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Added new parser for .tid files produced by SBE26.
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| function sample_data = SBE26Parse( filename, mode ) | ||
| %SBE26PARSE Parses a .tid data file from a Seabird SBE26 | ||
| % TP logger. | ||
| % | ||
| % This function is able to read in a .tid data file retrieved | ||
| % from a Seabird SBE26 Temperature and Pressure Logger. It is | ||
| % assumed the file consists in the following columns: | ||
| % | ||
| % - measurement number | ||
| % - date and time (mm/dd/yyyy HH:MM:SS) of beginning of measurement | ||
| % - pressure in psia | ||
| % - temperature in degrees Celsius | ||
| % | ||
| % Inputs: | ||
| % filename - cell array of files to import (only one supported). | ||
| % mode - Toolbox data type mode. | ||
| % | ||
| % Outputs: | ||
| % sample_data - Struct containing sample data. | ||
| % | ||
| % Author: Guillaume Galibert <guillaume.galibert@utas.edu.au> | ||
| % | ||
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| % | ||
| % Copyright (c) 2016, Australian Ocean Data Network (AODN) and Integrated | ||
| % Marine Observing System (IMOS). | ||
| % All rights reserved. | ||
| % | ||
| % Redistribution and use in source and binary forms, with or without | ||
| % modification, are permitted provided that the following conditions are met: | ||
| % | ||
| % * Redistributions of source code must retain the above copyright notice, | ||
| % this list of conditions and the following disclaimer. | ||
| % * Redistributions in binary form must reproduce the above copyright | ||
| % notice, this list of conditions and the following disclaimer in the | ||
| % documentation and/or other materials provided with the distribution. | ||
| % * Neither the name of the AODN/IMOS nor the names of its contributors | ||
| % may be used to endorse or promote products derived from this software | ||
| % without specific prior written permission. | ||
| % | ||
| % THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| % AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| % IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| % ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE | ||
| % LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| % CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF | ||
| % SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS | ||
| % INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN | ||
| % CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | ||
| % ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE | ||
| % POSSIBILITY OF SUCH DAMAGE. | ||
| % | ||
| narginchk(1,2); | ||
|
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| if ~iscellstr(filename) | ||
| error('filename must be a cell array of strings'); | ||
| end | ||
|
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||
| % only one file supported currently | ||
| filename = filename{1}; | ||
|
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| formatSpec = '%*d %f %f %f %f %f %f %f %f'; | ||
|
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| % read in every line in the file | ||
| try | ||
| fid = fopen(filename, 'rt'); | ||
| data = textscan(fid, formatSpec, 'Delimiter', {' ', '/', ':'}, 'MultipleDelimsAsOne', true); | ||
|
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| fclose(fid); | ||
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| catch e | ||
| if fid ~= -1, fclose(fid); end | ||
| rethrow(e); | ||
| end | ||
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| Y = data{3}; | ||
| M = data{1}; | ||
| D = data{2}; | ||
| H = data{4}; | ||
| MN = data{5}; | ||
| S = data{6}; | ||
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| time = datenum(Y, M, D, H, MN+2, S); % we assume a measurement is averaged over 4 minutes | ||
| pressure = data{7} * 0.6894757; % 1psi = 0.6894757dbar | ||
| temperature = data{8}; | ||
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| % create sample data struct, | ||
| % and copy all the data in | ||
| sample_data = struct; | ||
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| sample_data.toolbox_input_file = filename; | ||
| sample_data.meta.featureType = mode; | ||
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| sample_data.meta.instrument_make = 'Seabird'; | ||
| sample_data.meta.instrument_model = 'SBE26'; | ||
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| sample_data.meta.instrument_firmware = ''; | ||
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| sample_data.meta.instrument_serial_no = ''; | ||
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| sample_data.meta.instrument_sample_interval = median(diff(time*24*3600)); | ||
|
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| sample_data.dimensions = {}; | ||
| sample_data.variables = {}; | ||
|
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| % generate time data from header information | ||
| sample_data.dimensions{1}.name = 'TIME'; | ||
| sample_data.dimensions{1}.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.dimensions{1}.name, 'type'))); | ||
| sample_data.dimensions{1}.data = sample_data.dimensions{1}.typeCastFunc(time); | ||
| sample_data.dimensions{1}.comment = 'Time stamp corresponds to the centre of the measurement which lasts 4 minutes.'; | ||
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| sample_data.variables{end+1}.name = 'TIMESERIES'; | ||
| sample_data.variables{end}.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.variables{end}.name, 'type'))); | ||
| sample_data.variables{end}.data = sample_data.variables{end}.typeCastFunc(1); | ||
| sample_data.variables{end}.dimensions = []; | ||
| sample_data.variables{end+1}.name = 'LATITUDE'; | ||
| sample_data.variables{end}.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.variables{end}.name, 'type'))); | ||
| sample_data.variables{end}.data = sample_data.variables{end}.typeCastFunc(NaN); | ||
| sample_data.variables{end}.dimensions = []; | ||
| sample_data.variables{end+1}.name = 'LONGITUDE'; | ||
| sample_data.variables{end}.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.variables{end}.name, 'type'))); | ||
| sample_data.variables{end}.data = sample_data.variables{end}.typeCastFunc(NaN); | ||
| sample_data.variables{end}.dimensions = []; | ||
| sample_data.variables{end+1}.name = 'NOMINAL_DEPTH'; | ||
| sample_data.variables{end}.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.variables{end}.name, 'type'))); | ||
| sample_data.variables{end}.data = sample_data.variables{end}.typeCastFunc(NaN); | ||
| sample_data.variables{end}.dimensions = []; | ||
|
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| % create a variable for each parameter | ||
| coordinates = 'TIME LATITUDE LONGITUDE NOMINAL_DEPTH'; | ||
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| % dimensions definition must stay in this order : T, Z, Y, X, others; | ||
| % to be CF compliant | ||
| sample_data.variables{end+1}.dimensions = 1; | ||
| sample_data.variables{end }.name = 'PRES_REL'; | ||
| sample_data.variables{end }.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.variables{end}.name, 'type'))); | ||
| sample_data.variables{end }.data = sample_data.variables{end}.typeCastFunc(pressure); | ||
| sample_data.variables{end }.coordinates = coordinates; | ||
| % let's document the constant pressure atmosphere offset previously | ||
| % applied by SeaBird software on the absolute presure measurement | ||
| sample_data.variables{end}.applied_offset = sample_data.variables{end}.typeCastFunc(-14.7*0.689476); | ||
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| sample_data.variables{end+1}.dimensions = 1; | ||
| sample_data.variables{end }.name = 'TEMP'; | ||
| sample_data.variables{end }.typeCastFunc = str2func(netcdf3ToMatlabType(imosParameters(sample_data.variables{end}.name, 'type'))); | ||
| sample_data.variables{end }.data = sample_data.variables{end}.typeCastFunc(temperature); | ||
| sample_data.variables{end }.coordinates = coordinates; | ||
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| end |