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Re: [science-iwg] New viz project follow up

Philip,

Yeah, might as well. I think they would be a good fit.

Jay

On Tue, May 26, 2015 at 1:21 PM, Austenfeld, Marcel <maustenfeld@xxxxxxxxxxxxxx> wrote:
Hello Phillip,

funny that you asked. Today I wrote a mail to a ImageJ2 developer and architect Curtis Rueden which I know from the last ImageJ conferences regarding ImageJ2 to clarify some questions from today.

Best regards

Marcel


________________________________
Von: science-iwg-bounces@xxxxxxxxxxx [science-iwg-bounces@xxxxxxxxxxx]" im Auftrag von "Philip Wenig [philip.wenig@xxxxxxxxxxxxx]
Gesendet: Dienstag, 26. Mai 2015 18:26
An: science-iwg@xxxxxxxxxxx
Betreff: Re: [science-iwg] New viz project follow up

Hi folks,

would it make sense to ask Wayne Rasband, respectively the NIH and the ImageJ2 team to join the Science WG? Or is this an too early stage?

I just think of "the earlier the better". Currently, I'm struggling a bit to resolve all 3rd party library dependencies for ChemClipse ... especially the NetCDF library dependencies are hard to resolve. As ImageJ2 is re-designed, potential pitfalls could be addressed beforehand.


Philip

Am 26.05.2015 um 17:55 schrieb Matt.Gerring@xxxxxxxxxxxxx<mailto:Matt.Gerring@xxxxxxxxxxxxx>:
Hello Jay,

I have no idea what I am agreeing to in agreeing to help but I am sure we can think of something along the way!

Integrating imglib2 looks like a very helpful line of attack for us and we are happy to have learnt about it from Marcel.

Matt


From: science-iwg-bounces@xxxxxxxxxxx<mailto:science-iwg-bounces@xxxxxxxxxxx> [mailto:science-iwg-bounces@xxxxxxxxxxx] On Behalf Of Jay Jay Billings
Sent: 26 May 2015 16:23
To: Science Industry Working Group
Subject: Re: [science-iwg] New viz project follow up

Very good! Thanks Marcel!
Jay

On Tue, May 26, 2015 at 11:05 AM, Austenfeld, Marcel <maustenfeld@xxxxxxxxxxxxxx<mailto:maustenfeld@xxxxxxxxxxxxxx>> wrote:
Hello Jay,

you can list me in the proposal as an initial committer if that is possible and I can help.

Best regards

Marcel

Von: science-iwg-bounces@xxxxxxxxxxx<mailto:science-iwg-bounces@xxxxxxxxxxx> [mailto:science-iwg-bounces@xxxxxxxxxxx<mailto:science-iwg-bounces@xxxxxxxxxxx>] Im Auftrag von Jay Jay Billings
Gesendet: Dienstag, 26. Mai 2015 16:38
An: Science Industry Working Group

Betreff: Re: [science-iwg] New viz project follow up

Matt and Marcel,

I think you have provided a sufficient discussion of imaging capabilities that we can Imaging to the scope, especially since I know how much tech are in both DAWNSci and Bio7 for dealing with images.
I wanted to address your emails collectively since I think the proposed capabilities intersect and/or complement each other. At this point I am not looking to define a single architecture, but to collect existing viz technologies in the SWG under one project. The very next step after we get an initial contribution composed of these technologies will be to define the architecture and plan the (multi-institutional) work to implement it.
In the beginning we can have both the IPlottingSystem/IDataset infrastructure from DAWNSci and Marcel's ImageJ-based tools from Bio7 sitting side by side in the same project. Once we deal with all the necessary CQs and IP issues, we can look at the next steps, like building a bridge from Marcel's existing ImageJ capabilities to IDataSet or getting around the SWT_AWT bridge (which, btw, doesn't seem to be a problem on our Linux machines).
So, that all being said, can I count on a code contribution from each of you for the viz project (IPlottingSystem/IDataset from DAWNSci and Image-J based tools from Bio7) and list you in the proposal as initial committers?
Jay

On Tue, May 26, 2015 at 8:24 AM, <Matt.Gerring@xxxxxxxxxxxxx<mailto:Matt.Gerring@xxxxxxxxxxxxx>> wrote:
Marcel,

Thanks. Java2D in Swing is awesome but any solution that requires the SWT-AWT bridge would be unacceptable from the perspective of us becoming part of it. The imglib2 stuff looks good however one of us will investigate if we can bridge the imglib2 algorithms with IDataset, perhaps something like:

Img<FloatType> img = DatasetImgFactory.wrapImg(iDataset);
… // Do some ImageJ filters
iDataset = DatasetImgFactory.unwrapImg(img);

Or maybe the array will modify in-place, so the unwrap is not needed, we’ll see :) This kind of thing is done with other classes which wrap data in order to bridge gaps in the functionality for instance with BoofCV<http://boofcv.org/>.

Sincerely,

Matt

From: Austenfeld, Marcel [mailto:maustenfeld@xxxxxxxxxxxxxx<mailto:maustenfeld@xxxxxxxxxxxxxx>]
Sent: 26 May 2015 12:13
To: Science Industry Working Group; Gerring, Matt (DLSLtd,RAL,LSCI); science-iwg@xxxxxxxxxxx<mailto:science-iwg@xxxxxxxxxxx>
Subject: AW: Re: [science-iwg] New viz project follow up

Hello Matt,


1.      This is indeed separated in ImageJ2.

2.      I had some painful experiences with that but I have a running Linux SWT_AWT implementation with the help of some changed Albireo sources (I started to investigate ImageJ2). However the image data visualization from ImageJ1 don’t has to be a Swing panel it can be converted to a SWT image. To convert the whole ImageJ interface to SWT is possible but in SWT_AWT easier to maintain. I selected a hybrid with SWT tabs.

3.      In addition I tried the way: Swing->embedded in JavaFX->embedded in SWT which also worked as an easy SWT_AWT alternative. However I think this could be a little bit less effective than the SWT_AWT bridge though I didn’t tested it much.


Best regards

Marcel



Von: science-iwg-bounces@xxxxxxxxxxx<mailto:science-iwg-bounces@xxxxxxxxxxx> [mailto:science-iwg-bounces@xxxxxxxxxxx] Im Auftrag von Matt.Gerring@xxxxxxxxxxxxx<mailto:Matt.Gerring@xxxxxxxxxxxxx>
Gesendet: Dienstag, 26. Mai 2015 12:52
An: science-iwg@xxxxxxxxxxx<mailto:science-iwg@xxxxxxxxxxx>; mike.milinkovich@xxxxxxxxxxx<mailto:mike.milinkovich@xxxxxxxxxxx>
Betreff: Re: [science-iwg] New viz project follow up

Hello Marcel,

Couple of problems we have had with ImageJ were:
1. Hard coded links between data and visualization which I think were solved in ImageJ2 but we have not tried it yet
2. The viewer is swing and using the AWT-SWT bridge on linux can be risky

Sincerely,

Matt

From: science-iwg-bounces@xxxxxxxxxxx<mailto:science-iwg-bounces@xxxxxxxxxxx> [mailto:science-iwg-bounces@xxxxxxxxxxx] On Behalf Of Austenfeld, Marcel
Sent: 26 May 2015 11:41
To: science-iwg@xxxxxxxxxxx<mailto:science-iwg@xxxxxxxxxxx>; mike.milinkovich@xxxxxxxxxxx<mailto:mike.milinkovich@xxxxxxxxxxx>
Subject: Re: [science-iwg] New viz project follow up


Hello,



I already wrote this to Jay to bring in my image library experience.



As an image lib I would highly recommend ImageJ (public domain) and (or) it extension ImageJ2:



http://imagej.nih.gov/ij/



which is the fastest Java imaging library around.



ImageJ2 (BSD):



https://github.com/imagej/imagej/



is a redesign of ImageJ with a more flexible data model using ImgLib2:



http://imglib2.net/



"ImageJ2 is a new version of ImageJ<http://imagej.net/> seeking to strengthen both the software and its community. Internally, it is a total redesign of ImageJ, but it is backwards compatible with ImageJ 1.x via a "legacy layer" and features a user interface closely modeled after the original.......ImageJ2 completely isolates the image processing logic from the graphical user interface (UI), allowing ImageJ2 commands to be used in many contexts...."



Please note that ImageJ1 is still actively developed by it’s developer Wayne Rasband , too, and is a fantastic imaging library easy to use (with many examples only).



Using this lib with the Bio-Formats package you can open all kind of image formats:



http://www.openmicroscopy.org/site/products/bio-formats



Note that these libs are coming from microscopy imaging but are used in very different domains!



If you would like to open geospatial or GIS formats then I think you should use the GeoTools libs:



http://www.geotools.org/.



There is also a Java JNI lib available for the GDAL library which is the Swiss Army tool for geospatial raster or vector formats (integrated in almost all GIS tools):



http://trac.osgeo.org/gdal/wiki/GdalOgrInJava



Anothermulti pupose image library actively! developed is the Apache Commons Imaging lib:



https://commons.apache.org/proper/commons-imaging/



Some other links to free or proprietary libs can be found on the ImageJ website:



http://imagej.nih.gov/ij/links.html





However checkout the ImageJ libs. You will be surprised what you can do with it:



http://imagej.nih.gov/ij/docs/guide/146.html





Best regards



Marcel





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