segysak 0.2.7

SEG-Y Seismic Data Inspection and Manipulation Tools using Xarray

Access the full documentation for SEGY-SAK from readthedocs

SEGY-SAK aims to be your Python Swiss Army Knife for Seismic Data.

To do this SEGY-SAK offers two things; a commandline interface (CLI) for inspecting and converting SEGY data to a more friendly format called NETCDF4, and by providing convienience functions for the data using xarray. We try hard to load the data the same way everytime so your functions will work no-matter which cube/line you load. The xarray conventions we use are outlined in the documentation.

Why NETCDF4? Well, NETCDF4 is a fancy type of enclosed file binary format that allows for faster indexing and data retreival than SEGY. We try our best to scan in the header information and to make it easy (or easier) to load SEGY in different formats, different configuration (2D, 2D gathers, 3D, 3D gathers). We do all this with the help of segyio which is a lower level interface to SEGY. If you stick to our xarray format of files we also offer utility functions to return to SEGY so you can export to other software.

Current Capabilities

• CLI:

  • Convert 2D, 3D and gathers type SEGY to NETCDF4 and back. The NETCDF4 files are one line open with xarray.open_dataset.

  • Extract sub-volumes via cropping xline and inline.

  • Read EBCIDC header.

  • Perform a limited header scan.

• Xarray and Python API:

  • Load 2D, 3D and gathers type SEGY to a xarray.Dataset.

  • Access header information and text headers in Python with conveience functions.

  • Select traces by UTM X and Y coordinates.

Installation

SEGY-SAK can be installed by using pip or python setuptools, we also provide an environment.yml for use with conda.

Python Package Index via pip

From the command line run the pip package manager

pip install segysak

Install from source

Clone the SEGY-SAK Github repository and in the top level directory run setuptools via

python setup.py install

CLI Quick Start

The command line interface (CLI) provides an easy tool to convert or manipulate SEG-Y data. In your Python command-line environment it can be accessed by calling segysak.

For a full list of options run

segysak --help

Any SEG-Y files converted using the convert command. For example

segysak convert test.segy

Can be loaded into Python using xarray.

test = xarray.open_dataset('test.SEISNC')

xarray seismic specification seisnc

The xarray seismic specification termed seisnc can be used by segysak to output NETCDF4 files is more performant for Python operations than standard SEG-Y. Unlike SEG-Y, xarray compatable files fit neatly into the Python scientific stack providing operations like lazy loading, easy slicing, compatability with multi-core and multi-node operations using dask as well as important features such as labelled axes and coordinates.

This specification is not meant to be prescriptive but outlines some basic requirements for xarray datasets to work with SEGYSAK functionality.

SEGY-SAK uses the convention .seisnc for the suffix on NETCDF4 files it creates. These files are datasets with specific 1D and 2D coordiates and have a single variable called data. The data variable contains the seismic cube volume or 2D line traces. Attributes can be used to provide further metadata about the cube.

3D and 3D Gathers

SEGY-SAK uses the convention labels of iline, xline and offset to describe the bins of 3D data. Vertical dimensions are twt and depth. A typical xarray dataset created by SEGY-SAK will return for example

>>> seisnc_3d = segysak.segy_loader('test3d.sgy', iline=189, xline=193)
>>> seisnc_3d.dims

Frozen(SortedKeysDict({'iline': 61, 'xline': 202, 'twt': 850}))

2D and 2D Gathers

For 2D data SEGY-SAK uses the dimensino labels cdp and offset. This allows the package to distinguish between 2D and 3D data to allow automation on saving and convience wrappers. The same vertical dimensions apply as for 3D. A typical xarray in 2D format would return

>>> seisnc_2d = segysak.segy_loader('test2d.sgy', cdp=21)
>>> seisnc_2d.dims

Frozen(SortedKeysDict({'cdp': 61, 'twt': 850}))

Coordinates

If the cdpx and cdpy byte locations are specified during loading the SEGY the coordinates will be populated from the headers with the variable names cdp_x and cdp_y. These will have dimensions equivalent to the horizontal dimensions of the data (iline, xline for 3D and cdp for 2D).

Attributes

Any number of attributes can be added to a siesnc file. Currently the following attributes are extracted or reserved for use by SEGY-SAK.

• ns number of samples per trace

• ds sample interval

• text ebcidc header as ascii text

• measurement_sys vertical units of the data

• d3_domain vertical domain of the data

• epsg data epsg code

• corner_points corner points of the dataset in grid coordinates

• corner_points_xy corner points of the dataset in xy

• source_file name of the file the dataset was created from

• srd seismic reference datum of the data in vertical units measurement_sys and d3_domain

• datatype the data type e.g. amplitude, velocity, attribute

• percentiles this is an array of approximate percentile values created during scanning from SEGY. Primarily this is useful for plotting by limiting the dynamic range of the display. The percentiles are in percent 0, 0.1, 10, 50, 90, 99.9 & 100.

Complete Documentation

The complete documentation for SEGY-SAK can be found at readthedocs