def command_init(args):
'''
Execution of command init
'''
def setup(parser):
parser.add_option('--force',
dest='force',
action='store_true',
help='overwrite existing project directory')
parser, options, args = cl_parse('init', args, setup)
if len(args) != 1:
help_and_die(parser, 'missing argument')
else:
fn_config = args[0]
if not os.path.isfile(fn_config):
die('config file missing: %s' % fn_config)
conf = load(filename=fn_config)
config.check(conf)
if ((not options.force) and (os.path.isdir(conf.project_dir))):
die('project dir exists: %s; use force option' % conf.project_dir)
else:
if os.path.isdir(conf.project_dir):
shutil.rmtree(conf.project_dir)
os.mkdir(conf.project_dir)
conf.dump(filename=os.path.join(conf.project_dir, 'seiscloud.config'))
dst = os.path.join(conf.project_dir, 'catalog.pf')
if conf.catalog_origin == 'file':
src = conf.catalog_fn
shutil.copyfile(src, dst)
else:
if conf.catalog_origin == 'globalcmt':
orig_catalog = catalog.GlobalCMT()
else: # geofon
orig_catalog = catalog.Geofon()
events = orig_catalog.get_events(time_range=(util.str_to_time(
conf.tmin), util.str_to_time(conf.tmax)),
magmin=conf.magmin,
latmin=conf.latmin,
latmax=conf.latmax,
lonmin=conf.lonmin,
lonmax=conf.lonmax)
selevents = [ev for ev in events if ev.magnitude <= conf.magmax]
model.dump_events(selevents, dst)
print('Project directory prepared "%s"' % conf.project_dir)
def command_init(args):
'''
Execution of command init
'''
def setup(parser):
parser.add_option('--force',
dest='force',
action='store_true',
help='overwrite existing project directory')
parser, options, args = cl_parse('init', args, setup)
if len(args) != 1:
help_and_die(parser, 'missing argument')
else:
fn_config = args[0]
if not os.path.isfile(fn_config):
die('config file missing: %s' % fn_config)
conf = load(filename=fn_config)
config.check(conf)
if ((not options.force) and (os.path.isdir(conf.project_dir))):
die('project directory exists: %s; use force option' %
conf.project_dir)
else:
if os.path.isdir(conf.project_dir):
shutil.rmtree(conf.project_dir)
os.mkdir(conf.project_dir)
conf.dump(filename=os.path.join(conf.project_dir, 'seiscloud.config'))
src, dst = conf.catalog_fn, os.path.join(conf.project_dir,
'catalog.pf')
shutil.copyfile(src, dst)
print('Project directory prepared "%s"' % conf.project_dir)
def command_plot(args):
'''
Execution of command plot
'''
def setup(parser):
parser.add_option('--force',
dest='force',
action='store_true',
help='overwrite existing project directory')
parser, options, args = cl_parse('plot', args, setup)
if len(args) != 1:
help_and_die(parser, 'missing argument')
else:
fn_config = args[0]
if not os.path.isfile(fn_config):
die('config file missing: %s' % fn_config)
conf = load(filename=fn_config)
config.check(conf)
if not os.path.isdir(conf.project_dir):
die('project directory missing: %s' % conf.project_dir)
resdir = os.path.join(conf.project_dir, 'clustering_results')
if not os.path.isdir(resdir):
die('clustering results missing: %s' % resdir)
plotdir = os.path.join(conf.project_dir, 'clustering_plots')
resdir = os.path.join(conf.project_dir, 'clustering_results')
if not (options.force):
if (os.path.isdir(plotdir)):
die('clustering plot directory exists; use force option')
if options.force:
if (os.path.isdir(plotdir)):
shutil.rmtree(plotdir)
os.mkdir(plotdir)
simmat_temporal_fn = os.path.join(conf.project_dir, 'simmat_temporal.npy')
simmat_clustered_fn = os.path.join(conf.project_dir,
'simmat_clustered.npy')
if not os.path.isfile(simmat_temporal_fn):
die('similarity matrix does not exists: %s; ' +
'use seiscloud matrix first' % simmat_temporal_fn)
if not os.path.isfile(simmat_clustered_fn):
die('similarity matrix does not exists: %s; ' +
'use seiscloud matrix first' % simmat_clustered_fn)
new_catalog_fn = os.path.join(conf.project_dir,
'events_to_be_clustered.pf')
if not os.path.isfile(new_catalog_fn):
die('catalog of selected events does not exists: %s; ' +
'use seiscloud matrix and seiscloud cluster first' %
new_catalog_fn)
events = model.load_events(new_catalog_fn)
eventsclusters = sccluster.load_obj(
os.path.join(resdir, 'processed.eventsclusters'))
clusters = sccluster.load_obj(os.path.join(resdir, 'processed.clusters'))
scplot.plot_all(events, eventsclusters, clusters, conf, resdir, plotdir)
print('Seiscloud plots prepared in "%s"' % plotdir)
def command_cluster(args):
'''
Execution of command cluster
'''
def setup(parser):
parser.add_option('--force',
dest='force',
action='store_true',
help='overwrite existing project directory')
parser.add_option('--view',
dest='view',
action='store_true',
help='view similarity matrix after clustering')
parser.add_option(
'--savefig',
dest='savefig',
action='store_true',
help='save figure of similarity matrix after clustering')
parser, options, args = cl_parse('cluster', args, setup)
if len(args) != 1:
help_and_die(parser, 'missing argument')
else:
fn_config = args[0]
if not os.path.isfile(fn_config):
die('config file missing: %s' % fn_config)
conf = load(filename=fn_config)
config.check(conf)
if not os.path.isdir(conf.project_dir):
die('project directory missing: %s' % conf.project_dir)
resdir = os.path.join(conf.project_dir, 'clustering_results')
if not (options.force):
if (os.path.isdir(resdir)):
die('clustering result directory exists; use force option')
if options.force:
if (os.path.isdir(resdir)):
shutil.rmtree(resdir)
os.mkdir(resdir)
simmat_temporal_fn = os.path.join(conf.project_dir, 'simmat_temporal.npy')
if not os.path.isfile(simmat_temporal_fn):
die('similarity matrix does not exists: %s; ' +
'use seiscloud matrix first' % simmat_temporal_fn)
new_catalog_fn = os.path.join(conf.project_dir,
'events_to_be_clustered.pf')
if not os.path.isfile(new_catalog_fn):
die('catalog of selected events does not exists: %s; ' +
'use seiscloud matrix first' % new_catalog_fn)
simmat_temp = sccluster.load_similarity_matrix(simmat_temporal_fn)
events = model.load_events(new_catalog_fn)
eventsclusters = sccluster.dbscan(simmat_temp, conf.dbscan_nmin,
conf.dbscan_eps,
conf.sw_force_cluster_all)
clusters = sccluster.get_clusters(events, eventsclusters)
if min(eventsclusters) == -1:
noise_cluster_empty = False
else:
noise_cluster_empty = True
sccluster.save_all(events, eventsclusters, clusters, conf, resdir)
simmat_clus = sccluster.get_simmat_clustered(events, eventsclusters,
clusters, conf, resdir,
simmat_temp)
simmat_clustered_fn = os.path.join(conf.project_dir,
'simmat_clustered.npy')
sccluster.save_similarity_matrix(simmat_clus, simmat_clustered_fn)
print('I run seiscloud for the project in "%s"' % conf.project_dir)
n_clusters = len(clusters)
if not noise_cluster_empty:
n_clusters = n_clusters - 1
print(str(n_clusters) + ' cluster(s) found')
simmat_fig_fn = os.path.join(conf.project_dir,
'simmat_clustered.' + conf.figure_format)
if options.view and options.savefig:
scplot.view_and_savefig_similarity_matrix(simmat_clus, simmat_fig_fn,
'Sorted after clustering')
else:
if options.view:
scplot.view_similarity_matrix(simmat_clus,
'Sorted after clustering')
if options.savefig:
scplot.savefig_similarity_matrix(simmat_clus, simmat_fig_fn,
'Sorted after clustering')
for cluster in clusters:
selevents = clusters[cluster]
median = sccluster.get_median(selevents, conf)
fn_median = os.path.join(resdir,
'median_cluster' + str(cluster) + '.pf')
model.dump_events([median], fn_median)
# print(cluster,len(selevents))
print('Similarity matrix after clustering computed and stored as "%s"' %
simmat_clustered_fn)
if options.savefig:
print('Similarity matrix figure saved as "%s"' % simmat_fig_fn)
def command_matrix(args):
'''
Execution of command matrix
'''
def setup(parser):
parser.add_option('--force',
dest='force',
action='store_true',
help='overwrite existing project directory')
parser.add_option('--view',
dest='view',
action='store_true',
help='view similarity matrix')
parser.add_option('--savefig',
dest='savefig',
action='store_true',
help='save figure of similarity matrix')
parser, options, args = cl_parse('matrix', args, setup)
if len(args) != 1:
help_and_die(parser, 'missing argument')
else:
fn_config = args[0]
if not os.path.isfile(fn_config):
die('config file missing: %s' % fn_config)
conf = load(filename=fn_config)
config.check(conf)
if not os.path.isdir(conf.project_dir):
die('project directory missing: %s' % conf.project_dir)
simmat_temporal_fn = os.path.join(conf.project_dir, 'simmat_temporal.npy')
if ((not options.force) and (os.path.isfile(simmat_temporal_fn))):
die('similarity matrix exists: %s; use force option' %
simmat_temporal_fn)
catalog_ref_fn = os.path.join(conf.project_dir, 'catalog.pf')
if os.path.isfile(catalog_ref_fn):
allevents = model.load_events(catalog_ref_fn)
else:
die('catalog missing: %s' % catalog_ref_fn)
if conf.sw_simmat:
if not os.path.isfile(conf.sim_mat_fn):
die('similarity matrix missing: %s' % conf.sim_mat_fn)
if conf.sim_mat_type == 'binary':
if os.path.isfile(conf.sim_mat_fn):
simmat = sccluster.load_similarity_matrix(conf.sim_mat_fn)
else:
die('cannot read similarity matrix: %s' % conf.sim_mat_fn)
else:
die('ascii format for similarity matrix not yet implemented')
if len(allevents) != len(simmat):
print(len(allevents), len(simmat))
die('clustering stopped, number of events ' +
'differs from matrix size')
new_catalog_fn = os.path.join(conf.project_dir,
'events_to_be_clustered.pf')
model.dump_events(allevents, new_catalog_fn)
else:
if conf.metric in config.acceptable_mt_based_metrics:
events = [ev for ev in allevents if ev.moment_tensor is not None]
else:
events = [ev for ev in allevents]
new_catalog_fn = os.path.join(conf.project_dir,
'events_to_be_clustered.pf')
model.dump_events(events, new_catalog_fn)
simmat = sccluster.compute_similarity_matrix(events, conf.metric)
sccluster.save_similarity_matrix(simmat, simmat_temporal_fn)
simmat_fig_fn = os.path.join(conf.project_dir,
'simmat_temporal.' + conf.figure_format)
if options.view and options.savefig:
scplot.view_and_savefig_similarity_matrix(simmat, simmat_fig_fn,
'Sorted chronologically')
else:
if options.view:
scplot.view_similarity_matrix(simmat, 'Sorted chronologically')
if options.savefig:
scplot.savefig_similarity_matrix(simmat, simmat_fig_fn,
'Sorted chronologically')
print('Similarity matrix computed and stored as "%s"' % simmat_temporal_fn)
if options.savefig:
print('Similarity matrix figure saved as "%s"' % simmat_fig_fn)