Pyrocko GF store file format

Sebastian Heimann

Abstract

This document describes the storage file formats used for the Green’s function (GF) databases in the Pyrocko-GF framework 1.

Overview

A Pyrocko-GF store is an ordinary file system directory with a specific interal structure. It must contain one mandatory file and may contain several optional files and sub-directories with specific names (section Directory layout). The mandatory file must be named config and contains the GF store’s meta information in the YAML format (section The config file). Any non-empty GF store additionally contains two platform-independent binary files: a file named index and a file named traces (section Binary files).

The binary files index and traces are designed to be simple. Conceptually, both files together define the mapping of a scalar integer number (the low-level index) to snippets of regularly sampled time series (referred to as traces). Each trace is composed of a floating point array of GF samples, the time instant of its first sample and the number of elements in the array. All traces in the GF store share the same sampling rate.

A discrete, truncated, and sparse version of the GF is stored. Precisely, the stored samples are

G[j,i] = G[j(x_s, x_r, k), i(t)], \qquad \textrm{with} \qquad  i \in [i_{\textrm{min}}[j], i_{\textrm{max}}[j]] \qquad \textrm{and} \qquad  j \in [0, N-1],

where j is the combined integer low-level index, a mapping of source coordinates x_s, receiver coordinates x_r and the GF component k, and i is a mapping of the time t. Values outside of the time range of stored values are treated with repeating end-points, as

G[j, i<i_{\textrm{min}}[j]] = G[j, i_{\textrm{min}}[j]] \qquad \textrm{ and } \qquad G[j, i>i_{\textrm{max}}[j]] = G[j, i_{\textrm{max}}[j]].

The GF must be sampled at exact multiples of the sampling interval \Delta t, at times t_i = i \; \Delta t. The instant t = 0 corresponds to the time of the impulse-like source excitation.

How physical coordinates and component number (x_s, x_r, k) map into the low-level index j is specified in the meta information of the GF store. Different mappings are available to support different source-receiver geometries and to exploit problem symmetries.

Directory layout

The following table lists the entries of a GF store. Not all entries must be present.

GF store directory contents

File name

File type

Description

config

YAML file

Store meta-information, extent and index mapping (The config file).

index

binary file

GF trace metadata (The index file).

traces

binary file

GF trace sample data (The traces file).

decimated

sub-directory

Directory with decimated variants of the store.

phases

sub-directory

Directory with travel-time interpolation tables.

extra

sub-directory

Directory with extra information. Used to to store backend-specific modelling input parameters.

The config file

The config file contains all meta information needed to correctly interpret the stored Green’s function. It may additionally contain information about the modelling code, the earth model used, author information, citations, etc. Its file format is the widely used YAML format, which provides a good compromise between machine and human readability. It contains a common set of entries available for all GF types plus extra entries for specific GF types.

See the Pyrocko reference manual for lists of available entries:

Binary files

All numbers are encoded in little endian format. Real numbers are encoded as IEEE 754 32-bit or 64-bit floating-point values.

The index file

The index file of the GF store is composed of a 12-byte header and a sequence of 24-byte records, one record for each trace in the database. The following tables define there internal structure.

Index file header (12 bytes)

nrecords

8-byte unsigned int

Total number of records (traces) in the store N.

deltat

4-byte float

Common sampling interval \Delta t of the GF traces.

Index file record (24 bytes)

data_offset

8-byte unsigned int

Byte offset of first sample of the GF trace in the traces file. Special flag values are 0: trace is missing, 1: all samples in the trace are zero, 2: trace is short (one or two samples long).

itmin

4-byte signed int

Temporal onset of the GF trace in number of samples i_{\textrm{min}}[j].

nsamples

4-byte unsigned int

Number of samples in the GF trace: i_{\textrm{max}}[j] - i_{\textrm{min}}[j] + 1.

begin_value

4-byte float

Value the GF trace’s first sample G[j, i_{\textrm{min}}[j]], typically zero. This value is used when the GF trace has to be extrapolated to times t < t_{i_{\textrm{min}}[j]}.

end_value

4-byte float

Value the GF trace’s last sample G[j, i_{\textrm{max}}[j]], typically zero, or the static offset – This value is used when the GF trace has to be extrapolated to times t < t_{i_{\textrm{min}}[j]}.

The traces file

The traces file of the GF store is composed of 32 bytes of empty space at the beginning, followed by zero or more trace data allocations (GF trace sample arrays). Offset and length of each allocated trace are given in the index record. First and last value of the trace data must match their counterparts in the index record, begin_value and end_value. This redundancy can be used for integrity checks. No allocation is made for short traces, i.e. traces with 2 samples, representing step functions.

1

Sebastian Heimann, Hannes Vasyura-Bathke, Henriette Sudhaus, Marius Paul Isken, Marius Kriegerowski, Andreas Steinberg, and Torsten Dahm: A Python framework for efficient use of pre-computed Green’s functions in seismological and other physical forward and inverse source problems (2019, submitted)