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]> 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]>
> *Sent:* Wednesday, 13 December 2017 7:57 p.m.
> *To:* Gib Bogle
> *Cc:* Dženan Zukić; [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]> 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]> on behalf of Gib
>> Bogle <g.bogle-1/[email protected]>
>> *Sent:* Wednesday, 13 December 2017 5:57 p.m.
>> *To:* Dženan Zukić
>> *Cc:* [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]>
>> *Sent:* Wednesday, 13 December 2017 4:22 p.m.
>> *To:* Gib Bogle
>> *Cc:* Lowekamp, Bradley (NIH/NLM/LHC) [C]; Matt McCormick;
>> [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]>
>> 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
>>
>>
>

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