Bug 494 – 3D Manager unable to "Add Image"

Bug 494 - 3D Manager unable to "Add Image"


Summary:	3D Manager unable to "Add Image"

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P1 major
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2012-09-17 14:50 CDT by Jan Brocher
Modified:	2013-07-07 10:54 CDT
CC List:	2 users (show)

See Also:

Attachments
System and Version Information (97.67 KB, text/plain) 2012-09-17 14:50 CDT, Jan Brocher

Description Jan Brocher 2012-09-17 14:50:21 CDT

Created attachment 75
System and Version Information

The 3D Manager suddenly is not able to add the features in an image of the segmentation map to the manager after segmentation when pressing the "Add Image" button. This was perfectly working before the update to ImageJ 1.47c and/or before the Fiji updates until at least 10th of September 2012.

Comment 1 Johannes Schindelin 2012-09-17 20:09:34 CDT

I am sorry, I do not quite understand what you mean by "3D Manager". Could you point me to a menu entry (in the style of File>New>Script) and explain step by step what I have to do to reproduce the issue? Thanks.

Comment 2 Johannes Schindelin 2012-09-18 16:15:33 CDT

The reply by private mail:

-- snipsnap --
Thanks for the fast reply and sorry for the confusion. Hope to be able to make it clearer by this mail.

I installed the "3D Roi Manager and 3D Analysis" (from: http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start) plugin developed by Thomas Boudier longer time ago.

It worked perfectly fine until one of the last version updates of ImageJ (from v1.47a to v1.47b or c) or Fiji.

The problem occurs in the "Plugins>3D>3D Manager".

Image segmentation after plugin start works but afterwards the "Add Image" button opens up the expected Log window with the information about the objects found while they are not added to the ROI manager (the latter also shows a smaller ROI display window as usual, which might be connected to the problem).
The plugin files have not been changed since then and re-installation of the plugin did not solve the problem.

Thanks for addressing the problem.

Comment 3 Wayne Rasband 2012-09-18 19:12:03 CDT

The 3D Manager assumes the ROI Manager is using an AWT List but, in ImageJ 1.47c and later, it uses a JList. This change was made because the ROI Manager was unbearably slow when loading loading large ROI sets (e.g., 50,000 ROIs). I will try to modify the 3D Manager so that it works with ImageJ 1.47c and later.

Comment 4 Johannes Schindelin 2012-09-18 20:05:35 CDT

Good to know. This change breaks quite a couple of plugins I wrote over the years for some users. FWIW I needed to access the AWT list to get the ROIs in their displayed order, there is no other API to get at them in that way.

Comment 5 Johannes Schindelin 2012-09-18 20:34:35 CDT

Also, it would be nice if the fix did not prevent the plugin from running in ImageJ versions prior to 1.47c. Thanks!

Comment 6 Wayne Rasband 2012-09-18 20:41:25 CDT

The getRoisAsArray() method should return the ROIs in the displayed order. For example, this test program lists the ROIs in the displayed order.

  rm = RoiManager.getInstance();
  rois = rm.getRoisAsArray();
  for (i=0; i<rois.length; i++)
     print(i+" "+rois[i].getName());

Comment 7 Wayne Rasband 2012-09-28 18:21:41 CDT

There is a new version of the 3D ROI Manager at

  http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

that avoids this bug by being independent the ROI Manager.

Comment 8 Johannes Schindelin 2013-07-07 10:03:43 CDT

Jan, does this resolve your issue?

Comment 9 Johannes Schindelin 2013-07-07 10:54:13 CDT

On Sun, 7 Jul 2013, BioVoxxel wrote:

> This issue was solved with the new version of the 3D Roi Manager.
> Thanks,
> Jan