the digital grain size project: grain size estimates from images of sediment

The Digital Grain Size Project: grain size estimates from images of sediment

Daniel Buscombe

Grand Canyon Monitoring & Research Center

U.S. Geological Survey, Flagstaff, AZ.

[email protected]

Collaborators:

Martin Austin, Daniel Conley, Gerd Masselink, Alex Nimmo-Smith (UoP)

Dave Rubin, Jessie Lacy, Jon Warrick, Chris Sherwood, Guy Gelfenbaum, Bruce Jaffe, Curt Storlazzi, Paul Grams, Scott Wright, Ted Melis (USGS)

Ian Miller (Wash. SeaGrant)

Jon Williams (ABPmer)

Dayton Dove (BGS)

Joe Wheaton (USU)

Technical Support: Hank Chezar (USGS) Gerry Hatcher (USGS) Robert Wyland (USGS) Bob Tusso (USGS)

Thanks

Outline

• Why take pictures of sediment?

• How do you estimate grain size from those images?

• How do you take suitable pictures?

• Software (the Digital Grain Size Project)

• The future

Why take pictures of sediment?

Huge increase in temporal resolution and/or spatial coverage No physical samples required You can’t always visit your field site

Temporal Resolution

How do you estimate grain size

from those images?

• Deterministic versus statistical

• Evolution of methods

• Current method

No 'background' intensity against which to threshold Subjective choice of filter sizes and operation sequences Difficult to design a 'universal‘ algorithm which works equally well Non-diffuse reflectance, particle overlap, marks/scratches,etc

Deterministic

Statistical – Rubin (2004)

Rubin (2004) J. Sed. Res

Characterize features without directly measuring them Circumnavigate problem of detecting grains

But reliant on calibration Errors introduced by calibration Buscombe (2008), Sedimentary Geology

Buscombe and Masselink (2009), Sedimentology

Statistical

Could also use spectra, fractals and variograms

Grain size found as 2pi times typical grain-scale wavenumber

1. Requires neither calibration nor advanced image processing algorithms 2. Direct statistical estimate, grid-by-number style, of mean of all intermediate axes

Buscombe, Rubin & Warrick (2010) Journal of Geophysical Research

Rk 2

Statistical – Buscombe et al (2010)

•Generic & transferable expressions for particle size mean and standard deviation •No calibration or tunable parameters •Supported using a simple theoretical model

Buscombe & Rubin (2012) Journal of Geophysical Research

Statistical – Buscombe and Rubin (2012)

Global wavelet power spectrum

Short sequences

Non-stationarity, aperiodic

Non-Gaussian distributions

Statistical – Buscombe (2013)

Buscombe (2013) Sedimentology

Tested with a wide range of sediments

Skill Buscombe (2013) Sedimentology

How do you take suitable pictures?

• Exposed sediment

• Submerged sediment

• Biogenic?

• Mud?

Praa Sands, UK Dan Conley, Plymouth University

Dave Rubin, USGS

Praa Sands, UK

Buscombe, Conley, Nimmo-Smith, Rubin (in prep)

Colorado River in Grand Canyon

Dave Rubin, USGS

Paul Grams, USGS

Ted Melis, USGS

100 microns

300 microns

Slapton Sands, UK Gerd Masselink, Plymouth University

Buscombe, PhD thesis (2008)

Strait of Juan de Fuca

Elwha River Dungeness Spit Port Angeles

Jon Warrick, USGS

Ian Miller, UCSC

How do you take suitable pictures?

• Exposed sediment

• Submerged sediment

• Biogenic?

• Mud?

Praa Sands, UK A paddle constructed from a dive fin (1) is pushed back and forth by waves, turning a ratcheting speed-reducer in an oil-filled cylinder (2). The rotating output wheel of the speed-reducer (3) pulls down on the chain (4), which raises the video camera (5). When the chain on the wheel (3) passes its the lowest position, the ratchet allows the camera to fall to the bed …

… and a tilt sensor turns on a battery-powered video camera (5) and solid-state recorder (6) to collect a video

Buscombe et al (2014), Limnology & Oceanography Methods

Gra

in s

ize

(mm

)

Grain size (mm)

Inverse relationship between flow speed and bed grain size • Weak flow, preferential selection of fines, leaving coarse lag • Stronger flow, more equal mobilisation, lag appears finer

Bottom orbital velocity

Praa Sands, UK Buscombe, Conley, Nimmo-Smith, Rubin (in prep)

Decreasing vertical gradient with increasing shear (less selective resuspension with increasing shear)

Buscombe, Conley, Nimmo-Smith, Rubin (in prep)

Praa Sands, UK

Image from holographic camera

High energy

Low energy

The Santa Cruz Seafloor Observatory Dave Rubin, USGS

Jessie Lacy, USGS

Curt Storlazzi, USGS

Chris Sherwood, USGS

The Santa Cruz Seafloor Observatory

The Santa Cruz Seafloor Observatory

Buscombe et al (2014), Limnology & Oceanography Methods

Colorado River in Grand Canyon Rubin et al (2007), Sedimentary Geology

Bars: Eddies: Channel:

> 0.5 mm ~0.45 mm < 0.4mm

~500 m

Lower Marble Canyon, 2009-12

Above LCR confluence, 2009 – 2014:

UK Continental Shelf Dayton Dove, BGS

Images courtesy of British Geological Survey

The Digital Grain Size Project

Matlab tools Python tools Web/cloud application

Resolution

Matlab tools https://github.com/dbuscombe-usgs/DGS

Resolution

Image courtesy of British Geological Survey


Cropping




Select/cycle through images

Set resolution Save results

Calculate Select ROI

Filter

IMG1931

Mean = 7.7 pixels Median = 7.22 D75-D25 = 13.67 Skewness = 0.17


IMG2008



IMG2016



IMG1936



pip install pyDGS

git clone https://github.com/dbuscombe-usgs/pyDGS.git

python setup.py install

import DGS

density = 10 # process every 10 lines

res = 0.01 # mm/pixel

doplot = 0 # don't make plots

image_folder = '/home/sed_images'

DGS.dgs(image_folder,density,doplot,res)

image_file = '/home/sed_images/my_image.png'

mnsz, srt, sk, kurt, pd = DGS.dgs(image_file,density,doplot,res)

Python tools https://github.com/dbuscombe-usgs/pyDGS

Used by (at least) 47 institutions in 12 countries US Geological Survey, USA

Dept. of Ecology, State of Washington, USA

Northwest Hydraulic Consultants, Canada

Northern Arizona University, USA

Dartmouth College, USA

Johns Hopkins University, USA

University of California Santa Cruz, USA

Franklin and Marshall College, USA

University of California Los Angeles, USA

Utah State University, USA

Southwest Research Institute, Boulder, USA

Universidad EAFIT, Colombia

University of Washington, USA

Oregon State University, USA

University of California Davis, USA

University of Pennsylvania, USA

Brigham Young University, USA

University of Calgary, Canada

University of Texas at Austin, USA

Geoengineers Inc. USA

University of Delaware, USA

Western Washington University, USA

River Design Group Inc., USA

GMA Hydrology Inc. USA

Iowa State University, USA

U.S. Forest Service, USA

Queens University Belfast, UK

Freie Universitat Berlin, Germany

Instituto Superior Technico, Portugal

Plymouth University, UK

Institut de Physique du Globe du Paris, France

Deltares, the Netherlands

Imperial College London, UK

Durham University, UK

Technical University Delft, the Netherlands

University of Queensland, Australia

University of Sydney, Australia

University of Auckland, New Zealand

Tsinghua University, China

Zhejiang University, China

University of Liverpool, UK

Centre Européen de Recherche et d'Enseignement des Géosciences de l'Environnement, France

Heriot-Watt University, UK

Instituto de Ciencias Agrarias, Spain

Université de Caen Basse Normandie, France

British Geological Survey, UK

University of Leicester, UK

What’s next?

Digital Grain Size in the web browser?

Current USGS-CDI proposal in review

What’s next?

Images courtesy of Gary Barton,USGS Idaho Water Science Center Glen Canyon, AZ Dec 2014

mixed sand/gravel/veg

Areal coverage of sediment types?

Image courtesy Raleigh Martin, UCLA

Image courtesy Jon Warrick, USGS

Areal map of sediment sizes?

Size in pixels

Thanks for listening

• Python: https://pypi.python.org/pypi/pyDGS

pip install pyDGS

https://github.com/dbuscombe-usgs/pyDGS

python setup.py install

• Matlab: https://github.com/dbuscombe-usgs/DGS

• Web application … watch this space

Daniel Buscombe

Grand Canyon Monitoring & Research Center

U.S. Geological Survey, Flagstaff, AZ.

[email protected]

the digital grain size project: grain size estimates from images of sediment

Science

uk buscombe

calibration buscombe

statistical buscombe

rubin warrick

pictures of sediment

usgs praa sands

plymouth university

sedimentology statistical