Rename folder matlab_tools -> +simnibsMATLAB

simnibs/+simnibsMATLAB/@gifti/gifti.m

@@ -0,0 +1,179 @@
+classdef gifti
+% GIfTI Geometry file format class
+% Geometry format under the Neuroimaging Informatics Technology Initiative
+% (NIfTI):
+%                 http://www.nitrc.org/projects/gifti/
+%                      http://nifti.nimh.nih.gov/
+%__________________________________________________________________________
+% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+    properties
+
+        metadata (1,1) struct = struct % TODO: short documentation here.
+
+        label (1,1) struct = struct % TODO: short documentation here.
+
+        data (1,:) cell = struct % TODO: short documentation here.
+
+        mat % TODO: add size, class and default value restrictions here.
+
+        faces % TODO: add size, class and default value restrictions here.
+
+        vertices % TODO: add size, class and default value restrictions here.
+
+        cdata (1,1) struct = struct % TODO: short documentation here.
+
+        indices % TODO: add size, class and default value restrictions here.
+
+    end % properties
+
+    methods
+
+        function this = gifti(varargin)
+        % GIfTI Geometry file format class
+        % Geometry format under the Neuroimaging Informatics Technology Initiative
+        % (NIfTI):
+        %                 http://www.nitrc.org/projects/gifti/
+        %                      http://nifti.nimh.nih.gov/
+        %__________________________________________________________________________
+        % Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
+
+        % Guillaume Flandin
+        % $Id: gifti.m 7621 2019-06-20 16:58:59Z guillaume $
+
+            switch nargin
+
+                case 0
+
+                    this = simnibsMATLAB.gifti(giftistruct) ;
+
+                case 1
+                    if isa(varargin{1},'simnibsMATLAB.gifti')
+                        this = varargin{1};
+
+                    elseif isstruct(varargin{1})
+                        f       = {'faces', 'face', 'tri' 'vertices', 'vert', 'pnt', 'cdata', 'indices'};
+                        ff      = {'faces', 'faces', 'faces', 'vertices', 'vertices', 'vertices', 'cdata', 'indices'};
+                        [c, ia] = intersect(f,fieldnames(varargin{1}));
+                        if ~isempty(c)
+
+                            for i=1:length(c)
+                                fieldName = ff{ia(i)} ;
+                                this.(fieldName) = varargin{1}.(c{i}) ;
+                            end
+                            if isfield(varargin{1},'mat')
+                                this.mat = varargin{1}.mat ;
+                            end
+                        elseif isempty(setxor(fieldnames(varargin{1}), {'metadata','label','data'}))
+                            this = this ;
+                        else
+                            error('[GIFTI] Invalid structure.');
+                        end
+
+                    elseif ishandle(varargin{1})
+
+                        this = struct('vertices',get(varargin{1},'Vertices'), ...
+                                      'faces',   get(varargin{1},'Faces'));
+                        if ~isempty(get(varargin{1},'FaceVertexCData'))
+                              this.cdata = get(varargin{1},'FaceVertexCData');
+                        end
+                        this = simnibsMATLAB.gifti(this);
+
+                    elseif isnumeric(varargin{1})
+
+                        this = simnibsMATLAB.gifti;
+                        this.cdata = varargin{1};
+
+                    elseif iscell(varargin{1}) && numel(varargin{1}) == 1 && isnumeric(varargin{1}{1})
+                        this = simnibsMATLAB.gifti;
+                        for i=1:size(varargin{1}{1},2)
+                            this.data{i}.metadata = struct([]);
+                            this.data{i}.space    = [];
+                            this.data{i}.attributes.Intent = 'NIFTI_INTENT_NONE';
+                            this.data{i}.attributes.DataType = 'NIFTI_TYPE_FLOAT32';
+                            this.data{i}.attributes.Dim = size(varargin{1}{1},1);
+                            this.data{i}.data     = single(varargin{1}{1}(:,i));
+                        end
+
+                    elseif ischar(varargin{1})
+
+                        if size(varargin{1},1)>1
+                            this = simnibsMATLAB.gifti(cellstr(varargin{1}));
+                            return;
+                        end
+                        [~,~,e] = fileparts(varargin{1});
+                        if strcmpi(e,'.mat')
+                            try
+                                this = simnibsMATLAB.gifti(load(varargin{1}));
+                            catch
+                                error('[GIFTI] Loading of file %s failed.', varargin{1});
+                            end
+                        elseif ismember(lower(e),{'.asc','.srf','.mgh','.mgz','.pial',...
+                                '.white','.inflated','.nofix','.orig','.smoothwm',...
+                                '.sphere','.reg','.surf','.curv','.area','.sulc','.annot'})
+                            this = freesurfer_read(varargin{1});
+                            this = simnibsMATLAB.gifti(this);
+                        elseif strcmpi(e,'.vtk')
+                            this = mvtk_read(varargin{1});
+                            this = simnibsMATLAB.gifti(this);
+                        elseif strcmpi(e,'.obj')
+                            this = obj_read(varargin{1});
+                            this = simnibsMATLAB.gifti(this);
+                        elseif strcmpi(e,'.ply')
+                            this = ply_read(varargin{1});
+                            this = simnibsMATLAB.gifti(this);
+                        elseif strcmpi(e,'.off')
+                            this = off_read(varargin{1});
+                            this = simnibsMATLAB.gifti(this);
+                        elseif strcmpi(e,'.stl')
+                            this = stl_read(varargin{1});
+                            this = simnibsMATLAB.gifti(this);
+                        elseif strcmpi(e,'.mz3')
+                            this = mz3_read(varargin{1});
+                            this = simnibsMATLAB.gifti(this);
+                        else
+                            this = gifti_read(varargin{1},giftistruct);
+                            this = simnibsMATLAB.gifti(this);
+                        end
+
+                    elseif iscellstr(varargin{1})
+                        fnames = varargin{1};
+                        this(numel(fnames)) = simnibsMATLAB.gifti(giftistruct);
+                        for i=1:numel(fnames)
+                            this(i) = simnibsMATLAB.gifti(fnames{i});
+                        end
+
+                    else
+                        error('[GIFTI] Invalid object construction.');
+                    end
+
+                otherwise
+                    error('[GIFTI] Invalid object construction.');
+            end % switch
+        end % function
+    end % methods
+end % classdef
+
+%==========================================================================
+function s = giftistruct
+s = struct(...
+    'metadata', ...
+        struct(...
+            'name',       {}, ...
+            'value',      {} ...
+        ), ...
+    'label', ...
+        struct(...
+            'name',       {}, ...
+            'index',      {} ...
+        ), ...
+    'data', ...
+        struct(...
+            'attributes', {}, ...
+            'metadata',   struct('name',{}, 'value',{}), ...
+            'space',      {}, ...
+            'data',       {} ...
+        ) ...
+    );
+
+end % function

simnibs/matlab_tools/expand_to_center_surround.m → simnibs/+simnibsMATLAB/expand_to_center_surround.m

@@ -37,14 +37,14 @@
 s.N=[];
 s.multichannel=[];
 s.phis_surround=[];
-s=parse_input(s,varargin{:});
+s=simnibsMATLAB.parse_input(s,varargin{:});
 
 fn_in  = [tempname,'.mat'];
 fn_out = [tempname,'.mat'];
 save(fn_in,'-struct','tdcslist', '-v7')
 
 % Run expand_to_center_surround
-cmdstr = [simnibs_cli_call('expand_to_center_surround') ...
+cmdstr = [simnibsMATLAB.simnibs_cli_call('expand_to_center_surround') ...
            ' -S ' fn_in ' -p ' subpath ' -F ' fn_out ];
 fn = fieldnames(s);
 for k=1:numel(fn)
@@ -76,4 +76,3 @@
 S_out = load(fn_out);
 delete(fn_in);
 delete(fn_out);
-

simnibs/matlab_tools/get_data_and_scaleLimits.m → simnibs/+simnibsMATLAB/get_data_and_scaleLimits.m

@@ -1,10 +1,10 @@
 function [data, name, scaleLimits, varargout] = get_data_and_scaleLimits(m,field_idx,datatype,scaleLimits)
 % returns the data, the field name and fills in the scaleLimits (if they
 % are empty); optionally, also the element sizes are returned
-% 
+%
 % USAGE:
-%  [data, name, scaleLimits] = get_data_and_scaleLimits(m,field_idx,datatype,scaleLimits)
-%  [data, name, scaleLimits, elemsizes] = get_data_and_scaleLimits(m,field_idx,datatype,scaleLimits)
+%  [data, name, scaleLimits] = simnibsMATLAB.get_data_and_scaleLimits(m,field_idx,datatype,scaleLimits)
+%  [data, name, scaleLimits, elemsizes] = simnibsMATLAB.get_data_and_scaleLimits(m,field_idx,datatype,scaleLimits)
 %
 % The scale limits are determined as follows:
 % [0 absmax] for positive-only data;
@@ -33,18 +33,18 @@
 if isempty(scaleLimits)||(nargout>3)
     if strcmpi(datatype,'tet')
         % tet volumes
-        elemsizes=mesh_get_tetrahedron_sizes(m);
+        elemsizes=simnibsMATLAB.mesh_get_tetrahedron_sizes(m);
     elseif strcmpi(datatype,'tri')
         % triangle areas
-        elemsizes=mesh_get_triangle_sizes(m);
+        elemsizes=simnibsMATLAB.mesh_get_triangle_sizes(m);
     else % node data
         if ~isempty(m.triangles)&&~isempty(m.tetrahedra)
             disp('Both tets and triangles found: Ambiguity to assign sizes to nodes')
             error('mesh has to contain either tets or triangles, not both');
         end
         if isempty(m.triangles)
             % use tet volumes to get node sizes
-            elemsizes=mesh_get_tetrahedron_sizes(m);
+            elemsizes=simnibsMATLAB.mesh_get_tetrahedron_sizes(m);
             elemsizes=elemsizes/4;
             nodesizes=zeros(size(m.nodes,1),1);
             for i=1:size(m.tetrahedra,1)
@@ -53,7 +53,7 @@
             elemsizes=nodesizes;
         else
             % use tri areas to get node sizes
-            elemsizes=mesh_get_triangle_sizes(m);          
+            elemsizes=simnibsMATLAB.mesh_get_triangle_sizes(m);
             elemsizes=elemsizes/3;
             nodesizes=zeros(size(m.nodes,1),1);
             for i=1:size(m.triangles,1)
@@ -70,9 +70,9 @@
 % get element postions if needed
 if nargout>4
     if strcmpi(datatype,'tet')
-        varargout{2}=mesh_get_tetrahedron_centers(m);
+        varargout{2}=simnibsMATLAB.mesh_get_tetrahedron_centers(m);
     elseif strcmpi(datatype,'tri')
-        varargout{2}=mesh_get_triangle_centers(m);
+        varargout{2}=simnibsMATLAB.mesh_get_triangle_centers(m);
     else
         varargout{2}=m.nodes;
     end
@@ -86,11 +86,11 @@
     else
         dataHlp=data;
     end
-    
+
     idx=~isnan(dataHlp);
     dataHlp=dataHlp(idx);
     elemsizesHlp=elemsizes(idx);
-    
+
     [dataHlp,idx] = sort(dataHlp);
     elemsizesHlp=elemsizesHlp(idx);
     elemsizesHlp=cumsum(elemsizesHlp);
@@ -106,4 +106,4 @@
         absmax=max([-dataHlp(idx) scaleLimits(2)]);
         scaleLimits = [-absmax absmax];
     end
-end
+end

simnibs/matlab_tools/get_fields_at_coordinates.m → simnibs/+simnibsMATLAB/get_fields_at_coordinates.m

@@ -23,18 +23,18 @@
 if ischar(mesh)
     assert(exist(mesh, 'file') == 2, ['Could not find mesh file ' mesh])
     fn_mesh = mesh;
-    is_temp = false; 
+    is_temp = false;
 else
     is_temp = true;
     fn_mesh = [tempname '.msh'];
-    mesh_save_gmsh4(mesh, fn_mesh)
+    simnibsMATLAB.mesh_save_gmsh4(mesh, fn_mesh)
 end
 
 fn_in = [tempname,'.csv'];
 csvwrite(fn_in, coords);
 
 % Run mni2subject_coords
-[status,result] = system([simnibs_cli_call('get_fields_at_coordinates')...
+[status,result] = system([simnibsMATLAB.simnibs_cli_call('get_fields_at_coordinates')...
                          ' -m ' fn_mesh ' -s ' fn_in, ' --out_fill ' out_fill]);
 if status ~= 0
     if is_temp
@@ -60,4 +60,4 @@
 end
 delete(fn_in);
 
-end
+end

simnibs/matlab_tools/mesh_extract_regions.m → simnibs/+simnibsMATLAB/mesh_extract_regions.m

@@ -3,15 +3,15 @@
 % deletes unused nodes, elment_data entries and updates the node numbers
 %
 % USAGE:
-%   m=mesh_extract_regions(m, [,'OptionName',OptionValue,...]) 
+%   m=mesh_extract_regions(m, [,'OptionName',OptionValue,...])
 %
 %   m: input mesh
-%  
+%
 %   Options are set using the option name followed by the value.
 %   elemtype: determines the element type to extract
 %             ('tri', 'tet' or 'both'; standard: 'both')
 %   region_idx: extracts the elements with the given region numbers
-%   keepAllNodes: when set to true, do not remove unused nodes and 
+%   keepAllNodes: when set to true, do not remove unused nodes and
 %                 do not update node numbers (standard: false)
 %   node_idx: indices of the nodes to keep (standard: keep all)
 %   tri_idx: indices of the triangles to keep
@@ -22,7 +22,7 @@
 %  m=mesh_extract_regions(m, 'elemtype','tet'); % delete all triangles
 %  m=mesh_extract_regions(m, 'region_idx', [5 1005]);
 %             % keep tetrahedra and triangles with region numbers 5 or 1005
-%         
+%
 % A. Thielscher 11-Apr-2018, based on prior code from M. Windhoff
 % A.Thielscher: updated 03-Oct-2018, added 'node_idx', 'tri_idx' and
 %               'tet_idx' options
@@ -57,7 +57,7 @@
 if nargin<1
     error('at least one argument is needed');
 end
-s=parse_input(s,varargin{:});
+s=simnibsMATLAB.parse_input(s,varargin{:});
 
 keepTri=false;
 keepTet=false;
@@ -85,7 +85,7 @@
              idx_kept_tri = idx_kept_tri | m.triangle_regions==s.region_idx(i);
         end
     end
-    
+
     if ~isempty(s.tri_idx)
         if islogical(s.tri_idx)&&length(s.tri_idx)~=size(m.triangles,1)
             error('logical index must have same length as number of triangles')
@@ -107,7 +107,7 @@
              idx_kept_tet = idx_kept_tet | m.tetrahedron_regions==s.region_idx(i);
         end
     end
-    
+
     if ~isempty(s.tet_idx)
         if islogical(s.tet_idx)&&length(s.tet_idx)~=size(m.tetrahedra,1)
             error('logical index must have same length as number of tets')
@@ -128,7 +128,7 @@
 else
     idx_kept_nodes(unique(m.triangles(idx_kept_tri,:)))=true;
     idx_kept_nodes(unique(m.tetrahedra(idx_kept_tet,:)))=true;
-    
+
     if ~isempty(s.node_idx)
         if islogical(s.node_idx)&&length(s.node_idx)~=size(m.nodes,1)
             error('logical index must have same length as number of nodes')
@@ -139,7 +139,7 @@
             s.node_idx=idx_hlp;
         end
         idx_kept_nodes = idx_kept_nodes&s.node_idx;
-        
+
         % delete affected triangles and tets
         idx_kept_tri=idx_kept_tri&(sum(idx_kept_nodes(m.triangles),2)==3);
         idx_kept_tet=idx_kept_tet&(sum(idx_kept_nodes(m.tetrahedra),2)==4);
@@ -168,7 +168,7 @@
     if ~isempty(m.element_data{i}.tridata)
         m.element_data{i}.tridata=m.element_data{i}.tridata(idx_kept_tri,:);
     end
-    
+
     if ~isempty(m.element_data{i}.tetdata)
         m.element_data{i}.tetdata=m.element_data{i}.tetdata(idx_kept_tet,:);
     end