add scritps and functions, based in R.Patel PhD Thesis tutorial

custom_scripts/AutomateEntireSoft.m

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+% This is an example to automate entire Eddy detection and tracking software
+% and also to visualize outputs. Each section elucidates different aspect
+% of automatization.
+clc; clear
+% =====Input arguments for set_up_data_regional=====%
+NetCDF_files_path = '~/Desktop/Satellite_data/MADT-SLA/';
+ssh_NetCDF_name = 'sla';
+lat_NetCDF_name = 'lat';
+lon_NetCDF_name = 'lon';
+lonlimit = [100, 175];
+latlimit = [-35, -70];
+ssh_save_path = '~/Documents/MATLAB/OceanEddies-master/Myssh';
+%=======
+% Preprocessing data for complete run
+set_up_NRTdata_regional(NetCDF_files_path, ssh_NetCDF_name, lat_NetCDF_name, lon_NetCDF_name, ...
+    lonlimit, latlimit, ssh_save_path)
+
+%% Detection and tracking of eddies
+clear;
+% =====Input arguments for complete_run=====%
+% My SLA data archived in \textbf{Myssh} directory 
+ssh_path = '~/Documents/MATLAB/OceanEddies-master/Myssh/';
+% I save my outputs at \textbf{MyRuns/MyEddies} and \textbf{MyTracks} directories. 
+% Note: Both directory will be generated by script if not exist at provided location. 
+% Furthermore, it will also generate directories for modified eddies and track if you 
+% had allowed eddy to unassociate. i.e 'yes' at fake eddy argument. 
+eddies_save_path = '~/Documents/MATLAB/OceanEddies-master/MyRuns/MyEddies/eddies'; 
+tracks_save_path = '~/Documents/MATLAB/OceanEddies-master/MyRuns/MyTracks/tracks';
+% These are extra outputs more detail please follow up text in section 3
+viewer_data_save_path = '~/Documents/MATLAB/OceanEddies-master/MyRuns/';
+viewer_path = '~/Documents/MATLAB/OceanEddies-master/MyRuns/Extra_viewer/';
+%========
+% running software
+complete_run(ssh_path, eddies_save_path, tracks_save_path, 'yes', viewer_data_save_path, viewer_path)
+
+%% Visualization of eddies track after filtering by lifespan
+clear;
+% =====Input arguments for plotTrack=====%
+path = '~/Documents/MATLAB/OceanEddies-master/MyRuns/modified_tracks';
+cycfilename = 'cyclonic_tracks_processed.mat';
+acycfilename = 'anticyc_tracks_processed.mat';
+load([path, cycfilename])
+load([path, acyfilename])
+% I would filter eddies whose lifespan is \geq 28days
+filter_day = 28;
+% global_coastline.txt file contains global longitudes and latitude
+coast = load('global_coastline.txt');
+xtick = 100:10:175;
+ytick = -70:5:-35;
+%======
+% Filtering and plotting
+plotTrack(cyclonic_tracks, anticyc_tracks, filter_day, coast, xtick, ytick)

custom_scripts/EddyAnimation.m

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+% This script generates an Animation to identify desired edd(y)ies for
+% further analysis
+%
+% NOTE: SLA overlaid by contours of 0.1 0.4 and 0 m
+% - with center position obtained from the Algorithms
+% NOTE: This is only for cyclonic eddies, for anticyclonic eddies make
+% changes, suggested below
+%===============
+% Ramkrushn Patel, IMAS/UTAS
+%===============
+
+% CONTENTS:
+% 1) Loading Sea Surface Height data
+% 2) Loading Eddies locations
+% 3) Preparing Movie
+
+%% 1) Loading Sea Surface Height data
+clear; clc;
+
+old_path = pwd;
+ssh_path =  '~/Desktop/Satellite_data/JoanModelRun/';
+cd(ssh_path)
+%
+filenames = dir('ssh_*.mat');
+nfiles = length(filenames);
+%
+load lon.mat
+load lat.mat
+load dates.mat
+%
+cd(old_path)
+
+%% 2) Loading Eddies location
+
+eddy_path = '~/Documents/MATLAB/OceanEddies-master/MyRuns/JoanEddy/';
+fname = 'chelton_structured_tracks.mat';
+load([eddy_path, fname])
+
+% Extracting variables
+e_sign = eddies_t.cyc;
+% get only cyclonic eddies/anticyclonic eddies
+cyc = e_sign == 1; % -1 for cyclonic % ---------- Change here for type of eddies 
+%
+e_lon = eddies_t.x(cyc); % eddies center longitude
+e_lat = eddies_t.y(cyc); % eddies center latitude
+e_trackday = eddies_t.track_day(cyc); % tracked date
+e_id = eddies_t.id(cyc); % eddies id
+
+% Loading coastlines
+c = load('~/Documents/MATLAB/Construction_Site/global_coastline.txt'); % Coast Line
+
+%% 3) Preparing movie
+close all
+h = figure(11);
+set(h, 'Position', [100 678 560 420])
+% ==Prepare Video file==
+vidObj = VideoWriter('EddyAnimationACyc.avi'); %==== Change file name if you re-run the script
+fps = 7;
+vidObj.FrameRate = fps;
+vidObj.Quality = 100;
+open(vidObj)
+%
+for fInd = 1:nfiles
+    disp(['Current File: ', int2str(fInd)])
+    %
+    load([ssh_path, filenames(fInd).name]) % SLA data
+    time = num2str(dates(fInd));
+    time = datestr(datenum(time,'yyyymmdd'));
+    %
+    % Getting eddies for the day
+    da_id = dates(fInd);
+    ind = find(e_trackday == da_id);
+
+    % Plotting
+    % Background MSLA 
+    pcolor(lon, lat, data); shading interp 
+    caxis([-0.5, 0.5])
+    colormap(redblue(length(-0.5:0.02:0.5) - 1))
+    colorbar
+    hold on
+    % Plotting eddies
+    plot(e_lon(ind), e_lat(ind), '.m', 'MarkerSize', 20) 
+    text(e_lon(ind), e_lat(ind), num2str(e_id(ind)),'color','k','fontsize', 14, 'fontweigh','bold') % numbering eddies
+    % Ensuring closed contours
+    contour(lon, lat, data, [-0.1, -0.1], '-', 'linewidth', 1, 'color', 'b');
+    contour(lon, lat, data, [0.1, 0.1], '-', 'linewidth', 1, 'color', 'r');
+
+    % ======
+    plot(c(:,1), c(:,2), 'k-', 'LineWidth', 3);
+    s1 = sprintf('Day %d Date: %s', fInd, time);
+    title(s1, 'fontsize', 14, 'fontweigh', 'bold')
+    M(fInd) = getframe(h); %#ok 
+    clf
+    clear data time s1 ind da_id
+end
+writeVideo(vidObj, M)
+close(vidObj)
+clear M h

custom_scripts/ReadMe.md

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+# Custom Scripts to extend functionality of OceanEddies software
+*This ReadMe.md belongs to **custom_scripts** directory*
+
+## Author
+Ramkrushnbhai S. Patel $^{1,2}$
+
+1: [Institute for Marine and Antarctic Studies](https://www.imas.utas.edu.au), [University of Tasmania](https://www.utas.edu.au), Hobart, Tasmania, Australia
+
+2: [Australian Research Council Centre of Excellence for Climate Extremes](https://climateextremes.org.au), University of Tasmania, Hobart, Tasmania, Australia
+
+## ABOUT
+The *custom_scripts* directory provides the scripts that automatise the detection and tracking of eddies using Faghmous et al. 2015 software.  
+## CONTENTS
+Directory | Description
+--------- | ----------
+custom_scripts | Collection of preprossing, post-processing and analyses scripts
+txt file | global coastline data
+ReadMe | -
+
+### Example scripts
+*AutomateEntireSoft.m* : demonstrates how to automate the software from altimetry data\
+*idealizedmodelautomate.m* : demonstrates how to automate the software from idealised model output data\
+*EddyAnimation.m* : makes movie to identify specific types of eddies\
+
+
+### Preprocessing functions
+*set_up_NRTdata_regional.m* : prepares near-real-time daily SLA maps for the software\
+*set_up_DTdata_regional.m* : prepares delay-mode daily SLA maps for the software with modified area-map algorithm\
+*set_up_data_3D2daily.m* : converts 3D.mat file to daily to conform complete_run.m function input\
+*set_up_data_3D2dailyModel.m* : flexible compare to 3D2daily function\
+**
+
+### Supporting functions
+*plotTrack.m* : visualise eddies track redily after the detection for the quick summary
+
+### Contact
+If you have any question or feedback, please raise an issue in [OceanEddiesToolbox](https://github.com/rampatels/OceanEddiesToolbox.git) repository.