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Installing OpenSeaSeis

This is a quick note to describe how to download and install the OpenSeaSeis Java based seismic processing system and viewer under the windows linux subsystem (WSL). To install WSL and Seismic Unix please refer to my previous blog post. I found OpenSeaSeis installed very easily in my windows WSL/ubuntu setup.

  1. Download the master file from John Stockwell’s Github page. On the Github page to the right is a green button labelled Code. I downloaded the zip package in windows and unzipped it to my linux home directory in a subdirectory called seaseis. Its important that you use a sub-directory.
  2. From within the OpenSeaSeis-Master directory I just ran
    • ./make_seaseis.sh
    • Originally I was using gcc version 7.5.0 but on 28/12/2022 I installed using gcc version 11.3.0 for Ubuntu 22.04
    • My Ubuntu install probably already had Java and FFTW libraries installed, so that might also need to be done before seaseis compilation
    • Check java version with java -version and javac – version and if java is not installed then for Ubuntu (sudo apt-get install default-jre and sudo apt-get install default-jdk )
    • The compilation starts and here is a screenshot taken after a few minutes, while modules are still compiling.
  • I think compilation took around 5 minutes on my laptop. There were some errors in the last stage regarding html help files but I ignored these.
  • On 28/12/2022 I installed using gcc version 11.3.0 for Ubuntu 22.04 and I did get the same compilation errors for src/cs/jni/csNativeSegyReader.cc, src/cs/jni/csNativeSeismicReader.cc and src/cs/jni/csNativeRSFReader.cc . I managed to circumvent these with a quick hack that commented the offensive lines out. A better fix is needed.
  • By the way before running the command I did look in the doc directory where John has helpfully included all the relevant installation instructions and a users manual.
  • The binary files are installed one directory above the OpenSeaSeis-master directory, so in my case they were in my userid/seaseis – which is where I wanted them.
  • bash: export PATH=${PATH}:/userid/seaseis/bin and put this command in your .bashrc file
  • log out and log back in to activate the shell and paths
  • commands
    1. seisseis -h is for the command line interface
    2. xseaseis.sh runs the interactive flow building
    3. seaview.sh runs the seismic viewer
  • Enjoy OpenSeaSeis !!
    • The viewer includes spectra, filter and AGC support as well as the ability to support multiple sections, trace header overlays, remap SEGY headers etc.
    • The interactive job builder is just really a way to edit ASCII job files and submit them. Its a bit clunky, but could be a good way to learn the seaseis syntax. personally since I know seismic unix I wouldn’t be planning on learning seaseis also although in the past I’ve found the seaseis SEGD option to be very useful.

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Seismic Unix on Windows

In this post I wanted to briefly summarise the stages I went through to install seismic unix under the windows linux subsystem (WSL). There are other ways to get seismic unix running under windows (just google it !), and believe me I’ve used them all over the years. The WSL route is the closest I’ve come to something that’s easy, fast and offers all the functionality you need including sharing files between windows and linux. Please also note that I did this install a few years ago, but am putting a few updates here (May 2022). My notes might still not be very accurate.

  1. Windows Linux Subsystem 1 or 2 ?
    1. there are plenty of online blogs for this, but try the official microsoft help page. My installed used WSL1 but version 2 is now available and covered in the link above. WSL2 is supposed to be quicker, but there are some network differences and issues to overcome. If you have Windows11 then you can use the latest WSL distribution which automatically handles linux graphics applications. See this page here for windows 11 options. By default under WSL you install the Linux Ubuntu distribution which should then let you install seismic unix very easily. Other distributions are available as per the following screenshot (March 2022).
  1. Once you have installed linux and setup your user name and password you generally need to upgrade/update the installation using the following commands:
    • sudo apt-get update
    • sudo apt-get upgrade
  2. The following commands will install c-compiler and various development libraries needed to install seismic unix. The fortran compiler and possibly other items are optional, but this is what I did prior to installing seismic unix.
    • sudo apt-get install build-essential
    • sudo apt-get install gfortran
    • sudo apt-get install libx11-dev
    • sudo apt-get install libxt-dev
    • sudo apt-get install freeglut3-dev
    • sudo apt-get install libxmu-dev libxi-dev
    • sudo apt-get install libc6
  1. X-Windows System (graphics)
    • Newer versions of WSL will support WSLg as described in this recent microsoft post for Windows 11. However I only have windows 10 and WSL 1 – so I havn’t tested this route. I used the vcxsrv server to enable graphics applications. There are other possible options (for example via MobaXterm), but I know that this way works. You could follow this blog page which describes how to install and test a linux desktop, but particularly focused on vcxsrv and xfce4. Once I have xfce4 installed you can run it to obtain a full linux experience on your windows machine. However I just use vcxsrv to launch graphical windows from seismic unix under windows and it seems to work just fine.
    • One of the main issues seems to be connecting the linux DISPLAY variable to the X-server vcxsrv (as described in the blog page above). There are differences here between WSL1 and WSL2, with WSL2 using different networking protocols. Some users report issues with the firewall automatically blocking the connection – so you may need to make a firewall rule to get it to work properly. If you experience a problem here there are plenty of possible online solutions available.
  2. I also installed an xeyes to check the graphics are working via sudo apt-get install x11-apps
    • xeyes
  1. I like to keep linux and windows files separated by default, so the way I work is to make a new windows directory under Documents called linuxshare and then various project subdirectories for segy files etc. I can then access that from linux by typing
    • cd /mnt/c/Users/<your windows user id>/Documents/linuxshare
    • (I also have an alias setup in .bashrc so I can change easily to that directory).
  2. You will need to download the latest seismic unix from the current main website. The version as of March 2022 is V44 release 23. The installation instructions are found from the main website and these seem to be pretty comprehensive although I’ve done the install so many times that I admit to not following the instructions.
    • The recommended directory for install is /usr/local/cwp but personally I’ve always just used cwp.
    • The critical thing is to setup your CWPHOME variable e.g. export $CWPROOT=/usr/local/cwp
    • test using suplane|suximage

Enjoy seismic processing and quality control in seismic unix.

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Seismic Quality Control: Geo2X geo2view

In a previous post I compiled a brief review of the free SeiSee software for quality control of SEGY data, including trace headers. I’ve also compared SeiSee to a newer viewer SeisTopia. In this post I briefly review GEO2View which has recently been released by applied geophysics company Geo2x. Thanks to Alan Richardson of Ausar Geophysical for pointing it out to me. I’ve used the same data for my SeiSee/SeisTopia reviews which is a 12935 trace migrated stack released by USGS from the 2018 Matrix Survey with shot records from the same line.

Display of stacked seismic section. The variable scale display is very fast (and useful for long lines).
Shot record displays with trace header readout (to left) and plots of header attributes above the shots.
  1. License: Unfortunately not covered by any standard license agreements such as GNU.
  2. Hardware: Windows 10
  3. Support: The authors have pledged to release new features and support the viewer.
  4. Data Input/Output
    • Supports SEGY rev1 /Seismic Unix (SU) and SEG2 formats.
    • SEGY can also be exported.
  5. Seismic Display
    • Fairly standard but high quality seismic displays in wiggle or variable density in four colourbars which are fixed.
  6. Trace Header QC
    • Simple but effective trace readouts with ability to dump headers to ascii files.
    • Useful section info summary and ability to export headers.
  7. Processing Options
    • Basic AGC and bandpass only as of June 2021 (filtering options probably a bit abstract for many users).

Verdict:

SeisTopia has slightly more options, particularly from the seismic processing and 3D QC point of view. The neat ability of SeiSee to rapidly QC an entire directory is missing from other viewers covered here.

I liked the Geo2X viewer and it might have an exciting future if it is supported and developed as planned. Will it ever topple SeiSee from the pinnacle of free QC viewers….well, only time will tell.

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Free Seismic Data Repositories

In this post I provide an incomplete list of links to free seismic data repositories. Feel free to add your favorites using the comments to this page. Many governments are now seeing the benefit of releasing data to research. There is a now a lot of data out there !

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Seismic Quality Control: SeisTopia

In a previous post I compiled a brief review of the free SeiSee software for quality control of SEGY data, including trace headers. In this post I briefly review SeisTopia which has very recently (May 2021) been released by Kev Roberts. Please also see here for a review of Geo2View. I used the same data for my SeiSee review which is a 12935 trace migrated stack released by USGS from the 2018 Matrix Survey with shot records from the same line.

SeisTopia Preudo Relief Display
  1. License
    • Both viewers are free to download but are not covered by any standard license agreements (e.g. GNU).
    • I did find that Windows Defender anti-virus flags the colourbar editor shipped with SeisTopia. I’ve scanned this file with Bitdefender and it is totally clean. In any case you will not need the colourbar editor unless you plan to load customised colourbars.
  2. Hardware
    • SeisTopia and SeiSee both run under Windows10, but the newer versions of SeiSee also run under Linux.
  3. Support
    • Both viewers are officially unsupported, however SeiSee has been around for many years, many people are familiar with it and the developer does seem to release updates every few years. The recent release of SeiSee code could lead to extended 3rd party support in the future.
  4. Data Input/Output
    • The SeisTopia user has to select (or drop in) one file at a time which is less useful than SeiSee for QC of multiple files in a single directory, switching between many files and comparing headers etc.
    • SeiSee will read seismic unix and CGG format files, as well as SEGY. SeisTopia will read up to SEGY Rev1.
    • SeiSee allows the user to edit/export SEGY files and modify headers.
  5. Seismic Display
    • The SeisTopia viewer options are nicely laid out and of excellent quality, probably better than SeiSee but sometimes slower as the files buffer from disk. The mouse wheel can be used to quickly change parameter values as well as to scroll the seismic displays. The mouse buttons can be used to quickly zoom in/out of the displays. It’s all very intuitive and the help file is quickly accessible if you need it.
    • I loaded 5Gb of shot records very quickly into SeisTopia and it was impressively quick to scroll through the file for quality control. I was able to view windowed Amplitude Spectra, test bandpass filters and FK filters.
  6. Trace Header QC
    • SeisTopia pops the trace headers into a different window and the user can scroll up and down the section to see how the header values change. Two headers can be selected for the seismic display, with a third header available for a graphic type overlay (useful for elevation for example).
    • A 3D map viewer can be used to select inlines, crosslines and timeslices and make maps of header values (e.g. fold, elevation) so as a 3D Viewer SeisTopic far exceeds the capabilities of SeiSee and comes into territory previously occupied by OpenDtect. Other 3D viewers are also available for quality control of seismic data.
  7. Processing Options
    • Both viewers have similar display options such as AGC and Bandpass Filter, SeisTopia has a few additional extra options such as t-squared gain, instantaneous attributes, a pseudo relief option and the ability to perform a windowed FK display as well as a normal amplitude spectrum.
  • SeisTopia Trace QC display
  • SeisTopia FK display and dip annotation
SeisTopia Screen Displays

Verdict:

I liked the new SeisTopia viewer, found it trivial to learn with intuitive high quality displays. I’ve put the icon right next to SeiSee on my desktop and I intend to use SeisTopia more often in the future. That said, if you are already a heavy SeiSee user then there is probably no strong reason to switch viewers. SeiSee offers more header editing features and SeisTopia offers more processing QC displays and 3D displays. Also checkout my review of Geo2View which is an alternative free windows based viewer.

There are of course literally tens of commercially available seismic viewers. Its always amazed me that more (or ?any) companies didn’t release a “lite” version of their viewers to enable quality control. Many contractors now offer free licenses (or cloud based) viewers for client QC during a processing project and this is certainly something I would recommend that the client asks for.

My review for the BotoSeis interface for Seismic Unix, as well as other viewers and free seismic processing systems should be coming later this month.

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Seismic Quality Control: SeiSee

As advertised in a previous post we aim to review and compare freely available tools for seismic quality control. The standard bearer is most definitely SeiSee from DMNG . It seems to have been around for ever, but as of May 2021, version 22.6 dated 2017 appears to be the latest available (older versions are available on other links). More on SeiSee can be found here and on the original DMNG download site together with other codes such as SegDSee which is a similar viewer but for SEG-D format files. Also available and dated March 2021 is SeiSeeMp which is a slightly simplified tool but available multi-platform (including Linux) and for which source code is available.

I can understand that some of these download sites may not appear too friendly for those of you with highly security minded IT departments and those without administrator privilege’s. If you have these difficulties and would still like to use SeiSee then we recommend that you use your own laptop or you can contact us and we can come up with a cloud based solution which will suit your needs. Although free, SeiSee is a very useful piece of software and its well worth suffering the paperwork with your IT staff to get it installed. As far as we know the install exe is free of any virus or bugs and works out of the box on any windows system.

The above screenshot shows a typical SeiSee QC session featuring files in a given directory (left tab), middle tab (trace, EBCDIC or binary header) and seismic display with frequency spectrum. The software is fairly easy to use. If you have any difficulties then feel free to ask me via the comments to this post and I will try and help. Some comments and tips:

  • The seismic display is probably not the very best, but I find it very quick and perfectly good enough for simple data diagnostics. If I need to make figures as part of the QC then I would normally use Seismic Unix for this. SeiSee is great for a few screen snapshots for example by PrtScr or Windows key-Shift-S sequence.
  • The display is practically instantaneous and you can look at any SEGY file including stacks, shots or velocity cubes.
  • Seismic data processing is limited to bandpass filtering, AGC scaling and wiggle/variable area displays. There is an inversion option but that is not acoustic impendence inversion, it just reverses the display polarity.
  • You can read and edit 3D volumes in SeiSee also – for example to extract a given inline or crossline (although its a bit slow for this compared to something like Petrel or OpenDtect).
  • Trace headers can be edited and exported, although normally I would do this in Seismic Unix.
  • One feature I like is that you can simultaneously QC many SEGY files in the same directory. I find this useful, for example, to check all the binary or trace headers of many files together just by flicking back and forwards. I have sometimes managed to crash SeiSee doing this, but it is quick to get back in and carry on where you left off.

In our next post we will make some comparisons with other available software for QC, such as the newly released SeisTopia and Geo2View. In our view SeiSee is an indispensable windows based tool for quality control of seismic data, particularly trace headers.

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Free Software for Seismic Quality Control

A few weeks ago I saw a few posts on linkedin featuring the authors “top ten” windows based software for geoscience based tasks. Unfortunately I can’t find a link to these posts, maybe someone can help me out so I can link to them ?

In this series I wanted to make some notes on a topic that I’m asked about a lot namely “How do I view and QC seismic data for free ?”.

A normal starting point is the Wikipedia page Comparison of Free Geophysics Software. This list here from Ivan V. Dmitriev also contains some additional links to Matlab routines and navigation software.

I also have a slide in my online (and free !) seismic processing course which I am aiming to improve during this series of posts. The slide is attached to this post but note that none of the links will currently work since it’s just an image.

I should note up front that since I’ve been using Seismic Unix for many years I am rather biased in its favour and will likely recommend that it is the best software for many simple seismic processing and visualisation tasks. See my blog post here for how to duplicate my seismic unix install which is to use seismic unix under the windows linux subsystem (WSL). I’m happy to use the free packages for QC and verification. Infact they are often better for this than commercial packages for 2D. Only basic 3D processing/visualisation is available in freeware. I use commercial packages for production processing, linking gathers to stack sections, interactive processing etc. I’d be a bit uneasy doing anything fully commercial using freeware unless I had independently compared results with something commercial.

So future posts will inform readers on:

  • Tricks and scripts for the autogeneration of images for inclusion and comparison within powerpoint (in prep).
  • Preparing a post featuring installation and comparisons of the various GUI available for seismic unix such as botoseis or OpenSeaSeis . The latter post can be found here.
    • Tools generally lacking in freeware are:
      • Velocity analysis/velocity model building tools
      • Anisotropy derivation tools
      • Interactive testing/parameter verification tools
      • Multi-threaded Applications (but again if doing 2D or shot by shot processing its easy to do this in scripts).
      • SRME
      • Statics derivation/geometry handling.
      • 3D denoise (or 3D processing in general other than some free 3D modelling and imaging codes out there).
  • Comparisons and reviews of Windows based QC software such as g-viewer and SeiSee. This is my SeiSee review and here is a review of the recently released SeisTopia and Geo2View seismic data viewers.
  • Here is an overview of OpenSeaSeis – its installation and type of things that it may be useful for.
  • Incomplete wishlist of things that could be included in a free seismic viewer to make it more useful:
    1. Image comparison tools such as difference/wipe/flip (trivial to do, but not present in ?any? free viewers).
    2. Overlay tools e.g. seismic and velocity model
  • One of my contacts referred me to SPAC-RT for QC of seismic noise in passive seismic methods.
  • Notes on commercially available seismic processing software
  • Anything anyone else thinks would be interesting or useful – please make comments !!

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Useful Links

One of the things we did when we first built websites in the late 1990’s was to provide lists of links which might be useful to other people. Better search engines and dominant marketplaces have limited the use of a “List of Links”. Undeterred by fashion, here are the various links to areas I’ve found useful in recent months, particularly regarding the geoscience consulting business. Practically all consultants have a website and actively use connections within LinkedIn, however, in geoscience there is not a single place to go for clients to find commercially available products and consulting services. Or if there is please let me know about it.

Please feel free to add your own favourite links in the comments and I will add them to the list.

LinkDescription
Seismic Data Repositories


Links to free seismic and well data
WebsiteG&G project based and Consulting Services
xcovermatch talent to hosted projects and provides hosted virtual workstations (backed by Shell). Not too many projects presently, but one to watch maybe.
proteusprobably not a major player in G&G to date, but could be a future option if more projects are added and it gains traction beyond the engineering sphere.
syntillicaproblem solving and consulting services across the energy industry
nudgeexchangefreelancer marketplace for energy industry
WebsiteTraining Course Websites
book-4Listings of various training courses available, both free and paid.
tonntaMay as well link myself ! We provide a shopfront for consultants to sell services such as consulting time, documents, codes, training courses and manuals.
WebsiteGenerally Useful Marketplace Listings
seg marketplacecomprehensive listing of geophysical companies and suppliers, but could use a website refresh.
petromehrasHas comprehensive listings of all types of software used in the energy industry
WebsiteConsultants Marketplaces and Job Listings (also with links)
A variety pf marketplace websites can be used to find consultants in the IT sector at rock bottom prices, but these are rarely used in geoscience. The concept is good but some of the projects offered might be considered questionable at best. Typical examples include freelancer upwork truelancer toptal peopleperhour
fiverrA few G&G services on offer from freelancers on this website
job listingsA variety of websites such as indeed simplyhired glassdoor jooble
oilandgasjobsearchfocussed job listings for oul and gas industry
PetroplanVariety of G&G job related services available
working smartprovides listings of available consultants and also job searches
sub-surface-globalconsultancy link given here, other services on offer such as jobs listings.
rigzonejob listings

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Final Pentominoes Post: the code works !!

Probably two weeks have passed since the initial failure of the original code logic to find a solution to fit all 12 Pentominoes into a 12 by 5 space. After ironing out a few bugs in the initial code, it did manage to find solutions for 5,8,10 and one time 11 pieces. However, even after running overnight, it failed to find a solution to the full 12 piece problem. I think the code is sound, it’s just that it relies on chance to find a solution and with the large number of iterations required to solve for 12 pieces it is just very unlikely to randomly be selected. Eventually it should work – I might run this exe on an AWS cloud based PC which can easily be left to run for a week if required.

The following modifications in the logic resulted in success (and some very spaghetti like code.)

  1. The piece order can now be read in from data statements, and in the future can be made random. Normally I start off with the “X” pentomino since there are fewer possible starting solutions (this piece has no reflections or rotations).
  2. For a given starting position for piece1 the code evaluates all possible legal positions for piece2,3,4…and so on until no more solutions are found. It then moves back onto the next position of the previous piece until a full solution is found for all 12 pieces. This way ensures that the solutions tested run from left to right, so this algorithm has a kind of natural packing whilst still being a brute force search. If left to run “forever” this code should eventually find all 1010 possible solutions for the 12×5 fitting problem.

This version of the code has already produced two out of the 1010 solutions with the same starting position for the X piece. I’m happy that my initial goal has been achieved, within the timeframe assigned. Remaining tasks (which probably do not merit further posts) are:

  1. truly random piece order, starting with user decided starting piece.
  2. bring in piece reflections
  3. Only reflect or rotate pieces which need it (at the moment all pieces are rotated which is a bit wasteful.
  4. Simplify code logic and introduce more subroutines to reduce duplicated code.
  5. More advanced “hole checking” routines to reduce some spurious interim solutions
  6. Algorithm to weight solutions to proceed to faster convergence.
  7. Version which will find all possible solutions.
  8. Bring in some AI algorithms
  9. Recode in Python or something other than BASIC.

Watch this space for any progress reported !