http://imagej.273.s1.nabble.com/Calculating-atan2-on-pixels-from-two-input-images-in-a-macro-tp5007758p5007761.html
out how to get access to the images and buffers you need. Something like
> Hi Adam,
> There is likely a more elegant solution to your question, but until it's
> posted a way to speed up your macro is to put the pixels values for each
> image into arrays and then index them based on the image dimensions. It's
> one of the work arounds suggested for the macro language limitation to 1D
> arrays.
> Using the arrays avoids switching between the three images. It will still
> be limited in speed compared to a plugin and may require a lot of memory
> for the arrays (dependent on your image size). But it will be faster than
> switching between the images and it might get you by until a better
> solution is posted.
> I've pasted an edited version of your code below.
> Best,
> George
>
>
> selectImage(U);
> w = getWidth();
> h = getHeight();
>
> UArray=newArray(w*h);
> QArray=newArray(w*h);
>
> selectImage(U);
> for (y=0; y<h; y++) {
> for (x=0; x<w; x++) {
> UArray[x+(h*y)]=getPixel(x, y);
> }
> }
>
> selectImage(Q);
> for (y=0; y<h; y++) {
> for (x=0; x<w; x++) {
> QArray[x+(h*y)]=getPixel(x, y);
> }
> }
>
> newImage("Ψ", "32-bit", w, h, 1);
> for (y=0; y<h; y++) {
> for (x=0; x<w; x++) {
> setPixel(x, y, 0.5*atan2(UArray[x+(h*y)],QArray[x+(h*y)]));
> }
> }
> updateDisplay();
>
>
> On Thu, May 15, 2014 at 2:46 PM,
[hidden email] <
[hidden email]
> >wrote:
>
> > Hello all,
> >
> > *My Question:*
> > Is there a way of creating a new image (in a reasonable amount of time)
> > from
> > the atan2 value calculated from the pixel values of two input images, in
> an
> > imageJ macro? Can this be done within a macro or will this require a
> script
> > or plugin?
> >
> > *Background on what I'm doing and what I've attempted:*
> > I have been writing a macro to calculate intensity (/I/), degree of
> linear
> > polarization (/p/), and angle of polarization (Ψ) from a set of four
> > photographs taken with a polarizing filter at different angles (0, 45,
> 90,
> > 135) ( addition info on polarimetry measurements
> > <
> >
>
https://casper.berkeley.edu/astrobaki/index.php/Polarization#Stokes_Q__U:_linear_polarization> > >
> > ). I have created the macro work on multiple sets of such images.
> >
> > I am able to calculate /I/ & /p/ without to much trouble using the image
> > calculator and the process>math functions. I have hit a roadblock with
> > calculating Ψ though. The formula to calculate Ψ is:
> >
> > Ψ = 0.5*atan(/U///Q/)
> >
> > U & Q are stokes parameters calculated from intensity values from the
> > images (see link above)
> >
> > Unfortunately atan have different values depending on the sign of the two
> > inputs, so I cannot simply divide U by Q and take the atan of the value
> > like
> > this:
> >
> > imageCalculator("Divide create 32-bit", "U","Q");
> > selectWindow("Result of U");
> > run("Macro...", "code=v=0.5*atan(v)");
> >
> > The atan2 function takes the different values into account but requires
> two
> > inputs and must be iterated over each pixel. I've tried the code below
> but
> > it is incredibly slow.
> >
> > selectImage(U);
> > w = getWidth();
> > h = getHeight();
> > newImage("Ψ", "32-bit", w, h, 1)
> > for (y=0; y<h; y++) {
> > for (x=0; x<w; x++) {
> > selectImage(U)
> > Upixel=getPixel(x, y);
> > selectImage(Q)
> > Qpixel=getPixel(x, y);
> > setPixel(x, y, 0.5*atan2(Upixel, Qpixel))
> > }
> > }
> > updateDisplay();
> >
> > Fiji has the Image Expression Parser which does exactly what I want
> > (0.5*atan2(A,B)), but at least I haven't figured out a way to pass
> > arguments
> > to the Parser from a macro.
> >
> > I know this is possible to calculate within a plugin, but I have yet to
> > find
> > one that I can incorporate into my macro. Any idea how to calculate this
> in
> > my macro would be appreciated. Would this particular task be better
> suited
> > to a script or plugin? I can post my code thus far if it would be
> helpful.
> >
> > Thanks,
> > Adam Blake
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > View this message in context:
> >
>
http://imagej.1557.x6.nabble.com/Calculating-atan2-on-pixels-from-two-input-images-in-a-macro-tp5007758.html> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>