Apply to all files...

[Wilson R S (AT)]

I am thinking someone would probably have already wrote this code/macro, but can't find it...

I want to apply a macro to all files within a certain folder and all its subfolders. I can see how this works in theory with getFileList(Directory), but just can't seem to get the code quite rite.

Any help would be much appreciated.

Rhod

[pang]

Hi, I have following codes might help you. You may want to modify a
little bit to suit your need.

run("Set Measurements...", "area mean standard min integrated median
area_fraction stack limit display redirect=None decimal=3");
run("Clear Results");

dir1 = getDirectory("Choose  Directory ");
list = getFileList(dir1);

setBatchMode(false);
for (i=0;i<list.length;i++) {
   

      if (endsWith(list[i],"tif") || endsWith(list[i],"TIF")){
      open(dir1+ list[i]);
      run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
      run("Measure");
      close();
      }
     else if (endsWith(list[i],"/")) {
     idx2=lengthOf(list[i])-1;
     
     dir2=dir1+substring(list[i],0,idx2);
     list2 = getFileList(dir2);
     for (j=0;j<list2.length;j++) {
     if (endsWith(list2[j],"tif") || endsWith(list2[j],"TIF")){
      open(dir2+"\\"+ list2[j]);
      run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
      run("Measure");
      close();
      }
}
   }

}

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Wilson R S (AT)
Sent: Wednesday, April 06, 2011 9:02 AM
To: [hidden email]
Subject: Apply to all files...

I am thinking someone would probably have already wrote this code/macro,
but can't find it...

I want to apply a macro to all files within a certain folder and all its
subfolders. I can see how this works in theory with
getFileList(Directory), but just can't seem to get the code quite rite.

Any help would be much appreciated.

Rhod

[Albert Cardona-2]

2011/4/6 Wilson R S (AT) <[hidden email]>:
> I am thinking someone would probably have already wrote this code/macro, but can't find it...
>
> I want to apply a macro to all files within a certain folder and all its subfolders. I can see how this works in theory with getFileList(Directory), but just can't seem to get the code quite rite.
>
> Any help would be much appreciated.
>
> Rhod


Considering you want subdirectories as well, I'd do it with a python script:

basedir = "/path/to/root/dir/"

for root, dirs, files in os.walk(basedir):
  for file in files:
    # do something to each file

See examples in Jython here:

http://pacific.mpi-cbg.de/Jython_Scripting



--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona

[Carnë Draug]

Hi Rhod,

I wrote a function some time ago to do it. It returns an array with
all files inside a directory with a specific extension and is
recursive (also looks inside the subdirectory).  It also uses other
functions I wrote to manipulate arrays. I pasted it all on
http://pastebin.com/wtQMSBwm

I'd recommend you place all of them in macros/Library.txt so all your
macros can access them. You can call the function as

file_list = get_cleansed_file_list (dir, extension);

Hope it helps

Carnë

On 6 April 2011 14:02, Wilson R S (AT) <[hidden email]> wrote:
> I am thinking someone would probably have already wrote this code/macro, but can't find it...
>
> I want to apply a macro to all files within a certain folder and all its subfolders. I can see how this works in theory with getFileList(Directory), but just can't seem to get the code quite rite.
>
> Any help would be much appreciated.
>
> Rhod

[Crowell Elizabeth]

Hello,

You are right, you want a recursive loop that uses getFileList, and this
macro is already available from the ImageJ website :
http://rsbweb.nih.gov/ij/macros/BatchProcessFolders.txt
In this macro, the "processFiles" function is the recursive loop that
goes through all folders and subfolders.  Every time an image file is
encountered, the function "processFile" is run.  Use of the countFiles
function is optional.

Normally you simply need to add a few lines in the "processFiles"
function for the commands you want to run on each image, and this macro
should work for you.  Just let me know if you encounter any problem.

Kind Regards,
Elizabeth Crowell




Wilson R S (AT) a écrit :
> I am thinking someone would probably have already wrote this code/macro, but can't find it...
>
> I want to apply a macro to all files within a certain folder and all its subfolders. I can see how this works in theory with getFileList(Directory), but just can't seem to get the code quite rite.
>
> Any help would be much appreciated.
>
> Rhod
>  


--

Elizabeth CROWELL

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Institut Pasteur
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Tel :  [phone]
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