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

Why don't you try reading it with:
tyepdef RGBPixel<unsigned short> PixelType;

Embedded thumbnails might be ignored by the reader, it is definitely worth
a shot trying Brad's suggestion.

Regards,
Dženan

On Tue, Dec 12, 2017 at 6:36 PM, Gib Bogle <g.bogle-1/[email protected]> wrote:

> Thanks Brad.  The situation is complicated by the fact that there are 3
> channels (three colours).  Tiffsplit is able to split the file into 396 127
> MB TIFFs and 396 thumbnail TIFFs.  Irfanview can open one of the TIFFs, and
> it tells me that it is 4656x4656 and 48 bitsperpixel.  That is, it contains
> 3 16-bit images of that size.  Nothing is displayed in Irfanview - I'm
> rather surprised that it could open it at all.
>  I'll try using that example, but the double complication of the included
> thumbnails and the 3 colours might stymie it.
>
> Cheers, Gib
> ________________________________________
> From: Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp-2loH/[email protected]>
> Sent: Wednesday, 13 December 2017 3:51 a.m.
> To: Matt McCormick; Gib Bogle
> Cc: [email protected]
> Subject: Re: [ITK] [ITK-users] Getting info from a very big image file
>
> Gib,
>
> I have not tested this, but the LSMImageIO is derived from the
> TIFFImageIO,  and LSMImageIO::Read does just call TIFFImageIO. So the
> chances are very good that it supports streamed reading.
>
> I updated the TIFFImageIO to support stream reading of the individual
> pages in the TIFF stack some time ago.
>
> You may find the following example useful to determining if the
> functionality is there:
> https://github.com/InsightSoftwareConsortium/ITK/blob/master
> /Examples/IO/ImageReadExtractWrite.cxx
>
>
> You can see the usage of “UpdateOutputInformation” followed by the
> ExtractImageFilter, this can be a very powerful and efficient pattern for
> working with large images. The ExtractImageFilter can be used to create a
> 3D to 2D image from it’s input volume.
>
> Brad
>
>
> On 12/11/17, 10:56 PM, "Matt McCormick" <[email protected]>
> wrote:
>
>     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
>     The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
>     ________________________________________
>     Community mailing list
>     [email protected]
>     http://public.kitware.com/mailman/listinfo/community
>
>
> 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