2018-03-20 22:05 CET

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IDProjectCategoryView StatusLast Update
0001370Orfeo Toolbox (OTB)Generalpublic2017-04-05 10:08
Assigned Topoughov 
PlatformLinuxOSUbuntuOS Version16.04
Summary0001370: Segmentation algorithm doesn't segment the whole image
DescriptionWhen running the otbcli_segmentation shell script, the algorithm doesn't perform the segmentation across the whole image. Sometimes I receive the error:

2017 Mar 16 11:30:06 : Application.logger (INFO) Using watershed segmentation.

2017 Mar 16 11:30:06 : Application.logger (INFO) Large scale segmentation mode which output vector data

Computing watershed segmentation: 33% [**************** ]2017 Mar 16 11:30:27 : Application.logger (FATAL) The following error occurred during application execution : /home/mrashad/dashboard/otb/install-stable/include/ITK-4.10/itkWatershedSegmentTreeGenerator.hxx:437:
itk::ERROR: itk::watershed::SegmentTreeGenerator::MergeSegments:: An unexpected and fatal error has occurred. This is probably the result of overthresholding of the input image.

However, sometimes it reaches 100%, but still produces the same result.

I've tested this on the watershed and meanshift algorithms getting the same error both times.

I had this issue with Pleiades imagery on a much smaller scale, but it is a much larger issue when dealing with Worldview 3 imagery.

Is this a known issue, or is there a parameter I should be adding?
Steps To Reproducewv3_segimg = "/home/williamray/Documents/Building_Recognition/Worldview3/Mexico/image_clip.tif"
segments = "segments.shp"
wv3_segs = "wv3_segs.kea"
# segmentation

os.system("/home/williamray/OTB-5.8.0-Linux64/bin/otbcli_Segmentation -in %s -mode.vector.out %s -filter meanshift" %(wv3_segimg, segments))

    os.system("gdal_rasterize -a DN -tr 2 2 -ot UInt32 -of KEA %s %s" %(segments, wv3_segs))

    rastergis.populateStats(wv3_segs, True, True)
TagsNo tags attached.
Attached Files




Ludovic (developer)


I tried to reproduce your problem with WorldView2 and Pleiades images, but without success.

Could you give us your images where the problem is present (Pleiades or Worldview3) with a link to an host (since the limit on Mantis is of ~2MB) or even the steps to recreate your input data ?



wray_qurus (reporter)

Unfortunately, due to licensing I can't share the imagery. I have played around with several parameters and am getting more stable results now. I believe it is a combination of the area of interest extent, the number of bands and the resolution of the imagery I'm using.


Ludovic (developer)

It is unfortunate, but is it possible to reproduce this bug with images publicly available?

I know that its can take you some time to reproduce this bug with other data, but without that I am not able to fix the problem.

Nevertheless, I am glad that you have find a work around to perform full image segmentation.


poughov (administrator)

Changing to "feedback". We can't investigate unless able to reproduce.

-Issue History
Date Modified Username Field Change
2017-03-16 12:50 wray_qurus New Issue
2017-03-16 12:50 wray_qurus File Added: Segmentation.JPG
2017-03-17 11:37 Ludovic Status new => acknowledged
2017-03-20 10:36 Ludovic Note Added: 0004072
2017-03-22 12:15 wray_qurus Note Added: 0004076
2017-03-23 11:09 Ludovic Note Added: 0004078
2017-04-05 10:08 poughov Note Added: 0004088
2017-04-05 10:08 poughov Assigned To => poughov
2017-04-05 10:08 poughov Status acknowledged => feedback
+Issue History