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Ticket #35 (closed enhancement: moved)

Opened 2007-03-19T11:18:44-05:00

Last modified 2014-01-09T13:11:34-06:00

More intelligent usage of Bio-Formats

Reported by: curtis Owned by: curtis
Priority: critical Milestone: visbio4.0
Component: visbio Severity: fatal
Keywords: Cc:
Blocked By: Blocking:

Description (last modified by curtis)

VisBio was migrated from its own importer code from the pre-Bio-Formats era, to using Bio-Formats directly for much of its import logic. The migration is incomplete, however, as VisBio still performs some redundant operations:

  • VisBio does its own file stitching, rather than relying on Bio-Formats's improved FileStitcher and AxisGuesser classes.
  • VisBio maintains its own multidimensional position arrays, but that logic is being migrated into Bio-Formats. Doing so will let FileStitcher provide an API offering more fine-grained control over numerical block axis assignments, as well as allow SDTReader to accurately report its spectral and lifetime dimension components.

There is a significant amount of VisBio logic that should be torn out and thrown away in favor of leaning on Bio-Formats. (This is not really a waste of good code, since it was this same code that formed the basis of Bio-Formats in the first place, and has continued to drive the corresponding features in Bio-Formats. That is, code originally written for VisBio keeps finding its way into the Bio-Formats library, making the original VisBio implementation, ironically, obsolete.)

Change History

comment:1 Changed 2007-03-19T13:15:41-05:00 by curtis

  • Milestone set to visbio4.0

comment:2 Changed 2007-10-31T16:54:48-05:00 by curtis

  • Severity set to fatal

This ticket includes usage of Bio-Formats's "sub-C" logic (getChannelDimLengths and getChannelDimTypes).

comment:3 Changed 2014-01-09T13:11:34-06:00 by curtis

  • Status changed from new to closed
  • Resolution set to moved
  • Description modified