scripts for chl quality control and vicarious calibration of CTD fluorometers

Author: hsosik

Chl/SPIROPAchl_importfile.m

@@ -0,0 +1,58 @@
+function SPIROPAchl = importfile(workbookFile, sheetName, dataLines)
+%IMPORTFILE Import data from a spreadsheet
+%  SPIROPACHL = IMPORTFILE(FILE) reads data from the first worksheet in
+%  the Microsoft Excel spreadsheet file named FILE.  Returns the data as
+%  a table.
+%
+%  SPIROPACHL = IMPORTFILE(FILE, SHEET) reads from the specified
+%  worksheet.
+%
+%  SPIROPACHL = IMPORTFILE(FILE, SHEET, DATALINES) reads from the
+%  specified worksheet for the specified row interval(s). Specify
+%  DATALINES as a positive scalar integer or a N-by-2 array of positive
+%  scalar integers for dis-contiguous row intervals.
+%
+%  Example:
+%  SPIROPAchl = importfile("\\sosiknas1\Lab_data\SPIROPA\CHL\SPIROPAchl.xlsx", "chl", [2, 3887]);
+%
+%  See also READTABLE.
+%
+% Auto-generated by MATLAB on 01-Nov-2019 08:23:42
+
+%% Input handling
+
+% If no sheet is specified, read first sheet
+if nargin == 1 || isempty(sheetName)
+    sheetName = 1;
+end
+
+% If row start and end points are not specified, define defaults
+if nargin <= 2
+    dataLines = [2, 3887];
+end
+
+%% Setup the Import Options
+opts = spreadsheetImportOptions("NumVariables", 28);
+
+% Specify sheet and range
+opts.Sheet = sheetName;
+opts.DataRange = "A" + dataLines(1, 1) + ":AB" + dataLines(1, 2);
+
+% Specify column names and types
+opts.VariableNames = ["Cruise", "Cast", "Niskin", "TargetDepth", "Replicate", "VolFilt", "FilterSize", "VolExtracted", "Sample", "Acetone", "DilutionDuringReading", "Chl_Cal_Filename", "tau_Calibration", "Fd_Calibration", "Rb", "Ra", "blank", "Rbblank", "Rablank", "Chlugl", "Phaeougl", "Cal_Date", "Fluorometer", "Labnotebookandpagenumber", "Comments", "quality_flag", "Sample1", "Acetone1"];
+opts.SelectedVariableNames = ["Cruise", "Cast", "Niskin", "TargetDepth", "Replicate", "VolFilt", "FilterSize", "VolExtracted", "Sample", "Acetone", "DilutionDuringReading", "Chl_Cal_Filename", "tau_Calibration", "Fd_Calibration", "Rb", "Ra", "blank", "Rbblank", "Rablank", "Chlugl", "Phaeougl", "Cal_Date", "Fluorometer", "Labnotebookandpagenumber", "Comments", "quality_flag", "Sample1", "Acetone1"];
+opts.VariableTypes = ["categorical", "double", "double", "double", "categorical", "double", "double", "double", "double", "double", "double", "categorical", "double", "double", "double", "double", "double", "double", "double", "double", "double", "datetime", "string", "categorical", "categorical", "double", "double", "double"];
+opts = setvaropts(opts, 22, "InputFormat", "");
+opts = setvaropts(opts, 23, "WhitespaceRule", "preserve");
+opts = setvaropts(opts, [1, 5, 12, 23, 24, 25], "EmptyFieldRule", "auto");
+
+% Import the data
+SPIROPAchl = readtable(workbookFile, opts, "UseExcel", false);
+
+for idx = 2:size(dataLines, 1)
+    opts.DataRange = "A" + dataLines(idx, 1) + ":AB" + dataLines(idx, 2);
+    tb = readtable(workbookFile, opts, "UseExcel", false);
+    SPIROPAchl = [SPIROPAchl; tb]; %#ok<AGROW>
+end
+
+end

Chl/compare_extract_BTL.m

@@ -0,0 +1,62 @@
+% Import SPIROPAchl spreadsheet
+% Import CTD-only bottle summary file for each SPIROPA cruise
+% Produce BTLmatch with same number of rows as SPIROPAchl
+% Plot extracted Chl vs BTL_chl_fluorescence for each cruise
+%
+% Heidi M. Sosik, Woods Hole Oceanographic Institution; November 2019
+
+%AR29
+load('\\sosiknas1\Lab_data\SPIROPA\20180414_AR29\fromOlga\p_11_ar29_BTL_data_v2.mat');
+AR29_BTL = p_11_ar29_BTL_data_v2; clear p_11_ar29_BTL_data_v2
+ARcolnum = [1 2 19 25]; %cast, niskin, pressure, FL-chl?
+
+%RB1904
+load('\\sosiknas1\Lab_data\SPIROPA\20180503_RB1904\fromOlga\rb1904_BTL_data.mat');
+RB1904_BTL = rb1904_BTL_data; clear rb1904_BTL_data
+RBcolnum = [1 2 20 26 36]; %cast, niskin, depth, FL-chl, FL-V
+
+%TN368
+load('\\sosiknas1\Lab_data\SPIROPA\20190705_TN368\fromOlga\tn368_BTL_data.mat')
+TN368_BTL = tn368_BTL_data; clear tn368_BTL_data
+TNcolnum = [1 2 20 26 36]; %cast, niskin, depth, FL-chl, FL-V
+
+SPIROPAchl = SPIROPAchl_importfile("\\sosiknas1\Lab_data\SPIROPA\CHL\SPIROPAchl.xlsx", "chl", [2, 3887]);
+
+ARrow = find(SPIROPAchl.Cruise == 'AR29');
+RBrow = find(SPIROPAchl.Cruise == 'RB1904');
+TNrow = find(SPIROPAchl.Cruise == 'TN368');
+
+BTLmatch = NaN(size(SPIROPAchl,1),5);
+indmatch = NaN(size(ARrow));
+for ii = 1:length(ARrow)
+    indmatch(ii) = find(AR29_BTL(:,ARcolnum(1)) == SPIROPAchl.Cast(ARrow(ii)) & AR29_BTL(:,ARcolnum(2)) == SPIROPAchl.Niskin(ARrow(ii)));
+end
+BTLmatch(ARrow,1:4) = AR29_BTL(indmatch,ARcolnum);
+
+indmatch = NaN(size(RBrow));
+for ii = 1:length(RBrow)
+    indmatch(ii) = find(RB1904_BTL(:,ARcolnum(1)) == SPIROPAchl.Cast(RBrow(ii)) & RB1904_BTL(:,RBcolnum(2)) == SPIROPAchl.Niskin(RBrow(ii)));
+end
+BTLmatch(RBrow,:) = RB1904_BTL(indmatch,RBcolnum);
+
+indmatch = NaN(size(TNrow));
+for ii = 1:length(TNrow)
+    indmatch(ii) = find(TN368_BTL(:,TNcolnum(1)) == SPIROPAchl.Cast(TNrow(ii)) & TN368_BTL(:,TNcolnum(2)) == SPIROPAchl.Niskin(TNrow(ii)));
+end
+BTLmatch(TNrow,:) = TN368_BTL(indmatch,TNcolnum);
+
+ARrow = find(SPIROPAchl.Cruise == 'AR29' & SPIROPAchl.FilterSize == 0);
+RBrow = find(SPIROPAchl.Cruise == 'RB1904' & SPIROPAchl.FilterSize == 0);
+TNrow = find(SPIROPAchl.Cruise == 'TN368' & SPIROPAchl.FilterSize == 0);
+
+figure
+plot(BTLmatch(ARrow,4), SPIROPAchl.Chlugl(ARrow), '.')
+title('AR29')
+
+figure
+plot(BTLmatch(RBrow,4), SPIROPAchl.Chlugl(RBrow), '.')
+title('RB1904')
+
+figure
+plot(BTLmatch(TNrow,4), SPIROPAchl.Chlugl(TNrow), '.')
+title('TN368')

Tools/btlmat2table.m

@@ -6,7 +6,8 @@
 %to handle highly non-standard column labels, create and save a table data
 %type for easier handling in MATLAB
 
-file2load = 'C:\work\SPIROPA\ar29_bottle_data_Apr_2019.mat';
+%file2load = 'C:\work\SPIROPA\ar29_bottle_data_Apr_2019.mat';
+file2load = 'C:\work\SPIROPA\RB1904\rb1904_bottle_data_Jul_2019.mat';
 if ~exist(file2load,'file')
     [FileName,PathName] = uigetfile('*.mat','Select BTL mat file');
     file2load = fullfilename(PathName, FileName);