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Re: split channels and all files in a directory

Posted by melkor2.0 on Apr 07, 2011; 4:45pm
URL: http://imagej.273.s1.nabble.com/split-channels-and-all-files-in-a-directory-tp3685101p3685112.html

Thank you very much, the problem is the naming of the images, I want to
separate their channels and then tell the program which images I need to
combine, and then I would need the name of the new image to tell the program
to analyze particles...
Anyway I liker the way of process all files in a directory :)

On 7 April 2011 16:41, vlabrador <[hidden email]> wrote:

> Hi Ramon:
>
> These are the instructions we use to process all the files in a directory:
>
> ******
> origen = getDirectory("Images to process");
> destino = getDirectory("Results");
> lista = getFileList(origen);
> setBatchMode(true);
> for (i=0; i<lista.length; i++) {
>        showProgress(i+1, lista.length);
>        open(origen+lista[i]);
>        nombre = lista[i];
>         (MACRO FUNCTIONS/INSTRUCTIONS HERE)
>        saveAs(".tiff", destino + nombre);
>        close();
>        }
> ******
>
> "Origen" and "destino" are just the names we have given to the variables
> (the path to the Directory and folder where you have your images and where
> you want to save your results).
>
> "nombre" is another variable to save the result image with the same name as
> the original image.
>
> To select a window use this instruction: selectWindow("NAME OF THE
> WINDOW");
>
> An easy way to work with the 3 resultant images after splitting channels is
> to rename the original image:
>
> *******
>         rename("A");
>        run("Split Channels");
>        selectWindow("C2-A");
> *******
>
>
> I hope you find this information useful.
>
> Kind regards,
>
> Veronica
>
>
>
> On Thu, 7 Apr 2011 16:14:38 +0200, Ramon Guirado <[hidden email]>
> wrote:
>
>> In fact I don't know how to identify the new windows created as a result
>> of
>> the image calculation...
>>
>> On 7 April 2011 16:04, Ramon Guirado <[hidden email]> wrote:
>>
>>  Hi, I'm trying to write a macro able to open all the files in a
>>> directory,
>>> split the channels of the images and analyze particles in this separated
>>> channels as well as the composite between some of them (they will be also
>>> binarized, etc...). I have just done small macros using the macro
>>> recorder,
>>> so I don't know how to do it, I'm trying to get the identity of every
>>> image
>>> in a directory and then I guess after the image calculator, I will have
>>> to
>>> identify the new windows just created so they are processed as well, and
>>> then do that recursively, but I feel a little bit lost... which would be
>>> the
>>> easiest way to proceed? by know I'll try to understand the macro posted
>>> by Carnë Draug..
>>>
>>> Thanks,
>>>
>>>
>>> ramon
>>>
>>>