Merge branch 'python3' into ma_py3_merge

apps/lassie

@@ -13,7 +13,7 @@ logger = logging.getLogger('main')
 
 def d2u(d):
     if isinstance(d, dict):
-        return dict((k.replace('-', '_'), v) for (k, v) in d.iteritems())
+        return dict((k.replace('-', '_'), v) for (k, v) in d.items())
     else:
         return d.replace('-', '_')
 
@@ -21,7 +21,7 @@ def d2u(d):
 def str_to_time(s):
     try:
         return util.str_to_time(s)
-    except util.TimeStrError, e:
+    except util.TimeStrError as e:
         raise lassie.LassieError(str(e))
 
 
@@ -83,7 +83,7 @@ def cl_parse(command, args, setup=None):
     usage = subcommand_usages[command]
     descr = subcommand_descriptions[command]
 
-    if isinstance(usage, basestring):
+    if isinstance(usage, str):
         usage = [usage]
 
     susage = '%s %s' % (program_name, usage[0])
@@ -147,7 +147,7 @@ def command_init(args):
     else:
         stations_path = 'STATIONS_PATH'
 
-    print '''%%YAML 1.1
+    print('''%%YAML 1.1
 --- !lassie.Config
 
 ## Configuration file for Lassie, your friendly earthquake detector
@@ -242,7 +242,7 @@ detector_threshold: 150.
 ## directory
 save_figures: true
 
-## Mapping of phase ID to phase definition in cake syntax (used e.g. in the 
+## Mapping of phase ID to phase definition in cake syntax (used e.g. in the
 ## CakePhaseShifter config sections)
 tabulated_phases:
 - !pf.TPDef
@@ -252,7 +252,7 @@ tabulated_phases:
   id: 's'
   definition: 'S,s'
 
-## Mapping of earthmodel ID  to the actual earth model in nd format (used in 
+## Mapping of earthmodel ID  to the actual earth model in nd format (used in
 ## the CakePhaseShifter config sections)
 earthmodels:
 - !lassie.CakeEarthmodel
@@ -280,7 +280,7 @@ earthmodels:
     120.0 8.15 4.57 3.3
 ''' % dict(
         stations_path=stations_path,
-        s_data_paths=s_data_paths)
+        s_data_paths=s_data_paths))
 
 
 def command_search(args):
@@ -356,7 +356,7 @@ def command_search(args):
             nparallel=nparallel,
             bark=options.bark)
 
-    except lassie.LassieError, e:
+    except lassie.LassieError as e:
         die(str(e))
 
 

src/common.py

@@ -107,7 +107,7 @@ class HasPaths(Object):
 
         if path is None:
             return None
-        elif isinstance(path, basestring):
+        elif isinstance(path, str):
             return extra(
                 op.normpath(xjoin(self._basepath, xjoin(path_prefix, path))))
         else:

src/config.py

 import logging
 import os.path as op
 
-from pyrocko.guts import Object, String, Float, Timestamp, List, Bool
+from pyrocko.guts import String, Float, Timestamp, List, Bool
 from pyrocko import model, guts
-from pyrocko.fdsn import station as fs
+from pyrocko.io import stationxml
 from pyrocko.gf import TPDef
 
 from lassie import receiver, ifc, grid, geo
@@ -182,7 +182,7 @@ class Config(HasPaths):
                             z=station.depth))
 
             if self.stations_stationxml_path:
-                sx = fs.load_xml(filename=fp(self.stations_stationxml_path))
+                sx = stationxml.load_xml(filename=fp(self.stations_stationxml_path))
                 for station in sx.get_pyrocko_stations():
                     self._receivers.append(
                         receiver.Receiver(

src/core.py

@@ -39,8 +39,7 @@ class Detection(Object):
 
 def check_data_consistency(p, config):
     receivers = config.get_receivers()
-    nslc_ids = p.nslc_ids.keys()
-    nsl_ids = [nslc_id[:3] for nslc_id in nslc_ids]
+    nsl_ids = [nslc_id[:3] for nslc_id in p.nslc_ids.keys()]
     r_ids = [r.codes for r in receivers]
 
     r_not_in_p = []
@@ -92,7 +91,7 @@ def zero_fill(trs, tmin, tmax):
         d[tr.nslc_id].append(tr)
 
     trs_out = []
-    for nslc, trs_group in d.iteritems():
+    for nslc, trs_group in d.items():
         if not all(tr.deltat == trs_group[0].deltat for tr in trs_group):
             logger.warn('inconsistent sample rate, cannot merge traces')
             continue
@@ -272,13 +271,11 @@ def search(
             100.0*2.0*tpad / (tinc+2.0*tpad)))
 
         iwin = -1
-        for trs in p.chopper(
-                tmin=tmin_win, tmax=tmax_win, tinc=tinc, tpad=tpad,
+
+        for trs in p.chopper(tmin=tmin_win, tmax=tmax_win, tinc=tinc, tpad=tpad,
                 want_incomplete=config.fill_incomplete_with_zeros,
                 trace_selector=lambda tr: tr.nslc_id[:3] in station_index):
-
             iwin += 1
-
             trs_ok = []
             for tr in trs:
                 if tr.ydata.size == 0:
@@ -320,7 +317,6 @@ def search(
                 dataset = ifc.preprocess(
                     trs, wmin-tpeaksearch, wmax+tpeaksearch,
                     tshift_max - tshift_min, deltat_cf)
-
                 if not dataset:
                     continue
 
@@ -507,7 +503,6 @@ def search(
             io.save([tr_stackmax, tr_stackmax_indx], ifm_path_template)
 
             del frames
-
         logger.info('end processing time window group: %s - %s' % (
             util.time_to_str(tmin_win),
             util.time_to_str(tmax_win)))

src/grid.py

+from builtins import range
 import math
 import numpy as num
 from pyrocko.guts import Object, Float
@@ -184,7 +185,7 @@ def geometrical_normalization(grid, receivers):
     ngridpoints, nstations = distances.shape
     norm_map = num.zeros(ngridpoints)
 
-    for istation in xrange(nstations):
+    for istation in range(nstations):
         dists_station = distances[:, istation]
 
         dist_min = num.floor(num.min(dists_station) / delta_ring) * delta_ring

src/ifc.py

+from __future__ import print_function
 import logging
-from collections import defaultdict
 import numpy as num
+from collections import defaultdict
 from scipy.signal import fftconvolve
 from pyrocko.guts import Object, String, Float, Bool, StringChoice, List, Dict
-from pyrocko import trace, autopick, util, model, gui_util
+from pyrocko import trace, autopick, util, model
+from pyrocko.gui import util as gui_util
 from pyrocko import marker as pmarker
 from lassie import shifter, common, geo
 

src/plot.py

-import os
+from builtins import range
 import numpy as num
 
-from pyrocko import automap, plot, util
+from pyrocko.plot import automap
+from pyrocko import plot, util
 from lassie import grid as gridmod, geo
 
 km = 1000.
@@ -375,7 +376,7 @@ def plot_detection(
     if movie:
         ani = FuncAnimation(
             fig, update,
-            frames=list(xrange(iframe_min, iframe_max+1))[::10] + [None],
+            frames=list(range(iframe_min, iframe_max+1))[::10] + [None],
             interval=20.,
             repeat=False,
             blit=True)

src/shifter.py

 import logging
 import hashlib
-from StringIO import StringIO
+from io import BytesIO
 import os.path as op
 import numpy as num
-from pyrocko.guts import Object, Float, String
+from pyrocko.guts import Object, Float, String   # noqa
 from pyrocko import cake, spit, util
 from pyrocko.gf import meta
 from lassie import geo
@@ -96,14 +96,16 @@ class CakePhaseShifter(Shifter):
         return op.join(self._cache_path, ehash + '.spit')
 
     def ttt_hash(self, earthmodel, phases, x_bounds, x_tolerance, t_tolerance):
-        f = StringIO()
+        f = BytesIO()
+        earthmodel.profile('z').dump(f)
         earthmodel.profile('vp').dump(f)
         earthmodel.profile('vs').dump(f)
         earthmodel.profile('rho').dump(f)
-        f.write(','.join(phase.definition() for phase in phases))
+
+        f.write(b','.join(phase.definition().encode() for phase in phases))
         x_bounds.dump(f)
         x_tolerance.dump(f)
-        f.write('%f' % t_tolerance)
+        f.write(str(t_tolerance).encode())
         s = f.getvalue()
         h = hashlib.sha1(s).hexdigest()
         f.close()

src/snuffling.py

 import copy
 import os
 import numpy as num
-from pyrocko import util, gui_util, model, orthodrome, pile, snuffler, \
-        marker as pmarker
-from pyrocko.snuffling import Snuffling, Param, Choice, Switch
+from pyrocko import util, model, orthodrome, pile
+from pyrocko.gui import snuffler
+from pyrocko.gui import marker as pmarker
+from pyrocko.gui import util as gui_util
+from pyrocko.gui.snuffling import Snuffling, Param, Choice, Switch
 from lassie import geo, ifc
 
 
@@ -96,6 +98,7 @@ class LassieSnuffling(Snuffling):
         # self.add_trigger('read Lassie config', self.fail)
         self.set_live_update(True)
         self.markers_compare = []
+        self.detections = []
         self.fig = None
         self.fframe = None
         self.grid = self.config.get_grid()
@@ -118,8 +121,8 @@ class LassieSnuffling(Snuffling):
                 mode='all',
                 trace_selector=lambda x: x.station == "SMAX",
                 fallback=True):
-            tr_smax = filter(lambda x: x.location == '', traces)
-            tr_i = filter(lambda x: x.location == 'i', traces)
+            tr_smax = [tr for tr in traces if tr.location == '']
+            tr_i = [tr for tr in traces if tr.location == 'i']
             if not tr_i:
                 tr_i = [None] * len(tr_smax)
 
@@ -171,7 +174,7 @@ class LassieSnuffling(Snuffling):
 
     def filter_visible(self, markers):
         vtmin, vtmax = self.get_viewer().get_time_range()
-        return filter(lambda x: vtmin < x.tmin < vtmax, markers)
+        return [x for x in markers if vtmin < x.tmin < vtmax]
 
     def show_comparison(self):
         '''
@@ -224,7 +227,7 @@ class LassieSnuffling(Snuffling):
             self.fig = self.fframe.gcf()
 
         ax = self.fig.add_subplot(111)
-        compare_events = map(lambda x: x.get_event(), markers_compare)
+        compare_events = [x.get_event() for x in markers_compare]
         associated_events = [compare_events[a[1]] for a in detections_success]
         magnitudes = [e.get_event().magnitude for e in markers_compare]
         detected_magnitudes = [e.magnitude for e in associated_events]
@@ -253,6 +256,8 @@ def __snufflings__():
 def snuffle(config):
     global _lassie_config
     _lassie_config = copy.deepcopy(config)
+    for _ifc in _lassie_config.image_function_contributions:
+        _ifc.setup(config)
 
     def load_snuffling(win):
         s = LassieSnuffling()