[ImageJ-devel] Bug? using ConnectedComponents and LabelRegion(s) with ImageJFunctions.wrapByte(ImagePlus imp)

[Jay Warrick]

Curtis - Thanks so much for digging. This focuses my efforts greatly. 

Tobias - If you see this email... I noticed that you are listed as author of the ConnectedComponents class. Any thoughts as I dig in?

Thanks,

Jay

> On Jun 30, 2015, at 12:34 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> 
> Hi Jay,
> 
> Interesting bug. I did some digging. The two Img<UnsignedByteType> instances are identical in terms of dimensionality and pixel values, so that isn't the culprit.
> 
> I also tried disabling the labeling computation for SCIFIO to see if it was an issue of tainted state, but the order of computation doesn't seem to make a difference either.
> 
> I also stepped a bit with the debugger and certainly the issue is inside of ConnectedComponents.labelAllConnectedComponents. On line 115, the value of numLabels comes back as 2 for the SCIFIO image and 1 for the IJ1 image. Digging deeper becomes tricky due to the multithreadedness of the algorithm, but I fear that's what you'll have to do in order to isolate the difference in behavior.
> 
> Regards,
> Curtis
> 
> On Tue, Jun 30, 2015 at 1:01 AM, Jay Warrick <warrick at wisc.edu <mailto:warrick at wisc.edu>> wrote:
> Hi All,
> 
> I am getting different behavior using the new ConnectedComponents class of imglib2-algorithm depending on whether I get and Img<UnsignedByteType> from a SCIFIO ImageOpener vs. when I get the same image as an Img<UnsignedByteType> by wrapping an ImagePlus. In the SCIFIO case, ConnectedComponents finds the expected single circle while with a wrapped ImagePlus, it doesn't find any regions.
> 
> Any thoughts/fixes? Might there be something occurring during the wrapping process to cause an issue? Here is a tiny commented maven project with the example scenario.
> 
> https://github.com/jaywarrick/ConnectedComponentsTest <https://github.com/jaywarrick/ConnectedComponentsTest>
> 
> The tiny .tif I'm using is included in the project but is loaded by a string path. Thus, you need to retype the path to the image to match your computer, but that should be it. Sorry... wasn't sure how to avoid that easily.
> 
> Thanks for your help,
> 
> Jay
> 
> 
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