wolffd@0: function h=som_show_add(mode,D,varargin)
wolffd@0: 
wolffd@0: %SOM_SHOW_ADD Shows hits, labels and trajectories on SOM_SHOW visualization
wolffd@0: %
wolffd@0: % h = som_show_add(mode, D, ['argID',value,...])
wolffd@0: %
wolffd@0: %  som_show_add('label',sMap)
wolffd@0: %  som_show_add('hit',som_hits(sMap,sD))
wolffd@0: %  som_show_add('traj',som_bmus(sMap,sD))
wolffd@0: %  som_show_add('comet',som_bmus(sMap,sD))
wolffd@0: %  som_show_add('comet',inds, 'markersize', [1 0.2])
wolffd@0: % 
wolffd@0: %  Input and output arguments ([]'s are optional): 
wolffd@0: %   mode    (string) operation mode 'label', 'hit', 'traj', 'comet'
wolffd@0: %   D       (varies) depending on operation mode
wolffd@0: %      In 'label' mode gives the labels  
wolffd@0: %           (struct) map struct, the .labels field of which is used
wolffd@0: %           (cell array of strings) size munits x number_of_labels
wolffd@0: %      In 'hit' mode gives the hit histogram(s)
wolffd@0: %           (matrix) size munits x k, if k>1, D gives hit histograms 
wolffd@0: %                    for k different sets of data (e.g. k classes).     
wolffd@0: %      In 'traj' and 'comet' modes gives the trace of the trajectory
wolffd@0: %           (vector) size N x 1, D(1) is the current and D(end) 
wolffd@0: %                    is oldest item of the trajectory
wolffd@0: %   [argID, (string) Additional arguments are given as argID, value
wolffd@0: %    value] (varies) pairs. Depend on the operation mode (see below).                   
wolffd@0: %
wolffd@0: %   h    (vector)    handles to the created objects
wolffd@0: %
wolffd@0: % Here are the valid argument IDs and corresponding values. Most of 
wolffd@0: % them depend on the operation mode: 
wolffd@0: %
wolffd@0: % all modes
wolffd@0: %   'SubPlot'   (vector) which subplots are affected (default: current)
wolffd@0: %               (string) 'all': all subplots are affected 
wolffd@0: % mode = 'label'
wolffd@0: %   'TextSize'  (scalar) text size in points
wolffd@0: %   'TextColor' (string) ColorSpec, 'xor' or 'none': label color 
wolffd@0: %
wolffd@0: % mode = 'hit'
wolffd@0: %   'EdgeColor'  (string) ColorSpec, 'none' 
wolffd@0: %   'MarkerSize' (scalar) maximum marker size
wolffd@0: %  if k == 1, 
wolffd@0: %   'Marker'     (string) 'lattice', Matlab's built-in markerstyles, 'none'
wolffd@0: %   'MarkerColor'(string) Colorspec, 'none': fill color for markers
wolffd@0: %   'Text'       (string) 'on', 'off':  whether to write the number of hits
wolffd@0: %   'TextColor'  (string) ColorSpec, 'xor': text color if Text is 'on'
wolffd@0: %   'TextSize'   (scalar) text font size in points if Text is 'on'
wolffd@0: %  if k > 1, 
wolffd@0: %   'SizeFactor' (string) 'common', 'separate': size scaling
wolffd@0: %   'Marker'     (string) 'lattice', Matlab's built-in markerstyles, 'pie', 'none' 
wolffd@0: %                (cell array) size k x 1, marker style for each histogram
wolffd@0: %   'MarkerColor'(string) Colorspec, 'none': fill color for markers
wolffd@0: %                (matrix) size k x 3, color for each histogram
wolffd@0: %
wolffd@0: % mode = 'traj'
wolffd@0: %   'TrajWidth'  (scalar) basic trajectory line width in points
wolffd@0: %   'WidthFactor'(string) 'hit' or 'equal': effect of hits on line width 
wolffd@0: %   'TrajColor'  (string) ColorSpec, 'xor': color for trajectory line
wolffd@0: %   'Marker'     (string) 'lattice', Matlab's built-in markerstyles, 'none'
wolffd@0: %   'MarkerSize' (scalar) basic marker size (in points)
wolffd@0: %   'SizeFactor' (string) 'equal', 'hit' (equal size/size depends on freq.) 
wolffd@0: %   'MarkerColor'(string) Colorspec, 'none': color of markers
wolffd@0: %   'EdgeColor'  (string) ColorSpec, 'none': edgecolor of markers 
wolffd@0: %
wolffd@0: % mode = 'comet'
wolffd@0: %   'Marker'     (string) 'lattice', Matlab's built-in markerstyles
wolffd@0: %   'MarkerColor'(string) ColorSpec, 'none': color for the markers
wolffd@0: %                (matrix) size N x 3, RGB color for each step 
wolffd@0: %   'EdgeColor'  (string) ColorSpec, 'none': edgecolor for markers
wolffd@0: %   'MarkerSize' (vector) size 1 x 2, size of comet core and tail
wolffd@0: % 
wolffd@0: % For more help, try 'type som_show_add' or check out online documentation.
wolffd@0: % See also SOM_SHOW.
wolffd@0: 
wolffd@0: %%%%%%%%%%%% DETAILED DESCRIPTION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: %
wolffd@0: % som_show_add 
wolffd@0: %
wolffd@0: % PURPOSE 
wolffd@0: %
wolffd@0: %  Shows hits, labels and trajectories on SOM_SHOW visualization
wolffd@0: %
wolffd@0: % SYNTAX
wolffd@0: %
wolffd@0: %  h = som_show_add(mode, D); 
wolffd@0: %  h = som_show_add(..., 'argID', value);
wolffd@0: %
wolffd@0: % DESCRIPTION 
wolffd@0: %
wolffd@0: % The SOM_SHOW function makes the basic visualization of the SOM.
wolffd@0: % With SOM_SHOW_ADD one can set labels, hit histogarms or different 
wolffd@0: % trajectories on this visualization.
wolffd@0: %
wolffd@0: %  labels (mode = 'label')
wolffd@0: %
wolffd@0: % Labels are strings describing the units. They may be, e.g., a result
wolffd@0: % of SOM_AUTOLABEL function. Labels are centered on the unit so that
wolffd@0: % multiple labels are in a column.
wolffd@0: %
wolffd@0: %  hit histograms (mode = 'hit')
wolffd@0: %
wolffd@0: % Hit histograms indicate how the best matching units of a data
wolffd@0: % set/some data sets are distribited on a SOM. The hit histogram can
wolffd@0: % be calculated using function SOM_HITS.
wolffd@0: %
wolffd@0: %  trajectories (mode = 'traj' or mode = 'comet')
wolffd@0: %
wolffd@0: % Trajectories show the best matching units for a data set that is
wolffd@0: % time (or any ordered) series. It may be either a line connecting the
wolffd@0: % consecutive best matching units ('traj' mode) or a "comet"
wolffd@0: % trajectory where the current (first sample in D) best matching unit
wolffd@0: % has biggest marker and the oldest (last sample) has smallest
wolffd@0: % marker ('comet' mode).
wolffd@0: %
wolffd@0: % NOTE: that the SOM_SHOW_ADD function can only be applied to
wolffd@0: % figures that have been drawn by SOM_SHOW.
wolffd@0: % 
wolffd@0: % KNOWN BUGS
wolffd@0: %
wolffd@0: % for 'hit' mode, if the given hit matrix is all zeros, a series of 
wolffd@0: % error messages is generated
wolffd@0: % 
wolffd@0: % REQUIRED INPUT ARGUMENTS
wolffd@0: %
wolffd@0: % mode     (string) Visuzalization mode 
wolffd@0: %                   'label'  map labeling
wolffd@0: %                   'hit'    hit histograms
wolffd@0: %                   'traj'   line style trajectory
wolffd@0: %                   'comet'  comet style trajectory 
wolffd@0: %
wolffd@0: % D (vector, map struct, cell array of strings) Data
wolffd@0: %
wolffd@0: % The valid value of D depends on the visualization mode:
wolffd@0: %
wolffd@0: %  Mode       Valid D
wolffd@0: %  'label'    map struct or Mxl cell array of strings, where
wolffd@0: %              M is number of map units and l maximum numer of
wolffd@0: %              labels in unit.
wolffd@0: %
wolffd@0: %  'hit'      Mx1 vector or MxK matrix, where M is number of map
wolffd@0: %             units and K is number of hit histograms (of K
wolffd@0: %             different classes of data) to be shown
wolffd@0: %
wolffd@0: %  'comet'    Lx1 vector of best matchig unit indices that have to
wolffd@0: %  'traj'     be in range of the map that is in the figure. L is 
wolffd@0: %             the length of trajectory
wolffd@0: %             
wolffd@0: % OPTIONAL INPUT ARGUMENTS
wolffd@0: %
wolffd@0: % Optional arguments must be given as 'argument identifier', value
wolffd@0: % -pairs. This section is divided in four parts because each mode
wolffd@0: % functions in a different way, though they may have same identifier
wolffd@0: % names.
wolffd@0: %
wolffd@0: % If user specifies an identifier that is not operational in the
wolffd@0: % specified mode, the functions gives a warning message. If the
wolffd@0: % identifier does not exist in any mode the execution is terminated
wolffd@0: % and an error message is returned.
wolffd@0: %
wolffd@0: % GENERAL OPTIONAL INPUT ARGUMENTS (in all modes)
wolffd@0: %
wolffd@0: % 'SubPlot'     Target subplots in the figure    
wolffd@0: %      (vector) Subplots' ordinal numbers in a vector. By default
wolffd@0: %               the target is the current subplot (see GCA).
wolffd@0: %      (string) String 'all' means all subplots. 
wolffd@0: %
wolffd@0: % 'Marker'      Data marker (not in use in 'label' mode)
wolffd@0: %      (string) 'none': sets the markers off
wolffd@0: %               'lattice': sets the marker shape according to the
wolffd@0: %                lattice of the underlying map, i.e. it gives
wolffd@0: %                rectangles if underlying map lattice is 'rect' and
wolffd@0: %                hexagons for 'hexa', respectively
wolffd@0: %               any of the Matlab's built-in marker styles: 'o', 's',
wolffd@0: %               'd', 'v', '^', '<' ,'> ', 'p', 'h', 'x', '.', '*', '+'
wolffd@0: %      
wolffd@0: %               NOTE that '.','x','+' or '*' are not recommended since
wolffd@0: %               they have only edgecolor and many visualizations are 
wolffd@0: %               based on _face_ color. 
wolffd@0: %
wolffd@0: %               NOTE there is an important difference between built-in
wolffd@0: %               markers. If figure size is changed the 'lattice'
wolffd@0: %               markers are rescaled but the built-in markers stay at
wolffd@0: %               fixed size, and consequently, the size unit for
wolffd@0: %               'lattice' markers is normalized but for built-in
wolffd@0: %               markers the size is given in points. For 'lattice'
wolffd@0: %               markers size 1 means the size of the map unit.
wolffd@0: %
wolffd@0: %               NOTE that in 'hit' mode there are some additional features.
wolffd@0: %
wolffd@0: % 'EdgeColor'   Sets edgecolor for the markers (not in use in 'label' mode)
wolffd@0: %      (string) ColorSpec, e.g. 'r',  gives each edge the specified color
wolffd@0: %               'none': sets markers edges invisible 
wolffd@0: %               Default is 'none' - except if MarkerColor is set to 'none' the
wolffd@0: %               defaults is 'black'.
wolffd@0: %
wolffd@0: % OPTIONAL INPUT ARGUMENTS mode 'label'
wolffd@0: %
wolffd@0: % Labels are centered on the unit so that multiple labels are in
wolffd@0: % a single column.
wolffd@0: %
wolffd@0: % 'SubPlot'     see General Optional Input Arguments 
wolffd@0: %
wolffd@0: % 'TextSize'    Text size for labels
wolffd@0: %      (scalar) Text size in points. Default is 10.
wolffd@0: %
wolffd@0: % 'TextColor'   Text color
wolffd@0: %      (string) ColorSpec specifies the text color for all labels 
wolffd@0: %               'xor': gives Matlab's "xor" text color mode where the 
wolffd@0: %                label color depends on background color     
wolffd@0: %               'none': sets labels invisble (but creates the objects)
wolffd@0: %
wolffd@0: % OPTIONAL INPUT ARGUMENTS mode 'hit'
wolffd@0: %
wolffd@0: % The function in mode 'hit' depends on the input argument size. If
wolffd@0: % only one hit histogram is drawn (K==1), it is possible to show the
wolffd@0: % hits using numbers. This is not possible for multiple hit
wolffd@0: % histograms (K>1).
wolffd@0: %
wolffd@0: % 'SubPlot'     see General Optional Input Arguments 
wolffd@0: %        
wolffd@0: % 'Marker'      Marker style(s)
wolffd@0: %      (string) As in General Optional Input Arguments. In addition 
wolffd@0: %               'pie': sets pie charts for markers. The size of the
wolffd@0: %                pie in each unit describes the number of total hits in the
wolffd@0: %                unit and the share of each sector is the relative amount of
wolffd@0: %                hits in each class (requires multiple histograms). Color for
wolffd@0: %                each class is set by MarkerColor. Default coloring 
wolffd@0: %                is hsv(K), where K is the number of hit histograms (classes).
wolffd@0: %      (cell array) size K x 1, of built-in marker style characters. K is
wolffd@0: %               number of histograms (classes), i.e., same as size(D,2)
wolffd@0: %               where D is the second input argument. Cell value is
wolffd@0: %               valid only if multiple histograms are specified (K>1). 
wolffd@0: % 
wolffd@0: %               NOTE if multiple histograms (classes) are specified
wolffd@0: %               and Marker is one of the built-in marker styles or
wolffd@0: %               'lattice', the markers are drawn in size order from
wolffd@0: %               largest to smallest. This insures that all markers are
wolffd@0: %               visible (or at least their edges are). But if two
wolffd@0: %               markers for different classes in the same node were of
wolffd@0: %               same size, the other would be totally hidden. In order
wolffd@0: %               to prevent this, the markers for different classes are
wolffd@0: %               shifted different amounts from the exact centre of the
wolffd@0: %               unit. (Evidently, if Marker is 'pie' this problem does
wolffd@0: %               not exist.)
wolffd@0: %
wolffd@0: %               Default marker is 'lattice' for one histogram and
wolffd@0: %               'pie' for multiple histograms.
wolffd@0: %
wolffd@0: % 'MarkerColor' Marker color(s) 
wolffd@0: %      (string) ColorSpec gives all markers the same color
wolffd@0: %               'none': leaves the markes transparent (only edges are visible)
wolffd@0: %      (matrix) size K x 3, RGB triples for each histogram class
wolffd@0: %               giving each hit histogram an own color
wolffd@0: %
wolffd@0: %               NOTE that markers '*','+','x', or '.' cannot use 
wolffd@0: %               MarkerColor since these objects have no face (fill)
wolffd@0: %               color. For them only EdgeColor matters.
wolffd@0: % 
wolffd@0: % 'MarkerSize'  Maximum size for marker
wolffd@0: %      (scalar) set the _maximum_ marker size that corresponds to
wolffd@0: %               maximum hit count. If Marker is 'pie' or 'lattice' the 
wolffd@0: %               MarkerSize is in normalized scale: 1 correspons to unit size.
wolffd@0: %               If Marker is one of the built-in styles, MarkerSize is given
wolffd@0: %               in points.  
wolffd@0: %               
wolffd@0: %               Marker        Default MarkerSize  
wolffd@0: %               'lattice'      1 (normalized units)
wolffd@0: %               'pie'          1 (normalized units) 
wolffd@0: %               'o','s', etc.  6 (points)
wolffd@0: %
wolffd@0: % 'SizeFactor'  Defines the scaling of the marker sizes in multiple
wolffd@0: %               histogram case (when Marker is one of the built-in marker 
wolffd@0: %               styles or 'lattice').
wolffd@0: %      (string) 'separate' (the default) means that marker size shows 
wolffd@0: %                the share of the data which hits the unit compared to 
wolffd@0: %                amount of data in that class. That is, the size of
wolffd@0: %                markers show the relative distribution of data on the map 
wolffd@0: %                in each class separately. The maximum size is SizeFactor.       
wolffd@0: %               'common' means that marker size shows the distribution of
wolffd@0: %                the data in the different classes compared to 
wolffd@0: %                _the total amount of data_. 
wolffd@0: %
wolffd@0: % 'EdgeColor'   Sets edgecolor for the markers, see General
wolffd@0: %               Optional Input Arguments. Default is 'none' -
wolffd@0: %               except if MarkerColor is 'none' or Marker is
wolffd@0: %               'x','*,'x', or '.'. In these cases default EdgeColor is 'black'. 
wolffd@0: %
wolffd@0: % 'Text'        Write/don't write the number of hits on the
wolffd@0: %               units. This option is not in use for multiple histograms.
wolffd@0: %      (string) 'on' or 'off' (the default)
wolffd@0: %
wolffd@0: % 'TextColor'   Text color 
wolffd@0: %      (string) ColorSpec gives each letter the same color
wolffd@0: %               'xor' gives a "xor" coloring for the text
wolffd@0: %
wolffd@0: % 'TextSize'    Text size (in points)    
wolffd@0: %      (scalar) text size in points, default is 10
wolffd@0: %
wolffd@0: % OPTIONAL INPUT ARGUMENTS mode 'traj'
wolffd@0: %
wolffd@0: % Input D is a Nx1 vector of N BMU indices that describe the trace of the 
wolffd@0: % comet. First element D(1) is "newest" and D(end) "oldest". Note
wolffd@0: % that at least two indeces are expected: size of D must be at
wolffd@0: % least 2x1.
wolffd@0: %
wolffd@0: % 'SubPlot'     see General Optional Input Arguments
wolffd@0: %
wolffd@0: % 'TrajColor'   Color for trajectory line
wolffd@0: %      (string) ColorSpec gives each marker the same color, 'w' by default
wolffd@0: %               'none' sets the marker fill invisible: only edges are shown
wolffd@0: %
wolffd@0: % 'TrajWidth'   Maximum width of trajectory line
wolffd@0: %      (scalar) width in points. Default is 3.
wolffd@0: %
wolffd@0: % 'WidthFactor' Shows how often edge between two units has been traversed.
wolffd@0: %      (string) 'hit': the size of the marker shows how frequent the
wolffd@0: %                trajectory visits the unit (TrajWidth sets the
wolffd@0: %                maximum size). This is the default.
wolffd@0: %               'equal': all lines have the same width (=TrajWidth)
wolffd@0: %
wolffd@0: % 'Marker'      Marker style, see General Optional Input
wolffd@0: %               Arguments. Default is 'o'.
wolffd@0: %    
wolffd@0: %               NOTE Marker style 'lattice' is not valid in mode 'traj'.
wolffd@0: %               NOTE Markers can be turned off by setting MarkerSize to zero.
wolffd@0: %
wolffd@0: % 'MarkerSize'  Maximum size of markers
wolffd@0: %      (scalar) Default is 12 (points).
wolffd@0: %
wolffd@0: % 'SizeFactor'  Sets the frequency based marker size or constant marker size.                  
wolffd@0: %      (string) 'hit': the size of the marker shows how frequent the
wolffd@0: %                trajectory visits the unit (MarkerSize sets the
wolffd@0: %                maximum size). This is the default.
wolffd@0: %               'equal': all markers have th esame size (=MarkerSize)
wolffd@0: %
wolffd@0: % 'MarkerColor' The fill color(s) for hit markers
wolffd@0: %      (string) ColorSpec gives each marker the same color, default is 'w'
wolffd@0: %               'none' sets the marker fill invisible: only edges are shown
wolffd@0: %
wolffd@0: %               NOTE markers '*','+','x', or '.' can't use MarkerColor since
wolffd@0: %               these objects have no face (fill) color: only EdgeColor
wolffd@0: %               matters for these markers.
wolffd@0: % 
wolffd@0: % 'EdgeColor'   see General Optional Input Arguments. Default is
wolffd@0: %               'none' - except if MarkerColor is 'none' or Marker
wolffd@0: %               is 'x','*','x', or '.'. In these cases default
wolffd@0: %               EdgeColor is 'white'. 
wolffd@0: %
wolffd@0: % OPTIONAL INPUT ARGUMENTS mode 'comet'
wolffd@0: %
wolffd@0: % Input D is a Nx1 vector of N BMU indices that describe the trace of
wolffd@0: % the comet. First element D(1) is "newest" and D(end) "oldest". Note
wolffd@0: % that at least two indeces are expected: size of D must be at least
wolffd@0: % 2x1.
wolffd@0: %
wolffd@0: % 'SubPlot'     see General Optional Input Arguments 
wolffd@0: %
wolffd@0: % 'Marker'      Marker style, see General Optional Input
wolffd@0: %               Arguments. Default is 'lattice'.
wolffd@0: %
wolffd@0: % 'MarkerColor' The fill color(s) for comet markers
wolffd@0: %      (string) ColorSpec gives each marker the same color, default is 'w'
wolffd@0: %               'none' sets the marker fill invisible: only edges are shown 
wolffd@0: %      (matrix) size N x 3, consisting of RGB triples as rows 
wolffd@0: %               sets different color for each marker. This may be
wolffd@0: %               used to code the time series using color/grayscale.
wolffd@0: %
wolffd@0: %               NOTE Markers '*','+','x', or '.' can't use MarkerColor
wolffd@0: %               since these objects have no face (fill) color: only 
wolffd@0: %               EdgeColor matters for these markers.
wolffd@0: % 
wolffd@0: % 'EdgeColor'   see General Optional Input Arguments. Default is
wolffd@0: %               'none' - except if MarkerColor is 'none' or Marker
wolffd@0: %               is 'x','*,'x', or '.'. In these cases default 
wolffd@0: %               EdgeColor is 'white'. 
wolffd@0: %
wolffd@0: % 'MarkerSize'  The size of "comet core" and tail 
wolffd@0: %      (vector) size 1 x 2: first element sets the size for the marker
wolffd@0: %               representing D(1) and the second set size for D(end)
wolffd@0: %               the size (area) of the markes between these changes linearly.
wolffd@0: %               Note that size units for 'lattice' marker style are
wolffd@0: %               normalized so that 1 means map unit size but for built-in
wolffd@0: %               marker styles the size is given points.
wolffd@0: %
wolffd@0: %               Marker          default value
wolffd@0: %               'lattice'        [0.8 0.1]
wolffd@0: %               'o','v', etc.    [20 4]
wolffd@0: %
wolffd@0: % OUTPUT ARGUMENTS
wolffd@0: %
wolffd@0: % h (vector) handles to all objects created by the function
wolffd@0: % 
wolffd@0: % OBJECT TAGS
wolffd@0: %
wolffd@0: %  Field Tag in every object is set to
wolffd@0: %
wolffd@0: %   'Lab'  for objects created in mode 'label'
wolffd@0: %   'Hit'                -"-           'hit'
wolffd@0: %   'Traj'               -"-           'traj'
wolffd@0: %   'Comet'              -"-           'comet'
wolffd@0: %
wolffd@0: % EXAMPLES
wolffd@0: %
wolffd@0: % Not yet ready
wolffd@0: %
wolffd@0: % SEE ALSO
wolffd@0: %             
wolffd@0: %  som_show       Basic map visualization
wolffd@0: %  som_show_clear Clear hit marks, labels or trajectories from current figure. 
wolffd@0: 
wolffd@0: % Copyright (c) 1999-2000 by the SOM toolbox programming team.
wolffd@0: % http://www.cis.hut.fi/projects/somtoolbox/             
wolffd@0: 
wolffd@0: % Version 2.0beta Johan 131199
wolffd@0: 
wolffd@0: %% Check arguments %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: error(nargchk(2,Inf,nargin))     % check no. of input args
wolffd@0: 
wolffd@0: % Get data from the SOM_SHOW figure, exit if error
wolffd@0: 
wolffd@0: [handles,msg,lattice,msize,dim]=vis_som_show_data('all',gcf);    
wolffd@0: error(msg);                    
wolffd@0: 
wolffd@0: munits=prod(msize);
wolffd@0: % Initialize some variables: these must exist later; 
wolffd@0: % the default values are set by subfunctions
wolffd@0: 
wolffd@0: Property=init_properties;
wolffd@0: Property.handles=handles; 
wolffd@0: 
wolffd@0: %%% Check mode and that D is of right type & size for that mode 
wolffd@0: % mode has to be string
wolffd@0: if ~vis_valuetype(mode,{'string'}),
wolffd@0:   error('String value expected for first input argument (mode).');
wolffd@0: else                
wolffd@0:   mode=lower(mode); % case insensitive
wolffd@0:   mode_=mode;       % 'mode' is internal variable; 
wolffd@0:                     % for program constructs 'mode_' is shown to
wolffd@0:                     % user in some error messags
wolffd@0: end
wolffd@0: 
wolffd@0: switch mode         % check mode
wolffd@0:  case 'hit'
wolffd@0:   %%% Hit histogram visualization: vector [msize k]
wolffd@0:  
wolffd@0:   if ~vis_valuetype(D,{'nxm'}),
wolffd@0:     error('Hit visualization: a matrix expected for data input.');
wolffd@0:   elseif size(D,1) ~= prod(msize)
wolffd@0:     error('Hit visualization: data and map size do not match.');
wolffd@0:   end
wolffd@0:   % Multiple hit histograms
wolffd@0:   if size(D,2)>1
wolffd@0:     mode='mhit';
wolffd@0:     % Hit count musn't be negative
wolffd@0:     if any(D(:)<0),
wolffd@0:       error('Hit visualization: negative hit count in data not allowed!');
wolffd@0:     end
wolffd@0:   end
wolffd@0:  
wolffd@0:  case {'traj','comet'}
wolffd@0:   %%% Trajectory like visualizations
wolffd@0:   
wolffd@0:   if ~vis_valuetype(D,{'nx1'}),
wolffd@0:     error('Trajectory/Comet: a Nx1 vector expected for data input.');
wolffd@0:   elseif any(D>prod(msize))| any(D<1),
wolffd@0:     error('Trajectory/Comet: BMU indices out of range in data input.');
wolffd@0:   elseif any(fix(D)~=D),
wolffd@0:     warning('Trajectory/Comet: BMU indices not integer. Rounding...');
wolffd@0:   elseif size(D,1)<2
wolffd@0:     error('At least two BMU indexes expected.');
wolffd@0:   end
wolffd@0:   
wolffd@0:  case  'label' 
wolffd@0:   %%% Label visualizations
wolffd@0:   
wolffd@0:   if isstruct(D),                  % check if D is a map
wolffd@0:     [tmp,ok,tmp]=som_set(D);
wolffd@0:     if all(ok) & strcmp(D.type,'som_map') 
wolffd@0:       ;
wolffd@0:     else
wolffd@0:       error('Map struct is invalid!');
wolffd@0:     end
wolffd@0:     % Size check
wolffd@0:     if length(msize) ~= length(D.topol.msize) | ...
wolffd@0: 	  munits ~= prod(D.topol.msize),
wolffd@0:       error(['The size of the input map and the map in the figure' ...
wolffd@0: 	     ' do not match.']);
wolffd@0:     end
wolffd@0:     D=D.labels;
wolffd@0:     % Cell input  
wolffd@0:   elseif vis_valuetype(D,{'2Dcellarray_of_char'}) 
wolffd@0:     ;
wolffd@0:     % Char input   
wolffd@0:   elseif vis_valuetype(D,{'char_array'}),
wolffd@0:     D=cellstr(D);
wolffd@0:   else
wolffd@0:     error(['Labels has to be in a map struct or in a cell array' ...
wolffd@0: 	   ' of strings']);
wolffd@0:   end
wolffd@0:   if size(D,1) ~= munits
wolffd@0:     error(['The number of labels does not match the size of the map' ...
wolffd@0: 	   ' in the figure.']);
wolffd@0:   end
wolffd@0:  otherwise
wolffd@0:   error('Invalid visualization mode.');
wolffd@0: end  
wolffd@0: 
wolffd@0: if rem(length(varargin),2)
wolffd@0:   error('Mismatch in identifier-value pairs or wrong input argument order.');
wolffd@0: end
wolffd@0: 
wolffd@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: %  read in optional arguments
wolffd@0: 
wolffd@0: for i=1:2:length(varargin),
wolffd@0:   %% Check that all argument types are strings
wolffd@0:   
wolffd@0:   if ~ischar(varargin{i})
wolffd@0:     error('Invalid identifier name or input argument order.');
wolffd@0:   end
wolffd@0:   
wolffd@0:   %% Lower/uppercase in identifier types doesn't matter: 
wolffd@0:   
wolffd@0:   identifier=lower(varargin{i});     % identifier (lowercase)
wolffd@0:   value=varargin{i+1};
wolffd@0:   
wolffd@0:   % Check property identifiers and values and store the values.
wolffd@0:   % Struct used_in is set to initiate warning messages:
wolffd@0:   % if a don't care propersty is set, the user is warned.
wolffd@0:   
wolffd@0:   switch identifier  
wolffd@0:    case 'marker'
wolffd@0:     %%% Marker for hits or trajectories
wolffd@0:     switch mode
wolffd@0:      case 'mhit'
wolffd@0:       if vis_valuetype(value,{'markerstyle'}) | ...
wolffd@0: 	    (vis_valuetype(value,{'string'}) & ...
wolffd@0: 	     any(strcmp(value,{'lattice','pie'}))),
wolffd@0: 	; % ok
wolffd@0:       elseif vis_valuetype(value,{'cellcolumn_of_char'}),
wolffd@0: 	if size(value,1) ~= size(D,2)
wolffd@0: 	  error([' If a cell of Markers is specified its size must be' ...
wolffd@0: 		 ' number_of_hit_histograms x 1.']);
wolffd@0: 	else
wolffd@0: 	  for i=1:size(D,2),
wolffd@0: 	    if ~vis_valuetype(value{i},{'markerstyle'})
wolffd@0: 	      error('Cell input for ''Marker'' contains invalid styles.')
wolffd@0: 	    end
wolffd@0: 	  end
wolffd@0: 	end
wolffd@0:       else
wolffd@0: 	error([' Invalid ''Marker'' in case of multiple hit histograms.' ...
wolffd@0: 	       char(10) ' See detailed documentation.'])
wolffd@0:       end
wolffd@0:      case {'comet','hit'}
wolffd@0:       if vis_valuetype(value,{'markerstyle'}) | isempty(value),
wolffd@0: 	% ok;
wolffd@0:       elseif ischar(value) & strcmp(value,'lattice'),
wolffd@0: 	% ok;
wolffd@0:       else
wolffd@0: 	error(['Marker must be Matlab''s marker style, or string' ...
wolffd@0: 	       ' ''lattice''.']);
wolffd@0:       end
wolffd@0:      case 'traj'
wolffd@0:       if ~vis_valuetype(value,{'markerstyle'}) & ~isempty(value),
wolffd@0: 	error('In mode ''traj'' Marker must be one of Matlab''s built-in marker styles');
wolffd@0:       end
wolffd@0:     end
wolffd@0:     used_in.comet=1;           % Set relevance flags
wolffd@0:     used_in.traj=1;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=1;
wolffd@0:     used_in.mhit=1;
wolffd@0:     
wolffd@0:    case 'markersize'
wolffd@0:     %%% Marker for hits or trajectories
wolffd@0:     switch mode 
wolffd@0:      case 'comet'
wolffd@0:       if ~vis_valuetype(value,{'1x2'}) & ~isempty(value), 
wolffd@0: 	error('In mode ''comet'' MarkerSize'' must be a 1x2 vector.');
wolffd@0:       end
wolffd@0:      case {'hit','traj'}
wolffd@0:       if ~vis_valuetype(value,{'1x1'}) & ~isempty(value), 
wolffd@0: 	error(['In mode ''' mode_ ...
wolffd@0: 	       ''' ''MarkerSize'' must be a scalar.']);
wolffd@0:       end
wolffd@0:     end
wolffd@0:     used_in.comet=1;           % Set relevance flags
wolffd@0:     used_in.traj=1;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=1;
wolffd@0:     used_in.mhit=1;
wolffd@0:     
wolffd@0:    case 'sizefactor'   
wolffd@0:     %%% Hit dependent size factor
wolffd@0:     switch mode
wolffd@0:      case 'traj'
wolffd@0:       if ~vis_valuetype(value,{'string'}) | ...
wolffd@0: 	    ~any(strcmp(value,{'hit', 'equal'})),
wolffd@0: 	error(['In mode ''traj'' ''SizeFactor'' must be ' ...
wolffd@0: 	       'string ''equal'' or ''hit''.']);
wolffd@0:       end
wolffd@0:      case 'mhit'
wolffd@0:       if ~vis_valuetype(value,{'string'}) | ...
wolffd@0: 	    ~any(strcmp(value,{'common', 'separate'})),
wolffd@0: 	error(['In mode ''hit'' ''SizeFactor'' must be ' ...
wolffd@0: 	       'string ''common'' or ''separate''.']);
wolffd@0:       end
wolffd@0:     end
wolffd@0:     used_in.comet=0;           % Set relevance flags
wolffd@0:     used_in.traj=1;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=0;
wolffd@0:     used_in.mhit=1;
wolffd@0:     
wolffd@0:    case 'markercolor'
wolffd@0:     %%% Markercolor
wolffd@0:     switch mode
wolffd@0:      case 'comet' 
wolffd@0:       if ~vis_valuetype(value,{'colorstyle','1x3rgb'}) & ...
wolffd@0: 	    ~vis_valuetype(value,{'nx3rgb',[size(D,1) 3]},'all') & ...
wolffd@0: 	    ~isempty(value),
wolffd@0: 	error(['MarkerColor in mode ''comet'' must be a ColorSpec,' ...
wolffd@0: 	       ' string ''none'' or Mx3 matrix of RGB triples.']);
wolffd@0:       end
wolffd@0:      case 'mhit'
wolffd@0:       if ~vis_valuetype(value,{[size(D,2) 3],'nx3rgb'},'all') & ...
wolffd@0: 	    ~vis_valuetype(value,{'colorstyle','1x3rgb'}),
wolffd@0: 	error([' If multiple hit histograms in mode ''hit'' are' ...
wolffd@0: 	       char(10) ...
wolffd@0: 	       ' given MarkerColor must be ColorSpec or a Kx3 matrix' ...
wolffd@0: 	       char(10)...
wolffd@0: 	       ' of RGB triples where K is the number of histograms.']);
wolffd@0:       end
wolffd@0:      case 'hit'
wolffd@0:       if ~vis_valuetype(value,{'colorstyle','1x3rgb'}) & ...
wolffd@0: 	    ~isempty(value),
wolffd@0: 	error(['MarkerColor in mode ''hit'' ' ...
wolffd@0: 	       'must be a ColorSpec or string ''none''.']);
wolffd@0:       end
wolffd@0:      case 'traj'
wolffd@0:       if ~vis_valuetype(value,{'colorstyle','1x3rgb'}) & ...
wolffd@0: 	    ~isempty(value),
wolffd@0: 	error(['MarkerColor in mode ''traj'' ' ...
wolffd@0: 	       'must be a ColorSpec or string ''none''.']);
wolffd@0:       end
wolffd@0:     end
wolffd@0:     
wolffd@0:     used_in.comet=1;           % Set relevance flags
wolffd@0:     used_in.traj=1;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=1;
wolffd@0:     used_in.mhit=1;
wolffd@0:     
wolffd@0:    case 'edgecolor'
wolffd@0:     %%% Color for marker edges
wolffd@0:     if ~vis_valuetype(value,{'colorstyle','1x3rgb'}) & ~isempty(value),
wolffd@0:       error('''EdgeColor'' must be a ColorSpec or string ''none''.')
wolffd@0:     end
wolffd@0:     
wolffd@0:     used_in.comet=1;           % Set relevance flags
wolffd@0:     used_in.traj=1;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=1;
wolffd@0:     used_in.mhit=1;
wolffd@0:     
wolffd@0:    case 'text'
wolffd@0:     %%% Labeling for trajectories/hits
wolffd@0:     switch mode
wolffd@0:      case 'hit'
wolffd@0:       %%% Hit count using numbers?
wolffd@0:       if isempty(value),
wolffd@0: 	value='off';
wolffd@0:       elseif vis_valuetype(value,{'string'}) & ...
wolffd@0: 	    ~any(strcmp(value,{'on','off'})),
wolffd@0: 	error('Value for Text in mode ''hit'' should be ''on'' or ''off''.');
wolffd@0:       else
wolffd@0: 	; % ok
wolffd@0:       end
wolffd@0:      %case 'traj','comet'
wolffd@0:      % if ~vis_valuetype(value,{'char_array','cellcolumn_of_char'}) & ...
wolffd@0:      %	    ~isempty(value)
wolffd@0:      %	 error('Value for Text is of wrong type or size.')
wolffd@0:      % elseif ischar(value)
wolffd@0:      %	value=strcell(value) % ok, convert to cell
wolffd@0:      % end
wolffd@0:      % if size(traj_label,1)~=size(D,1)
wolffd@0:      %	error(['The number of labels in Text and the length of the' ...
wolffd@0:      % 	       ' trajectory do not match.']);
wolffd@0:      % end
wolffd@0:      case 'label'
wolffd@0:       ; % not used
wolffd@0:     end
wolffd@0:     used_in.comet=0;            % Set relevance flags
wolffd@0:     used_in.traj=0;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=1;
wolffd@0:     used_in.mhit=0;
wolffd@0:     
wolffd@0:    case 'textsize'
wolffd@0:     %%% Text size for labels
wolffd@0:     
wolffd@0:     if ~vis_valuetype(value,{'1x1'}) & ~isempty(value), 
wolffd@0:       error('TextSize must be scalar.');
wolffd@0:     end
wolffd@0:     used_in.comet=0;            % Set relevance flags
wolffd@0:     used_in.traj=0;
wolffd@0:     used_in.label=1;
wolffd@0:     used_in.hit=1;
wolffd@0:     used_in.mhit=0;
wolffd@0:     
wolffd@0:    case 'textcolor'
wolffd@0:     %%% Color for labels
wolffd@0:     
wolffd@0:     if ~vis_valuetype(value,{'colorstyle','1x3rgb','xor'}) & ~isempty(value),
wolffd@0:       error('''TextColor'' must be ColorSpec, ''xor'' or ''none''.')
wolffd@0:     end
wolffd@0:     used_in.comet=0;            % Set relevance flags
wolffd@0:     used_in.traj=0;
wolffd@0:     used_in.label=1;
wolffd@0:     used_in.hit=1;
wolffd@0:     used_in.mhit=0;
wolffd@0:     
wolffd@0:    case 'trajwidth'
wolffd@0:     %%% Basic line width for a line trajectory
wolffd@0:     if ~vis_valuetype(value,{'1x1'}) & ~isempty(value), 
wolffd@0:       error('TrajWidth must be a scalar.');
wolffd@0:     end
wolffd@0:     used_in.comet=0;            % Set relevance flags
wolffd@0:     used_in.traj=1; 
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=0;
wolffd@0:     used_in.mhit=0;
wolffd@0:     
wolffd@0:    case 'widthfactor'
wolffd@0:     %%% Hit factor for a line trajectory
wolffd@0:     if ~vis_valuetype(value,{'string'}) | ...
wolffd@0: 	  ~any(strcmp(value,{'hit', 'equal'})),
wolffd@0:       error(['In mode ''traj'' ''WidthFactor'' must be ' ...
wolffd@0: 	     'string ''equal'' or ''hit''.']);
wolffd@0:     end
wolffd@0:     used_in.comet=0;            % Set relevance flags
wolffd@0:     used_in.traj=1;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=0;
wolffd@0:     used_in.mhit=0;
wolffd@0:     
wolffd@0:    case 'trajcolor'
wolffd@0:     %%% Color for trajectory line
wolffd@0:     
wolffd@0:     if ~vis_valuetype(value,{'colorstyle','1x3rgb','xor'}) & ~isempty(value),
wolffd@0:       error('''TrajColor'' must be a ColorSpec or string ''xor''.')
wolffd@0:     end
wolffd@0:     used_in.comet=0;            % Set relevance flags
wolffd@0:     used_in.traj=1;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=0;
wolffd@0:     used_in.mhit=0;
wolffd@0:     
wolffd@0:    case 'uselabel' 
wolffd@0:     %%% Which labels to show
wolffd@0:     error('Not yet implemented.');
wolffd@0:    
wolffd@0:    case 'shift'
wolffd@0:     if ~vis_valuetype(value,{'1x1'}) | ((value < 0) | (value > 1)),
wolffd@0:       error('''Shift'' must be a scalar in range [0,1].')
wolffd@0:     end
wolffd@0:     used_in.comet=0;            % Set relevance flags
wolffd@0:     used_in.traj=0;
wolffd@0:     used_in.label=0;
wolffd@0:     used_in.hit=0;
wolffd@0:     used_in.mhit=1;
wolffd@0:     
wolffd@0:    case 'subplot'
wolffd@0:     %%% The subplots which are affected 
wolffd@0:     
wolffd@0:     if vis_valuetype(value,{'1xn','nx1','string'}), 
wolffd@0:       if ischar(value),
wolffd@0: 	if ~strcmp(value,'all'),
wolffd@0: 	  error('Only valid string value for subplot indices is ''all''.');
wolffd@0: 	else
wolffd@0: 	  value=1:length(handles);
wolffd@0: 	end
wolffd@0:       elseif any(value<1) | any(value>length(handles)),
wolffd@0: 	error('Subplot indices must be in range 1...number_of_subplots!');
wolffd@0:       end
wolffd@0:     elseif ~isempty(value)
wolffd@0:       error('Invalid subplot indices!');
wolffd@0:     end
wolffd@0:     used_in.comet=1;              % Set relevance flags
wolffd@0:     used_in.traj=1;
wolffd@0:     used_in.label=1;
wolffd@0:     used_in.hit=1;
wolffd@0:     used_in.mhit=1;
wolffd@0:     
wolffd@0:    otherwise
wolffd@0:     error([ 'Unknown identifier ''' identifier '''.']);
wolffd@0:   end
wolffd@0:   
wolffd@0:   % Warn user if the property that was set has no effect in the 
wolffd@0:   % selected visuzlization mode
wolffd@0: 
wolffd@0:   if ~getfield(used_in, mode),
wolffd@0:     warning(['Property ''' identifier ''' has no effect in mode ''' ...
wolffd@0: 	       mode_ '''.']);
wolffd@0:   else 
wolffd@0:     Property=setfield(Property,identifier,value);
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: % set default subplot
wolffd@0: if isempty(Property.subplot)
wolffd@0:   % search the subplot number for current axis
wolffd@0:   value=find(gca==handles);    
wolffd@0:   if isempty(value) | value>length(handles) 
wolffd@0:     error('SubPlot default value setting: current axis is not in the figure!');
wolffd@0:   else
wolffd@0:     Property.subplot=value;
wolffd@0:   end
wolffd@0: end
wolffd@0:   
wolffd@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: %%%%%%% Main switch: select the right subfunction %%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: switch mode
wolffd@0:  case 'hit'
wolffd@0:   h_=hit(D, lattice, msize, Property);  
wolffd@0:  case 'mhit'
wolffd@0:   h_=mhit(D, lattice, msize, Property);  
wolffd@0:  case 'label'
wolffd@0:   h_=label(D, lattice, msize, Property);
wolffd@0:  case 'traj'
wolffd@0:   h_=traj(D, lattice, msize, Property);
wolffd@0:  case 'comet'
wolffd@0:   %error('Not yet implemented.'); 
wolffd@0:   h_=comet(D, lattice, msize, Property);
wolffd@0:  otherwise
wolffd@0:   error('Whoops! Internal error: unknown mode!');
wolffd@0: end
wolffd@0: 
wolffd@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: %% Build output if necessary %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: if nargout>0
wolffd@0:   h=h_;
wolffd@0: end
wolffd@0: 
wolffd@0: %%%% SUBFUNCTIONS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: function h_=hit(Hits, lattice, msize, Property);  
wolffd@0: 
wolffd@0: % number of map units
wolffd@0: munits=prod(msize);
wolffd@0: 
wolffd@0: % subplots
wolffd@0: p=Property.subplot;
wolffd@0: handles=Property.handles;
wolffd@0: 
wolffd@0: % Set default marker
wolffd@0: if isempty(Property.marker),
wolffd@0:   if strcmp(Property.text,'on')
wolffd@0:     Property.marker='none';
wolffd@0:   else
wolffd@0:     Property.marker='lattice';
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default markersize
wolffd@0: if isempty(Property.markersize)
wolffd@0:   if strcmp(Property.marker,'none'),
wolffd@0:     warning('MarkerSize is not meaningful since Marker is set to ''none''.');
wolffd@0:   elseif strcmp(Property.marker,'lattice'),
wolffd@0:     Property.markersize=1; % normalized size
wolffd@0:   else
wolffd@0:     Property.markersize=12; % points
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default colors
wolffd@0: if ~isempty(Property.markercolor),
wolffd@0:   if strcmp(Property.marker,'none')
wolffd@0:     warning('MarkerColor is not used since Marker is set to ''none''.');
wolffd@0:     Property.markercolor=[]; % not used
wolffd@0:   else
wolffd@0:     ; % ok
wolffd@0:   end
wolffd@0: elseif any(strcmp(Property.marker,{'+','*','.','x'})),
wolffd@0:   % these don't use fill color: 'none' will cause default
wolffd@0:   % edgecolor to be 'k'.
wolffd@0:   Property.markercolor='none'; 
wolffd@0: else
wolffd@0:   Property.markercolor='k';
wolffd@0: end
wolffd@0: 
wolffd@0: if ~isempty(Property.edgecolor),
wolffd@0:   if strcmp(Property.marker,'none')
wolffd@0:     warning(['EdgeColor is not used since Marker is set to' ...
wolffd@0: 	     ' ''none''.']);
wolffd@0:   else
wolffd@0:     ; %ok 
wolffd@0:   end
wolffd@0: elseif ~strcmp(Property.markercolor,'none'),
wolffd@0:   Property.edgecolor='none';
wolffd@0: else
wolffd@0:   Property.edgecolor='k';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default text
wolffd@0: if isempty(Property.text),
wolffd@0:   Property.text='off';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default textsize
wolffd@0: if isempty(Property.textsize)
wolffd@0:   Property.textsize=10;
wolffd@0: elseif strcmp(Property.text,'off')  
wolffd@0:   warning('TextSize not used as hits are not set to be shown as numbers.');
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default textcolor
wolffd@0: if isempty(Property.textcolor)
wolffd@0:   Property.textcolor='w';
wolffd@0: elseif strcmp(Property.text,'off')  
wolffd@0:   warning('TextColor not used as hits are not set to be shown as numbers.');
wolffd@0: end
wolffd@0: 
wolffd@0: %% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: h_=[];          % this variable is for collecting the object handles
wolffd@0: 
wolffd@0: % Select the drawing mode 
wolffd@0: 
wolffd@0: if ~strcmp(Property.marker,'none') 
wolffd@0:   
wolffd@0:   %%%%% Draw spots %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0:   
wolffd@0:   % unit coordinates 
wolffd@0:   coord=som_vis_coords(lattice,msize);
wolffd@0:   
wolffd@0:   % Calculate the size of the spots
wolffd@0:   mx=max(Hits);
wolffd@0:   
wolffd@0:   if mx==0,
wolffd@0:     % nothing to draw!
wolffd@0:     h_=[]; 
wolffd@0:     return
wolffd@0:   else
wolffd@0:     Size=sqrt(Hits./mx);      
wolffd@0:   end
wolffd@0:   % coordinates for non-zero hits (only those are drawn)
wolffd@0:   coord=coord(Size~=0,:);
wolffd@0:   Size=Size(Size~=0);
wolffd@0:   N=size(Size,1);
wolffd@0:   
wolffd@0:   % som_cplane can't draw one unit with arbitrary
wolffd@0:   % coordinates as it its mixed with msize:
wolffd@0:   if size(coord,1)==1 & strcmp(Property.marker,'lattice'),
wolffd@0:     Size=[Size;Size];
wolffd@0:     coord=[coord;coord];
wolffd@0:   end
wolffd@0:   
wolffd@0:   for i=1:length(p),
wolffd@0:     % Set axes
wolffd@0:     axes(handles(p(i)));
wolffd@0:     % Get hold state and caxis
wolffd@0:     memhold=ishold; cax=caxis;     
wolffd@0:     hold on;
wolffd@0:     
wolffd@0:     switch Property.marker
wolffd@0:      case 'lattice'
wolffd@0:       h_(i,1)=som_cplane(lattice, coord, Property.markercolor, ...
wolffd@0: 			 Property.markersize*Size);
wolffd@0:      otherwise  
wolffd@0:       [S,m]=som_grid(lattice, [N 1],...
wolffd@0: 		     'Coord',coord, ...
wolffd@0: 		     'Line','none',...
wolffd@0: 		     'Marker',Property.marker,...
wolffd@0: 		     'MarkerColor',Property.markercolor,...
wolffd@0: 		     'MarkerSize', Size*Property.markersize);
wolffd@0:       h_=[h_;m(:)];
wolffd@0:     end
wolffd@0:     
wolffd@0:     % Restore hold state
wolffd@0:     if ~memhold         
wolffd@0:       hold off;
wolffd@0:     end
wolffd@0:   end
wolffd@0:   
wolffd@0:   % Set edgecolor
wolffd@0:   if strcmp(Property.marker,'lattice')
wolffd@0:     set(h_,'edgecolor',Property.edgecolor);
wolffd@0:   else
wolffd@0:     set(h_,'markeredgecolor',Property.edgecolor);
wolffd@0:   end
wolffd@0: end
wolffd@0:   
wolffd@0: if strcmp(Property.text,'on'),
wolffd@0:   %%%%% Draw numbers %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%    
wolffd@0: 
wolffd@0:   % Do numbers
wolffd@0:   Hits=reshape(Hits,[munits 1]);
wolffd@0:   labels=cell([munits 1]);
wolffd@0:   for i=1:length(Hits)
wolffd@0:     if Hits(i)              % zero hit won't be shown
wolffd@0:       labels(i)={num2str(Hits(i))};
wolffd@0:     end
wolffd@0:   end
wolffd@0: 
wolffd@0:   for i=1:length(p),
wolffd@0:     axes(handles(p(i)));    % Set axes
wolffd@0:     memhold=ishold;         % Get hold state
wolffd@0:     hold on;
wolffd@0:     [S,m,l,t]=som_grid(lattice, msize, ...
wolffd@0: 		       'Line','none',...
wolffd@0: 		       'Marker','none', ...
wolffd@0: 		       'Label',labels, ...
wolffd@0: 		       'LabelColor', Property.textcolor, ...
wolffd@0: 		       'LabelSize', Property.textsize);
wolffd@0:     % Get handles
wolffd@0:     h_=[h_;t(:)];
wolffd@0:     
wolffd@0:     % Restore hold state and caxis
wolffd@0:     if ~memhold     
wolffd@0:       hold off;
wolffd@0:     end
wolffd@0:     caxis(cax);
wolffd@0:   end
wolffd@0: 
wolffd@0:   % Remove zero object handles (missing objects)
wolffd@0:   h_=setdiff(h_,0);
wolffd@0: end
wolffd@0: 
wolffd@0: %% Set object tags (for som_show_clear) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: set(h_,'Tag','Hit')
wolffd@0: 
wolffd@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: function h_=mhit(Hits, lattice, msize, Property);  
wolffd@0: 
wolffd@0: % number of map units
wolffd@0: munits=prod(msize);
wolffd@0: 
wolffd@0: % subplots
wolffd@0: p=Property.subplot;
wolffd@0: handles=Property.handles;
wolffd@0: 
wolffd@0: 
wolffd@0: % Set default marker
wolffd@0: if isempty(Property.marker),
wolffd@0:   Property.marker=lattice;
wolffd@0: end
wolffd@0: 
wolffd@0: % variable 'mode' indicates which kind of markers are used:
wolffd@0: 
wolffd@0: if iscell(Property.marker),
wolffd@0:   mode='marker';
wolffd@0: elseif vis_valuetype(Property.marker,{'markerstyle'}),
wolffd@0:   mode='marker';
wolffd@0: elseif strcmp(Property.marker,'pie'),
wolffd@0:   mode='pie';
wolffd@0: else
wolffd@0:   mode='lattice';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default size scaling
wolffd@0: if isempty(Property.sizefactor)
wolffd@0:   Property.sizefactor='separate';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default markersize 
wolffd@0: if isempty(Property.markersize)
wolffd@0:   if any(strcmp(mode,{'lattice','pie'})),
wolffd@0:     Property.markersize=1; % normalized
wolffd@0:   else
wolffd@0:     Property.markersize=12;  % points
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default colors
wolffd@0: 
wolffd@0: if isempty(Property.markercolor),
wolffd@0:   Property.markercolor=hsv(size(Hits,2));
wolffd@0: end
wolffd@0: 
wolffd@0: if isempty(Property.edgecolor),
wolffd@0:   if vis_valuetype(Property.markercolor,{'none'}),
wolffd@0:     Property.edgecolor='k';
wolffd@0:   else
wolffd@0:     Property.edgecolor='none';
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default shift
wolffd@0: if isempty(Property.shift)
wolffd@0:   Property.shift=0;
wolffd@0: end
wolffd@0: 
wolffd@0: %% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: h_=[];          % this variable is for collecting the object handles
wolffd@0: 
wolffd@0: switch mode
wolffd@0:   case {'marker','lattice'}
wolffd@0:    % Number of hits histograms
wolffd@0:    n_Hits=size(Hits,2);
wolffd@0:    % Calculate the size of the spots
wolffd@0:    
wolffd@0:    if strcmp(Property.sizefactor,'common')
wolffd@0:      mx=max(max(Hits));
wolffd@0:      if mx==0 % nothing to draw!
wolffd@0:        h_=[]; return
wolffd@0:      end
wolffd@0:      spotSize=sqrt(Hits./mx);
wolffd@0:    else
wolffd@0:      mx=repmat(max(Hits),munits,1);
wolffd@0:      mx(mx==0)=1; % Prevent division by zero
wolffd@0:      spotSize=sqrt(Hits./mx);
wolffd@0:    end
wolffd@0:    
wolffd@0:    %%% Make spotSize
wolffd@0:    
wolffd@0:    %reshape Size to a vector [spotSizeforHist(:,1); spotSizeforHist(:,2);...]
wolffd@0:    spotSize=spotSize(:);
wolffd@0:    
wolffd@0:    % indices for non-zero hits (only those are drawn)
wolffd@0:    notZero=find(spotSize ~= 0);
wolffd@0:    
wolffd@0:    % Drop zeros away from spotSize
wolffd@0:    spotSize=spotSize(notZero);
wolffd@0:    
wolffd@0:    % Order spots so that bigger will be drawn first, so that they 
wolffd@0:    % won't hide smaller ones
wolffd@0:    [dummy, sizeOrder]=sort(spotSize); sizeOrder=sizeOrder(end:-1:1);
wolffd@0:    spotSize=spotSize(sizeOrder);
wolffd@0:    
wolffd@0:    %%% Make unit coordinates 
wolffd@0:    coord=som_vis_coords(lattice,msize);
wolffd@0:    
wolffd@0:    move=repmat(linspace(-.1,.1,n_Hits),size(coord,1),1)*Property.shift;
wolffd@0:    move=repmat(move(:),1,2);
wolffd@0:    
wolffd@0:    % do n_Hits copies of unit coordinates so that they match spotSize
wolffd@0:    coord=repmat(coord,n_Hits,1)+move;
wolffd@0:    
wolffd@0:    % Drop zeros away from coords and order
wolffd@0:    coord=coord(notZero,:);
wolffd@0:    coord=coord(sizeOrder,:);
wolffd@0:    
wolffd@0:    %%% Make unit colors
wolffd@0:    
wolffd@0:    if vis_valuetype(Property.markercolor,{'nx3'}),
wolffd@0:      % If multiple colors Copy unit colors so that they match spotSize
wolffd@0:      color=Property.markercolor(reshape(repmat([1:n_Hits]',1,munits)',...
wolffd@0: 					munits*n_Hits,1),:);
wolffd@0:      % drop zeros away & order
wolffd@0:      color=color(notZero,:);
wolffd@0:      color=color(sizeOrder,:);
wolffd@0:    else
wolffd@0:      % only on color
wolffd@0:      color=Property.markercolor;
wolffd@0:    end
wolffd@0:    
wolffd@0:    %%% Make unit markers
wolffd@0:    
wolffd@0:    if iscell(Property.marker),
wolffd@0:      %marker shows class: 
wolffd@0:      marker=char(Property.marker);
wolffd@0:      marker=marker(reshape(repmat([1:n_Hits]',1,munits)',...
wolffd@0: 			   munits*n_Hits,1),:);
wolffd@0:      % Drop zeros, order & make to cell array (for som_grid)
wolffd@0:      marker=marker(notZero,:);
wolffd@0:      marker=cellstr(marker(sizeOrder,:));
wolffd@0:    else
wolffd@0:      marker=Property.marker;
wolffd@0:    end
wolffd@0: 
wolffd@0:    % som_cplane can't draw one unit with arbitrary
wolffd@0:    % coordinates as it its mixed with msize:
wolffd@0:    if size(coord,1)==1 & strcmp(mode,'lattice'),
wolffd@0:      spotSize = [spotSize; spotSize];
wolffd@0:      coord = [coord; coord];
wolffd@0:    end
wolffd@0: 
wolffd@0:    N=length(notZero); % for som_grid visuzalization routine
wolffd@0:  case 'pie'
wolffd@0:   % marker 'pie' requires size parameter totHits
wolffd@0:   if strcmp(mode,'pie')
wolffd@0:     coord=som_vis_coords(lattice, msize);
wolffd@0:     notZero=sum(Hits,2)>0;
wolffd@0:     Hits=Hits(notZero,:);
wolffd@0:     coord=coord(notZero,:);
wolffd@0:     N=size(notZero,1);
wolffd@0:     totHits=sqrt(sum(Hits,2)./max(sum(Hits,2)));
wolffd@0:   end
wolffd@0:   
wolffd@0:   % som_pieplane can't draw one unit with arbitrary
wolffd@0:   % coordinates as it its mixed with msize:
wolffd@0:   if size(coord,1)==1,
wolffd@0:     Hits= [Hits; Hits];
wolffd@0:     coord = [coord; coord];
wolffd@0:   end
wolffd@0:  otherwise
wolffd@0:   error('Whoops: internal error. Bad mode in subfunction mhit');
wolffd@0: end
wolffd@0: 
wolffd@0: for i=1:length(p),    %%% Main loop begins
wolffd@0:   % Set axis
wolffd@0:   axes(handles(p(i)));
wolffd@0:   % Get hold state and caxis 
wolffd@0:   memhold=ishold; cax=caxis;
wolffd@0:   hold on;
wolffd@0:   
wolffd@0:   switch mode
wolffd@0:    case 'lattice'
wolffd@0:     h_(i,1)=som_cplane(lattice, coord, color, spotSize*Property.markersize);
wolffd@0:    case 'marker'
wolffd@0:     [S,m]=som_grid(lattice, [N 1],...
wolffd@0: 		   'Coord',coord, ...
wolffd@0: 		   'Line','none',...
wolffd@0: 		   'Marker',marker,...
wolffd@0: 		   'MarkerColor',color,...
wolffd@0: 		   'MarkerSize', spotSize*Property.markersize);
wolffd@0:     h_=[h_;m(:)];
wolffd@0:    case 'pie'
wolffd@0:     h_(i)=som_pieplane(lattice, coord, ...
wolffd@0: 		       Hits, Property.markercolor, ...
wolffd@0: 		       totHits*Property.markersize);
wolffd@0:   end
wolffd@0:   
wolffd@0:   % Restore hold state and caxis
wolffd@0:   if ~memhold         
wolffd@0:     hold off;
wolffd@0:   end
wolffd@0:   caxis(cax);
wolffd@0: end
wolffd@0: 
wolffd@0: % Set edgecolor
wolffd@0: if any(strcmp(mode,{'lattice','pie'})),
wolffd@0:   set(h_,'edgecolor',Property.edgecolor);
wolffd@0: else
wolffd@0:   set(h_,'markeredgecolor',Property.edgecolor);
wolffd@0: end
wolffd@0: 
wolffd@0: %% Set object tags (for som_show_clear) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: set(h_,'Tag','Hit')
wolffd@0: 
wolffd@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: function h_=label(Labels, lattice, msize, Property)
wolffd@0: 
wolffd@0: % number of map units
wolffd@0: munits=prod(msize);
wolffd@0: 
wolffd@0: % subplots and handles
wolffd@0: p=Property.subplot;
wolffd@0: handles= Property.handles;
wolffd@0: 
wolffd@0: % Set default text size
wolffd@0: if isempty(Property.textsize)   % default point size
wolffd@0:   Property.textsize=10;
wolffd@0: end
wolffd@0: 
wolffd@0: % Check color/set default
wolffd@0: if isempty(Property.textcolor),                   
wolffd@0:   Property.textcolor='k';
wolffd@0: end
wolffd@0: 
wolffd@0: % handles will be collected in h_ for output
wolffd@0: h_=[];                            
wolffd@0: 
wolffd@0: %%% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: for i=1:length(p);
wolffd@0:   % set axes
wolffd@0:   axes(handles(p(i)));
wolffd@0:   % store hold state and caxis (for some reason matlab may 
wolffd@0:   % change caxis(!?)
wolffd@0:   memhold=ishold;
wolffd@0:   hold on;
wolffd@0:   cax=caxis;
wolffd@0:   
wolffd@0:   % Write labels
wolffd@0:   [S,m,l,t]=som_grid(lattice, msize, ...
wolffd@0: 		     'Line','none', ...
wolffd@0: 		     'Marker', 'none', ...
wolffd@0: 		     'Label', Labels, ...
wolffd@0: 		     'LabelColor', Property.textcolor,  ...
wolffd@0: 		     'LabelSize', Property.textsize);
wolffd@0:   % Get handles
wolffd@0:   h_=[h_;m(:);l(:);t(:)];
wolffd@0:   
wolffd@0:   % reset hold state and caxis
wolffd@0:   if ~memhold
wolffd@0:     hold off;
wolffd@0:   end
wolffd@0:   caxis(cax);
wolffd@0: end
wolffd@0: 
wolffd@0: %%% Set object tags %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: set(h_,'Tag','Lab');
wolffd@0:   
wolffd@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: function h_=traj(bmu, lattice, msize, Property)
wolffd@0: 
wolffd@0: % number of map units
wolffd@0: munits=prod(msize);
wolffd@0: 
wolffd@0: % subplots and handles
wolffd@0: p=Property.subplot;
wolffd@0: handles=Property.handles;
wolffd@0: 
wolffd@0: % Set default text color
wolffd@0: %if isempty(Property.textcolor),                   
wolffd@0: %  Property.textcolor='k';
wolffd@0: %end
wolffd@0: 
wolffd@0: % Set default text size
wolffd@0: %if isempty(Property.textsize)
wolffd@0: %  Property.textsize=10;
wolffd@0: %end
wolffd@0: 
wolffd@0: % Set default marker
wolffd@0: if isempty(Property.marker)
wolffd@0:   Property.marker='o';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default markersize
wolffd@0: if isempty(Property.markersize)
wolffd@0:   Property.markersize=10;
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default markercolor
wolffd@0: if isempty(Property.markercolor)
wolffd@0:   Property.markercolor='w';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default sizefactor
wolffd@0: if isempty(Property.sizefactor)
wolffd@0:   %Property.sizefactor=0;
wolffd@0:   Property.sizefactor='hit';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default trajwidth
wolffd@0: if isempty(Property.trajwidth)
wolffd@0:   Property.trajwidth=3;
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default widthfactor
wolffd@0: if isempty(Property.widthfactor)
wolffd@0:   Property.widthfactor='hit';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default trajcolor
wolffd@0: if isempty(Property.trajcolor)
wolffd@0:   Property.trajcolor='w';
wolffd@0: end
wolffd@0: 
wolffd@0: % if no labels, do a empty cell array for syntax reasons
wolffd@0: %if isempty(Property.text),
wolffd@0: %  Property.text=cell(munits,1);
wolffd@0: %end
wolffd@0: 
wolffd@0: h_=[];                    % handles will be collected in h_ for output    
wolffd@0: l=length(bmu);            % length of trajectory
wolffd@0: C=sparse(munits, munits); % init a connection matrix
wolffd@0: 
wolffd@0: %%%%%% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: % Calculate the connection matrix that describes the trajectory
wolffd@0: for i=1:l-1,
wolffd@0:   % The following if structure removes the possible redundancy due
wolffd@0:   % to travels in both directions between two nodes of trajectory 
wolffd@0:   % (i.e. reflexivity) 
wolffd@0:   I=bmu(i+1);J=bmu(i);
wolffd@0:   %if bmu(i)>bmu(i+1)
wolffd@0:   
wolffd@0:   %else 
wolffd@0:   %  I=bmu(i);J=bmu(i+1);
wolffd@0:   %end
wolffd@0:   C(I,J)=C(I,J)+1;
wolffd@0: end
wolffd@0: 
wolffd@0: % transitive connections are equal
wolffd@0: C=C+C';
wolffd@0: % drop reflexive conncetions away
wolffd@0: C=spdiags(zeros(munits,1),0,C);
wolffd@0: 
wolffd@0: % Do labels of trajectory nodes
wolffd@0: 
wolffd@0: %traj_lab=cell(munits,1);
wolffd@0: hits=zeros(munits,1);
wolffd@0: 
wolffd@0: for i=1:l,
wolffd@0: %  traj_lab{bmu(i)}=strvcat(traj_lab{bmu(i)},Property.text{i});
wolffd@0:   hits(bmu(i))=(hits(bmu(i))+1);
wolffd@0: end
wolffd@0: 
wolffd@0: % Calculate unit coordinates
wolffd@0: unit_coord=som_vis_coords(lattice, msize);
wolffd@0: 
wolffd@0: % Calculate line width
wolffd@0: if strcmp(Property.widthfactor,'equal')
wolffd@0:   TrajWidth=(C>0)*Property.trajwidth;
wolffd@0: else
wolffd@0:   TrajWidth=Property.trajwidth.*sqrt(C./max(max(C)));
wolffd@0: end
wolffd@0: 
wolffd@0: % Calculate marker sizes
wolffd@0: if strcmp(Property.sizefactor,'hit')
wolffd@0:   MarkerSize=Property.markersize*sqrt(hits/max(hits));
wolffd@0: else
wolffd@0:   MarkerSize=Property.markersize*(hits>0);
wolffd@0: end
wolffd@0: 
wolffd@0: for i=1:length(p),
wolffd@0:   axes(handles(p(i)));
wolffd@0:   % Get hold state and caxis
wolffd@0:   memhold=ishold; cax=caxis;
wolffd@0:   hold on;
wolffd@0: 
wolffd@0:   	%'Label', traj_lab, ...
wolffd@0: 	%'LabelColor', Property.textcolor, ...
wolffd@0: 	%'LabelSize', Property.textsize, ...
wolffd@0: 
wolffd@0:   % Draw
wolffd@0:   [S,m,l,t,s]=som_grid(C,msize,'coord',unit_coord,...
wolffd@0: 	'Line','-', ...
wolffd@0: 	'LineColor', Property.trajcolor, ...
wolffd@0: 	'LineWidth', TrajWidth, ...
wolffd@0: 	'Marker', Property.marker, ...
wolffd@0: 	'MarkerColor', Property.markercolor, ...
wolffd@0: 	'MarkerSize', MarkerSize);
wolffd@0:   
wolffd@0:   % Restore hold state and caxis
wolffd@0:   if ~memhold   
wolffd@0:     hold off;
wolffd@0:   end
wolffd@0:   caxis(cax);
wolffd@0:   % Get handles
wolffd@0:   h_=[h_;m(:);l(:);t(:);s(:)];
wolffd@0: end
wolffd@0: 
wolffd@0: %% Set object tags %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  
wolffd@0: 
wolffd@0: set(h_,'Tag','Traj');
wolffd@0: 
wolffd@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: function h_=comet(bmu, lattice, msize, Property)
wolffd@0: 
wolffd@0: % number of map units
wolffd@0: munits=prod(msize);
wolffd@0: 
wolffd@0: % subplots and handles
wolffd@0: p=Property.subplot;
wolffd@0: handles=Property.handles;
wolffd@0: 
wolffd@0: % Set default text color
wolffd@0: %if isempty(Property.textcolor),                   
wolffd@0: %  Property.textcolor='k';
wolffd@0: %end
wolffd@0: 
wolffd@0: %% Set default text size
wolffd@0: %if isempty(Property.textsize)
wolffd@0: %  Property.textsize=10;
wolffd@0: %end
wolffd@0: 
wolffd@0: % Set default marker
wolffd@0: if isempty(Property.marker)
wolffd@0:   Property.marker='o';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default markersize
wolffd@0: if isempty(Property.markersize),
wolffd@0:   if strcmp(Property.marker,'lattice'),
wolffd@0:     Property.markersize=linspace(0.8,0.1,length(bmu))';
wolffd@0:   else 
wolffd@0:     Property.markersize=sqrt(linspace(400,16,length(bmu)))';
wolffd@0:   end
wolffd@0: else
wolffd@0:   if strcmp(Property.marker,'lattice'),
wolffd@0:     Property.markersize=linspace(Property.markersize(1),...
wolffd@0: 				 Property.markersize(2), ...
wolffd@0: 				 length(bmu))';
wolffd@0:   else
wolffd@0:     Property.markersize=sqrt(linspace(Property.markersize(1).^2,...
wolffd@0: 				      Property.markersize(2).^2, ...
wolffd@0: 				      length(bmu)))';
wolffd@0: 
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default markercolor
wolffd@0: if isempty(Property.markercolor)
wolffd@0:   Property.markercolor='w';
wolffd@0: end
wolffd@0: 
wolffd@0: % Set default edgecolor
wolffd@0: if isempty(Property.edgecolor),
wolffd@0:   if vis_valuetype(Property.markercolor,{'nx3rgb'}),
wolffd@0:     Property.edgecolor='none';
wolffd@0:   else
wolffd@0:     Property.edgecolor=Property.markercolor;
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: h_=[];l_=[];              % handles will be collected in h_ for output       
wolffd@0: N_bmus=length(bmu);       % length of trajectory
wolffd@0: 
wolffd@0: % if no labels, do a empty cell array for syntax reasons
wolffd@0: %if isempty(Property.text),
wolffd@0: %  Property.text=cell(N_bmus,1);
wolffd@0: %end
wolffd@0: 
wolffd@0: %%%%%% Action %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: % Calculate unit coordinates for trajectory points
wolffd@0: unit_coord=som_vis_coords(lattice, msize);
wolffd@0: coord=unit_coord(bmu,:);
wolffd@0: 
wolffd@0: % Make labels for the _unique_ units that the comet hits
wolffd@0: 
wolffd@0: unique_bmu=unique(bmu);               % count units
wolffd@0: %N_labels=length(unique_bmu);    
wolffd@0: %traj_lab=cell(N_labels,1);            % cell for labels
wolffd@0: %label_coord=unit_coord(unique_bmu,:); % label coordinates
wolffd@0: 
wolffd@0: % Make labels
wolffd@0: %for i=1:N_bmus,
wolffd@0: %  index=find(unique_bmu==bmu(i));
wolffd@0: %  traj_lab{index}=strvcat(traj_lab{index},Property.text{i});
wolffd@0: %end
wolffd@0: 
wolffd@0: %Main loop for drawing comets
wolffd@0: for i=1:length(p),
wolffd@0:   % set axis
wolffd@0:   axes(handles(p(i)));
wolffd@0: 
wolffd@0:   % Get hold state and caxis
wolffd@0:   memhold=ishold; cax=caxis;
wolffd@0:   hold on;
wolffd@0:   
wolffd@0:   if strcmp(Property.marker,'lattice'),
wolffd@0:     % Draw: marker is a patch ('hexa','rect')
wolffd@0:      l_=som_cplane(lattice, coord, Property.markercolor, ...
wolffd@0: 		  Property.markersize);
wolffd@0:      
wolffd@0:      % Set edgecolor
wolffd@0:      set(l_,'edgecolor',Property.edgecolor);
wolffd@0:   else
wolffd@0:     % Draw: other markers than 'hexa' or 'rect'
wolffd@0:      [S,m,l,t,s]=som_grid(lattice, [N_bmus 1], 'coord', coord,...
wolffd@0: 			  'Line','none', ...
wolffd@0: 			  'Marker', Property.marker, ...
wolffd@0: 			  'MarkerColor', Property.markercolor, ...
wolffd@0: 			  'MarkerSize',Property.markersize);
wolffd@0:      
wolffd@0:      % Set edgecolor
wolffd@0:      set(m, 'markeredgecolor', Property.edgecolor);
wolffd@0:      
wolffd@0:      % Get handles from markers
wolffd@0:      h_=[h_;l_(:);m(:);l(:);t(:);s(:)];
wolffd@0:   end
wolffd@0:   
wolffd@0:   % Set labels
wolffd@0:   %[S,m,l,t,s]=som_grid(lattice, [N_labels 1], 'coord', label_coord,...
wolffd@0:   %		       'Marker','none','Line','none',...
wolffd@0:   %		       'Label', traj_lab, ...
wolffd@0:   %		       'LabelColor', Property.textcolor, ...
wolffd@0:   %		       'LabelSize', Property.textsize);
wolffd@0:   % Get handles from labels
wolffd@0:   %h_=[h_;m(:);l(:);t(:);s(:)];
wolffd@0: 
wolffd@0:   % Restore hold state and caxis
wolffd@0:   if ~memhold   
wolffd@0:     hold off;
wolffd@0:   end
wolffd@0:   caxis(cax);
wolffd@0: end
wolffd@0: 
wolffd@0: %% Set object tags %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  
wolffd@0: 
wolffd@0: set(h_,'Tag','Comet');
wolffd@0: 
wolffd@0: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wolffd@0: 
wolffd@0: 
wolffd@0: function P=init_properties;
wolffd@0: 
wolffd@0: % Initialize an empty property struct
wolffd@0: 
wolffd@0: P.marker=[];
wolffd@0: P.markersize=[];
wolffd@0: P.sizefactor=[];
wolffd@0: P.markercolor=[];
wolffd@0: P.edgecolor=[];
wolffd@0: P.trajwidth=[];
wolffd@0: P.widthfactor=[];
wolffd@0: P.trajcolor=[];
wolffd@0: P.text=[];
wolffd@0: P.textsize=[];
wolffd@0: P.textcolor=[];
wolffd@0: P.subplot=[];
wolffd@0: P.shift=[];