get_result_point to backend, plotting import only when needed

apps/beat

@@ -12,13 +12,14 @@ import shutil
 
 from optparse import OptionParser
 
-from beat import heart, config, utility, inputf, plotting
+from beat import heart, config, utility, inputf
 from beat.models import load_model, Stage, estimate_hypers, sample
-from beat.backend import TextChain 
+from beat.backend import TextChain
 from beat.sampler import SamplingHistory
 from beat.sources import MTSourceWithMagnitude
 from beat.utility import list2string
 from numpy import savez, atleast_2d
+from beat import backend
 
 from pyrocko import model, util
 from pyrocko.trace import snuffle
@@ -445,7 +446,7 @@ def command_import(args):
             stage.load_results(
                 model=problem.model, stage_number=-1, load='full')
 
-            point = plotting.get_result_point(stage, problem.config, 'max')
+            point = backend.get_result_point(stage, problem.config, 'max')
             n_sources = problem.config.problem_config.n_sources
 
             source_params = problem.config.problem_config.priors.keys()
@@ -482,10 +483,10 @@ def command_update(args):
 
         parser.add_option(
             '--parameters',
-            default=['structure'], type='string',
+            default=[], type='string',
             action='callback', callback=list_callback,
-            help='Parameters to update; "structure, hypers, hierarchicals". '
-                 'Default: ["structure"] (config file-structure only)')
+            help='Parameters to update; "hypers, hierarchicals". '
+                 'Default: [] (config file-structure only)')
 
         parser.add_option(
             '--mode', dest='mode',
@@ -1059,6 +1060,7 @@ def command_build_gfs(args):
 
 def command_plot(args):
 
+    from beat import plotting
     command_str = 'plot'
 
     def setup(parser):
@@ -1151,7 +1153,6 @@ def command_plot(args):
             dest='build',
             action='store_true',
             help='Build models during problem loading.')
-
     plots_avail = plotting.available_plots()
 
     details = '''Available <plot types> are: %s or "all". Multiple plots can be
@@ -1387,17 +1388,13 @@ def command_export(args):
         model=problem.model, stage_number=options.stage_number,
         load='trace', chains=[-1])
 
-    trace_name = 'chain--1.csv'
-    results_path = pjoin(problem.outfolder, config.results_dir_name)
-    logger.info('Saving results to %s' % results_path)
-    util.ensuredir(results_path)
-
-    results_trace = pjoin(stage.handler.stage_path(-1), trace_name)
-    shutil.copy(results_trace, pjoin(results_path, trace_name))
-
-    point = plotting.get_result_point(
+    point = backend.get_result_point(
         stage, problem.config, point_llk=options.post_llk)
 
+    mpoint = dict()
+    for var in problem.varnames:
+        mpoint[var] = atleast_2d(stage.mtrace.get_values(var).mean())
+
     for datatype, composite in problem.composites.items():
         logger.info(
             'Exporting "%s" synthetics for "%s" likelihood parameters:' % (
@@ -1407,6 +1404,9 @@ def command_export(args):
                 varname, list2string(value.ravel().tolist())))
 
         results = composite.assemble_results(point)
+        results_path = pjoin(problem.outfolder, config.results_dir_name)
+        logger.info('Saving results to %s' % results_path)
+        util.ensuredir(results_path)
 
         if datatype == 'seismic':
             from pyrocko import io
@@ -1435,7 +1435,7 @@ def command_export(args):
             if hasattr(sc.parameters, 'update_covariances'):
                 if sc.parameters.update_covariances:
                     logger.info('Saving velocity model covariance matrixes...')
-                    composite.update_weights(point)
+                    composite.update_weights(mpoint)
                     for wmap in composite.wavemaps:
                         pcovs = {
                             list2string(dataset.nslc_id):
@@ -1444,23 +1444,10 @@ def command_export(args):
 
                         outname = pjoin(
                             results_path, '%s_C_vm_%s' % (
-                                datatype, wmap._mapid))
-                        logger.info('"%s" to: %s' % (wmap._mapid, outname))
+                                datatype, wmap.name))
+                        logger.info('"%s" to: %s' % (wmap.name, outname))
                         savez(outname, **pcovs)
 
-                logger.info('Saving data covariance matrixes...')
-                for wmap in composite.wavemaps:
-                    dcovs = {
-                        list2string(dataset.nslc_id):
-                        dataset.covariance.data
-                        for dataset in wmap.datasets}
-
-                    outname = pjoin(
-                        results_path, '%s_C_d_%s' % (
-                            datatype, wmap._mapid))
-                    logger.info('"%s" to: %s' % (wmap._mapid, outname))
-                    savez(outname, **dcovs)
-
         elif datatype == 'geodetic':
             for ifgs, attribute in heart.results_for_export(
                     results, datatype=datatype):

src/backend.py

@@ -38,6 +38,7 @@
 from beat.utility import load_objects, dump_objects, \
     ListArrayOrdering, ListToArrayBijection
 from beat.covariance import calc_sample_covariance
+from beat import utility
 
 from pyrocko import util
 from time import time
@@ -830,6 +831,58 @@ def load_sampler_params(project_dir, stage_number, mode):
         sample_p_outname)
     return load_objects(stage_path)
 
+def get_result_point(stage, config, point_llk='max'):
+    """
+    Return point of a given stage result.
+
+    Parameters
+    ----------
+    stage : :class:`models.Stage`
+    config : :class:`config.BEATConfig`
+    point_llk : str
+        with specified llk(max, mean, min).
+
+    Returns
+    -------
+    dict
+    """
+    if config.sampler_config.name == 'Metropolis':
+        if stage.step is None:
+            raise AttributeError(
+                'Loading Metropolis results requires'
+                ' sampler parameters to be loaded!')
+
+        sc = config.sampler_config.parameters
+        from beat.sampler.metropolis import get_trace_stats
+        pdict, _ = get_trace_stats(
+            stage.mtrace, stage.step, sc.burn, sc.thin)
+        point = pdict[point_llk]
+
+    elif config.sampler_config.name == 'SMC':
+        llk = stage.mtrace.get_values(
+            varname='like',
+            combine=True)
+
+        posterior_idxs = utility.get_fit_indexes(llk)
+
+        point = stage.mtrace.point(idx=posterior_idxs[point_llk])
+
+    elif config.sampler_config.name == 'PT':
+        params = config.sampler_config.parameters
+        llk = stage.mtrace.get_values(
+            varname='like',
+            burn=int(params.n_samples * params.burn),
+            thin=params.thin)
+
+        posterior_idxs = utility.get_fit_indexes(llk)
+
+        point = stage.mtrace.point(idx=posterior_idxs[point_llk])
+
+    else:
+        raise NotImplementedError(
+            'Sampler "%s" is not supported!' % config.sampler_config.name)
+
+    return point
 
 def concatenate_traces(mtraces):
     """

src/plotting.py

@@ -10,7 +10,6 @@
 
 from beat import utility
 from beat.models import Stage
-from beat.sampler.metropolis import get_trace_stats
 from beat.heart import init_seismic_targets, init_geodetic_targets
 from beat.colormap import slip_colormap
 
@@ -473,60 +472,6 @@ def plot_log_cov(cov_mat):
     plt.colorbar(im)
     plt.show()
 
-
-def get_result_point(stage, config, point_llk='max'):
-    """
-    Return point of a given stage result.
-
-    Parameters
-    ----------
-    stage : :class:`models.Stage`
-    config : :class:`config.BEATConfig`
-    point_llk : str
-        with specified llk(max, mean, min).
-
-    Returns
-    -------
-    dict
-    """
-    if config.sampler_config.name == 'Metropolis':
-        if stage.step is None:
-            raise AttributeError(
-                'Loading Metropolis results requires'
-                ' sampler parameters to be loaded!')
-
-        sc = config.sampler_config.parameters
-        pdict, _ = get_trace_stats(
-            stage.mtrace, stage.step, sc.burn, sc.thin)
-        point = pdict[point_llk]
-
-    elif config.sampler_config.name == 'SMC':
-        llk = stage.mtrace.get_values(
-            varname='like',
-            combine=True)
-
-        posterior_idxs = utility.get_fit_indexes(llk)
-
-        point = stage.mtrace.point(idx=posterior_idxs[point_llk])
-
-    elif config.sampler_config.name == 'PT':
-        params = config.sampler_config.parameters
-        llk = stage.mtrace.get_values(
-            varname='like',
-            burn=int(params.n_samples * params.burn),
-            thin=params.thin)
-
-        posterior_idxs = utility.get_fit_indexes(llk)
-
-        point = stage.mtrace.point(idx=posterior_idxs[point_llk])
-
-    else:
-        raise NotImplementedError(
-            'Sampler "%s" is not supported!' % config.sampler_config.name)
-
-    return point
-
-
 def plot_quadtree(ax, data, target, cmap, colim, alpha=0.8):
     """
     Plot UnwrappedIFG displacements on the respective quadtree rectangle.