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kasra-hosseini / obspyDMT

A Python toolbox for the query, retrieval, processing and management of seismological data sets, including very large, heterogeneous and/or dynamically growing ones.
http://kasra-hosseini.github.io/obspyDMT/
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Couldn't write catalog object to QuakeML #55

Open okling opened 4 years ago

okling commented 4 years ago

Hi Kasra,

I had an issue in writing event catalog (Quake ML) after updating Obspy.

I was trying to download waveforms using the following command:

obspyDMT --datapath Alaska_M6.5 --min_date 2018-08-14 --max_date 2018-08-16 --sta="*" --net="BW" --station_rect="1/22/40/52" --loc "*" --cha "HHZ" --event_rect="-180/-160/45/55" --min_mag 6.0 --preset 0 --offset 7200 --sampling_rate 20 --instrument_correction --corr_unit "DIS" --pre_filt "0.001, 0.005, 10, 20" --data_source all --event_catalog "NEIC_USGS" --req_parallel

But I received this error message and no ML file was written in the EVENT-INFO folder:

--------------------------------------------------------------------------------
           obspyDMT (obspy Data Management Tool)

    Python Toolbox for Retrieving, Processing and Management of
            Large Seismological Datasets

:copyright:
The ObsPy Development Team (devs@obspy.org)

Developed by Kasra Hosseini
email: kasra.hosseinizad@earth.ox.ac.uk

:license:
GNU General Public License, Version 3
(http://www.gnu.org/licenses/gpl-3.0-standalone.html)
--------------------------------------------------------------------------------

obspyDMT primary mode: event_based

=================================
Waveforms will be retrieved from:
BGR,ETH,EMSC,GEONET,GFZ,ICGC,INGV,IPGP,IRIS,ISC,KNMI,KOERI,LMU,NCEDC,NIEP,NOA,ODC,ORFEUS,RESIF,RASPISHAKE,SCEDC,TEXNET,USGS,USP
=================================

Event(s) are based on:  NEIC_USGS
#Divisions: 0

Assembling 1 xml files...
1,
cleaning up the temporary folder.

0.14046099999999995 sec to retrieve the event info form NEIC.

#N LAT       LON       DEP DATETIME             MAG  AUTH  EV_ID              FLY  
--------------------------------------------------------------------------------
1    51.423  -178.026  34  2018-08-15T21:56:56  6.5  None  20180815_215656.a  NAN
--------------------------------------------------------------------------------

Number of events/intervals: 1
Time for retrieving and saving the event info: 0:00:00

Couldn't write catalog object to QuakeML as:
>>:  'NoneType' object has no attribute 'id'
Proceed without ..

#Events after filtering: 1

Here are my current packages:

python                    3.7.3                h5b0a415_0    conda-forge
obspy                     1.2.1            py37h03ebfcd_1    conda-forge
obspydmt                  2.2.5                     dev_0    <develop>
basemap                   1.2.1            py37hd1be537_2    conda-forge
basemap-data-hires        1.2.1                         0    conda-forge

The data set cannot be updated (e.g. adding more stations/channels). Any ideas on this? Thanks for your help!

Cheers, Angel

kasra-hosseini commented 4 years ago

Hi Angel, Could you please try the new version of obspyDMT (2.2.7). Indeed, there were some inconsistencies between obspyDMT and the latest version of obspy. Thank you for reporting this.

kasra-hosseini commented 4 years ago

Here is the output:

=================================
Waveforms will be retrieved from:
BGR,ETH,EMSC,GEONET,GFZ,ICGC,INGV,IPGP,IRIS,ISC,KNMI,KOERI,LMU,NCEDC,NIEP,NOA,ODC,ORFEUS,RESIF,RASPISHAKE,SCEDC,TEXNET,USGS,USP
=================================

Event(s) are based on:  NEIC_USGS
#Divisions: 0

Assembling 1 xml files...
1,
cleaning up the temporary folder.

0.394233689 sec to retrieve the event info form NEIC.

#N LAT       LON       DEP DATETIME             MAG  AUTH  EV_ID              FLY
--------------------------------------------------------------------------------
1    51.423  -178.026  34  2018-08-15T21:56:56  6.5  None  20180815_215656.a  NAN
--------------------------------------------------------------------------------

Number of events/intervals: 1
Time for retrieving and saving the event info: 0:00:00

#Events after filtering: 1

=============
metadata mode
=============
initializing files and directories...DONE
check the availability: BGR
okling commented 4 years ago

Hi Angel, Could you please try the new version of obspyDMT (2.2.7). Indeed, there were some inconsistencies between obspyDMT and the latest version of obspy. Thank you for reporting this.

Hi Kasra, thanks for the quick response! It is fixed in the master branch, but it is not fixed in the routing_client branch, which has the option --eida_token_path. In the master branch, it gives this message: obspyDMT: error: no such option: --eida_token_path. Could you implement this option to the master branch or also resolve the compatibility in the routing_client branch?

Thanks again!

okling commented 4 years ago

Hi Kasra, I have found another problem with writing QuakeML catalog even in the master branch. So instead of a ML catalog catalog.ml in the EVENTS-INFO folder, a file called catalog.ml.pkl is written. When I'm trying to open (pickle) it, it gives me the following message:

>>> import obspy
>>> import pickle
>>> ev_load = open("catalog.ml.pkl","r")
>>> ev_pkl = pickle.load(ev_load)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/aling/anaconda3/envs/obspy/lib/python3.7/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 0: invalid start byte

If reading in binary,

>>> ev_load = open("catalog.ml.pkl","rb")
>>> ev_pkl = pickle.load(ev_load)
/home/aling/anaconda3/envs/obspy/lib/python3.7/site-packages/obspy/core/util/attribdict.py:97: UserWarning: Setting attribute "preferred_mag" which is not a default attribute ("event_descriptions", "comments", "picks", "amplitudes", "focal_mechanisms", "origins", "magnitudes", "station_magnitudes", "resource_id", "event_type", "event_type_certainty", "creation_info", "preferred_origin_id", "preferred_magnitude_id", "preferred_focal_mechanism_id").
  warnings.warn(msg)
/home/aling/anaconda3/envs/obspy/lib/python3.7/site-packages/obspy/core/util/attribdict.py:97: UserWarning: Setting attribute "preferred_mag_type" which is not a default attribute ("event_descriptions", "comments", "picks", "amplitudes", "focal_mechanisms", "origins", "magnitudes", "station_magnitudes", "resource_id", "event_type", "event_type_certainty", "creation_info", "preferred_origin_id", "preferred_magnitude_id", "preferred_focal_mechanism_id").
  warnings.warn(msg)
/home/aling/anaconda3/envs/obspy/lib/python3.7/site-packages/obspy/core/util/attribdict.py:97: UserWarning: Setting attribute "preferred_author" which is not a default attribute ("event_descriptions", "comments", "picks", "amplitudes", "focal_mechanisms", "origins", "magnitudes", "station_magnitudes", "resource_id", "event_type", "event_type_certainty", "creation_info", "preferred_origin_id", "preferred_magnitude_id", "preferred_focal_mechanism_id").
  warnings.warn(msg)

Thanks for your help!