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Zeffiro developer: A regular push adding the changes made in the curr…
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…ent local repository to the remote origin. Contents of the folders ./data/ and ./profile/ are ignored. The update necessitates creating a personal access token.
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@sampsapursiainen
sampsapursiainen committed Oct 9, 2024
1 parent ae2e401 commit 8c90dd6
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Showing 6 changed files with 194 additions and 189 deletions.
142 changes: 71 additions & 71 deletions +utilities/+brainstorm2zef/+m/zef_bst_create_compartment_data.m
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Original file line number Diff line number Diff line change
Expand Up @@ -8,56 +8,56 @@
if length(fieldnames(zef_bst.subject_struct)) > 0
subject_struct = zef_bst.subject_struct;
else
subject_struct = bst_get('Subject');
subject_struct = bst_get('Subject');
end
else
subject_struct = bst_get('Subject');
else
subject_struct = bst_get('Subject');
end

if isfield(zef_bst,'subject_folder')
if not(isempty(char(zef_bst.subject_folder)))
subject_folder = zef_bst.subject_folder;
else
subject_folder = bst_get('ProtocolInfo').SUBJECTS;
end
if not(isempty(char(zef_bst.subject_folder)))
subject_folder = zef_bst.subject_folder;
else
subject_folder = bst_get('ProtocolInfo').SUBJECTS;
end
else
subject_folder = bst_get('ProtocolInfo').SUBJECTS;
subject_folder = bst_get('ProtocolInfo').SUBJECTS;
end

if isempty(zef_bst.compartment_files)

aux_type = '';

zef_bst.compartment_files = cell(0);
for i = 1 : length(zef_bst.compartment_list)
if (isfield(subject_struct,['i' zef_bst.compartment_list{i}]))
aux_ind = subject_struct.(['i' zef_bst.compartment_list{i}]);
aux_type = 'Surface';
else
aux_ind = find(ismember({subject_struct.Surface.Comment},zef_bst.compartment_list{i}),1);
aux_type = 'Surface';
if isempty(aux_ind)
aux_ind = find(ismember({subject_struct.Anatomy.Comment},zef_bst.compartment_list{i}),1);
aux_type = 'Anatomy';
end
end
aux_type = '';

zef_bst.compartment_files = cell(0);
for i = 1 : length(zef_bst.compartment_list)
if (isfield(subject_struct,['i' zef_bst.compartment_list{i}]))
aux_ind = subject_struct.(['i' zef_bst.compartment_list{i}]);
aux_type = 'Surface';
else
aux_ind = find(ismember({subject_struct.Surface.Comment},zef_bst.compartment_list{i}),1);
aux_type = 'Surface';

if isempty(aux_ind)
aux_ind = find(ismember({subject_struct.Anatomy.Comment},zef_bst.compartment_list{i}),1);
aux_type = 'Anatomy';
end
end

if not(isempty(aux_ind))
mesh_file_ind = mesh_file_ind + 1;
if isequal(aux_type,'Surface')
zef_bst.compartment_files{mesh_file_ind} = [subject_folder filesep subject_struct.Surface(aux_ind).FileName];
elseif isequal(aux_type,'Anatomy')
zef_bst.compartment_files{mesh_file_ind} = [subject_folder filesep subject_struct.Anatomy(aux_ind).FileName];
end
if not(isempty(aux_ind))
mesh_file_ind = mesh_file_ind + 1;
if isequal(aux_type,'Surface')
zef_bst.compartment_files{mesh_file_ind} = [subject_folder filesep subject_struct.Surface(aux_ind).FileName];
elseif isequal(aux_type,'Anatomy')
zef_bst.compartment_files{mesh_file_ind} = [subject_folder filesep subject_struct.Anatomy(aux_ind).FileName];
end

end
end
end
end

else
for i = 1 : length(zef_bst.compartment_files)
if not(exist(zef_bst.compartment_files{i},'file'))
zef_bst.compartment_files{i} = fullfile(subject_folder,zef_bst.compartment_files{i});
zef_bst.compartment_files{i} = fullfile(subject_folder,zef_bst.compartment_files{i});
end
end
end
Expand All @@ -66,53 +66,53 @@
compartment_types = cell(1,n_surface_meshes);
surface_mesh_type = '';
for i = 1 : n_surface_meshes
surface_mesh_type = load(zef_bst.compartment_files{i},'Comment');
surface_mesh_type = surface_mesh_type.Comment;
if not(ismember(surface_mesh_type,zef_bst.compartment_list))
[subject_struct, ~, surface_index] = bst_get('SurfaceFile', zef_bst.compartment_files{i});
surface_mesh_type = subject_struct.Surface(surface_index).SurfaceType;
end
compartment_types{i} = surface_mesh_type;
surface_mesh_type = load(zef_bst.compartment_files{i},'Comment');
surface_mesh_type = surface_mesh_type.Comment;
if not(ismember(surface_mesh_type,zef_bst.compartment_list))
[subject_struct, ~, surface_index] = bst_get('SurfaceFile', zef_bst.compartment_files{i});
surface_mesh_type = subject_struct.Surface(surface_index).SurfaceType;
end
compartment_types{i} = surface_mesh_type;
end

surface_mesh_order = zeros(n_surface_meshes,1);
surface_counter = 0;
surface_counter = 0;
for i = 1 : length(zef_bst.compartment_list)
I = find(ismember(compartment_types,zef_bst.compartment_list{i}));
n_found = length(I);
surface_mesh_order(I) = [1:n_found]' + surface_counter;
surface_counter = surface_counter + n_found;
I = find(ismember(compartment_types,zef_bst.compartment_list{i}));
n_found = length(I);
surface_mesh_order(I) = [1:n_found]' + surface_counter;
surface_counter = surface_counter + n_found;
end

zef_bst.compartment_files = zef_bst.compartment_files(surface_mesh_order);
compartment_types = compartment_types(surface_mesh_order);

surface_meshes = struct;
for i = 1 : n_surface_meshes

compartment_struct = load(zef_bst.compartment_files{i});

if isfield(compartment_struct, 'Vertices')
surface_meshes(i).Name = compartment_types{i};
surface_meshes(i).Type = compartment_types{i};
surface_meshes(i).Color = [];
surface_meshes(i).Points = zef_bst.unit_conversion*compartment_struct.Vertices;
surface_meshes(i).Triangles = compartment_struct.Faces;
end
if isfield(compartment_struct, 'Vertices')
surface_meshes(i).Name = compartment_types{i};
surface_meshes(i).Type = compartment_types{i};
surface_meshes(i).Color = [];
surface_meshes(i).Points = zef_bst.unit_conversion*compartment_struct.Vertices;
surface_meshes(i).Triangles = compartment_struct.Faces;
end

if isfield(compartment_struct,'Cube')
if not(isempty(compartment_struct.InitTransf))
A = compartment_struct.InitTransf{2};
else
compartment_struct.InitTransf{2} = A;
end
surface_meshes_aux = utilities.brainstorm2zef.m.zef_bst_get_atlas_surfaces(zef,compartment_struct,zef_bst.n_inflation_steps,zef_bst.transform_cell,compartment_types{i});
if length(fieldnames(surface_meshes)) > 0
surface_meshes = [surface_meshes surface_meshes_aux];
else
surface_meshes = surface_meshes_aux;
end
end
if isfield(compartment_struct,'Cube')
if not(isempty(compartment_struct.InitTransf))
A = compartment_struct.InitTransf{2};
else
compartment_struct.InitTransf{2} = A;
end
surface_meshes_aux = utilities.brainstorm2zef.m.zef_bst_get_atlas_surfaces(zef,compartment_struct,zef_bst.n_inflation_steps,zef_bst.transform_cell,compartment_types{i});
if length(fieldnames(surface_meshes)) > 0
surface_meshes = [surface_meshes surface_meshes_aux];
else
surface_meshes = surface_meshes_aux;
end
end

end

Expand All @@ -121,9 +121,9 @@
n_surface_meshes = size(compartment_settings,1);
ind_vec_aux = zeros(n_surface_meshes,1);
for i = 1 : n_surface_meshes
if size(surface_meshes(i).Points,1) >= 4
ind_vec_aux(i) = 1;
end
if size(surface_meshes(i).Points,1) >= 4
ind_vec_aux(i) = 1;
end
end
ind_vec_aux = find(ind_vec_aux);
surface_meshes = surface_meshes(ind_vec_aux);
Expand Down
76 changes: 37 additions & 39 deletions +utilities/+brainstorm2zef/+m/zef_bst_create_project.m
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Original file line number Diff line number Diff line change
Expand Up @@ -9,27 +9,27 @@
end

if nargin < 4
input_mode = 1;
input_mode = 1;
end

if nargin < 3
run_type = 1;
run_type = 1;
end

if nargin < 2
project_file_name = '';
project_file_name = '';
end

zef_bst = utilities.brainstorm2zef.m.zef_bst_get_settings(settings_file_name, zef_bst);

zeffiro_path = fileparts(which('zeffiro_interface'));

if evalin("base","exist('zef', 'var');")
run([zeffiro_path filesep 'm' filesep 'zef_close_all.m']);
run([zeffiro_path filesep 'm' filesep 'zef_close_all.m']);
end

if isempty(fieldnames(zef))
zef = zeffiro_interface('start_mode','nodisplay','verbose_mode',zef_bst.verbose_mode,'use_gpu',zef_bst.use_gpu,'parallel_processes',zef_bst.parallel_processes,'always_show_waitbar',zef_bst.always_show_waitbar);
zef = zeffiro_interface('start_mode','nodisplay','verbose_mode',zef_bst.verbose_mode,'use_gpu',zef_bst.use_gpu,'parallel_processes',zef_bst.parallel_processes,'always_show_waitbar',zef_bst.always_show_waitbar);
end

zef = zef_add_bounding_box(zef);
Expand All @@ -44,20 +44,20 @@

[aux_path, aux_file] = fileparts(settings_file_name);
if isequal(run_type,1)
[compartment_settings, surface_meshes, zef] = utilities.brainstorm2zef.m.zef_bst_create_compartment_data(settings_file_name, zef_bst, zef);
writecell(compartment_settings, fullfile(aux_path,[aux_file '_compartment_settings.dat']));
save(fullfile(aux_path,[aux_file '_surface_meshes.mat']),'surface_meshes','-v7.3');
[compartment_settings, surface_meshes, zef] = utilities.brainstorm2zef.m.zef_bst_create_compartment_data(settings_file_name, zef_bst, zef);
writecell(compartment_settings, fullfile(aux_path,[aux_file '_compartment_settings.dat']));
save(fullfile(aux_path,[aux_file '_surface_meshes.mat']),'surface_meshes','-v7.3');
else
compartment_settings = readcell(fullfile(aux_path,[aux_file '_compartment_settings.dat']));
load(fullfile(aux_path,[aux_file '_surface_meshes.mat']));
compartment_settings = readcell(fullfile(aux_path,[aux_file '_compartment_settings.dat']));
load(fullfile(aux_path,[aux_file '_surface_meshes.mat']));
end

n_surface_meshes = size(compartment_settings,1);
ind_vec_aux = zeros(n_surface_meshes,1);
for i = 1 : n_surface_meshes
if size(surface_meshes(i).Points,1) >= 4
ind_vec_aux(i) = 1;
end
if size(surface_meshes(i).Points,1) >= 4
ind_vec_aux(i) = 1;
end
end
ind_vec_aux = find(ind_vec_aux);
surface_meshes = surface_meshes(ind_vec_aux);
Expand All @@ -71,32 +71,30 @@
ind_vec_aux = zeros(n_surface_meshes,1);
h_waitbar = zef_waitbar(0, 'Creating project.');
for i = 1 : n_surface_meshes
zef_waitbar(i/n_surface_meshes,h_waitbar,'Creating project.');
surface_names_aux = {surface_meshes.Name};
i_aux = find(ismember(surface_names_aux,compartment_settings{i,2}),1);
if not(isempty(i_aux))
ind_vec_aux(i) = 1;
zef = zef_add_compartment(zef);
zef.([zef.compartment_tags{1} '_name']) = [compartment_settings{i,4} ' : ' compartment_settings{i,2}];
zef.([zef.compartment_tags{1} '_points']) = surface_meshes(i_aux).Points;
zef.([zef.compartment_tags{1} '_triangles']) = surface_meshes(i_aux).Triangles(:,[1 3 2]);
zef.([zef.compartment_tags{1} '_submesh_ind']) = size(surface_meshes(i_aux).Triangles,1);
zef.([zef.compartment_tags{1} '_sigma']) = compartment_settings{i,10};
zef.([zef.compartment_tags{1} '_activity']) = compartment_settings{i,12};
if not(isempty(surface_meshes(i_aux).Color))
zef.([zef.compartment_tags{1} '_color']) = surface_meshes(i_aux).Color;
end
zef = zef_build_compartment_table(zef);
end
end

ind_vec_aux = find(ind_vec_aux);
zef_waitbar(i/n_surface_meshes,h_waitbar,'Creating project.');
surface_names_aux = {surface_meshes.Name};
i_aux = find(ismember(surface_names_aux,compartment_settings{i,2}),1);
if not(isempty(i_aux))
ind_vec_aux(i) = 1;
zef = zef_add_compartment(zef);
zef.([zef.compartment_tags{1} '_name']) = [compartment_settings{i,4} ' : ' compartment_settings{i,2}];
zef.([zef.compartment_tags{1} '_points']) = surface_meshes(i_aux).Points;
zef.([zef.compartment_tags{1} '_triangles']) = surface_meshes(i_aux).Triangles(:,[1 3 2]);
zef.([zef.compartment_tags{1} '_submesh_ind']) = size(surface_meshes(i_aux).Triangles,1);
zef.([zef.compartment_tags{1} '_sigma']) = compartment_settings{i,10};
zef.([zef.compartment_tags{1} '_activity']) = compartment_settings{i,12};
if not(isempty(surface_meshes(i_aux).Color))
zef.([zef.compartment_tags{1} '_color']) = surface_meshes(i_aux).Color;
end
zef = zef_build_compartment_table(zef);
end
end

I_on = find(zef_bst.compartment_on_vec);
ind_vec_aux = find(ind_vec_aux(I_on));
ref_vec_vol = find(ref_vec_vol(ind_vec_aux));
ref_vec_surf = find(ref_vec_surf(ind_vec_aux));

ref_vec_vol = find(ref_vec_vol);
ref_vec_surf = find(ref_vec_surf);

zef.refinement_on = 1;
zef.mesh_smoothing_on = zef_bst.mesh_smoothing_on;
zef.distance_smoothing_on = zef_bst.distance_smoothing_on;
Expand All @@ -111,18 +109,18 @@
zef.refinement_volume_compartments = ref_vec_vol;
zef.mesh_resolution = zef_bst.mesh_resolution;
zef.use_fem_mesh_inflation = zef_bst.inflation_on;
zef.fem_mesh_inflation_strength = zef_bst.inflation_strength;
zef.fem_mesh_inflation_strength = zef_bst.inflation_strength; if zef.([zef.temp_var_0 '_on'])
zef.max_surface_face_count = zef_bst.surface_mesh_density;
zef.priority_mode = zef_bst.priority_mode;
zef.extensive_relabeling = zef_bst.extensive_relabeling;

run(zef_bst.import_settings);

zef = zef_turn_compartment_onoff(zef,zef_bst.compartment_on_vec)
zef = zef_turn_compartment_onoff(zef,[zef_bst.compartment_on_vec 1]);
zef = zef_process_meshes(zef);

if not(isempty(zef_bst.labeling_priority))
zef = zef_update_labeling_priority(zef,[],zef_bst.labeling_priority);
zef = zef_update_labeling_priority(zef,[],zef_bst.labeling_priority);
end

if not(isempty(char(project_file_name)))
Expand Down
3 changes: 3 additions & 0 deletions m/zef_create_sensors.m
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,9 @@
{'visible_list','[]'}
{'names_visible','1'}
{'color_table','[]'}
{'electrode_impedance', '2000'}
{'electrode_inner_radius', '2'}
{'electrode_outer_radius', '5'}
{'get_functions','cell(0)'}};

for i = 1 : length(field_cell_default)
Expand Down
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