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Sundermeyer MAR 550 Spring 2013 1 Laboratory in Oceanography: Data and Methods MAR550, Spring 2013 Miles A. Sundermeyer Image Processing/Analysis.

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Presentation on theme: "Sundermeyer MAR 550 Spring 2013 1 Laboratory in Oceanography: Data and Methods MAR550, Spring 2013 Miles A. Sundermeyer Image Processing/Analysis."— Presentation transcript:

1 Sundermeyer MAR 550 Spring 2013 1 Laboratory in Oceanography: Data and Methods MAR550, Spring 2013 Miles A. Sundermeyer Image Processing/Analysis

2 Sundermeyer MAR 550 Spring 2013 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 Sundermeyer MAR 550 Spring 2013 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 Sundermeyer MAR 550 Spring 2013 4 Image Processing/Analysis Image Processing Toolbox/Introduction/Image Types in the Toolbox Image TypeInterpretation 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 Sundermeyer MAR 550 Spring 2013 5 Image Processing/Analysis Image Processing Toolbox/Introduction/Image Types in the Toolbox The Separated Color Planes of an RGB Image

6 Sundermeyer MAR 550 Spring 2013 6 Image Processing/Analysis Image Processing Toolbox/Introduction/Image Types in the Toolbox red greenblue

7 Sundermeyer MAR 550 Spring 2013 7 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies by: G. A. Stuart (2007)

8 Sundermeyer MAR 550 Spring 2013 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

9 Sundermeyer MAR 550 Spring 2013 9 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d)

10 Sundermeyer MAR 550 Spring 2013 10 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(:)));

11 Sundermeyer MAR 550 Spring 2013 11 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d) Identify ‘dark bits’ >> bkgcutoff = 165; >> darkbits = find(ambkg<bkgcutoff & ~(ambkg==nan));

12 Sundermeyer MAR 550 Spring 2013 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');

13 Sundermeyer MAR 550 Spring 2013 13 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d)

14 Sundermeyer MAR 550 Spring 2013 14 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d)

15 Sundermeyer MAR 550 Spring 2013 15 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d)

16 Sundermeyer MAR 550 Spring 2013 16 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d)

17 Sundermeyer MAR 550 Spring 2013 17 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d)

18 Sundermeyer MAR 550 Spring 2013 18 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d)

19 Sundermeyer MAR 550 Spring 2013 19 Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d)

20 Sundermeyer MAR 550 Spring 2013 20 Two-Dimensional dye variance Inferred Eddy Diffusivity Time (s) Area of Ellipse (m 2 )  H = 2.3 x 10 -5 m 2 s -1 Observed area Fitted slope Image Processing/Analysis Image Processing Toolbox Example: Lab Studies (cont’d) Calculate growth rate of dye variance to determine effective horizontal diffusivity

21 Sundermeyer MAR 550 Spring 2013 21 Laboratory in Oceanography: Data and Methods MAR550, Spring 2013 Miles A. Sundermeyer Image Processing/Analysis Part II

22 Sundermeyer MAR 550 Spring 2013 22 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

23 Sundermeyer MAR 550 Spring 2013 23 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) Example: >> 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')

24 Sundermeyer MAR 550 Spring 2013 24 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');...

25 Sundermeyer MAR 550 Spring 2013 25 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];

26 Sundermeyer MAR 550 Spring 2013 26 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 gauge Unable to gauge Audubon Field Station Fresh Pond (velocity only) Margaret's Brook (velocity only) Current Inlet (approximate location) Inlet does not connect to this channel Water Column sampling Zylfee Brook (velocity only) TBD

27 Sundermeyer MAR 550 Spring 2013 27 Image Processing/Analysis Mapping Toolbox Example: Allens Pond Nutrient Loading / Tidal Flushing Study Case Studies in Estuarine Dynamics (MAR620), Spring 2008

28 Sundermeyer MAR 550 Spring 2013 28 Image Processing/Analysis Mapping Toolbox Example: Allens Pond Nutrient Loading / Tidal Flushing Study Case Studies in Estuarine Dynamics (MAR620), Spring 2008

29 Sundermeyer MAR 550 Spring 2013 29 Image Processing/Analysis Mapping Toolbox Example: Allens Pond Nutrient Loading / Tidal Flushing Study Case Studies in Estuarine Dynamics (MAR620), Spring 2008

30 Sundermeyer MAR 550 Spring 2013 30 Image Processing/Analysis Mapping Toolbox Example: Allens Pond Nutrient Loading / Tidal Flushing Study Case Studies in Estuarine Dynamics (MAR620), Spring 2008

31 Sundermeyer MAR 550 Spring 2013 31 Image Processing/Analysis Mapping Toolbox Example: Allens Pond Nutrient Loading / Tidal Flushing Study Case Studies in Estuarine Dynamics (MAR620), Spring 2008

32 Sundermeyer MAR 550 Spring 2013 32 Image Processing/Analysis Mapping Toolbox Useful Tidbits: Mass GIS website: http://www.mass.gov/mgis/massgis.htm


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