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

Tue Sep 20 09:06:35 EDT 2016

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<mailto: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<mailto:tevain at telecom-paristech.fr>]
Sent: Dienstag, 20. September 2016 10:35
To: D'Isidoro Fabio
Cc: insight-users at itk.org<mailto: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<mailto:fisidoro at ethz.ch>>
À: insight-users at itk.org<mailto: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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