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Bug 806 - Trackmate LoG detector
Trackmate LoG detector
Product: Fiji
Classification: Unclassified
Component: Plugins
PC Windows
: P4 normal
Assigned To: Jean-Yves Tinevez
Depends on:
Reported: 2014-06-20 05:30 CDT by Sébastien Tosi
Modified: 2014-06-25 10:02 CDT
4 users (show)

See Also:

Description Sébastien Tosi 2014-06-20 05:30:24 CDT
Trackmate LoG detector apprently runs endlessly without providing any output (tested on different time-lapses and for different threshold values). DoG is working fine.

Information about your version of Java:

  os.arch => amd64 => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc. => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07 => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc. => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: E:\
  imagej.dir => E:\

Information about the version of each plugin:

Activated update sites:
ImageJ: (last check:20140620040617)
Fiji: (last check:20140618220039)
MOSAIC ToolSuite: (last check:20140618180410)
Comment 1 Jean-Yves Tinevez 2014-06-20 05:43:59 CDT
After full update on a Mac, I cannot reproduce.
I therefore need a PC to investigate. Please standby.
Comment 2 Sébastien Tosi 2014-06-20 06:05:20 CDT
To be more specific the plugin does not completely freeze but the "preview" button simply stays grayed out endlessly. It is possible to proceed to the next step but then no spot are detected.
Comment 3 Jean-Yves Tinevez 2014-06-20 14:57:32 CDT
I tested on my win7 PC x64, and everything is working fine, from LoG to 3D viewing of tracks. I can only suspect some problems with the Mosaic update site. Could you try to remove it?
Comment 4 Sébastien Tosi 2014-06-25 09:19:36 CDT
If I remove MOSAIC update site the LoG detector is indeed working normally.
Comment 5 Jean-Yves Tinevez 2014-06-25 09:21:12 CDT
Woao that's crazy.
I guess they depend on a custom imglib2. If it's ok with you I will close this bug and put a warning on the TrackMate page.
Comment 6 Sébastien Tosi 2014-06-25 09:23:20 CDT
Please do so!
Comment 7 Jean-Yves Tinevez 2014-06-25 09:24:53 CDT

They somehow impact the FFT code used for LoG (which explains why only the LoG detector is affected):

25/06/14 16:29:25,214 [0x0-0x1fb1fb].org.fiji: Exception in thread "TrackMate preview detection thread" java.lang.NoSuchMethodError: net.imglib2.algorithm.fft2.FFTConvolution.setNumThreads(I)V
25/06/14 16:29:25,215 [0x0-0x1fb1fb].org.fiji: 	at fiji.plugin.trackmate.detection.LogDetector.process(
25/06/14 16:29:25,215 [0x0-0x1fb1fb].org.fiji: 	at fiji.plugin.trackmate.TrackMate$
25/06/14 16:29:25,215 [0x0-0x1fb1fb].org.fiji: 	at net.imglib2.multithreading.SimpleMultiThreading.startAndJoin(
25/06/14 16:29:25,215 [0x0-0x1fb1fb].org.fiji: 	at fiji.plugin.trackmate.TrackMate.execDetection(
25/06/14 16:29:25,215 [0x0-0x1fb1fb].org.fiji: 	at fiji.plugin.trackmate.gui.panels.detector.LogDetectorConfigurationPanel$
Comment 8 Johannes Schindelin 2014-06-25 10:02:34 CDT
Thanks all!

The problem with the incompatible ImgLib2 versions will hopefully be addressed in October at a hackathon dedicated to releasing a first stable version of ImgLib2. The API should evolve in a SemVer-compatible manner from then on.