[ITK] Getting ImageType for TIFF

[Bill Lorensen]

How are you displaying the unsigned short image? Many viewers cannot
properly display unsigned short.
On Aug 14, 2014 7:23 AM, "Мар'ян Климов" <nekto1989 at gmail.com> wrote:

> Hi,
>
> I've tried different methods. Reading to RGBPixel<unsigned char>, then
> using RGBToLuminanceImageFilter and MultiplyImageFilter (2 ^ 8) produces
> the same visually proper image. Reading directly to <unsigned short, 2>
> fails. Looks like this is bug in TIFFImageIO and not in the way it is being
> called.
> http://itk-users.7.n7.nabble.com/TiffIO-strange-behaviour-td32215.html
>
> Marian
>
>
> 2014-08-13 23:55 GMT+03:00 Мар'ян Климов <nekto1989 at gmail.com>:
>
>> Hi Matt,
>>
>> I hope this is proper cmakelists.txt. I'm used to using ITK connected
>> through *.props into Visual Studio solution.
>>
>> Best regards,
>> Marian
>>
>>
>>
>> 2014-08-13 22:52 GMT+03:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>> Hi Marian,
>>>
>>> Thanks for the update.  Offhand, I am not seeing the issue.
>>>
>>> Could you please post a SSCCE [1], i.e. CMakeLists.txt, the code, and
>>> the input data?
>>>
>>> Thanks,
>>> Matt
>>>
>>> [1] http://sscce.org/
>>>
>>> On Wed, Aug 13, 2014 at 2:27 PM, Мар'ян Климов <nekto1989 at gmail.com>
>>> wrote:
>>> > {
>>> >     typedef unsigned short PixelType;
>>> >     typedef itk::Image<PixelType, 2> ImageType;
>>> >     auto reader = itk::ImageFileReader<
>>> > ImageType>::New();
>>> >     reader->SetFileName("D:/TestData/input/input.tif");
>>> >     reader->SetImageIO(itk::TIFFImageIO::New());
>>> >
>>> >     typedef unsigned short OutputPixelType;
>>> >     typedef itk::Image<OutputPixelType, 2> OutputImageType;
>>> >
>>> >     auto writer = itk::ImageFileWriter<OutputImageType>::New();
>>> >     writer->SetFileName("D:/TestData/output/ushort_to_ushort.tif");
>>> >     auto image_io = itk::TIFFImageIO::New();
>>> >     image_io->SetPixelType(itk::ImageIOBase::SCALAR);
>>> >     writer->SetImageIO(image_io);
>>> >     writer->SetInput(reader->GetOutput());
>>> >     writer->Update(); //produces completely black
>>> >     }
>>> >
>>> >     {
>>> >     typedef itk::RGBAPixel<char> PixelType;
>>> >     typedef itk::Image<PixelType, 2> ImageType;
>>> >     auto reader = itk::ImageFileReader<ImageType>::New();
>>> >     reader->SetFileName("D:/TestData/input/input.tif");
>>> >     reader->SetImageIO(itk::TIFFImageIO::New());
>>> >     reader->Update();
>>> >
>>> >     typedef unsigned short OutputPixelType;
>>> >     typedef itk::Image<OutputPixelType, 2> OutputImageType;
>>> >
>>> >     auto input_image = reader->GetOutput();
>>> >     auto output_image = OutputImageType::New();
>>> >     output_image->CopyInformation(input_image);
>>> >     output_image->SetRegions(input_image->GetLargestPossibleRegion());
>>> >     output_image->Allocate();
>>> >     itk::ImageRegionConstIterator<ImageType>
>>> const_iterator(input_image,
>>> > input_image->GetLargestPossibleRegion());
>>> >     itk::ImageRegionIterator<OutputImageType>
>>> > rescaled_iterator(output_image,
>>> output_image->GetLargestPossibleRegion());
>>> >     for (const_iterator.GoToBegin(), rescaled_iterator.GoToBegin();
>>> > !const_iterator.IsAtEnd(); ++const_iterator, ++rescaled_iterator)
>>> >       {
>>> >       const PixelType& pixel = const_iterator.Get();
>>> >       rescaled_iterator.Set(((pixel.GetAlpha() * 16 + pixel.GetRed())
>>> * 16 +
>>> > pixel.GetGreen()) * 16 + pixel.GetBlue());
>>> >       }
>>> >
>>> >     auto writer = itk::ImageFileWriter<OutputImageType>::New();
>>> >     writer->SetFileName("D:/TestData/output/rgba_char_to_ushort.tif");
>>> >     auto image_io = itk::TIFFImageIO::New();
>>> >     image_io->SetPixelType(itk::ImageIOBase::SCALAR);
>>> >     writer->SetImageIO(image_io);
>>> >     writer->SetInput(output_image);
>>> >     writer->Update(); //output looks the same
>>> >     }
>>> >
>>> >
>>> > 2014-08-13 20:50 GMT+03:00 Matt McCormick <matt.mccormick at kitware.com
>>> >:
>>> >>
>>> >> Hi Marian,
>>> >>
>>> >>
>>> >> If
>>> >>
>>> >>   itk::Image< unsigned  short, 2 >
>>> >>
>>> >> is used for the ImageType, does it work (note the dimension
>>> >> specification).
>>> >>
>>> >> HTH,
>>> >> Matt
>>> >>
>>> >> On Wed, Aug 13, 2014 at 1:47 PM, Мар'ян Климов <nekto1989 at gmail.com>
>>> >> wrote:
>>> >> > Hi,
>>> >> >
>>> >> > How to properly read 32-bit TIFF? I need to get itk::Image<unsigned
>>> >> > short>
>>> >> > on output. If I use it as ImageType for ImageFileReader, it is read
>>> as
>>> >> > fully
>>> >> > black (checked contrast with Image Watch and it is for sure
>>> completely
>>> >> > empty). If I read it with pixel type RGBPixel<unsigned char> or
>>> >> > RGBAPixel<unsigned char>, it is read properly. But I need to
>>> convert it
>>> >> > manually to unsigned short after this. So what is the proper way of
>>> >> > reading
>>> >> > it? Do I need to create templated methods for every pixeltype with
>>> >> > conversions to unsigned short?
>>> >> >
>>> >> > Best regards,
>>> >> > Marian
>>> >> >
>>> >> > _______________________________________________
>>> >> > Community mailing list
>>> >> > Community at itk.org
>>> >> > http://public.kitware.com/mailman/listinfo/community
>>> >> >
>>> >
>>> >
>>>
>>
>>
>
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