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Bug 728 - Analyze Particles / Add To Manager in BatchMode
Analyze Particles / Add To Manager in BatchMode
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Linux
: P5 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-04-11 09:42 CDT by Niko Ehrenfeuchter
Modified: 2014-04-30 03:44 CDT
2 users (show)

See Also:

Attachments
analyzeparticles_batchmode.ijm (252 bytes, text/plain)
2014-04-11 09:42 CDT, Niko Ehrenfeuchter

Description Niko Ehrenfeuchter 2014-04-11 09:42:36 CDT 
Created attachment 143
analyzeparticles_batchmode.ijm

I think I found a bug in current ImageJ/Fiji:

When running "Analyze Particles" from within a macro with the "add" parameter in Batch Mode, nothing is added to the ROI Manager. To reproduce, use the attached macro code - if you move the "setBatchMode(false);" statement below the "Analyze Particles" call the ROI Manager will remain empty.

I came across this as suddenly one of my macros stopped working. If I remember correctly this still used to work like 3 or 4 weeks ago.

Cheers
Niko
Comment 1 Wayne Rasband 2014-04-12 19:52:17 CDT 
Analyze Particles does work with the ROI Manager in batch mode but the ROI Manager is hidden and it is deleted when you exit batch mode. Your test macro will work as expected if you move "setBatchMode(false)" to the end of the macro, as follows:

  setBatchMode(true);
  run("Blobs (25K)");
  setAutoThreshold("Default");
  run("Analyze Particles...", "circularity=0.50-1.00 exclude clear add");
  roiManager("Show All with labels");
  setBatchMode(false);

This behavior has not changed since ImageJ 1.41.
Comment 2 Johannes Schindelin 2014-04-29 11:00:40 CDT 
Is this issue resolved? If so, please do not leave it open.
Comment 3 Niko Ehrenfeuchter 2014-04-30 03:44:36 CDT 
(Sorry for the delay, just back from vacation.)

According to Wayne, the behavior hasn't changed in a while, so I probably missed a change in our macro here. Closing the issue as invalid for now.