[Insight-users] Possible bug in Gipl file not being recognized
Raghavendra Chandrashekara
rc3@doc.ic.ac.uk
Mon, 31 Mar 2003 12:04:10 +0100
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Hi Luis,
Sorry the for the delay in replying. I've attached the entire image as
it's quite a small one.
Thanks,
Raghavendra.
Luis Ibanez wrote:
> Hi Raghavendra,
>
> The ramp.gipl file was added to Testing after the 1.2 release.
> You can get it through CVS at:
> http://www.itk.org/cgi-bin/cvsweb.cgi/Insight/Testing/Data/Baseline/IO/?cvsroot=Insight
>
>
> ---
>
> Your test shows that your Gipl file is ok.
>
> What seems to be failing is the testing criteria of the GIPL
> reader for recognizing your file as a gipl-file.
>
> Could you please post the header (just the header, not the data)
> of your GIPL file. It should have an extra field, or a missing
> field that is making the GiplImageIO reject the file.
>
> You can also check the GiplImageIO.cxx file in Insight/Code/IO
> and verify the revision criteria in the method "CanReadFile()".
>
>
>
> Thanks
>
>
> Luis
>
>
>
> ----------------------------------------
>
> Raghavendra Chandrashekara wrote:
>
>> Just to be on the safe side I cleaned our copy of the ITK repository,
>> updated it again, and built everything from scratch. Unfortunately the
>> ramp.gipl image doesn't seem to be there anymore so I couldn't check the
>> program with the test image. Has the image been removed from the
>> Release-1-2-0 branch?
>>
>> Here's the code that I am using:
>>
>> #include <iostream>
>> #include <iomanip>
>>
>> #include "itkImage.h"
>> #include "itkImageFileReader.h"
>> #include "itkGiplImageIO.h"
>> #include "itkImageFileWriter.h"
>>
>> /* Program reads a GIPL image and writes it out again. */
>> int main(int argc, char** argv)
>> {
>> if (argc != 3) {
>> std::cout << std::setiosflags(std::ios::left) << "GIPLIOTest reads an
>> input image file and writes it out again." << std::endl
>> << std::endl
>> << "Usage: GIPLIOTest input.gipl output.gipl" << std::endl
>> << std::endl
>> << "Where:" << std::endl
>> << std::endl
>> << std::setw(30) << "input.gipl" << std::setw(50) << "is the input
>> image" << std::endl
>> << std::setw(30) << "output.gipl" << std::setw(50) << "is the
>> output
>> filename" << std::endl;
>> exit(1);
>> }
>>
>> typedef short PixelType;
>> typedef itk::Image<PixelType, 3> ImageType;
>> typedef itk::ImageFileReader<ImageType> ReaderType;
>> typedef itk::ImageFileWriter<ImageType> WriterType;
>> itk::GiplImageIO::Pointer pGiplImageIO = itk::GiplImageIO::New();
>>
>> try {
>> ReaderType::Pointer pReader = ReaderType::New();
>> WriterType::Pointer pWriter = WriterType::New();
>>
>> // pReader->SetImageIO(pGiplImageIO);
>>
>> pReader->SetFileName(argv[1]);
>> pWriter->SetFileName(argv[2]);
>>
>> pWriter->SetInput(pReader->GetOutput());
>>
>> pWriter->Update();
>> }
>> catch (itk::ExceptionObject& ex) {
>> std::cout << "Exception object caught!" << std::endl;
>> std::cout << ex << std::endl;
>> exit(1);
>> }
>>
>> return 0;
>> }
>>
>> When I uncomment out the line that sets the GIPL IO object then
>> everything
>> works fine! So it looks like the image that I am using is alright.
>>
>> Thanks,
>>
>> Raghavendra
>>
>> ----- Original Message -----
>> From: "Luis Ibanez" <luis.ibanez@kitware.com>
>> To: "Raghavendra Chandrashekara" <rc3@doc.ic.ac.uk>
>> Cc: <Insight-users@public.kitware.com>
>> Sent: Friday, March 28, 2003 1:28 PM
>> Subject: Re: [Insight-users] Possible bug in itkAnalyzeImageIO? : Gipl
>> not
>> being found
>>
>>
>>
>>> Hi Raghavendra,
>>>
>>> Yeap, the code looks right.
>>>
>>> 1) Could you post the piece of code you are using for
>>> reading the gipl file ?
>>>
>>> 2) Could you try reading the gipl test file
>>> that is available in
>>>
>>> Insight/Testing/Data/Baseline/IO
>>>
>>> the file name is
>>>
>>> ramp.gipl
>>>
>>> If this test file works, this may mean that there
>>> is something particular in your gipl file that
>>> prevents the reader from recognizing the format.
>>>
>>> Note that checking the extension .gipl is only the
>>> initial part of the test. Readers verify the content
>>> of the file in order to make sure they are capable
>>> of processing the file.
>>>
>>>
>>> Thanks
>>>
>>> Luis
>>>
>>>
>>> --------------------------
>>>
>>> Raghavendra Chandrashekara wrote:
>>>
>>>> Hi Luis,
>>>>
>>>> There is a line registering the GiplImageIOFactory but it is on line
>>>> 98,
>>>> this is the code:
>>>>
>>>> void
>>>> ImageIOFactory::RegisterBuiltInFactories()
>>>> {
>>>> static bool firstTime = true;
>>>>
>>>> static SimpleMutexLock mutex;
>>>> {
>>>> // This helper class makes sure the Mutex is unlocked
>>>> // in the event an exception is thrown.
>>>> MutexLockHolder<SimpleMutexLock> mutexHolder( mutex );
>>>> if( firstTime )
>>>> {
>>>> ObjectFactoryBase::RegisterFactory( DicomImageIOFactory::New() );
>>>> ObjectFactoryBase::RegisterFactory( MetaImageIOFactory::New() );
>>>> ObjectFactoryBase::RegisterFactory( PNGImageIOFactory::New() );
>>>> ObjectFactoryBase::RegisterFactory( VTKImageIOFactory::New() );
>>>> ObjectFactoryBase::RegisterFactory( GiplImageIOFactory::New() );
>>>> ObjectFactoryBase::RegisterFactory( AnalyzeImageIOFactory::New());
>>>> firstTime = false;
>>>> }
>>>> }
>>>>
>>>> }
>>>>
>>>> Does it look correct to you? I'm using Release-1-2-0 also.
>>>>
>>>> Thanks,
>>>>
>>>> Raghavendra.
>>>>
>>>> ----- Original Message -----
>>>> From: "Luis Ibanez" <luis.ibanez@kitware.com>
>>>> To: "Raghavendra Chandrashekara" <rc3@doc.ic.ac.uk>
>>>> Cc: <insight-users@public.kitware.com>
>>>> Sent: Friday, March 28, 2003 12:31 PM
>>>> Subject: Re: [Insight-users] Possible bug in itkAnalyzeImageIO? : Gipl
>>>
>>>
>> not
>>
>>>> being found
>>>>
>>>>
>>>>
>>>>
>>>>> Hi Raghavendra,
>>>>>
>>>>> It looks like the GiplImageIO factory
>>>>> is not being found.
>>>>>
>>>>> Could you please double check the file
>>>>>
>>>>> Insight/Code/IO
>>>>>
>>>>> itkImageIOFactory.cxx
>>>>>
>>>>> and see if in line 99, the following
>>>>> line is not commented out :
>>>>>
>>>>>
>>>>> ObjectFactoryBase::RegisterFactory( GiplImageIOFactory::New() );
>>>>>
>>>>>
>>>>> This lines registers the Gipl reader/writer
>>>>> in the factory mechanism.
>>>>>
>>>>> (I'm assuming you are using ITK version 1.2)
>>>>>
>>>>>
>>>>>
>>>>> Regards,
>>>>>
>>>>>
>>>>>
>>>>> Luis
>>>>>
>>>>>
>>>>> ---------------------------------------------
>>>>> Raghavendra Chandrashekara wrote:
>>>>>
>>>>>
>>>>>> Hi Kent,
>>>>>>
>>>>>> Okay I tried the patch that you sent. Now another exception is
>>>>>> thrown,
>>>>>
>>>>>
>>>> this
>>>>
>>>>
>>>>>> time by the itkImageFileReader class:
>>>>>>
>>>>>> Exception object caught!
>>>>>>
>>>>>> itk::ImageFileReaderException (0x815ace8)
>>>>>> Location: "Unknown"
>>>>>> File: /vol/vipdata/packages/InsightCVS/Code/IO/itkImageFileReader.txx
>>>>>> Line: 94
>>>>>> Description: Could not create IO object for file
>>>>>> ../../Data/Synthetic/cube.gipl
>>>>>>
>>>>>> Does this mean that the gipl image is not being recognised by any of
>>>>>
>>>>>
>> the
>>
>>>> IO
>>>>
>>>>
>>>>>> classes?
>>>>>>
>>>>>> Raghavendra.
>>>>>>
>>>>>> ----- Original Message -----
>>>>>> From: "Kent Williams" <kent@mail.psychiatry.uiowa.edu>
>>>>>> To: "Raghavendra Chandrashekara" <rc3@doc.ic.ac.uk>
>>>>>> Sent: Wednesday, March 19, 2003 6:46 PM
>>>>>> Subject: Re: [Insight-users] Possible bug in itkAnalyzeImageIO?
>>>>>>
>>>>>>
>>>>>> I don't know why you're getting that far into CanRead, since the 1.2
>>>>>
>>>>>
>>>> version
>>>>
>>>>
>>>>>> of itkAnalyzeImageIO.cxx checks for valid extensions first before
>>>>>
>>>>>
>> trying
>>
>>>> to
>>>>
>>>>
>>>>>> open the file.
>>>>>>
>>>>>> I think that it's incorrect to throw an exception in CanRead
>>>>>> anyway; my
>>>>>> suggestion to you is to patch around line 1000 in that file thusly:
>>>>>>
>>>>>> CHANGE:
>>>>>> if( local_InputStream.fail() )
>>>>>> {
>>>>>> ExceptionObject exception(__FILE__, __LINE__);
>>>>>> exception.SetDescription("File cannot be read");
>>>>>> throw exception;
>>>>>> }
>>>>>> local_InputStream.read( (char *)&(this->m_hdr), sizeof(struct
>>>>>
>>>>>
>>>> dsr) );
>>>>
>>>>
>>>>>> if( local_InputStream.eof() )
>>>>>> {
>>>>>> ExceptionObject exception(__FILE__, __LINE__);
>>>>>> exception.SetDescription("Unexpected end of file");
>>>>>> throw exception;
>>>>>> }
>>>>>> TO:
>>>>>> if( local_InputStream.fail() )
>>>>>> {
>>>>>> return false;
>>>>>> }
>>>>>> local_InputStream.read( (char *)&(this->m_hdr), sizeof(struct
>>>>>
>>>>>
>>>> dsr) );
>>>>
>>>>
>>>>>> if( local_InputStream.eof() )
>>>>>> {
>>>>>> return false;
>>>>>> }
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Insight-users mailing list
>>>>>> Insight-users@public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Insight-users mailing list
>>>>> Insight-users@public.kitware.com
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Insight-users mailing list
>>> Insight-users@public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>
>>
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>>
>
>
>
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