Add example images and usage example

.gitignore

@@ -0,0 +1 @@
+*.DS_Store

@hilospeckle/hilospeckle.m

@@ -46,6 +46,7 @@
     end
 
     properties (Hidden)
+        doVectorisedCamOTF=true
         verbose = false
         padded %boolean - true if images were padded
         impLo %The "Lo" image
@@ -65,6 +66,13 @@
                 return
             end
 
+            try 
+                gpuDevice
+            catch
+                obj.doGPU=false;
+                fprintf('Disabling GPU acceleration: no device found\n')
+            end
+
             obj.uniformIm = uniformIm;
             obj.speckleIm = speckleIm;
             obj.runHiLo;
@@ -183,24 +191,45 @@ function showResults(obj)
 
 
 
-        function pixel = createCameraOTF(~, imWidth, imHeight)
+        function pixel = createCameraOTF(obj, imWidth, imHeight)
             % Tested and produces something that looks plausible
-            pixel = ones(imHeight, imWidth);
 
+
+            X = (2 * (1:imWidth) - imWidth) * pi / imWidth;
+            Y = (2 * (1:imHeight) - imHeight) * pi / imHeight;
+
+            if obj.doVectorisedCamOTF %Faster but doesn't yield exactly the same answer as the loop
+                [xx,yy] = meshgrid(X,Y);
+
+                pixel=sin(xx) .* sin(yy) ./ (xx .* yy);
+
+                f=(xx == 0 & yy ~= 0);
+                t = sin(yy(f))./yy(f);
+                pixel(f)=t;
+
+                f=(xx ~= 0 & yy == 0);
+                t = sin(xx(f))./xx(f);
+                pixel(f)=t;
+
+                f=(xx == 0 & yy == 0);
+                pixel(f)=1;
+
+                pixel(pixel<0) = 0;
+                return
+            end
+
+            pixel = ones(imHeight, imWidth,'single');
             for x = 1:imWidth
                 for y = 1:imHeight
 
-                    x1 = (2 * x - imWidth) * pi / imWidth;
-                    y1 = (2 * y - imHeight) * pi / imHeight;
-
-                    if x1 ~= 0 && y1 ~= 0
-                        pixel(y,x) = sin(x1) * sin(y1) / x1 / y1;
+                    if X(x) ~= 0 && Y(y) ~= 0
+                        pixel(y,x) = sin(X(x)) * sin(Y(y)) / (X(x) * Y(y));
 
-                    elseif x1 == 0 && y1 ~= 0
-                        pixel(y,x) = sin(y1) / y1;
+                    elseif X(x) == 0 && Y(y) ~= 0
+                        pixel(y,x) = sin(Y(y)) / Y(y);
 
-                    elseif x1 ~= 0 && y1 == 0
-                        pixel(y,x) = sin(x1) / x1;
+                    elseif X(x) ~= 0 && Y(y) == 0
+                        pixel(y,x) = sin(X(x)) / X(x);
                     %otherwise it's a one
                     end
 
@@ -213,7 +242,7 @@ function showResults(obj)
 
 
         function pixel = createImagingOTF(obj, numericalAperture, wavelengthInNM, sizeX,  sizeY)
-            % Tested but tends to yield zero arrays
+            % Tested and seem to yield something meaningful
             BandWidth = 2 * numericalAperture / (wavelengthInNM * 1E-9);
             scaleUnits = obj.magnification / (obj.pixelSize * 1E-6) / BandWidth;
 

@hilospeckle/runHiLo.m

@@ -144,9 +144,15 @@ function runHiLo(obj)
 
             obj.impLo = obj.impLo .* obj.eta;
             obj.HiloFinal(:,:,ii) = obj.impLo + obj.impHi;
-            
+
         end %for ii = 1:size(obj.uniformIm,3)
         obj.HiloFinal(obj.HiloFinal<0)=0;
         obj.HiloFinal = uint16(obj.HiloFinal/max(obj.HiloFinal(:))*2^16);
-        fprintf('\nCompleted in %0.1f s\n', toc)
+        T=toc;
+        if T<2
+            fprintf('\nCompleted in %0.3f s\n', T)
+        else
+            fprintf('\nCompleted in %0.1f s\n', T)
+        end
+
 end % hilo

README.md

@@ -2,6 +2,24 @@
 
 This is a very basic MATLAB implementation of the HiLo algorithm for structured illumination. 
 
+## Usage
+```
+H=hilospeckle(ImageUniform, ImageSpeckle); %Run and show result image
+
+clf, imagesc(H.HiloFinal), axis equal off %re-plot result image
+
+%Change a setting and re-run
+H.targetThickness=4; 
+H.runHiLo
+H.showResults
+
+%Swap the speckle image with the unform image and re-run to compare with above
+H.speckleIm = H.uniformIm;
+H.runHiLo
+figure
+H.showResults
+```
+
 
 ###
 References

example_images/Readme.txt

@@ -0,0 +1,21 @@
+
+HiLo_ImageJ_result_image.tiff was produced the by the HiLo ImageJ plugin using the "uniform_image" and "structured_speckle_image" with settings:
+
+
+Camera gain: 0.15
+Readout noise: 1.64
+Magnification: 40
+Pixel size: 22.2
+Illumination wavelength: 488
+Detection wavelength: 520
+Illumination NA: 0.30
+Detection NA: 0.40
+
+Depth field multiplier: 2.0
+HiLo weighting: 3.0
+
+
+
+The image shows GFP-labeled neurons in a mouse cortex slice and comes from the Mertz lab home page: http://biomicroscopy.bu.edu/resources/4
+
+These images can be used to validate the output of the MATLAB code with respect to that produced by ImageJ.