Thursday, December 23, 2010

Raplee Ridge in 3D

Raplee Ridge was infamous in my structural geology lab.  It was our last project due by the end of finals week.  We had to measure strike and dip using lidar and lidarviewer and create a geologic map using an aerial photo.  We did so by using color descriptions and relative age of formations.  We used ArcDesktop and utilized topology.

The dataset provided to us was of very high quality.  After a bit of processing using what I learned about GRASS today, I loaded up nvis.  Raplee Ridge is beautiful.  I didn't quite get that from the project.  In fact, looking at these views, one can very quickly get an idea what the structure was that we were trying to tease apart from the lidar data using lidarviewer!


I just received Open Source GIS: A Grass GIS Approach, 3rd edition.  Time to learn!

Tuesday, December 21, 2010

QGIS Plugin Scripting: Revisited

I learned, rather hurriedly, how to script QGIS plugins for a class.  I came away unimpressed with the class hierarchy (I got lost and certain methods I needed seemed misplaced and therefore hard to find).

But now that QGIS alone is becoming a viable replacement for other software, I'm motivated to try scripting plugins again.

So I'll be taking a look at moving over the apparent dip script and cross section script to the QGIS interface.  If all goes well, I'll actually have a nice way to distribute them via the QGIS plugin repository.

Monday, December 20, 2010

Topo Profile Script Results

For the better part of the day, I wrote a topo profile script.  It allows the use of a cross section line of any geometry in a GIS to determine a topographic profile.  I probably implemented it in all the wrong ways, but it works well!    The distances for every point do in fact add up to the total line distance... and the cell values are spot on.  Very good.

As usual, scripted using Python with all the usual suspects (GDAL, OGR) but with a new comer: Numpy.

Basically, you tell it: where to find your cross section line, DEM, and a sample interval distance.  Assuming everything is projected right, it plots points.  It uses those points to sample the raster for elevations (cell values).  It also keeps cumulative track of distances between points.  It generates a shapefile with that data.  It also produces a tab delimited text file with the same data (but arguably easier to import into various graphing tools).

So we end up with something like the following (note that the profile graph was not generated by the script, just the elevation and distance data):
Generated points on a cross section line of various trends (El Mayor rupture region).  Point interval is 20 m; line vertices, start and end points, are always sampled.

Units are in meters, no vertical exaggeration.  Was created at 1:6000 scale. Zero is sea-level.
Yes, I was lazy and didn't label my axes.

I don't recommend reading ARC GRID rasters into this program as it has no smart way of dealing with massive datasets.  I kind of recommend using GeoTiffs for that reason... and clip to your work area or cross section.

The script is a mess... I'll release it eventually.  Especially if someone asks for it.

Thanks to OpenTopography for the data that I used to test this script :)

Sunday, December 19, 2010

Topo Profile: The Next Script

I'll be scripting a topo profile extractor based on cross section lines of arbitrary geometry.  It'll have the ability to scale how many elevation points you want based on distance between points.  Eventually it might find some use in conjunction with my apparent dip script (e.g., another column in the output with the apparent dip value, so it can be plotted as a marker with distance).

It should be pretty painless.  I've downloaded (for fun) a tiny slice of point cloud data for the El Mayor-Cucapah Earthquake rupture from OpenTopography.  I'll be testing cross section lines across that slice.  It's a good set since there are areas where there's no data (I didn't fill the nulls).

I think the goal of my winter is to simply script the tools to make life easier for the next two quarters.

And have fun while doing it :-0

I should note that the El Mayor data is affiliated with UC Davis.  Cool.

Friday, December 17, 2010

Updated: Geologic Symbology for QGIS

I am currently working on creating markerline SVGs for QGIS, since 1.7 trunk now allows for creation of most symbols found on geologic maps.  So far I have the following SVGs that are directly using the FGDC specifications (from their EPS files):

  • Anticline arrows (black and magenta)
  • Syncline arrows (black and magenta)
  • Asymmetric syncline arrows (black and magenta)
  • Downthrown symbol for normal faults
  • Sawtooth symbol for thrust faults
  • Left and right lateral fault symbols
Note that these do not include lines.  Those can be easily created using the QGIS symbology interface.  Generally, lines are 0.25 and 0.375 mm (0.38 in QGIS 1.7 trunk; does not allow thousandths) wide.  See FGDC guidelines if you're interested in following their standard; but frankly, as someone dear to me would say, cartography isn't always about following rules...

Take a look and/or use them here.

QGIS + GRASS = Topology

Today I embarked on a mission to figure out a workflow in QGIS that includes topology.  After searching around, I found that GRASS is fully-topological.

After playing around with GRASS, I think I have found my workflow.  I can now create contact boundaries, create centroids within them in a separate layer (boundaries + centroids = areas/polygons), and generate appropriately labeled polygons automatically.

The trick was (1) understanding how to attribute using the QGIS interface to GRASS, and (2) realizing that the Split tool needs a double click to create a vertex that can snap.

So perhaps my days requiring Arc are numbered.  Now I just need to get QGIS Trunk to compile for its awesome new symbology features.

Oh, if you haven't tried using GRASS since before QGIS 1.7, you might want to try.  Its interface is a bit more intuitive and it is way less crash prone.

Thickness of Bedding (Stratigraphy)

I imagine a script that could take elevation data (say, a raster derived from DEM) and calculate bedding thickness might be useful.

The workflow would involve:
  1. Loading a DEM
  2. Overlaying the DEM with remote imagery that has visible bedding
  3. Drawing a polygon over bedding where you need to find the approximate thickness
  4. Process the elevation data within the polygon to find the bedding thickness
    1. This would probably require generating a slope raster, perhaps average slope over the area within the polygon, measuring the various required distances and hope for the best...
Python w/Numpy and GDAL would be utilized.

Wednesday, December 15, 2010

Measuring Azimuth of a Line in a GIS

In order to find the apparent dip of bedding, strikes must be projected into a cross section line. The azimuth of that segment of cross section line must be found.

I did this in my GIS apparent dip script by creating a geospatial straight-edge and using it as a protractor.

Using a point on the cross section line at which a projected strike line intersects as the origin, I offset to the west a known distance (in this case, 0.5 map units, or as is often the case, 0.5 meters).  From that offset, I have OGR create a line feature that goes due north for 20 or so map units.  The line also extends 20 map units due south from the offset point (we want to make sure we can intersect the cross section line no matters its trend).  The idea is the straight-edge/protractor will intersect the cross section line providing it isn't trending due north.

Once the straight-edge intersects, we have a distance from our known offset point.  It is then a simple matter of using inverse tangent to find the angle that the cross section line makes from the north.

But what happens if the due north straight-edge NEVER intersects the cross section line?  Given how small of a distance it is offset from the line to the west, we can easily assume that the two lines are essentially parallel.  Thus we call the azimuth of that segment of cross section line 000° azimuth.

All of this, of course, is automated in a Python script and it is a measure made every time a projected strike line intersects the cross section line.  It does this because cross section lines can change direction.

By the way, if you have a geologic problem that would benefit from scripting, leave a comment.  If it is something that would be useful to me, I just might write a script.  Keep in mind I am an undergraduate student, so there will be a limited number of useful ideas :-)

Tuesday, December 14, 2010

Apparent Dip Script Initial Release

I've made the Apparent Dip script much more robust.  Get the latest gzip'd tarball here with my test datasets.  It requires Python with OGR.  I'll probably license it under the GPL (haven't really thought about it).

It is very cool though still not very polished and has a few caveats (read the commented code).

I think I've solved some of the obvious and easiest problems.

Brown lines are projected strike lines.  Magenta is the cross section line.  The apparent dip in the red box has its information shown in the dialog.

adip is the calculated apparent dip.  Dipdir, strike, and tdip (true dip) are copied from the original strike and dip and are really only useful for cross referencing or checking validity of the calculated apparent dip.  xsec is the name of the cross section and xsecaz is the azimuth of the cross section approximately where the projected strike line crosses.

Monday, December 13, 2010

Using GIS as an Apparent Dip Calculator

Today I prototyped half the Python script to calculate apparent dips from strike and dip point data and a cross section line.  So far, the script takes an arbitrary cross section, buffers it, selects the strike and dips within that buffer, and then projects lines from the strike of each of those points.  Then, the script finds the intersection of each of those lines with the cross section line.

The difficulty in finding the apparent dip is that one cannot assume the cross section line maintains one trend.  Nor is there a built-in OGR function (to my knowledge) that finds the angle(s) of intersection between two lines.

I solved this problem by creating an arbitrary north-south trending line offset a known distance from the determined intersection point.  From there it is super easy to find the azimuth of the cross section line!  Note that this method will fail on cross section lines oriented exactly north-south.

Next step: making the calculated apparent dips accessible with distances along the cross section line.

Projected Strikes in Magenta, Cross Section Line in Green.  Note that rotated strike and dip symbols pivot around the point's geographic coordinate, thus the appearance of offset (the strike lines go right through the point).  Buffer was 100 meters.  Arbitrary north-south oriented lines aren't in this screen shot. Viewed in QGIS.

Sunday, December 12, 2010

Winter Break Plans

I hope that, within the next few weeks, I will have done at least two of the following:

  1. Create geologic map symbols using SVG format for QGIS (I already have a E-W oriented S/D symbol for rotation using Dip Direction; removes a step ;-))
  2. Figure out a good way to emulate Arc's topology in QGIS: contact lines to unit polygons.
  3. Write a script to calculate apparent dips using strike and dip point data within a buffered cross section line
  4. Find out what Vrui does with regards to projection of geographic coordinates
  5. Relax

Wednesday, December 8, 2010

LidarViewer and Projected Coordinates

For Structural Geology lab, we were instructed to use the open sourced LidarViewer to measure strike and dips on a LIDAR point cloud of Raplee Ridge.  LidarViewer relies on an open sourced library and GUI called Vrui.  Both are products of UC Davis.

LidarViewer uses Vrui to display the LIDAR point cloud in 3D.  Vrui uses WGS 84 as its geodetic coordinate system.

Oddly, I cannot figure out what that PCS is.  It looks like a Mercator given the magnitude of the units.  Yet, the eastings and northings always mismatches the various projections found in QGIS.  World Mercator?  Nope.  At times it seemed rather non-linear.

Does anyone know what the heck Vrui is doing to get its 2D coordinates?  It is using WGS 84, so a false easting and northing would be nice to have...

I attempted understanding the code, but Vrui, being C++ code, is so abstracted that I can't make heads or tails of what is going on (I profess my love of Python!).  Perhaps it is taking whatever the projection was of the LIDAR point cloud?  If so, then the Raplee Ridge data has a very odd projection.  At least, odd in that I can't find a good match for it.

Knowing what the PCS is would be helpful in the future: I could take strike and dips plus have the coordinates saved to a file.  I like efficiency.

Monday, December 6, 2010

GIS and Cross Sections

I had the realization that a python script could take all your strike and dip data, project the strikes out some distance from each point, intersect a cross section line, find the apparent dip using the dip attribute from the S/D feature class, and provide distances along that section line to each projected strike along with apparent dips in a table.  I do believe that a QGIS plugin that does this would be extremely handy.  Heck, it might be handier yet to allow extracting a topographic profile along that section line too.

Sounds like a good winter project.  And it would save a load of time later on.

Monday, November 29, 2010

Group Geology Projects

It is the last week of lecture at UC Davis.  It is understandably difficult to get everyone's schedule to align in order to finish up group projects... as a group.

For now, I'm relying on Google Docs to allow group members to collaborate on finalizing the presentation and written report.  I have no idea how well this will work.

In the end, I'll take all the changes from the written report and put it into the master LaTeX document for printing.

While LaTeX is very portable, the world of Microsoft forbids it.  So I export my LaTeX documents to OpenDocument format.  Generally, that works good enough.  Then I save as a Word Doc in Open Office and import it to Google Docs or forward the .doc for collaboration.  Why should I use LaTeX when I have to go through these steps for collaboration?  Mainly, it outputs beautiful pages without any work, cross referencing figures can't be easier, and... BibTeX.  Bibliography can be a joy!

Finals are next week.

Saturday, November 27, 2010

QGIS 1.6 Released

Time to map more geology in a GIS:  QGIS 1.6 is out of the oven!  Mac users can get it here  and everyone else, here.

This release is already awesome, because it has a remote sensing and geology-friendly splash screen.

Friday, November 19, 2010

Georeferencing with GDAL 1.7 and QGIS 1.6 Trunk

Yesterday I set out to georeference the field map I made during the trip to Carrizo Plain National Monument.  I did not expect it to go quickly.  It did.

There is a plugin available for QGIS 1.6 Trunk that provides a very robust way to easily georeference images using GDAL.

You simply load the raster, plot points at your control points on the map (such as graticule crossings), choose a transformation (helmert, linear, polynomial 1-3, thin plate spline), an output raster name, and your target projection.  Then tell it to have at it.

If you've georeferenced using ArcMap 9.3, you'll find the interface in this QGIS plugin to be a bit different.  Instead of having to pan back and forth, zoom in and out, as in ArcMap, you have two views to work with in QGIS.  The plugin view provides only the image you are georeferencing and then there's the map view in the main QGIS window.  As you georeference your point by some coordinate (e.g., decimal degrees or UTM), those points show up in red within the main QGIS window (providing you're in the area you are trying to georeference the raster to).  Thus you can verify your georeferencing as you plot without having to pan and zoom!  I hope I'm being clear on this, because it is a fantastic way to georeference.

Also, as you generate points, they show up in a table below the raster.  You can modify the x and y coordinate for each of those points as necessary.  That is a true time saver.  Finally, you can save your points to a file for future use.

Another great feature with the GDAL georeference plugin is that it can generate a script for you.  I can see this being incredibly useful if you need to batch georeference maps from a class.  Of course, the problem of reliable scans with minimal pixel deviations may ruin such plans.

Sunday, November 14, 2010

Searching for Faults

This is a geology blog, get your head out of the drama gutter.

The trip to Carrizo Plain, as I shall discuss in depth at a later time, consisted of surface mapping (quaternary  stuff) and finding faults alongs the San Andreas.

It was fun.  Especially as it was the first time the professor had ever been out there with students.  So we all got to learn things like: just because there's a road does not mean there isn't a fence blocking the way :-)

And of course we learned about geological stuff and puzzled out offsets of ridges and drainages to help build a case for the presence of faults.

More later...

Friday, November 12, 2010

Carrizo Plain

Tomorrow, November 13, I will be heading out with my structural geology I class to Carrizo Plain National Monument.

I have no idea what the agenda is, but you can bet the San Andreas 1857 scarp will be involved.  There examples of pressure ridges, sag ponds, beheaded and displaced channels, anticlines, synclines, marine sediments, fluvial sediments, and so much more.  

I'll have my Canon G11 and a GPS receiver so that I can spatially correlate images by time.  

Since I have no idea what the agenda is, I made two simple maps: north and south Carrizo Plain.  They use a mosaic of the Taft and Cayuma 30x60 minute USGS quads and have a graticule in NAD83 UTM 11N (thanks to QGIS 1.6 Trunk).  I reprojected the DRGs into NAD 83 UTM 11N so that the graticule will be compatible with my GPS.  The great news about Zone 11N is that the west standard line is so very close to our field location.  I can take comfort in *very* minimal scale distortion :-)  The declination, by the way, on November 13 at the field area, will be 13.13 degrees.

If I had more time, I'd find my 8 Gb micro-SD card (probably impossible) and load OpenStreetMap data along with for the area contours.

Anyway, it should be a nice weekend if the weather cooperates.  We'll be learning how to map structures.  I hope that the agenda is such that I won't be sprinting traverses...

A report will follow this overnight trip.

By the way, I got to sit in on a career retrospective brown-bag by Dr. Eldridge Moores today.  

Thursday, November 11, 2010

Lyx 2.0.0 Beta 1 Released

Everyone that knows LaTeX loves it; mostly for it taking care of document formatting (letting you concentrate on writing) and producing beautifully typeset equations.

Once you've learned LaTeX, it's good to go on to the next step.  That would be Lyx.  Lyx is a graphical interface to LaTeX, and frankly, you have to use it to understand how much of a time saver it is.   Writing LaTeX documents / research papers will never be the same :-)

Those with Macs can now fetch Lyx 2.0 Beta 1.   See the feature list.  Windows binaries are sure to follow. 

My favorite feature of Lyx 2.0 Beta 1?  Spell checking on Macs works out of the box!

Wednesday, November 10, 2010

Blender and Geology

Anyone out there ever use Blender to help solve or visualize geologic problems?  I suspect it would be handy in structural geology.  It is scriptable: Python!

I once tried to make a fence diagram using processed seismic imagery from the NRPA (National Petroleum Reserve, Alaska) in Blender, but given the lack of time I had, I failed miserably.  The idea was to see how strata may correlate between shot lines.  This was for a Basin Analysis class.

Eventually I gave up and did it the old fashioned way.  Results from that were apparently pretty good!

Drawing Mohr Circles

This may seem obvious to many Structural Geologists, but I rather enjoyed usng OS X's Grapher to graph a parametric equation of the Mohr Circle.  I also plotted fracture planes and the Mohr-Coloumb Criterion at all of the appropriate angles.  It was my first go of it, so perhaps I missed something important.  But it looks really good.

Monday, November 8, 2010

Open Stratigraphy Log

While I took sedimentology, I created a stratigraphic log using Inkscape.

I forgot about it until now.  It is based on the Nichols (2009) stratigraphy log, but I added a column meant for recording GPS waypoints, photo numbers, and other notes.   This form is field tested.

Download the Stratigraphy Log as a (PDF) (SVG -- for editing the log).

Use and misuse however you like, but please try to keep the attributions somewhere on the log. :-)

It look a lot of time to get this log right and so I really hope it is useful to anyone recording section in the field.  Let me know!

Note: I think the log is different enough from Nichols' that I'm releasing it under Creative Commons Attribute-By. So feel free to modify for your own use! I will revise it on occasion but this is a fairly solid product (though the form does intrude into the right-hand 1" margin, but most printers can handle that!)

Thursday, November 4, 2010

Quick Python Script: Cross Section Topography

I wanted to see if it were possible to take a bunch of map measurements and create an SVG file with topographic cross section.  Turns out it is easy to do, once you find the right Python module.

I installed svg.charts, piped my measurements out to a CSV file (x,y) with the first line as a header, and generated a plot of the topography using my script.  I then loaded the topography into Inkscape, trashed the extraneous vectors (e.g., symbology, axes, legend), and scaled to the on-the-map cross section length and appropriately scaled height.  Remember that cross sections must always have the vertical scale be the same as the horizontal scale.

I could continue on and finish the cross section in Inkscape, except I doubt my TAs would approve.  So I printed it out and traced over the topography.  It matched up with the cross section line perfectly.  Hopefully the next time I'll be more efficient at this.

Although, I was considering that I could have avoided hand measurements by scanning the map and doing the following in a GIS:

  • Plot a point on top of each index contour on the cross section line
  • Give each point the appropriate elevation attribute
  • Generate a distance vs. elevation plot using a QGIS script
  • Use my script and scale appropriately using Inkscape
I won't post the script unless I'm asked.  It's really trivial, though.  But perhaps gnuplot would have been a little faster :-)

Sunday, October 31, 2010

Buyer Beware: Microsoft Office 2011 for Macintosh, Academic License

I just finished reading the academic license for Microsoft's latest Office suite for OS X.  The academic license is very restrictive and may prove to make the $99 cost not economical.

The reason is that the academic license of Office is permanently installed on the first Mac it is installed onto.  Thus, if your computer goes out to pasture, you're out of luck and will need to get a new license.  Other licenses for Office 2011 allow a one-time transfer to another computer.

Update: Feb 16, 2011. Here's what I'm referring to within the academic license:
"'a. One Copy per Device. The software license is permanently assigned to the device on which the software is initially activated. That device is the “licensed device.”'

This does not appear on any other license.  In fact, other licenses have specific transfer rights.  The academic license does not.

I did not decipher this in the license itself, but be aware that the box says "One user, One Mac."  This seems to imply only the academic user that bought it can use it.  But I don't see how that could be enforceable without causing a lot of headaches for users.  The One Mac, in this case, REALLY means One Mac.  Not One Mac install at a time.

So, it may be better, if you need office on a Mac, to buy the Office for Home & Business edition if you want the software to have longevity.  Other people have lamented the fact that it can't be installed on a laptop and desktop simultaneously so long as you use only one at a time.  But Apple Pages has the same restriction.

What am I going to do?  Continue using Office 2007 in a Windows virtual machine.  But usually I rock it with MacTeX and Lyx, anyway.

Update, Nov 7 2010: I should note that the Microsoft Office 2010 for Windows Academic license is a full-blown license with no transfer restrictions.  It, apparently, can also be installed on a portable machine owned by the single user.  The license is also $20 less.  I have to wonder if the onerous restrictions in Office for Mac 2011 is purposeful: Microsoft would prefer you not use OSX, and so provides some justification via licensing.  Microsoft, those restrictions are a net negative, in my case. Sorry. 

Structural Geology and Python

As I journey through Structural Geology, I'm compiling (no pun intended) a set of python scripts.  These scripts, for example, include Mohr circle formulas, and calculations of apparent and true dip.  Direction cosines are only a matter of time.

This is a good study method.  Writing the scripts, while trivial, makes me reflect on why the formulas work.  Later on, they could be integrated into a GUI (perhaps using Tkinter or QT).  

These scripts might also be integrated later on into more complicated scripts designed to solve geologic problems.  I am writing them as modules and I am including docstrings as I go. 

Friday, October 29, 2010


libLAS is a library that processes the LAS LiDAR format.  It is now, apparently, available in the OSGEO4W repository.  OSGEO4W is a set of applications and libraries compiled for Windows by the most awesome OSGEO project; it is a complete environment to work with many raster (OGR) and vector formats (GDAL).  The packaging system also includes Python, which is great for geoprocessing scripts.  It also includes QGIS stable and experimental.  This OSGEO4W is the way to go if you're using Windows!

Anyway, libLAS as compiled with OSGEO4W can immediately process LAS formatted LiDAR data into OGR supported formats using las2ogr. For example, you could download LAS point cloud data and immediately get a GeoTIFF with all vertical reprojections applied.  Neat-o.

Of course, if you don't want to try installing OSGEO, you could try one of their Live DVDs or VMWare images.  But I highly doubt the LibLAS software has made it in version 4.01 (it was released August 26).

It is only a matter of time before libLAS and las2ogr makes it into OGR packages for OS X 10.6.

Happy geoprocessing and happy Halloween.  It's back to constructing Mohr circles and plotting lines and planes on stereonets.

Tuesday, October 19, 2010

OpenTopography, GDAL, and the San Andreas Fault is a resource for a limited, but massive, set of LIDAR point data. LIDAR is a LASER-based method to determine topography. It is pretty dang nice when you want to look at the details of topography at a very large scale.

GDAL can process the returned LIDAR data. I've been using GeoTIFFs, since it is lossless, and isn't an ESRI specified format. GDAL is open source.

gdal_contour, gdaldem are two GDAL tools you will want to use if you want to visualize LIDAR data.

LIDAR at Wallace Creek

This image shows a LIDAR DEM that has been processed using the GDAL toolset.  A hillshade has been generated using gdaldem and its defaults.  A 5 m contour interval is shown, but there is also a 1 m contour interval in the legend.  I turned it off because it obscured the hillshade.  Imagine doing a 1 m contour interval on USGS DEM data: not a bright idea!  This LIDAR data was downloaded at a scale of 1 m per cell (I haven't verified that is what I actually received, but it certainly looks great at incredibly large scales).  I must note what you probably have noted:  that is some awful labeling.  The labeling engine in QGIS (used to display this data) is still under serious work;  patience is necessary.  Until then,Inkscape is a good way to manually, and deliberately, label your maps.

Notice at the center of the image there is an offset of two stream channels.  Both have an offset at the same time.  And if you look closely, you can see a faint trace of the San Andreas Fault.  This is Wallace Creek!  So if you wanted proof that the San Andreas fault is a right-lateral strike-slip fault, here it is.  Please note that this creek has been beheaded by cummulative offset, not by a single event.  The old stream channel is towards the west (left).

It is worth noting that the trace of the fault really stands out when you generate a slope map.  Distinct breaks in slope are great for finding faults or landslides.  At such large scales, you can really understand the geomorphology of a region.

Sunday, June 6, 2010


Looks like this summer I will be helping to finish off a very large data set of geology for USDA Forest Service.  It is even hooked into a relational database.  There is some potential for mapping part of a forest.  But there are two key problems: it's in the Franciscan and I've yet to map anything besides stratigraphic columns.

Tuesday, May 25, 2010

Owens Lake

Owens Lake is being a pain in my behind.  I wasn't expecting the kinds of research on the lake that I'm finding out about.  Where's the sequence stratigraphy and stratigraphic columns?  It's all chemical!  Core OL-92, etc., exists but researchers only use them for stable isotopes and rock-flour studies.

Update: I found a great paper that includes sequence stratigraphy of trenches at paleoseismic study sites:
Bacon, Steven N., Silvio K. Pezzopane, and Raymond M. Burke. 2003. Paleoseismology on the Owens Valley Fault and Latest Quaternary Stratigraphy in Owens Valley near Lone Pine, eastern California. Unpublished Final Technical Report for the US Geological Survey, National Earthquake Hazards Reduction Program (NEHRP). Arcata, CA.

Sunday, April 11, 2010

Ore Deposits

For entertainment, I have been reading portions of J.M. Guilbert and C.F. Park Jr.'s The Geology of Ore Deposits.

I wanted to read it in order to understand chromite deposits.  In my opinion, my thirst for knowledge on that topic has been sated.  However, now I have found out that it has a few sections devoted towards ores developed by chemical and mechanical sedimentation.  Awesome.

Saturday, March 20, 2010

Point Reyes

I will be headed to Point Reyes tomorrow.  There is an incredible assortment of geology there.  I'll be sure to look for as many sedimentary structures as I can find.  I will have my G11, which should allow for some excellent photographic detail.

The annotated Kolob Canyon photo will have to wait a little longer...

In other news, I am taking Basin Analysis this Spring quarter.  In addition to that, I'll be learning about environmental applications in GIS, Non-Renewable Resources (lecture-based inorganic chemistry in disguise), and paleoclimatology.  Should be a very nice multidisciplinary quarter.

Saturday, March 13, 2010

Useful Software for Geology Majors

If you're studying geology and are a computer geek, I have some ideas that you may not have thought of. But knowing how resourceful most computer geeks are, I am sure you have found similar things.

OSXStereonet can take input planes and lines (e.g., strike/dip, trend/plunge) and take care of important calculations often made on a stereonet.  It can do a cylindrical and conical best-fit, find poles to all planes, generate Kamb contours, and much more.  This software is a must for all geology majors and professionals.  OS X only.


Mendeley is not open source, but it does use a few open sourced libraries such as QT.  But that isn't important.  What is important is that it helps you manage journal articles for writing research papers in a very natural way. It automatically extracts metadata from downloaded PDFs and fills in the bibliographic details.  If the software thinks it doesn't have everything, it'll prompt you.  But best of all, it has a built in PDF reader that allows for highlighting and note taking... plus those same PDFs can be uploaded to Mendeley servers for syncing with other computers!  Or, share your bibliography using the Mendeley website.  It can also create a customizable organized directory tree of all the papers you have loaded into it.  I use it to categorize articles, take notes,  and export references to BibTex.  Others may want to use it to cite while you write in documents.  What is key with this software is that it does not get in my way!  With software like this, who needs Dark Age software like EndNote or an amazingly cluttered desktop? For OSX, Windows, and Linux.


Anki replace Mnemosyne as my favored flashcard software.  Mnemosyne has not seen a release in over a year.

Anki is open source software  and is flash card program that uses algorithms that prevents wasting time on cards you know. It schedules cards based your rankings.  It allows you to use LaTeX and paste in arbitrary raster images from the clipboard.  Must have for those that need to memorize material.  It is cross-platform.


Mnemosyne lets you modify the LaTeX preamble. So you can add packages which can make inputing cards much faster. I use the package mhchem. It typesets chemical equations or formulas using input that is very natural for most people familiar with chemistry. It aligns numbers in equations very nicely. Get it and typeset your flashcards using that package. Its documentation is a very easy read.


LaTeXiT is for MacOSX. What better way to put your favorite TeX formulas into most any other OSX software. It is really fantastic. Double joy when you find that Grapher that comes with OSX can give LaTeX formatting for formulas that you used to generate graphs! Of course GNUPlot is probably necessary for your research papers. If you have OSX Snow Leopard, follow these instructions to compile GNUPlot.

The Periodic Table

The Periodic Table is a OSX Dashboard widget. It isn't a must have but damn is it convenient to find out very quickly ion charges and atomic mass! Now where is a good isotopes widget? ;-)

PDF-XChange Viewer

PDF-XChange Viewer is for Windows but free. Unlike Adobe Acrobat Reader (for the vast majority of PDFs I have used), but like OSX's Preview, it can do annotations. For slideshow heavy courses where the professor posts before lecture, this is a must have. It also has drawing tools and a highlighter. Be careful though as some PDF readers might get confused with abundant annotations and stack them atop each other and refuse to let you rearrange them.


Inkscape is the de-facto open source software for creating vector-based graphics.  It's for MacOS X, Windows, and Linux.  However, you need the latest XQuartz environment for MacOS X for it to run.  If you need to redraft infinitely scalable sketches from your field book, look no further.  But if you can afford Adobe Illustrated, or your department has it on their lab computers, I suppose you might be better off.  But at least, with this, you can work on diagram-based assignments at home.  Inkscape can also be a terrific way to create forms for use in the field.  It export to PDF.

Adobe Illustrator
This software needs no introduction.  If you're having problems with Inkscape, picking up an academic license of Illustrator might be a worthwhile solution.  Illustrator is great for finishing off maps exported from ArcGIS.  It can also help you draw various things handy to structural geology such as balanced cross sections and strain ellipses.


On OSX v10.4 and greater, use rsync -aE /Volume/thumbdrive /Users/username/somebackuplocation regularly to backup your thumbdrives without copying data that has not changed. -E might not be useful copying off a FAT32 thumbdrive but it is there in case OSX can actually use those file attribute data on the HFS+ side. Definitely use it if you're backing up to a HFS+ external drive or vice versa. -a is archive mode which sets a bunch of flags that ensures you get a quality backup.  But, timemachine is rather nice, too.  It's really an overglorified, but awesome, rsync :-)


Synctoy is software for Windows.  It is an easy to use method to sync files between disks, flash drives, networks, and so on.  If you operate Windows, and maintain files on a fallible flash drive, you better keep backups on your other computers.  Synctoy makes backups faster by only copying files that are new or have been updated.

Friday, March 5, 2010

Zions National Park, Part 1

In June of 2004, I visited Zions National Park in southern Utah.  I took an incredible number of photographs, but at the time I did not know much about geology.  Thus features that now look obvious to me were not features at all.

As I look through my photos, I can spot faint sedimentary structures.  My camera at the time was 3.1 megapixels.  It certainly could not resolve fine details from afar; and that's all I have!

This first image has what appears to be planar laminations at the base of the formation.  I believe that I can discern some cross stratification above that.  If I had more time, I would trace them so that they are evident.  In my original photos they can be seen pretty easily but for personal reasons I prefer not distributing my master copies.

In the second image, I can barely make out more obvious signs of cross stratification at center left by the dark linear feature.  They're dipping to the right, so one might say that water was flowing in that direction.

In the next post, I'll actually annotate the features on a really nice photo!  It is a closer view of photo two on this post.

Monday, March 1, 2010

Trough Cross-Stratification

This photograph was taken about a mile east of Butte Community College on the Durham-Pentz Highway.

I am the person in the photo.  Unfortunately, I am awful for  a scale due to perspective.

This is a roadcut and it clearly shows trough cross-stratification, perhaps from a stream.  The structures that clues us in are the abundance of smiley faces.  These are created as subaqueous dunes migrate and their troughs cuts off previously deposited dune peaks.

Streams have these kinds of structures at the thalweg or just above it.  The thalweg is the deepest, and often the fastest, part of a stream.  It is what develops cut banks. The fastest, outside portion of a stream's meander cuts into terraces creating a cut bank.  The interior portion of the meander develops a point bar.  If sediment were deposited above the trough cross-stratification, we might see fining upwards and current ripples.  That would indicate a pointbar.  If we could see sediment below this structure, we might see mud from overbank deposits.  That is Walther's Law: vertical succession of beds shows differences in lateral environments (providing unconformities do not exist!).

If you click on the photo, you should notice that the grain sizes are pretty apparent.  They are medium to coarse, though I lean towards coarse.  That would be an additional line of evidence that this was deposited by a stream.

I cannot say for certain which direction this stream flowed.  From this perspective it is either in or out of the photograph.  But I would hazard to guess water flows in to the photograph since the troughs seem to be dipping that way.

In summary, this is a cut-and-fill structure which represents the bottom of a stream!  Cool!

USC's SedPak

SedPak is software written by the geology department at the University of South Carolina.  So University of North Carolina has the wonderful rock and mineral texture library, and USC has SedPak.

SedPak is freely available and uses the motif graphical user interface in X11/XOrg.  It works very well on Ubuntu 9.10.  This is in stark contrast to FUZZIM, which is only available as a PowerPC binary for Mac OS9.  To my knowledge, there is no source code available for it and there is only one place to get the binary (all those GOPHER links? Very much dead).  It may forever be locked up in the confines of Mac Classic environments running within OSX (or in SheepShaver PowerPC emulator software).

At first glance, its interface is more confusing than FUZZIM.  SedPak uses a server-client interface (common in the *nix world), which can break if a database file has incorrect data.  Despite that, it looks pretty powerful and has many ways to visualize data.  For example, you can create a facies file to help describe the facies deposited in a basin.  A chronostratigraphic log can be generated, as well as sand-silt ratios.  In addition, wells can be defined, and specific portions of basin sediments can be isolated by using the sea level curve.  Carbonates can be included in models and hydrocarbon development can be tracked.

It has a GUI with many tools to *visually* design surfaces, sea level curves, temperature curves, and more.  For those that know spreadsheet-fu, data can be manually entered to create more precise environment models.  From what I understand, SedPak it uses a geometric model rather than the "fuzzy" model employed in FUZZIM.  It is blazingly fast yet seems to take into account most things that FUZZIM does.

I have much to learn about this software and the concepts that drive it.

Friday, February 26, 2010

Canon G11

The Canon G11 has fantastic macro abilities, very reasonable noise at high ISO, and a great lens.  For those three reasons, I highly recommend it for taking field photos in nearly any conditions.  Of course, a bonus feature is RAW which means you, as the geologist, can adjust pictures using a very wide range of available tones.  Why use a 8bit JPEG burned with white balance and tone curves when you can have unadulterated *nearly* 16bit RAW?  Besides, posterization is unacceptable and JPEG is king of that.

One problem of the G11:  At 6.1mm (28mm film), the lens does distort light at the fringes; that's typical.  However, Digital Photo Professional, included with the camera, fixes that in a pinch with minimal cropping.

If you still need convincing of RAW, please see 
Ron Bigelow's incredible website.  Particularly, see "Why RAW."  Leave JPEGs for the party at camp.

Friday, February 19, 2010

The Generic Geologist

I am not going to be a generic geologist.  I took optical mineralogy, or "how to use the petrographic microscope", but I will not be taking the other petrology courses.  Instead, I am aiming for a Bachelor's of Arts in Geology with a mixture of other, perhaps equally  important, classwork.

To offset the fact that I won't be experienced in determining the exact igneous or metamorphic rock based on modes of minerals, I'll be focusing on sedimentology.  I am also focusing on the environmental aspects of geology.  Finally, I have developed a program to cluster GIS coursework.

I do not plan on staying in academia.  I think I will be quite satisfied as a field technician with a plethora of knowledge and skills that are ancillary to geology.  

The BA allows me to explore all kinds of areas without spending time in courses learning skills that flood the marketplace.  It is a valid reason, though it does certainly have drawbacks.  However I am willing to accept those drawbacks for a different career path.

Sunday, January 31, 2010

A Terrible Blogger

What have I been doing instead of describing a photo of trough ripples?  I have been writing a sedimentology lab report using Apple's Pages and a paper using LaTeX for an upper division writing class.  I must say, it is rather refreshing to use LaTeX.  Pages has a lot of unpredictable quirks.  Still, it has its charms.

Thursday, January 28, 2010

The iPad in Geology Education

I carefully followed yesterday's reveal of the Apple iPad.  I was interested in it because I use technology in the classroom to take notes, view slides, and other important tasks (such as keeping track of data in lab).  I'm not particularly interested in a Netbook because they have proven to be unreliable; I want something that lasts years.  However, the tablet is interesting because it comes from a company known for reliable computers.  But more than that, it could be used for taking notes in class, keeping track of data, while staying connected.

Despite the introduction of iWork for the iPad, I do not see how this device could be useful in an academic setting.  Perhaps if I were the one presenting slideshows using Keynote, it would be interesting.  But I'm the student.  I listen to lectures and take notes, and I prefer, if possible, to do so paperless.  

Currently I use my aging laptop to take notes on slides exported to PDF.  My preferred software package to do that is PDF-XChange Viewer.  I can make comments on specific slides, highlight ideas and comment on them, and even do some basic diagramming using primitive shapes.  Naturally, for some classes, I have to use a pad of paper for complicated drawings.  Unfortunately, I do not see how I can do any of that on an iPad.  

The next problem is a problem of data integrity.  I keep all of my data on a flashdrive and I make daily backups to my laptop using SyncToy.  The iPad glaringly lacks a USB port.  That is also a handicap for those times when I need files from a fellow student (such as field photos).

The keyboard on the iPad looks large but appears to be largely a single-hand affair.  I doubt I could type fast enough to keep up in lecture.  And certainly I would have to buy the case/stand to do so somewhat ergonomically.  Furthermore, I would not want to lug around an Apple Aluminum keyboard with accompanying stand all day long.  Another negative is that it lacks a Unix environment.  I love using LaTeX for my reference laden papers and math-based homework; not a chance of doing so on the iPad.

So at this point, the iPad seems to lack PDF annotations, a USB port, and most likely it has a very slow input interface.  I would have to try typing on an iPad to really know.

What can I see this being useful for?  I think a few pundits have already indicated that it is more of a leave-at-home device.  You can take it into any room, lounge around, surf the web, check e-mail, and read books.  Thus if you have an iPhone, you can leave it to phone calls while in the home.  With the iWork suite, you could potentially be productive with it.  Perhaps you wake up in the middle of the night with a great thesis: turn on the iPad and clumsily type it out.

I do not have plans to buy this device in its first iteration.  In fact, I'm still looking for the perfect device.  I'm surprised Apple did not refresh their Macbook Pro line; I'm a bit more interested in their 13" variant.

I will post a new interpretation soon; it will be on ripples.  I've a great picture for that, although it lacks scale!  Stay tuned.

Tuesday, January 5, 2010

Fort Bragg: Glass Beach Marine Terrace Sorting

Fort Bragg, CA exists on a marine terrace.  Its tectonic genesis I'll leave for another day.  The wave cut cliffs exposing the sediments of these terraces vary.  Here in March of 2009, I found part of a terrace eroding towards the city just south of Glass Beach, revealing conglomerate.  A quarter was used for scale (thankfully!).  Remember, you can always click on the image to view it (middle click to view in a new tab in Firefox or right click or command click to see a menu where you can open the photo in a new window or tab).

In these particular photos, there appears to be conglomerate in normal grading (as opposed to reverse grading).  It goes from very large (often discoid) pebbles to small pebbles to granules.   This graded bedding appears to be largely clast-supported (orthoconglomerate).

Why might this graded bedding be occurring along the coast within a terrace?  Given that the pebbles are very well rounded, they were likely deposited by a stream or were weathered away regularly by wave action prior to uplift.

 If this feature were in fact caused by fluvial processes, the larger clasts would be indicative of very rapid flows which were able to move and deposit large pebbles (perhaps by saltation or rolling). Most of the coarse to medium grain sands AND smaller pebbles would have been entrained within the flow.   These clasts probably washed out into the sea.  Eventually the stream velocity decreased, dropping out smaller pebbles and coarser sand.  Then the whole process repeated itself.

One should also note that at the bottom of this graded bedding there is a jumble of large and small pebbles with coarse sand; perhaps this indicates rapid stream velocity changes at the start of a flooding event?

Finally, if this were a feature created by wave action, it might be said that material may have been deposited into the ocean by mass wasting.  Providing that the ocean at this location was shallow enough, wave action could slowly wear down the larger clasts by abrasion.  Storms, perhaps, cause this mass wasting.  The exact mechanism for this kind of sorting under these conditions is a little iffy to me.  But perhaps I'll revisit this later when I've learned more.  However, I believe that fluvial conditions are more apt for this situation as water intensely sheds westward off the Coastal Ranges all along the north coast of California.  Since this is in a terrace, perhaps it represents an uplifted portion of an old stream channel (note that Pudding Creek is a several blocks north of here)?  Sea levels, of course, have not always been where they are now; so it is reasonable that the ultimate baselevel for this stream could have been further out (a shoreline shift).

Perhaps I'll use this opportunity to disclaim any accuracy in my interpretations of photographs I've taken over the last ten years.  First of all, I am a very fresh geology student and so I will be wrong and miss important indicators regularly.  Second of all, I'm relying on only the details in the photographs and my spotty memory.  However, do feel free to elucidate what I might have missed and/or explain pertinent processes.

Saturday, January 2, 2010

Winter 2010 Geology at UC Davis

This winter quarter I will be studying sediments & stratigraphy (GEL 109/109L), environmental geology (GEL 134), and the "history of life" (GEL 103/103L).

I will be collecting a lot of knowledge and tools this quarter.  Thus, as I progress, I will post photographs from my extensive photograph library and try to explain them.

Last quarter I took classes very fundamental to geology: earth materials and optical mineralogy.  However, it is rather difficult to blog on the scale of minerals.  Fortunately this quarter will finally allow me to apply principles of geology to the many sweeping landscapes I have photographed over the last decade.  By the next academic year (2010-2011) I will be taking structure and should be able to interpret geological phenomenon even more.

The image above is of the sandstone formations at Sächsische Schweiz National Park in Saxony, Germany.  I took this photograph during my 2009 summer vacation.