Can I use libjpeg to read JPEGs with an alpha channel?

Have you already tried libjpeg-turbo? It is supposed to be able to decode RGBA and there is already a Java wrapper for it.

Even if you store your images as 4 channel jpeg images, there's no standardized way I know of how to specify the color format in the jpeg file.

The JFIF standard assumes YCbCr.

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.

This is how I compiled libjpeg-turbo for linux 64-bit:

$ 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

This is how I run Fiji with the correct library path and classpath, to include libjpeg-turbo:

$ 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

This is a small jython script to read such jpeg+alpha files:

######
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()
####

The problem: no matter what flag I use (the '0' above in the call to decompress) from the TJ class (see http://libjpeg-turbo.svn.sourceforge.net/viewvc/libjpeg-turbo/trunk/java/doc/org/libjpegturbo/turbojpeg/TJ.html), I cannot get the jpeg to load.

Here's the error message:

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 

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.