Re: Trouble with active windows within a loop

Posted by Herbie on Apr 04, 2018; 9:31pm
URL: http://imagej.273.s1.nabble.com/Trouble-with-active-windows-within-a-loop-tp5020382p5020383.html

Good day Samantha,

did you try using the ImageJ macro recorder?

For Java and JavaScript it gives me:

IJ.run(imp, "8-bit", "");

Please note that this is has been cross-posted to the ImageJ-Forum.

Regards

Herbie

:::::::::::::::::::::::::::::::::::
Am 04.04.18 um 22:42 schrieb moxed:

> Scripting newbie here, having trouble calling windows to the front in a for
> loop. As a brief example, I'm trying to write a script (jython) that will
> loop through an array of images and convert them to 8-bit and also set a
> particular threshold.
>
> I can't seem to get the convert to 8bit command to work on all images in the
> array. It looks like only the last image is acted upon.
>
> I think I need to be able to call an image to the front, using the image
> title or ID, but I can't figure out how to do that. Any advice would be
> great.
> (In my real code there are a number of more manipulations, and also more
> than 2 files being processed)
>
>      import os
>      from java.io import File
>      from ij import IJ, Macro, ImagePlus, WindowManager
>      from ij.process import ImageStatistics as IS, ImageProcessor
>      from ij.measure import Measurements
>      from ij.process import ImageConverter
>
>
>      wt_path = "C:/wt.tif"
>      dic_path = "C:/dic.tif"
>
>      wt = IJ.openImage(wt_path)
>      dic = IJ.openImage(dic_path)
>
>      imp = [wt, dic]
>
>      for img in imp:
>          IJ.getImage()
>       IJ.run("8-bit")
>       if img == dic:
>       maxThreshold = wt.getStatistics(Measurements.MIN_MAX).max
>       IJ.setThreshold(0.50*maxThreshold, maxThreshold)
>       print img, "mxt=", maxThreshold
>       else:
>       maxThreshold = img.getStatistics(Measurements.MIN_MAX).max
>       IJ.setThreshold(0.20*maxThreshold, maxThreshold)
>       print img, "mxt=", maxThreshold
>
>
>      print end
>
> The threshold function works perfect, but I can't for the life of me get the
> 8 bit to run.  Only the last image in the array `dic` is converted.
>
> I've also tried:
>      for img in imp:
> ImageConverter.convertToGray8(img)
>
> But that throws an error:
>> TypeError: convertToGray8(): self arg can't be coerced to
>> ij.process.ImageConverter
>
>
> I can't figure out how to call a specific image either by window title or by
> image ID.
>
>
>
> --
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>
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>

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