<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Verdana;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 2.0cm 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="DE-CH" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Ok, thanks. Moe specifically I am using now
<u>Visual Studio 2017 Preview</u>.<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"><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">Fabio.</span><span 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"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Dženan Zukić [mailto:dzenanz@gmail.com]
<br>
<b>Sent:</b> Mittwoch, 12. </span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">April 2017 21:54<br>
<b>To:</b> D'Isidoro Fabio <fisidoro@ethz.ch><br>
<b>Cc:</b> Matt McCormick <matt.mccormick@kitware.com>; insight-users@itk.org<br>
<b>Subject:</b> Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif">Hi Fabio,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif">let me give it a try with VS2017 and Wrapping+NumPy. I will report back when I have an update.<o:p></o:p></span></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif">Regards,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif">Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)<o:p></o:p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Wed, Apr 12, 2017 at 2:16 PM, D'Isidoro Fabio <<a href="mailto:fisidoro@ethz.ch" target="_blank">fisidoro@ethz.ch</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<p class="MsoNormal">Thank you. I am trying to build ITK Wrap Python with Module_BridgeNumPy=ON with Visual Studio 2017.<br>
<br>
I get the following type of errors:<br>
<br>
12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\xstring(1905,26): error G3F63BFAE: constexpr variable '_Memcpy_move_offset' must be initialized by a constant expression<br>
12> static constexpr size_t _Memcpy_move_offset = offsetof(_Mydata_t, _Bx);<br>
12> ^ ~~~~~~~~~~~~~~~~~~~~~~~~<br>
12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\stdexcept:23:21: note: in instantiation of template class 'std::basic_string<char, std::char_traits<char>, std::allocator<char> >' requested here<br>
12> : _Mybase(_Message.c_str())<br>
12> ^<br>
12>C:/Program Files (x86)/Microsoft Visual Studio/Preview/Community/VC/Tools/MSVC/14.10.25017/include\xstring:1905:48: note: cast that performs the conversions of a reinterpret_cast is not allowed in a constant expression<br>
12> static constexpr size_t _Memcpy_move_offset = offsetof(_Mydata_t, _Bx);<br>
12> ^<br>
12>C:/Program Files (x86)/Windows Kits/10/Include/10.0.10586.0/ucrt\stddef.h:38:32: note: expanded from macro 'offsetof'<br>
12> #define offsetof(s,m) ((size_t)&reinterpret_cast<char const volatile&>((((s*)0)->m)))<br>
<br>
<br>
The build worked with Visual Studio 2015 instead.<br>
<br>
Can I fix this issue with Visual Studio 2017 somehow?<br>
<br>
Thank you.<br>
<br>
----------------------------------------------------------------------<br>
Fabio D’Isidoro - PhD Student<br>
Institute of Biomechanics<br>
HPP O 14<br>
Hönggerbergring 64<br>
8093 Zürich, Switzerland<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><br>
-----Original Message-----<br>
From: Matt McCormick [mailto:<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>]<br>
Sent: Montag, 3. April 2017 20:41<br>
To: D'Isidoro Fabio <<a href="mailto:fisidoro@ethz.ch" target="_blank">fisidoro@ethz.ch</a>><br>
Cc: <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>
Subject: Re: [ITK-users] ITK Python: numpy to itk image (and viceversa)<br>
<br>
Hallo Fabio,<br>
<br>
<br>
> I use ITK with Python Wrap. I need to interface my Python code with a<br>
> Cython-wrapped C++ code that takes only numpy array as input and<br>
> returns numpy array as output.<br>
<br>
Cool. By the way, you may be interested in scikit-build [1], which is a good way to build Cython-wrapped C++ code. We are using it for the ITK and SimpleITK Python packages, and it has good Cython and CMake support.<br>
<br>
<br>
> Hence, I need to convert the Python itk images into numpy array to be<br>
> given as input to the wrapped C++ code, and then convert the numpy<br>
> array in output from the wrapped C++ code back into python itk images.<br>
><br>
><br>
><br>
> Question 1) How can I do that in an efficient way? I found some posts<br>
> on itk.PyBuffer but I could not find anywhere any reference on how to<br>
> install it on my itk wrap build.<br>
<br>
Yes, itk.PyBuffer works great for that. Please review a PR for some additional documentation:<br>
<br>
<a href="https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18" target="_blank">
https://github.com/InsightSoftwareConsortium/ITKBridgeNumPy/pull/18</a><br>
<br>
This has been available in ITK for a few releases as a Remote module, which can be enabled by setting<br>
<br>
Module_BridgeNumPy=ON<br>
<br>
in ITK's CMake configuration.<br>
<br>
<br>
Since ITK 4.11.0, it is easier to build since it does not require the NumPy headers.<br>
<br>
<br>
In current ITK Git master (to be 4.12.0) the module is enabled by default.<br>
<br>
<br>
Nightly ITK Python packages for ITK Git master are now being built:<br>
<br>
<a href="https://github.com/InsightSoftwareConsortium/ITKPythonPackage" target="_blank">
https://github.com/InsightSoftwareConsortium/ITKPythonPackage</a><br>
<br>
macOS and Linux are available. Windows packages will be available over the coming weeks.<br>
<br>
<br>
<br>
> Question 2) The purpose of writing a part of my algorithm in C++ is to<br>
> speed up the code. If the conversion between python itk images and<br>
> numpy arrays is slow, I would lose all the speed gain obtained with the C++ implementation.<br>
> Are there better ways to deal with that?<br>
<br>
The newer versions ITKBridgeNumPy use a NumPy array view, which does not do any copies during the conversion, and it is very fast.<br>
<br>
<br>
HTH,<br>
Matt<br>
<br>
<br>
[1] <a href="http://scikit-build.org/" target="_blank">http://scikit-build.org/</a><br>
_____________________________________<br>
Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
<br>
Visit other Kitware open-source projects at<br>
<a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
<br>
Kitware offers ITK Training Courses, for more information visit:<br>
<a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
<br>
Please keep messages on-topic and check the ITK FAQ at:<br>
<a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
<br>
Follow this link to subscribe/unsubscribe:<br>
<a href="http://public.kitware.com/mailman/listinfo/insight-users" target="_blank">http://public.kitware.com/mailman/listinfo/insight-users</a><o:p></o:p></p>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</div>
</body>
</html>