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imageCalculator in macro

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jlongy

imageCalculator in macro

Dear ImageJ Mailing List -

I'm trying to automate a series of ImageCalculator commands with an ImageJ macro after asking the user to choose which images to work with.
It's not working, I suspect some syntax problem I can't identify. I'd greatly appreciate any help at all, I've been round and round the archives but don't know what I'm looking for!

Thank you in advance,
Jennifer

-------------------------------
var msNIR;
var msR;
var idNIR;
var idR;
macro "myMacro" {
// Assumes at least 2 open images, asks user to choose the images to add together
allopen=newArray(nImages+1);
if (nImages==0)
exit("open some images!!");
else {
setBatchMode(true);
for(i=1; i<nImages+1; i++){
selectImage(i);
allopen[i] = getTitle;
}
}
allopen[0] = "Choose open image";
//Create dialog box to ask user to identify the two images
//Return user choices to appropriate variables
title = "Select Choices";
width = 512; height = 512;
Dialog.create("Select Choices");
Dialog.addChoice("NIR:", allopen, msNIR);
Dialog.addChoice("Red:", allopen, msR);
Dialog.show();
msNIR=Dialog.getChoice();
msR=Dialog.getChoice();

selectWindow(msNIR);
idNIR = getImageID();
selectWindow(msR);
idR = getImageID();
// All the above seems to work fine! I can put in print commands and I get back reasonable image names and id numbers
imageCalculator("Add create", idNIR, idR); // This is where it goes wrong! This line won't execute!
}

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Michael Schmid

Re: imageCalculator in macro

Hi Jennifer,

you have set BatchMode, so the resulting image won't be displayed.
You can add at the end
setBatchMode("exit and display");

Then all images created during the BatchMode macro will be shown.

Michael
________________________________________________________________
On Apr 2, 2015, at 11:07, Longyear, Jennifer wrote:

> Dear ImageJ Mailing List -
>
> I'm trying to automate a series of ImageCalculator commands with an ImageJ macro after asking the user to choose which images to work with.
> It's not working, I suspect some syntax problem I can't identify. I'd greatly appreciate any help at all, I've been round and round the archives but don't know what I'm looking for!
>
> Thank you in advance,
> Jennifer
>
> -------------------------------
> var msNIR;
> var msR;
> var idNIR;
> var idR;
> macro "myMacro" {
> // Assumes at least 2 open images, asks user to choose the images to add together
> allopen=newArray(nImages+1);
> if (nImages==0)
> exit("open some images!!");
> else {
> setBatchMode(true);
> for(i=1; i<nImages+1; i++){
> selectImage(i);
> allopen[i] = getTitle;
> }
> }
> allopen[0] = "Choose open image";
> //Create dialog box to ask user to identify the two images
> //Return user choices to appropriate variables
> title = "Select Choices";
> width = 512; height = 512;
> Dialog.create("Select Choices");
> Dialog.addChoice("NIR:", allopen, msNIR);
> Dialog.addChoice("Red:", allopen, msR);
> Dialog.show();
> msNIR=Dialog.getChoice();
> msR=Dialog.getChoice();
>
> selectWindow(msNIR);
> idNIR = getImageID();
> selectWindow(msR);
> idR = getImageID();
> // All the above seems to work fine! I can put in print commands and I get back reasonable image names and id numbers
> imageCalculator("Add create", idNIR, idR); // This is where it goes wrong! This line won't execute!
> }
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

jlongy

Re: imageCalculator in macro

Michael,
Thank you so much!
Jennifer

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Schmid
Sent: 02 April 2015 11:05
To: [hidden email]
Subject: Re: imageCalculator in macro

Hi Jennifer,

you have set BatchMode, so the resulting image won't be displayed.
You can add at the end
setBatchMode("exit and display");

Then all images created during the BatchMode macro will be shown.

Michael
________________________________________________________________
On Apr 2, 2015, at 11:07, Longyear, Jennifer wrote:

> Dear ImageJ Mailing List -
>
> I'm trying to automate a series of ImageCalculator commands with an ImageJ macro after asking the user to choose which images to work with.
> It's not working, I suspect some syntax problem I can't identify. I'd greatly appreciate any help at all, I've been round and round the archives but don't know what I'm looking for!
>
> Thank you in advance,
> Jennifer
>
> -------------------------------
> var msNIR;
> var msR;
> var idNIR;
> var idR;
> macro "myMacro" {
> // Assumes at least 2 open images, asks user to choose the images to
> add together allopen=newArray(nImages+1); if (nImages==0)
> exit("open some images!!");
> else {
> setBatchMode(true);
> for(i=1; i<nImages+1; i++){
> selectImage(i);
> allopen[i] = getTitle;
> }
> }
> allopen[0] = "Choose open image";
> //Create dialog box to ask user to identify the two images //Return
> user choices to appropriate variables title = "Select Choices"; width
> = 512; height = 512; Dialog.create("Select Choices");
> Dialog.addChoice("NIR:", allopen, msNIR); Dialog.addChoice("Red:",
> allopen, msR); Dialog.show(); msNIR=Dialog.getChoice();
> msR=Dialog.getChoice();
>
> selectWindow(msNIR);
> idNIR = getImageID();
> selectWindow(msR);
> idR = getImageID();
> // All the above seems to work fine! I can put in print commands and
> I get back reasonable image names and id numbers imageCalculator("Add create", idNIR, idR); // This is where it goes wrong! This line won't execute!
> }
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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