Task #10646 (closed)
Opened 11 years ago
Closed 10 years ago
Bug: Colour rendering broken for big images
| Reported by: | rleigh | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | 5.0.0-rc1 |
| Component: | Insight | Version: | 4.4.9 |
| Keywords: | n.a. | Cc: | ux@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description
Using /ome/apache_repo/4951/DG70_07_b_02_.zip on howe/dev_4_4. This is a 4-channel nd2 file, and is "big".
See attached screenshots. Greyscale rendering of individual channels works. Colour rendering, even of single channels, just returns completely black tiles.
This appears to affect Insight only.
Attachments (4)
Change History (18)
Changed 11 years ago by rleigh
comment:1 Changed 11 years ago by rleigh
Note that this issue does not affect gretzky/develop.
comment:2 Changed 11 years ago by rleigh
Also note that thumbnails are also black.
comment:3 Changed 10 years ago by jburel
- Resolution set to invalid
- Status changed from new to closed
- Version set to 4.4.9
Working on develop (see Roger's comment), no plan to review the dev_4_4 since develop is now becoming our "main" branch.
Closing
comment:4 Changed 10 years ago by rleigh
While it was seen to work on develop, will it work if imported on a 4.4 system which is later upgraded to 5.0 rather than imported afresh?
comment:5 Changed 10 years ago by jburel
- Milestone changed from Unscheduled to 5.0.0-beta2
- Resolution invalid deleted
- Status changed from closed to reopened
Good point,
I did not think about that case.
comment:6 Changed 10 years ago by rleigh
When we next do a DB upgrade testing session, if we could import this prior to the upgrade we can test it then.
comment:7 Changed 10 years ago by jburel
- Cc ux@… added
Petr do you mind checking with an "upgraded"image?
comment:8 Changed 10 years ago by pwalczysko
The image is imported on omero4-demo server in anticipation of the upgrade. Will check the result tomorrow (or after the upgrade proceeds).
user-8
comment:9 Changed 10 years ago by pwalczysko
Imported the .nd2 file to omero4 server into a dev_4_4 db and then upgrade to omero5 db was performed. After this, the images was checked by Insight OMERO.insight-5.0.0-beta2-RC2-263-4de9f1f-ice33-b508-mac.
The problem on omero4 (=dev 5 upgraded db, dev 5 server) is there just like reported here for Howe (=dev_4_4 server, dev_4_4 db,). See screenshot.
comment:10 Changed 10 years ago by jburel
the black thumbnail problem has been fixed by https://github.com/openmicroscopy/openmicroscopy/pull/1871
comment:11 Changed 10 years ago by jburel
The same problem in web.
The image imported using FS indicates that the pyramid is not ready
comment:12 Changed 10 years ago by pwalczysko
The image from FS-import is ready now - but unlike reported above, also this image has black thumb and is black when color is on. See screenshot.
comment:13 Changed 10 years ago by jburel
- Owner changed from jburel to mlinkert
- Status changed from reopened to accepted
Passing to melissa to check if there is not an issue with that specific file
comment:14 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from accepted to closed
PR opened: https://github.com/openmicroscopy/bioformats/pull/822
This not a general problem with big images, but rather specific to certain .nd2 files. Resetting the alpha value to 255 in Insight for each of the channel colors should also fix the problem.
greyscale