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/mesh/zef_process_meshes.m

@@ -22,6 +22,7 @@
 reuna_p_inf = cell(0);
 reuna_submesh_ind = cell(0);
 reuna_type = cell(0);
+reuna_mesh_ind = [];
 
 compartment_tags = eval('zef.compartment_tags');
 for k = 1 : length(compartment_tags)
@@ -55,6 +56,7 @@
         reuna_type{i,4} = compartment_tags{k};
         reuna_submesh_ind{i} = eval(var_11);
         mean_vec = repmat(mean(reuna_p{i},1),size(reuna_p{i},1),1);
+reuna_mesh_ind(i) = k;
 
         for t_ind = 1 : length(eval(var_1))
 
@@ -330,6 +332,7 @@
 zef.reuna_p_inf = reuna_p_inf;
 zef.reuna_submesh_ind = reuna_submesh_ind;
 zef.reuna_type = reuna_type;
+zef.reuna_mesh_ind = reuna_mesh_ind;
 
 if nargout == 0
     assignin('base','zef',zef);

m/zef_choose_domain_labels.m

@@ -12,9 +12,9 @@
 
 submesh_vec = cell2mat(zef.reuna_submesh_ind);
 n_subcompartments = length(submesh_vec);
-n_compartments = length(zef.compartment_tags);
+n_compartments = length(zef.reuna_mesh_ind);
 subcompartment_labeling_priority_vec = zeros(n_subcompartments,1);
-compartment_labeling_priority_vec = zeros(n_compartments,1);
+compartment_labeling_priority_vec = zeros(length(zef.reuna_mesh_ind),1);
 
 priority_vec = flipud([1:n_subcompartments]');
 priority_vec_compartments = flipud([1:n_compartments]');
@@ -25,12 +25,12 @@
 
 for i = 1 : length(zef.reuna_p)
 
-     compartment_labeling_priority_vec(i) = zef.([zef.compartment_tags{i} '_labeling_priority']);
+     compartment_labeling_priority_vec(i) = zef.([zef.compartment_tags{zef.reuna_mesh_ind(i)} '_labeling_priority']);
 
     for j = 1 : length(zef.reuna_submesh_ind{i})
 
      counter_ind = counter_ind + 1;
-      subcompartment_labeling_priority_vec(counter_ind) = zef.([zef.compartment_tags{i} '_labeling_priority']);
+      subcompartment_labeling_priority_vec(counter_ind) = zef.([zef.compartment_tags{zef.reuna_mesh_ind(i)} '_labeling_priority']);
 
     end
 end
@@ -53,7 +53,7 @@
 labeling_priority_vec_aux = subcompartment_labeling_priority_vec(label_array);
 for i = 1 : ordinal_index-1
 [priority_val priority_ind] = min(labeling_priority_vec_aux,[],2);
-labelin_priority_vec_aux(ind_vec_aux + (priority_ind-1)*n_labels) = NaN; 
+labeling_priority_vec_aux(ind_vec_aux + (priority_ind-1)*n_labels) = NaN; 
 end
 [priority_val priority_ind] = min(labeling_priority_vec_aux,[],2);
 priority_ind = sub2ind(size(label_array),[1:size(label_array,1)]',priority_ind);

m/zef_fix_sensors_get_functions_array_size.m

@@ -10,6 +10,7 @@
 end
 zef.([zef.current_sensors '_get_functions_aux']) = cell(1,n_sensors);
 zef.([zef.current_sensors '_get_functions_aux_ind']) = setdiff([1:size(zef.([zef.current_sensors '_get_functions']),2)],find(cellfun(@isempty, zef.([zef.current_sensors '_get_functions']))));
+zef.([zef.current_sensors '_get_functions_aux'])(zef.([zef.current_sensors '_get_functions_aux_ind'])) = zef.([zef.current_sensors '_get_functions'])(zef.([zef.current_sensors '_get_functions_aux_ind'])); 
 zef.([zef.current_sensors '_get_functions']) = zef.([zef.current_sensors '_get_functions_aux']);
 
 zef = rmfield(zef,[zef.current_sensors '_get_functions_aux']);

m/zef_init.m

@@ -322,6 +322,7 @@
 zef_data.distance_smoothing_on = 1;
 zef_data.smoothing_steps_dist = 0.9;
 zef_data.reuna_submesh_ind = cell(0);
+zef_data.reuna_mesh_ind = [];
 
 zef.fieldnames = fieldnames(zef_data);
 

m/zef_open_forward_and_inverse_options.m

@@ -94,7 +94,7 @@
 
 zef.h_menu_move_one_step_up_in_labeling_priority.MenuSelectedFcn = 'zef = zef_update_labeling_priority(zef,''one step up'');';
 zef.h_menu_move_one_step_down_in_labeling_priority.MenuSelectedFcn = 'zef = zef_update_labeling_priority(zef,''one step down'');';
-zef.h_menu_move_to_bottom_in_labeling_priority.MenuSelectedFcn = 'zef = zef_update_labeling_priority(zef,''top'');';
+zef.h_menu_move_to_top_in_labeling_priority.MenuSelectedFcn = 'zef = zef_update_labeling_priority(zef,''top'');';
 zef.h_menu_move_to_bottom_in_labeling_priority.MenuSelectedFcn = 'zef = zef_update_labeling_priority(zef,''bottom'');';
 
 zef.h_refinement_volume_on.Value = zef.refinement_volume_on;

m/zef_update_labeling_priority.m

@@ -11,32 +11,39 @@
     use_settings = 1;
 end
 
+n_compartments = length(zef.reuna_mesh_ind); 
+
 if use_settings
 
 item_selected = zef.h_labeling_priority_order.Value; 
 [~,~,labeling_priority_vec] = zef_choose_domain_labels(zef,[],1);
-labeling_priority_vec = labeling_priority_vec(:)';
+[~, labeling_priority_vec] = sort(labeling_priority_vec);
+
+labeling_priority_vec = (labeling_priority_vec(:)');
 
 if isequal(update_type,'one step up')
 if item_selected > 1
 labeling_priority_vec = [labeling_priority_vec(1:item_selected-2) labeling_priority_vec(item_selected) labeling_priority_vec(item_selected-1) labeling_priority_vec(item_selected+1:end)];
 end
 elseif isequal(update_type,'one step down')
- if item_selected < length(labeling_priority_vec)
+if item_selected < length(labeling_priority_vec)
 labeling_priority_vec = [labeling_priority_vec(1:item_selected-1) labeling_priority_vec(item_selected+1) labeling_priority_vec(item_selected) labeling_priority_vec(item_selected+2:end)];
- end
- elseif isequal(update_type,'top')
-labeling_priority_vec = [labeling_priority_vec(item_selected) labeling_priority_vec(1:item_selected-1) labeling_priority_vec(1:item_selected+1)]; 
+end
+elseif isequal(update_type,'top')
+labeling_priority_vec = [labeling_priority_vec(item_selected) labeling_priority_vec(1:item_selected-1) labeling_priority_vec(item_selected+1:end)]; 
 elseif isequal(update_type,'bottom')
-labeling_priority_vec = [labeling_priority_vec(1:item_selected-1) labeling_priority_vec(1:item_selected+1) labeling_priority_vec(item_selected)];
+labeling_priority_vec = [labeling_priority_vec(1:item_selected-1) labeling_priority_vec(item_selected+1:end) labeling_priority_vec(item_selected)];
 end
 
 end
 
-items = cell(length(zef.compartment_tags),1);
-for i = 1 : length(zef.compartment_tags) 
-zef.([zef.compartment_tags{labeling_priority_vec(i)} '_labeling_priority']) = i;
-items{i} = zef.([zef.compartment_tags{labeling_priority_vec(i)} '_name']);
+%labeling_priority_vec_1 = fliplr(labeling_priority_vec);
+%labeling_priority_vec = labeling_priority_vec_2(labeling_priority_vec_1);
+
+items = cell(n_compartments,1);
+for i = 1 : n_compartments
+zef.([zef.compartment_tags{zef.reuna_mesh_ind(labeling_priority_vec(i))} '_labeling_priority']) = i;
+items{i} = zef.([zef.compartment_tags{zef.reuna_mesh_ind(labeling_priority_vec(i))} '_name']);
 end
 
 if use_settings

plugins/StripTool/zef_strip_tool_plot.m

@@ -39,7 +39,7 @@ function zef_strip_tool_plot(zef)
 for i = 1 : strip_struct.strip_n_contacts
 
 [contacts, ~, triangle_ind_aux] = zef_get_strip_contacts(i,strip_struct,zef);
-h_strip_contact = trimesh(contacts(:,2:4),points{1}(:,1),points{1}(:,2),points{1}(:,3));
+h_strip_contact = trimesh(contacts(:,1:3),points{1}(:,1),points{1}(:,2),points{1}(:,3));
 h_strip_contact.FaceColor = [0 0 0];
 h_strip_contact.EdgeColor = 'none';
 h_strip_contact.Tag = 'additional: strip contact';