Re: [ITK-users] Getting info from a very big image file

Hi Gib,

Call

 reader->UpdateOutputInformation();

instead of

  reader->Update();

to get the LargestPossibleRegion populated without loading the pixel buffer.


The image IO has to support streaming to read in only a
RequestedRegion -- unfortunately, I do not think the LSMImageIO
supports this at this time.

HTH,
Matt

On Mon, Dec 11, 2017 at 10:44 PM, Gib Bogle <g.bogle-1/[email protected]> wrote:
> Hello,
>
>
> I am wanting to work with a 50 GB LSM file (3D).  The first step is to be
> able to get the image info: width, height and depth.  I have code that works
> on a small LSM file
>
>
>     im_u16 = reader->GetOutput();
>     width = im_u16->GetLargestPossibleRegion().GetSize()[0];
>     height = im_u16->GetLargestPossibleRegion().GetSize()[1];
>     depth = im_u16->GetLargestPossibleRegion().GetSize()[2];
>
>
> but I see that to do this the whole image must be loaded into memory.  When
> I start the program running with the big file I can see that it is going to
> exceed the host machine's 32 GB.  Is there a way to get the image dimensions
> without loading the whole image?  What I am hoping to do is split the file
> into 2D TIFF files - is there any way to extract a 2D slice without reading
> the whole image?  Or will I be forced to run on a  machine with more than 50
> GB of RAM?
>
>
> Thanks in advance for any suggestions.
>
>
> Best regards
>
> Gib
>
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users