Adding MATLAB scripts for SI and main figures

AaltoAtoms/MATLAB/Createc data import tools/BiasOffset.m

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+function [offset] = BiasOffset(options)
+
+arguments
+    options.file char = 'no'
+    options.path char = 'no'
+end
+
+%BIASOFFSET Check the bias offset of a VERT spectrum
+%   Call in a loop for several spectra
+%   Optional name-value pair inputs
+%       - file: VERT file name
+%       - path: path to said VERT file
+%   Output:
+%       - offset: the bias where the current crosses zero [mV]
+%
+%   NOTE: USE WITH METALS ONLY! Does not work with a gap at Fermi
+
+%% Import the data
+% Get a file and path in case it wasn't supplied
+if strcmp(options.file, 'no')
+    [file, path] = uigetfile('*.VERT',...
+        'Select the files to plot', ...
+        'Multiselect', 'off');
+else
+    file = options.file;
+    path = options.path;
+end
+
+% Exit in case no files were imported
+if isfloat(file)
+    disp('No file selected: exiting')
+    return;
+end
+
+% Get the correct data line
+A = regexp(fileread([path '\' file]),'\n','split');
+dataLine = find(contains(A,'DATA'), 1, 'last') + 2;
+
+[Bias, I, ~] = ImportVERTfile([path '\' file], [dataLine, inf]);
+
+%% Find the bias where current crosses zero
+
+% If the spectra have several directions, use only the forward direction
+[Bias, ia, ~] = unique(Bias, 'stable');
+I = I(ia);
+
+% Also, make sure the current vector is unique. Sometimes it is not.
+[I, ib, ~] = unique(I, 'stable');
+Bias = Bias(ib);
+
+% Interpolate to get the offset
+offset = interp1(I, Bias, 0);
+
+
+end
+

AaltoAtoms/MATLAB/Createc data import tools/CustomVERTImport.m

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+function [Data, header] = CustomVERTImport(options)
+    arguments
+        options.files = 'no';
+        options.path = 'no';
+        options.normalisation string = 'IMax';
+        options.direction string = 'all';
+        options.BiasUnit char = 'mV'
+        options.correctBiasOffset logical = true;
+    end
+
+%CUSTOMVERTIMPORT Imports all your Createc VERT files, however you like them
+%   Imports VERT Files (see import functions for details), applies
+%   normalisations.
+%   Inputs (name-value pairs):
+%       - files: the list of VERT files to be plotted. Default opens a file
+%      browser.
+%       - path: path to the folder containing the VERT files. Default opens
+%       a file browser.
+%       - normalisation: How to normalise the data
+%           - 'raw' (default): plotting raw data (with NaN values removed)
+%           - 'IMax': normalise all spectra with the current at the start
+%           of the spectrum.
+%           - 'StartNorm': normalise all spectra to the starting value
+%           - 'avg': normalise each spectra to it's mean
+%       - direction: which direction to take the spectra
+%           - 'all' (default): plot all points in the files
+%           - 'fwd': plot only the forward direction of bias sweeps
+%           - 'bwd': -||- backward direction
+%           - 'avg': averages the points in the forward and backward
+%           directions
+%       - BiasUnit: either 'mV' (default) or 'V' for volts
+%       - correctBiasOffset: apply a simple bias offset (default true)
+%   More optional inputs can be added as needed!
+%   Outputs:
+%       - h: handle to the generated figure
+%       - data: A struct with a bunch of stuff like Bias, I, dIdV etc.
+%       - header: Header of the first file to see what's what
+%
+% Adapted from PlotVERTFunction 3.9.2021
+% Example on how to call the function:
+%   >> % [Data, header] = CustomVERTImport('files', files, ...
+%           'path', path,...
+%           'direction', 'fwd',...
+%           'normalisation', 'avg');
+
+%% Import
+% Use the supplied path and files if able
+if strcmp(options.files, 'no')
+    [files, path] = uigetfile('*.VERT',...
+        'Select the files to plot', ...
+        'Multiselect', 'on');
+else
+    files = options.files;
+    path = options.path;
+end
+
+% Exit in case no files were imported
+if isfloat(files)
+    disp('No file selected: exiting')
+    return;
+end
+
+%% Initialize necessary parameters
+% Number of point spectra (NP). Also, read a VERT file to know what's what
+if ischar(files)
+    % One spectrum
+    NP = 1;
+
+    % Get the correct data line
+    A = regexp(fileread([path files]),'\n','split');
+    dataLine = find(contains(A,'DATA'), 1, 'last') + 2;
+
+    [Bias, ~, ~] = ImportVERTfile([path files], [dataLine, inf]);
+    header = ImportVERTHeader([path files]);
+
+    if options.correctBiasOffset
+        Bias = Bias - BiasOffset('file', files, 'path', path);
+    end
+else
+    % Several spectra
+    NP = length(files);
+
+    % Get the correct data line
+    A = regexp(fileread([path files{1}]),'\n','split');
+    dataLine = find(contains(A,'DATA'), 1, 'last') + 2;
+
+    [Bias, ~, ~] = ImportVERTfile([path files{1}], [dataLine, inf]);
+    header = ImportVERTHeader([path files{1}]);
+
+    % Line length from headers
+    Pos1 = [header.XPos_nm, header.YPos_nm];
+
+    Header2 = ImportVERTHeader([path files{end}]);
+    Pos2 = [Header2.XPos_nm, Header2.YPos_nm];
+
+    LineLength = norm(Pos2- Pos1);
+%         LineDist = linspace(0, LineLength, NP);
+    Line_nm = [0 LineLength];
+
+    if options.correctBiasOffset
+        Bias = Bias - BiasOffset('file', files{1}, 'path', path);
+    end
+end
+
+% Get rid of NaN values
+Bias = rmmissing(Bias);
+
+% Remove duplicate points from the beginning and end
+NSearch = 40;
+
+[~,iStart,~] = unique(Bias(1:NSearch), 'last');
+NEStart = iStart(end);
+
+[~,iEnd,~] = unique(Bias(end-NSearch+1:end), 'first');
+NEEnd = length(Bias) - NSearch + max(iEnd);
+
+% Indexing works without sorting
+BiasFilt = Bias(NEStart:NEEnd);
+
+% Number of energy points: one way, both ways, or average
+if strcmp(options.direction, 'all')
+    NE = length(BiasFilt);
+else
+    NE = length(unique(BiasFilt));
+end
+
+% Mid point initialisation: reverts to NEEnd if the spectrum only has one
+% direction
+NEMid = find(Bias == min(Bias), 1);
+
+% In case the starting bias is smaller than the end
+if NEMid == NEStart
+    NEMid = find(Bias == max(Bias) ,1);
+end
+
+% dIdV and I matrix initialisation
+dIdV = zeros(NE, NP);
+I = zeros(NE, NP);
+
+%% Extract the data
+for ii = 1:NP
+    % Filename initialisation based on NP
+    if NP ~= 1
+        filename = [path files{ii}];
+        VertGain = GetHeaderParam('VertManGain', 'files',files{ii}, 'path', path);
+    else
+        filename = [path files];
+        VertGain = header.VertManGain;
+    end
+
+    [~, I_cur, LIX] = ImportVERTfile(filename, [dataLine, inf]);
+
+    % Get rid of NaNs
+    LIX = rmmissing(LIX);
+    I_currm = rmmissing(I_cur);
+
+    % Fix the current with preamp gain value
+    % (Note that 'GainPreamplifier' is the scanning preamp gain)
+    if VertGain ~= 9
+        I_currm = I_currm.*10^(9 - VertGain);
+    end
+
+    %% Directions
+    % If the spectra are taken in one direction, things get simple
+
+    if length(BiasFilt) == length(unique(BiasFilt))
+%         disp('No backward direction: plotting forward direction instead')
+        dIdV(:,ii) = LIX(NEStart:NEEnd);
+        I(:,ii) = I_currm(NEStart:NEEnd);
+
+    else
+         % Take the backward and forward channels
+        LIXfw = LIX(NEStart:NEMid);
+        LIXbw = flipud(LIX(NEMid:NEEnd));
+
+        Ifw = I_currm(NEStart:NEMid);
+        Ibw = flipud(I_currm(NEMid:NEEnd));
+
+        switch options.direction
+            case 'all'
+                % won't work nicely with heat maps with several directions
+                dIdV(:,ii) = LIX(NEStart:NEEnd);
+                I(:,ii) = I_currm(NEStart:NEEnd);
+
+            case 'avg'
+                dIdV(:,ii) = (LIXfw + LIXbw)/2;.../mean(I_cur(1:NEStart));
+                I(:,ii) = (Ifw + Ibw)/2;
+
+            case 'fwd'
+                dIdV(:,ii) = LIXfw;
+                I(:,ii) = Ifw;
+
+            case 'bwd'
+                % If the spectra are only taken in one direction, take the
+                % forward direction instead
+
+                dIdV(:,ii) = LIXbw;
+                I(:,ii) = Ibw;
+
+        end
+    end
+
+    %% Normalisations
+    switch options.normalisation
+        case 'raw'
+            continue
+
+        case 'IMax'
+            dIdV(:,ii) = dIdV(:,ii)./I(1, ii);
+
+        case 'StartNorm'
+            dIdV(:,ii) = dIdV(:,ii)./dIdV(1, ii);
+
+        case 'avg'
+            dIdV(:,ii) = dIdV(:,ii)./mean(dIdV(:,ii));
+    end
+
+end
+
+%% Adjust the bias vector based on directions
+switch options.direction
+    case 'all'
+        % Default initialisation is good: no need to do anything
+    case 'bwd'
+        BiasFilt = flipud(Bias(NEMid:NEEnd));
+    otherwise
+        BiasFilt = Bias(NEStart:NEMid);
+end
+
+%% Bias unit
+if strcmp(options.BiasUnit, 'V')
+    BiasFilt = 1e-3.*BiasFilt;
+end
+
+%% Produce the data struct
+% Always available ones
+Data.files = files;
+Data.path = path;
+Data.dIdV = dIdV;
+Data.Bias = BiasFilt;
+Data.I = I;
+Data.NP = NP;
+Data.NE = NE;
+
+% Conditional ones
+if NP > 1
+    Data.LineLength = LineLength;
+else
+    Data.LineLength = [];
+end
+
+
+end
+

AaltoAtoms/MATLAB/Createc data import tools/GetHeaderParam.m

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+function [param] = GetHeaderParam(paramName, options)
+    arguments
+        paramName char
+        options.files = 'no'
+        options.path = 'no'
+    end
+
+%GETHEADERPARAM Returns the value(s) of a VERT file header parameter
+% Inputs:
+%   - paramName: char with the parameter name needed (see ImportVertHeader
+%   for the list of parameter names)
+%   - files: the files from which the header will be extracted. Default
+%   opens a file browser.
+%   - path: path of said files.
+% Output:
+%   - param: a vector of numerical parameter values
+%
+% FIXME: One path per function call: use loops to go through several paths
+% FIXME: Make param a struct or cell array to store multiple types of
+% header parameters.
+
+%% File names and path
+% Use the supplied path and files if able
+if strcmp(options.files, 'no')
+    [files, path] = uigetfile('*.VERT',...
+        'Select the files to plot', ...
+        'Multiselect', 'on');
+else
+    files = options.files;
+    path = options.path;
+end
+
+% Exit in case no files were imported
+if isfloat(files)
+    disp('No file selected: exiting')
+    return;
+end
+
+%% Do the header imports in a loop
+% Number of point spectra (NP)
+if ischar(files)
+    % One spectrum
+    NP = 1;
+else
+    % Several spectra
+    NP = length(files);
+end
+
+% FIXME: taking only numerical values for now
+param = zeros(1,NP);
+
+if NP == 1
+    header = ImportVERTHeader([path '/' files]);
+%     param = getfield(header, paramName);
+    param = header.(paramName);
+else
+    for ii = 1:NP
+        header = ImportVERTHeader([path '/' files{ii}]);
+        param(ii) = header.(paramName);
+    end
+end
+