[ITK] Getting ImageType for TIFF
Matt McCormick
matt.mccormick at kitware.com
Sat Aug 16 12:56:42 EDT 2014
Hi Marian,
Sounds great. I added the file to the regression test suite. Please
review [1] this patch [2].
Thanks,
Matt
[1] http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/PerformAGerritReview/index.html#perform-a-gerrit-review
[2] http://review.source.kitware.com/#/c/16705/
On Fri, Aug 15, 2014 at 4:53 AM, Мар'ян Климов <nekto1989 at gmail.com> wrote:
> Hi,
>
> I don't mind. After changes that Ivan Kubarev proposed this image is being
> read to unsigned short properly for me. Problem may be the same for 64-bit
> TIFF.
>
> Marian
>
>
> 2014-08-14 17:18 GMT+03:00 Matt McCormick <matt.mccormick at kitware.com>:
>
>> Thanks for the nice example!
>>
>>
>> I have been able to reproduce the output. If it is a bug, can the
>> given image be added to the repository as part of a unit test?
>>
>> Thanks,
>> Matt
>>
>> On Thu, Aug 14, 2014 at 9:51 AM, Мар'ян Климов <nekto1989 at gmail.com>
>> wrote:
>> > 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
>> >>> Community at itk.org
>> >>> http://public.kitware.com/mailman/listinfo/community
>> >>>
>> >
>
>
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