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First version of map plotting routines
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‎auxil/plot_maps.m‎

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function plot_maps(Data, Mdata, variables, depths, sz, basename, varargin)
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% plot_maps This function is part of the
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% MATLAB toolbox for accessing Argo float data.
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%
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% USAGE:
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% plot_maps(Data, Mdata, variables, basename, varargin)
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%
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% DESCRIPTION:
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% This function plots maps of values for the specified variable(s)
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% and float(s) at the given depth(s).
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%
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% PREREQUISITE:
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% (S)prof file(s) for the specified float(s) must exist locally.
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%
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% INPUTS:
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% Data : struct that must contain the PRES field and the given
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% variables (_ADJUSTED fields are used if available)
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% Mdata : struct that must contain the WMO_ID field
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% variables : cell array with names of the measured fields (e.g., {'DOXY'})
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% depths : array of the depths to be plotted
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% sz : sz defines the size of plotted points
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% basename : if not empty, create png files of all plots;
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% the file names will be <variable>_<depth>dbar.png
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%
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% OPTIONAL INPUTS:
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% 'caxis',[cmin cmax] : specify the minimum and maximum value to be
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% shown (for all variables and depths)
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% default: automatic scaling for each variable and depth
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% separately
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% 'qc',flags : show only values with the given QC flags (array)
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% 0: no QC was performed;
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% 1: good data;
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% 2: probably good data;
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% 3: probably bad data that are potentially correctable;
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% 4: bad data;
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% 5: value changed;
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% 6,7: not used;
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% 8: estimated value;
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% 9: missing value
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% default setting: 0:9 (all flags)
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% See Table 7 in Bittig et al.:
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% https://www.frontiersin.org/files/Articles/460352/fmars-06-00502-HTML-r1/image_m/fmars-06-00502-t007.jpg
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% 'raw',raw : plot raw, i.e., unadjusted data if set to 'yes';
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% default: 'no' (i.e., plot adjusted data if
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% available)
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% 'no_strict': plot only adjusted data, skip floats
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% that have only raw data available
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%
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% OUTPUT: None.
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%
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% AUTHORS:
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% H. Frenzel, J. Sharp, A. Fassbender (NOAA-PMEL), N. Buzby (UW)
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%
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% CITATION:
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% H. Frenzel, J. Sharp, A. Fassbender, N. Buzby, 2022. OneArgo-Mat:
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% A MATLAB toolbox for accessing and visualizing Argo data.
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% Zenodo. https://doi.org/10.5281/zenodo.6588041
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%
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% LICENSE: oneargo_mat_license.m
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%
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% DATE: JUNE 1, 2022 (Version 1.0.1)
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global Settings;
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if nargin < 5
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warning(['Usage: plot_maps(Data, Mdata, variables, depth, basename, ', ...
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'[, varargin])'])
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return;
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end
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% set defaults
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cax = [];
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depth = [];
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raw = 'no'; % plot adjusted data by default
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qc_flags = 0:9; % use all data
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title_add = '';
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% parse optional arguments
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for f = 1:2:length(varargin)-1
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if strcmpi(varargin{f}, 'caxis')
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cax = varargin{f+1};
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elseif strcmpi(varargin{f}, 'raw')
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raw = varargin{f+1};
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elseif strcmpi(varargin{f}, 'qc')
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qc_flags = varargin{f+1};
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else
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warning('unknown option: %s', varargin{f});
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end
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end
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floats = fieldnames(Data);
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nfloats = length(floats);
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if ~nfloats
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warning('no floats found in Data structure')
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return
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end
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float_ids = fieldnames(Mdata);
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nvars = length(variables);
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ndepths = length(depths);
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nplots = ndepths * nvars;
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if nplots > Settings.max_plots
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warning(['too many plots requested - use fewer depths and/or variables', ...
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newline, 'or increase Settings.max_plots if possible'], ...
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warn_insert)
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return
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end
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% unless 'raw' is specified, plot adjusted data
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show_var = ones(nvars, nfloats); % default: assume adjusted values are available
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if strncmpi(raw,'y',1)
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[title_added{1:nvars}] = deal([title_add, ' [raw values]']);
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else
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[title_added{1:nvars}] = deal(title_add);
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for v = 1:nvars
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% if all floats have adjusted values available for a variable,
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% they will be used instead of raw values
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has_adj = 0;
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for f = 1:nfloats
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% the "_ADJUSTED" variable usually exists, but it may not
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% be filled with actual values
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if isfield(Data.(floats{f}),[variables{v}, '_ADJUSTED']) && ...
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sum(isfinite(Data.(floats{f}).([variables{v}, '_ADJUSTED'])(:)))
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has_adj = has_adj + 1;
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elseif strcmpi(raw, 'no_strict')
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warning(['adjusted values for %s for float %s are not ',...
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'available;\nits values will not be shown'], ...
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variables{v}, floats{f});
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show_var(v,f) = 0;
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has_adj = has_adj + 1; % needed for check below
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else
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warning(['adjusted values for %s for float %s are not available,',...
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' showing raw values for all profiles instead'], ...
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variables{v}, floats{f});
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title_added{v} = [title_added{v}, ' [raw values]'];
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break
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end
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end
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if has_adj == nfloats
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variables{v} = [variables{v}, '_ADJUSTED'];
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end
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end
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end
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[lon_lim, lat_lim, Data] = get_lon_lat_lims(Data);
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% Set lat and lon limits
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latlim = [lat_lim(1)-Settings.pad_lat, lat_lim(2)+Settings.pad_lat];
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lonlim = [lon_lim(1)-Settings.pad_lon, lon_lim(2)+Settings.pad_lon];
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% Adjust limits outside range to minimum and maximum limits
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latlim(latlim < -90) = -90;
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latlim(latlim > 90) = 90;
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% use 0..360 range if all points are near the dateline
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if isfield(Data.(floats{1}), 'ALT_LON')
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lonlim(lonlim < 0) = 0;
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lonlim(lonlim > 360) = 360;
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use_alt_lon = 1;
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else % using a range of -180..180
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lonlim(lonlim < -180) = -180;
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lonlim(lonlim > 180) = 180;
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use_alt_lon = 0;
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end
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% vertical interpolation to depths with regular intervals
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for f = 1:nfloats
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Datai.(floats{f}) = depth_interp(Data.(floats{f}), qc_flags, 'raw', raw);
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end
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for v = 1:nvars
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if ~any(show_var(v,:))
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fprintf('None of the specified floats have adjusted %s values, skipping the plot\n', ...
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variables{v})
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continue
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end
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[long_name, units] = get_var_name_units(variables{v});
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for d = 1:ndepths
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for f = 1:nfloats
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[mini,idz] = min(abs(Datai.(floats{f}).PRES(:,1) - depths(d)));
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if mini < 2 % interpolated depths are at 2 dbar intervals
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break
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end
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end
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if mini > 2
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warning('The requested depth level (%d dbar) was not found and will be skipped.', ...
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depths(d))
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continue;
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end
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f1 = figure;
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if isfield(Settings, 'colormap')
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cmap = colormap(Settings.colormap);
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else
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cmap = colormap;
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end
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geoaxes;
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hold on;
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% Set geographic limits for figure
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geolimits(latlim,lonlim)
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geobasemap grayland
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if ~isempty(cax)
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caxis(cax)
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end
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for f = 1:nfloats
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if ~show_var(v,f)
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continue;
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end
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if size(Datai.(floats{f}).(variables{v}), 1) < idz
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warning('Float %s did not reach %d dbar', floats{f}, ...
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depths(d))
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continue
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end
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if use_alt_lon
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lon{f} = Data.(floats{f}).ALT_LON(1,:);
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else
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lon{f} = Data.(floats{f}).LONGITUDE(1,:);
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end
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good_pts = ~isnan(Datai.(floats{f}).(variables{v})(idz,:));
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if ~isempty(good_pts)
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geoscatter(Data.(floats{f}).LATITUDE(1,good_pts), lon{f}(good_pts), ...
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sz,Datai.(floats{f}).(variables{v})(idz,good_pts), '.')
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caxis
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end
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end
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title(sprintf('%s %s at %d dbar%s', long_name, units, ...
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depths(d), title_added{v}), 'FontSize', 14);
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colorbar
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if ~isempty(basename)
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fn_png = sprintf('%s_%s_%ddbar.png', basename, variables{v}, depths(d))
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print(f1, '-dpng', fn_png);
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end
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end
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end

‎show_maps.m‎

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function good_float_ids = show_maps(float_ids, variables, depths, varargin)
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% show_profiles This function is part of the
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% MATLAB toolbox for accessing Argo float data.
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%
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% USAGE:
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% good_float_ids = show_maps(float_ids, variables, depths, varargin)
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%
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% DESCRIPTION:
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% This an intermediary function that downloads profile(s) for the given
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% float(s) and calls plot_maps to create the plot(s).
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%
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% INPUTS:
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% float_ids : WMO ID(s) of the float(s)
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% variables : cell array of variable(s) or one variable as a string
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% depths : depth levels to show (dbar)
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%
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% OPTIONAL INPUTS:
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% 'caxis',[cmin cmax] : specify the minimum and maximum value to be
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% shown (for all variables and depths);
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% default: automatic scaling for each variable and depth
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% separately
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% 'float_profs',fp : cell array with per-float indices of the profiles to
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% be shown, as returned by select_profiles
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% 'png',basename: if basename is not empty, png files will be created
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% for all plots; the file names will be
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% <basename>_<variable>_<depth>dbar.png
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% 'qc',flags : show only values with the given QC flags (as an array)
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% 0: no QC was performed;
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% 1: good data;
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% 2: probably good data;
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% 3: probably bad data that are potentially correctable;
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% 4: bad data;
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% 5: value changed;
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% 6,7: not used;
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% 8: estimated value;
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% 9: missing value
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% default setting: 0:9 (all flags)
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% See Table 7 in Bittig et al.:
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% https://www.frontiersin.org/files/Articles/460352/fmars-06-00502-HTML-r1/image_m/fmars-06-00502-t007.jpg
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% 'raw',raw : plot raw, i.e., unadjusted data if set to 'yes';
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% default: 'no' (i.e., plot adjusted data if available)
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% 'no_strict': plot only adjusted data, skip floats
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% that have only raw data available
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% 'size',sz : sz (positive integer) defines the size of plotted
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% points (default: 200)
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%
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% OUTPUT:
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% good_float_ids : array of the float IDs whose Sprof files were
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% successfully downloaded or existed already
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%
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% AUTHORS:
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% H. Frenzel, J. Sharp, A. Fassbender (NOAA-PMEL), N. Buzby (UW)
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%
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% CITATION:
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% H. Frenzel, J. Sharp, A. Fassbender, N. Buzby, 2022. OneArgo-Mat:
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% A MATLAB toolbox for accessing and visualizing Argo data.
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% Zenodo. https://doi.org/10.5281/zenodo.6588041
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%
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% LICENSE: oneargo_mat_license.m
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%
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% DATE: JUNE 1, 2022 (Version 1.0.1)
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global Settings;
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% make sure Settings is initialized
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if isempty(Settings)
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initialize_argo();
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end
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% assign empty arrays to the return value in case of early return
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good_float_ids = [];
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if isempty(float_ids)
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warning('no floats specified')
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return
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end
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% set defaults
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if nargin < 3
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warning('Usage: show_maps(float_ids, variables, depths, varargin)');
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return
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end
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float_profs = [];
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basename = [];
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sz = 200;
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varargpass= {};
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% parse optional arguments
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for i = 1:2:length(varargin)-1
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if strcmpi(varargin{i}, 'float_profs')
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float_profs = varargin{i+1};
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elseif strcmpi(varargin{i}, 'size')
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if round(varargin{i+1}) > 0
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sz = round(varargin{i+1});
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else
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warning('size must be a positive integer')
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end
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elseif strcmpi(varargin{i}, 'png')
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basename = varargin{i+1};
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else
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if strcmpi(varargin{i}, 'qc')
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if min(varargin{i+1}) < 0 || max(varargin{i+1}) > 9
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warning('only QC flags 0..9 are allowed!')
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continue; % don't add it to varargpass
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end
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end
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varargpass = [varargpass, varargin{i:i+1}];
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end
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end
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if ~strcmp(Settings.mapping, 'native')
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warning('This function is only implemented for the native Matlab geofunctions')
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return
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end
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% convert requested variable to cell array if necessary and
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% discard unknown variables
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variables = check_variables(variables, 'warning', ...
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'unknown sensor will be ignored');
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% if float profiles were specified, make sure that there are no empty
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% arrays; if so, disregard these floats
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if ~isempty(float_profs)
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no_profs = cellfun(@isempty, float_profs);
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if any(no_profs)
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warning('No profiles specified for float(s):');
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disp(float_ids(no_profs))
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float_ids(no_profs) = [];
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float_profs(no_profs) = [];
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end
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end
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% download prof and Sprof files if necessary
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good_float_ids = download_multi_floats(float_ids);
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if isempty(good_float_ids)
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warning('no valid floats found')
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else
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avail_vars = check_float_variables(good_float_ids, variables, ...
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'warning', 'Not available in all specified floats');
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tic
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[Data, Mdata] = load_float_data(good_float_ids, avail_vars, ...
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float_profs);
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toc
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plot_maps(Data, Mdata, avail_vars, depths, sz, basename, varargpass{:});
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end

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