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Re: Directionality Results Table

Posted by ctrueden on Jul 17, 2015; 9:39pm
URL: http://imagej.273.s1.nabble.com/Directionality-Results-Table-tp5013624p5013625.html

Hi Nathan,

Try using batch mode.

http://imagejdocu.tudor.lu/doku.php?id=faq:macros:how_can_i_speed_up_a_macro
http://imagej.net/developer/macro/functions.html#setBatchMode

Regards,
Curtis

On Fri, Jul 17, 2015 at 3:55 PM, Nathan Hotaling <[hidden email]> wrote:

> Hello All,
>
> I am trying to incorporate the directionality plugin into a macro I'm
> writing and would like to have it analyze an image and then have the
> histogram of orientations be saved into a file.  I don't need a plot, and
> ideally I'd like no windows to pop-up while its analyzing.
>
> My problem is that with the code I have below I get three windows that
> pop-up: the results, a plot, and a summary window.  I can save the results
> table and close it but I can't seem to access the plot and the summary
> window from the macro to close them.  Ideally, one of two options would be
> possible:
>
> 1) I access the Directionality plugin without opening any windows and just
> save a histogram of the results (don't need the Gaussian fit that it does
> either) to a .csv
> 2) I access the Directionality plugin and close the plot and summary
> windows and save the results to a .csv
>
> Either is fine, one is obviously a little more clean but I'd take either.
> The reason why the other windows are a problem is because I'd like to batch
> analyze a few hundred images at a time and thus after analyzing the images
> I have to manually close hundreds of pop-up windows (also the hundreds of
> open windows tend to hog a lot of RAM).
>
> Thanks in advance.
>
>     open(name0);
>         run("Invert");
>             run("Skeletonize");
>                     run("Directionality", "method=[Fourier components]
> nbins=180 histogram=-90 display_table");
>             saveAs("Results", path19);
>                 run("Close");
>                     close();
>                 run("Close All");
>
> I'm working with the latest release of FIJI.  I've also attached an
> example segmented image.
>
> Nathan
>
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>

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