batch processing for a selection of images

[Finn Peters]

Hi everyone,

I wanted to ask if there is a possibility to apply the
process/batch/macro function to all open images or only a selection of
images within a folder? To batch process all images of a folder is
somewhat inconvenient for me.

cheers,
Finn

[Volker Baecker]

Hello,
to me this is a very important point as well. I wrote a plugin called
Macro_IO_Settings (http://www.mri.cnrs.fr/index.php?m=82) that allows to
setup a list of input files (even if they are in different folders). See
page 18 of http://dev.mri.cnrs.fr/attachments/8/remote-imagej-slides.pdf
to get an idea of how it looks like.
The list is then available from within a plugin. It would be nice if the
process/batch/macro could use this or something similar for its input-files.
Volker
 
On 14/04/11 13:05, Finn Peters wrote:
> Hi everyone,
>
> I wanted to ask if there is a possibility to apply the
> process/batch/macro function to all open images or only a selection of
> images within a folder? To batch process all images of a folder is
> somewhat inconvenient for me.
>
> cheers,
> Finn

[Albert Cardona-2]

2011/4/14 Volker Baecker <[hidden email]>:
> Hello,
> to me this is a very important point as well. I wrote a plugin called
> Macro_IO_Settings (http://www.mri.cnrs.fr/index.php?m=82) that allows to
> setup a list of input files (even if they are in different folders). See
> page 18 of http://dev.mri.cnrs.fr/attachments/8/remote-imagej-slides.pdf
> to get an idea of how it looks like.
> The list is then available from within a plugin. It would be nice if the
> process/batch/macro could use this or something similar for its input-files.
> Volker


You could do it with python: walk a directory and its subdirectories,
inspect each file name and decide if you run the macro, command or
plugin on it. In Fiji, open the "File - New - Script", select
"Language - Python", and type something like:

import os

folder = "/path/to/folder"

for root, dirs, files in os.walk(folder):
  for filename in files:
    if -1 = filename.find("path-of-the-name-we-want"):
      imp = IJ.openImage(root + "/" + filename)
      IJ.run(imp, "Gaussian Blur...", "sigma=2")
      IJ.save(imp, "/new/path/to/" + filename)


Each file of the folder and all its subfolders will be walked.
At each iteration, the root and the files are given, and also any
present subdirectories of root (the "dirs").

Albert

--
http://albert.rierol.net

[Cammer, Michael]

The macro language can get a list of all files in a directory (and can search directories recursively).  We use this to, for example, process all files ending with ".tif" or to process all the "red#####" files one way and "green#######" another way.  For an idea how to implement, start by looking at look at getDirectory(string) at http://rsbweb.nih.gov/ij/developer/macro/functions.html
Cheers,
Michael

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Finn Peters
Sent: Thursday, April 14, 2011 7:06 AM
To: [hidden email]
Subject: batch processing for a selection of images

Hi everyone,

I wanted to ask if there is a possibility to apply the
process/batch/macro function to all open images or only a selection of
images within a folder? To batch process all images of a folder is
somewhat inconvenient for me.

cheers,
Finn

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=================================

[Michael Schmid]

Hi Finn,

if you want to do some processing for all images open in ImageJ, you  
can use a very simple macro:

for (i=1; i<=nImages; i++) {
   selectImage(i);
   processImage();  //or simply put your processing commands here.
}

function processImage() {
   run("Smooth");
   //or whatever operation(s) you like...
   //Make sure you leave no new images open,
   //and don't close the current image.
}

Michael
________________________________________________________________

On 14 Apr 2011, at 13:05, Finn Peters wrote:

> Hi everyone,
>
> I wanted to ask if there is a possibility to apply the process/
> batch/macro function to all open images or only a selection of  
> images within a folder? To batch process all images of a folder is  
> somewhat inconvenient for me.
>
> cheers,
> Finn

[melkor2.0]

Hello, What if operating with all the files within a directory, you want to
separate the channels and make compositions? you should have to identify the
new windows and include in the macro to continue operating... in my case I
want to separate the channels of all the files within a directory, and make
those compositions

On 14 April 011 15:13, Michael Schmid <[hidden email]> wrote:

> Hi Finn,
>
> if you want to do some processing for all images open in ImageJ, you can
> use a very simple macro:
>
> for (i=1; i<=nImages; i++) {
>  selectImage(i);
>  processImage();  //or simply put your processing commands here.
> }
>
> function processImage() {
>  run("Smooth");
>  //or whatever operation(s) you like...
>  //Make sure you leave no new images open,
>  //and don't close the current image.
> }
>
> Michael
> ________________________________________________________________
>
>
> On 14 Apr 2011, at 13:05, Finn Peters wrote:
>
>  Hi everyone,
>>
>> I wanted to ask if there is a possibility to apply the process/batch/macro
>> function to all open images or only a selection of images within a folder?
>> To batch process all images of a folder is somewhat inconvenient for me.
>>
>> cheers,
>> Finn
>>
>

[Albert Cardona-2]

2011/4/14 Ramon <[hidden email]>:
> Hello, What if operating with all the files within a directory, you want to
> separate the channels and make compositions? you should have to identify the
> new windows and include in the macro to continue operating... in my case I
> want to separate the channels of all the files within a directory, and make
> those compositions


Then don't use a macro. Macros work best for recording a sequence of
commands and then wrapping that in a loop and apply it to many images
or many slices of an image.

If your macro opens new windows, its complexity will escalate very
quickly--it's all related to the central concept of the "current
image" in ImageJ. When the current image changes in an unpredictable
way, it's time to use something other than a macro. For example, use a
plugin instead, or a script in python that gives you the same power of
a plugin without having to compile or care about class types.

Albert

--
http://albert.rierol.net

[Michael Schmid]

Hi Ramon,

no problem, you can easily adapt the macro for the case that you want  
to create new windows:

imgArray = newArray(nImages);
for (i=0; i<nImages; i++) {
   selectImage(i+1);
   imgArray[i] = getImageID();
}

//now we have a list of all open images, we can work on it:

for (i=0; i< imgArray.length; i++) {
   selectImage(imgArray[i]);
   //do whatever you like, whether it creates new images or not.
   //e.g.
   if (nSlices() > 1)
      run("Make Montage...");
}


Michael
________________________________________________________________

On 14 Apr 2011, at 15:21, Ramon wrote:

> Hello, What if operating with all the files within a directory, you  
> want to
> separate the channels and make compositions? you should have to  
> identify the
> new windows and include in the macro to continue operating... in my  
> case I
> want to separate the channels of all the files within a directory,  
> and make
> those compositions
>
> On 14 April 011 15:13, Michael Schmid <[hidden email]> wrote:
>
>> Hi Finn,
>>
>> if you want to do some processing for all images open in ImageJ,  
>> you can
>> use a very simple macro:
>>
>> for (i=1; i<=nImages; i++) {
>>  selectImage(i);
>>  processImage();  //or simply put your processing commands here.
>> }
>>
>> function processImage() {
>>  run("Smooth");
>>  //or whatever operation(s) you like...
>>  //Make sure you leave no new images open,
>>  //and don't close the current image.
>> }
>>
>> Michael
>> ________________________________________________________________
>>
>>
>> On 14 Apr 2011, at 13:05, Finn Peters wrote:
>>
>>  Hi everyone,
>>>
>>> I wanted to ask if there is a possibility to apply the process/
>>> batch/macro
>>> function to all open images or only a selection of images within  
>>> a folder?
>>> To batch process all images of a folder is somewhat inconvenient  
>>> for me.
>>>
>>> cheers,
>>> Finn
>>>
>>

[Finn Peters]

Hi Michael,

thanks a lot, this is just what I was looking for.

cheers,

Finn

> Hi Finn,
>
> if you want to do some processing for all images open in ImageJ, you
> can use a very simple macro:
>
> for (i=1; i<=nImages; i++) {
>   selectImage(i);
>   processImage();  //or simply put your processing commands here.
> }
>
> function processImage() {
>   run("Smooth");
>   //or whatever operation(s) you like...
>   //Make sure you leave no new images open,
>   //and don't close the current image.
> }
>
> Michael
> ________________________________________________________________
>
> On 14 Apr 2011, at 13:05, Finn Peters wrote:
>
>> Hi everyone,
>>
>> I wanted to ask if there is a possibility to apply the
>> process/batch/macro function to all open images or only a selection
>> of images within a folder? To batch process all images of a folder is
>> somewhat inconvenient for me.
>>
>> cheers,
>> Finn
>