Merge branch 'master' into fix_318

CHANGELOG.txt

@@ -1,12 +1,13 @@
+
 Master:
 ph5
  * made pep8 compliant
  * update all modules to use a standardized logger (issue #213)
- * cleanup comments and remove commented out code (issue #216) 
+ * cleanup comments and remove commented out code (issue #216)
  * replace deprecated optparse with argparse module.
  * update ph5 to better install c requirements
 ph5.utilities.ph5
- * add helpfile to utilities folder. Have not added pointer in setup.py as yet. 
+ * add helpfile to utilities folder. Have not added pointer in setup.py as yet.
  * Typing ph5 shows user the choices for help information.
  * Usage: ph5 pforma (lists info about pforma)https://github.com/PIC-IRIS/PH5/pull/new/helpfile
 ph5.clients.ph5toms
@@ -36,6 +37,8 @@ ph5.clients.ph5tostationxml
  * Limit number of asynchronous processes
  * Remove storage format from the sxml channel level to be compatible with sxml version 1.1
  * ph5tostationxml now correctly handles stations with multiple deployments (issue #318)
+ * Add a new custom iris namespace attribute called iris:PH5ReportNum to the network StationXML element
+ * Remove the report number from the alternateCode value in the network StationXML element
 ph5.utilities.ph5validate
  * add data time checking
 ph5.utilities.sort_kef_gen.py
@@ -79,6 +82,9 @@ ph5.entry_points
       (2) entry points for use by setup.
 ph5.help
  * calls entry_points to print the short descriptions in alpha-order.
+ph5.utilities.set_deploy_times
+ * An optional  additional argument, --auto-correct, has been added. This argument permits the function to automatically change a .kef file's deploy times and pickup times.
+ * Times are changed to the floor and ceiling seconds that are defined by the start and end time of trace data to which the kef file refers.
 
 v4.1.2:
 ph5.utilities.ph5validate
@@ -230,7 +236,7 @@ v4.0.2
 
 v4.0.1
 - ph5.clients.ph5tostationxml
-  * updated to work with latest obspy response code 
+  * updated to work with latest obspy response code
 
 v4.0.0
 - Initial Release

ph5/CONTRIBUTORS.txt

@@ -7,3 +7,4 @@ Jacobs, Katie
 Pacheco, Celia
 Thomas, David
 Accardo, Natalie
+Ronan, Tim

ph5/clients/ph5toms.py

@@ -550,13 +550,14 @@ def create_trace(self, station_to_cut, mp=False):
                 elif self.format.upper() == "SEGY1" or \
                         self.format.upper() == "SEGY2":
                     # These values are used to create the SEG-Y headers
-                    obspy_trace.stats.receiver_id = stc.receiver_n_i
+                    obspy_trace.stats.receiver_id = stc.station
                     obspy_trace.stats.ttype = trace.ttype
                     obspy_trace.stats.byteorder = trace.byteorder
                     obspy_trace.stats.elevation = float(stc.elev)
                     obspy_trace.stats.component = stc.component
                     obspy_trace.stats.response = self.get_response_obj(stc)
                     obspy_trace.stats.array = stc.array_code
+                    obspy_trace.stats.das = stc.das
                     obspy_trace.stats.shot_id = stc.shot_id
                     obspy_trace.stats.shot_lat = stc.shot_lat
                     obspy_trace.stats.shot_lng = stc.shot_lng

ph5/clients/ph5tostationxml.py

@@ -505,13 +505,19 @@ def create_obs_network(self):
         if obs_stations:
             obs_network = inventory.Network(
                 self.experiment_t[0]['net_code_s'])
-            obs_network.alternate_code = \
-                self.experiment_t[0]['experiment_id_s']
             obs_network.description = self.experiment_t[0]['longname_s']
             start_time, end_time = self.get_network_date()
             obs_network.start_date = UTCDateTime(start_time)
             obs_network.end_date = UTCDateTime(end_time)
             obs_network.total_number_of_stations = self.total_number_stations
+            extra = AttribDict({
+                    'PH5ReportNum': {
+                        'value': self.experiment_t[0]['experiment_id_s'],
+                        'namespace': self.manager.iris_custom_ns,
+                        'type': 'attribute'
+                    }
+                })
+            obs_network.extra = extra
             obs_network.stations = obs_stations
             return obs_network
         else:

ph5/utilities/set_deploy_pickup_times.py

@@ -7,9 +7,13 @@
 import logging
 import time
 import re
-from ph5.core import timedoy
+import datetime
+from ph5.core import timedoy, kefx, ph5api
+from kef2ph5 import add_references
+from math import floor, ceil
 
-PROG_VERSION = '2018.268'
+
+PROG_VERSION = '2019.197'
 LOGGER = logging.getLogger(__name__)
 
 os.environ['TZ'] = 'UTC'
@@ -65,14 +69,8 @@ def _epoch(self, epoch_l):
         self.type_s = 'BOTH'
 
 
-#
-# Read Command line arguments
-#
-
-
 def get_args():
-    global ARRAY_FILE, DEPLOY, PICKUP
-
+    global ARRAY_FILE, DEPLOY, PICKUP, AUTO_CORRECT, NICKNAME, PATH
     parser = argparse.ArgumentParser(
                                 formatter_class=argparse.RawTextHelpFormatter)
     parser.usage = (" set_deploy_pickup_times -a Array_t_xxx.kef "
@@ -85,19 +83,36 @@ def get_args():
                         help="The Array_t_xxx.kef file to modify.",
                         metavar="array_kef", required=True)
 
-    parser.add_argument("-d", "--deploy-time", dest="deploy_time",
+    parser.add_argument("-n", "--nickname", default="master.ph5",
+                        type=str, metavar="nickname", required=False,
+                        help="Name of the PH5 file.", dest="nickname")
+
+    parser.add_argument("-p", "--ph5path", action="store", default=".",
+                        help=("Comma separated list of paths to ph5 "
+                              "experiments."),
+                        type=str, metavar="ph5path", required=False,
+                        dest="path")
+
+    parser.add_argument("-dt", "--deploy-time", dest="deploy_time",
                         help="Array deployment time: YYYY:JJJ:HH:MM:SS",
-                        metavar="deploy_time", required=True)
+                        metavar="deploy_time", required=False)
 
-    parser.add_argument("-p", "--pickup-time", dest="pickup_time",
+    parser.add_argument("-pt", "--pickup-time", dest="pickup_time",
                         help="Array pickup time: YYYY:JJJ:HH:MM:SS",
-                        metavar="pickup_time", required=True)
+                        metavar="pickup_time", required=False)
 
-    args = parser.parse_args()
+    parser.add_argument("-ac", "--auto-correct", dest="auto_correct",
+                        help="Assigns the metadata deploy and pickup times"
+                             "to time stamps calculated by the PH5 traces.",
+                        metavar="auto_correct", required=False, default=False)
 
+    args = parser.parse_args()
+    NICKNAME = args.nickname
+    PATH = args.path
     ARRAY_FILE = args.array_kef
     DEPLOY = args.deploy_time
     PICKUP = args.pickup_time
+    AUTO_CORRECT = args.auto_correct
 
 
 def barf(fh, of, dep_time, pu_time):
@@ -148,28 +163,75 @@ def barf(fh, of, dep_time, pu_time):
             of.write("\t%s\n" % line)
 
 
+def kefTables(kef_file, NICKNAME, PATH):
+
+    k = kefx.Kef(ARRAY_FILE)
+    k.open()
+    while True:
+        n = k.read(10000)
+        if n == 0:
+            LOGGER.error("Kef file is empty")
+            break
+        # Get Das_g references
+        ret = k.strip_receiver_g()
+        if ret:
+            add_references(ret)
+
+            # Make sure Array_t_xxx, Event_t_xxx, and Offset_t_aaa_sss exist
+            arrays, events, offsets = k.strip_a_e_o()
+
+
 def main():
-    global ARRAY_FILE, DEPLOY, PICKUP
+    global ARRAY_FILE, DEPLOY, PICKUP, AUTO_CORRECT, NICKNAME, PATH
 
     get_args()
-
     if not os.path.exists(ARRAY_FILE):
         LOGGER.error("Can't open {0}!".format(ARRAY_FILE))
         sys.exit()
     else:
         fh = open(ARRAY_FILE)
         mdir = os.path.dirname(ARRAY_FILE)
         base = os.path.basename(ARRAY_FILE)
-        base = '_' + base
+        base = 'autocortime_{0}'.format(base)
         of = open(os.path.join(mdir, base), 'w+')
-        LOGGER.info("Opened: {0}".join(os.path.join(mdir, base)))
-
-    dep_time = PH5_Time(passcal_s=DEPLOY)
-
-    pu_time = PH5_Time(passcal_s=PICKUP)
-
-    barf(fh, of, dep_time, pu_time)
-
+        # LOGGER.info("Opened: {0}".join(os.path.join(mdir, base)))
+    if AUTO_CORRECT:
+        ph5_api_object = ph5api.PH5(path=PATH, nickname=NICKNAME)
+        ph5_api_object.read_array_t_names()
+        if not ph5_api_object.Array_t_names:
+            LOGGER.error("No arrays or no events defined in ph5 file."
+                         "Can not continue!")
+            ph5_api_object.close()
+            sys.exit()
+        LOGGER.info("Writing updated kef file: {0}".format(of.name))
+        for array_name in ph5_api_object.Array_t_names:
+            ph5_api_object.read_array_t(array_name)
+            arraybyid = ph5_api_object.Array_t[array_name]['byid']
+            arrayorder = ph5_api_object.Array_t[array_name]['order']
+            for ph5_station in arrayorder:
+                station_list = arraybyid.get(ph5_station)
+                for deployment in station_list:
+                    station_len = len(station_list[deployment])
+                    for st_num in range(0, station_len):
+                        station = station_list[deployment][st_num]
+                        true_deploy, true_pickup = \
+                            ph5_api_object.get_extent(
+                                das=station['das/serial_number_s'],
+                                component=station['channel_number_i'],
+                                sample_rate=station['sample_rate_i'])
+                        julian_tdeploy = (
+                            datetime.datetime.fromtimestamp(floor(true_deploy))
+                            .strftime('%Y:%j:%H:%M:%S'))
+                        julian_tpickup = (
+                            datetime.datetime.fromtimestamp(ceil(true_pickup))
+                            .strftime('%Y:%j:%H:%M:%S'))
+                        dep_time = PH5_Time(passcal_s=julian_tdeploy)
+                        pu_time = PH5_Time(passcal_s=julian_tpickup)
+                        barf(fh, of, dep_time, pu_time)
+    else:
+        dep_time = PH5_Time(passcal_s=DEPLOY)
+        pu_time = PH5_Time(passcal_s=PICKUP)
+        barf(fh, of, dep_time, pu_time)
     of.close()
     fh.close()