One can now export code instead of running commands with Lead-DBS.

connectomics/ea_perform_lc.m

@@ -46,6 +46,8 @@ function ea_perform_lc(options)
 disp('*** Done.');
 
 %% functional parts
+
+
 disp('*** Performing functional parts of LEAD-Connectome...');
 
 if options.lc.func.compute_CM % create functional connectivity matrix

ea_export.m

@@ -0,0 +1,33 @@
+function ea_export(options)
+% This function exports jobs created by the GUI of Lead-DBS. It is
+% distributed within Lead-DBS toolbox (www.lead-dbs.org)
+% __________________________________________________________________________________
+% Copyright (C) 2016 Charite University Medicine Berlin, Movement Disorders Unit
+% Andreas Horn
+
+
+
+[fn,pth]=uiputfile('*.m','Specify location for new job file...','lead_job.m');
+if ~fn % user pressed cancel
+    return
+end
+exp=ea_gencode(options,'options');
+
+fID=fopen([pth,fn],'w');
+
+% export comments
+fprintf(fID,'%s\n',['% - Lead-DBS Job created on ',date,':']);
+fprintf(fID,'%s\n',['% --------------------------------------']);
+fprintf(fID,'\n');
+fprintf(fID,'\n');
+
+for e=1:length(exp)
+    fprintf(fID,'%s\n',exp{e});
+end
+fprintf(fID,'\n');
+fprintf(fID,'%s\n','% Execute job:');
+fprintf(fID,'%s\n','% ---------------------------------------');
+fprintf(fID,'\n');
+fprintf(fID,'%s\n',['ea_run(''run'',options);']);
+
+edit([pth,fn]);

ea_exportisovolume.m

@@ -51,16 +51,17 @@ function ea_exportisovolume(elstruct,options)
     nii{side}(:)=nan;
     XYZ=[X{side},Y{side},Z{side},ones(length(X{side}),1)]';
     XYZ=Vol.mat\XYZ; % to voxel space.
-    XYZ=round(XYZ(1:3,:)');
+    XYZ=(XYZ(1:3,:)');
     % repeat the above but in voxel space..
     clear bb
-    bb(1,:)=[min(XYZ(:,1)),max(XYZ(:,1))];
-    bb(2,:)=[min(XYZ(:,2)),max(XYZ(:,2))];
-    bb(3,:)=[min(XYZ(:,3)),max(XYZ(:,3))];
+            bb(1,:)=[round(min(XYZ(:,1))),round(max(XYZ(:,1)))];
+            bb(2,:)=[round(min(XYZ(:,2))),round(max(XYZ(:,2)))];
+            bb(3,:)=[round(min(XYZ(:,3))),round(max(XYZ(:,3)))];
     clear XI YI ZI
     [XI,YI,ZI]=meshgrid([bb(1,1):bb(1,2)],[bb(2,1):bb(2,2)],[bb(3,1):bb(3,2)]);
     warning('off')
-    F = scatteredInterpolant(XYZ(:,1),XYZ(:,2),XYZ(:,3),double(V{side}));
+
+    F = scatteredInterpolant(XYZ(:,1),XYZ(:,2),XYZ(:,3),double(V{side}),'natural');
     warning('on')
     F.ExtrapolationMethod='none';
 
@@ -131,19 +132,21 @@ function ea_exportisovolume(elstruct,options)
                     XYZ=[[X{1};-X{2}],[Y{1};Y{2}],[Z{1};Z{2}],ones(length([X{1};X{2}]),1)]';
             end
             XYZ=Vol.mat\XYZ; % to voxel space.
-            XYZ=round(XYZ(1:3,:)');
+            XYZ=(XYZ(1:3,:)');
             % repeat the above but in voxel space..
             clear bb
-            bb(1,:)=[min(XYZ(:,1)),max(XYZ(:,1))];
-            bb(2,:)=[min(XYZ(:,2)),max(XYZ(:,2))];
-            bb(3,:)=[min(XYZ(:,3)),max(XYZ(:,3))];
+            bb(1,:)=[round(min(XYZ(:,1))),round(max(XYZ(:,1)))];
+            bb(2,:)=[round(min(XYZ(:,2))),round(max(XYZ(:,2)))];
+            bb(3,:)=[round(min(XYZ(:,3))),round(max(XYZ(:,3)))];
             clear XI YI ZI
             [XI,YI,ZI]=meshgrid([bb(1,1):bb(1,2)],[bb(2,1):bb(2,2)],[bb(3,1):bb(3,2)]);
 
 
 
             warning('off');
-            F = scatteredInterpolant(XYZ(:,1),XYZ(:,2),XYZ(:,3),double([V{1};V{2}]));
+
+            F = scatteredInterpolant(XYZ(:,1),XYZ(:,2),XYZ(:,3),double([V{1};V{2}]),'natural');
+
 
             F.ExtrapolationMethod='none';
             warning('on');

ea_run.m

@@ -0,0 +1,97 @@
+function ea_run(cmd,options)
+% This function is the main execution function of Lead-DBS. It is
+% distributed within Lead-DBS toolbox (www.lead-dbs.org)
+% __________________________________________________________________________________
+% Copyright (C) 2016 Charite University Medicine Berlin, Movement Disorders Unit
+% Andreas Horn
+
+
+try
+    options.lc=load([fileparts(which('lead')),filesep,'connectomics',filesep,'lc_options.mat']);
+catch
+    options.lc=[];
+end
+
+if options.d3.autoserver && options.d3.write
+    choice = questdlg('Are you sure you want to export results to the server automatically?', ...
+        'Auto Server-Export', ...
+        'Cancel','Yes','Cancel');
+    % Handle response
+    switch choice
+        case 'Cancel'
+            return
+    end
+end
+
+clc
+uipatdirs=getappdata(gcf,'uipatdir');
+
+if isempty(uipatdirs)
+    uipatdirs={'No Patient Selected'};
+end
+
+prefs=ea_prefs('');
+if length(uipatdirs)>1 && ~isempty(which('parpool')) && prefs.pp.do % do parallel processing if available and set in ea_prefs.
+    try delete(gcp); end
+    pp=parpool(prefs.pp.profile,prefs.pp.csize);
+
+    for pat=1:length(uipatdirs)
+        % set patient specific options
+        opts{pat}=options;
+        opts{pat}.root=[fileparts(uipatdirs{pat}),filesep];
+        [~,thispatdir]=fileparts(uipatdirs{pat});
+        opts{pat}.patientname=thispatdir;
+    end
+
+    parfor pat=1:length(uipatdirs)
+
+        % run main function
+        try
+            switch cmd
+                case 'run'
+                    ea_autocoord(opts{pat});
+                case 'export'
+                    ea_error('Exporting code not optimized for parallel processing as of yet. Please turn off parallel processing in ea_prefs.m');
+            end
+        catch
+            warning([opts{pat}.patientname,' failed. Please run this patient again and adjust parameters. Moving on to next patient.' ]);
+        end
+
+    end
+    delete(pp);
+
+else
+
+    for pat=1:length(uipatdirs)
+        % set patient specific options
+        options.root=[fileparts(uipatdirs{pat}),filesep];
+        [root,thispatdir]=fileparts(uipatdirs{pat});
+        options.patientname=thispatdir;
+        % run main function
+
+        if length(uipatdirs)>1 % multi mode. Dont stop at errors.
+            try
+                switch cmd
+                    case 'run'
+                        ea_autocoord(options);
+                    case 'export'
+                        ea_export(options);
+                end
+            catch
+                warning([options.patientname,' failed. Please run this patient again and adjust parameters. Moving on to next patient.' ]);
+            end
+        else
+            switch cmd
+                case 'run'
+                    ea_autocoord(options);
+                case 'export'
+                    ea_export(options);
+            end
+        end
+    end
+end
+
+
+
+
+