Working with 3D seismic data in Python using segyio and numpy (mostly)

Between 2 and 3 years ago I started turning my long time passion for image processing, and particularly morphological image processing, to the task of fault segmentation.

At the time I shared my preliminary code, of which I was very happy, in a Jupyter notebook, which you can run interactively at this GitHub repository.

Two areas need improvement to get that initial workflow closer to a production one. The first one is on the image processing and morphology side; I am thinking of including: a better way to clean-up very short faults; pruning to eliminate spurious segments in the skeletonization result; the von Mises distribution instead of standard distribution to filter low dip angles. I know how to improve all those aspects, and have some code snippets sitting around in various locations on my Mac, but I am not quite ready to push for it.

The second area, on the seismic side, is ability to work with 3D data. This has been a sore spot for some time.

Enter segyio, a fast, open-source library, developed precisely to work with SEGY files. To be fair, segyio has been around for some time, as I very well know from being a member of the Software Underground community (swung), but it was only a month or so ago that I started tinkering with it.

This post is mostly to share back with the community what I’ve learned in my very first playground session (with some very helpful tips from Jørgen Kvalsvik, a fellow member of swung, and one of the creators of segyio), which allowed me to create a 3D fault segmentation volume (and have lots of fun in the process) from a similarity (or discontinuity) volume.

The workflow, which you can run interactively at this segyio-notebooks GitHub repository (look for the 01 – Basic tutorial) is summarized pictorially in Figure 1, and comprises the steps below:

  • use segy-io to import two seismic volumes in SEGY file format from the F3 dataset, offshore Netherlands, licensed CC-BY-SA: a similarity volume, and an amplitude volume (with dip steered median filter smoothing applied)
  • manipulate the similarity to create a discontinuity/fault volume
  • create a fault mask and display a couple of amplitude time slices with superimposed faults
  • write the fault volume to SEGY file using segy-io, re-using the headers from the input file

Figure 1. Naive 3D seismic fault segmentation workflow in Python.


Get the notebooks on GitHub (look for the 01 – Basic tutorial)

Feedback is welcome.


DISCLAIMER: The steps outlined in the tutorial are not intended as a production-quality fault segmentation workflow. They work reasonably well on the small, clean similarity volume, artfully selected for the occasion, but it is just a simple example.

Seismic terrain displays


A couple of years ago I stumbled in a great 2001 paper by Beyer [1] on The Leading Edge. Being interested in visualization techniques I was drawn by the display in Figure 1 (which is a low resolution copy from Figure 2 in the paper). But what really amazed me was the suggestion that a display like this could be created in a few minutes, without doing any interpretation, by just manipulating instantaneous phase slices. With the only condition of having data of fair quality, this promised to be an awesome reconnaissance tool.


Figure 1 – Copyright SEG

The theory

The idea that instantaneous phase is a great attribute for interpretation has been around for a long time. There is, for example, a 1989 Exploration Geophysics paper by Duff and Mason [2]. These two authors argue that amplitude time slices are a suboptimal choice, and that instantaneous phase slices should be preferred. They give three reasons:

1) on amplitude time slices only relatively strong events remain above the bias level after gain and scaling. Weak events are submerged below the bias and remain unmappable.  Although it is the topic of a future post, it is worth mentioning I think this effect is exacerbated by the common but unfortunate choice of a divergent color palette with white in the middle. White is so bright (I call it white hole) that even more low amplitude events become indiscernible.

2) discrete boundaries corresponding to unique positions on the wavelet are displayed on instantaneous phase slices – this intra wavelet detail is lost on amplitude slices.

After-Duff-Mason 2

Figure 2 – after Duff and Mason, Figure 2

3) instantaneous time slices give DIRECTLY the sense of time dip for dipping events. In Figure 2 I show 2 parallel dipping reflectors, represented by 5 (non consecutive) traces, and 2 (non-consecutive) instantaneous phase slices (at arbitrary t1 an t2). I marked 5 discrete phase events for the top dipping reflector. The sense of time dip is given (with appropriate color palette) by the sense of color transition. Conversely, this intra wavelet detail would be lost on the amplitude time slices, with amplitudes between the black center trace and the red traces, and amplitudes between the red traces and the green traces lost within a single broad zone. The difference is probably not as dramatic nowadays with the increase in dynamic ranges available, but using instantaneous phase slices still remains advantageous for detailed mapping.

Beyer’s seismic terrain is just a natural extension of the instantaneous time slice as ( quoted from [1]):”… it then follows that the instantaneous phase (-180 deg to +180 deg) can simply be rescaled to the wavelength in ms of pseudoseismic two-way time… Seismic terrain can be thought of as a type of instantaneous wavelength generated from instantaneous phase along a time slice”. With reference to the top dipping reflector in Figure 3, the method allows generating converting the brown phase segment to the dipping blue segment (and similarly the yellow phase segment to the dipping green segment for bottom dipping event).


Figure 3

The practice – Petrel

Let’s see how we can create a terrain display similar to that in Figure 1 using Petrel.

Raw data

The process starts with migrated seismic data, from which we need generate both the phase and frequency component to get us the instantaneous wavelength.

For this tutorial I use a public seismic dataset (BPA9901) available on the Norwegian Public Data Portal. In Figure 4 below I am showing an amplitude time slice (above the Chalk) from the migrated seismic volume.


Figure 4

Step 1 – generate phase component

The first step is to generate an instantaneous phase attribute volume. This is found in the volume attributes. In Figure 5 below I am showing the instantaneous phase slice corresponding to the amplitude time slice of Figure 4.

*** N.B. *** If significant regional dips are observed in the seismic data, care should be taken in some cases  it may be beneficial (please see comment section) to remove them through flattening prior to the terrain generation.

Figure 5

Figure 5

Step 2 – generate frequency component

This is the trickiest part. In theory to get the instantaneous wavelength we would have to calculate the instantaneous frequency and divide the  instantaneous frequency attribute can be very noisy and can have spurious values in areas of low amplitude in the input data. A good practical alternative is to measure a single value of the dominant wavelet period T in an area of relatively flat reflections near the zone of interest as I am showing in Figure 6.

For the more avid readers, this is all explained quite nicely in Beyer (quoted from [1]): “Complex trace relationships dictate that the wavelength is the phase component divided by the frequency component. Thus one may be compelled to derive the seismic terrain by dividing the extracted instantaneous phase by the  extracted instantaneous frequency (carefully applying unit conversion of 1000 ms/ 360 deg or 2.78). However extracted instantaneous frequency tends to include spurious values in low amplitudes (approaching infinity according to literature and practice which correspond to poor data quality zones. Instantaneous frequency or even averaged instantaneous frequency renders the seismic terrain noisy, unrealistic, and misleading. Years of extensive use have shown that  single value of visually estimated dominant wavelet period (i.e. cycles per second) produces a very high-quality seismic terrain that closely fits the seismic events over wide areas”.


Figure 6

Step 3 – generate the instantaneous wavelength (seismic terrain)

Having estimated the dominant wavelet period T (in ms) , I can now use it to generate the instantaneous wavelength. We are essentially converting the data from the range [-180 180] deg to the range [-T/2 T/2] ms.

In Petrel I do it in the calculator with a formula of the type:

terrain=(((instantaneous phase +180)*T/2)/180)

The actual formula used is shown on the top row of Figure 7 below. You will notice that it isn’t exactly the same as the above formula. I added 1 to 180 to avoid division of zero values, e.g.:

(([-180 180]+180)*28/180) = ([0 180]*28/180) = ([0 5040]/180) % not good!


(([-180 180]+181)*28/180) = ([1 181]*28/180) = ([28 5068]/180) % good!

Once the division is performed I subtract T/2 again.

Notice from Figure 7 that because we added 181 but divided by 180 there is a small adjustment to be made by hand. I get this small adjustment by double clicking on the output volume to get the statistics. In this case it is +-0.16 ms, so I run a second time the formula (bottom row, Figure 7), this time subtracting T/2 +0.16 instead of just T/2.


Figure 7

Step 4 – display seismic terrain.

There are two options in Petrel to display the resulting seismic terrain volume:

Option 1 – display bump mapped terrain slices in 2D or 3D window

This is my preferred option for scanning up and down through the terrain slices. The bump mapping effect is done by double clicking on the terrain survey with a 2D or 3D window open and selected, in the Style tab>Intersection  tab. In Figure 8 I am showing the bump mapped terrain slice corresponding to the instantaneous phase time slice of Figure 5.


Figure 8

Option 2 – display selected horizons of interest in 3D window

One may want to create a display such as the one in Figure 1, which for me is intended for a later stage, when integrating perhaps with extracted amplitude or attribute anomalies highlighting hydrocarbon presence.

As often in Petrel there are different ways of achieving the same result. This is how I do it. First, I create a flat surface, with a TWT value corresponding to the slice I am interested in (as in Figure 9, left panel). Then I extract and append to this surface the terrain values from that slice of interest (as in Figure 9, right panel).

Figure 9

Figure 9

Figure 10

Figure 10

Finally, in the calculations tab, I add a constant time shift corresponding to the time associated with the slice  of interest: notice the difference in Z value between the left panel in Figure 10 (before the calculation), and the right panel (after the calculation). It is also necessary to use the extracted value as visual vertical position as illustrated in Figure 11.

Figure 11

Figure 11

I am showing the result in Figure 12. This is the same terrain slice as in Figure 8.

terrain_slice extracted

Figure 12


As a quick QC I am displaying in Figure 13 a vertical section (corresponding to the thick black line in Figure 12) from the input seismic data, with the extracted surface drawn as a thin black line.

The terrain deteriorates to the far left as we approach the edge of the survey, with fold decreasing and noise increasing, and there is a cycle skip towards the far right. But all in all I think  this is a very good result: it captures the faults well, and the whole process took less than 20 minutes with no picking.


Figure 13


This method has one limitation: the maximum fault throws or stratigraphic relief (in milliseconds) that can be mapped is equal to the period T.


I wish to thank DONG Energy for agreeing to the publication of the seismic images, which were generated using company licensed Petrel.

** UPDATE **

A few readers asked clarifications on what the benefits and potential uses are of using this attribute. The short answer is that this is in fact a pseudo-horizon that tracks dipping  seismic events accurately within the range of the period of the dominant frequency period (as seen in Figure 13), which makes it an excellent reconnaissance tool.  A good quality first pass map can be made in minutes in areas where detailed mapping can take days.  An excellent example is Figure 16 in the original paper [1].  More details can be found in the last two paragraphs of the paper:  Reservoir-scale structural data from seismic terrain and Fast 3-D screening. 


[1] Beyer, L. (2001). – Rapid 3-D screening with seismic terrain: deepwater Gulf of Mexico examplesThe Leading Edge, 20 (4), 386–395.

[2] Duff, B.A., and Mason, D.J. (1989) – The instantaneous-phase time slice: A crucial display for enhancing 3-D interpretationExploration Geophysics 20 (2) 213 – 217