Hi Jay, >In confirmation of this, when I look in that package within the formats-api-5.0.7.jar artifact, none of these readers exist.
Proprietary readers are in the formats-gpl component[1]. formats-api just provides base interfaces. For downloads I would recommend looking at the OME downloads pages[2] or, of course, using Maven to pull in the formats-gpl dependency. Note that scifio-bf-compat does not pull in formats-gpl itself - it just provides the framework for adapting Bio-Foramts classes. Best, Mark [1] https://github.com/openmicroscopy/bioformats/tree/develop/components/formats-gpl [2] http://downloads.openmicroscopy.org/bio-formats/5.0.7/ On Tue, Mar 3, 2015 at 3:54 PM, Jay Warrick <jay.w.warr...@gmail.com> wrote: > 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 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 <ctrue...@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 > > 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.warr...@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). 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] >> >> >> >> _______________________________________________ >> ImageJ-devel mailing list >> ImageJ-devel@imagej.net >> http://imagej.net/mailman/listinfo/imagej-devel >> >> > > > _______________________________________________ > ImageJ-devel mailing list > ImageJ-devel@imagej.net > http://imagej.net/mailman/listinfo/imagej-devel > >
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