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SPLS_Toolbox_Dev_2022/dp_spls_standalone/PackagingLog.html

@@ -13,5 +13,5 @@
 Creating the install agent URL file...
 Web based installer created at /volume/DP_FEF/ScrFun/ScriptsRepository/SPLS_Toolbox_Dev_2022/dp_spls_standalone/for_redistribution/MyAppInstaller_web.install.
 Packaging complete.
-Elapsed packaging time was: 26 seconds.
+Elapsed packaging time was: 21 seconds.
 </pre></html>

SPLS_Toolbox_Dev_2022/dp_spls_standalone_Dev_2022.m

@@ -59,14 +59,6 @@ function dp_spls_standalone_Dev_2022(datafile)
 % LV can be stored in separate rows
 ff = 1;
 
-if ~isfield(input, 'data_collection')
-    try input.data_collection.Diag = input.Diag;
-        input.data_collection.sites = input.sites;
-    catch ME
-        disp('Please give information about diagnoses (input.Diag) and sites (input.sites)');
-    end
-end
-
 % check if a validation set is set up => extract it before starting the
 % analysis
 val_labels=[];
@@ -75,46 +67,46 @@ function dp_spls_standalone_Dev_2022(datafile)
         validation_folds = round(100/input.validation_set);
         switch input.val_stratification % take out validation set depending on 1) diagnosis, 2) sites, 3) both
             case 1
-                val_labels = input.data_collection.Diag;
+                val_labels = input.Diag;
             case 2
-                for i=1:size(input.data_collection.sites,1)
-                    val_labels(i,1) = find(input.data_collection.sites(i,:));
+                for i=1:size(input.sites,1)
+                    val_labels(i,1) = find(input.sites(i,:));
                 end
             case 3
-                for i=1:size(input.data_collection.sites,1)
-                    val_labels(i,1) = input.data_collection.Diag(i,1)*10 + find(input.data_collection.sites(i,:));
+                for i=1:size(input.sites,1)
+                    val_labels(i,1) = input.Diag(i,1)*10 + find(input.sites(i,:));
                 end
         end
         output.validation_indices = nk_CVpartition2(1, validation_folds, val_labels);
         analysis_set = sort(output.validation_indices.TrainInd{1,1});
         validation_set = sort(output.validation_indices.TestInd{1,1});
     else
-        analysis_set = ones(size(input.data_collection.Diag,1),1)>0;
+        analysis_set = ones(size(input.Diag,1),1)>0;
         validation_set = ~analysis_set;
     end
 
 else
-    analysis_set = ones(size(input.data_collection.Diag,1),1)>0;
+    analysis_set = ones(size(input.Diag,1),1)>0;
     validation_set = ~analysis_set;
 end
 
 X_val = X(validation_set,:);
 Y_val = Y(validation_set,:);
-Diag_val = input.data_collection.Diag(validation_set,:);
+Diag_val = input.Diag(validation_set,:);
 DiagNames_val = input.DiagNames(validation_set,:);
 sites_val = input.sites(validation_set,:);
 
 X_ana = X(analysis_set,:);
 Y_ana = Y(analysis_set,:);
-Diag_ana = input.data_collection.Diag(analysis_set,:);
+Diag_ana = input.Diag(analysis_set,:);
 DiagNames_ana = input.DiagNames(analysis_set,:);
 sites_ana = input.sites(analysis_set,:);
 
 try Covars_ana = input.covariates(analysis_set,:);
     Covars_val = input.covariates(validation_set,:);
 catch
-    Covars_ana = nan(size(input.data_collection.Diag(analysis_set,:),1),1);
-    Covars_val = nan(size(input.data_collection.Diag(validation_set,:),1),1);
+    Covars_ana = nan(size(input.Diag(analysis_set,:),1),1);
+    Covars_val = nan(size(input.Diag(validation_set,:),1),1);
 end
 
 if input.framework == 4
@@ -209,8 +201,8 @@ function dp_spls_standalone_Dev_2022(datafile)
     end
 
     if ~input.corrected_log(ff)
-        Covars_ana = nan(size(input.data_collection.Diag(analysis_set,:),1),1);
-        Covars_val = nan(size(input.data_collection.Diag(validation_set,:),1),1);
+        Covars_ana = nan(size(input.Diag(analysis_set,:),1),1);
+        Covars_val = nan(size(input.Diag(validation_set,:),1),1);
         correction_target = 3;
     end