Bug: ROI points display

[wmoore]

This may be a duplicate, but just in case...

Importing modelgolgi.mod from test_images_good/imod I get an image where the min and max are 0 (totally black image - but this is expected), but the ROIs on the image don't show up in Insight (haven't tried web yet).

More details in comments below...

[mlinkert]

All IMOD files will contain completely black images - that is expected. The reason to have them in test_images_good is that they contain plenty of ROIs (and this is a supported format, so we do need to be testing it even if it's not interesting).

That exception is down to the RomioPixelBuffer? attempting to map an entire timepoint of data into memory at once, which in this case is 1781 * 1594 * 476 * 3 = ~3.77 GB. There isn't much that I can do about it, so removing myself as owner.

[wmoore]

There are no ROIs shown in Insight on the 2 files mentioned above, although they are in the DB

omero@howe:~$ psql omero
psql (8.4.8)
Type "help" for help.

omero=# select * from roi where image=8724;
 id  | description | permissions | keywords | namespaces | version | creation_id | external_id | group_id | owner_id | update_id | image | source 
-----+-------------+-------------+----------+------------+---------+-------------+-------------+----------+----------+-----------+-------+--------
 254 |             |          -8 | {}       | {}         |         |       70800 |             |       53 |      155 |     70800 |  8724 |       
 255 |             |          -8 | {}       | {}         |         |       70800 |             |       53 |      155 |     70800 |  8724 |       
 256 |             |          -8 | {}       | {}         |         |       70800 |             |       53 |      155 |     70800 |  8724 |       
(3 rows)

omero=# select * from roi where image=7646;
 id  | description | permissions | keywords | namespaces | version | creation_id | external_id | group_id | owner_id | update_id | image | source 
-----+-------------+-------------+----------+------------+---------+-------------+-------------+----------+----------+-----------+-------+--------
 251 |             |          -8 | {}       | {}         |         |       64213 |             |       53 |      155 |     64213 |  7646 |       
(1 row)

[mlinkert]

That's expected as part of #3215, though, right?

[wmoore]

I think #3215 is about import of ROIs etc, not display in Insight.

They don't show up in Insight because more than 1 shape within an ROI is on the same plane, and some have no plane (

# select id, theZ, theT, theC from shape where roi in (255);

  id  | thez | thet | thec 
------+------+------+------
 4288 |  267 |      |     
 4287 |  267 |      |     
 ...   
 4274 |  254 |      |     
 4273 |  253 |      |     
 4272 |  252 |      |     
 4271 |  250 |      |     
 4270 |  250 |      |     
...
 4258 |  250 |      |     
 4257 |  250 |      |     
 4256 |  249 |      |     
 4255 |  248 |      |     
 4254 |  247 |      |     
 4253 |  246 |      |     
 4252 |  245 |      |     
 4251 |  243 |      |     
 4250 |  243 |      |     
 4249 |  242 |      |     
 4248 |      |      |     
 4247 |      |      |     
 4246 |  242 |      |     
 4245 |  241 |      |        
...

[jburel]

duplicate see #10097