Home > fmri > utils > slice_overlay_contour.m

slice_overlay_contour

PURPOSE ^

Function to display + manage slice display

SYNOPSIS ^

function varargout = slice_overlay(action, varargin);

DESCRIPTION ^

 Function to display + manage slice display 
 Slice display works on a global structure SO
 with fields 
  - img - array of images to display
        - img structs contain fields
             vol - vol struct info (see spm_vol)
             cmap - colormap for this image
             nancol - color for NaN. If scalar, this is an index into
                    the image cmap.  If 1x3 vector, it's a colour
             prop - proportion of intensity for this cmap/img 
                    if = Inf, gives split cmap effect where values of 
                    this cmap override previous image cmap values
             func - function to apply to image before scaling to cmap
                    (and therefore before min/max thresholding. E.g. a func of
                    'i1(i1==0)=NaN' would convert zeros to NaNs
             range - 2x1 vector of values for image to distribute colormap across
                    the first row of the colormap applies to the first
                    value in 'range', and the last value to the second
                    value in 'range'
             outofrange - behavior for image values to the left and
                    right of image limits in 'range'.  Left means
                    colormap values < 1, i.e for image values <
                    range(1), if (range(1)<range(2)), and image values >
                    range(1) where (range(1)>range(2)). If missing,
                    display min (for Left) and max (for Right) value from colormap. 
                    Otherwise should be a 2 element cell array, where
                    the first element is the colour value for image values
                    left of 'range', and the second is for image values
                    right of 'range'.  Scalar values for
                    colour index the colormap, 3x1 vectors are colour
                    values.  An empty array attracts default settings
                    appropriate to the mode - i.e. transparent colour (where 
                    SO.prop ~= Inf), or split colour.  Empty cells
                    default to 0. 0 specifies that voxels with this
                    colour do not influence the image (split =
                    background, true = black)
            hold  - resampling order for image (see spm_sample_vol) -
                    default 1
            background - value when resampling outside image - default
                    NaN
            
 - transform - either - 4x4 transformation to apply to image slice position,
             relative to mm given by slicedef, before display
               or     - text string, one of axial, coronal, sagittal
                        These orientations assume the image is currently
                        (after its mat file has been applied) axially
                        oriented
 - slicedef - 2x3 array specifying dimensions for slice images in mm
             where rows are x,and y of slice image, and cols are neg max dim,
             slice separation and pos max dim
 - slices   - vector of slice positions in mm in z (of transformed image)
 - figure    - figure handle for slice display figure
 - area      struct with fields
                  position - bottom left, x size y size 1x4 vector of
                      area in which to display slices
                  units    - one of
                    inches,centimeters,normalized,points,{pixels}
                  halign - one of left,{center},right
                  valign - one of top,{middle},bottom
 - xsliceno  - no of slices to display across figure (defaults to an optimum)
 - refreshf  - flag - if set or empty, refresh axis info for figure
             else assume this is OK
 - cbar      - if empty, missing, no colourbar.  If an array of integers, then 
             indexes img array, and makes colourbar for each cmap for
             that img.  Cbars specified in order of appearance L->R
 - labels - struct can be absent (-> default numerical labels)
                  empty (SO.labels = []) (no labels) or contain fields 
                  colour - colour for label text 
                  size - font size in units normalized to slice axes 
                  format - if = cell array of strings =
                  labels for each slice in Z.  If is string, specifies
                  sprintf format string for labelling in distance of the
                  origin (Xmm=0, Ymm=0) of each slice from plane containing
                  the AC, in mm, in the space of the transformed image
  
  
 V 0.7 1/8/00  
 More or less  beta - take care.  Please report problems to  
 Matthew Brett matthew@mrc-cbu.cam.ac.uk

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SUBFUNCTIONS ^

SOURCE CODE ^

0001 function varargout = slice_overlay(action, varargin);
0002 % Function to display + manage slice display
0003 % Slice display works on a global structure SO
0004 % with fields
0005 %  - img - array of images to display
0006 %        - img structs contain fields
0007 %             vol - vol struct info (see spm_vol)
0008 %             cmap - colormap for this image
0009 %             nancol - color for NaN. If scalar, this is an index into
0010 %                    the image cmap.  If 1x3 vector, it's a colour
0011 %             prop - proportion of intensity for this cmap/img
0012 %                    if = Inf, gives split cmap effect where values of
0013 %                    this cmap override previous image cmap values
0014 %             func - function to apply to image before scaling to cmap
0015 %                    (and therefore before min/max thresholding. E.g. a func of
0016 %                    'i1(i1==0)=NaN' would convert zeros to NaNs
0017 %             range - 2x1 vector of values for image to distribute colormap across
0018 %                    the first row of the colormap applies to the first
0019 %                    value in 'range', and the last value to the second
0020 %                    value in 'range'
0021 %             outofrange - behavior for image values to the left and
0022 %                    right of image limits in 'range'.  Left means
0023 %                    colormap values < 1, i.e for image values <
0024 %                    range(1), if (range(1)<range(2)), and image values >
0025 %                    range(1) where (range(1)>range(2)). If missing,
0026 %                    display min (for Left) and max (for Right) value from colormap.
0027 %                    Otherwise should be a 2 element cell array, where
0028 %                    the first element is the colour value for image values
0029 %                    left of 'range', and the second is for image values
0030 %                    right of 'range'.  Scalar values for
0031 %                    colour index the colormap, 3x1 vectors are colour
0032 %                    values.  An empty array attracts default settings
0033 %                    appropriate to the mode - i.e. transparent colour (where
0034 %                    SO.prop ~= Inf), or split colour.  Empty cells
0035 %                    default to 0. 0 specifies that voxels with this
0036 %                    colour do not influence the image (split =
0037 %                    background, true = black)
0038 %            hold  - resampling order for image (see spm_sample_vol) -
0039 %                    default 1
0040 %            background - value when resampling outside image - default
0041 %                    NaN
0042 %
0043 % - transform - either - 4x4 transformation to apply to image slice position,
0044 %             relative to mm given by slicedef, before display
0045 %               or     - text string, one of axial, coronal, sagittal
0046 %                        These orientations assume the image is currently
0047 %                        (after its mat file has been applied) axially
0048 %                        oriented
0049 % - slicedef - 2x3 array specifying dimensions for slice images in mm
0050 %             where rows are x,and y of slice image, and cols are neg max dim,
0051 %             slice separation and pos max dim
0052 % - slices   - vector of slice positions in mm in z (of transformed image)
0053 % - figure    - figure handle for slice display figure
0054 % - area      struct with fields
0055 %                  position - bottom left, x size y size 1x4 vector of
0056 %                      area in which to display slices
0057 %                  units    - one of
0058 %                    inches,centimeters,normalized,points,{pixels}
0059 %                  halign - one of left,{center},right
0060 %                  valign - one of top,{middle},bottom
0061 % - xsliceno  - no of slices to display across figure (defaults to an optimum)
0062 % - refreshf  - flag - if set or empty, refresh axis info for figure
0063 %             else assume this is OK
0064 % - cbar      - if empty, missing, no colourbar.  If an array of integers, then
0065 %             indexes img array, and makes colourbar for each cmap for
0066 %             that img.  Cbars specified in order of appearance L->R
0067 % - labels - struct can be absent (-> default numerical labels)
0068 %                  empty (SO.labels = []) (no labels) or contain fields
0069 %                  colour - colour for label text
0070 %                  size - font size in units normalized to slice axes
0071 %                  format - if = cell array of strings =
0072 %                  labels for each slice in Z.  If is string, specifies
0073 %                  sprintf format string for labelling in distance of the
0074 %                  origin (Xmm=0, Ymm=0) of each slice from plane containing
0075 %                  the AC, in mm, in the space of the transformed image
0076 %
0077 %
0078 % V 0.7 1/8/00
0079 % More or less  beta - take care.  Please report problems to
0080 % Matthew Brett matthew@mrc-cbu.cam.ac.uk
0081 
0082 global SO
0083 
0084 if nargin < 1
0085   action = 'display';
0086 else
0087   action = lower(action);
0088 end
0089 
0090 switch action
0091  case 'checkso'
0092   checkso;
0093  case 'getcmap'
0094   varargout = {getcmap(varargin{1})};
0095  case 'volmaxmin'
0096   [mx mn] = volmaxmin(varargin{1});
0097   varargout = {mx, mn};
0098  case 'display'
0099 
0100 % check and/or initialise SO struct
0101 checkso;
0102 
0103 % get coordinates for plane
0104 X=1;Y=2;Z=3;
0105 dims = SO.slicedef;
0106 xmm = dims(X,1):dims(X,2):dims(X,3);
0107 ymm = dims(Y,1):dims(Y,2):dims(Y,3);
0108 zmm = SO.slices;
0109 [y x] = meshgrid(ymm,xmm');
0110 vdims = [length(xmm),length(ymm),length(zmm)];
0111 
0112 % no of slices, and panels (an extra for colorbars)
0113 nslices = vdims(Z);
0114 minnpanels = nslices;
0115 cbars = 0;
0116 if is_there(SO,'cbar')
0117   cbars = length(SO.cbar);
0118   minnpanels = minnpanels+cbars;
0119 end
0120 
0121 % get figure data
0122 % if written to, the axes may be specified already
0123 figno = figure(SO.figure);
0124 
0125 % (re)initialize axes and stuff
0126 
0127 % check if the figure is set up correctly
0128 if ~SO.refreshf
0129   axisd = flipud(findobj(SO.figure, 'Type','axes','Tag', 'slice overlay panel'));
0130   npanels = length(axisd);
0131   if npanels < vdims(Z)+cbars;
0132     SO.refreshf = 1;
0133   end
0134 end
0135 if SO.refreshf
0136   % clear figure and axis store
0137   clf
0138   axisd = [];
0139 
0140   % prevent print inversion problems
0141   set(figno,'InvertHardCopy','off');
0142   
0143   % calculate area of display in pixels
0144   parea = SO.area.position;
0145   if ~strcmp(SO.area.units, 'pixels')
0146     ubu = get(SO.figure, 'units');
0147     set(SO.figure, 'units','pixels');
0148     tmp = get(SO.figure, 'Position');
0149     ascf = tmp(3:4);
0150     if ~strcmp(SO.area.units, 'normalized')
0151       set(SO.figure, 'units',SO.area.units);
0152       tmp = get(SO.figure, 'Position');
0153       ascf = ascf ./ tmp(3:4);
0154     end
0155     set(figno, 'Units', ubu);
0156     parea = parea .* repmat(ascf, 1, 2);
0157   end
0158   asz = parea(3:4);
0159   
0160   % by default, make most parsimonious fit to figure
0161   yxratio = length(ymm)*dims(Y,2)/(length(xmm)*dims(X,2));
0162   if ~is_there(SO, 'xslices')
0163     % iteration needed to optimize, surprisingly.  Thanks to Ian NS
0164     axlen(X,:)=asz(1):-1:1;
0165     axlen(Y,:)=yxratio*axlen(X,:);
0166     panels = floor(asz'*ones(1,size(axlen,2))./axlen);
0167     estnpanels = prod(panels);
0168     tmp = find(estnpanels >= minnpanels);
0169     if isempty(tmp)
0170       error('Whoops, cannot fit panels onto figure');
0171     end
0172     b = tmp(1); % best fitting scaling
0173     panels = panels(:,b);
0174     axlen = axlen(:, b);
0175   else
0176     % if xslices is specified, assume X is flush with X figure dimensions
0177     panels(X) = SO.xsliceno;
0178     axlen(X) = asz(X)/panels(X);
0179   end
0180   
0181   % Axis dimensions are in pixels.  This prevents aspect ratio rescaling
0182   panels(Y) = ceil(minnpanels/panels(X));
0183   axlen(Y) = axlen(X)*yxratio;
0184   
0185   % centre (etc) panels in display area as required
0186   divs = [Inf 2 1];the_ds = [0;0];
0187   the_ds(X) = divs(strcmp(SO.area.halign, {'left','center','right'}));
0188   the_ds(Y) = divs(strcmp(SO.area.valign, {'bottom','middle','top'}));
0189   startc = parea(1:2)' + (asz'-(axlen.*panels))./the_ds;
0190   
0191   % make axes for panels
0192   r=0;c=1;
0193   npanels = prod(panels);
0194   lastempty = npanels-cbars;
0195   for i = 1:npanels
0196     % panel userdata
0197     if i<=nslices
0198       u.type = 'slice';
0199       u.no   = zmm(i);
0200     elseif i > lastempty
0201       u.type = 'cbar';
0202       u.no   = i - lastempty;
0203     else
0204       u.type = 'empty';
0205       u.no   = i - nslices;
0206     end
0207     axpos = [r*axlen(X)+startc(X) (panels(Y)-c)*axlen(Y)+startc(Y) axlen'];
0208     axisd(i) = axes(...
0209     'Parent',figno,...
0210     'XTick',[],...
0211     'XTickLabel',[],...
0212     'YTick',[],...
0213     'YTickLabel',[],...
0214     'Box','on',...
0215     'XLim',[1 vdims(X)],...
0216     'YLim',[1 vdims(Y)],...
0217     'Units', 'pixels',...
0218     'Position',axpos,...
0219     'Tag','slice overlay panel',...
0220     'UserData',u);
0221     r = r+1;
0222     if r >= panels(X)
0223       r = 0;
0224       c = c+1;
0225     end
0226   end
0227 end
0228 
0229 % sort out labels
0230 if is_there(SO,'labels')
0231   labels = SO.labels;
0232   if iscell(labels.format)
0233     if length(labels.format)~=vdims(Z)
0234       error(...
0235       sprintf('Oh dear, expecting %d labels, but found %d',...
0236           vdims(Z), length(labels.contents)));
0237     end
0238   else
0239     % format string for mm from AC labelling
0240     fstr = labels.format;
0241     labels.format = cell(vdims(Z),1);
0242     acpt = SO.transform * [0 0 0 1]';
0243     for i = 1:vdims(Z)
0244       labels.format(i) = {sprintf(fstr,zmm(i)-acpt(Z))};
0245     end
0246   end
0247 end
0248 
0249 % modify colormaps with any new colours
0250 nimgs = length(SO.img);
0251 lrn = zeros(nimgs,3);
0252 cmaps = cell(nimgs);
0253 for i = 1:nimgs
0254   cmaps(i)={SO.img(i).cmap};
0255   lrnv = {SO.img(i).outofrange{:}, SO.img(i).nancol};
0256   for j = 1:length(lrnv)
0257     if prod(size(lrnv{j}))==1
0258       lrn(i,j) = lrnv{j};
0259     else
0260       cmaps(i) = {[cmaps{i}; lrnv{j}(1:3)]};
0261       lrn(i,j) = size(cmaps{i},1);
0262     end
0263   end
0264 end
0265 
0266 % cycle through slices displaying images
0267 nvox = prod(vdims(1:2));
0268 pandims = [vdims([2 1]) 3]; % NB XY transpose for display
0269 
0270 zimg = zeros(pandims);
0271 for i = 1:nslices
0272   ixyzmm = [x(:)';y(:)';ones(1,nvox)*zmm(i);ones(1,nvox)];
0273   img = zimg;
0274   
0275   % construct overlay
0276   for j = 1:nimgs    
0277     if ~any(ismember(j,SO.contours))
0278       thisimg = SO.img(j);
0279       
0280       % to voxel space of image
0281       vixyz = inv(SO.transform*thisimg.vol.mat)*ixyzmm;
0282       % raw data
0283       i1 = spm_sample_vol(thisimg.vol,vixyz(X,:),vixyz(Y,:),vixyz(Z,:), ...
0284       [thisimg.hold thisimg.background]);
0285       if is_there(thisimg, 'func')
0286     eval(thisimg.func);
0287       end
0288       % transpose to reverse X and Y for figure
0289       i1 = reshape(i1, vdims(1:2))';
0290       % rescale to colormap
0291       [csdata badvals]= scaletocmap(...
0292       i1,...
0293       thisimg.range(1),...
0294       thisimg.range(2),...
0295       cmaps{j},...
0296       lrn(j,:));
0297       % take indices from colormap to make true colour image
0298       iimg = reshape(cmaps{j}(csdata(:),:),pandims);
0299       tmp = repmat(logical(~badvals),[1 1 3]);
0300       if thisimg.prop ~= Inf % truecolor overlay
0301     img(tmp) = img(tmp) + iimg(tmp)*thisimg.prop;
0302       else % split colormap effect
0303     img(tmp) = iimg(tmp);
0304       end
0305     end
0306   end
0307 
0308   % threshold out of range values
0309   img(img>1) = 1;
0310   
0311   image('Parent', axisd(i),...
0312     'CData',img);
0313   if is_there(SO,'labels')
0314     text('Parent',axisd(i),...
0315     'Color', labels.colour,...
0316     'FontUnits', 'normalized',...
0317     'VerticalAlignment','bottom',...
0318     'HorizontalAlignment','left',...
0319     'Position', [1 1],...
0320     'FontSize',labels.size,...
0321     'String', labels.format{i});
0322   end
0323    
0324   % add contours if desired
0325   for j = 1:nimgs 
0326     if any(ismember(j,SO.contours))
0327       thisimg = SO.img(j);
0328       % to voxel space of image
0329       vixyz = inv(SO.transform*thisimg.vol.mat)*ixyzmm;
0330       % raw data
0331       i1 = spm_sample_vol(thisimg.vol,vixyz(X,:),vixyz(Y,:),vixyz(Z,:), ...
0332       [thisimg.hold thisimg.background]);
0333       if is_there(thisimg, 'func')
0334     eval(thisimg.func);
0335       end
0336       % transpose to reverse X and Y for figure
0337       i1 = reshape(i1, vdims(1:2))';
0338       
0339       % add contour plot
0340       axes(axisd(i));
0341       set(axisd(i),'NextPlot','add');
0342       contour(i1,[thisimg.range(1) thisimg.range(1)],thisimg.linestr)
0343     end
0344   end
0345 end
0346 
0347 for i = (nslices+1):npanels
0348    set(axisd(i),'Color',[0 0 0]);
0349 end
0350 % add colorbar(s)
0351 for i = 1:cbars
0352   axno = axisd(end-cbars+i);
0353   cbari = SO.img(SO.cbar(i));
0354   cml = size(cbari.cmap,1);
0355   p = get(axno, 'Position');; % position of last axis
0356   cw = p(3)*0.2;
0357   ch = p(4)*0.75;
0358   pc = p(3:4)/2;
0359   [axlims idxs] = sort(cbari.range);
0360   a=axes(...
0361       'Parent',figno,...
0362       'XTick',[],...
0363       'XTickLabel',[],...
0364       'Units', 'pixels',...
0365       'YLim', axlims,...   
0366       'FontUnits', 'normalized',...
0367       'FontSize', 0.075,...
0368       'YColor',[1 1 1],...
0369       'Tag', 'cbar',...
0370       'Box', 'off',...
0371       'Position',[p(1)+pc(1)-cw/2,p(2)+pc(2)-ch/2,cw,ch]...
0372       );
0373   ih = image('Parent', a,...
0374     'YData', axlims(idxs),...     
0375     'CData', reshape(cbari.cmap,[cml,1,3]));
0376 
0377 end
0378 
0379 % end switch action
0380 end
0381 
0382 return
0383 
0384 function checkso
0385 % checks and fills SO structure
0386 global SO
0387 
0388 % figure
0389 if is_there(SO, 'figure')
0390   try
0391     if ~strcmp(get(SO.figure,'Type'),'figure')
0392       error('Figure handle is not a figure')
0393     end
0394   catch
0395     error('Figure handle is not a valid figure')
0396   end
0397 else
0398   % no figure handle. Try spm figure, then gcf
0399   SO.figure = spm_figure('FindWin', 'Graphics'); 
0400   if isempty(SO.figure)
0401     SO.figure = gcf;
0402   end
0403 end
0404 % set defaults for SPM figure
0405 if strcmp(get(SO.figure, 'Tag'),'Graphics')
0406   SO.area.position = [0 0 1 0.92]; % position figure nicely for SPM
0407   SO.area.units = 'normalized';
0408   SO.area.valign = 'top';
0409 end
0410 
0411 % orientation; string or 4x4 matrix
0412 orientn = [];
0413 SO = set_def(SO, 'transform', 'axial');
0414 if ischar(SO.transform)
0415   orientn = find(strcmpi(SO.transform, {'axial','coronal','sagittal'}));
0416   if isempty(orientn)
0417     error(sprintf('Unexpected orientation %s', SO.transform));
0418   end
0419   ts = [0 0 0 0 0 0 1 1 1;...
0420       0 0 0 pi/2 0 0 1 -1 1;...
0421       0 0 0 pi/2 0 -pi/2 -1 1 1];
0422   SO.transform = spm_matrix(ts(orientn,:));
0423 end
0424 % default slice size, slice matrix depends on orientation
0425 if ~is_there(SO,'slicedef' | ~is_there(SO, 'slices'))
0426   % take image sizes from first image
0427   V = SO.img(1).vol;
0428   D = V.dim(1:3);
0429   T = SO.transform * V.mat;
0430   vcorners = [1 1 1; D(1) 1 1; 1 D(2) 1; D(1:2) 1; ...
0431          1 1 D(3); D(1) 1 D(3); 1 D(2:3) ; D(1:3)]';
0432   corners = T * [vcorners; ones(1,8)];
0433   SC = sort(corners');
0434   vxsz = sqrt(sum(T(1:3,1:3).^2));
0435   
0436   SO = set_def(SO, 'slicedef',...
0437     [SC(1,1) vxsz(1) SC(8,1);SC(1,2) vxsz(2) SC(8,2)]);
0438   SO = set_def(SO, 'slices',[SC(1,3):vxsz(3):SC(8,3)]);
0439 end
0440 
0441 % no colourbars by default
0442 SO = set_def(SO, 'cbars', []);
0443 
0444 % always refresh figure window, by default
0445 SO = set_def(SO, 'refreshf', 1);  
0446 
0447 % labels
0448 defstruct = struct('colour',[1 1 1],'size',0.075,'format', '%+30f');
0449 if ~isfield(SO, 'labels') % no field, -> default
0450   SO.labels = defstruct;
0451 elseif ~isempty(SO.labels) % empty -> no labels
0452   % colour for slice labels
0453   SO.labels = set_def(SO.labels, 'colour', defstruct.colour); 
0454   % font size normalized to image axis
0455   SO.labels = set_def(SO.labels, 'size', defstruct.size); 
0456   % format string for slice labels
0457   SO.labels = set_def(SO.labels, 'format', defstruct.format); 
0458 end
0459                      
0460 % figure area stuff
0461 defarea = struct('position',[0 0 1 1],'units','normalized');
0462 SO = set_def(SO, 'area', defarea);
0463 if ~is_there(SO.area, 'position')
0464   SO.area = defarea;
0465 end
0466 if ~is_there(SO.area,'units')
0467   if (all(SO.area.position>=0 & SO.area.position<=1))
0468     SO.area.units = 'normalized';
0469   else
0470     SO.area.units = 'pixels';
0471   end
0472 end
0473 SO.area = set_def(SO.area,'halign', 'center');
0474 SO.area = set_def(SO.area,'valign', 'middle');
0475 
0476 % fill various img arguments
0477 % would be nice to use set_def, but we can't
0478 
0479 % set colour intensities as we go
0480 remcol = 1;
0481 for i = 1:length(SO.img)
0482   if ~is_there(SO.img(i),'hold')
0483     SO.img(i).hold = 1;
0484   end
0485   if ~is_there(SO.img(i),'background')
0486     SO.img(i).background = NaN;
0487   end
0488   if ~is_there(SO.img(i),'prop')
0489     % default is true colour
0490     SO.img(i).prop = remcol/(length(SO.img)-i+1);
0491     remcol = remcol - SO.img(i).prop;
0492   end
0493   if ~is_there(SO.img(i),'range')
0494     [mx mn] = volmaxmin(SO.img(i).vol);
0495     SO.img(i).range = [mn mx];
0496   end
0497   if ~is_there(SO.img(i),'cmap')
0498     if SO.img(i).prop == Inf; % split map
0499       SO.img(i).cmap = check_map(i, 'spm_cols');
0500     else                  % true colour
0501       SO.img(i).cmap = check_map(i, 'actc');
0502     end
0503   end  
0504   if ~is_there(SO.img(i),'outofrange')
0505     % this can be complex, and depends on split/true colour
0506     if SO.img(i).prop == Inf % split colour
0507       if xor(SO.img(i).range(1) < SO.img(i).range(2), ...
0508          SO.img(i).range(2) < 0)
0509     SO.img(i).outofrange = {[0],size(SO.img(i).cmap,1)};
0510       else
0511     SO.img(imgno).outofrange={[1], [0]};
0512       end
0513     else            % true colour
0514       SO.img(i).outofrange = {1,size(SO.img(i).cmap,1)};
0515     end
0516   end
0517   for j=1:2
0518     if isempty(SO.img(i).outofrange{j})
0519       SO.img(i).outofrange(j) = {0};
0520     end
0521   end
0522   if ~is_there(SO.img(i),'nancol')
0523     SO.img(i).nancol = 0;
0524   end
0525 end  
0526 return
0527 
0528 function tf = is_there(a, fname)
0529 % returns true if field fname is present in struct a, and not empty
0530 tf = isfield(a, fname);
0531 if tf
0532   tf = ~isempty(getfield(a, fname));
0533 end
0534 return
0535 
0536 function [img, badvals]=scaletocmap(inpimg,mn,mx,cmap,lrn)
0537 img = (inpimg-mn)/(mx-mn);  % img normalized to mn=0,mx=1
0538 cml = size(cmap,1);
0539 if cml==1 % values between 0 and 1 -> 1
0540   img(img>=0 & img<=1)=1;
0541 else
0542   img = img*(cml-1)+1;
0543 end
0544 outvals = {img<1, img>cml, isnan(img)};
0545 img= round(img);
0546 badvals = zeros(size(img));
0547 for i = 1:length(lrn)
0548   if lrn(i)
0549     img(outvals{i}) = lrn(i);
0550   else
0551     badvals = badvals | outvals{i};
0552     img(outvals{i}) = 1;
0553   end    
0554 end
0555 return
0556 
0557 function st = set_def(st, fld, def)
0558 if ~is_there(st, fld)
0559   st = setfield(st, fld, def);
0560 end
0561 
0562 function cm = check_map(idx, mapstr)
0563 try
0564   load(mapstr)
0565 catch
0566   error(sprintf(['No colormap defined for image %d, '...
0567          'and default map %s is not on the path'],...
0568         idx, mapstr));
0569 end
0570 cm = eval(mapstr);
0571 return
0572 
0573 function [mx,mn] = volmaxmin(vol)
0574 mx = -Inf;mn=Inf;
0575 for i=1:vol.dim(3),
0576   tmp = spm_slice_vol(vol,spm_matrix([0 0 i]),vol.dim(1:2),[0 NaN]);
0577   tmp = tmp(find(finite(tmp(:))));
0578   if ~isempty(tmp)
0579     mx = max([mx; tmp]);
0580     mn = min([mn; tmp]);
0581   end
0582 end
0583 return
0584 
0585 function cmap = getcmap(acmapname)
0586 % get colormap of name acmapname
0587 if ~isempty(acmapname)
0588   cmap = evalin('base',acmapname,'[]');
0589   if isempty(cmap) % not a matrix, is it...
0590     % a colour name?
0591     tmp = strcmp(acmapname, {'red','green','blue'});
0592     if any(tmp)
0593       cmap = zeros(64,3);
0594       cmap(:,tmp) = ((0:63)/63)';
0595     else
0596       % a .mat file?
0597       [p f e] = fileparts(acmapname);
0598       acmat = fullfile(p, [f '.mat']);
0599       if exist(acmat, 'file')
0600     s = struct2cell(load(acmat));
0601     cmap = s{1};
0602       end
0603     end
0604   end
0605 end
0606 if size(cmap, 2)~=3
0607   warning('Colormap was not an N by 3 matrix')
0608   cmap = [];
0609 end

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