Task #12110 (closed)
BUG:bfconvert exports only one channel using -z and -timepoint arguments
| Reported by: | bramalingam | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | minor | Milestone: | 5.1.0 |
| Component: | General | Version: | 5.0.0 |
| Keywords: | n.a. | Cc: | |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | n.a. |
Description
Image used :
No of z-sections : 20
No of Time points : 1
No of Channels : 3
Error :
The default export seems to export only one channel, (it is expected to convert all 3 channels).
Command line call :
ls29010:tools bramalingam$ ./bfconvert /Users/bramalingam/Desktop/Batch_Image_Export/SMN10ul03_R3D_D3D.dv.ome.tif -compression LZW -z 1 /Users/bramalingam/Desktop/test11q.ome.tif
/Users/bramalingam/Desktop/Batch_Image_Export/SMN10ul03_R3D_D3D.dv.ome.tif
OMETiffReader initializing /Users/bramalingam/Desktop/Batch_Image_Export/SMN10ul03_R3D_D3D.dv.ome.tif
Reading IFDs
Populating metadata
[OME-TIFF] -> /Users/bramalingam/Desktop/test11q.ome.tif [OME-TIFF]
Exception in thread "main" loci.formats.FormatException?: Plane index:21 must be < 3
at loci.formats.FormatWriter?.checkParams(FormatWriter?.java:386)
at loci.formats.out.TiffWriter?.saveBytes(TiffWriter?.java:174)
at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:201)
at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:187)
at loci.formats.FormatWriter?.saveBytes(FormatWriter?.java:136)
at loci.formats.ImageWriter?.saveBytes(ImageWriter?.java:205)
at loci.formats.tools.ImageConverter?.convertPlane(ImageConverter?.java:551)
at loci.formats.tools.ImageConverter?.testConvert(ImageConverter?.java:487)
at loci.formats.tools.ImageConverter?.main(ImageConverter?.java:681)
Change History (2)
comment:1 Changed 9 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.0
- Resolution set to fixed
- Status changed from new to closed
comment:2 Changed 9 years ago by Melissa Linkert <melissa@…>
- Remaining Time set to 0
(In [3976f3f94d40ef343153ff44d2f2ab1e5798c691/bioformats.git] on branch develop) bfconvert: fix plane indexing in the output file(s)
PR open: https://github.com/openmicroscopy/bioformats/pull/1555