Ticket #398 (closed enhancement: fixed)
Opened 2009-05-26T16:07:51-05:00
Last modified 2011-02-02T04:45:00-06:00
Better support for N-dimensional data
| Reported by: | curtis | Owned by: | curtis |
|---|---|---|---|
| Priority: | major | Milestone: |
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| Component: | bio-formats | Severity: | serious |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: |
Description
Eliminate IFormatReader.getChannelDimTypes and IFormatReader.getChannelDimLengths, in favor of more comprehensive getDimTypes and getDimLengths methods, which return all used dimensions in correct rasterization order.
- OME dimensions include: X, Y, Z, C, T
- Examples of non-OME dimensions:
- lifetime bins
- excitation wavelength
- polarization
- screen
- plate
- well
- field
Advantages:
- fully capable of expressing N-dimensional image data
- allows for XZ scans and other spatial configurations
- eliminates the need for DimensionOrder and Interleaved core metadata
Work to do:
- Rework ChannelSeparator a little
- It should always "pull" XY to the front
- Rework DimensionSwapper; it is more complex now
- Rework DataBrowser to use new methods, displaying extra sliders as before
- Rework FileStitcher and AxisGuesser a bit
- Guessed axes become new dimensions
- Change anywhere else that calls getChannelDim* methods
- InCell reader can be retrofitted to use this new functionality
- Certain other readers can benefit as well: Flex, Fluoview, ...
- Initially, conversion to OME-TIFF with bfconvert should throw an exception if any dimensions beyond 5D exist, since there is nowhere in the OME-XML schema to store the extra dimensional information