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Merge pull request #479 from aodn/2.5.35
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2.5.35
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@ggalibert
ggalibert authored Oct 11, 2017
2 parents 25470a1 + 3d541ad commit 837cf01
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Showing 9 changed files with 122 additions and 55 deletions.
33 changes: 28 additions & 5 deletions AutomaticQC/imosSalinityFromPTQC.m
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@

if ~strcmp(type, 'variables'), return; end

param = {'PSAL'};
salinityName = {'PSAL'};

% let's handle the case we have multiple same param distinguished by "_1",
% "_2", etc...
Expand All @@ -73,7 +73,7 @@
end
end

iParam = strcmpi(paramName, param);
iParam = strcmpi(paramName, salinityName);

if any(iParam)
% get the flag values with which we flag good and out of range data
Expand All @@ -93,11 +93,16 @@

% initialise all flags to non QC'd
flags = ones(lenData, 1, 'int8')*rawFlag;
depthFlags = ones(lenData, 1, 'int8')*rawFlag;
pressureFlags = ones(lenData, 1, 'int8')*rawFlag;

% we look for flags from pressure, conductivity and temperature data to give them
% to salinity as well
paramNames = {'DEPTH', 'PRES_REL', 'PRES', 'TEMP', 'CNDC'};
paramNames = {'TEMP', 'CNDC'};
depthName = {'DEPTH'};
pressureNames = {'PRES_REL', 'PRES'};

isDepth = false;
for i=1:length(sample_data.(type))
% let's handle the case we have multiple same param distinguished by "_1",
% "_2", etc...
Expand All @@ -111,12 +116,30 @@
end
end
end
iParam = strcmpi(paramName, paramNames);
if any(iParam)

if any(strcmpi(paramName, paramNames))
flags = max(flags, sample_data.(type){i}.flags(:));
end

if any(strcmpi(paramName, pressureNames))
pressureFlags = max(pressureFlags, sample_data.(type){i}.flags(:));
end

if any(strcmpi(paramName, depthName))
isDepth = true;
depthFlags = max(depthFlags, sample_data.(type){i}.flags(:));
end
end

% in case DEPTH has been inferred from a neighbouring sensor when PRES
% or PRES_REL failed, we only consider DEPTH flags
if isDepth
flags = max(flags, depthFlags);
else
flags = max(flags, pressureFlags);
end


if isMatrix
% we fold the vector back into a matrix
data = reshape(data, [len1, len2, len3]);
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6 changes: 4 additions & 2 deletions Graph/checkMooringPresDiffs.m
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Original file line number Diff line number Diff line change
Expand Up @@ -289,12 +289,14 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
'Layer', 'top');

if isPlottable
iOthersLogical = false(max(iOthers), 1);
iOthersLogical(iOthers) = true;
iNan = isnan(hLineVar);
if any(iNan)
hLineVar(iNan) = [];
instrumentDesc(iNan) = [];
iOthersLogical(iNan) = [];
end
iOthers = iOthers - (min(iOthers)-1);

datetick(hAxPressDiff, 'x', 'dd-mm-yy HH:MM:SS', 'keepticks');
datetick(hAxPress, 'x', 'dd-mm-yy HH:MM:SS', 'keepticks');
Expand All @@ -313,7 +315,7 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
xscale = 0.75;
end
hYBuffer = 1.1 * (2*(fontSizeAx + fontSizeLb));
hLegend = legendflex(hAxPress, instrumentDesc(iOthers),...
hLegend = legendflex(hAxPress, instrumentDesc(iOthersLogical),...
'anchor', [6 2], ...
'buffer', [0 -hYBuffer], ...
'ncol', nCols,...
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9 changes: 5 additions & 4 deletions Graph/lineMooring1DVar.m
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Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,11 @@ function lineMooring1DVar(sample_data, varName, isQC, saveToFile, exportDir)
qcParam = get(mWh, 'UserData');
yLim = get(hAxMooringVar, 'YLim');
for i=1:lenSampleData
if isfield(qcParam, 'inWater')
iVar = getVar(sample_data{iSort(i)}.(typeVar), varName);

if iVar && isfield(qcParam, 'inWater')
dataVar = sample_data{iSort(i)}.(typeVar){iVar}.data;

line([qcParam(iSort(i)).inWater, qcParam(iSort(i)).inWater, NaN, qcParam(iSort(i)).outWater, qcParam(iSort(i)).outWater], ...
[yLim, NaN, yLim], ...
'Parent', hAxMooringVar, ...
Expand All @@ -271,9 +275,6 @@ function lineMooring1DVar(sample_data, varName, isQC, saveToFile, exportDir)
iTime = getVar(sample_data{i}.dimensions, 'TIME');
xLine = sample_data{iSort(i)}.dimensions{iTime}.data;

iVar = getVar(sample_data{iSort(i)}.(typeVar), varName);
dataVar = sample_data{iSort(i)}.(typeVar){iVar}.data;

if strcmpi(varName, 'TIME')
xLine(1) = [];
dataVar = diff(dataVar)*24*3600;
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122 changes: 79 additions & 43 deletions Preprocessing/depthPP.m
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Original file line number Diff line number Diff line change
Expand Up @@ -568,10 +568,14 @@
iSecond = secondNearestInst(iCurSam);

if iSecond == 0 && iFirst ~= 0
tidalAmplitudeComment = ' Tidal amplitude is not accurate.';
if sample_data{nearestInsts{iCurSam}(iFirst)}.meta.depth < sample_data{iCurSam}.meta.depth
warningDepthComment = ' Tidal amplitude is not accurate.';
else
warningDepthComment = ' Mooring knock downs performed by strong current events are either not detected or inaccurate.';
end
fprintf('%s\n', ['Warning : ' descSam{iCurSam} ...
' has its actual depth inferred from only one neighbouring pressure sensor ' ...
'on mooring.' tidalAmplitudeComment]);
'on mooring.' warningDepthComment]);
% we found only one sensor
presIdxOther = getVar(sample_data{nearestInsts{iCurSam}(iFirst)}.variables, 'PRES');
presRelIdxOther = getVar(sample_data{nearestInsts{iCurSam}(iFirst)}.variables, 'PRES_REL');
Expand All @@ -595,64 +599,28 @@
'precision at a deployed depth)'];
end

% compute pressure at current sensor using trigonometry and
% assuming sensors repartition on a line between the
% nearest pressure sensor and the mooring's anchor
%
% the only drawback is that tidal amplitude is
% flattenned by static value of siteDepth
if isfield(sample_data{iCurSam}, 'site_nominal_depth')
if ~isempty(sample_data{iCurSam}.site_nominal_depth)
siteDepth = sample_data{iCurSam}.site_nominal_depth;
end
end

if isfield(sample_data{iCurSam}, 'site_depth_at_deployment')
if ~isempty(sample_data{iCurSam}.site_depth_at_deployment)
siteDepth = sample_data{iCurSam}.site_depth_at_deployment;
end
end

if isSensorTargetDepth
nominalHeightOther = siteDepth - sample_data{nearestInsts{iCurSam}(iFirst)}.instrument_nominal_depth;
nominalHeightCurSensor = siteDepth - sample_data{iCurSam}.instrument_nominal_depth;
else
nominalHeightOther = sample_data{nearestInsts{iCurSam}(iFirst)}.instrument_nominal_height;
nominalHeightCurSensor = sample_data{iCurSam}.instrument_nominal_height;
end

% theta is the angle between the vertical and line
% formed by the sensors
%
% cos(theta) = heightOther/nominalHeightOther
% and
% cos(theta) = heightCurSensor/nominalHeightCurSensor
%
% computedDepth = nominalSiteDepth - nominalHeightCurSensor * (nominalSiteDepth - zOther) / nominalHeightOther
%
% pressure = density*gravity*depth
%
% compute depth of the nearest sensor from its pressure
if ~isempty(sample_data{iCurSam}.geospatial_lat_min) && ~isempty(sample_data{iCurSam}.geospatial_lat_max)
% compute depth with Gibbs-SeaWater toolbox
% depth ~= - gsw_z_from_p(relative_pressure, latitude)
if sample_data{iCurSam}.geospatial_lat_min == sample_data{iCurSam}.geospatial_lat_max
zOther = - gsw_z_from_p(relPresOther, sample_data{iCurSam}.geospatial_lat_min);
computedDepthComment = ['depthPP: Depth inferred from only one neighbouring pressure sensor ' ...
descOtherSam{iCurSam}{iFirst + 1} ', using the Gibbs-SeaWater toolbox ' ...
'(TEOS-10) v3.06 from latitude and ' presComment '.' tidalAmplitudeComment];
'(TEOS-10) v3.06 from latitude and ' presComment '.' warningDepthComment];
else
meanLat = sample_data{iCurSam}.geospatial_lat_min + ...
(sample_data{iCurSam}.geospatial_lat_max - sample_data{iCurSam}.geospatial_lat_min)/2;
zOther = - gsw_z_from_p(relPresOther, meanLat);
computedDepthComment = ['depthPP: Depth inferred from only one neighbouring pressure sensor ' ...
descOtherSam{iCurSam}{iFirst + 1} ', using the Gibbs-SeaWater toolbox ' ...
'(TEOS-10) v3.06 from mean latitude and ' presComment '.' tidalAmplitudeComment];
'(TEOS-10) v3.06 from mean latitude and ' presComment '.' warningDepthComment];
end
else
% without latitude information, we assume 1dbar ~= 1m
zOther = relPresOther;
computedDepthComment = ['depthPP: Depth inferred from only one neighbouring pressure sensor ' ...
descOtherSam{iCurSam}{iFirst + 1} ' with ' presComment ', assuming 1dbar ~= 1m.' tidalAmplitudeComment];
descOtherSam{iCurSam}{iFirst + 1} ' with ' presComment ', assuming 1dbar ~= 1m.' warningDepthComment];
end
clear relPresOther;

Expand All @@ -664,8 +632,76 @@
zOther = interp1(tOther, zOther, tCur);
clear tOther tCur;

computedDepth = siteDepth - nominalHeightCurSensor * (siteDepth - zOther) / nominalHeightOther;
if sample_data{nearestInsts{iCurSam}(iFirst)}.meta.depth < sample_data{iCurSam}.meta.depth
% compute pressure at current sensor using trigonometry and
% assuming sensors repartition on a line between the
% nearest pressure sensor and the mooring's anchor
%
% the only drawback is that tidal amplitude is
% flattenned by static value of siteDepth
if isfield(sample_data{iCurSam}, 'site_nominal_depth')
if ~isempty(sample_data{iCurSam}.site_nominal_depth)
siteDepth = sample_data{iCurSam}.site_nominal_depth;
end
end

if isfield(sample_data{iCurSam}, 'site_depth_at_deployment')
if ~isempty(sample_data{iCurSam}.site_depth_at_deployment)
siteDepth = sample_data{iCurSam}.site_depth_at_deployment;
end
end

if isSensorTargetDepth
nominalHeightOther = siteDepth - sample_data{nearestInsts{iCurSam}(iFirst)}.instrument_nominal_depth;
nominalHeightCurSensor = siteDepth - sample_data{iCurSam}.instrument_nominal_depth;
else
nominalHeightOther = sample_data{nearestInsts{iCurSam}(iFirst)}.instrument_nominal_height;
nominalHeightCurSensor = sample_data{iCurSam}.instrument_nominal_height;
end

% theta is the angle between the vertical and line
% formed by the sensors
%
% cos(theta) = heightOther/nominalHeightOther
% and
% cos(theta) = heightCurSensor/nominalHeightCurSensor
%
% computedDepth = nominalSiteDepth - nominalHeightCurSensor * (nominalSiteDepth - zOther) / nominalHeightOther
%
% pressure = density*gravity*depth
%
computedDepth = siteDepth - nominalHeightCurSensor * (siteDepth - zOther) / nominalHeightOther;
else
% compute pressure at current sensor assuming sensors
% repartition on a vertical line between current sensor
% and the nearest. This is the best we can do as we can't
% have any idea of the angle of the mooring with one
% pressure sensor.
%
% computedDepth = depthOther + distOtherCurSensor
% computedHeight = heightOther - distOtherCurSensor
%
% vertical axis is positive down when talking about
% depth
if isSensorTargetDepth
distOtherCurSensor = sample_data{iCurSam}.instrument_nominal_depth - sample_data{nearestInsts{iCurSam}(iFirst)}.instrument_nominal_depth;
signOtherCurSensor = sign(distOtherCurSensor);

distOtherCurSensor = abs(distOtherCurSensor);
else
distOtherCurSensor = sample_data{nearestInsts{iCurSam}(iFirst)}.instrument_nominal_height - sample_data{iCurSam}.instrument_nominal_height;
signOtherCurSensor = -sign(distOtherCurSensor);
% 0 => two sensors at the same depth
% 1 => current sensor is deeper than other sensor
% -1 => current sensor is lower than other sensor

distOtherCurSensor = abs(distOtherCurSensor);
end

computedDepth = zOther + signOtherCurSensor*distOtherCurSensor;
end
clear zOther;

elseif iSecond ~= 0 && iFirst ~= 0
presIdxFirst = getVar(sample_data{nearestInsts{iCurSam}(iFirst)}.variables, 'PRES');
presRelIdxFirst = getVar(sample_data{nearestInsts{iCurSam}(iFirst)}.variables, 'PRES_REL');
Expand Down
5 changes: 5 additions & 0 deletions Preprocessing/rinkoDoPP.m
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Expand Up @@ -95,6 +95,11 @@
else
if depthIdx > 0
depth = sam.(depthType){depthIdx}.data;

% any depth values <= -5 are discarded (reminder, depth is
% positive down), this allow use of gsw_p_from_z without error.
depth(depth <= -5) = NaN;

if ~isempty(sam.geospatial_lat_min) && ~isempty(sam.geospatial_lat_max)
% compute depth with Gibbs-SeaWater toolbox
% relative_pressure ~= gsw_p_from_z(-depth, latitude)
Expand Down
2 changes: 1 addition & 1 deletion imosToolbox.m
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ function imosToolbox(auto, varargin)
%

% Set current toolbox version
toolboxVersion = ['2.5.34 - ' computer];
toolboxVersion = ['2.5.35 - ' computer];

if nargin == 0, auto = 'manual'; end

Expand Down
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Binary file modified imosToolbox_Win32.exe
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