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Ticket #493 (closed defect: fixed)

Opened 2010-05-20T10:28:33-05:00

Last modified 2010-07-13T16:57:53-05:00

Series beyond 456 do not appear in ImageJ plugin

Reported by: melissa Owned by: curtis
Priority: critical Milestone: bio-formats-4.2
Component: plugins Severity: serious
Keywords: Cc: ruben.munoz@…
Blocked By: Blocking:

Description (last modified by curtis)

When opening data/fake/curtis/520series&series=520&sizeX=96&sizeY=48.fake, the series dialog appears as expected but series beyond 456 are not displayed in the dialog.

The display option was "Hyperstack", and the only option checked was "Autoscale".

Change History

comment:1 Changed 2010-06-02T15:21:31-05:00 by curtis

  • Status changed from new to assigned

This works on my system with the 520series fake dataset. Melissa, is it still broken for you? If so, what is your OS and Java version?

comment:2 Changed 2010-06-02T19:20:33-05:00 by melissa

Yes, it's still broken for me with trunk r6450.

OS: Ubuntu 9.10
ImageJ version: 1.43u

$ java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) Server VM (build 16.3-b01, mixed mode)

comment:3 Changed 2010-06-03T15:25:23-05:00 by curtis

  • Description modified

Seems to be Linux-specific. I was able to duplicate your problem on Ubuntu 9.10, at least. It also does not seem to be an issue with the layout manager. I tried switching from GridLayout to FormLayout for the masterPanel, and it made no difference.

However, on my system, the series beyond 233 disappear, not 456. It may be an issue with the number of total pixels vertically in a ScrollPane, or something strange with the interaction with the GenericDialog's GridBagLayout.

Unless you have any further insight into this problem immediately, we may want to push to 4.2.1, because it will probably not be a quick fix.

comment:4 Changed 2010-06-03T16:09:56-05:00 by curtis

  • Status changed from assigned to closed
  • Resolution set to fixed

In r6466, I changed the code to suppress the thumbnails if more than 200 series, showing only checkboxes. I also fixed a bug when seriesCount % 256 == 0, and switched over to FormLayout from GridLayout, since I observed an exception relating to GridLayout on some systems.

There is a remaining problem when seriesCount gets extremely large. On my Ubuntu 9.10 box, seriesCount much beyond 1200 stalled; e.g., with seriesCount=10000, my system stalled with 100% CPU for longer than I was willing to wait for the dialog, busy doing some native X flush operation. Similarly on Mac OS X 10.6, seriesCount=3000 popped up reasonably fast, but seriesCount=5000 did not appear after many seconds of waiting.

We may want to implement an alternative GUI for seriesCount>1000. Perhaps the user could simply type in the desired series numbers as a comma-separated list, using dashes to indicate ranges.

comment:5 Changed 2010-07-09T12:55:02-05:00 by melissa

  • Milestone bio-formats-4.2 deleted

Milestone bio-formats-4.2 deleted

comment:6 Changed 2010-07-13T16:57:53-05:00 by melissa

  • Milestone set to bio-formats-4.2