My mistake was using roi = rm.select(i), which returns None.
I needed roi = rm.getRoi(i), which returns an Roi.
On 13/02/2018 21:22, Aryeh Weiss wrote:
>
> I am trying to define an ROI within which teh particle analyzer will
> operate.
>
> so I tried the following
>
> imp.setRoi(rm.select(i)) #rm is an existing RoiManager
>
should be imp.setRoi(rm.getRoi(i))
>
> IJ.run(imp, "Analyze Particles...", "size=1-Infinity summarize
> in_situ")
>
> but this measured on the entire image.
>
> I also tried
>
> options = PA.SHOW_SUMMARY
> parameters = PA.AREA
> rt = ResultsTable()
>
> myPA = PA(options, parameters, rt, 1,100000 )
>
> ip - imp.getProcessor()
>
> roi = rm.select(i)
>
should be rm.getRoi()
>
> imp.setRoi(roi)
> ip.setRoi(roi)
> imp.updateAndDraw()
> myPA.analyze(imp, ip)
>
> In both cases, the measurement is done over the entire image, and not
> within the ROI.
>
> What am I doing wrong?
>
> --aryeh
>
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
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