OmeisImporter operates on loci.formats classes

Fixed a compile error in OmeisImporter regarding the convolution between
legacy delegator classes and refactored live classes.

OmeisImporter will operate exclusively on loci.formats.IFormatReader
objects for the time being. This is due to its dependency on the Reader
wrapper extensions, such as ChannelSeparater, ChannelFiller and
fileStichter - which do not have SCIFIO equivalents.

Once those classes are converted, OmeisImporter should be refactored out
of loci.formats imports and the delegators in those classes should use
the ReaderAdapter class to delegate.
Copied OMEXML services to ome.xml.services

Created a copy of OMEXMLService and its Impl class in ome.xml.services.
The originals in loci.formats.services will remain and become delegators.
Migrated OMEXML Translation classes

Added the necessary classes for translation to OMEXML from the currently
supported SCIFIO formats, including a base OMEMetadata.

Note these translators are not yet fully functional.
Ordered inner classes within formats

Organized the inner classes within each Format into a more natural
progression.
Migrated APNGWriter

Updated loci.formats.out.APNGWriter with a refactored SCIFIO delegator.
Updated copyright header for SCIFIO classes

The copyright header has been added/updated for all migrated SCIFIO
classes.
Bug fix: CoreMetadata convert method

loci.formats.CoreMetadata's conversion method, to generate
ome.scifio.CoreMetadata, now properly sets each axis length, and sets
the total number of planes.
AbstractReader sets current filename

AbstractReader now uses its pre-existing currentId variable by setting
the current file name whenever the source is set.
Bug fix: FormatTools

ome.scifio.util.FormatTools now properly passes plane counts instead of
image counts for several methods.

Additionally, when checking plane parameters, the file id is verified
instead of the stream, to allow for fake file checking (which currently
can not have a RandomAccessxxxStream instantiated)
Corrected CoreMetadata planeSize calculation

Multiply planes instead of adding them.
Added sezpoz and imglib to loci-plugins build.prop

The loci-plugins ant targets will now include the sezpoz and imglib on
the classpath, which was necessary for scifio dependencies.
Changed return type of CoreMetadata#convert

The loci.formats.CoreMetadata#convert method will now return an
ome.scifio.CoreImageMetadata which has a 1:1 relationship with the
loci.formats.CoreMetadata, instead of trying to generate a complete
CoreMetadata array.

Thus it is up to the calling program to assemble the CoreMetadata
appropriately.
Updated CoreMetadata generation in ReaderAdapter

The SCIFIOReaderAdapter now generates an ome.scifio.CoreMetadata object
once on creation, and when changing the source - instead of constantly
converting every time the getter method is called.

In addition it now takes properly constructs a CoreMetadata object from
individually converting each series' loci.formats.CoreMetadata to a
CoreImageMetadata object.
Corrected loci.formats.in.APNG reader construction

The delegating APNGReader was mistakenly creating an
ome.scifio.ICSReader for delegation.

It now creates an ome.scifio.APNGReader as intended.
Removed unnecessary setSource calls to delegates

The ICSReader and APNGReader in loci.formats.in were unnecessarily
calling setSource after setId was invoked on the parent reader.

The setId shell in the SCIFIOFormatReader already calls setSource.
Corrected CoreMetadata generation in SCIFIOReaders

The SCIFIOFormatReader now initializes the ome.scifio.CoreMetadata array
before trying to access it, and builds a number of
loci.formats.CoreMetadata equal to the series count.
ome.scifio.Readers reset CoreMetadata

When setting the Metadata for an ome.scifio.Reader, the AbstarctReader
will now re-initialize the CoreMetadata, instead of continuously adding
to it.
Restricted axes list to Bio-Formats compatible

When determining the axis order for SCIFIO axes, only the standard
bio-formats dimensions will be considered for the time being, to
preserve backwards compatibility.

This should eventually be modified to detect if the order request comes
from loci.formats or ome.scifio classes and respond appropriately.
Created ome.xml.meta.MetadataTools

Copied existing scifio MetadataTools class to ome.xml.meta.

This class will contain all MetadataStore/MetadataRetrieve methods,
facilitating the removal of these classes from SCIFIO, and allowing
delegation from loci.formats/Bio-Formats classes.
Trimmed MetadataTools classes

ome.xml.meta.MetadataTools now contains all methods pertinent to working
with MetadataStores and MetadataRetrieves. Equivalent methods for
working with ome.scifio.CoreMetadata objects remain in
ome.scifio.util.MetadataTools.

loci.formats.MetadataTools has had all functional code removed
(transferred to ome.xml.meta.MetadataTools) and now properly, fully
delegates.