Initial commit

README.md

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+# salinity-correction-toolbox
+Set of matlab scripts to identify correction coefficients for salinity data taken from CTD rossette and glider
+
+The plot_socib_rv_adcp is a set of python scripts and functions developed at SOCIB to plot the data collected by a SBE911+ CTD mounted onboard the SOCIB Research Vessel. They are able to plot the main variables stored into the cnv files and plot them interpolate the profiles over the longitude dimension.
+
+## Prerequisites:
+The following libraries need to be added into salinity-correction-toolbox/ext/ directory:
+
+- SOCIB Glider Toolbox v1.0.0 - https://github.com/socib/glider_toolbox
+- GSW - https://github.com/TEOS-10/GSW-Matlab
+- m_map - https://www.eoas.ubc.ca/~rich/map.html
+- mexcdf - https://github.com/dcherian/tools/tree/master/netcdf/mexcdf/snctools
+- seawater - http://www.cmar.csiro.au/datacentre/ext_docs/seawater.htm
+
+
+## The following features are already implemented in the toolbox:
+ctd-correction-pack
+glider-correction-pack
+
+
+## The following features are planned or in development:
+
+
+## Legacy
+This toolbox is based on the previous code developed at SOCIB by Dr Krissy Reeve and Dr John T. Allen. 
+
+## Copyright
+
+Copyright (C) 2013-2018 ICTS SOCIB - Servei d'observació i predicció costaner de les Illes Balears http://www.socib.es
+
+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, either version 3 of the License, or (at your option) any later version.
+
+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.
+
+You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

lib/ctd-salinity-correction-pack/res/config/ctd_sc_set_ancillary_paths.m

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+function set_ancillary_paths(DeploymentInfo)
+
+global MainPath
+global Path 
+global OPERATIONAL_MODE 
+global ONLINE_MODE
+global TEST_MODE 
+
+
+Path.main = MainPath.main;
+Path.dataCtdL1Thredds = MainPath.dataCtdL1Thredds;
+Path.dataInsituSalinityRaw = MainPath.dataPortasal;
+Path.dataCtd = [MainPath.dataCtd,DeploymentInfo.researchVesselName,'/', DeploymentInfo.instrumentName,'/rawArchive/',DeploymentInfo.deploymentYear,'/',DeploymentInfo.deploymentName,'/'];
+Path.dataCTDInsituCalHistory = MainPath.dataCTDInsituCalHistory;
+
+switch OPERATIONAL_MODE
+    case 1 % when working in the office network
+        Path.figs = [];
+        Path.dataOut = [];
+    case 0 % when NOT working in the office network
+        Path.figs = []; % paths to figures       
+        Path.dataOut = []; % paths to data
+end
+
+switch ONLINE_MODE
+    case 0 % when NOT working with internet connetion
+    case 1 % when working with internet connetion
+end
+
+switch TEST_MODE
+    case 0 % when NOT testing  
+        Path.figs = [Path.main,'out/prod/figs/']; % paths to figures
+        Path.dataOut = [Path.main,'out/prod/data/']; % paths to data 
+    case 1 % when testing
+        Path.figs = [Path.main,'out/test/figs/']; % paths to figures
+        Path.dataOut = [Path.main,'out/test/data/']; % paths to data
+end
+
+Path.code = [Path.main,'src/']; % path to the source code
+Path.libraries = [Path.main,'ext/']; % path to external libraries
+Path.resources = [Path.main,'res/']; % path to resources like configuration files and ancillary images
+
+% paths through data folders
+Path.dataCtdBtl = [Path.dataCtd,'BOTTLE/'];
+Path.dataCtdBinAvgHalfm = [Path.dataCtd,'PROCESSED_SOCIB_halfm/'];
+Path.dataCtdBtlMat = [Path.dataOut,'ctd_btl_mat/'];
+Path.dataInsituSalinityConverted = [Path.dataOut,'insitu_salinity_mat/'];
+
+Path.dataCorrectionFiles = [Path.dataOut,'correction_data/correction_files/'];
+Path.dataCorrectedMat = [Path.dataCorrectionFiles,'corrected_mat/'];
+Path.dataCorrectedMat5mBinAvg = [Path.dataCorrectedMat,'corrected_mat_5m_bin_avg/'];
+Path.dataCorrectedMatHalfmBinAvg = [Path.dataCorrectedMat,'corrected_mat_halfm_bin_avg/'];
+Path.dataCorrectedMatHalfmBinAvgAll = [Path.dataCorrectedMat,'ctd_all_data_halfm_corrected/'];
+Path.dataCorrectedNc = [Path.dataCorrectionFiles,'corrected_nc/'];
+Path.dataCorrectedNc5mBinAvg = [Path.dataCorrectedNc,'corrected_nc_5m_bin_avg/'];
+Path.dataCorrectedNcHalfmBinAvg = [Path.dataCorrectedNc,'corrected_nc_halfm_bin_avg/'];
+Path.dataCorrectionCoefficients = [Path.dataOut,'correction_data/correction_coefficients/'];
+Path.dataCorrectionCoefficientsMat = [Path.dataCorrectionCoefficients,'correction_coefficients_mat/'];
+Path.dataCorrectionCoefficientsNc = [Path.dataCorrectionCoefficients,'correction_coefficients_nc/'];
+
+
+% path through figures folders
+Path.figsTSdiagsAllCruisesThreddsL1 = [Path.figs,'ts_diag_all_cruises_thredds_L1/'];
+Path.figsTSdiagsSingleCruisesThreddsL1 = [Path.figsTSdiagsAllCruisesThreddsL1,'single_cruises/'];
+Path.figsTSdiagsSingleCruisesThreddsL1Zoom = [Path.figsTSdiagsSingleCruisesThreddsL1,'zoom/'];
+Path.figsTSdiagsComparedCruisesThreddsL1 = [Path.figsTSdiagsAllCruisesThreddsL1,'compared_cruises/'];
+Path.figsResidualsInsituSalinity = [Path.figs,'residuals_insitu_salinity/'];
+Path.figsTSdiagsWithWithoutCorrections = [Path.figs,'ts_diag_with_without_corrections/'];
+Path.figsTSdiagsCorrectedReference = [Path.figs,'ts_diag_corrected_reference/'];
+Path.figsTSdiagsCorrectedReferenceHalfmSingle = [Path.figsTSdiagsCorrectedReference,'halfm_single/'];
+Path.figsTSdiagsCorrectedReferenceHalfmAll = [Path.figsTSdiagsCorrectedReference,'halfm_all/'];
+
+end

lib/ctd-salinity-correction-pack/src/ctd_salinity_correction_main.m

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+
+% set_main_paths;
+% [deploymentName, ncL1FileName, DIR, instrumentName] = stage_0_select_datasets;
+% set_ancillary_paths(deploymentName, instrumentName);
+% create_out_directories;
+
+choice = {'PHASE 1. Load Cruise Data', ...
+          'PHASE 2. Preliminary Results', ...
+          'PHASE 3. Default Salinity Correction', ...
+          'PHASE 3a. Manual Salinity Correction', ...
+          'PHASE 4. Apply Correction Results', ...
+          'PHASE 5. Write L1_corr Data Files'};
+
+choiceFunction = {'[CtdBtl, InsituSal, DIR, ncL1FileName, DeploymentInfo] = phase_1_select_cruise_data', ...
+    'phase_2_preliminary_results(DIR)', ...
+    '[unique_sensor, rmX] = phase_3_salinity_corrections(DIR, DeploymentInfo, choice(3))', ...
+    '[unique_sensor, rmX] = phase_3_salinity_corrections(DIR, DeploymentInfo, choice(4))', ...
+    'fnameOutPath = phase_4_apply_salinity_correction_results(DeploymentInfo, DIR, ncL1FileName, unique_sensor)', ...%'Stage_7a_mbtl_insitu_SAL_matchup()', ... %original argument: manual_outlier_removal set to 0 or 1
+    'write_L1_corr_data_files(fnameOutPath)'};
+
+d = dialog('Position',[80 250 550 410],'Name','CTD Salinity Correction Pack');       
+firstButtonY = 365;
+firstButtonWidth = 350;
+firstButtonX = 10;
+firstBttonHeight = 40;
+% txt = uicontrol('Parent',d,...
+%        'Style','text',...
+%        'Position',[20 80 210 40],...
+%        'String','Select a color');
+[x,~]=imread('LogoSocib.png');
+I2=imresize(x, [102 113]);
+socibLogo=uicontrol('Parent',d,...
+            'units','pixels',...
+            'position',[10 30 113 102],...
+            'cdata',I2);
+
+[x,~]=imread('ctdSocib.jpg');
+I2=imresize(x, [202 140]);
+ctdLogo=uicontrol('Parent',d,...
+            'units','pixels',...
+            'position',[380 162 140 202],...
+            'cdata',I2);
+
+[x,~]=imread('jericoLogo.jpg');
+I2=imresize(x, [102 183]);
+jericoLogo=uicontrol('Parent',d,...
+            'units','pixels',...
+            'position',[150 30 183 102],...
+            'cdata',I2);
+
+
+[~,n] = size(choice);
+count = 0;
+for i = 1:n
+    stage(i) = uicontrol('Parent',d,...
+       'Position',[firstButtonX firstButtonY - count firstButtonWidth firstBttonHeight],...
+       'String',choice(i),...
+       'fontSize',12, ...
+       'Callback',choiceFunction{i}, ...
+       'Interruptible', 'on');
+    count = count + 45;
+end
+
+
+
+
+
+
+
+
+

lib/ctd-salinity-correction-pack/src/phase_1/listncfiles.m

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+function listncfiles
+
+global MainPath
+
+fprintf(1,'Connecting to SOCIB Data Discovery API...\n');
+JsonQuery = webread('http://apps.socib.es/DataDiscovery/list-deployments?');
+
+fprintf(1,'Listing available netCDF files from thredds...\n\n');
+for i = 1:length(JsonQuery) % keep only deploymnts info from RV CTD. id 172 and 448 and 640 belong to SCB-SBE9001 and SCB-SBE9002 and UTM-SBE9001
+    if JsonQuery{i}.platform.jsonInstrumentList.id == 172 || JsonQuery{i}.platform.jsonInstrumentList.id == 448 || JsonQuery{i}.platform.jsonInstrumentList.id == 640 || JsonQuery{i}.platform.jsonInstrumentList.id == 642 || JsonQuery{i}.platform.jsonInstrumentList.id == 650
+        FilteredJsonQuery{i,:} = JsonQuery{i};
+        fprintf(1,[char(JsonQuery{i}.name),'\n']);
+    end
+end
+
+FilteredJsonQuery =  FilteredJsonQuery(~cellfun('isempty',FilteredJsonQuery)); % remove empty cells
+
+for i = 1:length(FilteredJsonQuery) % create cell arrays with list of opendap and file server links to nc files
+    ncFilesListOpendap{i} = FilteredJsonQuery{i}.platform.jsonInstrumentList.ncOpendapLink;
+    ncFilesListFileServer{i} = FilteredJsonQuery{i}.platform.jsonInstrumentList.ncFileCatalogLink;
+end
+
+NcFilesList.opendap = ncFilesListOpendap; 
+NcFilesList.fileServer = ncFilesListFileServer;
+save([MainPath.dataCtdL1Thredds, 'NcFilesList.mat'], 'NcFilesList');
+
+
+end

lib/ctd-salinity-correction-pack/src/phase_1/phase_1_select_cruise_data.m

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+function [CtdBtl, InsituSal, DIR, ncL1FileName, DeploymentInfo] = phase_1_select_cruise_data
+
+set_main_paths('salinity_ctd');
+
+[ncL1FileName, DIR, DeploymentInfo] = stage_0_select_datasets;
+
+ctd_sc_set_ancillary_paths(DeploymentInfo);
+
+create_out_directories;
+
+InsituSal = stage_4_read_insitu_salinity_data(DeploymentInfo);
+
+CtdBtl = stage_6a_read_dotbtl_files(DeploymentInfo);
+
+end

lib/ctd-salinity-correction-pack/src/phase_1/stage_0_select_datasets.m

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+function [ncL1FileName, DIR, DeploymentInfo] = stage_0_select_datasets
+
+global MainPath
+global ONLINE_MODE
+
+DataPname = MainPath.dataCtdL1Thredds;
+
+if ONLINE_MODE == 0
+    DIR = dir(fullfile(DataPname,'*.nc')); %list of accessible files in downloaded files folder
+elseif ONLINE_MODE == 1
+    %listncfiles; % list accessible files in thredds
+    NcFilesList = load(fullfile(DataPname,'NcFilesList.mat'));
+    NcFilesList = NcFilesList.NcFilesList;
+    RANGE = length(NcFilesList.fileServer);
+    for i = 1:RANGE
+        NcFilesListSplit(i).name = strsplit(char(NcFilesList.fileServer(i)),'/');
+        DIR(i).name = NcFilesListSplit(i).name{10};
+        DIR(i).pathToFile = NcFilesList.fileServer(i);
+    end
+
+end
+
+% list of files to select deployment
+for i = 1:length(DIR)
+    %list(i,:) = DIR(i).name;
+    list{i} = DIR(i).name;
+end
+[indx,tf] = listdlg('ListString',list,'SelectionMode','single','ListSize',[450,650]);
+
+if ONLINE_MODE == 0
+    %ncL1FileName = char(list(indx,:));
+    ncL1FileName = char(list{indx});
+elseif ONLINE_MODE == 1
+    %download file from thredds
+%     URL = char(NcFilesList.fileServer(indx));
+%     ncL1FileName = char(list(indx,:));
+    URL = char(NcFilesList.fileServer(indx));
+    ncL1FileName = char(list{indx});
+    urlwrite(URL,[DataPname, ncL1FileName]);
+end
+
+deploymentName = regexprep(ncL1FileName,'L1_','','ignorecase'); %remove L1 from file name to be used as parameter to locate further files (btl, insituSal, etc)
+deploymentName = deploymentName(1:end-3);
+deploymentYear = deploymentName(end-9:end-6);
+
+dum = strsplit(deploymentName,'_');
+
+DeploymentInfo.deploymentCode = dum{1};
+DeploymentInfo.researchVesselName = strrep(dum{2},'-','_');
+DeploymentInfo.instrumentName = upper(dum{3});
+DeploymentInfo.deploymentDate = dum{4};
+DeploymentInfo.deploymentName = deploymentName;
+DeploymentInfo.deploymentYear = deploymentYear;
+
+% deploymentYear = deploymentName(30:33);
+
+% if ~isnan(strfind(deploymentName,'scb-sbe9002'));
+%     instrumentName = 'SCB-SBE9002';
+% elseif ~isnan(strfind(deploymentName,'scb-sbe9001'));
+%     instrumentName = 'SCB-SBE9001';    
+% elseif ~isnan(strfind(deploymentName,'utm-sbe9001'));
+%     instrumentName = 'UTM-SBE9001'; 
+% elseif ~isnan(strfind(deploymentName,'nat-sbe9001'));
+%     instrumentName = 'NAT-SBE9001'; 
+% end
+
+end
+