Task #4114 (new)
Opened 13 years ago
Last modified 11 years ago
Better support for N-dimensional data — at Initial Version
Reported by: | curtis | Owned by: | curtis |
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Priority: | major | Milestone: | OMERO-Beta4.4 |
Component: | Bio-Formats | Version: | n.a. |
Keywords: | n.a. | Cc: | |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
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
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