Sunday, February 21, 2016

February's Baking Challenge: Molten Chocolate Cake

This year I decided to take on Cake Baking Bucket List challenge. Each month I am baking a different cake, learning some new tricks, and honing my skills.

February's cake is a molten chocolate cake. One of the things I love about the recipe is that it make 4 individual cakes, perfect for having a couple friends over for dinner. It's also extremely simple and fast. The cakes bake in 12 minutes, and since you want to serve them warm, there is hardly any wait time. I made them after dinner on Friday night, and the whole process took about 30 minutes from initial prep to first bite.

Once I had the cakes placed on dessert plates, I sprinkled them with powdered sugar and topped them with a small scoop of vanilla bean ice cream. Delicious!

Edit: we just ate the remaining two cakes last night (they'll keep 5 days in a airtight Tupperware in the fridge), and I drizzled some caramel sauce over the top once I added the scoop of ice cream. Amazing! Caramel sauce and vanilla bean ice cream: that is definitely my recommended way to serve these.

Friday, February 12, 2016

Dissertation is available online

Hi Guys,
  A couple weeks ago ProQuest published my dissertation online.  Most institutional libraries will have access to it through a subscription to ProQuest's Thesis and Dissertations Database. 

  I also want to make it available to those that don't have access to a university library, so I am hosting it on Google Drive.

  If you would like to view/download a copy of "The relationship between oceanic transform fault segmentation, seismicity, and thermal structure," you can find a link to it here.

Sunday, February 7, 2016

The Ultimate Cake Baking Bucket List: A Monthly Cake Challenge

As one of my goals for 2016, I decided I want to expand my skills in the kitchen. I love baking, so why not find a way to challenge myself and make some tasty treats at the same time?

Enter the
Ultimate Cake Baking Bucket List. The list, which assigns a cake to bake for each month of the year, is designed to introduce the baker to multiple techniques while also, making them more confident and comfortable behind the stove. 

January's cake was a citrus angel food cake. I postponed making it until this weekend, as I thought it would be a fun activity to do while hiding out from the Super Bowl madness occurring just down the road from us (we're only 10 minutes from the stadium, and live right along the public rail line). 

One thing I noticed about some of the recipes on Food & Wine is that they don't list out all the steps, which can be a bit confusing. For example, the recipe for the angel food cake lists heavy cream and powdered sugar in the ingredients list. The directions never mention these ingredients though. From the picture and the ingredients themselves, it's obvious they want to make a simple icing to drizzle on the cake, but it would be nice if they mentioned that.

I followed the recipe almost exactly as it appears on the webpage, with a couple exceptions:
  1. My egg whites would not whip up into stiff peaks no matter how much I beat them in the KitchenAid until I added more cream of tartar. I believe this possibly due to the grated lemon zest preventing the egg whites from forming good structure.

    To over come this, I gradually added additional cream of tartar, approximately 1/4 teaspoon at a time. The recipe calls for 1 teaspoon, and it total I think I used about 2.5. One nice thing I learned, adding additional cream of tartar does not seem to affect the recipe at all. Yeah!
  2. The icing: the recipe mentions 2 tablespoons heavy cream and 1 cup confectioner's sugar. I used 1.5 tablespoons whole milk (I didn't have heavy cream), and 1/2 tablespoons homemade vanilla extract (I'll make a post later on how to make the extract). Once the cake was cooled and out of the pan, I just mixed up the icing with a metal whisk and drizzled it over the cake.

This cake is light, airy, and very delicious. The zest and fresh lemon juice really give the cake a nice pop of citrus flavor without making it tart. I was honestly surprised just how flavorful this cake was, as plain angel cake is so mild and generally a bit boring on it's own.

I did have some trouble getting the cake off the bottom of the pan, until I started cutting it. I used a non-stick angel food pan, but since angel food batter climbs the walls of your pan as it bakes, I am not sure how much the non-stick coating actually helps. I need to get a nice rubber or silicon icing spreader that I can also use to separate the cake from the pan for easy removal. You'll notice in my pics that the cake was still on the bottom part of the pan when I iced it. 

(sorry for the dirty pan in the pic, my husband had just sauteed some veggies)

Sunday, January 17, 2016

Learning QGIS - a simple tutorial

One of my goals for early 2016 is to learn how to use QGIS, a freely available open source Geographic Information System.

I have been an ArcGIS user for years, and consider myself fairly proficient. If you're a student and your university has a site license for ArcGIS, you can actually get a free personal license, good for one year from the date of install. The ability to have ArcGIS installed on my personal machine, and not having to rely on remote desktop connections, really helped facilitate my research during the last couple years. I have an Apple laptop, but I found that if I allocate sufficient memory (4 GB) and hard disk space to my Windows virtual machine, I can run ArcGIS quite happily. ArcGIS is extremely powerful, but it is also prohibitively expensive for many individuals and for small organizations, and is also Windows-only at this time. I am not sure where I will end up working at this time, and I certainly cannot assume I will have access to ArcGIS when I get there. As such, I feel that it behooves me to learn alternative solutions for any GIS needs I have.

QGIS provides many of the same powerful analysis tools as ArcGIS, thanks to its integration with other open source GIS tools, such GDALGRASS GISPostGIS, and MapServer.

GDAL is a translator library for raster and vector data, allowing you to transform your data into a number of different projections (coordinate reference frames) and data formats. It can generate hillshade, compute statistics on a grid file, etc.

GRASS GIS provides a lot of the analytical, modeling, and image processing tools found in QGIS. The difference between GRASS GIS and QGIS can be confusing as GRASS GIS can be also used as a standalone GIS. Earlier versions of GRASS did not include a GUI; commands were run via a command shell and results were displayed using the X11 windowing system. QGIS interfaces directly with GRASS to provide a nice user-interface, that folks already familiar with ArcGIS might be more comfortable with. Also, to my knowledge GRASS does not integrate directly with MapServer. Early versions of QGIS did not integrate with GRASS. Those early versions of QGIS could still handle a lot of GIS needs, but it did not have a lot of the analytical tools that GRASS did.

PostGIS brings geospatial capabilities to PostgreSQL databases, allowing you to run queries and perform database operations based off geometries, locations, etc. This tool is what provides QGIS with its database capabilities.

MapServer allows for the publishing of geospatial data on the web, and provides a suite of interactive mapping tools. QGIS uses MapServer to allow you to publish your maps to web.

The most recent version of QGIS (v. 2.12) brings together these individual tools, along with a number of others, in a nicely packaged open source software that is a serious competitor to ArcGIS.

My first project:

For my first project, I decided to create a map of the Discovery Transform Fault.

To create this image:
  1. I brought in an ASCII Grid file (.asc) of the bathymetry data, using Layer --> Add Layer --> Add Raster Layer. This brings the grid file in as a grayscale image.

  2. To change the color, double-click on the layer, then go Style --> Render Type --> singleband pseudocolor. Now you can select your colormap, choose between continuous and discrete modes, create classes, and adjust your bounds just as you can in ArcGIS.

  3. You can create the hillshade effect by going to Raster --> Analysis --> DEM. Under mode you will find options for computing slope, aspect, hillshade, etc. 

  4. Once your hillshade layer is created, move it down below your grid layer in the layers panel. Then, go to Layer Properties for your grid, and set a transparency so you can see the hillshade through the data. 

  5. The plate boundary line that you see on the map was brought in as a geotiff. To make the white background transparent, you go to Layer Properties --> Transparency and set the RGB values to 255.

  6. Next I added the earthquake data, the purple circles that are sized by magnitude. The earthquake data was in a comma-separated file (.csv) so I went to Layers -->Add Layer --> Add Delimited Text Layer.

    QGIS does a great job of reading the file and determining that the first row of data is actually the header row. I simply selected which columns represented the X field and Y field and clicked OK. It then asks you to choose a Coordinate Reference System (CRS) for the data. Select the appropriate projection, hit OK, and the data should show up on your map.

    To size the points by magnitude (you can also color by attribute as well), double-click the layer to bring up Layer Properties --> Style and change Single Symbol to Graduated. Under Method, select size, and for Column, select the attribute (in my case "Mw") that you want to size by. Now you can choose what mode to break by (equal interval, natural breaks, pretty breaks, etc.).

    As with any context menu, you can hit "apply" before you hit "OK" to see how the data will look before you completely exit the menu. 

  7. Now that we have all the data in QGIS, it's time to make the actual map. First, hit the New Print Composer icon (white rectangle w/ yellow asterisk) or go to Project --> New Print Composer.

  8. Select Layout --> Add Map, and then drag using your mouse or trackpad to draw a box where you want the map to appear. Once you let go on the mouse or trackpad, your data will pop into view. You can adjust the visible bounds of your data under Item Properties.

  9. Under Item Properties for the Map object, you will also find options for adding a geographic grid, or graticule, as I did above.

  10. The Add Scalebar and Add Legend options are tucked away under Layout. Each time you choose to add an item under Layout, you'll need to draw a box on your map so the composer knows where to place it. You can always move these items after the fact.

  11. If you do not want all your layers to show up in the legend, simply uncheck Auto Update under Item Properties and the select the layer you wish to remove and hit the minus icon. The icon of the pencil on the paper allows you to edit the names of the visible layers.  The legend item has a "columns" option under Item Properties. This will enable you to have your layers added side-by-side, versus stacked vertically. The icon that looks like a funnel with filter the legend by map content. For my map, this meant that for certain sized earthquakes not visible in my map extents, the corresponding legend entry was removed.

  12. before filtering legend for map content

    after filtering legend for map content

  13. Once you have your map the way you want it, you can easily export it as an image, PDF, or SVG file.

One thing I noticed was that even though I used a continuous colormap for the bathymetry data, the legend shows the colorbar as discrete color blocks. It would be better show a gradual change in color from blue to red. When you first set the colorbar for the layer, the icon for the spectral colormap does show this gradation of colors, so this should be something QGIS can do. I haven't looked into this too much yet, but if I find a solution, I'll post about it.

For a lot of helpful QGIS tutorials, complete with downloadable datasets so you can easily follow along, check out They start out with tutorials on basic map-making and go all the way through advanced statistical analyses of your data. It's a tremendously useful site if you really want to learn QGIS.

Thursday, January 7, 2016

AGU and Post Docs

Well, my re-dedication to my blog hit a brief snafu as AGU ended up being crazy as usual and last minute postdoc applications (*fingers crossed*) took up the rest of my time.

AGU was fun, as always, and completely crazy due to the sheer number of talks and posters, as usual. It was great to meet up with friends, catch up with colleagues, and, of course, catch some great talks and posters.

I presented a poster on my global characterization of mid-ocean ridge transform fault structure and the relationship between fault segmentation and the underlying fault thermal structure, which controls the width of the seismogenic zone. You can view and download a high-res PNG version of my poster here: AGU poster.

Below is a low-res screen grab:

It is stuff I have presented before as preliminary results, but the work is now finalized. I have been working on my global characterization of fault structure for a few years now, updating it as new versions of global bathymetric grids become available. My committee and I decided to hold off on publishing it until we finalize the scaling relation work, as combining the two makes for a much stronger paper. Of course, all of this is now published in my dissertation. Writing this all up for publication in a journal will be one of my top goals over the next couple of months.

Speaking of my dissertation, a link to the PDF document be found here: Dissertation. ProQuest has the final version, and once it is officially published online, I'll write a new post and include the direct link.

Oh, due to said postdoc applications, my AGU poster ended up being put together much later than anticipated. I ended up using AGU's own poster printing services provided by Copy Central. For $119, I received a high-res full color 3' x 5' poster printed on heavyweight paper. It looked amazing, and for the convenience of picking it up at the conference the morning of my presentation, it was worth every penny. I highly recommend their services.

Tuesday, December 15, 2015

Long Time, No Blog

Well, it has been a LONG time since I have posted on my blog, ~ 2.5 years. I did not even realize it had been that long until I checked this evening.

A lot has happened over the last 2.5 years, here are a just few examples:
  • Just this past October I successfully defended my Ph.D. at the University of New Hampshire. My dissertation is entitled "The Relationship Between Oceanic Transform Fault Segmentation, Seismicity, and Thermal Structure." I'll post a link to it once it's available online, and I'll include the abstract below
  • In September, 2014 my first paper related to my PhD research was published:
    Wolfson-Schwehr, M., Boettcher, M.S., McGuire, J.J., and Collins, J.A., 2014, The relationship between seismicity and fault structure on the Discovery transform fault, East Pacific Rise: Geochemistry, Geophysics, Geosystems, v. 15, no. 9, p. 3698–3712, doi: 10.1002/2014GC005445.
  • On October 23, 2013 I gave a talk at the USGS Menlo Park. I admit that standing up on the podium, in front of all the flags and facing many of my committee chair's colleagues (she was a Mendenhall Fellow there), was a bit intimidating. Everyone there was very welcoming, however, and I really enjoyed the day. The talk is available to watch online here
  • On October 30, 2015 I gave my second web-streamed talk at the University of Texas Institute of Geophysics. This was my first post-defense talk, and it was definitely more relaxed than many of my others. It was quite fun to be flown down from northern Cali for a couple days and to get to tour the facilities and meet with many of the researchers. This talk is also available online, and can be watched here.  
  • In 2013 I co-convened my first AGU session on oceanic transform faults, and in 2014 I did it again! It was really nice to be able to bring the oceanic transform fault community together, and we're hoping to make this a biennial occurrence. 
  • And, on a personal note: In Aug. 2014, I gave birth my son, Lincoln. He's our first child, and such a joyous addition to our family. 

So that pretty much catches you up on all the major things I believe. I know I have said this before, but I am going to recommit to this blog once again and try to update on a regular basis. It's AGU week now, so that should give me some good material to blog about.

Oh, and here is the abstract for my dissertation:

Monica Wolfson-Schwehr
University of New Hampshire, December, 2015

Mid-ocean ridge transform faults (RTFs) are typically viewed as geometrically simple, with fault lengths readily constrained by the ridge-transform intersections. This relative simplicity, combined with well-constrained slip rates, make them an ideal environment for studying strike-slip earthquake behavior. As the resolution of available bathymetric data over oceanic transform faults continues to improve, however, it is being revealed that the geometry and structure of these faults can be complex, including such features as intra-transform pull-apart basins, intra-transform spreading centers, and cross-transform ridges. To better determine the resolution of structural complexity on RTFs, as well as the prevalence of RTF segmentation, fault structure is delineated on a global scale. Segmentation breaks the fault system up into a series of subparallel fault strands separated by an extensional basin, intra-transform spreading center, or fault step. RTF segmentation occurs across the full range of spreading rates, from faults on the ultraslow portion of the Southwest Indian Ridge to faults on the ultrafast portion of the East Pacific Rise (EPR). It is most prevalent along the EPR, which hosts the fastest spreading rates in the world and has undergone multiple changes in relative plate motion over the last couple of million years. Earthquakes on RTFs are known to be small, to scale with the area above the 600C isotherm, and to exhibit some of the most predictable behaviors in seismology. In order to determine whether segmentation affects the global RTF scaling relations, the scalings are recomputed using an updated seismic catalog and fault database in which RTF systems are broken up according to their degree of segmentation (as delineated from available bathymetric datasets). No statistically significant differences between the new computed scaling relations and the current scaling relations were found, though a few faults were identified as outliers. Finite element analysis is used to model 3-D RTF fault geometry assuming a viscoplastic rheology in order to determine how segmentation affects the underlying thermal structure of the fault. In the models, fault segment length, length and location along fault of the intra-transform spreading center, and slip rate are varied. A new scaling relation is developed for the critical fault offset length (OC) that significantly reduces the thermal area of adjacent fault segments, such that adjacent segments are fully decoupled at 4OC . On moderate to fast slipping RTFs, offsets 5 km are sufficient to significantly reduce the thermal influence between two adjacent transform fault segments. The relationship between fault structure and seismic behavior was directly addressed on the Discovery transform fault, located at 4S on the East Pacific Rise. One year of microseismicity recorded on an OBS array, and 24 years of Mw 5.4 earthquakes obtained from the Global Centroid Moment Tensor catalog, were correlated with surface fault structure delineated from high-resolution multibeam bathymetry. Each of the 15 Mw 5.4 earthquakes was relocated into one of five distinct repeating rupture patches, while microseismicity was found to be reduced within these patches. While the endpoints of these patches appeared to correlate with structural features on the western segment of Discovery, small step-overs in the primary fault trace were not observed at patch boundaries. This indicates that physical segmentation of the fault is not the primary control on the size and location of large earthquakes on Discovery, and that along-strike heterogeneity in fault zone properties must play an important role. 

Friday, May 3, 2013

Reordering columns/rows in a shapefile in ArcGIS

I recently created a shapefile in ArcGIS of my oceanic transform fault data. I started off with two separate files: a shapefile of points that simply contained a latitude/longitude and name for each fault; and a polyline shape file that contained the length measurements and the start/end points. I combined these two shapefiles in ArcMap using the "Join Data" command, and selecting to join the data based on spatial location. The result was a single polyline shapefile, that included all the original polyline attributes as well as all the related attributes (name, center lat/long) from the point file.

The problem was that the shapefile was not ordered the way I wanted it. In ArcMap you can reorder rows by ascending/descending values by double-clicking on the column header, or move columns simply by clicking on the header and dragging it over. The problem is that this only applies to your view of the shapefile attribute table, and the reordering is not actually saved to the shapefile itself. If you close out ArcMap, open a new map, reimport the shapefile, everything is back to the original order.

There is a free plugin tool for ArcGIS that is quite powerful and can solve these issues for you: ET GeoWizards. There are both free and paid versions of this toolbox, but I found the free version did exactly what I need. This toolbox is pretty impressive, and includes tools for feature translation, where shapefile objects are moved by a user-specified distance, filling holes in polygons, generalizing features, creating clusters from points, and a whole suite of other functions.

In order to reorder the columns and sort the rows in your shapefile, you can find the necessary commands under "Basic." The "Order Fields" command lets you select which fields you want to use from your original shapefile and specify the order in which they should appear. The "Sort Shapes" command lets you select which columns you want to sort the data by (you can select more than one), and whether you want them in ascending or descending order.

Another great toolbox plugin for ArcMap is Jenness Enterprises' Tools for Graphics and Shapes.  If you are looking for a tool to calculate spheroidal (geodesic) length of features in your shapefile, this is the tool for you. While this toolbox includes many of the same functions as the GeoWizards plugin, it also has many unique tools as well.  I have found that having both toolboxes has made working in ArcMap a much more pleasant experience. I wrote up a blogpost on the Tools for Graphics and Shapes plug-in back in 2010.