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InLineAnalysis.m
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InLineAnalysis.m
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classdef InLineAnalysis < handle
%INLINEANALYSIS Summary of this class goes here
% Detailed explanation goes here
% The handle class as representing objects whose identity is independent of the values of their properties
properties
meta=struct();
cfg=struct();
instrument = struct();
end
methods
% Constructor
function obj = InLineAnalysis(cfg_file_name)
% Pre-initialization
% Add path to library of functions
addpath('lib', 'instruments', 'packages', 'packages/datetick2_doy', ...
'packages/spectral_color', 'packages/TEOS-10_subset');
% Object Initilization
obj = obj@handle();
% Post initialization
if nargin ~= 0
[~, ~, ext] = fileparts(cfg_file_name);
switch ext
case '.json'
cfg = obj.ReadCfgJSON(cfg_file_name);
case '.m'
cfg = obj.ReadCfgM(cfg_file_name);
otherwise
error('Unknown configuration file type.');
end
obj.meta = cfg.meta;
obj.cfg = cfg.process;
% Format cfg in flag
cfg_flag_buf = obj.cfg.flag;
obj.cfg.flag = struct();
obj.cfg.flag.skip = cfg_flag_buf.skip;
% Set all instruments with default parameters
for i = fieldnames(cfg.instruments)'; i = i{1};
obj.cfg.flag.(i) = struct();
for p = fieldnames(cfg_flag_buf.default)'; p = p{1};
switch p
case {'tot', 'filt'}
% Overwrite tot|filt specific parameters
for sp = fieldnames(cfg_flag_buf.default.(p))'; sp = sp{1};
obj.cfg.flag.(i).(p).(sp) = cfg_flag_buf.default.(p).(sp);
end
otherwise
% Overwrite with instrument specific parameters (both filt and tot)
obj.cfg.flag.(i).tot.(p) = cfg_flag_buf.default.(p);
obj.cfg.flag.(i).filt.(p) = cfg_flag_buf.default.(p);
end
end
end
% Set instruments with specific parameters
% Note: orders of the parameters in the cfg files matters
for i = fieldnames(cfg.instruments)'; i = i{1};
if isfield(cfg_flag_buf, i)
for p = fieldnames(cfg_flag_buf.(i))'; p = p{1};
switch p
case {'tot', 'filt'}
% Overwrite tot|filt specific parameters
for sp = fieldnames(cfg_flag_buf.(i).(p))'; sp = sp{1};
obj.cfg.flag.(i).(p).(sp) = cfg_flag_buf.(i).(p).(sp);
end
otherwise
% Overwrite with instrument specific parameters (both filt and tot)
obj.cfg.flag.(i).tot.(p) = cfg_flag_buf.(i).(p);
obj.cfg.flag.(i).filt.(p) = cfg_flag_buf.(i).(p);
end
end
end
end
% Initialize each instrument
for i = fieldnames(cfg.instruments)'; i = i{1};
switch cfg.instruments.(i).model
case {'NMEA','SC701','GP32','GPS32Tara','GP32Tara','GPSSC701Tara','19X','GPS19X','GPSCOMPASSAT'}
obj.instrument.(i) = NMEA(cfg.instruments.(i));
case {'TSG', 'SBE45', 'SBE3845'}
obj.instrument.(i) = TSG(cfg.instruments.(i));
case 'atlasTSG'
obj.instrument.(i) = atlasTSG(cfg.instruments.(i));
case {'FTH', 'ADU100', 'ADU200'}
obj.instrument.(i) = FTH(cfg.instruments.(i));
case 'ACS'
obj.instrument.(i) = ACS(cfg.instruments.(i));
case 'AC9'
obj.instrument.(i) = AC9(cfg.instruments.(i));
case 'HBB'
obj.instrument.(i) = HBB(cfg.instruments.(i));
% case 'BB3'
% obj.instrument.(i) = BB3(cfg.instruments.(i));
% case 'WSCD'
% obj.instrument.(i) = WSCD(cfg.instruments.(i));
case {'LISST', 'LISST100X'}
obj.instrument.(i) = LISST100X(cfg.instruments.(i));
case 'LISST200X'
obj.instrument.(i) = LISST200X(cfg.instruments.(i));
case {'LISSTTau', 'LISSTTAU', 'TAU'}
obj.instrument.(i) = LISSTTau(cfg.instruments.(i));
case 'ECO'
obj.instrument.(i) = ECO(cfg.instruments.(i));
case 'FL'
obj.instrument.(i) = FL(cfg.instruments.(i));
case {'BB', 'BB3'}
obj.instrument.(i) = BB(cfg.instruments.(i));
case {'CD', 'WSCD'}
obj.instrument.(i) = CD(cfg.instruments.(i));
case 'ALFA'
obj.instrument.(i) = ALFA(cfg.instruments.(i));
case 'PAR'
obj.instrument.(i) = PAR(cfg.instruments.(i));
otherwise
error('Instrument not supported: %s.', cfg.instruments.(i).model);
end
end
% Set optional default parameters
if ~isfield(obj.cfg,'instruments2run')
obj.cfg.instruments2run = fieldnames(obj.instrument)';
end
end
fprintf('%s config file loaded in ILA structure\n', cfg_file_name)
end
% Pre-Process
function ReadRaw(obj)
% Read was renamed to ReadRaw on Oct 19, 2018
for i=obj.cfg.instruments2run; i = i{1};
if ~isfield(obj.instrument, i)
error('Instrument2run "%s" does not match any instrument name in the cfg file: %s', ...
i, strjoin(fieldnames(obj.instrument), ' / '))
else
fprintf('READ RAW: %s\n', i);
obj.instrument.(i).ReadRaw(obj.cfg.days2run, obj.cfg.force_import, true);
end
end
end
function ReadRawDI(obj)
for i=obj.cfg.instruments2run; i = i{1};
if any(strcmp(i,obj.cfg.di.skip))
fprintf('READ DI: Skip %s\n', i);
else
fprintf('READ DI: %s\n', i);
obj.instrument.(i).ReadRawDI(obj.cfg.days2run, obj.cfg.force_import, true);
end
end
end
function Sync(obj)
% Note: Run all days loaded (independent of days2run)
for i=obj.cfg.instruments2run; i = i{1};
if any(strcmp(i,obj.cfg.sync.skip))
fprintf('SYNC: Skip %s\n', i);
else
fprintf('SYNC: %s\n', i);
obj.instrument.(i).Sync(obj.cfg.sync.delay.(i));
end
end
end
function SplitDetect (obj, MinFiltPeriod, szFilt)
if nargin < 2
MinFiltPeriod = 65;
szFilt = 10;
elseif nargin < 3
szFilt = 10;
end
fprintf('Detecting %s filter events...\n', obj.cfg.qcref.view);
obj.instrument.FLOW.data = SplitDetect(obj.cfg.qcref.view,...
obj.instrument.(obj.cfg.qcref.view).data, obj.instrument.FLOW.data, MinFiltPeriod, szFilt);
fprintf('Done\n');
end
function AutoQC (obj, level)
tolerance = obj.cfg.qc.AutoQC_tolerance;
saturation_threshold = obj.cfg.qc.AutoQC_Saturation_Threshold;
if isempty(tolerance)
tolerance.dissolved.a = 3;
tolerance.dissolved.c = 3;
tolerance.filtered.a = 3;
tolerance.filtered.c = 3;
tolerance.total.a = 3;
tolerance.total.c = 3;
elseif isempty(saturation_threshold)
saturation_threshold.a = 50;
saturation_threshold.c = 50;
saturation_threshold.bb = 4000;
elseif nargin < 2
level = 'raw';
end
instru = fieldnames(obj.instrument);
for i=obj.cfg.instruments2run; i = i{1};
if any(contains(i,{'AC','BB','PAR','ALFA'}))
if ~isempty(obj.instrument.(i).(level).fsw)
% fprintf('Deleting bad values from %s filtered data ...\n', i);
if any(contains(i,'AC'))
lambda.a = obj.instrument.(i).lambda_a;
lambda.c = obj.instrument.(i).lambda_c;
bb_dark = [];
elseif any(contains(i,'BB3'))
lambda.bb = obj.instrument.(i).lambda;
bb_dark = obj.instrument.(instru{contains(instru, 'BB3')}).dark;
elseif any(contains(i,{'HBB', 'HyperBB'}))
lambda.bb = obj.instrument.(i).lambda;
bb_dark = [];
end
if any(contains(i,{'AC','BB'}))
[obj.instrument.(i).(level).fsw, bad_spec, Nbad] = AutoQC(i, obj.instrument.(i).(level).fsw,...
lambda, tolerance.filtered, bb_dark, saturation_threshold);
obj.instrument.(i).(level).bad = [obj.instrument.(i).(level).bad; bad_spec];
end
if any(contains(i,'AC'))
fprintf('%4.2f%% of absorption and %4.2f%% of attenuation spectra deleted from %s filtered %s data\n',...
Nbad.a, Nbad.c, i, level);
elseif any(contains(i,'BB'))
fprintf('\n')
fprintf('\n')
fprintf('Data percentage deleted from %s filtered %s data:\n', i, level)
lineseg = '-------+';
headseg = ' %i |';
dataseg = ' %2.2f%% |';
lin = '-----------+';
head = '| lambda |';
dat = ' %% deleted |';
for ii = 1:size(Nbad.bb,2)
lin = [lin lineseg];
head = [head headseg];
dat = [dat dataseg];
end
lin = [lin '+\n'];
head = [head '\n'];
dat = [dat '\n'];
fprintf(head, lambda.bb)
fprintf(lin);
fprintf(dat, Nbad.bb)
% for ii = 1:size(Nbad.bb,2)
% fprintf('%4.2f%% of beta%i deleted from %s filtered data\n',...
% Nbad.bb(ii), lambda.bb(ii), i);
% end
end
else
warning('No filtered data loaded: Skip');
end
if ~isempty(obj.instrument.(i).(level).tsw)
% % fprintf('Deleting bad values from %s total data ...\n', i);
if any(contains(i,'AC'))
lambda.a = obj.instrument.(i).lambda_a;
lambda.c = obj.instrument.(i).lambda_c;
elseif any(contains(i,'BB'))
lambda.bb = obj.instrument.(i).lambda;
elseif any(contains(i,'PAR'))
foo = obj.instrument.(i).(level).tsw.par./obj.instrument.PAR.scale > 4500 ...
| obj.instrument.(i).(level).tsw.par./obj.instrument.PAR.scale < 0;
obj.instrument.(i).(level).tsw(foo,:) = [];
% get percentage of data deleted
foo = sum(foo) / size(obj.instrument.(i).(level).tsw, 1) * 100;
elseif any(contains(i,'ALFA'))
alf_ar = table2array(obj.instrument.(i).(level).tsw);
toqc = repmat(~contains(obj.instrument.(i).(level).tsw.Properties.VariableNames, ...
{'dt', 'WL'}), size(alf_ar,1),1);
% clean with derivative
clean_cycles = 50;
foo = 0;
for ii = progress(1:clean_cycles)
alfa_deriv = [zeros(1, size(alf_ar, 2)); diff(alf_ar, [], 1)];
prc_deriv = repmat(prctile(alfa_deriv, 95), size(alf_ar,1),1);
toclean = toqc & alfa_deriv > 1.5*prc_deriv & alfa_deriv(:,1) < 0.6;
alf_ar(toclean) = NaN;
foo = foo + sum(toclean(:));
end
% clean with absolute values
alfa_prc = repmat(prctile(alf_ar, 95), size(alf_ar,1),1);
toclean = toqc & alfa_deriv > 1.5*alfa_prc;
alf_ar(toclean) = NaN;
foo = foo + sum(toclean(:));
% rebuild table
obj.instrument.(i).(level).tsw = array2table(alf_ar, 'VariableNames', ...
obj.instrument.(i).(level).tsw.Properties.VariableNames);
% get percentage of data deleted
foo = foo / sum(toqc(:));
end
if any(contains(i,{'AC','BB'}))
[obj.instrument.(i).(level).tsw, bad_spec, Nbad] = AutoQC(i, obj.instrument.(i).(level).tsw,...
lambda, tolerance.total, bb_dark, saturation_threshold);
obj.instrument.(i).(level).bad = [obj.instrument.(i).(level).bad; bad_spec];
end
if any(contains(i,'AC'))
fprintf('%4.2f%% of absorption and %4.2f%% of attenuation spectra deleted from %s total %s data\n',...
Nbad.a, Nbad.c, i, level);
elseif any(contains(i,'BB'))
fprintf('\n')
fprintf('\n')
fprintf('Data percentage deleted from %s total %s data:\n', i, level)
lineseg = '-------+';
headseg = ' %i |';
dataseg = ' %2.2f%% |';
lin = '-----------+';
head = '| lambda |';
dat = ' %% deleted |';
for ii = 1:size(Nbad.bb,2)
lin = [lin lineseg];
head = [head headseg];
dat = [dat dataseg];
end
lin = [lin '+\n'];
head = [head '\n'];
dat = [dat '\n'];
fprintf(head, lambda.bb)
fprintf(lin);
fprintf(dat, Nbad.bb)
elseif any(contains(i,{'PAR', 'ALFA'}))
fprintf('%.3f%% of %s %s values deleted\n', foo, level, i);
end
else
warning('No total data loaded: Skip');
end
if ~isempty(obj.instrument.(i).(level).diw)
% fprintf('Deleting bad values from %s dissolved data...\n', i);
if any(contains(i,'AC'))
lambda.a = obj.instrument.(i).lambda_a;
lambda.c = obj.instrument.(i).lambda_c;
elseif any(contains(i,'BB'))
lambda.bb = obj.instrument.(i).lambda;
end
if any(contains(i,{'AC','BB'}))
[obj.instrument.(i).(level).diw, bad_spec, Nbad] = AutoQC(i, obj.instrument.(i).(level).diw,...
lambda, tolerance.dissolved, obj.instrument.(instru{contains(instru, 'BB3')}).dark,...
saturation_threshold, true);
obj.instrument.(i).(level).bad = [obj.instrument.(i).(level).bad; bad_spec];
end
if any(contains(i,'AC'))
fprintf('%4.2f%% of absorption and %4.2f%% of attenuation spectra deleted from %s dissolved %s data\n',...
Nbad.a, Nbad.c, i, level);
elseif any(contains(i,'BB'))
fprintf('\n')
fprintf('\n')
fprintf('Data percentage deletred from %s dissolved %s data:\n', i, level)
lineseg = '-------+';
headseg = ' %i |';
dataseg = ' %2.2f%% |';
lin = '-----------+';
head = '| lambda |';
dat = ' %% deleted |';
for ii = 1:size(Nbad.bb,2)
lin = [lin lineseg];
head = [head headseg];
dat = [dat dataseg];
end
lin = [lin '+\n'];
head = [head '\n'];
dat = [dat '\n'];
fprintf(head, lambda.bb)
fprintf(lin);
fprintf(dat, Nbad.bb)
end
end
fprintf('AutoQC [Done]\n')
else
fprintf('No AutoQC for %s [Done]\n', i)
end
end
end
function SpectralQC (obj, instru, level, save_figure, toClean)
if nargin < 3
error('Not enough input argument')
elseif nargin == 3
save_figure = false;
toClean = {'',''};
elseif nargin == 4
toClean = {'',''};
elseif nargin > 5
error('Too many input argument')
end
if size(toClean,2) < 2 || ~iscell(toClean)
error("Indicate the table and variable names in cell array, e.g. {'p', 'ap'} to clean ACS product visualising ap spectra")
end
for i=obj.cfg.instruments2run; i = i{1};
if any(contains(i,instru))
fprintf('%s Spectral QCs\n', i);
[user_selection] = SpectralQC(obj.instrument.(i), obj.cfg.days2run, i, level, ...
save_figure, obj.meta.cruise, toClean);
% Apply user selection
if ~isempty(user_selection)
if ~isfolder(obj.instrument.(i).path.ui); mkdir(obj.instrument.(i).path.ui); end
obj.instrument.(i).DeleteUserSelection(user_selection, level{:}, toClean);
if strcmp(level{:}, 'prod')
obj.instrument.(i).DeleteUserSelection(user_selection, 'qc', {'tsw', strrep(toClean{2}, 'p', '')});
end
% Save user selection
if strcmp(toClean{1}, 'diw')
filename = fullfile(obj.instrument.(i).path.ui, [i '_QCDI_Specific_UserSelection.mat']);
else
filename = fullfile(obj.instrument.(i).path.ui, [i '_QCpickSpecific_UserSelection.mat']);
end
obj.update_userselection_bad(filename, user_selection, false, level{:}, toClean);
end
end
end
end
function visProd_timeseries(obj)
for i=obj.cfg.instruments2run; i = i{1};
if any(~contains(i, {'FLOW', 'FTH', 'Flow'}))
fprintf('%s products time series plots\n', i);
ifieldn = fieldnames(obj.instrument.(i).prod);
for j=1:size(ifieldn,1)
if ~strcmp(ifieldn{j}, 'FiltStat') && ~strcmp(ifieldn{j}, 'QCfailed') && ...
~isempty(obj.instrument.(i).prod.(ifieldn{j}))
if contains(i, {'BB'})
visProd_timeseries(obj.instrument.(i).prod.(ifieldn{j}), i, ...
obj.instrument.(i).lambda);
elseif contains(i, {'AC'})
visProd_timeseries(obj.instrument.(i).prod.(ifieldn{j}), i, ...
obj.instrument.(i).lambda_c);
else
visProd_timeseries(obj.instrument.(i).prod.(ifieldn{j}), i);
end
end
end
end
end
end
function Stretch(obj)
% Note: Run all days loaded (independent of days2run)
for i=obj.cfg.instruments2run; i = i{1};
if any(strcmp(i,obj.cfg.stretch.skip))
fprintf('STRETCH: Skip %s\n', i);
else
fprintf('STRETCH: %s\n', i);
obj.instrument.(i).Stretch(obj.cfg.stretch.delta.(i));
end
end
end
function QCRef(obj)
if isempty(obj.instrument.(obj.cfg.qcref.view).data.dt)
error('%s data table is empty, make sure to view the instrument you are trying to process or load your data before running QCref', ...
obj.cfg.qcref.view)
end
switch obj.cfg.qcref.mode
case 'ui'
%% create new FTH data for missing data
% round date time to second
obj.instrument.FLOW.data.dt = datenum(floor(datevec(obj.instrument.FLOW.data.dt)));
% delete duplicates (bug in flowcontrol software)
[~, L, ~] = unique(obj.instrument.FLOW.data.dt,'first');
indexToDump = not(ismember(1:numel(obj.instrument.FLOW.data.dt),L));
obj.instrument.FLOW.data(indexToDump, :) = [];
obj.instrument.FLOW.data(~isfinite(obj.instrument.FLOW.data.dt),:) = [];
% Fresh selection does not take into account previous QC
% TOTAL and FILTERED Sections
fh = fig(31);
title(['\fontsize{22}Switch position QC:' newline '\fontsize{18}Select total (t; \color{red}red\color{black}) and filtered (f; \color{green}green\color{black}) sections' newline '\fontsize{14}Press q to save and quit (close graph to cancel and quit)'], 'interpreter', 'tex');
fprintf('Select total (t; red) and filtered (f; green) sections (q to save)\n');
yyaxis('left');
plot(obj.instrument.(obj.cfg.qcref.reference).data.dt,...
obj.instrument.(obj.cfg.qcref.reference).data.(obj.instrument.(obj.cfg.qcref.reference).view.varname), ...
'k', 'LineWidth', obj.instrument.(obj.cfg.qcref.reference).view.varcol);
ylim([-0.1 1.1]);
ax = gca; ax.YColor = 'k';
ylabel('Switch position')
yyaxis('right');
plot(obj.instrument.(obj.cfg.qcref.view).data.dt,...
obj.instrument.(obj.cfg.qcref.view).data.(obj.instrument.(obj.cfg.qcref.view).view.varname)(:,obj.instrument.(obj.cfg.qcref.view).view.varcol),'.');
if contains(obj.cfg.qcref.view, 'AC')
ylabel([obj.instrument.(obj.cfg.qcref.view).view.varname ' ' ...
num2str(round(obj.instrument.(obj.cfg.qcref.view).('lambda_ref')(obj.instrument.(obj.cfg.qcref.view).view.varcol),0)) 'nm'])
elseif contains(obj.cfg.qcref.view, 'BB')
ylabel([obj.instrument.(obj.cfg.qcref.view).view.varname ' ' ...
num2str(round(obj.instrument.(obj.cfg.qcref.view).('lambda')(obj.instrument.(obj.cfg.qcref.view).view.varcol),0)) 'nm'])
else
ylabel([obj.instrument.(obj.cfg.qcref.view).view.varname obj.instrument.(obj.cfg.qcref.view).view.varcol]);
end
datetick2_doy();
legend('switch position (1=filtered | 0=total)', obj.instrument.(obj.cfg.qcref.view).view.varname, 'FontSize', 14, 'AutoUpdate','off')
[user_selection.total, user_selection.filtered] = guiSelectOnTimeSeries(fh);
obj.instrument.(obj.cfg.qcref.reference).ApplyUserInput(user_selection.total, 'total');
obj.instrument.(obj.cfg.qcref.reference).ApplyUserInput(user_selection.filtered, 'filtered');
filename = fullfile(obj.instrument.(obj.cfg.qcref.reference).path.ui, 'QCRef_UserSelection.mat');
if all(isfile(strrep(filename, '.mat', '.json')) & ~isfile(filename))
file_selection = json_to_mat(strrep(filename, '.mat', '.json'));
save(filename, 'file_selection')
end
if isfile(filename)
% Load file
load(filename, 'file_selection');
if obj.cfg.qcref.remove_old
% Remove old (days2run) selections
if ~isempty(file_selection.total)
sel = min(obj.cfg.days2run) <= file_selection.total(:,1) & file_selection.total(:,1) < max(obj.cfg.days2run) + 1;
file_selection.total(sel,:) = [];
end
if ~isempty(file_selection.filtered)
sel = min(obj.cfg.days2run) <= file_selection.filtered(:,1) & file_selection.filtered(:,1) < max(obj.cfg.days2run) + 1;
file_selection.filtered(sel,:) = [];
end
end
% Add new user selection
file_selection.total = [file_selection.total; user_selection.total];
file_selection.filtered = [file_selection.filtered; user_selection.filtered];
else
file_selection = user_selection;
end
% Save user selection
if ~isfolder(obj.instrument.(obj.cfg.qcref.reference).path.ui)
mkdir(obj.instrument.(obj.cfg.qcref.reference).path.ui);
end
save(filename, 'file_selection');
case 'load'
fprintf('QCRef LOAD: %s\n', obj.cfg.qcref.reference);
% Load previous QC and apply it
filename = fullfile(obj.instrument.(obj.cfg.qcref.reference).path.ui, 'QCRef_UserSelection.mat');
if all(isfile(strrep(filename, '.mat', '.json')) & ~isfile(filename))
file_selection = json_to_mat(strrep(filename, '.mat', '.json'));
save(filename, 'file_selection')
end
if isfile(filename)
load(filename, 'file_selection');
% Remove selection from days before & after days2run
if ~isempty(file_selection.total)
sel = file_selection.total(:,2) < min(obj.cfg.days2run) | max(obj.cfg.days2run) + 1 < file_selection.total(:,1);
file_selection.total(sel,:) = [];
end
if ~isempty(file_selection.filtered)
sel = file_selection.filtered(:,2) < min(obj.cfg.days2run) | max(obj.cfg.days2run) + 1 < file_selection.filtered(:,1);
file_selection.filtered(sel,:) = [];
end
% Apply selection
if ~isempty(file_selection.total)
obj.instrument.(obj.cfg.qcref.reference).ApplyUserInput(file_selection.total, 'total');
end
if ~isempty(file_selection.filtered)
obj.instrument.(obj.cfg.qcref.reference).ApplyUserInput(file_selection.filtered, 'filtered');
end
fh = fig(31);
title(['\fontsize{22}Switch position QC:' newline '\fontsize{18}Previous selection applied' newline 'Make sure filtered and total are properly seleceted'], 'interpreter', 'tex');
fprintf('Select total (t; red) and filtered (f; green) sections (q to save)\n');
yyaxis('left');
plot(obj.instrument.(obj.cfg.qcref.reference).data.dt,...
obj.instrument.(obj.cfg.qcref.reference).data.(obj.instrument.(obj.cfg.qcref.reference).view.varname), ...
'k', 'LineWidth', obj.instrument.(obj.cfg.qcref.reference).view.varcol);
ylim([-0.1 1.1]);
ax = gca; ax.YColor = 'k';
ylabel('Switch position')
yyaxis('right');
plot(obj.instrument.(obj.cfg.qcref.view).data.dt,...
obj.instrument.(obj.cfg.qcref.view).data.(obj.instrument.(obj.cfg.qcref.view).view.varname)(:,obj.instrument.(obj.cfg.qcref.view).view.varcol),'.');
if contains(obj.cfg.qcref.view, 'AC')
ylabel([obj.instrument.(obj.cfg.qcref.view).view.varname ' ' ...
num2str(round(obj.instrument.(obj.cfg.qcref.view).('lambda_ref')(obj.instrument.(obj.cfg.qcref.view).view.varcol),0)) 'nm'])
elseif contains(obj.cfg.qcref.view, 'BB')
ylabel([obj.instrument.(obj.cfg.qcref.view).view.varname ' ' ...
num2str(round(obj.instrument.(obj.cfg.qcref.view).('lambda')(obj.instrument.(obj.cfg.qcref.view).view.varcol),0)) 'nm'])
else
ylabel([obj.instrument.(obj.cfg.qcref.view).view.varname obj.instrument.(obj.cfg.qcref.view).view.varcol]);
end
datetick2_doy();
legend('switch position (1=filtered | 0=total)', obj.instrument.(obj.cfg.qcref.view).view.varname, 'FontSize', 14, 'AutoUpdate','off')
else
fprintf(['Warning: ' filename ' not found\n'])
end
case 'skip'
fprintf('WARNING: Reference is not QC.\n');
otherwise
error('Unknown mode.');
end
end
function Split(obj)
% Note: Run all days loaded (independent of days2run)
for i=obj.cfg.instruments2run; i = i{1};
if isempty(obj.instrument.(i).data)
error('%s data table is empty', i)
end
if any(strcmp(i, obj.cfg.split.skip))
fprintf('SPLIT: Skip %s (copy data to next level)\n', i);
obj.instrument.(i).raw.tsw = obj.instrument.(i).data;
elseif strcmp(obj.instrument.(i).split.mode, 'None')
fprintf('SPLIT: Not available for %s\n', i);
else
fprintf('SPLIT: %s\n', i);
obj.instrument.(i).Split(obj.instrument.(obj.cfg.split.reference),...
obj.cfg.split.buffer.(i));
end
end
end
function Bin(obj)
% Note: Run all days loaded (independent of days2run)
for i=obj.cfg.instruments2run; i = i{1};
obj.instrument.(i).bin.tsw = table();
obj.instrument.(i).bin.fsw = table();
if any(strcmp(i,obj.cfg.bin.skip))
fprintf('BIN: Skip %s (copy data to next level)\n', i);
obj.instrument.(i).bin.tsw = obj.instrument.(i).raw.tsw;
obj.instrument.(i).bin.fsw = obj.instrument.(i).raw.fsw;
else
fprintf('BIN: %s\n', i);
obj.instrument.(i).Bin(obj.cfg.bin.bin_size.(i),...
obj.cfg.bin.prctile_detection,...
obj.cfg.bin.prctile_average,...
obj.cfg.parallel,...
obj.cfg.bin.mode);
% obj.cfg.bin.method,...
end
end
end
function BinDI(obj)
%%% NOTE: For DIW QC is done before the Binning %%%
% Note: Run all days loaded (independent of days2run)
for i=obj.cfg.instruments2run; i = i{1};
if any(strcmp(i,obj.cfg.di.skip))
fprintf('BIN DI: Skip %s\n', i);
else
fprintf('BIN DI: %s\n', i);
obj.instrument.(i).BinDI(obj.cfg.di.bin.bin_size,...
obj.cfg.bin.prctile_detection,...
obj.cfg.bin.prctile_average,...
obj.cfg.parallel);
% obj.cfg.bin.method,...
end
end
end
% Flag is DEPRECATED: Use skip to move data to next level
function Flag(obj)
% Automatic selection of good and bad data
% Note: Run all days loaded (independent of days2run)
% add all instrument from instrument2run into the skip so that flag
% never bugs
obj.cfg.flag.skip = [obj.cfg.flag.skip; obj.cfg.instruments2run(:)];
for i=obj.cfg.instruments2run; i = i{1};
if any(strcmp(i,obj.cfg.flag.skip))
fprintf('FLAG: Skip %s (copy data to next level)\n', i);
obj.instrument.(i).qc.tsw = obj.instrument.(i).bin.tsw;
obj.instrument.(i).qc.fsw = obj.instrument.(i).bin.fsw;
else
fprintf('FLAG: %s\n', i);
obj.instrument.(i).Flag(obj.cfg.flag.(i))
end
end
end
function QC(obj)
% Check if remove data when flow below threshold
if isfield(obj.cfg.qc, 'remove_when_flow_below')
if islogical(obj.cfg.qc.remove_when_flow_below)
if obj.cfg.qc.remove_when_flow_below
flow_threshold = 0.5;
rm_with_flow = true;
else
rm_with_flow = false;
end
elseif isnumeric(obj.cfg.qc.remove_when_flow_below)
flow_threshold = obj.cfg.qc.remove_when_flow_below;
rm_with_flow = true;
else
rm_with_flow = false;
end
else
rm_with_flow = false;
end
% select flow while rounding timestamps
if ~isempty(obj.instrument.FLOW.raw.tsw)
flow_level = 'raw';
elseif ~isempty(obj.instrument.FLOW.bin.tsw)
flow_level = 'bin';
elseif ~isempty(obj.instrument.FLOW.qc.tsw)
flow_level = 'qc';
else
warning('Flow data not loaded')
flow_level = 'raw';
end
obj.instrument.FLOW.(flow_level).tsw = round_timestamp(obj.instrument.FLOW.(flow_level).tsw);
% remove sections with low flow
for i=obj.cfg.qc.specific.run(:)'; i = i{1};
if ~any(strcmp(obj.cfg.instruments2run, i)); continue; end
% round timestamps
if ~isempty(obj.instrument.(i).qc.fsw)
obj.instrument.(i).qc.fsw = round_timestamp(obj.instrument.(i).qc.fsw);
end
if ~isempty(obj.instrument.(i).qc.tsw)
obj.instrument.(i).qc.tsw = round_timestamp(obj.instrument.(i).qc.tsw);
end
if rm_with_flow
remove_low_flow(obj, i, flow_level, flow_threshold)
end
end
fooflow = obj.instrument.FLOW.(flow_level).tsw;
% Manual quality check of the data resulting in good and bad data
switch obj.cfg.qc.mode
case 'ui'
if obj.cfg.qc.global.active
% Display interactive figure
foo = obj.instrument.(obj.cfg.qc.global.view{:});
fh=visFlag(foo.raw.tsw, foo.raw.fsw, foo.qc.tsw, foo.suspect.tsw,...
foo.qc.fsw, foo.suspect.fsw, foo.view.varname, foo.view.varcol,...
foo.raw.bad, fooflow, obj.instrument.FLOW.view.spd_variable);
title('\fontsize{22}\color{red}Global QC: \fontsize{18}\color{black}Press t to trash section (press q to save)', 'interpreter', 'tex');
fprintf('Global QC: Press t to trash section (press q to save)\n');
user_selection = guiSelectOnTimeSeries(fh);
% For each instrument
for i=obj.cfg.qc.global.apply(:)'; i = i{1};
if ~any(strcmp(obj.cfg.instruments2run, i)); continue; end
% Apply user selection
obj.instrument.(i).DeleteUserSelection(user_selection);
% Save user selection
filename = fullfile(fileparts(obj.instrument.(i).path.ui), 'QCGlobal_UserSelection.mat');
if ~isfolder(fileparts(fileparts(obj.instrument.(i).path.ui)))
mkdir(fileparts(fileparts(obj.instrument.(i).path.ui)));
end
obj.update_userselection_bad(filename, user_selection, obj.cfg.qc.remove_old);
end
else
% Load previous globalQC if file exists and apply
for i=obj.cfg.qc.global.apply(:)'; i = i{1};
if ~any(strcmp(obj.cfg.instruments2run, i)); continue; end
filename = fullfile(fileparts(obj.instrument.(i).path.ui), 'QCGlobal_UserSelection.mat');
if all(isfile(strrep(filename, '.mat', '.json')) & ~isfile(filename))
file_selection = json_to_mat(strrep(filename, '.mat', '.json'));
save(filename, 'file_selection')
end
if isfile(filename)
fprintf('QC LOAD Global selection: %s ... ', i);
load(filename, 'file_selection');
fprintf('done\n')
obj.instrument.(i).DeleteUserSelection(file_selection.bad);
end
end
end
if obj.cfg.qc.specific.active
% For each instrument
for i=obj.cfg.qc.specific.run(:)'; i = i{1};
if ~any(strcmp(obj.cfg.instruments2run, i)); continue; end
if ~isfolder(obj.instrument.(i).path.ui); mkdir(obj.instrument.(i).path.ui); end
if contains(i, 'AC')
channel = {'a', 'c'};
elseif contains(i, {'TSG', 'SBE45', 'SBE3845'})
if ~strcmp(obj.instrument.(i).qc.tsw.Properties.VariableNames, 's')
channel = {obj.instrument.(i).temperature_variable, 'c'};
else
channel = {obj.instrument.(i).temperature_variable, 's'};
end
end
if contains(i, {'AC', 'TSG', 'SBE45', 'SBE3845'}) && ~obj.cfg.qc.qc_once_for_all
for j = channel
% Display interactive figure
fh=visFlag(obj.instrument.(i).raw.tsw, obj.instrument.(i).raw.fsw, ...
obj.instrument.(i).qc.tsw, obj.instrument.(i).suspect.tsw, obj.instrument.(i).qc.fsw, ...
obj.instrument.(i).suspect.fsw, j{:}, obj.instrument.(i).view.varcol,...
obj.instrument.(i).raw.bad, fooflow, obj.instrument.FLOW.view.spd_variable);
title(['\fontsize{22}\color{red}' i ' QC of "' j{:} '" only:' newline '\fontsize{18}\color{black}Press t to trash section (press q to save)'], 'interpreter', 'tex');
fprintf([i ' QC of "' j{:} '" only: Press t to trash section (press q to save)\n']);
% Get user selection
user_selection = guiSelectOnTimeSeries(fh);
% Apply user selection
obj.instrument.(i).DeleteUserSelection(user_selection, 'qc', ['tsw' j]);
obj.instrument.(i).DeleteUserSelection(user_selection, 'qc', ['fsw' j]);
% Save user selection
filename = fullfile(obj.instrument.(i).path.ui, [i '_QCSpecific_UserSelection.mat']);
obj.update_userselection_bad(filename, user_selection, obj.cfg.qc.remove_old, ...
'qc', ['tsw' j]);
obj.update_userselection_bad(filename, user_selection, obj.cfg.qc.remove_old, ...
'qc', ['fsw' j]);
clf(52)
end
elseif contains(i, 'ALFA') && ~obj.cfg.qc.qc_once_for_all
channel = obj.instrument.(i).qc.tsw.Properties.VariableNames;
channel(contains(channel, {'dt', '_avg_sd', '_avg_n'})) = [];
for j = channel
% delete crazy values
if contains(j{:}, 'WL')
obj.instrument.(i).qc.tsw.(j{:})(obj.instrument.(i).qc.tsw.(j{:}) > 1000 | obj.instrument.(i).qc.tsw.(j{:}) < 540) = NaN;
else
obj.instrument.(i).qc.tsw.(j{:})(obj.instrument.(i).qc.tsw.(j{:}) > 100) = NaN;
end
fh=visFlag(obj.instrument.(i).raw.tsw, obj.instrument.(i).raw.fsw, ...
obj.instrument.(i).qc.tsw, obj.instrument.(i).suspect.tsw, obj.instrument.(i).qc.fsw, ...
obj.instrument.(i).suspect.fsw, j{:}, obj.instrument.(i).view.varcol,...
obj.instrument.(i).raw.bad, fooflow, obj.instrument.FLOW.view.spd_variable);
title(['\fontsize{22}\color{red}' i ' QC of "' j{:} '" only:' newline '\fontsize{18}\color{black}Press t to trash section (press q to save)'], 'interpreter', 'tex');
fprintf([i ' QC of "' j{:} '" only: Press t to trash section (press q to save)\n']);
% Get user selection
user_selection = guiSelectOnTimeSeries(fh);
% Apply user selection
obj.instrument.(i).DeleteUserSelection(user_selection, 'qc', ['tsw' j]);
% Save user selection
filename = fullfile(obj.instrument.(i).path.ui, [i '_QCSpecific_UserSelection.mat']);
obj.update_userselection_bad(filename, user_selection, obj.cfg.qc.remove_old, ...
'qc', ['tsw' j]);
clf(52)
end
else
if ~isempty(obj.instrument.(i).raw.tsw)
fh=visFlag(obj.instrument.(i).raw.tsw, obj.instrument.(i).raw.fsw, obj.instrument.(i).qc.tsw, ...
obj.instrument.(i).suspect.tsw, obj.instrument.(i).qc.fsw, obj.instrument.(i).suspect.fsw, ...
obj.instrument.(i).view.varname, obj.instrument.(i).view.varcol,...
obj.instrument.(i).raw.bad, fooflow, obj.instrument.FLOW.view.spd_variable);
else
fh=visFlag([], [], obj.instrument.(i).qc.tsw, obj.instrument.(i).suspect.tsw, ...
obj.instrument.(i).qc.fsw, obj.instrument.(i).suspect.fsw,...
obj.instrument.(i).view.varname, obj.instrument.(i).view.varcol, ...
obj.instrument.(i).raw.bad, fooflow, obj.instrument.FLOW.view.spd_variable);
end
title(['\fontsize{22}\color{red}' i ' QC all variables:' newline '\fontsize{18}\color{black}Press t to trash section (press q to save)'], 'interpreter', 'tex');
fprintf([i ' QC all: Press t to trash section (press q to save)\n']);
user_selection = guiSelectOnTimeSeries(fh);
% Apply user selection
obj.instrument.(i).DeleteUserSelection(user_selection);
% Save user selection
filename = fullfile(obj.instrument.(i).path.ui, [i '_QCSpecific_UserSelection.mat']);
obj.update_userselection_bad(filename, user_selection, obj.cfg.qc.remove_old);
end
end
end
if ~obj.cfg.qc.global.active && ~obj.cfg.qc.specific.active
fprintf('WARNING: Quality check is NOT performed.\n');
end
case 'load'
% Load previous QC files and apply them
% if obj.cfg.qc.global.active
for i=obj.cfg.qc.global.apply(:)'; i = i{1};
if ~any(strcmp(obj.cfg.instruments2run, i)); continue; end
fprintf('QC LOAD Global selection: %s ... ', i);
filename = fullfile(fileparts(obj.instrument.(i).path.ui), 'QCGlobal_UserSelection.mat');
if all(isfile(strrep(filename, '.mat', '.json')) & ~isfile(filename))
file_selection = json_to_mat(strrep(filename, '.mat', '.json'));
save(filename, 'file_selection')
end
if isfile(filename)
load(filename, 'file_selection');
fprintf('done\n')
obj.instrument.(i).DeleteUserSelection(file_selection.bad);
else
fprintf(['Warning: ' filename ' not found\n'])
end
end
% end
if obj.cfg.qc.specific.active
for i=obj.cfg.qc.specific.run(:)'; i = i{1};
if ~any(strcmp(obj.cfg.instruments2run, i)); continue; end
fprintf('QC LOAD Specific slection: %s ... ', i);
filename = fullfile(obj.instrument.(i).path.ui, [i '_QCSpecific_UserSelection.mat']);
if all(isfile(strrep(filename, '.mat', '.json')) & ~isfile(filename))
file_selection = json_to_mat(strrep(filename, '.mat', '.json'));
save(filename, 'file_selection')
end
if isfile(filename)
fprintf('done\n')
load(filename, 'file_selection');
sel_toload = fieldnames(file_selection);
for j = 1:size(sel_toload, 1)
% Keep only selection of the day2run
file_selection.(sel_toload{j})(any(file_selection.(sel_toload{j}) < min(obj.cfg.days2run) | ...
file_selection.(sel_toload{j}) > max(obj.cfg.days2run)+1, 2)) = [];
if ~isempty(file_selection.(sel_toload{j}))
if contains(i, 'AC')
channel = strsplit(sel_toload{j}, 'bad_');
foo = strsplit(channel{end}, '_');
if size(foo, 2) == 1
level = 'qc';
channel = channel(end);
elseif size(foo, 2) == 2
level = 'qc';
channel = foo;
elseif size(foo, 2) == 3
level = foo{1};
channel = foo(2:3);
end
obj.instrument.(i).DeleteUserSelection(file_selection.(sel_toload{j}), ...
level, channel);
else
obj.instrument.(i).DeleteUserSelection(file_selection.(sel_toload{j}));
end
end
end
else
fprintf(['Warning: ' filename ' not found\n'])
end
fprintf('QC LOAD Specific pick selection: %s ... ', i);
filename = fullfile(obj.instrument.(i).path.ui, [i '_QCpickSpecific_UserSelection.mat']);
if all(isfile(strrep(filename, '.mat', '.json')) & ~isfile(filename))
file_selection = json_to_mat(strrep(filename, '.mat', '.json'));
save(filename, 'file_selection')
end
if isfile(filename)
% load hand picked bad values
fprintf('done\n')
load(filename, 'file_selection');
sel_picktoload = fieldnames(file_selection);
for j = progress(1:size(sel_picktoload, 1))
% Keep only selection of the day2run
file_selection.(sel_picktoload{j})(any(file_selection.(sel_picktoload{j}) < min(obj.cfg.days2run) | ...
file_selection.(sel_picktoload{j}) > max(obj.cfg.days2run)+1, 2)) = [];
if ~isempty(file_selection.(sel_picktoload{j}))
channel = strsplit(sel_picktoload{j}, 'bad_');
foo = strsplit(channel{end}, '_');
if size(foo, 2) == 1
level = 'qc';
channel = {'all'};
elseif size(foo, 2) == 2
level = 'qc';
channel = foo;
elseif size(foo, 2) == 3
level = foo{1};
channel = foo(2:3);
end
if contains(i, 'AC')
obj.instrument.(i).DeleteUserSelection(file_selection.(sel_picktoload{j}), ...
level, channel);
if strcmp(level, 'prod')
obj.instrument.(i).DeleteUserSelection(file_selection.(sel_picktoload{j}), ...
'qc', {'tsw', strrep(channel{2}, 'p', '')});
end
else
obj.instrument.(i).DeleteUserSelection(file_selection.(sel_picktoload{j}), level);
if strcmp(level, 'prod')
obj.instrument.(i).DeleteUserSelection(file_selection.(sel_picktoload{j}), 'qc');
end
end
end
end
else
fprintf(['Warning: ' filename ' not found\n'])
end
end
end
if ~obj.cfg.qc.global.active && ~obj.cfg.qc.specific.active
fprintf('WARNING: Quality check is NOT performed.\n');
end
case 'skip'
fprintf('WARNING: Quality Check is NOT performed.\n');
otherwise
error('Unknown mode.');
end
end
function QCDI(obj)
%%% NOTE: For DIW QC is done before the Binning %%%
% Manual quality check of the data resulting in good and bad data
% Check if qc level is empty for each instrument
for i=obj.cfg.instruments2run; i = i{1};
if isempty(obj.instrument.(i).qc.diw)
obj.instrument.(i).qc.diw = obj.instrument.(i).raw.diw;
end
end
switch obj.cfg.di.qc.mode
case 'ui'
% For each instrument
for i=obj.cfg.instruments2run; i = i{1};
if ~any(strcmp(obj.cfg.instruments2run, i)) || any(strcmp(obj.cfg.di.skip, i)); continue; end
% Display interactive figure
foo = obj.instrument.(i); %(obj.instrument.(i).dt, ;
if isempty(foo.qc.diw)
error('Empty qc diw \n');
end
% create folder for user input
filename = fullfile(obj.instrument.(i).path.ui, [i '_QCDI_UserSelection.mat']);
if all(isfile(strrep(filename, '.mat', '.json')) & ~isfile(filename))
file_selection = json_to_mat(strrep(filename, '.mat', '.json'));
save(filename, 'file_selection')
end
if ~isfolder(obj.instrument.(i).path.ui); mkdir(obj.instrument.(i).path.ui); end
ColorSet = lines(2);
fh = fig(52); hold('on');
if contains(i, 'AC') && ~obj.cfg.di.qc.qc_once_for_all
channel = {'a', 'c'};
for j = 1:size(channel,2)
plot(foo.qc.diw.dt, foo.qc.diw.(channel{j})(:,foo.view.varcol), 'o', 'Color', ColorSet(j,:));
title([i ' QC of "' channel{j} '" only' newline 'Press t to trash section (press q to save)']);
ylabel(channel{j});
datetick2_doy();
set(datacursormode(fh), 'UpdateFcn', @data_cursor_display_date);
% Get user selection
user_selection = guiSelectOnTimeSeries(fh);
% Apply user selection
obj.instrument.(i).DeleteUserSelection(user_selection, 'qc', ['diw' channel(j)]);
% Save user selection
obj.update_userselection_bad(filename, user_selection, obj.cfg.di.qc.remove_old, ...
'qc', ['diw' channel(j)]);
clf(52)
end
else
plot(foo.qc.diw.dt, foo.qc.diw.(foo.view.varname)(:,foo.view.varcol), 'o', 'Color', ColorSet(1,:));
ylabel(foo.view.varname);
title([i ' QC all' newline 'Trash full section pressing t (q to save)']);
datetick2_doy();