[ImageJ-devel] Scifio question - how to use (recently updated) bioformats proprietary formats (programmatically)
Jay Warrick
jay.w.warrick at gmail.com
Tue Mar 3 15:54:27 CST 2015
Hi Curtis,
Super helpful feedback. Thanks for the tips on leveraging the newest OME stuff.
Re: Problem 1 - Did some debugging. As you already know, the scifio-bf-compat dependency is pulling in the formats-api-5.0.7.jar artifact which contains some crucial classes for all this. Critical to matching a file with an appropriate reader is the loci.formats.ImageReader class which has a static method (getDefaultReaderClasses()) that should populate a cache of readers based on the readers.txt file (short example snippet in listing #1). As you can see from the snippet, the readers are expected to be contained within the loci.formats.in package. During population of this cache, each attempt to load a class listed in the file is met with a ClassNotFoundException. In confirmation of this, when I look in that package within the formats-api-5.0.7.jar artifact, none of these readers exist. Thus, the cache of readers does not get populated and Scifio is not able to match my file with any reader. Seems like this is the issue, right? However, it would seem like this would affect almost ANY proprietary format, which tells me I am likely doing something weird if this hasn't come up yet in feedback from others.
Suggestions? I re-downloaded the artifact directly from maven.imagej.net <http://maven.imagej.net/> again to check. I change the extension to zip and looked in the corresponding folder and did not find any of the readers I would expect.
%%%%%%%%%%%%%%
Listin #1 - short snippet of readers.txt file.
%%%%%%%%%%%%%%
# standalone readers with unique file extensions
loci.formats.in.PGMReader # pgm
loci.formats.in.FitsReader # fits
loci.formats.in.PCXReader # pcx
> On Mar 3, 2015, at 11:28 AM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
> Hi Jay,
>
> > I thought it used to be automatic upon adding the scifio and
> > scifio-bf-compat dependencies.
>
> Yeah, that's correct.
>
> > A "limited" list of 30 formats show up in the DefaultFormatService
> > currently and don't include ND2.
>
> The format that supports ND2 (and all Bio-Formats formats) is the "Bio-Formats Compatibility Format" at the front of your list.
>
> You'll need to debug into the code to find out why the BioFormatsFormat is not being selected properly for your ND2 file.
>
> > It looks like the parent pom of scifio-bf-compat (pom-scijava)
> > specifies <bio-formats.version>5.0.7</bio-formats.version>.
> > Is it likely to be "risky" to leverage the most recent changes
> > for ND2 compatibility?
>
> Yes, it will not work. The scifio-bf-compat component has not yet been updated to use the Bio-Formats 5.1.x codebase.
>
> The good news is: updating it to use the OME 5.1 API was easy. I pushed a branch:
>
> https://github.com/scifio/scifio-bf-compat/compare/ome-5.1 <https://github.com/scifio/scifio-bf-compat/compare/ome-5.1>
>
> You can use it during development by:
>
> * Cloning scifio-bf-compat.
> * Switching to the ome-5.1 branch.
> * Importing scifio-bf-compat into your Eclipse.
> * Setting your project's bio-formats.version property to 5.1.0-SNAPSHOT.
> * Setting your project's scifio-bf-compat.version property to 1.11.1-SNAPSHOT.
>
> And then Eclipse should switch to a project coupling for scifio-bf-compat and use the branch.
>
> But you'll want to stay on a corresponding branch of your own project development until the OME 5.1.0 release.
>
> Regards,
> Curtis
>
> On Tue, Mar 3, 2015 at 10:42 AM, Jay Warrick <jay.w.warrick at gmail.com <mailto:jay.w.warrick at gmail.com>> wrote:
> Hi All,
>
> I have 2 problems you all hopefully have suggestions for... (thanks in advance)
>
> Problem 1:
>
> I'm interested in opening ND2 file format programmatically in Java via a SCIFIO object used with an ImageJ context but can't seem to get it to work. (see listing A) Error message indicates format not found.
>
> Hopefully relevant details of what I am currently doing with maven imports are below. (see listing B)
>
> Suggestions? Is there a BioFormats dependency I am not bringing in that is necessary to expose/discover all the additional proprietary formats or do I have to add the proprietary formats myself using a combination of a bioformats artifact I'm not aware of and adding each format using the mechanism provided by scifio-bf-compat? I thought it used to be automatic upon adding the scifio and scifio-bf-compat dependencies. Any help is appreciated. I looked in scifio tutorials but couldn't figure it out. Sorry.
>
> Problem 2:
>
> After resolution of problem 1, I'd like to leverage recent changes to the bioformats package that addresses a bug in ND2 metadata handling that was affecting me (https://trac.openmicroscopy.org.uk/ome/ticket/12548 <https://trac.openmicroscopy.org.uk/ome/ticket/12548>). The link suggests using bioformats 5.1.x vs 5.0.x which also requires use a few other updated jars (as noted near end of ticket). Suggestions on the best way to do this given my use case? It looks like the parent pom of scifio-bf-compat (pom-scijava) specifies <bio-formats.version>5.0.7</bio-formats.version>. Is it likely to be "risky" to leverage the most recent changes for ND2 compatibility?
>
> Thanks,
>
> Jay
>
> %%%%%%%%%%%%%
> Listing A
> %%%%%%%%%%%%%
>
> final SCIFIO scifio = new SCIFIO(ij.getContext());
> Reader reader;
> try
> {
> reader = scifio.initializer().initializeReader(nd2File, new SCIFIOConfig().checkerSetOpen(true));
> }
> catch (Exception e)
> {
> e.printStackTrace();
> return false;
> }
>
>
> %%%%%%%%%%%%%
> Listing B
> %%%%%%%%%%%%%
>
> My project parent pom is
>
> <parent>
> <groupId>net.imagej</groupId>
> <artifactId>pom-imagej</artifactId>
> <version>5.12.0</version>
> </parent>
>
> I have the following maven dependencies
>
> <dependency>
> <groupId>io.scif</groupId>
> <artifactId>scifio</artifactId>
> </dependency>
> <dependency>
> <groupId>io.scif</groupId>
> <artifactId>scifio-bf-compat</artifactId>
> <scope>runtime</scope>
> </dependency>
>
> A "limited" list of 30 formats show up in the DefaultFormatService currently and don't include ND2. (see Listing C)
>
>
> %%%%%%%%%%%%%
> Listing C
> %%%%%%%%%%%%%
>
> (*) Formats in DefaultFormatService
>
> ImageJ ij = new ImageJ();
> Set<Format> formats = ij.scifio().format().getAllFormats();
>
> returns
>
> [Bio-Formats Compatibility Format, Animated PNG, Audio Video Interleave, Windows Bitmap, DICOM, Encapsulated PostScript, Flexible Image Transport System, Simulated data, Graphics Interchange Format, Image Cytometry Standard, JPEG-2000, JPEG, Java source code, Multiple Network Graphics, Micro-Manager, NRRD, OBF, PCX, Portable Gray Map, Text, Zip, QuickTime, PICT, plugin:class io.scif.ome.formats.OMEXMLFormat, Tile JPEG, QuickTime, plugin:class io.scif.ome.formats.OMETIFFFormat, Tagged Image File Format, Minimal TIFF, Tagged Image File Format]
>
>
>
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