Task #5914 (closed)
Bug: Import ome file with PhysicalSizeZ = 0.0
| Reported by: | jburel | Owned by: | cxallan |
|---|---|---|---|
| Priority: | major | Milestone: | OMERO-Beta4.3.1 |
| Component: | Import | Version: | n.a. |
| Keywords: | n.a. | Cc: | jamoore, cxallan |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2011-07-07 (1) |
Description
Try to import the following file specification/Samples/compliant-hcs-sample.ome.
PhysicalSizeZ = 0.0.
loci.formats.FormatException: loci.common.services.ServiceException: java.lang.IllegalArgumentException: 0.0 must not be null and positive. at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:259) at loci.formats.FormatReader.setId(FormatReader.java:1072) at loci.formats.ImageReader.setId(ImageReader.java:670) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
The stylesheet is maybe not valid or not applied
Change History (16)
comment:1 Changed 13 years ago by jmoore
- Milestone changed from OMERO-Beta4.3 to OMERO-Beta4.3.1
comment:2 Changed 13 years ago by ajpatterson
Data file is incorrect.
comment:3 Changed 13 years ago by Andrew J Patterson <ajpatterson@…>
- Remaining Time set to 0
- Resolution set to fixed
- Status changed from new to closed
(In [5e3660b6f038434d6367fd3499c4050dc83363b1/ome.git] on branch develop) Fixing PhysicalSizeZ to valid value Close #5914
comment:4 Changed 13 years ago by ajpatterson
- Resolution fixed deleted
- Status changed from closed to reopened
comment:5 Changed 13 years ago by ajpatterson
After chat with Chris the data file is not invalid for its 2010-04 schema. When I manually run the file through the transforms the value is upgraded unchanged to 2010-06 and then correctly striped as invalid by the upgrade to 2011-06. I will revert the change I made to the files.
comment:6 Changed 13 years ago by Andrew J Patterson <ajpatterson@…>
(In [8bf75285321ad79d307903e89f5dca06486bd87e/ome.git] on branch develop) Undo fix to PhysicalSizeZ as 0.0 valid (see #5914)
comment:7 Changed 13 years ago by ajpatterson
<xsd:attribute name="PhysicalSizeZ" use="optional" type="PositiveFloat">
So It is optional but if present it must be > 0.
Think this must be a bug in the reader?
comment:8 Changed 13 years ago by ajpatterson
- Owner changed from ajpatterson to cxallan
- Status changed from reopened to accepted
comment:9 Changed 13 years ago by Chris Allan <callan@…>
(In [52e60a27eb162dcd2747850b968b891da913293a/bioformats.git]) Added additional debugging. (See #5914)
comment:10 Changed 13 years ago by Chris Allan <callan@…>
- Resolution set to fixed
- Status changed from accepted to closed
(In [47ea2d764f0da18465406c0b13089b45a11d6d72/bioformats.git]) Execution of 2010-04 to 2010-06 update stylesheet restored. (Fixes #5914)
comment:11 Changed 13 years ago by Chris Allan <callan@…>
(In [52e60a27eb162dcd2747850b968b891da913293a/bioformats.git]) Added additional debugging. (See #5914)
comment:12 Changed 13 years ago by Chris Allan <callan@…>
(In [47ea2d764f0da18465406c0b13089b45a11d6d72/bioformats.git]) Execution of 2010-04 to 2010-06 update stylesheet restored. (Fixes #5914)
comment:13 Changed 13 years ago by Chris Allan <callan@…>
(In [52e60a27eb162dcd2747850b968b891da913293a/bioformats.git]) Added additional debugging. (See #5914)
comment:14 Changed 13 years ago by Chris Allan <callan@…>
(In [47ea2d764f0da18465406c0b13089b45a11d6d72/bioformats.git]) Execution of 2010-04 to 2010-06 update stylesheet restored. (Fixes #5914)
comment:15 Changed 13 years ago by Chris Allan <callan@…>
(In [52e60a27eb162dcd2747850b968b891da913293a/bioformats.git]) Added additional debugging. (See #5914)
comment:16 Changed 13 years ago by Chris Allan <callan@…>
(In [47ea2d764f0da18465406c0b13089b45a11d6d72/bioformats.git]) Execution of 2010-04 to 2010-06 update stylesheet restored. (Fixes #5914)
Moving to 4.3.1 for handling