126 lines
6.1 KiB
Matlab
126 lines
6.1 KiB
Matlab
function DataTable = nappGenerateSpectra(DataTable,varargin)
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%nappGenerateSpectra reduces the dimension of images to generate spectra
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%
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% nappGenerateSpectra(FileList,tmpDataSelection)
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%
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% *input*
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% FileList: data table
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% tableSelection (optional): logical array to filter data table
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% tableVariable (optional): select source: image(default),'imageRoh'
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% mode: mean (default) averages the sequence iterations; sum adds them
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%
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% *output*
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% with mode mean the spectrum will be saved in the table variable spectrum_countsPerSecond
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% with mode sum the spectrum will be saved in the table variable spectrum_counts
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%
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% FIXME: spectrum_counts is not implemented yet.
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% Define conditions and defaults of input
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defaultTableVariable = 'image';
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expectedTableVariable = {'image','imageRoh'};
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defaultMode = 'mean';
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expectedMode = {'mean','sum','trapz'};
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defaultEkinStart = 0;
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defaultEkinEnd = 0;
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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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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,'iterationRange',[0:0]);
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addParameter(p,'eKinStart',defaultEkinStart,@isnumeric)
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addParameter(p,'eKinEnd',defaultEkinEnd,@isnumeric)
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parse(p,DataTable,varargin{:});
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% add empty variable to table
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existColumn = strcmp('spectrum_countsPerSecond',p.Results.DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.spectrum_countsPerSecond = cell(size(p.Results.DataTable,1),1);
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end
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existColumn = strcmp('spectrum_counts',p.Results.DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.spectrum_counts = cell(size(p.Results.DataTable,1),1);
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end
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existColumn = strcmp('logGenerateRange',p.Results.DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logGenerateRange = NaN(size(p.Results.DataTable,1),2);
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end
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existColumn = strcmp('logGenerateDate',p.Results.DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logGenerateDate = cellstr(repmat(' ',size(p.Results.DataTable,1),1));
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end
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existColumn = strcmp('logGenerateMode',p.Results.DataTable.Properties.VariableNames);
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if ~any(existColumn)
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DataTable.logGenerateDate = 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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% create empty variables
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tmp_3 = cell(size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
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tmp_6 = cell(size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
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tmp_4 = NaN(size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
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tmp_5 = NaN(size(p.Results.DataTable(p.Results.tableSelection,:),1),1);
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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},'h5') % let's do NEXAFS first.
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% Get index of EkinStart and EkinEnd
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if (p.Results.eKinStart) == 0
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tmp_1 = 1;
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else
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tmp_1 = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii} >= p.Results.eKinStart,1);
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end
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if (p.Results.eKinEnd) == 0
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tmp_2 = length(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii});
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else
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tmp_2 = find(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii} >= p.Results.eKinEnd,1);
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end
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if contains(p.Results.mode,'trapz')
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tmp_3(ii,1)= {trapz(p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(tmp_1:tmp_2),...
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p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(tmp_1:tmp_2,:))'};
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elseif (contains(p.Results.mode,'sum') | contains(p.Results.mode,'mean'))
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tmp_3(ii,1) = {sum(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(tmp_1:tmp_2,:),1)'}; %#ok<*AGROW>
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end
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% log
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tmp_4(ii,1) = p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(tmp_1);
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tmp_5(ii,1) = p.Results.DataTable(p.Results.tableSelection,:).scientaEkin_eV{ii}(tmp_2);
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elseif endsWith(p.Results.DataTable(p.Results.tableSelection,:).name{ii},'ibw') % then do Igorfiles
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if p.Results.iterationRange(1) == 0
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startRange = 1;
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endRange = size(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii},2);
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else
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startRange = p.Results.iterationRange(1);
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endRange = p.Results.iterationRange(2);
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end
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if (contains(p.Results.mode,'mean') | contains(p.Results.mode,'trapz'))
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tmp_6(ii,1)= {mean(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,startRange:endRange),2)};
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elseif contains(p.Results.mode,'sum')
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tmp_3(ii,1) = {sum(p.Results.DataTable(p.Results.tableSelection,:).(p.Results.tableVariable){ii}(:,startRange:endRange),2)}; %#ok<*AGROW>
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end
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% log
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tmp_4(ii,1) = startRange;
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tmp_5(ii,1) = endRange;
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end
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end
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% write results to table
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DataTable.spectrum_counts(p.Results.tableSelection) = tmp_3;
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DataTable.spectrum_countsPerSecond(p.Results.tableSelection) = tmp_6;
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% write log to table
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DataTable.logGenerateMode(p.Results.tableSelection,:) = cellstr(repmat(p.Results.mode,size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
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DataTable.logGenerateRange(p.Results.tableSelection,:) = [tmp_4 tmp_5];
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DataTable.logGenerateDate(p.Results.tableSelection,:) = cellstr(repmat(datestr(now),size(p.Results.DataTable(p.Results.tableSelection,:),1),1));
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end |