Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....
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Re: [Plastic-devs] Idenitifying different subsets [was Re: Also....
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From: John T. <jon...@gm...> - 2006-08-30 10:58:06
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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?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>
--
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AstroGrid/VOTech
&
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Skype:johndavidtaylor <skype:johndavidtaylor?chat>
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