Added new tolerance_track_lnn for interpolating eddies to connect tracks, updated track_lnn to load

 eddies dynamically.

Author: warmkar

track_lnn.m

@@ -0,0 +1,35 @@
+function [ amps, geospeeds, lats, lons, pxcounts, pixels, surface_areas ] = get_eddy_attributes( eddy_dir, eddy_file_initial, dates)
+%GET_EDDY_ATTRIBUTES Summary of this function goes here
+%   Detailed explanation goes here
+
+amps = cell(size(dates));
+geospeeds = cell(size(dates));
+lats = cell(size(dates));
+lons = cell(size(dates));
+pxcounts = cell(size(dates));
+pixels = cell(size(dates));
+surface_areas = cell(size(dates));
+for i = 1:length(dates)
+    disp(i)
+    try
+        temp = load([eddy_dir eddy_file_initial '_' num2str(dates(i)) '.mat']);
+    catch
+        disp(['Error loading file: ', eddy_dir, eddy_file_initial, '_', num2str(dates(i)), '.mat']);
+        continue;
+    end
+    names = fieldnames(temp);
+    if length(names) == 1
+        eddies = temp.(names{1});
+    end
+    amps{i} = [eddies.Amplitude];
+    geospeeds{i} = [eddies.MeanGeoSpeed];
+    surface_areas{i} = [eddies.SurfaceArea];
+    lats{i} = [eddies.Lat];
+    lons{i} = [eddies.Lon];
+    stats = [eddies.Stats];
+    pxcounts{i} = [stats.Area];
+    pixels{i} = {stats.PixelIdxList};
+end
+
+end
+

track_lnn/lib/get_eddy_attributes.m

@@ -0,0 +1,21 @@
+function [ eddy_lifetimes ] = get_eddy_lifetimes( eddy_counts, tracks  )
+%GET_EDDY_LIFETIMES Summary of this function goes here
+%   Detailed explanation goes here
+
+eddy_lifetimes = cell(size(eddy_counts));
+for i = 1:length(eddy_counts)
+    eddy_lifetimes{i} = ones(1, eddy_counts(i));
+end
+
+for i = 1:length(tracks)
+    curr_track = tracks{i};
+    track_length = size(curr_track, 1);
+    for j = 1:size(curr_track, 1)
+        curr_date_index = curr_track(j, 3);
+        curr_eddy_index = curr_track(j, 4);
+        eddy_lifetimes{curr_date_index}(curr_eddy_index) = track_length;
+    end
+end
+
+end
+

track_lnn/lib/get_eddy_lifetimes.m

@@ -0,0 +1,20 @@
+function [ track_indexes ] = get_eddy_track_index( eddy_counts, tracks )
+%GET_EDDY_TRACK_INDEX Summary of this function goes here
+%   Detailed explanation goes here
+
+track_indexes = cell(size(eddy_counts));
+for i = 1:length(eddy_counts)
+    track_indexes{i} = nan(eddy_counts(i), 1);
+end
+
+for i = 1:length(tracks)
+    curr_track = tracks{i};
+    for j = 1:size(curr_track, 1)
+        curr_date_index = curr_track(j, 3);
+        curr_eddy_index = curr_track(j, 4);
+        track_indexes{curr_date_index}(curr_eddy_index) = i;
+    end
+end
+
+end
+

track_lnn/lib/get_eddy_track_index.m

@@ -0,0 +1,16 @@
+function [ tags ] = make_track_tags( tracks, eddy_types )
+%MAKE_TRACK_TAGS Make tags for eddy in tracks based on eddy type cell array
+%   Detailed explanation goes here
+
+tags = cell(size(tracks));
+for i = 1:length(tracks);
+    tags{i} = nan(size(tracks{i}, 1), 1);
+    for j = 1:size(tracks{i}, 1)
+        date_index = tracks{i}(j, 3);
+        eddy_index = tracks{i}(j, 4);
+        tags{i}(j) = eddy_types{date_index}(eddy_index);
+    end
+end
+
+end
+

track_lnn/lib/make_track_tags.m

@@ -0,0 +1,128 @@
+function prepare_eddy_data_for_viewer( viewer_data_save_dir, dates, eddy_dir, ...
+    cyclonic_tracks, anticyclonic_tracks, ssh_dir)
+%PREPARE_EDDY_DATA_FOR_VIEWER Prepare data for the viewer
+% Input:
+%   viewer_data_save_dir: where to save data for track viewer
+%   dates: 1D array of dates for data
+%   eddy_dir: directory where you save eddy from eddyscan
+%   cyclonic_tracks: tracks for cyclonic eddies
+%   anticyclonic_tracks: tracks for anticyclonic eddies
+%   ssh_dir: directory where you save ssh data slices
+addpath('/project/expeditions/alindell/FullEddyViewer/data_code/');
+%% Prepare directory for saving
+if ~exist(viewer_data_save_dir, 'dir')
+    mkdir(viewer_data_save_dir);
+end
+
+pixel_save_dir = [viewer_data_save_dir 'pixel_data/'];
+if ~exist(pixel_save_dir, 'dir')
+    mkdir(pixel_save_dir);
+end
+
+disp('saving pixel data');
+load([ssh_dir 'lat.mat']);
+load([ssh_dir 'lon.mat']);
+save([pixel_save_dir 'lat.mat'], 'lat');
+save([pixel_save_dir 'lon.mat'], 'lon');
+
+%% Cyclonic attributes
+disp('getting eddies attributes, will take a long time (about 30mins for 900 time slices)');
+
+ if ~isempty(cyclonic_tracks)
+     [ cyc_amps, cyc_geospeeds, cyc_lats, cyc_lons, cyc_pxcounts, cyc_pixels, cyc_surface_areas ] = ...
+         get_eddy_attributes(eddy_dir, 'cyclonic', dates);
+
+    cyc_types = cell(size(dates));
+    for i = 1:length(dates)
+        cyc_types{i} = zeros(size(cyc_lats{i}));
+    end
+    for i = 1:length(cyclonic_tracks)
+        for j = 1:size(cyclonic_tracks{i},1)
+            if length(cyclonic_tracks{i}(1,:)) == 5
+                if cyclonic_tracks{i}(j,5) ~= 0
+                    flagged_eddy_timestep = cyclonic_tracks{i}(j,3);
+                    flagged_eddy_index = cyclonic_tracks{i}(j,4);
+                    cyc_types{flagged_eddy_timestep}(flagged_eddy_index) = cyclonic_tracks{i}(j,5);
+                end
+            end
+        end
+    end
+    
+    cyclonic_tags = make_track_tags(cyclonic_tracks, cyc_types);
+    save([viewer_data_save_dir 'cyclonic_tags.mat'], 'cyclonic_tags');
+
+    cyc_eddy_counts = zeros(length(cyc_lats), 1);
+    for i = 1:length(cyc_lats)
+        cyc_eddy_counts(i) = length(cyc_lats{i});
+    end
+
+    cyc_lifetimes = get_eddy_lifetimes(cyc_eddy_counts, cyclonic_tracks);
+    cyc_eddy_track_indexes = get_eddy_track_index(cyc_eddy_counts, cyclonic_tracks);
+
+    attribute_to_save = {'amps', 'geospeeds', 'lats', 'lons', 'pxcounts', 'surface_areas', 'lifetimes', 'eddy_track_indexes', 'types'};
+    disp('saving cyclonic attributes')
+    for i = 1:length(attribute_to_save)
+        curr_attribute = attribute_to_save{i};
+        save([viewer_data_save_dir 'cyc_' curr_attribute '.mat'], ['cyc_' curr_attribute]);
+    end
+
+    if ~exist([pixel_save_dir 'cyclonic/'], 'dir')
+        mkdir([pixel_save_dir 'cyclonic/']);
+    end
+
+    disp('saving cyclonic pixels')
+    for i = 1:length(dates)
+        data = cyc_pixels{i};
+        save([pixel_save_dir 'cyclonic/pixels_' num2str(dates(i)) '.mat'], 'data');
+    end
+end
+
+%% Anticyclonic attributes
+if ~isempty(anticyclonic_tracks)
+    [ ant_amps, ant_geospeeds, ant_lats, ant_lons, ant_pxcounts, ant_pixels, ant_surface_areas ] = ...
+        get_eddy_attributes(eddy_dir, 'anticyc', dates);
+
+    ant_types = cell(size(dates));
+    for i = 1:length(dates)
+        ant_types{i} = zeros(size(ant_lats{i}));
+    end
+    for i = 1:length(anticyclonic_tracks)
+        for j = 1:size(anticyclonic_tracks{i},1)
+            if length(anticyclonic_tracks{i}(1,:)) == 5
+                if anticyclonic_tracks{i}(j,5) ~= 0
+                    flagged_eddy_timestep = anticyclonic_tracks{i}(j,3);
+                    flagged_eddy_index = anticyclonic_tracks{i}(j,4);
+                    ant_types{flagged_eddy_timestep}(flagged_eddy_index) = anticyclonic_tracks{i}(j,5);
+                end
+            end
+        end
+    end
+
+    anticyclonic_tags = make_track_tags(anticyclonic_tracks, ant_types);
+    save([viewer_data_save_dir 'anticyclonic_tags.mat'], 'anticyclonic_tags');
+
+    ant_eddy_counts = zeros(length(ant_lats), 1);
+    for i = 1:length(ant_lats)
+        ant_eddy_counts(i) = length(ant_lats{i});
+    end
+
+    ant_lifetimes = get_eddy_lifetimes(ant_eddy_counts, anticyclonic_tracks);
+    ant_eddy_track_indexes = get_eddy_track_index(ant_eddy_counts, anticyclonic_tracks);
+
+    attribute_to_save = {'amps', 'geospeeds', 'lats', 'lons', 'pxcounts', 'surface_areas', 'lifetimes', 'eddy_track_indexes', 'types'};
+    for i = 1:length(attribute_to_save)
+        curr_attribute = attribute_to_save{i};
+        save([viewer_data_save_dir 'ant_' curr_attribute '.mat'], ['ant_' curr_attribute]);
+    end
+
+    if ~exist([pixel_save_dir 'anticyclonic/'], 'dir')
+        mkdir([pixel_save_dir 'anticyclonic/']);
+    end
+
+    for i = 1:length(dates)
+        data = ant_pixels{i};        
+        save([pixel_save_dir 'anticyclonic/pixels_' num2str(dates(i)) '.mat'], 'data');
+    end
+end
+
+end