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--- blogtng:2012-10-28:imglib2_first_test [2012/10/28 15:53] – created kota
+++ blogtng:2012-10-28:imglib2_first_test [2016/05/24 12:46] (current) – external edit 127.0.0.1
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+====== 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>