Displaying a 32-bit image with NaN values (ImageJ)

Question

I wrote a multilanguage 3-D image denoising ImageJ plugin that does some operations on an image and returns the denoised image as a 1-D array. The 1-D array contains NaN values (around the edges). The 1-D array is converted back into an image stack and displayed. It is simply black. I saved the image stack and opened it in ImageJ again. I moved my cursor over the image and saw the values change as they should. In some places (where I presume the neurone is) the pixels values were in the range of 1000-4000 . Yet, the whole image was simply pitch black. Here is a snippet of the code that converts the array into an image-stack at the end:

# Image-denoising routines written in C (this is where the nan values are introduced)
fimg = JNApackage.NativeCodeJNA.NativeCall(InputImgArray, medfiltArray, int(searchradius), int(patchradius), beta , int(x), int(y), int(z))



# Optimal Inverse Anscombe Transform (Some more operations in Jython)
fimg = InverseAnscombe.InvAnscombe(fimg)

InputImg.flush()

outputstack = ImageStack(x, y, z )  

for i in xrange(0, z):  
    # Get the slice at index i and assign array elements corresponding to it.
    outputstack.setPixels(fimg[int(i*x*y):int((i+1)*x*y)], i+1)

print 'Preparing denoised image for display '
outputImp = ImagePlus("Output Image", outputstack)    
#print "OutputImage Stats:"
Stats = StackStatistics(outputImp)
print "mean:", Stats.mean, "minimum:", Stats.min, "maximum:", Stats.max 

outputImp.show()

Any help as to what is going on?

Answer 1

The display range of your image might not be set correctly.

Try

outputImp.resetDisplayRange()

or

outputImp.setDisplayRange(Stats.min, Stats.max)

See the ImagePlus javadoc for more info.