Aerial Footage of the Casperkill Creek

In support of the Environmental Studies focus on the Casparkill Watershed, we recorded a flight above the Casparkill Creek, from its source to its mouth in the Hudson River, a distance of about 10 miles. The course was covered by 6 separate flights, as shown below. We also flew a course over the Casparkill’s biggest tributary, the Fonteyn Kill.

Click on a red or green line segment to see a drone video of the corresponding section of the Casperkill Creek, flown north to south. (Click on the yellow line segment to see a drone video of the Fonteyn Kill.)

Casperkill section 1 Casperkill section 2 Casperkill section 3 Casperkill section 4 Casperkill section 5 Casperkill section 6 Fonteyn Kill
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3D Modeling a Thirteenth-Century Dove

The Eucharistic Dove, one of only a few left in existence, is found behind glass in the Frances Lehman Loeb Art Center, making it a difficult piece to investigate closely. Academic Computing Services students, Dylan MacDonald, Zechariah Lee, and Sufyan Abbasi, under the guidance of Amy Laughlin and Professor Andrew Tallon, were put to the task of producing a 3D model that preserves the texture of the Dove for closer inspection.

The model was produced using a technique called photogrammetry, which is the process of stitching together a 3D model based on a sequence of images. The technique combines novel application of computer vision with classical projection mapping that produces stunning results. The software used was Agisoft Photoscan, an industry standard photogrammetry software that allows users to stitch together an orbit of still photos into a 3D model, like so:

As a proof of concept, we began with trying to model a candlestick, donated to us by Professor Tallon, which had similar properties as the Eucharistic Dove in size and luster. Due to the reflective surface of the candlestick, we found that using a green screen was out of the question since the shades of green were reflecting off of the object and projected onto the model. After trying different techniques, we discovered that shooting with a white background in the Loeb photo studio proved to be the best way to eliminate any unwanted reflections in our model.

Once we took photos of all angles of the Dove (over 200 pictures total), we used Adobe Photoshop to mask out the backgrounds and loaded the images into Photoscan. There, a second masking process was done to tell the software the bounds of the object to be generated.

Once Photoscan was finished processing the files, we were left with a .obj file that formed the 3D model of the Dove, a .tif file that dictated the texture, (shown below) and a .mta file that maps the texture to the 3D model.

Next, we loaded the model into Blender, an open source 3D modeling software. Here, we made edits to the generated 3D model, such as filling in the bottom area of the Dove where photos were not available.

Finally, the model was ready to be published on SketchFab, an online publishing platform for 3D models, which allows users to manipulate the model in 3D space and view the model in virtual reality. 

From start to end, the process took about a semester for the initial research and testing, and half a semester for photographing the Dove and making edits to the model. Dylan and Zech worked on masking the Dove in Photoshop and Photoscan and generating the 3D model in Photoscan, and Sufyan worked with Blender to make the edits to the model.

Eucharistic Dove by Vassar College on Sketchfab

We hope that you enjoy the Dove as much as we enjoyed producing the model. If you have a project idea involving 3D modeling and need some help,  please contact Amy Laughlin in Academic Computing Services in CIS.

 

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Working with Dual USB headsets for input and output (Mac OSX)

I wish I had known this years ago when I ran the Media Cloisters! It turns out you can connect multiple USB inputs and outputs on Macs. This is great if you want to team-edit video or record two people at once. You’ll need two USB headsets for this to work.

Getting Two USB Headsets to Work:

This is built-in functionality for Mac OSX. Plug in both headphones, then open Audio Midi setup from /Applications/Utilities.

searching for Midi

Find the Audio Midi Setup by searching “midi” in the spotlight

Click the plus in the lower left corner and choose “Create Multi-Output Device.”

Make two usb headsets play together!

Make two usb headsets play together!

Check the checkboxes beside both headphones.

Uncheck the built-in output.

Uncheck the built-in output.

If you want to rename your new virtual device, you can double click the new entry in the list on the left and give it a name like “Both headphones.”

In System Preferences, you can now set the output to go to your new Multi-Output Device.

Setting up Two USB Headphones Mics

A similar arrangement will work to create two USB inputs. Create an aggregate device for the USB headsets.

Make two mics record on separate channels!

Make two mics record on separate channels!

Check the appropriate boxes.

To record in Audacity onto two separate channels, choose “(Stereo) Recording Channels” as your input:

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High-Performance Computing at Vassar

What is HPC?
Have you ever tried to run some code or perform some data analysis on your personal computer, and it ended up taking several hours or even days to finish? Frequently, we interact with data sets or projects that are simply too taxing for a single computer (even a very powerful one) to complete. This happens very frequently in a variety of fields across disciplines. High-Performance Computing (or HPC as it is known) is a field in technology concerned with providing advanced computing resources to researchers in order to speed up their data processing or modeling projects. Typically, these computing resources take the form of what is known as a computing “cluster”, which is really just a fancy name for a large number of computers that are all connected together and process data in unison.

Who can benefit from HPC?
-Students
-Faculty
-Non-Faculty Researchers
-Administrative Staff

HPC at Vassar (on-campus)
Here at Vassar, we have a computing cluster named “Junior” that was built in 2010. Junior has been used by many faculty and students over the years to run countless analyses and simulations for coursework and research in the Sciences and Humanities. The big advantage of using a system like Junior is that it has what’s called a job scheduler program installed. In Junior’s case, the scheduler program is called SLURM. Slurm enables users to submit the code or analysis that they want to run, and then the system will automatically load the required packages and software to complete the job, and output it into a user-specified format. This means that a user can submit a job that might take the system several days to finish, and then go and work on something else while awaiting the results, confident that work is being performed by the automated processes on the computer the whole time.

HPC at Vassar (off-campus/remote)
Here at Vassar, we have access to off-campus HPC resources as well:

  1. Through an agreement with the NSF-supported XSEDE system (The Extreme Science and Engineering Discovery Environment), Vassar researchers are able to apply for computing allocations on a variety of cluster environments that provide abundant libraries of packages, software, compilers, and user interfaces. The best part – It’s completely 100% free for Vassar! Your tax dollars are hard at work creating and maintaining this extensive network of HPC resources for use by all researchers.
  2. Vassar has an agreement with Amazon Web Services (or AWS) to provide for Virtual computing environments hosted in Amazon’s many data centers around the country. While we do pay by the hour for resources through AWS, the scalability and versatility afforded to us through this system are incredibly useful. Computing environments can be built and made accessible to the end-user very quickly and easily by administrators on campus. 
  3. We are exploring additional resources such as Google Cloud, Microsoft Azure, products from IBM, and partnerships with other colleges and universities with more robust computing infrastructure. We are also looking into avenues for the upgrade and/or replacement of Junior.

HPC Projects & Initiatives at Vassar
Many faculty at Vassar have been involved in using HPC in the course of their research and teaching. Courses and projects in BiologyChemistryCognitive Science, Computer Science, Mathematics, and Physics & Astronomy all make use of Junior and other HPC resources for course work and projects.

Just a few of the specific HPC projects underway or already completed include:

  • Chemistry Molecular research by Franco Caruso and Miriam Rossi which utilized Materials Studio in a cluster environment and has resulted in the publication of two successful journal submissions with a third in progress.
  • Biology research on viruses and bacteria using QIIME and other genetic analysis tools on both the local cluster and in AWS by David Esteban.
  • Deep learning research and course work using GPU-enhanced computational systems in the cloud by Joshua de Leeuw
  • Computational Quantum Chemistry research by Leah I. Bendavid on XSEDE.

Find out More!
If you’re interested in learning more about HPC, or getting in touch with other people at Vassar who are using HPC resources, please email Chris Gahn, the ACS Consultant for the Sciences.

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Making Posters and Fliers at Vassar Spring 2018

by Baynard Bailey

Making Posters at Vassar Presentation (link requires VC gmail login)

illustrator environment pencil imac

You can use any software you like to create posters or fliers. The most common applications used are Adobe Illustrator and MS Powerpoint. The goal is to create a .pdf that can be shared with the printer. Adobe Illustrator is available in the library electronic classroom and the 24 hour space of the library (AKA DMZ).

Here are some ACS created tutorials for creating academic posters with Adobe Illustrator:

  1. Graphic Design Tutorial (12 minutes)
  2. Illustrator Tutorial (25 minutes)
  3. Exporting Tutorial (4 minutes)

Print jobs smaller 11″x17″ or smaller go to the Copy Center, and can be picked up at the post office counter in college center.

Print jobs larger than 11″x17″ go to Media Resources, which is in the basement of the College Center. Further details and to submit a print job please visit https://servicedesk.vassar.edu/catalog_items/307242-poster-request

If you would like to arrange training for faculty or classes, please email acs@vassar.edu

If you are hosting a poster event or poster session, please contact campus activities to reserve their foam boards and/or easels: campusactivities@vassar.edu

I’ve helped many classes create posters for academic purposes. Here are various poster sets created by students I’ve trained (some links require VC login):

 For additional inspiration, here are some useful links:

For a list of upcoming public workshops keep an eye the events listed in our Moodle site or visit http://pages.vassar.edu/dissco/events/

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Digital Storytelling Work at Vassar

I love teaching digital storytelling workshops to classes at Vassar. The students seem to enjoy it and the faculty are pretty happy with the results. Departments include French, Japanese, Psychology, Education and Anthropology. I was reviewing students’ examples in preparation for the upcoming LACOL panel and I was blown away by all the amazing and diverse work done by the students.

Here’s a quick summary of the kinds of digital storytelling projects that I have helped classes with over the years:

French – Digital Storybooks for FREN 206 with Mark Andrews, Tom Parker and Susan Hiner.

Japanese – Digital Storybooks for 200- and 300-level courses with Peipei Qiu and Hiromi Dollase.

Psychology – End-of-term research presentations with Mark Cleaveland’s students

Education – Semester-long collaborations with Adolescent Literacy students and their middle school partners (workshops every week)

Anthropology – A variety of uses, including digital ethnographies and engaged research

We use Final Cut Pro X at Vassar for these classes. FCP X is a powerful and easy-to-use editor. It is available in the Library’s Electronic Classroom and Digital Media Zone. Students with Macs can get a 30-day free trial license.

The goals vary by classes. Sometimes the professor wants a rich medium to tell a story. In Mark’s class, he wanted polished presentations that acted as crucibles to bring together all their research. For 

Lessons Learned:

  • Provide lots of support
  • Don’t assume the students know how to do things
  • Sound is more important than video
  • Things improve with iteration
  • Set clear expectations 
  • More faculty / instructional technologist collaboration is better
  • It is helpful if the faculty member can model or provide examples
  • Allow time for things to go wrong
  • Try to keep track of where you put things
  • Measure success by faculty “happiness” level

This is an example of a digital ethnography.

4m20s

This was produced for community engaged research:

t=33s

This is an example from a final group project for a Psychology class.

t=27s

French 206

t=1:25

Japanese stories (behind Moodle login Moodle

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Main Campus Orthomosaic

The VSA organization Vassar Urban Enrichment asked us to create an aerial image of the entire main campus (i.e. not including the Vassar Farm, Townhouses, golf course, etc.) After a few tries with the ACS drone, we determined that the wifi signal it uses to communicate with its controller was insufficient for handling the distance we needed and the occasional obstacles in between. Drone pilot Chad Fust then used his own drone, which uses an RF signal, rather than wifi, and we were able to complete the project in two sections. The result is a merge (“orthomosaic”) of about 900 individual photos.

 

(Link to website)

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Puzzle Pieces

We recently used the drone for a fun project: getting an aerial photo of a large sculpture project. Sculpture student Antoine Robinson had created an interactive art project, comprised of 30 plywood boxes painted with a design. Passersby will be able to move the boxes around to “solve the puzzle,” or create their own arrangement.

Puzzle Sculpture

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Beaver Pond

Prof. Lynn Christenson of the Environmental Studies program and Keri VanCamp of the Collins Field Station are interested in using the drone to acquire various types of imaging of the Vassar Farm and Ecological Preserve. One area of focus is the beaver pond, which they’d like to view from above at different times of the year and over the years. After several unsuccessful attempts, we were able to collect a series of 200 images and stitch them together into the following visualization.

 

(Link to website)

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