Re: Macro/plugin for image calculations: is this possible?

Posted by J PIke on May 16, 2007; 4:43pm
URL: http://imagej.273.s1.nabble.com/Macro-plugin-for-image-calculations-is-this-possible-tp3687283p3687286.html

As you say it is does seem quiet managable. However, I've written a macro which I'm having a problem getting to work (below). If I put in a value instead of a getResult command it works fine e.g.

Replace:

NIRcal = getResult("Mean",nResults-1);

with:

NIRcal = "value=70.000";

I find this strange as if I display NIRcal e.g. print(NIRcal) it shows the value that I want it to use. It just refuses to use this value in the divide operation.....

 
        x = 1400
        y = 900
        w = 200
        h = 200
        CarRef = "value=18.000"
        run("16-bit");
        makeRectangle(x, y, w, h);
        run("Set Measurements...", "  mean standard min redirect=None decimal=3");
        run("Measure");
        IH = getHeight();
        IW = getWidth();
        makeRectangle(0, 0, IW, IH);
        run("Multiply...", CarRef);
        NIRcal = getResult("Mean",nResults-1);
        run("Divide...", NIRcal);
        makeRectangle(x, y, w, h);
        run("Measure");

Cheers

James

       

Harry Parker wrote

Hello J,

What you want to do is quite easy using a macro. Writing a plugin won't be necessary.

The Macro Recorder is your friend. Read up on how to use it. (Just run it and do what you do to manually calculate your images. Then edit the resulting file to make it more general and allow the  operator to select the files to use.)

If you haven't already, read up the pages of the ImageJ macro language and scan the macro functions page. Scan the list of prewritten macros for valuable examples.

Give it a try and let us know if you get stuck.
 

--  
Harry Parker  
Senior Systems Engineer  
Digital Imaging Systems, Inc.

----- Original Message ----
From: J PIke <[e-mail]>
To: [e-mail]
Sent: Friday, May 11, 2007 1:30:14 PM
Subject: Macro/plugin for image calculations: is this possible?

I have been normalizing images and creating composite images successfully
using imageJ and have written some simple macros to speed up the processing
of the large quantities of images I am analysing. I now want to speed things
up further, the problem which I'm not sure is surmountable is that the
output from one calculation or measurement is the input for the next
calculation.

Briefly, these are pairs of images of the same target captured at different
wavelengths (a,b), the images are normalized to a calibration panel which is
in the image field, a mathematical function is then applied to the 2 images
to create a composite image:

A = (a x 18) / calibration panel value for a
B = (b x 18) / calibration panel value for b

Final composite image = (A – B)/(A + B)

Does somebody know whether it is feasible to write a plugin which when fed
two raw images will output the desired composite image? If so any pointers?

Thanks

P.S. If you’re curious this is to calculate an index of photosynthetic
biomass, the final image is the normalized difference vegetation index
(NDVI) and the two wavelengths are near infrared and red.

--
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