Bug fix for lowerbound truncation of colormap and support for scaled …

…transparency
canlab · Sep 13, 2023 · 7136038 · 7136038
1 parent 157bb94
commit 7136038
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Showing 2 changed files with 32 additions and 10 deletions.
diff --git a/CanlabCore/@image_vector/render_on_surface.m b/CanlabCore/@image_vector/render_on_surface.m
@@ -65,6 +65,19 @@
 %       'colormap' argument as well, otherwise this does nothing and a
 %       warning is thrown.
 %
+%   **'scaledtransparency':**
+%       Transparency is a function of voxel value, lower values are more transparent. This will look very
+%       strange without an underlay. To create an underlay render a two duplicate surfaces and invoke
+%       render_on_surface only on the second duplicate.
+%   
+%    **'transcontrast':** 
+%       If scaledtransparency is used transparency alpha values are a linear function of the data. This 
+%       option makes them a sigmoidal function of the data with higher values disproportionately opaque and
+%       lower values disproportionately transparent. This argument is followed by a scalar value which 
+%       specifies how steep the sigmoidal part of the contrast curve should be. It works like a contrast 
+%       curve in photoshop, but only affects alpha transparency, not colormapping, and therefore does not 
+%       alter the data being shown.
+%
 % :Outputs:
 %
 %   **renders colors on surfaces:**
@@ -152,6 +165,8 @@
 dolegend = true;
 doindexmap = false;
 splitcolors = {};
+doscaledtrans = 0;
+enhance_contrast = @(x1)(x1);
 
 allowable_keyword_value_pairs = {'clim' 'color' 'colormap' 'colormapname' 'axis_handle' 'pos_colormap' 'neg_colormap'};
 
@@ -202,8 +217,13 @@
 
                 doindexmap = true;
 
-
-
+            case 'scaledtransparency'
+                doscaledtrans = 1;
+
+            case 'transcontrast'
+                k = varargin{i+1};
+                enhance_contrast = @(x1)(2*((1./(1+exp(-k.*x1)))-0.5));
+
             case allowable_keyword_value_pairs
 
                 eval([varargin{i} ' = varargin{i+1}; varargin{i+1} = [];']);
@@ -335,6 +355,9 @@
 % Needed to map to vertices later
 [~, ~, mesh_struct] = reconstruct_image(obj);                % get volume data for slices
 
+% fixes colormap out of range bug
+mesh_struct.voldata(mesh_struct.voldata < min(clim)) = min(clim);
+
 % Deal with edge interpolation effects
 % problem is that vertices near empty (zero) voxels get interpolated down to zero
 % solution: map all non-zero voxels to lowest limit value
@@ -454,6 +477,13 @@
     set(surface_handles(i), 'CDataMapping', 'direct')
     set(surface_handles(i), 'EdgeColor', 'none');
 
+    if doscaledtrans
+        z = c/max(abs(c));
+        z = enhance_contrast(z);
+        set(surface_handles(i), 'FaceVertexAlphaData',abs(z));
+        set(surface_handles(i), 'FaceAlpha', 'interp');
+    end
+
 end
 
 % Colorbars - legend

diff --git a/CanlabCore/fmridisplay_helper_functions/render_blobs.m b/CanlabCore/fmridisplay_helper_functions/render_blobs.m
@@ -102,14 +102,6 @@
 %         curve in photoshop, but only affects alpha transparency, not colormapping, and therefore does not 
 %         alter the data being shown.
 %
-%      **'transcontrast':** 
-%         If scaledtransparency is used transparency alpha values are a linear function of the data. This 
-%         option makes them a sigmoidal function of the data with higher values disproportionately opaque and
-%         lower values disproportionately transparent. This argument is followed by a scalar value which 
-%         specifies how steep the sigmoidal part of the contrast curve should be. It works like a contrast 
-%         curve in photoshop, but only affects alpha transparency, not colormapping, and therefore does not 
-%         alter the data being shown.
-%
 %
 %   **OTHER OPTIONS:**
 %