[ITK-users] [ITK] 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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>
>
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> ________________________________
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>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
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