Get "Direction (°)" from Directionality using an IJ1 Macro

Development
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#1

Hello,

I’m trying to write a macro that utilizes the Analyze > Directionality plugin. After running the plugin, a (what appears to be a) javascript window pops up and displays generated statistics from the analysis. I want to extract the value of the “Direction (°)” and assign that value to a variable in my macro.

I have tried using “getResult” but the table doesn’t seem to be a normal FIJI Result table (aside from its irregular name). So the solution here didn’t seem relevant to me.

Does anyone know how to do this?

Below is the code that I am working with. The unsuccessful things that I have tried are commented out.

run("Z Project...", "projection=[Average Intensity]");
run("8-bit");
run("Directionality", "method=[Local gradient orientation] nbins=90 histogram=-90");
//IJ.renameResults("Directionality analysis for AVG_0096 (using Local gradient orientation)","Results");
//getResult("Direction (°)",1)
#2

The getResult() and IJ.renameResults() macro functions do not work with the table produced by the Directionality plugin because it is a JTable. There may be a way in a script or plugin to get a reference to this JTable (it’s not listed in the Window menu) and to access its cells.

2 Likes
#3

As @Wayne said, the displayed table is not an ImageJ ResultsTable. You can resort to scripting as explained in the plugin documentation:

For example, you can use the following Groovy script from the script editor:

#@ ImagePlus imp
#@ ResultsTable rt

import fiji.analyze.directionality.Directionality_

d = new Directionality_()

d.setImagePlus(imp)
d.computeHistograms()
d.fitHistograms()

result = d.getFitAnalysis()

mainDirection = Math.toDegrees(result[0][0])

rt.incrementCounter()
rt.addValue("Main Direction", mainDirection)
rt.show("Results")

If you save this script in a subfolder of Fiji’s scripts directory, e.g. as ./Fiji.app/scripts/Analyze/Get_Main_Direction.groovy, and restart Fiji, you’ll then be able to run it from the menu and record its usage with the macro recorder, which will record something like:

run("Get Main Direction");

Subsequently you can get the value from the standard results table in the way you tried.

4 Likes
#4

Wow thank you! Great to learn about this technique!

#5

I came across this thread trying to batch the Directionality analysis. For anyone interested here is an implementation for batch processing and returning all 4 Directionality parameters in a results table:

https://bitbucket.org/davemason/gvy_batchdirectionality/src/master/

Thanks to @imagejan for the code to get me started!

#6

Dear Jan,
This seems to be a good solution, but I am not getting the groovy code to work. I first copied the example code into a new Fiji sheet and changed it to record ‘dispersal’ because that is my interest from Directionality. I saved the code as a groovy file in scripts and created an ‘Analyze’ folder and saved it there. Then after restarting FIJI it still tells me "unrecognized command.
the macro I am writing:

run("Duplicate...", "title=temp");
run("Select None");
setTool("elliptical");
waitForUser("Selection","Select an elipse around the line you want to analyze");
run("8-bit");
run("Directionality", "method=[Local gradient orientation] nbins=90 histogram=-90");
run("Get_Dispersal.groovy");
Ldisp = getResult()
{close("temp");}

How to fix?
Best,
Freerk

#7

The macro command to call the script needs to correspond to the menu entry, not the file name.

That means, if you saved your script e.g. under Fiji.app/scripts/My_Scripts/Get_Dispersal.groovy, it will show up in the menu at My Scripts > Get Dispersal, and the macro recorder will record the following command when you run it:

run("Get Dispersal");