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LOCI projects are now located on GitHub. The Bio-Formats project can be found here.

Ticket #263 (closed task: fixed)

Opened 2008-03-19T14:11:39-05:00

Last modified 2010-08-16T15:58:17-05:00

Bio-Formats configuration dialog

Reported by: curtis Owned by: curtis
Priority: major Milestone:
Component: plugins Severity: serious
Keywords: Cc:
Blocked By: Blocking:

Description

The Bio-Formats-related plugins have many options with enough complexity that the suite would benefit from a Preferences window to allow easy configuration. Things to include in this configuration dialog include:

  • Availability of QuickTime for Java
  • Toggle between QTJava and native QT logic
  • Availability of official Nikon ND2 plugin
  • Toggle between Nikon ND2 and BF ND2 logic
  • Ability to upgrade to latest version of Bio-Formats, similar to ImageJ updater
  • Availability of various component libraries (in case JARs are separated)
  • Availability of native JPEG2000 codec, and ability to install it if needed
  • Lurawave license code
  • Behavior of SDT reader

To assist with this, consider an addition to the IFormatHandler API that identifies such configuration options in some standard way. If we can come up with a good solution, the configuration dialog would be simplified as it could simply iterate over known configuration options for each reader & writer.

Change History

comment:1 Changed 2008-03-19T15:28:45-05:00 by curtis

More things the configuration checking logic should be able to do:

  • Check to make sure there are no old JAR files in any of the folders (plugins, jre/lib/ext, /Library/Java/Extensions, /System/Library/Java/Extensions, etc.).
  • After installing a native library, check whether a restart of ImageJ/Java is necessary, and if so, notify the user.

comment:2 Changed 2008-05-02T16:33:29-05:00 by curtis

  • Cc curtis@… added

comment:3 Changed 2008-05-02T16:44:47-05:00 by curtis

  • Cc curtis@… removed

comment:4 Changed 2008-05-02T16:51:24-05:00 by curtis

The Bio-Formats configuration dialog plugin now exists in the source:trunk/loci/plugins/config package. Currently it can do everything mentioned above, EXCEPT:

  • Ability to upgrade to latest version of Bio-Formats, similar to ImageJ updater
  • Ability to install native JPEG2000 codec if needed
  • Ability to install or upgrade any other missing libraries
  • Checking common paths for old or duplicate JARs

All of the above features fall under the umbrella of installation and upgrade, and will be handled in a modular Bio-Formats Installer plugin. However, this plugin will be easily accessible from the configuration dialog via a "Check my system and install missing libraries" button in large, friendly letters.

comment:5 Changed 2009-01-07T11:11:31-06:00 by melissa

  • Milestone changed from bio-formats-m2 to bio-formats-4.0.0

comment:6 Changed 2009-02-17T12:04:22-06:00 by melissa

(In [4812]) Added ImageJ plugin that will download the latest trunk, daily or stable build. This plugin is automatically called if upgrade checking is enabled and a new stable version is detected; it can also be called manually using Plugins>LOCI>Upgrade LOCI Plugins. Closes #327, see #263.

comment:7 Changed 2009-03-11T16:47:59-05:00 by curtis

  • Milestone changed from bio-formats-4.0.0 to bio-formats-4.1.0

comment:8 Changed 2009-10-21T07:28:47-05:00 by melissa

  • Milestone bio-formats-4.1 deleted

comment:9 Changed 2010-08-16T15:58:17-05:00 by curtis

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

Ability to install native JPEG2000 codec if needed

Bio-Formats decodes JPEG2000 in pure Java now, so this is no longer needed.

Ability to install or upgrade any other missing libraries Checking common paths for old or duplicate JARs

The Fiji Updater largely obviates the need for this functionality.

Hence, I am closing this ticket!