[vtkusers] [vtk-developers] [EXTERNAL] vtk 6.3 and vtk 7.0

Wed Jul 1 11:44:51 EDT 2015

Is there some way that java.nio API’s can help here?
Possibly the ByteBuffer or MappedByteBuffer:
http://docs.oracle.com/javase/8/docs/api/java/nio/ByteBuffer.html
http://docs.oracle.com/javase/8/docs/api/java/nio/MappedByteBuffer.html

Gerrick

From: vtkusers [mailto:vtkusers-bounces at vtk.org] On Behalf Of Berk Geveci
Sent: Wednesday, July 01, 2015 9:03 AM
To: Alexandre Dufour
Cc: vtkdev; vtkusers at vtk.org
Subject: Re: [vtkusers] [vtk-developers] [EXTERNAL] vtk 6.3 and vtk 7.0

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?

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.

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.

Best,
-berk

On Wed, Jul 1, 2015 at 9:00 AM, Alexandre Dufour <adufour at pasteur.fr<mailto:adufour at pasteur.fr>> wrote:
Hi,

I am not familiar with the nitty-gritty of the wrapping aspects, but as a Java-based user (icy.bioimageanalysis.org<http://icy.bioimageanalysis.org>), 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.

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…

My 2 (unexperienced) cents. Very excited about this anyhow!!

Alexandre

—
Alexandre Dufour, PhD

Senior Research Fellow @ Biological Image Analysis<http://www.bioimageanalysis.org> group
Institut Pasteur<http://www.pasteur.fr/en>, Dpt. of Cell Biology & Infection, Paris campus (France)
CNRS UMR 3691 “Pathological and Physiological Cell Dynamics”

Meet Icy<http://icy.bioimageanalysis.org>, the next-generation Bioimage Informatics platform

On 30 Jun 2015, at 15:46, Utkarsh Ayachit <utkarsh.ayachit at kitware.com<mailto:utkarsh.ayachit at kitware.com>> wrote:

Gerrick,

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.

Utkarsh

On Mon, Jun 29, 2015 at 6:04 PM Gerrick Bivins <Gerrick.Bivins at halliburton.com<mailto:Gerrick.Bivins at halliburton.com>> wrote:
“* 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.”

Where can I find more information about this?
Does the “Zero copy array refactor” expose this framework to wrapped languages, Java in particular?
Currently the duplication of data is one of the things holding up adoption of VTK in our application.

Gerrick

From: vtk-developers [mailto:vtk-developers-bounces at vtk.org<mailto:vtk-developers-bounces at vtk.org>] On Behalf Of David E DeMarle
Sent: Monday, June 29, 2015 9:42 AM
To: vtkdev; vtkusers at vtk.org<mailto:vtkusers at vtk.org>
Subject: [EXTERNAL] [vtk-developers] vtk 6.3 and vtk 7.0

Hey vtkers,

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.

We'd are putting out a 6.3 out in order to:
* 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.
* 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.

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.

If all goes well we'll have a release candidate for 6.3 next week.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909<tel:518-881-4909>
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 intended recipient (or authorized to receive information for the intended recipient), please contact the sender by reply e-mail and delete all copies of this message.
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