%% 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