[ITK] Getting ImageType for TIFF

[Мар'ян Климов]

Image Watch during debugging in Visual Studio.
Windows Photo Viewer after results dumped to disk.


2014-08-14 15:35 GMT+03:00 Bill Lorensen <bill.lorensen at gmail.com>:

> 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
>>>> >> >
>>>> >
>>>> >
>>>>
>>>
>>>
>>
>> _______________________________________________
>> Community mailing list
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>>
>>
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