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nappMATLAB-toolbox/import/nappFileList.m
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function ListFiles = nappFileList(dataPath,varargin)
% nappFileList lists all XAS, PE, and picture data of a specific beam
% time. Analyser and sample settings such as pass energy, lens mode,
% temperature, position, and pressure are added.
%
%
% * listFiles = nappFileList('2019\April_NanoXAS') imports data from beam
% time folder on local computer, generates a new matlab table 'listFiles'
% in the current workspace, and a csv file from data in the
% 'SC_Data/2019/April_NanoXAS' .
%
% * listFiles = nappFileList('2019\April_NanoXAS',listFiles) imports data from beam
% time folder on local computer, adds data to the existing matlab table
% 'listFiles' in the current workspace, and a csv file from data in the
% 'SC_Data/2019/April_NanoXAS' .
%
% Input Arguments
%
% * dataPath, mandatory: year and name of folder that holds the beam time data.
% Text string with format year/name of folder: '2019/April_NanoXAS'
% * DataTable, optional: DataTable to which imported data is added.
% * 'mode','local'; default: imports from local server address
% * 'mode','nappDrive'; imports from napp drive. Needs to be mounted.
% * 'mode','localNew'; imports only new files that have not yet been
% imported. Needs existing data table as input.
% * 'mode','nappDrivePick'; lets user select files in file browser window. Default address is Napp beam time folder.
% * 'mode','localPick'; lets user select files in file browser window. Default address is local beam time folder.
%
% Dependencies
%
% * beam time folder must be located at server/NAPP/SC Data/dataPath.
% dataPath is user input. server needs to be defined at line ~100 of this
% function.
% * XPS data in igor *.ibw format need to be in SES subfolder
% * Photos in *.bmp format need to be in Photos folder
% * NEXAFS data in *.h5 format need to be in NEXAFS subfolder
% * Labview pressure and temperature log need to be in Pressure subfolder.
% * Uses the IgorPro importer for Matlab:
% https://ch.mathworks.com/matlabcentral/fileexchange/42679-igor-pro-file-format-ibw-to-matlab-variable
% * needs at least 1 .*ibw file in the SES subfolder
%
%
% Output
%
% * ListFiles: Matlab table listing XPS, NEXAFS, and photo files with settings
% * YYYYmmm_DataList.csv (2019Apr_DataList.csv): Semicolon separated ASCII
% file for import to Excel in beamtime folder
%
%
% Further info
%
% * Do not run while SES or NEXAFS data are being recorded. Data will be
% lost by SES software.
% * Region iterations are averaged during import
% * counts are normalised to 1s dwell time during import. That is, the
% counts are in cps after import.
%
%
% Matlab Version
%
% * Matlab 2018a or higher
%
%
% See also TABLE IBWread h5read DIR LabView_importData
%
%%
%
% TODO
%
% * FIXME: Add videos and jpg
%
%% Updated
%
% * January 2020, added new h5 file structure and naming convention.
% * March 2021, added possibility to work on local file structure
% * March 2021, added Lens Mode as column (have not tested this for older
% NEXAFS files).
% * April 2021, X-ray kinetic energy and images are now made unique
% * March 2022, input now using varargin
% * March 2022, strict data structure required for local and remote sources
%% Input
% Define conditions and defaults of input
defaultMode = 'local';
expectedMode = {'local','nappDrive','localNew','nappDrivePick','localPick'};
defaultImportLabView = 'on';
expectedImportLabView = {'on','off'};
% Parse input
p = inputParser;
addRequired(p,'dataPath');
addOptional(p,'DataTable',@istable);
addParameter(p,'mode',defaultMode,...
@(x) any(validatestring(x,expectedMode)));
addParameter(p,'importLabView',defaultImportLabView,...
@(x) any(validatestring(x,expectedImportLabView)));
parse(p,dataPath,varargin{:});
%% Data Paths
%
% Mac and Windows use different notations to address network drives. For
% windows, we use the UNC naming convention. This is a more recent way to
% address mounted drives that does not rely on the use of drive letters.
% The letters might be different for the same drive on different computer.
if contains(p.Results.mode,'local')
% Data server address
if ismac
server = '/Users/bartels-rausch/Forschung_Einsam/PSI_SLS/';
elseif ispc
server = userpath;
end
elseif contains(p.Results.mode,'nappDrive')
% Data server address
if ismac
server = '/Volumes/';
elseif ispc
server = '\\fs03\';
end
end
dataPath = fullfile(server,'NAPP','SC Data',dataPath);
% Data Paths to subdirectories for specific files:
dataPath_XPS = fullfile(dataPath, 'SES');
dataPath_Photo = fullfile(dataPath, 'Photos');
dataPath_NEXAFS = fullfile(dataPath, 'NEXAFS');
dataPath_LabView = fullfile(dataPath, 'Pressure');
%
if ~isfolder(dataPath_XPS)
warning('There is something wrong with the path. Check for typo and that the drives are mounted')
disp('There is something wrong with the path. Check for typo and that the drives are mounted')
disp('I quit now')
return
end
%% Naming Convention
%
% See: MATLAB Programming Style Guidelines, by Richard Johnson
%
% * Variable: mixed case words starting with lower case: credibleThreat, qualityOfLife
% * Variables with a large scope should have meaningful names. Variables
% with a small scope can have short names.
% * A convention on pluralisation should be followed consistently.
% * Named constants (including globals) should be all uppercase using
% underscore to separate words. MAX_ITERATIONS, COLOR_RED
% * Structure names should begin with a capital letter: SegmentData.length
% * The prefix n should be used for variables representing the number of
% objects. A MATLAB-specific addition is the use of m for number of rows
% (based on matrix notation). nFiles, mRows
% * Iterator variables should be named or prefixed with i. for iPosition =
% 1:nPositions, ii, ij, ik....
% * Functions should have meaningful names written in lower case.
% computetotalwidth(), Avoid compwid();
%
%% Query beam time folder content
%
% We use MATLAB's 'dir' command which writes the content of a folder into a
% structure with the following fields:
%
% * name
% * folder
% * date
% * bytes
% * isdir
% * datenum
%
% XPS data: Create a structure 'TmpFileList{1}' with all Igor files in the
% directory and its subfolders (1st level). The '\N*' at the beginning is
% important. Otherwise hidden files starting with a . will also be listed.
% Obviously, Igor file names from SES software and h5 file names from Epics
% (NEXAFS) need to start with an N, otherwise change the search term below:
%
% THE ** notation needs a recent version of Matlab, 2014 does not work.
if endsWith(p.Results.mode,'Pick')
% select files (Xps or Nexafs, ignoring photos) to be imported from data directory
% (data can be taken from any directory; files need to be in same directory)
[filePick,pathPick] = uigetfile({'*.ibw;*.h5'},...
'Select One or More Files', dataPath,...
'MultiSelect', 'on');
% make lists for Nexafs and for XPS
if ischar(filePick)
filePick = {filePick};
end
filePickXps = filePick(endsWith(filePick,'.ibw'));
filePickNexafs = filePick(endsWith(filePick,'.h5'));
if isempty(filePickXps)
TmpFileList{1} = dir([dataPath_XPS filesep '**' filesep '*.trallalla']);
else
for ii = 1:size(filePickXps,2)
TmpFileList{1}(ii,1) = dir([pathPick filePickXps{ii}]);
end
end
if isempty(filePickNexafs)
TmpFileList{2} = dir([dataPath_NEXAFS filesep '**' filesep '*.trallalla']);
else
for ii = 1:size(filePickNexafs,2)
TmpFileList{2}(ii,1) = dir([pathPick filePickNexafs{ii}]);
end
end
% make a empty file list for photos, to be consitent with code
TmpFileList{3} = dir([dataPath_Photo filesep '**' filesep '*.trallalla']);
else
% SES files in IGOR format list all files, then get rid of system files
TmpFileList{1} = dir([dataPath_XPS filesep '**' filesep '*.ibw']);
TmpFileList{1} = TmpFileList{1}(find(~cellfun(@isempty,regexp({TmpFileList{1}.name},'^[a-zA-Z0-9]\w*')))); %#ok<FNDSB>
% EPICS files in h5 format list all files, then get rid of system files
TmpFileList{2} = dir([dataPath_NEXAFS filesep '**' filesep '*.h5']);
TmpFileList{2} = TmpFileList{2}(find(~cellfun(@isempty,regexp({TmpFileList{2}.name},'^[a-zA-Z0-9]\w*')))); %#ok<FNDSB>
% Photos list all files, then get rid of system files
TmpFileList{3} = dir([dataPath_Photo filesep '**' filesep '*.bmp']);
TmpFileList{3} = TmpFileList{3}(find(~cellfun(@isempty,regexp({TmpFileList{3}.name},'^[a-zA-Z0-9]\w*')))); %#ok<FNDSB>
% The second line of code filters all files that start with Numbers or
% letters. All system files starting with a . or ~ are discarded.
% only process new files
if (istable(p.Results.DataTable) & matches(p.Results.mode,'localNew')) % do this only if previous list was input to function call
tmpXpsFiles = endsWith(p.Results.DataTable.name,'.ibw'); % get XPS files in current data table
tmpMissingFiles = ~ismember({TmpFileList{1}(:).name},p.Results.DataTable.name(tmpXpsFiles,:)); % find those files that are yet imported
TmpFileList{1} = TmpFileList{1}(tmpMissingFiles);
tmpNexafsFiles = endsWith(p.Results.DataTable.name,'.h5'); % get XPS files in current data table
tmpMissingFiles = ~ismember({TmpFileList{2}(:).name},p.Results.DataTable.name(tmpNexafsFiles,:)); % find those files that are yet imported
TmpFileList{2} = TmpFileList{2}(tmpMissingFiles);
tmpPhotoFiles = endsWith(p.Results.DataTable.name,'.bmp'); % get XPS files in current data table
tmpMissingFiles = ~ismember({TmpFileList{3}(:).name},p.Results.DataTable.name(tmpPhotoFiles,:)); % find those files that are yet imported
TmpFileList{3} = TmpFileList{3}(tmpMissingFiles);
end
end
% get date of last and first .ibw file in folder .
tmp.fileinfo = dir([dataPath_XPS '/*.ibw']);
if isempty(tmp.fileinfo)
warning('There appears to be no file in the SES folder. Add at least one file first.')
disp('There appears to be no file in the SES folder. Add at least one file first.')
disp('I quit now')
return
end
try
tmp.fileinfo = dir([dataPath_XPS '/*.ibw']);
filedate_first = tmp.fileinfo(1).datenum;
clearvars name tmp
catch
disp('Error getting ibw file date.')
end
%% Import XPS data to get SES settings
%
% Uses the IgorPro importer for Matlab:
% https://ch.mathworks.com/matlabcentral/fileexchange/42679-igor-pro-file-format-ibw-to-matlab-variable
%
% Normally, Matlab stops when an error occurs. I use 'try' to force Matlab
% to continue even if an error occurs. Matlab will instead print a warning,
% as defined after the 'catch'. Error might occur when single data files
% can't be read. If a warning comes up, check the corresponding data file
% and try to resolve it. I suggest to rename these original data files that
% are damaged, or not complete (because measurement was aborted) to
% "ignore_filename".
for ii = 1:size(TmpFileList{1},1) % cycle through each XPS file
try
PE = IBWread([TmpFileList{1}(ii).folder filesep TmpFileList{1}(ii).name]); % read XPS file
catch
warning('Problem reading the Igor file')
disp('Problem reading the Igor file')
fprintf('Number %.0f: %s \n',ii,[TmpFileList{1}(ii).folder filesep TmpFileList{1}(ii).name])
end
fclose('all');
try
%% Convert SES meta data into variables
%
% Upon import, all meta data are written into _WaveNotes_ variable.
% Here, I select the meta data for each setting and write those
% into individual variables that are then added to the list.
% Split the WaveNotes text string into individual strings at each line break.
% (This is a work-around. Did not manage to select values with regexp
% function only.)
tmp = regexp(PE.WaveNotes, '\r', 'split');
% Then, read out the values into variables using a combination of string operations:
% Start date/time of measurement
PE.creationDate = datevec([char(regexp(tmp{29},'((?<=Date=).*)','match')) ...
' ' char(regexp(tmp{30},'((?<=Time=).*)','match'))]);
% Pass energy
PE.passEnergy = str2double(char(regexp(tmp{5},'((?<=Pass Energy=).*)','match')));
% Dwell time (or step time)
PE.dwellTime = str2double(char(regexp(tmp{15},'((?<=Step Time=).*)','match')));
% Energy step
PE.scientaEkinStep = str2double(char(regexp(tmp{14},'((?<=Energy Step=).*)','match')));
% Region name
PE.regionName = char(regexp(tmp{3},'((?<=Region Name=).*)','match'));
% Acquisition Mode
PE.acquisitionMode = char(regexp(tmp{9},'((?<=Acquisition Mode=).*)','match'));
% kinetic energy
for n = 1:size(PE.y,1)
PE.x(n)= PE.x0(1) + (n-1)*PE.dx(1);
end
% lens mode
PE.lensMode = char(regexp(tmp{4},'((?<=Lens Mode=).*)','match'));
% define iterations
%
% There is a BUG in this code. The SES file apparently has the same
% structure for 1 seq. iteration and several reg. iterations and
% several seq. iterations and 1 region iteration.
if PE.Ndim == 3
PE.regionIterations = size(PE.y,2);
PE.sequenceIterations = size(PE.y,3);
elseif PE.Ndim == 2
PE.regionIterations = 1;
PE.sequenceIterations = size(PE.y,2);
else
PE.regionIterations = 1;
PE.sequenceIterations = size(PE.y,2);
end
% average region iterations
if PE.Ndim == 3
PE.y = squeeze(mean(PE.y,2));
elseif PE.Ndim == 2
% PE.y = squeeze(mean(PE.y,2));
end
% normalise data to 1ms
PE.y = PE.y .* 1000 ./ PE.dwellTime;
% Pass energy
PE.passEnergy = str2double(char(regexp(tmp{5},'((?<=Pass Energy=).*)','match')));
catch
warning('Problem reading the PE variable')
disp('Problem reading the PE variable')
fprintf('Number %.0f: %s \n',ii,[TmpFileList{1}(ii).folder filesep TmpFileList{1}(ii).name])
end
%% Write SES meta data variables into XPS FileList structure
try
TmpFileList{1}(ii).creationDate = PE.creationDate;
TmpFileList{1}(ii).image = PE.y;
TmpFileList{1}(ii).spectrum_counts = NaN;
TmpFileList{1}(ii).spectrum_countsPerSecond = NaN;
TmpFileList{1}(ii).xRayEkin_eV = NaN;
TmpFileList{1}(ii).xRayEkinRange_eV = [NaN NaN];
% SES pass energy
TmpFileList{1}(ii).scientaPassEnergy_eV = PE.passEnergy; % in eV
% SES dwell time
TmpFileList{1}(ii).scientaDwellTime_ms = PE.dwellTime; % in ms
% SES region Name
TmpFileList{1}(ii).regionName = PE.regionName;
TmpFileList{1}(ii).scientaAcquisitionMode = PE.acquisitionMode;
% SES kinetic energy window
TmpFileList{1}(ii).scientaEkinRange_eV = [PE.x(1) PE.x(end)];
TmpFileList{1}(ii).scientaEkinStep_eV = PE.scientaEkinStep;
TmpFileList{1}(ii).scientaEkin_eV = PE.x;
% Beamline Intensity (I0 during NEXAFS)
TmpFileList{1}(ii).beamlineInt = cell(1);
% SES lens mode
TmpFileList{1}(ii).scientaLensMode = PE.lensMode;
TmpFileList{1}(ii).scientaRegionIterations = PE.regionIterations;
TmpFileList{1}(ii).scientaSequenceIterations = PE.sequenceIterations;
TmpFileList{1}(ii).imageRoh = PE.y;
TmpFileList{1}(ii).spectrum_countsPerSecondRoh = NaN;
TmpFileList{1}(ii).importDate = datestr(now);
try
TmpFileList{1}(ii).analysisDir = file.mFile;
catch
TmpFileList{1}(ii).analysisDir = pwd;
end
catch
warning('Problem with a XPS data file for XPS list')
disp('Problem with a XPS data file for XPS list')
fprintf('Number %.0f: %s \n',ii,[TmpFileList{1}(ii).folder filesep TmpFileList{1}(ii).name])
fprintf('Number %.0f: %s \n',ii,datestr(TmpFileList{1}(ii).datenum))
end
end
disp('*************************************************')
disp('* Voila: Done reading & writing XPS data! *')
disp('*************************************************')
%% Read and write NEXAFS meta data
%
% The h5 file is much nicer organised, so we do not need string operations
% to select individual meta data. The data can be directly addressed and
% written into the list structure:
% if datenum(filedate_first) >= datenum('31-Dec-2017 23:59:00') %('31-Dec-2019 23:59:00')
for ii = 1:size(TmpFileList{2},1) % do this for each list element
%if ~isempty(h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/energy'))
% creation date of file
TmpFileList{2}(ii).creationDate = datevec(NaN);
try
% read data
%if datenum(filedate_first) <= datenum('21-Nov-2020 00:01:00') % Date not exaclty certain.
try
TmpImage= h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/spectrum');
%else
catch
try
TmpImage = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/scienta spectrum');
catch
TmpImage = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/detector/data'); % pre-2020 (?) h5 structure
end
end
% 21.8.20 changed from spectrum to scienta spectrum, later
% switched back to spectrum.
% Spectrum
TmpFileList{2}(ii).spectrum_counts = NaN;
TmpFileList{2}(ii).spectrum_countsPerSecond = NaN;
% import Photon Energy (cols)
try
TmpXrayEkin = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/energy'); % X-ray excitation energy; Photon energy in eV
TmpXrayEkin(TmpXrayEkin==0)=[];
catch
TmpXrayEkin = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/PhotonEnergy'); % X-ray excitation energy; Photon energy in eV
TmpXrayEkin(TmpXrayEkin==0)=[];
end
if isempty(TmpXrayEkin)
TmpFileList{2}(ii).xRayEkinRange_eV = [NaN NaN];
else
TmpFileList{2}(ii).xRayEkinRange_eV = [TmpXrayEkin(1) TmpXrayEkin(end)];
end
% Make unique
[TmpFileList{2}(ii).xRayEkin_eV, ind] = unique(TmpXrayEkin);
TmpFileList{2}(ii).image = TmpImage(:,ind);
TmpFileList{2}(ii).image = TmpImage(:,ind);
% NEXAFS pass energy
try
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/PassEnergy'); % in eV
TmpFileList{2}(ii).scientaPassEnergy_eV = str2double(tmp(1));
catch
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/PassEnergy'); % in eV
if tmp(1) == 1
TmpFileList{2}(ii).scientaPassEnergy_eV = 20;
elseif tmp(1) == 2
TmpFileList{2}(ii).scientaPassEnergy_eV = 50;
elseif tmp(1) == 3
TmpFileList{2}(ii).scientaPassEnergy_eV = 100;
elseif tmp(1) == 4
TmpFileList{2}(ii).scientaPassEnergy_eV = 200;
end
end
% NEXAFS dwell time
if datenum(filedate_first) >= datenum('1-Feb-2020 23:59:00')
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/ScientaStepTime')*1000; % in ms
else
try
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/StepTime')*1000; % in ms
catch
try
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/StepTime')*1000; % in ms
catch
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/ScientaStepTime')*1000;
end
end
end
TmpFileList{2}(ii).scientaDwellTime_ms = tmp(1);
% NEXAFS region Name
if TmpFileList{2}(ii).xRayEkinRange_eV(:,1) <= 530 && TmpFileList{2}(ii).xRayEkinRange_eV(:,2) >= 530
TmpFileList{2}(ii).regionName = 'O K-edge NEXAFS';
else
TmpFileList{2}(ii).regionName = 'NEXAFS';
end
% Acquisition mode
try
TmpFileList{2}(ii).scientaAcquisitionMode = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/AcquisitionMode');
catch
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/AcquireMode');
if tmp(1) == 0
TmpFileList{2}(ii).scientaAcquisitionMode = "Swept";
elseif tmp(1) == 1
TmpFileList{2}(ii).scientaAcquisitionMode = "Fixed";
end
clear tmp
end
if strcmp(TmpFileList{2}(ii).scientaAcquisitionMode,'Fixed')
% NEXAFS kinetic energy window - fixed mode
try
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/ScientaCenterEnergy'); % in eV
catch
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/ScientaCenterEnergy'); % in eV
end
TmpFileList{2}(ii).scientaEkinRange_eV = [tmp(1)-TmpFileList{2}(ii).scientaPassEnergy_eV/20 tmp(1)+TmpFileList{2}(ii).scientaPassEnergy_eV/20];
TmpFileList{2}(ii).scientaEkinStep_eV = NaN;
TmpFileList{2}(ii).scientaEkin_eV = linspace(TmpFileList{2}(ii).scientaEkinRange_eV(:,1)...
,TmpFileList{2}(ii).scientaEkinRange_eV(:,2),size(TmpFileList{2}(ii).image,1))';
else
% NEXAFS kinetic energy window - scan mode
try
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/ScientaLowEnergy'); % in eV
tmp2 = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/ScientaHighEnergy');
catch
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/LowEnergy'); % in eV
tmp2 = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/HighEnergy');
end
TmpFileList{2}(ii).scientaEkinRange_eV = [tmp(1) tmp2(1)];
clearvars tmp
try
TmpFileList{2}(ii).scientaEkinStep_eV = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/StepSize');
catch
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/StepSize');
TmpFileList{2}(ii).scientaEkinStep_eV = abs(tmp(1));
end
TmpFileList{2}(ii).scientaEkin_eV = [TmpFileList{2}(ii).scientaEkinRange_eV(:,1):TmpFileList{2}(ii).scientaEkinStep_eV(1):TmpFileList{2}(ii).scientaEkinRange_eV(:,2)]';
end
clearvars tmp
% read I_0
try
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/i0');
catch
end
try
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/RM2I0');
catch
end
try
TmpFileList{2}(ii).beamlineInt = abs(tmp(ind));
catch
TmpFileList{2}(ii).beamlineInt = NaN(size(ind,1),1);
end
% Lens Mode
try
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/LensMode');
TmpFileList{2}(ii).scientaLensMode = tmp{1};
catch
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/LensMode');
TmpFileList{2}(ii).scientaLensMode = num2str(tmp(1));
end
clearvars tmp
try
TmpFileList{2}(ii).scientaRegionIterations = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/NumIterations');
catch
tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/NumIterations');
TmpFileList{2}(ii).scientaRegionIterations = tmp(1);
end
TmpFileList{2}(ii).scientaSequenceIterations = 1;
catch
warning('Problem with a NEXAFS data file in NEXAFS list')
disp('Problem with a NEXAFS data file in NEXAFS list')
fprintf('Number %.0f: %s \n',ii,[TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name])
fprintf('Number %.0f: %s \n',ii,datestr(TmpFileList{2}(ii).datenum))
end
TmpFileList{2}(ii).imageRoh = TmpFileList{2}(ii).image;
TmpFileList{2}(ii).spectrum_countsPerSecondRoh = TmpFileList{2}(ii).spectrum_countsPerSecond;
% log
TmpFileList{2}(ii).importDate = datestr(now);
try
TmpFileList{2}(ii).analysisDir = file.mFile;
catch
TmpFileList{2}(ii).analysisDir = pwd;
end
end
% else
% for ii = 1:size(TmpFileList{2},1) % do this for each list element
% try
% % NEXAFS pass energy
% tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/PassEnergy'); % in eV
% % TODO: Confirm that this assignment is correct. (The number refer to the list number in epics software)
% if tmp(1) == 1
% TmpFileList{2}(ii).passEnergy_eV = {[20]};
% elseif tmp(1) == 2
% TmpFileList{2}(ii).passEnergy_eV = {[50]};
% elseif tmp(1) == 3
% TmpFileList{2}(ii).passEnergy_eV = {[100]};
% elseif tmp(1) == 4
% TmpFileList{2}(ii).passEnergy_eV = {[200]};
% end
%
% % NEXAFS dwell time
% if datenum(filedate_first) >= datenum('1-Feb-2020 23:59:00')
% tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/ScientaStepTime')*1000; % in ms
%
% else
% tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/StepTime')*1000; % in ms
% end
% TmpFileList{2}(ii).dwellTime_ms = tmp(1);
% % NEXAFS region Name
% TmpFileList{2}(ii).regionName = 'NEXAFS';
% % FIXME: Can we differentiate O K-edge, N K-edge, C K-edge based on the h5-file meta data?
%
% % NEXAFS kinetic energy window
% tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/LowEnergy'); % in eV
% tmp2 = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/HighEnergy');
% TmpFileList{2}(ii).kinRange_eV = [tmp(1) tmp2(1)];
%
% % Lens mode
% tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/LensMode');
% TmpFileList{2}(ii).scientaLensMode = tmp{1};
% clearvars tmp
% catch
% warning('Problem with a NEXAFS data file in NEXAFS list')
% disp('Problem with a NEXAFS data file in NEXAFS list')
% fprintf('Number %.0f: %s \n',ii,[TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name])
% fprintf('Number %.0f: %s \n',ii,datestr(TmpFileList{2}(ii).datenum))
% end
%
% end
% end
disp('*************************************************')
disp('* Voila: Done reading and writing NEXAFS data! *')
disp('*************************************************')
%% Create Picture List
%
% The file structure needs same number of fields as SES and NEXAFS data.
% Set them to NaN (Not-a-Number).
for ii = 1:size(TmpFileList{3},1) % do this for each picture in the list
TmpFileList{3}(ii).creationDate = datevec(NaN);
TmpFileList{3}(ii).image = NaN;
TmpFileList{3}(ii).spectrum_counts = NaN;
TmpFileList{3}(ii).spectrum_countsPerSecond = NaN;
TmpFileList{3}(ii).xRayEkin_eV = NaN;
TmpFileList{3}(ii).xRayEkinRange_eV = [NaN NaN];
TmpFileList{3}(ii).scientaPassEnergy_eV = NaN;
TmpFileList{3}(ii).scientaDwellTime_ms = NaN;
TmpFileList{3}(ii).regionName = ' ';
TmpFileList{3}(ii).scientaAcquisitionMode = ' ';
TmpFileList{3}(ii).scientaEkinRange_eV = [NaN NaN];
TmpFileList{3}(ii).scientaEkinStep_eV = NaN;
TmpFileList{3}(ii).scientaEkin_eV = NaN;
TmpFileList{3}(ii).beamlineInt = cell(1);
TmpFileList{3}(ii).scientaLensMode = ' ';
TmpFileList{3}(ii).scientaRegionIterations = NaN;
TmpFileList{3}(ii).scientaSequenceIterations = NaN;
TmpFileList{3}(ii).imageRoh = {NaN};
TmpFileList{3}(ii).spectrum_countsPerSecondRoh = NaN;
TmpFileList{3}(ii).importDate = ' ';
TmpFileList{3}(ii).analysisDir = ' ';
end
%% Merge lists into one
%
% get index of non-empty structures
tf =~cellfun(@isempty,TmpFileList);
% merge the non-empty list structures into one structure
ListFiles = cat(1,TmpFileList{tf});
% remove lines with empty images
for ii = 1:size(ListFiles,1)
tmpLogic(ii) = isempty(ListFiles(ii).image);
noncells = tmpLogic;
end
ListFiles(noncells) = [];
clearvars -except ListFiles server dataPath* p
%%
%% Sort by date
% First, we need to convert into a table, because structures can not be sorted:
ListFiles = struct2table(ListFiles,'AsArray',true);
% Then, we sort the table based on the time (6th column, datenum)
ListFiles = sortrows(ListFiles,6);
% Then, remove un-needed columns
ListFiles = removevars(ListFiles,{'bytes','isdir'});
disp('*************************************************')
disp('* Voila: Done creating data list! *')
disp('*************************************************')
%% Import LabView data
%
if matches(p.Results.importLabView,'on')
if isfolder(dataPath_LabView) % verify that this folder exists.
try
% Get list of all files in that folder
TmpFileList = dir([dataPath_LabView filesep '**' filesep '20*.dat']);
% import LabView data
LabView = LabView_importData(fullfile(TmpFileList(1).folder,TmpFileList(1).name)); % Overwrite LabView data in workspace, if this is the first import
if size(TmpFileList,1) > 1 % for additional data files, add these to the LabView data structure.
for ii = 2:size(TmpFileList,1)
LabView = LabView_importData(fullfile(TmpFileList(ii).folder,TmpFileList(ii).name),LabView);
end
end
catch
warning('Problem with LabView file')
disp('Problem reading LabView file')
end
end
disp('*************************************************')
disp('* Voila: Done reading LabView data! *')
disp('*************************************************')
clearvars TmpFileList
try
% combine data and/or rename
LabView = LabView_combine(LabView);
catch
warning('Problem with LabView file')
disp('Problem merging LabView files')
disp('Check number of columns for each file')
end
%% Extent list with LabView data
%Query time of each data file and get LabView log for that time.
for ii = 1:size(ListFiles,1)
try
% The time of the data and the logging of LabView are not
% necessarily occurring at precisely the same time. So, here define
% a time range (50 seconds) and get all
% data between these times.
tse1 = tsdata.event('Start',datenum(ListFiles.datenum(ii)),'Datenum');
tse2 = tsdata.event('End',datenum(ListFiles.datenum(ii)+seconds(50)),'Datenum');
tmp = gettsbetweenevents(LabView.merge,tse1,tse2);
if ~isempty(tmp.Data) % only do this if LabView data are not missing (because data logging was off).
% Cryo-holder set T (Sample holder temperature is in field ts.Data:1)
ListFiles.sampleTemp_dC(ii) = tmp.Data(1,1); % in �C (only get data in first row of tmp)
% Cell pressure
% (TODO: Pick correct Baratron read out: either field: ts.Data 4,8,and 9)
ListFiles.cellPressure_mbar(ii) = tmp.Data(1,4); % in mbar
% vapour pressure over ice:
if ListFiles.cellPressure_mbar(ii) >= 0
% Marti, J., and K. Mauersberger, Geophys. Res.Lett., 20, 363?366, 1993.
% gives parameterisation from 169 - 273K in Pa. (log10(p)= A1/T+B)
A_1 = -2663.5;
B_1 = 12.537;
ListFiles.iceTemp_dC(ii) = A_1/(log10(ListFiles.cellPressure_mbar(ii)*100)-B_1)-273.15;
else
ListFiles.iceTemp_dC(ii) = NaN;
end
if datenum(ListFiles.datenum(ii)) >= datenum('04-Mar-2019 13:30:00') % import additional data, logged after 03/2019
ListFiles.smplX_mm(ii) = tmp.Data(1,10);
ListFiles.smplY_mm(ii) = tmp.Data(1,11);
ListFiles.smplZ_mm(ii) = tmp.Data(1,12);
ListFiles.sealingTemp(ii) = tmp.Data(1,13);
else % if these sub-set of data is not logged, set to NaN
ListFiles.smplX_mm(ii) = NaN;
ListFiles.smplY_mm(ii) = NaN;
ListFiles.smplZ_mm(ii) = NaN;
ListFiles.sealingTemp(ii) = NaN;
end
else % if there are no LabView data stored, set all entries to NaN
ListFiles.sampleTemp_dC(ii) = NaN;
ListFiles.iceTemp_dC(ii) = NaN;
ListFiles.cellPressure_mbar(ii) = NaN;
ListFiles.smplX_mm(ii) = NaN;
ListFiles.smplY_mm(ii) = NaN;
ListFiles.smplZ_mm(ii) = NaN;
ListFiles.sealingTemp(ii) = NaN;
end
clearvars tmp
catch
warning('Problem merging LabView data into data table')
disp('Problem merging LabView data into data table')
%fprintf('Number %.0f: %s \n',ii,[ListFiles.folder(ii) filesep ListFiles.name(ii)])
%fprintf('Number %.0f: %s \n',ii,datestr(ListFiles.datenum(ii)))
end
end
disp('*************************************************')
disp('* Voila: Done writing LabView data! *')
disp('*************************************************')
end
%% Make table nicer
%
if ~iscell(ListFiles.spectrum_countsPerSecond)
ListFiles.spectrum_countsPerSecond = cell(size(ListFiles,1),1);
end
if ~iscell(ListFiles.spectrum_counts)
ListFiles.spectrum_counts = cell(size(ListFiles,1),1);
end
if ~iscell(ListFiles.xRayEkin_eV)
ListFiles.xRayEkin_eV = cell(size(ListFiles,1),1);
end
if ~iscell(ListFiles.scientaEkin_eV)
for ii = 1:size(ListFiles,1)
tmp{ii,:} = ListFiles.scientaEkin_eV(ii,:);
end
ListFiles.scientaEkin_eV = tmp;
end
% rename date fields and delete those fields not needed
[ListFiles.lastModifiedDatestr] = ListFiles.date;
[ListFiles.lastModifiedDatenum] = ListFiles.datenum;
ListFiles = removevars(ListFiles, {'date','datenum'});
% Copy Ekin Data
existColumn = strcmp('scientaEkinRoh_eV',ListFiles.Properties.VariableNames);
if any(existColumn)
ListFiles = removevars(ListFiles,'scientaEkinRoh_eV');
end
existColumn = strcmp('scientaEkinRoh_eV',ListFiles.Properties.VariableNames);
if ~any(existColumn)
% save current ekin data before they are modified
ListFiles.scientaEkinRoh_eV= ListFiles.scientaEkin_eV;
end
if ~iscell(ListFiles.scientaEkinRoh_eV)
for ii = 1:size(ListFiles,1)
tmp{ii,:} = ListFiles.scientaEkinRoh_eV(ii,:);
end
ListFiles.scientaEkinRoh_eV = tmp;
end
% work around for table variables with fitting results having the wrong
% size:
% first delete the old entries
existColumn = strcmp('peakPosition',ListFiles.Properties.VariableNames);
if any(existColumn)
ListFiles = removevars(ListFiles,'peakPosition');
end
existColumn = strcmp('peakArea',ListFiles.Properties.VariableNames);
if any(existColumn)
ListFiles = removevars(ListFiles,'peakArea');
end
existColumn = strcmp('peakFWHM',ListFiles.Properties.VariableNames);
if any(existColumn)
ListFiles = removevars(ListFiles,'peakFWHM');
end
% then re-create them with right size
% 11/22 change to 5 entries from 4.
existColumn = strcmp('peakPosition',ListFiles.Properties.VariableNames);
if ~any(existColumn)
% save current ekin data before they are modified
ListFiles.peakPosition= NaN(size(ListFiles,1),5);
end
existColumn = strcmp('peakArea',ListFiles.Properties.VariableNames);
if ~any(existColumn)
% save current ekin data before they are modified
ListFiles.peakArea= NaN(size(ListFiles,1),5);
end
existColumn = strcmp('peakFWHM',ListFiles.Properties.VariableNames);
if ~any(existColumn)
% save current ekin data before they are modified
ListFiles.peakFWHM= NaN(size(ListFiles,1),5);
end
existColumn = strcmp('sample',ListFiles.Properties.VariableNames);
if ~any(existColumn)
ListFiles.sample = cellstr(repmat(' ',size(ListFiles,1),1));
end
% add the imported data to previous list (if passed to function upon call)
if istable(p.Results.DataTable) % do this only if previous list was input to function call
% find table variables that are missing in ListFiles
existColumn = strcmp('sample',p.Results.DataTable.Properties.VariableNames);
if ~any(existColumn)
p.Results.DataTable.sample = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
end
tmpMissing = ~ismember(p.Results.DataTable.Properties.VariableNames,ListFiles.Properties.VariableNames);
% find all table variables that are cells
tmpCell = cellfun(@(x) iscell(p.Results.DataTable.(x)), p.Results.DataTable.Properties.VariableNames);
% find all table variables that are numbers
tmpNumber = cellfun(@(x) isnumeric(p.Results.DataTable.(x)), p.Results.DataTable.Properties.VariableNames);
% table variabes that hold cells and are missing
tmpCellVariables = p.Results.DataTable.Properties.VariableNames(tmpMissing & tmpCell);
% table variables that hold numbers and are missing
tmpNumberVariables = p.Results.DataTable.Properties.VariableNames(tmpMissing & tmpNumber);
% add empty table variables for missing cell and for number variables
if ~isempty(tmpCellVariables)
for i = 1: size(p.Results.DataTable(:,tmpMissing & tmpCell),2)
ListFiles = addvars(ListFiles,cell(size(ListFiles,1),1),'NewVariableNames',tmpCellVariables{i});
end
end
if ~isempty(tmpNumberVariables)
for i = 1: size(p.Results.DataTable(:,tmpMissing & tmpNumber),2)
ListFiles = addvars(ListFiles,nan(size(ListFiles,1),1),'NewVariableNames',tmpNumberVariables{i});
end
end
% % % sort the tables, if they have not the same order
% tmpCompareTables = cellfun(@isequal, ListFiles.Properties.VariableNames', p.Results.DataTable.Properties.VariableNames');
%
% if ~all(tmpCompareTables)
% indexDifferenzes = find(ismember(p.Results.DataTable.Properties.VariableNames',ListFiles.Properties.VariableNames(~tmpCompareTables)','rows'));
% nameListFiles =ListFiles.Properties.VariableNames(~tmpCompareTables);
%
% for ii = 1:size(indexDifferenzes,1)
% tmpIndx = find(ismember(p.Results.DataTable.Properties.VariableNames',nameListFiles{ii},'rows'));
% tmpPreviousVarName = p.Results.DataTable.Properties.VariableNames{tmpIndx-1};
% ListFiles = movevars(ListFiles,nameListFiles{ii},'After',tmpPreviousVarName);
% fprintf("%s comes after %s \n", nameListFiles{ii},tmpPreviousVarName)
% end
%
% end
% merge tables (append imported data to previous table)
ListFiles = [p.Results.DataTable; ListFiles];
% Then, we sort the table based on the time (datenum)
ListFiles = sortrows(ListFiles,'lastModifiedDatenum');
end
%% Export
ExportList = removevars(ListFiles, {'image', 'spectrum_counts', 'spectrum_countsPerSecond', 'scientaEkin_eV', 'beamlineInt', 'imageRoh', 'scientaEkinRoh_eV', 'xRayEkin_eV'});
% TODO check windows formatting
try
% write a ;-separated list for export to excel.
writetable(ExportList,fullfile(dataPath,[datestr(ExportList.lastModifiedDatenum(1),'mmmYYYY') '_DataList.csv']),'Delimiter',',');
if ispc
% and open in Excel; works only on Windows Machines
winopen(fullfile(dataPath,[datestr(ExportList.lastModifiedDatenum(1),'mmmYYYY') '_DataList.csv']));
end
catch
warning('Problem writing Excel File (*.csv). Make sure it is not open in Excel')
end
disp('*************************************************')
disp('* Voila: nappFileList.m finished ! *')
disp('*************************************************')
end
function LabView = LabView_importData(fullFileName,varargin)
%
% LabView_importData reads data log ASCII files stored by LabView into
% a Matlab time series.
%
% LabView = LabView_importData(A) imports file A
% and stores its content as time series in a structure called "LabView".
%
% LabView = LabView_importData(A,LabView) imports file A
% and appends its content as time series to the LabView structure.
%
%
% Example
% LabView = LabView_importData('exmpl.dat',LabView)
%
% Input
% * Napp_chamber_file: Complete and absolute path to the Napp chamber log file.
% * LabView: name of output structure. Always call this'LabView'
%
% Output
% * LabView: time series, the name starting with "ts"
% followed by date and time the recording started.
%
% See also LABVIEW_COMBINE, LABVIEW_PLOT, LABVIEW_CUTDATA
%
%% Data Structure
%
% Data structure before 4.3.2019
% col 1: Date
% col 2: Time
% col 3: Reservoir "Pressure 1" - Unit "1 water" - mbar -> ts.Data:2
% col 4: Reservoir "Pressure 2" - Unit "2 other" - mbar -> ts.Data:3
% col 5: Baratron 1 - cell - 1mbar max - mbar -> ts.Data:4
% col 6: Baratron 2 - cell - 10mbar max - mbar -> ts.Data:8
% col 7: Baratron 3 - cell - 0.05mbar max - mbar -> ts.Data:9
% col 8: Baratron 4 - - mbar
% col 9: Temp.Ice Sample - �C -> ts.Data:1
% col 10: Temp.Heated Sample
% col 11: none
% col 12: Temp. Reservoir "Cooler 1" - �C -> ts.Data:5
% col 13: Temp. Reservoir "Cooler 2" - �C -> ts.Data:6
% col 14: Flow He(cryoholder) - l/min -> ts.Data:7
% col 15: none
% col 16: none
%
% Data structure after 4.3.2019
% col 1: Date
% col 2: Time
% col 3: Reservoir "Pressure 1" - Unit "1 water" - mbar -> ts.Data:2
% col 4: Reservoir "Pressure 2" - Unit "2 other" - mbar -> ts.Data:3
% col 5: Baratron 1 - cell - 1mbar max - mbar -> ts.Data:4
% col 6: Baratron 2 - cell - 10mbar max - mbar -> ts.Data:8
% col 7: Baratron 3 - cell - 0.05mbar max - mbar -> ts.Data:9
% col 8: Baratron 4 - - mbar
% col 9: Temp.Ice Sample - �C -> ts.Data:1
% col 10: Temp.Heated Sample
% col 11: Temp. Reservoir "Cooler 1" - �C -> ts.Data:5
% col 12: Temp. Reservoir "Cooler 2" - �C -> ts.Data:6
% col 13: Flow He(cryoholder) - l/min -> ts.Data:7
% col 14: Flow gas 1
% col 15: Pressure chamber - mbar
% col 16: x-position of cryoholder - mm -> ts.Data:10
% col 17: y-position of cryoholder - mm -> ts.Data:11
% col 18: z-position of cryoholder - mm -> ts.Data:12
% col 19: nothing
% col 20: Temp.Sealing - �C -> ts.Data:13
%%
% Create an InputParser object
p = inputParser;
% Add inputs to the scheme.
defaultAppendToStructure = 0;
addRequired(p,'fullFileName',@isfile);
addOptional(p,'appendToStructure',defaultAppendToStructure,@isstruct);
% Parse the inputs.
parse(p,fullFileName,varargin{:})
%%
% get filedate
[~,name,~] = fileparts(p.Results.fullFileName);
tmp = strsplit(name,'_PC');
filedate = datenum(tmp{1},'yyyy-mm-dd_HH.MM.SS');
clearvars name tmp
%%
% parse structure to append to
if isstruct(p.Results.appendToStructure)
LabView = p.Results.appendToStructure;
end
%%
if datenum(filedate) <= datenum('04-Mar-2019 13:30:00')
fid = fopen(p.Results.fullFileName);
data = textscan(fid, ...
'%s %s %f %f %f %f %f %f %f %f %f %f %f %f %f %f',...
'HeaderLines',1); % data file has 2 text columns, followed by 14 numeric columns
fclose(fid);
% define time series
LabView.(['ts_' datestr(datenum([char(data{1}{1}), char(data{2}{1})],'dd.mm.yyyyHH:MM:SS'),'YYYYmmdd_HHMM')]) ...
= timeseries([data{9} data{3} data{4} data{5} data{12} ...
data{13} data{14} data{6} data{7}] , ...
datestr(datenum([char(data{1}), char(data{2})],...
'dd.mm.yyyyHH:MM:SS'),0));
LabView.(['ts_' datestr(datenum([char(data{1}{1}), char(data{2}{1})],'dd.mm.yyyyHH:MM:SS'),'YYYYmmdd_HHMM')]).Name ...
= 'Readout Napp Chamber raw signal';
clear fid ans formatOut nans t x
elseif datenum(filedate) >= datenum('15-Sep-2021 01:00:00') && datenum(filedate) <= datenum('01-Apr-2023 01:00:00')
% during this time, date and time were in american format.
fid = fopen(p.Results.fullFileName);
data = textscan(fid, ...
'%s %s %s %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f',...
'HeaderLines',1); %
fclose(fid);
% the date formating in the dat file is really messed up. Try to make
% it consitent with MATLAB. The problem is that MATLAB does not
% understand 1 digit month and hours.
%
%
% Split the date in column 1 into year,month,day
newDateSplit = cellfun(@(x) split(char(x),'/'),data{1},'UniformOutput', false);
% Split the time in column 2 into hours, minutes, seconds
newTimeSplit = cellfun(@(x) split(char(x),':'),data{2},'UniformOutput', false);
% combine both with the am/pm string in column 3 to a new datestring
customDateStr = cellfun(@(x,y,z) [datestr(datenum([str2double(x{3}),str2double(x{1}),str2double(x{2}),str2double(y{1}),str2double(y{2}),str2double(y{3})])), ' ', char(z)], newDateSplit,newTimeSplit,data{3}, 'uniformOutput',false) ;
% define time series
LabView.(['ts_' datestr(customDateStr{1},'YYYYmmdd_HHMM')]) ...
= timeseries([data{10} data{4} data{5} data{6} data{12} ...
data{13} data{14} data{7} data{8} data{17} data{18} data{19} data{21}], ...
customDateStr);
LabView.(['ts_' datestr(customDateStr{1},'YYYYmmdd_HHMM')]).Name ...
= 'Readout Napp Chamber raw signal';
clearvars fid ans formatOut nans t x new* custom*
elseif datenum(filedate) >= datenum('01-Apr-2023 02:00:00')
fid = fopen(p.Results.fullFileName);
data = textscan(fid, ...
'%s %s %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f',...
'HeaderLines',1);
% data file has 2 text columns, followed by 18 numeric columns (THE AM
% PM IS MISSING and some changes to the LabView file. Confirm with Luca....)
fclose(fid);
% define time series
LabView.(['ts_' datestr(datenum([char(data{1}{1}), char(data{2}{1})],'dd.mm.yyyyHH:MM:SS'),'YYYYmmdd_HHMM')]) ...
= timeseries([data{9} data{3} data{4} data{5} data{11} ...
data{12} data{20} data{6} data{7} data{15} data{16} data{17} data{19}] , ...
datestr(datenum([char(data{1}), char(data{2})],...
'dd.mm.yyyyHH:MM:SS'),0));
LabView.(['ts_' datestr(datenum([char(data{1}{1}), char(data{2}{1})],'dd.mm.yyyyHH:MM:SS'),'YYYYmmdd_HHMM')]).Name ...
= 'Readout Napp Chamber raw signal';
clear fid ans formatOut nans t x
else
fid = fopen(p.Results.fullFileName);
data = textscan(fid, ...
'%s %s %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f',...
'HeaderLines',1); % data file has 2 text columns, followed by 14 numeric columns
fclose(fid);
% define time series
LabView.(['ts_' datestr(datenum([char(data{1}{1}), char(data{2}{1})],'dd.mm.yyyyHH:MM:SS'),'YYYYmmdd_HHMM')]) ...
= timeseries([data{9} data{3} data{4} data{5} data{11} ...
data{12} data{13} data{6} data{7} data{16} data{17} data{18} data{20}] , ...
datestr(datenum([char(data{1}), char(data{2})],...
'dd.mm.yyyyHH:MM:SS'),0));
LabView.(['ts_' datestr(datenum([char(data{1}{1}), char(data{2}{1})],'dd.mm.yyyyHH:MM:SS'),'YYYYmmdd_HHMM')]).Name ...
= 'Readout Napp Chamber raw signal';
clear fid ans formatOut nans t x
end
end
function data_structure = LabView_combine(data_structure)
% LabView_combine can be used to merge time series into one.
%
% LabView = LabView_combine(LabView) merges all timeseries in the structure
% LabView into the new timeseries "merge"
% and adds this timeseries to the LabView structure
%
%
% Input
% * data_structure: name of the structure holding the time series
%
% Output
% * data_structure.merge: New time series combining all ts in this structure
%
% See also LABVIEW_IMPORTDATA, LABVIEW_PLOT
% delete previous merged data
if isfield(data_structure,'merge')
data_structure = rmfield(data_structure, 'merge');
end
% sort them chronologically
data_structure = orderfields(data_structure);
% query list of time series
list_ts = fieldnames(data_structure);
% and merge all of them into one time series
for ii = 1:length(list_ts)
if ii == 1
data_structure.merge = data_structure.(list_ts{1});
else
data_structure.merge = append(data_structure.merge,data_structure.(list_ts{ii}));
end
end
end
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