Creating a 3D model of a surface with QGIS

The easiest method I have found for creating a 3D model from a digital elevation model (DEM) is with the QGIS plugin [DEMto3D]. Simply add the DEM into the plugin, and you can adjust the model’s base height, z exaggeration, etc., The model can take awhile to create if the DEM file is large. 
The plugin creates a STL file that can then be added into Meshlab or other 3D viewers for further manipulation. The model should also be easy to georeference based on obtaining the extent coordinates within QGIS. The plugin was designed for 3D printing landscapes. 


Integrating Endnote with Ulysses III

As an academic researcher it saves a lot of time to use a bibliography database to automatically output citations in the correct format. Although Pages and Word have direct plug-in capability and is easy to use, often I find myself working in a text editor such as Ulysses III.

Currently I am using Endnote X6, however, it is likely other bibliography databases that have a scan paper function will work as well. To insert citations into Ulysses III so that Endnote will recognize them follow the format guides below.

Steps for generating bibliography with Endnote

  1. Save finished paper as Word .rtf
  2. Open up Endnote, and select Tools > Format Paper. Navigate to the saved file and Endnote will scan the paper and generate a new .rtf file with a bibliography in your chosen Endnote style.

Formatting guide for inserting citations into Ulysses III:

Copy each desired reference within Endnote and then \ Paste reference within Ulysses III.  To avoid using the backslash you can also modify {} as a markup symbol

Ulysses III tips

For author and date:
\{Hurst, 2002 #1796}

Results example:
(Hurst 2002)

For multiple citations:
\{Hurst, 2002 #1796}\{Hurst, 2010 #1636}
\{Hurst, 2010 #1636}\{Johnson, 2011 #739}

Results example:
(Hurst 2002, 2010)
(Hurst 2010; Johnson et al., 2011)

Add prefix to citation:
\{e.g.,\Hurst, 2010 #1636}

Results example:

(e.g., Hurst 2010)

Note:  To get the prefix citation to work you must add the backslash within the RTF document prior to Endnote scanning.  Ulysses removes \ on export to RTF.

Add page numbers:

\{Hurst, 2010 #1636:23-30}

Results example:

(e.g., Hurst, 2010:23-30)

Year only:

Hurst states \{, 2010 #1636} the following

Results example:

Hurst states (2010) the following

Bulletproof espresso

Bulletproof espresso

Bulletproof coffee consists of blending organic coffee, grass fed butter, and MCT oil into a rich and creamy drink. The benefits are introducing your body to healthy fats that increases clarity and helps to maintain weight through a healthy metabolism.
While I am not sold on the health benefits, it does make a delicious drink.

I enjoy espresso on occasion and I wanted to develop a method that incorporates the idea of bulletproof coffee, and at the same time reduce the time and number of steps necessary to make the drink. This is really easy, and all you need is the ability to make espresso. I have used this method with my pump driven machine, and I think it will also work with a pressure driven machine or a stovetop.

Simply add the grass fed butter directly with the espresso coffee into the filter. I typically only use one spoon scoop of butter. Then run your machine. The result is a buttery rich espresso. The final step is to add a couple tablespoons of the MCT oil. Voilà

Submitting high resolution graphs and figures for publication from iWork’s Pages and Numbers

Recently I submitted a new manuscript for publication.  Within the manuscript I have several figures and line drawings that I created within Numbers and Pages.  Publishers typically require line drawings to be saved in Tiff format and have a resolution of 1200 dpi.

In the past, I copy and pasted my figures and line drawings into Keynote using a really big custom slide.  After scaling up the figure to match the large slide size,  I would then export the Keynote slide as a Tiff and then modify the image size setting and resolution within Photoshop.

This method requires many unnecessary steps.

The easy way is to print the Pages or Numbers document at 1200 dpi resolution and save it as a PDF file.  Then open up the PDF in Photoshop, select the page with the figure or line drawing that you are working on, crop the image, and then save as a Tiff.  That is it.  Repeat for each figure or line drawing.

With this method it is now really easy to use Pages to manage figures, tables, and line drawings for publication.  I typically have one Pages document that contains all of my text, and another Pages document that contains all of my figures, line drawings, and tables.

Pompeii World Heritage Site

Archaeological Areas of Pompei, Herculaneum and Torre Annunziata


The site of Pompeii is part of the world heritage site that also includes Herculaneum, and Torre Annunziata. Pompeii was inscribed onto the world heritage list in 1997. The famous volcanic explosion on the 24th of August 79 A.D. tragically sealed the fate of many. The entire town as it stood in 79 A.D is fairly well represented, and to walk these streets is to really get a sense and feel for what urban life was like in a Roman town.

Map Location

My wife and I visited this site in January of 2012, and we like to call it our “prehoneymoon” trip. We took our awesome vacation prior to our wedding rather than before.

Pompeii is located along the eastern coast of Italy in the shadow of Mount Vesuvius. We were based in Rome for our trip so we took a train from Rome, to Naples, and then another to Pompeii. A highly recommended excursion from Rome. My wife and I do not speak Italian, however, it was an adventurous and interesting way to see other aspects of Italy.

In my introductory classes in archaeology as an undergraduate, Pompeii was always a site included in the textbook. An example of a static snapshot of what life was like at one point of time sealed by a volcanic eruption.

To see this site in person is an experience I will never forget. The greatest heritage aspect of this site, in my opinion, is the ability to walk an entire town. Walking through amphitheaters, a colosseum, a bakery, prostitute houses, temples, residential homes, etc. is a unique heritage experience.

A feeling of tragedy permeates the entire site, and a question of why we never seem able to learn our lessons from history. Mount Vesuvius will likely erupt again one day and will likely bury the city of Naples. Yet, people continue to live in the path of the volcano with each generation tempting fate.

Place of Ill Repute



Chavín de Huántar

Chavín de Huántar

At over 10,000 feet Chavín is the highest cultural world heritage site in the Americas.

Chavín was inscribed onto the World Heritage list in 1985.

The main occupations at Chavín date between 850-200 B.C. An early ceremonial center that contains a series of sunken courts and platform mounds. Depictions of animals that originate in the Amazonian basin indicate exchange between neighboring peoples was an important aspect of this society. This site represents an early Andean civilization and the development of a socially stratified society.

The Lanzón stone is a rock pillar in the shape of a lance and is located in Building B at the site.

The Chavín de Huántar site and the Lanzón stone has been laser scanned by CyArk, with detailed images and 3D models for viewing.


World Heritage: First Steps


Our heritage begins approximately 2 million years ago. An early hominid Homo habilis “handy man” began making simple pebble tools. This is our first evidence of our ancestors making and using tools.

Stone tools are not easy to make. Knowledge of rock properties and how to manipulate the properties of the rock to control how the rock fractures is required to make a stone tool.

The significance of this moment in time is the knowledge exhibited in making stone tools. This knowledge illustrates a culture had developed. It is not enough for one person to figure out how to make a stone tool by chance. After learning of the advantages of chipping stone for tools, these early people transmitted this knowledge to others in the group and to future generations. This is culture, this is heritage.

Discoveries of Homo habilis crania remains indicate this group had a larger brain size than previous generations. The larger brain size likely allowed for the development of higher order cognitive reasoning and the development of a culture.

Louis Leakey discovered, in the 1930s, these simple pebble stone tools in a sediment layer sandwiched between volcanic ash layers in Olduvai Gorge. Olduvai Gorge is located in the East African Rift Valley. The rift valley formed from the continental plate pulling apart and exposing ancient sedimentary layers dating to the development of our early ancestors. Potassium-Argon (K-Ar) dating of the ash layers provided an estimate of when these tools were made.

Louis Leakey defined the process of making these pebble tools and called it Oldowan technology after Olduvai Gorge. Oldowan technology is the oldest known cultural tradition preserved in earth's heritage record.

First Steps: World Heritage Sites

Ngorongoro Conservation Area, located in the United Republic of Tanzania, was inscribed onto the world heritage list in 1979. This 809,440 ha site encompasses Ngorongoro Crater, the world's largest caldera, and Olduvai Gorge. The famous Lake Laetoli footprints, discovered by Mary Leakey, is also located in the park. The Lake Laetoli footprints provide evidence of early bipedalism approximately 3.6 million years ago.

Ngorongoro is also home to a diverse population of ungulates and the highest density of mammalian predators in Africa such as the lion. The Maasai, a pastoralist people, also inhabit a portion of the park for the grassland.


Having a New Baby

My wife and I went in for an induction on November 4th, just four days earlier than the November 8th due date. Things had progressed well and active labor began first thing in the morning.

We were ready as we could be to have a baby. We had attended all of the parenting and birthing classes, and had the baby’s room all set, car seats ready, etc. We were both mentally prepared, but being prepared and going through labor and having a baby are two different things.

I was calm cool and collected as labor progressed. This was our first baby after all, so I was prepared for a long day. Then things began to speed up a bit. My wife is now at a 5, a hour later a 7. The epidural that was suppose to relieve pain did not work and only one side of her body was free from pain. The contractions became more frequent and the pain more intense. All I could do from a husbands perspective was to hold on to my wife’s hand tightly and talk her through each contraction.

Another 30 minutes goes by and we are already at a 10. Now this is getting serious. My long day of preparing to have a baby has come to an end, and the time is now. My wife started to push with each contraction now trying to get the baby to drop the rest of the way down. Our doctor had not made it into the room yet, but the nurse was trying to get the baby into position. The nurse now can feel an ear and the baby’s head needs to straighten out. While the nurse is getting all of the gear ready for the doctor to deliver the baby she encourages my wife to keep on pushing through each contraction. A slight fear of mine at this point is that a push will now expel the baby onto the floor and nobody is there to catch him. I secretly hope at this point my wife is not doing that great of a job at pushing.

Then the doctor arrives. To speed up the delivery of the baby he is going to use a vacuum pump. I guess my worry of pushing the baby out onto the floor is unfounded. The vacuum goes in, and now we are really pushing. A head appears. Then another push, a baby is delivered and while being dried off is placed onto my wife’s chest. We now have a baby. The look of bewilderment on my wife’s face as she looked at the baby and then to me must have been a mirror of my own expression.

It did not seem real, and at the same time it was one of the most real experiences of my life.

The only other experience that I had that came close to this was the feeling of spiritual connection with the world while hiking a mountain range in Montana. I had climbed above timber line and was amongst the rocks of a weathered scree field. Being part rock hound I began to examine a few of the more interesting rocks and notice sea shell fossils within them. The rock on top of this mountain was laid down by an ancient sea that buried and preserved the fossils that had then been uplifted by the collision of continental plates, a process taking millions of years. It felt both unreal and the most real connection I had ever had with the universe.

Productivity and National Novel Writing Month Competition?

Start your typewriters, computers, iPads, pencils, etc. November is the national novel writing month, or NoNaWritMo for short. Each November would be writers attempt to write that novel within a month. The goal is to reach 50,000 words in 30 days. That is 1667 words per day.

The NoNaWritMo competition started in 1999 and only 21 writers competed. The competition has grown exponentially and last years competition welcomed 341,375 participants of which 38,438 finished the 50,000 word goal a 11% rate of success. Published novels derived from the competition include Sara Gruen’s Water for Elephants and Marissa Meyer’s Cinder.

The goal of NoNaWritMo is to just write. Lots of people have an idea for a novel, and if they just had that time to write they would produce a bestseller. This is also the problem with writing that thesis, dissertation, and journal article.

I encounter the dreaded writers block on occasion. It is also difficult to get back in the swing of writing after finishing field season. Writing is a different type of mental activity. This past field season I attempted to just write something everyday. I started an archaeology type novel, after all, I have plenty of good stories and people to base characters on. I also started writing this blog. It is difficult to do research based writing in the field, to much mental activity after a long day. So by writing, writing just anything, I was attempting to keep the mental activity of writing up in the hopes that it would improve and make me more productive in my research based writing.

The extracurricular writing has helped. Although it has been more difficult to keep up with fun writing while out of the field since there are so many manuscripts to write and finally finish. However, I think the idea of writing, and writing just anything, everyday, can help students with writing their term papers, and thesis or dissertations.

In honor of NoNaWritMo I started a writing challenge with students and colleagues. A few of my students and colleagues are a little past due in getting that chapter finished for a thesis, finishing a manuscript, and also finally writing that novel. For our competition, to keep it on a level playing field, I proposed that research base writing would count double. So to reach the 50,000 word goal for November a participant would have to write 25,000 words. Writing can consist of a mix of research and non research writing. The important thing is to just write everyday. My hope is that the participants will produce a few drafts of chapters, manuscripts, and a novel.

My wife and I are expecting our first baby the beginning of this month. Therefore it is easy to challenge my students, if I can write with a newborn in my arm than so can you! We will see how that works out! After writing this blog I can now add 601 words to my count for the day. Take that fellow NoNaWritMo competitors.

Keeping track of NoNaWritMo

To keep track of the competition’s progress, and to also provide extra motivation, I set up an iWorks Numbers spreadsheet within iCloud. Each participant has their on sheet to enter their word count for the day. I set formulas to add up the totals and I have an interacting bar chart to compare each participants progress. With the new iWorks you can collaborate together on the same document. Each participant is allowed to enter their own word count everyday. It is working great so far.

iPhone (ios) for use in archaeology: essential apps

Carrying a portable computer and camera in one small package is great for archaeological field work. I have relied upon my iPhone in the field for the past four seasons. Currently, I have the iPhone 5, which had a significant camera upgrade from the iPhone 4. It now has a great macro mode, and I use it to take great shots of artifacts in the lab. Here is an updated list of apps I use in the field.


Topo maps is a relatively inexpensive app for downloading and viewing USGS 7.5 minute quadrangle maps of the United States. The app provides a grid view of the topo quadrangles, and to download a map you simply click on one of the maps (for free). The real value of the app is that it uses your iPhones GPS capabilities to show your location on the topo map. You can set a waypoint, but what I mainly use it for is viewing my location on the topo map so that I can orient myself to the paper topo map that I carry with me in the field. It also uses the iPhones compass function and will also orient the map based on the direction you are facing.


GIS Roam

This is the best GIS app I have found. ESRI has some basic apps out for use on the iPhone, but I found these apps to be limited and too reliant upon their public cloud system. With GIS Roam you can view shapefiles and raster files of your project area right on your iPhone. You can also edit and add new data. Transferring files to the iPhone is a bit cumbersome, you have to do it through iTunes, but I found that it works rather well. It is a 10 dollar data connect fee to transfer the files. The major limitation of this app is that you are limited to the GPS accuracy of the iPhone. So you would not want to rely upon your iPhone for accuracy within a few meters, but within 20 meters the iPhone is accurate enough for site scale plotting and management.


Bento is a database. I use it for storing site information, c14 ages, etc., any information that I might need to have with me in the field. Unfortunately, they have discontinued Bento and is no longer supported. There is a rumor going around that Apple will include a Bento like product in their next iWorks update, which is already a few years over due.


If you have a phone signal than you can use soilweb. It uses your iPhone’s GPS location to determine the soil series that you are standing upon. Now there is no need to carry the County NRCS soils series book with you into the field if you have a connection.



As mentioned earlier, the iPhone camera just keeps getting better and better. Sure you can take better photos with an SLR, but who wants to carry around that bulky thing?

Check out this National Geographic blog on the use of the iPhone 5s camera.

One of Manitou Springs’, CO water fountains



I use the iPhones basic notes app, for record keeping, however, there is a multitude of other writing apps, you can PDF forms as well.