Ticket #542 (closed defect: fixed)
Opened 2010-08-27T17:08:42-05:00
Last modified 2010-10-04T13:55:28-05:00
Multi-series stitching is incorrect
| Reported by: | curtis | Owned by: | melissa |
|---|---|---|---|
| Priority: | major | Milestone: |
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| Component: | bio-formats | Severity: | serious |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: |
Description
When stitching a dataset with multiple image series distributed across multiple files:
$ cd 'wiscscan/jayne/long term test xyz' $ showinf -stitch 'test longterm xyz_C1_TP1_SP0.tiff'
The file pattern is correctly detected. However, Bio-Formats only acknowledges two series, based on SP1 and SP2 file sets—the SP0 files are apparently ignored.
It also gets the axes wrong:
$ java loci.formats.AxisGuesser 'test longterm xyz_C1_TP1_SP0.tiff' File = /Volumes/data/wiscscan/jayne/long term test xyz/test longterm xyz_C1_TP1_SP0.tiff Pattern = /Volumes/data/wiscscan/jayne/long term test xyz/test longterm xyz_C<1-2>_TP<1-114>_SP<0-2>.tiff Pattern is valid. Reading first file [Fatal Error] :1:1: Content is not allowed in prolog. Reading IFDs Populating metadata Checking comment style Populating OME metadata [done] dimOrder = XYCZT (uncertain) sizeZ = 1 sizeT = 20 sizeC = 1 Axis types: <1-2> C (prefix = test longterm xyz_C) <1-114> T (prefix = _TP) <0-2> ? (prefix = _SP) Adjusted dimension order = XYCTZ (uncertain)
The misdetected "sizeT = 20" for a single TIFF is expected, but because the dimension order is uncertain, that axis should be remapped to Z rather than stacking with the 114 external T elements (which is what's happening).
Change History
comment:1 Changed 2010-10-04T13:55:28-05:00 by melissa
- Status changed from new to closed
- Resolution set to fixed
(In [7021]) Updated FileStitcher and FilePattern to better handle multi-series datasets in which the series axis is spread across multiple files. Closes #296, closes #542.
Note that datasets such as S<0-2>_T<0-10>.lif with each file containing multiple series are still unsupported. However, attempting to stitch datasets of this type will result in an informative exception.