Task #5359 (closed)
BUG: Some Volocity datasets with embedded pixel data do not open
| Reported by: | mlinkert | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | OMERO-Beta4.3 |
| Component: | Bio-Formats | Version: | n.a. |
| Keywords: | n.a. | Cc: | |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2011-06-16 (14) |
Description
Embedded pixel data can be stored in the "library clipping" format; this is not currently supported. The dimensions of the images can be retrieved and the offset to the pixel data can be found, but the pixels themselves are encoded somehow.
The pixels do not appear to be compressed; in fact, the total number of bytes is slightly larger than the number of raw bytes expected. Most of the pixel values appear to be stored without any sort of encoding, but every so often there are ~3-16 bytes of encoded data that do not correspond to the real pixel values.
Change History (10)
comment:1 Changed 8 years ago by Melissa Linkert <melissa@…>
comment:2 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [158e6170cc5a824b269170f5c9e3d09f20574803/bioformats.git]) A few fixes for embedded library clipping data.
This at least allows the correct dimensions and offsets to be used.
However, there is still some work left to be done in order to have the
pixel data correctly read from clipping files.
See #5359.
comment:3 Changed 8 years ago by mlinkert
- Status changed from new to accepted
comment:4 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [275ec8baecff9424c3f3800489e5ceecdf795c9b/bioformats.git]) Read the offset to the pixel data, instead of hard-coding it.
See #5359.
comment:5 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [275ec8baecff9424c3f3800489e5ceecdf795c9b/bioformats.git]) Read the offset to the pixel data, instead of hard-coding it.
See #5359.
comment:6 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [6f8c5e8dc8856cce8c89f78af7c24364184a746e/bioformats.git]) A little progress on setting up the clipping decoder.
It needs work though; the encoded sections are still not decoded
properly. See #5359.
comment:7 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [6f8c5e8dc8856cce8c89f78af7c24364184a746e/bioformats.git]) A little progress on setting up the clipping decoder.
It needs work though; the encoded sections are still not decoded
properly. See #5359.
comment:8 Changed 8 years ago by jburel
- Sprint changed from 2011-06-02 (13) to 2011-06-16 (14)
Moved from sprint 2011-06-02 (13)
comment:9 Changed 8 years ago by Melissa Linkert <melissa@…>
- Remaining Time set to 0
- Resolution set to fixed
- Status changed from accepted to closed
(In [649e4a9e737e84896f589d3d7eda9dc7556a8e6f/bioformats.git]) Fix decoding of clipping data.
Closes #5359.
comment:10 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [649e4a9e737e84896f589d3d7eda9dc7556a8e6f/bioformats.git]) Fix decoding of clipping data.
Closes #5359.
(In [158e6170cc5a824b269170f5c9e3d09f20574803/bioformats.git]) A few fixes for embedded library clipping data.
This at least allows the correct dimensions and offsets to be used.
However, there is still some work left to be done in order to have the
pixel data correctly read from clipping files.
See #5359.