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Package io.scif

Provides the interfaces and default implementations for the components of SCIFIO, and the context for instantiating these components.

See: Description

Package io.scif Description

Provides the interfaces and default implementations for the components of SCIFIO, and the context for instantiating these components.

Please refer to the FAQ for answers to commonly asked questions.

Support for a given image format in SCIFIO is established by implementing the Format interface. Each Format consists of six types of components:

The intended workflow in SCIFIO takes an image source through the following steps:

  1. Use each discovered Format's Checker to determine if that Format is compatible with the image source.
  2. If a match is found, use a Parser to extract the format-specific Metadata from the image source. Format-specific information is also used at this point to populate the associated ImageMetadata information.
  3. Now that we have a Metadata object, it can be attached to a Reader and used to open image Planes.
  4. If we want to save these planes to a different Format, we need to use Translators to convert our parsed Metadata to the destination Metadata. This could be done by translating to and from an intermediary - e.g. an open exchange format, like OME-XML. Or, it could be done by simply translating from the source's ImageMetadata to the destination.
  5. The translated Metadata is then attached to an appropriate Writer, and Planes opened by the Reader are passed, as desired, to the Writer for saving to an output source.

The SCIFIO class wraps Context instances and provides convenient access to many services.

This package also contains an ImageMetadata interface and default implementation. ImageMetadata is use as a format-agnostic representation of common image attributes. SCIFIO follows the OME syntax of what is an "image" - in that top-level is really a dataset, which are arbitrary lists of one or more images. Images are the pixel containers, and metadata can exist at both the image and dataset level.

Changes since Bio-Formats

Future plans

NB: items with an asterisk (*) are of unknown merit and may or may not be implemented, pending discussion.
Author:
Mark Hiner
See Also:
Format, SCIFIO
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