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Merge pull request #390 from aodn/2.5.20
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2.5.20
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@ggalibert
ggalibert committed Nov 21, 2016
2 parents 7fc6700 + 39c8081 commit cd3ae8d
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Showing 16 changed files with 95 additions and 30 deletions.
11 changes: 9 additions & 2 deletions AutomaticQC/imosHistoricalManualSetQC.m
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Expand Up @@ -57,8 +57,15 @@
paramsLog = [];

% read manual QC file for this dataset
[mqcPath, mqcFile, ~] = fileparts(sample_data.toolbox_input_file);
mqcFile = fullfile(mqcPath, [mqcFile, '.mqc']);
mqcFile = [sample_data.toolbox_input_file, '.mqc'];

% we need to migrate any remnants of the old file naming convention
% for .mqc files.
[mqcPath, oldMqcFile, ~] = fileparts(sample_data.toolbox_input_file);
oldMqcFile = fullfile(mqcPath, [oldMqcFile, '.mqc']);
if exist(oldMqcFile, 'file')
movefile(oldMqcFile, mqcFile);
end

if exist(mqcFile, 'file')
load(mqcFile, '-mat', 'mqc');
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12 changes: 10 additions & 2 deletions AutomaticQC/readQCparameter.m
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Expand Up @@ -64,8 +64,16 @@
if ~ischar(QCtest), error('QCtest must be a string'); end
if ~ischar(param), error('param must be a string'); end

[pqcPath, pqcFile, ~] = fileparts(rawDataFile);
pqcFile = fullfile(pqcPath, [pqcFile, '.pqc']);
pqcFile = [rawDataFile, '.pqc'];

% we need to migrate any remnants of the old file naming convention
% for .pqc files.
[pqcPath, oldPqcFile, ~] = fileparts(rawDataFile);
oldPqcFile = fullfile(pqcPath, [oldPqcFile, '.pqc']);
if exist(oldPqcFile, 'file')
movefile(oldPqcFile, pqcFile);
end

pqc = struct([]);

if exist(pqcFile, 'file')
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12 changes: 10 additions & 2 deletions AutomaticQC/writeQCparameter.m
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Expand Up @@ -61,8 +61,16 @@ function writeQCparameter(rawDataFile, QCtest, param, value)
if ~ischar(QCtest), error('QCtest must be a string'); end
if ~ischar(param), error('param must be a string'); end

[pqcPath, pqcFile, ~] = fileparts(rawDataFile);
pqcFile = fullfile(pqcPath, [pqcFile, '.pqc']);
pqcFile = [rawDataFile, '.pqc'];

% we need to migrate any remnants of the old file naming convention
% for .pqc files.
[pqcPath, oldPqcFile, ~] = fileparts(rawDataFile);
oldPqcFile = fullfile(pqcPath, [oldPqcFile, '.pqc']);
if exist(oldPqcFile, 'file')
movefile(oldPqcFile, pqcFile);
end

pqc = struct([]);

if exist(pqcFile, 'file'), load(pqcFile, '-mat', 'pqc'); end
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34 changes: 28 additions & 6 deletions FlowManager/displayManager.m
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Expand Up @@ -478,8 +478,16 @@ function dataSelectCallback(ax, type, range)
flags = flagFunc(panel, graphs, sample_data{setIdx}, vars);

% write/update manual QC file for this dataset
[mqcPath, mqcFile, ~] = fileparts(sample_data{setIdx}.toolbox_input_file);
mqcFile = fullfile(mqcPath, [mqcFile, '.mqc']);
mqcFile = [sample_data{setIdx}.toolbox_input_file, '.mqc'];

% we need to check first that there is not any remnants from
% the old .mqc file naming convention
[mqcPath, oldMqcFile, ~] = fileparts(sample_data{setIdx}.toolbox_input_file);
oldMqcFile = fullfile(mqcPath, [oldMqcFile, '.mqc']);
if exist(oldMqcFile, 'file')
movefile(oldMqcFile, mqcFile);
end

mqc = struct([]);

if exist(mqcFile, 'file'), load(mqcFile, '-mat', 'mqc'); end
Expand Down Expand Up @@ -552,8 +560,15 @@ function resetManQCCallback()
end
end

[mqcPath, mqcFile, ~] = fileparts(sample_data{resetIdx(j)}.toolbox_input_file);
mqcFile = fullfile(mqcPath, [mqcFile, '.mqc']);
mqcFile = [sample_data{resetIdx(j)}.toolbox_input_file, '.mqc'];

% we need to migrate any remnants of the old file naming convention
% for .mqc files.
[mqcPath, oldMqcFile, ~] = fileparts(sample_data{resetIdx(j)}.toolbox_input_file);
oldMqcFile = fullfile(mqcPath, [oldMqcFile, '.mqc']);
if exist(oldMqcFile, 'file')
movefile(oldMqcFile, mqcFile);
end

if exist(mqcFile, 'file')
delete(mqcFile);
Expand Down Expand Up @@ -594,8 +609,15 @@ function resetPropQCCallback()
end
end

[pqcPath, pqcFile, ~] = fileparts(sample_data{resetIdx(j)}.toolbox_input_file);
pqcFile = fullfile(pqcPath, [pqcFile, '.pqc']);
pqcFile = [sample_data{resetIdx(j)}.toolbox_input_file, '.pqc'];

% we need to migrate any remnants of the old file naming convention
% for .pqc files.
[pqcPath, oldPqcFile, ~] = fileparts(sample_data{resetIdx(j)}.toolbox_input_file);
oldPqcFile = fullfile(pqcPath, [oldPqcFile, '.pqc']);
if exist(oldPqcFile, 'file')
movefile(oldPqcFile, pqcFile);
end

if exist(pqcFile, 'file')
delete(pqcFile);
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20 changes: 15 additions & 5 deletions GUI/mainWindow.m
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Expand Up @@ -254,8 +254,8 @@ function mainWindow(...
buttons = findall(tb);

zoomoutb = findobj(buttons, 'TooltipString', 'Zoom Out');
zoominb = findobj(buttons, 'TooltipString', 'Zoom In');
panb = findobj(buttons, 'TooltipString', 'Pan');
zoominb = findobj(buttons, 'TooltipString', 'Zoom In (Ctrl+z)');
panb = findobj(buttons, 'TooltipString', 'Pan (Ctrl+a)');
datacursorb = findobj(buttons, 'TooltipString', 'Data Cursor');

buttons(buttons == tb) = [];
Expand Down Expand Up @@ -318,11 +318,16 @@ function mainWindow(...
set(hToolsLineCastVarNonQC, 'callBack', {@displayLineCastVar, false});
set(hToolsLineCastVarQC, 'callBack', {@displayLineCastVar, true});
end
hHelpMenu = uimenu(fig, 'label', 'Help');
hHelpWiki = uimenu(hHelpMenu, 'label', 'IMOS Toolbox Wiki');
hHotKeyMenu = uimenu(fig, 'label', 'Hot Keys');
uimenu(hHotKeyMenu, 'Label', 'Enable zoom', 'Accelerator', 'z', 'Callback', @(src,evt)zoom(fig, 'on'));
uimenu(hHotKeyMenu, 'Label', 'Enable pan', 'Accelerator', 'a', 'Callback', @(src,evt)pan( fig, 'on'));
uimenu(hHotKeyMenu, 'Label', 'Disable zoom/pan', 'Accelerator', 'q', 'Callback', @disableZoomAndPan);

hHelpMenu = uimenu(fig, 'label', 'Help');
hHelpWiki = uimenu(hHelpMenu, 'label', 'IMOS Toolbox Wiki');

%set menu callbacks
set(hHelpWiki, 'callBack', @openWikiPage);
set(hHelpWiki, 'callBack', @openWikiPage);

%% Widget Callbacks

Expand Down Expand Up @@ -634,6 +639,11 @@ function displayLineMooringVar(source,ev, isQC)

end

function disableZoomAndPan(source, ev)
pan(fig, 'off');
zoom(fig, 'off');
end

function displayLineCastVar(source,ev, isQC)
%DISPLAYLINECASTVAR Opens a new window where all the
% variables collected by the CTD cast are line-plotted.
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16 changes: 8 additions & 8 deletions IMOS/imosParameters.txt
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Expand Up @@ -133,7 +133,7 @@ SW, 1, surface_downwelling_shortwave_flux_in_air,
SWPD, 0, sea_surface_peak_swell_wave_from_direction, degree, clockwise, true north, W, 999999.0, 0.0, 360.0, float
SWPD_MAG, 0, sea_surface_peak_swell_wave_from_direction, degree, clockwise, magnetic north, W, 999999.0, 0.0, 360.0, float
SWPP, 0, sea_surface_peak_swell_wave_period, Second, , , W, 999999.0, 0.0, 100.0, float
SWSH, 1, sea_surface_swell_wave_significant_height, m, up, sea surface, W, 999999.0, 0.0, 100.0, float
SWSH, 1, sea_surface_swell_wave_significant_height, m, , , W, 999999.0, 0.0, 100.0, float
SW_NET, 1, surface_net_upward_shortwave_flux, W m-2, , , F, 999999.0, , , float
TAU, 1, magnitude_of_surface_downward_stress, Pascal, , , F, 999999.0, , , float
TEMP, 1, sea_water_temperature, degrees_Celsius,, , T, 999999.0, -2.5, 40.0, float
Expand All @@ -145,7 +145,7 @@ TRAJECTORY, 0, unique_identifier_for_each_trajectory_feature_instance_i
UCUR, 1, eastward_sea_water_velocity, m s-1, , , V, 999999.0, -10.0, 10.0, float
UCUR_MAG, 0, magnetic_eastward_sea_water_velocity, m s-1, , , V, 999999.0, -10.0, 10.0, float
UWND, 1, eastward_wind, m s-1, , , M, 999999.0, , , float
VAVH, 1, sea_surface_wave_significant_height, m, up, sea surface, W, 999999.0, 0.0, 100.0, float
VAVH, 1, sea_surface_wave_significant_height, m, , , W, 999999.0, 0.0, 100.0, float
VAVT, 1, sea_surface_wave_zero_upcrossing_period, Second, , , W, 999999.0, 0.0, 100.0, float
VBSC, 0, volumetric_backscatter_coefficient, m-1 sr-1, , , E, 999999.0, , , float
VCUR, 1, northward_sea_water_velocity, m s-1, , , V, 999999.0, -10.0, 10.0, float
Expand Down Expand Up @@ -176,16 +176,16 @@ VWND, 1, northward_wind,
WCUR, 1, upward_sea_water_velocity, m s-1, , , V, 999999.0, -5.0, 5.0, float
WDIR, 1, wind_to_direction, degree, clockwise, true north, M, 999999.0, 0.0, 360.0, float
WDIRF_AVG, 1, wind_from_direction, degree, clockwise, true north, M, 999999.0, 0.0, 360.0, float
WHTE, 0, sea_surface_wave_significant_height_of_highest_one_tenth, m, up, sea surface, W, 999999.0, 0.0, 100.0, float
WHTH, 0, sea_surface_wave_significant_height_of_highest_one_third, m, up, sea surface, W, 999999.0, 0.0, 100.0, float
WHTE, 0, sea_surface_wave_significant_height_of_highest_one_tenth, m, , , W, 999999.0, 0.0, 100.0, float
WHTH, 0, sea_surface_wave_significant_height_of_highest_one_third, m, , , W, 999999.0, 0.0, 100.0, float
WPFM, 1, sea_surface_wave_mean_period_from_variance_spectral_density_first_frequency_moment, Second, , , W, 999999.0, 0.0, 100.0, float
WPMH, 0, sea_surface_wave_zero_crossing_period, Second, , , W, 999999.0, 0.0, 100.0, float
WPSM, 1, sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment, Second, , , W, 999999.0, 0.0, 100.0, float
WPTE, 0, sea_surface_wave_period_of_highest_one_tenth, Second, , , W, 999999.0, 0.0, 100.0, float
WPTH, 0, sea_surface_wave_period_of_highest_one_third, Second, , , W, 999999.0, 0.0, 100.0, float
WMPP, 0, sea_surface_wave_maximum_zero_crossing_period, Second, , , W, 999999.0, 0.0, 100.0, float
WMSH, 0, sea_surface_wave_zero_crossing_mean_height, m, up, sea surface, W, 999999.0, 0.0, 100.0, float
WMXH, 0, sea_surface_wave_maximum_height, m, up, sea surface, W, 999999.0, 0.0, 100.0, float
WMSH, 0, sea_surface_wave_zero_crossing_mean_height, m, , , W, 999999.0, 0.0, 100.0, float
WMXH, 0, sea_surface_wave_maximum_height, m, , , W, 999999.0, 0.0, 100.0, float
WPDI, 0, sea_surface_wave_from_direction_at_variance_spectral_density_maximum, degree, clockwise, true north, W, 999999.0, 0.0, 360.0, float
WPDI_MAG, 0, sea_surface_wave_from_direction_at_variance_spectral_density_maximum, degree, clockwise, magnetic north, W, 999999.0, 0.0, 360.0, float
WPDIT, 0, sea_surface_wave_to_direction_at_variance_spectral_density_maximum, degree, clockwise, true north, W, 999999.0, 0.0, 360.0, float
Expand All @@ -195,12 +195,12 @@ WSPD, 1, wind_speed,
WSPD_AVG, 1, wind_speed, m s-1, , , M, 999999.0, , , float
WSPD_MIN, 1, wind_speed, m s-1, , , M, 999999.0, , , float
WSPD_MAX, 1, wind_speed, m s-1, , , M, 999999.0, , , float
WSSH, 0, sea_surface_wave_spectral_significant_height, m, up, sea surface, W, 999999.0, 0.0, 100.0, float
WSSH, 0, sea_surface_wave_spectral_significant_height, m, , , W, 999999.0, 0.0, 100.0, float
WWAV, 1, sea_surface_wind_wave_to_direction, degree, clockwise, true north, W, 999999.0, 0.0, 360.0, float
WWDS, 0, sea_surface_wind_wave_directional_spread, degree, clockwise, true north, W, 999999.0, 0.0, 360.0, float
WWPD, 0, sea_surface_peak_wind_sea_wave_from_direction, degree, clockwise, true north, W, 999999.0, 0.0, 360.0, float
WWPD_MAG, 0, sea_surface_peak_wind_sea_wave_from_direction, degree, clockwise, magnetic north, W, 999999.0, 0.0, 360.0, float
WWPP, 0, sea_surface_peak_wind_sea_wave_period, Second, , , W, 999999.0, 0.0, 100.0, float
WWSH, 1, sea_surface_wind_wave_significant_height, m, up, sea surface, W, 999999.0, 0.0, 100.0, float
WWSH, 1, sea_surface_wind_wave_significant_height, m, , , W, 999999.0, 0.0, 100.0, float
XCO2_AIR, 1, mole_fraction_of_carbon_dioxide_in_air, 1e-6, , , K, 999999.0, , , float
XCO2_WATER, 0, mole_fraction_of_carbon_dioxide_in_sea_water, 1e-6, , , K, 999999.0, , , float
6 changes: 5 additions & 1 deletion NetCDF/exportNetCDF.m
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Expand Up @@ -53,7 +53,7 @@
if ~ischar(dest), error('dest must be a string'); end

% check that destination is a directory
[stat atts] = fileattrib(dest);
[stat, atts] = fileattrib(dest);
if ~stat || ~atts.directory || ~atts.UserWrite
error([dest ' does not exist, is not a directory, or is not writeable']);
end
Expand Down Expand Up @@ -644,6 +644,10 @@ function putAtts(fid, vid, var, template, templateFile, netcdfType, dateFmt, mod

% each att is a struct field
atts = fieldnames(template);

% let's process them in the alphabetical order regardless of the case
[~, iSort] = sort(lower(atts));
atts = atts(iSort);
for k = 1:length(atts)

name = atts{k};
Expand Down
2 changes: 1 addition & 1 deletion Parser/SBE19Parse.m
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Expand Up @@ -252,7 +252,7 @@
sample_data.variables{end}.name = 'TIME';
sample_data.variables{end}.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.variables{end}.name, 'type')));
sample_data.variables{end}.data = sample_data.variables{end}.typeCastFunc([descendingTime, ascendingTime]);
sample_data.variables{end}.comment = 'First value over profile measurement';
sample_data.variables{end}.comment = 'First value over profile measurement.';

sample_data.variables{end+1}.dimensions = dimensions;
sample_data.variables{end}.name = 'DIRECTION';
Expand Down
2 changes: 1 addition & 1 deletion Parser/readXR420.m
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Expand Up @@ -178,7 +178,7 @@
sample_data.variables{end}.name = 'TIME';
sample_data.variables{end}.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.variables{end}.name, 'type')));
sample_data.variables{end}.data = sample_data.variables{end}.typeCastFunc([descendingTime, ascendingTime]);
sample_data.variables{end}.comment = 'First value over profile measurement';
sample_data.variables{end}.comment = 'First value over profile measurement.';

sample_data.variables{end+1}.dimensions = dimensions;
sample_data.variables{end}.name = 'DIRECTION';
Expand Down
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