Bioformats in Julia?

Specific Domains Data
15

Just to get you started…

using JavaCall

try
    # init JVM wtih bioformats_package.jar on classpath
    JavaCall.init(["-ea", "-Xmx1024M", "-Djava.class.path=bioformats_package.jar"])
end

# import java classes
const JChannelFiller = @jimport loci.formats.ChannelFiller
const JChannelSeparator = @jimport loci.formats.ChannelSeparator
const JOMEXMLServiceImpl = @jimport loci.formats.services.OMEXMLServiceImpl
const JOMEXMLMetadata = @jimport loci.formats.ome.OMEXMLMetadata
const JOMEXMLService = @jimport loci.formats.services.OMEXMLService
const JMetadataStore = @jimport loci.formats.meta.MetadataStore

# example of how get_angles function may look like
function get_angles(obj, full_filename)
    ret = []
    try
        # same as `new ChannelFiller()`
        # empty tuple `()` here means that constructor doesn't take any args
        r = JChannelFiller(())

        # same as new ChannelSeparator(r)
        # again, first argument - `(JChannelFiller,)` - a tuple of input types
        # the rest - `r` - is a list of actual arguments
        r = JChannelSeparator((JChannelFiller,), r)

        # same as `new OMEXMLServiceImpl()`
        OMEXMLService = JOMEXMLServiceImpl(())

        # same as `meta = OMEXMLService.createMEXMLMetadata()`
        meta = jcall(OMEXMLService, "createOMEXMLMetadata", JOMEXMLMetadata, ())

        # same as `r.setMetadataStore(meta)`
        jcall(r, "setMetadataStore", Void, (JMetadataStore,), meta)
        ...
    end
end

As you may guess, I know nothing about the domain or BioFormats, so it’s mostly just a hint for you to see how it may look like. Basically, you need to learn how to:

  1. Add .jar files using JavaCall.init()
  2. Import Java classes using @jimport.
  3. Create new objects using constructor syntax, e.g. r = JChannelFiller(()).
  4. Call methods using jcall, e.g. jcall(r, "setMetadataStore", Void, (JMetadataStore,), meta).

So I think it’s pretty doable.

Note that this example requires bioformats_package.jar and some other lib because creating ChannelFiller throws:

ClassNotFoundException: loci.formats.in.SlideBook6Reader

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