Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #9228 (new)

Opened 7 years ago

Last modified 3 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)

AllPixels.bsh (910 bytes) - added by mlinkert-x 7 years ago.
timing.ijm (404 bytes) - added by mlinkert-x 7 years ago.

Download all attachments as: .zip

Change History (10)

Changed 7 years ago by mlinkert-x

Changed 7 years ago by mlinkert-x

comment:1 Changed 7 years ago by mlinkert

These commits:

https://github.com/openmicroscopy/bioformats/commit/ccfdb78b4979112d87c3afb3c2d25c4d93a7f0aa
https://github.com/openmicroscopy/bioformats/commit/62c862c4f51838ca63201115ec9c6f27bc179332

bring the output of timing.ijm down to:

Plain IJ1: 654ms, Bio-Formats: 5816ms

and the output of the BeanShell? script to:

create reader: 700 ms
create metadata structure: 144 ms
initialize file: 2877 ms
read all images: 229 ms

Still not as good as we'd like, but it's progress.

Last edited 7 years ago by mlinkert (previous) (diff)

comment:2 Changed 7 years ago by mlinkert

  • Milestone changed from OMERO-4.4.x to OMERO-4.4.1

comment:3 Changed 7 years ago by mlinkert

  • Sprint set to 2012-08-28 (3)

comment:4 Changed 6 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 6 years ago by mlinkert

  • Milestone changed from OMERO-4.4.3 to OMERO-4.5
  • Sprint 2012-09-11 (4) deleted

comment:7 Changed 3 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled

comment:8 Changed 3 years ago by sbesson

  • Milestone changed from Unscheduled to OME-Files
  • Version set to OMERO-5.2.0
Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.152458 sec.)

We're Hiring!