Changed the default image loading to brighten all

src/c/Shaders/ViewAlignedVolumePS.hlsl

@@ -61,7 +61,7 @@ float4 ViewAlignedVolumePS( VS_OUTPUT input ) : SV_TARGET
 
 		color.rgb += (lightMod*intensity*channelColor[i].rgb);
 		unlitComposite += intensity*channelColor[i].rgb;
-		alphaComposite += intensity*channelColor[i].rgb*channelColor[i].a;
+		alphaComposite += intensity*channelColor[i].rgb*channelColor[i].a/2.0f;
 	}
 
 	float maxComponent = max(max(unlitComposite.r,unlitComposite.g),unlitComposite.b);

src/matlab/+D3d/+UI/AutoTransferFunction.m

@@ -13,7 +13,7 @@ function AutoTransferFunction(im)
         N = histcounts(curIm(curIm>0),255);
         
         forwardSum = cumsum(N);
-        lowerBound = forwardSum > sum(N)*0.05;
+        lowerBound = forwardSum > sum(N)*0.1;
         l = find(lowerBound,1,'first');
         if (isempty(l))
             lb(c) = 0;
@@ -36,7 +36,7 @@ function AutoTransferFunction(im)
     for c=1:size(im,4)
         channelData(c).minVal = lb(c)/255;
         channelData(c).maxVal = ub(c)/255;
-        channelData(c).alphaMod = 0.1;
+        channelData(c).alphaMod = 0.5;
     end
     D3d.UI.Ctrl.SetUserData(imageData,ucolors,channelData);
     D3d.UI.Ctrl.UpdateCurrentState();

src/matlab/+D3d/@Viewer/Shaders/ViewAlignedVolumePS.hlsl

@@ -61,7 +61,7 @@ float4 ViewAlignedVolumePS( VS_OUTPUT input ) : SV_TARGET
 
 		color.rgb += (lightMod*intensity*channelColor[i].rgb);
 		unlitComposite += intensity*channelColor[i].rgb;
-		alphaComposite += intensity*channelColor[i].rgb*channelColor[i].a;
+		alphaComposite += intensity*channelColor[i].rgb*channelColor[i].a/2.0f;
 	}
 
 	float maxComponent = max(max(unlitComposite.r,unlitComposite.g),unlitComposite.b);

src/matlab/+D3d/LoadImage.m

-%LOADIMAGE D3d.LoadImage( im, bufferNum, frameNumber)
+%LOADIMAGE D3d.LoadImage( im, bufferNum, frameNumber, nonNormalized)
 
-function LoadImage( im, bufferNum, frameNumber )
+function im8 = LoadImage( im, bufferNum, frameNumber, dontNormalized )
     global D3dIsOpen
     if (isempty(D3dIsOpen) || ~D3dIsOpen)
         error('You need to open the viewer before you can load images! Call D3d.Open first.');
@@ -20,6 +20,10 @@ function LoadImage( im, bufferNum, frameNumber )
         error('You can only load one frame at a time!');
     end
     
+    if (~exist('nonNormalized','var') || isempty(dontNormalized))
+        dontNormalized = false;
+    end
+
     bufferType = 'original';
     if (bufferNum==2)
         bufferType = 'processed';
@@ -30,7 +34,11 @@ function LoadImage( im, bufferNum, frameNumber )
         im = permute(im,[1,2,5,4,3]);
     end
     
-    im8 = ImUtils.ConvertType(im,'uint8',true);
+    if (dontNormalized)
+        im8 = ImUtils.ConvertType(im,'uint8');
+    else
+        im8 = ImUtils.BrightenImages(im,'uint8');
+    end
     if (isempty(frameNumber))
         D3d.Viewer.LoadTexture(im8,bufferType);
     else

src/matlab/+D3d/Open.m

@@ -81,7 +81,7 @@ function [varargout] = Open( im, imData, imagePath, mesagePkgStr )
     
     %% open the region chooser if the image is too big
     if (any(imData.Dimensions>2048))
-        D3d.UI.InitializeMipFigure(im,imData,imData.imageDir,true);
+        D3d.UI.InitializeMipFigure(im,imData);
         if (nargout>1)
             varargout{2} = [];
         end
@@ -107,17 +107,17 @@ function [varargout] = Open( im, imData, imagePath, mesagePkgStr )
         end
         
         if (size(im,5)<imData.NumberOfFrames)
-            D3d.LoadImage(im(:,:,:,:,1),1,1);
+            im8 = D3d.LoadImage(im(:,:,:,:,1),1,1);
             D3d.Update();
-            loadTransFunc(imData,im);
+            loadTransFunc(imData,im8);
             for t=2:size(im,5)
                 D3d.LoadImage(im(:,:,:,:,t),1,t);
             end
         else
             for t=1:size(im,5)
-                D3d.LoadImage(im(:,:,:,:,t),1,t);
+                im8 = D3d.LoadImage(im(:,:,:,:,t),1,t);
             end
-            loadTransFunc(imData,im);
+            loadTransFunc(imData,im8);
             D3d.Update();
         end
     else