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

I've created a discourse topic, Brad.  I don't have a way of creating a smaller 2D image file (the compressed size is 57 MB).


Cheers, Gib

________________________________
From: Lowekamp, Bradley (NIH/NLM/LHC) [C] <blowekamp-2loH/[email protected]>
Sent: Friday, 15 December 2017 2:56 a.m.
To: Gib Bogle; [email protected]
Cc: [email protected]
Subject: Re: [ITK-users] [ITK] Getting info from a very big image file

Hello,

I have been paying attention to ITK Discourse discourse.itk.org<http://discourse.itk.org/> where the mailing list has migrated too. So I haven’t noticed this topic the past couple days.

I’d suggest creating a topic in ITK discourse and share the details of your image produced by tiffinfo, and trying to get an image that you can share.

Brad

From: Gib Bogle <g.bogle-1/[email protected]>
Date: Wednesday, December 13, 2017 at 7:58 PM
To: "[email protected]" <[email protected]>
Cc: "[email protected]" <[email protected]>
Subject: Re: [ITK-users] [ITK] Getting info from a very big image file


The print command is:



    std::cout << adaptor->GetPixel(index) << std::endl;

no way to cast it, as far as I can see.

________________________________
From: Richard Beare <[email protected]>
Sent: Thursday, 14 December 2017 12:09 p.m.
To: Gib Bogle
Cc: Dženan Zukić; [email protected]
Subject: Re: [ITK-users] [ITK] Getting info from a very big image file

Another long shot - any chance that windows printing is interpreting the unsigned short as a multi-byte character type (equivalent of the issues when printing unsigned char pixels) - try casting to int when displaying to see if it changes anything.

On Thu, Dec 14, 2017 at 8:22 AM, Gib Bogle <g.bogle-1/[email protected]<mailto:g.bogle-1/[email protected]>> wrote:

I modified the VectorImageToImageAdaptor example to get this:



    typedef itk::RGBPixel<unsigned short> PixelType;
    typedef itk::VectorImage<PixelType,2> ImageType_u16;
    ImageType_u16::Pointer image;

    typedef itk::ImageFileReader<ImageType_u16> ReaderType;
    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName(filename);
    reader->Update();
    image = reader->GetOutput();

    int width = image->GetLargestPossibleRegion().GetSize()[0];
    int height = image->GetLargestPossibleRegion().GetSize()[1];
    int depth = image->GetLargestPossibleRegion().GetSize()[2];
    printf("Image dimensions: width, height: %d %d\n",width,height);
    printf("NumberOfComponentsPerPixel: %d\n", image->GetNumberOfComponentsPerPixel());

    typedef itk::VectorImageToImageAdaptor<PixelType, 2> ImageAdaptorType;
    ImageAdaptorType::Pointer adaptor = ImageAdaptorType::New();
    adaptor->SetExtractComponentIndex(0);
    adaptor->SetImage(image);

    itk::Index<2> index;
    index[0] = 3084;
    index[1] = 3072;

    std::cout << adaptor->GetPixel(index) << std::endl;



The size of the image is reported correctly (4656x4656) but although the number of components is shown as 4, GetPixel returns three values (2 0 0), at a location where I know (from ImageJ) that the green channel has a pixel value of more than 2000.

________________________________
From: Richard Beare <[email protected]<mailto:[email protected]>>
Sent: Wednesday, 13 December 2017 7:57 p.m.
To: Gib Bogle
Cc: Dženan Zukić; [email protected]<mailto:[email protected]>
Subject: Re: [ITK-users] [ITK] Getting info from a very big image file

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-1/[email protected]<mailto:g.bogle-1/[email protected]>> 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 <[email protected]<mailto:[email protected]>> on behalf of Gib Bogle <g.bogle-1/[email protected]<mailto:[email protected]>>
Sent: Wednesday, 13 December 2017 5:57 p.m.
To: Dženan Zukić
Cc: [email protected]<mailto:[email protected]>
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 <[email protected]<mailto:[email protected]>>
Sent: Wednesday, 13 December 2017 4:22 p.m.
To: Gib Bogle
Cc: Lowekamp, Bradley (NIH/NLM/LHC) [C]; Matt McCormick; [email protected]<mailto:[email protected]>
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-1/[email protected]<mailto: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]<mailto:blowekamp-2loH/[email protected]>>
Sent: Wednesday, 13 December 2017 3:51 a.m.
To: Matt McCormick; Gib Bogle
Cc: [email protected]<mailto:[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]<mailto:[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]<mailto: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
    >
    >
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