http://imagej.273.s1.nabble.com/Macro-for-beginners-tp5010322p5010325.html
I'd add one small thing.. often computers add annoying little files like
> Hi Toufic,
> Here is what I propose. It may be clear enough to answer your questions. I
> added few remarks to clarify.
> Hope it helps !!!
>
> Eric
>
>
> // Gets the name of directories with file separator "\"
>
> input=getDirectory("Choose an Input Folder");
> output=getDirectory("Choose an Output folder");
> Bckgrd=getDirectory("Choose a Background folder");
>
> // goes faster without dispalying images
> setBatchMode(true);
>
>
> // Open the Bcgrd Image
> open(Bckgrd + "background.tif");
>
> // array of names of files in alphabetical order (no needs for specific
> names)
> list = getFileList(input);
>
> //needs open and close brackets to define the input folder loop
> for (i = 0; i < list.length; i++) {
> open(input + list[i]);
> title1=getTitle();
> imageCalculator("Subtract create",list[i] , "background.tif");
> title2=getTitle();
>
> // Save the file with the name "Bckg_"+ original title
> saveAs("jpeg", output+"Bckg_"+title2);
>
> // close the images
> close();
> selectWindow(title1);
> close();
> } // end of loop
>
> selectWindow( "background.tif");
> close();
>
> Le 05/11/2014 20:36, Toufic El Arnaout a écrit :
>
> Hello everyone,I am new to ImageJ and Fiji. I know well now how to use
>> basic macro for batch mode for all basic analysis functions, but cases with
>> variables to read and save. Please help me correct the macro below in red
>> (sorry for the long email).. it will be needed for now and future similar
>> ones.
>> a- I have images in let's say folder A in C:.b- I want those images to
>> have their background removed using image "background.tif".c- Then have the
>> output image for each saved in folder B in C:.d- I might be wrong in some
>> cases, but the setBatchMode was probably added below in a wrong way because
>> I found it in tutorials. I may also have the input and output entries
>> wrongly placed. In addition, I may not need the images to be all opened
>> after processing...e- The sixth line entry, called action is wrong as the
>> software says (I also found it here:
http://fiji.sc/How_to_apply_a_>> common_operation_to_a_complete_directory)
>> Furthermore, let me know how to call the files in this macro. I think
>> this macro assumes that the file name is 0, and next one is 1, 2, 3 etc?
>> What if the file name in stupid cases for example is
>> 1_2014-10-31-153821-0200? and the next one is *-0201, etc (because
>> otherwise, simply renaming 1000 files in Windows by selecting all will make
>> them called 1, 1 (2), 1 (3), etc.... and I assume will be complicated for
>> me to understand for i, i + 1, i + 2 rule...toufic
>>
>>
>> input = "C:\\A\\";output = "C:\\B\\";
>> setBatchMode(true);list = getFileList(input);for (i = 0; i < list.length;
>> i++) action(input, output, list[i]);
>> open(input + filename);open("C:\\background.tif");selectWindow(filename);run("Subtract
>> Background...", "rolling=40 light");imageCalculator("Subtract create",
>> "background.tif", input);selectWindow("Result of
>> background.tif");saveAs("jpeg", output);
>> setBatchMode(false);
>>
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
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