Created SCIFIO Cell package

The SCIFIOCell series of classes facilitate creating an imgplus
(SCIFIOImgPlus) that uses the CellImg principles of dynamically loading
pixel information as it's requested.

Cells allow an image to be broken down into manageable bits, so that
images too large for memory can still be viewed and operated on.

The SCIFIOCellCache performs actual caching operatings, allowing
operations on cells to persist after the cell falls out of scope. It
uses an in-memory weak reference cache for fast memory action, and an
Ehcache back-end for its disk caching capabilities (and general memory
management).

This change also involves migrating ImgOpener and ImgSaver from Imglib
to SCIFIO (as these classes use SCIFIO to perform their IO operations,
and SCIFIO uses Imglib).
Added image, plane index to getColorTable

The HasColorTable API can now specify the image and plane index of the
desired ColorTable.
Added Parse signature to JPEG2k Parser

As the JPEG2000 format has been replaced by the JPEG2000Format.Parser,
added a parse(RAIS, Metadata, long maxOffset) signature to support the
same functionality as the legacy parser.
Adjusted ByteArrayPlane construction

A byte array is now allocated by using FormatTools.bytesPerPixel for the
pixel type, instead of directly dividing the bits per pixel by 8 (as
there can be bits per pixel that aren't evenly divisible by 8).
Refactored translator naming

The OME translators have now been consolidated to a single class, of the
non-ome name (e.g. "APNGTranslator"). These classes are containers for
one or more nested class that perform the actual translation.
Converted TIFFJAI Format

The loci.formats TiffJAIReader was converted to SCIFIO components in
ome.scifio as TIFFJAIFormat.
Converted MinimalTIFF Reader

Translated the loci.formats MinimalTIFF reader to SCIFIO components in
ome.scifio, as MinimalTIFFFormat. Supporting classes (TiffParser and
TiffCompression) were updated as well, and the scifio Codec interface
was marked as Contextual (the abstract codec heirarchy already extended
AbstractContextual, but MinimalTIFFFormat required Codecs to guarantee
context).

The TIFF/BaseTIFF/OME-TIFF heirarchy will be preserved via intra-format
dependencies on specific components.
Converted TIFFFormat

The loci.formats TiffReader and TiffWriter were consolidated to SCIFIO
components in ome.scifio as TIFFFormat. The supporting TiffSaver was
also copied to SCIFIO.

As TIFFFormat extended BaseTiffReader, it was also marked deprecated
(although its logic is restricted to a BaseTIFFParser in the new
TIFFFormat).

The TiffDelegateReader was also marked deprecated although it should
still function as normal.
Converted OME-TIFF format

Translated the loci.formats OMETiffReader and Writer to SCIFIO
components in ome.scifio, consolidated to the OMETIFFFormat.

Added required "getOriginalMetadata" method to OMEXMLService as well.
Removed Bio-Formats from test-suite dependencies

Some Bio-Formats readers were superceding OME-TIFF for testing.
Eventually the test-suite will be completely converted for SCIFIO
classes. For now it is enough to remove Bio-Formats from the classpath,
and the one reference to Bio-Formats readers in the FormatReader test.
Added "exact" flag to TranslatorService

Translators (via the underlying PluginAttributeService) can now be
queried with an "exact" flag. If true, the translator must match both
Metadata classes exactly. If false, "isassignablefrom" is tested.
Updated uses as needed.
Added dummy EPSFormat Translator

Added an empty translator from ome.scifio.Metadata to EPSFormatMetadata.
This is to facilitate the EPS to OMEXML translator (which was looking
for an exact translator for EPSMetadata, which didn't exist).
Converted ZipFormat

The loci.formats ZipReader has been converted to SCIFIO components in
an ome.scifio ZipFormat.
Added getBinning method to OMEXMLMetadataService

This method was necessary for the MicromanagerFormat conversion.
Converted MicromanagerReader

The loci.formats MicromanagerReader has been translated to SCIFIO
components in the ome.scifio MicromanagerFormat. The loci.formats reader
is marked deprecated and now delegates to the SCIFIO Format.
Fixed ImageMetadata population

When populating ImageMetadata using an OMEXMLMetadata, was accidentally
counting size Z as both Z and T axis lengths. Fixed.
Changed default calibration values

ImgOpener should now populate default calibration values of 1.0 instead
of NaN, to allow computations that assume calibration values to be
performed.
Fixed ImgSaver workflow

Updated signatures to prevent infinite loop/NPE

Also force translation to SCIFIO Metadata, to trigger format-specific
translation processees.
Moved ReadImage to scifio unit tests

Updated for ImgOpener modified API. This allows the IO component to be
completely removed from imglib.
Added ImgOpener flags.

Should really consolidate these signatures to a single key,value list...