Macro: How can I create an output files with a name related to the input file?

Usage & Issues
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#1

Hi,

I am very new to programming and have the following issue:

I wrote a Macro which loads images from a user chosen Directory, for instance, “islet1”.

Now I want my images the Macro creates to be saved in a new file on my desktop, termed with the name of the chosen file+_Results, so for the above example: “islet1_results”.

Is that somehow possible? I managed to create an output file but I get stuck when creating a flexible connection to the original file name.

Also I want to save it on my Desktop. Is there a command for that? I only found the command for saving it in the user folder.

This is my very primitive attempt so far:

Bild2

I hope, somebody can help me.

#2

Hi @consti1511 ,

you can keep track of the original image name by using the following at the beginning of the script:

originalName = getTitle();

Possibly there is a file extension at the end of your original file name. You could remove it as follows

originalNameWithoutExt = replace( originalName , ".tif" , "" );

You can then reuse it later on in the macro to define the result image name

resultName = originalNameWithoutExt + "_result.tif";
2 Likes
#3

Good day,

here is a demo macro that does what you want, at least on a mac:

open();
fileName = File.nameWithoutExtension;
path2Desktop = getDirectory("home") + "Desktop/";
save( path2Desktop + fileName + "_results.tif" );

Paste the code to an empty macro window (Plugins >> New >> Macro) and run it.

In general you will have to learn how to use the ImageJ macro language. Here
https://imagej.nih.gov/ij/developer/macro/functions
is a commented list with the available functions and here
https://imagej.nih.gov/ij/developer/macro/macros.html
you find a description of the language.

Regards

Herbie

#4

Hi @anon96376101 Thank you! Thats it!!

Actually I meant a folder, not a file to save on the Desktop, but I changed it a bit and now it works.

However, somehow I am not able to save anything inside the folder. That is what I tried so far.

//Create output directory
home = getDirectory("home") + "Desktop/";
fileName = File.nameWithoutExtension;
folderName = fileName + "_results";
File.makeDirectory(home + folderName);

outputdir = (home + folderName);


//Saving 
selectWindow(ImageTitle + "_Dapi");
saveAs("tiff" + outputdir);

selectWindow(ImageTitle + "_Dapi-inside");
saveAs("tiff", outputdir);

I do not receive an error message, but the folder is empty and the images are not saved anywhere else…

Does anybody know, where the mistake is?

Thanks again for your help!!

#5

Again a demo macro:

open();
fileName = File.nameWithoutExtension;
path2Folder = getDirectory("home") + "Desktop/" + fileName + "_results/";
if ( File.exists( path2Folder) < 1 ) File.makeDirectory( path2Folder );
save( path2Folder + fileName + "_Dapi.tif" );

Please note that in general you need to generate the directory only once.
And please study the documents I’ve mentioned earlier.

HTH

Herbie

#6

Hi @consti1511,

The path used in saveAs has to include the filename as well.

Instead of this:

selectWindow(ImageTitle + "_Dapi");
saveAs("tiff", outputdir);

try this:

newImageName = ImageTitle + "_Dapi.tif";
selectWindow(ImageTitle + "_Dapi");
saveAs("tiff", outputdir+File.separator+newImageName);

The list of macro functions explains the required arguments for the functions, and links to many examples, as @anon96376101 mentioned.

Hope this helps.

How to make a macro ask for a file name before saving a generic Results.xls file?
#7

I got it now, thank you very much!!