westpa 2022.12__cp313-cp313-macosx_10_13_x86_64.whl

westpa/cli/tools/w_reweight.py

@@ -0,0 +1,780 @@
+import logging
+import warnings
+
+import numpy as np
+
+from westpa.tools import WESTMasterCommand, WESTParallelTool
+
+from westpa.tools.kinetics_tool import WESTKineticsBase, AverageCommands, generate_future
+from westpa.core import h5io
+
+
+from westpa.mclib import mcbs_ci_correl
+
+from westpa.core.reweight import reweight_for_c, FluxMatrix
+
+
+warnings.filterwarnings('ignore', category=DeprecationWarning)
+warnings.filterwarnings('ignore', category=RuntimeWarning)
+warnings.filterwarnings('ignore', category=FutureWarning)
+
+log = logging.getLogger('w_reweight')
+
+
+def _2D_eval_block(
+    iblock, start, stop, nstates, data_input, name, mcbs_alpha, mcbs_nsets, mcbs_acalpha, do_correl, mcbs_enable, estimator_kwargs
+):
+    # As our reweighting estimator is a weird function, we can't use the general mclib block.
+    results = []
+    for istate in range(nstates):
+        for jstate in range(nstates):
+            if istate == jstate:
+                continue
+            estimator_kwargs.update(dict(istate=istate, jstate=jstate, nstates=nstates))
+
+            dataset = {'indices': np.array(list(range(start - 1, stop - 1)), dtype=np.uint16)}
+
+            ci_res = mcbs_ci_correl(
+                dataset,
+                estimator=reweight_for_c,
+                alpha=mcbs_alpha,
+                n_sets=mcbs_nsets,
+                autocorrel_alpha=mcbs_acalpha,
+                subsample=(lambda x: x[0]),
+                do_correl=do_correl,
+                mcbs_enable=mcbs_enable,
+                estimator_kwargs=estimator_kwargs,
+            )
+            results.append((name, iblock, istate, jstate, (start, stop) + ci_res))
+
+    return results
+
+
+def _1D_eval_block(
+    iblock, start, stop, nstates, data_input, name, mcbs_alpha, mcbs_nsets, mcbs_acalpha, do_correl, mcbs_enable, estimator_kwargs
+):
+    # As our reweighting estimator is a weird function, we can't use the general mclib block.
+    results = []
+    for istate in range(nstates):
+        # A little hack to make our estimator play nice, as jstate must be there.
+        # For 1D datasets (state probabilities, etc), the argument isn't used in our estimator,
+        # and so any variable which has the proper type is fine.
+        estimator_kwargs.update(dict(istate=istate, jstate=istate, nstates=nstates))
+
+        dataset = {'indices': np.array(list(range(start - 1, stop - 1)), dtype=np.uint16)}
+
+        ci_res = mcbs_ci_correl(
+            dataset,
+            estimator=reweight_for_c,
+            alpha=mcbs_alpha,
+            n_sets=mcbs_nsets,
+            autocorrel_alpha=mcbs_acalpha,
+            subsample=(lambda x: x[0]),
+            do_correl=do_correl,
+            mcbs_enable=mcbs_enable,
+            estimator_kwargs=estimator_kwargs,
+        )
+        results.append((name, iblock, istate, (start, stop) + ci_res))
+
+    return results
+
+
+def _pop_eval_block(
+    iblock,
+    start,
+    stop,
+    nstates,
+    data_input,
+    name,
+    mcbs_alpha,
+    mcbs_nsets,
+    mcbs_acalpha,
+    do_correl,
+    mcbs_enable,
+    estimator_kwargs,
+    **kwargs
+):
+    # As our reweighting estimator is a weird function, we can't use the general mclib block.
+    # A little hack to make our estimator play nice, as jstate must be there.
+    # For 1D datasets (state probabilities, etc), the argument isn't used in our estimator,
+    # and so any variable which has the proper type is fine.
+    estimator_kwargs.update(dict(istate=0, jstate=0, nstates=nstates))
+
+    estimator_kwargs.update({'indices': np.array(list(range(start - 1, stop - 1)), dtype=np.uint16), 'stride': 1})
+    # cpdef reweight_for_c(rows, cols, obs, flux, insert, indices, nstates, nbins, state_labels, state_map, nfbins, istate, jstate, stride, bin_last_state_map, bin_state_map, return_obs, obs_threshold=1):
+    # ['nbins', 'rows', 'state_map', 'nfbins', 'bin_state_map', 'cols', 'jstate', 'flux', 'istate', 'return_obs', 'bin_last_state_map', 'insert', 'nstates', 'indices', 'state_labels', 'obs']
+    # cpdef reweight_for_c(stride, obs_threshold=1):
+
+    ci_res = reweight_for_c(**estimator_kwargs)[...].reshape(-1, nstates).sum(axis=1)
+
+    return ci_res
+
+
+class RWMatrix(WESTKineticsBase, FluxMatrix):
+    subcommand = 'init'
+    default_kinetics_file = 'reweight.h5'
+    default_output_file = 'reweight.h5'
+    help_text = 'create a color-labeled transition matrix from a WESTPA simulation'
+    description = '''\
+Generate a colored transition matrix from a WE assignment file. The subsequent
+analysis requires that the assignments are calculated using only the initial and
+final time points of each trajectory segment. This may require downsampling the
+h5file generated by a WE simulation. In the future w_assign may be enhanced to optionally
+generate the necessary assignment file from a h5file with intermediate time points.
+Additionally, this analysis is currently only valid on simulations performed under
+either equilibrium or steady-state conditions without recycling target states.
+
+-----------------------------------------------------------------------------
+Output format
+-----------------------------------------------------------------------------
+
+The output file (-o/--output, by default "reweight.h5") contains the
+following datasets:
+
+  ``/bin_populations`` [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.
+
+  ``/iterations`` [iteration]
+    *(Structured -- see below)*  Sparse matrix data from each
+    iteration.  They are reconstructed and averaged within the
+    w_reweight {kinetics/probs} routines so that observables may
+    be calculated.  Each group contains 4 vectors of data:
+
+      flux
+        *(Floating-point)* The weight of a series of flux events
+      cols
+        *(Integer)* The bin from which a flux event began.
+      cols
+        *(Integer)* The bin into which the walker fluxed.
+      obs
+        *(Integer)* How many flux events were observed during this
+        iteration.
+
+-----------------------------------------------------------------------------
+Command-line options
+-----------------------------------------------------------------------------
+'''
+
+    def __init__(self, parent):
+        super().__init__(parent)
+        self.parent = parent
+        self.assignments_file = None
+
+    def add_args(self, parser):
+        cogroup = parser.add_argument_group('calculation options')
+        cogroup.add_argument(
+            '-s',
+            '--sampling-frequency',
+            dest='sampling_frequency',
+            choices=['timepoint', 'iteration'],
+            default='timepoint',
+            help='''Observe for transition events with a lag
+                             time corresponding to either each weighted ensemble
+                             iteration (``iteration``) or each sub-iteration
+                             timepoint (``timepoint``) (default: %(default)s).
+                             For each pair of bins, store the sum of fluxes
+                             in a given iteration (['flux']). Similarly,
+                             for each bin, store the sum of weights in the bin
+                             over all observation points for a given iteration
+                             (['bin_populations']).''',
+        )
+
+    def process_args(self, args):
+        self.output_file = h5io.WESTPAH5File(args.output, 'w', creating_program=True)
+        self.assignments_file = h5io.WESTPAH5File(args.assignments, 'r')
+        # Force a build of the transition matrix at the iteration level.
+        self.sampling_frequency = 'iteration' if self.assignments_file.attrs['subsampled'] is True else args.sampling_frequency
+
+    def go(self):
+        # This function exists in FluxMatrix, and is not currently portable.
+        # That is, it assumes all properties are properly initialized (self.assignments_file, etc)
+        # TO DO : make it portable.
+        pi = self.progress.indicator
+        with pi:
+            self.w_postanalysis_matrix()
+
+
+class RWReweight(AverageCommands):
+    help_text = 'Parent class for all reweighting routines, as they all use the same estimator code.'
+
+    def __init__(self, parent):
+        super().__init__(parent)
+        self.parent = parent
+        self.assignments_file = None
+
+    def add_args(self, parser):
+        cogroup = parser.add_argument_group('calculation options')
+        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 process_args(self, args):
+        self.obs_threshold = args.obs_threshold
+
+    def accumulate_statistics(self, start_iter, stop_iter):
+        '''
+        This function pulls previously generated flux matrix data into memory.
+        The data is assumed to exist within an HDF5 file that is available
+        as a property.
+        The data is kept as a single dimensional numpy array to use with the
+        cython estimator.
+        '''
+        # This is designed to pull in the flux data...
+        rows = []
+        cols = []
+        obs = []
+        flux = []
+        insert = [0] * (start_iter)
+
+        # Actually, I'm not sure we need to start this at start_iter...
+        # ... as it's keyed to the iteration, we need to make sure that the index
+        # matches with the iteration (particularly for 'insert').
+        # It's just easier to load all the data, although we could just start insert as a list of length
+        # start_iter.
+        for iiter in range(start_iter, stop_iter):
+            iter_grp = self.kinetics_file['iterations']['iter_{:08d}'.format(iiter)]
+
+            rows.append(iter_grp['rows'][...])
+            cols.append(iter_grp['cols'][...])
+            obs.append(iter_grp['obs'][...])
+            flux.append(iter_grp['flux'][...])
+            # 'insert' is the insertion point for each iteration; that is,
+            # at what point do we look into the list for iteration X?
+            insert.append(iter_grp['rows'][...].shape[0] + insert[-1])
+        self.rows = np.concatenate(rows)
+        self.cols = np.concatenate(cols)
+        self.obs = np.concatenate(obs)
+        self.flux = np.concatenate(flux)
+        assert insert[-1] == len(self.rows)
+        self.insert = np.array(insert, dtype=np.intc)
+
+    def generate_reweight_data(self):
+        '''
+        This function ensures all the appropriate files are loaded, sets
+        appropriate attributes necessary for all calling functions/children,
+        and then calls the function to load in the flux matrix data.
+        '''
+
+        self.open_files()
+        self.open_assignments()
+
+        self.nfbins = self.kinetics_file.attrs['nrows']
+        self.npts = self.kinetics_file.attrs['npts']
+        self.state_map = self.assignments_file['state_map'][...]
+        self.state_labels = self.assignments_file['state_labels'][...]
+
+        # Copying this over to make it more convenient...
+        self.output_file.replace_dataset('state_labels', data=self.assignments_file['state_labels'][...])
+        # ... as we'll need it for ploterr.
+
+        assert self.nstates == len(self.state_labels)
+        assert self.nfbins == self.nbins * self.nstates
+
+        start_iter, stop_iter, _ = self.iter_range.iter_start, self.iter_range.iter_stop, self.iter_range.iter_step
+
+        # This function call loads up all the flux matrix data and stores it in memory.
+        # We just give our cython estimator all the information it needs beforehand, as
+        # the nature of the bootstrap means we can't know what iterations we'll actually need before
+        # the routine is called.
+
+        self.accumulate_statistics(start_iter, stop_iter)
+
+
+class RWRate(RWReweight):
+    subcommand = 'kinetics'
+    help_text = 'Generates rate and flux values from a WESTPA simulation via reweighting.'
+    default_kinetics_file = 'reweight.h5'
+    default_output_file = 'reweight.h5'
+    description = '''\
+Calculate average rates from weighted ensemble data using the postanalysis
+reweighting scheme. Bin assignments (usually "assign.h5") and pre-calculated
+iteration flux matrices (usually "reweight.h5") data files must have been
+previously generated using w_reweight matrix (see "w_assign --help" and
+"w_reweight init --help" for information on generating these files).
+
+-----------------------------------------------------------------------------
+Output format
+-----------------------------------------------------------------------------
+The output file (-o/--output, usually "kinrw.h5") contains the following
+dataset:
+
+  /avg_rates [state,state]
+    (Structured -- see below) State-to-state rates based on entire window of
+    iterations selected.
+
+  /avg_total_fluxes [state]
+    (Structured -- see below) Total fluxes into each state based on entire
+    window of iterations selected.
+
+  /avg_conditional_fluxes [state,state]
+    (Structured -- see below) State-to-state fluxes based on entire window of
+    iterations selected.
+
+If --evolution-mode is specified, then the following additional datasets are
+available:
+
+  /rate_evolution [window][state][state]
+    (Structured -- see below). State-to-state rates 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.
+
+  /target_flux_evolution [window,state]
+    (Structured -- see below). Total flux into a given macro state based on
+    windows of iterations of varying width, as in /rate_evolution.
+
+  /conditional_flux_evolution [window,state,state]
+    (Structured -- see below). State-to-state fluxes based on windows of
+    varying width, as in /rate_evolution.
+
+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 observable as evaluated within
+    this window, in units of inverse tau.
+
+  ci_lbound
+    (Floating-point) Lower bound of the confidence interval of the observable
+    within this window, in units of inverse tau.
+
+  ci_ubound
+    (Floating-point) Upper bound of the confidence interval of the observable
+    within this window, in units of inverse tau.
+
+  stderr
+    (Floating-point) The standard error of the mean of the observable
+    within this window, in units of inverse tau.
+
+  corr_len
+    (Integer) Correlation length of the observable 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, parent):
+        super().__init__(parent)
+        self.parent = parent
+        self.assignments_file = None
+
+    def w_postanalysis_reweight(self):
+        '''
+        This function ensures the data is ready to send in to the estimator and
+        the bootstrapping routine, then does so. Much of this is simply setting
+        up appropriate args and kwargs, then passing them in to the
+        'run_calculation' function, which sets up future objects to send to the
+        work manager. The results are returned, and then written to the
+        appropriate HDF5 dataset.
+        This function is specific for the rates and fluxes from the reweighting
+        method.
+        '''
+        self.generate_reweight_data()
+        pi = self.progress.indicator
+
+        # start_iter, stop_iter, step_iter = self.iter_range.iter_start, self.iter_range.iter_stop, self.iter_range.iter_step
+        # start_pts = list(range(start_iter, stop_iter, step_iter))
+        start_iter = self.iter_range.iter_start
+        stop_iter = self.iter_range.iter_stop
+
+        indices = np.array(list(range(start_iter - 1, stop_iter - 1)), dtype=np.uint16)
+        submit_kwargs = dict(
+            pi=pi, nstates=self.nstates, start_iter=self.start_iter, stop_iter=self.stop_iter, step_iter=self.step_iter
+        )
+
+        # Due to the way our estimator is written, we're using the same dataset every time.  We're just returning different values.
+        submit_kwargs['dataset'] = {'indices': indices}
+        submit_kwargs['estimator_kwargs'] = {}
+        submit_kwargs['estimator_kwargs'].update(
+            dict(
+                rows=self.rows,
+                cols=self.cols,
+                obs=self.obs,
+                flux=self.flux,
+                insert=self.insert,
+                bin_last_state_map=np.tile(np.arange(self.nstates, dtype=int), self.nbins),
+                bin_state_map=np.repeat(self.state_map[:-1], self.nstates),
+                nfbins=self.nfbins,
+                state_labels=self.state_labels,
+                return_obs='R',  # Set to a default, here, but we explicitly set it later.
+                state_map=self.state_map,
+                nbins=self.nbins,
+            )
+        )
+
+        # Calculate averages for the simulation, then report, if necessary.
+
+        # The dataset options are what we pass on to the estimator...
+        submit_kwargs['estimator_kwargs']['return_obs'] = 'R'
+        avg_rates = self.run_calculation(eval_block=_2D_eval_block, name='Average Rates', dim=2, do_averages=True, **submit_kwargs)
+        avg_rates['expected'] *= self.npts - 1
+        avg_rates['ci_ubound'] *= self.npts - 1
+        avg_rates['ci_lbound'] *= self.npts - 1
+        self.output_file.replace_dataset('avg_rates', data=avg_rates[1])
+
+        submit_kwargs['estimator_kwargs']['return_obs'] = 'F'
+        avg_conditional_fluxes = self.run_calculation(
+            eval_block=_2D_eval_block, name='Average Flux', dim=2, do_averages=True, **submit_kwargs
+        )
+        avg_conditional_fluxes['expected'] *= self.npts - 1
+        avg_conditional_fluxes['ci_ubound'] *= self.npts - 1
+        avg_conditional_fluxes['ci_lbound'] *= self.npts - 1
+        self.output_file.replace_dataset('avg_conditional_fluxes', data=avg_conditional_fluxes[1])
+
+        # Now, print them!
+
+        # We've returned an average, but it still exists in a timeslice format.  So we need to return the 'last' value.
+        if self.display_averages:
+            self.print_averages(avg_conditional_fluxes[1], '\nfluxes from state to state:', dim=2)
+            self.print_averages(avg_rates[1], '\nrates from state to state:', dim=2)
+
+        # Do a bootstrap evolution.
+
+        submit_kwargs['estimator_kwargs']['return_obs'] = 'R'
+        rate_evol = self.run_calculation(eval_block=_2D_eval_block, name='Rate Evolution', dim=2, **submit_kwargs)
+        rate_evol['expected'] *= self.npts - 1
+        rate_evol['ci_ubound'] *= self.npts - 1
+        rate_evol['ci_lbound'] *= self.npts - 1
+        self.output_file.replace_dataset('rate_evolution', data=rate_evol, shuffle=True, compression=9)
+
+        submit_kwargs['estimator_kwargs']['return_obs'] = 'F'
+        flux_evol = self.run_calculation(eval_block=_2D_eval_block, name='Conditional Flux Evolution', dim=2, **submit_kwargs)
+        flux_evol['expected'] *= self.npts - 1
+        flux_evol['ci_ubound'] *= self.npts - 1
+        flux_evol['ci_lbound'] *= self.npts - 1
+        self.output_file.replace_dataset('conditional_flux_evolution', data=rate_evol, shuffle=True, compression=9)
+
+    def go(self):
+        pi = self.progress.indicator
+        with pi:
+            self.w_postanalysis_reweight()
+
+
+class RWStateProbs(RWReweight):
+    subcommand = 'probs'
+    help_text = 'Calculates color and state probabilities via reweighting.'
+    default_kinetics_file = 'reweight.h5'
+    description = '''\
+Calculate average populations from weighted ensemble data using the postanalysis
+reweighting scheme. Bin assignments (usually "assign.h5") and pre-calculated
+iteration flux matrices (usually "reweight.h5") data files must have been
+previously generated using w_reweight matrix (see "w_assign --help" and
+"w_reweight init --help" for information on generating these files).
+
+-----------------------------------------------------------------------------
+Output format
+-----------------------------------------------------------------------------
+
+The output file (-o/--output, usually "direct.h5") contains the following
+dataset:
+
+  /avg_state_probs [state]
+    (Structured -- see below) Population of each state across entire
+    range specified.
+
+  /avg_color_probs [state]
+    (Structured -- see below) Population of each ensemble across entire
+    range specified.
+
+If --evolution-mode is specified, then the following additional datasets are
+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.
+
+  /color_prob_evolution [window][state]
+    (Structured -- see below). Ensemble 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 observable as evaluated within
+    this window, in units of inverse tau.
+
+  ci_lbound
+    (Floating-point) Lower bound of the confidence interval of the observable
+    within this window, in units of inverse tau.
+
+  ci_ubound
+    (Floating-point) Upper bound of the confidence interval of the observable
+    within this window, in units of inverse tau.
+
+  stderr
+    (Floating-point) The standard error of the mean of the observable
+    within this window, in units of inverse tau.
+
+  corr_len
+    (Integer) Correlation length of the observable 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 w_postanalysis_stateprobs(self):
+        '''
+        This function ensures the data is ready to send in to the estimator and
+        the bootstrapping routine, then does so. Much of this is simply setting
+        up appropriate args and kwargs, then passing them in to the
+        'run_calculation' function, which sets up future objects to send to the
+        work manager. The results are returned, and then written to the
+        appropriate HDF5 dataset.
+        This function is specific for the color (steady-state) and macrostate
+        probabilities from the reweighting method.
+        '''
+        self.generate_reweight_data()
+        pi = self.progress.indicator
+
+        start_iter, stop_iter, step_iter = self.iter_range.iter_start, self.iter_range.iter_stop, self.iter_range.iter_step
+        start_pts = list(range(start_iter, stop_iter, step_iter))
+        indices = np.array(list(range(start_iter - 1, stop_iter - 1, step_iter)), dtype=np.uint16)
+        submit_kwargs = dict(
+            pi=pi, nstates=self.nstates, start_iter=self.start_iter, stop_iter=self.stop_iter, step_iter=self.step_iter
+        )
+
+        # Due to the way our estimator is written, we're using the same dataset every time.  We're just returning different values.
+        submit_kwargs['dataset'] = {'indices': indices}
+        submit_kwargs['estimator_kwargs'] = {}
+        submit_kwargs['estimator_kwargs'].update(
+            dict(
+                rows=self.rows,
+                cols=self.cols,
+                obs=self.obs,
+                flux=self.flux,
+                insert=self.insert,
+                bin_last_state_map=np.tile(np.arange(self.nstates, dtype=int), self.nbins),
+                bin_state_map=np.repeat(self.state_map[:-1], self.nstates),
+                nfbins=self.nfbins,
+                state_labels=self.state_labels,
+                return_obs='C',  # Set to a default, but we explicitly set it later.
+                state_map=self.state_map,
+                nbins=self.nbins,
+            )
+        )
+
+        # Calculate averages for the simulation, then report, if necessary.
+
+        # The dataset options are what we pass on to the estimator...
+        submit_kwargs['estimator_kwargs']['return_obs'] = 'C'
+        avg_color_probs = self.run_calculation(
+            eval_block=_1D_eval_block, name='Average Color (Ensemble) Probability', dim=1, do_averages=True, **submit_kwargs
+        )
+        self.output_file.replace_dataset('avg_color_probs', data=avg_color_probs[1])
+
+        submit_kwargs['estimator_kwargs']['return_obs'] = 'S'
+        avg_state_probs = self.run_calculation(
+            eval_block=_1D_eval_block, name='Average State Probability', dim=1, do_averages=True, **submit_kwargs
+        )
+        self.output_file.replace_dataset('avg_state_probs', data=avg_state_probs[1])
+
+        # Now, print them!
+
+        # We've returned an average, but it still exists in a timeslice format.  So we need to return the 'last' value.
+        if self.display_averages:
+            self.print_averages(avg_color_probs[1], '\naverage color probabilities:', dim=1)
+            self.print_averages(avg_state_probs[1], '\naverage state probabilities:', dim=1)
+
+        # Do a bootstrap evolution.
+
+        submit_kwargs['estimator_kwargs']['return_obs'] = 'C'
+        color_evol = self.run_calculation(
+            eval_block=_1D_eval_block, name='Color (Ensemble) Probability Evolution', dim=1, **submit_kwargs
+        )
+        self.output_file.replace_dataset('color_prob_evolution', data=color_evol, shuffle=True, compression=9)
+
+        submit_kwargs['estimator_kwargs']['return_obs'] = 'S'
+        state_evol = self.run_calculation(eval_block=_1D_eval_block, name='State Probability Evolution', dim=1, **submit_kwargs)
+        self.output_file.replace_dataset('state_pop_evolution', data=state_evol, shuffle=True, compression=9)
+
+        # Little different, here.  Do a non-bootstrap evolution.
+        # Just use the work manager and the estimator without the bootstrap code, which is problematic for a dataset like this.
+        # We'll be adding this in later.
+        if False:
+            submit_kwargs['estimator_kwargs']['return_obs'] = 'P'
+            submit_kwargs['pi'] = None
+            futures = []
+            bin_pops = []
+            for iblock, start in enumerate(start_pts):
+                stop = min(start + step_iter, stop_iter)
+                # TODO: below line references uninitialized variable `do_averages`. Removed for now to satisfy
+                # flake8 since code never runs because of `if False`. Needs to be dealt with if this changes
+                # if self.evolution_mode == 'cumulative' or do_averages is True:
+                if self.evolution_mode == 'cumulative':
+                    windowsize = int(self.evol_window_frac * (stop - start_iter))
+                    block_start = max(start_iter, stop - windowsize)
+                else:  # self.evolution_mode == 'blocked'
+                    block_start = start
+                future_kwargs = dict(
+                    iblock=iblock,
+                    start=block_start,
+                    stop=stop,
+                    # nstates=self.nstates,
+                    mcbs_alpha=self.mcbs_alpha,
+                    mcbs_nsets=self.mcbs_nsets,
+                    mcbs_acalpha=self.mcbs_acalpha,
+                    do_correl=self.do_correl,
+                    name='Bin Population Evolution',
+                    mcbs_enable=self.mcbs_enable,
+                    data_input={},
+                    **submit_kwargs
+                )
+                # print(future_kwargs)
+                futures.append(generate_future(self.work_manager, 'Bin Pop Evolution', _pop_eval_block, future_kwargs))
+            # bin_evol = self.run_calculation(eval_block=_pop_eval_block, name='Bin Population Evolution', dim=1, **submit_kwargs)
+            # bin_evol = bin_evol.reshape(-1, 2)
+            for future in self.work_manager.as_completed(futures):
+                # pi.progress += iblock / step_iter
+                bin_pops.append(future.get_result(discard=True))
+            hist = self.output_file.replace_dataset('histograms', data=bin_pops, shuffle=True, compression=9)
+            hist.attrs['iter_start'] = start_iter
+            hist.attrs['iter_stop'] = stop_iter
+            import ast
+
+            binbounds = []
+            midpoints = []
+            for i in self.assignments_file['bin_labels']:
+                binbounds.append(ast.literal_eval(i)[0][0])
+            # This is probably crap, so...
+            binbounds.append(ast.literal_eval(self.assignments_file['bin_labels'][-1])[0][1])
+            # binbounds.append(binbounds[-1]+1)
+            for i in range(1, len(binbounds)):
+                midpoints.append(((binbounds[i] - binbounds[i - 1]) / 2) + binbounds[i - 1])
+            self.output_file.replace_dataset('binbounds_0', data=binbounds, shuffle=True, compression=9)
+            self.output_file.replace_dataset('midpoints_0', data=midpoints, shuffle=True, compression=9)
+            self.output_file.replace_dataset('n_iter', data=list(range(start_iter, stop_iter)), shuffle=True, compression=9)
+
+    def go(self):
+        pi = self.progress.indicator
+        with pi:
+            self.w_postanalysis_stateprobs()
+
+
+class RWAll(RWMatrix, RWStateProbs, RWRate):
+    subcommand = 'all'
+    help_text = 'Runs the full suite, including the generation of the flux matrices.'
+    default_kinetics_file = 'reweight.h5'
+    default_output_file = 'reweight.h5'
+    description = '''\
+A convenience function to run init/kinetics/probs. Bin assignments,
+including macrostate definitions, are required. (See
+"w_assign --help" for more information).
+
+For more information on the individual subcommands this subs in for, run
+w_reweight {init/kinetics/probs} --help.
+
+-----------------------------------------------------------------------------
+Command-line options
+-----------------------------------------------------------------------------
+'''
+
+    def go(self):
+        pi = self.progress.indicator
+        with pi:
+            self.w_postanalysis_matrix()
+            self.w_postanalysis_reweight()
+            self.w_postanalysis_stateprobs()
+
+
+# Just a convenience class to average the observables.
+class RWAverage(RWStateProbs, RWRate):
+    subcommand = 'average'
+    help_text = 'Averages and returns fluxes, rates, and color/state populations.'
+    default_kinetics_file = 'reweight.h5'
+    default_output_file = 'reweight.h5'
+    description = '''\
+A convenience function to run kinetics/probs. Bin assignments,
+including macrostate definitions, are required. (See
+"w_assign --help" for more information).
+
+For more information on the individual subcommands this subs in for, run
+w_reweight {kinetics/probs} --help.
+
+-----------------------------------------------------------------------------
+Command-line options
+-----------------------------------------------------------------------------
+'''
+
+    def go(self):
+        pi = self.progress.indicator
+        with pi:
+            self.w_postanalysis_reweight()
+            self.w_postanalysis_stateprobs()
+
+
+class WReweight(WESTMasterCommand, WESTParallelTool):
+    prog = 'w_reweight'
+    subcommands = [RWMatrix, RWAverage, RWRate, RWStateProbs, RWAll]
+    subparsers_title = 'reweighting kinetics analysis scheme'
+
+
+def entry_point():
+    warnings.warn('{} is being deprecated.  Please use WESS, WEED or the haMSM plugin instead.'.format(WReweight.prog))
+    WReweight().main()
+
+
+if __name__ == '__main__':
+    entry_point()