trouble defining an ROI in python

Posted by Aryeh Weiss on
URL: http://imagej.273.s1.nabble.com/trouble-defining-an-ROI-in-python-tp5020088.html

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
     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)
     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: [phone]


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