Zeffiro developer: A regular push adding the changes made in the curr…

…ent local repository to the remote origin. Contents of the folders ./data/ and ./profile/ are ignored. The update necessitates creating a personal access token.

m/zef_init_parcellation.m

@@ -32,6 +32,26 @@
     zef.use_parcellation = 0;
 end;
 
+if not(isfield(zef,'parcellation_roi_name'));
+    zef.parcellation_roi_name{1} = 'User-defined ROI';
+end;
+
+if not(isfield(zef,'parcellation_roi_center'));
+    zef.parcellation_roi_center = [0 0 0];
+end;
+
+if not(isfield(zef,'parcellation_roi_radius'));
+    zef.parcellation_roi_radius = 10;
+end;
+
+if not(isfield(zef,'parcellation_roi_color'));
+    zef.parcellation_roi_color = [0.56078 0.91373 1];
+end;
+
+if not(isfield(zef,'parcellation_roi_selected'));
+    zef.parcellation_roi_selected = 1;
+end;
+
 zef.time_series_tools_dir = fileparts(which('zef_time_series_plot.m'));
 zef.time_series_tools_name_list = cell(0);
 zef.time_series_tools_file_list = cell(0);

m/zef_parcellation_default.m

@@ -1,31 +1,31 @@
 %Copyright © 2018- Sampsa Pursiainen & ZI Development Team
 %See: https://github.com/sampsapursiainen/zeffiro_interface
-function [c_table,c_points] = zef_parcellation_default(void)
+function [c_table,c_points] = zef_parcellation_default(zef)
 
 c_table = cell(0);
 c_points = cell(0);
 c_ind = 0;
 
-submesh_ind = evalin('base','zef.submesh_ind');
+submesh_ind = eval('zef.submesh_ind');
 if isempty(submesh_ind)
-    submesh_ind = ones(size(evalin('base','zef.brain_ind')));
+    submesh_ind = ones(size(eval('zef.brain_ind')));
 end
 
-if evalin('base','zef.parcellation_merge')
-    c_table = evalin('base','zef.parcellation_colortable');
-    c_points = evalin('base','zef.parcellation_points');
+if eval('zef.parcellation_merge')
+    c_table = eval('zef.parcellation_colortable');
+    c_points = eval('zef.parcellation_points');
 else
-    evalin('base','zef.parcellation_selected = [];');
+    eval('zef.parcellation_selected = [];');
 end
 
-s_interp_ind = evalin('base','zef.source_interpolation_ind{1}');
+s_interp_ind = eval('zef.source_interpolation_ind{1}');
 
 t_ind = 1 + length(c_table);
 
 c_table{t_ind}{1} = 'SG';
-c_points_aux = evalin('base','zef.source_positions');
+c_points_aux = zef.source_positions';
 c_points_aux = [[0:size(c_points_aux,1)-1]' c_points_aux];
-c_table{t_ind}{4} = zeros(size(c_points,1),1);
+c_table{t_ind}{4} = zeros(size(c_points_aux,1),1);
 
 c_points{t_ind} = c_points_aux;
 
@@ -36,21 +36,21 @@
 visible_vec = [];
 color_cell = cell(0);
 aux_brain_ind = [];
-compartment_tags = evalin('base','zef.compartment_tags');
+compartment_tags = eval('zef.compartment_tags');
 for k = 1 : length(compartment_tags)
     var_0 = ['zef.' compartment_tags{k} '_on'];
     var_1 = ['zef.' compartment_tags{k} '_sigma'];
     var_2 = ['zef.' compartment_tags{k} '_priority'];
     var_3 = ['zef.' compartment_tags{k} '_visible'];
-    color_str = evalin('base',['zef.'  compartment_tags{k}  '_color']);
-    on_val = evalin('base',var_0);
+    color_str = eval(['zef.'  compartment_tags{k}  '_color']);
+    on_val = eval(var_0);
     if on_val
         i = i + 1;
 
         c_str = compartment_tags{k};
 
-        if ismember(evalin('base',['zef.' c_str '_sources']),[1 2])
-            I = find(evalin('base','zef.domain_labels(zef.brain_ind)')==i);
+        if ismember(eval(['zef.' c_str '_sources']),[1 2])
+            I = find(eval('zef.domain_labels(zef.brain_ind)')==i);
             submesh_ind_aux = unique(submesh_ind(I));
             if isempty(submesh_ind_aux)
                 submesh_ind_aux = 1;
@@ -61,11 +61,11 @@
                 I_aux = find(submesh_ind(I)==submesh_ind_aux(ell_ind));
                 J = unique(s_interp_ind(I(I_aux),:));
                 if length(submesh_ind_aux) > 1
-                    c_table{t_ind}{2}{c_ind,1} = [evalin('base',['zef.' c_str '_name']) ' ' num2str(submesh_ind_aux(ell_ind))];
+                    c_table{t_ind}{2}{c_ind,1} = [eval(['zef.' c_str '_name']) ' ' num2str(submesh_ind_aux(ell_ind))];
                 else
-                    c_table{t_ind}{2}{c_ind,1} = [evalin('base',['zef.' c_str '_name'])];
+                    c_table{t_ind}{2}{c_ind,1} = [eval(['zef.' c_str '_name'])];
                 end
-                c_table{t_ind}{3}(c_ind,1:3) = evalin('base',['zef.' c_str '_color']);
+                c_table{t_ind}{3}(c_ind,1:3) = eval(['zef.' c_str '_color']);
                 c_table{t_ind}{3}(c_ind,5) =  c_ind;
                 c_table{t_ind}{5}(c_ind,:) = [i submesh_ind_aux(ell_ind)];
                 c_table{t_ind}{4}(J) = c_ind;

m/zef_parcellation_roi_add.m

@@ -0,0 +1,10 @@
+function zef = zef_parcellation_roi_add(zef)
+
+zef.parcellation_roi_selected = 1;
+zef.parcellation_roi_center = [0 0 0; zef.parcellation_roi_center];
+zef.parcellation_roi_radius = [10 zef.parcellation_roi_radius];
+zef.parcellation_roi_color = [0.56078 0.91373 1; zef.parcellation_roi_color];
+zef.parcellation_roi_name = [{'Used-defined ROI'} zef.parcellation_roi_name];
+zef = zef_update_parcellation(zef);
+
+end

m/zef_parcellation_roi_delete.m

@@ -0,0 +1,19 @@
+function zef = zef_parcellation_roi_delete(zef)
+
+I = [1 : size(zef.parcellation_roi_center,1)];
+I = setdiff(I,zef.parcellation_roi_selected);
+if not(isempty(I))
+zef.parcellation_roi_center = zef.parcellation_roi_center(I,:);
+zef.parcellation_roi_color = zef.parcellation_roi_color(I,:);
+zef.parcellation_roi_radius = zef.parcellation_roi_radius(I);
+zef.parcellation_roi_name = zef.parcellation_roi_name(I);
+else
+zef.parcellation_roi_center = [0 0 0];
+zef.parcellation_roi_radius = [10];
+zef.parcellation_roi_color = [0.56078 0.91373 1];
+zef.parcellation_roi_name = [{'Used-defined ROI'}];
+end
+zef.parcellation_roi_selected = 1;
+zef = zef_update_parcellation(zef);
+
+end

m/zef_parcellation_roi_embed.m

@@ -0,0 +1,39 @@
+%Copyright © 2018- Sampsa Pursiainen & ZI Development Team
+%See: https://github.com/sampsapursiainen/zeffiro_interface
+function [c_table,c_points] = zef_parcellation_roi_embed(zef)
+
+c_table = cell(0);
+c_points = cell(0);
+
+if eval('zef.parcellation_merge')
+    c_table = eval('zef.parcellation_colortable');
+    c_points = eval('zef.parcellation_points');
+else
+    eval('zef.parcellation_selected = [];');
+end
+
+t_ind = length(c_table);
+
+t_ind = t_ind + 1;
+
+c_table{t_ind}{1} = 'ROI';
+
+c_points_aux = [];
+c_table{t_ind}{4} = [];
+start_index = 0;
+for i = 1 : size(zef.parcellation_roi_center,1)
+c_points_aux_0 = zef.source_positions;
+c_points_aux_1 = c_points_aux_0(find(sqrt(sum((c_points_aux_0-zef.parcellation_roi_center(i,:)).^2,2))<= zef.parcellation_roi_radius(i)),:);
+c_points_aux = [c_points_aux ; [[start_index:start_index + size(c_points_aux_1,1)-1]' c_points_aux_1]];
+start_index = start_index + size(c_points_aux_1,1); 
+c_table{t_ind}{4} = [c_table{t_ind}{4} ; i*ones(size(c_points_aux_1,1),1)];
+c_table{t_ind}{2}{i,1} = zef.parcellation_roi_name{i};
+c_table{t_ind}{3}(i,1:3) = zef.parcellation_roi_color(i,:);
+c_table{t_ind}{3}(i,5) =  i;
+end
+
+c_points{t_ind} = c_points_aux;
+c_table{t_ind}{3}(:,1:3) = round(255*c_table{t_ind}{3}(:,1:3));
+c_table{t_ind}{4} = c_table{t_ind}{4}(:);
+
+end

m/zef_parcellation_roi_pick_center.m

@@ -0,0 +1,9 @@
+function zef = zef_parcellation_roi_pick_center(zef)
+
+if isempty(findobj(allchild(zef.h_axes1),'Type','DataTip'))~=1
+    zef.h_datatip = findobj(allchild(zef.h_axes1),'Type','DataTip');
+    zef.parcellation_roi_center(zef.parcellation_roi_selected,:) = [h_datatip(1).X h_datatip(1).Y h_datatip(1).Z];
+    zef.h_parcellation_roi_center.String = num2str(zef.parcellation_roi_center(zef.parcellation_roi_selected,:));
+end
+
+end

m/zef_parcellation_roi_pick_color.m

@@ -0,0 +1,11 @@
+function zef = zef_parcellation_roi_pick_color(zef)
+
+color_vec = uisetcolor;
+if not(isequal(color_vec,0))
+    color_str = num2str(color_vec);
+    zef.h_parcellation_roi_color.String = color_str;
+    zef.h_parcellation_roi_color.BackgroundColor = color_vec;
+    zef.parcellation_roi_color(zef.parcellation_roi_selected,:) = color_vec;
+end
+
+end

m/zef_parcellation_roi_plot.m

@@ -0,0 +1,19 @@
+function zef_parcellation_roi_plot(zef)
+
+[s_x,s_y,s_z] = sphere(100);
+h_axes1 = zef.h_axes1;
+hold(h_axes1,'on');
+h_parcellation_roi_sphere = findobj(h_axes1,'Tag','additional: parcellation roi');
+delete(h_parcellation_roi_sphere);
+for i = 1 : size(zef.parcellation_roi_center,1)
+s_x_2 = zef.parcellation_roi_radius(i)*s_x + zef.parcellation_roi_center(i,1);
+s_y_2 = zef.parcellation_roi_radius(i)*s_y + zef.parcellation_roi_center(i,2);
+s_z_2 = zef.parcellation_roi_radius(i)*s_z + zef.parcellation_roi_center(i,3);
+h_plot = surf(h_axes1,s_x_2,s_y_2,s_z_2);
+set(h_plot,'facealpha',1,'edgecolor','none','facecolor',zef.parcellation_roi_color(i,:),'tag','additional: parcellation roi');
+end
+
+drawnow;
+hold(h_axes1,'off');
+
+end