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 |
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Priority: | critical | Milestone: |
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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: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