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SVMCrossVal.git
somtoolbox2
som_set.m
starting som prediction fine-tuned class-performance visualisation
Christoph Budziszewski
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4dbef18
at 2009-01-21 16:34:25
som_set.m
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function [sS, ok, msgs] = som_set(sS, varargin) %SOM_SET Create and check SOM Toolbox structs, give values to their fields. % % [sS, ok, msgs] = som_set(sS, [field, contents, ...]) % % sM = som_set(sM,'name','SOM#1.1'); % [dummy,ok,msgs] = som_set(sData); % sT = som_set('som_topol','msize',[10 10],'lattice','hexa'); % [sTrain,ok] = som_set(sTrain,'algorithm','lininit'); % [sN,ok,msgs] = som_set('som_norm'); % % Input and output arguments ([]'s are optional): % sS the target struct % (struct) a SOM Toolbox structure (not visualization struct) % (string) structure identifier (see below) % the updated/created structure is returned % [field, (string) field to be given value to (see below) % contents] (varies) the contents for the field % % ok (vector) status for each field-contents pair (1=ok) % msgs (cellstr) status string for each field-contents pair (''=ok) % % There can be arbitrarily many field-contents pairs. If there % are _no_ field-content pairs, and the first argument is a struct, % the fields of the struct are checked for validity. % % Valid struct and corresponding field identifiers: % 'som_map' : 'codebook', 'labels', 'mask', 'neigh', 'name', % 'topol', 'msize, 'lattice', 'shape', % 'trainhist', 'comp_names', 'comp_norm', % 'som_data' : 'data', 'labels', 'name', 'comp_names', 'comp_norm', % 'label_names' % 'som_topol' : 'msize', 'lattice', 'shape' % 'som_norm' : 'method', 'params', 'status' % 'som_train' : 'algorithm', 'data_name', 'mask', 'neigh', % 'radius_ini', 'radius_fin', 'alpha_ini', 'alpha_type', % 'trainlen', 'time' % 'som_grid' : 'lattice', 'shape', 'msize', 'coord', % 'line', 'linecolor', 'linewidth', % 'marker', 'markersize', 'markercolor', 'surf', % 'label', 'labelcolor', 'labelsize' % checking given values has not been implemented yet! % % For more help, try 'type som_set' or check out online documentation. % See also SOM_INFO, SOM_MAP_STRUCT, SOM_DATA_STRUCT, SOM_VS1TO2. %%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % som_set % % PURPOSE % % Create and set values for fields of SOM Toolbox structs (except % visualization struct). Can also be used to check the validity of structs. % % SYNTAX % % sMap = som_set('som_map'); % sData = som_set(sData); % sNorm = som_set(...,'field',contents,...); % [sTopol,ok] = som_set(sTopol,...); % [sTrain,ok,msgs] = som_set('som_train',...); % % DESCRIPTION % % The function is used to create and set values for fields of SOM % Toolbox structs, except visualization structs. The given values are % first checked for validity, and if they are not valid, an error % message is returned. The function can also be used to check the % validity of all the fields of the struct by supplying a struct as % the first and only argument. % % NOTE: Using SOM_SET to create structures does _not_ guarantee that the % structs are valid (try e.g. sM = som_set('som_map'); som_set(sM)). The % initial values that the function gives to the fields of the structs are % typically invalid. It is recommended that when creating map or data % structs, the corresponding functions SOM_MAP_STRUCT and SOM_DATA_STRUCT % are used instead of SOM_SET. However, when giving values for the fields, % SOM_SET tries to guarantee that the values are valid. % % If a string is given as the first argument, the corresponding % structure is first created and the field-content pairs are then % applied to it. % % There can be arbitrarily many field-contents pairs. The pairs % are processed sequentially one pair at a time. For each pair, % the validity of the contents is checked and the corresponding % items in the returned 'ok'-vector and 'msgs'-cellstring are set. % - if the contents is ok, the status is set to 1 and message to '' % - if the contents is suspicious, status is set to 1, but a % message is produced % - if the contents is invalid, status is set to 0 and an error % message is produced. The contents are _not_ given to the field. % If there is only one output argument, the status and messages % for each pair are printed to standard output. % % The different field-contents pairs have no effect on each other. % If a field is given a value multiple times, the last valid one % stays in effect. % % In some cases, the order of the given fields is significant. % For example in the case of 'som_map', the validity of some fields, % like '.comp_names', depends on the input space dimension, which is % checked from the '.data' field (dim = size(sD.data,2) to be specific). % Therefore, the '.data' field (or '.codebook' field in case of map % struct) should always be given a value first. Below is a list of % this kind of dependancies: % % som_map: 'comp_names', 'comp_norm', 'msize', 'topol.msize', % 'labels' and 'mask' depend on 'codebook' % new value for 'codebook' should have equal size to the old % one (unless the old one was empty) % som_data: 'comp_names' and 'comp_norm' depend on 'data' % new value for 'data' should have equal dimension (size(data,2)) % as the old one (unless the old one was empty) % % KNOWN BUGS % % Checking the values given to som_grid struct has not been % implemented. Use SOM_GRID function to give the values. % % REQUIRED INPUT ARGUMENTS % % sS The struct. % (struct) A SOM Toolbox struct. % (string) Identifier of a SOM Toolbox struct: 'som_map', % 'som_data', 'som_topol', 'som_norm' or 'som_train' % % OPTIONAL INPUT ARGUMENTS % % field (string) Field identifier string (see below). % contents (varies) Value for the field (see below). % % Below is the list of valid field identifiers for the different % SOM Toolbox structs. % % 'som_map' (map struct) % 'codebook' : matrix, size [munits, dim] % 'labels' : cell array of strings, % size [munits, maximum_number_of_labels] % 'topol' : topology struct (prod(topol.msize)=munits) % 'mask' : vector, size [dim, 1] % 'neigh' : string ('gaussian' or 'cutgauss' or 'bubble' or 'ep') % 'trainhist' : struct array of train structs % 'name' : string % 'comp_names' : cellstr, size [dim, 1], e.g. {'c1','c2','c3'} % 'comp_norm' : cell array, size [dim, 1], of cell arrays % of normalization structs % Also the following can be used (although they are fields % of the topology struct) % 'msize' : vector (prod(msize)=munits) % 'lattice' : string ('rect' or 'hexa') % 'shape' : string ('sheet' or 'cyl' or 'toroid') % % 'som_data' (data struct) % 'data' : matrix, size [dlen, dim] % 'name' : string % 'labels' : cell array of strings, % size [dlen, m] % 'comp_names' : cellstr, size [dim, 1], e.g. {'c1','c2','c3'} % 'comp_norm' : cell array, size [dim, 1], of cell arrays % of normalization structs % 'label_names' : cellstr, size [m, 1] % % 'som_topol' (topology struct) % 'msize' : vector % 'lattice' : string ('rect' or 'hexa') % 'shape' : string ('sheet' or 'cyl' or 'toroid') % % 'som_norm' (normalization struct) % 'method' : string % 'params' : varies % 'status' : string ('done' or 'undone' or 'uninit') % % 'som_train' (train struct) % 'algorithm' : string ('seq' or 'batch' or 'lininit' or 'randinit') % 'data_name' : string % 'mask' : vector, size [dim, 1] % 'neigh' : string ('gaussian' or 'cutgauss' or 'bubble' or 'ep') % 'radius_ini' : scalar % 'radius_fin' : scalar % 'alpha_ini' : scalar % 'alpha_type' : string ('linear' or 'inv' or 'power') % 'trainlen' : scalar % 'time' : string % % 'som_grid' (grid struct) : checking the values has not been implemented yet! % 'lattice' : string ('rect' or 'hexa') or % (sparce) matrix, size munits x munits % 'shape' : string ('sheet' or 'cyl' or 'toroid') % 'msize' : vector, size 1x2 % 'coord' : matrix, size munits x 2 or munits x 3 % 'line' : string (linespec, e.g. '-', or 'none') % 'linecolor' : RGB triple or string (colorspec, e.g. 'k') or % munits x munits x 3 (sparce) matrix or cell % array of RGB triples % 'linewidth' : scalar or munits x munits (sparce) matrix % 'marker' : string (markerspec, e.g. 'o', or 'none') or % munits x 1 cell or char array of these % 'markersize' : scalar or munits x 1 vector % 'markercolor' : RGB triple or string (colorspec, e.g. 'k') % 'surf' : [], munits x 1 or munits x 3 matrix of RGB triples % 'label' : [] or munits x 1 char array or % munits x l cell array of strings % 'labelcolor' : RGB triple or string (colorspec, e.g. 'g' or 'none') % 'labelsize' : scalar % % OUTPUT ARGUMENTS % % sS (struct) the created / updated struct % ok (vector) length = number of field-contents pairs, gives % validity status for each pair (0=invalid, 1 otherwise) % msgs (cellstr) length = number of field-contents pairs, gives % error/warning message for each pair ('' if ok) % % EXAMPLES % % To create a struct: % sM = som_set('som_map'); % sD = som_set('som_data'); % sTo = som_set('som_topol'); % sTr = som_set('som_train'); % sN = som_set('som_norm'); % sG = som_set('som_grid'); % % To check the the contents of a struct: % som_set(sS); % [dummy,ok] = som_set(sS); % [dummy,ok,msgs] = som_set(sS); % % To give values to fields: % sTo = som_set(sTo,'msize',[10 10],'lattice','hexa','shape','toroid'); % sM = som_set('som_map','codebook',rand(100,4),'topol',sTo); % % SEE ALSO % % som_info Prints information the given struct. % som_map_struct Create map struct. % som_data_struct Create data struct. % som_topol_struct Create topology struct. % som_train_struct Create training struct. % som_grid Create and visualize grid struct. % som_vs1to2 Conversion from version 1.0 structs to 2.0. % som_vs2to1 Conversion from version 2.0 structs to 1.0. % Copyright (c) 1999-2000 by the SOM toolbox programming team. % http://www.cis.hut.fi/projects/somtoolbox/ % Version 2.0beta juuso 101199 130300 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% create struct if necessary if ischar(sS), switch sS case 'som_map', sS=struct('type', 'som_map', ... 'codebook', [], ... 'topol', som_set('som_topol'), ... 'labels', cell(1), ... 'neigh', 'gaussian', ... 'mask', [], ... 'trainhist', cell(1), ... 'name', '',... 'comp_names', {''}, ... 'comp_norm', cell(1)); case 'som_data', sS=struct('type', 'som_data', ... 'data', [], ... 'labels', cell(1), ... 'name', '', ... 'comp_names', {''}, ... 'comp_norm', cell(1), ... 'label_names', []); case 'som_topol', sS=struct('type', 'som_topol', ... 'msize', 0, ... 'lattice', 'hexa', ... 'shape', 'sheet'); case 'som_train', sS=struct('type', 'som_train', ... 'algorithm', '', ... 'data_name', '', ... 'neigh', 'gaussian', ... 'mask', [], ... 'radius_ini', NaN, ... 'radius_fin', NaN, ... 'alpha_ini', NaN, ... 'alpha_type', 'inv', ... 'trainlen', NaN, ... 'time', ''); case 'som_norm', sS=struct('type', 'som_norm', ... 'method', 'var', ... 'params', [], ... 'status', 'uninit'); case 'som_grid', sS=struct('type','som_grid',... 'lattice','hexa',... 'shape','sheet',... 'msize',[1 1],... 'coord',[],... 'line','-',... 'linecolor',[.9 .9 .9],... 'linewidth',0.5,... 'marker','o',... 'markersize',6,... 'markercolor','k',... 'surf',[],... 'label',[],... 'labelcolor','g',... 'labelsize',12); otherwise ok=0; msgs = {['Unrecognized struct type: ' sS]}; sS = []; return; end elseif isstruct(sS) & length(varargin)==0, % check all fields fields = fieldnames(sS); if ~any(strcmp('type',fields)), error('The struct has no ''type'' field.'); end k = 0; for i=1:length(fields), contents = getfield(sS,fields{i}); if ~strcmp(fields{i},'type'), varargin{k+1} = fields{i}; varargin{k+2} = contents; k = k + 2; else if ~any(strcmp(contents, ... {'som_map','som_data','som_topol','som_train','som_norm'})), error(['Unknown struct type: ' contents]); end end end end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% set field values p = ceil(length(varargin)/2); ok = ones(p,1); msgs = cell(p,1); for i=1:p, field = varargin{2*i-1}; content = varargin{2*i}; msg = ''; isok = 0; si = size(content); isscalar = (prod(si)==1); isvector = (sum(si>1)==1); isrowvector = (isvector & si(1)==1); if isnumeric(content), iscomplete = all(~isnan(content(:))); ispositive = all(content(:)>0); isinteger = all(content(:)==ceil(content(:))); isrgb = all(content(:)>=0 & content(:)<=1) & size(content,2)==3; end switch sS.type, case 'som_map', [munits dim] = size(sS.codebook); switch field, case 'codebook', if ~isnumeric(content), msg = '''codebook'' should be a numeric matrix'; elseif size(content) ~= size(sS.codebook) & ~isempty(sS.codebook), msg = 'New ''codebook'' must be equal in size to the old one.'; elseif ~iscomplete, msg = 'Map codebook must not contain NaN''s.'; else sS.codebook = content; isok=1; end case 'labels', if isempty(content), sS.labels = cell(munits,1); isok = 1; elseif size(content,1) ~= munits, msg = 'Length of labels array must be equal to the number of map units.'; elseif ~iscell(content) & ~ischar(content), msg = '''labels'' must be a string array or a cell array/matrix.'; else isok = 1; if ischar(content), content = cellstr(content); elseif ~iscellstr(content), l = prod(size(content)); for j=1:l, if ischar(content{j}), if ~isempty(content{j}), msg = 'Invalid ''labels'' array.'; isok = 0; break; else content{j} = ''; end end end end if isok, sS.labels = content; end end case 'topol', if ~isstruct(content), msg = '''topol'' should be a topology struct.'; elseif ~isfield(content,'msize') | ... ~isfield(content,'lattice') | ... ~isfield(content,'shape'), msg = '''topol'' is not a valid topology struct.'; elseif prod(content.msize) ~= munits, msg = '''topol''.msize does not match the number of map units.'; else sS.topol = content; isok = 1; end case 'msize', if ~isnumeric(content) | ~isvector | ~ispositive | ~isinteger, msg = '''msize'' should be a vector with positive integer elements.'; elseif prod(content) ~= munits, msg = '''msize'' does not match the map size.'; else sS.topol.msize = content; isok = 1; end case 'lattice', if ~ischar(content), msg = '''lattice'' should be a string'; elseif ~strcmp(content,'rect') & ~strcmp(content,'hexa'), msg = ['Unknown lattice type: ' content]; sS.topol.lattice = content; isok = 1; else sS.topol.lattice = content; isok = 1; end case 'shape', if ~ischar(content), msg = '''shape'' should be a string'; elseif ~strcmp(content,'sheet') & ~strcmp(content,'cyl') & ... ~strcmp(content,'toroid'), msg = ['Unknown shape type:' content]; sS.topol.shape = content; isok = 1; else sS.topol.shape = content; isok = 1; end case 'neigh', if ~ischar(content), msg = '''neigh'' should be a string'; elseif ~strcmp(content,'gaussian') & ~strcmp(content,'ep') & ... ~strcmp(content,'cutgauss') & ~strcmp(content,'bubble'), msg = ['Unknown neighborhood function: ' content]; sS.neigh = content; isok = 1; else sS.neigh = content; isok = 1; end case 'mask', if size(content,1) == 1, content = content'; end if ~isnumeric(content) | size(content) ~= [dim 1], msg = '''mask'' should be a column vector (size dim x 1).'; else sS.mask = content; isok = 1; end case 'name', if ~ischar(content), msg = '''name'' should be a string.'; else sS.name = content; isok = 1; end case 'comp_names', if ~iscell(content) & ~ischar(content), msg = '''comp_names'' should be a cell string or a string array.'; elseif length(content) ~= dim, msg = 'Length of ''comp_names'' should be equal to dim.'; else if ischar(content), content = cellstr(content); end if size(content,1)==1, content = content'; end sS.comp_names = content; isok = 1; end case 'comp_norm', if ~iscell(content) & length(content)>0, msg = '''comp_norm'' should be a cell array.'; elseif length(content) ~= dim, msg = 'Length of ''comp_norm'' should be equal to dim.'; else isok = 1; for j=1:length(content), if ~isempty(content{j}) & (~isfield(content{j}(1),'type') | ... ~strcmp(content{j}(1).type,'som_norm')), msg = 'Each cell in ''comp_norm'' should be either empty or type ''som_norm''.'; isok = 0; break; end end if isok, sS.comp_norm = content; end end case 'trainhist', if ~isstruct(content) & ~isempty(content), msg = '''trainhist'' should be a struct array or empty.'; else isok = 1; for j=1:length(content), if ~isfield(content(j),'type') | ~strcmp(content(j).type,'som_train'), msg = 'Each cell in ''trainhist'' should be of type ''som_train''.'; isok = 0; break; end end if isok, sS.trainhist = content; end end otherwise, msg = ['Invalid field for map struct: ' field]; end case 'som_data', [dlen dim] = size(sS.data); switch field, case 'data', [dummy dim2] = size(content); if prod(si)==0, msg = '''data'' is empty'; elseif ~isnumeric(content), msg = '''data'' should be numeric matrix.'; elseif dim ~= dim2 & ~isempty(sS.data), msg = 'New ''data'' must have the same dimension as old one.'; else sS.data = content; isok = 1; end case 'labels', if isempty(content), sS.labels = cell(dlen,1); isok = 1; elseif size(content,1) ~= dlen, msg = 'Length of ''labels'' must be equal to the number of data vectors.'; elseif ~iscell(content) & ~ischar(content), msg = '''labels'' must be a string array or a cell array/matrix.'; else isok = 1; if ischar(content), content = cellstr(content); elseif ~iscellstr(content), l = prod(size(content)); for j=1:l, if ~ischar(content{j}), if ~isempty(content{j}), msg = 'Invalid ''labels'' array.'; isok = 0; j break; else content{j} = ''; end end end end if isok, sS.labels = content; end end case 'name', if ~ischar(content), msg = '''name'' should be a string.'; else sS.name = content; isok = 1; end case 'comp_names', if ~iscell(content) & ~ischar(content), msg = '''comp_names'' should be a cell string or a string array.'; elseif length(content) ~= dim, msg = 'Length of ''comp_names'' should be equal to dim.'; else if ischar(content), content = cellstr(content); end if size(content,1)==1, content = content'; end sS.comp_names = content; isok = 1; end case 'comp_norm', if ~iscell(content) & length(content)>0, msg = '''comp_norm'' should be a cell array.'; elseif length(content) ~= dim, msg = 'Length of ''comp_norm'' should be equal to dim.'; else isok = 1; for j=1:length(content), if ~isempty(content{j}) & (~isfield(content{j}(1),'type') | ... ~strcmp(content{j}(1).type,'som_norm')), msg = 'Each cell in ''comp_norm'' should be either empty or type ''som_norm''.'; isok = 0; break; end end if isok, sS.comp_norm = content; end end case 'label_names', if ~iscell(content) & ~ischar(content) & ~isempty(content), msg = ['''label_names'' should be a cell string, a string array or' ... ' empty.']; else if ~isempty(content), if ischar(content), content = cellstr(content); end if size(content,1)==1, content = content'; end end sS.label_names = content; isok = 1; end otherwise, msg = ['Invalid field for data struct: ' field]; end case 'som_topol', switch field, case 'msize', if ~isnumeric(content) | ~isvector | ~ispositive | ~isinteger, msg = '''msize'' should be a vector with positive integer elements.'; else sS.msize = content; isok=1; end case 'lattice', if ~ischar(content), msg = '''lattice'' should be a string'; elseif ~strcmp(content,'rect') & ~strcmp(content,'hexa'), msg = ['Unknown lattice type: ' content]; sS.lattice = content; isok = 1; else sS.lattice = content; isok = 1; end case 'shape', if ~ischar(content), msg = '''shape'' should be a string'; elseif ~strcmp(content,'sheet') & ~strcmp(content,'cyl') & ... ~strcmp(content,'toroid'), msg = ['Unknown shape type: ' content]; sS.shape = content; isok = 1; else sS.shape = content; isok = 1; end otherwise, msg = ['Invalid field for topology struct: ' field]; end case 'som_train', switch field, case 'algorithm', if ~ischar(content), msg = '''algorithm'' should be a string.'; else sS.algorithm = content; isok = 1; end case 'data_name', if ~ischar(content), msg = '''data_name'' should be a string'; else sS.data_name = content; isok = 1; end case 'neigh', if ~ischar(content), msg = '''neigh'' should be a string'; elseif ~isempty(content) & ~strcmp(content,'gaussian') & ~strcmp(content,'ep') & ... ~strcmp(content,'cutgauss') & ~strcmp(content,'bubble'), msg = ['Unknown neighborhood function: ' content]; sS.neigh = content; isok = 1; else sS.neigh = content; isok = 1; end case 'mask', if size(content,1) == 1, content = content'; end dim = size(content,1); %[munits dim] = size(sS.data); if ~isnumeric(content) | size(content) ~= [dim 1], msg = '''mask'' should be a column vector (size dim x 1).'; else sS.mask = content; isok = 1; end case 'radius_ini', if ~isnumeric(content) | ~isscalar, msg = '''radius_ini'' should be a scalar.'; else sS.radius_ini = content; isok = 1; end case 'radius_fin', if ~isnumeric(content) | ~isscalar, msg = '''radius_fin'' should be a scalar.'; else sS.radius_fin = content; isok = 1; end case 'alpha_ini', if ~isnumeric(content) | ~isscalar, msg = '''alpha_ini'' should be a scalar.'; else sS.alpha_ini = content; isok = 1; end case 'alpha_type', if ~ischar(content), msg = '''alpha_type'' should be a string'; elseif ~strcmp(content,'linear') & ~strcmp(content,'inv') & ... ~strcmp(content,'power') & ~strcmp(content,'constant') & ~strcmp(content,''), msg = ['Unknown alpha type: ' content]; sS.alpha_type = content; isok = 1; else sS.alpha_type = content; isok = 1; end case 'trainlen', if ~isnumeric(content) | ~isscalar, msg = '''trainlen'' should be a scalar.'; else sS.trainlen = content; isok = 1; end case 'time', if ~ischar(content), msg = '''time'' should be a string'; else sS.time = content; isok = 1; end otherwise, msg = ['Invalid field for train struct: ' field]; end case 'som_norm', switch field, case 'method', if ~ischar(field), msg = '''method'' should be a string.'; else sS.method = content; isok = 1; end case 'params', sS.params = content; isok = 1; case 'status', if ~ischar(content), msg = '''status'' should be a string'; elseif ~strcmp(content,'done') & ~strcmp(content,'undone') & ... ~strcmp(content,'uninit'), msg = ['Unknown status type: ' content]; sS.status = content; isok = 1; else sS.status = content; isok = 1; end otherwise, msg = ['Invalid field for normalization struct: ' field]; end case 'som_grid', if any(strcmp(field,{'lattice', 'shape', 'msize', 'coord',... 'line', 'linecolor', 'linewidth', ... 'marker', 'markersize', 'markercolor', 'surf', ... 'label', 'labelcolor', 'labelsize'})), warning('No checking done on field identifier or content.'); sS = setfield(sS,field,content); isok = 1; else msg = ['Invalid field for grid struct: ' field]; end otherwise, error('Unrecognized structure.'); end msgs{i} = msg; ok(i) = isok; end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% return if nargout < 2, for i=1:p, if ~isempty(msgs{i}), if ~ok(i), fprintf(1,'[Error! '); else fprintf(1,'[Notice '); end fprintf(1,'in setting %s] ',varargin{2*i-1}); fprintf(1,'%s\n',msgs{i}); end end end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%