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SVMCrossVal.git
somtoolbox2
som_cplane.m
starting som prediction fine-tuned class-performance visualisation
Christoph Budziszewski
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at 2009-01-21 16:34:25
som_cplane.m
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function h=som_cplane(varargin) %SOM_CPLANE Visualize one 2D component plane, U-matrix or color plane. % % h=som_cplane(lattice, msize, color, [s], [pos]) % h=som_cplane(topol, color, [s], [pos]) % % som_cplane('hexa', [10 5], 'none'); % som_cplane('rect', [10 5], 'r'); % som_cplane(sM.topol, sM.codebook(:,1)); % U = som_umat(sM); som_cplane('hexaU',sM.topol.msize,U(:)); % % Input and output arguments ([]'s are optional): % lattice (string) 'hexa', 'rect' (component planes) % 'hexaU', 'rectU' (corresponding U-matrices) % (matrix) defines the patch (see function VIS_PATCH). % msize (vector) 1x2 vector defines grid size (M=prod(msize)) % (matrix) Mx2 matrix gives explicit coordinates for each node % topol (struct) map or topology struct % color color for the nodes % (matrix) Mx1 matrix gives indexed colors for the units % Mx3 matrix of RGB triples gives explicit % color for each unit % (Note: in case of U-matrix, the number of color % values is 4*prod(msize)-2*sum(msize)+1, not prod(msize)) % (string) ColorSpec gives the same color for each node % 'none' draws black edges only. % [s] (matrix) size Mx1, gives individual size scaling for each node % (scalar) gives the same size for each node, default=1. % Additional features: see 'type som_cplane' % This argument is ignored if the lattice is 'rectU' or 'hexaU'. % [pos] (vector) a 1x2 vector that determines position of origin, % default is [1 1]. % % h (scalar) the object handle for the PATCH object % % Axis are set to the 'ij' mode with equal spacing and turned off if % 'pos' is not given. If 'lattice' is 'rect', 'hexa', 'rectU' or % 'hexaU' the node (a,b) has coordinates (a,b) (+pos), except on the % even numbered rows on the 'hexa' and 'hexaU' grids where the % coordinates are (a,b+0.5) (+pos). % % For more help, try 'type som_cplane' or check out online documentation. % See also SOM_PIEPLANE, SOM_PLOTPLANE, SOM_BARPLANE, VIS_PATCH, % SOM_VIS_COORDS %%%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % som_cplane % % PURPOSE % % Visualizes a 2D component plane or u-matrix % % SYNTAX % % h = som_cplane(topol, color) % h = som_cplane(lattice, msize, color) % h = som_cplane(lattice, msize, color) % h = som_cplane(..., size) % h = som_cplane(..., size, pos) % % DESCRIPTION % % Creates some basic visualizations of the SOM grid: the component plane and % the unified distance matrix. The routine draws the SOM grid as a patch % object according to the specifications given in the input arguments and % returns its object handle. % % Each unit of the map is presented by a polygon whose color, size, shape % and location can be specified in various ways. The usual procedure % is to choose the lattice and map size used in the map training. Then % the function creates the standard sheet shaped topological % representation of the map grid with hexagonal or rectangular units. % When the values from a map codebook component (or from SOM_UMAT) % are given to the function it produces an indexed coloring for the % units (as in SURF command). Another possibility is to give a fixed % RGB color for each unit explicitly. % % Special effects (variable unit size, location or shape) can be produced % giving different types of input variables. % % KNOWN BUGS % % Using 1x3 or 3x1 grids causes problem, as the MATLAB will treat the color % information vector 1x3 or 3x1 as a single RGB triple. So, using indexed % colors is not possible for this particular map size. % % It is not possible to specify explicit coordinates for map % consistig of just one unit as then the msize is interpreted as % map size. % % REQUIRED INPUT ARGUMENTS % % Note: M is the number of map units % % lattice The basic shape of the map units % % (string) 'hexa' or 'rect' creates standard component plane; % 'hexaU' or 'rectU' creates standard u-matrix. % (matrix) Lx2 matrix defines the cornes of an arbitary polygon to be used % as the unit marker. (L is the number of patch vertex: L=6 for % 'hexa' and L=4 for 'rect') % % msize The size of the map grid % % (vector) [n1 n2] vector defines the map size (height n1 units, width % n2 units, total M=n1 x n2 units). The units will be placed to their % topological locations to form a uniform hexagonal or rectangular grid. % (matrix) Mx2 matrix defines arbitrary coordinates for the M units % In this case the argument 'lattice' defines the unit form only. % % topol Topology of the map grid % % (struct) map or topology struct from which the topology is taken % % color Unit colors % % (string) (ColorSpec) gives the same color for each unit, 'none' % draws black unit edges only. % (vector) Mx1 column vector gives indexed color for each unit using the % current colormap (see help colormap). % (matrix) Mx3 matrix of RGB triples as rows gives each unit a fixed color. % % OPTIONAL INPUT ARGUMENTS % % Note: M is the number of map units. % Note: if unspecified or given empty values ('' or []) default % values are used for optional input arguments. % % s The size scaling factors for the units % % (scalar) scalar gives each unit the same size scaling: % 0 unit disappears (edges can be seen as a dot). % 1 by default unit has its normal size (ie. no scaling) % >1 unit overlaps others % (matrix) Mx1 double: each unit gets individual size scaling % % pos Position of origin % % (vector) This argument exists to be able drawing component planes % in arbitrary locations in a figure. Note the operation: % if this argument is given, the axis limits setting % part in the routine is skipped and the limits setting % will be left to be done by MATLAB's default % operation. % % OUTPUT ARGUMENTS % % h (scalar) handle to the created patch object % % OBJECT TAGS % % One object handle is returned: field Tag is set to % 'planeC' for component plane % 'planeU' for U-matrix % % FEATURES % % There are some extra features in following arguments % % size % - MxL matrix: radial scaling: the distance between % the center of node m and its kth vertex is scaled by % s(m,k). % - Mx1x2 matrix: the uniform scaling is done separately for % x- and y-directions % - MxLx2 matrix: the scaling is done separately to x- and y- % directions for each vertex. % % color % Each vertex may be given individual color. % The PATCH object interpolates the colors on the % face if shading is turned to interp. % - 1xMxL matrix: colormap index for each vertex % - LxMx3 matrix: RGB color for each vertex % % Note: In both cases (size and color) the ordering of the patch % vertices in the "built-in" patches is the following % % 'rect' 'hexa' % 1 3 1 % 2 4 5 2 % 6 3 % 4 % % The color interpolation result seem to depend on the order % in which the patch vertices are defined. Anyway, it gives % unfavourable results in our case especially with hexa grid: % this is a MATLAB feature. % % EXAMPLES % % m=som_make(rand(100,4),'msize',[6 5]) % make a map % % % show the first variable plane using indexed color coding % % som_cplane(m.topol.lattice,m.topol.msize,m.codebook(:,1)); % or som_cplane(m.topol,m.codebook(:,1)); % or som_cplane(m,m.codebook(:,1)); % % % show the first variable using different sized black units % % som_cplane(m,'k',m.codebook(:,1)); % % % Show the u-matrix. First we have to calculate it. % % Note: som_umat returns a matrix therefore we write u(:) to get % % a vector which contains the values in the proper order. % % u=som_umat(m); % som_cplane('hexaU', m.topol.msize, u(:)); % % % Show three first variables coded as RGB colors % % and turn the unit edges off % % h=som_cplane(m, m.codebook(:,1:3),1) % set(h,'edgecolor','none'); % % % Try this! (see section FEATURES) % % som_cplane('rect',[5 5],'none',rand(25,4)); % som_cplane('rect',[5 5],rand(1,25,4)); % % SEE ALSO % % som_barplane Visualize the map prototype vectors as bar diagrams % som_plotplane Visualize the map prototype vectors as line graphs % som_pieplane Visualize the map prototype vectors as pie charts % som_umat Compute unified distance matrix of self-organizing map % vis_patch Define the basic patches used in som_cplane % som_vis_coords The default 'hexa' and 'rect' coordinates in visualizations % Copyright (c) 1999-2000 by the SOM toolbox programming team. % http://www.cis.hut.fi/projects/somtoolbox/ % Version 2.0beta Johan 061099 juuso 151199 juuso 070600 %%% Check & Init arguments %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% [nargin, lattice, msize, color, s, pos]=vis_planeGetArgs(varargin{:}); error(nargchk(3, 5, nargin)); % check no. of input args is correct %% Translation? if nargin < 5 | isempty(pos) pos=NaN; % "no translation" flag elseif ~vis_valuetype(pos,{'1x2'}), error('Position of origin has to be given as an 1x2 vector.'); end %% Patchform %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% switch class(lattice) case 'char' % built-in patchforms pos=pos-1; switch lattice case {'hexa', 'hexaU'} patchform=vis_patch('hexa'); case {'rect', 'rectU'} patchform=vis_patch('rect'); otherwise error([ 'Lattice ' lattice ' not implemented!']); end case { 'double', 'sparse'} if vis_valuetype(lattice,{'nx2'}), patchform=lattice; % users patchform lattice='rect'; else error('Patchform matrix has wrong size'); end otherwise error('String or matrix expected for lattice.'); end l=size(patchform,1); % number of vertices planeType=lattice(end); % 'U' if umatrix otherwise something else if ~vis_valuetype(msize,{ '1x2', 'nx2'}), error('msize has to be given as 1x2 or nx2 vectors.'); end %% msize or coordinates %%%%%%%%%%%%%%%%%%%%%%% if size(msize,1)>1 % msize is coordinate matrix Nx2? if planeType == 'U', % don't accept u-matrix error('U-matrix visualization doesn''t work with free coordinates.'); end % set number of map unit and unit coordinates munits=size(msize,1); unit_coords=msize; msize=[munits 1]; if isnan(pos), % no translation is done here pos=[0 0]; % using [0 0] in order to prevent end % axis tightening in % vis_PlaneAxisProperties (arbitary coords!) else % msize is built-in lattice unit_coords=som_vis_coords(lattice,msize); % Calculate matrices x and y which 'moves' nodes % to the correct positions: % For U-matrix, the size has to be recalculated if planeType == 'U', xdim=2*msize(1)-1;ydim=2*msize(2)-1; else xdim=msize(1);ydim=msize(2); end munits=xdim*ydim; % Feature warning if munits == 3 warning('Problems with 1x3 and 3x1 maps. See documentation.'); end end %% Color matrix %%%%%%%%%%%%%%%%%%%%%%%%%%%%% if ~isnumeric(color) & ~ischar(color), error('Color matrix is invalid.'); else d=size(color); switch length(d) case 2 %% Flat colors if ischar(color) % Check for string 'none' if strcmp(color,'none'), color=NaN; end else if ~(d(1)== 1 & d(2) == 3) & ... ~(d(1) == munits & (d(2)==1 | d(2)==3)) error('Color data matrix has wrong size.'); elseif d(1)~=1 & d(2)==3 if any(color>1 | color<0) error('Color data matrix has invalid RGB values.'); end color=reshape(color,[1 munits 3]); % RGB colors elseif d(2)==1 color=color'; % indexed end end case 3 %% Interpolated colors if d(1) == 1 & d(2) == munits & d(3) == l, color=reshape(color, l, munits); elseif ~(d(1) == l & d(2) == munits & d(3) == 3) error('Color data matrix has wrong size.'); end otherwise error('Color data matrix has too many dimensions.'); end end %% Size matrix? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% if nargin < 4 | isempty(s), s=1; % default value for s (no scaling) elseif ~isnumeric(s) error('Size matrix is not numeric.'); end %%Determine the type of size matrix d=size(s); switch length(d) case 2 if (d(1)==1 & d(2)==1), % Each node gets the same, uniform scaling. s=s'; sx=s; sy=s; elseif (d(1)==munits & d(2)==l), % Each vertex is scaled radially respetc to the % node center. s=s'; sx=s; sy=s; elseif d(1)==munits & d(2)==1 % Each node gets an individual uniform scaling. sx=repmat(s',l,1); sy=sx; else error('Size matrix has wrong size.'); end case 3 if d(1)==munits & d(2)==1 & d(3)==2, % Each node is individually and uniformly % scaled separately to x- and y-directions. sx=repmat(shiftdim(s(:,:,1))',l,1); sy=repmat(shiftdim(s(:,:,2))',l,1); elseif d(1)==munits & d(2)==l & d(3)==2, % Each vertex is scaled separately to x- and y-directions % with respect to the node center. sx=shiftdim(s(:,:,1))'; sy=shiftdim(s(:,:,2))'; else error('Size matrix has wrong size.'); end otherwise error('Size matrix has too many dimensions.'); end % Size zero would cause division by zero. eps is as good (node disappears) % I tried first NaN, it works well otherwise, but the node is % then not on the axis and some commands may the work oddly. % The edge may be visible, though. sx(sx==0)=eps; sy(sy==0)=eps; % Rescale sizes for u-matrix if planeType=='U', sx=sx/2;sy=sy/2; end %%%% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Making grid. %%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Translation for each patch x=repmat(unit_coords(:,1)',l,1); y=repmat(unit_coords(:,2)',l,1); % patch vertex coordiantes nx=repmat(patchform(:,1),1,munits); ny=repmat(patchform(:,2),1,munits); % NB: The hexagons are not uniform in order to get even % y-coordinates for the nodes. This is handled by setting _axis scaling_ % so that the hexa-nodes look like uniform hexagonals. See % vis_PlaneAxisProperties %% Make and scale the final input for PATCH: % 1: combine translation and scaling of each patch x=(x./sx+nx).*sx; y=(y./sy+ny).*sy; %% 2: translation of origin (pos) if ~isnan(pos) x=x+pos(1);y=y+pos(2); % move upper left corner end % to pos %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Set axes properties %% Command view([0 90]) shows the map in 2D properly oriented ax=newplot; % set new plot vis_PlaneAxisProperties(ax,lattice,msize,pos); %% Draw the map! if ~isnan(color) h_=patch(x,y,color); else h_=patch(x,y,'k'); % empty grid set(h_,'FaceColor','none'); end %% Set object tag if planeType=='U' set(h_,'Tag','planeU'); else set(h_,'Tag','planeC'); end %%% Build output %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% if nargout>0, h=h_; end % Set h only, % if there really is output
