Struggling to open a list of images (.lif)

[Monarakl]

Hello,

After updating ImageJ, I have problems to run a macro, which
worked perfectly beforehand.

Now the macro works only for the first
image not for all the images that area saved in .lif format (as it
should work). Could anyone help me? Thank you in advance.

The macro
is:

path = getDirectory("SP8 Images");
path2 = getDirectory("Results
of Find Maxima");
listN3 = getFileList(path);
setBatchMode(true);
for
(i=0; i<listN3.length; i++) {
    incomingN3 =
path+File.separator+listN3[i];
    run("Bio-Formats Macro Extensions");

  run("Bio-Formats Windowless Importer", "open=incomingN3");
    title
= getTitle();
    run("Z Project...", "projection=[Max Intensity]");
   
run("Split Channels");
    selectWindow("C2-MAX_" +title);
   
run("Gamma...", "value=1.50");
    run("Gamma...", "value=1.50");
   
run("Gaussian Blur...", "sigma=1");
    run("Find Maxima...", "noise=500
output=Count");
    outFile = path2 +File.separator+ title;
   
saveAs("Measurements", outFile +".csv");
    run("Close");
}

print("
");
print("All done");

Monara


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[Wayne Rasband-2]

> On Mar 21, 2019, at 7:08 AM, MONARA ANGELIM <[hidden email]> wrote:
>
> Hello,
>
> After updating ImageJ, I have problems to run a macro, which
> worked perfectly beforehand.
>
> Now the macro works only for the first
> image not for all the images that area saved in .lif format (as it
> should work). Could anyone help me? Thank you in advance.

In the macro, change

   outFile = path2 +File.separator+ title;

to

   outFile = path2 + ”/“ + title;

and it should work as expected. “/” is a valid file separator on all operating systems, including Windows.

Here is the description of the getFileList() macro function:

Returns an array containing the names of the files in the specified directory path. The names of subdirectories have a "/" appended. For an example, see the ListFilesRecursively macro at

  https://imagej.nih.gov/ij/macros/ListFilesRecursively.txt

-wayne

> The macro
> is:
>
> path = getDirectory("SP8 Images");
> path2 = getDirectory("Results
> of Find Maxima");
> listN3 = getFileList(path);
> setBatchMode(true);
> for
> (i=0; i<listN3.length; i++) {
>    incomingN3 =
> path+File.separator+listN3[i];
>    run("Bio-Formats Macro Extensions");
>
>  run("Bio-Formats Windowless Importer", "open=incomingN3");
>    title
> = getTitle();
>    run("Z Project...", "projection=[Max Intensity]");
>
> run("Split Channels");
>    selectWindow("C2-MAX_" +title);
>
> run("Gamma...", "value=1.50");
>    run("Gamma...", "value=1.50");
>
> run("Gaussian Blur...", "sigma=1");
>    run("Find Maxima...", "noise=500
> output=Count");
>    outFile = path2 +File.separator+ title;
>
> saveAs("Measurements", outFile +".csv");
>    run("Close");
> }
>
> print("
> ");
> print("All done");
>
> Monara

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