Thursday, March 16, 2017

Camera research

Here's the latest installment of camera research.  A low def video camera with a large topside drove this round of research which was done by Kate Ostrikis in our Gloucester office.  We want high def, something that can be mounted on a pyramid or towed, video or still, waterproof.  Ideally it will be GPS enabled -- we're tired of merging GPS data into exif data.  Small size and good on battery since it could be used on small boats with low power availability.  


Comparison table:
Company
Product
Cost
Camera res
Screen size
Cable length
Recording
Ocean Systems
Splash Cam Deep Blue
 $   1,600
Hi Def

50'

JW Fisher
VRM-1 TOV-2
 $   5,000

5"


Aqua-Vu
HD700i
 $      700
720p hi def
7"
100'

Doyle Marine
Snake Mate
 $      900

7"
90'

GoPro
Hero5 Black
 $      550
4k video/12mp photo


GPS

Each has its drawbacks in terms of cost or ease of use or image quality or durability or GPS connections.
We're leaning toward using the gopro, but we need to figure out how to get a surface view and determine what happens to the GPS signal.  Maybe if we can get the gopro on a cable that plugs into or wifis to a phone for recording?

Kate's presentation is here (pdf 2.6mb).

Tuesday, January 10, 2017

Productivity tools

Happy New Year!
My routine in the first couple of week of the New Year is to archive my emails.  Unfortunately, I have 2600 emails in my Inbox, and my first step is to clean that out.  Unfortunately, we're having ANOTHER network slowdown, and I can barely access my emails.

So I'm focusing on a little challenge that has bugged me for many years: notes.  I take a prodigious amount of notes.  I do this for a variety of reasons: to keep busy, to help me remember things, to do lists, jotting down random thoughts, to record meetings, to record my daily activities, to record when someone calls and tells me something.  I also have a couple of files with "notes," including interesting articles from the web or that someone sent me or that I clipped out of a magazine.  How do I improve my access and use of that information?

Now that I've been in my current job for a decade, what am I supposed to do with notebooks and files full of notes?  Some issues come up every 5-7 years.  What's an efficient way to keep track of who I spoke to and what happened?  I think I need a searchable (digital) notebook.  Yes, I'm ready to move from my handwritten notes to a digital platform.  Some of my slowness to adopt digital notetaking is that it has been considered quite offensive to have electronics out and on at meetings (a no-no just a few years ago).  But it's becoming more acceptable.

There are two dueling products: Evernote and OneNote.  I installed Evernote on my phone a few years ago.  I have about 50 notes, mostly from jotting ideas down from scientific meetings.  Those notes are patiently waiting for me to do something with them.  OneNote is Microsoft's version.  I don't remember using OneNote, though it is possible I tried it out.

I headed to the Google-sphere to find 380,000 returns for my search Evernote vs OneNote.  Here's my assessment:
1. Since I'm essentially starting from scratch, importing/exporting functionality is not a requirement.  Evernote trumps OneNote here, but it doesn't matter for me.
2. Cost is a consideration.  I have a subscription to Office 365 at home and I have all Windows/Microsoft products at work.  OneNote is free right now, and even if it costs later on, it might be bundled with my Office 365 subscription.
3. I want robust webclipping.  Sounds like EndNote wins here, but OneNote can do it too.
4. Note tagging and searching.  Both can do this.
5. I want to be able to share notebooks with other people.  Both can do this.
6. Interface with Outlook maybe for project management?  OneNote only.
7. Aesthetics.  Sounds like this is a toss up based on individual preference.  I like that you can hand-write notes into OneNote, I like that you can have nested notes and a less linear note-taking process in OneNote.

So, OneNote it is.  Wish me luck.

Wednesday, March 30, 2016

ScanPot Day 1

Some of the folks I work with have been busy doing field work all winter, but I've been in the office for much of it.  So it was great to get back out on the water after a few months.  And we couldn't have picked a nicer day: sunny, 50 degrees, with <1 foot seas in Buzzards Bay.  A rare treat.


We were out on our first field day for a NFWF-funded project we call "ScanPot."  We're quantifying the efficiency of using sidescan sonar to identify lobster pots on the seafloor in flat-softer bottom (low backscatter) and rough-harder bottom (high backscatter).  We're partnering with a commercial lobsterman on the project and using his boat.

We're using a Klein3000 200/355 kHz sidescan we borrowed from the wonderful folks at MIT Seagrant.  We collect data onto a laptop running SonarPro v. 12.  We collected both the high and low resolution imagery, but only looked at the high resolution imagery on the survey.

Here's a shot of the Klein. We used a hand cable since we were in shallow water and only doing a few hours of survey work.
Here's our tow set up -l bracket aluminum on cylindrical posts.
Here's a stack of 4 lobster pots
Here's a lobster pot as imaged by the sidescan (it's the square white box near the bottom of the red circle)


We were hoping to image the pots at a 75 meter range, but beyond 50 meters the resolution was too compromised.  So we'll have to do our full surveying at a 50 meter range.

Friday, December 4, 2015

Sandwich eelgrass results

The area we studied in Sandwich does not have, as far as I know, previous maps or estimates of eelgrass coverage.  I don't know how old this meadow might be.  The closest previously mapped eelgrass is from aerial photographic analysis Mass DEP does.  They mapped a bed to the northwest.  There was also work done by Woods Hole Group, a consultant for a town beach nourishment project.  They mapped a small bed near the spit in the middle of the picture and some patches off a groin in the southeast corner of the picture below.  The US EPA identified this bed as a good location for a blue carbon study.  Eric Nelson of EPA snorkeled in the area to check it out and gave us two points indicating the approximate shoreward edge of the bed.  Those are the two bigger dots just south and east of the spit in the middle of the picture below.  The area is about 0.5 miles away from the meadow DEP mapped.
Our goal was to map the extent of the bed near the EPA points.

We mapped a total of 21.1 acres and interpolated 8.3 acres based on the aerial photo we had.  Total acreage = 29.4 acres.  This is less accurate than what we did in Cohasset since there is no previous information and there is a significant eelgrass-algae mix with many boulders.  The seaward side has a lot of Fucus algae which has large air bladders and looks the same as eelgrass in the sidescan.  We weren't sure if we made it to the southeastern extent of the bed with the sidescan, so we examined the 2013 USGS aerial photos.  Vegetation is really obvious in the aerials, but differentiating eelgrass and any type of algae in the aerials is impossible without groundtruthing.  Therefore, interpreting the aerial photo without groundtruthing is, well, a crapshoot.  We did due diligence and studied bathymetry to define a shoreward and seaward edge, but this is a tough area.  Take areas without groundtruthing with a grain of salt.

Here are some photos to give an idea of what it looks like on the bottom:

Patchy eelgrass
Dense eelgrass
Red algae found in deeper part of study area
Cobble bottom
The last image is from the spit that defined the northwestern edge of our study area.  It was a pretty cool spot.  As it deepened, more and more algae encrusted on the cobbles.


Wednesday, December 2, 2015

Cohasset eelgrass results

Here is the DEP map.  It was done by digitizing aerial photos flown in 2012 which were groundtruthed with underwater video.  Target scale 1:10,000.
84 acres of eelgrass (large meadow in the middle and small meadow to the southwest).

Here is our map. It was done by digitizing acoustic imagery collected in 2015 which we groundtruthed with underwater photos.  We used aerial photography to extend our survey to the north where we didn't have acoustic coverage.  Target scale 1:1,000. 
82.7 acres of eelgrass.  Since our survey didn't cover the northern part of this meadow, we double checked 2013 aerial photos to see that it was still there and then used part of the DEP 2012 delineation to add it on to our acoustic delineation.

Here are some photos to give an idea of what it looks like on the bottom:

Patchy eelgrass

Dense eelgrass

Granule-pebble bottom

Thursday, August 20, 2015

How is eelgrass mapped?


  • First we look at aerial photos (Google Maps/Earth, Bing, those flown for the state).
  • In some places, we run acoustics to look at deeper waters or cover time periods that we don't have aerial photos for. 
  • Then we get in the water with cameras to confirm (groundtruth) that we're identifying eelgrass and not algae.
  • These steps are illustrated below.

Is the dark shading in the aerial photo eelgrass in the center of Cohasset Harbor?



Step 1: Go out in a boat with sidescan and underwater camera.

The water is shallow where eelgrass grows and instruments are fairly sensitive to waves.  So use a small boat or jetski on a calm day.  Here we're using a Humminbird 698SI (200 kHz) sidescan. The transducer is mounted on a pole attached to the boat with a trolling motor bracket.
















This is the Humminbird 698SI sidescan unit. The  photo to the right shows the whole unit as it comes out of the box.  The next photo down shows the transducer on the pole and the processing (and GPS/nav) unit is the smaller computer screen mounted to the table in front of the boat driver.


This is the GoPro Hero2 camera on a line with a shackle for weight.  We set it up to automatically snap images every 2 seconds.  Before each station, we write the station number on a white board, take an image of the board, then toss the camera overboard and lower to seafloor then bring it up slowly. We record the lat/lon of the station on paper and using the waypoint feature on the Humminbird sidescan unit.  This works to about 20 feet.  Then more weight is needed.  Deeper than about 30 feet might need light too.






Step 2: Drive survey lines with the sidescan and drop camera overboard at stations throughout the survey area.  We can cover 150-200 acres in 4 hours.

The survey lines are in yellow.  We space the lines approximately 200 feet apart to achieve about 150% coverage of the sidescan.  We do that by eye using the chart on the Humminbird sidescan unit.  The drop camera stations are the white dots.  These were distributed on the fly in the field to achieve 6-10 stations per planned survey line.  In this survey we added survey lines to the northern section late in the day, on the fly.  We didn’t bring the deeper drop camera, so that area wasn’t included in the photo groundtruthing.









 Step 3: Process sidescan data in SonarTRX or CARIS HIPS-SIPS software, create mosaic.

Here is the mosaic, I don’t know why there are two blank sections –one in the middle toward the top and one in the northwest corner.  The data is there and when I zoom in and out it blinks on and off.
Step 4: Examine groundtruth photos and compare to sidescan and aerial photos.  Identify patterns in aerial photos and sidescan that are consistent with eelgrass (or other habitats like gravel).

The image below has the grass stations coded in green, sand in yellow, and sand-gravel in orange. The green outline was drawn by DEP on aerial photos from 2006.  All data files are available for download as kml/kmz files for opening in Google Earth.

Sidescan sonar mosaic (200 mb)
Lat/lon of photo stations with notes (2.2 kb)
Photos geotagged to the correct location (several per station) (514 kb)
DEP eelgrass polygons, statewide, 2006-2007 (107 kb)  metadata

Thursday, March 5, 2015

Ice

This has been the iciest winter we've seen on the South Coast of Massachusetts in a long time. I haven't been able to quantify this yet -- a NYTimes article said the Coast Guard severe ice bulletins were issued this year "for the first time in more than a decade."  The eastern shore of Buzzards Bay has been completely iced in.  This image was captured on February 25 by the Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA’s Aqua satellite (thank you to Greg Bettencourt, MADMF). We're wondering how this will impact eelgrass beds.


Quite a few folks have been taking videos.  Here are some links:
Brian Switzer, Woods Hole
My drone shots of NB Harbor
Peter Perriera drone shots of NB Harbor
Tom Dunlop, Vineyard Gazette story about Chappaquiddick Ferry battling ice
Tyler Fields photographs of Sea Ice (Buzzards Bay ice just south of Mass Maritime/Wareham)
The Buzzards Bay Coalition has some photos on its Facebook page