On Tue, Nov 5, 2013 at 6:16 PM, <science-iwg-request@xxxxxxxxxxx> wrote:
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Today's Topics:
1. Re: Review BoF EclipseCon (UOMo)
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Message: 1
Date: Tue, 5 Nov 2013 18:16:11 +0100
From: UOMo <uomo@xxxxxxxxxxx>
To: science-iwg@xxxxxxxxxxx
Subject: Re: [science-iwg] Review BoF EclipseCon
Message-ID:
<CAAGawe0a_u9KMZn9prfTidYKYoFcMeURnC6V_zUn2dJ5o=
Joeg@xxxxxxxxxxxxxx>
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Did I miss anything being wrong with "org.eclipse.science" or why would we
prefer "scisoft"?
As a matter of fact, the term "SciSoft" (maybe not so critical for a Java
sub-package, but still odd) seems to be used by a product or family of
Astrological products already:
Scisoft for Mac OSX Intel is a collection of astronomical software for Mac
OS X Intel >10.5 and above. It is similar to the ESO Scisoft (
http://www.eso.org/scisoft/) >distribution but is not an official ESO
product. More information is available >at http://scisoftosx.dyndns.org.
Read more: Scisoft for Mac - Free download and software reviews - CNET
Download.com<
http://download.cnet.com/Scisoft/3000-2053_4-41468.html#ixzz2jnAaOeLM>
http://download.cnet.com/Scisoft/3000-2053_4-41468.html#ixzz2jnAaOeLM
If "scisoft" was a thought, I'd like to think about "science", in the end
both would work, but trying to avoid clashes with other projects or
commercial products seem to be in the interest of Eclipse where possible,
see "Mylar" -> "Mylyn";-)
http://www.sci-soft.com/ is also a site with commercial products claiming
to be around for the last 20 years.
Werner
On Tue, Nov 5, 2013 at 6:00 PM, <science-iwg-request@xxxxxxxxxxx> wrote:
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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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http://de.linkedin.com/pub/philip-wenig/2a/4a8/877
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