added pearl data loader

c0deta1ker · Oct 23, 2022 · 3308454 · 3308454
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diff --git a/ADRESSTools_Dionysus/PESTools_PCC/Examples/Example_006_Testing_FileLoaders.mlx b/ADRESSTools_Dionysus/PESTools_PCC/Examples/Example_006_Testing_FileLoaders.mlx
diff --git a/...xamples/Example_Data/010_Au4f_hv=578eV.h5 → ...les/Example_Data/010_XPS_Au4f_hv=578eV.h5 b/...xamples/Example_Data/010_Au4f_hv=578eV.h5 → ...les/Example_Data/010_XPS_Au4f_hv=578eV.h5
diff --git a/...Examples/Example_Data/010_AuEF_hv=1050.h5 → ...ples/Example_Data/010_XPS_AuEF_hv=1050.h5 b/...Examples/Example_Data/010_AuEF_hv=1050.h5 → ...ples/Example_Data/010_XPS_AuEF_hv=1050.h5
diff --git a/ADRESSTools_Dionysus/PESTools_PCC/Examples/Example_Data/PEARL_ManipulatorScan.h5 b/ADRESSTools_Dionysus/PESTools_PCC/Examples/Example_Data/PEARL_ManipulatorScan.h5
diff --git a/ADRESSTools_Dionysus/PESTools_PCC/Examples/Example_Data/PEARL_MultiRegionScan2022.h5 b/ADRESSTools_Dionysus/PESTools_PCC/Examples/Example_Data/PEARL_MultiRegionScan2022.h5
diff --git a/ADRESSTools_Dionysus/PESTools_PCC/Examples/Example_Data/PEARL_XPSSpectrum.h5 b/ADRESSTools_Dionysus/PESTools_PCC/Examples/Example_Data/PEARL_XPSSpectrum.h5
diff --git a/ADRESSTools_Dionysus/PESTools_PCC/F006 - data saveloaders/load_pearl_data.m b/ADRESSTools_Dionysus/PESTools_PCC/F006 - data saveloaders/load_pearl_data.m
@@ -0,0 +1,105 @@
+function pearlStr = load_pearl_data(FileName, PathName)
+% pearlStr = load_adress_data(FileName, PathName)
+%   This function loads in the HDF5 data files of ARPES data from 
+%   the ADRESS beamline at the SLS. The output is a MATLAB
+%   data-structure that yields all the data and information. This function 
+%   should be used to load in a single ADRESS data-file that is unprocessed
+%   or has been previously processed using PESTools. Last updated in
+%   October 2022, and includes electrostatic tilt extraction.
+%
+%   REQ. FUNCTIONS:
+%   -   [data, axes, note]  = ReaderHDF5(fname);
+%   -   [DataXC,OffsE]      = SumScanXC(Energy,Data,maxLagE[,WinE]);
+%
+%   IN:
+%   -   FileName:           char of the input .h5 or .mat file-name.
+%   -   PathName:           char of the input .h5 or .mat directory path.
+%   -   Reset:              if equal to 1, then reset all previous processing upon loading, otherwise leave alone.
+%
+%   OUT:
+%   pearlStr - MATLAB data structure containing all fields below;
+%	 .(FileName):        string of the current filename of the data file.
+%	 .(H5file):          string of the raw .H5 filename of the data file.
+%	 .(Type):            string "Eb(k)", "Eb(k,i)", "Eb(kx,ky)" or "Eb(kx,kz)".
+%	 .(meta.info):       [1xN] char array of scan information.
+%	 .(meta.ep):         scalar of the Pass energy.
+%	 .(raw_data):        2Data [nEnergy x nAngle] or 3Data [nEnergy x nAngle xnScan] data array.
+%	 .(raw_tht):         [1×nAngle] row vector of angles.
+% 	 .(raw_eb):          [nEnergyx1] column vector of energy.
+%	 .(deb):             scalar of the Analyser resolution.
+%	 .(hv):              scalar or [1×nScan] row vector (if Scan parameter for 3Data data).
+%	 .(dhv):             scalar of the Beamline resolution.
+%	 .(tltM):            scalar or [1×nScan] row vector (if Scan parameter for 3Data data).
+%	 .(thtM):            scalar of the manipular Theta angle.
+%	 .(Temp):            scalar of the sample temperature.
+
+%% Default parameters
+if nargin < 1; FileName = ''; end
+if nargin < 2; PathName = ''; end
+if isempty(FileName);   FileName = '';  end
+if isempty(PathName);   PathName = '';  end
+% - Display text
+disp('Loading PEARL data...')
+% - Verifying inputs are characters
+FileName = char(FileName);
+PathName = char(PathName);
+
+%% 1 - Loading and reading in the HDF5 data file
+% - If no filename if defined, load in an empty data structure
+if isempty(FileName); return;
+% - Verify that a .h5 file has been parsed and load the variables
+elseif string(FileName(end-2:end)) == ".h5"
+    %% 1.1 -- Extracting file information
+    FileInfo = dir(char(string(PathName) + string(FileName))); 
+    TimeStamp = string(FileInfo.date);
+    %% 1.2 -- Extracting all of the miscellaneous variables
+    pearlStr = struct();
+    full_h5_file_name = char(string(PathName) + string(FileName));
+    % (1) Finding all the HDF5 Group Names
+    Type = "Spectrum";
+    group_names = string({h5info(full_h5_file_name).Groups.Name});
+    if group_names(1) == '/__DATA_TYPES__'; group_names(1) = []; end
+    % -- Filing through each group and extracting all the data
+    for i = 1:length(group_names)
+        % Validity check on group name
+        % ---- Ensuring the group name does not include prefix '/'
+        group_name = group_names(i); group_name = char(group_name); group_name = group_name(2:end);
+        % ---- Removing all spaces from the group name
+        group_name = strrep(group_name," ","_");
+        % Extracting element names
+        element_names = string({h5info(full_h5_file_name, char(group_names(i)+"/")).Datasets.Name});
+        % --- Filing through each element in the group
+        for j = 1:length(element_names)
+            % Validity check on element name
+            element_name = element_names(j);
+            % ---- Extracting the PEARL dataset
+            pearlStr.(group_name).(element_name) = h5read(full_h5_file_name, char(group_names(i)+"/"+element_names(j)));
+        end
+    end
+    %% 1.3 -- Extracting all of the data variables - 'scan 1'
+    if contains(group_names, "/scan 1")
+        % For custom 'MultiRegionScan' files
+        Type = "MultiRegionScan";
+        group_names = string({h5info(full_h5_file_name, char("/scan 1")).Groups.Name});
+        % -- Filing through each group and extracting all the data
+        for i = 1:length(group_names)
+            % ---- Ensuring the group name does not include prefix '/'
+            group_name = group_names(i); group_name = char(group_name); group_name = group_name(9:end);
+            % Extracting element names
+            element_names = string({h5info(full_h5_file_name, char(group_names(i)+"/")).Datasets.Name});
+            % --- Filing through each element in the group
+            for j = 1:length(element_names)
+                pearlStr.scan_1.(group_name).(element_names(j)) = h5read(full_h5_file_name, char(group_names(i)+"/"+element_names(j)));
+            end
+        end
+    end
+
+%% 2 - Reading in the .mat data that has been processed before
+elseif string(FileName(end-3:end)) == ".mat"
+    arpes_data  = load(char(string(PathName) + string(FileName)));
+    pearlStr     = arpes_data.pearlStr;
+    if isstruct(pearlStr) && isfield(pearlStr, 'FileName')
+        pearlStr.FileName = FileName(1:end-4);
+    end
+end
+end
diff --git a/ADRESSTools_Dionysus/PESTools_PCC/F006 - data saveloaders/load_sis_data.m b/ADRESSTools_Dionysus/PESTools_PCC/F006 - data saveloaders/load_sis_data.m
@@ -44,7 +44,6 @@
     dataStr.H5path      = char(PathName);
     dataStr.H5file      = char(FileName);
     H5full              = char(string(PathName) + string(FileName));
-
     %% -- Extracting all of the data variables
     datav_new           = struct();
     datav_new.value     = h5read(H5full,'/Electron Analyzer/Image Data');