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copied!<p>I have tried running libjpeg-turbo on color images that have an alpha channel and which have been saved with java's ImageIO as jpeg.</p> <p>This is how I compiled libjpeg-turbo for linux 64-bit:</p> <pre><code>$ autoreconf -fiv $ mkdir build $ cd build $ sh ../configure --with-java CPPFLAGS="-I$JAVA_HOME/include -I$JAVA_HOME/include/linux" $ make $ cd .. $ mkdir my-install $ cd build $ make install prefix=$PWD/../my-install libdir=$PWD/../my-install/lib64 </code></pre> <p>This is how I run Fiji with the correct library path and classpath, to include libjpeg-turbo:</p> <pre><code>$ cd Programming/fiji $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/../java/libjpeg-turbo/libjpeg-turbo/my-install/lib64 $ ./fiji -cp $PWD/../java/libjpeg-turbo/libjpeg-turbo/my-install/classes/turbojpeg.jar </code></pre> <p>This is a small jython script to read such jpeg+alpha files:</p> <pre> ###### path = "/home/albert/Desktop/t2/trakem2.1263462814399.1347985440.1111111/trakem2.mipmaps/0/17.07may04b_GridID02043_Insertion001_00013gr_00005sq_00014ex.tif.jpg" from org.libjpegturbo.turbojpeg import TJDecompressor, TJ from java.io import File, FileInputStream from java.awt.image import BufferedImage from jarray import zeros f = File(path) fis = FileInputStream(f) b = zeros(fis.available(), 'b') print len(b) fis.read(b) fis.close() d = TJDecompressor(b) print d.getWidth(), d.getHeight() bi = d.decompress(d.getWidth(), d.getHeight(), BufferedImage.TYPE_INT_ARGB, 0) ImagePlus("that", ColorProcessor(bi)).show() #### </pre> <p>The problem: no matter what flag I use (the '0' above in the call to decompress) from the TJ class (see <a href="http://libjpeg-turbo.svn.sourceforge.net/viewvc/libjpeg-turbo/trunk/java/doc/org/libjpegturbo/turbojpeg/TJ.html" rel="nofollow">http://libjpeg-turbo.svn.sourceforge.net/viewvc/libjpeg-turbo/trunk/java/doc/org/libjpegturbo/turbojpeg/TJ.html</a>), I cannot get the jpeg to load.</p> <p>Here's the error message:</p> <pre> Started turbojpeg.py at Thu Jun 02 12:36:58 EDT 2011 Traceback (most recent call last): File "", line 15, in at org.libjpegturbo.turbojpeg.TJDecompressor.decompressHeader(Native Method) at org.libjpegturbo.turbojpeg.TJDecompressor.setJPEGImage(TJDecompressor.java:89) at org.libjpegturbo.turbojpeg.TJDecompressor.(TJDecompressor.java:58) at sun.reflect.GeneratedConstructorAccessor10.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at org.python.core.PyReflectedConstructor.constructProxy(PyReflectedConstructor.java:210) java.lang.Exception: java.lang.Exception: tjDecompressHeader2(): Could not determine subsampling type for JPEG image </pre> <p>So it appears that either libjpeg-turbo cannot read jpeg with alpha as saved by ImageIO, or there is a very non-obvious setting in the call to "decompress" that I am unable to grasp.</p>

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