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

[robert tamburo]

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();
>>>>>>>>>
>>>>>>>>> _____________________________________
>>>>>>>>> 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.html
>>>>>>>>>
>>>>>>>>> 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://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20110630/fdb9e346/attachment.htm>