Day 30 - 7/24

Events presided over by: Dr. S. Stonedahl

Today was our last day of the summer research institute.  It's not super sad because we intend to continue in the fall, but it's still a little sad.  

Events: 
Final run through of the presentation.  
Moving stuff around 2nd Hayes.  (Between Dr. Stonedahl's two offices and the Hydrology lab)
And then we had the culminating Final Presentation!  

Getting ready

Obligatory photo with advisor

It was nerve wracking waiting to go FIRST.

The audience was a distinguished crowd full of faculty

and family...and they ALL waited expecting your brilliance.

We told them "we played with sand" and hoped to be done, but they still made us present.

We told them about our project...

And everyone was so dazzled by our greatness that none of the other groups wanted to present and everyone went home early...

Or at least they should have been.
In reality we got done, we got to stop stressing,

and we sat through many more presentations.  None of which were as good as our own. Dungeons and Dragons jokes may have been made...

Took some more obligatory photos

Successful completion of the Summer Research Institute!!!!
 Congrats!!
Great job presenting!
 Team Caleb was fabulous!!!!!

Day 29 - 7/23/15

We finished the presentation.
Practiced the presentation.
Revised the presentation.
Practiced the presentation.
Cleaned our Lewis research space.
Carted lots of stuff over to Hayes.
Practiced the presentation.
Were honored the hear the "Hyporheic Song"
Practiced the presentation.
Decided we were READY!!!!!

Day 28 - 7/22

Events presided over Dr Stonedahl
Guest appearances: loneliness

What we did.
    Began packing for the journey home
    staked a claim in Hayes hall
    disassembled the apparatus
    Compared EC data to concentration simulation

Day 27 - 7/21

Events presided over by Dr. S. Stonedahl
Guests: Dr. F. Prosise, engineering candidate #2 and Issac
What we did
     Further worked on PowerPoint
     Got particle tracking to work
     Time lapse process was begun
     Engineering lecture #2
    Created calibration solutions to be used in transferring Ec data into salt concentrations
   
   

Caleb working on calibration

Res-time Graph from particle tracking

Day 26 - 7/20

Events were partially presided over by Dr. S Stonedahl
Guest appearances: Dr. J Prosise and ENGR candidate 1 (I'm not good with names)
What we did
     As the lab was now a slightly more bearable temperature note books were removed from cooling
         chambers
     The constant head permeameter was dissembled brutally to strike fear into any other equipment that does not succumb to the will of the research overlords
     The falling head permeameter was lifted up upon a pedestal as it was determined to be the savior
           of the lab.
     The overlords took a hiatus to help determine the future of the engineering department.
     Another falling head permeameter was created so that they could fight in tandem the evil K-value
           problems
     The permeameters fought valiantly against the not understood K-value trend, but more errors
     appeared and overcame them.
     While the permeameter fought and pretty much let the whole realm down, the PowerPoint for
           Friday was executed by an overlord for being formatted weirdly.
     From its ashes rose a new PowerPoint, a superior PowerPoint, That is formatted correctly and will
           look totally kick butt and save the realm.

Day 5^2

Events presided over by Dr. S. Stonedahl, PhDictator.

Guest appearances by: Dr. F. Stonedahl, Malik Thalji, Issac Schwantes, Dr. Prosise, Prospective Student #187 from Montana, Prospective Student's Father

Guest blogger (thanks to slow "not-it" reflexes): Dr. F. Stonedahl

Today was "The Big One".  All of our lives have been spent training, building our skills, for this one day.  Previous apparatus runs were but pale shadows of the glorious success that will be hailed at the completion of this ultimate apparatus experiment.

(Essentially, it's the same setup as before, but hopefully all the bugs have been worked out, and this will result in glorious CLEAN data, magnificent photographic evidence, no abnormalities of flow, etc..)

So... the  time lapse camera was adjusted and started, the apparatus was started running with tap water for over an hour to get things settled down, then switched over to blue... Q measurements were taken at roughly ~15 minute intervals, and the EC meter was run continuously throughout, with periodic data downloads to prevent it from overrunning its (ridiculously small) storage limit.

Dr. S. Stonedahl and Caleb gaze in awe at the "Big One", as the clear water pushes the blue dye out.

Meanwhile, Caleb spent much time entering data in spreadsheets, 

In other news, as a result of unfavorable weather and faulty air conditioning, and the inside room temperature rose to approximately 451 degrees Fahrenheit, and all of the lab notebooks had to be soaked with blue dye water to prevent spontaneous combustion.  Ice buckets were also embraced, to help stave off heat exhaustion, heat stroke, and fiery death for as long as possible.  The time is 6:06, and the apparatus has not finished running yet, and only time will tell whether all of the brave researchers will survive to the completion of the experiment.  If you do not see a new blog post on this blog on Monday, assume the worst.  In that contingency, please send someone to Lewis Hall to collect all of our valuable data, so that our contribution to science will be recognized, and our sacrifice will not be in vain.

Day 24 - 7/16

What we did
    Finished cleaning apparatus
    Flowed water through apparatus
    Put dividers in the apparatus
    Took k values from both CH and FH permeameters

        Still slightly bothered by FH
    Began filling apparatus

    Finished filtering sand

    Washed sand

    Worked on presentation
    SRI lunch
    Increased brightness in time lapse video
    Made final adjustments to set up

   
What we will do
    Test 4 (final test)
    Permeameter work
   
 
   

Day Twenty-three - 7/15

Events presided over by: Dr. S. Stonedahl


What we did:
    Worked on cleaning out the Apparatus.
    Chose a new grid to use for next Apparatus test.
    Did more tests with falling head permeameter.
    Built a new method for having water flow into the Apparatus.
    Generated more timelapse videos for comparing computer model to Apparatus tests.

What we will do:
    Finish cleaning Apparatus.
    Fill Apparatus.
    Wire water distribution device.
    Make final checks.
    Adjust K-values for computer model, and compare videos.
    Test falling head permeameter.
    Test constant head permeameter.

Day Twenty-Two 7/14

Events presided over by: Dr. S. Stonedahl
Special guest appearances by: Issac Schwantes, Dr. Stratton, Dr. Ferm

What we did:
    Finished setting up for apparatus test.
    Began apparatus test.
    Wrote a program to take our photos and images and turn them into a time lapse video.
    Tested using a falling head test to calculate K-Values.
    Worked on Permeameter.
    Disposed of sand with the help of Issac Schwantes.
    Generated more head files to choose from for next apparatus test.
 

What we will do:
    Fix leaking divide
    Wash out the bottom of apparatus that still looks blue
    Run 0.125 grid, if we like it use it, if not we have a 0.75 we liked
    Mix up blue solution
    Fill TWO tap water garbage cans
    Monitor these solutions, to see if they change with time
    Begin filling apparatus for next test AFTER silicone has dried .
    Think about changing Q's issue and pump having to work harder at lower level, etc.
    Continue trying falling head tests
    Set up another constant head test (Intimidate the permeameter into working correctly, or something.)
    Work on presentation, make graphs, pick pictures, if we can't make graphs yet due to K value make a blue rectangle that says what you will put there.
    Modify matlab code so that it's ready to try to match conductivity data once we get K's
    So really we NEED to get consistent K values!!!!!!!!!!!!!!


 

Rough plan for timelapse movie creation

Setup:

Install these pre-requisite tools:
(These are command-line tools that I use on Linux, but there are Windows versions as well, and hopefully all the commands will work on it equally well.)

ImageMagick: http://www.imagemagick.org/script/binary-releases.php#windows (check if your computers are running a 64-bit or 32-bit OS... I bet it's 32-bit.)

FFMPEG: http://ffmpeg.zeranoe.com/builds/  (download the appropriate 32 or 64-bit "static" version)

General plan:

IMPORTANT:  1) Make sure you have a COMPLETE backup of your timelapse photos somewhere.  They are irreplaceable.  2) Also copy a couple images to a new testing folder, so you can try out running commands there without messing up your original files.  If you specify the file names in the wrong order with ImageMagick, you can accidentally overwrite your input files...

EDIT: Pre-processing step for the timelapse photos.  All of the photos will need cropped (and possibly rescaled) identically.  Imagemagick has a command that can do this for us.  (Note: usually "mogrify" changes the original files, but if you start with .JPG and give it the "-format png" option, it will turn each XYZ.JPG file into an XYZ.png file.

In a folder that contains only the timelapse photos that you want to crop, run something like this:

mogrify -format png -crop WxH+X+Y -resize <NEW_WIDTH>x *.JPG

where you replace W and H with the width/height of the cropped region, and X and Y with the pixel offsets.  The -resize <NEW_WIDTH> part is optional, and you may or may not want to do it, depending on how high-resolution of movie you'd like to output in the end... it will take the resulting crop and scale it down so that the image has the width you specify.
Be careful to leave the "x" and "+" signs in the command shown above.

Run NetLogo model to create a bunch of PNG files that match the timelapse photos... should create the same number of image frames here.  (EDIT: you may need to play around with the "pixels per patch" setting in NetLogo to get the exported images to be the same size as the cropped timelapse photos.)

In MatLab, write a script that takes the starting frame number from the timelapse images as an input, and goes through a loop that stacks (vertically? horizontally?) each model image with the paired real image, to make a new image called movie_frame_####.png.  To do this, have your MatLab script execute the external "montage" program (comes with ImageMagick, Google for examples) to stack two images together.

After you have all the movie_frame_####.png files, you can create a movie out of them using the FFMPEG software.  Something like this (all one line) should do the job:

ffmpeg -r 15 -i movie_frame_%04d.png -vcodec libx264 -crf 20 -pix_fmt yuv420p -r 30 sand_grid_movie.mp4

Change the first "15" above to control the frame rate (frames per second) for the frames going into the movie.  (Leave the later -r 30, which controls the frame rate for the output movie, and it seems like it's best to output at 30 FPS to be more compatible with different movie players...)

If the MP4 won't play in your windows movie player, for WMV output try:

ffmpeg -r 15 -i movie_frame_%04d.png -q:v 2 -r 30 sand_grid_movie.wmv

Lastly, I've done all of this stuff before, so if you run into problems, let me know, and I can help!

(Side note: both ImageMagick and FFMPEG have a myriad of other features, which you can find out more about on the web if you wish.)

Day Twenty-one - 7/13

Events Presided over by Dr. S Stonedahl
Guest appearances by Dr. F. Stonedahl and one of his research students, Nelly.

What we did
    Discussed improvements to testing procedure.
    Changed the basin method to a bucket and trash can method
    Emptied the Apparatus.
    Chose a grid for filling our Apparatus.
    Compiled a PowerPoint presentation.
    Went to lunch with Nelly and Dr. F Stonedahl

 

    Presented to Augustana students.

    Began filtering and cleaning sand and filling the apparatus.
   Dr. S Stonedahl stayed until 7:00 filling the apparatus.  This was her punishment for missing two days last week,

What we will do:
    Begin next Apparatus test.

Day Twenty - 7/10

Events NOT presided over by Dr. Stonedahl
Special guest appearances by: Connor Daws, Issac Schwantes, Kayla Gibson

What we did:
    Connor Daws assisted us in the lab today, and we probably would have died, were he not here.

Connor helping us siphon water

    Began our second apparatus test.
    Issac Schwantes came in and challenged us to find the next number in a confusing sequence.
    Ran tap water through the apparatus.
    Ran dyed water through the apparatus.

    Possibly solved the sequence.

Issac never showed up again to confirm if we were right.

   

Didn't even spill anything..

    Had a hiccup during running tap water second time.
    Took appropriate measurements.
   
What we will do next week:
    Prepare for setting up third apparatus test.
    Set up third apparatus test.
    Run third apparatus test.

Disclaimer: No animals were harmed in the making of this film.

Day Nineteen - 7/9

Events NOT presided over by Dr. S Stonedahl
Guest appearances by: Kayla Gibson

What we did:
    Filled apparatus for test two
    Began generating head files
    SRI lunch
    Finished filling apparatus

Ta-da

    Cleaned work station
    Made a check list for tomorrow

faces of focus

What we will do

    Test time lapse camera


    Replace batteries in time lapse camera
    Transfer tap water 1 into reservoir
    Set EC meter and Q value Equipment for testing
    Turn on pump
    Fill apparatus with tap water
    Turn sprinkler to a drizzle
    Take Q measurement every 15 minutes
    Run tap water for 2 hours

    Drain collection bin
    Transfer small amount of tap water to a bucket from reservoir, transfer pump also
    Drain remaining tap water from reservoir to original container
    Fill reservoir with blue water
    Collect data from EC meter and prepare for next liquid
    Set EC meter and Q value Equipment for testing
    Set time lapse camera for photos
    Transfer pump back turning to full volume
    Remove bucket once discharge is all blue
    Turn sprinkler to a drizzle
    Take Q measurement every 15 minutes
    Run blue water until all sand is blue
    Drain collection bin

    Transfer small amount of Blue water to a bucket from reservoir, transfer pump also
    Drain remaining Blue water from reservoir to original container
    Fill reservoir with tap water 2
    Collect data from EC meter and prepare for next liquid
    Set EC meter and Q value Equipment for testing
    Transfer pump back turning to full volume
    Remove bucket once discharge no longer blue
    Turn sprinkler to a drizzle
    Take Q measurement every 15 minutes
    Run tap water until all sand is no longer blue
    Collect data from EC meter
    Collect photos from time lapse
    Transfer left over tap water to container
    Drain collection bin

Day Eighteen - 7/8

Safety first.

Events presided over by Dr. S. Stonedahl
Special guest appearances by: Dr. F. Stonedahl, Dr. Ferm, Dr. Barakati, and Dr. Panah

Dr. Panah and Dr. Barakati visit.

What we did:
    Fixed the water distribution device.
    Removed sediments from the apparatus.

Caleb removing sediments from the apparatus.

    Chose a new head file to be used for the next apparatus set up.
    Generated more head files for modelling.
    Finished preparing the apparatus to be filled again.

Caleb warding off vampires.

Caleb watching as Caleb draws lines.

    Prepared a dye and salt solution to be ran through the apparatus.
    Cleaned more sand, and began filling the apparatus.

Caleb filling the apparatus.

What we will do:
    Fill the apparatus.
    Work on presentation.

Day Seventeen - 7/7

Events presided over by: Dr. S. Stonedahl
Special guest appearance by: Dr. F. Stonedahl

What we did:
    Measured Q values of the apparatus. (Volume of water coming out over time.)
    Graphed the measured Electrical Conductivities of previous apparatus tests.
    Discussed methods of improving the apparatus.

    Discussed how to improve lighting for the camera.
    Made a list of items to be purchased for executing these methods.
    Went to Menards and purchased the items we deemed necessary.

    Returned to the lab, and set up lighting for the camera.
    Discussed connectivity values for future apparatus set ups.

Day Sixteen - 7/6

IT WORKED