images to stack

[Agustin Lobo]

Hi!
Is there any way to add images by name to an stack? My images
are not in the same directory, and prefer not to move/copy them.
I can open them all and the use images to stack, but there are
too many and opening them all represents a memory problem.
I can easily have the names (with their paths) in a list, bit do not
know how to add each image to the stack (and close) within a loop.

Thanks
Agus

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[Agustin Lobo]

Answering myself:
I can open the image and the use
Add Slice, Select All in the new image, and Copy and Paste.
Specifically:
//stack of all CENTERED background images
//we take the name from the imasbackgroundBMP directory
//but actually read from the midastif20121217 where all images (not
only background) live
imasBMPFolder =
"//media/Iomega_HDD/JPIERA/alfacs20121217/MIDAS_alfacs20121217/imasbackgroundBMP/";
imasTIFFolder =
"/media/Iomega_HDD/JPIERA/alfacs20121217/MIDAS_alfacs20121217/midastif20121217/";
images = getFileList(imasBMPFolder);
print(images.length)
open(imasBMPFolder + images[1]);
inputPath = imasTIFFolder + File.nameWithoutExtension + ".tif";
close();
open(inputPath);
run("32-bit");
getStatistics(area, mean, min, max, std);
run("Subtract...", "value=" + mean);
setBatchMode(true);
for (i=1; i<images.length; i++){
        showProgress(i+1, images.length);
        open(imasBMPFolder + images[i]);
        bmpid = getImageID();
        inputima = File.nameWithoutExtension + ".tif";
        inputPath = imasTIFFolder + File.nameWithoutExtension + ".tif";
        selectImage(bmpid);
        close();
        run("Add Slice");
        sliceid = getImageID();
        open(inputPath);
        imaid2 = getImageID();
        run("32-bit");
        getStatistics(area, mean, min, max, std);
        run("Subtract...", "value=" + mean);
        selectWindow(inputima);
        run("Select All");
        run("Copy");
        selectImage(sliceid);
        run("Paste");
        selectWindow(inputima);
        close();
}

Agus

On Thu, Feb 14, 2013 at 5:49 PM, Agustin Lobo <[hidden email]> wrote:

> Hi!
> Is there any way to add images by name to an stack? My images
> are not in the same directory, and prefer not to move/copy them.
> I can open them all and the use images to stack, but there are
> too many and opening them all represents a memory problem.
> I can easily have the names (with their paths) in a list, bit do not
> know how to add each image to the stack (and close) within a loop.
>
> Thanks
> Agus

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Rasband, Wayne (NIH/NIMH) [E]]

On Feb 14, 2013, at 11:49 AM, Agustin Lobo wrote:

> Hi!
> Is there any way to add images by name to an stack? My images
> are not in the same directory, and prefer not to move/copy them.
> I can open them all and the use images to stack, but there are
> too many and opening them all represents a memory problem.
> I can easily have the names (with their paths) in a list, bit do not
> know how to add each image to the stack (and close) within a loop.

You can use the File>Import>Stack from List command, which opens a stack, or virtual stack, from a text file or URL containing a list of image file paths. The images can be in different folders but they must all be the same size and type.

This macro demonstrates how to generate a list of images and then use that list to open the images as a virtual stack:

   http://imagej.nih.gov/ij/macros/VirtualStackFromList.txt

And this one demonstrates how to how to open an image series from a remote server:

   http://imagej.nih.gov/ij/macros/OpenStackUsingURLs.txt

-wayne

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Agustin Lobo]

This alternative is a lot better and more elegant,
Thanks!
Agus



On Sat, Feb 16, 2013 at 3:43 PM, Rasband, Wayne (NIH/NIMH) [E]
<[hidden email]> wrote:

> On Feb 14, 2013, at 11:49 AM, Agustin Lobo wrote:
>
>> Hi!
>> Is there any way to add images by name to an stack? My images
>> are not in the same directory, and prefer not to move/copy them.
>> I can open them all and the use images to stack, but there are
>> too many and opening them all represents a memory problem.
>> I can easily have the names (with their paths) in a list, bit do not
>> know how to add each image to the stack (and close) within a loop.
>
> You can use the File>Import>Stack from List command, which opens a stack, or virtual stack, from a text file or URL containing a list of image file paths. The images can be in different folders but they must all be the same size and type.
>
> This macro demonstrates how to generate a list of images and then use that list to open the images as a virtual stack:
>
>    http://imagej.nih.gov/ij/macros/VirtualStackFromList.txt
>
> And this one demonstrates how to how to open an image series from a remote server:
>
>    http://imagej.nih.gov/ij/macros/OpenStackUsingURLs.txt
>
> -wayne
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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