[Insight-users] problem in using itkLabelOverlayImageFilter in 3D

robert tamburo robert.tamburo at gmail.com
Thu Jun 30 10:45:49 EDT 2011 

Perhaps it's not an ITK bug after all. Sounds like the viewer is displaying
the image incorrectly (ImageJ didn't work either).

On Thu, Jun 30, 2011 at 10:40 AM, john smith <mkitkinsightuser at gmail.com>wrote:

> I have noticed that when I open the output.hdr with Bioimage Suite I get
> the strange results. But when I open the output.hdr with itk snap, I do not
> have any problem.Do you know why is this happening? I will try to display it
> just using ITK libraries in my application. Should I expect to have problem?
>
> Thanks
>
>
> 2011/6/30 robert tamburo <robert.tamburo at gmail.com>
>
>> Actually, the documentation for AnalyzeImageIO indicates an RGB image is
>> an acceptable image format. Looks like there might be a bug.
>>
>>
>> On Thu, Jun 30, 2011 at 10:25 AM, robert tamburo <
>> robert.tamburo at gmail.com> wrote:
>>
>>> It appears the Analyze file format does not handle RGB images well
>>> (should an exception be thrown or concept checking catch this?). If you
>>> output the image as a meta or raw image (use .mhd or .raw file name
>>> extensions), results should be as expected.
>>>
>>>
>>> On Thu, Jun 30, 2011 at 9:48 AM, robert tamburo <
>>> robert.tamburo at gmail.com> wrote:
>>>
>>>> Can you send me Region.hdr and Result.hdr?
>>>>
>>>>
>>>> On Thu, Jun 30, 2011 at 9:46 AM, john smith <mkitkinsightuser at gmail.com
>>>> > wrote:
>>>>
>>>>> I have made this change in my previous code and now I do not get any
>>>>> errors. But when I run the algorithm I get very strange results. I get a
>>>>> volume with confused the red and blue colors and not the blue contour of the
>>>>> label image added on the initial grayscale 3D image. I hope someone could
>>>>> help as I cannot understand the reason why I am getting these results.
>>>>>
>>>>>
>>>>> Thanks in advance
>>>>>
>>>>> 2011/6/30 john smith <mkitkinsightuser at gmail.com>
>>>>>
>>>>>> I have made this change in my previous code and now I do not get any
>>>>>> errors. But when I run the algorithm I get very strange results. I send a
>>>>>> docx file including the two inputs and the output of
>>>>>> itkLabelOverlayImageFilter. I hope someone to help me as I cannot understand
>>>>>> the reason why I am getting these results.
>>>>>>
>>>>>> Thanks in advance
>>>>>>
>>>>>> 2011/6/30 john smith <mkitkinsightuser at gmail.com>
>>>>>>
>>>>>>> I have made this change in my previous code and now I do not get any
>>>>>>> errors. But when I run the algorithm I get very strange results. I send a
>>>>>>> docx file including the two inputs and the output of
>>>>>>> itkLabelOverlayImageFilter. I hope someone to help me as I cannot understand
>>>>>>> the reason why I am getting these results.
>>>>>>>
>>>>>>> Thanks in advance
>>>>>>>
>>>>>>> 2011/6/30 john smith <mkitkinsightuser at gmail.com>
>>>>>>>
>>>>>>>> I have made this change in my previous code and now I do not get any
>>>>>>>> errors. But when I run the algorithm I get very strange results. I send a
>>>>>>>> docx file including the two inputs and the output of
>>>>>>>> itkLabelOverlayImageFilter. I hope someone to help me as I cannot understand
>>>>>>>> the reason why I am getting these results.
>>>>>>>>
>>>>>>>> Thanks in advance
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 2011/6/30 john smith <mkitkinsightuser at gmail.com>
>>>>>>>>
>>>>>>>>> You have right. I will post the solution for 2D immediatly.
>>>>>>>>>
>>>>>>>>> Thanks for your response
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2011/6/30 robert tamburo <robert.tamburo at gmail.com>
>>>>>>>>>
>>>>>>>>>> Your typedef for RGBImageType does not have a template parameter
>>>>>>>>>> for dimension.
>>>>>>>>>>
>>>>>>>>>> Also, it'd be nice if you posted your solution to your previous
>>>>>>>>>> error for the benefit of other ITK users that may encounter the same
>>>>>>>>>> problem.
>>>>>>>>>>
>>>>>>>>>> On Thu, Jun 30, 2011 at 8:45 AM, john smith <
>>>>>>>>>> mkitkinsightuser at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hello to all,
>>>>>>>>>>>
>>>>>>>>>>> I had used the itkLabelOverlayImageFilter  in 2D and I didn;t
>>>>>>>>>>> have any problem. No I am trying to use tis filter in 3D. I have written
>>>>>>>>>>> exactly the same code but for 3D, and I get this error which I don't know
>>>>>>>>>>> what exactly means.
>>>>>>>>>>>
>>>>>>>>>>> the error is the following:
>>>>>>>>>>> error C2440: 'initializing' : cannot convert from
>>>>>>>>>>> 'itk::Concept::Detail::UniqueType_unsigned_int<__formal>' to
>>>>>>>>>>> 'itk::Concept::Detail::UniqueType_unsigned_int<__formal>'
>>>>>>>>>>>
>>>>>>>>>>> I hope someone could help me.
>>>>>>>>>>> Thanks in advance
>>>>>>>>>>>
>>>>>>>>>>> ///////////// code///////////
>>>>>>>>>>>  typedef itk::Image<unsigned char, 3>  ImageType;
>>>>>>>>>>>    ImageType::Pointer image1 = ImageType::New();
>>>>>>>>>>>    ImageType::Pointer image_label = ImageType::New();
>>>>>>>>>>>
>>>>>>>>>>>    typedef   unsigned char           InternalPixelType_add;
>>>>>>>>>>>    const     unsigned int    Dimension = 3;
>>>>>>>>>>>    typedef itk::Image< InternalPixelType_add, Dimension >
>>>>>>>>>>> InternalImageType_add;
>>>>>>>>>>>    typedef  itk::ImageFileReader< InternalImageType_add >
>>>>>>>>>>> ReaderType_add;
>>>>>>>>>>>
>>>>>>>>>>>     ReaderType_add::Pointer reader1 = ReaderType_add::New();
>>>>>>>>>>>     reader1->SetFileName( fileName.toStdString()  );
>>>>>>>>>>>     reader1->Update();
>>>>>>>>>>>     image1 = reader1->GetOutput();
>>>>>>>>>>>
>>>>>>>>>>>     ReaderType_add::Pointer reader2 = ReaderType_add::New();
>>>>>>>>>>>     reader2->SetFileName( "result.hdr"  );
>>>>>>>>>>>     reader2->Update();
>>>>>>>>>>>     image_label = reader2->GetOutput();
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>   typedef itk::RGBPixel<unsigned char> RGBPixelType;
>>>>>>>>>>>   typedef itk::Image<RGBPixelType> RGBImageType;
>>>>>>>>>>>
>>>>>>>>>>>   typedef itk::LabelOverlayImageFilter<ImageType, ImageType,
>>>>>>>>>>> RGBImageType>
>>>>>>>>>>>
>>>>>>>>>>> LabelOverlayImageFilterType;
>>>>>>>>>>>   LabelOverlayImageFilterType::Pointer labelOverlayImageFilter =
>>>>>>>>>>> LabelOverlayImageFilterType::New();
>>>>>>>>>>>   labelOverlayImageFilter->SetInput(image1);
>>>>>>>>>>>   labelOverlayImageFilter->SetLabelImage(image_label);
>>>>>>>>>>>  // labelOverlayImageFilter->SetOpacity(.5);
>>>>>>>>>>>   labelOverlayImageFilter->SetOpacity(1.0);
>>>>>>>>>>>   labelOverlayImageFilter->ResetColors(); // reset color map
>>>>>>>>>>>   labelOverlayImageFilter->AddColor(0, 0, 255); // fill color map
>>>>>>>>>>> with blue
>>>>>>>>>>>   labelOverlayImageFilter->SetBackgroundValue(0); // don't
>>>>>>>>>>> overlay the background, i.e., label 0
>>>>>>>>>>>   labelOverlayImageFilter->Update();
>>>>>>>>>>>
>>>>>>>>>>>   typedef  itk::ImageFileWriter< RGBImageType  > WriterType;
>>>>>>>>>>>   WriterType::Pointer writer = WriterType::New();
>>>>>>>>>>>   writer->SetFileName("output.hdr");
>>>>>>>>>>>   writer->SetInput(labelOverlayImageFilter->GetOutput());
>>>>>>>>>>>   writer->Update();
>>>>>>>>>>>
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>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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