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List: insight-users
Subject: Re: [ITK-users] [ITK] itk Python: origin of DICOM slice does not change
From: Matt McCormick <matt.mccormick () kitware ! com>
Date: 2016-09-20 18:14:23
Message-ID: CALzTN-Scn3xsRFQJX3mnnxX8fYn_=zyoytiw9cHGRKhOmPi2mA () mail ! gmail ! com
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A Python version of the example is available here:
http://review.source.kitware.com/#/c/21554/
On Tue, Sep 20, 2016 at 1:03 PM, Matt McCormick
<matt.mccormick@kitware.com> wrote:
> Hi Fabio,
>
> In the example, a 3D non-DICOM is written to the output (e.g. NRRD).
> Your code must have something different if it is writing 2D DICOM
> files. DicomImageReadWrite is also deprecated [1].
>
> DICOM writing support in ITK could be improved. It is recommended to
> write to other output formats.
>
> HTH,
> Matt
>
> [1] https://github.com/InsightSoftwareConsortium/ITK/blob/077527e86d96daf88663fda6bf7abeb1e92b9d9d/Examples/IO/DicomSeriesReadImageWrite.cxx#L22-L28
>
> On Tue, Sep 20, 2016 at 10:26 AM, D'Isidoro Fabio <fisidoro@ethz.ch> wrote:
> > Hi,
> >
> > I tried this
> >
> > ImageIOType = itk.GDCMImageIO
> > gdcmImageIO = ImageIOType.New()
> > reader.SetImageIO(gdcmImageIO)
> > reader.Update()
> >
> > ...
> >
> > writer_output.SetInput(filter.GetOutput())
> > writer_output.UseInputMetaDataDictionaryOff()
> > gdcmImageIO_output = ImageIOType.New()
> > writer_output.SetImageIO(gdcmImageIO_output)
> >
> > but the written DICOM image has default origin (0,0) mm and default spacing (1., \
> > 1.).
> > Also, the example "DicomImageReadWrite" too does not create a new instance of the \
> > gdcmImageIO.
> >
> >
> >
> > -----Original Message-----
> > From: Matt McCormick [mailto:matt.mccormick@kitware.com]
> > Sent: Dienstag, 20. September 2016 16:03
> > To: D'Isidoro Fabio
> > Cc: Dženan Zukić; insight-users@itk.org; Timothee Evain
> > Subject: Re: [ITK-users] [ITK] itk Python: origin of DICOM slice does not change
> >
> > 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@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@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@gmail.com]
> > > > Sent: Dienstag, 20. September 2016 14:46
> > > > To: D'Isidoro Fabio
> > > > Cc: Timothee Evain; insight-users@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@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@telecom-paristech.fr]
> > > > Sent: Dienstag, 20. September 2016 10:35
> > > > To: D'Isidoro Fabio
> > > > Cc: insight-users@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@ethz.ch>
> > > > À: insight-users@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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> > > >
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> > > >
> > > > Please keep messages on-topic and check the ITK FAQ at:
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> > > >
> > > > Please keep messages on-topic and check the ITK FAQ at:
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> > > >
> > > > Follow this link to subscribe/unsubscribe:
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> > > >
> > > >
> > > >
> > > >
> > > > _____________________________________
> > > > Powered by www.kitware.com
> > > >
> > > > Visit other Kitware open-source projects at
> > > > http://www.kitware.com/opensource/opensource.html
> > > >
> > > > Kitware offers ITK Training Courses, for more information visit:
> > > > http://www.kitware.com/products/protraining.php
> > > >
> > > > Please keep messages on-topic and check the ITK FAQ at:
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> > > >
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> > > >
_____________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php
Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ
Follow this link to subscribe/unsubscribe:
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