Yay! That solved it. Thanks. I wasn't aware that I needed to specify this third
dependency. For some reason, I didn't need when this last time I was working
with ND2 files. Just the 1st two dependencies at least appeared to suffice...
maybe something else I was doing at the time brought it in without my knowledge.
For documentation's sake for others, this appears to work. Thanks!!!
<dependency>
<groupId>io.scif</groupId>
<artifactId>scifio</artifactId>
</dependency>
<dependency>
<groupId>io.scif</groupId>
<artifactId>scifio-bf-compat</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>formats-gpl</artifactId>
</dependency>
Best,
Jay
> On Mar 4, 2015, at 8:45 AM, Mark Hiner <[email protected]> wrote:
>
> 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
>
> <https://github.com/openmicroscopy/bioformats/tree/develop/components/formats-gpl>
> [2] http://downloads.openmicroscopy.org/bio-formats/5.0.7/
> <http://downloads.openmicroscopy.org/bio-formats/5.0.7/>
>
> On Tue, Mar 3, 2015 at 3:54 PM, Jay Warrick <[email protected]
> <mailto:[email protected]>> 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 <http://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 <[email protected]
>> <mailto:[email protected]>> 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 <[email protected]
>> <mailto:[email protected]>> 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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>> <http://imagej.net/mailman/listinfo/imagej-devel>
>>
>>
>
>
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