Bug 509 – Segmentation Editor doesn't recognize existing label files anymore

Bug 509 - Segmentation Editor doesn't recognize existing label files anymore


Summary:	Segmentation Editor doesn't recognize existing label files anymore

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P5 major
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2012-10-04 13:22 CDT by Till
Modified:	2013-04-30 11:23 CDT
CC List:	2 users (show)

See Also:

Attachments
Information about your version of Java (70.06 KB, text/plain) 2012-10-04 13:22 CDT, Till

Description Till 2012-10-04 13:22:27 CDT

Created attachment 79
Information about your version of Java

Hi,

when I last used the Segmentation Editor (about half a year ago) the following was possible:
I created labels with the plugin Segmentation Editor on a TIFF stack. A file XXX.labels was created that showed these labels. After I clicked "OK" in the Segmentation Editor, I got two stacks, the original stack and the label stack. If I then ran the Segmentation Editor again, the same label file was re-used. In this manner I could modify previous label stacks. As long as it was compatible (regarding slices and file name), a saved label stack could even be loaded and modified at a later point (by running the Segmentation Editor on the image stack).

Now each time I open the Segmentation Editor on an image stack, a new label stack is created, no matter whether one already exists.

It would be great if this little bug could be solved...

Thanks,

Till

Comment 1 Till 2012-10-26 15:48:50 CDT

Hi,
I filed this bug three weeks ago and didn't get any answer yet. It would be great if someone could take a look at this issue.

Thanks,
Till

Comment 2 Johannes Schindelin 2012-10-26 16:22:37 CDT

I am very sorry that I am not at your service 24/7 :-P

Seriously again, I am on the last stretch of a three-week business trip, and I will be pretty busy when I come back home. So unfortunately this bug might need a while still.

Comment 3 Till 2012-12-04 09:40:34 CST

Hi,

I'd like to point your attention to this bug again, it might not be critical for many users, but it is for me...

Thanks,

Till

Comment 4 Daniel Hornung 2013-04-29 11:22:58 CDT

I had the same problem, but found out that fortunately the labels stack was recognized again after saving (Save as > AmiraMesh) and loading (Import > Amira) it again.

After browsing a bit through the code, I think this is because the calibration and size information are added to the image only when saving, although they are required for the image stack to be recognized as a valid labels stack.

A question to those developers who have more insight:

What use is the check for 

info.indexOf("CoordType") >= 0

in line 127 of AmiraParameters.java? To me it doesn't seem to be used anywhere else again, so maybe the check for the "Materials" info is enough?  Omitting the "CoordType" check should resolve this bug.

Comment 5 Johannes Schindelin 2013-04-29 11:59:25 CDT

Daniel, I think you're absolutely correct. That check is back from the days when we still had to verify from the file's first 1k that it is an AmiraMesh.

Would you have time to replace the check and verify that it fixes the bug? If so, I would really be very thankful not only for your work so far, but also for a pull request ;-)

Thanks!

Comment 6 Daniel Hornung 2013-04-29 14:40:56 CDT

Should be fixed by
https://github.com/quazgar/fiji/commit/867445bb8e39b1c14dcb9dcb477cf2140905a0c0

Comment 7 Johannes Schindelin 2013-04-30 11:23:02 CDT

Uploaded. Thank you so much, Daniel!