Task #13270 (new)
Opened 8 years ago
Last modified 6 years ago
Bug: images not matching with well placement
Reported by: | mtbcarroll | Owned by: | dgault |
---|---|---|---|
Priority: | major | Milestone: | Unscheduled |
Component: | Bio-Formats | Version: | n.a. |
Keywords: | OMEXMLReader | Cc: | bf@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
From inspecting the simple OME-XML for the attached plate one would expect the field names to describe their placement on the plate. However, if I import it and work around #13269 then the images aren't at all where I'd expect. Am I missing something simple?
Attachments (1)
Change History (7)
Changed 8 years ago by mtbcarroll
comment:1 Changed 8 years ago by mtbcarroll
- Version OMERO-5.2.0 deleted
comment:2 Changed 8 years ago by mtbcarroll
- Cc bf@… added; ux@… removed
- Component changed from Import to Bio-Formats
- Keywords OMEXMLReader added
This mangling looks like it happens at the Bio-Formats level: compare the mapping from row & column to image name before and after the attached OME-XML goes through showinf -omexml. (If this is user error, please just point me to the doc I missed!)
comment:3 Changed 8 years ago by mtbcarroll
Ha, and it seems to work much better if I decrement the image numbers by 1 in both their actual IDs and the ImageRefs to them (leaving the abovementioned mapping unchanged).
comment:4 Changed 8 years ago by mtbcarroll
- Owner changed from jburel to dgault
comment:5 Changed 6 years ago by mtbcarroll
Just confirmed on current OMERO develop which I'm guessing is at least BF 5.7.3.
comment:6 Changed 6 years ago by mtbcarroll
I just ran into this bug again with problem-name.ome.xml from https://trello.com/c/fbJ6jMvZ/399-ignores-plate-names-in-naming-fields -
mtbc@ls28101:/tmp$ < problem-name.ome.xml grep Image: <ImageRef ID="Image:1"/> <ImageRef ID="Image:2"/> <Image ID="Image:1" Name="First Image"> <Image ID="Image:2" Name="Second Image"> mtbc@ls28101:/tmp$ showinf -nopix -omexml-only problem-name.ome.xml | grep Image: <ImageRef ID="Image:1"/> <ImageRef ID="Image:1"/> <Image ID="Image:0" Name="First Image"> <Image ID="Image:1" Name="Second Image"> mtbc@ls28101:/tmp$
plate to import