[colours,scl_data]= calc_colours(img, set_value, do_colourbar)
Calculate a colour for each image element
Conductive (positive) areas are shown in red
Non-Conductive (negative) areas are shown in blue
PARAMETERS: img
- 1) an EIDORS image object, or a Ex1 vector
- 2) a 2D image matrix
Usage #1 (img is a Ex1 vector of element conductivities)
Cs = calc_colours( img);
patch(Xs,Ys,Zs,Cs);
Cs is Ex1x1 colourmap entries (if mapped_colour>0)
Ex1x3 colourmap entries (if mapped_colour==0)
Usage #2 (rimg is a MxN image matrix of reconstructed pixels):
img is an image structure with the image properties
c_img = calc_colours( rimg, img);
image( c_img );
c_img is MxN colourmap entries (if mapped_colour>0)
MxNx3 colourmap entries (if mapped_colour==0)
Usage #3 (img is string parameter value)
value = calc_colours( 'param' );
calc_colours( 'param', value );
eg. calc_colours('mapped_colour',127)
Use this to allow printing vector eps files to get around
a matlab bug with warning 'RGB color data not ...'
The following parameters are accepted
'greylev' (DEFAULT -.01): the colour of the ref_level.
Negative values indicate white background
For almost white, greylev=-.01; Black=> greylev=.01
'sat_adj' (DEFAULT .9): max G,B when R=1
'window_range' (DEFAULT .9); window colour range
Colour slope outside range is 1/3 of centre slope
'backgnd' ( DEFAULT [.5,.5,.15] ): image border colour
'ref_level' (DEFAULT 'auto') conductivity of centre of
colour mapping. 'auto' tries to estimate a good level.
'mapped_colour' (DEFAULT 127) number of colourmap entries
using mapped_colour allows matlab to print vector graphics to eps
setting mapped_colour=0 means to use RGB colours
'npoints' (DEFAULT 64) number of points accross the image
'clim' (DEFAULT []) crop colour display of values above clim
colour limit. values more different from ref_level are cropped.
if not specified or clim==[] => no limit
'cmap_type' Specify special colours (Default 'blue_red')
if 'draeger' use the Draegerwerk/Amato colourmap
if 'jet' use the matlab jet colourmap
'cb_shrink_move' shrink or move the colorbar. See eidors_colourbar
help for details.
'colourmap' Return the current EIDORS colormap.
Use as colormap(calc_colours('colourmap'))
PARAMETERS CAN BE SPECIFIED IN TWO WAYS
1. as an image parameter (ie clim in img.calc_colours.clim)
2. a second parameter to ( calc_colours(data, param2 )
where param2.calc_colours.clim= ... etc
3. parameter to calc_colours('clim')
Parameters specified as (1) will override (2)
PARAMETERS: do_colourbar
- show a Matlab colorbar with appropriate scaling
usage: c_img= calc_colours( img, clim );
image( c_img );
calc_colours( img, clim, 1); %now do colorbar
PARAMETERS: ref_lev
- if specified, override the global ref_level parameter0001 function [colours,scl_data]= calc_colours(img, set_value, do_colourbar) 0002 % [colours,scl_data]= calc_colours(img, set_value, do_colourbar) 0003 % Calculate a colour for each image element 0004 % 0005 % Conductive (positive) areas are shown in red 0006 % Non-Conductive (negative) areas are shown in blue 0007 % 0008 % PARAMETERS: img 0009 % - 1) an EIDORS image object, or a Ex1 vector 0010 % - 2) a 2D image matrix 0011 % 0012 % Usage #1 (img is a Ex1 vector of element conductivities) 0013 % 0014 % Cs = calc_colours( img); 0015 % patch(Xs,Ys,Zs,Cs); 0016 % 0017 % Cs is Ex1x1 colourmap entries (if mapped_colour>0) 0018 % Ex1x3 colourmap entries (if mapped_colour==0) 0019 % 0020 % Usage #2 (rimg is a MxN image matrix of reconstructed pixels): 0021 % img is an image structure with the image properties 0022 % 0023 % c_img = calc_colours( rimg, img); 0024 % image( c_img ); 0025 % 0026 % c_img is MxN colourmap entries (if mapped_colour>0) 0027 % MxNx3 colourmap entries (if mapped_colour==0) 0028 % 0029 % Usage #3 (img is string parameter value) 0030 % 0031 % value = calc_colours( 'param' ); 0032 % calc_colours( 'param', value ); 0033 % eg. calc_colours('mapped_colour',127) 0034 % Use this to allow printing vector eps files to get around 0035 % a matlab bug with warning 'RGB color data not ...' 0036 % 0037 % The following parameters are accepted 0038 % 0039 % 'greylev' (DEFAULT -.01): the colour of the ref_level. 0040 % Negative values indicate white background 0041 % For almost white, greylev=-.01; Black=> greylev=.01 0042 % 'sat_adj' (DEFAULT .9): max G,B when R=1 0043 % 'window_range' (DEFAULT .9); window colour range 0044 % Colour slope outside range is 1/3 of centre slope 0045 % 'backgnd' ( DEFAULT [.5,.5,.15] ): image border colour 0046 % 'ref_level' (DEFAULT 'auto') conductivity of centre of 0047 % colour mapping. 'auto' tries to estimate a good level. 0048 % 'mapped_colour' (DEFAULT 127) number of colourmap entries 0049 % using mapped_colour allows matlab to print vector graphics to eps 0050 % setting mapped_colour=0 means to use RGB colours 0051 % 'npoints' (DEFAULT 64) number of points accross the image 0052 % 'clim' (DEFAULT []) crop colour display of values above clim 0053 % colour limit. values more different from ref_level are cropped. 0054 % if not specified or clim==[] => no limit 0055 % 'cmap_type' Specify special colours (Default 'blue_red') 0056 % if 'draeger' use the Draegerwerk/Amato colourmap 0057 % if 'jet' use the matlab jet colourmap 0058 % 'cb_shrink_move' shrink or move the colorbar. See eidors_colourbar 0059 % help for details. 0060 % 0061 % 'colourmap' Return the current EIDORS colormap. 0062 % Use as colormap(calc_colours('colourmap')) 0063 % 0064 % PARAMETERS CAN BE SPECIFIED IN TWO WAYS 0065 % 1. as an image parameter (ie clim in img.calc_colours.clim) 0066 % 2. a second parameter to ( calc_colours(data, param2 ) 0067 % where param2.calc_colours.clim= ... etc 0068 % 3. parameter to calc_colours('clim') 0069 % 0070 % Parameters specified as (1) will override (2) 0071 % 0072 % PARAMETERS: do_colourbar 0073 % - show a Matlab colorbar with appropriate scaling 0074 % 0075 % usage: c_img= calc_colours( img, clim ); 0076 % image( c_img ); 0077 % calc_colours( img, clim, 1); %now do colorbar 0078 % 0079 % PARAMETERS: ref_lev 0080 % - if specified, override the global ref_level parameter 0081 % 0082 0083 % (C) 2005-2008 Andy Adler. License: GPL version 2 or version 3 0084 % $Id: calc_colours.html 2819 2011-09-07 16:43:11Z aadler $ 0085 0086 if nargin==0; error('calc_colours: expecting argument'); end 0087 if isstr(img) && strcmp(img,'UNIT_TEST'); do_unit_test; return; end 0088 0089 if ischar(img) 0090 % called as calc_colours('parameter' ... ) 0091 if nargin==1; 0092 colours= get_field(img); 0093 else 0094 colours= set_field(img, set_value); 0095 end 0096 return; 0097 0098 elseif isfield(img,'type') 0099 img_data= get_img_data( img ); 0100 pp=get_colours(img(1)) ; 0101 else 0102 img_data= img; 0103 0104 if nargin==1 0105 pp=get_colours( [] ); 0106 else 0107 pp=get_colours(set_value); 0108 end 0109 end 0110 0111 % Set default parameters 0112 if nargin < 3; do_colourbar = 0; end 0113 ref_lev = 'use_global'; 0114 0115 0116 if isempty(img_data) 0117 colours = 'k'; %black 0118 return; 0119 end 0120 0121 m= size(img_data,1); n=size(img_data,2); 0122 0123 % We can only plot the real part of data 0124 % Vectorize img_data here, it gets reshaped later 0125 [scl_data, ref_lev, max_scale] = ... 0126 scale_for_display( real(img_data(:)), pp.ref_level, pp.clim ); 0127 0128 backgnd= isnan(scl_data); 0129 scl_data(backgnd)= mean( scl_data(~backgnd)); 0130 0131 if pp.mapped_colour 0132 colours=set_mapped_colour(pp, backgnd, scl_data); 0133 colours= reshape( colours, m,n,[]); 0134 else 0135 [red,grn,blu] = blu_red_axis( pp, scl_data, backgnd ); 0136 colours= reshape( [red,grn,blu],m,n,3); 0137 end 0138 0139 % print colorbar if do_colourbar is specified 0140 if do_colourbar 0141 if ~pp.mapped_colour 0142 warning('Colorbar not available without mapped_colour option'); 0143 else 0144 eidors_colourbar(max_scale,ref_lev,pp.cb_shrink_move) 0145 end 0146 end 0147 0148 0149 %scaled data must go from -1 to 1 0150 function [red,grn,blu] = blu_red_axis( pp, scale_data, backgnd ) 0151 if ~isfield(pp,'cmap_type') 0152 pp.cmap_type = 'blue_red'; 0153 end; 0154 0155 % window data such that slope above w is 1/3 of that below 0156 % thus w is mapped to k st k/w = 3(1-k)/(1-w) -> k=3w/(1+2w) 0157 W= pp.window_range; K= 3*W/(1+2*W); 0158 scale_data= sign(scale_data) .* ( ... 0159 ( K/W* abs(scale_data) ) .* (abs(scale_data)<=W) + ... 0160 (K+K/W/3*(abs(scale_data)-W)) .* (abs(scale_data)> W) ); 0161 0162 switch pp.cmap_type 0163 case {'blue_red',''} 0164 [red,grn,blu]= blue_red_colours(pp,scale_data); 0165 case 'draeger' 0166 [red,grn,blu]= draeger_colours(pp,scale_data); 0167 case 'jet' 0168 [red,grn,blu]= jet_colours(pp,scale_data); 0169 case 'jetair' 0170 % Make most of the range for air -ve 0171 scd = (scale_data + 0.5)/0.6; 0172 [red,grn,blu]= jet_colours(pp,scd); 0173 otherwise 0174 error(['specified cmap_type not understood:',pp.cmap_type]); 0175 end 0176 0177 red(backgnd) = pp.backgnd(1); 0178 grn(backgnd) = pp.backgnd(2); 0179 blu(backgnd) = pp.backgnd(3); 0180 0181 function [red,grn,blu]= blue_red_colours(pp,scale_data); 0182 if 0 0183 D= sign(pp.greylev+eps); %force 0 to 1 0184 glev= abs(pp.greylev); 0185 F= 3*pp.sat_adj; 0186 0187 red= D*F*abs(scale_data+D/F) - D + (D==-1); 0188 red= red.*(red>0).*(red<1) + (red>=1); 0189 red= red*(1-glev) + glev; 0190 end 0191 ofs= (pp.greylev >= 0); % 1 if greylev>=0 0192 glev= abs(pp.greylev); 0193 0194 D= (2*ofs - 1); 0195 ofs= ofs - 2*(ofs==0); 0196 F= 3*pp.sat_adj; 0197 DF= D*F; D_F= D/F; 0198 0199 red= DF*abs(scale_data+D_F) - ofs; 0200 red= red.*(red>0).*(red<1) + (red>=1); 0201 0202 grn= DF*abs(scale_data ) - ofs; 0203 grn= grn.*(grn>0).*(grn<1) + (grn>=1); 0204 0205 blu= DF*abs(scale_data-D_F) - ofs; 0206 blu= blu.*(blu>0).*(blu<1) + (blu>=1); 0207 0208 if pp.greylev >=0 % Black background 0209 red= red*(1-glev) + glev; 0210 grn= grn*(1-glev) + glev; 0211 blu= blu*(1-glev) + glev; 0212 else 0213 red= red*(1-glev); 0214 grn= grn*(1-glev); 0215 blu= blu*(1-glev); 0216 end 0217 0218 function [red,grn,blu] = draeger_colours(pp,scale_data); 0219 grn= (-scale_data>0.2) .* (-scale_data - 0.2)/0.8; 0220 red=grn + ( scale_data>0.2) .* ( scale_data - 0.2)/0.8*2/3; 0221 0222 blu= (-scale_data>0.1) .* (-scale_data - 0.1)/0.1; 0223 blu(-scale_data>0.2) = 1; 0224 blu=blu + ( scale_data>0.2) .* ( scale_data - 0.2)/0.8*2/3; 0225 0226 % Sometimes this is just slightly > 1 0227 red(red>1) = 1; 0228 grn(grn>1) = 1; 0229 blu(blu>1) = 1; 0230 0231 function [red,grn,blu] = jet_colours(pp,scale_data); 0232 grn = 2*(3/4 - abs(scale_data)); 0233 grn(grn>1) = 1; grn(grn<0) = 0; 0234 0235 red = 1.5 - 2*abs(scale_data + 0.5); 0236 red(red>1) = 1; red(red<0) = 0; 0237 0238 blu = 1.5 - 2*abs(scale_data - 0.5); 0239 blu(blu>1) = 1; blu(blu<0) = 0; 0240 0241 function pp=get_colours( img ); 0242 global eidors_colours; 0243 pp= eidors_colours; 0244 0245 % override global if calc.colours specified 0246 try 0247 % DAMN Matlab should have syntax for this loop 0248 fds= fieldnames(img(1).calc_colours);%assume all are the same! 0249 for fdn= fds(:)'; 0250 fdn= fdn{1}; 0251 pp.( fdn ) = img(1).calc_colours.(fdn); 0252 end 0253 end 0254 0255 function BGI= backgndidx; 0256 BGI= 1; 0257 0258 function colours=set_mapped_colour(pp, backgnd, img_data) 0259 % need to generate a colourmap with pp.mapped_colour+1 elements 0260 % background pixel will be at entry #1. Thus for 0261 % mapped_colour= 3. CMAP = [backgnd,[-1 -.5 0 .5 1] 0262 % 0263 % Note: ensure patch uses 'direct' CDataMapping 0264 ncol= pp.mapped_colour; 0265 [red,grn,blu] = blu_red_axis( pp, ... 0266 [-1,linspace(-1,1,2*ncol - 1)]', backgndidx ); 0267 colormap([red,grn,blu]); 0268 % This is the line I wan't to write. However, matlab seems to waste 0269 % lots of memory to do it. Instead we break it into pieces 0270 % colours = fix( img_data * (ncol-1))' + ncol + 1; 0271 colours = img_data'; colours = colours * (ncol-1); 0272 colours = fix ( colours ); colours = colours + ncol + 1; 0273 colours(backgnd)= backgndidx; 0274 0275 function value= get_field(param); 0276 global eidors_colours; 0277 if strcmp(param,'colourmap') 0278 ncol= eidors_colours.mapped_colour; 0279 [red,grn,blu] = blu_red_axis( eidors_colours, ... 0280 [-1,linspace(-1,1,2*ncol - 1)]', backgndidx ); 0281 value= [red,grn,blu]; 0282 else 0283 value = getfield(eidors_colours, param); 0284 end 0285 0286 function value= set_field(param, value); 0287 global eidors_colours; 0288 eidors_colours = setfield(eidors_colours, param, value); 0289 value= eidors_colours; 0290 0291 % TESTS: 0292 function do_unit_test 0293 img = eidors_obj('image','test'); 0294 0295 img.calc_colours.mapped_colour = 127; 0296 img.calc_colours.ref_level = 'auto'; 0297 img.calc_colours.sat_adj = 0.9; 0298 img.calc_colours.window_range = 0.9; 0299 img.calc_colours.greylev = -0.01; 0300 0301 img.elem_data = [-2;0;0;0;1;3]; 0302 unit_test_cmp('cc01', calc_colours(img), [44; 128; 128; 128; 170; 254]); 0303 0304 imgk(1) = img; imgk(2) = img; 0305 unit_test_cmp('cc01', calc_colours(imgk), [44; 128; 128; 128; 170; 254]*[1,1]); 0306 0307 img.calc_colours.ref_level = 1; 0308 unit_test_cmp('cc02', calc_colours(img), [ 2; 86; 86; 86; 128; 212]); 0309 0310 img.calc_colours.greylev = -.1; 0311 img.calc_colours.mapped_colour = 0; 0312 img.elem_data = [-2;1;3]; 0313 cm= reshape([ 0, 0.9, 0.9; 0, 0.9, 0.0643; 0.27, 0.9, 0]',[3,1,3]); 0314 unit_test_cmp('cc03', calc_colours(img), cm,1e-3) 0315 0316 img.calc_colours.greylev = .1; 0317 cm= reshape([ 0.73, 1.0, 1.0; 0.1, 0.1, 0.1; 1.0, 0.9357, 0.1],[3,1,3]); 0318 unit_test_cmp('cc04', calc_colours(img), cm,1e-3) 0319 0320 calc_colours('greylev',0); 0321 calc_colours('sat_adj',1); 0322 calc_colours('mapped_colour',4); 0323 calc_colours('backgnd',[0.5,0.5,0.5]); 0324 cc= calc_colours('colourmap'); 0325 unit_test_cmp('cc05',cc, [2,2,2;4,4,4;2,4,4;0,1,4;0,0,0;4,1,0;4,4,2;4,4,4]/4,1e-4); 0326 0327 % TESTS TO WRITE 0328 % 'greylev' (DEFAULT -.01) 0329 % 'sat_adj' (DEFAULT .9) 0330 % 'window_range' (DEFAULT .9) 0331 % 'backgnd' ( DEFAULT [.5,.5,.15] ) 0332 % 'ref_level' (DEFAULT 'auto') 0333 % 'mapped_colour' (DEFAULT 127) 0334 % 'npoints' (DEFAULT 64) 0335 % 'clim' (DEFAULT []) 0336 % 'cmap_type' (Default blue-red) 0337