<div dir="ltr">Hi Stephan,<div> thanks for the information!</div><div><br></div><div> I should have read them in more detail :)</div><div><br></div><div> And thanks for the ITK introduction. I used VTK a bit, and CMake somtimes, and now I know they are trinity.</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/10/19 Stephan Saalfeld <span dir="ltr"><<a href="mailto:saalfeld@mpi-cbg.de" target="_blank">saalfeld@mpi-cbg.de</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Yili,<br>
<br>
that is you didn't read beyond the first paragraph of the introduction:<br>
<br>
<a href="http://bioinformatics.oxfordjournals.org/content/28/22/3009.full" target="_blank">http://bioinformatics.oxfordjournals.org/content/28/22/3009.full</a><br>
<br>
, or the first paragraph of the conclusion in the ImgLib1 workshop<br>
paper:<br>
<br>
<a href="http://fly.mpi-cbg.de/~preibisch/pubs/imagejpaper2010.pdf" target="_blank">http://fly.mpi-cbg.de/~preibisch/pubs/imagejpaper2010.pdf</a><br>
<br>
? Depressing for the authors ;).<br>
<br>
The other significant source of inspiration is ITK, if you don't know it<br>
yet, check it out, also very cool stuff:<br>
<br>
<a href="http://www.itk.org/" target="_blank">http://www.itk.org/</a><br>
<br>
Best,<br>
Stephan<br>
<div class="im"><br>
<br>
<br>
<br>
On Sat, 2013-10-19 at 17:13 +0800, Yili Zhao wrote:<br>
> Hi,<br>
> >> Its design was the most important source of inspiration for ImgLib2.<br>
> Thanks for this information.<br>
> When I read ImgLib2, I have a impression that its design has some similar<br>
> with other library.<br>
> Now I know this library is VIGRA :)<br>
><br>
> By the way, I can not access<br>
</div>> <a href="http://hci.iwr.uni-heidelberg.de/vigra" target="_blank">http://hci.iwr.uni-heidelberg.de/vigra</a><<a href="http://hci.iwr.uni-heidelberg.de/vigra/%E2%80%8E" target="_blank">http://hci.iwr.uni-heidelberg.de/vigra/%E2%80%8E</a>>/<br>
<div class="HOEnZb"><div class="h5">> currently.<br>
> Do others have this problem?<br>
><br>
><br>
> 2013/10/17 Johannes Schindelin <<a href="mailto:Johannes.Schindelin@gmx.de">Johannes.Schindelin@gmx.de</a>><br>
><br>
> > Hi Ullrich,<br>
> ><br>
> > a little background information for everybody else: Ullrich is the<br>
> > inventor and maintainer of VIGRA, an incredibly powerful C++ library to<br>
> > process and analyze images. Its design was the most important source of<br>
> > inspiration for ImgLib2. As a consequence, I was really delighted to meet<br>
> > Ullrich at the EuBIAS meeting in Barcelona last week. Among other things,<br>
> > we talked extensively about ways to interoperate between ImgLib2 and<br>
> > VIGRA, and the lack of support in VIGRA to read file formats via the<br>
> > Bio-Formats library.<br>
> ><br>
> > Also at that meeting, I got into contact with the OpenMole project, and in<br>
> > particular with Mark Hammons who not only explained patiently the benefits<br>
> > of the Scala language to me, but also pointed out the existence of the<br>
> > Avian VM, a small, embeddable, BSD-licensed Java Virtual Machine written<br>
> > in C++, with a tiny Just-In-Time compiler, just enough to make it a<br>
> > practical choice for running limited Java inside a C++ program/library:<br>
> > <a href="http://oss.readytalk.com/avian/" target="_blank">http://oss.readytalk.com/avian/</a><br>
> ><br>
> > It is actually very, very, *very* limited, as I found out when I tried to<br>
> > get it to run the bfconvert tool of Bio-Formats.<br>
> ><br>
> > But I did get it to run bfconvert. To be precise, in my hands, the 5MB<br>
> > executable compiled from my fork of Avian was able to run my<br>
> > (minimally-diverging) Bio-Formats v4.4.8 fork's<br>
> > loci.formats.tools.ImageConverter class to convert Fiji's icon.png (my<br>
> > standard example) to a .tiff file (although the colors are off, but<br>
> > running the same example with plain Java results in a byte-identical<br>
> > file).<br>
> ><br>
> > Although it is too early for proper benchmarking, things seem to be<br>
> > comparable between Java and Avian: while Java is slightly faster in what<br>
> > time(1) calls "real" time (~0.54s vs ~0.72s), in terms of "user" time<br>
> > roles are reversed (~0.70s vs ~0.63s). Roughly the same holds true for the<br>
> > dynamic Avian executable (which is only 11K and links to Avian's libjvm.so<br>
> > weighing in with a whopping 1.2M). The major benefit will most likely be<br>
> > space: linking to libjvm.so should be enough, the standard Java classes<br>
> > are included therein. So you can get Java support in VIGRA (or any other<br>
> > C++ project) by adding a library that is slightly larger than one<br>
> > megabyte.<br>
> ><br>
> > Now to some more detailed explanations about the challenges I faced, for<br>
> > the technically-inclined.<br>
> ><br>
> > On the Bio-Formats side, there are two major and one minor (and one micro)<br>
> > issue:<br>
> ><br>
> > - to enable logging, Bio-Formats uses a cute hack called<br>
> > ReflectedUniverse, which is basically a scripting language for Java<br>
> > itself. However, it uses regular expressions, something that Avian's<br>
> > class library does not yet support.<br>
> ><br>
> > - Bio-Formats uses a concurrent hashmap in loci.common.Location.<br>
> > Concurrency (JSR-166) is not supported by Avian's class library yet.<br>
> ><br>
> > - in loci.formats.gui.LegacyQTTools, the value of the java.library.path<br>
> > property is used without checking whether the property is null (unset).<br>
> ><br>
> > - some debug logging in Bio-Formats uses String.format() (not yet<br>
> > supported by Avian's class library).<br>
> ><br>
> > All of these issues could be worked around in the code calling<br>
> > Bio-Formats: there is no need to use the ImageConverter class (which<br>
> > enables the logging), the concurrent hashmap could be faked by extending<br>
> > the non-concurrent hashmap (and just not bothering with the concurrency<br>
> > because we will most likely instantiate one VM per Bio-Formats call), the<br>
> > java.library.path property could be initialized to a dummy value and the<br>
> > logging could be switched off completely.<br>
> ><br>
> > On the Avian side, I am happy to report that I only had to extend the<br>
> > class library (apart from one bug fix that I will contribute upstream<br>
> > later this week). In particular, I had to<br>
> ><br>
> > - make RandomAccessFile support writing<br>
> ><br>
> > - provide three dummy AWT classes because Bio-Formats actually links to<br>
> > them, but does not use them by default<br>
> ><br>
> > - provide a couple of interfaces and exceptions that were not yet included<br>
> > in Avian<br>
> ><br>
> > - implement a minimal java.io.DataOutputStream<br>
> ><br>
> > - provide a FileChannel for RandomAccessFiles (i.e. implement getChannel)<br>
> ><br>
> > - implement java.lang.Boolean's parse(String) method<br>
> ><br>
> > - implement java.lang.Character's isISOControl(char) method<br>
> ><br>
> > - implement fake byte order methods for ByteBuffers (they are hardcoded to<br>
> > big endian, but that is what Bio-Formats required in my test)<br>
> ><br>
> > - provide a dummy SimpleDateFormat which actually does not work, but does<br>
> > not need to<br>
> ><br>
> > - add toString(long[]) to java.util.Arrays<br>
> ><br>
> > - teach Avian's pseudo regular expressions about "\\", i.e. the backslash<br>
> ><br>
> > For the moment, all of these changes are contained in hodge podge<br>
> > work-in-progress commits which I will clean up over the next few days. You<br>
> > can see them here (the linked pages will update whenever I get around to<br>
> > clean up the commits):<br>
> ><br>
> > <a href="https://github.com/dscho/avian/compare/bio-formats" target="_blank">https://github.com/dscho/avian/compare/bio-formats</a><br>
> > <a href="https://github.com/dscho/bioformats/compare/v4.4.8...avian" target="_blank">https://github.com/dscho/bioformats/compare/v4.4.8...avian</a><br>
> ><br>
> > Since VIGRA and ImgLib2 share design concepts, and since SCIFIO supports<br>
> > ImgLib2 natively, I think that my plan to extend the test to SCIFIO after<br>
> > cleaning up my Avian fork is sound.<br>
> ><br>
> > Once that is done, I will add unit tests that our trusty Jenkins will run<br>
> > whenever SCIFIO (or Avian) changes, to ensure that things continue to<br>
> > work. These unit tests will be extended as needed, e.g. when someone finds<br>
> > out that an important use case requires more changes in Avian, still.<br>
> ><br>
> > This way to call Bio-Formats and SCIFIO could become the default C++ entry<br>
> > point into those libraries.<br>
> ><br>
> > Summary: I showed that Bio-Formats/SCIFIO support for VIGRA and other C++<br>
> > libraries is feasible through the BSD-licensed embeddable Java virtual<br>
> > machine "Avian". I am confident that I can clean up my patches this week<br>
> > still, to be contributed to the Avian project.<br>
> ><br>
> > Ciao,<br>
> > Johannes<br>
> ><br>
> > _______________________________________________<br>
> > ImageJ-devel mailing list<br>
> > <a href="mailto:ImageJ-devel@imagej.net">ImageJ-devel@imagej.net</a><br>
> > <a href="http://imagej.net/mailman/listinfo/imagej-devel" target="_blank">http://imagej.net/mailman/listinfo/imagej-devel</a><br>
> ><br>
><br>
><br>
><br>
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> <a href="mailto:ImageJ-devel@imagej.net">ImageJ-devel@imagej.net</a><br>
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<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Yili Zhao
</div>