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Ticket #1311 (closed defect: fixed)

Opened 2012-07-11T10:33:12-05:00

Last modified 2012-07-12T10:47:05-05:00

Process > Binary > Make Binary sometimes fails

Reported by: bdezonia Owned by: bdezonia
Priority: major Milestone: imagej2-b3-headless
Component: Legacy Compatibility Version:
Severity: serious Keywords:
Cc: Blocked By:

Description (last modified by bdezonia)

Process > Binary > Make Binary does not work the same as IJ1 for all image types.

It works with Boats (1-bit black and white).
It fails with Organ of Corti (data is treated as a 8-bit Color hyperstack rather than a 1-bit hyperstack).
It fails with Clown (data is black and white but stays 8-bit rather than 1-bit)

It fails with a 32-bit version of Bridge. In IJ1 open bridge, change type to 32-bit, run Make Binary and its fine. In IJ2 open bridge, change type to 32-bit float, run Make Binary, and then all values are 255. Editing Brightness/Contrast to match IJ1's values before running the Make Binary command had no effect on results.

Change History

comment:1 Changed 2012-07-11T10:46:53-05:00 by bdezonia

  • Description modified

comment:2 Changed 2012-07-11T11:14:45-05:00 by bdezonia

  • Description modified

comment:3 Changed 2012-07-11T16:37:56-05:00 by bdezonia

With commit 843ba423554ac55947b92a66721e95870e802cee all file types now becoming binary as needed.

However the issue of bridge being all 255's is not yet fixed. That may be a different bug altogether. Investigating.

comment:4 Changed 2012-07-11T17:17:11-05:00 by bdezonia

The code that correctly handles the binary type tracking is slowing down harmonization of all 8-bit images. We'll need to find a more efficient way to handle this before the release.

comment:5 Changed 2012-07-12T09:48:30-05:00 by bdezonia

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

The issue where a float version of the bridge is all 255 is an issue with thresholding. The IJ1 plugin is returning the image as all 255's. It uses thresholds to calc pixel values. I think we are not handling thresholds at all at the moment. Opening that issue as a new ticket.

Closing this ticket.

comment:6 Changed 2012-07-12T10:47:05-05:00 by bdezonia

  • Milestone changed from imagej-2.0.0-beta4 to imagej-2.0.0-beta3