Remove obsolete FileList.mat and nappScale.m. nappScale is replaced by nappNorm.m which does however not yet include the NEXAFS processing. WIP
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function DataTable = nappScale(DataTable,varargin)
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%NAPPSCALE Normalize XPS and NEXAFS spectra.
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% The peak of the same region or of a different region with identical
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% SES file number (same sequence iteration) can be used for XPS data.
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% NEXAFS spectra can be normed to their area or to the intensity
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% at an energy range of choice.
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%
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% For XPS ('.ibw') data, NAPPSCALE divides spectra of one region
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% (regionOld, default is C1s) by the fitted peak area taken from a
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% spectrum of the same sequence but different region (regionNew, default
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% is O1s). The same sequence iteration is identified by the SES file
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% number and acquisition time. For NEXAFS ('.h5') data, NAPPSCALE
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% normalizes spectra to the mean intensity or to the integrated area over
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% a chosen photon-energy interval.
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%
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% DataTable = NAPPSCALE(DataTable) normalizes spectra in the input table
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% using default options and returns the updated table with
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% normalized spectra in the variable spectrum_countsNorm.
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%
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% DataTable = NAPPSCALE(DataTable, tableSelection) restricts
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% normalization to rows where tableSelection is true. The length
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% of tableSelection must match the height of DataTable.
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%
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% DataTable = NAPPSCALE(DataTable, tableSelection, energyStart, energyEnd)
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% additionally specifies an energy interval used to normalize NEXAFS
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% spectra ('.h5' data)
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%
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% DataTable = NAPPSCALE(..., Name, Value) customizes the source variable,
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% normalization mode, line region mapping, and peak selection via
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% Name-Value arguments (see below):
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%
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%
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% Required input
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% --------------
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% DataTable
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% Table containing spectroscopy data and metadata.[web:2]
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% Depending on file type and options, the function uses:
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% - name : file name, used to distinguish 'ibw'
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% and 'h5' and to construct regionNew
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% file names (XPS)
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% - spectrum_counts : 1D spectrum (cell of numeric)
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% - spectrum_countsPerSecond
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% : 1D spectrum normalized to rate
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% - spectrum_countsNorm : (created/overwritten) normalized
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% spectrum
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% - peakArea : numeric vector of fitted peak areas
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% (XPS, one row per region)
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% - lastModifiedDatenum : datenum time stamp used to find the
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% matching regionNew spectrum
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% - xRayEkin_eV : photon energy axis (NEXAFS)
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%
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% Optional positional input
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% -------------------------
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% tableSelection
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% Logical vector selecting rows in DataTable to normalize.
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% Default: all rows true
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%
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% energyStart, energyEnd
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% Photon-energy limits (in eV) that define the normalization
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% interval for NEXAFS spectra ('.h5').
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% Type : numeric scalars
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% Use : required for 'intensity' or 'area' mode on '.h5' data.
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%
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% Name-Value arguments
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% --------------------
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% 'tableVariable'
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% Name of the spectral variable to be normalized.[web:10]
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% Type : char or string
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% Values : 'spectrum_countsPerSecond' (default)
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% 'spectrum_counts'
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% 'spectrum_countsNorm'
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%
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% 'regionOld'
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% XPS region name of the spectra to be normalized ('.ibw').
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% Used for file-name replacement when searching the reference
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% region
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% Type : char or string
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% Values : 'C1s' (default) | 'O1s' | 'N1s' | 'Cl2p'
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%
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% 'regionNew'
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% XPS region name that provides the reference peak area used for
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% normalization.
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% Type : char or string
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% Values : 'O1s' (default) | 'C1s' | 'N1s'
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%
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% 'peakNumber'
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% Index of the peak in the peakArea vector used as normalization
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% reference for XPS data.
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% Type : positive integer scalar
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% Default: 1
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%
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% 'mode'
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% Normalization mode.
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% Type : char or string
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% Values : 'area' (default)
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% 'intensity'
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%
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% Behaviour:
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% - For '.ibw' (XPS)
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% 'area' : divide selected spectra by the chosen peakArea
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% of the corresponding regionNew spectrum.
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% 'intensity' : currently not implemented (warning printed).
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% - For '.h5' (NEXAFS)
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% 'intensity' : divide spectra by the mean intensity over
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% [energyStart, energyEnd].
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% 'area' : divide spectra by the integrated area under
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% the curve over [energyStart, energyEnd]
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% (trapz).
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%
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% Output
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% ------
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% DataTable
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% Updated input table with normalized spectra and log variables.
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% The function ensures the following variables:
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%
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% spectrum_countsNorm
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% Cell array containing the normalized spectrum for each
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% processed row. Existing values are overwritten.
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%
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% logScaleRange
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% Numeric matrix with two columns. For '.h5' rows, stores the
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% [energyStart energyEnd] interval used for normalization.
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%
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% logScaleMode
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% Cell array of character vectors with the mode ('area' or
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% 'intensity') used for each normalized row.
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%
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% logScaleDate
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% Cell array of character vectors containing the time stamp of
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% the normalization (datestr(now)).
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%
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% Notes
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% -----
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% - All selected entries in the chosen tableVariable must contain
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% non-empty spectra; otherwise, the function throws an error.
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% - For XPS data, regionOld and the tableSelection filter must refer to
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% the same region; regionNew is found by name replacement and by
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% matching date and time to locate the correct reference spectrum.
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% - For NEXAFS data, the function supports both increasing and decreasing
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% photon-energy axes when locating the normalization interval.
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% Define conditions and defaults of input
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defaultTableVariable = 'spectrum_countsPerSecond';
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expectedTableVariable = {'spectrum_counts','spectrum_countsPerSecond','spectrum_countsNorm'};
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defaultMode = 'area';
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expectedMode = {'intensity','area'};
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defaultRegionOld = 'C1s';
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expectedRegionOld = {'O1s','C1s','N1s','Cl2p'};
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defaultRegionNew = 'O1s';
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expectedRegionNew = {'O1s','C1s','N1s'};
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defaultPeakNumber = 1;
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defaultTableSelection = true(size(DataTable,1));
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% Parse input
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p = inputParser;
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addRequired(p,'DataTable',@istable);
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addOptional(p,'tableSelection',defaultTableSelection,@islogical);
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addOptional(p,'energyStart',@isnumeric)
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addOptional(p,'energyEnd',@isnumeric)
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addParameter(p,'tableVariable',defaultTableVariable,...
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@(x) any(validatestring(x,expectedTableVariable)));
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addParameter(p,'regionOld',defaultRegionOld,...
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@(x) any(validatestring(x,expectedRegionOld)));
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addParameter(p,'regionNew',defaultRegionNew,...
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@(x) any(validatestring(x,expectedRegionNew)));
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addParameter(p,'peakNumber',defaultPeakNumber);
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addParameter(p,'mode',defaultMode,...
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@(x) any(validatestring(x,expectedMode)));
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parse(p,DataTable,varargin{:});
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% add empty variable to table
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existColumn = strcmp('spectrum_countsNorm',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.spectrum_countsNorm = cell(size(DataTable,1),1);
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end
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existColumn = strcmp('logScaleRange',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logBackgroundRange = NaN(size(DataTable,1),2);
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end
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existColumn = strcmp('logScaleMode',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logBackgroundMode = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
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end
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existColumn = strcmp('logScaleDate',DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logBackgroundDate = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
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end
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% check input (all elements of input variable need to have non-zero size)
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if ~all(cell2mat(cellfun(@size,p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable),'UniformOutput',false)),'all')
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disp('The table variable appears to be empty. I quit now')
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error('The table variable appears to be empty.')
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end
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% repeat this for all columns in input.
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for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
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if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')
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% get name and date of input file and replace old region with new
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% region. This will be the files where the peak area is taken from.
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tmpName = replace(p.Results.DataTable(p.Results.tableSelection,:).name{ii}, ...
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p.Results.regionOld,p.Results.regionNew);
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tmpDate = p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatenum(ii);
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% select spectra based on the new names and dates of original file
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tmpDataSelection = contains(p.Results.DataTable.name,tmpName)...
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& ismember(year(p.Results.DataTable.lastModifiedDatenum),year(tmpDate))...
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& ismember(month(p.Results.DataTable.lastModifiedDatenum),month(tmpDate))...
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& ismember(day(p.Results.DataTable.lastModifiedDatenum),day(tmpDate))...
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& ismember(hour(p.Results.DataTable.lastModifiedDatenum),hour(tmpDate))...
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& ismember(minute(p.Results.DataTable.lastModifiedDatenum),minute(tmpDate));
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% check peak area
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existColumn = strcmp('peakArea',DataTable.Properties.VariableNames);
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if any(existColumn)
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if isnan(DataTable( tmpDataSelection,:).peakArea(p.Results.peakNumber))
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disp('The peak area appears to be empty. I quit now')
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disp(DataTable( tmpDataSelection,:).name{ii})
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error('The peak area appears to be empty.')
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end
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else
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disp('The data table appear to have not peak area column. I quit now')
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error('No peak area column')
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end
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% do the norming
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if contains(p.Results.mode,'area')
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DataTable(p.Results.tableSelection,:).spectrum_countsNorm{ii} = ...
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DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}...
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./ DataTable( tmpDataSelection,:).peakArea(p.Results.peakNumber);
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elseif contains(p.Results.mode,'intensity')
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disp('Intensity mode not yet programmed for XPS data')
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end
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elseif endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')
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% if ~exist(p.Results.energyStart) | ~exist(p.Results.energyEnd)
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% disp('The energy region used for normalisation appears to be empty. I quit now')
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% error('The energy region used to normalise appears to be empty.')
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% end
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if contains(p.Results.mode,'intensity')
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if p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1)...
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< p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)
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% prepare Data
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[xData, yData] = prepareCurveData(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}...
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, p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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% MEAN
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b_1 = find(xData >= p.Results.energyStart,1);
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b_2 = find(xData >= p.Results.energyEnd,1);
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b_mean = mean(yData(b_1:b_2));
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elseif p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1)...
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> p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)
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% prepare Data
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[xData, yData] = prepareCurveData( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}...
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, p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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% MEAN
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b_1 = find(xData <= p.Results.energyStart,1);
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b_2 = find(xData <= p.Results.energyEnd,1);
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b_mean = mean(yData(b_2:b_1));
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else
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disp('Warning: Issue with NEXAFS_col_scaling')
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end
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tmp_3(:,1) = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}...
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./b_mean;
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DataTable(p.Results.tableSelection,:).spectrum_countsNorm{ii} = tmp_3;
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clearvars tmp_3
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elseif contains(p.Results.mode,'area')
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if p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1)...
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< p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)
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% prepare Data
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[xData, yData] = prepareCurveData( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}...
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, p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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% Area
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b_1 = find(xData >= p.Results.energyStart,1);
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b_2 = find(xData >= p.Results.energyEnd,1);
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b_area = trapz(xData(b_1:b_2),yData(b_1:b_2));
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elseif p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1)...
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> p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)
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% prepare Data
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[xData, yData] = prepareCurveData( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}...
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, p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
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% MEAN
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b_1 = find(xData <= p.Results.energyStart,1);
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b_2 = find(xData <= p.Results.energyEnd,1);
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b_area = trapz(xData(b_2:b_1),yData(b_2:b_1));
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else
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disp('Warning: Issue with NEXAFS_col_scaling')
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end
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tmp_3(:,1) = p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}...
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./b_area;
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DataTable(p.Results.tableSelection,:).spectrum_countsNorm{ii} = tmp_3;
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clearvars tmp_3
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end
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end
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end
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% write log to table
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DataTable.logScaleMode(p.Results.tableSelection,:) = cellstr(repmat(p.Results.mode,size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
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if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')
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DataTable.logScaleRange(p.Results.tableSelection,:) = repmat([p.Results.energyStart p.Results.energyEnd],size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
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end
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DataTable.logScaleDate(p.Results.tableSelection,:) = cellstr(repmat(datestr(now),size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
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end
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