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

Tue Dec 12 23:57:59 EST 2017

Hi Dzenan,

I did:

#include "itkRGBPixel.h"

typedef RGBPixel<unsigned short> PixelType;

but VS2010 tells me "Error: RGBPixel is not a template"

Cheers, Gib

________________________________
From: Dženan Zukić <dzenanz at gmail.com>
Sent: Wednesday, 13 December 2017 4:22 p.m.
To: Gib Bogle
Cc: Lowekamp, Bradley (NIH/NLM/LHC) [C]; Matt McCormick; insight-users at itk.org
Subject: 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 at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> 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 at mail.nih.gov<mailto:blowekamp at mail.nih.gov>>
Sent: Wednesday, 13 December 2017 3:51 a.m.
To: Matt McCormick; Gib Bogle
Cc: insight-users at itk.org<mailto:insight-users at itk.org>
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" <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>> 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 at auckland.ac.nz<mailto:g.bogle at auckland.ac.nz>> 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
    >
    >
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