Exporting for multivariate analysis

So, you have a bunch of analyses in your StrataBugs database that have, of course, been nicely QC’d and you want to do some statistical analysis. Apart from the built in clustering offered through the taxon panel, we don’t do a lot of exploratory stats like Q/R mode cluster analysis, Principal Components etc. So, you have to export the data. Up until recently, you can only export one well at a time through the “Save As” mechanism on the Analyses tab in Samples & Interpretations. This is all well and good, but what if you need to combine data from more than one well? If you export into multiple spreadsheets, then unless the fauna/flora are identical, you’re going to end up with having to manually paste in each spreadsheet carefully, so the columns all line up correctly. Major headache.

Fortunately there’s now a Multi-well sample analysis export built into Organiser, and Lawrence Febo has kindly shared this simple graphic to explain the export steps … thanks Lawrence, and enjoy …

StrataBugs and Java updates

Here at StrataData towers we’ve been working to prepare for the next major release of StrataBugs, which will likely to be called v3.0 and involve some database updates. It’s also going to be built on the latest version of Java. Things have been happening in the Java world. Many of you will have noticed that Oracle have stopped freely licencing Java except for personal use: you are now required to buy (for a nominal fee) a licence for Java itself before you can run any Java-based software. Fear not, however, as there are open source builds of Java available to download with no licensing restrictions. The current version of StrataBugs, version 2.1.1, will require version 7 or 8 of java, and there are various builds available for you to use. To simplify, we have created a downloadable bundle of StrataBugs with the Azul Zulu version of Java 8; with this you can run StrataBugs without having to “install” Java on your machine. This means that you will also not be pestered about Java updates.

We have also made available an intermediate version between v2.1.1 and v3.0, which we’re calling v2.1.1-14, which uses the latest Java 14. In this case, a tailored version of Java 14 is bundled with the download. It is fully compatible with your v2.1/v2.1.1 database, and can be used in place of your existing installation. The advantage of using Java 14 is that it responds to screen sizing better. High resolution “4k” screens are becoming more common – if you look at your Windows display properties, and it shows that your fonts etc. are displayed at 200% or 250%, then you’re likely to be running a 4k screen. In its default setting, StrataBugs will be unusable, as the contents of the windows will “outgrow” the window borders. With Java 8 there is a workaround to this: but it does look slightly pixelated. With Java 14, scaling works correctly and the windows and dialogs are sharp.

You can download this new version but you will need a licence update to run it: we are only releasing this version to current (2020) maintenance holders.

Get in touch with support@stratadata.co.uk if you want more information, or for any other StrataBugs queries.


Do your homework

These challenging times of self isolation and home working will hugely disrupt the working practices of many of you, whilst for others who already work in an office at home, your working life might remain largely unaffected by the current crisis.

For people who usually work in an office with a server based database you have a few options available to manage how you can work remotely. The strategy you choose will be based on the availability of resources and the need to integrate with others.

The basics. To run StrataBugs you will need two things: a licence and a connection to a database. There are many different configurations for both these things, and they both can either be provided centrally on a network, or to distributed stand alone machines.

The licence

We usually provide permanent licences to a server or a hardware key (dongle). In the server model, as long as you’re connected to the server and the server has a licence available, then it can be “checked out” for the duration of your session and it automoatically returns to the pool when you close. We can also extend this model to provide a licence that can be checked out from the server for a continuous period of time, up to a set limited number of days. During this period, the licence can be used independently of the network. If you look at the Control Panel Config options, and the option for “Licence check in/out from server” is not greyed out, then your licence server has this enabled. This is useful for workers due to be working off line for example at rig site where a network connection to the server is not guaranteed, but could also be used for periods of home working.

Checked out licences reduce the number of remaining licences available to others, so its use should be carefully managed to avoid people being uncessarily locked out while a licence isn’t actually required.

For individual licence holders we usually issue a dongle. This is provided with a matched licence file and has the advantage that it can be moved from machine to machine, giving the same flexibility as a server licence without the need for a network. The disadvantage is the need to have a driver installed on each machine before the dongle will be recognised.

We can also licence individual machines based on their host ID(s) which are a unique aspect of the machine’s hardware. We do not issue permanant licences for individual machines because this would remove the flexibility to transfer between multiple machines or upgrade hardware.

For these exceptional times, if you would be normally able to connect to your company licence server but are unable temporarily to do so, then we can issue a temporary licence, if you provide us with the hostid. When sending us the hostid, please copy and paste the text rather than sending a screenshot to reduce the chances of retyping it incorrectly.

The database

In StrataBugs you can set up one or more connections to databases. For most, you will only have one database that you connect to all of the time, but if that database is on a server, then when working remotely that server might be unreachable or simply too slow or intermittent to adequately work. One tip here: if you have the option, used a wired connection i.e. an ethernet cable, into your router, rather than a WiFi connection. We have found that database connections frequently get dropped when used over WiFi. Although we try to trap these instances and allow you to reconnect within StrataBugs, this isn’t always reliable.

If you find that you can’t work effectively using the remote server connection, then you can set up a connection to a local database. We use a file based database system called h2 which provides good performance for a single user. There is an h2 database called “demo” which you’ll find in the StrataBugs data folder. All the connection details for getting started with the h2 demo database are given on this page.

The demo database will obviously not contain any of the data you will have been working on in your server database. If you do need to carry on working where you left off, you have two options.


Firstly, before leaving the office, or if you can connect to the server remotely, you could run the Organiser module and run the guided export for all the data you’re working on. Use the default file format .sbg since this will best preserve the data for version 2.1 – older more obsolete formats like DEX have some deficiences for some data types. Save the export file to a folder location that you will be able to access offline.

When reconnected to the local database, you go through the Organiser guided import procedure, generally “adding all” as you go, and this will give you a new copy of the data into your local database that you can now work on.

Create database

There is a second option here. In the Wells and Outcrops module, there is a option for a Project (which is a list of wells and associated groups and templates) called “Create DB” which allows you to create a standalone database whch contains all of the project data. This avoids the import/merge steps of the above, but be warned, it places a heavy demand on the server and should only be run locally or over a fast enough network. It’s also sensitive to any errors in the data, so don’t be too optimistic that it will work first time! In this process, you start with an empty h2 database which just contains the table structure and some ancilliary data. See the help for a link to this database. At the end of the process you will have a file containing an h2 database which just contains your project data. One omission however is that it will not contain “Global” chart templates. See below.

Chart templates

If you use the export/import method, or you want to use global templates that the “Create database” step does not (yet) provide, you might want to also export some of your server’s global well blocks. You can do this from the “Chart/template” menu in the Charts & Templates module. If your well block uses groups and sets then these will be exported along with the panels that make up the well block. This also creates a .sbg file which you can import using the guided import of the Organiser module.


Don’t forget to backup your database file – nobody can replace this if it gets corrupted and you might lose all your data. On the connection settings there is a handy backup reminder prompt which pops up when you close the database.


Regardless of the method you use to get started, sooner or later you will want to get all that new or changed data back into your server database. The only option here is the reverse of the export/import method described above, except this time you’re exporting from the local database and importing back into the server database. If you have a lot of wells in your local database, remember to keep a note of which ones you’ve touched. The Oganiser guided import will allow you to see exactly what’s changed and give you the option to deal with any conflicts that arise during the merge.

As always, contact us if you need any help in managing your data.


Multi-well header loading

Many thanks to Lawrence Febo (Chevron USA) for this post…

A very useful StrataBugs feature, though perhaps overlooked, is the bulk well importer using the Organiser interface.

Step 1: Prepare a spreadsheet with your well header data as shown below. Four fields are required for each well (Name, Code, Location, and TD), though others can be added.  In the US Gulf of Mexico, additional identifiers may be added, such as the OCS Numbers (Outer Continental Shelf).

Step 2: Choose the Organiser Module, then select File>Open file…>XLS Well headers…(Figure 2).  After selecting the Excel file, you will need to select the depth units for the wells.  Be sure to bulk load wells that have the same depth units. Do not import a mix of wells where some are in meters and others are in feet. If you do, then they will all go into the database in the units selected.

Figure 3 – View of an individual well in the list and the fields that get populated in the database.

Step 3: Once the well headers are read into the workspace, the last step is to Match the wells from the workspace into the database (Figure 4). You can choose “add all” if they are all new. Figure 4 – Final steps > select “Match all” first, and then “Add all” of the unmatched wells. Any wells left unmatched will be excluded when you close the dialog.



Using SVG files in Microsoft Office

One of the consequences of moving to an integrated java based charting system in version 2.1 was that we lost the ability to generate Windows Metafiles (.wmf) from the chart program. The wmf format was a good vector based graphics format meaning that, for the graphics packages that could decode the files, the lines appeared sharp regardless of the scale it was plotted at. They were well supported by earlier versions of Windows and Microsoft Office, but more recent editions of Windows do not always render them very well. Unfortunately we have not been able to find a reliable code library that would created wmf files from our java code.

The alternatives are to create PDF files, which are vector based, or use the SVG format. The latter, which is short for Scaleable Vector Graphics, is an open graphics standard which is theoretically readable by a wide variety of software. We have found that although SVG files can be easily read by browsers like Internet Explorer, support was lacking in Microsoft Office. In Office, you needed to insert PDF files or bitmaps. These don’t always look optimal in Excel or Powerpoint.

Now, with the latest builds of Office, Microsoft have made good on their promise to be able to import SVG files. You will need a recent version – those who have an Office 365 subscription or similar will probably have received the update by now – specifically version 1705.

From the StrataBugs chart menus use the Export option and change the file type selector to show .SVG files. Create your file. Then in Office use the Insert Illustrations menu, select your file.

For large correlation charts which create large VGS files – particularly if you’re using logs and lithologies, the Office apps can get a bit sluggish, but otherwise it does reliably support the chart in pin sharp detail. Try it.

More information here: https://support.office.com/en-gb/article/Insert-SVG-images-and-icons-in-Office-2016-e2459f17-3996-4795-996e-b9a13486fa79

This file was 42Mb, and Powerpoint struggles, but it can read the file faithfully …




Backup your databases

In recognition of World Backup Day (no?, me neither), a quick run through the hows and whys of backing up your StrataBugs database.

Backing up your system seems a obvious no-brainer, but take a few minutes to consider what you’re backing up, why you’re doing it, and how you  might recover the database, should it be necessary.

There are two main reasons to take a backup: the most obvious being a hard drive or system failure, a fire, or theft, that results in an unrecoverable data loss. The other reason, sometimes overlooked, is the need to go back to an earlier database state in the event of accidental data loss by deleting, mistaken editing, or even a programming error (I know, I know, highly unlikley, but let’s move on..).

For the first, you need a copy – any copy – on some kind of media that isn’t the computer that StrataBugs is installed on. Most sensibly this means an external drive or memory stick that isn’t stored (and fire damaged/stolen with) the computer itself, OR, files copied ino the cloud using Dropbox or similar services. The only real pitfall of this approach is that you need to ideally make multiple copies on different media and make sure you know which ones are most up to date. In the event of a system failure you want to be able to go straight back to the most recent copy without having to try to work out which of your myriad sources of backup contained the latest database.

For users of stand-alone databases, you only really need concern yourself with the database file(s) in the /Data folder ending in .db or .mdb, since this is the only file that we can’t restore for you. All the rest of the StrataBugs files can be downloaded afresh, or supplied by us.

For users of server-based databases like SQL Server and Oracle, this backup issue is out of your hands, and one would assume that server custodians would have a backup schedule fully in place. It’s worth asking however, how often the backups are performed.

Going back to an earlier state of data is more problematic if your backup schedule always involves overwriting the previous backup copy. You might be able to recover a database, but what if you discovered a previous problem that has only just come to light, or a loss of data that pre-dates your last backup? For this reason, you should keep snapshot copies stretching back say, every day for a week, then every month for a year, then each year.

Another way to create an effective backup, particularly for server based databases, it to export the data through Organiser, or through the process that creates project databases in the Wells & Outcrops module. In this way you can selectively restore data through the usual import mechanism.

To make this process as painless as possible, a recent addition to the Connection properties dialog for H2 databases allows you to Prompt for backup:

If you have this feature switched on, you will get the following dialog pop up whenever you exit from the system:

You can use this to quickly create a dated compressed backup file onto your chosen media. If you need to recover your database from the file, you need to unzip the database snapshot into the StrataBugs data folder, and provided your connection and database name are the same as the backup, you can be back up and running immediately.

Don’t let your backup be the one thing that you always meant to get around to doing … but never quite made it. If you haven’t done it recently – do it today!


Why doesn’t StrataBugs always look right?

You get a shiny new computer with a nice high resolution screen but when you start up StrataBugs, the text font looks too small so you can hardly read it, and some windows are clipped so you can’t see everything that’s supposed to be there without enlarging it. Moreover, every time you get a simple dialog box pop-up, the icon, instead of looking like this:

NotClipped(Windows 7, 100%)

is clipped, like this:

clipped(Windows 10, 125%)

So, what’s going on? Well, it’s possible in Windows to set your display preferences so that text fonts and other windows components are made larger and more readable, without sacrificing the overall number of pixels available on screen (unlike, say, lowering the overall screen resolution, which doesn’t look good on modern flat screen monitors). As higher resolution monitors have become the norm, the default settings on a new Windows installation is actually for this preference to be set to 125%, so you might already have enlarged text without realising it. The problem is that a lot of software, and this includes the Java library code that StrataBugs uses, doesn’t respond in a uniform way to the font size change, resulting in the general loss of beauty described above.

In general, if you’re running a recent update of StrataBugs, you will have seen that the text is reduced in size compared to the general Windows font sizes, so that the text and other components fit into the StrataBugs windows as they are designed. Older builds (including v2.0), will have parts of some of the dialogs missing, where the window is too small to accommodate the enlarged controls. We’ve been tweaking things again recently, to get around the tiny menu font sizes and the clipping you see above, which makes life a bit easier on the eyes.

We would also recommend that you don’t opt for the ultra high resolution 4K screens for Windows, as the application will look tiny, however this doesn’t affect the Mac community, as the scaling for their Retina displays is already built into the libraries. We’ve always bemoaned the lack of pixels available on standard issue laptops with a resolution of 1366 x 768, which is the bare minimum of space you need. More pixels are definitely better, as long as you can still read it.

The best solution, for now, is to right-click on your desktop background, select Display Preferences and reset the size to 100% ….


You might find this a bit tricky to start with, but you might also like the extra screen “real estate” that this gives you. If after a while you still find yourself squinting at the screen, try moving your chair closer, or visit an optician and invest in a new pair of glasses!

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Time for a spring clean? Episode 2: Schemes

In this second post about giving your database a spring spruce-up, I’m going to outline some tips for cleaning up your list of schemes.

You are mostly going to be working in the Schemes & Interpretations module. Select Schemes > Strataigraphic schemes to bring up the Schemes window.

Go to the full post…

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Time for a spring clean? Episode 1: Taxa and Groups

Spring is in the air here in the UK and I for one have forgotten my new year’s resolutions. Blow away the cobwebs and embrace the new season feeling virtuous by spending a little time spring-cleaning your StrataBugs database. All databases need ongoing tidying up, organising and pruning. It need not be a huge job – a little dusting here and there to keep things in shape will go a long way if performed frequently. Perhaps get into the habit of performing these tasks at the end of each project.
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Welcome to StrataBlog

Welcome to the StrataData blog! We will be running this blog in addition to our formal help site, blogging about all things StrataBugs: hints for improving your workflow, handy tips and tricks, and everything new from the development desk. You can sign up below to receive posts direct to your inbox. Please feel free to leave your comments for us and the rest of the StrataBugs community!

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