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Bug 300 - Graph cut segmentation cannot be run twice
Graph cut segmentation cannot be run twice
Status: RESOLVED REMIND
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Graph cut segmentation cannot be run ...
Depends on:
Blocks:
 
Reported: 2011-04-16 14:41 CDT by G. Landini
Modified: 2012-01-06 00:22 CST
1 user (show)

See Also:
Description G. Landini 2011-04-16 14:41:49 CDT 
[Enter details of the problem or bug and how to reproduce it here.]

Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => amd64
  os.name => Linux
  os.version => 2.6.37.1-1.2-desktop
  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.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /usr/lib64/jvm/java
  fiji.dir => /home/gabriel/fiji

Information about the version of each plugin:

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Comment 1 G. Landini 2011-04-16 14:45:26 CDT 
I can segment an image, but if I need to change the Potts weight and re-segment it, the plugin does nothing. 
Maybe one should be able to re-segment as many times as possible to fine tune the Potts weight.
Comment 2 Jan Funke 2011-04-18 15:30:14 CDT 
Is it possible that you provide a step-by-step description and maybe even the image you are trying to segment? Is there some output on the console? I can't reproduce your bug...
Comment 3 G. Landini 2011-04-18 15:44:05 CDT 
Well I now realise that yes I can run it twice... (different machine) I could not last time I tried.

I also run into a problem when Toggle overlay off, which I get this error (not always):
java.lang.NullPointerException
        at Graph_Cut$GraphCutWindow.toggleOverlay(Graph_Cut.java:440)
        at Graph_Cut$GraphCutWindow$1$1.run(Graph_Cut.java:243)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)



Furthermore, wouldn't it make sense to re-segment the image automatically as soon as one releases the Potts weight slider?

And another question... why does the result gets hat blocky?
Cheers
G.
Comment 4 Jan Funke 2011-04-21 12:14:31 CDT 
Can you see if the development version (branch "graphcut") works for the overlay problem you reported?

I don't think that automatic segmentation on slider changes is what everyone wants. For big images this can take a while.

The blockyiness comes from the Potts-term in a 4-neighborhood. The development version (branch "graphcut") uses a 8-neighborhood which helps a little. You can also give a gray-scale image for local Potts weights. However, the interface needs some cleanup.
Comment 5 Johannes Schindelin 2011-04-23 10:16:17 CDT 
For easier testing, I checked out that branch, built the plugin and uploaded it to http://pacific.mpi-cbg.de/snaps/Graph_Cut.jar
Comment 6 G. Landini 2011-04-23 13:01:57 CDT 
Thanks Dscho for making the jar file and thanks Jan, this new version seems much more useful, and I have not had the loss of control I originally had.

I hope the feedback below is useful to improve the plugin.

I appreciate that with more sliders updating the image every time it might take long to update on large images, but isn't that what everybody would do anyway? 
I doubt that a user would move the sliders but do not segment the image after that. Possible, but not very likely, no? 
The only reason I see why not to update with slider change is if for every movement of the slider the segmentation is computed. I think that lots of plugins have this undesirable behaviour (for example Kai's excellent volume viewer and 3D interactive surface plot). The computation should be done when the slider is *released*, not while it is being moved. (Easy to say, no idea how this could be achieved).
What about a checkbox that lets you have both behaviours (update result with slider change or something like that)?

Another idea: having the colour overlay show the result and then have a button to generate the mask at the end, like the Create Result button of the Trainable Segmentation?

Observation, the colours chosen for the thresholded overlay will be very difficult to see for deuteranopes (green colour blinds). What about changing this to blue and yellowish orange? 

The 2nd slider is very sensitive for small settings but not so much for large ones. Maybe introducing some scaling, like taking the logarithm or the square root of the slider position value would morethe control easoer?

Related to this, it would be useful to know what the slider values are, so one can reproduce settings. Maybe a text box next to the slider reporting the setting values? Or make it possible to call the segmentation from a macro with the position of the 3 sliders. 

I could not find a difference iin the results by changing the third slider.
The "Create sequence" button is also a mystery. :-)

But in all, yest the results look much better than the previous version.
Cheers

Gabriel
Comment 7 Johannes Schindelin 2011-10-20 02:10:15 CDT 
So... can we close this bug?
Comment 8 G. Landini 2011-10-20 11:19:43 CDT 
You can close it, but as mentioned before the interface of this plugin is not right or particularly useful despite this being a potentially useful plugin.

1. What this should have is a listener on the slider that computes the overlay when released or when the value changes.
Then the "Segment image" button should open the binarised image of the current overlay shown... but the overlay is not computed unless you segment the image, so one does not know what is being segmented. It would be very useful to have such interactivity like in other thresholder plugins.

2. There is no way of repeating the segmentation as it is impossible to know what the slider setting is, let alone reproduce it.
It seems to me tricky to control 1001 settings with a 165 or so pixel slider. What this needs is a box that reports the setting of the slider and allows entry of any number by hand if required.

3. Overlay colours (red and green...) are not use *at all* for colour blind people. These should be blue & yellow or green & magenta; there is little excuse to do it otherwise.

4. It is not recordable.
Comment 9 Johannes Schindelin 2012-01-06 00:22:41 CST 
Hopefully Jan will address the issues some day.