Images to Stack

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Images to Stack

Alex-2
This seems like it should be an easy one but I can't figure out how to merge all open images (ImagePlus Objects) to a stack in my Jython script.
Any help would be greatly appreciated.
Thanks
Alex

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Re: Images to Stack

Albert Cardona-2
See: https://www.ini.uzh.ch/~acardona/fiji-tutorial/#grabbing-an-open-image

See where it grabs the list of open images from the WindowManager. Then create an ImageStack and add all the .getProcessor() as slices.

Albert


> On Jul 6, 2018, at 10:06 PM, Alex <[hidden email]> wrote:
>
> This seems like it should be an easy one but I can't figure out how to merge all open images (ImagePlus Objects) to a stack in my Jython script.
> Any help would be greatly appreciated.
> Thanks
> Alex
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Images to Stack

Alex-2
 Thanks Albert ...

Hugely helpful resource.  It does raise a question though.  In ImageJ scripting it appears there are multiple ways to achieve the same result.  For exampleusing IJ.run() or IJ.saveas() vs. lower level level APIs.  What is the best practice for when each should be used?
Alex

    On Saturday, July 7, 2018, 3:08:44 AM PDT, Albert Cardona <[hidden email]> wrote:  
 
 See: https://www.ini.uzh.ch/~acardona/fiji-tutorial/#grabbing-an-open-image

See where it grabs the list of open images from the WindowManager. Then create an ImageStack and add all the .getProcessor() as slices.

Albert


> On Jul 6, 2018, at 10:06 PM, Alex <[hidden email]> wrote:
>
> This seems like it should be an easy one but I can't figure out how to merge all open images (ImagePlus Objects) to a stack in my Jython script.
> Any help would be greatly appreciated.
> Thanks
> Alex
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html 

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Re: Images to Stack

Albert Cardona-2
Best practice: readability first.

I tend to use the "low"-level API (ImageJ's classes) because I know it well and is well documented. But that's because of my particular circumstance.

Albert

> On Jul 7, 2018, at 1:47 PM, Alex <[hidden email]> wrote:
>
> Thanks Albert ...
>
> Hugely helpful resource.  It does raise a question though.  In ImageJ scripting it appears there are multiple ways to achieve the same result.  For exampleusing IJ.run() or IJ.saveas() vs. lower level level APIs.  What is the best practice for when each should be used?
> Alex
>
>    On Saturday, July 7, 2018, 3:08:44 AM PDT, Albert Cardona <[hidden email]> wrote:  
>
> See: https://www.ini.uzh.ch/~acardona/fiji-tutorial/#grabbing-an-open-image
>
> See where it grabs the list of open images from the WindowManager. Then create an ImageStack and add all the .getProcessor() as slices.
>
> Albert
>
>
>> On Jul 6, 2018, at 10:06 PM, Alex <[hidden email]> wrote:
>>
>> This seems like it should be an easy one but I can't figure out how to merge all open images (ImagePlus Objects) to a stack in my Jython script.
>> Any help would be greatly appreciated.
>> Thanks
>> Alex
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html 
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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