Obsinfo Overview

Introduction

obsinfo is a Python standalone application for creating FDSN-standard (StationXML) data and metadata for ocean bottom seismometers using standardized, easy-to-read information files in YAML or JSON formats. The advantages of obsinfo are the following:

  • Easier input user format, as YAML and JSON syntax is simpler than XML

  • Flexibility to change configurations avoiding rewriting or modifying a new StationXML file each time (DRY, don’t repeat yourself)

  • Avoiding redundancy

  • Extreme autonomy of operation from Internet connections, being text-based

  • Adapting StationXML to OBS-specific functionality

  • Simple interface to other systems, such as AROL-based Yasmine

Unlike general systems like Yasmine/AROL, obsinfo is conceived to reflect the vast variability of OBS equipment and the fact that changes on the field are common and cannot be planned in advance. Emergency procedures such as changing an equipment component or a stage in the high seas need to be taken into account. The fact that the editing of information needs to occur without necessarily a connection to a central database is a consideration too. Therefore, the choice has been made to avoid a GUI such as Yasmine and make obsinfo totally text-based using regular files. At the same time, every effort has been made to stay compatible with AROL, which is based on an earlier version of obsinfo itself, v0.106, so AROL yaml files can be imported into obsinfo. However, as of this publication, some differences exist which are documented here.

Lack of redundancy and reusability is achieved by creating a repository of instrumentations which is referenced time and again by different campaigns. Flexibility is achieved by permitting these instrumentations to have several selectable configurations. as well as the ability to make punctual changes to any field via channel modifications (see Advanced Topics).

Object Model

_images/object_model.jpg

The reference manual is organized around the object model, in pages that describe each particular class. The object hierarchy starts in Class Network. You can navigate from one class to the other by using the Relationships section.

Information Files

The system is based on “information files” in JSON or YAML format as input, filled in by appropriate actors and broken down into different categories to remove redundancy and simplify input as much as possible. Information files are taken as input and converted first to an obsinfo object, which in turn gets converted to an obs_py object, finally output as a StationXML file.

There are 6 main file types:

Name

Description

Filled by

When filled

campaign

Lists of stations facilities and participants, plus desired verification. NOT NEEDED FOR PROCESSING

Chief scientist

after a data collection campaign

network

Deployed stations, their instruments and parameters

OBS facility

after a campaign

instrumentation

Instrument description

OBS facility

new/changed instruments

instrument_components

sensors

components

dataloggers

Description of basic components

OBS facility -or- component manufacturer

when there are new are new components or calibrations

response_stage

Description of stages

digitizers, amplifiers/filters)

OBS facility -or- component manufacturer

when there are new components or calibrations

filter

Description of filters amplifiers and digitizers used in stages

OBS facility -or- component manufacturer

when there are new components or calibrations

Only the campaign and network files are OBS-specific. The instrumentation files and their subfiles could be replaced by existing standards such as RESP files or the NRL (Nominal Response Library), but obsinfo provides a simpler and more standards-compliant way to specify the components, and it can automatically calculate response sensitivities based on gains and filter characteristics (using obsPy). obsinfo instrumentation files could also be used to make RESP-files and NRL directories, if so desired.

File Hierarchy

It is recommended to arrange the information files in a file hierarchy such as this:

/authors (contains files used in headers of other information files)
/network
/instrumentation
/sensors
/preamplifiers
/dataloggers
[/instrumentation_componenent]/stages
[instrumentation_componenent]/stages/filters

where [instrumentation_componenent] = sensors, preamplifiers or dataloggers.

The hierarchy is completely up to the user, including the names of the folders/directories. In fact, it is perfectly possible to put all the information in a single file, although it is not recommended as reusability of filters, stages or components depends on independent files.

To reference a file from within another file, use the JREF syntax:

authors: - {$ref: "../authors/Wayne_Crawford.author.yaml#author"}

The effect of this directive is at the core of the philosophy of obsinfo, as it is this mechanism which allows reuse: it substitutes the content of the key author within the file ../authors/Wayne_Crawford.author.yaml as the value of the key authors. If you want to include the complete file, remove the #author anchor.

File Naming Convention

While there is flexibility about the folder hierarchy, information files must follow the following naming convention:

<descriptive file name>.<obsinfo file type>.<file format>

where

<descriptive file name> usually includes vendor and configuration shorthand to make the file easily identifiable by users,

<obsinfo file type> is one of campaign, network, instrumentation, sensor, preamplifier, datalogger, stage, filter

<file format> is one of yml, yaml or json.

Examples:

  • TI_ADS1281_FIR1.stage.yml is a stage with a Texas Instruments FIR filter nested in it, in YAML format.

  • BBOBS.INSU-IPGP.network.json is a network of broad-band stations deployed by INSU IPGP, in JSON format.

There are three resources to look up the exact syntax for each information file. One is the Introduction which takes you step by step building a typical hierarchy of information files. The different Classes pages have a complete explanation of all the attributes in the class. Unless otherwise noted, attributes in the file have the same syntax as attributes in the class. The third resource is the formal syntax of the file, which is a JSON schema, which is always referenced in the Class page.

File Metadata

All information files contain common metadata

  • format_version: - This is a required field. It reflects the template version against which this file must be validated

  • revision: - Revision information (date in particular) to keep change control of file.

    • date: - date of revision

    • authors: - authors of revision, usually a reference to an author file

  • notes: - Optional extra information which will not be put in final metadata.

  • yaml_anchors: - YAML anchors to avoid redundancy, for advanced YAML users. Here is a guide on how to use YAML anchors.

Python architecture

Executables

The following command-line executables perform the main tasks:

  • makeSTATIONXML: generates StationXML files from a network + instrumentation information files

$ python3 makeStationXML -h

displays all the options of makeStationXML.

To create a StationXML file from a file called <filename>, type:

$ python3 makeStationXML.py [options] filename
  • obsinfo-validate: validates an information file against its schema

  • obsinfo-print: prints a summary of an information file

The following command-line executables make scripts to run specific data conversion software:

  • obsinfo-make_LCHEAPO_scripts: Makes scripts to convert LCHEAPO data to miniSEED

  • obsinfo-make_SDPCHAIN_scripts: Makes scripts to drift correct miniSEED data and package them for FDSN-compatible data centers

Package and Modules

The package name is obsinfo

obsinfo.main contains code to initialize the main obsinfo routine, to read and potentially validate main (network) information file and to write StationXML file

obsinfo.network and obsinfo.instrumentation contain the main code to process the corresponding information files.

obsinfo.OBSMetadata contains code to read and validate information files in either YAML or JSON formats.

obsinfo.misc contains miscellaneous code, currently deprecated and unsupported, which is not used anymore in the application

obspy.addons contains modules specific to proprietary systems:

  • obspy.addons.LCHEAPO creates scripts to convert LCHEAPO OBS data to miniSEED using the lc2ms software

  • obspy.addons.SDPCHAIN creates scripts to convert basic miniSEED data to OBS-aware miniSEED using the SDPCHAIN software suite

  • obspy.addons.OCA creates JSON metadata in a format used by the Observatoire de la Cote d’Azur to create StationXML

Auxiliary subdirectories

obsinfo/data/schema

data/schema contains JSON Schema for each file type.

obsinfo/_examples/

Contains example information files and scripts:

  • _examples/Information_Files contains a complete set of information files

    • _examples/Information_Files/network contains network files

    • _examples/Information_Files/instrumentation contains instrumentation, instrument_components, response and filter files.

  • _examples/scripts contains bash scripts to look at and manipulate these files using the executables. Running these scripts is a good way to make sure your installation works, looking at the files they work on is a good way to start making your own information files.

obsinfo/tests/

Contains test cases and code using unittest.py. The tests are performed either on the information files under test/data or on _examples.

Comments on versioning

We use standard MAJOR.MINOR.MAINTENANCE version numbering but, while the system is in prerelease:

  • MAJOR==0

  • MINOR increments every time the information file structure changes in a non-backwards-compatible way

  • MAINTENANCE increments when the code changes or the file structure changes in a backwards-compatible way

Current version: v0.110

Resources

Installation and Startup Guide <InstallStartup>

Tutorial <Tutorial1>

Class Reference Pages <class11>

Information File Templates <FILE>

For the YAML specification, see YAML . For a tutorial, see YAML Tutorial

For the JSON specification, see JSON . For a tutorial, see JSON Tutorial

For the JREF notation, see JREF Notation

For the StationXML reference, see FDSN StationXML Reference