Added functions to do all the work for the user

Author: warmkar

complete_run.m

@@ -0,0 +1,278 @@
+function complete_run(ssh_path, eddies_save_path, tracks_save_path, fake_eddies, viewer_data_save_path, viewer_path, varargin)
+% NOTE: Please provide full path names for all paths.
+%
+% The purpose of this function is to automate the entire gauntlet of
+% running all of the code to go from having only MATLAB SSH data to getting
+% the data set up to be viewed on the tracks viewer. This function should
+% automate the following steps:
+% 1. Scan SSH data for eddies
+% 2. Save detected eddies
+% 3. Build LNN tracks for these eddies (Possibly with fake eddies, if the
+%    user of the script wants fake eddies)
+% 4. Format and process saved data so that it can be viewed in Hung's
+%    viewer that we include
+%
+% NOTE: The process of turning NetCDF file data into MATLAB data is
+% partially left up to the user to do. A function will be provided that
+% will accomplish this for the user, but the user will have to provide the
+% variable names for what the SSH data is called, what the Latitude data is
+% called, and what the Longitude data is called. Also, the user will either
+% have to have this function generate a dates array (that is, what day each
+% day of SSH data relates to) for it, or they will have to generate their
+% own. Code will be provided in the NetCDf to MATLAB data function to
+% assist with generating this dates array.
+% Also, this script will not open the viewer for the user, it will leave
+% that action up to the user. To open the viewer, all the user has to do is
+% run the start_track_viewer script inside the tracks_viewer directory.
+
+p = inputParser;
+defaultLat = NaN;
+defaultLon = NaN;
+defaultDates = NaN;
+defaultAreaMap = NaN;
+defaultScanType = 'v2';
+defaultMinPixelSize = 9;
+defaultThresholdStep = 0.05;
+defaultSSHUnits = 'centimeters';
+defaultPaddingFlag = true;
+
+addRequired(p, 'ssh_dir');
+addRequired(p, 'eddies_save_path');
+addRequired(p, 'fake_eddies');
+
+addParameter(p, 'lat', defaultLat);
+addParameter(p, 'lon', defaultLon);
+addParameter(p, 'dates', defaultDates);
+addParameter(p, 'area_map', defaultAreaMap);
+addParameter(p, 'scan_type', defaultScanType);
+addParameter(p, 'minimumArea', defaultMinPixelSize, @isnumeric);
+addParameter(p, 'thresholdStep', defaultThresholdStep, @isnumeric);
+addParameter(p, 'isPadding', defaultPaddingFlag);
+addParameter(p, 'sshUnits', defaultSSHUnits);
+
+parse(p, ssh_path, eddies_save_path, fake_eddies, varargin{:});
+
+lat = p.Results.lat;
+lon = p.Results.lon;
+dates = p.Results.dates;
+area_map = p.Results.area_map;
+scan_type = p.Results.scan_type;
+minimumArea = p.Results.minimumArea;
+thresholdStep = p.Results.thresholdStep;
+isPadding = p.Results.isPadding;
+SSH_Units = p.Results.sshUnits;
+if ~strcmp(ssh_path(end), '/')
+    ssh_path = strcat(ssh_path, '/');
+end
+if ~strcmp(eddies_save_path(end), '/')
+    eddies_save_path = strcat(eddies_save_path, '/');
+end
+if ~strcmp(tracks_save_path(end), '/')
+    tracks_save_path = strcat(tracks_save_path, '/');
+end
+if ~strcmp(viewer_data_save_path(end), '/')
+    viewer_data_save_path = strcat(viewer_data_save_path, '/');
+end
+ssh_names = get_ssh_names(ssh_path);
+if isnan(lat)
+    vars = load([ssh_path, 'lat.mat']);
+    names = fieldnames(vars);
+    lat = vars.(names{1});
+end
+if isnan(lon)
+    vars = load([ssh_path, 'lon.mat']);
+    names = fieldnames(vars);
+    lon = vars.(names{1});
+end
+if isnan(dates)
+    vars = load([ssh_path, 'dates.mat']);
+    names = fieldnames(vars);
+    dates = vars.(names{1});
+end
+if isnan(area_map)
+    vars = load([ssh_path, 'area_map.mat']);
+    names = fieldnames(vars);
+    area_map = vars.(names{1});
+end
+if ~exist(eddies_save_path, 'dir')
+    mkdir(eddies_save_path);
+end
+old_path = cd('eddyscan/');
+disp('Scanning SSH data for eddies');
+for i = 1:length(ssh_names)
+    disp(['Iteration ', num2str(i)]);
+    vars = load(ssh_names{i});
+    names = fieldnames(vars);
+    ssh_data = vars.(names{1});
+    ant_eddies = scan_single(ssh_data, lat, lon, dates(i), 'anticyc', scan_type, area_map, 'sshUnits', SSH_Units,...
+                             'thresholdStep', thresholdStep, 'minimumArea', minimumArea, 'isPadding', isPadding);
+    par_save([eddies_save_path, 'anticyc_', num2str(dates(i)), '.mat'], ant_eddies);
+    cyc_eddies = scan_single(ssh_data, lat, lon, dates(i), 'cyclonic', scan_type, area_map, 'sshUnits', SSH_Units,...
+                             'thresholdStep', thresholdStep, 'minimumArea', minimumArea, 'isPadding', isPadding);
+    par_save([eddies_save_path, 'cyclonic_', num2str(dates(i)), '.mat'], cyc_eddies);
+end
+cd(old_path);
+% Track eddies and save tracks
+if ~exist(tracks_save_path, 'dir')
+    mkdir(tracks_save_path);
+end
+if ~exist(viewer_data_save_path, 'dir')
+    mkdir(viewer_data_save_path);
+end
+old_path = cd('track_lnn/');
+disp('Tracking eddies');
+if strcmp(fake_eddies, 'yes')
+    anticyclonic_tracks = tolerance_track_lnn(eddies_save_path, 'anticyc', 1, 1, minimumArea);
+    cyclonic_tracks = tolerance_track_lnn(eddies_save_path, 'cyclonic', 1, 1, minimumArea);
+    modified_eddies_path = [viewer_data_save_path, 'modified_eddies/'];
+    modified_tracks_path = [viewer_data_save_path, 'modified_tracks/'];
+    if ~exist(modified_eddies_path, 'dir')
+        mkdir(modified_eddies_path);
+    end
+    if ~exist(modified_tracks_path, 'dir')
+        mkdir(modified_tracks_path);
+    end
+    disp('Modifying eddy data to include fake eddies (for the sake of the tracks)');
+    process_eddies_and_tracks_tolerance('anticyc', dates, eddies_save_path, anticyclonic_tracks, modified_eddies_path, modified_tracks_path);
+    process_eddies_and_tracks_tolerance('cyclonic', dates, eddies_save_path, cyclonic_tracks, modified_eddies_path, modified_tracks_path);
+    vars = load([modified_tracks_path, 'anticyc_tracks_processed.mat']);
+    s = fieldnames(vars);
+    anticyclonic_tracks = vars.(s{1});
+    vars = load([modified_tracks_path, 'cyclonic_tracks_processed.mat']);
+    s = fieldnames(vars);
+    cyclonic_tracks = vars.(s{1});
+    eddies_save_path = modified_eddies_path;
+else
+    anticyclonic_tracks = track_lnn(eddies_save_path, 'anticyc', 1); % Change this so it can be an optional argument in input parser
+    cyclonic_tracks = track_lnn(eddies_save_path, 'cyclonic', 1); % Same as above
+end
+save([tracks_save_path, 'anticyclonic_tracks.mat'], 'anticyclonic_tracks');
+save([tracks_save_path, 'cyclonic_tracks.mat'], 'cyclonic_tracks');
+% Set up data for viewer
+disp('Preparing data for viewer');
+prepare_eddy_data_for_viewer(viewer_data_save_path, dates, eddies_save_path, cyclonic_tracks, anticyclonic_tracks, ssh_path);
+cd(old_path);
+% Deleting old viewer files
+files = dir([viewer_path, 'SSH/']);
+old_path = cd([viewer_path, 'SSH/']);
+for i = 1:length(files)
+    file = files(i).name;
+    if ~strcmp(file, '.') && ~strcmp(file, '..')
+        if files(i).isdir
+            rmdir(file, 's');
+        else
+            delete(file);
+        end
+    end
+end
+files = dir([viewer_path, 'track_data/']);
+cd([viewer_path, 'track_data/']);
+for i = 1:length(files)
+    file = files(i).name;
+    if ~strcmp(file, '.') && ~strcmp(file, '..')
+        if files(i).isdir
+            rmdir(file, 's');
+        else
+            delete(file);
+        end
+    end
+end
+files = dir([viewer_path, 'attributes/']);
+cd([viewer_path, 'attributes/']);
+for i = 1:length(files)
+    file = files(i).name;
+    if ~strcmp(file, '.') && ~strcmp(file, '..')
+        if files(i).isdir
+            rmdir(file, 's');
+        else
+            delete(file);
+        end
+    end
+end
+files = dir([viewer_path, 'pixels_data/']);
+cd([viewer_path, 'pixels_data/']);
+for i = 1:length(files)
+    file = files(i).name;
+    if ~strcmp(file, '.') && ~strcmp(file, '..')
+        if files(i).isdir
+            rmdir(file, 's');
+        else
+            delete(file);
+        end
+    end
+end
+cd(old_path);
+% Copying new viewer files into place
+files = dir(ssh_path);
+for i = 1:length(files)
+    file = files(i).name;
+    if ~strcmp(file, '.') && ~strcmp(file, '..')
+        copyfile([ssh_path, file], [viewer_path, 'SSH/', file]);
+    end
+end
+files = dir(tracks_save_path);
+for i = 1:length(files)
+    file = files(i).name;
+    if ~strcmp(file, '.') && ~strcmp(file, '..')
+        copyfile([tracks_save_path, file], [viewer_path, 'track_data/', file]);
+    end
+end
+files = dir(viewer_data_save_path);
+for i = 1:length(files)
+    file = files(i).name;
+    if ~strcmp(file, '.') && ~strcmp(file, '..')
+        if ~files(i).isdir
+            if strcmp(file, 'anticyclonic_tags.mat') || strcmp(file, 'cyclonic_tags.mat')
+                copyfile([viewer_data_save_path, file], [viewer_path, 'track_data/', file]);
+            else
+                copyfile([viewer_data_save_path, file], [viewer_path, 'attributes/', file]); 
+            end
+        end
+    end
+end
+files = dir([viewer_data_save_path, 'pixel_data/']);
+for i = 1:length(files)
+    file = files(i).name;
+    if ~strcmp(file, '.') && ~strcmp(file, '..')
+        copyfile([viewer_data_save_path, 'pixel_data/', file], [viewer_path, 'pixels_data/', file]);
+    end
+end 
+
+end
+
+function par_save(path, eddies)%#ok
+save(path, 'eddies');
+end
+
+function [ssh_names] = get_ssh_names(path)
+% path is the path to the eddies directory
+% type is anticyclonic or cyclonic
+if ~strcmp(path(end), '/')
+    path = strcat(path, '/');
+end
+files = dir(path);
+x = 0;
+for i = 1:length(files)
+    if ~isempty(strfind(files(i).name, 'ssh_'))
+        x = x + 1;
+    end
+end
+ssh_names = cell(x, 1);
+x = 1;
+for i = 1:length(files)
+    if files(i).isdir && ~isequal(files(i).name, '.') && ~isequal(files(i).name, '..')
+        rec_names = get_ssh_names([path, files(i).name, '/']);
+        for j = 1:length(rec_names)
+            ssh_names{x} = rec_names{j};
+            x = x + 1;
+        end
+        continue;
+    end
+    file = files(i).name;
+    [~, name, ext] = fileparts([path, file]);
+    if ~isempty(strfind(name, 'ssh_')) && strcmp(ext, '.mat')
+        ssh_names{x} = [path, file];
+        x = x + 1;
+    end
+end
+end