Inverse masking, outlining of colorbar bins in map, colorbar aligned tick labels

- Keep everything outside of a mask image (inverse masking; added to contextual menu for mask button)
- Create outlines for each bin in your colormap (as one image; added to outline dropdown menu for overlays)
- Tick labels were not aligned to the edges of the colorbar or to colorbar bins (and were not centered)
- Added warning when tick labels purposefully do not align to colorbar bins
- When binarizing underlays, number of bins in the colormap is no longer manipulable to prevent some bugs. Use the color buttons in the underlay data panel to assign different colors than those used by the colormap

Author: alexteghipco

GUIs/oSelect.mlapp

@@ -1,4 +1,4 @@
-function [cMap,cData,cbData,ticks,tickLabels] = colormapper(data,varargin)
+function [cMap,cData,cbData,ticks,tickLabels,m] = colormapper(data,varargin)
 % This function generates a colormap using various specifications.
 %
 % Mandatory arguments------------------------------------------------------ 
@@ -50,6 +50,7 @@
 % [cMap,cData,cbData,ticks,tickLabels] = colormapGenerator(data,'colormap','delta','colorSpacing','even','colorBins',1000,'colorSpecial','randomizeClusterColors','invertColors','false')
 
 % Defaults
+m = [];
 options = struct('colormap', 'jet','colorSpacing','even','colorBins',1000,'colorSpecial','none','invertColors','false','limits',[min(data) max(data)],'sulci',[],'gyri',[],'thresh',[]);
 optionNames = fieldnames(options);
 
@@ -80,6 +81,8 @@
             warning('Colormap is adjusted...if centering on zero must have even number of color bins')
             options.colorBins=options.colorBins-1;
         end
+    case 'even'
+        %options.colorBins = options.colorBins+1;
 end
 
 % create colormap if a string is passed in...otherwise interpolate colors
@@ -293,15 +296,23 @@
     % this is the default option. All values between limits will get a
     % color from your colormap.
     case 'even'
-        cbData = linspace(min(options.limits),max(options.limits),options.colorBins);
+        cbData = linspace(min(options.limits),max(options.limits),options.colorBins+1);
         % this will split your colormap into negative and positive values.
         % Negative stuff gets half the colormap. positive stuff gets the other
         % half.
-        ticks = linspace(min(options.limits),max(options.limits),11);
-        tickLabels = ticks;
+        if length(cbData) <= 21
+            ticks = cbData;
+        else
+            ticks = linspace(min(options.limits),max(options.limits),21);
+            warning('Colorbar labels are in the correct position but may not match the location of each bin on the colormap because you have too many bins in your colormap and we cannot display ticks for all of them')
+        end
 
+        tickLabels = ticks;
         tf = cbData >= data;
-        [~,m] = max(tf,[],2);
+        [~,m] = min(fliplr(tf), [], 2);
+        m = size(tf, 2) - m + 1;
+        id = find(m > options.colorBins);
+        m(id) = options.colorBins; % we need to clip everything above the limit to the last colorbin
         cData = cMap(m,:);
 
     case 'center on zero'

brainSurfer.mlapp

@@ -237,7 +237,7 @@
 end
 
 % Get clusters if they are needed
-if options.clusterThresh ~= 0 | options.grow ~= 0 | strcmpi(options.outline,'map') | strcmpi(options.binarize,'clusters') == 1 | ~isempty(options.priorClusters)
+if options.clusterThresh ~= 0 | options.grow ~= 0 | strcmpi(options.outline,'map') | strcmpi(options.outline,'bins') | strcmpi(options.binarize,'clusters') == 1 | ~isempty(options.priorClusters)
     if ~isempty(options.UI)
         d.Message = ['Finding blobs...this may take some time if you have large blobs in your map'];
         d.Value = 0.1;
@@ -302,20 +302,35 @@
     options.clusters = dataClust;
 end
 
+% Bin-based outlines are a little different too...we will turn bins into
+% clusters...
+if strcmpi(options.outline,'bins')
+   % other outline functions have to occur before colormapping so this is
+   % temporary...
+   warning('This option is still under development!!! It may break lots of things.')
+   [colormapMapTmp,cDataTmp,colormapdataMapTmp,ticksTicksTmp,tickslabelsTmp,m] = colormapper(dataT{:},'colormap',options.colormap{1},'colorSpacing',options.colorSpacing{1},'colorBins',options.colorBins{1},'colorSpecial',options.colorSpecial{1},'invertColors',options.invertColors{1},'limits',[min(options.limits{1}) max(options.limits{1})],'thresh',options.thresh{1});
+   un = unique(m);
+   clear dataClust
+   for i = 1:length(un)
+       dataClust{i} = find(m == un(i));
+   end
+end
+
 % Turn clusters into boundaries if necessary
 if ~strcmpi(options.outline,'none') | options.grow ~= 0
     if ~isempty(options.UI)
         d.Message = ['Fetching boundary vertices...'];
         d.Value = 0.2;
     end
-        dataClust_all = dataClust;
-        if strcmpi(options.outline,'roi')
-            dataClust2 = getClusterBoundary(dataClust, underlays.(hemi).Faces);
-            dataClust = cellfun(@(x,y) setdiff(x,intersect(vertcat(dataClust2{:}),x)),dataClust,dataClust2, 'UniformOutput', false);
-        end
-
-        dataClust = getClusterBoundary(dataClust, underlays.(hemi).Faces);       
-        hz = horzcat(dataT{:});
+    
+    dataClust_all = dataClust;
+    if strcmpi(options.outline,'roi')
+        dataClust2 = getClusterBoundary(dataClust, underlays.(hemi).Faces);
+        dataClust = cellfun(@(x,y) setdiff(x,intersect(vertcat(dataClust2{:}),x)),dataClust,dataClust2, 'UniformOutput', false);
+    end
+    
+    dataClust = getClusterBoundary(dataClust, underlays.(hemi).Faces);
+    hz = horzcat(dataT{:});
 
     for clusteri = 1:length(dataClust)
         % if you are doing an outline we need to get mean value for
@@ -474,7 +489,9 @@
 for di = 1:length(dataTS)
     %if length(dataTS) == 1 | (length(dataTS) > 1  & (isempty(options.multiCmap) | isempty(options.multiCmapTicks) | isempty(options.multiCbData)))
     if length(dataTS) == 1 | length(dataTS) > 1 | isempty(options.multiCmapTicks) | isempty(options.multiCbData)
-        [colormapMapTmp,cDataTmp,colormapdataMapTmp,ticksTicksTmp,tickslabelsTmp] = colormapper(dataTS{di},'colormap',options.colormap{di},'colorSpacing',options.colorSpacing{di},'colorBins',options.colorBins{di},'colorSpecial',options.colorSpecial{di},'invertColors',options.invertColors{di},'limits',[min(options.limits{di}) max(options.limits{di})],'thresh',options.thresh{di});
+        if  ~strcmpi(options.outline,'bins')
+            [colormapMapTmp,cDataTmp,colormapdataMapTmp,ticksTicksTmp,tickslabelsTmp] = colormapper(dataTS{di},'colormap',options.colormap{di},'colorSpacing',options.colorSpacing{di},'colorBins',options.colorBins{di},'colorSpecial',options.colorSpecial{di},'invertColors',options.invertColors{di},'limits',[min(options.limits{di}) max(options.limits{di})],'thresh',options.thresh{di});
+        end
         colormap{di}.map = colormapMapTmp;
         cData{di} = cDataTmp;
         colormap{di}.dataMap = colormapdataMapTmp;
@@ -625,11 +642,16 @@
 % find alpha mapping for each "color" here. transp.map will be this.
 % transp.vals can be alph from below.
 try
-    transp.map = ones(size(colormap{1}.dataMap))*options.opacity;
+    if strcmpi(options.colorSpacing,'even')
+        transp.map = ones(1,length(colormap{1}.dataMap)-1)*options.opacity;
+    else
+        transp.map = ones(size(colormap{1}.dataMap))*options.opacity;
+    end
 catch
     transp.map = ones(size(options.multiCbData,1),1)*options.opacity;
 end
 
+
 % if strcmpi(options.inclZero,'off') & isempty(s)
 %    id = find(all(horzcat(dataTS{:}) == 0,2)==1);
 %    transp.vals(id) = 0;

scripts/patch/colormapper.m

@@ -226,12 +226,18 @@
        id2 = find(lo < options.binarize);
        lo(id1) = 1;
        lo(id2) = 0.01;
+       options.colorBins = 2;
+       [~,mi] = min(options.limits);
+       options.limits(mi) = 0;
     end
     if ~isempty(options.rh)
         id1 = find(ro >= options.binarize);
         id2 = find(ro < options.binarize);
         ro(id1) = 1;
         ro(id2) = 0.01;
+        options.colorBins = 2;
+        [~,mi] = min(options.limits);
+        options.limits(mi) = 0;
     end
 end
 
@@ -270,13 +276,19 @@
 if isempty(options.limits) || ~isempty(options.binarize)
     if ~isempty(options.lh) && ~isempty(options.rh)
         tmp = [los; ros];
-        options.limits(1,1) = min(tmp);
+        if isempty(options.binarize)
+            options.limits(1,1) = min(tmp);
+        end
         options.limits(1,2) = max(tmp);
     elseif ~isempty(options.lh) && isempty(options.rh)
-        options.limits(1,1) = min(options.lh);
+        if isempty(options.binarize)
+            options.limits(1,1) = min(options.lh);
+        end
         options.limits(1,2) = max(options.lh);
     elseif isempty(options.lh) && ~isempty(options.rh)
-        options.limits(1,1) = min(options.rh);
+        if isempty(options.binarize)
+            options.limits(1,1) = min(options.rh);
+        end
         options.limits(1,2) = max(options.rh);
     end
 end