plastic-devs — Plastic Developers

Re: [Plastic-devs] spectrum load message

[Thomas B. <bo...@ne...>]

Hi Mark,


> So I've revised my proposal, as follows:
> 
>    boolean ivo://votech.org/spectrum/loadFromURL( String url, String id,
>                                                   Map meta )
> 
>       Loads a spectrum or SED. id is an identifier as for the VOTable
>       load message - use the URL if there's no reason to do otherwise.
>       The meta argument is a map/struct containing additional
>       information about the type of data found at url which encodes
>       the spectrum. The entries of this map take the form of
>       utype->value pairs, where the keys (utypes) are as defined
>       in the SSAP specification, e.g. "Access.Format" for MIME
>       type. As many or few of these entries as are known may be
>       filled in.
> 
> (...)
> 
> Sending this message should be easy to implement by an SSAP client
> (e.g. AstroScope) which wants to pass the spectrum selection on to
> viewers, since it can just scoop up the fields from the relevant
> row of the SSAP response VOTable and pass them on in a Map without
> having to know or care what they mean.

I agree, this sounds sensible and pragmatic to me.

> This message can of course be used to pass spectra around which
> do not result from actual SSAP queries, since you can add metadata
> map entries by hand as if they'd come from SSAP (or just leave the
> metadata map empty).

Indeed, it is important to leave the door open for spectra *not* coming
from an SSAP service (eg. local files, MySpace account). For those
spectra, we certainly won't have all the metadata Isa has described, and
it will be up to the spectrum tool to try to obtain needed metadata from
the spectrum itself.
Thus, I think we should precise that tools sending a
ivo://votech.org/spectrum/loadFromURL message should give as many
metadata information as they can, but that no parameter is really
'compulsory'.

Cheers,

Thomas

[Plastic-devs] wiki organisation

[Mark T. <m.b...@br...>]

All,

the current organisation of descriptions for the standard and 
proposed messages on the wiki (one table row per message) does not 
encourage detailed descriptions.  We have had many long discussions 
on some of these messages which are now buried in the list archives 
somewhere and hard to locate.

I suggest it would be a good idea to have a wiki page for each message
(e.g. SpectrumLoadFromURL), which would make it easier to record
properly detailed definitions of what each message, along with each
of its arguments, is supposed to mean.  These pages could also host 
the the various debates, clarifications, compromises etc which are
associated with the message, for historical interest and to inform
future debates about new messages or changes to existing ones.  
There would still a central page listing the messages and linking
to these per-message pages of course.

The question of who has the time or enthusiasm to re-organise the
existing documentation in this way is another matter however...

Mark

-- 
Mark Taylor   Astronomical Programmer   Physics, Bristol University, UK
m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/~mbt/

Re: [Plastic-devs] spectrum load message

[Mark T. <m.b...@br...>]

On Tue, 12 Sep 2006, Isa Barbarisi wrote:

> Dear Mark,
> 
> I agree with the approach about defining additional arguments in the 
> message related more to the type of object (spectrum) than to the 
> format  of this object (votable, fits..). In fact, this is what we tried 
> to do when we defined the first SSAP definition.
> During the process of implementation of VOSpec, we found that only a few 
> parameters are needed to manipulate most of the spectra formats. Of 
> course, not all the possible spectra serializations can be used in 
> VOSpec, but that collection of parameters allows our application to 
> display thousand of spectra in different formats from ~15 different 
> projects.
> 
> List of parameters:  C: compulsory - O: Optional
> ------------------------------------------------------------------------------------------------------------------------------------------- 
> 
> Title - <title> - C - e.g. "ISO SWS01  Spectrum Target: M31_BULGE"
> URL - <url> - C - e.g.   
> "http://pma.i....../jsp/product.jsp?obsno=40001501"
> ServerTitle - <server_title> - O - e.g. "ISO Data Archive"
> WaveLengthColumnName - <wave_column_name> - C - e.g. SWAAWAVE
> FluxColumnName - <flux_column_name> - C - e.g. SWAAFLUX
> WaveUnitsScaleq  - <wave_units_scaleq>  - C - e.g. 1.E-6
> WaveUnitsDimeq  - <wave_units_dimeq>  - C - e.g.  L
> FluxUnitsScaleq    - <flux_units_scaleq>    - C - e.g. 1.E-23
> FluxUnitsDimeq    - <flux_units_dimeq>    - C - e.g. MT-2
> Ra   - <ra> - O - e.g 10.691809995
> Dec - <dec> - O - e.g    41.27003
> Format - <format> - C - e.g spectrum/fits 
> --------------------------------------------------------------------------------------------------------------------------------------------- 
> 
> 
> Our proposal is to have (at least) all the compulsory fields in the 
> message, so VOSpec (as message consumer) and e.g. Aladin and Astroscope 
> (as message senders) could be immediately updated to load spectra using it.
> Note that all the information requested is already present in the 
> existing SSAP services, and it is going to be included (perhaps with 
> some minimal syntax changes) in the next SSAP specification.

Isa,

thanks for your message.  I hadn't given much thought to these additional
metadata items.  I suppose in most cases they can be obtained from
the spectrum itself after retrieval, but in some cases the information
is available before retrieval (and useful) because the relevant fields 
are filled in for each row of the SSAP response table.

So I've revised my proposal, as follows:

   boolean ivo://votech.org/spectrum/loadFromURL( String url, String id,
                                                  Map meta )

      Loads a spectrum or SED. id is an identifier as for the VOTable
      load message - use the URL if there's no reason to do otherwise.
      The meta argument is a map/struct containing additional 
      information about the type of data found at url which encodes 
      the spectrum. The entries of this map take the form of 
      utype->value pairs, where the keys (utypes) are as defined 
      in the SSAP specification, e.g. "Access.Format" for MIME
      type. As many or few of these entries as are known may be
      filled in.

Discussions on the SSAP standard including the most recent
draft can be found at http://www.ivoa.net/twiki/bin/view/IVOA/SsaInterface
(see sec 7.5 of the SSA query interface V0.95 doc).

Sending this message should be easy to implement by an SSAP client 
(e.g. AstroScope) which wants to pass the spectrum selection on to
viewers, since it can just scoop up the fields from the relevant 
row of the SSAP response VOTable and pass them on in a Map without 
having to know or care what they mean.

VO-friendly spectrum viewers such as VOSpec should be well-equipped 
to receive and act on such messages, since in order to understand
SSAP queries which they already do, they must know how to make
sense of fields keyed by utypes in this way.  The various optional
and compulsory parameters that you describe above can be included,
as well as any others that may be available.

And an added bonus is that decisions about what metadata items 
are/can be/should be passed by the message is taken care of by the
DAL/DM groups whose job it is to worry about such things, rather 
than us plastickers who (well, speaking for myself) may not 
understand spectra so well.

This message can of course be used to pass spectra around which
do not result from actual SSAP queries, since you can add metadata
map entries by hand as if they'd come from SSAP (or just leave the
metadata map empty).

Opinions?

Mark

-- 
Mark Taylor   Astronomical Programmer   Physics, Bristol University, UK
m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/~mbt/

Re: [Plastic-devs] spectrum load message

[Isa B. <Isa...@sc...>]

Dear Mark,

I agree with the approach about defining additional arguments in the 
message related more to the type of object (spectrum) than to the 
format  of this object (votable, fits..). In fact, this is what we tried 
to do when we defined the first SSAP definition.
During the process of implementation of VOSpec, we found that only a few 
parameters are needed to manipulate most of the spectra formats. Of 
course, not all the possible spectra serializations can be used in 
VOSpec, but that collection of parameters allows our application to 
display thousand of spectra in different formats from ~15 different 
projects.

List of parameters:  C: compulsory - O: Optional
------------------------------------------------------------------------------------------------------------------------------------------- 

Title - <title> - C - e.g. "ISO SWS01  Spectrum Target: M31_BULGE"
URL - <url> - C - e.g.   
"http://pma.i....../jsp/product.jsp?obsno=40001501"
ServerTitle - <server_title> - O - e.g. "ISO Data Archive"
WaveLengthColumnName - <wave_column_name> - C - e.g. SWAAWAVE
FluxColumnName - <flux_column_name> - C - e.g. SWAAFLUX
WaveUnitsScaleq  - <wave_units_scaleq>  - C - e.g. 1.E-6
WaveUnitsDimeq  - <wave_units_dimeq>  - C - e.g.  L
FluxUnitsScaleq    - <flux_units_scaleq>    - C - e.g. 1.E-23
FluxUnitsDimeq    - <flux_units_dimeq>    - C - e.g. MT-2
Ra   - <ra> - O - e.g 10.691809995
Dec - <dec> - O - e.g    41.27003
Format - <format> - C - e.g spectrum/fits 
--------------------------------------------------------------------------------------------------------------------------------------------- 


Our proposal is to have (at least) all the compulsory fields in the 
message, so VOSpec (as message consumer) and e.g. Aladin and Astroscope 
(as message senders) could be immediately updated to load spectra using it.
Note that all the information requested is already present in the 
existing SSAP services, and it is going to be included (perhaps with 
some minimal syntax changes) in the next SSAP specification.

I would like to have your opinion about this and hopefully discuss it in 
Moscow, if some of you are coming.

Cheers,
Isa



Mark Taylor wrote:

>Plastic Pals,
>
>I have documented a new proposed message for loading spectra at
>
>   http://eurovotech.org/twiki/bin/view/VOTech/PlasticMessagesProposal
>
>I had discussions with various people at Strasbourg about this;
>it is unlike the votable/loadFromURL and fits/image/loadFromURL
>messages in that it relates to the semantic content (it's a spectrum)
>rather than the data format (it's a FITS file) of the resource
>at the URL.  The reason for this is that there is a very wide range
>of possible serializations of a spectrum/SED (FITS 1-d array, FITS
>binary or ascii table, VOTable, FITS or VOTable serialisations of
>DM spectral data model as described at
>http://www.ivoa.net/internal/IVOA/IvoaDataModel/spec98c.pdf, ...),
>trying to cope with all possibilities could lead to an explosion
>in the number of messages.
>
>There are arguments for and against doing it this way, but on pragmatic
>grounds I think this is the most workable solution.  If you disagree,
>feel free to continue the debate here.
>
>Mark
>
>  
>

[Plastic-devs] spectrum load message

[Mark T. <m.b...@br...>]

Plastic Pals,

I have documented a new proposed message for loading spectra at

   http://eurovotech.org/twiki/bin/view/VOTech/PlasticMessagesProposal

I had discussions with various people at Strasbourg about this;
it is unlike the votable/loadFromURL and fits/image/loadFromURL
messages in that it relates to the semantic content (it's a spectrum)
rather than the data format (it's a FITS file) of the resource
at the URL.  The reason for this is that there is a very wide range
of possible serializations of a spectrum/SED (FITS 1-d array, FITS
binary or ascii table, VOTable, FITS or VOTable serialisations of
DM spectral data model as described at
http://www.ivoa.net/internal/IVOA/IvoaDataModel/spec98c.pdf, ...),
trying to cope with all possibilities could lead to an explosion
in the number of messages.

There are arguments for and against doing it this way, but on pragmatic
grounds I think this is the most workable solution.  If you disagree,
feel free to continue the debate here.

Mark

-- 
Mark Taylor   Astronomical Programmer   Physics, Bristol University, UK
m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/~mbt/

Re: [Plastic-devs] spectrum messaging

[Mark T. <m.b...@br...>]

On Fri, 8 Sep 2006, John Taylor wrote:

> 
> 
> Isa Barbarisi wrote:
> > Hi all,
> > sorry for my silence on this but I was on leave.. :-)
> >
> > Noel is right, currently VOSpec implements an old version of Plastic 
> > where the list of supported messages was left empty, this to indicate 
> > "all messages".
> >   
> Perhaps, I should have made the hub still support this "mode" for older 
> versions of the spec, but felt that since the Plastic community is still 
> relatively small it would be OK to ask people to update.  Apologies if 
> this has caused you any inconvenience.
> > We have managed to send spectra from VOQuest to VOSpec by the 
> > ivo://votech.org/votable/load message, sending the votable as String 
> > argument. And I can also send/receive spectra from Topcat&Others using 
> > the same messages, votable/load and votable/loadFromURL, getting the 
> > arguments and calling our internal methods to visualize them in VOSpec.
> > So no spectra messages have been used in VOSpec and this was kind of 
> > working around the issue.. so I'm actually happy to know about the 
> > beginning of this discussion, so that I could update the plastic 
> > implementation in VOSpec for spectra transfers, hopefully in the next 
> > release before Moscow.
> >   
> Then we'll have to work quickly.  We've had some discussions here at the 
> VOTech meeting (pity you couldn't make it!) and Mark is going to post 
> the ideas on the wiki soon.

Isa,

As John said, we discussed this in Strasbourg.  The conclusion 
seemed to be that the best thing would be to introduce a new
message with the semantics "load spectrum", with an additional 
arguments specifying the format (VOTable, Spectral Data Model FITS 
serialization, 1-d FITS array, ...) that the data was in.

This is not the approach that we've taken with previous messages, 
which have concentrated on the data format (VOTable, FITS) rather 
than the data semantics (source catalogue, 2-d image).  However,
spectra/SEDs seem in practice to be a bit different in that there 
are many different ways that they can be serialized.  So for 
pragmatic reasons I think this is the best way forward.
I'm planning to write a draft definition of such a message on
the wiki shortly.  However, if you disagree with this approach,
please post your arguments here shortly.  Incidentally, what 
formats can VOSpec load spectra from?

Mark
   
-- 
Mark Taylor   Astronomical Programmer   Physics, Bristol University, UK
m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/~mbt/

Re: [Plastic-devs] spectrum messaging

[John T. <jd...@ro...>]

Isa Barbarisi wrote:
> Hi all,
> sorry for my silence on this but I was on leave.. :-)
>
> Noel is right, currently VOSpec implements an old version of Plastic 
> where the list of supported messages was left empty, this to indicate 
> "all messages".
>   
Perhaps, I should have made the hub still support this "mode" for older 
versions of the spec, but felt that since the Plastic community is still 
relatively small it would be OK to ask people to update.  Apologies if 
this has caused you any inconvenience.
> We have managed to send spectra from VOQuest to VOSpec by the 
> ivo://votech.org/votable/load message, sending the votable as String 
> argument. And I can also send/receive spectra from Topcat&Others using 
> the same messages, votable/load and votable/loadFromURL, getting the 
> arguments and calling our internal methods to visualize them in VOSpec.
> So no spectra messages have been used in VOSpec and this was kind of 
> working around the issue.. so I'm actually happy to know about the 
> beginning of this discussion, so that I could update the plastic 
> implementation in VOSpec for spectra transfers, hopefully in the next 
> release before Moscow.
>   
Then we'll have to work quickly.  We've had some discussions here at the 
VOTech meeting (pity you couldn't make it!) and Mark is going to post 
the ideas on the wiki soon.

All the best,
John






> Isa
>
>
>
> Noel Winstanley wrote:
>
>   
>> Hi.
>> I don't know if there's any messages defined for spectra.
>>
>> at the moment the workbench bundles an in-process jar of vospec, and  
>> controls it directly using direct method calls - no plastic here.
>>
>> Although there is a standalone version of vospec, I've not managed to  
>> send it any messages it'll respond to. I beleive it's implemented to  
>> the early version of the plastic spec where you can leave the list of  
>> supported messages empty to indicate 'all messages'.
>>
>> IIRC, I was told by the ESAC folk that there's a new version of  
>> vospec in the pipeline - so maybe this is a good time to define some  
>> spectra messages.
>>
>> noel.
>>
>>
>> On 15 Aug 2006, at 10:18, Mark Taylor wrote:
>>
>>  
>>
>>     
>>> Chaps,
>>>
>>> what message/s is/are currently used for the transfer of spectra
>>> over PLASTIC?  Presumably it is done between the workbench and
>>> VO-Spec, though when VO-Spec registers it doesn't appear to
>>> indicate which messages it supports.  I suppose the answer is
>>> ivo://votech.org/votable/loadFromURL; if that's the case, is there
>>> a standard way to know which columns of the VOTable mean what?
>>>
>>> An alternative (and one that I'd like to see) would be
>>> ivo://votech.org/fits/spectrum/loadFromURL, which would make sense
>>> sitting next to  fits/image/loadFromURL.
>>>
>>> Mark
>>>
>>> -- 
>>> Mark Taylor   Astronomical Programmer   Physics, Bristol  
>>> University, UK
>>> m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/ 
>>> ~mbt/
>>>
>>>
>>> ---------------------------------------------------------------------- 
>>> ---
>>> Using Tomcat but need to do more? Need to support web services,  
>>> security?
>>> Get stuff done quickly with pre-integrated technology to make your  
>>> job easier
>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache  
>>> Geronimo
>>> http://sel.as-us.falkag.net/sel? 
>>> cmd=lnk&kid=120709&bid=263057&dat=121642
>>> _______________________________________________
>>> Plastic-devs mailing list
>>> Pla...@li...
>>> https://lists.sourceforge.net/lists/listinfo/plastic-devs
>>>
>>>    
>>>
>>>       
>> -------------------------------------------------------------------------
>> Using Tomcat but need to do more? Need to support web services, security?
>> Get stuff done quickly with pre-integrated technology to make your job easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>> _______________________________________________
>> Plastic-devs mailing list
>> Pla...@li...
>> https://lists.sourceforge.net/lists/listinfo/plastic-devs
>>  
>>
>>     
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Plastic-devs mailing list
> Pla...@li...
> https://lists.sourceforge.net/lists/listinfo/plastic-devs
>
>   

-- 
------------------------------------------------------------------------
AstroGrid/VOTech
&
Institute for Astronomy, Edinburgh
Skype:johndavidtaylor <skype:johndavidtaylor?chat>

------------------------------------------------------------------------

Re: [Plastic-devs] spectrum messaging

[Isa B. <Isa...@sc...>]

Hi all,
sorry for my silence on this but I was on leave.. :-)

Noel is right, currently VOSpec implements an old version of Plastic 
where the list of supported messages was left empty, this to indicate 
"all messages".
We have managed to send spectra from VOQuest to VOSpec by the 
ivo://votech.org/votable/load message, sending the votable as String 
argument. And I can also send/receive spectra from Topcat&Others using 
the same messages, votable/load and votable/loadFromURL, getting the 
arguments and calling our internal methods to visualize them in VOSpec.
So no spectra messages have been used in VOSpec and this was kind of 
working around the issue.. so I'm actually happy to know about the 
beginning of this discussion, so that I could update the plastic 
implementation in VOSpec for spectra transfers, hopefully in the next 
release before Moscow.

Isa



Noel Winstanley wrote:

>Hi.
>I don't know if there's any messages defined for spectra.
>
>at the moment the workbench bundles an in-process jar of vospec, and  
>controls it directly using direct method calls - no plastic here.
>
>Although there is a standalone version of vospec, I've not managed to  
>send it any messages it'll respond to. I beleive it's implemented to  
>the early version of the plastic spec where you can leave the list of  
>supported messages empty to indicate 'all messages'.
>
>IIRC, I was told by the ESAC folk that there's a new version of  
>vospec in the pipeline - so maybe this is a good time to define some  
>spectra messages.
>
>noel.
>
>
>On 15 Aug 2006, at 10:18, Mark Taylor wrote:
>
>  
>
>>Chaps,
>>
>>what message/s is/are currently used for the transfer of spectra
>>over PLASTIC?  Presumably it is done between the workbench and
>>VO-Spec, though when VO-Spec registers it doesn't appear to
>>indicate which messages it supports.  I suppose the answer is
>>ivo://votech.org/votable/loadFromURL; if that's the case, is there
>>a standard way to know which columns of the VOTable mean what?
>>
>>An alternative (and one that I'd like to see) would be
>>ivo://votech.org/fits/spectrum/loadFromURL, which would make sense
>>sitting next to  fits/image/loadFromURL.
>>
>>Mark
>>
>>-- 
>>Mark Taylor   Astronomical Programmer   Physics, Bristol  
>>University, UK
>>m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/ 
>>~mbt/
>>
>>
>>---------------------------------------------------------------------- 
>>---
>>Using Tomcat but need to do more? Need to support web services,  
>>security?
>>Get stuff done quickly with pre-integrated technology to make your  
>>job easier
>>Download IBM WebSphere Application Server v.1.0.1 based on Apache  
>>Geronimo
>>http://sel.as-us.falkag.net/sel? 
>>cmd=lnk&kid=120709&bid=263057&dat=121642
>>_______________________________________________
>>Plastic-devs mailing list
>>Pla...@li...
>>https://lists.sourceforge.net/lists/listinfo/plastic-devs
>>
>>    
>>
>
>
>-------------------------------------------------------------------------
>Using Tomcat but need to do more? Need to support web services, security?
>Get stuff done quickly with pre-integrated technology to make your job easier
>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>_______________________________________________
>Plastic-devs mailing list
>Pla...@li...
>https://lists.sourceforge.net/lists/listinfo/plastic-devs
>  
>

[Plastic-devs] Spectra messages

[Noel W. <Noe...@ma...>]

Hi chaps.
We've talked about it - could someone (not me, as I don't think I  
know enough), write down the proposal for Spectrum messages?

sorry to be pushy - would like to  get this settled (and implemented)  
quickly.

cheers
noel

Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....

[John T. <jd...@ro...>]

Whoops - I meant to send this to the list.

Marco Comparato wrote:
> John Taylor wrote:
>> I think this would be useful, but we need to agree on how to do it - 
>> it sounds like currently different apps do different things on 
>> receipt of an empty list.  So...VisIVO ignores it...does Topcat 
>> create an empty subset...and what does Aladin do?
>
> Hi John,
>
> VisIVO does not ignore it, it creates an empty selection, that's why a
> showObjects message with an empty list would be for us a "clear
> selection" message.
>
> Cheers,
> Marco
>
> P.S. why did you write a private message? Isn't it a proper message for
> the mailing list?
>

-- 
------------------------------------------------------------------------
AstroGrid/VOTech
&
Institute for Astronomy, Edinburgh
Skype:johndavidtaylor <skype:johndavidtaylor?chat>

------------------------------------------------------------------------

Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....

[R H. <ric...@co...>]

On Wed, 30 Aug 2006, John Taylor wrote:

> R Holbrey wrote:
>>
>>>>
>>>> For errors, I guess the user could expect this from eirik, but might
>>>> not these params be useful in another workflow? For the number of
>>>> clusters, it seems more sensible to have a showObjects message where
>>>> the elements of the rows array might look like
>>>>
>>>> {1,1,1,2,2,3,4,4,3,3}
>>>>
>>>> for a 10-row table, with 4 clusters identified ie rows 1-3 belong to
>>>> cluster 1. As I read showObjects at the moment, this would result in 4
>>>> messages and then more for "other details". This kind of
>>>> multiplication of messages seems dangerously confusing to me, harder
>>>> to implement and more likely to lead to less understanding.
>>> Sure - we could do it this way instead.   The purpose of the showObjects
>>> message is to tell a visualiser to select a set of rows.  We want to
>>> make sure that we keep it generic, and it doesn't have any
>>> Eirik-specific information in there.  However, the ability to be able to
>>> identify subsets in the set is quite generally useful I think.   The
>>> format of the message at the moment is
>>> showObjects(tableId, rows[])
>>>
>>> We can change this to
>>> showObjects(tableId, rows[], groupId)
>>> (which is what I proposed above, and would require a separate message
>>> for each group)
>>> or
>>> showObjects(tableId, rows[], groupId[])
>>>
>>
>> I see how the first one works, though I don't know how other apps
>> would then know how many clusters to expect.
> They wouldn't know how many clusters...do they need to?
>> I don't quite get how the second showObjects would work, unless (as I
>> suggested above) groups are matched to table rows in rows[], in which
>> case groupId[] seems superfluous...?
> I might have misunderstood what you were proposing  - I thought this was
> it...the addition of a groupId[] mask that identifies the group each row
> belongs to.

I expect you have it better than I do ... you're keeping rows for 
compatability ? (ie one of rows or groupId could be the mask)


>>
>> If I might make another suggestion, it would be for an optional
>> argument as a string to identify the form of analysis, to jog the
>> user's memory and which would optionally be stored in a votable
>> header. It might look like:
>>
>> "clustering by mclust v1.2, Bic=5, groups=4 (based on Bmag, Rmag, Imag)"
>>
>> Also, I'd be tempted to call this thing showClusters( .. ).
> This could be done quite easily with an optional "description" parameter
> in the first of the showObjects messages I suggested above.  Can I just
> try to nail down what you're wanting to achieve here, and why the
> existing message doesn't suffice?  So, Eirik has run its algorithms and
> identified 3 clusters.  It sends 3 showObjects messages in quick
> succession to Topcat, which creates 3 subsets from them.  You bring up a
> scatterplot, and there are your 3 clusters, ready to be overlaid on the
> full dataset in different colours.  You don't even need a "groupId" to
> do this.
>
> Am I misunderstanding what you want to do?

You could probably get by working as you suggest, but my feeling is that 
it is seriously flawed for anything beyond demo usage. The problem comes 
in the user knowing that the 3 clusters sent to topcat the first time are 
different from the 4 clusters sent in the next analysis and the 5 clusters 
sent ... I hope you get the idea.

Also, at some point, you probably want to save the preferred clustering 
with the data (as an extra column, presumably), so you'll need to combine 
the 3/4/5 etc clusters into one item somehow. I imagine this is do-able in 
topcat, but, as before, which of the dozens of clusters to choose from ... 
unless you can work it out from the optional message (I've missed 
this option somewhere, but it still sounds messy).


regards,
Richard

>
>
>>
>> regards,
>> Richard
>>
>> ps wasn't there a suggestion a while back for a "showColumns(int
>> cols[])" ?
> Yes - I think it's still needed.  I think we settled on something like
> showColumns(tableId, cols[], [optionsHashTable])#fragment
>
> John
>
>>
>>
>>> I don't have any strong opinions either way - the latter has the benefit
>>> that it does keep all the groups together.
>>>
>>> Whichever is adopted the groupId should be an optional parameter.  In
>>> fact, I'd prefer to see it tacked on in an optional struct at the end
>>> showObjects(tableId, rows[], [options])
>>> with
>>> options={groupdId=int[]}
>>>
>>> to allow for future expansion.
>>>
>>>
>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>>
>>>> More bluntly, I'd say it was shoe-horning... what happens if someone
>>>> requests a regression or a pca/fa with clustering on top (please stop,
>>>> I hear you cry ;)
>>> No no...go on...
>>>>
>>>> An eirik api, anyone?
>>>>
>>>> R
>>>>
>>>>
>>>>
>>>> On Tue, 22 Aug 2006, John Taylor wrote:
>>>>
>>>>> I'll need to be reminded about exactly what you want to do....
>>>>> IIRC  the use cases include:
>>>>>
>>>>> 1) User loads VOTable into Eirik, through Eirik identifies (say) 3
>>>>> interesting columns, sends a message to Topcat
>>>>> ivo://.../selectColumns#plot_3d
>>>>> 2) User loads VOTable into Eirik, through Eirik identifies 4
>>>>> interesting columns, sends a message to Weka
>>>>> ivo://.../selectColumns#set_active_cols. User then runs a clustering
>>>>> algorithm on those columns.
>>>>> 3) User wants to display the clusters in VisIVO.  Weka sends messages
>>>>> to VisIVO ivo://..../showObjects#highlight. Each message has an extra
>>>>> optional argument of groupId that VisIVO maps to a different colour.
>>>>> Similarly Eirik could do the clustering (through R), and display the
>>>>> results through A.N.Other display program.
>>>>>
>>>>> 4) User loads a VOTable into TabView, decides on a set of columns for
>>>>> further investigation in Eirik.  TabView instructs Eirik to load the
>>>>> table, then sends a message ivo://.../selectColumns#set_active_cols
>>>>>
>>>>> In all these cases, the bit after the # is just a message fragment
>>>>> that I made up - each application can define its own.
>>>>>
>>>>> John
>>>>>
>>>>>
>>>>>
>>>>> R Holbrey wrote:
>>>>>> On Tue, 22 Aug 2006, John Taylor wrote:
>>>>>>
>>>>>>> I think we got it!  At least, the window comes up, and by hitting
>>>>>>> random buttons like a monkey I can get plots to appear.
>>>>>>
>>>>>> cheers John,
>>>>>>
>>>>>> maybe now I can teach the monkey how to do showobjects. What was the
>>>>>> latest on that btw? I've been struggling to think how eirik would
>>>>>> understand it, and it needs work, the kind of been wanting to get on
>>>>>> with.
>>>>>>
>>>>>> If it's not desirable to expand plastic the way I was wondering a
>>>>>> while back, I'm starting to think eirik should define his own api
>>>>>> as, basically, requests to various r functions eg to do clustering.
>>>>>> (At the moment it seems like to do this through plastic would
>>>>>> require a new votable to be written and passed back, which I think
>>>>>> inordinately clumsy).
>>>>>>
>>>>>> R
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> R Holbrey wrote:
>>>>>>>>
>>>>>>>> After going to the bowels of NT and back, I realised I missed a
>>>>>>>> rather crucial file (doh), but the weird thing is, this still
>>>>>>>> doesn't cause trouble on my main xp machine. Presumably it finds
>>>>>>>> the file elsewhere, but I'm darned if I can replicate the problem,
>>>>>>>> unless I move to my ageing old compaq.
>>>>>>>>
>>>>>>>> I've uploaded a zip (built with 7-zip, which is GPL) and rar
>>>>>>>> (better compression than either, I suspect) of the bundle with the
>>>>>>>> missing r source file, so I'd be grateful if you would give it
>>>>>>>> another crack. Maybe then I can get on with my life...
>>>>>>>>
>>>>>>>> R
>>>>>>>>
>>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>>
>>>>>>>>> Still no luck I'm afraid...and nothing helpful (in the way of
>>>>>>>>> diagnostics) appears on the commandline.
>>>>>>>>> J
>>>>>>>>>
>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>
>>>>>>>>>> one thing I forgot was to set yet another environment variable,
>>>>>>>>>> R_HOME, so that RDLL in the .bat should really look like eg
>>>>>>>>>>
>>>>>>>>>> set R_HOME=c:\Program Files\R\R-2.3.1
>>>>>>>>>> set RDLL=%R_HOME%\bin
>>>>>>>>>>
>>>>>>>>>> with %RDLL% in the path (these should appear in your path after
>>>>>>>>>> running the .bat from the command prompt??). Oddly though the
>>>>>>>>>> "depends" utility (from ms visualc - do you happen to have it?)
>>>>>>>>>> tells me, on my old laptop that there are no bindings to the
>>>>>>>>>> Rdll at all and several other key libraries. Looks like I'd
>>>>>>>>>> better reboot this one and go check...
>>>>>>>>>>
>>>>>>>>>> R
>>>>>>>>>>
>>>>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Richard,
>>>>>>>>>>> I'm using the latest R: 2.3.1 , java 1.5.0_06 and my path is:
>>>>>>>>>>> C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program
>>>>>>>>>>>
>>>>>>>>>>> Files\ATI Technologies\ATI Control Panel;C:\Program
>>>>>>>>>>> Files\QuickTime\QTSystem\;C:\Program Files\Python;C:\Program
>>>>>>>>>>> Files\Java\jdk1.5.0_06\bin;E:\jdt\applications\maven-2.0\bin;E:\jdt\applications\maven-1.0.2\bin;C:\Program
>>>>>>>>>>>
>>>>>>>>>>> Files\Putty;E:\jdt\applications\apache-ant-1.6.5\bin;C:\Program
>>>>>>>>>>> Files\Java\jdk1.5.0_06\jre\bin\client;C:\Program Files\SSH
>>>>>>>>>>> Communications Security\SSH Secure Shell
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> thanks John,
>>>>>>>>>>>>
>>>>>>>>>>>> can you post me the versions of R, java and anything else you
>>>>>>>>>>>> can think of you're using and your path. I'll try some
>>>>>>>>>>>> different machines and I'll look up my old version of Visual
>>>>>>>>>>>> C. APparently there was a utility there called "depends" which
>>>>>>>>>>>> allowed you to see what dynamic libraries were in use (this
>>>>>>>>>>>> kind of thing is free in linux of course ;)
>>>>>>>>>>>>
>>>>>>>>>>>> R
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Richard,
>>>>>>>>>>>>> We're getting there.  The install worked pretty much out of
>>>>>>>>>>>>> the box (all my dlls were in the right place I think).  Eirik
>>>>>>>>>>>>> fires up OK and plastic and ACR integration works.  However,
>>>>>>>>>>>>> the test data set isn't loaded, and any attempt to load a
>>>>>>>>>>>>> VOTable causes Eirik to bomb out. Is there any way I can get
>>>>>>>>>>>>> some diagnostic info for you?
>>>>>>>>>>>>>
>>>>>>>>>>>>> John
>>>>>>>>>>>>>
>>>>>>>>>>>>> PS
>>>>>>>>>>>>> Any particular reason to use RAR?  I only have a "free trial"
>>>>>>>>>>>>> RAR decoder on my machine....zip is more common!
>>>>>>>>>>>>>
>>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I've tried to post an xp versionjust now on the wiki:
>>>>>>>>>>>>>> http://eurovotech.org/twiki/bin/view/VOTech/EirikDemo
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> which has had plenty of hacks and papering although I did
>>>>>>>>>>>>>> manage to sort out one of the things that was bogging me
>>>>>>>>>>>>>> down all week.. (actually, a compiler error, if you must
>>>>>>>>>>>>>> know..). You need to tell it where R and Java are in the
>>>>>>>>>>>>>> path (see batch file), but I trust you'll let me know how
>>>>>>>>>>>>>> this goes ;)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> What platform were you trying to run on? I think it would
>>>>>>>>>>>>>> probably be an idea to track these things, so that at least
>>>>>>>>>>>>>> we can advise when not to bother...
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Richard
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Richard,
>>>>>>>>>>>>>>> It's now complaining about missing libstdc++.so.6
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I think our OS installations here are a) not the most
>>>>>>>>>>>>>>> up-to-date b) a bit sparse.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I could ask Horst to install the missing libraries, but I
>>>>>>>>>>>>>>> think we have to be able to cope with the situation where
>>>>>>>>>>>>>>> the user can't get this stuff installed and make eirik as
>>>>>>>>>>>>>>> independent of any shared libs as possible, regardless of
>>>>>>>>>>>>>>> the size.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> John
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> fairly small, so attached mine! (might work if you create
>>>>>>>>>>>>>>>> links libXinerama.so and libXinerama.so.1 also in your
>>>>>>>>>>>>>>>> path.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Logo: probably shouldn't really rely on it, but I might
>>>>>>>>>>>>>>>> change it when I have an idle minute, so the web link
>>>>>>>>>>>>>>>> should do for now.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> R
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> ...could you send me a copy of your logo for putting on
>>>>>>>>>>>>>>>>>>> the web site?
>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>> J
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Xinerama is kind of optional with qt and I just left it
>>>>>>>>>>>>>>>>>> in by default. When I go through another 2-hour compile
>>>>>>>>>>>>>>>>>> I might take it out to see what happens... otherwise you
>>>>>>>>>>>>>>>>>> might visit http://rpm.pbone.net and do an advanced
>>>>>>>>>>>>>>>>>> search for your linux distro and libXinerama, choosing
>>>>>>>>>>>>>>>>>> the libXinerama-<ver>-i386.rpm if anything comes up.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> eg. for fedora 5 this might turn out as
>>>>>>>>>>>>>>>>>> ftp://ftp.univie.ac.at/systems/linux/fedora/5/i386/os/Fedora/RPMS/libXinerama-1.0.1-1.2.i386.rpm
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> click,save and then run
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> rpm -Uvh libXinerama-1.0.1-1.2.i386.rpm
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> as root.
>>>>>>>>>>>>>>>>> Not root on this machine, alas, so might have to just try
>>>>>>>>>>>>>>>>> stuffing it on the library path, assuming I can get hold
>>>>>>>>>>>>>>>>> of it.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Still having teething troubles with windows (you
>>>>>>>>>>>>>>>>>> probably guessed) but it is working and I'm fairly
>>>>>>>>>>>>>>>>>> hopeful of getting a demo out this week (I forgot things
>>>>>>>>>>>>>>>>>> like windows doesn't let you overwrite files whilst
>>>>>>>>>>>>>>>>>> they're still open...). At the moment it seems to die if
>>>>>>>>>>>>>>>>>> you tried to load several files one after the other.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> A version of my (slightly crude) logo lies at
>>>>>>>>>>>>>>>>>> http://www.comp.leeds.ac.uk/richardh/eirik/xpm/Eirikship.png
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Cheers!  Can I rely on that URL or should I take a copy?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>
>
>
>

Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....

[John T. <jon...@gm...>]

R Holbrey wrote:
>
>>>
>>> For errors, I guess the user could expect this from eirik, but might
>>> not these params be useful in another workflow? For the number of
>>> clusters, it seems more sensible to have a showObjects message where
>>> the elements of the rows array might look like
>>>
>>> {1,1,1,2,2,3,4,4,3,3}
>>>
>>> for a 10-row table, with 4 clusters identified ie rows 1-3 belong to
>>> cluster 1. As I read showObjects at the moment, this would result in 4
>>> messages and then more for "other details". This kind of
>>> multiplication of messages seems dangerously confusing to me, harder
>>> to implement and more likely to lead to less understanding.
>> Sure - we could do it this way instead.   The purpose of the showObjects
>> message is to tell a visualiser to select a set of rows.  We want to
>> make sure that we keep it generic, and it doesn't have any
>> Eirik-specific information in there.  However, the ability to be able to
>> identify subsets in the set is quite generally useful I think.   The
>> format of the message at the moment is
>> showObjects(tableId, rows[])
>>
>> We can change this to
>> showObjects(tableId, rows[], groupId)
>> (which is what I proposed above, and would require a separate message
>> for each group)
>> or
>> showObjects(tableId, rows[], groupId[])
>>
>
> I see how the first one works, though I don't know how other apps 
> would then know how many clusters to expect.
They wouldn't know how many clusters...do they need to?
> I don't quite get how the second showObjects would work, unless (as I 
> suggested above) groups are matched to table rows in rows[], in which 
> case groupId[] seems superfluous...?
I might have misunderstood what you were proposing  - I thought this was 
it...the addition of a groupId[] mask that identifies the group each row 
belongs to.
>
> If I might make another suggestion, it would be for an optional 
> argument as a string to identify the form of analysis, to jog the 
> user's memory and which would optionally be stored in a votable 
> header. It might look like:
>
> "clustering by mclust v1.2, Bic=5, groups=4 (based on Bmag, Rmag, Imag)"
>
> Also, I'd be tempted to call this thing showClusters( .. ).
This could be done quite easily with an optional "description" parameter 
in the first of the showObjects messages I suggested above.  Can I just 
try to nail down what you're wanting to achieve here, and why the 
existing message doesn't suffice?  So, Eirik has run its algorithms and 
identified 3 clusters.  It sends 3 showObjects messages in quick 
succession to Topcat, which creates 3 subsets from them.  You bring up a 
scatterplot, and there are your 3 clusters, ready to be overlaid on the 
full dataset in different colours.  You don't even need a "groupId" to 
do this.

Am I misunderstanding what you want to do?


>
> regards,
> Richard
>
> ps wasn't there a suggestion a while back for a "showColumns(int 
> cols[])" ?
Yes - I think it's still needed.  I think we settled on something like
showColumns(tableId, cols[], [optionsHashTable])#fragment

John

>
>
>> I don't have any strong opinions either way - the latter has the benefit
>> that it does keep all the groups together.
>>
>> Whichever is adopted the groupId should be an optional parameter.  In
>> fact, I'd prefer to see it tacked on in an optional struct at the end
>> showObjects(tableId, rows[], [options])
>> with
>> options={groupdId=int[]}
>>
>> to allow for future expansion.
>>
>>
>
>>
>>
>>
>>
>>
>>
>>>
>>> More bluntly, I'd say it was shoe-horning... what happens if someone
>>> requests a regression or a pca/fa with clustering on top (please stop,
>>> I hear you cry ;)
>> No no...go on...
>>>
>>> An eirik api, anyone?
>>>
>>> R
>>>
>>>
>>>
>>> On Tue, 22 Aug 2006, John Taylor wrote:
>>>
>>>> I'll need to be reminded about exactly what you want to do....
>>>> IIRC  the use cases include:
>>>>
>>>> 1) User loads VOTable into Eirik, through Eirik identifies (say) 3
>>>> interesting columns, sends a message to Topcat
>>>> ivo://.../selectColumns#plot_3d
>>>> 2) User loads VOTable into Eirik, through Eirik identifies 4
>>>> interesting columns, sends a message to Weka
>>>> ivo://.../selectColumns#set_active_cols. User then runs a clustering
>>>> algorithm on those columns.
>>>> 3) User wants to display the clusters in VisIVO.  Weka sends messages
>>>> to VisIVO ivo://..../showObjects#highlight. Each message has an extra
>>>> optional argument of groupId that VisIVO maps to a different colour.
>>>> Similarly Eirik could do the clustering (through R), and display the
>>>> results through A.N.Other display program.
>>>>
>>>> 4) User loads a VOTable into TabView, decides on a set of columns for
>>>> further investigation in Eirik.  TabView instructs Eirik to load the
>>>> table, then sends a message ivo://.../selectColumns#set_active_cols
>>>>
>>>> In all these cases, the bit after the # is just a message fragment
>>>> that I made up - each application can define its own.
>>>>
>>>> John
>>>>
>>>>
>>>>
>>>> R Holbrey wrote:
>>>>> On Tue, 22 Aug 2006, John Taylor wrote:
>>>>>
>>>>>> I think we got it!  At least, the window comes up, and by hitting
>>>>>> random buttons like a monkey I can get plots to appear.
>>>>>
>>>>> cheers John,
>>>>>
>>>>> maybe now I can teach the monkey how to do showobjects. What was the
>>>>> latest on that btw? I've been struggling to think how eirik would
>>>>> understand it, and it needs work, the kind of been wanting to get on
>>>>> with.
>>>>>
>>>>> If it's not desirable to expand plastic the way I was wondering a
>>>>> while back, I'm starting to think eirik should define his own api
>>>>> as, basically, requests to various r functions eg to do clustering.
>>>>> (At the moment it seems like to do this through plastic would
>>>>> require a new votable to be written and passed back, which I think
>>>>> inordinately clumsy).
>>>>>
>>>>> R
>>>>>
>>>>>>
>>>>>>
>>>>>> R Holbrey wrote:
>>>>>>>
>>>>>>> After going to the bowels of NT and back, I realised I missed a
>>>>>>> rather crucial file (doh), but the weird thing is, this still
>>>>>>> doesn't cause trouble on my main xp machine. Presumably it finds
>>>>>>> the file elsewhere, but I'm darned if I can replicate the problem,
>>>>>>> unless I move to my ageing old compaq.
>>>>>>>
>>>>>>> I've uploaded a zip (built with 7-zip, which is GPL) and rar
>>>>>>> (better compression than either, I suspect) of the bundle with the
>>>>>>> missing r source file, so I'd be grateful if you would give it
>>>>>>> another crack. Maybe then I can get on with my life...
>>>>>>>
>>>>>>> R
>>>>>>>
>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>
>>>>>>>> Still no luck I'm afraid...and nothing helpful (in the way of
>>>>>>>> diagnostics) appears on the commandline.
>>>>>>>> J
>>>>>>>>
>>>>>>>> R Holbrey wrote:
>>>>>>>>>
>>>>>>>>> one thing I forgot was to set yet another environment variable,
>>>>>>>>> R_HOME, so that RDLL in the .bat should really look like eg
>>>>>>>>>
>>>>>>>>> set R_HOME=c:\Program Files\R\R-2.3.1
>>>>>>>>> set RDLL=%R_HOME%\bin
>>>>>>>>>
>>>>>>>>> with %RDLL% in the path (these should appear in your path after
>>>>>>>>> running the .bat from the command prompt??). Oddly though the
>>>>>>>>> "depends" utility (from ms visualc - do you happen to have it?)
>>>>>>>>> tells me, on my old laptop that there are no bindings to the
>>>>>>>>> Rdll at all and several other key libraries. Looks like I'd
>>>>>>>>> better reboot this one and go check...
>>>>>>>>>
>>>>>>>>> R
>>>>>>>>>
>>>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>>>
>>>>>>>>>> Hi Richard,
>>>>>>>>>> I'm using the latest R: 2.3.1 , java 1.5.0_06 and my path is:
>>>>>>>>>> C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program 
>>>>>>>>>>
>>>>>>>>>> Files\ATI Technologies\ATI Control Panel;C:\Program
>>>>>>>>>> Files\QuickTime\QTSystem\;C:\Program Files\Python;C:\Program
>>>>>>>>>> Files\Java\jdk1.5.0_06\bin;E:\jdt\applications\maven-2.0\bin;E:\jdt\applications\maven-1.0.2\bin;C:\Program 
>>>>>>>>>>
>>>>>>>>>> Files\Putty;E:\jdt\applications\apache-ant-1.6.5\bin;C:\Program
>>>>>>>>>> Files\Java\jdk1.5.0_06\jre\bin\client;C:\Program Files\SSH
>>>>>>>>>> Communications Security\SSH Secure Shell
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>
>>>>>>>>>>> thanks John,
>>>>>>>>>>>
>>>>>>>>>>> can you post me the versions of R, java and anything else you
>>>>>>>>>>> can think of you're using and your path. I'll try some
>>>>>>>>>>> different machines and I'll look up my old version of Visual
>>>>>>>>>>> C. APparently there was a utility there called "depends" which
>>>>>>>>>>> allowed you to see what dynamic libraries were in use (this
>>>>>>>>>>> kind of thing is free in linux of course ;)
>>>>>>>>>>>
>>>>>>>>>>> R
>>>>>>>>>>>
>>>>>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Richard,
>>>>>>>>>>>> We're getting there.  The install worked pretty much out of
>>>>>>>>>>>> the box (all my dlls were in the right place I think).  Eirik
>>>>>>>>>>>> fires up OK and plastic and ACR integration works.  However,
>>>>>>>>>>>> the test data set isn't loaded, and any attempt to load a
>>>>>>>>>>>> VOTable causes Eirik to bomb out. Is there any way I can get
>>>>>>>>>>>> some diagnostic info for you?
>>>>>>>>>>>>
>>>>>>>>>>>> John
>>>>>>>>>>>>
>>>>>>>>>>>> PS
>>>>>>>>>>>> Any particular reason to use RAR?  I only have a "free trial"
>>>>>>>>>>>> RAR decoder on my machine....zip is more common!
>>>>>>>>>>>>
>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> I've tried to post an xp versionjust now on the wiki:
>>>>>>>>>>>>> http://eurovotech.org/twiki/bin/view/VOTech/EirikDemo
>>>>>>>>>>>>>
>>>>>>>>>>>>> which has had plenty of hacks and papering although I did
>>>>>>>>>>>>> manage to sort out one of the things that was bogging me
>>>>>>>>>>>>> down all week.. (actually, a compiler error, if you must
>>>>>>>>>>>>> know..). You need to tell it where R and Java are in the
>>>>>>>>>>>>> path (see batch file), but I trust you'll let me know how
>>>>>>>>>>>>> this goes ;)
>>>>>>>>>>>>>
>>>>>>>>>>>>> What platform were you trying to run on? I think it would
>>>>>>>>>>>>> probably be an idea to track these things, so that at least
>>>>>>>>>>>>> we can advise when not to bother...
>>>>>>>>>>>>>
>>>>>>>>>>>>> Richard
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Richard,
>>>>>>>>>>>>>> It's now complaining about missing libstdc++.so.6
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I think our OS installations here are a) not the most
>>>>>>>>>>>>>> up-to-date b) a bit sparse.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I could ask Horst to install the missing libraries, but I
>>>>>>>>>>>>>> think we have to be able to cope with the situation where
>>>>>>>>>>>>>> the user can't get this stuff installed and make eirik as
>>>>>>>>>>>>>> independent of any shared libs as possible, regardless of
>>>>>>>>>>>>>> the size.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> John
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> fairly small, so attached mine! (might work if you create
>>>>>>>>>>>>>>> links libXinerama.so and libXinerama.so.1 also in your 
>>>>>>>>>>>>>>> path.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Logo: probably shouldn't really rely on it, but I might
>>>>>>>>>>>>>>> change it when I have an idle minute, so the web link
>>>>>>>>>>>>>>> should do for now.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> R
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ...could you send me a copy of your logo for putting on
>>>>>>>>>>>>>>>>>> the web site?
>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>> J
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Xinerama is kind of optional with qt and I just left it
>>>>>>>>>>>>>>>>> in by default. When I go through another 2-hour compile
>>>>>>>>>>>>>>>>> I might take it out to see what happens... otherwise you
>>>>>>>>>>>>>>>>> might visit http://rpm.pbone.net and do an advanced
>>>>>>>>>>>>>>>>> search for your linux distro and libXinerama, choosing
>>>>>>>>>>>>>>>>> the libXinerama-<ver>-i386.rpm if anything comes up.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> eg. for fedora 5 this might turn out as
>>>>>>>>>>>>>>>>> ftp://ftp.univie.ac.at/systems/linux/fedora/5/i386/os/Fedora/RPMS/libXinerama-1.0.1-1.2.i386.rpm 
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> click,save and then run
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> rpm -Uvh libXinerama-1.0.1-1.2.i386.rpm
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> as root.
>>>>>>>>>>>>>>>> Not root on this machine, alas, so might have to just try
>>>>>>>>>>>>>>>> stuffing it on the library path, assuming I can get hold
>>>>>>>>>>>>>>>> of it.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Still having teething troubles with windows (you
>>>>>>>>>>>>>>>>> probably guessed) but it is working and I'm fairly
>>>>>>>>>>>>>>>>> hopeful of getting a demo out this week (I forgot things
>>>>>>>>>>>>>>>>> like windows doesn't let you overwrite files whilst
>>>>>>>>>>>>>>>>> they're still open...). At the moment it seems to die if
>>>>>>>>>>>>>>>>> you tried to load several files one after the other.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> A version of my (slightly crude) logo lies at
>>>>>>>>>>>>>>>>> http://www.comp.leeds.ac.uk/richardh/eirik/xpm/Eirikship.png 
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Cheers!  Can I rely on that URL or should I take a copy?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>


-- 
------------------------------------------------------------------------
AstroGrid/VOTech
&
Institute for Astronomy, Edinburgh
Skype:johndavidtaylor <skype:johndavidtaylor?chat>

------------------------------------------------------------------------

Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....

[Marco C. <mc...@oa...>]

John Taylor wrote:
> 
> Thomas Boch wrote:
> 
>>Hi John,
>>
>>Being able to identify groups within tables might also be interest for
>>me (in Aladin). I don't quite understand at which level the groupId is
>>defined. Could you elaborate a bit more, and give an example ?
>>  
> 
> Hi Thomas - the use case we're thinking of is that Eirik (say) runs a 
> clustering algorithm on the VOTable and identifies (say) 3 clusters.  It 
> would be nice if Eirik could then ask Aladin to display those 3 clusters 
> in different colours, or using different symbols.  I'd prefer to keep 
> the groupings at an abstract level, rather than Eirik specifying the 
> colours or symbols itself and allow the receiving application to decide 
> what to do with them.  e.g. VisIVO could map from groupIds to colours, 
> Aladin from groupIds to symbols, and Topcat could map each group to a 
> different subset...whatever makes sense for the receiving application.

Dear all application devs,

what do you think about clearing the selection? I think it would be
useful to have a way to clear a selection or a multiple selection (see
groups). Maybe the simplest way to do that would be to send a showObject
message with an empty array of rows. As an example: if the user makes a
selection in Aladin the selected points will be highlighted in all
VisIVO's visualization windows displaying the dataset, but if you
clear the selection in Aladin (clicking on an empty region) the
selection will remain active in VisIVO,  in this case it would be great
to receive an empty list of objects to show.

Cheers,
Marco

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....

[R H. <ric...@co...>]

On Tue, 29 Aug 2006, John Taylor wrote:

> R Holbrey wrote:
>>
>> I guess this would be a good thing to hammer out a bit more at the
>> hackathon, but I'm still not quite getting there. Let's take the
>> clustering example abit further. R easily has a dozen different routines
>>  and many possible parameter settings.
>>
>> In fact, one of the harder things to decide up front is whether you
>> want to set the number of clusters or whether you want some kind of
>> estimate. My idea for eirik is that you might want to do two, three or
>> more clusterings to get a feel how things are going and that,
>> crucially, eirik should start you off with the fastest/dirtiest.
>>
>> The way I read showObjects here is that for each cluster identified,
>> you send back a message saying show these objects, say for those in
>> cluster 1. Then another message for objects in cluster 2 etc. But
>>
>>  - how many clusters in all?
>>  - what kind of errors were given (possibly on each)?
>>  - what other parameters were assumed? (variables used to cluster,
>> types of cluster etc)

> You could put any such extra information into the VOTable that you send
> to other apps.

mmm... but this would imply a separate votable for each clustering/bit of 
analysis, which seems rather cumbersome to me. I'd prefer to pass back a 
clustering to topcat (say) and then, when the user is happy, s/he can same 
the preferred clustering results as an extra column in a votable.

>>
>> For errors, I guess the user could expect this from eirik, but might
>> not these params be useful in another workflow? For the number of
>> clusters, it seems more sensible to have a showObjects message where
>> the elements of the rows array might look like
>>
>> {1,1,1,2,2,3,4,4,3,3}
>>
>> for a 10-row table, with 4 clusters identified ie rows 1-3 belong to
>> cluster 1. As I read showObjects at the moment, this would result in 4
>> messages and then more for "other details". This kind of
>> multiplication of messages seems dangerously confusing to me, harder
>> to implement and more likely to lead to less understanding.
> Sure - we could do it this way instead.   The purpose of the showObjects
> message is to tell a visualiser to select a set of rows.  We want to
> make sure that we keep it generic, and it doesn't have any
> Eirik-specific information in there.  However, the ability to be able to
> identify subsets in the set is quite generally useful I think.   The
> format of the message at the moment is
> showObjects(tableId, rows[])
>
> We can change this to
> showObjects(tableId, rows[], groupId)
> (which is what I proposed above, and would require a separate message
> for each group)
> or
> showObjects(tableId, rows[], groupId[])
>

I see how the first one works, though I don't know how other apps would 
then know how many clusters to expect. I don't quite get how the second 
showObjects would work, unless (as I suggested above) groups are matched 
to table rows in rows[], in which case groupId[] seems superfluous...?

If I might make another suggestion, it would be for an optional argument 
as a string to identify the form of analysis, to jog the user's memory and 
which would optionally be stored in a votable header. It might look like:

"clustering by mclust v1.2, Bic=5, groups=4 (based on Bmag, Rmag, Imag)"

Also, I'd be tempted to call this thing showClusters( .. ).

regards,
Richard

ps wasn't there a suggestion a while back for a "showColumns(int cols[])" 
?


> I don't have any strong opinions either way - the latter has the benefit
> that it does keep all the groups together.
>
> Whichever is adopted the groupId should be an optional parameter.  In
> fact, I'd prefer to see it tacked on in an optional struct at the end
> showObjects(tableId, rows[], [options])
> with
> options={groupdId=int[]}
>
> to allow for future expansion.
>
>

>
>
>
>
>
>
>>
>> More bluntly, I'd say it was shoe-horning... what happens if someone
>> requests a regression or a pca/fa with clustering on top (please stop,
>> I hear you cry ;)
> No no...go on...
>>
>> An eirik api, anyone?
>>
>> R
>>
>>
>>
>> On Tue, 22 Aug 2006, John Taylor wrote:
>>
>>> I'll need to be reminded about exactly what you want to do....
>>> IIRC  the use cases include:
>>>
>>> 1) User loads VOTable into Eirik, through Eirik identifies (say) 3
>>> interesting columns, sends a message to Topcat
>>> ivo://.../selectColumns#plot_3d
>>> 2) User loads VOTable into Eirik, through Eirik identifies 4
>>> interesting columns, sends a message to Weka
>>> ivo://.../selectColumns#set_active_cols. User then runs a clustering
>>> algorithm on those columns.
>>> 3) User wants to display the clusters in VisIVO.  Weka sends messages
>>> to VisIVO ivo://..../showObjects#highlight. Each message has an extra
>>> optional argument of groupId that VisIVO maps to a different colour.
>>> Similarly Eirik could do the clustering (through R), and display the
>>> results through A.N.Other display program.
>>>
>>> 4) User loads a VOTable into TabView, decides on a set of columns for
>>> further investigation in Eirik.  TabView instructs Eirik to load the
>>> table, then sends a message ivo://.../selectColumns#set_active_cols
>>>
>>> In all these cases, the bit after the # is just a message fragment
>>> that I made up - each application can define its own.
>>>
>>> John
>>>
>>>
>>>
>>> R Holbrey wrote:
>>>> On Tue, 22 Aug 2006, John Taylor wrote:
>>>>
>>>>> I think we got it!  At least, the window comes up, and by hitting
>>>>> random buttons like a monkey I can get plots to appear.
>>>>
>>>> cheers John,
>>>>
>>>> maybe now I can teach the monkey how to do showobjects. What was the
>>>> latest on that btw? I've been struggling to think how eirik would
>>>> understand it, and it needs work, the kind of been wanting to get on
>>>> with.
>>>>
>>>> If it's not desirable to expand plastic the way I was wondering a
>>>> while back, I'm starting to think eirik should define his own api
>>>> as, basically, requests to various r functions eg to do clustering.
>>>> (At the moment it seems like to do this through plastic would
>>>> require a new votable to be written and passed back, which I think
>>>> inordinately clumsy).
>>>>
>>>> R
>>>>
>>>>>
>>>>>
>>>>> R Holbrey wrote:
>>>>>>
>>>>>> After going to the bowels of NT and back, I realised I missed a
>>>>>> rather crucial file (doh), but the weird thing is, this still
>>>>>> doesn't cause trouble on my main xp machine. Presumably it finds
>>>>>> the file elsewhere, but I'm darned if I can replicate the problem,
>>>>>> unless I move to my ageing old compaq.
>>>>>>
>>>>>> I've uploaded a zip (built with 7-zip, which is GPL) and rar
>>>>>> (better compression than either, I suspect) of the bundle with the
>>>>>> missing r source file, so I'd be grateful if you would give it
>>>>>> another crack. Maybe then I can get on with my life...
>>>>>>
>>>>>> R
>>>>>>
>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>
>>>>>>> Still no luck I'm afraid...and nothing helpful (in the way of
>>>>>>> diagnostics) appears on the commandline.
>>>>>>> J
>>>>>>>
>>>>>>> R Holbrey wrote:
>>>>>>>>
>>>>>>>> one thing I forgot was to set yet another environment variable,
>>>>>>>> R_HOME, so that RDLL in the .bat should really look like eg
>>>>>>>>
>>>>>>>> set R_HOME=c:\Program Files\R\R-2.3.1
>>>>>>>> set RDLL=%R_HOME%\bin
>>>>>>>>
>>>>>>>> with %RDLL% in the path (these should appear in your path after
>>>>>>>> running the .bat from the command prompt??). Oddly though the
>>>>>>>> "depends" utility (from ms visualc - do you happen to have it?)
>>>>>>>> tells me, on my old laptop that there are no bindings to the
>>>>>>>> Rdll at all and several other key libraries. Looks like I'd
>>>>>>>> better reboot this one and go check...
>>>>>>>>
>>>>>>>> R
>>>>>>>>
>>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>>
>>>>>>>>> Hi Richard,
>>>>>>>>> I'm using the latest R: 2.3.1 , java 1.5.0_06 and my path is:
>>>>>>>>> C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program
>>>>>>>>> Files\ATI Technologies\ATI Control Panel;C:\Program
>>>>>>>>> Files\QuickTime\QTSystem\;C:\Program Files\Python;C:\Program
>>>>>>>>> Files\Java\jdk1.5.0_06\bin;E:\jdt\applications\maven-2.0\bin;E:\jdt\applications\maven-1.0.2\bin;C:\Program
>>>>>>>>> Files\Putty;E:\jdt\applications\apache-ant-1.6.5\bin;C:\Program
>>>>>>>>> Files\Java\jdk1.5.0_06\jre\bin\client;C:\Program Files\SSH
>>>>>>>>> Communications Security\SSH Secure Shell
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>
>>>>>>>>>> thanks John,
>>>>>>>>>>
>>>>>>>>>> can you post me the versions of R, java and anything else you
>>>>>>>>>> can think of you're using and your path. I'll try some
>>>>>>>>>> different machines and I'll look up my old version of Visual
>>>>>>>>>> C. APparently there was a utility there called "depends" which
>>>>>>>>>> allowed you to see what dynamic libraries were in use (this
>>>>>>>>>> kind of thing is free in linux of course ;)
>>>>>>>>>>
>>>>>>>>>> R
>>>>>>>>>>
>>>>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Richard,
>>>>>>>>>>> We're getting there.  The install worked pretty much out of
>>>>>>>>>>> the box (all my dlls were in the right place I think).  Eirik
>>>>>>>>>>> fires up OK and plastic and ACR integration works.  However,
>>>>>>>>>>> the test data set isn't loaded, and any attempt to load a
>>>>>>>>>>> VOTable causes Eirik to bomb out. Is there any way I can get
>>>>>>>>>>> some diagnostic info for you?
>>>>>>>>>>>
>>>>>>>>>>> John
>>>>>>>>>>>
>>>>>>>>>>> PS
>>>>>>>>>>> Any particular reason to use RAR?  I only have a "free trial"
>>>>>>>>>>> RAR decoder on my machine....zip is more common!
>>>>>>>>>>>
>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> I've tried to post an xp versionjust now on the wiki:
>>>>>>>>>>>> http://eurovotech.org/twiki/bin/view/VOTech/EirikDemo
>>>>>>>>>>>>
>>>>>>>>>>>> which has had plenty of hacks and papering although I did
>>>>>>>>>>>> manage to sort out one of the things that was bogging me
>>>>>>>>>>>> down all week.. (actually, a compiler error, if you must
>>>>>>>>>>>> know..). You need to tell it where R and Java are in the
>>>>>>>>>>>> path (see batch file), but I trust you'll let me know how
>>>>>>>>>>>> this goes ;)
>>>>>>>>>>>>
>>>>>>>>>>>> What platform were you trying to run on? I think it would
>>>>>>>>>>>> probably be an idea to track these things, so that at least
>>>>>>>>>>>> we can advise when not to bother...
>>>>>>>>>>>>
>>>>>>>>>>>> Richard
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Richard,
>>>>>>>>>>>>> It's now complaining about missing libstdc++.so.6
>>>>>>>>>>>>>
>>>>>>>>>>>>> I think our OS installations here are a) not the most
>>>>>>>>>>>>> up-to-date b) a bit sparse.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I could ask Horst to install the missing libraries, but I
>>>>>>>>>>>>> think we have to be able to cope with the situation where
>>>>>>>>>>>>> the user can't get this stuff installed and make eirik as
>>>>>>>>>>>>> independent of any shared libs as possible, regardless of
>>>>>>>>>>>>> the size.
>>>>>>>>>>>>>
>>>>>>>>>>>>> John
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> fairly small, so attached mine! (might work if you create
>>>>>>>>>>>>>> links libXinerama.so and libXinerama.so.1 also in your path.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Logo: probably shouldn't really rely on it, but I might
>>>>>>>>>>>>>> change it when I have an idle minute, so the web link
>>>>>>>>>>>>>> should do for now.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> R
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ...could you send me a copy of your logo for putting on
>>>>>>>>>>>>>>>>> the web site?
>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>> J
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Xinerama is kind of optional with qt and I just left it
>>>>>>>>>>>>>>>> in by default. When I go through another 2-hour compile
>>>>>>>>>>>>>>>> I might take it out to see what happens... otherwise you
>>>>>>>>>>>>>>>> might visit http://rpm.pbone.net and do an advanced
>>>>>>>>>>>>>>>> search for your linux distro and libXinerama, choosing
>>>>>>>>>>>>>>>> the libXinerama-<ver>-i386.rpm if anything comes up.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> eg. for fedora 5 this might turn out as
>>>>>>>>>>>>>>>> ftp://ftp.univie.ac.at/systems/linux/fedora/5/i386/os/Fedora/RPMS/libXinerama-1.0.1-1.2.i386.rpm
>>>>>>>>>>>>>>>> click,save and then run
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> rpm -Uvh libXinerama-1.0.1-1.2.i386.rpm
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> as root.
>>>>>>>>>>>>>>> Not root on this machine, alas, so might have to just try
>>>>>>>>>>>>>>> stuffing it on the library path, assuming I can get hold
>>>>>>>>>>>>>>> of it.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Still having teething troubles with windows (you
>>>>>>>>>>>>>>>> probably guessed) but it is working and I'm fairly
>>>>>>>>>>>>>>>> hopeful of getting a demo out this week (I forgot things
>>>>>>>>>>>>>>>> like windows doesn't let you overwrite files whilst
>>>>>>>>>>>>>>>> they're still open...). At the moment it seems to die if
>>>>>>>>>>>>>>>> you tried to load several files one after the other.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> A version of my (slightly crude) logo lies at
>>>>>>>>>>>>>>>> http://www.comp.leeds.ac.uk/richardh/eirik/xpm/Eirikship.png
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Cheers!  Can I rely on that URL or should I take a copy?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>
>
>
>

Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....

[John T. <jon...@gm...>]

Thomas Boch wrote:
> Hi John,
>
> Being able to identify groups within tables might also be interest for
> me (in Aladin). I don't quite understand at which level the groupId is
> defined. Could you elaborate a bit more, and give an example ?
>   
Hi Thomas - the use case we're thinking of is that Eirik (say) runs a 
clustering algorithm on the VOTable and identifies (say) 3 clusters.  It 
would be nice if Eirik could then ask Aladin to display those 3 clusters 
in different colours, or using different symbols.  I'd prefer to keep 
the groupings at an abstract level, rather than Eirik specifying the 
colours or symbols itself and allow the receiving application to decide 
what to do with them.  e.g. VisIVO could map from groupIds to colours, 
Aladin from groupIds to symbols, and Topcat could map each group to a 
different subset...whatever makes sense for the receiving application.

As you say below, we want to keep things simple for applications that 
aren't interested in such complications!


>   
>> Whichever is adopted the groupId should be an optional parameter.  In
>> fact, I'd prefer to see it tacked on in an optional struct at the end
>> showObjects(tableId, rows[], [options])
>> with
>> options={groupdId=int[]}
>>
>> to allow for future expansion.
>>     
>
> The more I think about it, the more I agree that an optional struct is
> the right way to keep simplicity for simple things, yet giving some
> flexibility for more advanced ones. I think it is very important to keep
> the 'entry cost' to PLASTIC as low as possible, otherwise most people
> won't use it.
>
> Cheers,
>
> Thomas
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Plastic-devs mailing list
> Pla...@li...
> https://lists.sourceforge.net/lists/listinfo/plastic-devs
>
>   

Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....

[Thomas B. <bo...@ne...>]

Hi John,

Being able to identify groups within tables might also be interest for
me (in Aladin). I don't quite understand at which level the groupId is
defined. Could you elaborate a bit more, and give an example ?

> Whichever is adopted the groupId should be an optional parameter.  In
> fact, I'd prefer to see it tacked on in an optional struct at the end
> showObjects(tableId, rows[], [options])
> with
> options={groupdId=int[]}
> 
> to allow for future expansion.

The more I think about it, the more I agree that an optional struct is
the right way to keep simplicity for simple things, yet giving some
flexibility for more advanced ones. I think it is very important to keep
the 'entry cost' to PLASTIC as low as possible, otherwise most people
won't use it.

Cheers,

Thomas

[Plastic-devs] Idenitifying different subsets [was Re: Also....

[John T. <jd...@ro...>]

R Holbrey wrote:
>
> I guess this would be a good thing to hammer out a bit more at the 
> hackathon, but I'm still not quite getting there. Let's take the 
> clustering example abit further. R easily has a dozen different routines
>  and many possible parameter settings.
>
> In fact, one of the harder things to decide up front is whether you 
> want to set the number of clusters or whether you want some kind of 
> estimate. My idea for eirik is that you might want to do two, three or 
> more clusterings to get a feel how things are going and that, 
> crucially, eirik should start you off with the fastest/dirtiest.
>
> The way I read showObjects here is that for each cluster identified, 
> you send back a message saying show these objects, say for those in 
> cluster 1. Then another message for objects in cluster 2 etc. But
>
>  - how many clusters in all?
>  - what kind of errors were given (possibly on each)?
>  - what other parameters were assumed? (variables used to cluster, 
> types of cluster etc)
You could put any such extra information into the VOTable that you send 
to other apps.
>
> For errors, I guess the user could expect this from eirik, but might 
> not these params be useful in another workflow? For the number of 
> clusters, it seems more sensible to have a showObjects message where 
> the elements of the rows array might look like
>
> {1,1,1,2,2,3,4,4,3,3}
>
> for a 10-row table, with 4 clusters identified ie rows 1-3 belong to 
> cluster 1. As I read showObjects at the moment, this would result in 4 
> messages and then more for "other details". This kind of 
> multiplication of messages seems dangerously confusing to me, harder 
> to implement and more likely to lead to less understanding.
Sure - we could do it this way instead.   The purpose of the showObjects 
message is to tell a visualiser to select a set of rows.  We want to 
make sure that we keep it generic, and it doesn't have any 
Eirik-specific information in there.  However, the ability to be able to 
identify subsets in the set is quite generally useful I think.   The 
format of the message at the moment is
showObjects(tableId, rows[])

We can change this to
showObjects(tableId, rows[], groupId)
(which is what I proposed above, and would require a separate message 
for each group)
or
showObjects(tableId, rows[], groupId[])

I don't have any strong opinions either way - the latter has the benefit 
that it does keep all the groups together.

Whichever is adopted the groupId should be an optional parameter.  In 
fact, I'd prefer to see it tacked on in an optional struct at the end
showObjects(tableId, rows[], [options])
with
options={groupdId=int[]}

to allow for future expansion.








>
> More bluntly, I'd say it was shoe-horning... what happens if someone 
> requests a regression or a pca/fa with clustering on top (please stop, 
> I hear you cry ;)
No no...go on...
>
> An eirik api, anyone?
>
> R
>
>
>
> On Tue, 22 Aug 2006, John Taylor wrote:
>
>> I'll need to be reminded about exactly what you want to do....
>> IIRC  the use cases include:
>>
>> 1) User loads VOTable into Eirik, through Eirik identifies (say) 3 
>> interesting columns, sends a message to Topcat 
>> ivo://.../selectColumns#plot_3d
>> 2) User loads VOTable into Eirik, through Eirik identifies 4 
>> interesting columns, sends a message to Weka 
>> ivo://.../selectColumns#set_active_cols. User then runs a clustering 
>> algorithm on those columns.
>> 3) User wants to display the clusters in VisIVO.  Weka sends messages 
>> to VisIVO ivo://..../showObjects#highlight. Each message has an extra 
>> optional argument of groupId that VisIVO maps to a different colour.
>> Similarly Eirik could do the clustering (through R), and display the 
>> results through A.N.Other display program.
>>
>> 4) User loads a VOTable into TabView, decides on a set of columns for 
>> further investigation in Eirik.  TabView instructs Eirik to load the 
>> table, then sends a message ivo://.../selectColumns#set_active_cols
>>
>> In all these cases, the bit after the # is just a message fragment 
>> that I made up - each application can define its own.
>>
>> John
>>
>>
>>
>> R Holbrey wrote:
>>> On Tue, 22 Aug 2006, John Taylor wrote:
>>>
>>>> I think we got it!  At least, the window comes up, and by hitting 
>>>> random buttons like a monkey I can get plots to appear.
>>>
>>> cheers John,
>>>
>>> maybe now I can teach the monkey how to do showobjects. What was the 
>>> latest on that btw? I've been struggling to think how eirik would 
>>> understand it, and it needs work, the kind of been wanting to get on 
>>> with.
>>>
>>> If it's not desirable to expand plastic the way I was wondering a 
>>> while back, I'm starting to think eirik should define his own api 
>>> as, basically, requests to various r functions eg to do clustering. 
>>> (At the moment it seems like to do this through plastic would 
>>> require a new votable to be written and passed back, which I think 
>>> inordinately clumsy).
>>>
>>> R
>>>
>>>>
>>>>
>>>> R Holbrey wrote:
>>>>>
>>>>> After going to the bowels of NT and back, I realised I missed a 
>>>>> rather crucial file (doh), but the weird thing is, this still 
>>>>> doesn't cause trouble on my main xp machine. Presumably it finds 
>>>>> the file elsewhere, but I'm darned if I can replicate the problem, 
>>>>> unless I move to my ageing old compaq.
>>>>>
>>>>> I've uploaded a zip (built with 7-zip, which is GPL) and rar  
>>>>> (better compression than either, I suspect) of the bundle with the 
>>>>> missing r source file, so I'd be grateful if you would give it 
>>>>> another crack. Maybe then I can get on with my life...
>>>>>
>>>>> R
>>>>>
>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>
>>>>>> Still no luck I'm afraid...and nothing helpful (in the way of 
>>>>>> diagnostics) appears on the commandline.
>>>>>> J
>>>>>>
>>>>>> R Holbrey wrote:
>>>>>>>
>>>>>>> one thing I forgot was to set yet another environment variable, 
>>>>>>> R_HOME, so that RDLL in the .bat should really look like eg
>>>>>>>
>>>>>>> set R_HOME=c:\Program Files\R\R-2.3.1
>>>>>>> set RDLL=%R_HOME%\bin
>>>>>>>
>>>>>>> with %RDLL% in the path (these should appear in your path after 
>>>>>>> running the .bat from the command prompt??). Oddly though the 
>>>>>>> "depends" utility (from ms visualc - do you happen to have it?) 
>>>>>>> tells me, on my old laptop that there are no bindings to the 
>>>>>>> Rdll at all and several other key libraries. Looks like I'd 
>>>>>>> better reboot this one and go check...
>>>>>>>
>>>>>>> R
>>>>>>>
>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>
>>>>>>>> Hi Richard,
>>>>>>>> I'm using the latest R: 2.3.1 , java 1.5.0_06 and my path is:
>>>>>>>> C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program 
>>>>>>>> Files\ATI Technologies\ATI Control Panel;C:\Program 
>>>>>>>> Files\QuickTime\QTSystem\;C:\Program Files\Python;C:\Program 
>>>>>>>> Files\Java\jdk1.5.0_06\bin;E:\jdt\applications\maven-2.0\bin;E:\jdt\applications\maven-1.0.2\bin;C:\Program 
>>>>>>>> Files\Putty;E:\jdt\applications\apache-ant-1.6.5\bin;C:\Program 
>>>>>>>> Files\Java\jdk1.5.0_06\jre\bin\client;C:\Program Files\SSH 
>>>>>>>> Communications Security\SSH Secure Shell
>>>>>>>>
>>>>>>>>
>>>>>>>> R Holbrey wrote:
>>>>>>>>>
>>>>>>>>> thanks John,
>>>>>>>>>
>>>>>>>>> can you post me the versions of R, java and anything else you 
>>>>>>>>> can think of you're using and your path. I'll try some 
>>>>>>>>> different machines and I'll look up my old version of Visual 
>>>>>>>>> C. APparently there was a utility there called "depends" which 
>>>>>>>>> allowed you to see what dynamic libraries were in use (this 
>>>>>>>>> kind of thing is free in linux of course ;)
>>>>>>>>>
>>>>>>>>> R
>>>>>>>>>
>>>>>>>>> On Mon, 21 Aug 2006, John Taylor wrote:
>>>>>>>>>
>>>>>>>>>> Hi Richard,
>>>>>>>>>> We're getting there.  The install worked pretty much out of 
>>>>>>>>>> the box (all my dlls were in the right place I think).  Eirik 
>>>>>>>>>> fires up OK and plastic and ACR integration works.  However, 
>>>>>>>>>> the test data set isn't loaded, and any attempt to load a 
>>>>>>>>>> VOTable causes Eirik to bomb out. Is there any way I can get 
>>>>>>>>>> some diagnostic info for you?
>>>>>>>>>>
>>>>>>>>>> John
>>>>>>>>>>
>>>>>>>>>> PS
>>>>>>>>>> Any particular reason to use RAR?  I only have a "free trial" 
>>>>>>>>>> RAR decoder on my machine....zip is more common!
>>>>>>>>>>
>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>
>>>>>>>>>>> I've tried to post an xp versionjust now on the wiki:
>>>>>>>>>>> http://eurovotech.org/twiki/bin/view/VOTech/EirikDemo
>>>>>>>>>>>
>>>>>>>>>>> which has had plenty of hacks and papering although I did 
>>>>>>>>>>> manage to sort out one of the things that was bogging me 
>>>>>>>>>>> down all week.. (actually, a compiler error, if you must 
>>>>>>>>>>> know..). You need to tell it where R and Java are in the 
>>>>>>>>>>> path (see batch file), but I trust you'll let me know how 
>>>>>>>>>>> this goes ;)
>>>>>>>>>>>
>>>>>>>>>>> What platform were you trying to run on? I think it would 
>>>>>>>>>>> probably be an idea to track these things, so that at least 
>>>>>>>>>>> we can advise when not to bother...
>>>>>>>>>>>
>>>>>>>>>>> Richard
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Richard,
>>>>>>>>>>>> It's now complaining about missing libstdc++.so.6
>>>>>>>>>>>>
>>>>>>>>>>>> I think our OS installations here are a) not the most 
>>>>>>>>>>>> up-to-date b) a bit sparse.
>>>>>>>>>>>>
>>>>>>>>>>>> I could ask Horst to install the missing libraries, but I 
>>>>>>>>>>>> think we have to be able to cope with the situation where 
>>>>>>>>>>>> the user can't get this stuff installed and make eirik as 
>>>>>>>>>>>> independent of any shared libs as possible, regardless of 
>>>>>>>>>>>> the size.
>>>>>>>>>>>>
>>>>>>>>>>>> John
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> fairly small, so attached mine! (might work if you create 
>>>>>>>>>>>>> links libXinerama.so and libXinerama.so.1 also in your path.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Logo: probably shouldn't really rely on it, but I might 
>>>>>>>>>>>>> change it when I have an idle minute, so the web link 
>>>>>>>>>>>>> should do for now.
>>>>>>>>>>>>>
>>>>>>>>>>>>> R
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> R Holbrey wrote:
>>>>>>>>>>>>>>> On Thu, 17 Aug 2006, John Taylor wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ...could you send me a copy of your logo for putting on 
>>>>>>>>>>>>>>>> the web site?
>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>> J
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Xinerama is kind of optional with qt and I just left it 
>>>>>>>>>>>>>>> in by default. When I go through another 2-hour compile 
>>>>>>>>>>>>>>> I might take it out to see what happens... otherwise you 
>>>>>>>>>>>>>>> might visit http://rpm.pbone.net and do an advanced 
>>>>>>>>>>>>>>> search for your linux distro and libXinerama, choosing 
>>>>>>>>>>>>>>> the libXinerama-<ver>-i386.rpm if anything comes up.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> eg. for fedora 5 this might turn out as
>>>>>>>>>>>>>>> ftp://ftp.univie.ac.at/systems/linux/fedora/5/i386/os/Fedora/RPMS/libXinerama-1.0.1-1.2.i386.rpm 
>>>>>>>>>>>>>>> click,save and then run
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> rpm -Uvh libXinerama-1.0.1-1.2.i386.rpm
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> as root.
>>>>>>>>>>>>>> Not root on this machine, alas, so might have to just try 
>>>>>>>>>>>>>> stuffing it on the library path, assuming I can get hold 
>>>>>>>>>>>>>> of it.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Still having teething troubles with windows (you 
>>>>>>>>>>>>>>> probably guessed) but it is working and I'm fairly 
>>>>>>>>>>>>>>> hopeful of getting a demo out this week (I forgot things 
>>>>>>>>>>>>>>> like windows doesn't let you overwrite files whilst 
>>>>>>>>>>>>>>> they're still open...). At the moment it seems to die if 
>>>>>>>>>>>>>>> you tried to load several files one after the other.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> A version of my (slightly crude) logo lies at
>>>>>>>>>>>>>>> http://www.comp.leeds.ac.uk/richardh/eirik/xpm/Eirikship.png 
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Cheers!  Can I rely on that URL or should I take a copy?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>


-- 
------------------------------------------------------------------------
AstroGrid/VOTech
&
Institute for Astronomy, Edinburgh
Skype:johndavidtaylor <skype:johndavidtaylor?chat>

------------------------------------------------------------------------

Re: [Plastic-devs] spectrum messaging

[Mark T. <m.b...@br...>]

On Wed, 16 Aug 2006, Thomas Boch wrote:

> Mark,
> 
> 
> > (...)
> > 
> > So maybe
> > 
> >    1D:  ivo://votech.org/fits/line/loadFromURL
> >    2D:  ivo://votech.org/fits/image/loadFromURL
> >   3+D:  ivo://votech.org/fits/cube/loadFromURL
> 
> I think I like your suggestion. 
> 2 questions :
> 
> - How would FITS-extensions files fit into this scheme ?

Good question.  Possible answers:

  1. The array must be the primary HDU
  2. The array must be the first array-type HDU (may be primary, but
       if that's empty the first extension of type IMAGE)
  3. 1 and/or 2 unless the FITS URL has some kind of appendage to
       mark the extension ("#n" or "[n]" to denote extention number n?)
  4. 1 and/or 2 unless there's an optional message argument giving
       extension number (0 is primary, 1 is first extension)
  5. Mandatory message argument giving extension number 
       (0 is primary, 1 is first extension)

I probably favour 4.

Incidentally, we should in any case have an additional argument for
all these messages giving an identifier for the array, analogous
to the one sent in ivo://votech.org/votable/loadFromURL


> - If we want to send spectrum or timeseries serialized in VOTable,
> should we define a ivo://votech.org/votable/line/loadFromURL ? I am a
> bit worried by the multiplication of messages this solution would imply
> (though I don't see any better way).

My feeling is that you should have different message IDs for 
different data formats, but address the semantic issues using the
fragment mechanism that John has suggested (and until that's 
in place, just leave them to the user to work out).  The thinking 
behind this is that applications need to know what the data format
is in order to load it (and to know whether they will be able to),
but the question of whether it's sensible to load it is better
answered by a human.  So you don't have the message you mention 
above, but applications would advertise messages like

   ivo://votech.org/votable/loadFromURL#timeseries
   ivo://votech.org/votable/loadFromURL#spectrum

as appropriate.  The data is still a VOTable, and you might still 
want to load it into a generic table viewer such as TOPCAT.
The situation is different for 1,2,3-dimensional FITS arrays,
because a program that knows how to display a 1-d array
(typically a spectrum or time-series viewer) is not especially
likely to know how to display a 2-d array (typically a sky image).

There is room for argument in specific cases (including the one above)
about where the distinction between data format description and 
semantic hint lies, but (until anyone persuades me differently) 
I'd say that this is a good rule to answer questions about what 
functions require new messages to be defined.

Mark

-- 
Mark Taylor   Astronomical Programmer   Physics, Bristol University, UK
m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/~mbt/

Re: [Plastic-devs] spectrum messaging

[Thomas B. <bo...@ne...>]

Mark,


> (...)
> 
> So maybe
> 
>    1D:  ivo://votech.org/fits/line/loadFromURL
>    2D:  ivo://votech.org/fits/image/loadFromURL
>   3+D:  ivo://votech.org/fits/cube/loadFromURL

I think I like your suggestion. 
2 questions :

- How would FITS-extensions files fit into this scheme ?

- If we want to send spectrum or timeseries serialized in VOTable,
should we define a ivo://votech.org/votable/line/loadFromURL ? I am a
bit worried by the multiplication of messages this solution would imply
(though I don't see any better way).

Cheers,

Thomas

Re: [Plastic-devs] spectrum messaging

[Mark T. <m.b...@br...>]

On Tue, 15 Aug 2006, John Taylor wrote:

> Mark Taylor wrote:
> > Chaps,
> >
> > []
> >
> > An alternative (and one that I'd like to see) would be
> > ivo://votech.org/fits/spectrum/loadFromURL, which would make sense
> > sitting next to  fits/image/loadFromURL.
> >
> > Mark
> 
> I'd go with that, _unless_ there could ever be a need to load a 
> fits-format spectrum into a general fits image viewer (which wouldn't 
> know about fits/spectrum/...).  If there is such a need, then we could 
> go for ivo://votech.org/fits/image/loadFromURL#loadSpectrum (assuming 
> this "annotating with fragments" idea is accepted.)
> 
> John

Thinking slightly more carefully about it, I think what we need is
separate named messages for 1D, 2D and >=3D FITS arrays.
The 'image' one (though it doesn't currently say this explicitly in 
the message description) is probably understood already to mean 2D.
I *don't* think that this distinction would be best handled using 
fragments, since the difference refers to a well-defined 
characterisation of the type of data, not just how the client is
to understand it.

Naming is a bit of a problem; "cube" is often understood to mean 
high- rather than strictly 3-dimensional, so that's probably OK, 
but "spectrum" is not good for 1D since not all 1D arrays are
spectra (e.g. could be time series).

So maybe 

   1D:  ivo://votech.org/fits/line/loadFromURL
   2D:  ivo://votech.org/fits/image/loadFromURL
  3+D:  ivo://votech.org/fits/cube/loadFromURL

Fragments probably are the best way to distinguish between [uses for]
different physical meanings for some of these things, e.g.

  ivo://votech.org/fits/line/loadFromURL#spectrum
  ivo://votech.org/fits/line/loadFromURL#timeseries

though an application which can just plot graphs won't care
about the difference so would use the un-fragmented message.

Mark

-- 
Mark Taylor   Astronomical Programmer   Physics, Bristol University, UK
m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/~mbt/

Re: [Plastic-devs] spectrum messaging

[Noel W. <Noe...@ma...>]

Hi.
I don't know if there's any messages defined for spectra.

at the moment the workbench bundles an in-process jar of vospec, and  
controls it directly using direct method calls - no plastic here.

Although there is a standalone version of vospec, I've not managed to  
send it any messages it'll respond to. I beleive it's implemented to  
the early version of the plastic spec where you can leave the list of  
supported messages empty to indicate 'all messages'.

IIRC, I was told by the ESAC folk that there's a new version of  
vospec in the pipeline - so maybe this is a good time to define some  
spectra messages.

noel.


On 15 Aug 2006, at 10:18, Mark Taylor wrote:

> Chaps,
>
> what message/s is/are currently used for the transfer of spectra
> over PLASTIC?  Presumably it is done between the workbench and
> VO-Spec, though when VO-Spec registers it doesn't appear to
> indicate which messages it supports.  I suppose the answer is
> ivo://votech.org/votable/loadFromURL; if that's the case, is there
> a standard way to know which columns of the VOTable mean what?
>
> An alternative (and one that I'd like to see) would be
> ivo://votech.org/fits/spectrum/loadFromURL, which would make sense
> sitting next to  fits/image/loadFromURL.
>
> Mark
>
> -- 
> Mark Taylor   Astronomical Programmer   Physics, Bristol  
> University, UK
> m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/ 
> ~mbt/
>
>
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Re: [Plastic-devs] spectrum messaging

[John T. <jon...@gm...>]

Mark Taylor wrote:
> Chaps,
>
> []
>
> An alternative (and one that I'd like to see) would be
> ivo://votech.org/fits/spectrum/loadFromURL, which would make sense
> sitting next to  fits/image/loadFromURL.
>
> Mark
>   

I'd go with that, _unless_ there could ever be a need to load a 
fits-format spectrum into a general fits image viewer (which wouldn't 
know about fits/spectrum/...).  If there is such a need, then we could 
go for ivo://votech.org/fits/image/loadFromURL#loadSpectrum (assuming 
this "annotating with fragments" idea is accepted.)

John

[Plastic-devs] spectrum messaging

[Mark T. <m.b...@br...>]

Chaps,

what message/s is/are currently used for the transfer of spectra
over PLASTIC?  Presumably it is done between the workbench and
VO-Spec, though when VO-Spec registers it doesn't appear to 
indicate which messages it supports.  I suppose the answer is
ivo://votech.org/votable/loadFromURL; if that's the case, is there
a standard way to know which columns of the VOTable mean what?

An alternative (and one that I'd like to see) would be
ivo://votech.org/fits/spectrum/loadFromURL, which would make sense
sitting next to  fits/image/loadFromURL.

Mark

-- 
Mark Taylor   Astronomical Programmer   Physics, Bristol University, UK
m.b...@br... +44-117-928-8776 http://www.star.bris.ac.uk/~mbt/

Re: [Plastic-devs] Select or show colums message

[John T. <jon...@gm...>]

Hi Doug - welcome to the list.

Looks like Mark is thinking on the same lines - consider the motion carried.

John
> This is more a user interface thought than anything deep or meaningful.
>
> Given that the fragment is application specific, does this mean you 
> have to have descriptive fragments, so that the UI of the sending 
> application can provide enough info for a user to know what each 
> particular specialization does? In the example above, "plot", 
> "highlight" are easy, and "new_subset" is obvious enough but the 
> underscore makes it look ugly (from a UI view). An alternative would be 
> to add a way to ask the receiving application for a descriptive string 
> for a given fragment so that this could be used by the UI (maybe even 
> title and description if you wanted to add "tooltips" or some other 
> such mechanism).
>
> Doug
>
>
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Re: [Plastic-devs] Select or show colums message

[Doug B. <db...@cf...>]

On Jul 19, 2006, at 7:55 PM, John Taylor wrote:

> To take a specific example.  Topcat could do one of two things with a
> bunch of columns: create a new subset based on them, or create a plot
> (2D or 3D depending on the number of columns).
> It would register as understanding
> ivo://votech.org/votable/selectCols#plot
> ivo://votech.org/votable/selectCols#new_subset
>
> The fragment string is completely defined by Topcat - no other 
> agreement
> is needed with any other application, and no other application needs to
> understand what it means.  Instead, the sending application (e.g. Weka)
> strips off the fragments and uses them to populate its UI.  Thus it
> might offer the user the following options for the selected columns:
> send cols -> topcat -> plot
>                                -> new_subset
>                -> tabview-> highlight
>                -> Anomaly Detector
>
> [assuming tabview has registered with selectCols#highlight, and Anomaly
> Detector has registered just with selectCols]
> The appropriate fragment is then tacked on to any sent messages.

This is more a user interface thought than anything deep or meaningful.

Given that the fragment is application specific, does this mean you 
have to have descriptive fragments, so that the UI of the sending 
application can provide enough info for a user to know what each 
particular specialization does? In the example above, "plot", 
"highlight" are easy, and "new_subset" is obvious enough but the 
underscore makes it look ugly (from a UI view). An alternative would be 
to add a way to ask the receiving application for a descriptive string 
for a given fragment so that this could be used by the UI (maybe even 
title and description if you wanted to add "tooltips" or some other 
such mechanism).

Doug