[Insight-users] incorrect z-spacing in GDCM reading: oops

Wed May 11 14:27:00 EDT 2005

George,

	strtok is definitely one function I would strongly suggest not to use. 
Not only does it modify your input (so you cannot even use 
string::c_str()) but also it is not thread safe.

Anyway a nicer patch would be:

#include <iostream>

int main()
{
   float x,y,z;
   std::string s = "0.100000  \\0.200000\t\\0.300000  ";
   std::cout <<   sscanf( s.c_str(), "%f \\%f \\%f ", &x, &y, &z) << 
std::endl;
   std::cout << x << "," << y << "," << z << std::endl;
   return 1;
}

Seems to solve the problem. I am committing it to both gdcm CVS/ gdcm 
1.0 and ITK

Thanks,
Mathieu

Li, George (NIH/NCI) wrote:
> Mathieu and Jim:
> 
> The dicom file is generated from my own program, which can communicate 
> with several commercial treatment planning software, where dicom is used
> as standard image format. 
> 
> For more robust I/O, I would suggest to use fgets() then parse the entire 
> line with strtok() with "\\" as the deliminator. They are all C function 
> calls though. Therefore, a slight format change in the file won't corrupt 
> the reading.
> 
> Of course, it takes the performance as the expense. But, it does not cost 
> much.
> 
> Regards,
> 
> George
> 
> 
> -----Original Message-----
> From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com] 
> Sent: Wednesday, May 11, 2005 1:53 PM
> To: Miller, James V (Research)
> Cc: Li, George (NIH/NCI); insight-users at itk.org; Luis Ibanez
> Subject: Re: [Insight-users] incorrect z-spacing in GDCM reading: oops
> 
> 
> Jim,
> 
> 	Ok my mistake you are right sscanf is failing on that:
> 
> #include <iostream>
> 
> int main()
> {
>    float x,y,z;
>    std::string s = "0.000000  \\0.000000  \\0.000000  ";
>    std::cout <<   sscanf( s.c_str(), "%f\\%f\\%f", &x, &y, &z) << std::endl;
>    return 1;
> }
> 
> It only reads the first floating point value...
> 
> 
> George where did you get this DICOM file ?
> 
> I'll convert the sscanf to a more robust stringstream approach,
> 
> 
> Any suggestion welcome,
> Mathieu
> 
> 
> Miller, James V (Research) wrote:
> 
>>It looks like the ImagePositionPatients in these headers
>>are formatted like
>>
>>0.00000 \0.0000 \0.0000
>>
>>with a space before the "\".  Normally, these fields appears as
>>
>>0.0000\0.0000\0.0000
>>
>>I have never seen spaces before the "\", does DICOM allow this?
>>
>>Jim
>>
>>-----Original Message-----
>>From: insight-users-bounces+millerjv=crd.ge.com at itk.org
>>[mailto:insight-users-bounces+millerjv=crd.ge.com at itk.org]On Behalf Of 
>>Li, George (NIH/NCI)
>>Sent: Wednesday, May 11, 2005 12:44 PM
>>To: Li, George (NIH/NCI); 'Mathieu Malaterre'
>>Cc: 'insight-users at itk.org'; 'Luis Ibanez'
>>Subject: RE: [Insight-users] incorrect z-spacing in GDCM reading
>>
>>
>>Mathieu:
>>
>>Here are the dicom header information. The strings are direct dump, So 
>>should provide some info on the images. Hopefully, you can tell Me an 
>>alternative way to send images to you and test them from your End.
>>
>>Thanks,
>>
>>George
>>
>>
>>-----Original Message-----
>>From: Li, George (NIH/NCI)
>>Sent: Wednesday, May 11, 2005 12:38 PM
>>To: 'Mathieu Malaterre'
>>Cc: 'insight-users at itk.org'; 'Luis Ibanez'
>>Subject: RE: [Insight-users] incorrect z-spacing in GDCM reading
>>
>>
>>
>>Mathieu:
>>
>>I cannot send the 2 images as attachment, because they are 205KB each. 
>>I got a message from ITK, saying that there is limit of 40KB per mail 
>>And my following mail was discarded.
>>
>>Any other way I can send the images?
>>
>>Thanks,
>>
>>George
>>
>>
>>
>>-----Original Message-----
>>From: Li, George (NIH/NCI)
>>Sent: Wednesday, May 11, 2005 12:32 PM
>>To: 'Mathieu Malaterre'
>>Cc: 'Luis Ibanez'; insight-users at itk.org
>>Subject: RE: [Insight-users] incorrect z-spacing in GDCM reading
>>
>>
>>Thanks, Mathieu:
>>
>>I have included two image slices, together with their header 
>>information,
>>which is printed into text files from one of my own program. Actually, the
> 
> 
>>dicom image files are generated from my program, too. Theoretically, the 
>>syntax should follow dicom3 definition on 'Image Position Patient' /
> 
> 'Image 
> 
>>Orientation Patient'. I did not check how GDCM parses the string.
>>
>>The spacing should be 3.4mm, but GDCM got 1.00mm.
>>
>>Look forward to hearing from you.
>>
>>Thanks.
>>
>>George
>>
>>
>>-----Original Message-----
>>From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com]
>>Sent: Wednesday, May 11, 2005 12:00 PM
>>To: Li, George (NIH/NCI)
>>Cc: 'Luis Ibanez'; insight-users at itk.org
>>Subject: Re: [Insight-users] incorrect z-spacing in GDCM reading
>>
>>
>>George,
>>
>>	Your code looks fine. The algorithm for finding the z spacing is
> 
> kind
> 
>>of tricky. So I am wondering if:
>>
>>1. Your images might not have proper 'Image Position Patient' / 'Image
>>Orientation Patient'
>>
>>2. If they have, maybe gdcm is not able to parse the string properly.
>>
>>Could it be possible that you send me at least two images from this
>>dataset ?
>>
>>If not, you'll have to turn the code to be more verbose in particular
>>when entering the function:
>>
>>
>>     gdcm::SerieHelper::ImagePositionPatientOrdering
>>
>>Thanks,
>>Mathieu
>>
>>Li, George (NIH/NCI) wrote:
>>
>>
>>>Hi, Luis and ITK users:
>>>
>>>I recently tried to adopt the GDCM dicom code for loading dicom series 
>>>images, and then consequently saving images in dicom series. However, 
>>>when I read the images, the spacing in z-direction is incorrect, 
>>>leading to a compressed image
>>>in z-direction. Here is the related code, could you help me to identify 
>>>anything
>>>wrong?
>>>
>>>class CMDIDataITKIO
>>>{
>>>public:
>>> CMDIDataITKIO();
>>> virtual ~CMDIDataITKIO();
>>>public:
>>> void ReadGDCM_DicomImages(const char*, SeriesReaderType::Pointer);
>>> void WriteGDCM_DicomImages(const char*, ImageType::Pointer);
>>>private:
>>> // initiate in the ctor, and raise clean flag in dtor.
>>> GDCMImageIOType::Pointer m_gdcmIO;
>>> GDCMSeriesNames::Pointer m_gdcmNames;
>>> SeriesReaderType::Pointer m_gdcmReader;
>>>}
>>>
>>>
>>>void CMDIDataITKIO::ReadGDCM_DicomImages(const char* folderName,
>>>                                                                      
>>>SeriesReaderType::Pointer reader)
>>>{
>>>if(!m_gdcmIO) m_gdcmIO = GDCMImageIOType::New();
>>>if(!m_gdcmNames) m_gdcmNames = GDCMSeriesNames::New();
>>>
>>>// Get the DICOM filenames from the directory
>>>m_gdcmNames->SetInputDirectory(folderName);
>>>
>>>reader->SetFileNames( m_gdcmNames->GetInputFileNames() );
>>>reader->SetImageIO( m_gdcmIO );
>>>
>>>try {
>>> reader->Update();
>>>   }
>>>catch (itk::ExceptionObject &excp) {
>>> std::cerr << "Exception thrown while writing the image" << 
>>>std::endl;
>>> std::cerr << excp << std::endl;
>>>   }
>>>}
>>>Thanks,
>>>
>>>George
>>>
>>>
>>>
>>>----------------------------------------------------------------------
>>>--
>>>
>>>_______________________________________________
>>>Insight-users mailing list
>>>Insight-users at itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
>>
>>_______________________________________________
>>Insight-users mailing list
>>Insight-users at itk.org 
>>http://www.itk.org/mailman/listinfo/insight-users
>>
>>
> 
> 