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.

+utilities/+brainstorm2zef/+m/+postprocessing_script_bank/zef_bst_return_project_structure.m

@@ -0,0 +1 @@
+assignin('base','zef',zef);

+utilities/+brainstorm2zef/+m/+postprocessing_script_bank/zef_bst_save_project_structure.m

@@ -0,0 +1 @@
+zef = zef_save(zef,project_file_name,project_file_folder,1);

+utilities/+brainstorm2zef/+m/+run_script_bank/zef_bst_create_finite_element_mesh.m

@@ -0,0 +1 @@
+zef = zef_create_finite_element_mesh(zef);

+utilities/+brainstorm2zef/+m/zef_bst_edit_project.m

@@ -0,0 +1,18 @@
+function zef_bst_edit_project
+
+h_parent = get(gcbo,'Parent');
+addpath(h_parent.folder_name);
+h_text_1 = findobj(h_parent.Children,'Tag','setup_file');
+
+[folder_name,file_name] = fileparts(h_text_1.String);
+
+project_file_name = [folder_name filesep file_name '.mat'];
+
+if not(isequal(exist(project_file_name),2))
+zef = zeffiro_interface('start_mode','nodisplay','import_to_new_project',h_text_1.String,'save_project',project_file_name,'exit_zeffiro',true);
+addpath(h_parent.folder_name);
+end
+
+zef = zeffiro_interface('start_mode','display','open_project',project_file_name);
+
+end

+utilities/+brainstorm2zef/+m/zef_bst_import_settings.m

@@ -0,0 +1,12 @@
+zef = zef_add_bounding_box(zef);
+zef.exclude_box = 1;
+zef.max_surface_face_count = 0.5;
+zef.mesh_smoothing_on = 1;
+zef.mesh_resolution = 3;
+zef.refinement_on = 1;
+zef.refinement_surface_on = 1;
+import_compartment_list_aux = zef_get_active_compartments(zef);
+import_compartment_list_aux = import_compartment_list_aux(end-2:end-1);
+import_compartment_list_aux = import_compartment_list_aux(:)';
+zef.refinement_surface_compartments = [-1 import_compartment_list_aux];
+zef_mesh_tool;

+utilities/+brainstorm2zef/+m/zef_bst_plugin_close.m

@@ -0,0 +1,7 @@
+function zef_bst_plugin_close
+
+addpath(gcbo().folder_name)
+rmpath(gcbo().folder_name)
+closereq;
+
+end

+utilities/+brainstorm2zef/+m/zef_bst_plugin_start.m

@@ -0,0 +1,68 @@
+
+function zef_bst_plugin_start(folder_name)
+
+h_fig = figure(...
+    'PaperUnits',get(0,'defaultfigurePaperUnits'),...
+    'Units','normalized',...
+    'OuterPosition',[0.5 0.5 0.25 0.25],...
+    'Renderer',get(0,'defaultfigureRenderer'),...
+    'Visible','on',...
+    'Color',get(0,'defaultfigureColor'),...
+    'CloseRequestFcn','utilities.brainstorm2zef.m.zef_bst_plugin_close;',...
+    'CurrentAxesMode','manual',...
+    'IntegerHandle','off',...
+    'NextPlot',get(0,'defaultfigureNextPlot'),...
+    'Colormap',[0 0 0.5625;0 0 0.625;0 0 0.6875;0 0 0.75;0 0 0.8125;0 0 0.875;0 0 0.9375;0 0 1;0 0.0625 1;0 0.125 1;0 0.1875 1;0 0.25 1;0 0.3125 1;0 0.375 1;0 0.4375 1;0 0.5 1;0 0.5625 1;0 0.625 1;0 0.6875 1;0 0.75 1;0 0.8125 1;0 0.875 1;0 0.9375 1;0 1 1;0.0625 1 1;0.125 1 0.9375;0.1875 1 0.875;0.25 1 0.8125;0.3125 1 0.75;0.375 1 0.6875;0.4375 1 0.625;0.5 1 0.5625;0.5625 1 0.5;0.625 1 0.4375;0.6875 1 0.375;0.75 1 0.3125;0.8125 1 0.25;0.875 1 0.1875;0.9375 1 0.125;1 1 0.0625;1 1 0;1 0.9375 0;1 0.875 0;1 0.8125 0;1 0.75 0;1 0.6875 0;1 0.625 0;1 0.5625 0;1 0.5 0;1 0.4375 0;1 0.375 0;1 0.3125 0;1 0.25 0;1 0.1875 0;1 0.125 0;1 0.0625 0;1 0 0;0.9375 0 0;0.875 0 0;0.8125 0 0;0.75 0 0;0.6875 0 0;0.625 0 0;0.5625 0 0],...
+    'DoubleBuffer','off',...
+    'Name','ZEFFIRO-Brainstorm plugin',...
+    'NumberTitle','off',...
+    'HandleVisibility','callback',...
+    'DeleteFcn','closereq;',...
+    'Tag','zeffiro_bst_plugin',...
+    'UserData',[],'ToolBar','none','MenuBar','none',...
+    'WindowStyle',get(0,'defaultfigureWindowStyle'),...
+    'Resize',get(0,'defaultfigureResize'),...
+    'PaperPosition',get(0,'defaultfigurePaperPosition'),...
+    'PaperSize',[20.99999864 29.69999902],...
+    'PaperType',get(0,'defaultfigurePaperType'),...
+    'InvertHardcopy',get(0,'defaultfigureInvertHardcopy'),...
+    'ScreenPixelsPerInchMode','manual' );
+
+file_name = 'BrainStorm2Zeffiro_import.zef';
+subfolder_name = ['+utilities' filesep '+brainstorm2zef' filesep 'data'];
+
+h_button_1 = uicontrol('Style','pushbutton','Parent',h_fig,'Visible','on','Units','normalized','Position',[0.60 0.80 0.35 0.15],'String','Select file','Callback','utilities.brainstorm2zef.m.zef_bst_setup_file;');
+h_button_2 = uicontrol('Style','pushbutton','Parent',h_fig,'Visible','on','Units','normalized','Position',[0.60 0.35 0.35 0.15],'String','Reset project','Callback','utilities.brainstorm2zef.m.zef_bst_reset_project;');
+h_button_3 = uicontrol('Style','pushbutton','Parent',h_fig,'Visible','on','Units','normalized','Position',[0.60 0.20 0.35 0.15],'String','Edit project','Callback','utilities.brainstorm2zef.m.zef_bst_edit_project;');
+h_button_5 = uicontrol('Style','pushbutton','Parent',h_fig,'Visible','on','Units','normalized','Position',[0.60 0.05 0.35 0.15],'String','Run script','Callback','utilities.brainstorm2zef.m.zef_bst_run;');
+
+run_script_list = dir([folder_name filesep '+utilities' filesep '+brainstorm2zef' filesep '+m' filesep '+run_script_bank']);
+run_script_list = {run_script_list().name}'; 
+run_script_list = run_script_list(3:end);
+
+postprocessing_script_list = dir([folder_name filesep '+utilities' filesep '+brainstorm2zef' filesep '+m' filesep '+postprocessing_script_bank']);
+postprocessing_script_list = {postprocessing_script_list().name}'; 
+postprocessing_script_list = postprocessing_script_list(3:end);
+
+for i = 1 : length(run_script_list)
+[~,name_string] = fileparts(run_script_list{i});
+run_script_list{i} = name_string;
+end
+
+for i = 1 : length(postprocessing_script_list)
+[~,name_string] = fileparts(postprocessing_script_list{i});
+postprocessing_script_list{i} = name_string;
+end
+
+h_popmenu_1 = uicontrol('Style','popupmenu','Parent',h_fig,'Visible','on','Units','normalized','Position',[0.05 0.05 0.35 0.1],'String',postprocessing_script_list,'Tag','postprocessing_script');
+h_popmenu_2 = uicontrol('Style','popupmenu','Parent',h_fig,'Visible','on','Units','normalized','Position',[0.05 0.35 0.35 0.1],'String',run_script_list,'Tag','run_script');
+
+h_text_1 = uicontrol('Style','text','Parent',h_fig,'Units','normalized','String',[folder_name filesep subfolder_name filesep file_name],'HorizontalAlignment','left','Position',[0.05 0.55 0.9 0.2],'BackgroundColor',[0.9 0.9 0.9],'Tag','setup_file');
+h_text_2 = uicontrol('Style','text','Parent',h_fig,'Units','normalized','String','Postprocessing script:','HorizontalAlignment','left','Position',[0.05 0.15 0.35 0.1],'BackgroundColor',[0.94 0.94 0.94]);
+h_text_3 = uicontrol('Style','text','Parent',h_fig,'Units','normalized','String','Run script:','HorizontalAlignment','left','Position',[0.05 0.45 0.35 0.1],'BackgroundColor',[0.94 0.94 0.94]);
+
+h_axes = uiaxes('Parent',h_fig,'visible','on','Units','normalized','Position',[0.05 0.775 0.375 0.20],'FontSize',0.587962962962963,'Tag','image_axes','BackgroundColor',[0.94 0.94 0.94],'Visible','off');
+imagesc(h_axes,imread([folder_name filesep 'fig' filesep 'zeffiro_logo.png'], 'BackgroundColor', [0.94 0.94 0.94]));
+
+addprop(h_fig,'folder_name');
+set(h_fig,'folder_name',folder_name);

+utilities/+brainstorm2zef/+m/zef_bst_reset_project.m

@@ -0,0 +1,19 @@
+function zef_bst_reset_project
+
+h_parent = get(gcbo,'Parent');
+addpath(h_parent.folder_name);
+h_text_1 = findobj(h_parent.Children,'Tag','setup_file');
+
+[folder_name,file_name] = fileparts(h_text_1.String);
+
+project_file_name = [folder_name filesep file_name '.mat'];
+
+if isequal(exist(project_file_name),2)
+delete(project_file_name)
+end
+
+zef = zeffiro_interface('start_mode','nodisplay','import_to_new_project',h_text_1.String,'save_project',project_file_name,'exit_zeffiro',true);
+addpath(h_parent.folder_name);
+disp('Done.')
+
+end

+utilities/+brainstorm2zef/+m/zef_bst_run.m

@@ -0,0 +1,29 @@
+function zef_bst_run
+
+h_parent = get(gcbo,'Parent');
+addpath(h_parent.folder_name);
+h_text_1 = findobj(h_parent.Children,'Tag','setup_file');
+h_popupmenu_1 = findobj(h_parent.Children,'Tag','postprocessing_script');
+h_popupmenu_2 = findobj(h_parent.Children,'Tag','run_script');
+
+[project_file_folder, project_file_name] = fileparts(h_text_1.String);
+
+project_file_name = [project_file_name '.mat'];
+
+if not(isequal(exist(project_file_name),2))
+zef = zeffiro_interface('start_mode','nodisplay','import_to_new_project',h_text_1.String,'save_project',[project_file_folder filesep project_file_name],'exit_zeffiro',true);
+addpath(h_parent.folder_name);
+end
+
+run_script_name = ['utilities.brainstorm2zef.m.run_script_bank'];
+run_script_name = [run_script_name '.' h_popupmenu_2.String{h_popupmenu_2.Value}];
+
+postprocessing_script_name = ['utilities.brainstorm2zef.m.postprocessing_script_bank'];
+postprocessing_script_name = [postprocessing_script_name '.' h_popupmenu_1.String{h_popupmenu_1.Value}];
+
+zef = zeffiro_interface('start_mode','nodisplay','open_project',[project_file_folder filesep project_file_name],'run_script',run_script_name,'exit_zeffiro',true);
+addpath(h_parent.folder_name);
+eval(postprocessing_script_name);
+disp('Done.')
+
+end

+utilities/+brainstorm2zef/+m/zef_bst_setup_file.m

@@ -0,0 +1,13 @@
+function zef_bst_setup_file
+
+h_parent = get(gcbo,'Parent');
+addpath(h_parent.folder_name);
+h_text_1 = findobj(h_parent.Children,'Tag','setup_file');
+
+folder_name = get(h_parent,'folder_name');
+
+[file_name folder_name] = uigetfile('*.zef','Select setup file', folder_name);
+
+h_text_1.String = [folder_name filesep file_name];
+
+end

m/import/zef_bst_2_zef_sensors.m

@@ -8,6 +8,7 @@
 sensor_orientations = [];
 sensor_ind = [];
 sensor_tag_cell = cell(0);
+scaling_constant = 1000;
 
 if not(isempty(varargin))
     sensor_type = varargin{1};
@@ -45,6 +46,8 @@
 
 end
 
+sensor_positions = scaling_constant*sensor_positions;
+
 sensor_ind = sensor_ind(:);
 sensor_tag_cell = sensor_tag_cell(:);
 

m/import/zef_bst_2_zef_surface.m

@@ -7,6 +7,7 @@
 surface = [];
 subject = [];
 surface_properties = [];
+scaling_constant = 1000;
 
 if not(isempty(varargin))
     subject = varargin{1};
@@ -44,7 +45,7 @@
     end
 
     if isfield(surface_data,'Vertices')
-        vertices = surface_data.Vertices;
+        vertices = scaling_constant*surface_data.Vertices;
     end
 
     if isfield(surface_data,'Faces')

m/zef_downsample_surfaces.m

@@ -6,12 +6,16 @@
 
 zef.h = zef_waitbar(0,1,'Resampling surfaces.');
 zef.temp_time = now;
+relative_resolution_vec = zef_find_relative_resolution(zef);
 zef.number_of_compartments = length(zef.compartment_tags);
+active_compartment_ind = 0;
 
 for zef_k = 1 : zef.number_of_compartments
     zef.temp_var_0 = zef.compartment_tags{zef_k};
+    zef.temp_patch_data.scaling = eval(['zef.' zef.temp_var_0 '_scaling;']);
 
     if eval(['zef.' zef.temp_var_0 '_on'])
+        active_compartment_ind = active_compartment_ind + 1;
         if eval(['isfield(zef,"' zef.temp_var_0 '_points_original_surface_mesh")'])
             if eval(['not(isempty(zef.' zef.temp_var_0 '_points_original_surface_mesh))'])
                 zef.temp_patch_data.vertices_all = eval(['zef.' zef.temp_var_0 '_points_original_surface_mesh;']);
@@ -49,10 +53,10 @@
                 zef.temp_patch_data.vertice_ind_aux(zef.temp_patch_data.unique_faces_ind) = [1:length(zef.temp_patch_data.unique_faces_ind)];
                 zef.temp_patch_data.faces = zef.temp_patch_data.vertice_ind_aux(zef.temp_patch_data.faces);
                 zef.temp_patch_data.vertices = zef.temp_patch_data.vertices_all(zef.temp_patch_data.unique_faces_ind,:);
-                zef.temp_patch_data_aux = zef_set_surface_resolution(zef,zef.temp_patch_data,zef.max_surface_face_count);
+                zef.temp_patch_data_aux = zef_set_surface_resolution(zef,zef.temp_patch_data,zef.max_surface_face_count*relative_resolution_vec(active_compartment_ind));
                 zef.temp_patch_data_aux.vertices = zef_smooth_surface(zef.temp_patch_data_aux.vertices,zef.temp_patch_data_aux.faces,1e-2,1);
                 if eval(['zef.' zef.temp_var_0 '_sources'])
-                    if isempty(zef.temp_patch_data_aux.vertices) || isempty(zef.temp_patch_data_aux.vertices) || zef.bypass_inflate
+                    if isempty(zef.temp_patch_data_aux.vertices) || zef.bypass_inflate
                         zef.temp_patch_data_aux.vertices_inflated = [];
                     else
                         [zef.temp_patch_data_aux.vertices_inflated] = zef_inflate_surface(zef,zef.temp_patch_data_aux.vertices,zef.temp_patch_data_aux.faces);
@@ -67,7 +71,7 @@
         else
             zef.temp_patch_data.faces = zef.temp_patch_data.faces_all;
             zef.temp_patch_data.vertices = zef.temp_patch_data.vertices_all;
-            zef.temp_patch_data_aux = zef_set_surface_resolution(zef,zef.temp_patch_data,zef.max_surface_face_count);
+            zef.temp_patch_data_aux = zef_set_surface_resolution(zef,zef.temp_patch_data,zef.max_surface_face_count*relative_resolution_vec(active_compartment_ind));
             zef.temp_patch_data_aux.vertices = zef_smooth_surface(zef.temp_patch_data_aux.vertices,zef.temp_patch_data_aux.faces,1e-2,1);
             if eval(['zef.' zef.temp_var_0 '_sources']) > 0
                 zef.temp_patch_data_aux.vertices_inflated = zef_inflate_surface(zef,zef.temp_patch_data_aux.vertices,zef.temp_patch_data_aux.faces);

m/zef_figure_tool.m

@@ -47,7 +47,6 @@
     'InvertHardcopy',get(0,'defaultfigureInvertHardcopy'),...
     'ScreenPixelsPerInchMode','manual' );
 
-
 zef.h_zeffiro.Units = 'normalized';
 
 zef.h_zeffiro.ContextMenu = uicontextmenu(zef.h_zeffiro);

m/zef_find_relative_resolution.m

@@ -0,0 +1,99 @@
+function relative_resolution_vec = zef_find_relative_resolution(zef)
+
+[active_compartments, source_compartments] = zef_get_active_compartments(zef);
+
+source_compartments = find(ismember(active_compartments,source_compartments));
+
+relative_resolution_vec = ones(size(active_compartments));
+
+if zef.refinement_on
+
+if zef.refinement_surface_on
+
+rel_num_vec_aux = zef.refinement_surface_number(:).*ones(length(zef.refinement_surface_compartments),1);
+
+for i = 1 : length(zef.refinement_surface_compartments)
+
+if isequal(zef.refinement_surface_compartments(i),-1)
+
+relative_resolution_vec(source_compartments) = (4.^rel_num_vec_aux(i)).*relative_resolution_vec(source_compartments);
+
+else
+
+relative_resolution_vec(zef.refinement_surface_compartments(i)) = (4.^rel_num_vec_aux(i)).*relative_resolution_vec(zef.refinement_surface_compartments(i));
+
+end
+
+end
+
+end
+
+if zef.refinement_surface_on_2
+
+rel_num_vec_aux = zef.refinement_surface_number_2(:).*ones(length(zef.refinement_surface_compartments_2),1);
+
+for i = 1 : length(zef.refinement_surface_compartments_2)
+
+if isequal(zef.refinement_surface_compartments_2(i),-1)
+
+relative_resolution_vec(source_compartments) = (4.^rel_num_vec_aux(i)).*relative_resolution_vec(source_compartments);
+
+else
+
+relative_resolution_vec(zef.refinement_surface_compartments_2(i)) = (4.^rel_num_vec_aux(i)).*relative_resolution_vec(zef.refinement_surface_compartments_2(i));
+
+end
+
+end
+
+end
+
+
+if zef.refinement_volume_on
+
+rel_num_vec_aux = zef.refinement_volume_number(:).*ones(length(zef.refinement_volume_compartments),1);
+
+for i = 1 : length(zef.refinement_volume_compartments)
+
+if isequal(zef.refinement_volume_compartments(i),-1)
+
+relative_resolution_vec(source_compartments) = (4.^rel_num_vec_aux(i)).*relative_resolution_vec(source_compartments);
+
+else
+
+relative_resolution_vec(zef.refinement_volume_compartments(i)) = (4.^rel_num_vec_aux(i)).*relative_resolution_vec(zef.refinement_volume_compartments(i));
+
+end
+
+end
+
+end
+
+if zef.refinement_volume_on_2
+
+rel_num_vec_aux = zef.refinement_volume_number_2(:).*ones(length(zef.refinement_volume_compartments_2),1);
+
+for i = 1 : length(zef.refinement_volume_compartments_2)
+
+if isequal(zef.refinement_volume_compartments_2(i),-1)
+
+relative_resolution_vec(source_compartments) = (4.^rel_num_vec_aux(i)).*relative_resolution_vec(source_compartments);
+
+else
+
+relative_resolution_vec(zef.refinement_volume_compartments_2(i)) = (4.^rel_num_vec_aux(i)).*relative_resolution_vec(zef.refinement_volume_compartments_2(i));
+
+end
+
+end
+
+end
+
+
+
+end
+
+end
+
+
+