Re: Remove slices from a virtual stack

Posted by Michael Doube on
URL: http://imagej.273.s1.nabble.com/Remove-slices-from-a-virtual-stack-tp3690894p3690898.html

Never mind,

I discovered the VirtualStack class and hacked a very quick plugin:

http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/VirtualDelete.java

Mike

Michael Doube wrote:

> Hi all
>
> Is there a quick way to remove slices from a virtual stack?
>
> I have several GB of microCT slices that I drag 'n drop in their
> directory (i.e. drag 'n drop the directory), but then I want to remove
> the first 300 or so slices and the last 300 or so slices so that I can
> crop the stack without running out of RAM (the result of the crop
> operation is not a virtual stack so must be smaller than IJ's allocated
> memory).
>
> I have automated a slice range deletion with this macro, however it's
> very slow as it has to open each image before deleting it.
>
>
> macro "Delete Slice Range [b]"{
> Dialog.create("Delete Slice Range");
> Dialog.addMessage("Inclusive range of slices to delete");
> Dialog.addNumber("First", getSliceNumber());
> Dialog.addNumber("Last", getSliceNumber());
> Dialog.show();
> first = Dialog.getNumber();
> last = Dialog.getNumber();
> setBatchMode(true);
> deletable = last - first +1;
> for (deleted = 0; deleted < deletable; deleted++){
> showStatus("Deleting slices...");
> showProgress(deleted/(deletable-1));
> setSlice(first);
> run("Delete Slice");
>
> }
>
> }
>
>
> Can I simply dereference the images on the hard disk from the virtual
> stack instead?  I.e. tell the the virtual stack to no longer include
> images within a specified range?  Another approach might be to create a
> new virtual stack with the desired images by defining the new slice
> range in File->Import->Image Sequence... and closing the original.
>
>
> Mike
>  

--
Dr Michael Doube  BPhil BVSc PhD MRCVS
Research Associate
Department of Bioengineering
Imperial College London
South Kensington Campus
London  SW7 2AZ
United Kingdom