[ImageJ-devel] Scifio question - how to use (recently updated) bioformats proprietary formats (programmatically)

Wed Mar 4 08:45:59 CST 2015

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.warrick at 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 <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
>
> 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>
> 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]
>>
>>
>>
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>>
>>
>
>
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