[Insight-users] Analyze Image Orientation problem
Luis Ibanez
luis.ibanez at kitware.com
Tue Mar 31 18:55:12 EDT 2009
Hi Alex,
Both of the two things that you are observing are normal:
A) The run-time error is still there, because the default image type
of the Junction filter is still an image of pixel type "long".
In order to avoid this problem, you instantiate the filter type
by specifying the second template parameters.
B) The compilation error is normal, because you are instantiating
the writer with the input image type, instead of redefining the
output image type.
What you want to do is the following:
typedef itk::Image<unsigned short, 3> InputImageType;
typedef itk::Image<unsigned short, 3> OutputImageType;
typedef itk::ImageFileReader<InputImageType> ReaderType;
typedef itk::JunctionDetectionFilter<
InputImageType, OutputImageType> DetectorType;
typedef itk::ImageFileWriter<
DetectorType::OutputImageType> WriterType;
Note that now the JunctionDetectionFilter has two explicit template arguments.
Please let us know if you still find any problem,
Thanks
Luis
--------
BTW: Thanks for posting your review to the Insight Journal paper.
-----------------------------------------------------------------------------
On Tue, Mar 31, 2009 at 6:49 PM, Oleksandr Dzyubak <adzyubak at gmail.com> wrote:
> Hi Luis,
>
> Thanks for quick response.
>
> a) I have to use the Analyze format in my image processing.
> b) I agree that pixel type Long is not a must.
> c) At the last resort I would use image cast in a filter pipeline.
>
> d) I have downloaded and tried the attachment with your corrections.
> So I deleted my working directory and started all over.
>
> 1) If I use your attachment "as is", I get the runtime error message
> below.
>
> ********** Runtime Error *********
> From writer: ExceptionObject caught !
>
> itk::ExceptionObject (0x9923830)
> Location: "void itk::AnalyzeImageIO::DefineHeaderObjectDataType()"
> File:
> /mnt/Public/Root_BUILDS/Lenny/InsightToolkit_3_12/InsightToolkit-3.12.0/Code/IO/itkAnalyzeImageIO.cxx
> Line: 630
> Description: itk::ERROR: AnalyzeImageIO(0x9923840): Pixel Type Unknown
>
> real 62m59.119s
> user 59m44.896s
> sys 0m14.581s
> *********
>
> 2) And I get a compile error if I make a change in "main".
>
> typedef itk::Image<unsigned short, 3> ImageType;
> typedef itk::ImageFileReader<ImageType> ReaderType;
> typedef itk::JunctionDetectionFilter<ImageType> DetectorType;
> // typedef itk::ImageFileWriter<DetectorType::OutputImageType> WriterType;
> typedef itk::ImageFileWriter<ImageType> WriterType;
>
> ************ Compile Error ********
> /mnt/Public/Programs/ITK_Test/Skeletons/Automatic_Junction_Detection/Src/itkJunctionDetectionFilter3DTest.cxx:
> In function ‘int main(int, char**)’:
> /mnt/Public/Programs/ITK_Test/Skeletons/Automatic_Junction_Detection/Src/itkJunctionDetectionFilter3DTest.cxx:83:
> error: no matching function for call to
> ‘itk::ImageFileWriter<itk::Image<short unsigned int, 3u>
>>::SetInput(itk::Image<long int, 3u>*)’
> /usr/local/include/InsightToolkit/IO/itkImageFileWriter.txx:58: note:
> candidates are: void itk::ImageFileWriter<TInputImage>::SetInput(const
> TInputImage*) [with TInputImage = itk::Image<short unsigned int, 3u>]
> make[2]: ***
> [CMakeFiles/itkJunctionDetectionFilter3DTest.dir/itkJunctionDetectionFilter3DTest.o]
> Error 1
> make[1]: *** [CMakeFiles/itkJunctionDetectionFilter3DTest.dir/all] Error 2
> make: *** [all] Error 2
> **********
>
>
> Regards,
>
> Alex
>
>
> Luis Ibanez wrote:
>>
>> Hi Oleksandr,
>>
>>
>> It seems that you are getting two separate errors.
>>
>>
>>
>> A) The first one is a warning and refers to image orientation.
>> In this case, I would suggest to simply not use the Analyze
>> file format. Have you considered using nifti ?
>>
>>
>> B) The second one is also a limitation on the pixel
>> type supported by Analyze. The Junction filter uses
>> Long as the pixel type of the output image. This seems
>> to be an unnecessary restriction though.
>>
>> The simple solution is to make the filter templated also
>> over the output image type, and to provide the current
>> output image type as the default for that template argument.
>>
>> Please find attached the modified files, in which you
>> can replace the output image type for the junction filter.
>>
>>
>>
>> C) The compilation error that you are reporting indicates
>> that you are not declaring consistently the image type
>> at the output of the filter, and the corresponding
>> file writer.
>>
>> if you are going to connect:
>>
>> writer->SetInput( filter->GetOutput() )
>>
>> the the output of the filter *must* be of the same type
>> as the image type of the writer, *or* you could use a
>> cast image filter in the middle.
>>
>> The Junction filter is templated only over the input
>> image type, therfore, it looks like you would have to
>> go for inserting a CastImageFilter between the junction
>> filter and the writer (if you want to use the Analyze
>> file format).
>>
>> Or.... use the attached files.
>>
>>
>>
>> Regards,
>>
>>
>> Luis
>>
>>
>> -----------------------
>> Oleksandr Dzyubak wrote:
>>>
>>> Quick question though. I am mostly working with the Analyze format
>>> images.
>>> I know that is an additional headache but...
>>>
>>> So if I just run the program as above but with the Analyze format images,
>>> I am getting an "exception caught":
>>>
>>> ========================WARNING: In
>>> /mnt/Public/Root_BUILDS/Lenny/InsightToolkit_3_12/InsightToolkit-3.12.0/Code/IO/itkAnalyzeImageIO.cxx,
>>> line 1345
>>> AnalyzeImageIO (0x86fb840): ERROR: Analyze 7.5 File Format Only Allows
>>> RPI, PIR, and RIP Orientation
>>>
>>> ExceptionObject caught !
>>>
>>> itk::ExceptionObject (0x86fb830)
>>> Location: "void itk::AnalyzeImageIO::DefineHeaderObjectDataType()"
>>> File:
>>> /mnt/Public/Root_BUILDS/Lenny/InsightToolkit_3_12/InsightToolkit-3.12.0/Code/IO/itkAnalyzeImageIO.cxx
>>> Line: 630
>>> Description: itk::ERROR: AnalyzeImageIO(0x86fb840): Pixel Type Unknown
>>> ==========================
>>>
>>> On the other hand if I change the typedef to fit into the Analyze
>>> requirements,
>>>
>>> typedef itk::Image<unsigned short, 3> ImageType;
>>> typedef itk::ImageFileReader<ImageType> ReaderType;
>>> typedef itk::JunctionDetectionFilter<ImageType>
>>> DetectorType;
>>> // typedef itk::ImageFileWriter<DetectorType::OutputImageType>
>>> WriterType;
>>> typedef itk::ImageFileWriter<ImageType> WriterType;
>>>
>>> I am getting the compile error:
>>>
>>> ****************** Begin Error ***********
>>>
>>> [100%] Building CXX object
>>> CMakeFiles/itkJunctionDetectionFilter3DTest.dir/itkJunctionDetectionFilter3DTest.o
>>>
>>> /mnt/Public/Programs/ITK_Test/Skeletons/Automatic_Junction_Detection/Src/itkJunctionDetectionFilter3DTest.cxx:
>>> In function ‘int main(int, char**)’:
>>>
>>> /mnt/Public/Programs/ITK_Test/Skeletons/Automatic_Junction_Detection/Src/itkJunctionDetectionFilter3DTest.cxx:83:
>>> error: no matching function for call to
>>> ‘itk::ImageFileWriter<itk::Image<short unsigned int, 3u>
>>> >::SetInput(itk::Image<short int, 3u>*)’
>>> /usr/local/include/InsightToolkit/IO/itkImageFileWriter.txx:58: note:
>>> candidates are: void itk::ImageFileWriter<TInputImage>::SetInput(const
>>> TInputImage*) [with TInputImage = itk::Image<short unsigned int, 3u>]
>>> make[2]: ***
>>> [CMakeFiles/itkJunctionDetectionFilter3DTest.dir/itkJunctionDetectionFilter3DTest.o]
>>> Error 1
>>> make[1]: *** [CMakeFiles/itkJunctionDetectionFilter3DTest.dir/all] Error
>>> 2
>>> make: *** [all] Error 2
>>>
>>> ****************** End Error ***********
>>>
>>> Any solution for that?
>>>
>>> Thanks,
>>> Alex
>>>
>>> Luis Ibanez wrote:
>>>
>>>>
>>>> Hi Oleksandr,
>>>>
>>>> I just finished reviewing this paper:
>>>> http://www.insight-journal.org/browse/publication/324
>>>>
>>>> The code was missing a bunch of "typename" keywords,
>>>> which is the usual problem of code developed in Windows
>>>> with Visual Studio 6.0.
>>>>
>>>> Please find attached the .tgz file with the corrections
>>>> required to compile it in GCC. (gcc 4.3.2, GNU/Linux
>>>> Ubuntu 8.10).
>>>>
>>>> Please give it a try at this modified code and let us
>>>> know if you find any problem.
>>>>
>>>> Note that you should compile this code for Release,
>>>> and allow it to run for at least 15min for the 2D
>>>> case, for it to finish processing the image.
>>>>
>>>>
>>>> BTW: If you find the paper useful, please take the
>>>> time of contributing a review for it. In this way
>>>> we will be able to integrate this paper code into
>>>> ITK in the near future.
>>>>
>>>>
>>>>
>>>> Regards,
>>>>
>>>>
>>>> Luis
>>>>
>>>>
>>>>
>>>> ---------------------------
>>>> Oleksandr Dzyubak wrote:
>>>>
>>>>> Thanks Luis,
>>>>>
>>>>> You were right on that one. So we are getting close.
>>>>> Now I am getting a family of errors as below concerning
>>>>> the variable "was not declared in this scope"...
>>>>>
>>>>> ********* Errors begin ********
>>>>> itkJunctionDetectionFilter.txx:78: error: expected `;' before
>>>>> ‘wallDister’
>>>>> itkJunctionDetectionFilter.txx:79: error: ‘wallDister’ was not declared
>>>>> in this scope
>>>>> .......
>>>>> etc.
>>>>> ********* Errors end ********
>>>>>
>>>>> Alex
>>>>>
>>>
>>>
>
>
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