bartels-rausch
00d34110db
Both Scienta (.ibw) and SpecsLab (.xy) raw files capture multidimensional XPS data but use different terminology to structure it. Scienta uses "Region Iterations" and "Sequence Iterations". SpecsLab organizes data by "Groups" or "Regions" (different elemental energy sweeps), "Scans" (time-resolved repetitions), and "Curves". Scienta Region Iterations are automatically averaged to improve the signal-to-noise ratio, while Scienta Sequence Iterations and SpecsLab Scans are preserved to keep the time-resolved data. For SpecsLab files specifically, distinct Regions are split into separate table rows. Ultimately, the preserved time-resolved data is saved in the table's image variable as a 2D matrix ([Energy bins × Sequence iterations/Scans]). File type handling: Added .xy as a recognized XPS format. Currently, the script differentiates data types strictly by file extension (NEXAFS: .h5, XPS: .ibw and .xy). This extension-based differentiation needs to be improved in future updates. Metadata parsing: Implemented global header scanning for .xy files to correctly extract instrument parameters (Acquisition Mode, Lens Mode, Slit, Workfunction) located before the first region block. Timezone alignment: Added timestamp conversion for .xy files from UTC to local time (Europe/Zurich) to ensure synchronization with LabView logs. Region separation: Modified .xy parsing to append a _RegX suffix to filenames. This correctly splits single .xy files that contain multiple elements or energy sweeps into distinct table rows so they can be processed individually. Import efficiency: Added an originalFileName variable. The script now cross-references the input DataTable and skips files that have already been imported to reduce execution time on re-runs. Testing status: Processing of .xy data has currently only been tested and debugged with nappGenerateSpectra and nappPlot. Compatibility with other functions in the suite remains untested.
313 lines
14 KiB
Matlab
313 lines
14 KiB
Matlab
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 |