| Re: [science-iwg] Review BoF EclipseCon |
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Today's Topics:
1. Re: Review BoF EclipseCon (Philip Wenig)
----------------------------------------------------------------------
Message: 1
Date: Tue, 05 Nov 2013 08:35:55 +0100
From: Philip Wenig <philip.wenig@xxxxxxxxxxxxxx>
To: science-iwg@xxxxxxxxxxx
Subject: Re: [science-iwg] Review BoF EclipseCon
Message-ID: <52789FDB.4000102@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
Hi Matt,
that sounds reasonable. I like the idea to have the IDN notation
"org.eclipse.scisoft.xxx" and extension points for different
implementations. We should also include a section for algorithms.
Probably an export format extension point would be also fine to create
scientific images ready for publication e.g. with R or other tools.
org.eclipse.scisoft
org.eclipse.scisoft.1d
org.eclipse.scisoft.2d
org.eclipse.scisoft.3d
org.eclipse.scisoft.ui
org.eclipse.scisoft.ui.1d
org.eclipse.scisoft.ui.2d
org.eclipse.scisoft.ui.3d
Extensions:
org.eclipse.scisoft.supplier.savitzkygolay
org.eclipse.scisoft.supplier.firstdeviation
org.eclipse.scisoft.supplier.seconddeviation
...
org.eclipse.scisoft.ui.supplier.swtchart
org.eclipse.scisoft.ui.supplier.xygraph
org.eclipse.scisoft.ui.supplier.javafx
That's just an idea.
Best Regards,
Philip
Am 04.11.2013 10:32, schrieb Matt.Gerring@xxxxxxxxxxxxx:
>
> Hi Philip,
>
> Yes I would propose something which is swappable i.e. the plotting is
> well separated from the algorithm/data. So plotting details do not
> leak into eclipse parts, instead they interact with an interface. Any
> design we choose should have to be abstract -- including from
> underlying plot objects (draw2d figures, javafx scene graphs, jogl
> objects etc. are all not in the interface!).
>
> At Diamond, we have had several plotting engines (3) in the past, so
> we have learned this over a hard earned period of time. It would mean
> that anyone could contribute a plotting system (by extension point)
> and that any user from the group can swap plotting whenever they need
> -- providing there is an implementation. I can imagine that we would
> want to swap the javafx 1D plotting into the interface fairly soon! --
> tying ourselves to any particular plotting engine would be a bad idea.
> Although I am a fan (most of the time) and would-be contributor to
> xy-graph.
>
> I would be willing to send around the interfaces with examples how to
> use them later this month if people want that. I suggest that the
> package be org.eclipse.scisoft.xxx where scisoft stands for scientific
> software.
>
> Nomenclature: Can we name the plotting type after the dimensionality
> of the data? This gives room in the nomenclature to have a name for
> images which cannot be called 3D -- so they must be 2D!
>
> *Xy-graphs, scatter, pie, area* - *1D* (e.g.
> XY-Graphs are1D data shown with two axes)
>
> *Images, surfaces, contours, vector plots* - *2D* (Note surfaces are
> 2D data shown with 3 axes and using 3D scene graph)
>
> *Iso-surface, other volume rendering* - *3D*? (They are slices
> from 3D data)
>
> Best Regards,
>
> Matt
>
> *From:*science-iwg-bounces@xxxxxxxxxxx
> [mailto:science-iwg-bounces@xxxxxxxxxxx] *On Behalf Of *Philip Wenig
> *Sent:* 02 November 2013 11:45
> *To:* science-iwg@xxxxxxxxxxx
> *Subject:* Re: [science-iwg] Review BoF EclipseCon
>
> Hi Matt,
>
> I think that's a great idea to have APIs and abstract respectively
> generalized methods and views for 2D and 3D data. Attached are two
> screenshots of DAWN and OpenChrom. Both screenshots show profiles,
> despite the fact that both have completely different data models (XRD
> and GC/MS). Hence, it would be great to have an unified and flexible
> API. Moreover, it would be great use the existing knowledge and to
> build upon the interfaces and methods that are already available in
> DAWN, Bioclipse, OpenChrom and others.
>
> ----------------------------------
> Profile Views
> ----------------------------------
> 2D / 3D
> Variable measurement units and descriptions for each Axis
> 1st Derivative
> 2nd Derivative
> ...
> Overlay
>
> ----------------------------------
> Profile Methods
> ----------------------------------
> Smoothing Algorithms (Savitzky-Golay, ...)
> Peak Detektion (1st Derivative, ..., Deconvolution, ...)
> Peak Integration (Gaussian model, ...)
> Peak Fitting (Correlation Optimized Warping, Dynamic Time Warping, ...)
> ...
>
> In my opinion, such abstract handling of profile data would make it
> much more easier for others (students, post-docs, scientists, ...) to
> implement additional algorithms. Furthermore, data from different
> detectors like XRD, NMR, GC/FID, GC/MS MS/MS could be handled in an
> unified way as long as it produces profile data. In addition, all
> specific calculations can still be executed by specialized frameworks
> for e.g. XRD (DAWN) or GC/MS (OpenChrom). Wouldn't that be great?
>
> /"As long as your going to be thinking anyway, think big."/ Donald Trump
>
>
> Cheers,
> Philip
>
> Am 01.11.2013 16:09, schrieb Matt.Gerring@xxxxxxxxxxxxx
> <mailto:Matt.Gerring@xxxxxxxxxxxxx>:
>
> Hi Philip,
>
>
>
> Yes it was a very positive step, well done in getting it organised. I am willing to write the documents and circulate these for agreement as we agreed.
>
>
>
> Diamond are able and, subject to review, interested in providing interfaces and a reference implementation for all of the features mentioned in the meeting, including everything in Jans recent email. I have a concrete idea of how this could happen and we can detail this in the documents. We would obviously start gradually so that the searches of license agreement can be performed on each API provided. In fact even more gradual than that - we should agree on interfaces of each module, I can provide the starting point for these too including examples of how to use the API. The APIs are elegant and powerful to use and I hope you will like them.
>
>
>
> Since the talk I did at eclipse con was not busily attended, I am looking forward to the video of the demonstration being available on the youtube channel. Then people can see how cool the features the team here has worked on are, and decide if they are interested in working with us.
>
>
>
> Best Regards,
>
>
>
> Matt
>
>
>
> -----Original Message-----
>
> From:science-iwg-bounces@xxxxxxxxxxx <mailto:science-iwg-bounces@xxxxxxxxxxx> [mailto:science-iwg-bounces@xxxxxxxxxxx] On Behalf Of Philip Wenig
>
> Sent: 01 November 2013 13:17
>
> To:science-iwg@xxxxxxxxxxx <mailto:science-iwg@xxxxxxxxxxx>
>
> Subject: [science-iwg] Review BoF EclipseCon
>
>
>
> Hi folks,
>
>
>
> the BoF was fantastic, wasn't it!
>
> I really feel that the time has come to bring our idea of a scientific working group to reality :-).
>
>
>
>
>
> Best
>
> Philip
>
>
>
>
>
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. Philip Wenig
>
> http://www.openchrom.net
>
> https://www.xing.com/profile/Philip_Wenig
> http://de.linkedin.com/pub/philip-wenig/2a/4a8/877
> ~~~~~~~~~~~~~~~~~~~~~~~~
>
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--
~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Philip Wenig
http://www.openchrom.net
https://www.xing.com/profile/Philip_Wenig
http://de.linkedin.com/pub/philip-wenig/2a/4a8/877
~~~~~~~~~~~~~~~~~~~~~~~~
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