Laboratory in Oceanography: Data and Methods

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Laboratory in Oceanography Data and Methods
Image Processing/Analysis

• MAR599, Spring 2009
• Miles A. Sundermeyer

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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

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Image Processing/Analysis Image Processing
Toolbox/Product Overview

• Loading and writing images
• To read an image, use imread
• Example
• gtgt imfinfo('pout2.png')
• gtgt I imread('pout.tif')
• gtgt imshow(I)
• gtgt whos I
• gtgt
• gtgt II imread(StarWars.tif)
• gtgt whos II
• gtgt imshow(StarWars(,,13)
• gtgt
• gtgt imwrite (II(,,13), StarWars.png')

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Image Processing/Analysis Image Processing
Toolbox/Introduction/Image Types in the Toolbox
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Image Processing/Analysis Image Processing
Toolbox/Introduction/Image Types in the Toolbox
The Separated Color Planes of an RGB
Image            
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Image Processing/Analysis Image Processing
Toolbox/Introduction/Image Types in the Toolbox
red
green
blue
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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies by G. A. Stuart (2007)
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Image Processing/Analysis Image Processing Toolbox

• Example Lab Studies (contd)
• The time evolution of a centrally injected patch
  of green dye was observed in response to a preset
  sequence of 8 mixing events

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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies (contd)
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Image Processing/Analysis Image Processing Toolbox

• Example Lab Studies (contd)
• Computing and subtracting image background
• gtgt bkgd blkproc(newa,5 5,50 50,_at_(x)
  nanmedian(x()))

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Image Processing/Analysis Image Processing Toolbox

• Example Lab Studies (contd)
• Identify dark bits
• gtgt bkgcutoff 165
• gtgt darkbits find(ambkgltbkgcutoff
• (ambkgnan))

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Image Processing/Analysis Image Processing Toolbox

• Example Lab Studies (contd)
• Linearly interpolate over masked portions of
  image
• gtgt newdarkbits griddata(Xgrid(lightbits),Ygr
  id(lightbits),a(lightbits), ...
• Xgrid(darkbits),Ygrid(darkbits),'l
  inear')

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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies (contd)
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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies (contd)
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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies (contd)
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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies (contd)
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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies (contd)
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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies (contd)
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Image Processing/Analysis Image Processing Toolbox
Example Lab Studies (contd)
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Image Processing/Analysis Image Processing Toolbox

• Example Lab Studies (contd)
• Calculate growth rate of dye variance to
  determine effective horizontal diffusivity

Two-Dimensional dye variance
kH 2.3 x 10-5 m2 s-1
Area of Ellipse (m2)
Inferred Eddy Diffusivity
Observed area
Fitted slope
Time (s)
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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

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Image Processing/Analysis Mapping Toolbox/Getting
Started/Your First Maps

• Loading and plotting simple map data
• Example
• gtgt worldmap world create an empty map axis
• gtgt load coast load and plot coastlines
• gtgt plotm(lat, long)
• Example
• gtgt h worldmap('Europe') create a new map axes
  for Europe
• gtgt and add data to the map
• gtgt geoshow('landareas.shp', 'FaceColor', 0.15
  0.5 0.15)
• gtgt geoshow('worldlakes.shp', 'FaceColor', 'cyan')
• gtgt geoshow('worldrivers.shp', 'Color', 'blue')
• gtgt geoshow('worldcities.shp', 'Marker', '.',
  'MarkerEdgeColor', 'red')

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Image Processing/Analysis Mapping Toolbox/Getting
Started/Your First Maps

• The Map Viewer is an interactive tool for
  browsing map data
• Example
• gtgt mapview
• gtgt To import Mapping Toolbox demo data, change
  directory to
• gtgt cd(fullfile(matlabroot,'toolbox','map','mapdemo
  s'))
• gtgt (can also get here by navigating to
  'toolbox/map/mapdemos')
• gtgt Import a vector data layer
• gtgt boston_roads shaperead('boston_roads.shp')
• ...

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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
• gtgt lat 45.6 -23.47 78 long 13 -97.45 165

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

• Useful Tidbits
• Mass GIS website http//www.mass.gov/mgis/massgis
  .htm