Merge pull request #279 from rmodrak/fix_get_synthetics

Station metadata now gets passed by default to get_synthetics

docs/install/index.rst

@@ -32,7 +32,7 @@ Unpack seismic waveforms used by examples:
 .. code::
 
     bash ./data/examples/unpack.bash
-    bash ./data/tests/unpack.bash
+    bash ./data/tests/download.bash
 
 
 Finally, install PyGMT:

mtuq/greens_tensor/base.py

@@ -24,7 +24,8 @@ class GreensTensor(Stream):
         `ObsPy documentation <https://docs.obspy.org/packages/autogen/obspy.core.stream.Stream.html>`_
         for more information. 
 
-    """
+"""
+
     def __init__(self, 
             traces=None, 
             station=None, 
@@ -102,13 +103,6 @@ def _set_components(self, components):
 
     def _preallocate(self):
         """ Preallocates structures used by `get_synthetics`
-
-        .. note:
-
-            Every time ``get_synthetics(inplace=True)`` is called, the numeric 
-            trace data get overwritten. Every time ``_set_components`` is 
-            called, the traces get overwritten.  The stream itself never gets
-            overwritten.
         """
         nc, nr, nt = self._get_shape()
 
@@ -148,10 +142,10 @@ def _allocate_stream(self, stats=None):
         """
         nc, nr, nt = self._get_shape()
 
-        if not stats:
-            stats = []
+        if stats is None:
+            stats = list()
             for component in self.components:
-                stats += [self[0].stats.copy()]
+                stats.append(deepcopy(self.station))
                 stats[-1].update({'npts': nt, 'channel': component})
 
         stream = Stream()
@@ -291,7 +285,7 @@ def select(self, selector):
         return selected
 
 
-    def get_synthetics(self, source, components=None, stats=None, mode='apply', **kwargs):
+    def get_synthetics(self, source, components=['Z','R','T'], stats=None, mode='apply', **kwargs):
         """ Generates synthetics through a linear combination of time series
 
         Returns an MTUQ `Dataset`
@@ -307,7 +301,25 @@ def get_synthetics(self, source, components=None, stats=None, mode='apply', **kw
 
         ``stats`` (`obspy.Trace.Stats` object):
         ObsPy Stats object that will be attached to the synthetics
-        
+        (Defaults to `GreensTensor` `station` attributes.)
+
+
+        .. note::
+
+          Different ways of generating synthetics are possible (including in-place
+          methods suitable for use in mtuq/grid_search.py):
+
+             - When ``get_synthetics(inplace=True)`` is called, the existing 
+               stream and trace objects are reused, and only the numeric trace
+               data gets overwritten
+
+             - When ``get_synthetics(inplace=False)`` is called, new stream and trace
+               objects are allocated
+
+             - When ``_set_components()`` is called prior to 
+              ``get_synthetics(inplace=True)``, the existing stream is reused but
+              new trace objects are allocated
+
         """
         if mode=='map':
             if components is None:
@@ -322,6 +334,12 @@ def get_synthetics(self, source, components=None, stats=None, mode='apply', **kw
             return synthetics
 
         elif mode=='apply':
+            if stats is not None:
+                print("get_synthetics() stats keyword argument can only be "
+                      "used with mode='apply'")
+
+                warnings.warn("Ignoring stats keyword argument.")
+
             synthetics = Dataset()
             for tensor in self:
                 synthetics.append(tensor.get_synthetics(

mtuq/io/clients/CPS_SAC.py

@@ -22,10 +22,6 @@
 ]
 
 
-# disply prominent warning
-print('CPS client still under testing')
-
-
 class Client(ClientBase):
     """  CPS database client
 

mtuq/io/readers/SAC.py

@@ -68,8 +68,11 @@ def read(filenames, station_id_list=None, event_id=None, tags=[]):
     for station_id in data_sorted:
          streams += [data_sorted[station_id]]
 
-    # check for duplicate components
     for stream in streams:
+        # check for duplicate components
+        check_components(stream)
+
+        # check for that all traces have same time sampling
         check_components(stream)
 
     # collect event metadata
@@ -81,7 +84,7 @@ def read(filenames, station_id_list=None, event_id=None, tags=[]):
 
     # collect station metadata
     for stream in streams:
-        stream.station = _get_station(stream, preliminary_origin)
+        stream.station = _get_station(stream)
 
     # create MTUQ Dataset
     return Dataset(streams, id=event_id, tags=tags)
@@ -133,26 +136,28 @@ def _get_origin(stream, event_id):
         })
 
 
-def _get_station(stream, origin, attach_sac_headers=True):
+def _get_station(stream):
     """ Extracts station metadata from SAC headers
-    """
-    #
-    # extract metadata from ObsPy structures
-    #
-    meta = deepcopy(stream[0].meta.__dict__)
-
-    sac_headers = meta.pop('sac')
-
-    # remove channel-specific attributes
-    for attr in ['channel', 'component']:
-        if attr in meta:
-            meta.pop(attr)
+    """ 
+    stats = stream[0].stats
+    sac_headers = stream[0].stats.sac
 
-    #
+    #       
     # populate station object
-    #
-    station = Station(meta)
-
+    #       
+    station = Station()
+
+    station.update({
+        'network': stream[0].stats.network,
+        'station': stream[0].stats.station,
+        'location': stream[0].stats.location,
+        'sampling_rate': stream[0].stats.sampling_rate,
+        'npts': stream[0].stats.npts,
+        'delta': stream[0].stats.delta,
+        'starttime': stream[0].stats.starttime,
+        'endtime': stream[0].stats.endtime,
+        })
+
     station.update({
         'id': '.'.join([
             stream[0].stats.network,
@@ -168,20 +173,18 @@ def _get_station(stream, origin, attach_sac_headers=True):
     except:
         raise Exception(
             "Could not determine station location from SAC headers.")
-
+    
     try:
         station.update({
             'station_elevation_in_m': sac_headers.stel,
             'station_depth_in_m': sac_headers.stdp})
-    except:
+    except: 
         pass
-
-    if attach_sac_headers:
-        station.sac = sac_headers
-
+
     return station
 
 
+
 def _glob(filenames):
    # glob any wildcards
    _list = list()