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

Tue Sep 20 10:02:32 EDT 2016

Hi Fabio,

Also, if

  writer_output.SetImageIO(gdcmImageIO)

is called, and gdcmImageIO is being re-used, then gdcmImageIO will
re-use its MetaDataDictionary. So a new instance of GDCMImageIO
shoulrd be passed to avoid using the old MetaDataDictionary.

HTH,
Matt

On Tue, Sep 20, 2016 at 9:14 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Hi Fabio,
>
> As suggested by Tim, call  ->UseInputMetaDataDictionaryOff() to use
> the Origin from the itk::Image. The MetaDataDictionary tags will
> indicate an Origin that is not correct.
>
> HTH,
> Matt
>
> On Tue, Sep 20, 2016 at 9:06 AM, D'Isidoro  Fabio <fisidoro at ethz.ch> wrote:
>> Hi,
>>
>>
>>
>> It doesn’t work.
>>
>>
>>
>> Filter.GetOuput() already has the new origin (I can print it and it’s
>> right). Something wrong is in the writing process.
>>
>>
>>
>> By the way, I noticed this problem occurs for change of the origin and of
>> rescaling intensities. It does not occur for changes in size and spacing.
>>
>>
>>
>> Regards,
>>
>> Fabio
>>
>>
>>
>> From: Dženan Zukić [mailto:dzenanz at gmail.com]
>> Sent: Dienstag, 20. September 2016 14:46
>> To: D'Isidoro Fabio
>> Cc: Timothee Evain; insight-users at itk.org
>> Subject: Re: [ITK-users] [ITK] itk Python: origin of DICOM slice does not
>> change
>>
>>
>>
>> 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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