_reader.open('r')
assignments_file = h5py.File(self.assignments_filename, mode='r')
output_file = h5io.WESTPAH5File(self.output_filename, mode='w')
pi = self.progress.indicator
count = self.count
timepoint = self.timepoint
nbins = assignments_file.attrs['nbins'] + 1
assignments_ds = assignments_file['assignments']
iter_start, iter_stop = self.iter_range.iter_start, self.iter_range.iter_stop
iter_count = iter_stop - iter_start
h5io.check_iter_range_least(assignments_ds, iter_start, iter_stop)
nsegs = assignments_file['nsegs'][h5io.get_iteration_slice(
assignments_file['nsegs'], iter_start, iter_stop)]
output_file.create_dataset('n_iter',
dtype=n_iter_dtype,
data=list(range(iter_start, iter_stop)))
seg_count_ds = output_file.create_dataset('nsegs',
dtype=numpy.uint,
shape=(iter_count, nbins))
matching_segs_ds = output_file.create_dataset(
'seg_ids',
shape=(iter_count, nbins, count),
dtype=seg_id_dtype,
chunks=h5io.calc_chunksize((iter_count, nbins, count),
seg_id_dtype),
shuffle=True,
compression=9)
weights_ds = output_file.create_dataset('weights',
shape=(iter_count, nbins,
count),
dtype=weight_dtype,
chunks=h5io.calc_chunksize(
(iter_count, nbins, count),
weight_dtype),
shuffle=True,
compression=9)
what = self.what
with pi:
pi.new_operation('Finding matching segments', extent=iter_count)
for iiter, n_iter in enumerate(range(iter_start, iter_stop)):
assignments = numpy.require(assignments_ds[
h5io.get_iteration_entry(assignments_ds, n_iter) +
numpy.index_exp[:, timepoint]],
dtype=westpa.binning.index_dtype)
all_weights = self.data_reader.get_iter_group(
n_iter)['seg_index']['weight']
# the following Cython function just executes this loop:
#for iseg in xrange(nsegs[iiter]):
# segs_by_bin[iseg,assignments[iseg]] = True
segs_by_bin = assignments_list_to_table(
nsegs[iiter], nbins, assignments)
for ibin in range(nbins):
segs = numpy.nonzero(segs_by_bin[:, ibin])[0]
seg_count_ds[iiter, ibin] = min(len(segs), count)
if len(segs):
weights = all_weights.take(segs)
if what == 'lowweight':
indices = numpy.argsort(weights)[:count]
elif what == 'highweight':
indices = numpy.argsort(weights)[::-1][:count]
else:
assert what == 'random'
indices = numpy.random.permutation(len(weights))
matching_segs_ds[iiter,
ibin, :len(segs)] = segs.take(indices)
weights_ds[iiter,
ibin, :len(segs)] = weights.take(indices)
del segs, weights
del assignments, segs_by_bin, all_weights
pi.progress += 1
class WSelectTool(WESTParallelTool):
prog='w_select'
description = '''\
Select dynamics segments matching various criteria. This requires a
user-provided prediate function. By default, only matching segments are
stored. If the -a/--include-ancestors option is given, then matching segments
and their ancestors will be stored.
-----------------------------------------------------------------------------
Predicate function
-----------------------------------------------------------------------------
Segments are selected based on a predicate function, which must be callable
as ``predicate(n_iter, iter_group)`` and return a collection of segment IDs
matching the predicate in that iteration.
The predicate may be inverted by specifying the -v/--invert command-line
argument.
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, by default "select.h5") contains the following
datasets:
``/n_iter`` [iteration]
*(Integer)* Iteration numbers for each entry in other datasets.
``/n_segs`` [iteration]
*(Integer)* Number of segment IDs matching the predicate (or inverted
predicate, if -v/--invert is specified) in the given iteration.
``/seg_ids`` [iteration][segment]
*(Integer)* Matching segments in each iteration. For an iteration
``n_iter``, only the first ``n_iter`` entries are valid. For example,
the full list of matching seg_ids in the first stored iteration is
``seg_ids[0][:n_segs[0]]``.
``/weights`` [iteration][segment]
*(Floating-point)* Weights for each matching segment in ``/seg_ids``.
-----------------------------------------------------------------------------
Command-line arguments
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WSelectTool,self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.output_filename = None
self.predicate = None
self.invert = False
self.include_ancestors = False
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
sgroup = parser.add_argument_group('selection options')
sgroup.add_argument('-p', '--predicate-function', metavar='MODULE.FUNCTION',
help='''Use the given predicate function to match segments. This function
should take an iteration number and the HDF5 group corresponding to that
iteration and return a sequence of seg_ids matching the predicate, as in
``match_predicate(n_iter, iter_group)``.''')
sgroup.add_argument('-v', '--invert', dest='invert', action='store_true',
help='''Invert the match predicate.''')
sgroup.add_argument('-a', '--include-ancestors', action ='store_true',
help='''Include ancestors of matched segments in output.''')
ogroup = parser.add_argument_group('output options')
ogroup.add_argument('-o', '--output', default='select.h5',
help='''Write output to OUTPUT (default: %(default)s).''')
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
predicate = get_object(args.predicate_function,path=['.'])
if not callable(predicate):
raise TypeError('predicate object {!r} is not callable'.format(predicate))
self.predicate = predicate
self.invert = bool(args.invert)
self.include_ancestors = bool(args.include_ancestors)
self.output_filename = args.output
def go(self):
self.data_reader.open('r')
output_file = h5io.WESTPAH5File(self.output_filename, mode='w')
pi = self.progress.indicator
iter_start, iter_stop = self.iter_range.iter_start, self.iter_range.iter_stop
iter_count = iter_stop - iter_start
output_file.create_dataset('n_iter', dtype=n_iter_dtype, data=range(iter_start,iter_stop))
current_seg_count = 0
seg_count_ds = output_file.create_dataset('n_segs', dtype=numpy.uint, shape=(iter_count,))
matching_segs_ds = output_file.create_dataset('seg_ids', shape=(iter_count,0), maxshape=(iter_count,None),
dtype=seg_id_dtype,
chunks=h5io.calc_chunksize((iter_count,1000000), seg_id_dtype),
shuffle=True, compression=9)
weights_ds = output_file.create_dataset('weights', shape=(iter_count,0), maxshape=(iter_count,None),
dtype=weight_dtype,
chunks=h5io.calc_chunksize((iter_count,1000000), weight_dtype),
shuffle=True,compression=9)
with pi:
pi.new_operation('Finding matching segments', extent=iter_count)
# futures = set()
# for n_iter in xrange(iter_start,iter_stop):
# futures.add(self.work_manager.submit(_find_matching_segments,
# args=(self.data_reader.we_h5filename,n_iter,self.predicate,self.invert)))
# for future in self.work_manager.as_completed(futures):
for future in self.work_manager.submit_as_completed(((_find_matching_segments,
(self.data_reader.we_h5filename,n_iter,self.predicate,self.invert),
{}) for n_iter in xrange(iter_start,iter_stop)),
self.max_queue_len):
n_iter, matching_ids = future.get_result()
n_matches = len(matching_ids)
if n_matches:
if n_matches > current_seg_count:
current_seg_count = len(matching_ids)
matching_segs_ds.resize((iter_count,n_matches))
weights_ds.resize((iter_count,n_matches))
current_seg_count = n_matches
seg_count_ds[n_iter-iter_start] = n_matches
matching_segs_ds[n_iter-iter_start,:n_matches] = matching_ids
weights_ds[n_iter-iter_start,:n_matches] = self.data_reader.get_iter_group(n_iter)['seg_index']['weight'][sorted(matching_ids)]
del matching_ids
pi.progress += 1
if self.include_ancestors:
pi.new_operation('Tracing ancestors of matching segments', extent=iter_count)
from_previous = set()
current_seg_count = matching_segs_ds.shape[1]
for n_iter in xrange(iter_stop-1, iter_start-1, -1):
iiter = n_iter - iter_start
n_matches = seg_count_ds[iiter]
matching_ids = set(from_previous)
if n_matches:
matching_ids.update(matching_segs_ds[iiter, :seg_count_ds[iiter]])
from_previous.clear()
n_matches = len(matching_ids)
if n_matches > current_seg_count:
matching_segs_ds.resize((iter_count,n_matches))
weights_ds.resize((iter_count,n_matches))
current_seg_count = n_matches
if n_matches > 0:
seg_count_ds[iiter] = n_matches
matching_ids = sorted(matching_ids)
matching_segs_ds[iiter,:n_matches] = matching_ids
weights_ds[iiter,:n_matches] = self.data_reader.get_iter_group(n_iter)['seg_index']['weight'][sorted(matching_ids)]
parent_ids = self.data_reader.get_iter_group(n_iter)['seg_index']['parent_id'][sorted(matching_ids)]
from_previous.update(parent_id for parent_id in parent_ids if parent_id >= 0) # filter initial states
del parent_ids
del matching_ids
pi.progress += 1
class WPDist(WESTParallelTool):
prog='w_pdist'
description = '''\
Calculate time-resolved, multi-dimensional probability distributions of WE
datasets.
-----------------------------------------------------------------------------
Source data
-----------------------------------------------------------------------------
Source data is provided either by a user-specified function
(--construct-dataset) or a list of "data set specifications" (--dsspecs).
If neither is provided, the progress coordinate dataset ''pcoord'' is used.
To use a custom function to extract or calculate data whose probability
distribution will be calculated, specify the function in standard Python
MODULE.FUNCTION syntax as the argument to --construct-dataset. This function
will be called as function(n_iter,iter_group), where n_iter is the iteration
whose data are being considered and iter_group is the corresponding group
in the main WEST HDF5 file (west.h5). The function must return data which can
be indexed as [segment][timepoint][dimension].
To use a list of data set specifications, specify --dsspecs and then list the
desired datasets one-by-one (space-separated in most shells). These data set
specifications are formatted as NAME[,file=FILENAME,slice=SLICE], which will
use the dataset called NAME in the HDF5 file FILENAME (defaulting to the main
WEST HDF5 file west.h5), and slice it with the Python slice expression SLICE
(as in [0:2] to select the first two elements of the first axis of the
dataset). The ``slice`` option is most useful for selecting one column (or
more) from a multi-column dataset, such as arises when using a progress
coordinate of multiple dimensions.
-----------------------------------------------------------------------------
Histogram binning
-----------------------------------------------------------------------------
By default, histograms are constructed with 100 bins in each dimension. This
can be overridden by specifying -b/--bins, which accepts a number of different
kinds of arguments:
a single integer N
N uniformly spaced bins will be used in each dimension.
a sequence of integers N1,N2,... (comma-separated)
N1 uniformly spaced bins will be used for the first dimension, N2 for the
second, and so on.
a list of lists [[B11, B12, B13, ...], [B21, B22, B23, ...], ...]
The bin boundaries B11, B12, B13, ... will be used for the first dimension,
B21, B22, B23, ... for the second dimension, and so on. These bin
boundaries need not be uniformly spaced. These expressions will be
evaluated with Python's ``eval`` construct, with ``numpy`` available for
use [e.g. to specify bins using numpy.arange()].
The first two forms (integer, list of integers) will trigger a scan of all
data in each dimension in order to determine the minimum and maximum values,
which may be very expensive for large datasets. This can be avoided by
explicitly providing bin boundaries using the list-of-lists form.
Note that these bins are *NOT* at all related to the bins used to drive WE
sampling.
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file produced (specified by -o/--output, defaulting to "pdist.h5")
may be fed to plothist to generate plots (or appropriately processed text or
HDF5 files) from this data. In short, the following datasets are created:
``histograms``
Normalized histograms. The first axis corresponds to iteration, and
remaining axes correspond to dimensions of the input dataset.
``/binbounds_0``
Vector of bin boundaries for the first (index 0) dimension. Additional
datasets similarly named (/binbounds_1, /binbounds_2, ...) are created
for additional dimensions.
``/midpoints_0``
Vector of bin midpoints for the first (index 0) dimension. Additional
datasets similarly named are created for additional dimensions.
``n_iter``
Vector of iteration numbers corresponding to the stored histograms (i.e.
the first axis of the ``histograms`` dataset).
-----------------------------------------------------------------------------
Subsequent processing
-----------------------------------------------------------------------------
The output generated by this program (-o/--output, default "pdist.h5") may be
plotted by the ``plothist`` program. See ``plothist --help`` for more
information.
-----------------------------------------------------------------------------
Parallelization
-----------------------------------------------------------------------------
This tool supports parallelized binning, including reading of input data.
Parallel processing is the default. For simple cases (reading pre-computed
input data, modest numbers of segments), serial processing (--serial) may be
more efficient.
-----------------------------------------------------------------------------
Command-line options
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WPDist,self).__init__()
# Parallel processing by default (this is not actually necessary, but it is
# informative!)
self.wm_env.default_work_manager = self.wm_env.default_parallel_work_manager
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.input_dssynth = WESTDSSynthesizer(default_dsname='pcoord')
self.iter_range = IterRangeSelection(self.data_reader)
self.iter_range.include_args['iter_step'] = False
self.binspec = None
self.output_filename = None
self.output_file = None
self.dsspec = None
self.wt_dsspec = None # dsspec for weights
# These are used during histogram generation only
self.iter_start = None
self.iter_stop = None
self.ndim = None
self.ntimepoints = None
self.dset_dtype = None
self.binbounds = None # bin boundaries for each dimension
self.midpoints = None # bin midpoints for each dimension
self.data_range = None # data range for each dimension, as the pairs (min,max)
self.ignore_out_of_range = False
self.compress_output = False
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
parser.add_argument('-b', '--bins', dest='bins', metavar='BINEXPR', default='100',
help='''Use BINEXPR for bins. This may be an integer, which will be used for each
dimension of the progress coordinate; a list of integers (formatted as [n1,n2,...])
which will use n1 bins for the first dimension, n2 for the second dimension, and so on;
or a list of lists of boundaries (formatted as [[a1, a2, ...], [b1, b2, ...], ... ]), which
will use [a1, a2, ...] as bin boundaries for the first dimension, [b1, b2, ...] as bin boundaries
for the second dimension, and so on. (Default: 100 bins in each dimension.)''')
parser.add_argument('-o', '--output', dest='output', default='pdist.h5',
help='''Store results in OUTPUT (default: %(default)s).''')
parser.add_argument('-C', '--compress', action='store_true',
help='''Compress histograms. May make storage of higher-dimensional histograms
more tractable, at the (possible extreme) expense of increased analysis time.
(Default: no compression.)''')
parser.add_argument('--loose', dest='ignore_out_of_range', action='store_true',
help='''Ignore values that do not fall within bins. (Risky, as this can make buggy bin
boundaries appear as reasonable data. Only use if you are
sure of your bin boundary specification.)''')
igroup = parser.add_argument_group('input dataset options').add_mutually_exclusive_group(required=False)
igroup.add_argument('--construct-dataset',
help='''Use the given function (as in module.function) to extract source data.
This function will be called once per iteration as function(n_iter, iter_group)
to construct data for one iteration. Data returned must be indexable as
[seg_id][timepoint][dimension]''')
igroup.add_argument('--dsspecs', nargs='+', metavar='DSSPEC',
help='''Construct probability distribution from one or more DSSPECs.''')
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
self.input_dssynth.h5filename = self.data_reader.we_h5filename
self.input_dssynth.process_args(args)
self.dsspec = self.input_dssynth.dsspec
# Carrying an open HDF5 file across a fork() seems to corrupt the entire HDF5 library
# Open the WEST HDF5 file just long enough to process our iteration range, then close
# and reopen in go() [which executes after the fork]
with self.data_reader:
self.iter_range.process_args(args)
self.wt_dsspec = SingleIterDSSpec(self.data_reader.we_h5filename, 'seg_index', slice=numpy.index_exp['weight'])
self.binspec = args.bins
self.output_filename = args.output
self.ignore_out_of_range = bool(args.ignore_out_of_range)
self.compress_output = args.compress or False
def go(self):
self.data_reader.open('r')
pi = self.progress.indicator
pi.operation = 'Initializing'
with pi:
self.output_file = h5py.File(self.output_filename, 'w')
h5io.stamp_creator_data(self.output_file)
self.iter_start = self.iter_range.iter_start
self.iter_stop = self.iter_range.iter_stop
# Construct bin boundaries
self.construct_bins(self.parse_binspec(self.binspec))
for idim, (binbounds, midpoints) in enumerate(izip(self.binbounds, self.midpoints)):
self.output_file['binbounds_{}'.format(idim)] = binbounds
self.output_file['midpoints_{}'.format(idim)] = midpoints
# construct histogram
self.construct_histogram()
# Record iteration range
iter_range = self.iter_range.iter_range()
self.output_file['n_iter'] = iter_range
self.iter_range.record_data_iter_range(self.output_file['histograms'])
self.output_file.close()
@staticmethod
def parse_binspec(binspec):
namespace = {'numpy': numpy,
'inf': float('inf')}
try:
binspec_compiled = eval(binspec,namespace)
except Exception as e:
raise ValueError('invalid bin specification: {!r}'.format(e))
else:
if log.isEnabledFor(logging.DEBUG):
log.debug('bin specs: {!r}'.format(binspec_compiled))
return binspec_compiled
def construct_bins(self, bins):
'''
Construct bins according to ``bins``, which may be:
1) A scalar integer (for that number of bins in each dimension)
2) A sequence of integers (specifying number of bins for each dimension)
3) A sequence of sequences of bin boundaries (specifying boundaries for each dimension)
Sets ``self.binbounds`` to a list of arrays of bin boundaries appropriate for passing to
fasthist.histnd, along with ``self.midpoints`` to the midpoints of the bins.
'''
if not isiterable(bins):
self._construct_bins_from_scalar(bins)
elif not isiterable(bins[0]):
self._construct_bins_from_int_seq(bins)
else:
self._construct_bins_from_bound_seqs(bins)
if log.isEnabledFor(logging.DEBUG):
log.debug('binbounds: {!r}'.format(self.binbounds))
def scan_data_shape(self):
if self.ndim is None:
dset = self.dsspec.get_iter_data(self.iter_start)
self.ntimepoints = dset.shape[1]
self.ndim = dset.shape[2]
self.dset_dtype = dset.dtype
def scan_data_range(self):
'''Scan input data for range in each dimension. The number of dimensions is determined
from the shape of the progress coordinate as of self.iter_start.'''
self.progress.indicator.new_operation('Scanning for data range', self.iter_stop-self.iter_start)
self.scan_data_shape()
dset_dtype = self.dset_dtype
ndim = self.ndim
dsspec = self.dsspec
try:
minval = numpy.finfo(dset_dtype).min
maxval = numpy.finfo(dset_dtype).max
except ValueError:
minval = numpy.iinfo(dset_dtype).min
maxval = numpy.iinfo(dset_dtype).max
data_range = self.data_range = [(maxval,minval) for _i in xrange(self.ndim)]
#futures = []
#for n_iter in xrange(self.iter_start, self.iter_stop):
#_remote_min_max(ndim, dset_dtype, n_iter, dsspec)
# futures.append(self.work_manager.submit(_remote_min_max, args=(ndim, dset_dtype, n_iter, dsspec)))
#for future in self.work_manager.as_completed(futures):
for future in self.work_manager.submit_as_completed(((_remote_min_max, (ndim, dset_dtype, n_iter, dsspec), {})
for n_iter in xrange(self.iter_start, self.iter_stop)),
self.max_queue_len):
bounds = future.get_result(discard=True)
for idim in xrange(ndim):
current_min, current_max = data_range[idim]
current_min = min(current_min, bounds[idim][0])
current_max = max(current_max, bounds[idim][1])
data_range[idim] = (current_min, current_max)
self.progress.indicator.progress += 1
def _construct_bins_from_scalar(self, bins):
if self.data_range is None:
self.scan_data_range()
self.binbounds = []
self.midpoints = []
for idim in xrange(self.ndim):
lb, ub = self.data_range[idim]
# Advance just beyond the upper bound of the range, so that we catch
# the maximum in the histogram
ub *= 1.01
boundset = numpy.linspace(lb,ub,bins+1)
midpoints = (boundset[:-1] + boundset[1:]) / 2.0
self.binbounds.append(boundset)
self.midpoints.append(midpoints)
def _construct_bins_from_int_seq(self, bins):
if self.data_range is None:
self.scan_data_range()
self.binbounds = []
self.midpoints = []
for idim in xrange(self.ndim):
lb, ub = self.data_range[idim]
# Advance just beyond the upper bound of the range, so that we catch
# the maximum in the histogram
ub *= 1.01
boundset = numpy.linspace(lb,ub,bins[idim]+1)
midpoints = (boundset[:-1] + boundset[1:]) / 2.0
self.binbounds.append(boundset)
self.midpoints.append(midpoints)
def _construct_bins_from_bound_seqs(self, bins):
self.binbounds = []
self.midpoints = []
for boundset in bins:
boundset = numpy.asarray(boundset)
if (numpy.diff(boundset) <= 0).any():
raise ValueError('boundary set {!r} is not strictly monotonically increasing'.format(boundset))
self.binbounds.append(boundset)
self.midpoints.append((boundset[:-1]+boundset[1:])/2.0)
def construct_histogram(self):
'''Construct a histogram using bins previously constructed with ``construct_bins()``.
The time series of histogram values is stored in ``histograms``.
Each histogram in the time series is normalized.'''
self.scan_data_shape()
iter_count = self.iter_stop - self.iter_start
histograms_ds = self.output_file.create_dataset('histograms', dtype=numpy.float64,
shape=((iter_count,) + tuple(len(bounds)-1 for bounds in self.binbounds)),
compression=9 if self.compress_output else None)
binbounds = [numpy.require(boundset, self.dset_dtype, 'C') for boundset in self.binbounds]
self.progress.indicator.new_operation('Constructing histograms',self.iter_stop-self.iter_start)
task_gen = ((_remote_bin_iter, (iiter, n_iter, self.dsspec, self.wt_dsspec, 1 if iiter > 0 else 0, binbounds,
self.ignore_out_of_range), {})
for (iiter,n_iter) in enumerate(xrange(self.iter_start, self.iter_stop)))
#futures = set()
#for iiter, n_iter in enumerate(xrange(self.iter_start, self.iter_stop)):
# initpoint = 1 if iiter > 0 else 0
# futures.add(self.work_manager.submit(_remote_bin_iter,
# args=(iiter, n_iter, self.dsspec, self.wt_dsspec, initpoint, binbounds)))
#for future in self.work_manager.as_completed(futures):
#future = self.work_manager.wait_any(futures)
#for future in self.work_manager.submit_as_completed(task_gen, self.queue_size):
log.debug('max queue length: {!r}'.format(self.max_queue_len))
for future in self.work_manager.submit_as_completed(task_gen, self.max_queue_len):
iiter, n_iter, iter_hist = future.get_result(discard=True)
self.progress.indicator.progress += 1
# store histogram
histograms_ds[iiter] = iter_hist
del iter_hist, future
class WFluxanlTool(WESTTool):
prog='w_fluxanl'
description = '''\
Extract fluxes into pre-defined target states from WEST data,
average, and construct confidence intervals. Monte Carlo bootstrapping
is used to account for the correlated and possibly non-Gaussian statistical
error in flux measurements.
All non-graphical output (including that to the terminal and HDF5) assumes that
the propagation/resampling period ``tau`` is equal to unity; to obtain results
in familiar units, divide all fluxes and multiply all correlation lengths by
the true value of ``tau``.
'''
output_format_version = 2
def __init__(self):
super(WFluxanlTool,self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.output_h5file = None
self.output_group = None
self.target_groups = {}
self.fluxdata = {}
self.alpha = None
self.autocorrel_alpha = None
self.n_sets = None
self.do_evol = False
self.evol_step = 1
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
ogroup = parser.add_argument_group('output options')
ogroup.add_argument('-o', '--output', default='fluxanl.h5',
help='Store intermediate data and analysis results to OUTPUT (default: %(default)s).')
cgroup = parser.add_argument_group('calculation options')
cgroup.add_argument('--disable-bootstrap', '-db', dest='bootstrap', action='store_const', const=False,
help='''Enable the use of Monte Carlo Block Bootstrapping.''')
cgroup.add_argument('--disable-correl', '-dc', dest='correl', action='store_const', const=False,
help='''Disable the correlation analysis.''')
cgroup.add_argument('-a', '--alpha', type=float, default=0.05,
help='''Calculate a (1-ALPHA) confidence interval on the average flux'
(default: %(default)s)''')
cgroup.add_argument('--autocorrel-alpha', type=float, dest='acalpha', metavar='ACALPHA',
help='''Evaluate autocorrelation of flux to (1-ACALPHA) significance.
Note that too small an ACALPHA will result in failure to detect autocorrelation
in a noisy flux signal. (Default: same as ALPHA.)''')
cgroup.add_argument('-N', '--nsets', type=int,
help='''Use NSETS samples for bootstrapping (default: chosen based on ALPHA)''')
cgroup.add_argument('--evol', action='store_true', dest='do_evol',
help='''Calculate time evolution of flux confidence intervals (expensive).''')
cgroup.add_argument('--evol-step', type=int, default=1, metavar='ESTEP',
help='''Calculate time evolution of flux confidence intervals every ESTEP
iterations (default: %(default)s)''')
def process_args(self, args):
self.data_reader.process_args(args)
self.data_reader.open()
self.iter_range.data_manager = self.data_reader
self.iter_range.process_args(args)
self.output_h5file = h5py.File(args.output, 'w')
self.alpha = args.alpha
# Disable the bootstrap or the correlation analysis.
self.mcbs_enable = args.bootstrap if args.bootstrap is not None else True
self.do_correl = args.correl if args.correl is not None else True
self.autocorrel_alpha = args.acalpha or self.alpha
self.n_sets = args.nsets or mclib.get_bssize(self.alpha)
self.do_evol = args.do_evol
self.evol_step = args.evol_step or 1
def calc_store_flux_data(self):
westpa.rc.pstatus('Calculating mean flux and confidence intervals for iterations [{},{})'
.format(self.iter_range.iter_start, self.iter_range.iter_stop))
fluxdata = extract_fluxes(self.iter_range.iter_start, self.iter_range.iter_stop, self.data_reader)
# Create a group to store data in
output_group = h5io.create_hdf5_group(self.output_h5file, 'target_flux', replace=False, creating_program=self.prog)
self.output_group = output_group
output_group.attrs['version_code'] = self.output_format_version
self.iter_range.record_data_iter_range(output_group)
n_targets = len(fluxdata)
index = numpy.empty((len(fluxdata),), dtype=target_index_dtype)
avg_fluxdata = numpy.empty((n_targets,), dtype=ci_dtype)
for itarget, (target_label, target_fluxdata) in enumerate(fluxdata.iteritems()):
# Create group and index entry
index[itarget]['target_label'] = str(target_label)
target_group = output_group.create_group('target_{}'.format(itarget))
self.target_groups[target_label] = target_group
# Store per-iteration values
target_group['n_iter'] = target_fluxdata['n_iter']
target_group['count'] = target_fluxdata['count']
target_group['flux'] = target_fluxdata['flux']
h5io.label_axes(target_group['flux'], ['n_iter'], units=['tau^-1'])
# Calculate flux autocorrelation
fluxes = target_fluxdata['flux']
mean_flux = fluxes.mean()
fmm = fluxes - mean_flux
acorr = fftconvolve(fmm,fmm[::-1])
acorr = acorr[len(acorr)//2:]
acorr /= acorr[0]
acorr_ds = target_group.create_dataset('flux_autocorrel', data=acorr)
h5io.label_axes(acorr_ds, ['lag'], ['tau'])
# Calculate overall averages and CIs
#avg, lb_ci, ub_ci, correl_len = mclib.mcbs_ci_correl(fluxes, numpy.mean, self.alpha, self.n_sets,
# autocorrel_alpha=self.autocorrel_alpha, subsample=numpy.mean)
avg, lb_ci, ub_ci, sterr, correl_len = mclib.mcbs_ci_correl({'dataset': fluxes}, estimator=(lambda stride, dataset: numpy.mean(dataset)), alpha=self.alpha, n_sets=self.n_sets,
autocorrel_alpha=self.autocorrel_alpha, subsample=numpy.mean, do_correl=self.do_correl, mcbs_enable=self.mcbs_enable )
avg_fluxdata[itarget] = (self.iter_range.iter_start, self.iter_range.iter_stop, avg, lb_ci, ub_ci, sterr, correl_len)
westpa.rc.pstatus('target {!r}:'.format(target_label))
westpa.rc.pstatus(' correlation length = {} tau'.format(correl_len))
westpa.rc.pstatus(' mean flux and CI = {:e} ({:e},{:e}) tau^(-1)'.format(avg,lb_ci,ub_ci))
index[itarget]['mean_flux'] = avg
index[itarget]['mean_flux_ci_lb'] = lb_ci
index[itarget]['mean_flux_ci_ub'] = ub_ci
index[itarget]['mean_flux_correl_len'] = correl_len
# Write index and summary
index_ds = output_group.create_dataset('index', data=index)
index_ds.attrs['mcbs_alpha'] = self.alpha
index_ds.attrs['mcbs_autocorrel_alpha'] = self.autocorrel_alpha
index_ds.attrs['mcbs_n_sets'] = self.n_sets
self.fluxdata = fluxdata
self.output_h5file['avg_flux'] = avg_fluxdata
def calc_evol_flux(self):
westpa.rc.pstatus('Calculating cumulative evolution of flux confidence intervals every {} iteration(s)'
.format(self.evol_step))
for itarget, (target_label, target_fluxdata) in enumerate(self.fluxdata.iteritems()):
fluxes = target_fluxdata['flux']
target_group = self.target_groups[target_label]
iter_start = target_group['n_iter'][0]
iter_stop = target_group['n_iter'][-1]
iter_count = iter_stop - iter_start
n_blocks = iter_count // self.evol_step
if iter_count % self.evol_step > 0: n_blocks += 1
cis = numpy.empty((n_blocks,), dtype=ci_dtype)
for iblock in xrange(n_blocks):
block_iter_stop = min(iter_start + (iblock+1)*self.evol_step, iter_stop)
istop = min((iblock+1)*self.evol_step, len(target_fluxdata['flux']))
fluxes = target_fluxdata['flux'][:istop]
#avg, ci_lb, ci_ub, correl_len = mclib.mcbs_ci_correl(fluxes, numpy.mean, self.alpha, self.n_sets,
# autocorrel_alpha = self.autocorrel_alpha,
# subsample=numpy.mean)
avg, ci_lb, ci_ub, sterr, correl_len = mclib.mcbs_ci_correl({'dataset': fluxes}, estimator=(lambda stride, dataset: numpy.mean(dataset)), alpha=self.alpha, n_sets=self.n_sets,
autocorrel_alpha = self.autocorrel_alpha,
subsample=numpy.mean, do_correl=self.do_correl, mcbs_enable=self.mcbs_enable )
cis[iblock]['iter_start'] = iter_start
cis[iblock]['iter_stop'] = block_iter_stop
cis[iblock]['expected'], cis[iblock]['ci_lbound'], cis[iblock]['ci_ubound'] = avg, ci_lb, ci_ub
cis[iblock]['corr_len'] = correl_len
cis[iblock]['sterr'] = sterr
del fluxes
cis_ds = target_group.create_dataset('flux_evolution', data=cis)
cis_ds.attrs['iter_step'] = self.evol_step
cis_ds.attrs['mcbs_alpha'] = self.alpha
cis_ds.attrs['mcbs_autocorrel_alpha'] = self.autocorrel_alpha
cis_ds.attrs['mcbs_n_sets'] = self.n_sets
def go(self):
self.calc_store_flux_data()
if self.do_evol:
self.calc_evol_flux()
class WNTopTool(WESTTool):
prog='w_ntop'
description = '''\
Select walkers from bins . An assignment file mapping walkers to
bins at each timepoint is required (see``w_assign --help`` for further
information on generating this file). By default, high-weight walkers are
selected (hence the name ``w_ntop``: select the N top-weighted walkers from
each bin); however, minimum weight walkers and randomly-selected walkers
may be selected instead.
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, by default "ntop.h5") contains the following
datasets:
``/n_iter`` [iteration]
*(Integer)* Iteration numbers for each entry in other datasets.
``/n_segs`` [iteration][bin]
*(Integer)* Number of segments in each bin/state in the given iteration.
This will generally be the same as the number requested with
``--n/--count`` but may be smaller if the requested number of walkers
does not exist.
``/seg_ids`` [iteration][bin][segment]
*(Integer)* Matching segments in each iteration for each bin.
For an iteration ``n_iter``, only the first ``n_iter`` entries are
valid. For example, the full list of matching seg_ids in bin 0 in the
first stored iteration is ``seg_ids[0][0][:n_segs[0]]``.
``/weights`` [iteration][bin][segment]
*(Floating-point)* Weights for each matching segment in ``/seg_ids``.
-----------------------------------------------------------------------------
Command-line arguments
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WNTopTool,self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.assignments_filename = None
self.output_filename = None
self.what = None
self.timepoint = None
self.count = None
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
igroup = parser.add_argument_group('input options')
igroup.add_argument('-a', '--assignments', default='assign.h5',
help='''Use assignments from the given ASSIGNMENTS file (default: %(default)s).''')
sgroup = parser.add_argument_group('selection options')
sgroup.add_argument('-n', '--count', type=int, default=1,
help='''Select COUNT walkers from each iteration for each bin (default: %(default)s).''')
sgroup.add_argument('-t', '--timepoint', type=int, default=-1,
help='''Base selection on the given TIMEPOINT within each iteration. Default (-1)
corresponds to the last timepoint.''')
cgroup = parser.add_mutually_exclusive_group()
cgroup.add_argument('--highweight', dest='select_what', action='store_const', const='highweight',
help='''Select COUNT highest-weight walkers from each bin.''')
cgroup.add_argument('--lowweight', dest='select_what', action='store_const', const='lowweight',
help='''Select COUNT lowest-weight walkers from each bin.''')
cgroup.add_argument('--random', dest='select_what', action='store_const', const='random',
help='''Select COUNT walkers randomly from each bin.''')
parser.set_defaults(select_what='highweight')
ogroup = parser.add_argument_group('output options')
ogroup.add_argument('-o', '--output', default='ntop.h5',
help='''Write output to OUTPUT (default: %(default)s).''')
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
self.what = args.select_what
self.output_filename = args.output
self.assignments_filename = args.assignments
self.count = args.count
self.timepoint = args.timepoint
def go(self):
self.data_reader.open('r')
assignments_file = h5py.File(self.assignments_filename, mode='r')
output_file = h5io.WESTPAH5File(self.output_filename, mode='w')
pi = self.progress.indicator
count = self.count
timepoint = self.timepoint
nbins = assignments_file.attrs['nbins']+1
assignments_ds = assignments_file['assignments']
iter_start, iter_stop = self.iter_range.iter_start, self.iter_range.iter_stop
iter_count = iter_stop - iter_start
h5io.check_iter_range_least(assignments_ds, iter_start, iter_stop)
nsegs = assignments_file['nsegs'][h5io.get_iteration_slice(assignments_file['nsegs'], iter_start,iter_stop)]
output_file.create_dataset('n_iter', dtype=n_iter_dtype, data=range(iter_start,iter_stop))
seg_count_ds = output_file.create_dataset('nsegs', dtype=numpy.uint, shape=(iter_count,nbins))
matching_segs_ds = output_file.create_dataset('seg_ids', shape=(iter_count,nbins,count),
dtype=seg_id_dtype,
chunks=h5io.calc_chunksize((iter_count,nbins,count), seg_id_dtype),
shuffle=True, compression=9)
weights_ds = output_file.create_dataset('weights', shape=(iter_count,nbins,count),
dtype=weight_dtype,
chunks=h5io.calc_chunksize((iter_count,nbins,count), weight_dtype),
shuffle=True,compression=9)
what = self.what
with pi:
pi.new_operation('Finding matching segments', extent=iter_count)
for iiter, n_iter in enumerate(xrange(iter_start, iter_stop)):
assignments = numpy.require(assignments_ds[h5io.get_iteration_entry(assignments_ds, n_iter)
+ numpy.index_exp[:,timepoint]], dtype=westpa.binning.index_dtype)
all_weights = self.data_reader.get_iter_group(n_iter)['seg_index']['weight']
# the following Cython function just executes this loop:
#for iseg in xrange(nsegs[iiter]):
# segs_by_bin[iseg,assignments[iseg]] = True
segs_by_bin = assignments_list_to_table(nsegs[iiter],nbins,assignments)
for ibin in xrange(nbins):
segs = numpy.nonzero(segs_by_bin[:,ibin])[0]
seg_count_ds[iiter,ibin] = min(len(segs),count)
if len(segs):
weights = all_weights.take(segs)
if what == 'lowweight':
indices = numpy.argsort(weights)[:count]
elif what == 'highweight':
indices = numpy.argsort(weights)[::-1][:count]
else:
assert what == 'random'
indices = numpy.random.permutation(len(weights))
matching_segs_ds[iiter,ibin,:len(segs)] = segs.take(indices)
weights_ds[iiter,ibin,:len(segs)] = weights.take(indices)
del segs, weights
del assignments, segs_by_bin, all_weights
pi.progress += 1
class KinAvgSubcommands(WESTSubcommand):
'''Common argument processing for w_kinavg subcommands'''
def __init__(self, parent):
super(KinAvgSubcommands, self).__init__(parent)
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.kinetics_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
def stamp_mcbs_info(self, dataset):
dataset.attrs['mcbs_alpha'] = self.mcbs_alpha
dataset.attrs['mcbs_acalpha'] = self.mcbs_acalpha
dataset.attrs['mcbs_nsets'] = self.mcbs_nsets
def add_args(self, parser):
self.progress.add_args(parser)
self.data_reader.add_args(parser)
self.iter_range.include_args['iter_step'] = True
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument(
'-a',
'--assignments',
default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
# self.default_kinetics_file will be picked up as a class attribute from the appropriate subclass
iogroup.add_argument(
'-k',
'--kinetics',
default=self.default_kinetics_file,
help='''Populations and transition rates are stored in KINETICS
(default: %(default)s).''')
iogroup.add_argument(
'-o',
'--output',
dest='output',
default='kinavg.h5',
help='''Store results in OUTPUT (default: %(default)s).''')
cgroup = parser.add_argument_group(
'confidence interval calculation options')
cgroup.add_argument('--alpha',
type=float,
default=0.05,
help='''Calculate a (1-ALPHA) confidence interval'
(default: %(default)s)''')
cgroup.add_argument(
'--autocorrel-alpha',
type=float,
dest='acalpha',
metavar='ACALPHA',
help='''Evaluate autocorrelation to (1-ACALPHA) significance.
Note that too small an ACALPHA will result in failure to detect autocorrelation
in a noisy flux signal. (Default: same as ALPHA.)'''
)
cgroup.add_argument(
'--nsets',
type=int,
help=
'''Use NSETS samples for bootstrapping (default: chosen based on ALPHA)'''
)
cogroup = parser.add_argument_group('calculation options')
cogroup.add_argument(
'-e',
'--evolution-mode',
choices=['cumulative', 'blocked', 'none'],
default='none',
help='''How to calculate time evolution of rate estimates.
``cumulative`` evaluates rates over windows starting with --start-iter and getting progressively
wider to --stop-iter by steps of --step-iter.
``blocked`` evaluates rates over windows of width --step-iter, the first of which begins at
--start-iter.
``none`` (the default) disables calculation of the time evolution of rate estimates.'''
)
cogroup.add_argument(
'--window-frac',
type=float,
default=1.0,
help=
'''Fraction of iterations to use in each window when running in ``cumulative`` mode.
The (1 - frac) fraction of iterations will be discarded from the start of each window.'''
)
def open_files(self):
self.output_file = h5io.WESTPAH5File(self.output_filename,
'w',
creating_program=True)
h5io.stamp_creator_data(self.output_file)
self.assignments_file = h5io.WESTPAH5File(
self.assignments_filename,
'r') #, driver='core', backing_store=False)
self.kinetics_file = h5io.WESTPAH5File(
self.kinetics_filename,
'r') #, driver='core', backing_store=False)
if not self.iter_range.check_data_iter_range_least(
self.assignments_file):
raise ValueError(
'assignments data do not span the requested iterations')
if not self.iter_range.check_data_iter_range_least(self.kinetics_file):
raise ValueError(
'kinetics data do not span the requested iterations')
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(
1,
(self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.kinetics_filename = args.kinetics
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(
self.mcbs_alpha)
self.evolution_mode = args.evolution_mode
self.evol_window_frac = args.window_frac
if self.evol_window_frac <= 0 or self.evol_window_frac > 1:
raise ValueError(
'Parameter error -- fractional window defined by --window-frac must be in (0,1]'
)
class WSelectTool(WESTParallelTool):
prog = 'w_select'
description = '''\
Select dynamics segments matching various criteria. This requires a
user-provided prediate function. By default, only matching segments are
stored. If the -a/--include-ancestors option is given, then matching segments
and their ancestors will be stored.
-----------------------------------------------------------------------------
Predicate function
-----------------------------------------------------------------------------
Segments are selected based on a predicate function, which must be callable
as ``predicate(n_iter, iter_group)`` and return a collection of segment IDs
matching the predicate in that iteration.
The predicate may be inverted by specifying the -v/--invert command-line
argument.
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, by default "select.h5") contains the following
datasets:
``/n_iter`` [iteration]
*(Integer)* Iteration numbers for each entry in other datasets.
``/n_segs`` [iteration]
*(Integer)* Number of segment IDs matching the predicate (or inverted
predicate, if -v/--invert is specified) in the given iteration.
``/seg_ids`` [iteration][segment]
*(Integer)* Matching segments in each iteration. For an iteration
``n_iter``, only the first ``n_iter`` entries are valid. For example,
the full list of matching seg_ids in the first stored iteration is
``seg_ids[0][:n_segs[0]]``.
``/weights`` [iteration][segment]
*(Floating-point)* Weights for each matching segment in ``/seg_ids``.
-----------------------------------------------------------------------------
Command-line arguments
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WSelectTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_file = None
self.output_filename = None
self.predicate = None
self.invert = False
self.include_ancestors = False
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
sgroup = parser.add_argument_group('selection options')
sgroup.add_argument(
'-p',
'--predicate-function',
metavar='MODULE.FUNCTION',
help=
'''Use the given predicate function to match segments. This function
should take an iteration number and the HDF5 group corresponding to that
iteration and return a sequence of seg_ids matching the predicate, as in
``match_predicate(n_iter, iter_group)``.''')
sgroup.add_argument('-v',
'--invert',
dest='invert',
action='store_true',
help='''Invert the match predicate.''')
sgroup.add_argument(
'-a',
'--include-ancestors',
action='store_true',
help='''Include ancestors of matched segments in output.''')
ogroup = parser.add_argument_group('output options')
ogroup.add_argument(
'-o',
'--output',
default='select.h5',
help='''Write output to OUTPUT (default: %(default)s).''')
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
predicate = get_object(args.predicate_function, path=['.'])
if not callable(predicate):
raise TypeError(
'predicate object {!r} is not callable'.format(predicate))
self.predicate = predicate
self.invert = bool(args.invert)
self.include_ancestors = bool(args.include_ancestors)
self.output_filename = args.output
def go(self):
self.data_reader.open('r')
output_file = h5io.WESTPAH5File(self.output_filename, mode='w')
pi = self.progress.indicator
iter_start, iter_stop = self.iter_range.iter_start, self.iter_range.iter_stop
iter_count = iter_stop - iter_start
output_file.create_dataset('n_iter',
dtype=n_iter_dtype,
data=list(range(iter_start, iter_stop)))
current_seg_count = 0
seg_count_ds = output_file.create_dataset('n_segs',
dtype=numpy.uint,
shape=(iter_count, ))
matching_segs_ds = output_file.create_dataset(
'seg_ids',
shape=(iter_count, 0),
maxshape=(iter_count, None),
dtype=seg_id_dtype,
chunks=h5io.calc_chunksize((iter_count, 1000000), seg_id_dtype),
shuffle=True,
compression=9)
weights_ds = output_file.create_dataset('weights',
shape=(iter_count, 0),
maxshape=(iter_count, None),
dtype=weight_dtype,
chunks=h5io.calc_chunksize(
(iter_count, 1000000),
weight_dtype),
shuffle=True,
compression=9)
with pi:
pi.new_operation('Finding matching segments', extent=iter_count)
# futures = set()
# for n_iter in xrange(iter_start,iter_stop):
# futures.add(self.work_manager.submit(_find_matching_segments,
# args=(self.data_reader.we_h5filename,n_iter,self.predicate,self.invert)))
# for future in self.work_manager.as_completed(futures):
for future in self.work_manager.submit_as_completed(
((_find_matching_segments,
(self.data_reader.we_h5filename, n_iter, self.predicate,
self.invert), {})
for n_iter in range(iter_start, iter_stop)),
self.max_queue_len):
n_iter, matching_ids = future.get_result()
n_matches = len(matching_ids)
if n_matches:
if n_matches > current_seg_count:
current_seg_count = len(matching_ids)
matching_segs_ds.resize((iter_count, n_matches))
weights_ds.resize((iter_count, n_matches))
current_seg_count = n_matches
seg_count_ds[n_iter - iter_start] = n_matches
matching_segs_ds[n_iter -
iter_start, :n_matches] = matching_ids
weights_ds[n_iter - iter_start, :
n_matches] = self.data_reader.get_iter_group(
n_iter)['seg_index']['weight'][sorted(
matching_ids)]
del matching_ids
pi.progress += 1
if self.include_ancestors:
pi.new_operation('Tracing ancestors of matching segments',
extent=iter_count)
from_previous = set()
current_seg_count = matching_segs_ds.shape[1]
for n_iter in range(iter_stop - 1, iter_start - 1, -1):
iiter = n_iter - iter_start
n_matches = seg_count_ds[iiter]
matching_ids = set(from_previous)
if n_matches:
matching_ids.update(
matching_segs_ds[iiter, :seg_count_ds[iiter]])
from_previous.clear()
n_matches = len(matching_ids)
if n_matches > current_seg_count:
matching_segs_ds.resize((iter_count, n_matches))
weights_ds.resize((iter_count, n_matches))
current_seg_count = n_matches
if n_matches > 0:
seg_count_ds[iiter] = n_matches
matching_ids = sorted(matching_ids)
matching_segs_ds[iiter, :n_matches] = matching_ids
weights_ds[
iiter, :
n_matches] = self.data_reader.get_iter_group(
n_iter)['seg_index']['weight'][sorted(
matching_ids)]
parent_ids = self.data_reader.get_iter_group(n_iter)[
'seg_index']['parent_id'][sorted(matching_ids)]
from_previous.update(
parent_id for parent_id in parent_ids
if parent_id >= 0) # filter initial states
del parent_ids
del matching_ids
pi.progress += 1
class StateProbTool(WESTParallelTool):
prog = 'w_stateprobs'
description = '''\
Calculate average populations and associated errors in state populations from
weighted ensemble data. Bin assignments, including macrostate definitions,
are required. (See "w_assign --help" for more information).
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, usually "stateprobs.h5") contains the following
dataset:
/avg_state_pops [state]
(Structured -- see below) Population of each state across entire
range specified.
If --evolution-mode is specified, then the following additional dataset is
available:
/state_pop_evolution [window][state]
(Structured -- see below). State populations based on windows of
iterations of varying width. If --evolution-mode=cumulative, then
these windows all begin at the iteration specified with
--start-iter and grow in length by --step-iter for each successive
element. If --evolution-mode=blocked, then these windows are all of
width --step-iter (excluding the last, which may be shorter), the first
of which begins at iteration --start-iter.
The structure of these datasets is as follows:
iter_start
(Integer) Iteration at which the averaging window begins (inclusive).
iter_stop
(Integer) Iteration at which the averaging window ends (exclusive).
expected
(Floating-point) Expected (mean) value of the rate as evaluated within
this window, in units of inverse tau.
ci_lbound
(Floating-point) Lower bound of the confidence interval on the rate
within this window, in units of inverse tau.
ci_ubound
(Floating-point) Upper bound of the confidence interval on the rate
within this window, in units of inverse tau.
corr_len
(Integer) Correlation length of the rate within this window, in units
of tau.
Each of these datasets is also stamped with a number of attributes:
mcbs_alpha
(Floating-point) Alpha value of confidence intervals. (For example,
*alpha=0.05* corresponds to a 95% confidence interval.)
mcbs_nsets
(Integer) Number of bootstrap data sets used in generating confidence
intervals.
mcbs_acalpha
(Floating-point) Alpha value for determining correlation lengths.
-----------------------------------------------------------------------------
Command-line options
-----------------------------------------------------------------------------
'''
def __init__(self):
super(StateProbTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.output_file = None
self.assignments_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
def stamp_mcbs_info(self, dataset):
dataset.attrs['mcbs_alpha'] = self.mcbs_alpha
dataset.attrs['mcbs_acalpha'] = self.mcbs_acalpha
dataset.attrs['mcbs_nsets'] = self.mcbs_nsets
def add_args(self, parser):
self.progress.add_args(parser)
self.data_reader.add_args(parser)
self.iter_range.include_args['iter_step'] = True
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument(
'-a',
'--assignments',
default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
iogroup.add_argument(
'-o',
'--output',
dest='output',
default='stateprobs.h5',
help='''Store results in OUTPUT (default: %(default)s).''')
cgroup = parser.add_argument_group(
'confidence interval calculation options')
cgroup.add_argument('--alpha',
type=float,
default=0.05,
help='''Calculate a (1-ALPHA) confidence interval'
(default: %(default)s)''')
cgroup.add_argument(
'--autocorrel-alpha',
type=float,
dest='acalpha',
metavar='ACALPHA',
help='''Evaluate autocorrelation to (1-ACALPHA) significance.
Note that too small an ACALPHA will result in failure to detect autocorrelation
in a noisy flux signal. (Default: same as ALPHA.)'''
)
cgroup.add_argument(
'--nsets',
type=int,
help=
'''Use NSETS samples for bootstrapping (default: chosen based on ALPHA)'''
)
cogroup = parser.add_argument_group('calculation options')
cogroup.add_argument(
'-e',
'--evolution-mode',
choices=['cumulative', 'blocked', 'none'],
default='none',
help='''How to calculate time evolution of rate estimates.
``cumulative`` evaluates rates over windows starting with --start-iter and getting progressively
wider to --stop-iter by steps of --step-iter.
``blocked`` evaluates rates over windows of width --step-iter, the first of which begins at
--start-iter.
``none`` (the default) disables calculation of the time evolution of rate estimates.'''
)
def open_files(self):
self.output_file = h5io.WESTPAH5File(self.output_filename,
'w',
creating_program=True)
h5io.stamp_creator_data(self.output_file)
self.assignments_file = h5io.WESTPAH5File(
self.assignments_filename,
'r') #, driver='core', backing_store=False)
if not self.iter_range.check_data_iter_range_least(
self.assignments_file):
raise ValueError(
'assignments data do not span the requested iterations')
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(
1,
(self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(
self.mcbs_alpha)
self.evolution_mode = args.evolution_mode
def calc_state_pops(self):
start_iter, stop_iter = self.iter_range.iter_start, self.iter_range.iter_stop
nstates = self.nstates
state_map = self.state_map
iter_count = stop_iter - start_iter
pi = self.progress.indicator
pi.new_operation('Calculating state populations')
pops = h5io.IterBlockedDataset(
self.assignments_file['labeled_populations'])
iter_state_pops = numpy.empty((nstates + 1, ), weight_dtype)
all_state_pops = numpy.empty((iter_count, nstates + 1), weight_dtype)
avg_state_pops = numpy.zeros((nstates + 1, ), weight_dtype)
pops.cache_data(max_size='available')
try:
for iiter, n_iter in enumerate(xrange(start_iter, stop_iter)):
iter_state_pops.fill(0)
labeled_pops = pops.iter_entry(n_iter)
accumulate_state_populations_from_labeled(
labeled_pops,
state_map,
iter_state_pops,
check_state_map=False)
all_state_pops[iiter] = iter_state_pops
avg_state_pops += iter_state_pops
del labeled_pops
pi.progress += 1
finally:
pops.drop_cache()
self.output_file.create_dataset('state_pops',
data=all_state_pops,
compression=9,
shuffle=True)
h5io.stamp_iter_range(self.output_file['state_pops'], start_iter,
stop_iter)
self.all_state_pops = all_state_pops
avg_state_pops = numpy.zeros((nstates + 1, ), ci_dtype)
pi.new_operation('Calculating overall average populations and CIs',
nstates)
# futures = []
# for istate in xrange(nstates):
# futures.append(self.work_manager.submit(_eval_block,kwargs=dict(iblock=None,istate=istate,
# start=start_iter,stop=stop_iter,
# state_pops=all_state_pops[:,istate],
# mcbs_alpha=self.mcbs_alpha, mcbs_nsets=self.mcbs_nsets,
# mcbs_acalpha = self.mcbs_acalpha)))
# for future in self.work_manager.as_completed(futures):
def taskgen():
for istate in xrange(nstates):
yield (_eval_block, (),
dict(iblock=None,
istate=istate,
start=start_iter,
stop=stop_iter,
state_pops=all_state_pops[:, istate],
mcbs_alpha=self.mcbs_alpha,
mcbs_nsets=self.mcbs_nsets,
mcbs_acalpha=self.mcbs_acalpha))
for future in self.work_manager.submit_as_completed(
taskgen(), self.max_queue_len):
(_iblock, istate, ci_res) = future.get_result(discard=True)
avg_state_pops[istate] = ci_res
pi.progress += 1
self.output_file['avg_state_pops'] = avg_state_pops
self.stamp_mcbs_info(self.output_file['avg_state_pops'])
pi.clear()
maxlabellen = max(map(len, self.state_labels))
print('average state populations:')
for istate in xrange(nstates):
print(
'{:{maxlabellen}s}: mean={:21.15e} CI=({:21.15e}, {:21.15e})'.
format(self.state_labels[istate],
avg_state_pops['expected'][istate],
avg_state_pops['ci_lbound'][istate],
avg_state_pops['ci_ubound'][istate],
maxlabellen=maxlabellen))
def calc_evolution(self):
nstates = self.nstates
start_iter, stop_iter, step_iter = self.iter_range.iter_start, self.iter_range.iter_stop, self.iter_range.iter_step
start_pts = range(start_iter, stop_iter, step_iter)
pop_evol = numpy.zeros((len(start_pts), nstates), dtype=ci_dtype)
pi = self.progress.indicator
pi.new_operation('Calculating population evolution',
len(start_pts) * nstates)
# futures = []
# for iblock, start in enumerate(start_pts):
# if self.evolution_mode == 'cumulative':
# block_start = start_iter
# else: # self.evolution_mode == 'blocked'
# block_start = start
# stop = min(start+step_iter, stop_iter)
#
# for istate in xrange(nstates):
# future = self.work_manager.submit(_eval_block,kwargs=dict(iblock=iblock,istate=istate,
# start=block_start,stop=stop,
# state_pops=self.all_state_pops[block_start-start_iter:stop-start_iter,istate],
# mcbs_alpha=self.mcbs_alpha, mcbs_nsets=self.mcbs_nsets,
# mcbs_acalpha = self.mcbs_acalpha))
# futures.append(future)
def taskgen():
for iblock, start in enumerate(start_pts):
if self.evolution_mode == 'cumulative':
block_start = start_iter
else: # self.evolution_mode == 'blocked'
block_start = start
stop = min(start + step_iter, stop_iter)
for istate in xrange(nstates):
yield (_eval_block, (),
dict(
iblock=iblock,
istate=istate,
start=block_start,
stop=stop,
state_pops=self.all_state_pops[block_start -
start_iter:stop -
start_iter,
istate],
mcbs_alpha=self.mcbs_alpha,
mcbs_nsets=self.mcbs_nsets,
mcbs_acalpha=self.mcbs_acalpha))
#for future in self.work_manager.as_completed(futures):
for future in self.work_manager.submit_as_completed(
taskgen(), self.max_queue_len):
(iblock, istate, ci_res) = future.get_result(discard=True)
pop_evol[iblock, istate] = ci_res
pi.progress += 1
self.output_file.create_dataset('state_pop_evolution',
data=pop_evol,
shuffle=True,
compression=9)
pi.clear()
def go(self):
pi = self.progress.indicator
with pi:
pi.new_operation('Initializing')
self.open_files()
nstates = self.nstates = self.assignments_file.attrs['nstates']
state_labels = self.state_labels = self.assignments_file[
'state_labels'][...]
state_map = self.state_map = self.assignments_file['state_map'][
...]
if (state_map > nstates).any():
raise ValueError('invalid state mapping')
# copy metadata to output
self.output_file.attrs['nstates'] = nstates
self.output_file['state_labels'] = state_labels
# calculate overall averages
self.calc_state_pops()
# calculate evolution, if requested
if self.evolution_mode != 'none' and self.iter_range.iter_step:
self.calc_evolution()
class KinAvgSubcommands(WESTSubcommand):
'''Common argument processing for w_kinavg subcommands'''
def __init__(self, parent):
super(KinAvgSubcommands,self).__init__(parent)
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.kinetics_file = None
self.evolution_mode = None
self.mcbs_alpha = None
self.mcbs_acalpha = None
self.mcbs_nsets = None
def stamp_mcbs_info(self, dataset):
dataset.attrs['mcbs_alpha'] = self.mcbs_alpha
dataset.attrs['mcbs_acalpha'] = self.mcbs_acalpha
dataset.attrs['mcbs_nsets'] = self.mcbs_nsets
def add_args(self, parser):
self.progress.add_args(parser)
self.data_reader.add_args(parser)
self.iter_range.include_args['iter_step'] = True
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument('-a', '--assignments', default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
# self.default_kinetics_file will be picked up as a class attribute from the appropriate subclass
iogroup.add_argument('-k', '--kinetics', default=self.default_kinetics_file,
help='''Populations and transition rates are stored in KINETICS
(default: %(default)s).''')
iogroup.add_argument('-o', '--output', dest='output', default='kinavg.h5',
help='''Store results in OUTPUT (default: %(default)s).''')
cgroup = parser.add_argument_group('confidence interval calculation options')
cgroup.add_argument('--alpha', type=float, default=0.05,
help='''Calculate a (1-ALPHA) confidence interval'
(default: %(default)s)''')
cgroup.add_argument('--autocorrel-alpha', type=float, dest='acalpha', metavar='ACALPHA',
help='''Evaluate autocorrelation to (1-ACALPHA) significance.
Note that too small an ACALPHA will result in failure to detect autocorrelation
in a noisy flux signal. (Default: same as ALPHA.)''')
cgroup.add_argument('--nsets', type=int,
help='''Use NSETS samples for bootstrapping (default: chosen based on ALPHA)''')
cogroup = parser.add_argument_group('calculation options')
cogroup.add_argument('-e', '--evolution-mode', choices=['cumulative', 'blocked', 'none'], default='none',
help='''How to calculate time evolution of rate estimates.
``cumulative`` evaluates rates over windows starting with --start-iter and getting progressively
wider to --stop-iter by steps of --step-iter.
``blocked`` evaluates rates over windows of width --step-iter, the first of which begins at
--start-iter.
``none`` (the default) disables calculation of the time evolution of rate estimates.''')
cogroup.add_argument('--window-frac', type=float, default=1.0,
help='''Fraction of iterations to use in each window when running in ``cumulative`` mode.
The (1 - frac) fraction of iterations will be discarded from the start of each window.''')
def open_files(self):
self.output_file = h5io.WESTPAH5File(self.output_filename, 'w', creating_program=True)
h5io.stamp_creator_data(self.output_file)
self.assignments_file = h5io.WESTPAH5File(self.assignments_filename, 'r')#, driver='core', backing_store=False)
self.kinetics_file = h5io.WESTPAH5File(self.kinetics_filename, 'r')#, driver='core', backing_store=False)
if not self.iter_range.check_data_iter_range_least(self.assignments_file):
raise ValueError('assignments data do not span the requested iterations')
if not self.iter_range.check_data_iter_range_least(self.kinetics_file):
raise ValueError('kinetics data do not span the requested iterations')
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(1, (self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.kinetics_filename = args.kinetics
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(self.mcbs_alpha)
self.evolution_mode = args.evolution_mode
self.evol_window_frac = args.window_frac
if self.evol_window_frac <= 0 or self.evol_window_frac > 1:
raise ValueError('Parameter error -- fractional window defined by --window-frac must be in (0,1]')
class WCrawl(WESTParallelTool):
prog='w_crawl'
description = '''\
Crawl a weighted ensemble dataset, executing a function for each iteration.
This can be used for postprocessing of trajectories, cleanup of datasets,
or anything else that can be expressed as "do X for iteration N, then do
something with the result". Tasks are parallelized by iteration, and
no guarantees are made about evaluation order.
-----------------------------------------------------------------------------
Command-line options
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WCrawl,self).__init__()
# These are used throughout
self.progress = ProgressIndicatorComponent()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection(self.data_reader)
self.crawler = None
self.task_callable = None
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
tgroup = parser.add_argument_group('task options')
tgroup.add_argument('-c', '--crawler-instance',
help='''Use CRAWLER_INSTANCE (specified as module.instance) as an instance of
WESTPACrawler to coordinate the calculation. Required only if initialization,
finalization, or task result processing is required.''')
tgroup.add_argument('task_callable',
help='''Run TASK_CALLABLE (specified as module.function) on each iteration.
Required.''')
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
self.task_callable = get_object(args.task_callable, path=['.'])
if args.crawler_instance is not None:
self.crawler = get_object(args.crawler_instance, path=['.'])
else:
self.crawler = WESTPACrawler()
def go(self):
iter_start = self.iter_range.iter_start
iter_stop = self.iter_range.iter_stop
iter_count = iter_stop - iter_start
self.data_reader.open('r')
pi = self.progress.indicator
with pi:
pi.operation = 'Initializing'
self.crawler.initialize(iter_start, iter_stop)
try:
pi.new_operation('Dispatching tasks & processing results', iter_count)
task_gen = ((_remote_task, (n_iter, self.task_callable), {}) for n_iter in range(iter_start,iter_stop))
for future in self.work_manager.submit_as_completed(task_gen, self.max_queue_len):
n_iter, result = future.get_result(discard=True)
if self.crawler is not None:
self.crawler.process_iter_result(n_iter,result)
pi.progress += 1
finally:
pi.new_operation('Finalizing')
self.crawler.finalize()
class WNetworker(WESTTool):
prog = "w_networker"
description = """\
Makes a network file from a transition matrix that can be visualized
by most graph programs.
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, by default "network.gml") contains the network
as described by the transition matrix found in the transition matrix file
-----------------------------------------------------------------------------
Command-line arguments
-----------------------------------------------------------------------------
"""
def __init__(self):
super(WNetworker, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.tm_filename = None
self.postprocess_function = None
def add_args(self, parser):
self.data_reader.add_args(parser)
self.iter_range.add_args(parser)
igroup = parser.add_argument_group("input options")
# TODO: Get WESTPA h5 file and add some stuff from it into nodes
igroup.add_argument(
"-tm",
"--transition-matrix",
default="tm.h5",
help="""Use transition matrix from the"""
"""resulting h5 file of w_reweigh (default: %(default)s).""",
)
ogroup = parser.add_argument_group("output options")
ogroup.add_argument(
"-o",
"--output",
default="network.gml",
help="""Write output to OUTPUT (default: %(default)s).""",
)
ppgroup = parser.add_argument_group("postprocess options")
ppgroup.add_argument(
"--postprocess-function",
help=
"""Names a function (as in module.function) that will be called just prior
to saving the graph. The function will be called as ``postprocess(G, tm, prob)``
where ``G`` is the fully built networkx graph, ``tm`` is the transition matrix
used to build the graph and ``prob`` is the probability distribution used""",
)
self.progress.add_args(parser)
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args)
# Set the attributes according to arguments
self.output_filename = args.output
self.tm_filename = args.transition_matrix
if args.postprocess_function:
self.postprocess_function = get_object(args.postprocess_function,
path=["."])
def _load_from_h5(self, fname, istart, istop):
tmh5 = h5py.File(fname, "r")
# We will need the number of rows and columns to convert from
# sparse matrix format
nrows = tmh5.attrs["nrows"]
ncols = tmh5.attrs["ncols"]
# gotta average over iterations
tm = None
for it in range(istart, istop):
it_str = "iter_{:08}".format(it)
col = tmh5["iterations"][it_str]["cols"]
row = tmh5["iterations"][it_str]["rows"]
flux = tmh5["iterations"][it_str]["flux"]
ctm = coo_matrix((flux, (row, col)),
shape=(nrows, ncols)).toarray()
if tm is None:
tm = ctm
else:
tm += ctm
# We need to convert the "non-markovian" matrix to
# a markovian matrix here
# TODO: support more than 2 states
# Not as straight forward as it seems since there is the
# "unknown" state to deal with and it requires a funky
# fix to go from non-markovian to markovian matrix
nstates = 2
mnrows = int(nrows / nstates)
mncols = int(ncols / nstates)
mtm = numpy.zeros((mnrows, mncols), dtype=flux.dtype)
for i in range(mnrows):
for j in range(mncols):
mtm[i, j] = tm[i * 2:(i + 1) * 2, j * 2:(j + 1) * 2].sum()
mtm = mtm / len(tmh5["iterations"])
# Let's also get probabilities
bin_probs = tmh5["bin_populations"]
avg_bin_probs = numpy.average(bin_probs[istart:istop],
axis=0) / nstates
prob = avg_bin_probs.reshape(mnrows, nstates).sum(axis=1)
return mtm, prob
def read_tmfile(self, fname, istart, istop):
if fname.endswith(".h5"):
tm, prob = self._load_from_h5(fname, istart, istop)
else:
# TODO: error out
pass
return tm, prob
def save_graph(self, outname, graph):
# determine save function
if outname.endswith(".gml"):
func = nx.write_gml
else:
# TODO: error out
pass
func(graph, outname)
def go(self):
self.data_reader.open("r")
# Get the iterations we want to average the tm if needed
iter_start, iter_stop = self.iter_range.iter_start, self.iter_range.iter_stop
# Read transition matrix and probabilities
tm, prob = self.read_tmfile(self.tm_filename, iter_start, iter_stop)
# Start the progress indicator and work on the graph
pi = self.progress.indicator
with pi:
node_sizes = prob
edge_sizes = tm
pi.new_operation("Building graph, adding nodes",
extent=len(node_sizes))
G = nx.DiGraph()
for i in range(tm.shape[0]):
if node_sizes[i] > 0:
G.add_node(i, weight=float(node_sizes[i]))
pi.progress += 1
pi.new_operation("Adding edges", extent=len(edge_sizes.flatten()))
for i in range(tm.shape[0]):
for j in range(tm.shape[1]):
if edge_sizes[i][j] > 0:
G.add_edge(i, j, weight=float(edge_sizes[i][j]))
pi.progress += 1
if self.postprocess_function:
self.postprocess_function(G, tm, prob)
self.save_graph(self.output_filename, G)
class WPostAnalysisReweightTool(WESTTool):
prog ='w_postanalysis_reweight'
description = '''\
Calculate average rates from weighted ensemble data using the postanalysis
reweighting scheme. Bin assignments (usually "assignments.h5") and pre-calculated
iteration flux matrices (usually "flux_matrices.h5") data files must have been
previously generated using w_postanalysis_matrix.py (see "w_assign --help" and
"w_kinetics --help" for information on generating these files).
-----------------------------------------------------------------------------
Output format
-----------------------------------------------------------------------------
The output file (-o/--output, usually "kinrw.h5") contains the following
dataset:
/state_prob_evolution [window,state]
The reweighted state populations based on windows
/color_prob_evolution [window,state]
The reweighted populations last assigned to each state based on windows
/bin_prob_evolution [window, bin]
The reweighted populations of each bin based on windows. Bins contain
one color each, so to recover the original un-colored spatial bins,
one must sum over all states.
/conditional_flux_evolution [window,state,state]
(Structured -- see below). State-to-state fluxes based on windows of
varying width
The structure of the final dataset is as follows:
iter_start
(Integer) Iteration at which the averaging window begins (inclusive).
iter_stop
(Integer) Iteration at which the averaging window ends (exclusive).
expected
(Floating-point) Expected (mean) value of the rate as evaluated within
this window, in units of inverse tau.
-----------------------------------------------------------------------------
Command-line options
-----------------------------------------------------------------------------
'''
def __init__(self):
super(WPostAnalysisReweightTool, self).__init__()
self.data_reader = WESTDataReader()
self.iter_range = IterRangeSelection()
self.progress = ProgressIndicatorComponent()
self.output_filename = None
self.kinetics_filename = None
self.assignment_filename = None
self.output_file = None
self.assignments_file = None
self.kinetics_file = None
self.evolution_mode = None
def add_args(self, parser):
self.progress.add_args(parser)
self.data_reader.add_args(parser)
self.iter_range.include_args['iter_step'] = True
self.iter_range.add_args(parser)
iogroup = parser.add_argument_group('input/output options')
iogroup.add_argument('-a', '--assignments', default='assign.h5',
help='''Bin assignments and macrostate definitions are in ASSIGNMENTS
(default: %(default)s).''')
iogroup.add_argument('-k', '--kinetics', default='flux_matrices.h5',
help='''Per-iteration flux matrices calculated by w_postanalysis_matrix
(default: %(default)s).''')
iogroup.add_argument('-o', '--output', dest='output', default='kinrw.h5',
help='''Store results in OUTPUT (default: %(default)s).''')
cogroup = parser.add_argument_group('calculation options')
cogroup.add_argument('-e', '--evolution-mode', choices=['cumulative', 'blocked'], default='cumulative',
help='''How to calculate time evolution of rate estimates.
``cumulative`` evaluates rates over windows starting with --start-iter and getting progressively
wider to --stop-iter by steps of --step-iter.
``blocked`` evaluates rates over windows of width --step-iter, the first of which begins at
--start-iter.''')
cogroup.add_argument('--window-frac', type=float, default=1.0,
help='''Fraction of iterations to use in each window when running in ``cumulative`` mode.
The (1 - frac) fraction of iterations will be discarded from the start of each window.''')
cogroup.add_argument('--obs-threshold', type=int, default=1,
help='''The minimum number of observed transitions between two states i and j necessary to include
fluxes in the reweighting estimate''')
def open_files(self):
self.output_file = h5io.WESTPAH5File(self.output_filename, 'w', creating_program=True)
h5io.stamp_creator_data(self.output_file)
self.assignments_file = h5io.WESTPAH5File(self.assignments_filename, 'r')#, driver='core', backing_store=False)
self.kinetics_file = h5io.WESTPAH5File(self.kinetics_filename, 'r')#, driver='core', backing_store=False)
if not self.iter_range.check_data_iter_range_least(self.assignments_file):
raise ValueError('assignments data do not span the requested iterations')
if not self.iter_range.check_data_iter_range_least(self.kinetics_file):
raise ValueError('kinetics data do not span the requested iterations')
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(1, (self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.kinetics_filename = args.kinetics
self.evolution_mode = args.evolution_mode
self.evol_window_frac = args.window_frac
if self.evol_window_frac <= 0 or self.evol_window_frac > 1:
raise ValueError('Parameter error -- fractional window defined by --window-frac must be in (0,1]')
self.obs_threshold = args.obs_threshold
def go(self):
pi = self.progress.indicator
with pi:
pi.new_operation('Initializing')
self.open_files()
nstates = self.assignments_file.attrs['nstates']
nbins = self.assignments_file.attrs['nbins']
state_labels = self.assignments_file['state_labels'][...]
state_map = self.assignments_file['state_map'][...]
nfbins = self.kinetics_file.attrs['nrows']
npts = self.kinetics_file.attrs['npts']
assert nstates == len(state_labels)
assert nfbins == nbins * nstates
start_iter, stop_iter, step_iter = self.iter_range.iter_start, self.iter_range.iter_stop, self.iter_range.iter_step
start_pts = range(start_iter, stop_iter, step_iter)
flux_evol = np.zeros((len(start_pts), nstates, nstates), dtype=ci_dtype)
color_prob_evol = np.zeros((len(start_pts), nstates))
state_prob_evol = np.zeros((len(start_pts), nstates))
bin_prob_evol = np.zeros((len(start_pts), nfbins))
pi.new_operation('Calculating flux evolution', len(start_pts))
if self.evolution_mode == 'cumulative' and self.evol_window_frac == 1.0:
print('Using fast streaming accumulation')
total_fluxes = np.zeros((nfbins, nfbins), weight_dtype)
total_obs = np.zeros((nfbins, nfbins), np.int64)
for iblock, start in enumerate(start_pts):
pi.progress += 1
stop = min(start + step_iter, stop_iter)
params = dict(start=start, stop=stop, nstates=nstates, nbins=nbins,
state_labels=state_labels, state_map=state_map, nfbins=nfbins,
total_fluxes=total_fluxes, total_obs=total_obs,
h5file=self.kinetics_file, obs_threshold=self.obs_threshold)
rw_state_flux, rw_color_probs, rw_state_probs, rw_bin_probs, rw_bin_flux = reweight(**params)
for k in xrange(nstates):
for j in xrange(nstates):
# Normalize such that we report the flux per tau (tau being the weighted ensemble iteration)
# npts always includes a 0th time point
flux_evol[iblock]['expected'][k,j] = rw_state_flux[k,j] * (npts - 1)
flux_evol[iblock]['iter_start'][k,j] = start
flux_evol[iblock]['iter_stop'][k,j] = stop
color_prob_evol[iblock] = rw_color_probs
state_prob_evol[iblock] = rw_state_probs[:-1]
bin_prob_evol[iblock] = rw_bin_probs
else:
for iblock, start in enumerate(start_pts):
pi.progress += 1
stop = min(start + step_iter, stop_iter)
if self.evolution_mode == 'cumulative':
windowsize = max(1, int(self.evol_window_frac * (stop - start_iter)))
block_start = max(start_iter, stop - windowsize)
else: # self.evolution_mode == 'blocked'
block_start = start
params = dict(start=block_start, stop=stop, nstates=nstates, nbins=nbins,
state_labels=state_labels, state_map=state_map, nfbins=nfbins,
total_fluxes=None, total_obs=None,
h5file=self.kinetics_file)
rw_state_flux, rw_color_probs, rw_state_probs, rw_bin_probs, rw_bin_flux = reweight(**params)
for k in xrange(nstates):
for j in xrange(nstates):
# Normalize such that we report the flux per tau (tau being the weighted ensemble iteration)
# npts always includes a 0th time point
flux_evol[iblock]['expected'][k,j] = rw_state_flux[k,j] * (npts - 1)
flux_evol[iblock]['iter_start'][k,j] = start
flux_evol[iblock]['iter_stop'][k,j] = stop
color_prob_evol[iblock] = rw_color_probs
state_prob_evol[iblock] = rw_state_probs[:-1]
bin_prob_evol[iblock] = rw_bin_probs
ds_flux_evol = self.output_file.create_dataset('conditional_flux_evolution', data=flux_evol, shuffle=True, compression=9)
ds_state_prob_evol = self.output_file.create_dataset('state_prob_evolution', data=state_prob_evol, compression=9)
ds_color_prob_evol = self.output_file.create_dataset('color_prob_evolution', data=color_prob_evol, compression=9)
ds_bin_prob_evol = self.output_file.create_dataset('bin_prob_evolution', data=bin_prob_evol, compression=9)
ds_state_labels = self.output_file.create_dataset('state_labels', data=state_labels)
