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Merge pull request #797 from aodn/FeatQcFlag
(Feat) Add failed QC tests information into new ancillary variable [*]_failed_tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| function value = imosQCTest( testName ) | ||
| %imosQCTest Returns an appropriate QC flag_value (integer) | ||
| % given a qc test routine (String) | ||
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| % The value returned by this function is the power of 2 of the qc routine | ||
| % positional integer available in imosQCTests.txt. This is used to store | ||
| % information in a variable in the form of integers | ||
| % | ||
| % | ||
| % Inputs: | ||
| % | ||
| % testName - name of QC test | ||
| % | ||
| % Outputs: | ||
| % value - integer | ||
| % | ||
| % Author: Laurent Besnard <[email protected]> | ||
| % | ||
| % Example: | ||
| % | ||
| % value = imosQCTest( 'userManualQC'); | ||
| % | ||
| % | ||
| % assert(value==2) | ||
| % | ||
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| narginchk(1, 1); | ||
| if ~ischar(testName), error('field must be a string'); end | ||
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| value = ''; | ||
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| % open the IMOSQCFTests.txt file - it should be | ||
| % in the same directory as this m-file | ||
| path = ''; | ||
| if ~isdeployed, [path, ~, ~] = fileparts(which('imosToolbox.m')); end | ||
| if isempty(path), path = pwd; end | ||
| path = fullfile(path, 'IMOS'); | ||
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| fidS = -1; | ||
| try | ||
| % read in the QC sets | ||
| fidS = fopen([path filesep 'imosQCTests.txt'], 'rt'); | ||
| if fidS == -1, return; end | ||
| sets = textscan(fidS, '%s%f', 'delimiter', ',', 'commentStyle', '%'); | ||
| fclose(fidS); | ||
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| [~, idx] = ismember(testName, sets{1,1}); | ||
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| value = int32(2^sets{1,2}(idx)); % return the | ||
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| catch e | ||
| if fidS ~= -1, fclose(fidS); end | ||
| rethrow(e); | ||
| end | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| function values = imosQCTests() | ||
| %imosQCTests Returns a 1x2 cell array reading the info found in | ||
| %ImosQCTests.txt | ||
| % - the first one contains a list of QC routines | ||
| % - the second cell returns a positional integer for each routine | ||
| % | ||
| % Inputs: | ||
| % | ||
| % N.A. | ||
| % | ||
| % Outputs: | ||
| % 1x2 cell array | ||
| % | ||
| % Author: Laurent Besnard <[email protected]> | ||
| % | ||
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| % | ||
| % Copyright (C) 2023, Australian Ocean Data Network (AODN) and Integrated | ||
| % Marine Observing System (IMOS). | ||
| % | ||
| % This program is free software: you can redistribute it and/or modify | ||
| % it under the terms of the GNU General Public License as published by | ||
| % the Free Software Foundation version 3 of the License. | ||
| % | ||
| % This program is distributed in the hope that it will be useful, | ||
| % but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| % GNU General Public License for more details. | ||
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| % You should have received a copy of the GNU General Public License | ||
| % along with this program. | ||
| % If not, see <https://www.gnu.org/licenses/gpl-3.0.en.html>. | ||
| % | ||
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| % open the IMOSQCFTests file - it should be | ||
| % in the same directory as this m-file | ||
| path = ''; | ||
| if ~isdeployed, [path, ~, ~] = fileparts(which('imosToolbox.m')); end | ||
| if isempty(path), path = pwd; end | ||
| path = fullfile(path, 'IMOS'); | ||
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| fidS = -1; | ||
| try | ||
| % read in the QC sets | ||
| fidS = fopen([path filesep 'imosQCTests.txt'], 'rt'); | ||
| if fidS == -1, return; end | ||
| sets = textscan(fidS, '%s%f', 'delimiter', ',', 'commentStyle', '%'); | ||
| fclose(fidS); | ||
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| % rewrite sets with correct qc flag test values using the imosQCTest | ||
| % function | ||
| nQcFlags = length(sets{1}); | ||
| for k = 1:nQcFlags | ||
| sets{1,2}(k) = imosQCTest(sets{1,1}{k}); | ||
| end | ||
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| values = sets; | ||
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| catch e | ||
| if fidS ~= -1, fclose(fidS); end | ||
| rethrow(e); | ||
| end | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| % | ||
| % A list of all the toolbox QC routines flag values. This list is intended | ||
| % to by used by the qcFilterMain.m function to tag, for each data point, | ||
| % which QC test failed | ||
| % | ||
| % the positional integer value has to be strictly above 0 since 0 is used | ||
| % as a _FillValue | ||
| % | ||
| % QC routine, positional integer | ||
| userManualQC, 0 | ||
| imosCorrMagVelocitySetQC, 1 | ||
| imosDensityInversionSetQC, 2 | ||
| imosEchoIntensitySetQC, 3 | ||
| imosEchoIntensityVelocitySetQC, 4 | ||
| imosEchoRangeSetQC, 5 | ||
| imosErrorVelocitySetQC, 6 | ||
| imosGlobalRangeQC, 7 | ||
| imosHorizontalVelocitySetQC, 8 | ||
| imosImpossibleDateQC, 10 | ||
| imosImpossibleDepthQC, 11 | ||
| imosImpossibleLocationSetQC, 12 | ||
| imosInOutWaterQC, 13 | ||
| imosPercentGoodVelocitySetQC, 14 | ||
| imosRateOfChangeQC, 15 | ||
| imosRegionalRangeQC, 16 | ||
| imosSalinityFromPTQC, 17 | ||
| imosSideLobeVelocitySetQC, 18 | ||
| imosStationarityQC, 19 | ||
| imosSurfaceDetectionByDepthSetQC, 20 | ||
| imosTier2ProfileVelocitySetQC, 21 | ||
| imosTiltVelocitySetQC_probably_good,22 | ||
| imosTiltVelocitySetQC_bad, 23 | ||
| imosTimeSeriesSpikeQC, 24 | ||
| imosVerticalSpikeQC, 25 | ||
| imosVerticalVelocityQC, 26 |
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