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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Is there some way that java.nio API’s can help here?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Possibly the ByteBuffer or MappedByteBuffer:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://docs.oracle.com/javase/8/docs/api/java/nio/ByteBuffer.html">http://docs.oracle.com/javase/8/docs/api/java/nio/ByteBuffer.html</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://docs.oracle.com/javase/8/docs/api/java/nio/MappedByteBuffer.html">http://docs.oracle.com/javase/8/docs/api/java/nio/MappedByteBuffer.html</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Gerrick<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> vtkusers [mailto:vtkusers-bounces@vtk.org]
<b>On Behalf Of </b>Berk Geveci<br>
<b>Sent:</b> Wednesday, July 01, 2015 9:03 AM<br>
<b>To:</b> Alexandre Dufour<br>
<b>Cc:</b> vtkdev; vtkusers@vtk.org<br>
<b>Subject:</b> Re: [vtkusers] [vtk-developers] [EXTERNAL] vtk 6.3 and vtk 7.0<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I am fairly novice in Java so I apologize if this sounds naive. Doesn't Java do its own memory management and actually automatically move data from one memory location to another? How does one map a Java array to a C++ array and make sure
that it is not moved and of course garbage collected?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Interfacing to numpy arrays works fine because Python provides a buffer interface where it is guaranteed that a Python object holds a buffer (an array essentially) that does not move. The Python wrappers simply expose a functionality that
allows the C++ layer to get a pointer from a buffer object. Then this array can simply be passed to any C++ method that takes an array.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This is the only efficient way of sharing array between the two layers. Doing a "zero copy" array where each array access such as GetTuple() goes through a Java layer would be terribly inefficient and impractical. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal">-berk<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Wed, Jul 1, 2015 at 9:00 AM, Alexandre Dufour <<a href="mailto:adufour@pasteur.fr" target="_blank">adufour@pasteur.fr</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi,<o:p></o:p></p>
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<p class="MsoNormal">I am not familiar with the nitty-gritty of the wrapping aspects, but as a Java-based user (<a href="http://icy.bioimageanalysis.org" target="_blank">icy.bioimageanalysis.org</a>), I believe the issue has to do with the fact that transferring
some Java array down to a vtk structure (via any setJavaArray() method) always(?) implies a copy of said structure down to the C++ layer, hence the issue of duplication. This typically happens when your data/image structure is first handled on the Java side,
then passed over to VTK for rendering purposes.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Does this make sense? Is there any way around this? I doubted that for a while, but then remembered the good old Unsafe class in Java that might help do “dirty but efficient” communication…<o:p></o:p></p>
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<p class="MsoNormal">My 2 (unexperienced) cents. Very excited about this anyhow!!<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Alexandre<o:p></o:p></p>
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<p class="MsoNormal"><i><span style="color:black">—</span></i><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><i><span style="font-size:10.5pt;color:black">Alexandre Dufour, PhD</span></i></b><span style="font-size:10.5pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:6.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><i><span style="font-size:10.5pt;color:black">Senior Research Fellow @ </span></i><span style="font-size:10.5pt;color:black"><a href="http://www.bioimageanalysis.org" target="_blank"><i>Biological Image Analysis</i></a><i> group</i><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><a href="http://www.pasteur.fr/en" target="_blank"><i>Institut Pasteur</i></a><i>, Dpt. of Cell Biology & Infection, Paris campus (France)</i><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-size:10.5pt;color:black">CNRS UMR 3691 “Pathological and Physiological Cell Dynamics” </span></i><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:6.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><i><span style="font-size:10.5pt;color:black">Meet </span></i><span style="font-size:10.5pt;color:black"><a href="http://icy.bioimageanalysis.org" target="_blank"><i>Icy</i></a><i>, the next-generation Bioimage Informatics platform</i><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 30 Jun 2015, at 15:46, Utkarsh Ayachit <<a href="mailto:utkarsh.ayachit@kitware.com" target="_blank">utkarsh.ayachit@kitware.com</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">Gerrick,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The *new* zero copy design literally started a week or two ago, so it is in its infancy, but I will write a design document soon. It doesn't however do anything new for access through wrapped languages. What exactly is your use-case. I
am not sure what aspect is lacking in the current implementation in that regard.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Utkarsh<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Jun 29, 2015 at 6:04 PM Gerrick Bivins <<a href="mailto:Gerrick.Bivins@halliburton.com" target="_blank">Gerrick.Bivins@halliburton.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">“</span>* deprecate the existing zero copy array API in preparation for a significant refactoring
that will come in 7.0. The refactor will make zero copy arrays both simpler to use and perform better.”<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Where can I find more information about this?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Does the “Zero copy array refactor” expose this framework to wrapped languages, Java in particular?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Currently the duplication of data is one of the things holding up adoption of VTK in our application.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Gerrick</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> vtk-developers [mailto:<a href="mailto:vtk-developers-bounces@vtk.org" target="_blank">vtk-developers-bounces@vtk.org</a>]
<b>On Behalf Of </b>David E DeMarle<br>
<b>Sent:</b> Monday, June 29, 2015 9:42 AM<br>
<b>To:</b> vtkdev; <a href="mailto:vtkusers@vtk.org" target="_blank">vtkusers@vtk.org</a><br>
<b>Subject:</b> [EXTERNAL] [vtk-developers] vtk 6.3 and vtk 7.0</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hey vtkers,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">We are hoping to do a vtk 6.3 release in the next couple of weeks and then immediately follow that up with a 7.0 release.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">We'd are putting out a 6.3 out in order to:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">* deprecate the existing zero copy array API in preparation for a significant refactoring that will come in 7.0. The refactor will make zero copy arrays both simpler to use and
perform better.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">* package up all of the progress that has been made in the master branch's OpenGL2 surface and volume rendering. The vtkpython binaries will switch over to using the OpenGL2 back
end this release.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Please let us know if you have any feedback, critical bugs especially, and developers let us know if there is any work you have in a partially finished state that we should be sure
to get into 6.3.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">If all goes well we'll have a release candidate for 6.3 next week.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">David E DeMarle<br>
Kitware, Inc.<br>
R&D Engineer<br>
21 Corporate Drive<br>
Clifton Park, NY 12065-8662<br>
Phone: <a href="tel:518-881-4909" target="_blank">518-881-4909</a><o:p></o:p></p>
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<p class="MsoNormal">This e-mail, including any attached files, may contain confidential and privileged information for the sole use of the intended recipient. Any review, use, distribution, or disclosure by others is strictly prohibited. If you are not the
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<p class="MsoNormal">Please keep messages on-topic and check the VTK FAQ at: <a href="http://www.vtk.org/Wiki/VTK_FAQ" target="_blank">
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