<div dir="ltr"><div><div><div><div><div><div><div>Hello Fabio,<br><br></div>The main difference between itk.GetArrayFromImage() and itk.PyBuffer[ImageType].GetArrayFromImage() is that itk.GetAraryFromImage() is a wrapping of itk.PyBuffer[ImageType].GetArrayFromImage() in Python that automatically finds the type of the input image (and is a shorted command line). The reason why this worked but not itk.PyBuffer[ImageType.GetArrayFromImage() is because in the wrapping, if a filter is given instead of an image, the output of the filter will be used.<br><br></div>Which means that what really happen is that you gave a filter to a function (itk.PyBuffer[ImageType].GetArrayFromImage()) expecting an image.<br></div>If you want to work with the long command, you have to make sure that the input is an image:<br><br></div>image=source.GetOutput()<br>itk.PyBuffer[ImageType].GetArrayFromImage(image)<br><br></div>And then it should work.<br></div>Hope this helps,<br><br></div>Francois<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 2, 2017 at 11:20 AM, D'Isidoro Fabio <span dir="ltr"><<a href="mailto:fisidoro@ethz.ch" target="_blank">fisidoro@ethz.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div link="blue" vlink="purple" lang="DE-CH">
<div class="m_-869863128702153880WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi Francois,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">It works with your commands, the difference being the use of:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal">itk.GetArrayFromImage(source)<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">in your version, instead of:<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal">itk.PyBuffer[ImageType].<wbr>GetArrayFromImage(source)<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">in my version.<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">May you explain me the difference, and why using PyBuffer does not work for this case?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Also, when using VectorImage I get the error “No module named 'ITKQuadEdgeMeshPython'”. This is the only module that failed
in my ITK Python build. Is this a known bug or it was just for my build?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Thank you!<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Fabio.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u><u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"> Francois Budin [mailto:<a href="mailto:francois.budin@kitware.com" target="_blank">francois.budin@<wbr>kitware.com</a>]
<br>
<b>Sent:</b> Freitag, 28. April 2017 23:12<span class=""><br>
<b>To:</b> D'Isidoro Fabio <<a href="mailto:fisidoro@ethz.ch" target="_blank">fisidoro@ethz.ch</a>><br>
</span><b>Cc:</b> Lowekamp, Bradley (NIH/NLM/LHC) [C] <<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>>; <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>
<b>Subject:</b> Re: [ITK-users] [ITK] ITK PyBuffer get physical point coordinates<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<div>
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<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hello Fabio,<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">I was able to use this filter in Python. Here is the commands I typed:<br>
In [14]: ImageType=itk.Image[itk.<wbr>Vector[itk.F,2],2]<br>
<br>
In [15]: source=itk.<wbr>PhysicalPointImageSource[<wbr>ImageType].New()<br>
<br>
In [16]: source.SetSize([5,5])<br>
<br>
In [17]: source.SetOrigin([0,0])<br>
<br>
In [18]: source.SetSpacing([.5,.5])<br>
<br>
In [19]: source.Update()<br>
<br>
In [20]: itk.GetArrayFromImage(source)<br>
Out[20]: <br>
itkndarray([[[ 0. , 0. ],<br>
[ 0.5, 0. ],<br>
[ 1. , 0. ],<br>
[ 1.5, 0. ],<br>
[ 2. , 0. ]],<br>
<br>
[[ 0. , 0.5],<br>
[ 0.5, 0.5],<br>
[ 1. , 0.5],<br>
[ 1.5, 0.5],<br>
[ 2. , 0.5]],<br>
<br>
[[ 0. , 1. ],<br>
[ 0.5, 1. ],<br>
[ 1. , 1. ],<br>
[ 1.5, 1. ],<br>
[ 2. , 1. ]],<br>
<br>
[[ 0. , 1.5],<br>
[ 0.5, 1.5],<br>
[ 1. , 1.5],<br>
[ 1.5, 1.5],<br>
[ 2. , 1.5]],<br>
<br>
[[ 0. , 2. ],<br>
[ 0.5, 2. ],<br>
[ 1. , 2. ],<br>
[ 1.5, 2. ],<br>
[ 2. , 2. ]]], dtype=float32)<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">It also worked with VectorImages:<br>
<br>
In [22]: ImageType=itk.VectorImage[itk.<wbr>F,2]<br>
<br>
In [23]: source=itk.<wbr>PhysicalPointImageSource[<wbr>ImageType].New()<br>
<br>
In [24]: source.SetOrigin([0,0])<br>
<br>
In [25]: source.SetSize([5,5])<br>
<br>
In [26]: source.SetSpacing([.5,.5])<br>
<br>
In [27]: source.Update()<br>
<br>
In [28]: itk.GetArrayFromImage(source)<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal">To answer your questions:<u></u><u></u></p>
</div>
<p class="MsoNormal">1) This filter is only wrapped over image of vectors and vector images. You can have the list of types that are available in Python with itk.PhysicalPointImageSource.<wbr>GetTypes()<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">2) You may have a version of ITK Python for which VectorImage is not wrapped for PyBuffer. You can try to update your ITK Python [1]<u></u><u></u></p>
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<p class="MsoNormal">Hope this helps,<u></u><u></u></p>
</div>
<p class="MsoNormal">Francois<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal"><br>
[1] <a href="https://github.com/InsightSoftwareConsortium/ITKPythonPackage" target="_blank">https://github.com/<wbr>InsightSoftwareConsortium/<wbr>ITKPythonPackage</a><u></u><u></u></p>
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</div></div><div>
<p class="MsoNormal"><u></u> <u></u></p>
<div><div><div class="h5">
<p class="MsoNormal">On Fri, Apr 28, 2017 at 12:05 PM, D'Isidoro Fabio <<a href="mailto:fisidoro@ethz.ch" target="_blank">fisidoro@ethz.ch</a>> wrote:<u></u><u></u></p>
</div></div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
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<div><div><div class="h5">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Thank you for your reply.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="m_-869863128702153880m3566153338244404760msolistparagraph"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">1)</span><span style="font-size:7.0pt;color:#1f497d" lang="EN-US">
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">I have tried as a first step the following:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="text-indent:35.4pt">
<span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">DRRPhy =
</span><span style="font-size:9.5pt;font-family:Consolas;color:#6f008a" lang="EN-US">itk</span><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">.PhysicalPointImageSource[</span><span style="font-size:9.5pt;font-family:Consolas;color:#6f008a" lang="EN-US">i<wbr>tk</span><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">.Image[</span><span style="font-size:9.5pt;font-family:Consolas;color:#6f008a" lang="EN-US">itk</span><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">.Point[</span><span style="font-size:9.5pt;font-family:Consolas;color:#6f008a" lang="EN-US">itk</span><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">.F,
Dimension], Dimension]].New()</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">But I get the error:
</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="text-indent:35.4pt">
<span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">KeyError: "itkTemplate : No template (<class 'itkPointPython.itkPointF3'>, 3) for the itk::Image class"
</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="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.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:35.4pt">
<span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">sourceImage =
</span><span style="font-size:9.5pt;font-family:Consolas;color:#6f008a" lang="EN-US">itk</span><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">.PhysicalPointImageSource[</span><span style="font-size:9.5pt;font-family:Consolas;color:#6f008a" lang="EN-US">i<wbr>tk</span><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">.VectorImage[</span><span style="font-size:9.5pt;font-family:Consolas;color:#6f008a" lang="EN-US">itk</span><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">.F,
Dimension]].New()</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:35.4pt;text-autospace:none">
<span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">sourceImage.SetSize(size)</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:35.4pt;text-autospace:none">
<span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">sourceImage.SetSpacing(<wbr>spacing)</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:35.4pt;text-autospace:none">
<span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">sourceImage.SetOrigin(origin)</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:35.4pt;text-autospace:none">
<span style="font-size:9.5pt;font-family:Consolas;color:green" lang="EN-US">#DRRPhy.SetIndex(start) it does not work, how to set the start index?</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:35.4pt">
<span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">DRRPhy.SetDirection(direction)</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US"> </span><u></u><u></u></p>
<p class="m_-869863128702153880m3566153338244404760msolistparagraph"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">2)</span><span style="font-size:7.0pt;color:#1f497d" lang="EN-US">
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">However, using PyBuffer to get a numpy array form that does not work:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
</div></div><p class="MsoNormal" style="text-indent:35.4pt">
<span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">sourceImageArray =
</span><span style="font-size:9.5pt;font-family:Consolas;color:#6f008a" lang="EN-US">itk</span><span style="font-size:9.5pt;font-family:Consolas;color:black" lang="EN-US">. PyBuffer[ImageType].<wbr>GetArrayFromImage(sourceImage)</span><u></u><u></u></p><div><div class="h5">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">I get the error:
</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="text-indent:35.4pt">
<span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">AttributeError: '<wbr>itkPhysicalPointImageSourceVIF<wbr>3' object has no attribute 'GetLargestPossibleRegion'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Am I doing the right thing in point 1) ?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">How could I solve point 2) ?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Thank you !</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Fabio.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><u></u><u></u></p>
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<div style="border:none;border-top:solid #e1e1e1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"> Lowekamp,
Bradley (NIH/NLM/LHC) [C] [mailto:<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a><wbr>]
<br>
<b>Sent:</b> Donnerstag, 27. April 2017 23:16<br>
<b>To:</b> D'Isidoro Fabio <<a href="mailto:fisidoro@ethz.ch" target="_blank">fisidoro@ethz.ch</a>><br>
<b>Cc:</b> <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>
<b>Subject:</b> Re: [ITK] [ITK-users] ITK PyBuffer get physical point coordinates</span><u></u><u></u></p>
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</div>
<div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Hi!
<u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">You can generate an image of the physical locations of each pixel with the PhysicalPointImageSource filter:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="https://itk.org/Doxygen/html/classitk_1_1PhysicalPointImageSource.html" target="_blank">https://itk.org/Doxygen/html/<wbr>classitk_1_<wbr>1PhysicalPointImageSource.html</a><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<div>
<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.<u></u><u></u></p>
</div>
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<p class="MsoNormal"> <u></u><u></u></p>
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<div>
<p class="MsoNormal">After you generate the point image you should be able to convert to with the same method.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">HTH,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Brad<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Apr 27, 2017, at 4:58 PM, D'Isidoro Fabio <<a href="mailto:fisidoro@ethz.ch" target="_blank">fisidoro@ethz.ch</a>> wrote:<u></u><u></u></p>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Hallo,</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">I know it’s possible to get a numpy array of an itk image with:</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"> </span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">itk.PyBuffer[ImageType].<wbr>GetArrayFromImage(Image)</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"> </span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">Is it by any chance also possible to obtain a (flattended) numpy array of the physical coordinates of
the image pixels too?</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"> </span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">Thank you!</span><u></u><u></u></p>
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