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?
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.