====== ImgLib2, first test ======

I pretty much enjoyed [[http://imagejconf.tudor.lu/|ImageJ User and Developer conference 2012]] in Luxemburg. Interesting people from different areas in science, very exciting to see how people are doing image processing and analysis. Some of live notes could be found in [[https://twitter.com/cmci_|my time line]]. One of the great contribution for the third day was Bene Schmidt's work [[http://132.187.25.13/ij3d/?page=IntSeg_3D&category=Extensions|intseg_3D]], combining user clicking and active contour fitting in 3D. 

One of the core topic there was [[http://fiji.sc/ImgLib2|ImgLib2]], the generic image typ behind [[http://developer.imagej.net/|ImageJ2]]. 
After coming back home, I tested ImgLib2 with the Jython code below.

Results were:
Started testImgLib2.py at Sun Oct 28 16:41:57 CET 2012
  * ImgLib2 cursor 333 millisec
  * ImgLib2 for :  138 millisec
  * ImagePlus 152 millisec
  * ImageProcessor 114 millisec
  * Pixel Array 59 millisec
for loop using Img iterator is a bit faster than going through ImagePlus using classic nested for-loop. Even with the classic nested for-loop, using ImageProcessor was a bit faster than Img. The fastest is of course accessing pixels via pixel array. I only did this via ImagePlus, but there should be also some methods to extract an array from Img, which I did not test. 

Addendum: See also proper benchmark in the following link in ImageJ2 site:

http://developer.imagej.net/imglib-benchmarks

Thanks to Albert Cardona for commenting on this. 

<sxh python>
# first trial with ImageLib2
# iterations

from net.imglib2.img import ImagePlusAdapter

imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif")
img = ImagePlusAdapter.wrapReal(imp)

# accessing via ImagePlus
t3 = System.currentTimeMillis()
for i in range(imp.getHeight()):
	for j in range(imp.getWidth()):
#		print imp.getPixel(j, i)[0]
		imp.getPixel(j, i)[0]
				
t4 = System.currentTimeMillis()

# accessing via ImageProcessor
t5 = System.currentTimeMillis()
ip = imp.getProcessor()
for i in range(imp.getHeight()):
	for j in range(imp.getWidth()):
#		print ip.getPixelValue(j, i)
		ip.getPixelValue(j, i)
				
t6 = System.currentTimeMillis()

# ImgLib2 cursor
t1 = System.currentTimeMillis()
cursor = img.cursor()
cursor.fwd()
while cursor.hasNext():
	cursor.next()
#	print cursor.get()
	cursor.get()

t2 = System.currentTimeMillis()

t7 = System.currentTimeMillis()
for t in img:
#	print t.get()
	t.get()

t8 = System.currentTimeMillis()

# pixel array
t9 = System.currentTimeMillis()
pix = imp.getProcessor().getPixels()
for i in pix:
	i = i
#	print i

t10 = System.currentTimeMillis()	

print 'ImgLib2 cursor',(t2-t1), 'millisec'
print 'ImgLib2 for : ',(t8-t7), 'millisec'
print 'ImagePlus',(t4-t3), 'millisec'
print 'ImageProcessor',(t6-t5), 'millisec'
print 'Pixel Array',(t10-t9), 'millisec'
	
</sxh>