Re: Reducing virtual stack

Posted by jmutterer on May 02, 2021; 6:38pm
URL: http://imagej.273.s1.nabble.com/Reducing-virtual-stack-tp5024647p5024648.html

Dear Stein,
If you could list the remote directory, create a reduced list of files and
open this list with the "Stack from list" command.
See this example macro that builds and opens a list of files as a virtual
stack:

https://webcache.googleusercontent.com/search?q=cache:jd_q0eWMg2YJ:https://imagej.nih.gov/ij/macros/VirtualStackFromList.txt+&cd=1&hl=en&ct=clnk&gl=fr

Jerome.


On Sun, 2 May 2021 at 17:30, Stein Rørvik <[hidden email]> wrote:

> I have some large folders (usually 46GB each) of raw µCT data which I open
> as virtual stacks to quickly inspect if the data looks okay, before
> reconstructing it. This works as expected.
>
> These days I am working on samples that require the instrument flux
> correction to be turned off, due to an asymmetry in the way the samples are
> mounted. I therefore need to play through the stack to inspect to what
> degree the actual flux has drifted, to decide if the data needs to be
> re-acquired or can be used as is. Since the folder resides on a network
> disk which is too slow to allow slice animation, I reduce it using the
> Image → Stacks → Tools → Reduce command. This works, but I have noticed
> that the result stack is no longer virtual, but residing in memory. This
> makes the operation slow, especially if I choose a small reduction factor,
> as a lot of data then has to be read.
>
> So, is the conversion to memory resident stack really necessary, as I
> assume a virtual stack is just a list of pointers to files?  Then just the
> list could be reduced, instead of loading all files as a reduced stack.
>
> Stein
>
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>

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