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Task #12110 (closed)

Opened 8 years ago

Closed 7 years ago

Last modified 7 years ago

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 7 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 7 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)

Fixes #12110, fixes #12208.

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