Skip to content

Commit

Permalink
Merge pull request #383 from aodn/2.5.19
Browse files Browse the repository at this point in the history 
2.5.19
  • Loading branch information
@ggalibert
ggalibert authored Nov 9, 2016
2 parents 65452f9 + 178b408 commit 7fc6700
Show file tree
Hide file tree
Showing 7 changed files with 29 additions and 154 deletions.
10 changes: 7 additions & 3 deletions Preprocessing/depthPP.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -568,6 +568,12 @@
dimensions, ...
computedDepthComment, ...
coordinates);

% update vertical min/max from new computed DEPTH
sample_data{k}.geospatial_vertical_min = min(computedDepth);
sample_data{k}.geospatial_vertical_max = max(computedDepth);
sample_data{k}.comment = strrep(sample_data{k}.comment, 'NOMINAL_DEPTH', 'DEPTH min and max');

clear computedDepth;

history = sample_data{k}.history;
Expand All @@ -591,8 +597,6 @@
end

end

% update vertical min/max from new computed DEPTH
sample_data{k} = populateMetadata(sample_data{k});

clear curSam;
end
4 changes: 4 additions & 0 deletions Preprocessing/salinityPP.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -125,6 +125,10 @@
presName = 'instrument_nominal_depth';
end

% 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;

% pressure information needed for Salinity computation is either
% retrieved from gsw_p_from_z when latitude is available or by
% simply assuming 1dbar ~= 1m
Expand Down
167 changes: 17 additions & 150 deletions Util/populateMetadata.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -143,159 +143,26 @@

metadataChanged = true;
else
% Update from PRES if available
if ivPres > 0 || ivPresRel > 0
if ivPresRel == 0
% update from a relative pressure like SeaBird computes
% it in its processed files, substracting a constant value
% 10.1325 dbar for nominal atmospheric pressure
relPres = sample_data.variables{ivPres}.data - gsw_P0/10^4;
presComment = ['absolute '...
'pressure measurements to which a nominal '...
'value for atmospheric pressure (10.1325 dbar) '...
'has been substracted'];
iNanRelPres = isnan(relPres);
else
% update from a relative measured pressure
relPres = sample_data.variables{ivPresRel}.data;
presComment = ['relative '...
'pressure measurements (calibration offset '...
'usually performed to balance current '...
'atmospheric pressure and acute sensor '...
'precision at a deployed depth)'];
iNanRelPres = isnan(relPres);
end
if ~isempty(sample_data.geospatial_lat_min) && ~isempty(sample_data.geospatial_lat_max)
% compute vertical min/max with Gibbs-SeaWater toolbox (TEOS-10)
if sample_data.geospatial_lat_min == sample_data.geospatial_lat_max
computedDepth = - gsw_z_from_p(relPres, ...
sample_data.geospatial_lat_min);
computedMinDepth = - gsw_z_from_p(min(relPres(~iNanRelPres)), ...
sample_data.geospatial_lat_min);
computedMaxDepth = - gsw_z_from_p(max(relPres(~iNanRelPres)), ...
sample_data.geospatial_lat_min);
computedDepthComment = ['depthPP: Depth computed using the '...
'Gibbs-SeaWater toolbox (TEOS-10) v3.05 from latitude and '...
presComment '.'];
else
meanLat = sample_data.geospatial_lat_min + ...
(sample_data.geospatial_lat_max - sample_data.geospatial_lat_min)/2;

computedDepth = - gsw_z_from_p(relPres, meanLat);
computedMinDepth = - gsw_z_from_p(min(relPres(~iNanRelPres)), meanLat);
computedMaxDepth = - gsw_z_from_p(max(relPres(~iNanRelPres)), meanLat);
computedDepthComment = ['depthPP: Depth computed using the '...
'Gibbs-SeaWater toolbox (TEOS-10) v3.05 from mean latitude and '...
presComment '.'];
end
else
% without latitude information, we assume 1dbar ~= 1m
computedDepth = relPres;
computedMinDepth = min(relPres(~iNanRelPres));
computedMaxDepth = max(relPres(~iNanRelPres));
computedDepthComment = ['depthPP: Depth computed from '...
presComment ', assuming 1dbar ~= 1m.'];
end
% Update from NOMINAL_DEPTH if available
if ivNomDepth > 0
% Update from NOMINAL_DEPTH data
dataNominalDepth = sample_data.variables{ivNomDepth}.data;
iNan = isnan(dataNominalDepth);
dataNominalDepth = dataNominalDepth(~iNan);

if idHeight > 0
% ADCP
if all(sample_data.dimensions{idHeight}.data >= 0) % upward looking configuration
maxDistance = max(sample_data.dimensions{idHeight}.data); % HEIGHT_ABOVE_SENSOR is positive when upward
% update vertical min/max metadata from data
% we assume that depth data is reliable
if isempty(sample_data.geospatial_vertical_min) && isempty(sample_data.geospatial_vertical_max)

sample_data.geospatial_vertical_min = computedMinDepth - maxDistance;
sample_data.geospatial_vertical_max = computedMaxDepth;
comment = computedDepthComment;

if isempty(sample_data.comment)
sample_data.comment = comment;
elseif ~strcmpi(sample_data.comment, comment)
sample_data.comment = [sample_data.comment ' ' comment];
end

metadataChanged = true;
end
else % downward looking configuration
maxDistance = - min(sample_data.dimensions{idHeight}.data); % HEIGHT_ABOVE_SENSOR is negative when downward
% update vertical min/max metadata from data
% we assume that depth data is reliable
if isempty(sample_data.geospatial_vertical_min) && isempty(sample_data.geospatial_vertical_max)

sample_data.geospatial_vertical_min = computedMinDepth;
sample_data.geospatial_vertical_max = computedMaxDepth + maxDistance;
comment = computedDepthComment;

if isempty(sample_data.comment)
sample_data.comment = comment;
elseif ~strcmpi(sample_data.comment, comment)
sample_data.comment = [sample_data.comment ' ' comment];
end

metadataChanged = true;
end
end
else
% Not an ADCP, so we can update existing DEPTH dimension/variable from PRES data
if idDepth > 0
sample_data.dimensions{idDepth}.data = sample_data.dimensions{idDepth}.typeCastFunc(computedDepth);
comment = sample_data.dimensions{idDepth}.comment;
if isempty(comment)
sample_data.dimensions{idDepth}.comment = computedDepthComment;
elseif ~strcmpi(computedDepthComment, comment)
sample_data.dimensions{idDepth}.comment = [comment ' ' computedDepthComment];
end
metadataChanged = true;
end
if ivDepth > 0
sample_data.variables{ivDepth}.data = sample_data.variables{ivDepth}.typeCastFunc(computedDepth);
comment = sample_data.variables{ivDepth}.comment;
if isempty(comment)
sample_data.variables{ivDepth}.comment = computedDepthComment;
elseif ~strcmpi(computedDepthComment, comment)
sample_data.variables{ivDepth}.comment = [comment ' ' computedDepthComment];
end
metadataChanged = true;
end
verticalComment = ['Geospatial vertical min/max information has '...
'been filled using the NOMINAL_DEPTH.'];

if isempty(sample_data.geospatial_vertical_min) && isempty(sample_data.geospatial_vertical_max)

sample_data.geospatial_vertical_min = computedMinDepth;
sample_data.geospatial_vertical_max = computedMaxDepth;
comment = computedDepthComment;

metadataChanged = true;

if isempty(sample_data.comment)
sample_data.comment = comment;
elseif ~strcmpi(sample_data.comment, comment)
sample_data.comment = [sample_data.comment ' ' comment];
end
end
end
else
% Update from NOMINAL_DEPTH if available
if ivNomDepth > 0
% Update from NOMINAL_DEPTH data
dataNominalDepth = sample_data.variables{ivNomDepth}.data;
iNan = isnan(dataNominalDepth);
dataNominalDepth = dataNominalDepth(~iNan);

verticalComment = ['Geospatial vertical min/max information has '...
'been filled using the NOMINAL_DEPTH.'];

sample_data.geospatial_vertical_min = dataNominalDepth;
sample_data.geospatial_vertical_max = dataNominalDepth;

if isempty(sample_data.comment)
sample_data.comment = verticalComment;
elseif ~strcmpi(sample_data.comment, verticalComment)
sample_data.comment = [sample_data.comment ' ' verticalComment];
end

metadataChanged = true;
sample_data.geospatial_vertical_min = dataNominalDepth;
sample_data.geospatial_vertical_max = dataNominalDepth;

if isempty(sample_data.comment)
sample_data.comment = verticalComment;
elseif ~strcmpi(sample_data.comment, verticalComment)
sample_data.comment = [sample_data.comment ' ' verticalComment];
end

metadataChanged = true;
end
end

Expand Down
2 changes: 1 addition & 1 deletion imosToolbox.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ function imosToolbox(auto, varargin)
end

% Set current toolbox version
toolboxVersion = ['2.5.18 - ' computer];
toolboxVersion = ['2.5.19 - ' computer];

switch auto
case 'auto', autoIMOSToolbox(toolboxVersion, varargin{:});
Expand Down
Binary file modified imosToolbox_Linux64.bin
View file
Binary file not shown.
Binary file modified imosToolbox_Win32.exe
View file
Binary file not shown.
Binary file modified imosToolbox_Win64.exe
View file
Binary file not shown.

0 comments on commit 7fc6700

Please sign in to comment.