Minor updates

src/MATLAB/sandbox2.m

+%% read
+im = tiffReader('DAPI Olig2-514 GFAP-488 Dcx-647 Laminin-Cy3 Bcatenin-568 20x20');
+chan1_8 = uint8(im(:,:,:,1,1));
+
+%% threshold 
+chan1Bin = CudaMex('OtsuThresholdFilter',chan1_8,0.8);
+chan1Close = CudaMex('MorphClosure',chan1Bin,[3,3,2]);
+chan1Open = CudaMex('MorphOpening',chan1Close,[5,5,2]);
+
+%% draw
+figure
+imagesc(chan1_8(:,:,20))
+colormap gray
+figure
+imagesc(chan1Bin(:,:,20))
+colormap gray
+figure
+imagesc(chan1Close(:,:,20))
+colormap gray
+figure
+imagesc(chan1Open(:,:,20))
+colormap gray
\ No newline at end of file

src/c/CudaMex.vcxproj

@@ -59,9 +59,6 @@
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="Common\CHelpers.h" />
-    <ClInclude Include="Common\CudaImageBuffer.cuh">
-      <FileType>Document</FileType>
-    </ClInclude>
     <ClInclude Include="Common\Vec.h" />
     <ClInclude Include="Common\VecFuncs.h" />
     <ClInclude Include="CudaMex\MexCommand.h" />
@@ -71,6 +68,8 @@
     <ClInclude Include="Common\CudaUtilities.cuh">
       <FileType>Document</FileType>
     </ClInclude>
+    <None Include="Common\CudaProcessBuffer.cuh" />
+    <None Include="Common\CudaStorageBuffer.cuh" />
     <None Include="CudaMex\CudaMex.def" />
   </ItemGroup>
   <ItemGroup>

src/c/CudaMex.vcxproj.filters

@@ -127,14 +127,17 @@
     <None Include="CudaMex\CudaMex.def">
       <Filter>Resource Files</Filter>
     </None>
+    <None Include="Common\CudaProcessBuffer.cuh">
+      <Filter>Header Files</Filter>
+    </None>
+    <None Include="Common\CudaStorageBuffer.cuh">
+      <Filter>Header Files</Filter>
+    </None>
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="CudaMex\Process.h">
       <Filter>Header Files</Filter>
     </ClInclude>
-    <ClInclude Include="Common\CudaImageBuffer.cuh">
-      <Filter>Header Files</Filter>
-    </ClInclude>
     <ClInclude Include="Common\Vec.h">
       <Filter>Header Files</Filter>
     </ClInclude>

src/c/CudaMex/Process.cu

 #include "Process.h"
-#include "CudaImageBuffer.cuh"
+#include "CudaProcessBuffer.cuh"
 #include "CHelpers.h"
 
-CudaImageBuffer<MexImagePixelType>* g_cudaBuffer = NULL;
-CudaImageBuffer<MexImagePixelType>* g_cudaBuffer2 = NULL;
+CudaProcessBuffer<MexImagePixelType>* g_cudaBuffer = NULL;
+CudaProcessBuffer<MexImagePixelType>* g_cudaBuffer2 = NULL;
 
 void clear()
 {
@@ -16,13 +16,13 @@ void clear()
 void set(Vec<unsigned int> imageDims)
 {
 	if (g_cudaBuffer==NULL)
-		g_cudaBuffer = new CudaImageBuffer<unsigned char>(imageDims,true);
+		g_cudaBuffer = new CudaProcessBuffer<unsigned char>(imageDims,true);
 }
 
 void set2(Vec<unsigned int> imageDims)
 {
 	if (g_cudaBuffer2==NULL)
-		g_cudaBuffer2 = new CudaImageBuffer<unsigned char>(imageDims,true);
+		g_cudaBuffer2 = new CudaProcessBuffer<unsigned char>(imageDims,true);
 }
 
 void addConstant(const MexImagePixelType* image,  MexImagePixelType* imageOut, Vec<unsigned int> imageDims, double additive)
@@ -89,7 +89,7 @@ void gaussianFilter( const MexImagePixelType* image, MexImagePixelType* imageOut
 
 size_t getGlobalMemoryAvailable()
 {
-	CudaImageBuffer<unsigned char> cudaBuffer(1);
+	CudaProcessBuffer<unsigned char> cudaBuffer(1);
 	return g_cudaBuffer->getGlobalMemoryAvailable();
 }