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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thank you for your reply.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><span style="mso-list:Ignore">1)<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I have tried as a first step the following:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-indent:35.4pt"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">DRRPhy =
</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:#6F008A">itk</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">.PhysicalPointImageSource[</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:#6F008A">itk</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">.Image[</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:#6F008A">itk</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">.Point[</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:#6F008A">itk</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">.F,
Dimension], Dimension]].New()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">But I get the error:
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-indent:35.4pt"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">KeyError: "itkTemplate : No template (<class 'itkPointPython.itkPointF3'>, 3) for the itk::Image class"
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">So I guess I can’t generate an image with itk.Points as PixelType. Therefore I chose to use a VectorImage as ImageType
in Input to the PhysicalPointImageSource.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:35.4pt"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">sourceImage =
</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:#6F008A">itk</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">.PhysicalPointImageSource[</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:#6F008A">itk</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">.VectorImage[</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:#6F008A">itk</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">.F,
Dimension]].New()<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:35.4pt;text-autospace:none"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">sourceImage.SetSize(size)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:35.4pt;text-autospace:none"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">sourceImage.SetSpacing(spacing)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:35.4pt;text-autospace:none"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">sourceImage.SetOrigin(origin)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:35.4pt;text-autospace:none"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:green">#DRRPhy.SetIndex(start) it does not work, how to set the start index?</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:35.4pt"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">DRRPhy.SetDirection(direction)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><span style="mso-list:Ignore">2)<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">However, using PyBuffer to get a numpy array form that does not work:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-indent:35.4pt"><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">sourceImageArray =
</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:#6F008A">itk</span><span lang="EN-US" style="font-size:9.5pt;font-family:Consolas;color:black">.PyBuffer[ImageType].GetArrayFromImage(sourceImage)</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I get the error:
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-indent:35.4pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">AttributeError: 'itkPhysicalPointImageSourceVIF3' object has no attribute 'GetLargestPossibleRegion'<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Am I doing the right thing in point 1) ?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">How could I solve point 2) ?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thank you !<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Fabio.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp@mail.nih.gov]
<br>
<b>Sent:</b> Donnerstag, 27. April 2017 23:16<br>
<b>To:</b> D'Isidoro Fabio <fisidoro@ethz.ch><br>
<b>Cc:</b> insight-users@itk.org<br>
<b>Subject:</b> Re: [ITK] [ITK-users] ITK PyBuffer get physical point coordinates<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi! <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You can generate an image of the physical locations of each pixel with the PhysicalPointImageSource filter:<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://itk.org/Doxygen/html/classitk_1_1PhysicalPointImageSource.html">https://itk.org/Doxygen/html/classitk_1_1PhysicalPointImageSource.html</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Very recently added is the SetReferenceImage, which can be use to copy the meta data from one image to the parameters of this filter. If your version is not super recent then you can manually set the Size, Spacing, Origin, Direction and
StartIndex.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">After you generate the point image you should be able to convert to with the same method.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">HTH,<o:p></o:p></p>
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<p class="MsoNormal">Brad<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On Apr 27, 2017, at 4:58 PM, D'Isidoro Fabio <<a href="mailto:fisidoro@ethz.ch">fisidoro@ethz.ch</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Hallo,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">I know it’s possible to get a numpy array of an itk image with:</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">itk.PyBuffer[ImageType].GetArrayFromImage(Image)</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Is it by any chance also possible to obtain a (flattended) numpy array of the physical coordinates of the image pixels too?</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thank you!</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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