1. Laboratory in Oceanography: Data and Methods
Image Processing/Analysis
MAR599, Spring 2009
Miles A. Sundermeyer

2. Image Processing/Analysis Image Processing Toolbox/Product Overview
Overview of Image Processing Toolbox
A collection of functions that extend the capability of MATLAB numeric computing for image processing operations, including:
Spatial image transformations
Morphological operations
Neighborhood and block operations
Linear filtering and filter design
Transforms
Image analysis and enhancement
Image registration
Deblurring
Region of interest operations

3. Image Processing/Analysis Image Processing Toolbox/Product Overview
Loading and writing images
To read an image, use ‘imread’
Example:
>> imfinfo('pout2.png')
>> I = imread('pout.tif');
>> imshow(I)
>> whos I
>>
>> II = imread(‘StarWars.tif’);
>> whos II
>> imshow(StarWars(:,:,1:3);
>> imwrite (II(:,:,1:3), ‘StarWars.png');

4. Image Processing/Analysis
Image Processing Toolbox/Introduction/Image Types in the Toolbox
Image Type
Interpretation
Binary (aka bilevel)
Logical array of 0s and 1s, interpreted as b&w
Indexed (aka pseudocolor)
Array of class logical, uint8, uint16, single, or double whose pixel values are direct indices into an m-by-3 colormap.
Grayscale (aka intensity, gray scale, or gray level)
Array of class uint8, uint16, int16, single, or double whose pixel values specify intensity values.
Truecolor (aka RGB image )
An m-by-n-by-3 array of class uint8, uint16, single, or double whose pixel values specify intensity values.

5. Image Processing/Analysis
Image Processing Toolbox/Introduction/Image Types in the Toolbox
The Separated Color Planes of an RGB Image            

6. Image Processing/Analysis
Image Processing Toolbox/Introduction/Image Types in the Toolbox
red
green
blue

7. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies by:
G. A. Stuart (2007)
Next, I CONSIDERED MULTIPLE EDDY STIRRING, by placing multiple grid mixers in the same tank.
The same experimental parameters were USED AS IN THE SINGLE EXPERIMENTS.
THE ONLY difference was that multiple MIXERS WERE ACTUATED at a prescribed SEQUENCE
THE SCHEMATIC shows the approximate POSITIONS

8. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
The time evolution of a centrally injected patch of green dye was observed in response to a preset sequence of 8 mixing events
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

9. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

10. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
Computing and subtracting image background
>> bkgd = blkproc(newa,[5 5],[50 nanmedian(x(:)));
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

11. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
Identify ‘dark bits’
>> bkgcutoff = 165;
>> darkbits = find(ambkg<bkgcutoff
& ~(ambkg==nan));
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

12. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
Linearly interpolate over masked portions of image
>> newdarkbits = griddata(Xgrid(lightbits),Ygrid(lightbits),a(lightbits), ...
Xgrid(darkbits),Ygrid(darkbits),'linear');
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

13. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

14. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

15. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

16. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

17. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

18. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

19. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
HERE IS ANOTHER MOVIE, in this case it is the base run of a MULTIPLE EDDY experiment
THIS IS a SIMILAR PLANVIEW image of the entire tank.
SINGLE MIXER, SIDE MIRROR, ROTATING COUNTER CLOCK WISE, DYE INJECTED
‘THIS’ Video of an ENTIRE MULTIEDDY EXPERIMENT is a series of DIGITAL STILLS and is SPED UP SUBSTANTIALLY…
40 MINUTES are shown in 40 SECONDS
THE PICTURES were not UNIFORMLY SPACED (maybe a little jumpy).
AGAIN, you see a PLANVIEW image of the tank, SIDE MIRROR
IMPORTANT HERE is to notice when each mixer is ACTUATED and the resultant EDDY that is formed

20. Image Processing/Analysis Image Processing Toolbox
Example: Lab Studies (cont’d)
Calculate growth rate of dye variance to determine effective horizontal diffusivity
Two-Dimensional dye variance
kH = 2.3 x 10-5 m2 s-1
Inferred Eddy Diffusivity
Area of Ellipse (m2)
IMAGE PROCESSING WAS USED TO measured the rate of DYE spreading
The TOP FIGURE SHOWS….
THE 2D VARIANCE can be calculated
The OBSERVED DIFFUSIVITY can be estimated by GROWTH RATE OF THE Variance
Observed area
Fitted slope
Time (s)

21. Image Processing/Analysis
Mapping Toolbox/Getting Started/Product Overview
Overview of Mapping Toolbox
A collection of functions that extend the capability of MATLAB numeric computing for mapping and GIS operations, including:
Geospatial data import and access
Vector map data and geographic data structures
Geo-referenced images and data grids
Map projections and coordinates
Map display and interaction
Geographic calculations for vector and raster data
A map viewer and other graphical user interfaces

22. Image Processing/Analysis
Mapping Toolbox/Getting Started/Your First Maps
Loading and plotting simple map data
Example:
>> worldmap world % create an empty map axis
>> load coast % load and plot coastlines
>> plotm(lat, long)
>> h = worldmap('Europe') % create a new map axes for Europe
>> % and add data to the map
>> geoshow('landareas.shp', 'FaceColor', [ ])
>> geoshow('worldlakes.shp', 'FaceColor', 'cyan')
>> geoshow('worldrivers.shp', 'Color', 'blue')
>> geoshow('worldcities.shp', 'Marker', '.', 'MarkerEdgeColor', 'red')

23. Image Processing/Analysis
Mapping Toolbox/Getting Started/Your First Maps
The Map Viewer is an interactive tool for browsing map data
Example:
>> mapview
>> % To import Mapping Toolbox demo data, change directory to:
>> cd(fullfile(matlabroot,'toolbox','map','mapdemos'))
>> % (can also get here by navigating to 'toolbox/map/mapdemos')
>> % Import a vector data layer
>> boston_roads = shaperead('boston_roads.shp');
...

24. Image Processing/Analysis
Mapping Toolbox/Understanding Map Data/Understanding Vector Geo-Data
Points, Lines, Polygons
Vector geospatial data is used to represent linear features such as rivers, coastlines, boundaries, and highways
Example:
>> lat = [ ]; long = [ ];

25. Image Processing/Analysis
Mapping Toolbox
Example: Allens Pond Nutrient Loading / Tidal Flushing Study
Case Studies in Estuarine Dynamics (MAR620), Spring 2008
Sylvan Nurseries
Quanset Nurseries
Zylfee Brook
gauge
Tide gauge (still need datum)
Isaac's Brook
Unable to gauge
Audubon Field Station
Fresh Pond
(velocity only)
Margaret's Brook
Current Inlet (approximate location)
Inlet does not connect to this channel
Water Column sampling
(velocity only) TBD

26. Image Processing/Analysis
Mapping Toolbox
Example: Allens Pond Nutrient Loading / Tidal Flushing Study
Case Studies in Estuarine Dynamics (MAR620), Spring 2008
Next, I CONSIDERED MULTIPLE EDDY STIRRING, by placing multiple grid mixers in the same tank.
The same experimental parameters were USED AS IN THE SINGLE EXPERIMENTS.
THE ONLY difference was that multiple MIXERS WERE ACTUATED at a prescribed SEQUENCE
THE SCHEMATIC shows the approximate POSITIONS

27. Image Processing/Analysis
Mapping Toolbox
Example: Allens Pond Nutrient Loading / Tidal Flushing Study
Case Studies in Estuarine Dynamics (MAR620), Spring 2008
Next, I CONSIDERED MULTIPLE EDDY STIRRING, by placing multiple grid mixers in the same tank.
The same experimental parameters were USED AS IN THE SINGLE EXPERIMENTS.
THE ONLY difference was that multiple MIXERS WERE ACTUATED at a prescribed SEQUENCE
THE SCHEMATIC shows the approximate POSITIONS

28. Image Processing/Analysis
Mapping Toolbox
Example: Allens Pond Nutrient Loading / Tidal Flushing Study
Case Studies in Estuarine Dynamics (MAR620), Spring 2008
Next, I CONSIDERED MULTIPLE EDDY STIRRING, by placing multiple grid mixers in the same tank.
The same experimental parameters were USED AS IN THE SINGLE EXPERIMENTS.
THE ONLY difference was that multiple MIXERS WERE ACTUATED at a prescribed SEQUENCE
THE SCHEMATIC shows the approximate POSITIONS

29. Image Processing/Analysis
Mapping Toolbox
Example: Allens Pond Nutrient Loading / Tidal Flushing Study
Case Studies in Estuarine Dynamics (MAR620), Spring 2008
Next, I CONSIDERED MULTIPLE EDDY STIRRING, by placing multiple grid mixers in the same tank.
The same experimental parameters were USED AS IN THE SINGLE EXPERIMENTS.
THE ONLY difference was that multiple MIXERS WERE ACTUATED at a prescribed SEQUENCE
THE SCHEMATIC shows the approximate POSITIONS

30. Image Processing/Analysis
Mapping Toolbox
Example: Allens Pond Nutrient Loading / Tidal Flushing Study
Case Studies in Estuarine Dynamics (MAR620), Spring 2008
Next, I CONSIDERED MULTIPLE EDDY STIRRING, by placing multiple grid mixers in the same tank.
The same experimental parameters were USED AS IN THE SINGLE EXPERIMENTS.
THE ONLY difference was that multiple MIXERS WERE ACTUATED at a prescribed SEQUENCE
THE SCHEMATIC shows the approximate POSITIONS

31. Image Processing/Analysis
Mapping Toolbox
Useful Tidbits:
Mass GIS website: