[ITK-users] [ITK] itk Python: origin of DICOM slice does not change

[Dženan Zukić]

Hi Fabio,

did you try setting the origin directly on the result image:
filter->Update();
outImage=filter->GetOutput();
outImage->SetOrigin(new_origin);
writer_output->SetInput(outImage);

Regards,
Dženan


On Tue, Sep 20, 2016 at 8:34 AM, D'Isidoro Fabio <fisidoro at ethz.ch> wrote:

> Hi,
>
> I am currently using the command:
>
> writer_output.UseInputMetaDataDictionaryOff()
>
> If I don't use it, the image is saved with default origin (0,0) mm and
> default spacing (1., 1.).
>
> According to the manual for UseInputMetaDataDictionaryOff(), "this flag
> defines whether the MetaDataDictionary to use will be the one from the
> input image or the one already set in the ImageIO object." My understanding
> is that if I set it off, the DICOM slice will be written with current
> values (and not the input values), which is what I want. But this seems not
> to happen.
>
> Relevant parts of my code:
>
> filter.SetOutputOrigin( new_origin )
> writer_output.SetInput(filter.GetOutput())
> writer_output.UseInputMetaDataDictionaryOff()
> writer_output.SetImageIO(gdcmImageIO)
> writer_output.Update()
>
> Maybe the function UseInputMetaDataDictionaryOff() does not work properly
> for the itk with Python wrapping?
>
> Thanks for your answer.
>
> Fabio.
>
> -----Original Message-----
> From: Timothee Evain [mailto:tevain at telecom-paristech.fr]
> Sent: Dienstag, 20. September 2016 10:35
> To: D'Isidoro Fabio
> Cc: insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] itk Python: origin of DICOM slice does not
> change
>
> Hi,
>
> You refer to the DICOMImageReadWrite example. If you don't change the
> writing part, I think your problem comes from the fact that you assign the
> read metadata directly to the output ( ->UseInputMetaDataDictionaryOff()
> ) so the original origin will be saved.
>
> HTH,
>
> Tim
>
> ----- Mail original -----
> De: "D'Isidoro Fabio" <fisidoro at ethz.ch>
> À: insight-users at itk.org
> Envoyé: Lundi 19 Septembre 2016 22:09:39
> Objet: [ITK] [ITK-users] itk Python: origin of DICOM slice does not change
>
>
>
> Hi,
>
>
>
> Following the code ResampleImageFilter2.cxx, I am applying an Identity
> Transform to a single DICOM slice, I change the origin to
>
>
>
> output_origin = reader.GetOutput().GetOrigin() + offset
>
>
>
> and I write the transformed DICOM slice into a new DICOM slice (following
> the code DICOMImageReadAndWrite.cxx).
>
>
>
> I visualize the written DICOM slice with a viewer (it’s an itk-vtk
> segmentation software).
>
>
>
> The transformed DICOM slice looks as it should. Surprisingly however the
> viewer shows the original input values as origin. This is confirmed by the
> fact that if I read with an itk script the written DICOM slice again, and I
> print the information of the DICOM slice, the origin is still the original
> one and not the modified one.
>
>
>
> How could this be?
>
>
>
> Original DICOM slice:
>
>
>
>
>
>
>
> Transformed DICOM slice:
>
>
>
>
>
>
>
>
>
> Thank you for help,
>
>
>
> Fabio.
>
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