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+82
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function LopapTimeT = fitLopapBkgrd(LopapTimeT,lopapFitParameter)
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%FITLOPAPBKGRD fits and subtracts the background from Lopap data. Input is
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%a timetable with the processed data for both channels.
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%
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% LopapTimeT = fitLopapBkgrd(LopapTimeT) fits a linear background through 2
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% periods a 15 minutes at the beginning and at the end of the data set for
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% both channels.
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%
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% LopapTimeT = fitLopapBkgrd(LopapTimeT,'BkgrdPeriod',[datenum('14-Sep-2020 14:50:00')
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% datenum('14-Sep-2020 15:15:00'); datenum('14-Sep-2020 16:50:00')
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% datenum('14-Sep-2020 17:15:00')]) fits a linear background through 2
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% periods as specified by the time matrix for both channels: This matrix
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% holds the start time and end time in col1 and col2 of each line for
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% individual regions that are used to fit. The number of lines defines the
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% number of regions to be used to fit. All data outside these regions are
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% excluded from the fits.
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%
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% LopapTimeT = fitLopapBkgrd(LopapTimeT,'ChannelNumber',2) Processing is
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% restricted data of channel 2. Possible input are 1, 2, [1 2]. Default is [1 2]
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%
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% The optional input can also be combined:
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%
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% localFitBkgrd(LopapTimeT,'ChannelNumber', 1, 'FitType','exp1') fits data
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% in channel 1 with an exponential function. Standard FitType is linear
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% ('poly1').
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% Check the input: Is channel reasonable, is end-date after start-date?
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arguments
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LopapTimeT timetable
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lopapFitParameter.ChannelNumber double {mustBeMember(lopapFitParameter.ChannelNumber,[1,2])} = [1 2]
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lopapFitParameter.BkgrdPeriod double {mustBeLopapLaterDate(lopapFitParameter.BkgrdPeriod)} = ...
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[datenum(LopapTimeT.Time(1)+minutes(10)) datenum(LopapTimeT.Time(1)+minutes(25)); ...
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datenum(LopapTimeT.Time(end)-minutes(25)) datenum(LopapTimeT.Time(end)-minutes(10))]
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lopapFitParameter.FitType char ...
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{mustBeMember(lopapFitParameter.FitType,{'poly1','poly2','poly3','poly4','poly5','poly6','poly7','poly8','poly9','exp1','exp2'})} = "poly1"
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lopapFitParameter.TimeRangeToPlot
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end
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% gets index (row number) of data for given time periods
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for ii = 1:size(lopapFitParameter.BkgrdPeriod,1)
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index(ii,1) = find(datenum(LopapTimeT.Time) >= lopapFitParameter.BkgrdPeriod(ii,1),1);
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index(ii,2) = find(datenum(LopapTimeT.Time) >= lopapFitParameter.BkgrdPeriod(ii,2),1);
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end
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% gets index (row number) of data for given time periods
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for ii = 1:size(lopapFitParameter.TimeRangeToPlot,1)
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indexPlot(ii,1) = find(datenum(LopapTimeT.Time) >= lopapFitParameter.TimeRangeToPlot(ii,1),1);
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indexPlot(ii,2) = find(datenum(LopapTimeT.Time) >= lopapFitParameter.TimeRangeToPlot(ii,2),1);
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end
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% define data
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for ii = 1:size(lopapFitParameter.ChannelNumber,2)
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[xData, yData] = prepareCurveData( [], LopapTimeT.(['Ch #' num2str(lopapFitParameter.ChannelNumber(ii))]));
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clearvars excluded*
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%opts = rmfield(opts,'Exclude');
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% Set up fittype and options.
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ft = fittype( lopapFitParameter.FitType );
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% exclude all data outside the given time periods (based on the index):
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for ij = 1:size(lopapFitParameter.BkgrdPeriod,1)
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excludedRegion(:,ij) = excludedata( xData, yData, 'domain',...
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[index(ij) index(ij+size(lopapFitParameter.BkgrdPeriod,1))]);
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end
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excludedPoints = all(excludedRegion,2);
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opts = fitoptions( 'Method', 'LinearLeastSquares' );
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opts.Exclude = excludedPoints;
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% Fit model to data.
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[fitresult, ~] = fit( xData, yData, ft, opts );
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% Plot fit with data.
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figure( 'Name', ['Fit background Ch #' num2str(lopapFitParameter.ChannelNumber(ii))]);
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h = plot( fitresult, xData, yData, excludedPoints );
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legend( h, 'y', 'Excluded y', 'untitled fit 1', 'Location', 'NorthEast', 'Interpreter', 'none' );
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% Label axes
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ylabel( 'y', 'Interpreter', 'none' );
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grid on
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xlim([indexPlot(1,1) indexPlot(1,2)])
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% Subtract Background
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LopapTimeT.(['Ch #' num2str(lopapFitParameter.ChannelNumber(ii)) ' Bkgrd']) = ...
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LopapTimeT.(['Ch #' num2str(lopapFitParameter.ChannelNumber(ii))]) -fitresult(1:height(LopapTimeT));
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end
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end
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+32
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function [LopapTimeT, fitresult] = fitLopapCalibration(LopapTimeT,calib)
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%CREATEFIT(X,Y)
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% Create a fit.
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%
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% Data for 'untitled fit 1' fit:
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% X Input : x
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% Y Output: y
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% Output:
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% fitresult : a fit object representing the fit.
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% gof : structure with goodness-of fit info.
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%
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% See also FIT, CFIT, SFIT.
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% Auto-generated by MATLAB on 21-Sep-2020 11:28:06
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%% Fit: 'untitled fit 1'.
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[xData, yData] = prepareCurveData([0 calib.mean(3)],[0 calib.mixingRatio(1)]);
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% Set up fittype and options.
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ft = fittype( 'poly1' );
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% Fit model to data.
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[fitresult.calibChannel1, ~ ] = fit( xData, yData, ft );
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LopapTimeT.('Ch #1 Calib') = fitresult.calibChannel1(LopapTimeT.('Ch #1 Bkgrd'));
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[xData, yData] = prepareCurveData([0 calib.mean(4)],[0 calib.mixingRatio(2)]);
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% Fit model to data.
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[fitresult.calibChannel2, ~] = fit( xData, yData, ft );
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% calibrate
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LopapTimeT.('Ch #2 Calib') = fitresult.calibChannel2(LopapTimeT.('Ch #2 Bkgrd'));
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Executable
+37
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function [lopapReferenceWavelength, LopapDataCh1,LopapDataCh2,LopapSpecCh1,LopapSpecCh2]...
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= importLopap(lopapDateNum,fileLocation)
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%IMPORTLOPAP wraps import functions to read data from all Lopap files for one experiments
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% Check input to function, is the path correct?
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arguments
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lopapDateNum double
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fileLocation struct {mustBeLopapFolder(fileLocation, lopapDateNum)}
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end
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% generate full path name
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lopapPath = fullfile(fileLocation.server,fileLocation.dataPath,datestr(lopapDateNum,'yyyymmdd_HHMM'));
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% Import reference wavelength
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%
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% This reads the reference wavelength for both channels as recorded in the
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% *.dat file
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lopapReferenceWavelength = importLopapReferenceWavelength(fullfile(lopapPath,[datestr(lopapDateNum,'yyyymmdd_HHMM') '.dat']), [2, 3]);
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% Import data
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%
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% Here, we read the data from the Lopap .dat file into timetables, one for
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% each channel. This data holds the intensity at selected wavelength
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% divided by the reference wavelength. The information is thus the same as
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% shown in the "measurement plot" window of the Lopap software.
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[LopapDataCh1,LopapDataCh2] = importLopapDatFile(fullfile(lopapPath,[datestr(lopapDateNum,'yyyymmdd_HHMM') '.dat']), [6, Inf]);
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% Import spectra
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%
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% Here, we read the data from the Lopap .spec file into timetables, one for
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% each channel. The data hold the all spectra acquired during the
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% experiment. The information is thus the same as in the "spectrum plot"
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% window of the Lopap software.
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[LopapSpecCh1,LopapSpecCh2] = importLopapSpecFile(fullfile(lopapPath,[datestr(lopapDateNum,'yyyymmdd_HHMM') '.spec']), [1, Inf]);
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end
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+98
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function [LopapDataCh1, LopapDataCh2] = importLopapDatFile(filename, dataLines)
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%IMPORTLOPAPDATFILE Import data from a Lopap .dat file
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% [LopapDataCh1, LopapDataCh2] = importLopapDatFile(FILENAME) reads data
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% from Lopap .dat text file FILENAME for the default selection. Returns
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% the data as timetables for each Lopap channel with time in rows and
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% wavelength in columns.
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%
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% [LOPAPDATACH1, LOPAPDATACH2] = importLopapDatFile(FILE, DATALINES) reads
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% data for the specified row interval(s) of the Lopap .dat text file
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% FILENAME. Specify DATALINES as a positive scalar integer or a N-by-2
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% array of positive scalar integers for dis-contiguous row intervals.
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%
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% Example:
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% [LopapDataCh1, LopapDataCh2] = importLopapDatFile("20200619_1320.dat", [5, Inf]);
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%
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% See also READTABLE.
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%
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% Auto-generated by MATLAB on 14-Sep-2020 13:27:21
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%% Lopap Measurement Data Files (.dat)
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% The measurement data files contain the processed measurement values,
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% which were written while the running measurement. This file is constantly
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% updated while the measurement is running, thus even if the application is
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% terminated accidentally, this contains the measurement values until the
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% time of termination.
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%
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% *File Format* The file format is very straightforward.
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% A Measurement Data File consists of a header in which the file format and
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% the reference wavelengths for every spectrometer channel is recorded.
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% After this header, the data section starts. The data is arranged in a
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% chronological semicolon separated value list, with one line per sample
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% time. The first two columns give the date and the time of the data
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% sample. The following columns give the measurement values for every
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% measurement wavelength of the spectrometer channels. The spectrometer
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% channels are separated with the string ChX where "X" stands for the
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% spectrometer channel index. The very first line of the data section gives
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% the meaning of the columns in a sort form.
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%% Read header to string
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opts = delimitedTextImportOptions("NumVariables", 26);
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% Specify range and delimiter
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opts.DataLines = [5, 5];
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opts.Delimiter = ";";
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% Specify column names and types
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opts.VariableNames = ["Date", "Time", "Ch1", "VarName4", "VarName5", "VarName6", "VarName7", "VarName8", "VarName9", "VarName10", "VarName11", "VarName12", "VarName13", "VarName14", "Ch2", "VarName16", "VarName17", "VarName18", "VarName19", "VarName20", "VarName21", "VarName22", "VarName23", "VarName24", "VarName25", "VarName26"];
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opts.VariableTypes = ["string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string"];
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% Specify file level properties
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opts.ExtraColumnsRule = "ignore";
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opts.EmptyLineRule = "read";
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% Specify variable properties
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opts = setvaropts(opts, ["Date", "Time", "Ch1", "VarName4", "VarName5", "VarName6", "VarName7", "VarName8", "VarName9", "VarName10", "VarName11", "VarName12", "VarName13", "VarName14", "Ch2", "VarName16", "VarName17", "VarName18", "VarName19", "VarName20", "VarName21", "VarName22", "VarName23", "VarName24", "VarName25", "VarName26"], "WhitespaceRule", "preserve");
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opts = setvaropts(opts, ["Date", "Time", "Ch1", "VarName4", "VarName5", "VarName6", "VarName7", "VarName8", "VarName9", "VarName10", "VarName11", "VarName12", "VarName13", "VarName14", "Ch2", "VarName16", "VarName17", "VarName18", "VarName19", "VarName20", "VarName21", "VarName22", "VarName23", "VarName24", "VarName25", "VarName26"], "EmptyFieldRule", "auto");
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% Import the data
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variableNames = readmatrix(filename, opts);
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%% Input handling
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% If dataLines is not specified, define defaults
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if nargin < 2
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dataLines = [6, Inf];
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end
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%% Setup the Import Options and import the data
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clearvars opts
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opts = delimitedTextImportOptions("NumVariables", 26);
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% Specify range and delimiter
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opts.DataLines = dataLines;
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opts.Delimiter = ";";
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% Specify column names and types
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opts.VariableNames = variableNames(:);
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opts.VariableTypes = ["datetime", "datetime", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double"];
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% Specify file level properties
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opts.ExtraColumnsRule = "ignore";
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opts.EmptyLineRule = "read";
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opts.PreserveVariableNames = 1;
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% Specify variable properties
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opts = setvaropts(opts, "Date", "InputFormat", "dd.MM.yyyy");
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opts = setvaropts(opts, "Time", "InputFormat", "HH:mm:ss");
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opts = setvaropts(opts, ["Ch1", "Ch2"], "TrimNonNumeric", true);
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opts = setvaropts(opts, ["Ch1", "Ch2"], "ThousandsSeparator", ",");
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% Import the data
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T = readtable(filename, opts);
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T.Date.Format = 'dd.MM.uuuu HH:mm:ss';
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T.Time.Format = 'dd.MM.uuuu HH:mm:ss';
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columnCh2 = find(strcmp(opts.VariableNames,'Ch2') >=1,1);
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LopapDataCh1 = table2timetable(T(:,4:columnCh2-1),'RowTimes',T.Date + timeofday(T.Time));
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LopapDataCh2 = table2timetable(T(:,columnCh2+1:end),'RowTimes',T.Date + timeofday(T.Time));
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end
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+51
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function VarName2 = importLopapPrjFile(filename, dataLines)
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%IMPORTLOPAPPRJFILE Import data from a Lopap .prj text file
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% VARNAME2 = importLopapPrjFile(FILENAME) reads data from Lopap .prj text
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% file FILENAME for the default selection. Returns the data as column
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% vectors.
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%
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% VARNAME2 = importLopapPrjFile(FILE, DATALINES) reads data for the specified
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% row interval(s) of Lopap .prj text file FILENAME. Specify DATALINES as a
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% positive scalar integer or a N-by-2 array of positive scalar integers
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% for dis-contiguous row intervals.
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%
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% Example:
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% wavelengthCh1 = importLopapPrjFile("20200619_1320.prj", [10, 10]);
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%
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% See also READTABLE.
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%
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% Auto-generated by MATLAB on 15-Sep-2020 08:38:14
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%% Input handling
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% If dataLines is not specified, define defaults
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if nargin < 2
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dataLines = [10, Inf];
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end
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%% Setup the Import Options and import the data
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opts = delimitedTextImportOptions("NumVariables", 2);
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% Specify range and delimiter
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opts.DataLines = dataLines;
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opts.Delimiter = "=";
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% Specify column names and types
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opts.VariableNames = ["Var1", "VarName2"];
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opts.SelectedVariableNames = "VarName2";
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opts.VariableTypes = ["string", "string"];
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% Specify file level properties
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opts.ExtraColumnsRule = "ignore";
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opts.EmptyLineRule = "read";
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% Specify variable properties
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opts = setvaropts(opts, ["Var1", "VarName2"], "WhitespaceRule", "preserve");
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opts = setvaropts(opts, ["Var1", "VarName2"], "EmptyFieldRule", "auto");
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% Import the data
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tbl = readtable(filename, opts);
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%% Convert to output type
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VarName2 = tbl.VarName2;
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end
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@@ -0,0 +1,50 @@
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function referenceWavelength = importLopapReferenceWavelength(filename, dataLines)
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%IMPORTLOPAPREFERENCEWAVELENGTH IMPORT DATA FROM A TEXT FILE
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% REFERENCEWAVELENGTH = importReferenceWavelength(FILENAME) reads data from Lopap
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% .dat text file FILENAME for the default selection. Returns the data as
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% a string array with text string for channel 1 in 1st row and for channel
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% 2 in second row.
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%
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% REFERENCEWAVELENGTH = importReferenceWavelength(FILE, DATALINES) reads data for the specified
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% row interval(s) of text file FILENAME. Specify DATALINES as a
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% positive scalar integer or a N-by-2 array of positive scalar integers
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% for dis-contiguous row intervals.
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%
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% Example:
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% referenceWavelength = importReferenceWavelength("20200619_1320.dat", [2, 3]);
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%
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% See also READTABLE.
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%
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% Auto-generated by MATLAB on 14-Sep-2020 13:25:26
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%% Input handling
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% If dataLines is not specified, define defaults
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if nargin < 2
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dataLines = [2, Inf];
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end
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%% Setup the Import Options and import the data
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opts = delimitedTextImportOptions("NumVariables", 26);
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% Specify range and delimiter
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opts.DataLines = dataLines;
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opts.Delimiter = ";";
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% Specify column names and types
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opts.VariableNames = ["LOPAPlicmeasurementdatav01", "Var2", "Var3", "Var4", "Var5", "Var6", "Var7", "Var8", "Var9", "Var10", "Var11", "Var12", "Var13", "Var14", "Var15", "Var16", "Var17", "Var18", "Var19", "Var20", "Var21", "Var22", "Var23", "Var24", "Var25", "Var26"];
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opts.SelectedVariableNames = "LOPAPlicmeasurementdatav01";
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opts.VariableTypes = ["string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string", "string"];
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% Specify file level properties
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opts.ExtraColumnsRule = "ignore";
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opts.EmptyLineRule = "read";
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% Specify variable properties
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opts = setvaropts(opts, ["LOPAPlicmeasurementdatav01", "Var2", "Var3", "Var4", "Var5", "Var6", "Var7", "Var8", "Var9", "Var10", "Var11", "Var12", "Var13", "Var14", "Var15", "Var16", "Var17", "Var18", "Var19", "Var20", "Var21", "Var22", "Var23", "Var24", "Var25", "Var26"], "WhitespaceRule", "preserve");
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opts = setvaropts(opts, ["LOPAPlicmeasurementdatav01", "Var2", "Var3", "Var4", "Var5", "Var6", "Var7", "Var8", "Var9", "Var10", "Var11", "Var12", "Var13", "Var14", "Var15", "Var16", "Var17", "Var18", "Var19", "Var20", "Var21", "Var22", "Var23", "Var24", "Var25", "Var26"], "EmptyFieldRule", "auto");
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% Import the data
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||||
referenceWavelength = readmatrix(filename, opts);
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end
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||||
+86
@@ -0,0 +1,86 @@
|
||||
function [LopapSpecCh1, LopapSpecCh2] = importLopapSpecFile(filename, dataLines)
|
||||
%IMPORTLOPAPSPECFILE imports data from a Lopap .spec file
|
||||
% [LopapSpecCh1, LopapSpecCh2] = importLopapSpecFile(FILENAME) reads data
|
||||
% from Lopap .spec text file FILENAME for the default selection. Returns
|
||||
% the data as a timetable for each channel with time in rows and
|
||||
% wavelength in nm in columns.
|
||||
%
|
||||
% [LOPAPSPECCH1, LOPAPSPECCH2] = importLopapSpecFile(FILE, DATALINES) reads data for the specified
|
||||
% row interval(s) of text file FILENAME. Specify DATALINES as a
|
||||
% positive scalar integer or a N-by-2 array of positive scalar integers
|
||||
% for dis-contiguous row intervals.
|
||||
%
|
||||
% Example:
|
||||
% [LopapSpecCh1, LopapSpecCh2] = importLopapSpecFile("20200619_1320.spec", [1, Inf]);
|
||||
%
|
||||
% See also READTABLE.
|
||||
%
|
||||
% Auto-generated by MATLAB on 14-Sep-2020 16:40:15
|
||||
|
||||
%% Input handling
|
||||
|
||||
% If dataLines is not specified, define defaults
|
||||
if nargin < 2
|
||||
dataLines = [1, Inf];
|
||||
end
|
||||
|
||||
%% Setup the Import Options and import the data
|
||||
opts = delimitedTextImportOptions("NumVariables", 2051);
|
||||
|
||||
% Specify range and delimiter
|
||||
opts.DataLines = dataLines;
|
||||
opts.Delimiter = ";";
|
||||
|
||||
% Specify column names and types
|
||||
opts.VariableNames = ["VarName1", "VarName2", "VarName3", "VarName4", "VarName5", "VarName6", "VarName7", "VarName8", "VarName9", "VarName10", "VarName11", "VarName12", "VarName13", "VarName14", "VarName15", "VarName16", "VarName17", "VarName18", "VarName19", "VarName20", "VarName21", "VarName22", "VarName23", "VarName24", "VarName25", "VarName26", "VarName27", "VarName28", "VarName29", "VarName30", "VarName31", "VarName32", "VarName33", "VarName34", "VarName35", "VarName36", "VarName37", "VarName38", "VarName39", "VarName40", "VarName41", "VarName42", "VarName43", "VarName44", "VarName45", "VarName46", "VarName47", "VarName48", "VarName49", "VarName50", "VarName51", "VarName52", "VarName53", "VarName54", "VarName55", "VarName56", "VarName57", "VarName58", "VarName59", "VarName60", "VarName61", "VarName62", "VarName63", "VarName64", "VarName65", "VarName66", "VarName67", "VarName68", "VarName69", "VarName70", "VarName71", "VarName72", "VarName73", "VarName74", "VarName75", "VarName76", "VarName77", "VarName78", "VarName79", "VarName80", "VarName81", "VarName82", "VarName83", "VarName84", "VarName85", "VarName86", "VarName87", "VarName88", "VarName89", "VarName90", "VarName91", "VarName92", "VarName93", "VarName94", "VarName95", "VarName96", "VarName97", "VarName98", "VarName99", "VarName100", "VarName101", "VarName102", "VarName103", "VarName104", "VarName105", "VarName106", "VarName107", "VarName108", "VarName109", "VarName110", "VarName111", "VarName112", "VarName113", "VarName114", "VarName115", "VarName116", "VarName117", "VarName118", "VarName119", "VarName120", "VarName121", "VarName122", "VarName123", "VarName124", "VarName125", "VarName126", "VarName127", "VarName128", "VarName129", "VarName130", "VarName131", "VarName132", "VarName133", "VarName134", "VarName135", "VarName136", "VarName137", "VarName138", "VarName139", "VarName140", "VarName141", "VarName142", "VarName143", "VarName144", "VarName145", "VarName146", "VarName147", "VarName148", "VarName149", "VarName150", "VarName151", "VarName152", "VarName153", "VarName154", "VarName155", "VarName156", "VarName157", "VarName158", "VarName159", "VarName160", "VarName161", "VarName162", "VarName163", "VarName164", "VarName165", "VarName166", "VarName167", "VarName168", "VarName169", "VarName170", "VarName171", "VarName172", "VarName173", "VarName174", "VarName175", "VarName176", "VarName177", "VarName178", "VarName179", "VarName180", "VarName181", "VarName182", "VarName183", "VarName184", "VarName185", "VarName186", "VarName187", "VarName188", "VarName189", "VarName190", "VarName191", "VarName192", "VarName193", "VarName194", "VarName195", "VarName196", "VarName197", "VarName198", "VarName199", "VarName200", "VarName201", "VarName202", "VarName203", "VarName204", "VarName205", "VarName206", "VarName207", "VarName208", "VarName209", "VarName210", "VarName211", "VarName212", "VarName213", "VarName214", "VarName215", "VarName216", "VarName217", "VarName218", "VarName219", "VarName220", "VarName221", "VarName222", "VarName223", "VarName224", "VarName225", "VarName226", "VarName227", "VarName228", "VarName229", "VarName230", "VarName231", "VarName232", "VarName233", "VarName234", "VarName235", "VarName236", "VarName237", "VarName238", "VarName239", "VarName240", "VarName241", "VarName242", "VarName243", "VarName244", "VarName245", "VarName246", "VarName247", "VarName248", "VarName249", "VarName250", "VarName251", "VarName252", "VarName253", "VarName254", "VarName255", "VarName256", "VarName257", "VarName258", "VarName259", "VarName260", "VarName261", "VarName262", "VarName263", "VarName264", "VarName265", "VarName266", "VarName267", "VarName268", "VarName269", "VarName270", "VarName271", "VarName272", "VarName273", "VarName274", "VarName275", "VarName276", "VarName277", "VarName278", "VarName279", "VarName280", "VarName281", "VarName282", "VarName283", "VarName284", "VarName285", "VarName286", "VarName287", "VarName288", "VarName289", "VarName290", "VarName291", "VarName292", "VarName293", "VarName294", "VarName295", "VarName296", "VarName297", "VarName298", "VarName299", "VarName300", "VarName301", "VarName302", "VarName303", "VarName304", "VarName305", "VarName306", "VarName307", "VarName308", "VarName309", "VarName310", "VarName311", "VarName312", "VarName313", "VarName314", "VarName315", "VarName316", "VarName317", "VarName318", "VarName319", "VarName320", "VarName321", "VarName322", "VarName323", "VarName324", "VarName325", "VarName326", "VarName327", "VarName328", "VarName329", "VarName330", "VarName331", "VarName332", "VarName333", "VarName334", "VarName335", "VarName336", "VarName337", "VarName338", "VarName339", "VarName340", "VarName341", "VarName342", "VarName343", "VarName344", "VarName345", "VarName346", "VarName347", "VarName348", "VarName349", "VarName350", "VarName351", "VarName352", "VarName353", "VarName354", "VarName355", "VarName356", "VarName357", "VarName358", "VarName359", "VarName360", "VarName361", "VarName362", "VarName363", "VaLine truncated
|
||||
opts.VariableTypes = ["double", "datetime", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "double", "doubLine truncated
|
||||
|
||||
% Specify file level properties
|
||||
opts.ExtraColumnsRule = "ignore";
|
||||
opts.EmptyLineRule = "read";
|
||||
|
||||
% Specify variable properties
|
||||
opts = setvaropts(opts, "VarName2", "InputFormat", "HH:mm:ss dd.MM.yyyy");
|
||||
opts = setvaropts(opts, ["VarName1", "VarName2051"], "TrimNonNumeric", true);
|
||||
opts = setvaropts(opts, ["VarName1", "VarName2051"], "ThousandsSeparator", ",");
|
||||
|
||||
% Import the data
|
||||
T = readtable(filename, opts);
|
||||
|
||||
|
||||
|
||||
%% Import wavelength of spectrometer channels
|
||||
[pfad,name,~] = fileparts(filename);
|
||||
wavelengthCh1 = importLopapPrjFile([pfad filesep name '.prj'], [10, 10]);
|
||||
wavelengthCh1 = split(wavelengthCh1,",")';
|
||||
idx = cellfun(@isempty,wavelengthCh1);
|
||||
wavelengthCh1(idx) = "2000";
|
||||
|
||||
wavelengthCh2 = importLopapPrjFile([pfad filesep name '.prj'], [13, 13]);
|
||||
wavelengthCh2 = split(wavelengthCh2,",")';
|
||||
idx = cellfun(@isempty,wavelengthCh2);
|
||||
wavelengthCh2(idx) = "2000";
|
||||
|
||||
rows = T.VarName1 == 0;
|
||||
T.VarName2.Format = 'HH:mm:ss dd.MM.uuuu';
|
||||
LopapSpecCh1 = table2timetable(T(rows,3:end),'RowTimes',T.VarName2(rows));% LopapSpecCh1 = renamevars(LopapSpecCh1,1:width(LopapSpecCh1),wavelengthCh1)
|
||||
LopapSpecCh1.Properties.VariableNames = wavelengthCh1;
|
||||
|
||||
rows = T.VarName1 == 1;
|
||||
T.VarName2.Format = 'HH:mm:ss dd.MM.uuuu';
|
||||
LopapSpecCh2 = table2timetable(T(rows,3:end),'RowTimes',T.VarName2(rows));
|
||||
LopapSpecCh2.Properties.VariableNames = wavelengthCh2;
|
||||
|
||||
% Subtract spectrometer offset
|
||||
% Wenn Ihr direkt die
|
||||
% Spektren benutzen wollt (log(Iref/I), dann müßt Ihr erst den Dunkelstrom
|
||||
% des Spektrometers abziehen. Den kannst Du gut sehen, wenn die Lampe aus
|
||||
% ist. Der ist je nach Spektrometer aber meist unabhängig von der
|
||||
% Wellenlänge. Daher nehmen wir bei den alten Spektrometern (S2000 bei
|
||||
% Euch?) die Pixel 11-61 und ziehen diesen Mittelwert von allen Signalen
|
||||
% ab. Erst dann wird log(Iref/I0) gebildet:
|
||||
|
||||
LopapSpecCh1.Variables = LopapSpecCh1.Variables - mean(LopapSpecCh1{:,10:59},2);
|
||||
LopapSpecCh2.Variables = LopapSpecCh2.Variables - mean(LopapSpecCh2{:,10:59},2);
|
||||
|
||||
end
|
||||
+64
@@ -0,0 +1,64 @@
|
||||
function TimeRange = modifyLopapTimeRanges(TimeRange, LopapParameters, LopapDataCh1, LopapDataCh2)
|
||||
%
|
||||
if LopapParameters.Interactive == 1
|
||||
close all
|
||||
clc
|
||||
list = {'Data Range','Background Fit',...
|
||||
'Compare Spectrum #1','Compare Spectrum #2'};
|
||||
indx = listdlg('ListString',list,'PromptString',{'Choose parameter to modify,','then select region in figure'}...
|
||||
,'SelectionMode','single');
|
||||
if indx == 2
|
||||
prompt = {'Enter number of regions to fit the background:'};
|
||||
dlgtitle = 'Background Fit';
|
||||
dims = [1 40];
|
||||
definput = {'2'};
|
||||
answer = inputdlg(prompt,dlgtitle,dims,definput);
|
||||
end
|
||||
if indx >= 1
|
||||
clc
|
||||
close all
|
||||
figure( 'Name', 'LopapChannel 550','NumberTitle','off','Position',[10 100 550 800]);
|
||||
plot(datenum(LopapDataCh1.Time),LopapDataCh1.("485.5"));
|
||||
hold on
|
||||
datetick('x','dd.mm hh:MM','keeplimits','keepticks');
|
||||
ax = gca;
|
||||
yyaxis right
|
||||
plot(datenum(LopapDataCh2.Time),LopapDataCh2.("550.5"));
|
||||
datetick('x','dd.mm hh:MM','keeplimits','keepticks');
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
legend({'MeasData Ch#1','MeasData Ch#2'})
|
||||
% select regions in plot
|
||||
if indx == 1
|
||||
Roi.calibrationRange = drawline(ax,'Color','r');
|
||||
TimeRange.dataRange = [Roi.calibrationRange.Position(1,1) Roi.calibrationRange.Position(2,1)];
|
||||
pause(3)
|
||||
close all
|
||||
elseif indx == 2
|
||||
for ii = 1:str2double(answer)
|
||||
Roi.backgroundFit = drawline(ax,'Color','r');
|
||||
TimeRange.backgroundFit(ii,:) = [Roi.backgroundFit.Position(1,1) Roi.backgroundFit.Position(2,1)];
|
||||
end
|
||||
pause(3)
|
||||
close all
|
||||
elseif indx == 3
|
||||
Roi.specWithReagents = drawpoint(ax,'Color','r');
|
||||
TimeRange.specCompareOne = Roi.specWithReagents.Position(1,1);
|
||||
pause(3)
|
||||
close all
|
||||
elseif indx == 4
|
||||
Roi.specWithNitrite = drawpoint(ax,'Color','r');
|
||||
TimeRange.specCompareTwo = Roi.specWithNitrite.Position(1,1);
|
||||
pause(3)
|
||||
close all
|
||||
end
|
||||
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
save(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'],'TimeRange');
|
||||
end
|
||||
else
|
||||
disp('Variable LopapParameters.Interactive not set to 1: Modify data ranges manually has been skiped');
|
||||
end
|
||||
end
|
||||
+117
@@ -0,0 +1,117 @@
|
||||
function TimeRange = modifyLopapTimeRangesCalib(TimeRange, LopapParameters, LopapDataCh1, LopapDataCh2)
|
||||
%
|
||||
if LopapParameters.Interactive == 1
|
||||
close all
|
||||
clc
|
||||
list = {'Calibration Range','Background Fit','Mean ZeroAir','Mean Nitrit',...
|
||||
'Spectrum One','Spectrum Two'};
|
||||
indx = listdlg('ListString',list,'PromptString',{'Choose parameter to modify,','then select region in figure'}...
|
||||
,'SelectionMode','single');
|
||||
if indx == 2
|
||||
prompt = {'Enter number of regions to fit the background:'};
|
||||
dlgtitle = 'Background Fit';
|
||||
dims = [1 40];
|
||||
definput = {'2'};
|
||||
answer = inputdlg(prompt,dlgtitle,dims,definput);
|
||||
end
|
||||
if indx >= 1
|
||||
clc
|
||||
close all
|
||||
figure( 'Name', 'LopapChannel 550','NumberTitle','off','Position',[10 100 550 800]);
|
||||
plot(datenum(LopapDataCh1.Time),LopapDataCh1.("550.7"));
|
||||
hold on
|
||||
datetick('x','dd.mm hh:MM','keeplimits','keepticks');
|
||||
ax = gca;
|
||||
yyaxis right
|
||||
plot(datenum(LopapDataCh2.Time),LopapDataCh2.("550.5"));
|
||||
datetick('x','dd.mm hh:MM','keeplimits','keepticks');
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
legend({'MeasData Ch#1','MeasData Ch#2'})
|
||||
% select regions in plot
|
||||
if indx == 1
|
||||
Roi.calibrationRange = drawline(ax,'Color','r');
|
||||
TimeRange.calibrationRange = [Roi.calibrationRange.Position(1,1) Roi.calibrationRange.Position(2,1)];
|
||||
pause(3)
|
||||
close all
|
||||
elseif indx == 2
|
||||
for ii = 1:str2double(answer)
|
||||
Roi.backgroundFit = drawline(ax,'Color','r');
|
||||
TimeRange.backgroundFit(ii,:) = [Roi.backgroundFit.Position(1,1) Roi.backgroundFit.Position(2,1)];
|
||||
end
|
||||
pause(3)
|
||||
close all
|
||||
elseif indx == 3
|
||||
Roi.meanZeroAir = drawline(ax,'Color','r');
|
||||
TimeRange.MeanZeroAir = [Roi.meanZeroAir.Position(1,1) Roi.meanZeroAir.Position(2,1)];
|
||||
pause(3)
|
||||
close all
|
||||
elseif indx == 4
|
||||
Roi.meanNitriteStandard = drawline(ax,'Color','r');
|
||||
TimeRange.MeanNitriteStandard = [Roi.meanNitriteStandard.Position(1,1) Roi.meanNitriteStandard.Position(2,1)];
|
||||
pause(3)
|
||||
close all
|
||||
elseif indx == 5
|
||||
Roi.specCompareOne = drawpoint(ax,'Color','r');
|
||||
TimeRange.specCompareOne = Roi.specCompareOne.Position(1,1);
|
||||
pause(3)
|
||||
close all
|
||||
elseif indx == 6
|
||||
Roi.specCompareTwo = drawpoint(ax,'Color','r');
|
||||
TimeRange.specCompareTwo = Roi.specCompareTwo.Position(1,1);
|
||||
pause(3)
|
||||
close all
|
||||
end
|
||||
disp("***************************************************************")
|
||||
disp("* *")
|
||||
disp("* If modified, COPY THIS CODE TO YOUR SCRIPT *")
|
||||
disp("* *")
|
||||
disp("***************************************************************")
|
||||
|
||||
disp(" % State the start and end time of the calibration. Usually")
|
||||
disp(" % this is included zero air with R1&2, zero air with nitrite standard,")
|
||||
disp(" % zero air with R1&2")
|
||||
fprintf(" TimeRange.calibrationRange = [datenum('%s') datenum('%s')]; \n",datestr(TimeRange.calibrationRange(1)), datestr(TimeRange.calibrationRange(2)));
|
||||
disp(" % <Adapt>: State the time for the first spectrum that you like to")
|
||||
disp(" % compare (to confirm nitrite)")
|
||||
fprintf(" TimeRange.specCompareOne = datenum('%s'); \n", datestr(TimeRange.specCompareOne(1)));
|
||||
disp(" % <Adapt>: State the time for one spectrum of the second spectrum that")
|
||||
disp(" % you like to compare (to confirm nitrite)")
|
||||
fprintf(" TimeRange.specCompareTwo = datenum('%s'); \n", datestr(TimeRange.specCompareTwo(1)));
|
||||
disp(" % <Adapt>: Choose a start and end time for one as many intervals that can")
|
||||
disp(" % be used to fit the background. Background is the signal when R1&R2 was")
|
||||
disp(" % attached to the Lopap with zero air entering the sampling coil.")
|
||||
if size(TimeRange.backgroundFit,1) ==1
|
||||
fprintf(" TimeRange.backgroundFit = [datenum('%s') datenum('%s')]; \n",datestr(TimeRange.backgroundFit(1,1)), datestr(TimeRange.backgroundFit(1,2)))
|
||||
end
|
||||
if size(TimeRange.backgroundFit,1) ==2
|
||||
fprintf(" TimeRange.backgroundFit = [datenum('%s') datenum('%s'); datenum('%s') datenum('%s')]; \n",datestr(TimeRange.backgroundFit(1,1)), datestr(TimeRange.backgroundFit(1,2)),datestr(TimeRange.backgroundFit(2,1)), datestr(TimeRange.backgroundFit(2,2)))
|
||||
end
|
||||
if size(TimeRange.backgroundFit,1) ==3
|
||||
fprintf(" TimeRange.backgroundFit = [datenum('%s') datenum('%s'); datenum('%s') datenum('%s'); datenum('%s') datenum('%s')]; \n",datestr(TimeRange.backgroundFit(1,1)), datestr(TimeRange.backgroundFit(1,2)),datestr(TimeRange.backgroundFit(2,1)), datestr(TimeRange.backgroundFit(2,2)),datestr(TimeRange.backgroundFit(3,1)), datestr(TimeRange.backgroundFit(3,2)))
|
||||
end
|
||||
disp(" % <Adapt>: State the start and end time of data that can be used to")
|
||||
disp(" % calculate the mean of the zero air signal without nitrite")
|
||||
fprintf(" TimeRange.MeanZeroAir = [datenum('%s') datenum('%s')]; \n",datestr(TimeRange.MeanZeroAir(1)), datestr(TimeRange.MeanZeroAir(2)));
|
||||
disp(" % <Adapt>: State the start and end time of data that can be used to")
|
||||
disp(" % calculate the mean of the zero air signal with nitrite")
|
||||
fprintf(" TimeRange.MeanNitriteStandard = [datenum('%s') datenum('%s')]; \n",datestr(TimeRange.MeanNitriteStandard(1)), datestr(TimeRange.MeanNitriteStandard(2)));
|
||||
|
||||
disp("***************************************************************")
|
||||
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key after you have copied above text and when you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
|
||||
end
|
||||
|
||||
end
|
||||
else
|
||||
disp('Variable LopapParameters.Interactive not set to 1: Modify data ranges manually has been skiped');
|
||||
end
|
||||
end
|
||||
+13
@@ -0,0 +1,13 @@
|
||||
function mustBeLopapFolder(inputPath,inputDate)
|
||||
% MUSTBEFOLDER checks two things: First that the drive hosting the data
|
||||
% folder is accessible, i.e. that the windows server are mounted and that
|
||||
% there is no typo in the path and secondly that the folder name generated
|
||||
% from the experimental date exists.
|
||||
|
||||
if ~isfolder(fullfile(inputPath.server,inputPath.dataPath))
|
||||
error(['The folder ' fullfile(inputPath.server,inputPath.dataPath) ' appears not to be mounted. Check your network connection.'])
|
||||
end
|
||||
if ~isfolder(fullfile(inputPath.server,inputPath.dataPath,datestr(inputDate,'yyyymmdd_HHMM')))
|
||||
error(['The folder ' datestr(inputDate,'yyyymmdd_HHMM') ' appears not to exist. The windows shared drive seems to be mounted. Check the date.'])
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,7 @@
|
||||
function mustBeLopapLaterDate(input)
|
||||
% MUSTBELATERDATE checks that the start date comes before end date in
|
||||
% functions that require date ranges as input.
|
||||
if input(1,1) >= input(1,2)
|
||||
error(['First date (' datestr(input(1,1)) ') appears to be later than second one (',datestr(input(1,2)),').'])
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,14 @@
|
||||
function mustBeLopapReasonableDate(dateInput)
|
||||
% MUSTBEREASONABLEATE checks that a date is reaonalbe, that is after 1990
|
||||
% and before 2025
|
||||
|
||||
for ij = 1:length(dateInput)
|
||||
if datenum(dateInput(1,ij)) <= datenum('01-Jan-1999 01:00:00')
|
||||
error(['Date (' datestr(dateInput(1,ij)) ') appears to be earlier than 1999. Please check.'])
|
||||
end
|
||||
if datenum(dateInput(1,ij)) >= datenum('01-Jan-2025 01:00:00')
|
||||
error(['Date (' datestr(dateInput(1,ij)) ') appears to be later than 2025. Please check.'])
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
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@@ -0,0 +1,584 @@
|
||||
%% Lopap Template
|
||||
% Uses data from 16.9.2020 13h26
|
||||
%
|
||||
%% Info: How to use this
|
||||
%
|
||||
% # Make a copy of this file for each Lopap measurement. Name it
|
||||
% "Lopap"_date_time.m and store it in the folder with the Lopap data. %
|
||||
% Remove all the general text and comments in your file and add notes and
|
||||
% observations about the experiment.
|
||||
%
|
||||
% # You can run this script, publish it, or evaluate it section wise. For
|
||||
% new data run it section wise to carefully update the settings and to
|
||||
% observe the results.
|
||||
% # Once the data is loaded, you can also run individual sections only.
|
||||
% # Use the LabBook :: Chrono Notes section as lab book.
|
||||
% # First, you need to give the date and time of the Lopap measurement to
|
||||
% load and process the data.
|
||||
% # All sections that can be modified are marked with the word "<Adapt>:".
|
||||
% # You also need to give time regions such as for the background fit, as
|
||||
% well as to calculate means. There are several options how to do this
|
||||
%
|
||||
% * While running the experiments and observing the signal in the Lopap
|
||||
% software, you can enter the date and times directly in the LabBook :
|
||||
% Select data ranges section.
|
||||
% * You can manually select the regions in a plot. A window will pop up to
|
||||
% select the region to modify. To modify several regions, re-run this
|
||||
% section of the script. This overwrites the current settings.
|
||||
% * The times of the regions are stored in the "TimeRanges.mat" file. If it
|
||||
% exists, this is read; the LabBook : Select data ranges section is then
|
||||
% ignored.
|
||||
%% Info: Output & Variables
|
||||
%
|
||||
% * *lopapReferenceWavelength*: This _string variable_ holds text with
|
||||
% stating the reference wavelength for channel 1 and 2 used to process the
|
||||
% data by the Lopap software.
|
||||
% * *LopapDataCh1 & LopapDataCh2*: These _time tables_ hold the data that
|
||||
% have been processed by the Lopap Software during the data acquisition. It
|
||||
% contains the absorption for a number
|
||||
% of selected wavelength. The absorption is the log of the intensity at the
|
||||
% reference wavelength relative to the intensity at each wavelength of
|
||||
% interest. The timetables hold the time in each row and the wavelength in
|
||||
% the columns. The content is thus identical to that shown in the
|
||||
% "measurement window" of the Lopap software.
|
||||
% * *LopapSpecCh1,LopapSpecCh2*: The _time tables_ hold the full spectrum
|
||||
% for each time. Time is in the rows, wavelength in the columns. The
|
||||
% wavelength are read from the *.prj file, the spectra data from the *.spec
|
||||
% file. The information is identical to that shown in the "spectrum window"
|
||||
% of the Lopap software.
|
||||
%
|
||||
% * *TimeRanges.mat*: Time ranges after they have been manually modified. If
|
||||
% this file exists, the time range definitions in this script are ignored.
|
||||
% * *LopapMatlabDataDATE_TIME.mat*: Raw data and experimental settings.
|
||||
% Background subtraction and calibration are not saved in this file. When
|
||||
% this file exists, data will not be read from the windows server.
|
||||
% * *LopapDATE_TIME.mat*: Processed data - absorption with time (column 1
|
||||
% and 2: 'Ch #1' and 'Ch #2') after background (columns 3 and 4: 'Ch #1
|
||||
% Bkgrd' and 'Ch #2 Bkgrd') subtraction and calibration (columns 5 and 6:
|
||||
% 'Ch #1 Calib' and 'Ch #2 Calib') for one wavelength - that can be used
|
||||
% for further comparison with other experiments and discussion.
|
||||
%
|
||||
|
||||
%% Matlab: Initialise
|
||||
%
|
||||
% This starts Matlab and defines some common settings such as the path to
|
||||
% the Lopap data. Any modifications can be done at the end of this file in
|
||||
% where the local function _localInitializeMatlab_ is stored.
|
||||
|
||||
|
||||
% clear variables in workspace, clear text in command window
|
||||
clearvars
|
||||
clc
|
||||
% set the path to the data and define some custom colours for plotting
|
||||
[fileLocation, myColorMap] = localInitializeMatlab;
|
||||
% <Adapt>: Date when Lopap recording was started. Defines names of Lopap
|
||||
% files and folders. Seconds are irrelevant, but format is important.
|
||||
LopapParameters.MeasurementDate = datenum('16-Sep-2020 13:26:00');
|
||||
|
||||
%%
|
||||
|
||||
% Print info to command window
|
||||
|
||||
disp('The data is read from:');
|
||||
disp(fullfile(fileLocation.server,fileLocation.dataPath,datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM')));
|
||||
disp(' ')
|
||||
disp('Date of experiment:')
|
||||
disp(datestr(LopapParameters.MeasurementDate));
|
||||
disp(' ')
|
||||
disp('Date of analyis:')
|
||||
disp(datestr(today));
|
||||
|
||||
%% Process: Import data
|
||||
%
|
||||
% Reads and imports data from Lopap *.dat, *.spec, and *.prj files into:
|
||||
%
|
||||
% * *lopapReferenceWavelength*: This _string variable_ holds text with
|
||||
% stating the reference wavelength for channel 1 and 2 used to process the
|
||||
% data by the Lopap software.
|
||||
% * *LopapDataCh1 & LopapDataCh2*: These _time tables_ hold the data that
|
||||
% have been processed by the Lopap Software during the data acquisition. It
|
||||
% contains the absorption for a number
|
||||
% of selected wavelength. The absorption is the log of the intensity at the
|
||||
% reference wavelength relative to the intensity at each wavelength of
|
||||
% interest. The timetables hold the time in each row and the wavelength in
|
||||
% the columns. The content is thus identical to that shown in the
|
||||
% "measurement window" of the Lopap software.
|
||||
% * *LopapSpecCh1,LopapSpecCh2*: The _time tables_ hold the full spectrum
|
||||
% for each time. Time is in the rows, wavelength in the columns. The
|
||||
% wavelength are read from the *.prj file, the spectra data from the *.spec
|
||||
% file. The information is identical to that shown in the "spectrum window"
|
||||
% of the Lopap software.
|
||||
|
||||
|
||||
if isfile(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'])
|
||||
load(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'])
|
||||
else
|
||||
[LopapParameters.instrumentReferenceWavelength, LopapDataCh1,LopapDataCh2,LopapSpecCh1,LopapSpecCh2] ...
|
||||
= importLopap(LopapParameters.MeasurementDate,fileLocation);
|
||||
end
|
||||
|
||||
%% Matlab: Run mode
|
||||
%
|
||||
% <Adapt>:
|
||||
%
|
||||
% * runs without user interaction and without ability to modify data
|
||||
% ranges, when set to 0; use this to publish.
|
||||
% * if set to 1: stops for user interaction,
|
||||
% modify data ranges is enabled.Use this to run.
|
||||
LopapParameters.Interactive = 0;
|
||||
%% LabBook : ChronoNotes
|
||||
%
|
||||
% <Adapt>: Your notes go here
|
||||
%
|
||||
% * Nitritstandardlösung: 1g/l
|
||||
% * Nitritlösung: 0.01mg/l
|
||||
% * Volumenfluss 1: 26.08min für 5ml -> 0.192ml/min
|
||||
% * Volumenfluss 2: 26.33min für 5ml -> 0.190ml/min
|
||||
% * Pumpgeschwindigkeit: 10U/min
|
||||
% * Gasfluss: 2000ml/min
|
||||
% * *16.9.20 13h30*: Start instrument with water
|
||||
% * time: 2s/2s
|
||||
% * time: 80ms/4ms
|
||||
% * *16.9.20 13h00*: water -> R1 & R2, ABS closed
|
||||
%% LabBook : Measurement Settings
|
||||
%
|
||||
% <Adapt>: list the Lopap settings here:
|
||||
LopapParameters.concStandard = 0.01; % mg/l concentration of nitrite in standard used for calibration
|
||||
LopapParameters.flowReagents = 5./[26.08 26.33]; % ml/min, enter time for 5 ml
|
||||
LopapParameters.flowGas = 2000; % ml/min, take average of 10.
|
||||
LopapParameters.temperature = 298; % temp of gas flow in K
|
||||
LopapParameters.pressure = 1013; % pressure of gas flow in mbar
|
||||
|
||||
% <Adapt>: Choose a reference wavelength. Default is 650 nm.
|
||||
LopapParameters.wavelengthR = 650; %nm, reference intensity
|
||||
% <Adapt>: Choose a signal wavelength to calculate the absorption with time
|
||||
% from the spectra
|
||||
LopapParameters.wavelengthS = 534; %nm, signal intensity
|
||||
|
||||
%% LabBook : Define data ranges
|
||||
%
|
||||
% These settings are ignored if the TimesRanges.mat file exist. If you do
|
||||
% not want to use the data stored in the TimesRanges.mat file, you need to
|
||||
% delete it before running this section.
|
||||
%
|
||||
% These settings can be modified by selecting data ranges in a plot later.
|
||||
% So, you do not necessarily need to type the dates and times here.
|
||||
|
||||
if isfile(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'])
|
||||
load(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'])
|
||||
elseif ~exist('TimeRange','var')
|
||||
% <Adapt>: State the start and end time of the calibration. Usually
|
||||
% this is included zero air with R1&2, zero air with nitrite standard,
|
||||
% zero air with R1&2
|
||||
TimeRange.calibrationRange = [datenum('16-Sep-2020 13:55:00') datenum('16-Sep-2020 15:15:00')];
|
||||
% <Adapt>: State the time for one spectrum with R1&R2 without nitrite
|
||||
TimeRange.specWithReagents = datenum('2020-09-16 14:31:06');
|
||||
% <Adapt>: State the time for one spectrum with R1&R2 and nitrite
|
||||
TimeRange.specWithNitrite = datenum('2020-09-16 15:10:14');
|
||||
% <Adapt>: Choose a start and end time for one as many intervals that can
|
||||
% be used to fit the background. Background is the signal when R1&R2 was
|
||||
% attached to the Lopap with zero air entering the sampling coil.
|
||||
TimeRange.backgroundFit = [datenum('16-Sep-2020 14:29:28') datenum('16-Sep-2020 14:40:04');...
|
||||
datenum('16-Sep-2020 15:40:50') datenum('16-Sep-2020 15:51:06')];
|
||||
% <Adapt>: State the start and end time of data that can be used to
|
||||
% calculate the mean of the zero air signal without nitrate
|
||||
TimeRange.MeanZeroAir = [datenum('16-Sep-2020 14:28:42') datenum('16-Sep-2020 14:38:36')];
|
||||
% <Adapt>: State the start and end time of data that can be used to
|
||||
% calculate the mean of the zero air signal without nitrate
|
||||
TimeRange.MeanNitriteStandard = [datenum('16-Sep-2020 15:09:20') datenum('16-Sep-2020 15:18:30')];
|
||||
|
||||
save(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'],'TimeRange');
|
||||
else
|
||||
disp('Nothing done: TimeRange in Workspace used')
|
||||
end
|
||||
|
||||
%% Process: Modify data ranges
|
||||
%
|
||||
% Select the range to modify in the pop-up window and the number of fit
|
||||
% ranges for the background fit in the 2nd pop-up window. Then, a figure
|
||||
% will show, select the data ranges in the figure:
|
||||
%
|
||||
% * a line for calibration range, mean zero air and mean
|
||||
% nitrite standard. Select the range by keeping the mouse pushed while
|
||||
% moving from start to end time.
|
||||
% * a line for each background region, default is 2. Select the range by
|
||||
% keeping the mouse pushed while moving from start to end time.
|
||||
% * a point for spectrum with reagents and spectrum with nitrite. Click
|
||||
% once to select a specific time.
|
||||
%
|
||||
% * LopapParameters.Interactive needs to be 1 for this to run.
|
||||
%
|
||||
% # Run this section several times to modify several time regions
|
||||
% # Press cancel in the pop-up window if you do not want to modify any
|
||||
% region.
|
||||
|
||||
TimeRange = modifyLopapTimeRanges(TimeRange, LopapParameters, LopapDataCh1, LopapDataCh2);
|
||||
|
||||
%% Process: Find closest match of selected dates in data set
|
||||
%
|
||||
% The data is sampled at specific times with a certain interval. The
|
||||
% selected or chosen dates might not necessarily exactly match the data.
|
||||
% Here, closest match to the given dates are selected.
|
||||
|
||||
tmp.d1 = TimeRange.specWithReagents;
|
||||
tmp.d2 = LopapSpecCh1.Time;
|
||||
[~,ind1] = min(abs(bsxfun(@minus,datenum(tmp.d2),datenum(tmp.d1)')));
|
||||
TimeRange.specWithReagents = tmp.d2(ind1,:);
|
||||
|
||||
tmp.d1 = TimeRange.specWithNitrite ;
|
||||
tmp.d2 = LopapSpecCh1.Time;
|
||||
[~,ind1] = min(abs(bsxfun(@minus,datenum(tmp.d2),datenum(tmp.d1)')));
|
||||
TimeRange.specWithNitrite = tmp.d2(ind1,:);
|
||||
|
||||
% save current state of
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'])
|
||||
save(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'],'TimeRange');
|
||||
|
||||
%% LabBook: Data ranges used in this work
|
||||
%
|
||||
% This plots the
|
||||
|
||||
fprintf('Calibration range: %s to %s \n',datestr(TimeRange.calibrationRange(1)), datestr(TimeRange.calibrationRange(2)))
|
||||
for ii=1:size(TimeRange.backgroundFit,2)
|
||||
fprintf('Background range: %s to %s \n',datestr(TimeRange.backgroundFit(ii,1)), datestr(TimeRange.backgroundFit(ii,2)))
|
||||
end
|
||||
fprintf('Zero mean: %s to %s \n',datestr(TimeRange.MeanZeroAir(1)), datestr(TimeRange.MeanZeroAir(2)))
|
||||
fprintf('Nitrite mean: %s to %s \n',datestr(TimeRange.MeanNitriteStandard(1)), datestr(TimeRange.MeanNitriteStandard(2)))
|
||||
fprintf('Zero spectrum: %s \n',datestr(TimeRange.specWithReagents(1)))
|
||||
fprintf('Nitrite spectrum: %s \n',datestr(TimeRange.specWithNitrite(1)))
|
||||
|
||||
|
||||
%% Plot all data
|
||||
%
|
||||
% Here, we plot the data as shown in the "Measurement window" of the Lopap
|
||||
% software. That is, the processed $I^{*}_{i}$ data for all wavelength as
|
||||
% defined in the settings of the Lopap software.
|
||||
%
|
||||
%
|
||||
% For every measurement wavelength I_i the program calculates the
|
||||
% measurement (absorption) value I_i^* from the spectral intensity on the
|
||||
% measurement wavelength I_i and a reference wavelength I_r with the
|
||||
% following operation:
|
||||
%
|
||||
%
|
||||
% $$I^{*}_{i} = log_{10} (\frac{I_r}{I_i})$$
|
||||
%
|
||||
%
|
||||
%
|
||||
% The plots show time on the x-axis and the ABS intensity on the y axis for
|
||||
% each wavelength in separate graphs. One Figure for each Channel.
|
||||
|
||||
figure( 'Name', 'LopapChannel1','NumberTitle','off','Position',[10 100 550 700]);
|
||||
ch1s=stackedplot(LopapDataCh1);
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
for ii = 1:width(LopapDataCh1)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch1s.AxesProperties(ii).YLimits = [-0.4 -0.1];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
figure( 'Name', 'LopapChannel2','NumberTitle','off','Position',[600 100 550 700]);
|
||||
ch2s=stackedplot(LopapDataCh2);
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
for ii = 1:width(LopapDataCh2)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties(ii).YLimits = [-0.2 0.3];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Labbook: Notes to Figures
|
||||
%
|
||||
% * Kanal 2 ist stärker am rauschen.
|
||||
% * Ev. wegen Leck am T-Stück in der Absorptionskammer.
|
||||
|
||||
%% Plot selected data
|
||||
%
|
||||
% Here we plot the $I^{*}_{i}$ data for one wavelength only.
|
||||
|
||||
|
||||
figure( 'Name', 'LopapChannel1 550','NumberTitle','off','Position',[10 100 550 800]);
|
||||
% <Adapt>: The numbers in the curled brackets give wavelength for which you'd
|
||||
% like to display the data. The numbers need to be exactly match the
|
||||
% labels in the previous figure.
|
||||
ch1s=stackedplot(LopapDataCh1,{'550.7'});
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
%ch1s.AxesProperties.YLimits = [-0.4 -0.1];
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
|
||||
figure( 'Name', 'LopapChannel2 550','NumberTitle','off','Position',[600 100 550 800]);
|
||||
% <Adapt>: The numbers in the curled brackets give wavelength for which you'd
|
||||
% like to display the data. The numbers need to be exactly match the
|
||||
% labels in the previous figure
|
||||
ch2s=stackedplot(LopapDataCh2,{'550.5'});
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties.YLimits = [-0.2 0.3];
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap lopap* TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Plot several spectra
|
||||
%
|
||||
% * A spectrum is obtained from the spectrometer.
|
||||
% * This spectrum is averaged from multiple raw spectra with a given
|
||||
% integration time. Optionally the raw spectra can be boxcar averaged with
|
||||
% an adjustable boxcar window width. The recommended boxcar window width is
|
||||
% 10 Pixel.
|
||||
% * Then a background correction is performed: The mean of the values of
|
||||
% the background pixels, which contains no measurement signal, is
|
||||
% subtracted from the whole spectrum. The background pixels are freely
|
||||
% configurable.
|
||||
clc
|
||||
close all
|
||||
S = timerange(datestr(TimeRange.calibrationRange(1)), datestr(TimeRange.calibrationRange(2)));
|
||||
figure( 'Name', 'LopapSpectraWithTime','NumberTitle','off')
|
||||
T = LopapSpecCh1(S,:);
|
||||
plot3(repmat(str2double(T.Properties.VariableNames),[height(T),1]),repmat(T.Time,[1,width(T)]),T.Variables)
|
||||
% Set the viewing angle and the axis limits
|
||||
view(-25, 1)
|
||||
xlim([400 700])
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('Time')
|
||||
zlabel('Intensity')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Plot selected spectra
|
||||
%
|
||||
% Here, we plot a spectrum without ('R1&R2') and with nitrite
|
||||
% ('R1+nitrite&R2'') for each channel.
|
||||
clc
|
||||
close all
|
||||
figure('Name', 'LopapSelectedSpectra')
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),LopapSpecCh1{datestr(TimeRange.specWithReagents),:},...
|
||||
'DisplayName','#1 R1&R2') % a time where only R1&R2 was connected to the Lopap
|
||||
hold on
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),LopapSpecCh2{datestr(TimeRange.specWithReagents),:},...
|
||||
'DisplayName','#2 R1&R2','LineStyle','--') % a time where only R1&R2 was connected to the Lopap
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),LopapSpecCh1{datestr(TimeRange.specWithNitrite),:},...
|
||||
'DisplayName','#1 R1+nitrite&R2') % a time where nitrite in R1 was connected to the Lopap
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),LopapSpecCh2{datestr(TimeRange.specWithNitrite),:},...
|
||||
'DisplayName','#2 R1+nitrite&R2','LineStyle','--') % a time where nitrite in R1 was connected to the Lopap
|
||||
legend
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('Intensity')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process: Absorption spectrum
|
||||
%
|
||||
% Here, we reprocess the data to derive an absorption spectrum. This should
|
||||
% match the spectra shown for nitrite in the Lopap manual.
|
||||
%
|
||||
%
|
||||
%
|
||||
% <html>
|
||||
% <img src="../Bildschirmfoto2020-09-16um14.30.03.png" width="550">
|
||||
% </html>
|
||||
%
|
||||
clc
|
||||
close all
|
||||
indexR(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
indexR(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
|
||||
figure('Name', 'LopapAbsorbtionSpectra')
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),log10(LopapSpecCh1{datestr(TimeRange.specWithNitrite),...
|
||||
indexR(1)}./LopapSpecCh1{datestr(TimeRange.specWithNitrite),:})-log10(LopapSpecCh1{datestr(TimeRange.specWithReagents),...
|
||||
indexR(1)}./LopapSpecCh1{datestr(TimeRange.specWithReagents),:}),'DisplayName','#1 nitrite')
|
||||
hold on
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),log10(LopapSpecCh2{datestr(TimeRange.specWithNitrite),...
|
||||
indexR(2)}./LopapSpecCh2{datestr(TimeRange.specWithNitrite),:})-log10(LopapSpecCh2{datestr(TimeRange.specWithReagents),...
|
||||
indexR(2)}./LopapSpecCh2{datestr(TimeRange.specWithReagents),:}),'DisplayName','#2 nitrite','LineStyle','--')
|
||||
legend
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('ABS (log I_{r}/I_{i}')
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process :: Absorption with time
|
||||
%
|
||||
% Here, we reprocess the data to get the intensity with time for 1 chosen
|
||||
% signal wavelength and 1 reference wavelength. The data is identical to that
|
||||
% shown in the "measurement window" of the Lopap software.
|
||||
%
|
||||
% The data is written to the _LopapTimeT_ time table. Rows hold the time,
|
||||
% columns hold the processed signal for channel 1 and channel 2.
|
||||
%
|
||||
% It is important that the same signal wavelength and reference wavelength
|
||||
% are taken for the calibration and for the experimental data.
|
||||
|
||||
clc
|
||||
close all
|
||||
indexS(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthS,1);
|
||||
indexS(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthS,1);
|
||||
indexR(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
indexR(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
LopapTimeT = timetable(LopapSpecCh1.Time,log10(LopapSpecCh1{:,indexR(1)}./LopapSpecCh1{:,indexS(1)}),log10(LopapSpecCh2{:,indexR(2)}./LopapSpecCh1{:,indexS(2)}));
|
||||
LopapTimeT.Properties.VariableNames ={'Ch #1','Ch #2'};
|
||||
figure('Name', 'Lopap TimeTable')
|
||||
stackedplot(LopapTimeT,{{'Ch #1','Ch #2'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process :: Background
|
||||
%
|
||||
clc
|
||||
close all
|
||||
LopapTimeT = fitLopapBkgrd(LopapTimeT,'BkgrdPeriod',TimeRange.backgroundFit);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
%% Plot bkgrd corrected data
|
||||
%
|
||||
clc
|
||||
close all
|
||||
% Plot
|
||||
figure('Name', 'Lopap TimeTable Bkgrd')
|
||||
s=stackedplot(LopapTimeT,{{'Ch #1 Bkgrd','Ch #2 Bkgrd'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
s.AxesProperties.YLimits = [-0.01 0.3];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
|
||||
%% Process :: Calibrate
|
||||
%
|
||||
clc
|
||||
close all
|
||||
|
||||
S = timerange(datestr(TimeRange.MeanZeroAir(1)), datestr(TimeRange.MeanZeroAir(2)));
|
||||
TZ = LopapTimeT(S,:);
|
||||
S = timerange(datestr(TimeRange.MeanNitriteStandard(1)), datestr(TimeRange.MeanNitriteStandard(2)));
|
||||
TN = LopapTimeT(S,:);
|
||||
calib.mean = mean(TN{:,:},1) - mean(TZ{:,:},1);
|
||||
calib.std = std(TN{:,:},1);
|
||||
calib.mixingRatio = LopapParameters.concStandard./1000.*LopapParameters.flowReagents./1000./46.*6.022E23./...
|
||||
(246E17.*LopapParameters.flowGas).*1E12;
|
||||
|
||||
[LopapTimeT, calib.fitresult] = fitLopapCalibration(LopapTimeT,calib);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange* fitresult calib
|
||||
|
||||
fprintf('Detection limit channel #1 is %.0f ppt \n',calib.fitresult.calibChannel1(3.*calib.std(3)))
|
||||
fprintf('Detection limit channel #2 is %.0f ppt \n',calib.fitresult.calibChannel2(3.*calib.std(4)))
|
||||
|
||||
%% Plot calibrated data
|
||||
%
|
||||
clc
|
||||
close all
|
||||
% Plot
|
||||
figure('Name', 'Lopap TimeTable Calibrated')
|
||||
s=stackedplot(LopapTimeT,{{'Ch #1 Calib','Ch #2 Calib'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
s.AxesProperties.YLimits = [-100 2500];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange* fitresult calib
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Save the data
|
||||
%
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'])
|
||||
save(['Lopap' datestr(LopapParameters.MeasurementDate,'yyyyMMdd_hhmm') '.mat'],'LopapParameters','LopapTimeT','TimeRange')
|
||||
%% Local functions
|
||||
function [fileLocation, myColorMap] = localInitializeMatlab
|
||||
%INITIALIZEMATLAB Sets Lopap specific settings
|
||||
% Adds processing functions to path and defines file locations for mac, windows,
|
||||
% and Matlab online (which runs on unix)
|
||||
|
||||
% change working directory
|
||||
path = matlab.desktop.editor.getActiveFilename;
|
||||
[filepath,~,~] = fileparts(path);
|
||||
cd(filepath);
|
||||
|
||||
|
||||
% Data Server Address
|
||||
if ismac
|
||||
fileLocation.server = '/Volumes/';
|
||||
fileLocation.dataPath = 'data_2411/Lopap/Marc/';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('/Users/bartels-rausch/Documents/SwitchDrive/PSI_Matlab/Add-Ons');
|
||||
addpath('/Users/bartels-rausch/Documents/SwitchDrive/PSI_Matlab/Lopap/1.LOPAP_Restliche Daten');
|
||||
elseif ispc
|
||||
fileLocation.server = '\\fs00\'; %UNC name for file server that hosts Napp shared drive
|
||||
fileLocation.dataPath = 'data_2411\Lopap\Marc\';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('C:\Users\iezzi_l\switchdrive\Add-Ons');
|
||||
addpath('\\fs02\5601_surface_chemistry\People\Marc\Switchdrive\PSI_Matlab\Lopap\1.LOPAP_Restliche Daten');
|
||||
elseif isunix
|
||||
fileLocation.server = '/';
|
||||
fileLocation.dataPath = 'Lopap/';
|
||||
end
|
||||
|
||||
% Color maps
|
||||
myColorMap.red = colormap(autumn(7));
|
||||
myColorMap.blue = colormap(winter(7));
|
||||
|
||||
close all
|
||||
end
|
||||
|
||||
Binary file not shown.
@@ -0,0 +1,99 @@
|
||||
%% Compile LOPAP data
|
||||
% from different data set
|
||||
|
||||
%% Choose data
|
||||
%
|
||||
% * Choose the mat files with the Lopap timetables to be plotted
|
||||
% * For each data set, define the 0-time. This could be the time when you
|
||||
% turned on the UV, or when the flow was directed via the flow tube. This
|
||||
% depends on what you want to compare and plot
|
||||
%
|
||||
% The data is then imported and then transferred to relative time
|
||||
|
||||
% clear variables in workspace, clear text in command window
|
||||
clearvars
|
||||
clc
|
||||
% set the path to the data and define some custom colours for plotting
|
||||
[fileLocation, myColorMap] = localInitializeMatlab;
|
||||
|
||||
|
||||
% <Adapt>: data files to be loaded
|
||||
tmpFileList = {'Lopap20211201_1033.mat';...
|
||||
'Lopap20211115_1431.mat'};
|
||||
% <Adapt>: define 0-time for each data set to be loaded. This needs one
|
||||
% date for each data set.
|
||||
tmpRefTime = [datetime('01-Dec-2021 15:24:23');...
|
||||
datetime('15-Nov-2021 16:49:23')];
|
||||
% <Adapt>: define time window to be plotted, in seconds
|
||||
tmpPlotTime = -30*60:2:120*60; % 30 minutes prior, 2 s interval, 2 hours after event
|
||||
|
||||
%% Load data and process
|
||||
%
|
||||
for ii = 1: length(tmpFileList)
|
||||
% load data from mat file
|
||||
load(tmpFileList{ii},'LopapTimeT')
|
||||
% get time
|
||||
tmpX = duration(LopapTimeT.Time-tmpRefTime(ii));
|
||||
% interpolate HONO data (to have same time axis)
|
||||
tmpY = interp1(seconds(tmpX),LopapTimeT.HONO,...
|
||||
tmpPlotTime);
|
||||
|
||||
if ~exist('LopapData','var') % make new timetable if timetable does not exist
|
||||
% arrange in table
|
||||
LopapData = timetable(minutes(tmpPlotTime./60)',tmpY');
|
||||
LopapData = renamevars(LopapData,'Var1',tmpFileList{ii});
|
||||
else % or add new variable to existing timetable
|
||||
LopapData = addvars(LopapData,tmpY','NewVariableNames',tmpFileList{ii});
|
||||
end
|
||||
end
|
||||
% tidy up
|
||||
clearvars ii tmp* LopapTimeT
|
||||
%% Plot data
|
||||
figure
|
||||
stackedplot(LopapData)
|
||||
title('HONO in ppt')
|
||||
|
||||
|
||||
|
||||
%% Local functions
|
||||
|
||||
function [fileLocation, myColorMap] = localInitializeMatlab
|
||||
%INITIALIZEMATLAB Sets Lopap specific settings
|
||||
% Adds processing functions to path and defines file locations for mac, windows,
|
||||
% and Matlab online (which runs on unix)
|
||||
|
||||
% change working directory
|
||||
path = matlab.desktop.editor.getActiveFilename;
|
||||
[filepath,~,~] = fileparts(path);
|
||||
cd(filepath);
|
||||
|
||||
|
||||
% Data Server Address
|
||||
if ismac
|
||||
fileLocation.server = '/Volumes/';
|
||||
fileLocation.dataPath = 'data_2411/Lopap/';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('/Users/bartels-rausch/Documents/SwitchDrive/PSI_Matlab/Add-Ons');
|
||||
addpath('/Users/bartels-rausch/Documents/SwitchDrive/PSI_Matlab/Lopap/1.LOPAP_Restliche Daten');
|
||||
elseif ispc
|
||||
fileLocation.server = '\\fs00\'; %UNC name for file server that hosts Napp shared drive
|
||||
fileLocation.dataPath = 'data_2411\Lopap\';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('C:\Users\iezzi_l\switchdrive\Add-Ons');
|
||||
addpath('C:\Users\bletry_c\switchdrive\Add-Ons');
|
||||
addpath('C:\Users\iezzi_l\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
addpath('C:\Users\bletry_c\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
% addpath('\\fs02\5601_surface_chemistry\People\Marc\Switchdrive\PSI_Matlab\Add-Ons');
|
||||
% addpath('\\fs02\5601_surface_chemistry\People\Marc\Switchdrive\PSI_Matlab\Lopap\1.LOPAP_Restliche Daten');
|
||||
|
||||
elseif isunix
|
||||
fileLocation.server = '/';
|
||||
fileLocation.dataPath = 'Lopap/';
|
||||
end
|
||||
|
||||
% Color maps
|
||||
myColorMap.red = colormap(autumn(7));
|
||||
myColorMap.blue = colormap(winter(7));
|
||||
|
||||
close all
|
||||
end
|
||||
File diff suppressed because it is too large.
Load diff
Binary file not shown.
@@ -0,0 +1,656 @@
|
||||
%% Lopap Template
|
||||
% Uses data from 11.03.2021 09h51
|
||||
%
|
||||
%% Info: How to use this
|
||||
%
|
||||
% # Make a copy of this file for each Lopap measurement. Name it
|
||||
% "Lopap"_date_time.m and store it in the folder with the Lopap data. %
|
||||
% Remove all the general text and comments in your file and add notes and
|
||||
% observations about the experiment.
|
||||
%
|
||||
% # You can run this script, publish it, or evaluate it section wise. For
|
||||
% new data run it section wise to carefully update the settings and to
|
||||
% observe the results.
|
||||
% # Once the data is loaded, you can also run individual sections only.
|
||||
% # Use the LabBook :: Chrono Notes section as lab book.
|
||||
% # First, you need to give the date and time of the Lopap measurement to
|
||||
% load and process the data.
|
||||
% # All sections that can be modified are marked with the word "<Adapt>:".
|
||||
% # You also need to give time regions such as for the background fit, as
|
||||
% well as to calculate means. There are several options how to do this
|
||||
%
|
||||
% * While running the experiments and observing the signal in the Lopap
|
||||
% software, you can enter the date and times directly in the LabBook :
|
||||
% Select data ranges section.
|
||||
% * You can manually select the regions in a plot. A window will pop up to
|
||||
% select the region to modify. To modify several regions, re-run this
|
||||
% section of the script. This overwrites the current settings.
|
||||
% * The times of the regions are stored in the "TimeRanges.mat" file. If it
|
||||
% exists, this is read; the LabBook : Select data ranges section is then
|
||||
% ignored.
|
||||
%% ToDO
|
||||
%
|
||||
% * Analyse time delay of Lopap and and to exported variables. We need this
|
||||
% when looking at flow tube data.
|
||||
|
||||
%% Info: Output & Variables
|
||||
%
|
||||
% * *lopapReferenceWavelength*: This _string variable_ holds text with
|
||||
% stating the reference wavelength for channel 1 and 2 used to process the
|
||||
% data by the Lopap software.
|
||||
% * *LopapDataCh1 & LopapDataCh2*: These _time tables_ hold the data that
|
||||
% have been processed by the Lopap Software during the data acquisition. It
|
||||
% contains the absorption for a number
|
||||
% of selected wavelength. The absorption is the log of the intensity at the
|
||||
% reference wavelength relative to the intensity at each wavelength of
|
||||
% interest. The timetables hold the time in each row and the wavelength in
|
||||
% the columns. The content is thus identical to that shown in the
|
||||
% "measurement window" of the Lopap software.
|
||||
% * *LopapSpecCh1,LopapSpecCh2*: The _time tables_ hold the full spectrum
|
||||
% for each time. Time is in the rows, wavelength in the columns. The
|
||||
% wavelength are read from the *.prj file, the spectra data from the *.spec
|
||||
% file. The information is identical to that shown in the "spectrum window"
|
||||
% of the Lopap software.
|
||||
% * *LopapTimeT* This is the main results table:
|
||||
%
|
||||
% * time
|
||||
% * raw signal channel 1
|
||||
% * raw signal channel 2
|
||||
% * background subtracted channel 1
|
||||
% * background subtracted channel 2
|
||||
% * calibrated signal channel 1 in ppt
|
||||
% * calibrated signal channel 2 in ppt
|
||||
% * HONO in ppt (channel 2 -channel 1)
|
||||
%
|
||||
%
|
||||
% * *TimeRangesCalib.mat*: Time ranges after they have been manually modified. If
|
||||
% this file exists, the time range definitions in this script are ignored.
|
||||
% * *LopapMatlabDataDATE_TIMECalib.mat*: Raw data and experimental settings.
|
||||
% Background subtraction and calibration are not saved in this file. When
|
||||
% this file exists, data will not be read from the windows server.
|
||||
% * *LopapDATE_TIMECalib.mat*: Processed data - absorption with time (column 1
|
||||
% and 2: 'Ch #1' and 'Ch #2') after background (columns 3 and 4: 'Ch #1
|
||||
% Bkgrd' and 'Ch #2 Bkgrd') subtraction and calibration (columns 5 and 6:
|
||||
% 'Ch #1 Calib' and 'Ch #2 Calib') for one wavelength - that can be used
|
||||
% for further comparison with other experiments and discussion.
|
||||
|
||||
|
||||
%% Matlab: Initialise
|
||||
%
|
||||
% This starts Matlab and defines some common settings such as the path to
|
||||
% the Lopap data. Any modifications can be done at the end of this file in
|
||||
% where the local function _localInitializeMatlab_ is stored.
|
||||
|
||||
|
||||
% clear variables in workspace, clear text in command window
|
||||
clearvars
|
||||
clc
|
||||
% set the path to the data and define some custom colours for plotting
|
||||
[fileLocation, myColorMap] = localInitializeMatlab;
|
||||
% <Adapt>: Date when Lopap recording was started. Defines names of Lopap
|
||||
% files and folders. Seconds are irrelevant, but format is important.
|
||||
LopapParameters.MeasurementDate = datenum('11-March-2021 09:51:00');
|
||||
|
||||
%%
|
||||
|
||||
% Print info to command window
|
||||
|
||||
disp('The data is read from:');
|
||||
disp(fullfile(fileLocation.server,fileLocation.dataPath,datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM')));
|
||||
disp(' ')
|
||||
disp('Date of experiment:')
|
||||
disp(datestr(LopapParameters.MeasurementDate));
|
||||
disp(' ')
|
||||
disp('Date of analyis:')
|
||||
disp(datestr(today));
|
||||
|
||||
%% Process: Import data
|
||||
%
|
||||
% Reads and imports data from Lopap *.dat, *.spec, and *.prj files into:
|
||||
%
|
||||
% * *lopapReferenceWavelength*: This _string variable_ holds text with
|
||||
% stating the reference wavelength for channel 1 and 2 used to process the
|
||||
% data by the Lopap software.
|
||||
% * *LopapDataCh1 & LopapDataCh2*: These _time tables_ hold the data that
|
||||
% have been processed by the Lopap Software during the data acquisition. It
|
||||
% contains the absorption for a number
|
||||
% of selected wavelength. The absorption is the log of the intensity at the
|
||||
% reference wavelength relative to the intensity at each wavelength of
|
||||
% interest. The timetables hold the time in each row and the wavelength in
|
||||
% the columns. The content is thus identical to that shown in the
|
||||
% "measurement window" of the Lopap software.
|
||||
% * *LopapSpecCh1,LopapSpecCh2*: The _time tables_ hold the full spectrum
|
||||
% for each time. Time is in the rows, wavelength in the columns. The
|
||||
% wavelength are read from the *.prj file, the spectra data from the *.spec
|
||||
% file. The information is identical to that shown in the "spectrum window"
|
||||
% of the Lopap software.
|
||||
|
||||
|
||||
if isfile(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'])
|
||||
load(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'])
|
||||
else
|
||||
[LopapParameters.instrumentReferenceWavelength, LopapDataCh1,LopapDataCh2,LopapSpecCh1,LopapSpecCh2] ...
|
||||
= importLopap(LopapParameters.MeasurementDate,fileLocation);
|
||||
end
|
||||
|
||||
%% Matlab: Run mode
|
||||
%
|
||||
% <Adapt>:
|
||||
%
|
||||
% * runs without user interaction and without ability to modify data
|
||||
% ranges, when set to 0; use this to publish.
|
||||
% * if set to 1: stops for user interaction,
|
||||
% modify data ranges is enabled.Use this to run.
|
||||
LopapParameters.Interactive = 1;
|
||||
|
||||
%% LabBook : Measurement Settings % from 20.12.2020 template
|
||||
%
|
||||
% <Adapt>: list the Lopap settings here:
|
||||
LopapParameters.concStandard = 0.01; % mg/l concentration of nitrite in standard used for calibration
|
||||
LopapParameters.flowReagents = 5./[22+0/60 25+26/60]; % ml/min, enter time for 5 ml in minutes,
|
||||
% channel 1 and channel 2, first number is minutes, second is seconds.
|
||||
LopapParameters.flowGas = 396; % ml/min, at room temp and pressure, take average of 10.
|
||||
LopapParameters.temperature = 298; % temp of gas flow in K
|
||||
LopapParameters.pressure = 1013; % pressure of gas flow in mbar
|
||||
LopapParameters.flowGas = LopapParameters.flowGas.*LopapParameters.pressure ./LopapParameters.temperature...
|
||||
.*298.15./1013.25; % STP ml/min (as used in original LOPAP documents)
|
||||
|
||||
% <Adapt>: Choose a reference wavelength. Default is 650 nm.
|
||||
LopapParameters.wavelengthR = 650.3; %nm, reference intensity
|
||||
% <Adapt>: Choose a signal wavelength to calculate the absorption with time
|
||||
% from the spectra
|
||||
LopapParameters.wavelengthS = 530; %nm, signal intensity
|
||||
|
||||
%% LabBook : Define data ranges
|
||||
%
|
||||
% These settings are ignored if the TimesRanges.mat file exist. If you do
|
||||
% not want to use the data stored in the TimesRanges.mat file, you need to
|
||||
% delete it before running this section.
|
||||
%
|
||||
% These settings can be modified by selecting data ranges in a plot later.
|
||||
% So, you do not necessarily need to type the dates and times here.
|
||||
|
||||
if LopapParameters.Interactive == 1
|
||||
answer = questdlg('How would you like to set the data ranges of the experiment?', ...
|
||||
'Data range selection', ...
|
||||
'Read from script code','Read from mat file','Use from workspace','Read from script code');
|
||||
% Handle response
|
||||
switch answer
|
||||
case 'Read from script code'
|
||||
disp([answer 'OK. Data range will set as coded in the script.'])
|
||||
tmpDataRangeSource = 1;
|
||||
case 'Read from mat file'
|
||||
disp([answer 'OK. Data range will loaded from mat file in current directory.'])
|
||||
tmpDataRangeSource = 2;
|
||||
case 'Use from workspace'
|
||||
disp([answer 'OK. Data range in workspace variable will be used.'])
|
||||
tmpDataRangeSource = 3;
|
||||
case 'Cancel'
|
||||
disp('OK. Do nothing')
|
||||
tmpDataRangeSource = 0;
|
||||
end
|
||||
else
|
||||
if isfile(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'])
|
||||
tmpDataRangeSource = 2;
|
||||
disp([answer ' OK. Data range will loaded from mat file in current directory.'])
|
||||
elseif ~exist('TimeRange','var')
|
||||
tmpDataRangeSource = 1;
|
||||
disp([answer 'OK. Data range will set as coded in the script.'])
|
||||
elseif exist('TimeRange','var')
|
||||
tmpDataRangeSource = 3;
|
||||
disp(' OK. Data range in workspace variable will be used.')
|
||||
end
|
||||
end
|
||||
|
||||
if tmpDataRangeSource == 2
|
||||
load(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'])
|
||||
disp('TimeRange in TimeRange*.mat file in current directory used')
|
||||
disp('You need to delete the TimeRange variable in the workspace AND the TimeRange*.mat file in the current directory')
|
||||
disp('to use the dates entered in the script')
|
||||
disp('You keep to delete the TimeRange variable in the workspace AND delete TimeRange*.mat file in the current directory')
|
||||
disp('to use the dates saved in the workspace')
|
||||
elseif tmpDataRangeSource == 1
|
||||
% <Adapt> (Optional - comment if no needed) state the start and end
|
||||
% time of the time that you want to look at (to exclude very noisy
|
||||
% signal in the beginning and at the end of the data)
|
||||
TimeRange.calibrationRange = [datenum('15-Nov-2021 16:30:00') datenum('15-Nov-2021 17:20:00')];
|
||||
% <Adapt>: State the time for the first spectrum that you like to
|
||||
% compare (to confirm nitrite)
|
||||
TimeRange.specCompareOne = datenum('15-Nov-2021 16:49:30 ');
|
||||
% <Adapt>: State the time for one spectrum of the second spectrum that
|
||||
% you like to compare (to confirm nitrite)
|
||||
TimeRange.specCompareTwo = datenum('15-Nov-2021 17:02:00 ');
|
||||
% <Adapt>: Choose a start and end time for one as many intervals that can
|
||||
% be used to fit the background. Background is the signal when R1&R2 was
|
||||
% attached to the Lopap with zero air entering the sampling coil.
|
||||
TimeRange.backgroundFit = [datenum('15-Nov-2021 15:10:00') datenum('15-Nov-2021 15:50:00');...
|
||||
datenum('0-Dec-2021 16:26:00') datenum('0-Dec-2021 16:26:00')];
|
||||
% <Adapt>: State the start and end time of data that can be used to
|
||||
% calculate the mean of the zero air signal without nitrite
|
||||
TimeRange.MeanZeroAir = [datenum('04-Feb-2022 11:49:07') datenum('04-Feb-2022 11:59:14 ')];
|
||||
% <Adapt>: State the start and end time of data that can be used to
|
||||
% calculate the mean of the zero air signal with nitrite
|
||||
TimeRange.MeanNitriteStandard = [datenum('04-Feb-2022 12:26:28') datenum('04-Feb-2022 12:39:46')];
|
||||
|
||||
save(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'TimeRange');
|
||||
disp('TimeRange as coded in script used')
|
||||
|
||||
elseif tmpDataRangeSource == 3
|
||||
if exist('TimeRange','var')
|
||||
disp('TimeRange in Workspace used')
|
||||
disp('You need to delete the TimeRange variable in the workspace AND the TimeRange*.mat file in the current directory')
|
||||
disp('to use the dates entered in the script')
|
||||
elseif ~exist('TimeRange','var')
|
||||
warning('TimeRange in the Workspace was selected, but there is no TimeRange variable')
|
||||
end
|
||||
end
|
||||
|
||||
% confirm that all dates are reasonable
|
||||
tmp = fieldnames(TimeRange);
|
||||
for ii = 1:length(tmp)
|
||||
mustBeLopapReasonableDate(TimeRange.(tmp{ii}))
|
||||
end
|
||||
clearvars tmp*
|
||||
|
||||
%% Process: Modify data ranges
|
||||
%
|
||||
% Select the range to modify in the pop-up window and the number of fit
|
||||
% ranges for the background fit in the 2nd pop-up window. Then, a figure
|
||||
% will show, select the data ranges in the figure:
|
||||
%
|
||||
% * a line for calibration range, mean zero air and mean
|
||||
% nitrite standard. Select the range by keeping the mouse pushed while
|
||||
% moving from start to end time.
|
||||
% * a line for each background region, default is 2. Select the range by
|
||||
% keeping the mouse pushed while moving from start to end time.
|
||||
% * a point for spectrum with reagents and spectrum with nitrite. Click
|
||||
% once to select a specific time.
|
||||
%
|
||||
% * LopapParameters.Interactive needs to be 1 for this to run.
|
||||
%
|
||||
% # Run this section several times to modify several time regions
|
||||
% # Press cancel in the pop-up window if you do not want to modify any
|
||||
% region.
|
||||
|
||||
TimeRange = modifyLopapTimeRangesCalib(TimeRange, LopapParameters, LopapDataCh1, LopapDataCh2);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
save(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'],'TimeRange');
|
||||
|
||||
%% Process: Find closest match of selected dates in data set
|
||||
%
|
||||
% The data is sampled at specific times with a certain interval. The
|
||||
% selected or chosen dates might not necessarily exactly match the data.
|
||||
% Here, closest match to the given dates are selected.
|
||||
|
||||
tmp.d1 = TimeRange.specCompareOne;
|
||||
tmp.d2 = LopapSpecCh1.Time;
|
||||
[~,ind1] = min(abs(bsxfun(@minus,datenum(tmp.d2),datenum(tmp.d1)')));
|
||||
TimeRange.specCompareOne = tmp.d2(ind1,:);
|
||||
|
||||
tmp.d1 = TimeRange.specCompareTwo ;
|
||||
tmp.d2 = LopapSpecCh1.Time;
|
||||
[~,ind1] = min(abs(bsxfun(@minus,datenum(tmp.d2),datenum(tmp.d1)')));
|
||||
TimeRange.specCompareTwo = tmp.d2(ind1,:);
|
||||
|
||||
% save current state of
|
||||
clearvars -except Lopap* fileLocation myColorMap TimeRange*
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'LopapDataCh1','LopapDataCh2','LopapParameters','LopapSpecCh1','LopapSpecCh2')
|
||||
save(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'TimeRange');
|
||||
|
||||
%% LabBook: Data ranges used in this work
|
||||
%
|
||||
clc
|
||||
fprintf('Calibration range: %s to %s \n',datestr(TimeRange.calibrationRange(1)), datestr(TimeRange.calibrationRange(2)))
|
||||
for ii=1:size(TimeRange.backgroundFit,1)
|
||||
fprintf('Background range: %s to %s \n',datestr(TimeRange.backgroundFit(ii,1)), datestr(TimeRange.backgroundFit(ii,2)))
|
||||
end
|
||||
fprintf('Zero mean: %s to %s \n',datestr(TimeRange.MeanZeroAir(1)), datestr(TimeRange.MeanZeroAir(2)))
|
||||
fprintf('Nitrite mean: %s to %s \n',datestr(TimeRange.MeanNitriteStandard(1)), datestr(TimeRange.MeanNitriteStandard(2)))
|
||||
fprintf('Comparison Spectrum #1: %s \n',datestr(TimeRange.specCompareOne(1)))
|
||||
fprintf('Comparison Spectrum #2: %s \n',datestr(TimeRange.specCompareTwo(1)))
|
||||
|
||||
|
||||
%% Plot all data
|
||||
%
|
||||
% Here, we plot the data as shown in the "Measurement window" of the Lopap
|
||||
% software. That is, the processed $I^{*}_{i}$ data for all wavelength as
|
||||
% defined in the settings of the Lopap software.
|
||||
%
|
||||
%
|
||||
% For every measurement wavelength I_i the program calculates the
|
||||
% measurement (absorption) value I_i^* from the spectral intensity on the
|
||||
% measurement wavelength I_i and a reference wavelength I_r with the
|
||||
% following operation:
|
||||
%
|
||||
%
|
||||
% $$I^{*}_{i} = log_{10} (\frac{I_r}{I_i})$$
|
||||
%
|
||||
%
|
||||
%
|
||||
% The plots show time on the x-axis and the ABS intensity on the y axis for
|
||||
% each wavelength in separate graphs. One Figure for each Channel.
|
||||
|
||||
figure( 'Name', 'LopapChannel1','NumberTitle','off','Position',[10 100 550 700]);
|
||||
ch1s=stackedplot(LopapDataCh1);
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
for ii = 1:width(LopapDataCh1)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch1s.AxesProperties(ii).YLimits = [-0.4 -0.1];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
figure( 'Name', 'LopapChannel2','NumberTitle','off','Position',[600 100 550 700]);
|
||||
ch2s=stackedplot(LopapDataCh2);
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
for ii = 1:width(LopapDataCh2)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties(ii).YLimits = [-0.2 0.3];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
%% Plot all data :: selected time range
|
||||
%
|
||||
|
||||
TR = timerange(datestr(TimeRange.calibrationRange(1)),datestr(TimeRange.calibrationRange(2)));
|
||||
figure( 'Name', 'LopapChannel1','NumberTitle','off','Position',[10 100 550 700]);
|
||||
ch1s=stackedplot(LopapDataCh1(TR,:));
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
for ii = 1:width(LopapDataCh1)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch1s.AxesProperties(ii).YLimits = [-0.4 -0.1];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
figure( 'Name', 'LopapChannel2','NumberTitle','off','Position',[600 100 550 700]);
|
||||
ch2s=stackedplot(LopapDataCh2(TR,:));
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
for ii = 1:width(LopapDataCh2)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties(ii).YLimits = [-0.2 0.3];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
|
||||
%% Plot selected data in selected time range
|
||||
%
|
||||
% Here we plot the $I^{*}_{i}$ data for one wavelength only.
|
||||
|
||||
TR = timerange(datestr(TimeRange.calibrationRange(1)),datestr(TimeRange.calibrationRange(2)));
|
||||
figure( 'Name', 'LopapChannel1 550','NumberTitle','off','Position',[10 100 550 800]);
|
||||
% <Adapt>: The numbers in the curled brackets give wavelength for which you'd
|
||||
% like to display the data. The numbers need to be exactly match the
|
||||
% labels in the previous figure.
|
||||
ch1s=stackedplot(LopapDataCh1(TR,:),{'550.7'});
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
%ch1s.AxesProperties.YLimits = [-0.4 -0.1];
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
|
||||
figure( 'Name', 'LopapChannel2 550','NumberTitle','off','Position',[600 100 550 800]);
|
||||
% <Adapt>: The numbers in the curled brackets give wavelength for which you'd
|
||||
% like to display the data. The numbers need to be exactly match the
|
||||
% labels in the previous figure
|
||||
ch2s=stackedplot(LopapDataCh2(TR,:),{'550.5'});
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties.YLimits = [-0.2 0.3];
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap lopap* TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
%% Plot selected spectra
|
||||
%
|
||||
% Here, we plot a spectrum without ('R1&R2') and with nitrite
|
||||
% ('R1+nitrite&R2'') for each channel or which ever combination of spectra
|
||||
% that we have selected.
|
||||
clc
|
||||
close all
|
||||
figure('Name', 'LopapSelectedSpectra')
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),LopapSpecCh1{datestr(TimeRange.specCompareOne),:},...
|
||||
'DisplayName',['#1 ' datestr(TimeRange.specCompareOne) ]) % a time where only R1&R2 was connected to the Lopap
|
||||
hold on
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),LopapSpecCh2{datestr(TimeRange.specCompareOne),:},...
|
||||
'DisplayName',['#2 ' datestr(TimeRange.specCompareOne)],'LineStyle','--') % a time where only R1&R2 was connected to the Lopap
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),LopapSpecCh1{datestr(TimeRange.specCompareTwo),:},...
|
||||
'DisplayName',['#1 ' datestr(TimeRange.specCompareTwo)]) % a time where nitrite in R1 was connected to the Lopap
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),LopapSpecCh2{datestr(TimeRange.specCompareTwo),:},...
|
||||
'DisplayName',['#2 ' datestr(TimeRange.specCompareTwo)],'LineStyle','--') % a time where nitrite in R1 was connected to the Lopap
|
||||
legend
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('Intensity')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process: Absorption spectrum
|
||||
%
|
||||
% Here, we reprocess the data to derive an absorption spectrum. This should
|
||||
% match the spectra shown for nitrite in the Lopap manual.
|
||||
|
||||
|
||||
clc
|
||||
close all
|
||||
indexR(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
indexR(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
|
||||
figure('Name', 'LopapAbsorbtionSpectra')
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),log10(LopapSpecCh1{datestr(TimeRange.specCompareTwo),...
|
||||
indexR(1)}./LopapSpecCh1{datestr(TimeRange.specCompareTwo),:})-log10(LopapSpecCh1{datestr(TimeRange.specCompareOne),...
|
||||
indexR(1)}./LopapSpecCh1{datestr(TimeRange.specCompareOne),:}),'DisplayName','#1')
|
||||
hold on
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),log10(LopapSpecCh2{datestr(TimeRange.specCompareTwo),...
|
||||
indexR(2)}./LopapSpecCh2{datestr(TimeRange.specCompareTwo),:})-log10(LopapSpecCh2{datestr(TimeRange.specCompareOne),...
|
||||
indexR(2)}./LopapSpecCh2{datestr(TimeRange.specCompareOne),:}),'DisplayName','#2','LineStyle','--')
|
||||
legend
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('ABS (log I_{r}/I_{i}')
|
||||
title([datestr(TimeRange.specCompareOne) ' & ' datestr(TimeRange.specCompareTwo)])
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process :: Absorption with time
|
||||
%
|
||||
% Here, we reprocess the data to get the intensity with time for 1 chosen
|
||||
% signal wavelength and 1 reference wavelength. The data is identical to that
|
||||
% shown in the "measurement window" of the Lopap software.
|
||||
%
|
||||
% The data is written to the _LopapTimeT_ time table. Rows hold the time,
|
||||
% columns hold the processed signal for channel 1 and channel 2.
|
||||
%
|
||||
% It is important that the same signal wavelength and reference wavelength
|
||||
% are taken for the calibration and for the experimental data.
|
||||
|
||||
clc
|
||||
close all
|
||||
indexS(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthS,1);
|
||||
indexS(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthS,1);
|
||||
indexR(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
indexR(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
LopapTimeT = timetable(LopapSpecCh1.Time,log10(LopapSpecCh1{:,indexR(1)}./LopapSpecCh1{:,indexS(1)}),...
|
||||
log10(LopapSpecCh2{:,indexR(2)}./LopapSpecCh2{:,indexS(2)}));
|
||||
LopapTimeT.Properties.VariableNames ={'Ch #1','Ch #2'};
|
||||
figure('Name', 'Lopap TimeTable')
|
||||
stackedplot(LopapTimeT,{{'Ch #1','Ch #2'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process :: Background
|
||||
%
|
||||
% Currently a linear fit forced through 0.
|
||||
clc
|
||||
close all
|
||||
LopapTimeT = fitLopapBkgrd(LopapTimeT,'BkgrdPeriod',TimeRange.backgroundFit);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%%
|
||||
%
|
||||
clc
|
||||
close all
|
||||
% Plot
|
||||
figure('Name', 'Lopap TimeTable Bkgrd')
|
||||
s=stackedplot(LopapTimeT,{{'Ch #1 Bkgrd','Ch #2 Bkgrd'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
% s.AxesProperties.YLimits = [-0.01 0.6];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
|
||||
%% Process :: Calibrate
|
||||
%
|
||||
clc
|
||||
close all
|
||||
|
||||
S = timerange(datestr(TimeRange.MeanZeroAir(1)), datestr(TimeRange.MeanZeroAir(2)));
|
||||
TZ = LopapTimeT(S,:);
|
||||
S = timerange(datestr(TimeRange.MeanNitriteStandard(1)), datestr(TimeRange.MeanNitriteStandard(2)));
|
||||
TN = LopapTimeT(S,:);
|
||||
calib.mean = mean(TN{:,:},1) - mean(TZ{:,:},1);
|
||||
calib.std = std(TN{:,:},1);
|
||||
calib.mixingRatio = LopapParameters.concStandard./1000.*LopapParameters.flowReagents./1000./46.*6.022E23./...
|
||||
(246E17.*LopapParameters.flowGas).*1E12;
|
||||
|
||||
[LopapTimeT, calib.fitresult] = fitLopapCalibration(LopapTimeT,calib);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange* fitresult calib
|
||||
|
||||
fprintf('Detection limit channel #1 is %.0f ppt \n',calib.fitresult.calibChannel1(3.*calib.std(3)))
|
||||
fprintf('Detection limit channel #2 is %.0f ppt \n',calib.fitresult.calibChannel2(3.*calib.std(4)))
|
||||
|
||||
%% Plot calibrated data
|
||||
%
|
||||
clc
|
||||
close all
|
||||
% Plot
|
||||
figure('Name', 'Lopap TimeTable Calibrated')
|
||||
s=stackedplot(LopapTimeT,{{'Ch #1 Calib','Ch #2 Calib'}});
|
||||
title(['HONO in ppt, Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
% s.AxesProperties.YLimits = [-100 2500];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange* fitresult calib
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Save the data
|
||||
%
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'LopapDataCh1','LopapDataCh2','LopapParameters','calib','LopapSpecCh1','LopapSpecCh2')
|
||||
save(['Lopap' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'LopapParameters','LopapTimeT','TimeRange')
|
||||
%% Local functions
|
||||
function [fileLocation, myColorMap] = localInitializeMatlab
|
||||
%INITIALIZEMATLAB Sets Lopap specific settings
|
||||
% Adds processing functions to path and defines file locations for mac, windows,
|
||||
% and Matlab online (which runs on unix)
|
||||
|
||||
% change working directory
|
||||
path = matlab.desktop.editor.getActiveFilename;
|
||||
[filepath,~,~] = fileparts(path);
|
||||
cd(filepath);
|
||||
|
||||
|
||||
% Data Server Address
|
||||
if ismac
|
||||
fileLocation.server = '/Volumes/';
|
||||
fileLocation.dataPath = 'data_2411/Lopap/';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('/Users/bartels-rausch/SwitchDrive/PSI_Matlab/Add-Ons');
|
||||
addpath('/Users/bartels-rausch/SwitchDrive/PSI_Matlab/Lopap/1.LOPAP_Restliche Daten');
|
||||
elseif ispc
|
||||
fileLocation.server = '\\fs00\'; %UNC name for file server that hosts Napp shared drive
|
||||
fileLocation.dataPath = 'data_2411\Lopap\';
|
||||
% add Lopap functions and general add-ons to path
|
||||
|
||||
addpath('C:\Users\vieill_l\switchdrive\Add-Ons');
|
||||
|
||||
|
||||
addpath('C:\Users\vieill_l\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
|
||||
|
||||
elseif isunix
|
||||
fileLocation.server = '/';
|
||||
fileLocation.dataPath = 'Lopap/';
|
||||
end
|
||||
|
||||
% Color maps
|
||||
myColorMap.red = colormap(autumn(7));
|
||||
myColorMap.blue = colormap(winter(7));
|
||||
|
||||
close all
|
||||
end
|
||||
|
||||
Executable
BIN
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BIN
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@@ -0,0 +1,615 @@
|
||||
%% Lopap Template
|
||||
% Uses data from 20.12.2020 13h47
|
||||
%
|
||||
%% Info: How to use this
|
||||
%
|
||||
% # Make a copy of this file for each Lopap measurement. Name it
|
||||
% "Lopap"_date_time.m and store it in the folder with the Lopap data. %
|
||||
% Remove all the general text and comments in your file and add notes and
|
||||
% observations about the experiment.
|
||||
%
|
||||
% # You can run this script, publish it, or evaluate it section wise. For
|
||||
% new data run it section wise to carefully update the settings and to
|
||||
% observe the results.
|
||||
% # Once the data is loaded, you can also run individual sections only.
|
||||
% # Use the LabBook :: Chrono Notes section as lab book.
|
||||
% # First, you need to give the date and time of the Lopap measurement to
|
||||
% load and process the data.
|
||||
% # All sections that can be modified are marked with the word "<Adapt>:".
|
||||
% # You also need to give time regions such as for the background fit, as
|
||||
% well as to calculate means. There are several options how to do this
|
||||
%
|
||||
% * While running the experiments and observing the signal in the Lopap
|
||||
% software, you can enter the date and times directly in the LabBook :
|
||||
% Select data ranges section.
|
||||
% * You can manually select the regions in a plot. A window will pop up to
|
||||
% select the region to modify. To modify several regions, re-run this
|
||||
% section of the script. This overwrites the current settings. You need to
|
||||
% copy the output the the script to save your modified settings for the
|
||||
% next time.
|
||||
|
||||
%% ToDO
|
||||
%
|
||||
% * Analyse time delay of Lopap and and to exported variables. We need this
|
||||
% when looking at flow tube data.
|
||||
|
||||
%% Info: Output & Variables
|
||||
%
|
||||
% * *lopapReferenceWavelength*: This _string variable_ holds text with
|
||||
% stating the reference wavelength for channel 1 and 2 used to process the
|
||||
% data by the Lopap software.
|
||||
% * *LopapDataCh1 & LopapDataCh2*: These _time tables_ hold the data that
|
||||
% have been processed by the Lopap Software during the data acquisition. It
|
||||
% contains the absorption for a number
|
||||
% of selected wavelength. The absorption is the log of the intensity at the
|
||||
% reference wavelength relative to the intensity at each wavelength of
|
||||
% interest. The timetables hold the time in each row and the wavelength in
|
||||
% the columns. The content is thus identical to that shown in the
|
||||
% "measurement window" of the Lopap software.
|
||||
% * *LopapSpecCh1,LopapSpecCh2*: The _time tables_ hold the full spectrum
|
||||
% for each time. Time is in the rows, wavelength in the columns. The
|
||||
% wavelength are read from the *.prj file, the spectra data from the *.spec
|
||||
% file. The information is identical to that shown in the "spectrum window"
|
||||
% of the Lopap software.
|
||||
% * *LopapTimeT* This is the main results table:
|
||||
%
|
||||
% * time
|
||||
% * raw signal channel 1
|
||||
% * raw signal channel 2
|
||||
% * background subtracted channel 1
|
||||
% * background subtracted channel 2
|
||||
% * calibrated signal channel 1 in ppt
|
||||
% * calibrated signal channel 2 in ppt
|
||||
% * HONO in ppt (channel 2 -channel 1)
|
||||
%
|
||||
%
|
||||
% * *TimeRangesCalib.mat*: Time ranges after they have been manually modified. If
|
||||
% this file exists, the time range definitions in this script are ignored.
|
||||
% * *LopapMatlabDataDATE_TIMECalib.mat*: Raw data and experimental settings.
|
||||
% Background subtraction and calibration are not saved in this file. When
|
||||
% this file exists, data will not be read from the windows server.
|
||||
% * *LopapDATE_TIMECalib.mat*: Processed data - absorption with time (column 1
|
||||
% and 2: 'Ch #1' and 'Ch #2') after background (columns 3 and 4: 'Ch #1
|
||||
% Bkgrd' and 'Ch #2 Bkgrd') subtraction and calibration (columns 5 and 6:
|
||||
% 'Ch #1 Calib' and 'Ch #2 Calib') for one wavelength - that can be used
|
||||
% for further comparison with other experiments and discussion.
|
||||
|
||||
|
||||
%% Matlab: Initialise
|
||||
%
|
||||
% This starts Matlab and defines some common settings such as the path to
|
||||
% the Lopap data. Any modifications can be done at the end of this file in
|
||||
% where the local function _localInitializeMatlab_ is stored.
|
||||
|
||||
|
||||
% clear variables in workspace, clear text in command window
|
||||
clearvars
|
||||
clc
|
||||
% set the path to the data and define some custom colours for plotting
|
||||
[fileLocation, myColorMap] = localInitializeMatlab;
|
||||
% <Adapt>: Date when Lopap recording was started. Defines names of Lopap
|
||||
% files and folders. Seconds are irrelevant, but format is important.
|
||||
LopapParameters.MeasurementDate = datenum('20-Dez-2021 13:47:00');
|
||||
|
||||
%%
|
||||
|
||||
% Print info to command window
|
||||
|
||||
disp('The data is read from:');
|
||||
disp(fullfile(fileLocation.server,fileLocation.dataPath,datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM')));
|
||||
disp(' ')
|
||||
disp('Date of experiment:')
|
||||
disp(datestr(LopapParameters.MeasurementDate));
|
||||
disp(' ')
|
||||
disp('Date of analyis:')
|
||||
disp(datestr(today));
|
||||
|
||||
%% Process: Import data
|
||||
%
|
||||
% Reads and imports data from Lopap *.dat, *.spec, and *.prj files into:
|
||||
%
|
||||
% * *lopapReferenceWavelength*: This _string variable_ holds text with
|
||||
% stating the reference wavelength for channel 1 and 2 used to process the
|
||||
% data by the Lopap software.
|
||||
% * *LopapDataCh1 & LopapDataCh2*: These _time tables_ hold the data that
|
||||
% have been processed by the Lopap Software during the data acquisition. It
|
||||
% contains the absorption for a number
|
||||
% of selected wavelength. The absorption is the log of the intensity at the
|
||||
% reference wavelength relative to the intensity at each wavelength of
|
||||
% interest. The timetables hold the time in each row and the wavelength in
|
||||
% the columns. The content is thus identical to that shown in the
|
||||
% "measurement window" of the Lopap software.
|
||||
% * *LopapSpecCh1,LopapSpecCh2*: The _time tables_ hold the full spectrum
|
||||
% for each time. Time is in the rows, wavelength in the columns. The
|
||||
% wavelength are read from the *.prj file, the spectra data from the *.spec
|
||||
% file. The information is identical to that shown in the "spectrum window"
|
||||
% of the Lopap software.
|
||||
|
||||
|
||||
if isfile(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'])
|
||||
load(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'])
|
||||
else
|
||||
[LopapParameters.instrumentReferenceWavelength, LopapDataCh1,LopapDataCh2,LopapSpecCh1,LopapSpecCh2] ...
|
||||
= importLopap(LopapParameters.MeasurementDate,fileLocation);
|
||||
end
|
||||
|
||||
%% Matlab: Run mode
|
||||
%
|
||||
% <Adapt>:
|
||||
%
|
||||
% * runs without user interaction and without ability to modify data
|
||||
% ranges, when set to 0; use this to publish.
|
||||
% * if set to 1: stops for user interaction,
|
||||
% modify data ranges is enabled.Use this to run.
|
||||
LopapParameters.Interactive = 0;
|
||||
|
||||
%% LabBook : Measurement Settings
|
||||
%
|
||||
% <Adapt>: list the Lopap settings here:
|
||||
LopapParameters.concStandard = 0.01; % mg/l concentration of nitrite in standard used for calibration
|
||||
LopapParameters.flowReagents = 5./[22+0/60 25+26/60]; % ml/min, enter time for 5 ml in minutes,
|
||||
% channel 1 and channel 2, first number is minutes, second is seconds.
|
||||
LopapParameters.flowGas = 396; % ml/min, at room temp and pressure, take average of 10.
|
||||
LopapParameters.temperature = 298; % temp of gas flow in K
|
||||
LopapParameters.pressure = 1013; % pressure of gas flow in mbar
|
||||
LopapParameters.flowGas = LopapParameters.flowGas.*LopapParameters.pressure ./LopapParameters.temperature...
|
||||
.*298.15./1013.25; % STP ml/min (as used in original LOPAP documents,1 atm (1013 hPa) and 298.15K)
|
||||
|
||||
% <Adapt>: Choose a reference wavelength. Default is 650 nm.
|
||||
LopapParameters.wavelengthR = 650.3; %nm, reference intensity
|
||||
% <Adapt>: Choose a signal wavelength to calculate the absorption with time
|
||||
% from the spectra
|
||||
LopapParameters.wavelengthS = 530; %nm, signal intensity
|
||||
|
||||
%% LabBook : Define data ranges
|
||||
%
|
||||
% The time settings can be modified by selecting data ranges in a plot later.
|
||||
% So, you do not necessarily need to type the dates and times here.
|
||||
%
|
||||
% 11/2022 TBR: Removed the user choice. Data ranges are now ALWAYS read
|
||||
% from the script.
|
||||
|
||||
|
||||
% <Adapt>: % State the start and end time of the calibration. Usually
|
||||
% this is included zero air with R1&2, zero air with nitrite standard,
|
||||
% zero air with R1&2
|
||||
TimeRange.calibrationRange = [datenum('20-Dec-2021 15:00:00') datenum('20-Dec-2021 16:40:00')];
|
||||
% <Adapt>: State the time for the first spectrum that you like to
|
||||
% compare (to confirm nitrite)
|
||||
TimeRange.specCompareOne = datenum('20-Dec-2021 15:23:00');
|
||||
% <Adapt>: State the time for one spectrum of the second spectrum that
|
||||
% you like to compare (to confirm nitrite)
|
||||
TimeRange.specCompareTwo = datenum('20-Dec-2021 16:15:00');
|
||||
% <Adapt>: Choose a start and end time for one as many intervals that can
|
||||
% be used to fit the background. Background is the signal when R1&R2 was
|
||||
% attached to the Lopap with zero air entering the sampling coil.
|
||||
TimeRange.backgroundFit = [datenum('20-Dec-2021 15:10:58') datenum('20-Dec-2021 15:31:18'); datenum('20-Dec-2021 16:30:51') datenum('20-Dec-2021 16:25:11')];
|
||||
% <Adapt>: State the start and end time of data that can be used to
|
||||
% calculate the mean of the zero air signal without nitrite
|
||||
TimeRange.MeanZeroAir = [datenum('20-Dec-2021 15:25:00') datenum('20-Dec-2021 15:27:00')];
|
||||
% <Adapt>: State the start and end time of data that can be used to
|
||||
% calculate the mean of the zero air signal with nitrite
|
||||
TimeRange.MeanNitriteStandard = [datenum('20-Dec-2021 15:47:00') datenum('20-Dec-2021 15:49:00')];
|
||||
|
||||
|
||||
% confirm that all dates are reasonable
|
||||
tmp = fieldnames(TimeRange);
|
||||
for ii = 1:length(tmp)
|
||||
mustBeLopapReasonableDate(TimeRange.(tmp{ii}))
|
||||
end
|
||||
clearvars tmp*
|
||||
|
||||
%% Process: Modify data ranges
|
||||
%
|
||||
% Select the range to modify in the pop-up window and the number of fit
|
||||
% ranges for the background fit in the 2nd pop-up window. Then, a figure
|
||||
% will show, select the data ranges in the figure:
|
||||
%
|
||||
% * a line for calibration range, mean zero air and mean
|
||||
% nitrite standard. Select the range by keeping the mouse pushed while
|
||||
% moving from start to end time.
|
||||
% * a line for each background region, default is 2. Select the range by
|
||||
% keeping the mouse pushed while moving from start to end time.
|
||||
% * a point for spectrum with reagents and spectrum with nitrite. Click
|
||||
% once to select a specific time.
|
||||
%
|
||||
% * LopapParameters.Interactive needs to be 1 for this to run.
|
||||
%
|
||||
% # Run this section several times to modify several time regions
|
||||
% # Press cancel in the pop-up window if you do not want to modify any
|
||||
% region.
|
||||
|
||||
TimeRange = modifyLopapTimeRangesCalib(TimeRange, LopapParameters, LopapDataCh1, LopapDataCh2);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
% save(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'],'TimeRange');
|
||||
|
||||
|
||||
%% Process: Find closest match of selected dates in data set
|
||||
%
|
||||
% The data is sampled at specific times with a certain interval. The
|
||||
% selected or chosen dates might not necessarily exactly match the data.
|
||||
% Here, closest match to the given dates are selected.
|
||||
|
||||
tmp.d1 = TimeRange.specCompareOne;
|
||||
tmp.d2 = LopapSpecCh1.Time;
|
||||
[~,ind1] = min(abs(bsxfun(@minus,datenum(tmp.d2),datenum(tmp.d1)')));
|
||||
TimeRange.specCompareOne = tmp.d2(ind1,:);
|
||||
|
||||
tmp.d1 = TimeRange.specCompareTwo ;
|
||||
tmp.d2 = LopapSpecCh1.Time;
|
||||
[~,ind1] = min(abs(bsxfun(@minus,datenum(tmp.d2),datenum(tmp.d1)')));
|
||||
TimeRange.specCompareTwo = tmp.d2(ind1,:);
|
||||
|
||||
% save current state of
|
||||
clearvars -except Lopap* fileLocation myColorMap TimeRange*
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'LopapDataCh1','LopapDataCh2','LopapParameters','LopapSpecCh1','LopapSpecCh2')
|
||||
% save(['TimeRanges' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'TimeRange');
|
||||
|
||||
%% LabBook: Data ranges used in this work
|
||||
%
|
||||
fprintf('Calibration range: %s to %s \n',datestr(TimeRange.calibrationRange(1)), datestr(TimeRange.calibrationRange(2)))
|
||||
for ii=1:size(TimeRange.backgroundFit,1)
|
||||
fprintf('Background range: %s to %s \n',datestr(TimeRange.backgroundFit(ii,1)), datestr(TimeRange.backgroundFit(ii,2)))
|
||||
end
|
||||
fprintf('Zero mean: %s to %s \n',datestr(TimeRange.MeanZeroAir(1)), datestr(TimeRange.MeanZeroAir(2)))
|
||||
fprintf('Nitrite mean: %s to %s \n',datestr(TimeRange.MeanNitriteStandard(1)), datestr(TimeRange.MeanNitriteStandard(2)))
|
||||
fprintf('Comparison Spectrum #1: %s \n',datestr(TimeRange.specCompareOne(1)))
|
||||
fprintf('Comparison Spectrum #2: %s \n',datestr(TimeRange.specCompareTwo(1)))
|
||||
|
||||
|
||||
%% Plot all data
|
||||
%
|
||||
% Here, we plot the data as shown in the "Measurement window" of the Lopap
|
||||
% software. That is, the processed $I^{*}_{i}$ data for all wavelength as
|
||||
% defined in the settings of the Lopap software.
|
||||
%
|
||||
%
|
||||
% For every measurement wavelength I_i the program calculates the
|
||||
% measurement (absorption) value I_i^* from the spectral intensity on the
|
||||
% measurement wavelength I_i and a reference wavelength I_r with the
|
||||
% following operation:
|
||||
%
|
||||
%
|
||||
% $$I^{*}_{i} = log_{10} (\frac{I_r}{I_i})$$
|
||||
%
|
||||
%
|
||||
%
|
||||
% The plots show time on the x-axis and the ABS intensity on the y axis for
|
||||
% each wavelength in separate graphs. One Figure for each Channel.
|
||||
|
||||
figure( 'Name', 'LopapChannel1','NumberTitle','off','Position',[10 100 550 700]);
|
||||
stackedplot(LopapDataCh1);
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
for ii = 1:width(LopapDataCh1)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch1s.AxesProperties(ii).YLimits = [-0.4 -0.1];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
figure( 'Name', 'LopapChannel2','NumberTitle','off','Position',[600 100 550 700]);
|
||||
stackedplot(LopapDataCh2);
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
for ii = 1:width(LopapDataCh2)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties(ii).YLimits = [-0.2 0.3];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
%% Plot all data :: selected time range
|
||||
%
|
||||
|
||||
TR = timerange(datestr(TimeRange.calibrationRange(1)),datestr(TimeRange.calibrationRange(2)));
|
||||
figure( 'Name', 'LopapChannel1','NumberTitle','off','Position',[10 100 550 700]);
|
||||
stackedplot(LopapDataCh1(TR,:));
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
for ii = 1:width(LopapDataCh1)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch1s.AxesProperties(ii).YLimits = [-0.4 -0.1];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
figure( 'Name', 'LopapChannel2','NumberTitle','off','Position',[600 100 550 700]);
|
||||
stackedplot(LopapDataCh2(TR,:));
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
for ii = 1:width(LopapDataCh2)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties(ii).YLimits = [-0.2 0.3];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
|
||||
%% Plot selected data in selected time range
|
||||
%
|
||||
% Here we plot the $I^{*}_{i}$ data for one wavelength only.
|
||||
|
||||
TR = timerange(datestr(TimeRange.calibrationRange(1)),datestr(TimeRange.calibrationRange(2)));
|
||||
figure( 'Name', 'LopapChannel1 550','NumberTitle','off','Position',[10 100 550 800]);
|
||||
% <Adapt>: The numbers in the curled brackets give wavelength for which you'd
|
||||
% like to display the data. The numbers need to be exactly match the
|
||||
% labels in the previous figure.
|
||||
ch1s=stackedplot(LopapDataCh1(TR,:),{'550.7'});
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
%ch1s.AxesProperties.YLimits = [-0.4 -0.1];
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
|
||||
figure( 'Name', 'LopapChannel2 550','NumberTitle','off','Position',[600 100 550 800]);
|
||||
% <Adapt>: The numbers in the curled brackets give wavelength for which you'd
|
||||
% like to display the data. The numbers need to be exactly match the
|
||||
% labels in the previous figure
|
||||
ch2s=stackedplot(LopapDataCh2(TR,:),{'550.5'});
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties.YLimits = [-0.2 0.3];
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap lopap* TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
%% Plot selected spectra
|
||||
%
|
||||
% Here, we plot a spectrum without ('R1&R2') and with nitrite
|
||||
% ('R1+nitrite&R2'') for each channel or which ever combination of spectra
|
||||
% that we have selected.
|
||||
clc
|
||||
close all
|
||||
figure('Name', 'LopapSelectedSpectra')
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),LopapSpecCh1{datestr(TimeRange.specCompareOne),:},...
|
||||
'DisplayName',['#1 ' datestr(TimeRange.specCompareOne) ]) % a time where only R1&R2 was connected to the Lopap
|
||||
hold on
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),LopapSpecCh2{datestr(TimeRange.specCompareOne),:},...
|
||||
'DisplayName',['#2 ' datestr(TimeRange.specCompareOne)],'LineStyle','--') % a time where only R1&R2 was connected to the Lopap
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),LopapSpecCh1{datestr(TimeRange.specCompareTwo),:},...
|
||||
'DisplayName',['#1 ' datestr(TimeRange.specCompareTwo)]) % a time where nitrite in R1 was connected to the Lopap
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),LopapSpecCh2{datestr(TimeRange.specCompareTwo),:},...
|
||||
'DisplayName',['#2 ' datestr(TimeRange.specCompareTwo)],'LineStyle','--') % a time where nitrite in R1 was connected to the Lopap
|
||||
legend
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('Intensity')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process: Absorption spectrum
|
||||
%
|
||||
% Here, we reprocess the data to derive an absorption spectrum. This should
|
||||
% match the spectra shown for nitrite in the Lopap manual.
|
||||
|
||||
|
||||
clc
|
||||
close all
|
||||
indexR(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
indexR(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
|
||||
figure('Name', 'LopapAbsorbtionSpectra')
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),log10(LopapSpecCh1{datestr(TimeRange.specCompareTwo),...
|
||||
indexR(1)}./LopapSpecCh1{datestr(TimeRange.specCompareTwo),:})-log10(LopapSpecCh1{datestr(TimeRange.specCompareOne),...
|
||||
indexR(1)}./LopapSpecCh1{datestr(TimeRange.specCompareOne),:}),'DisplayName','#1')
|
||||
hold on
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),log10(LopapSpecCh2{datestr(TimeRange.specCompareTwo),...
|
||||
indexR(2)}./LopapSpecCh2{datestr(TimeRange.specCompareTwo),:})-log10(LopapSpecCh2{datestr(TimeRange.specCompareOne),...
|
||||
indexR(2)}./LopapSpecCh2{datestr(TimeRange.specCompareOne),:}),'DisplayName','#2','LineStyle','--')
|
||||
legend
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('ABS (log I_{r}/I_{i}')
|
||||
title([datestr(TimeRange.specCompareOne) ' & ' datestr(TimeRange.specCompareTwo)])
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process :: Absorption with time
|
||||
%
|
||||
% Here, we reprocess the data to get the intensity with time for 1 chosen
|
||||
% signal wavelength and 1 reference wavelength. The data is identical to that
|
||||
% shown in the "measurement window" of the Lopap software.
|
||||
%
|
||||
% The data is written to the _LopapTimeT_ time table. Rows hold the time,
|
||||
% columns hold the processed signal for channel 1 and channel 2.
|
||||
%
|
||||
% It is important that the same signal wavelength and reference wavelength
|
||||
% are taken for the calibration and for the experimental data.
|
||||
|
||||
clc
|
||||
close all
|
||||
indexS(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthS,1);
|
||||
indexS(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthS,1);
|
||||
indexR(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
indexR(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
LopapTimeT = timetable(LopapSpecCh1.Time,log10(LopapSpecCh1{:,indexR(1)}./LopapSpecCh1{:,indexS(1)}),...
|
||||
log10(LopapSpecCh2{:,indexR(2)}./LopapSpecCh2{:,indexS(2)}));
|
||||
LopapTimeT.Properties.VariableNames ={'Ch #1','Ch #2'};
|
||||
figure('Name', 'Lopap TimeTable')
|
||||
stackedplot(LopapTimeT,{{'Ch #1','Ch #2'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process :: Background
|
||||
%
|
||||
% Currently a linear fit forced through 0.
|
||||
clc
|
||||
close all
|
||||
LopapTimeT = fitLopapBkgrd(LopapTimeT,'BkgrdPeriod',TimeRange.backgroundFit,'TimeRangeToPlot',TimeRange.calibrationRange);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%%
|
||||
%
|
||||
clc
|
||||
close all
|
||||
% Plot
|
||||
TR = timerange(datestr(TimeRange.calibrationRange(1)),datestr(TimeRange.calibrationRange(2)));
|
||||
figure('Name', 'Lopap TimeTable Bkgrd')
|
||||
stackedplot(LopapTimeT(TR,:),{{'Ch #1 Bkgrd','Ch #2 Bkgrd'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
% s.AxesProperties.YLimits = [-0.01 0.6];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
|
||||
%% Process :: Calibrate
|
||||
%
|
||||
clc
|
||||
close all
|
||||
|
||||
S = timerange(datestr(TimeRange.MeanZeroAir(1)), datestr(TimeRange.MeanZeroAir(2)));
|
||||
TZ = LopapTimeT(S,:);
|
||||
S = timerange(datestr(TimeRange.MeanNitriteStandard(1)), datestr(TimeRange.MeanNitriteStandard(2)));
|
||||
TN = LopapTimeT(S,:);
|
||||
calib.mean = mean(TN{:,:},1) - mean(TZ{:,:},1);
|
||||
calib.std = std(TN{:,:},1);
|
||||
calib.stdZero = std(TZ{:,:},1);
|
||||
calib.mixingRatio = LopapParameters.concStandard./1000.*LopapParameters.flowReagents./1000./46.*6.022E23./...
|
||||
(246E17.*LopapParameters.flowGas).*1E12; % 246E17 are molecules in 1 ml at 298.15 K and 1013 hPa thus flow needs to be in these standard conditions!
|
||||
|
||||
[LopapTimeT, calib.fitresult] = fitLopapCalibration(LopapTimeT,calib);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange* fitresult calib
|
||||
disp("***************************************************************")
|
||||
disp("***************************************************************")
|
||||
fprintf('Detection limit channel #1 is %.0f ppt \n',calib.fitresult.calibChannel1(3.*calib.stdZero(3)))
|
||||
fprintf('Detection limit channel #2 is %.0f ppt \n',calib.fitresult.calibChannel2(3.*calib.stdZero(4)))
|
||||
disp("***************************************************************")
|
||||
fprintf('Calibration range: %s to %s \n',datestr(TimeRange.calibrationRange(1)), datestr(TimeRange.calibrationRange(2)))
|
||||
for ii=1:size(TimeRange.backgroundFit,1)
|
||||
fprintf('Background range: %s to %s \n',datestr(TimeRange.backgroundFit(ii,1)), datestr(TimeRange.backgroundFit(ii,2)))
|
||||
end
|
||||
|
||||
fprintf('Zero mean: %s to %s \n',datestr(TimeRange.MeanZeroAir(1)), datestr(TimeRange.MeanZeroAir(2)))
|
||||
fprintf('Nitrite mean: %s to %s \n',datestr(TimeRange.MeanNitriteStandard(1)), datestr(TimeRange.MeanNitriteStandard(2)))
|
||||
%% Plot calibrated data
|
||||
%
|
||||
close all
|
||||
% Plot
|
||||
TR = timerange(datestr(TimeRange.calibrationRange(1)),datestr(TimeRange.calibrationRange(2)));
|
||||
figure('Name', 'Lopap TimeTable Calibrated')
|
||||
s=stackedplot(LopapTimeT(TR,:),{{'Ch #1 Calib','Ch #2 Calib'}});
|
||||
title(['HONO in ppt, Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
% s.AxesProperties.YLimits = [-100 2500];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange* fitresult calib
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Save the data
|
||||
%
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'LopapDataCh1','LopapDataCh2','LopapParameters','calib','LopapSpecCh1','LopapSpecCh2')
|
||||
save(['Lopap' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') 'Calib.mat'],'LopapParameters','LopapTimeT','TimeRange')
|
||||
%% Local functions
|
||||
function [fileLocation, myColorMap] = localInitializeMatlab
|
||||
%INITIALIZEMATLAB Sets Lopap specific settings
|
||||
% Adds processing functions to path and defines file locations for mac, windows,
|
||||
% and Matlab online (which runs on unix)
|
||||
|
||||
% change working directory
|
||||
path = matlab.desktop.editor.getActiveFilename;
|
||||
[filepath,~,~] = fileparts(path);
|
||||
cd(filepath);
|
||||
|
||||
|
||||
% Data Server Address
|
||||
if ismac
|
||||
fileLocation.server = '/Volumes/';
|
||||
fileLocation.dataPath = 'data_2411/Lopap/';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('/Users/bartels-rausch/SwitchDrive/PSI_Matlab/Add-Ons');
|
||||
addpath('/Users/bartels-rausch/SwitchDrive/PSI_Matlab/Lopap/1.LOPAP_Restliche Daten');
|
||||
elseif ispc
|
||||
fileLocation.server = '\\fs00\'; %UNC name for file server that hosts Napp shared drive
|
||||
fileLocation.dataPath = 'data_2411\Lopap\';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('C:\Users\iezzi_l\switchdrive\Add-Ons');
|
||||
addpath('C:\Users\vieill_l\switchdrive\Add-Ons');
|
||||
addpath('C:\Users\bletry_c\switchdrive\Add-Ons');
|
||||
addpath('C:\Users\iezzi_l\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
addpath('C:\Users\vieill_l\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
addpath('C:\Users\bletry_c\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
|
||||
addpath('U:\SwitchDrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
addpath('U:\SwitchDrive\Add-Ons');
|
||||
elseif isunix
|
||||
fileLocation.server = '/';
|
||||
fileLocation.dataPath = 'Lopap/';
|
||||
end
|
||||
|
||||
% Color maps
|
||||
myColorMap.red = colormap(autumn(7));
|
||||
myColorMap.blue = colormap(winter(7));
|
||||
|
||||
close all
|
||||
end
|
||||
|
||||
Executable
+785
@@ -0,0 +1,785 @@
|
||||
%% Lopap Template
|
||||
% Uses data from 20211115_1431
|
||||
%
|
||||
%% Info: How to use this
|
||||
%
|
||||
% # Make a copy of this file for each Lopap measurement. Name it
|
||||
% "Lopap"_date_time.m and store it in the folder with the Lopap data. %
|
||||
% Remove all the general text and comments in your file and add notes and
|
||||
% observations about the experiment.
|
||||
%
|
||||
% # You can run this script, publish it, or evaluate it section wise. For
|
||||
% new data run it section wise to carefully update the settings and to
|
||||
% observe the results.
|
||||
% # Once the data is loaded, you can also run individual sections only.
|
||||
% # You may use the LabBook :: Chrono Notes section as lab book.
|
||||
% # All sections that can be modified are marked with the word "<Adapt>:".
|
||||
% # You also need to give time regions such as for the background fit, as
|
||||
% well as to calculate means. There are several options how to do this
|
||||
%
|
||||
% * While running the experiments and observing the signal in the Lopap
|
||||
% software, you can enter the date and times directly in the LabBook :
|
||||
% Select data ranges section.
|
||||
% * You can manually select the regions in a plot. A window will pop up to
|
||||
% select the region to modify. To modify several regions, re-run this
|
||||
% section of the script. This overwrites the current settings.
|
||||
% * The times of the regions are stored in the "TimeRanges.mat" file. If it
|
||||
% exists, this is read; the LabBook : Select data ranges section is then
|
||||
% ignored.
|
||||
%% Info: Output & Variables
|
||||
%
|
||||
% * *lopapReferenceWavelength*: This _string variable_ holds text with
|
||||
% stating the reference wavelength for channel 1 and 2 used to process the
|
||||
% data by the Lopap software.
|
||||
% * *LopapDataCh1 & LopapDataCh2*: These _time tables_ hold the data that
|
||||
% have been processed by the Lopap Software during the data acquisition. It
|
||||
% contains the absorption for a number
|
||||
% of selected wavelength. The absorption is the log of the intensity at the
|
||||
% reference wavelength relative to the intensity at each wavelength of
|
||||
% interest. The timetables hold the time in each row and the wavelength in
|
||||
% the columns. The content is thus identical to that shown in the
|
||||
% "measurement window" of the Lopap software.
|
||||
% * *LopapSpecCh1,LopapSpecCh2*: The _time tables_ hold the full spectrum
|
||||
% for each time. Time is in the rows, wavelength in the columns. The
|
||||
% wavelength are read from the *.prj file, the spectra data from the *.spec
|
||||
% file. The information is identical to that shown in the "spectrum window"
|
||||
% of the Lopap software.
|
||||
% * *LopapTimeT* This is the main results table:
|
||||
%
|
||||
% * time
|
||||
% * raw signal channel 1
|
||||
% * raw signal channel 2
|
||||
% * background subtracted channel 1
|
||||
% * background subtracted channel 2
|
||||
% * calibrated signal channel 1 in ppt
|
||||
% * calibrated signal channel 2 in ppt
|
||||
% * HONO in ppt (channel 2 -channel 1)
|
||||
%
|
||||
%
|
||||
% * *TimeRanges.mat*: Time ranges after they have been manually modified. If
|
||||
% this file exists, the time range definitions in this script are ignored.
|
||||
% * *LopapMatlabDataDATE_TIME.mat*: Raw data and experimental settings.
|
||||
% Background subtraction and calibration are not saved in this file. When
|
||||
% this file exists, data will not be read from the windows server.
|
||||
% * *LopapDATE_TIME.mat*: Processed data - absorption with time (column 1
|
||||
% and 2: 'Ch #1' and 'Ch #2') after background (columns 3 and 4: 'Ch #1
|
||||
% Bkgrd' and 'Ch #2 Bkgrd') subtraction and calibration (columns 5 and 6:
|
||||
% 'Ch #1 Calib' and 'Ch #2 Calib') for one wavelength - that can be used
|
||||
% for further comparison with other experiments and discussion. Also
|
||||
% exported is HONO in ppt (channel2-channel1 after calibration).
|
||||
%
|
||||
|
||||
%% Matlab: Initialise
|
||||
%
|
||||
% This starts Matlab and defines some common settings such as the path to
|
||||
% the Lopap data. Any modifications can be done at the end of this file in
|
||||
% where the local function _localInitializeMatlab_ is stored.
|
||||
|
||||
|
||||
% clear variables in workspace, clear text in command window
|
||||
clearvars
|
||||
clc
|
||||
% set the path to the data and define some custom colours for plotting
|
||||
[fileLocation, myColorMap] = localInitializeMatlab;
|
||||
% <Adapt>: Date when Lopap recording was started. Defines names of Lopap
|
||||
% files and folders. Seconds are irrelevant, but format is important.
|
||||
LopapParameters.MeasurementDate = datenum('15-Nov-2021 14:31:00');
|
||||
% <Adapt>: Date when Lopap calibration for this measurement was started.
|
||||
% Defines names of Lopap files and folders. Seconds are irrelevant, but
|
||||
% format is important.
|
||||
LopapParameters.CalibrationDate = datenum('11-March-2021 09:51:00');
|
||||
%%
|
||||
|
||||
% Print info to command window
|
||||
disp('The data is read from:');
|
||||
disp(fullfile(fileLocation.server,fileLocation.dataPath,datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM')));
|
||||
disp(' ')
|
||||
disp('Date of experiment:')
|
||||
disp(datestr(LopapParameters.MeasurementDate));
|
||||
try
|
||||
disp(' ')
|
||||
disp('Date of calibration:')
|
||||
disp(datestr(LopapParameters.CalibrationDate));
|
||||
catch
|
||||
end
|
||||
disp(' ')
|
||||
disp('Date of analyis:')
|
||||
disp(datestr(today));
|
||||
|
||||
%% Process: Import data
|
||||
%
|
||||
% Reads and imports data from Lopap *.dat, *.spec, and *.prj files and the
|
||||
% calibration results and settings from a *.mat file (*.mat file needs to
|
||||
% be in same folder as this file).
|
||||
%
|
||||
% * *lopapReferenceWavelength*: This _string variable_ holds text with
|
||||
% stating the reference wavelength for channel 1 and 2 used to process the
|
||||
% data by the Lopap software.
|
||||
% * *LopapDataCh1 & LopapDataCh2*: These _time tables_ hold the data that
|
||||
% have been processed by the Lopap Software during the data acquisition. It
|
||||
% contains the absorption for a number
|
||||
% of selected wavelength. The absorption is the log of the intensity at the
|
||||
% reference wavelength relative to the intensity at each wavelength of
|
||||
% interest. The timetables hold the time in each row and the wavelength in
|
||||
% the columns. The content is thus identical to that shown in the
|
||||
% "measurement window" of the Lopap software.
|
||||
% * *LopapSpecCh1,LopapSpecCh2*: The _time tables_ hold the full spectrum
|
||||
% for each time. Time is in the rows, wavelength in the columns. The
|
||||
% wavelength are read from the *.prj file, the spectra data from the *.spec
|
||||
% file. The information is identical to that shown in the "spectrum window"
|
||||
% of the Lopap software.
|
||||
% * *LopapParametersCalibration*: Holds the date, wavelength,
|
||||
% concentrations, flows, temperature & pressure of the calibration
|
||||
% measurement.
|
||||
% * *LopapCalibCalibration* holds the mean, standard deviation, mixing ratio
|
||||
% and fit results of the calibration. The fit results can be used to
|
||||
% calibrate this data-set. It's a linear fit via 0 of signal intensity vs.
|
||||
% HONO in ppt.
|
||||
|
||||
if isfile(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'])
|
||||
load(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'])
|
||||
disp('Lopap data loaded from mat file')
|
||||
else
|
||||
[LopapParameters.instrumentReferenceWavelength, LopapDataCh1,LopapDataCh2,LopapSpecCh1,LopapSpecCh2] ...
|
||||
= importLopap(LopapParameters.MeasurementDate,fileLocation);
|
||||
disp('Lopap data imported from intrument')
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'],'LopapDataCh1','LopapDataCh2','LopapParameters','LopapSpecCh1','LopapSpecCh2')
|
||||
end
|
||||
% if the calibration file exist, it will read the results and the
|
||||
% reference wavelength and signal wavelength from that file
|
||||
if isfile(['LopapMatlabData' datestr(LopapParameters.CalibrationDate,'yyyymmdd_HHMM') 'Calib.mat'])
|
||||
LopapParametersCalibration = load(['LopapMatlabData' datestr(LopapParameters.CalibrationDate,'yyyymmdd_HHMM') 'Calib.mat'],'LopapParameters');
|
||||
LopapCalibCalibration = load(['LopapMatlabData' datestr(LopapParameters.CalibrationDate,'yyyymmdd_HHMM') 'Calib.mat'],'calib');
|
||||
LopapParameters.wavelengthR = LopapParametersCalibration.LopapParameters.wavelengthR;
|
||||
LopapParameters.wavelengthS = LopapParametersCalibration.LopapParameters.wavelengthS;
|
||||
disp('Calibration data loaded from mat file')
|
||||
else
|
||||
% otherwise, you can choose these wavelength here
|
||||
disp('No calibration done yet!')
|
||||
% <Adapt>: Choose a reference wavelength. Default is 650 nm.
|
||||
LopapParameters.wavelengthR = 650; %nm, reference intensity
|
||||
% <Adapt>: Choose a signal wavelength to calculate the absorption with time
|
||||
% from the spectra
|
||||
LopapParameters.wavelengthS = 530; %nm, signal intensity
|
||||
|
||||
end
|
||||
%% Matlab: Run mode
|
||||
%
|
||||
% <Adapt>:
|
||||
%
|
||||
% * runs without user interaction and without ability to modify data
|
||||
% ranges, when set to 0; use this to publish.
|
||||
% * if set to 1: stops for user interaction,
|
||||
% modify data ranges is enabled.Use this to run.
|
||||
LopapParameters.Interactive = 1;
|
||||
|
||||
%% LabBook : Define data ranges
|
||||
%%
|
||||
% These settings can be modified by selecting data ranges in a plot later.
|
||||
% So, you do not necessarily need to type the dates and times here.
|
||||
|
||||
% <Adapt> (Optional - comment if no needed) state the start and end
|
||||
% time of the time that you want to look at (to exclude very noisy
|
||||
% signal in the beginning and at the end of the data)
|
||||
TimeRange.dataRange = [datenum('15-Nov-2021 16:30:00') datenum('15-Nov-2021 17:20:00')];
|
||||
% <Adapt>: State the time for the first spectrum that you like to
|
||||
% compare (to confirm nitrite)
|
||||
TimeRange.specCompareOne = datenum('15-Nov-2021 16:49:30');
|
||||
% <Adapt>: State the time for one spectrum of the second spectrum that
|
||||
% you like to compare (to confirm nitrite)
|
||||
TimeRange.specCompareTwo = datenum('15-Nov-2021 17:02:00');
|
||||
% <Adapt>: Choose a start and end time for one as many intervals that can
|
||||
% be used to fit the background. Background is the signal when R1&R2 was
|
||||
% attached to the Lopap with zero air entering the sampling coil.
|
||||
TimeRange.backgroundFit = [datenum('15-Nov-2021 15:10:00') datenum('15-Nov-2021 15:50:00')];% ;...
|
||||
% datenum('16-Sep-2020 15:40:50') datenum('16-Sep-2020 15:51:06')];
|
||||
|
||||
|
||||
|
||||
% confirm that all dates are reasonable
|
||||
tmp = fieldnames(TimeRange);
|
||||
for ii = 1:length(tmp)
|
||||
mustBeLopapReasonableDate(TimeRange.(tmp{ii}))
|
||||
end
|
||||
clearvars tmp*
|
||||
|
||||
%% Process: Modify data ranges
|
||||
%
|
||||
% Select the range to modify in the pop-up window and the number of fit
|
||||
% ranges for the background fit in the 2nd pop-up window. Then, a figure
|
||||
% will show, select the data ranges in the figure:
|
||||
%
|
||||
% * a line for calibration range, mean zero air and mean
|
||||
% nitrite standard. Select the range by keeping the mouse pushed while
|
||||
% moving from start to end time.
|
||||
% * a line for each background region, default is 2. Select the range by
|
||||
% keeping the mouse pushed while moving from start to end time.
|
||||
% * a point for spectrum with reagents and spectrum with nitrite. Click
|
||||
% once to select a specific time.
|
||||
%
|
||||
% * LopapParameters.Interactive needs to be 1 for this to run.
|
||||
%
|
||||
% # Run this section several times to modify several time regions
|
||||
% # Press cancel in the pop-up window if you do not want to modify any
|
||||
% region.
|
||||
|
||||
TimeRange = modifyLopapTimeRanges(TimeRange, LopapParameters, LopapDataCh1, LopapDataCh2);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
|
||||
|
||||
%% Process: Find closest match of selected dates in data set
|
||||
%
|
||||
% The data is sampled at specific times with a certain interval. The
|
||||
% selected or chosen dates might not necessarily exactly match the data.
|
||||
% Here, closest match to the given dates are selected.
|
||||
|
||||
tmp.d1 = TimeRange.specCompareOne;
|
||||
tmp.d2 = LopapSpecCh1.Time;
|
||||
[~,ind1] = min(abs(bsxfun(@minus,datenum(tmp.d2),datenum(tmp.d1)')));
|
||||
TimeRange.specCompareOne = tmp.d2(ind1,:);
|
||||
|
||||
tmp.d1 = TimeRange.specCompareTwo ;
|
||||
tmp.d2 = LopapSpecCh1.Time;
|
||||
[~,ind1] = min(abs(bsxfun(@minus,datenum(tmp.d2),datenum(tmp.d1)')));
|
||||
TimeRange.specCompareTwo = tmp.d2(ind1,:);
|
||||
|
||||
% save current state of
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'],'LopapDataCh1','LopapDataCh2','LopapParameters','LopapSpecCh1','LopapSpecCh2')
|
||||
|
||||
%% LabBook: Data ranges used in this work
|
||||
%
|
||||
% This plots the
|
||||
|
||||
for ii=1:size(TimeRange.backgroundFit,1)
|
||||
fprintf('Background range: %s to %s \n',datestr(TimeRange.backgroundFit(ii,1)), datestr(TimeRange.backgroundFit(ii,2)))
|
||||
end
|
||||
fprintf('Comparision Spectrum 1: %s \n',datestr(TimeRange.specCompareOne(1)))
|
||||
fprintf('Comparision Spectrum 2: %s \n',datestr(TimeRange.specCompareTwo(1)))
|
||||
|
||||
|
||||
%% Plot all data
|
||||
%
|
||||
% Here, we plot the data as shown in the "Measurement window" of the Lopap
|
||||
% software. That is, the processed $I^{*}_{i}$ data for all wavelength as
|
||||
% defined in the settings of the Lopap software.
|
||||
%
|
||||
%
|
||||
% For every measurement wavelength I_i the program calculates the
|
||||
% measurement (absorption) value I_i^* from the spectral intensity on the
|
||||
% measurement wavelength I_i and a reference wavelength I_r with the
|
||||
% following operation:
|
||||
%
|
||||
%
|
||||
% $$I^{*}_{i} = log_{10} (\frac{I_r}{I_i})$$
|
||||
%
|
||||
%
|
||||
%
|
||||
% The plots show time on the x-axis and the ABS intensity on the y axis for
|
||||
% each wavelength in separate graphs. One Figure for each Channel.
|
||||
|
||||
figure( 'Name', 'LopapChannel1','NumberTitle','off','Position',[10 100 550 700]);
|
||||
ch1s=stackedplot(LopapDataCh1);
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
for ii = 1:width(LopapDataCh1)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch1s.AxesProperties(ii).YLimits = [-0.4 -0.1];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
figure( 'Name', 'LopapChannel2','NumberTitle','off','Position',[600 100 550 700]);
|
||||
ch2s=stackedplot(LopapDataCh2);
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
for ii = 1:width(LopapDataCh2)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties(ii).YLimits = [-0.2 0.3];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
%% Plot all data :: selected time range
|
||||
%
|
||||
if isfield(TimeRange,'dataRange')
|
||||
TR = timerange(datestr(TimeRange.dataRange(1)),datestr(TimeRange.dataRange(2)));
|
||||
figure( 'Name', 'LopapChannel1','NumberTitle','off','Position',[10 100 550 700]);
|
||||
ch1s=stackedplot(LopapDataCh1(TR,:));
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
for ii = 1:width(LopapDataCh1)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch1s.AxesProperties(ii).YLimits = [-0.4 -0.1];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
figure( 'Name', 'LopapChannel2','NumberTitle','off','Position',[600 100 550 700]);
|
||||
ch2s=stackedplot(LopapDataCh2(TR,:));
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
for ii = 1:width(LopapDataCh2)
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties(ii).YLimits = [-0.2 0.3];
|
||||
end
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
%% Plot selected data with Notes
|
||||
%
|
||||
% Here we plot the $I^{*}_{i}$ data for one wavelength only.
|
||||
|
||||
if isfield(TimeRange,'dataRange')
|
||||
TR = timerange(datestr(TimeRange.dataRange(1)),datestr(TimeRange.dataRange(2)));
|
||||
end
|
||||
|
||||
ch1f = figure( 'Name', 'LopapChannel1 550','NumberTitle','off','Position',[10 100 550 800]);
|
||||
% <Adapt>: The numbers in the curled brackets give wavelength for which you'd
|
||||
% like to display the data. The numbers need to be exactly match the
|
||||
% labels in the previous figure.
|
||||
if isfield(TimeRange,'dataRange')
|
||||
ch1ax=plot(LopapDataCh1(TR,:).Time,LopapDataCh1(TR,:).('550.7'));
|
||||
else
|
||||
ch1ax=plot(LopapDataCh1.Time,LopapDataCh1.('550.7'));
|
||||
end
|
||||
title(LopapParameters.instrumentReferenceWavelength(1))
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
%ch1s.AxesProperties.YLimits = [-0.4 -0.1];
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
|
||||
ch2f = figure( 'Name', 'LopapChannel2 550','NumberTitle','off','Position',[600 100 550 800]);
|
||||
% <Adapt>: The numbers in the curled brackets give wavelength for which you'd
|
||||
% like to display the data. The numbers need to be exactly match the
|
||||
% labels in the previous figure
|
||||
if isfield(TimeRange,'dataRange')
|
||||
ch2ax=plot(LopapDataCh2(TR,:).Time,LopapDataCh2(TR,:).('550.5'));
|
||||
else
|
||||
ch2ax=plot(LopapDataCh2.Time,LopapDataCh2.('550.5'));
|
||||
end
|
||||
title(LopapParameters.instrumentReferenceWavelength(2))
|
||||
% <Adapt>: The numbers in the brackets give the lower and upper limit
|
||||
% of the y-axis. Adapt these to fit your data and remove the % sign.
|
||||
% ch2s.AxesProperties.YLimits = [-0.2 0.3];
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('Lab Time')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap lopap* TimeRange* ch1f ch2f
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% LabBook :: Annotate Figure
|
||||
%
|
||||
%
|
||||
% * 16:07 N2+water
|
||||
% * 16:23 N2+R1+R2
|
||||
% * 16:37 bubbles in the system
|
||||
% * 16:46 N2/O2/RH(78%)+NO2+ flow tube in line + LIGHT
|
||||
% * 17:05 N2/O2/RH(78%)+NO2+ flow tube in line è switch off light
|
||||
% * 17:15 Close ABS channel and switch the tubes of R1+R2 to the water
|
||||
% * 17:21 N2/O2/RH(78%) è open the ABS channel, bypass the reactor and close NO2 supply
|
||||
% * 17:30 N2 è switch off O2 supply and the humidifier
|
||||
% * 17:32 stop recording
|
||||
|
||||
% clc
|
||||
% ax = ch1f.CurrentAxes;
|
||||
% deltaT = 6;
|
||||
% eTime = datetime("25-Feb-2021 16:07:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh1.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh1(xPos,:).('550.7'),...
|
||||
% '\leftarrow N2+water');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 16:23:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh1.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh1(xPos,:).('550.7'),...
|
||||
% '\leftarrow N2+R1&R2');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 16:37:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh1.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh1(xPos,:).('550.7'),...
|
||||
% '\leftarrow Bubbles!');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 16:46:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh1.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh1(xPos,:).('550.7'),...
|
||||
% {['\leftarrow N2/O2/RH(78%)+NO2+'],[' flow tube in line + LIGHT']});
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 17:05:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh1.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh1(xPos,:).('550.7'),...
|
||||
% '\leftarrow light off');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 17:15:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh1.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh1(xPos,:).('550.7'),...
|
||||
% '\leftarrow close ABS, water');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 17:21:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh1.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh1(xPos,:).('550.7'),...
|
||||
% '\leftarrow N2/O2/RH(78%) ABS open');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% ax = ch2f.CurrentAxes;
|
||||
% deltaT = 6;
|
||||
% eTime = datetime("25-Feb-2021 16:07:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh2.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh2(xPos,:).('550.5'),...
|
||||
% '\leftarrow N2+water');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 16:23:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh2.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh2(xPos,:).('550.5'),...
|
||||
% '\leftarrow N2+R1&R2');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 16:37:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh2.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh2(xPos,:).('550.5'),...
|
||||
% '\leftarrow Bubbles!');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 16:46:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh2.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh2(xPos,:).('550.5'),...
|
||||
% {['\leftarrow N2/O2/RH(78%)+NO2+'],[' flow tube in line + LIGHT']});
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 17:05:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh2.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh2(xPos,:).('550.5'),...
|
||||
% '\leftarrow light off');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 17:15:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh2.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh2(xPos,:).('550.5'),...
|
||||
% '\leftarrow close ABS, water');
|
||||
% set(ht,'Rotation',90);
|
||||
%
|
||||
% eTime = datetime("25-Feb-2021 17:21:00")+minutes(deltaT);
|
||||
% xPos = find(LopapDataCh2.Time >= eTime,1);
|
||||
% ht = text(ax,eTime,LopapDataCh2(xPos,:).('550.5'),...
|
||||
% '\leftarrow N2/O2/RH(78%) ABS open');
|
||||
% set(ht,'Rotation',90);
|
||||
|
||||
|
||||
%% Plot selected spectra
|
||||
%
|
||||
% Compare to spectra to see if change is over whole wavelength or just
|
||||
% where nitrite absorbs.
|
||||
|
||||
clc
|
||||
close all
|
||||
figure('Name', 'LopapSelectedSpectra')
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),LopapSpecCh1{datestr(TimeRange.specCompareOne),:},...
|
||||
'DisplayName',['#1 ' datestr(TimeRange.specCompareOne) ]) % a time where only R1&R2 was connected to the Lopap
|
||||
hold on
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),LopapSpecCh2{datestr(TimeRange.specCompareOne),:},...
|
||||
'DisplayName',['#2 ' datestr(TimeRange.specCompareOne)],'LineStyle','--') % a time where only R1&R2 was connected to the Lopap
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),LopapSpecCh1{datestr(TimeRange.specCompareTwo),:},...
|
||||
'DisplayName',['#1 ' datestr(TimeRange.specCompareTwo)]) % a time where nitrite in R1 was connected to the Lopap
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),LopapSpecCh2{datestr(TimeRange.specCompareTwo),:},...
|
||||
'DisplayName',['#2 ' datestr(TimeRange.specCompareTwo)],'LineStyle','--') % a time where nitrite in R1 was connected to the Lopap
|
||||
legend
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('Intensity')
|
||||
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
%% Process: Absorption spectrum
|
||||
%
|
||||
% Here, we reprocess the data to derive an absorption spectrum. This should
|
||||
% match the spectra shown for nitrite in the Lopap manual.
|
||||
|
||||
clc
|
||||
close all
|
||||
indexR(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
indexR(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
|
||||
figure('Name', 'LopapAbsorbtionSpectra')
|
||||
plot(str2double(LopapSpecCh1.Properties.VariableNames),log10(LopapSpecCh1{datestr(TimeRange.specCompareTwo),...
|
||||
indexR(1)}./LopapSpecCh1{datestr(TimeRange.specCompareTwo),:})-log10(LopapSpecCh1{datestr(TimeRange.specCompareOne),...
|
||||
indexR(1)}./LopapSpecCh1{datestr(TimeRange.specCompareOne),:}),'DisplayName','#1')
|
||||
hold on
|
||||
plot(str2double(LopapSpecCh2.Properties.VariableNames),log10(LopapSpecCh2{datestr(TimeRange.specCompareTwo),...
|
||||
indexR(2)}./LopapSpecCh2{datestr(TimeRange.specCompareTwo),:})-log10(LopapSpecCh2{datestr(TimeRange.specCompareOne),...
|
||||
indexR(2)}./LopapSpecCh2{datestr(TimeRange.specCompareOne),:}),'DisplayName','#2','LineStyle','--')
|
||||
legend
|
||||
box ON
|
||||
grid ON
|
||||
% Add title and axis labels
|
||||
xlabel('wavelength [nm]')
|
||||
ylabel('ABS (log I_{r}/I_{i}')
|
||||
title([datestr(TimeRange.specCompareOne) ' & ' datestr(TimeRange.specCompareTwo)])
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
|
||||
%% Process :: Absorption with time
|
||||
%
|
||||
% Here, we reprocess the data to get the intensity with time for 1 chosen
|
||||
% signal wavelength and 1 reference wavelength. The data is identical to that
|
||||
% shown in the "measurement window" of the Lopap software.
|
||||
%
|
||||
% *The signal and the reference wavelength need to be identical to those
|
||||
% used for the calibration* and are therefore taken from the calibration
|
||||
% result file if present.
|
||||
%
|
||||
% The data is written to the _LopapTimeT_ time table. Rows hold the time,
|
||||
% columns hold the processed signal for channel 1 and channel 2. Did I
|
||||
% mention that it is important that the same signal wavelength and
|
||||
% reference wavelength are taken for the calibration and for the
|
||||
% experimental data.
|
||||
|
||||
clc
|
||||
close all
|
||||
indexS(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthS,1);
|
||||
indexS(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthS,1);
|
||||
indexR(1) = find(str2double(LopapSpecCh1.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
indexR(2) = find(str2double(LopapSpecCh2.Properties.VariableNames) >= LopapParameters.wavelengthR,1);
|
||||
LopapTimeT = timetable(LopapSpecCh1.Time,log10(LopapSpecCh1{:,indexR(1)}./LopapSpecCh1{:,indexS(1)}),...
|
||||
log10(LopapSpecCh2{:,indexR(2)}./LopapSpecCh2{:,indexS(2)}));
|
||||
LopapTimeT.Properties.VariableNames ={'Ch #1','Ch #2'};
|
||||
|
||||
TR = timerange(datestr(TimeRange.dataRange(1)),datestr(TimeRange.dataRange(2)));
|
||||
figure('Name', 'Lopap TimeTable')
|
||||
stackedplot(LopapTimeT(TR,:),{{'Ch #1','Ch #2'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process :: Background
|
||||
%
|
||||
% A linear background is fitted and subtracted (may be changed to
|
||||
% higher order). Background MUST be measured at the beginning
|
||||
% and at the end of the experiment for at least 30 minutes, ideally every
|
||||
% few hours. Background is R1&R2 with zero-air (or N2) entering the
|
||||
% stripping coil.
|
||||
|
||||
clc
|
||||
close all
|
||||
LopapTimeT = fitLopapBkgrd(LopapTimeT,'BkgrdPeriod',TimeRange.backgroundFit,'TimeRangeToPlot',TimeRange.dataRange);
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Plot bkgrd corrected data
|
||||
%
|
||||
clc
|
||||
close all
|
||||
% Plot
|
||||
TR = timerange(datestr(TimeRange.dataRange(1)),datestr(TimeRange.dataRange(2)));
|
||||
figure('Name', 'Lopap TimeTable Bkgrd')
|
||||
s=stackedplot(LopapTimeT(TR,:),{{'Ch #1 Bkgrd','Ch #2 Bkgrd'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
s.AxesProperties.YLimits = [-0.01 0.6];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange*
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
%% Process :: Calibrate
|
||||
%
|
||||
% The results from the calibration fits are used here to calibrate the
|
||||
% signal (intensity -> HONO in ppt).
|
||||
|
||||
clc
|
||||
close all
|
||||
if exist('LopapCalibCalibration','var')
|
||||
LopapTimeT.('Ch #1 Calib') = LopapCalibCalibration.calib.fitresult.calibChannel1(LopapTimeT.('Ch #1 Bkgrd'));
|
||||
LopapTimeT.('Ch #2 Calib') = LopapCalibCalibration.calib.fitresult.calibChannel2(LopapTimeT.('Ch #2 Bkgrd'));
|
||||
|
||||
disp('Settings of the calibration:')
|
||||
disp(' ')
|
||||
|
||||
fprintf('Flow Reagents: %.2f and %.2f ml/min \n',...
|
||||
LopapParametersCalibration.LopapParameters.flowReagents(1),...
|
||||
LopapParametersCalibration.LopapParameters.flowReagents(2));
|
||||
fprintf('Flow Gas: %.0f ml/min \n',...
|
||||
LopapParametersCalibration.LopapParameters.flowGas(1));
|
||||
fprintf('Temperature: %.0f K \n',LopapParametersCalibration.LopapParameters.temperature);
|
||||
fprintf('Pressure: %.0f mbar \n',LopapParametersCalibration.LopapParameters.pressure);
|
||||
fprintf('Reference Wavelength: %.0f nm \n',LopapParametersCalibration.LopapParameters.wavelengthR);
|
||||
fprintf('Sample Wavelength: %.0f nm \n',LopapParametersCalibration.LopapParameters.wavelengthS);
|
||||
|
||||
disp('Settings of this measurement')
|
||||
disp('')
|
||||
fprintf('Reference Wavelength: %.0f nm \n',LopapParameters.wavelengthR);
|
||||
fprintf('Sample Wavelength: %.0f nm \n',LopapParameters.wavelengthS);
|
||||
|
||||
% Plot
|
||||
TR = timerange(datestr(TimeRange.dataRange(1)),datestr(TimeRange.dataRange(2)));
|
||||
figure('Name', 'Lopap TimeTable Calibrated')
|
||||
s=stackedplot(LopapTimeT(TR,:),{{'Ch #1 Calib','Ch #2 Calib'}});
|
||||
title(['Lopap' datestr(LopapParameters.MeasurementDate)])
|
||||
s.AxesProperties.YLimits = [-100 2500];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange* fitresult calib
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
end
|
||||
|
||||
%% And Finally :: HONO
|
||||
%
|
||||
% * Channel 1 is from stripping coil 2. Its signal comes from NO2 and other
|
||||
% nitrogen oxides that yield nitrite in the stripping solution and/or dye
|
||||
% * Channel 2 is from stripping coil 1. Its signal comes from HONO plus
|
||||
% the impurities that are also collected in coil 2.
|
||||
%
|
||||
% HONO is thus calibrated signal coil 2 (Channel 1) - that of coil 1
|
||||
% (channel 2).
|
||||
|
||||
|
||||
close all
|
||||
if exist('LopapCalibCalibration','var')
|
||||
LopapTimeT.('HONO') = LopapTimeT.('Ch #1 Calib')-LopapTimeT.('Ch #2 Calib');
|
||||
|
||||
% Plot
|
||||
TR = timerange(datestr(TimeRange.dataRange(1)),datestr(TimeRange.dataRange(2)));
|
||||
figure('Name', 'HONO')
|
||||
s=stackedplot(LopapTimeT(TR,:),{'HONO'});
|
||||
s.Title=['HONO in ppt with time ' datestr(LopapParameters.MeasurementDate)];
|
||||
s.AxesProperties.YLimits = [-10 2500];
|
||||
clearvars -except Lopap* fileLocation myColorMap LopapParameters TimeRange* fitresult calib
|
||||
if LopapParameters.Interactive == 1
|
||||
distFig
|
||||
fprintf('press any key if you want to proceed\n')
|
||||
pause
|
||||
%%
|
||||
%
|
||||
close all
|
||||
end
|
||||
end
|
||||
%% Save the data
|
||||
%
|
||||
save(['LopapMatlabData' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'],'LopapDataCh1','LopapDataCh2','LopapParameters','LopapSpecCh1','LopapSpecCh2')
|
||||
save(['Lopap' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.mat'],'LopapParameters','LopapTimeT','TimeRange')
|
||||
% export to csv
|
||||
TT = LopapTimeT(:,{'HONO'});
|
||||
writetimetable(TT,['Lopap' datestr(LopapParameters.MeasurementDate,'yyyymmdd_HHMM') '.csv'])
|
||||
clearvars TT
|
||||
%% Local functions
|
||||
function [fileLocation, myColorMap] = localInitializeMatlab
|
||||
%INITIALIZEMATLAB Sets Lopap specific settings
|
||||
% Adds processing functions to path and defines file locations for mac, windows,
|
||||
% and Matlab online (which runs on unix)
|
||||
|
||||
% change working directory
|
||||
path = matlab.desktop.editor.getActiveFilename;
|
||||
[filepath,~,~] = fileparts(path);
|
||||
cd(filepath);
|
||||
|
||||
|
||||
% Data Server Address
|
||||
if ismac
|
||||
fileLocation.server = '/Volumes/';
|
||||
fileLocation.dataPath = 'data_2411/Lopap';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('/Users/bartels-rausch/SwitchDrive/PSI_Matlab/Add-Ons');
|
||||
addpath('/Users/bartels-rausch/SwitchDrive/PSI_Matlab/Lopap/1.LOPAP_Restliche Daten');
|
||||
elseif ispc
|
||||
fileLocation.server = '\\fs00\'; %UNC name for file server that hosts Napp shared drive
|
||||
fileLocation.dataPath = 'data_2411\Lopap';
|
||||
% add Lopap functions and general add-ons to path
|
||||
addpath('C:\Users\iezzi_l\switchdrive\Add-Ons');
|
||||
addpath('C:\Users\bletry_c\switchdrive\Add-Ons');
|
||||
addpath('C:\Users\vieill_l\switchdrive\Add-Ons');
|
||||
addpath('C:\Users\iezzi_l\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
addpath('C:\Users\bletry_c\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
addpath('C:\Users\vieill_l\switchdrive\Lopap\1.LOPAP_Restliche Daten');
|
||||
% addpath('\\fs02\5601_surface_chemistry\People\Marc\Switchdrive\PSI_Matlab\Add-Ons');
|
||||
% addpath('\\fs02\5601_surface_chemistry\People\Marc\Switchdrive\PSI_Matlab\Lopap\1.LOPAP_Restliche Daten');
|
||||
|
||||
elseif isunix
|
||||
fileLocation.server = '/';
|
||||
fileLocation.dataPath = 'Lopap/';
|
||||
end
|
||||
|
||||
% Color maps
|
||||
myColorMap.red = colormap(autumn(7));
|
||||
myColorMap.blue = colormap(winter(7));
|
||||
|
||||
close all
|
||||
end
|
||||
|
||||
|
||||
|
||||
Reference in new issue
Block a user