Segyio is a small LGPL licensed C library for easy interaction with SEG Y formatted seismic data, with language bindings for Python and Matlab. Segyio is an attempt to create an easy-to-use, embeddable, community-oriented library for seismic applications. Features are added as they are needed; suggestions and contributions of all kinds are very welcome.
- A low-level C interface with few assumptions; easy to bind to other languages.
- Read and write binary and textual headers.
- Read and write traces, trace headers.
- Easy to use and native-feeling python interface with numpy integration.
- xarray integration with netcdf_segy
Segyio does necessarily attempt to be the end-all of SEG-Y interactions; rather, we aim to lower the barrier to interacting with SEG-Y files for embedding, new applications or free-standing programs.
Additionally, the aim is not to support the full standard or all exotic (but correctly) formatted files out there. Some assumptions are made, such as:
- All traces in a file are assumed to be of the same sample size.
At this stage three different type of segy files can be read and written:
- Post-stack 3D volumes, sorted with respect to two header words (generally INLINE and CROSSLINE)
- Pre-stack 4D volumes, sorted with respect to three header words (generally INLINE, CROSSLINE, and OFFSET)
- Unstructured data
The writing functionality in segyio is largely meant to modify or adapt files. A file created from scratch is not necessarily a to-spec SEG-Y file, as we only necessarily write the header fields segyio needs to make sense of the geometry. It is still highly recommended that SEG-Y files are maintained and written according to specification, but segyio does not mandate this.
When segyio is built and installed, you're ready to start programming! For
examples and documentation, check out the examples in the python/examples
directory. If you're using python, pydoc is used, so fire up your favourite
python interpreter and type help(segyio) to get started.
To build and use segyio you need:
- A C99 compatible C compiler (tested mostly on gcc and clang)
- CMake version 2.8.8 or greater
- Python 2.7 or 3.x.
To build and install segyio, perform the following actions in your console:
git clone --recursive https://github.com/Statoil/segyio
cd segyio
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local
make
make install
Make install must be done as root for a system install; if you want to install
in your home directory, add -DCMAKE_INSTALL_PREFIX=~/ or some other
appropriate directory. Remember to update your $PATH! By default, only the
python bindings are built.
Passing recursive to git clone also fetches statoil/pycmake and
matthew-brett/multibuild. The former is cmake features for managing python
packages, and the latter tools for building OS X and linux binary packages for
pip.
To build the matlab bindings, invoke CMake with the option -DBUILD_MEX=ON. In
some environments the Matlab binaries are in a non-standard location, in which
case you need to help CMake find the matlab binaries by passing
-DMATLAB_ROOT=/path/to/matlab.
It's recommended to build in debug mode to get more warnings and to embed debug
symbols in the objects. Substituting Debug for Release in the
CMAKE_BUILD_TYPE is plenty.
Tests are located in the language/tests directories, and it's highly recommended that new features added are demonstrated for correctness and contract by adding a test. Feel free to use the tests already written as a guide.
After building segyio you can run the tests with ctest, executed from the
build directory.
Please note that to run the python examples you need to let your environment know
where to find the segyio python library. On linux (bash) this is accomplished
by being in the build directory and executing:
export PYTHONPATH=$PWD/python:$PYTHONPATH
We welcome all kinds of contributions, including code, bug reports, issues, feature requests and documentation. The preferred way of submitting a contribution is to either make an issue on github or by forking the project on github and making a pull request.
Alan Richardson has written a great little tool for using xarray with segy files, which he demos in this notebook
Small SEG Y formatted files are included in the repository for test purposes.
Phyiscally speaking the data is non-sensical, but it is reproducible by using
segyio. The tests file are located in the tests/test-data directory. To
reproduce the data file, build segyio and run the test program make-file.py,
make-ps-file.py, and make-rotated-copies.py as such:
python examples/make-file.py small.sgy 50 1 6 20 25
python examples/make-ps-file.py small-ps.sgy 10 1 5 1 4 1 3
python examples/make-rotated-copies.py small.sgy
If you have have small data files with a free license, feel free to submit it to the project!
Import useful libraries:
import segyio
import numpy as np
from shutil import copyfileOpen segy file and inspect it:
filename='name_of_your_file.sgy'
with segyio.open(filename, "r" ) as segyfile:
# Memory map file for faster reading (especially if file is big...)
segyfile.mmap()
# Print binary header info
print segyfile.bin
print segyfile.bin[segyio.BinField.Traces]
# Read headerword inline for trace 10
print segyfile.header[10][segyio.TraceField.INLINE_3D]
# Print inline and crossline axis
print segyfile.xlines
print segyfile.ilinesRead post-stack data cube contained in segy file:
# Read data along first xline
data = segyfile.xline[segyfile.xlines[1]]
# Read data along last iline
data = segyfile.iline[segyfile.ilines[-1]]
# Read data along 100th time slice
data = segyfile.depth_slice[100]
# Read data cube
data = segyio.tools.cube(filename)Read pre-stack data cube contained in segy file:
filename='name_of_your_prestack_file.sgy'
with segyio.open( filename, "r" ) as segyfile:
# Print offsets
print segyfile.offset
# Read data along first iline and offset 100: data [nxl x nt]
data=segyfile.iline[0,100]
# Read data along first iline and all offsets gath: data [noff x nxl x nt]
data=np.asarray([np.copy(x) for x in segyfile.iline[0:1,:]]
# Read data along first 5 ilines and all offsets gath: data [noff nil x nxl x nt]
data=np.asarray([np.copy(x) for x in segyfile.iline[0:5,:]]
# Read data along first xline and all offsets gath: data [noff x nil x nt]
data=np.asarray([np.copy(x) for x in segyfile.xline[0:1,:]])Read and understand fairly 'unstructured' data (e.g., data sorted in common shot gathers):
filename='name_of_your_prestack_file.sgy'
with segyio.open( filename, "r" ,ignore_geometry=True) as segyfile:
segyfile.mmap()
# Extract header word for all traces
segyfile.attributes(segyio.TraceField.SourceX)[:]
# Scatter plot sources and receivers color-coded on their number
plt.figure()
plt.scatter(segyfile.attributes(segyio.TraceField.SourceX)[:], segyfile.attributes(segyio.TraceField.SourceY)[:], c=segyfile.attributes(segyio.TraceField.NSummedTraces)[:], edgecolor='none')
plt.scatter(segyfile.attributes(segyio.TraceField.GroupX)[:], segyfile.attributes(segyio.TraceField.GroupY)[:], c=segyfile.attributes(segyio.TraceField.NStackedTraces)[:], edgecolor='none')Write segy file using same header of another file but multiply data by *2
input_file='name_of_your_input_file.sgy'
output_file='name_of_your_output_file.sgy'
copyfile(input_file, output_file)
with segyio.open( output_file, "r+" ) as src:
# multiply data by 2
for i in src.ilines:
src.iline[i] = 2*src.iline[i]Make segy file from sctrach
spec = segyio.spec()
filename='name_of_your_file.sgy'
spec = segyio.spec()
file_out = 'test1.sgy'
spec.sorting = 2
spec.format = 1
spec.samples = 30
spec.ilines = np.arange(10)
spec.xlines = np.arange(20)
with segyio.create(filename , spec) as f:
# write the line itself to the file and the inline number in all this line's headers
for ilno in spec.ilines:
f.iline[ilno] = np.zeros((len(spec.xlines),spec.samples),dtype=np.single)+ilno
f.header.iline[ilno] = { segyio.TraceField.INLINE_3D: ilno,
segyio.TraceField.offset: 0
}
# then do the same for xlines
for xlno in spec.xlines:
f.header.xline[xlno] = { segyio.TraceField.CROSSLINE_3D: xlno,
segyio.TraceField.TRACE_SAMPLE_INTERVAL: 4000
}Visualize data using sibling tool SegyViewer:
from PyQt4.QtGui import QApplication
import segyviewlib
qapp = QApplication([])
l= segyviewlib.segyviewwidget.SegyViewWidget('filename.sgy')
l.show()filename='name_of_your_file.sgy'
% Inspect segy
Segy_struct=SegySpec(filename,189,193,1);
% Read headerword inline for each trace
Segy.get_header(filename,'Inline3D')
%Read data along first xline
data= Segy.readCrossLine(Segy_struct,Segy_struct.crossline_indexes(1));
%Read cube
data=Segy.get_cube(Segy_struct);
%Write segy, use same header but multiply data by *2
input_file='input_file.sgy';
output_file='output_file.sgy';
copyfile(input_file,output_file)
data = Segy.get_traces(input_file);
data1 = 2*data;
Segy.put_traces(output_file, data1);
Segyio was initially written and is maintained by Statoil ASA as a free, simple, easy-to-use way of interacting with seismic data that can be tailored to our needs, and as contribution to the free software community.