Macro for Image sequence

[JakubD]

Hi all,

I am trying to make a macro to process data from MRI (usually many folders at once) in a way that I don't have to do anything else than set the input and output folders. The folder structure is the same for every measurement so, it is a viable approach.

The macro works just as it should untill the moment it is supposed to save the image sequence (alternating 5 or 10 images). It opens the file in folder structure, it creates a folder in the output folder, for an unknown reason it doesn't save anything and even doesn't show a sign of error, closes the images and moves on. Last folder gives an error in a way that there is some bracket expected.

Thank you in advance,
Jakub

Macro

input=input_images+input_folder;
output=output_images + output_folder;


setBatchMode(true);
list = getFileList(input);
list=Array.trim(list, list.length-3); //last 3 files in the folder don't contain images

for (i = 0; i < list.length; i++)
     save_all(input, output, list[i]);
setBatchMode(false);



function save_all(input, output, filename) {

input_file=filename+"pdata\\1\\2dseq";
file=input+input_file;

File.makeDirectory(output+filename)
       
open(file);

fileNameStack="2dseq.png"; //this can be anything as long as there are numbers of the stack position

run("Image Sequence... ", "format=PNG name="+fileNameStack+" digits=2 save=[output+filename]);
        close();
}

[Michael Schmid]

Hi Jakub,

if you write

  run("Image Sequence... ", "format=... save=[output+filename]);

it tries to save the image sequence in a directory named
"output+filename" (literally), not in a directory named according to the
contents of the variables output and filename.
So you need

  run("Image Sequence... ", "format=... save=["+output+filename+"]");

The square brackets are needed to avoid truncating the file path
(output+filename) in case there are spaces in it, they do not prevent
the contents from being interpreted as a String. Example:

   "...save=[/users/jakub/data 1/test 17.png]"

Michael

________________________________________________________________

On 2016-12-02 10:36, JakubD wrote:

> Hi all,
>
> I am trying to make a macro to process data from MRI (usually many folders
> at once) in a way that I don't have to do anything else than set the input
> and output folders. The folder structure is the same for every measurement
> so, it is a viable approach.
>
> The macro works just as it should untill the moment it is supposed to save
> the image sequence (alternating 5 or 10 images). It opens the file in folder
> structure, it creates a folder in the output folder, for an unknown reason
> it doesn't save anything and even doesn't show a sign of error, closes the
> images and moves on. Last folder gives an error in a way that there is some
> bracket expected.
>
> Thank you in advance,
> Jakub
>
> Macro
>
>
> input=input_images+input_folder;
> output=output_images + output_folder;
>
>
> setBatchMode(true);
> list = getFileList(input);
> list=Array.trim(list, list.length-3); //last 3 files in the folder don't
> contain images
>
> for (i = 0; i < list.length; i++)
>      save_all(input, output, list[i]);
> setBatchMode(false);
>
>
>
> function save_all(input, output, filename) {
>
> input_file=filename+"pdata\\1\\2dseq";
> file=input+input_file;
>
> File.makeDirectory(output+filename)
>
> open(file);
>
> fileNameStack="2dseq.png"; //this can be anything as long as there are
> numbers of the stack position
>
> run("Image Sequence... ", "format=PNG name="+fileNameStack+" digits=2
> save=[output+filename]);
> close();
> }
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Macro-for-Image-sequence-tp5017672.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[JakubD]

Hi Michael,

it works perfectly. Thank you a lot.

Jakub