bartels-rausch
2ec52b7ee7
beamtime/nappFileList.m - Fix h5 LensMode: translate numeric codes to descriptive text (e.g. 1 -> T_HiPPHAXPES) to match what .ibw files already store, applied across all three h5read fallback branches, not just the oldest-format one beamtime/nappGenerateSpectra.m - Bug fixes beamtime/nappPlot.m - Bug fixes import/importData.m (new) - Ground script for one beamtime: import (nappFileList, nappGenerateSpectra), sample/spot and photon-energy assignment per row range, campaign metadata (CustomProperties) and column descriptions/units set inline, tidy-up, and export to .csv/.mat/.h5 (via nappExportH5). Leaves FileList in the workspace for PublishReport.m and callOpenbisSync.m to run against afterward. import/nappExportH5.m (new) - Export FileList + campaign metadata + raw source files to a self-contained HDF5 archive - Low-level HDF5 API (H5F/H5G/H5D/H5A/H5T/H5S/H5P) to fix H5FD_truncate/"too many open files" errors from the top-level h5create/h5write functions each reopening the file internally - Explicit rowIndex attribute per row group, since HDF5 group listing order isn't guaranteed to match table row order openBIS/ (new) - nappSyncToOpenbis.py, callOpenbisSync.m, testpybis.m, README.md - openBIS sync pipeline: create-or-update per row matched by $name, correct lowercase property codes, timestamp formatting, parent linking, raw file upload, plot/photo/video thumbnail embedding, config/engine split for maintainability -- see README.md for full details
913 lines
43 KiB
Matlab
913 lines
43 KiB
Matlab
function hdl = nappPlot(DataTable,varargin)
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%NAPPLOT Plot photoelectron spectra and NEXAFS images from a data table.
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% hdl = NAPPLOT(DataTable) creates figures for all rows in DataTable
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% using the default visualization options and returns the handle(s) to
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% the generated figure(s).
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%
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% hdl = NAPPLOT(DataTable, tableSelection) restricts plotting to rows for
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% which tableSelection is true. The length of tableSelection must
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% match the height of DataTable.
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%
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% hdl = NAPPLOT(DataTable, tableSelection, Name, Value) additionally
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% customizes the data source, energy axis, layout mode, and figure
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% formatting using Name-Value arguments.
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%
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% NAPPLOT is a general-purpose visualization routine for spectroscopy
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% experiments that can display:
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% - NEXAFS images (h5)
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% - time-resolved XPS/Auger maps (ibw)
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% - 1D spectra from previously generated table variables
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% - interactive NEXAFS + Auger-Meitner views
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%
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% Required input
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% --------------
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% DataTable
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% Table that contains spectroscopy data and metadata.
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% Depending on the chosen tableVariable and energyScale, the
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% following variables are typically used:
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% - name : file name (string/char), used to
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% distinguish '.h5', '.ibw', '.xy'
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% - image : processed 2D image (cell of numeric)
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% - imageRoh : raw 2D image (cell of numeric)
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% - spectrum_counts : 1D spectrum (in arbitrary counts
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% - spectrum_countsPerSecond
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% : 1D spectrum (normalized to counts per second)
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% - spectrum_countsNorm : 1D normalized spectrum
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% - scientaEkin_eV : kinetic energy axis (cell of numeric)
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% - bindingEnergy_eV : binding energy axis (cell of numeric)
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% - xRayEkin_eV : photon energy axis (cell of numeric)
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% - scientaEkinRange_eV : [emin emax] for plotting
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% - xRayEkinRange_eV : [emin emax] for plotting
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% - lastModifiedDatestr : acquisition or file time stamp
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% - sample : (optional) sample name for titles
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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 of DataTable to plot.
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% Default: all rows true
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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 variable in DataTable to plot.
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% Type : char or string
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% Values : 'image' (default)
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% 'imageRoh'
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% 'spectrum_countsPerSecond'
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% 'spectrum_counts'
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% 'spectrum_countsNorm'
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%
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% 'energyScale'
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% Energy axis used for plotting
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% Type : char or string
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% Values : 'kinetic' (default) - use scientaEkin_eV
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% 'binding' - use bindingEnergy_eV
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% 'xRay' - use xRayEkin_eV
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% 'sweeps' - use column/iteration index
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%
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% 'mode'
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% Layout and plotting mode
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% Type : char or string
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% Values : 'AllInOne' (default)
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% - Plot all selected 1D spectra in a single axes
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% (overlaid).
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% 'OneEach'
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% - One figure per single spectrum or image.
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% 'iterations'
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% - Plot multiple iterations from a 2D stack in different
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% colors to show time/sequence evolution.
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% 'AugerMeitner'
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% - Extract and plot Auger-Meitner spectra at specified
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% photon energies for NEXAFS maps ('.h5').
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% 'interactive'
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% - Interactive layout for NEXAFS images with linked
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% Auger-Meitner and NEXAFS line cuts controlled by
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% mouse / data cursor callbacks.
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%
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% 'figureMode'
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% Overall figure formatting, size, and font presets.
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% Type : char or string
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% Values : 'screen' (default)
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% - Standard display window in pixels, moderate fonts.
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% 'powerpoint'
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% - Larger window and fonts optimized for slides.
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% 'word'
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% - Compact figure in centimeters for documents.
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%
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% 'plotStep'
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% Step size in iteration index for 'iterations' mode.
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% Type : positive numeric scalar
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% Default: 1 (plot every iteration)
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%
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% 'AugerMeitnerEnergies'
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% Photon energies (in eV) for 'AugerMeitner' mode
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% At each value, the function extracts one column from the image and
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% plots the corresponding Auger-Meitner electron spectrum.
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% Type : numeric vector
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%
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% Output
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% ------
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% hdl
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% Handle or array of handles to the generated figure(s)
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% For 'AllInOne' this is a single figure. For 'OneEach',
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% 'iterations', 'AugerMeitner', and 'interactive', hdl may contain
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% one handle per processed row.
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%
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% Notes
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% -----
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% - The function checks that the chosen tableVariable is non-empty for
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% all selected rows and throws an error otherwise.
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% - File type is inferred from the 'name' variable to distinguish h5,
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% ibw, and xy-type data
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% - Axis labels, limits, and titles are adapted automatically based on
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% energyScale, tableVariable, and available metadata (sample name,
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% time stamp)
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% - In 'interactive' mode, datacursor and mouse motion callbacks update
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% linked line plots for Auger-Meitner and NEXAFS traces.
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%% TODO
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%
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% TODO: Add averaging in image and in iteration plot
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% TODO: Make code nicer (NEXAFS plotting)
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% Define conditions and defaults of input
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defaultTableVariable = 'image';
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expectedTableVariable = {'image','imageRoh','spectrum_countsPerSecond','spectrum_counts','spectrum_countsNorm'};
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defaultMode = 'AllInOne';
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expectedMode = {'AllInOne','OneEach','iterations','AugerMeitner','interactive'};
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defaultFigureMode = 'screen';
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expectedFigureMode = {'screen','powerpoint','word'};
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defaultEnergyScale = 'kinetic';
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expectedEnergyScale = {'kinetic','binding','xRay','sweeps'};
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defaultTableSelection = true(size(DataTable,1),1);
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defaultPlotStep = 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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addParameter(p,'tableVariable',defaultTableVariable,...
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@(x) any(validatestring(x,expectedTableVariable)));
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addParameter(p,'mode',defaultMode,...
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@(x) any(validatestring(x,expectedMode)));
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addParameter(p,'figureMode',defaultFigureMode,...
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@(x) any(validatestring(x,expectedFigureMode)));
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addParameter(p,'energyScale',defaultEnergyScale,...
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@(x) any(validatestring(x,expectedEnergyScale)));
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addParameter(p,'plotStep',defaultPlotStep);
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addParameter(p,'AugerMeitnerEnergies',@isnumeric)
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parse(p,DataTable,varargin{:});
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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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% make figure, with options for output.
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if contains(p.Results.figureMode ,'screen') % standard
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alw = get(groot,'DefaultAxesLineWidth');
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fsz = get(groot,'DefaultAxesFontSize');
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lw = 2; %get(groot,'DefaultLineLineWidth');
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fnt = get(groot,'DefaultAxesFontName');
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loc = 'northeastoutside';
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unt = 'pixels';
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pos = [20 100 800 500];
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elseif contains(p.Results.figureMode,'powerpoint')
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alw = 2;
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fsz = 26;
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lw = 4;
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fnt = 'Helvetica Neue';
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loc = 'northeastoutside';
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unt = 'pixels';
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pos = [300 200 1280 720];
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elseif contains(p.Results.figureMode,'word')
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alw = 0.75;
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fsz = 10;
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lw = 0.5;
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fnt = 'Helvetica Neue';
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loc = 'southoutside';
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unt = 'centimeters';
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pos = [8 10 8 10];
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end
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if matches(p.Results.mode,'AugerMeitner')
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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},'h5')
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hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
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if size(p.Results.AugerMeitnerEnergies) >= 7
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tmp_color = colormap(parula(size(p.Results.AugerMeitnerEnergies,2)));
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else
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tmp_color = colormap(lines(size(p.Results.AugerMeitnerEnergies,2)));
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end
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% Create axes
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hold(gca,'on');
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for ij = 1:size(p.Results.AugerMeitnerEnergies,2)
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% find x-ray energy in data
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tmpXrayEnergy = find(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii} >= p.Results.AugerMeitnerEnergies(ij),1);
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hplot= plot( p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}, ...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,tmpXrayEnergy));
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hplot.LineWidth = lw;
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hold on
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end
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xlabel('Auger-Meitner electron energy [eV]')
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hYLabel = ylabel('Counts per dwell time');
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legend(string(p.Results.AugerMeitnerEnergies))
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end
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end
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end
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if matches(p.Results.tableVariable,'image') && matches(p.Results.mode,'interactive')
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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},'h5') % let's do NEXAFS first.
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hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',[20 100 1000 800]);
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tld = tiledlayout(2,2);
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tld.TileSpacing = 'compact';
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tld.Padding = 'compact';
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% image
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ax1= nexttile;
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img_handle = image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',ax1,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
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xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
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hXLabel = xlabel('# Photon energy, column number');
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hYLabel = ylabel('# Auger energy, column number');
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box(gca,'on');
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set( gca, ...
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'FontName' , fnt,'FontSize' , fsz );
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set([hXLabel, hYLabel], ...
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'FontName' , fnt);
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set([hXLabel, hYLabel] , ...
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'FontSize' , fsz );
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set(gca, ...
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'Box' , 'off' , ...
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'TickDir' , 'out' , ...
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'TickLength' , [.02 .02] , ...
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'XMinorTick' , 'on' , ...
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'YMinorTick' , 'off' , ...
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'XGrid' , 'on' , ...
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'XColor' , [0 0 0], ...
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'YColor' , [0 0 0], ...
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'LineWidth' , alw );
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hdl.Pointer = 'crosshair';
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ij= 1;
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ik=1;
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% Auger-Meitner
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ax2 = nexttile;
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hplot= plot(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,ij), p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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hplot.LineWidth = lw;
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hold on
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ylabel('A-M e energy [eV]')
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xlabel('Counts per dwell time');
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ax2.YDir = 'reverse';
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box(ax2,'on');
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set( ax2, ...
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'FontName' , fnt,'FontSize' , fsz );
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set([hXLabel, hYLabel], ...
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'FontName' , fnt);
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set([hXLabel, hYLabel] , ...
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'FontSize' , fsz );
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set(ax2, ...
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'Box' , 'off' , ...
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'TickDir' , 'out' , ...
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'TickLength' , [.02 .02] , ...
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'XMinorTick' , 'on' , ...
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'YMinorTick' , 'off' , ...
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'XGrid' , 'on' , ...
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'XColor' , [0 0 0], ...
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'YColor' , [0 0 0], ...
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'LineWidth' , alw );
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% NEXAFS
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ax3 = nexttile;
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hplot2= plot( p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}, ...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(ik,:));
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hplot2.LineWidth = lw;
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hold on
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xlabel('xray energy [eV]')
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hYLabel = ylabel('Counts per dwell time');
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box(ax3,'on');
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set( ax3, ...
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'FontName' , fnt,'FontSize' , fsz );
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set([hXLabel, hYLabel], ...
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'FontName' , fnt);
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set([hXLabel, hYLabel] , ...
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'FontSize' , fsz );
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set(ax3, ...
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'Box' , 'off' , ...
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'TickDir' , 'out' , ...
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'TickLength' , [.02 .02] , ...
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'XMinorTick' , 'on' , ...
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'YMinorTick' , 'off' , ...
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'XGrid' , 'on' , ...
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'XColor' , [0 0 0], ...
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'YColor' , [0 0 0], ...
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'LineWidth' , alw );
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if ~matches(p.Results.figureMode,'word')
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title(tld,p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
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end
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% % NOW set up datacursor - after all axes are created
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dcm = datacursormode(hdl);
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set(dcm, 'UpdateFcn', {@updatePlots, p.Results, ii, ax2, ax3, hplot, hplot2});
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set(dcm, 'Enable', 'on');
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set(dcm, 'SnapToDataVertex', 'off'); % Allows smooth mouse tracking
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set(dcm, 'DisplayStyle', 'window'); % or 'datatip' for tooltip style
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% Enable continuous update on mouse move
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set(hdl, 'WindowButtonMotionFcn', {@mouseMoveFcn, dcm, p.Results, ii, ax2, ax3, hplot, hplot2, ax1});
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end
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end
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end
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if matches(p.Results.tableVariable,'image') && ~matches(p.Results.mode,'AugerMeitner') && ~matches(p.Results.mode,'interactive')
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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},'h5') % let's do NEXAFS first.
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hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
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% Create axes
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hold(gca,'on');
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if matches(p.Results.energyScale,'sweep')
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image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
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xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
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hXLabel = xlabel('# Photon energy, column number');
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hYLabel = ylabel('# Auger energy, column number');
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else
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% Try to plot image with x and y
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try
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% interpolate, to have equal x spacing for image plot
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Xq = p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1):0.1:p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end);
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Vq = interp2(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},Xq,p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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image(Xq,p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
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Vq,'Parent',gca,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)]);
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ylim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,2)]);
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hXLabel = xlabel('Photon energy [eV]');
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hYLabel = ylabel('Auger energy [eV]');
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% if this does not work, plot without scaling (just with row and column numbers)
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catch
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image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
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axis(gca,'ij');
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set(gca,'Layer','top');
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ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
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xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
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hXLabel = xlabel('# Photon energy, column number');
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hYLabel = ylabel('# Auger energy, column number');
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end
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end
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box(gca,'on');
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if ~matches(p.Results.figureMode,'word')
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title(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Interpreter','none')
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end
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set( gca, ...
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'FontName' , fnt,'FontSize' , fsz );
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set([hXLabel, hYLabel], ...
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'FontName' , fnt);
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set([hXLabel, hYLabel] , ...
|
|
'FontSize' , 1.2*fsz );
|
|
|
|
set(gca, ...
|
|
'Box' , 'off' , ...
|
|
'TickDir' , 'out' , ...
|
|
'TickLength' , [.02 .02] , ...
|
|
'XMinorTick' , 'on' , ...
|
|
'YMinorTick' , 'off' , ...
|
|
'XGrid' , 'on' , ...
|
|
'XColor' , [0 0 0], ...
|
|
'YColor' , [0 0 0], ...
|
|
'LineWidth' , alw );
|
|
elseif endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')
|
|
|
|
if contains(p.Results.energyScale,'kinetic')
|
|
hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
|
|
|
|
% Create axes
|
|
hold(gca,'on');
|
|
image(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
|
|
1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
|
|
'Parent',gca,'CDataMapping','scaled');
|
|
axis(gca,'ij');
|
|
set(gca,'Layer','top');
|
|
if size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2) >= 2
|
|
ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
|
|
end
|
|
xlim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(end)]);
|
|
hXLabel = xlabel('Electron energy [eV]');
|
|
hYLabel = ylabel('Sequence iteration');
|
|
elseif contains(p.Results.energyScale,'binding')
|
|
hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
|
|
|
|
% Create axes
|
|
hold(gca,'on');
|
|
image(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},...
|
|
1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
|
|
'Parent',gca,'CDataMapping','scaled');
|
|
axis(gca,'ij');
|
|
set(gca,'Layer','top');
|
|
ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
|
|
% xlim([p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV(ii,2)]);
|
|
hXLabel = xlabel('Binding energy [eV]');
|
|
hYLabel = ylabel('Sequence iteration');
|
|
end
|
|
box(gca,'on');
|
|
existColumn = strcmp('sample',p.Results.DataTable.Properties.VariableNames);
|
|
if ~matches(p.Results.figureMode,'word')
|
|
if ~any(existColumn)
|
|
title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}],'Interpreter','none')
|
|
else
|
|
title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).sample{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}] ,'Interpreter','none')
|
|
end
|
|
end
|
|
set( gca, ...
|
|
'FontName' , fnt,'FontSize' , fsz );
|
|
set([hXLabel, hYLabel], ...
|
|
'FontName' , fnt);
|
|
set([hXLabel, hYLabel] , ...
|
|
'FontSize' , 1.2*fsz );
|
|
|
|
set(gca, ...
|
|
'Box' , 'off' , ...
|
|
'TickDir' , 'out' , ...
|
|
'TickLength' , [.02 .02] , ...
|
|
'XMinorTick' , 'on' , ...
|
|
'YMinorTick' , 'off' , ...
|
|
'XGrid' , 'on' , ...
|
|
'XColor' , [0 0 0], ...
|
|
'YColor' , [0 0 0], ...
|
|
'LineWidth' , alw );
|
|
end
|
|
end
|
|
end
|
|
if matches(p.Results.tableVariable,'imageRoh')
|
|
for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
|
|
if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5') % let's do NEXAFS first.
|
|
hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
|
|
|
|
% Create axes
|
|
hold(gca,'on');
|
|
% Try to plot image with x and y
|
|
try
|
|
image(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
|
|
axis(gca,'ij');
|
|
set(gca,'Layer','top');
|
|
xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii}(end)]);
|
|
ylim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,2)]);
|
|
hXLabel = xlabel('Photon energy [eV]');
|
|
hYLabel = ylabel('Auger energy [eV]');
|
|
% if this does not work, plot without scaling (just with row and column numbers)
|
|
catch
|
|
image(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},'Parent',gca,'CDataMapping','scaled');
|
|
axis(gca,'ij');
|
|
set(gca,'Layer','top');
|
|
ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},1)]);
|
|
xlim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
|
|
hXLabel = xlabel('# Photon energy, column number');
|
|
hYLabel = ylabel('# Auger energy, column number');
|
|
end
|
|
|
|
box(gca,'on');
|
|
set( gca, ...
|
|
'FontName' , fnt,'FontSize' , fsz );
|
|
set([hXLabel, hYLabel], ...
|
|
'FontName' , fnt);
|
|
set([hXLabel, hYLabel] , ...
|
|
'FontSize' , 1.2*fsz );
|
|
|
|
set(gca, ...
|
|
'Box' , 'off' , ...
|
|
'TickDir' , 'out' , ...
|
|
'TickLength' , [.02 .02] , ...
|
|
'XMinorTick' , 'on' , ...
|
|
'YMinorTick' , 'off' , ...
|
|
'XGrid' , 'on' , ...
|
|
'XColor' , [0 0 0], ...
|
|
'YColor' , [0 0 0], ...
|
|
'LineWidth' , alw );
|
|
elseif endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')
|
|
|
|
if contains(p.Results.energyScale,'kinetic')
|
|
hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
|
|
|
|
% Create axes
|
|
hold(gca,'on');
|
|
existColumn = strcmp('scientaEkinRoh_eV',DataTable.Properties.VariableNames);
|
|
if any(existColumn)
|
|
image(p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRoh_eV{ii},...
|
|
1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
|
|
'Parent',gca,'CDataMapping','scaled');
|
|
xlim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRoh_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRoh_eV{ii}(end)]);
|
|
|
|
else
|
|
image(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
|
|
1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
|
|
'Parent',gca,'CDataMapping','scaled');
|
|
xlim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(end)]);
|
|
|
|
end
|
|
axis(gca,'ij');
|
|
set(gca,'Layer','top');
|
|
ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
|
|
hXLabel = xlabel('Electron energy [eV]');
|
|
hYLabel = ylabel('Sequence iteration');
|
|
elseif contains(p.Results.energyScale,'binding')
|
|
hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
|
|
|
|
% Create axes
|
|
hold(gca,'on');
|
|
image(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},...
|
|
1:length(1:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)),...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}',...
|
|
'Parent',gca,'CDataMapping','scaled');
|
|
axis(gca,'ij');
|
|
set(gca,'Layer','top');
|
|
ylim([1 size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)]);
|
|
% xlim([p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV(ii,2)]);
|
|
hXLabel = xlabel('Binding energy [eV]');
|
|
hYLabel = ylabel('Sequence iteration');
|
|
|
|
end
|
|
box(gca,'on');
|
|
|
|
existColumn = strcmp('sample',p.Results.DataTable.Properties.VariableNames);
|
|
if ~matches(p.Results.figureMode,'word')
|
|
if ~any(existColumn)
|
|
title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}],'Interpreter','none')
|
|
else
|
|
title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).sample{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}] ,'Interpreter','none')
|
|
end
|
|
end
|
|
set( gca, ...
|
|
'FontName' , fnt,'FontSize' , fsz );
|
|
set([hXLabel, hYLabel], ...
|
|
'FontName' , fnt);
|
|
set([hXLabel, hYLabel] , ...
|
|
'FontSize' , 1.2*fsz );
|
|
|
|
set(gca, ...
|
|
'Box' , 'off' , ...
|
|
'TickDir' , 'out' , ...
|
|
'TickLength' , [.02 .02] , ...
|
|
'XMinorTick' , 'on' , ...
|
|
'YMinorTick' , 'off' , ...
|
|
'XGrid' , 'on' , ...
|
|
'XColor' , [0 0 0], ...
|
|
'YColor' , [0 0 0], ...
|
|
'LineWidth' , alw );
|
|
end
|
|
end
|
|
end
|
|
|
|
|
|
if contains(p.Results.tableVariable,'spectrum')
|
|
if contains(p.Results.mode,'OneEach')
|
|
for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
|
|
hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
|
|
|
|
% Create axes
|
|
hold(gca,'on');
|
|
if (contains(p.Results.energyScale,'kinetic') && (endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')))
|
|
hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}');
|
|
hplot.LineWidth = lw;
|
|
hXLabel = xlabel('Electron kinetic energy [eV]');
|
|
xlim([p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).scientaEkinRange_eV(ii,2)]);
|
|
|
|
elseif (contains(p.Results.energyScale,'binding') && (endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw')|| endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')))
|
|
hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}');
|
|
hplot.LineWidth = lw;
|
|
hXLabel= xlabel('Binding energy [eV]');
|
|
xlim([min(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii}) max(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii})]);
|
|
|
|
elseif (contains(p.Results.energyScale,'xRay') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5'))
|
|
hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii});
|
|
hplot.LineWidth = lw;
|
|
hXLabel = xlabel('Photon Energy eV');
|
|
try
|
|
xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkinRange_eV(ii,1) p.Results.DataTable(p.Results.tableSelection,:).xRayEkinRange_eV(ii,2)]);
|
|
catch
|
|
xlim([p.Results.DataTable(p.Results.tableSelection,:).xRayEkinRange_eV(ii,2) p.Results.DataTable(p.Results.tableSelection,:).xRayEkinRange_eV(ii,1)]);
|
|
end
|
|
end
|
|
if contains(p.Results.tableVariable,'Norm')
|
|
hYLabel = ylabel('Counts [arb. unit]');
|
|
elseif contains(p.Results.energyScale,'xRay')
|
|
hYLabel = ylabel('partial A-M.E.Y.');
|
|
else
|
|
hYLabel = ylabel('Counts per second');
|
|
end
|
|
|
|
|
|
box(gca,'on');
|
|
existColumn = strcmp('sample',p.Results.DataTable.Properties.VariableNames);
|
|
if ~matches(p.Results.figureMode,'word')
|
|
if ~any(existColumn)
|
|
title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}],'Interpreter','none')
|
|
else
|
|
try
|
|
title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).sample{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}] ,'Interpreter','none')
|
|
catch
|
|
title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).sample{ii}}] ,'Interpreter','none')
|
|
end
|
|
end
|
|
end
|
|
|
|
set( gca, ...
|
|
'FontName' , fnt,'FontSize' , fsz );
|
|
set([hXLabel, hYLabel], ...
|
|
'FontName' , fnt);
|
|
set([hXLabel, hYLabel] , ...
|
|
'FontSize' , 1.2*fsz );
|
|
|
|
set(gca, ...
|
|
'Box' , 'off' , ...
|
|
'TickDir' , 'out' , ...
|
|
'TickLength' , [.02 .02] , ...
|
|
'XMinorTick' , 'on' , ...
|
|
'YMinorTick' , 'off' , ...
|
|
'XGrid' , 'on' , ...
|
|
'XColor' , [0 0 0], ...
|
|
'YColor' , [0 0 0], ...
|
|
'LineWidth' , alw );
|
|
|
|
end
|
|
end
|
|
|
|
if contains(p.Results.mode,'AllInOne')
|
|
% generate colormap
|
|
|
|
hdl = figure('Name','AllInOneSpectrum','units', unt,'Position',pos);
|
|
if size(p.Results.DataTable(p.Results.tableSelection,:),1) >= 7
|
|
tmp_color = colormap(parula(size(p.Results.DataTable(p.Results.tableSelection,:),1)));
|
|
else
|
|
tmp_color = colormap(lines(size(p.Results.DataTable(p.Results.tableSelection,:),1)));
|
|
end
|
|
if contains(p.Results.energyScale,'kinetic')
|
|
% axes('Parent',gcf,'XDir','reverse')
|
|
hold(gca,'on');
|
|
for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
|
|
if (endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy'))
|
|
hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii},...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}','DisplayName',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Color',tmp_color(ii,:));
|
|
hplot.LineWidth = lw;
|
|
end
|
|
end
|
|
hXLabel = xlabel('Electron kinetic energy [eV]');
|
|
elseif contains(p.Results.energyScale,'binding')
|
|
axes('Parent',gcf,'XDir','reverse')
|
|
hold(gca,'on');
|
|
|
|
for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
|
|
if (endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy'))
|
|
hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii},...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}','DisplayName',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Color',tmp_color(ii,:));
|
|
hplot.LineWidth = lw;
|
|
end
|
|
end
|
|
hXLabel= xlabel('Binding energy [eV]');
|
|
elseif contains(p.Results.energyScale,'xRay')
|
|
hold(gca,'on');
|
|
for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
|
|
if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'h5')
|
|
hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).xRayEkin_eV{ii},...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},...
|
|
'DisplayName',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'Color',tmp_color(ii,:));
|
|
hplot.LineWidth = lw;
|
|
end
|
|
end
|
|
hXLabel = xlabel('Photon Energy eV');
|
|
end
|
|
if contains(p.Results.tableVariable,'Norm')
|
|
hYLabel = ylabel('Counts [arb. unit]');
|
|
elseif contains(p.Results.energyScale,'xRay')
|
|
hYLabel = ylabel('partial A-M.E.Y.');
|
|
else
|
|
hYLabel = ylabel('Counts per second');
|
|
end
|
|
|
|
|
|
box(gca,'on');
|
|
if ~matches(p.Results.figureMode,'word')
|
|
title('PE Spectra','Interpreter','none')
|
|
hlegend = legend(p.Results.DataTable(p.Results.tableSelection,:).name{:});
|
|
hlegend.FontSize = fsz;
|
|
hlegend.Interpreter = 'none';
|
|
hlegend.Location = loc;
|
|
set(legend, 'Interpreter','none')
|
|
end
|
|
set( gca, ...
|
|
'FontName' , fnt,'FontSize' , fsz );
|
|
set([hXLabel, hYLabel], ...
|
|
'FontName' , fnt);
|
|
set([hXLabel, hYLabel] , ...
|
|
'FontSize' , 1.2*fsz );
|
|
|
|
set(gca, ...
|
|
'Box' , 'off' , ...
|
|
'TickDir' , 'out' , ...
|
|
'TickLength' , [.02 .02] , ...
|
|
'XMinorTick' , 'on' , ...
|
|
'YMinorTick' , 'off' , ...
|
|
'XGrid' , 'on' , ...
|
|
'XColor' , [0 0 0], ...
|
|
'YColor' , [0 0 0], ...
|
|
'LineWidth' , alw );
|
|
|
|
|
|
|
|
end
|
|
|
|
|
|
end
|
|
if contains(p.Results.mode,'iterations')
|
|
% generate colormap
|
|
|
|
for ii = 1:size(p.Results.DataTable(p.Results.tableSelection,:),1)
|
|
if endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') || endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'xy')
|
|
|
|
hdl = figure('Name',p.Results.DataTable(p.Results.tableSelection,:).name{ii},'units', unt,'Position',pos);
|
|
if size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2) >= 7
|
|
tmp_color = colormap(parula(size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)));
|
|
else
|
|
tmp_color = colormap(lines(size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)));
|
|
end
|
|
|
|
% Create axes
|
|
hold(gca,'on');
|
|
|
|
if contains(p.Results.energyScale,'kinetic')
|
|
for ij = 1:p.Results.plotStep:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)
|
|
hplot= plot(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}',...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,ij),'Color',tmp_color(ij,:));
|
|
hplot.LineWidth = lw;
|
|
hold on
|
|
end
|
|
xlabel('Electron kinetic energy [eV]')
|
|
elseif contains(p.Results.energyScale,'binding')
|
|
%axes('Parent',gcf,'XDir','reverse')
|
|
|
|
for ij = 1:p.Results.plotStep:size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2)
|
|
hplot = plot(p.Results.DataTable(p.Results.tableSelection,:).bindingEnergy_eV{ii}',...
|
|
p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,ij),'Color',tmp_color(ii,:));
|
|
hplot.LineWidth = lw;
|
|
end
|
|
hXLabel = xlabel('Binding energy [eV]');
|
|
end
|
|
if contains(p.Results.tableVariable,'Norm')
|
|
hYLabel = ylabel('Counts [arb. unit]');
|
|
else
|
|
hYLabel = ylabel('Counts per second');
|
|
end
|
|
|
|
|
|
box(gca,'on');
|
|
if ~matches(p.Results.figureMode,'word')
|
|
title([{p.Results.DataTable(p.Results.tableSelection,:).name{ii} p.Results.DataTable(p.Results.tableSelection,:).sample{ii} p.Results.DataTable(p.Results.tableSelection,:).lastModifiedDatestr{ii}}] ,'Interpreter','none')
|
|
end
|
|
set( gca, ...
|
|
'FontName' , fnt,'FontSize' , fsz );
|
|
set([hXLabel, hYLabel], ...
|
|
'FontName' , fnt);
|
|
set([hXLabel, hYLabel] , ...
|
|
'FontSize' , 1.2*fsz );
|
|
|
|
set(gca, ...
|
|
'Box' , 'off' , ...
|
|
'TickDir' , 'out' , ...
|
|
'TickLength' , [.02 .02] , ...
|
|
'XMinorTick' , 'on' , ...
|
|
'YMinorTick' , 'off' , ...
|
|
'XGrid' , 'on' , ...
|
|
'XColor' , [0 0 0], ...
|
|
'YColor' , [0 0 0], ...
|
|
'LineWidth' , alw );
|
|
end
|
|
end
|
|
end
|
|
|
|
|
|
|
|
|
|
% Nested callback function
|
|
% function txt = updatePlots(~, event_obj, pResults, ii, ax2, ax3, hplot2, hplot3)
|
|
% pos = get(event_obj, 'Position');
|
|
% ij = round(pos(1));
|
|
% ik = round(pos(2));
|
|
%
|
|
% set(hplot2, 'XData', pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii}(:,ij));
|
|
% title(ax2, sprintf('Auger-Meitner (X index = %d)', ij));
|
|
%
|
|
% set(hplot3, 'YData', pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii}(ik,:));
|
|
% title(ax3, sprintf('NEXAFS (Y index = %d)', ik));
|
|
%
|
|
% % Create custom datatip text showing coordinates
|
|
% txt = {sprintf('X index: %d', ij), ...
|
|
% sprintf('Y index: %d', ik), ...
|
|
% sprintf('Intensity: %.2f', dataMatrix(ik, ij))};
|
|
% end
|
|
|
|
|
|
function mouseMoveFcn(~, ~, dcm, pResults, ii, ax2, ax3, hplot2, hplot3, ax1)
|
|
% Check if mouse is over the image axes
|
|
if gca == ax1
|
|
% Get current mouse position
|
|
cp = get(ax1, 'CurrentPoint');
|
|
ij = round(cp(1, 1)); % X index
|
|
ik = round(cp(1, 2)); % Y index
|
|
|
|
% Get the data matrix
|
|
dataMatrix = pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii};
|
|
|
|
% Ensure indices are within bounds
|
|
[nRows, nCols] = size(dataMatrix);
|
|
if ij >= 1 && ij <= nCols && ik >= 1 && ik <= nRows
|
|
% Update plots
|
|
set(hplot2, 'XData', dataMatrix(:, ij));
|
|
title(ax2, sprintf('Auger-Meitner (X index = %d)', ij));
|
|
|
|
set(hplot3, 'YData', dataMatrix(ik, :));
|
|
title(ax3, sprintf('NEXAFS (Y index = %d)', ik));
|
|
end
|
|
end
|
|
end
|
|
|
|
% Datatip callback - shows info
|
|
function txt = updatePlots(~, event_obj, pResults, ii, ax2, ax3, hplot2, hplot3)
|
|
try
|
|
pos = get(event_obj, 'Position');
|
|
ij = round(pos(1));
|
|
ik = round(pos(2));
|
|
|
|
dataMatrix = pResults.DataTable(pResults.tableSelection,:).(pResults.tableVariable){ii};
|
|
[nRows, nCols] = size(dataMatrix);
|
|
ij = max(1, min(ij, nCols));
|
|
ik = max(1, min(ik, nRows));
|
|
|
|
txt = {sprintf('X: %d', ij), ...
|
|
sprintf('Y: %d', ik), ...
|
|
sprintf('Intensity: %.2f', dataMatrix(ik, ij))};
|
|
catch
|
|
pos = get(event_obj, 'Position');
|
|
txt = {sprintf('X: %.1f', pos(1)), ...
|
|
sprintf('Y: %.1f', pos(2))};
|
|
end
|
|
end
|
|
end |