macro - array elements as options in run()

[ved sharma]

Hi,

I am writing a macro, where I create a newArray() to store names of all the open files. When I run Combine... command to combine the first two files (array elements [0] and [1]) as:

run("Combine...", "stack1=&filenames[0] stack2=&filenames[1]");

It gives me an error "filenames[0] is not a valid choice for Stack1". But, if I assign the array elements to different variables and pass those variables, then it works:

a = filenames[0];
b = filenames[1];
run("Combine...", "stack1=&a stack2=&b");

Is there a way to pass array elements as options to the run command?

Thanks,

Ved
________________________________
Ved Sharma, PhD
Department of Anatomy and Structural Biology
Albert Einstein College of Medicine
Bronx, New York

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[Aryeh Weiss]

Since I did not see another reply, I will suggest something.

On 8/23/15 6:21 AM, Ved Sharma wrote:

> Hi,
>
> I am writing a macro, where I create a newArray() to store names of all the open files. When I run Combine... command to combine the first two files (array elements [0] and [1]) as:
>
> run("Combine...", "stack1=&filenames[0] stack2=&filenames[1]");
>
> It gives me an error "filenames[0] is not a valid choice for Stack1". But, if I assign the array elements to different variables and pass those variables, then it works:
>
> a = filenames[0];
> b = filenames[1];
> run("Combine...", "stack1=&a stack2=&b");
>
> Is there a way to pass array elements as options to the run command?

Try the "old fashioned" way:

run("Combine...", "stack1="+filenames[0]+" stack2="+filenames[1]);

This explicitly builds the string, and does not depend on the parser's ability to understand
&filenames[0]

> Thanks,
>
> Ved
> ________________________________
> Ved Sharma, PhD
> Department of Anatomy and Structural Biology
> Albert Einstein College of Medicine
> Bronx, New York
>
>

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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[Cammer, Michael]

Make a loop that adds elements to a string.  Then put the string in the run command.

Like this


var thresholds = newArray(16, 32, 48, 64, 80);

// some other stuff here, then...

  outputString = "";
  for (t=0; t<thresholds.length; t++) {
     for (z=0; z<a.length; z++) {
       if ( (a[z]<thresholds[t]) || (b[z] < thresholds[t])  ) { a[z] = 0;  b[z] = 0; }
    }
    coef = calculateCoefficient(a, b);  
    outputString = outputString + coef + " \t ";
  }  // for t, report at each threshold
 
  print (outputString);



_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
http://microscopynotes.com/
Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Aryeh Weiss [[hidden email]]
Sent: Sunday, August 23, 2015 12:17 PM
To: [hidden email]
Subject: Re: macro - array elements as options in run()

Since I did not see another reply, I will suggest something.

On 8/23/15 6:21 AM, Ved Sharma wrote:

> Hi,
>
> I am writing a macro, where I create a newArray() to store names of all the open files. When I run Combine... command to combine the first two files (array elements [0] and [1]) as:
>
> run("Combine...", "stack1=&filenames[0] stack2=&filenames[1]");
>
> It gives me an error "filenames[0] is not a valid choice for Stack1". But, if I assign the array elements to different variables and pass those variables, then it works:
>
> a = filenames[0];
> b = filenames[1];
> run("Combine...", "stack1=&a stack2=&b");
>
> Is there a way to pass array elements as options to the run command?

Try the "old fashioned" way:

run("Combine...", "stack1="+filenames[0]+" stack2="+filenames[1]);

This explicitly builds the string, and does not depend on the parser's ability to understand
&filenames[0]

> Thanks,
>
> Ved
> ________________________________
> Ved Sharma, PhD
> Department of Anatomy and Structural Biology
> Albert Einstein College of Medicine
> Bronx, New York
>
>

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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

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[ved sharma]

Hi Aryeh,

Thanks for your reply!

The "old fashioned" way:
run("Combine...", "stack1="+filenames[0]+" stack2="+filenames[1]);

... does not work directly, because in my case filenames[] strings contain spaces. I got it to work by including square brackets as follows:
run("Combine...", "stack1=["+filenames[0]+"] stack2=["+filenames[1]+"]");

... which is OK except I found it a little cumbersome to match all the opening and closing square brackets. Would be much simpler if &filenames[] works!

Ved
________________________________
Ved Sharma, PhD
Department of Anatomy and Structural Biology
Albert Einstein College of Medicine
Bronx, New York

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[karvek]

Hi all,

I have the same problem of Ved but in my case the array is a sequence of number that I would like to use in a run command.

Very short, something like:
t = newArray(0, 30, 60, 90);
for (i=0, i++) {
run("Translate...", "interpolation=None slice y=sin(t[i]) x=cos(t[i]");
}

By using &t[i] there is no way to execute the Macro properly.
If I use "+t[i]+" then the value number is read as a string and cannot perform my operation.

Anyone have any clue how to do this?
Thanks.

Gabriele

[Jan Eglinger]

Hi Gabriele,

you have to use string concatenation in the correct way. The 'y=' and
'x=' are parts of the option string, the values you want to assign are
given by the sin() function:

     t = newArray(0, 30, 60, 90);
     for (i=0; i<t.length; i++) {
         run("Translate...", "interpolation=None slice y=" + sin(t[i]) +
" x=" + cos(t[i]) );
     }


Hope that helps,
Jan


On 28.01.2016 12:30, karvek wrote:

> Hi all,
>
> I have the same problem of Ved but in my case the array is a sequence of
> number that I would like to use in a run command.
>
> Very short, something like:
> t = newArray(0, 30, 60, 90);
> for (i=0, i++) {
> run("Translate...", "interpolation=None slice y=sin(t[i]) x=cos(t[i]");
> }
>
> By using &t[i] there is no way to execute the Macro properly.
> If I use "+t[i]+" then the value number is read as a string and cannot
> perform my operation.
>
> Anyone have any clue how to do this?
> Thanks.
>
> Gabriele
>

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