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acquifer-core API documentation

acquifer-core

See: Description

Packages 
Package Description
acquifer.core  
acquifer.core.im  
acquifer.core.im03  
acquifer.core.im04  

acquifer-core

This artifact can be used in most java programing environments provided the dependencies defined in the pom are available (Apache common...).
The artifact contains methods and classes to work with IM datasets.
For questions about this Java API, feel free to write a mail to support@acquifer.de.
The artifact is organized in sub-packages:

  • acquifer.core
  • This package contains data-structure such as Well, Plate and Dataset.
    These data-structures can be used with any IM version, and replicate the IM organisation : a plate is a collection of Well and a Dataset a collection of Images.

  • acquifer.core.im
  • This package is a "super" package for the related packages acquifer.core.im03/4.
    It contains classes which are mirrored in the im03/4 packages.
    In particular the classes are defined in a generic way in the im package, so that they can be adapted for both IM03/4 in the assoaciated im03/4 packages.
    Users should thus directly use the classes in the im03/im04 packages.
    However the documentation for most classes is in this super package.

    One important class for this multi-IM support is the MetadataParser class, it is responsible for extracting the metadata from IM filenames, and is thus IM-specific. Many classes in the im package, thus relies on a MetadataParser for their functioning.
    The metadataParser of the correct IM version is often defined as parameter of class constructor for classes of the im package.
    In the descendant classes (im03/4), this parameter disappear from the constructor, as we know which metadataParser to pass to the super constructor.


  • acquifer.core.im03
  • This is a mirror of the classes in acquifer.core.im, adapted to im03 datasets.
    You should use the classes in this package (ie import acquifer.core.im03.*) if you have IM03 datasets (filenames starting with "WE"). Refer to the mother classes in acquifer.core.im for the documentation.
  • acquifer.core.im04
  • This is a mirror of the classes in acquifer.core.im, adapted to im04 datasets.
    You should use the classes in this package (ie import acquifer.core.im04.*) if you have IM04 datasets (filenames starting with "-"). Refer to the mother classes in acquifer.core.im for the documentation.
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