[Insight-users] setSpacing() Ignored writing to files

[Bill Lorensen]

Felix,

Use itkChangeInformationImageFilter to change spacing,origin,direction...

Bill

On Jan 24, 2008 12:28 PM, <bollen at ipk-gatersleben.de> wrote:

> Hi Bill,
>
> Yes, a default value coming from MATLABs libtiff is 76px per inch-may I
> should try to change it on the data generation side...
>
> I know TIF (custom) tags themself are quite an issue. I have read
> through some posts regarding SetSpacing() and that its use is
> discouraged within ITK for obvious reasons.
>
> Could you give any suggestions how to circumvade the problem in
> reading/writing the TIFs with different spacing by setting the spacing
> manually?
>
> I tried to change the spacing directly on the caster->GetOutput()
> without effect as it is const I read. I am not shure how to properly
> change the spacing.
>
> Best Regards!
>
> Felix.
>
>
>
>
>
> Quoting Bill Lorensen <bill.lorensen at gmail.com>:
>
> > Felix,
> >
> > I just looked at the code in itkTIFFImageIO.cxx. We do in fact compute a
> > spacing on read if it exists. We don't write the spacing however.
> >
> > Here is the dilemma. TIFF supports units of measurement. Either inches,
> > centimeters or none. In itk, we don't specify units although for medical
> > imaging they are usually mm's. At write time, we don't know what units
> to
> > specify. We could assume mm's and convert that to cm's I guess.
> >
> > Bill
> > On Jan 24, 2008 11:08 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> >
> >> Felix,
> >>
> >> I don't believe that png supports spacing in the header. tiff might,
> but
> >> maybe we aren't writing the spacing. Can you file a bug following the
> >> procedure in:
> >>
> >> http://www.itk.org/Wiki/ITK_Procedure_for_Contributing_Bug_Fixes
> >>
> >> Thanks,
> >>
> >> Bill
> >>   On Jan 24, 2008 10:49 AM, Felix Bollenbeck <bollen at ipk-gatersleben.de
> >
> >> wrote:
> >>
> >> > Hi ITK Users!
> >> >
> >> > I'm having troubles writing the spacing to a transformed image.
> >> > Although the resampler gets the input-image spacing, the written
> image
> >> > which is read in the next iteration has the default [1 1] spacing
> >> > causing troubles.
> >> >
> >> > The images are written to tiff files and haven an initial spacing of
> >> > .37... after transformation and writing, i read files with [1 1]
> >> > spacing, although
> >> >
> >> >  resample->SetOutputSpacing(fixedImage->GetSpacing());
> >> >
> >> > and fixed image has [.37 .37]!
> >> >
> >> > I have tried png files too, in case this is a TIF specific issue
> same-so
> >> > I conclude it is my mistake here, but where?
> >> >
> >> > Thanks for your help,
> >> >
> >> > Felix.
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >  resample->SetSize(
>  fixedImage->GetLargestPossibleRegion().GetSize()
> >> > );
> >> >  resample->SetOutputOrigin(fixedImage->GetOrigin());
> >> >  resample->SetOutputSpacing(fixedImage->GetSpacing());
> >> >  resample->SetDefaultPixelValue(0);
> >> >  resample->Update();
> >> >
> >> > //#############
> >> >  const SpacingType outSpacing = resample->GetOutputSpacing();
> >> >  std::cout <<"SIZE spacing-out  " << outSpacing[0]<< "    " <<
> >> > outSpacing[1] << std::endl;
> >> > //#############
> >> >
> >> >
> >> >  typedef  unsigned char  OutputPixelType;
> >> >  typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
> >> >  typedef itk::CastImageFilter< FixedImageType,OutputImageType >
> >> > CastFilterType;
> >> >  typedef itk::ImageFileWriter< OutputImageType >  WriterType;
> >> >
> >> >
> >> >  WriterType::Pointer      writer =  WriterType::New();
> >> >  CastFilterType::Pointer  caster =  CastFilterType::New();
> >> >  writer->SetFileName(outImageName);
> >> >  caster->SetInput(resample->GetOutput());
> >> >  writer->SetInput(caster->GetOutput());
> >> >  writer->Update();
> >> > _______________________________________________
> >> > Insight-users mailing list
> >> > Insight-users at itk.org
> >> > http://www.itk.org/mailman/listinfo/insight-users
> >> >
> >>
> >>
> >
>
>
>
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