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

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

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');

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.

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

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

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

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

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

Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d) Computing and subtracting image background >> bkgd = blkproc(newa,[5 5],[50 50],@(x) 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

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

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

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

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

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

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

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

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

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

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)

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

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', [0.15 0.5 0.15]) >> geoshow('worldlakes.shp', 'FaceColor', 'cyan') >> geoshow('worldrivers.shp', 'Color', 'blue') >> geoshow('worldcities.shp', 'Marker', '.', 'MarkerEdgeColor', 'red')

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'); ...

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 = [45.6 -23.47 78]; long = [13 -97.45 165];

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

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

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

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

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

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

Image Processing/Analysis Mapping Toolbox Useful Tidbits: Mass GIS website: http://www.mass.gov/mgis/massgis.htm