Task #9228 (new)
Opened 12 years ago
Last modified 8 years ago
Investigate performance of TIFF-based readers
Reported by: | mlinkert | Owned by: | mlinkert |
---|---|---|---|
Priority: | minor | Milestone: | OME-Files |
Component: | Bio-Formats | Version: | OMERO-5.2.0 |
Keywords: | n.a. | Cc: | crueden-x, johannes.schindelin@…, jerome.mutterer@…, ppirrotte@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
See files in ome-tiff/johannes and zeiss-lsm/jerome/CONFOCAL*, and the attached ImageJ macro and BeanShell? script for testing.
For the OME-TIFF file and the ImageJ macro, the baseline timing is:
Plain IJ1: 531ms, Bio-Formats: 7669ms
For the OME-TIFF file and the BeanShell? script, the baseline timing is:
create reader: 677 ms create metadata structure: 1577 ms initialize file: 2004 ms read all images: 494 ms
...which basically means that constructing a reader and an OMEXMLMetadata is more expensive than calling setId. So the first priority is to reduce the amount of time required to set up, and then we can work on reducing the setId execution time so that it is closer to what we see when reading files with ImageJ's built-in TIFF reader.
Attachments (2)
Change History (10)
Changed 12 years ago by mlinkert-x
Changed 12 years ago by mlinkert-x
comment:1 Changed 12 years ago by mlinkert
comment:2 Changed 12 years ago by mlinkert
- Milestone changed from OMERO-4.4.x to OMERO-4.4.1
comment:3 Changed 12 years ago by mlinkert
- Sprint set to 2012-08-28 (3)
comment:4 Changed 12 years ago by jburel
- Sprint changed from 2012-08-28 (3) to 2012-09-11 (4)
Moved from sprint 2012-08-28 (3)
comment:5 Changed 12 years ago by mlinkert
- Milestone changed from OMERO-4.4.3 to OMERO-4.5
- Sprint 2012-09-11 (4) deleted
comment:6 Changed 11 years ago by mlinkert
See also this thread: http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2012-November/002319.html
comment:7 Changed 8 years ago by jamoore
- Milestone changed from 5.x to Unscheduled
comment:8 Changed 8 years ago by sbesson
- Milestone changed from Unscheduled to OME-Files
- Version set to OMERO-5.2.0
These commits:
https://github.com/openmicroscopy/bioformats/commit/ccfdb78b4979112d87c3afb3c2d25c4d93a7f0aa
https://github.com/openmicroscopy/bioformats/commit/62c862c4f51838ca63201115ec9c6f27bc179332
bring the output of timing.ijm down to:
and the output of the BeanShell? script to:
Still not as good as we'd like, but it's progress.