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Added time series plots
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‎auxil/plot_timeseries.m‎

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function plot_timeseries(Data, Mdata, variables, depth, basename, varargin)
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% plot_timeseries This function is part of the
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% MATLAB toolbox for accessing BGC Argo float data.
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%
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% USAGE:
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% plot_timeseries(Data, Mdata, variables, depth, basename, varargin)
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%
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% DESCRIPTION:
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% This function plots time series of one or more specified float(s) for
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% the specified variable(s).
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%
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% PREREQUISITE:
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% Sprof 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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% depth : array of depth levels to plot
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% basename : if not empty, create png files of all plots;
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% if per_float is used, the file names will be
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% <basename>_<WMOID>_<variable>.png,
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% if per_float is not used, the file names will be
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% <basename>_<variable>.png
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%
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% OPTIONAL INPUTS:
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% 'end',end_date : end date (in one of the following formats:
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% [YYYY MM DD HH MM SS] or [YYYY MM DD])
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% 'legend',legend : legend (string) can be 'yes' to show legend along with
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% plot (default) or 'no'
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% 'per_float',per_float : show time series separately for each float (1)
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% or all in one plot (0); default: 1
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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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% 'start',start_date : start date (in one of the following formats:
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% [YYYY MM DD HH MM SS] or [YYYY MM DD])
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% 'time_label',label : use either years or months ('m'); default depends
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% on length of time shown ('m' for up to 18 months,
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% 'title',title : title for the plot (default: "Depth: .. db"); an
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% empty string ('') suppresses the title
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% 'var2',variable : if variable is not empty, profiles of this second
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% variable will be plotted; if it is the same type as the
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% first variable (e.g., DOXY2 compared to DOXY), it will
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% be plotted using the same axes; otherwise, the right
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% axis will be used for the second variable
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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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% J. Plant, T. Maurer, Y. Takeshita (MBARI), D. Nicholson (WHOI),
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% and A. Gray (UW)
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%
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% CITATION:
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% H. Frenzel*, J. Sharp*, A. Fassbender, N. Buzby, J. Plant, T. Maurer,
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% Y. Takeshita, D. Nicholson, A. Gray, 2021. BGC-Argo-Mat: A MATLAB
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% toolbox for accessing and visualizing Biogeochemical Argo data.
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% Zenodo. https://doi.org/10.5281/zenodo.4971318.
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% (*These authors contributed equally to the code.)
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%
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% LICENSE: bgc_argo_mat_license.m
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%
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% DATE: DECEMBER 1, 2021 (Version 1.1)
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global Settings;
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if nargin < 5
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warning(['Usage: plot_timeseries(Data, Mdata, variables, depth, ', ...
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'basename [, varargin])'])
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return;
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end
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% set defaults
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per_float = 1; % show time series for each float in a separate plot
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raw = 'no'; % plot adjusted data by default
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title1 = []; % generate default titles
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qc_flags = 0:9; % use all data
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var2_orig = [];
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lgnd = 'yes';
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start_date = [];
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end_date = [];
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time_label = []; % used as flag
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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}, 'per_float')
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per_float = varargin{i+1};
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elseif strcmpi(varargin{i}, 'raw')
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raw = varargin{i+1};
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elseif strcmpi(varargin{i}, 'title')
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title1 = varargin{i+1};
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elseif strcmpi(varargin{i}, 'qc')
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qc_flags = varargin{i+1};
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elseif strcmpi(varargin{i}, 'var2')
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var2_orig = varargin{i+1};
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elseif strcmpi(varargin{i}, 'legend')
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lgnd = varargin{i+1};
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elseif strcmpi(varargin{i}, 'time_label')
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time_label = varargin{i+1};
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elseif strcmp(varargin{i}, 'start')
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if length(varargin{i+1}) == 3 || length(varargin{i+1}) == 6
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start_date = datenum(varargin{i+1});
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else
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warning(['dates should be in [YYYY MM DD HH MM SS] or ', ...
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'[YYYY MM DD] format']);
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end
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elseif strcmp(varargin{i}, 'end')
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if length(varargin{i+1}) == 3 || length(varargin{i+1}) == 6
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end_date = datenum(varargin{i+1});
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else
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warning(['dates should be in [YYYY MM DD HH MM SS] or ', ...
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'[YYYY MM DD] format']);
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end
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else
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warning('unknown option: %s', varargin{i});
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end
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end
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if ~isempty(var2_orig) && ~per_float
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warning('var2 can only be used with per float time series plots')
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return
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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(depth);
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if per_float
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nplots = nfloats * nvars * ndepths;
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warn_insert = 'floats, ';
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else
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nplots = nvars * ndepths;
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warn_insert = '';
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end
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if nplots > Settings.max_plots
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warning(['too many plots requested (%d) - use fewer %sdepths and/or variables', ...
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newline, 'or increase Settings.max_plots (%d) if possible'], ...
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nplots, warn_insert, Settings.max_plots)
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return
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end
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if ~isempty(var2_orig)
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[var2{1:nvars}] = deal(var2_orig); % default; may change later
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end
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[title_added{1:nvars}] = deal(''); % default; may change later
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% unless 'raw' is specified, plot adjusted data
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if strncmpi(raw,'y',1)
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if ~ischar(title1) || ~isempty(title1) % not added if title1 == ''
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[title_added{1:nvars}] = deal(' [raw values]');
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end
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else
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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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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 floats instead'], ...
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variables{v}, floats{f});
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if ~ischar(title1) || ~isempty(title1)
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title_added{v} = [title_added{v}, ' [raw values]'];
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end
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break
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end
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if ~isempty(var2_orig)
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if isfield(Data.(floats{f}),[var2_orig, '_ADJUSTED']) && ...
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sum(isfinite(Data.(floats{f}).([var2_orig, '_ADJUSTED'])(:)))
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has_adj = has_adj + 1;
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else
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warning(['adjusted values for %s for float %s ', ...
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'are not available, showing raw values for ', ...
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'all floats instead'], var2_orig, floats{f});
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if ~ischar(title1) || ~isempty(title1)
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title_added{v} = ' [raw values]';
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end
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break
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end
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end
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end
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if has_adj == nfloats * (1 + ~isempty(var2_orig))
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variables{v} = [variables{v}, '_ADJUSTED'];
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if ~isempty(var2_orig)
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var2{v} = [var2_orig, '_ADJUSTED'];
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end
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end
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end
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end
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if ~isempty(basename)
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[var2_insert{1:nvars}] = deal('');
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if ~isempty(var2_orig)
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for v = 1:nvars
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var2_insert{v} = sprintf('_%s', var2{v});
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end
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end
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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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% determine indices matching requested depths
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ndepths = length(depth);
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idx = cell(nfloats, ndepths);
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press = cell(nfloats, ndepths); % actual pressure levels used
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for d = 1:ndepths
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for f = 1:nfloats
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[mini, idx{f,d}] = min(abs(Datai.(floats{f}).PRES(:,1) - depth(d)));
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press{f,d} = Datai.(floats{f}).PRES(idx{f,d},1);
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if mini > Settings.depth_tol
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warning(['Closest depth level to requested %.1f db for ', ...
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'float %s is %.1f db'], depth(d), floats{f}, press{f,d});
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end
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end
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end
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for v = 1:nvars
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if ~isempty(var2_orig)
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same_var_type = strncmp(variables{v}, var2{v}, ...
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length(variables{v}) - ...
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9 * endsWith(variables{v}, '_ADJUSTED'));
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end
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for d = 1:ndepths
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if ~per_float
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% one figure per variable for all floats; make wide plot
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f1 = figure('Position',[20 20 800 400]);
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% reset color order
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set(gca,'ColorOrderIndex',1);
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hold(gca, 'on')
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end
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for f = 1:nfloats
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if per_float
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% one figure per variable for each float; make wide plot
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f1 = figure('Position',[20 20 800 400]);
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set(gca,'ColorOrderIndex',1);
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hold(gca, 'on')
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end
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plot(Datai.(floats{f}).TIME(1,:), ...
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Datai.(floats{f}).(variables{v})(idx{f,d},:), 'LineWidth', 2);
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xl = xlim;
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if ~isempty(start_date) || ~isempty(end_date)
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if ~isempty(start_date)
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xl(1) = start_date;
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end
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if ~isempty(end_date)
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xl(2) = end_date;
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end
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xlim(xl);
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end
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% determine type of time label based on length of time series
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if isempty(time_label)
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if xl(2) - xl(1) > 548 % in days; ~1.5 years
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time_label = 'y';
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else
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time_label = 'm';
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end
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end
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if strncmpi(time_label, 'y', 1)
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set(gca,'XTick',datenum([(2000:2030)' ones(31,1) ones(31,1)]));
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datetick('x','yyyy','keeplimits','keepticks');
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xlabel('Year','FontSize',14);
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else
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set(gca,'XTick',datenum([repelem((2000:2030)',12,1) ...
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repmat((1:12)',31, 1) ones(31*12,1)]));
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datetick('x','mm-yyyy','keeplimits','keepticks');
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xlabel('Month','FontSize',14);
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end
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[long_name, units] = get_var_name_units(variables{v});
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ylabel([long_name, ' ', units])
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if ~isempty(var2_orig)
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if ~same_var_type
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yyaxis right;
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end
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plot(Datai.(floats{f}).TIME(1,:), ...
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Datai.(floats{f}).(var2{v})(idx{f,d},:), 'LineWidth', 2);
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if ~same_var_type
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[long_name, units] = get_var_name_units(var2_orig);
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ylabel([long_name, ' ', units])
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end
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end
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if per_float
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hold off
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box on;
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if isempty(title1) && ~ischar(title1) % i.e., []
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if strcmp(lgnd, 'no') || ~isempty(var2_orig)
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% add float number to title instead
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title(sprintf('Depth: %d db (%s)%s', press{f,d}, ...
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floats{f}, title_added{v}));
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else % legend shows float number
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title(sprintf('Depth: %d db%s', press{f,d}, ...
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title_added{v}));
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end
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else
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title([title1, title_added{v}]);
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end
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if strcmp(lgnd,'yes')
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if isempty(var2_orig)
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legend(float_ids{f},'location','eastoutside',...
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'AutoUpdate','off');
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else
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legend({strrep(variables{v},'_','\_'); ...
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strrep(var2{v},'_','\_')}, ...
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'location', 'eastoutside', 'AutoUpdate', 'off');
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end
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end
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if ~isempty(basename)
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fn_png = sprintf('%s_%d_%s%s_%ddb.png', basename, ...
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Mdata.(float_ids{f}).WMO_NUMBER, variables{v}, ...
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var2_insert{v}, press{f,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
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if ~per_float
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hold off
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box on;
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if isempty(title1) && ~ischar(title1) % i.e., []
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if strcmp(lgnd, 'yes')
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title(sprintf('Depth: %d db%s', press{f,d}, ...
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title_added{v}));
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else
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title(sprintf('Depth: %d db (%s)%s', press{f,d}, ...
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floats{f}, title_added{v}));
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end
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else
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title([title1, title_added{v}]);
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end
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if strcmp(lgnd,'yes')
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legend(float_ids,'location','eastoutside',...
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'AutoUpdate','off');
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end
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if ~isempty(basename)
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fn_png = sprintf('%s_%s%s_%ddb.png', basename, variables{v}, ...
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var2_insert{v}, press{f,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
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end

‎initialize_argo.m‎

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@@ -69,6 +69,10 @@ function initialize_argo()
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Settings.temp_thresh = 0.2;
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Settings.dens_thresh = 0.03;
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% default value for deviation from requested depth level for time series
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% plots - if exceeded, a warning will be issued
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Settings.depth_tol = 5;
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% Settings.colormap = 'jet'; % uncomment and change as needed
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% colors for profile plots ("range" is for individual profiles using the

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