nappMATLAB-toolbox/import/QuickAndDirtyNexafsImport.m

function ListFiles = QuickAndDirtyNexafsImport(DataTable)



%% QuickAndDirtyNexafsImport
%
[filePick,pathPick] = uigetfile({'*.h5'},...
    'Select One or More Files',...
    'MultiSelect', 'on');
% make lists for Nexafs
if ischar(filePick)
    filePick = {filePick};
end

for ii = 1:size(filePick,2)
    TmpFileList{2}(ii,1) = dir([pathPick filePick{ii}]);
end


for ii = 1:size(filePick,2)
    try
        TmpImage= h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/spectrum');
        %else
    catch
        try
            TmpImage = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/scienta spectrum');
        catch
            TmpData = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/detector/data');
            %convert 3 dim matrix to 2 dim matrix
            for i = 1:size(TmpData,3)%iterations
                TmpImage(:,i) = TmpData(:,1,(i)); %#ok<*SAGROW>
            end



        end
    end
    % import Photon Energy (cols)
    try %general try to ensure that script does not stop upon errors.
        try
            TmpXrayEkin = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/energy'); % X-ray excitation energy; Photon energy in eV
            TmpXrayEkin(TmpXrayEkin==0)=[];
        catch
            TmpXrayEkin = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/PhotonEnergy'); % X-ray excitation energy; Photon energy in eV
            TmpXrayEkin(TmpXrayEkin==0)=[];
        end
        % Make unique
        [TmpFileList{2}(ii).xRayEkin_eV, ind] = unique(TmpXrayEkin);
        TmpFileList{2}(ii).image = TmpImage(:,ind);
        % NEXAFS pass energy
        try
            tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/PassEnergy'); % in eV
            TmpFileList{2}(ii).scientaPassEnergy_eV = str2double(tmp(1));
        catch
            tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/PassEnergy'); % in eV
            TmpFileList{2}(ii).scientaPassEnergy_eV = str2double(tmp(1));
        end
        % Acquisition mode
        try
            TmpFileList{2}(ii).scientaAcquisitionMode =  h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/AcquisitionMode');
        catch
            TmpFileList{2}(ii).scientaAcquisitionMode =  h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/AcquireMode');
        end
        if strcmp(TmpFileList{2}(ii).scientaAcquisitionMode,'Fixed')
            % NEXAFS kinetic energy window - fixed mode
            try
                tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/ScientaCenterEnergy'); % in eV
            catch
                tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/CenterEnergy'); % in eV
            end
            TmpFileList{2}(ii).scientaEkinRange_eV = [tmp(1)-TmpFileList{2}(ii).scientaPassEnergy_eV/20 tmp(1)+TmpFileList{2}(ii).scientaPassEnergy_eV/20];
            TmpFileList{2}(ii).scientaEkinStep_eV  = NaN;
            TmpFileList{2}(ii).scientaEkin_eV = linspace(TmpFileList{2}(ii).scientaEkinRange_eV(:,1)...
                ,TmpFileList{2}(ii).scientaEkinRange_eV(:,2),size(TmpFileList{2}(ii).image,1))';
        else
            % NEXAFS kinetic energy window - scan mode
            try
                tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/ScientaLowEnergy'); % in eV
                tmp2 = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/ScientaHighEnergy');
            catch
                tmp = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/LowEnergy'); % in eV
                tmp2 = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/HighEnergy');
            end
            TmpFileList{2}(ii).scientaEkinRange_eV = [tmp(1) tmp2(1)];
            try
                TmpFileList{2}(ii).scientaEkinStep_eV = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/scan 1/attrs/StepSize');
            catch
                TmpFileList{2}(ii).scientaEkinStep_eV = h5read([TmpFileList{2}(ii).folder filesep TmpFileList{2}(ii).name],'/entry/instrument/NDAttributes/StepSize');
            end
            TmpFileList{2}(ii).scientaEkin_eV = [TmpFileList{2}(ii).scientaEkinRange_eV(:,1):TmpFileList{2}(ii).scientaEkinStep_eV(1):TmpFileList{2}(ii).scientaEkinRange_eV(:,2)]';
        end
    catch
    end
end
%% Merge lists into one
%

% get index of non-empty structures
tf  =~cellfun(@isempty,TmpFileList);

% merge the non-empty list structures into one structure
ListFiles = cat(1,TmpFileList{tf});

% remove lines with empty images
for ii = 1:size(ListFiles,1)
    tmpLogic(ii) = isempty(ListFiles(ii).image);
    noncells    = tmpLogic;
end
ListFiles(noncells) = [];

clearvars -except ListFiles DataTable


%%



%% Sort by date
% rename date fields and delete those fields not needed
[ListFiles.lastModifiedDatestr] = ListFiles.date;
[ListFiles.lastModifiedDatenum] = ListFiles.datenum;

% First, we need to convert into a table, because structures can not be sorted:
ListFiles = struct2table(ListFiles,'AsArray',true);
% Then, we sort the table based on the time (6th column, datenum)
ListFiles = sortrows(ListFiles,6);
% Then, remove un-needed columns
ListFiles = removevars(ListFiles,{'bytes','isdir','date','datenum'});

% merge tables (append imported data to previous table)
if exist("DataTable",'var')
    ListFiles = outerjoinRowToTable(ListFiles,DataTable);
end
% Then, we sort the table based on the time (datenum)
ListFiles = sortrows(ListFiles,'lastModifiedDatenum');
end