[ImageJ-bugs] [Bug 1090] New: TrakEM2 : segmentation with polygon ROI not working

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1090

            Bug ID: 1090
           Summary: TrakEM2 : segmentation with polygon ROI not working
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: Benjamin.Pavie at cme.vib-kuleuven.be
                CC: Benjamin.Pavie at cme.vib-kuleuven.be

I watched the following video
http://www.ini.uzh.ch/~acardona/movies/arealist-create-and-edit.mp4 describing
how to segment in TrakEM2 and at 43 sec, it demonstrates how to use polygon ROI
tool to draw a ROI then use the FIT SPLINE option to get a perfect selection.
Unfortunately, using the last FIJI version available (ImageJ 1.49t), it
impossible to use the polygon ROI tool which is not working anymore. Using it
will just draw a tiny yellow square as a first point and refuse to add a new
one, getting stuck. You can't even unselect the ROI easily. 

According to Wayne Rasband who tested TrakEM2 in ImageJ 1.49s, 1.48, 1.47 and
1.46 and 1.44, it did not work in any of these earlier versions (I add this
comment for the forum):

quoted:
"The problem with the polygon ROI tool in TrakEM2 does not seem to be due to an
ImageJ API change in the last three years. I tried using the tool in ImageJ
1.49s, 1.48, 1.47 and 1.46 and it did not work in any of these earlier
versions..
(...)
The Polygon ROI tool in TrakEM2 does not work with ImageJ 1.44, released in
January 2011. I tried to revert to 1.43 but Fiji would not restart when I
downgraded to that version."

After a quick look of ImageJ source code of the ImageCanvas from ImageJ and the
DisplayCanvas of TrakEM2 plugin, it looks the problem is more coming from the
mouseMoved() method, which in DisplayCanvas doesn't look to manage the tools
Toolbar.POLYGON, Toolbar.POLYLINE, Toolbar.ANGLE.

It looks at some point DisplayCanvas  was taking care of them which will
explain why the video is working with using the Toolbar.POLYGON tool, but now
none of the above tools are doing anything.
Actually, it looks it was using something similar to ImageCanvas and that it
was commented and replaced by a threaded based class (see
https://github.com/trakem2/TrakEM2/blob/master/TrakEM2_/src/main/java/ini/trakem2/display/DisplayCanvas.java#L1317
and
https://github.com/trakem2/TrakEM2/blob/master/TrakEM2_/src/main/java/ini/trakem2/display/DisplayCanvas.java#L1373)
which doesn't handle the above tools.

I am not sure how to change that easily, since I do not know why the default
method has been replaced by the MouseMovedThread class for the mouse moved
event (you must had a good reason).

Information about your version of Java:

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

The up-to-date check says: UPDATEABLE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to:
C:\Users\u0094799\bin\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\u0094799\bin\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150614035343)
Fiji: http://fiji.sc/update/ (last check:20150605150752)

Files not up-to-date:
  03c47575 (LOCAL_ONLY) 20150511162009 plugins/3D_Convex_Hull.jar
  f79be975 (LOCAL_ONLY) 20150414165535 plugins/Auto_Focus.jar
  34e56692 (LOCAL_ONLY) 20150611165214 plugins/BoneJ_.jar
  1f12fc21 (LOCAL_ONLY) 20150610170354 plugins/IntSeg_3D.jar
  5f60d96e (LOCAL_ONLY) 20150427143733 plugins/Watershed_.jar
  6cbd979b (LOCAL_ONLY) 20150527103909 plugins/pagita_.jar

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