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

Richard Beare richard.beare at gmail.com
Wed Dec 13 01:57:13 EST 2017 

I guess there are a number of things you might want to check out.
1) Viewers that can handle 16 bit colour channels in tiffs - my guesses
would be itksnap, imageJ. Looks like you've succeeded with imageJ

2) Extracting a single channel - VectorImageToImageAdaptor

Can't see what is wrong with your code, but check the minimum as well, and
also confirm the pixel type with tiffinfo - perhaps it is signed?

On Wed, Dec 13, 2017 at 4:46 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:

> I just needed to put "itk::" before RGBPixel.  I still don't know how to
> get the R, G and B channels.  Are they in separate buffers?
> ------------------------------
> *From:* Insight-users <insight-users-bounces at itk.org> on behalf of Gib
> Bogle <g.bogle at auckland.ac.nz>
> *Sent:* Wednesday, 13 December 2017 5:57 p.m.
> *To:* Dženan Zukić
> *Cc:* insight-users at itk.org
> *Subject:* [FORGED] Re: [ITK-users] [ITK] Getting info from a very big
> image file
>
>
> 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> 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>
>> Sent: Wednesday, 13 December 2017 3:51 a.m.
>> To: Matt McCormick; Gib Bogle
>> Cc: 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>
>> 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>
>> 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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