Doing science with prototype Virtual Observatory tools?

July 01, 2003

Bob Mann1,2 and Mark Allen3
1. Institute for Astronomy, University of Edinburgh (rgm@roe.ac.uk)
2. Professeur invité, Université Louis Pasteur, Strasbourg
3. Centre de Données astronomiques, Strasbourg (allen@astro.u-strasbg.fr)

1 Introduction

As the Virtual Observatory (VO) takes shape, it is vital that there is a closed feedback loop between the developers of VO tools and the scientists who will use them, to ensure that the tools match the scientific requirements of the astronomical community. With that in mind, we undertook an exercise to see to what extent real science can be done with the existing first batch of VO prototype tools, primarily the tools created for the AVO First Light Demo in January 2003. Our approach was to take a science problem and to see if we could follow it through to the point of obtaining scientific results using available tools, and identifying the problems that arose along the way. We describe the results of this exercise in this note, and also supply the information required for other people to reproduce what we did. We stress that our goal was to test the existing tools scientifically, but not to do publication-quality science, so what follows does not include the same level of rigorous checking that we would apply in our own research!

2 Available data and tools

The AVO First Light Demo focuses on the manipulation of GOODS data using an extended version of the Aladin image tool from CDS, coupled with the Astronomy Catalogue Extractor (ACE), which is a web service wrapper to the SExtractor source extraction code. The AVO demo version of Aladin includes a source tree of image data covering the GOODS Chandra Deep Field South (CDFS) region, notably WFI (optical) and ISAAC (near-IR) data from ESO, multi-epoch ACS optical data from the HST and X-ray data from Chandra. Catalogues from these, and other data sets covering this region, are included in this tree, via links to the VizieR catalogue service at CDS. (These include a draft UBVRIJK catalogue created by the EIS team from their WFI and SOFI data: this was kindly made available for AVO development work by the EIS team, and should not be considered as being a scientifically validated EIS data product at this stage.) VizieR offers many formats for catalogue output, including VOTable. Attributes stored in VOTable files can be plotted using the VOPlot tool developed by VO-India project in collaboration with CDS. VOPlot can run as a standalone java application, or as an applet in a browser, and it has been integrated with VizieR, so that plots can be generated directly as part of the catalogue search procedure. Our exercise employed the publicly available VOPlot standalone version 1.0, and we note that VOPlot is currently in an early development phase. In fact many changes were being implemented during the running of this example, so the fixes implemented in the developmental June 12 version of VOPlot are noted. (Also a beta version of another tool, TOPCAT, became available after this exercise. We include a limited set of tests using TOPCAT in the appendix)

One of the great advantages of using an XML-based data format, such as VOTable, is that standard XSLT methods can be used to transform the data, so that they can be read into analysis tools developed outwith astronomy. In what follows, we give examples of using three such non-astronomical analysis tools: Mirage, a "Java-based software tool for exploratory analysis and visualization of classification and proximity structures of multi-dimensional numerical data" developed at Bell Labs (and utilised in the NVO January demonstrations); Weka, a "machine learning workbench" from the University of Waikato; and CViz, a "visualization tool designed for analyzing high-dimensional data in large, complex data sets", from IBM. Like VOPlot, all three of these tools are downloadable from the WWW as Java .jar files and are available free for academic use (although CViz currently so only for a finite time period): this is surely indicative of one future path of VO development, whereby astronomers can make use of applications developed in other disciplines, with the task for the VO developers being how to integrate these tools into their infrastructure, rather than developing bespoke astronomical applications themselves.

3 Example science topic: X-ray-detected EROs

Our testbed science problem follows the recent work of Roche, Almaini and Dunlop (astro-ph/0303206), who have studied the properties of Extremely Red Objects (EROs) in the GOODS CDFS field, as part of an on-going investigation of a galaxy evolution scenario in which the stellar mass of large elliptical galaxies seen at redshift zero is created in ultra-luminous dusty starbursts at high-redshift, like those detected in the submm using SCUBA, and possibly later passing through an AGN phase. One of the things that Roche et al. do to investigate this hypothesis is to seek associations between EROs (defined to be galaxies with I-K > 3.75) and Chandra sources in the GOODS CDFS field, to try and assess what fraction of EROs might contain obscured AGN, of the sort necessary to explain the spectrum of the hard X-ray background. We repeat that aspect of their work as our testbed science topic, seeking associations between the Chandra sources in the 1Ms CDFS catalogue of Giacconi et al. (2002) and the draft EIS UBVRIJK catalogue. We then investigate how the properties of those X-ray counterparts which are EROs compare with both the remaining counterparts of the X-ray sources which are not EROs and the remaining EROs which are not associated with X-ray sources. We also look for correlations between the X-ray and optical/NIR properties of the X-ray-detected EROs, and seek further information about them from the ACS data of the CDFS field.

4 Summary of the procedure followed in this exercise

In Figure 1 we show the layout of some of the datasets available in the CDFS field, using the Aladin component of the AVO demonstration prototype.


Figure 1. A summary plot of some of the data sets available in the CDFS area and used in this exercise, namely: SOFI near-IR (red square), ISAAC near-IR (dark blues squares), first epoch ACS (light blue squares), and Chandra sources (pink crosses), while the background image is a WFI V band preview.

The background image is a WFI V band preview image (i.e. the pixels in the original image are binned up to reduce the data volume) and the red square marks the boundary of the SOFI near-IR data, so that the area within the red square is the coverage of the EIS UBVRIJK catalogue. For comparison, the dark blue squares mark the area covered by the eight ISAAC fields used in the creation of the ERO catalogue analysed by Roche et al., so we are considering a significantly larger area of sky here. The pink crosses are the sources from the Chandra catalogue of Giacconi et al., and the light blue squares plot the fields from the first epoch of ACS observations.

In outline, our exercise proceeds as follows. We start by investigating the selection of EROs from the EIS UBVRIJK catalogue, by extracting a subset of the catalogue from VizieR in VOTable format and reading it into both VOPlot and Mirage: VOPlot reads VOTables directly, while we have to run an XSLT transform before reading the data into Mirage. We then perform the requisite I-K colour cut in the tools and display the ERO sample that we have just created.

Having seen how to select EROs, we then cross-match the Chandra and EIS catalogues, in preparation for investigating the properties of those associated sources which are EROs. Our cross-matching is simply done on proximity, with a matching radius of 2 arcsec, following Roche et al., and is performed within VizieR. Some manipulation in IDL is required to generate a VOTable containing the combined X-ray and optical/near-IR attributes of the matched sources, and we assess the validity of (a few of) these associations through the use of Aladin.

Our investigation into the properties of the X-ray-detected EROs then proceeds through the use of VOPlot, Mirage, Weka and CViz. Each of these is designed to explore multi-variate datasets like this, and we compare their performance in this task. This investigation identifies some interesting sources, so we use Aladin and ACE to extract further information about them, using one epoch of the ACS data in this field. Finally, we summarize our experience in undertaking this exercise and draw some conclusions from it.

5 A detiled walk-through of the procedure followed

5.1 Selection of EROs from the EIS 7-colour catalogue

The draft EIS 7-colour catalogue was interrogated within VizieR, to select a subsample of galaxies with K>17.5 (that marking roughly the brightest magnitude at which EROs are found) which was then exported in VOTable format. We extracted a magnitude-limited subsample of only 1000 sources, for our illustrative purposes: the VOTable for that subset is availabe here. (Selection of larger samples is also possible, taking into account the VizieR FAQ note for samples > 9999. ) We then sought to select EROs from that sample, using both VOPlot and Mirage. (It would be useful if VizieR could implement something analogous to "select count(*)" in SQL so that you could find out how many entries satisfy your selection criteria without having to extract them all, thereby helping in the setting of appopriate criteria.)

VOPlot can, of course, be launched straight from VizieR, but we ran it in its standalone version, loading the EIS subsample as a VOTable from disk, using VOPlot's simple Browse and Load process. To aid ERO selection, we defined an additional I-K column in our dataset, making use of VOPlot's Create new virtual columns mechanism, as shown in Figure 2:


Figure 2. Defining a new virtual column in VOPlot.

This process is simply performed, with the additional column readily defined in terms of the existing columns, through use of a set of basic mathematical functions. The Help pop-up lists a total of 18 functions, including logarithmic and trigonometric functions, so there is significant flexibility here, allowing both the investigation of positional properties and the creation of, say, optical/X-ray flux ratios when the optical photometry is supplied in magnitudes.

We then performed the I-K>3.75 colour cut by defining a filter on our dataset, as shown in Figure 3:


Figure 3. Defining a filter in VOPlot.

Again, this is simply done, using the Create new data subsets dialog box. Armed with our named ero filter, we then sought to plot I-K against I for the full sample of 1000 sources, and overplot our ERO subsample in such a way that it stood out. This should be readily done, since VOPlot has an Overlay option, which allows overplotting, and this can be used with a named Filter, like our ero selection. In practice, the resulting plot, shown in Figure 4


Figure 4. EROs selected from an (I-K) vs I colour-magnitude plot. Note the straight lines here and in other plots are due to the magnitude limits of the catalogue.

was not as clear as we had hoped. The main and overlaid plots can be distinguished by plotting symbols of different colour and/or shape. What we had wanted to do was to overlay our main plot with red diamonds by the ERO sample in blue diamonds, but, while VOPlot did perform both those operations, it then redrew the whole plot, as required to add notes of what the two symbols denoted, and, in doing so, the blue diamonds became overplotted by the red diamonds, so that the ERO subsample could not be distinguished. So, we had to resort to using blue crosses for the ERO filter, since these could still be seen after the red diamonds were replotted, but this leads to a somewhat unsatisfactory plot, as the ERO subsample does not readily stand out from the full sample. Unfortunately the current VOPlot version lacks a mechanism for exporting data manipulations made within the tool: in our example, it would be useful to be able to export a VOTable which might have contained the additional I-K column, but certainly would have contained an additional column which flagged the rows selected by our ero filter, ideally with the filter definition being recorded in a human-readable form in the <DESCRIPTION> element accompanying the <FIELD> element of the new column.

An analogous procedure can be followed in Mirage, once the data have been transformed into its format. This transformation is aided by starting from an XML format, like VOTable, as all that is required is the definition an XSL stylesheet expressing how the data are transformed and then a standard XSLT engine can be used to performed the transformation. Ray Plante produced an XSL stylesheet to convert from VOTable to Mirage format and posted it on the VOTable mailing list some time ago: it is available there at http://archives.us-vo.org/VOTable/0194.html. This needed to be modified slightly (changing the name of one attribute to look for) for use with VOTables downloaded from VizieR: the revised XSL stylesheet is available here. Armed with that stylesheet, conversion of the data takes just a one-line call to an XSLT engine. We used the Java version of Xalan, the free XSLT engine from Apache, for which the one-line call is of the form:

java org.apache.xalan.xslt.Process -in temp.vot -xsl vot2mirage.xml -out temp.mirage
to convert VOTable temp.vot into Mirage-format file temp.mirage: the Mirage version of the EIS subsample is available here. Mirage is launched with a command like the following:
java -Xmx750000000 -jar Mirage0.2.jar -data temp.mirage
where the -X specifies that Mirage be allocated a larger amount of memory than it would be assigned by default by the Java virtual machine. Once the data file has been loaded into Mirage, the user is first presented with a view of it in tabular form, as shown in Figure 5:


Figure 5. A table view of the data loaded into Mirage.

To define an extra column in Mirage to store the I-K colours, one does as shown in Figure 6,

Figure 6. Defining an additional column in Mirage.

using the addcol command. This works for this case, but it is less flexible than the mechanism for defining a new virtual column in VOPlot. One may only add a column which is the sum, difference or product of existing columns, and there is no possibility of using a numerical value in the place of the second column name: this restriction causes us a problem later, where we are not able to rescale our X-ray fluxes so that their numerical values are large enough to be handled by Mirage's axis-rescaling mechanisms. Mirage's selection mechanism is also somewhat less flexible than the filter procedure in VOPlot. To perform our ERO selection we type select Imag-Kmag 3.75 10.0 at the Mirage command line, since selections in Mirage have to be specified in terms of lower and upper limits to the values in pre-existing columns. Note that, in VOPlot, we could have made our ERO selection in one step, using a filter definition that included column numbers for both the I and K band magnitudes, whereas, in Mirage, it has to be a two-step process, with the definition of an extra column for I-K, followed by a selection of rows on the value in that new column.

Executing the select command in Mirage results in the highlighting of the rows in the table which satisfy the selection criteria, as shown in Figure 7:
Figure 7. Highlighting in the data table view rows selected by a select command.

If the selection had been made while a scatter plot had been displayed, the rows in the table satisfying the criterion would be overlaid, as shown for our EROs in an I-K vs I plot in Figure 8.

Figure 8. The ERO subsample in Mirage's I-K vs I colour-magnitude plot.

One of the neat things about Mirage is the way that a selection made in a plot making one sort of presentation can be propagated through to other plots generated within Mirage. So, for example, we could display a scatter plot of a different pair of attributes and the ERO points would continue to be appear in a different colour. Selections can also be made graphically with Mirage, which makes up for the lack of flexibility in the command line selection function: a rectangle or curve can be drawn in an existing scatter plot to select data, or one can even "paint" an area of the plot freehand, which would be very useful for selecting a cluster of points whose boundaries could not easily be expressed in simple range cuts on attributes. Another advantage that Mirage has over VOPlot is the ability to export data, so that we were able to write out, albeit into Mirage's own ASCII data format, both the version of our EIS sample with the added I-K column and the ERO subsample of that dataset.

5.2 Selection of counterparts to Chandra sources from the EIS catalogue

One of the biggest problems that we encountered in this exercise was the lack of a VO tool for the generic cross-matching of catalogues which can deliver its results in VOTable format. Since we were following the example of Roche et al. in making associations solely on the basis of proximity, with a matching radius of 2 arcsec, we resorted to a slightly clunky method using VizieR. VizieR is able to perform the matching of a list of targets, presented in Tab Separated Value (TSV) format in a file, against the catalogue it contains. So, the first step in our selection of counterparts to Chandra sources from the draft EIS catalogue was to extract from VizieR a TSV file containing the positions of all the Chandra sources in the catalogue of Giacconi et al.. This we then uploaded again into VizieR, using the List of Targets option, as described above and as shown in Figure 9 below:

Figure 9. Loading the Chandra source list into VizieR to match against the EIS catalogue.

While multiple output formats are listed for VizieR's output from this procedure, only the HTML table output worked perfectly, as shown in Figure 10

Figure 10. HTML table output from VizieR's cross-matching procedure.

Other output options generate "SIMBAD error" messages, are are currently not supported so we were not able to extract what we desired, a VOTable containing the X-ray and optical/near-IR magnitudes of the matched sources. In order to proceed with our exercise, we decided to create an ASCII file from the HTML file shown in Figure 10 and use a small IDL routine to match entries from it with entries in another ASCII file which contained the X-ray attributes extracted from VizieR for the same set of Chandra sources. (For those wishing to reproduce what we did, we provide the IDL file, the matched source file and the Chandra attribute file, the matched source VOTable output file, and the ERO subset VOTable, generated by including an I-K>3.75 colour cut in the IDL routine: note that the IDL code makes use of the readfmt routine from the Astrolib library.) We could have performed the source matching more easily using, for example, the CURSA package from Starlink, but this would not have returned results in VOTable format, which our quickly-written IDL code was able to. No doubt the situation will change soon, as VOTable becomes more widely supported by astronomical software packages, but this current lack of even a simple positional cross-matching tool that returns a VOTable is a frustration. (Re-attempting the matching procedure with VizieR, it was found that a cut down version of the tab separated file, where only the coordinates were present, as opposed to the full version returned by VizieR, could be used to obtain VOTable output of the matches. This VOTable of cross matches is linked here. In principle this table could be converted to a convenient format using an XSLT to generate the same result as done with the HTML table and IDL script above.)

5.3 Validation of associations made between Chandra and EIS sources

Whilst we did not attempt as rigorous a validation of the associations we had made between the Chandra and EIS sources as we would have in a real research project, we did check that the associations looked sensible, by loading our VOTable of cross-matched source information into Aladin and overlaying the error circles of the Chandra sources on an optical image of the region, marking the EIS catalogue sources. Figure 11 shows part of the results of this:

Figure 11. Chandra error circles (in red), plotted on an EIS/WFI B band images, with the positions of the EIS catalogue sources marked as blue crosses: note the apparent offset in the astrometric reference frames of the Chandra and EIS data.

The error circles in Figure 11 were created using Aladin's filter mechanism, which allows us to define the size of the circle to be drawn at each Chandra source position by using the values in the PosErr column of our cross-match VOTable, which records the uncertainties in the Chandra source positions listed in the Giacconi et al. catalogue. Figure 12 shows how this filter was defined in Aladin.

Figure 12. Defining a filter in Aladin, so that it will plot the error circles for all the Chandra sources.

The two bright galaxies in Figure 11 intrigued us, so we selected cutouts from three of the ACS frames in this field (F435W, F775W, F850LP) and created an RGB image from them in Aladin, on top of which we overlaid the Chandra error ellipses again and the positions of EIS catalogue sources. The result is shown in Figure 13:

Figure 13a. Zooming in on two of the Chandra/EIS associations; overlaying Chandra error circles (red) and EIS catalogue source positions (blue diamonds) on an RGB image created by Aladin from the F435W, F775W and F850LP ACS images of this field.
The AVO prototype also allows an SED of catalog data to be plotted. This is shown in figure 13b.

Figure 13b. SED of selected EROs.

Figure 11 indicates an apparent offset in the astrometric reference frames of the Chandra and EIS datasets. We tried to investigate this more thoroughly, by looking at the distribution of offsets between the matched X-ray and EIS source positions in the (RA,Dec) plane, but this proved impossible with the current versions of VOPlot and Mirage. VOplot 1.0 seems unable to handle RAs and Decs in decimal degrees. A developmental unreleased version of VOplot did however fix this problem, and allowed construction and plotting of columns of RA and Dec offsets, see Figure 13c.

Figure 13c. Positional offsets between the Chandra and EIS datasets. As noted above, Mirage allows the creation of a new column using only the sum, difference or product of two existing columns. This means that it is not possible to compute in Mirage a column to store the angular positional offsets in the RA and Dec directions in arcsec, which is really what is wanted. In the light of that, it was decided just to compute the difference between the RAs and Decs directly, neglecting the cos(dec) term for the angular distance in the RA direction and keeping the results in degrees, since that's what the original columns are in. Clearly, this resulted in very small numbers (of order 10-4 or 10-5), and it proved impossible to get Mirage to plot these values on a graph with sensibly-scaled axes - and the absence of a means of generating a new column by scaling the data values meant that it proved impossible to produce a useful plot of the distribution of positional offsets in Mirage, either.

5.4 Investigating the properties of X-ray detected EROs

In this section we describe our investigation of the properties of the X-ray detected EROs with the various tools described in Section 2 above. Our goal was to see how their properties compared with those of two other populations, the non-ERO counterparts for Chandra sources from the EIS catalogue, and the remaining EROs from the EIS catalogue which are not associated with Chandra sources.

5.4.1 VOPlot

VOPlot 1.0 had some problems loading the VOTable file containing the matched source information that we generated with our IDL routine. It seemed unable to match up some of the <FIELD> elements defining table columns with the appropriate column of data extracted from the <TABLEDATA> element. This is illustrated in Figure 14

Figure 14. Illustrating the column mismatch in VOPlot resulting from loading our VOTable: the axes say that this is a plot of PosErr against Match_dist, but the data values plotted are for Match_dist against EIS_RAJ2000.

which shows a plot labeled as being PosErr against Match_dist. In fact, the values plotted as being PosErr are, in fact, the values of Match_dist, the next column in the table, while those purporting to be Match_dist are actually those of EIS_RAJ2000 which is the column which follows it in the table. Also, trying to plot the Kmag column causes an ArrayIndexOutOfBoundsException to be thrown by VOPlot and the program was unable to display that plot. We have not tracked down the cause of this problem, but it does appear to be a problem with VOPlot and not with our VOTable: we checked that our file was a valid VOTable document by validating it against the VOTable schema, using the Java version of the Apache parser, Xerces, and the XSLT-transformed version of the data loaded into Mirage has no such mismatch between column titles and values. ( Subsequent tests with the developmental version of VOPlot show this bug to have been fixed)

Despite this, we were able to identify which column stored in VOPlot corresponded to which column in the VOTable, by comparing plots made with VOPlot and Mirage, and we were able to create new columns with names matching the correct columns of data values. This did not work completely, however, as we wanted to create a Total (0.5-10.0keV) X-ray flux, by adding the soft and hard band fluxes from the Chandra catalogue, but an exception was thrown when parsing the expression to set this up. This error seems to be present in both VOPlot 1.0 (where account of the row mis-labeling is taken into account), and with the developmental VOPlot.

Figure 15 shows one interesting plot that did result from our investigation with VOPlot using the columns already present in the table:

Figure 15. Hardness ratio against I-K colour for the Chandra-EIS associations by VOPlot.

This plots X-ray hardness ratio, HR> (defined to be HR=(H-S)/(H+S), where H and S are, respectively, the hard and soft band X-ray fluxes), against I-K colour, for all Chandra sources associated with EIS objects (red diamonds) and for the ERO subset (blue crosses underneath red diamonds). It is interesting to note that ERO counterparts are found across the full range of HR, implying that a number must harbour AGN, since passive ellipticals and dusty starbursts alone should be soft X-ray sources. A second noteworthy point is the hint of a difference in the I-K colour distribution as a function of HR for the ERO subsample. It appears that the harder EROs, with HR-0.4 occupy a narrower range of I-K space than the softer subsample.

5.4.2 Mirage

Similar procedures can be followed in Mirage. In Figure 16 we plot our analogue of Figure 15 from Roche et al., which plots the X-ray hardness ratio against total (0.5-10.0 keV) X-ray flux.

Figure 16. Hardness ratio against total (0.5-10.0 keV) X-ray flux for all the Chandra/EIS associations (blue), with the ERO subsample overlaid in red.

A problem with this plot results from the small numerical values of the X-ray fluxes (10-16 to 10-14 erg/s/cm2), which are too small for Mirage's axis rescaling procedure to work. Also, Mirage does not offer the capability of making logarithmic plots (although it does permit the input of externally generated columns with "addcolfrom" function). VOplot does allow logarithmic axes, by either the "log" checkbox next to the axis selection menus, and also by definition of new virtual columns using logarithm function. A benefit of using Mirage is the ability to work on multiple windows (plots) at the same time, with the concept of projecting selected subsets of data to the various plots.

5.4.3 Weka

We briefly investigated the exploration of our matched Chandra/EIS source list using Weka, which is a suite of data mining algorithms. Weka has its own data format, but our VOTable was readily converted to that format using a XSL stylesheet, which we make available here and which was created from the stylesheet for VOTable-to-Mirage transformation via a few modifications. We ran Xalan to perform the tranformation, as before, (yielding this ARFF file) which was loaded into Weka, which had been launched with the command java -jar weka.jar: Figure 17 shows the result of this procedure.

Figure 17. The Chandra/EIS dataset loaded into Weka, and with the attribute to be used in the clustering procedure selected.

Launching Weka brings up the Weka GUI Chooser, shown on the right, from which we have chosen the Weka Knowledge Explorer, on the left. We have loaded into that our dataset, and have selected a subset of attributes to study by the use of the check-boxes in the Preprocess pane. Note that statistical information about an attribute selected in the left hand pane is presented on the lower right hand pane. Our intention in loading the Chandra/EIS data into Weka was to use some of its clustering tools to see whether we could detect different populations in the multi-dimensional space defined by the nine band X-ray and optical/NIR photometry data we have for these sources. As an initial attempt at that, we just clicked on the Cluster tab in the Explorer window, which provided us with the means of launching one of Weka's clustering algorithms, details of which are given in the Weka book. We chose the default clustering algorithm, EM, with its default set of parameters, and chose to run it using 66% of our data as a training set. That yielded the following results pane:

Figure 18. The result of running Weka's default clustering algorithm (EM) on the 9-dimensional photometric data space created from the Chandra/EIS dataset.

Running the EM algorithm in this way on the 9-dimensional photometric space yields a set of nine clusters, but upon closer inspection of the results, two things become clear. Firstly, the two X-ray fluxes have effectively been ignored, since the clustering algorithm took their numerical values (10-16 to 10-14, in erg/s/cm2 recall) to be directly comparable to the optical magnitudes, so that the, essentially, all the sources had the same X-ray fluxes, so that the two fluxes would not distinguish between sources in their assignment to clusters. The second thing to note is that, if one ranks the nine clusters in order by the mean value of the magnitude of the cluster members in a particular optical band, then the ranking is almost identical across the seven optical/near-IR bands. This indicates that the spread in source colours is much smaller than the spread in source magnitudes - i.e. to lowest order, all sources have the same SED, and all that differs between them is an overall scaling in magnitude.

This is clearly not the result that we wanted to get from this exercise! The data space within which we should have sought clusters would have been one spanned by flux ratios, rather than fluxes, so that we found sets of source with different SED type, and with those fluxes normalised so that all of them would have similar weight in assigning cluster membership. Since Weka is intended to be an extensible data mining framework, rather than a comprehensive standalone tool, it does not provide many filters, such as we could use to perform this normalization, but, rather, it provides a mechanism whereby users can write small java classes to implement filters and have them run in Weka. Weka's Select attributes tab calls up algorithms to select the most discriminating attributes: for example, if we had run that with our input dataset, it would have eliminated the two X-ray fluxes. This would be a useful preprocessing step if we had normalised our data before loading them, since it probably would have reduced the dimensionality of the problem - and, hence, the time taken to run the clustering algorithm - by noting that the set of seven optical/near-IR magnitudes contain some redundancy, given that the spread of colours in the sample is smaller than the spread of magnitudes.

Weka has its own visualization capabilities, as illustrated in Figure 19:

Figure 19. Weka's visualization pane. The right hand portion shows condensed representations of the scatter plots of all pairs of attributes in the dataset, from which we have selected the HR vs K magnitude plot to display on the left, with points coloured accordingly to their I magnitude. An unusually red object has been selected from this plot, as indicated by the shaded rectangle around it.

To get this we clicked on Weka's Visualize tab, and selected HR and Kmag respectively from the menus for the X and Y axes. We then chose Imag from the Colour menu, so that the colour of the points is determined by their I band colour, as shown in the colour bar at the bottom of the plot. Weka allows us to select an instance from the dataset, and, in this plot, we have selected a source with an unusually red colour, indicated by the very faintness of its I band magnitude, given its magnitude at K. The right hand panel of this window displays the plots of all the pairs of attributes in the data set, and they can be selected by clicking on them. This is a nice feature, since, whilst they offer very condensed representations of their data, they do show which plots have structure in them (rather than just being randomly-populated scatter plots), so one could find the interesting set of plots to view by scanning over these previews, rather than having to look at each of them in turn.

5.4.3 CViz

The final application that we looked at in this study is CViz, which is a tool for visualizing clusters in data. It reads in data in CSV format, with the column names in the first row of the file: we provide the XSL stylesheet to convert from VOTable to CViz format and the resulting CSV file. CViz is launched by ivoking java on its .jar file, with additional command line options to set memory allocation, attach the HTML manual, etc, i.e.
java -cp ctour.jar -mx90M -Dmanual=manual/cviz.html -Dtext=%2 ControlPanel %1
Figure 20 shows a screenshot from CViz:

Figure 20. A screenshot showing CViz in action. In the top left is the main CViz window, which was used to load the dataset and select which attributes to use. The right hand plot shows the results of CViz's default clustering algorithm run on the data, which generated five clusters. Clicking on one of them produced the pane at the bottom, which shows the composition of the cluster, expressed as a comparison of the mean value of each attribute within the cluster members, against the mean value for the dataset as a whole.

To obtain this after launching CViz we loaded the Chandra/EIS dataset, using the Open Data File option from the File, and then, from the Select attributes to use pop up which then appeared, we select the flux/magnitude attributes, plus their uncertainties and the Hardness Ratio information. CViz then seeks clusters of points in that data space, using its default parameters, and displays them colour-coded in the right hand pane, in the projection of the data space that most separates them. Since CViz is designed for handling large amounts of data, it does not plot all the data points, but, rather, a square symbol to mark the centroid of each cluster, and a representative sample of points from the cluster, to indicate the dispersion about that centroid. By double clicking on one of the cluster names in the plot on the right we obtained the panel at the bottom of the figure, which describes the membership of the cluster in terms of how the mean value of each attribute differs between the cluster members and the dataset as a whole. As with the Weka clustering case, we see that CViz's clustering algorithm has basically divided the sample into slices by optical magnitude, due to the fact that the dispersion in the colours of the objects in the sample is lower than the dispersion in the overall scaling of their magnitude. So, once again, we should have applied some normalization to our data before running CViz's clustering algorithm to obtain meaningful results about possible different source populations. CViz appears not to offer much in the way of data filtering and manipulation methods, beyond the selection of which attributes to use, so we would have to have done this before loading the data into the software.

CViz does have some very nice features. It allows the user to merge the clusters that it has found automatically, in the case that s/he thinks they have been divided too far, and it can aid that process by marking the similarity between different clusters. What is particularly nice is its solution to the problem of how to present the use with multiple scatter plots, created from all the pairs of attributes in the dataset. It is interesting to compare how our four software packages do this. In VOPlot, the user would have to select manually the full set of pairs to plot and look at them one by one, while in Weka, the full set of plots is displayed, in condensed format, aiding the selection of the interesting ones. Mirage's solution is to display the set of plots one after the other, with a short pause between each, so that the user can stop the tour, if an interesting plot appears. This is very nice, but the jerky plotting procedure is a little hard on the eye, which is something that CViz handles much better. It also plots a tour through the set of scatter plots of pairs of attributes, but it does so with a smooth animation, so that the cloud of data points moves smoothly from one plot to the next. This is much easier to watch, and the movement of the data points in the position for the next plot is suggestive of whether that plot will be interesting, so it prompts the user to stop the tour and investigate an informative plot more closely.

5.5 Obtaining more information on X-ray detected EROs

As noted above, Figure 15 suggested a difference in the I-K colour distribution of EROs as a function of their X-ray hardness ratio, with the reddest EROs amongst the Chandra counterparts all being very soft X-ray sources. To investigate the properties of these sources in the high resolution ACS images we use the ACE web service to measure the sources with SExtractor, and determine whether they have a dominant optical nuclear component. This was done with the ACE configuration as shown in Figure 21.

Figure 21. The ACE configuration panel for SExtractor. Figure 22 shows a RGB image constructed from the ACS F850LP, F775W, and F435W bands, and overlaid with Chandra error ellipse, and the EIS position (again notice the offset). This object is clearly extended in the ACS image, and its SExtractor parameters (Low stellarity index) show there is no dominant nucleus.

Figure 22. RGB image of one of the most extreme EROs.

6. Discussion and Conclusions

This exercise was primarily intended to address the question "can real science be done with the first crop of prototype VO tools?", and our answer to that is a positive, if not completely definitive, "yes, just about". We believe that this exercise has reached the point of obtaining new science results using existing prototype VO tools, with our needing small workarounds in only one step where we had to use IDL to generate a VOTable which contained the combined X-ray and optical/NIR attributes of our cross-matched sources. This we only had to do because of an input formatting problem in VizieR which has subsequently been tracked down. As such, it is possible to follow this science problem through, from inception to generation of new results, using existing VO tools, and that is very encouraging.

The VO sceptic might next ask "but couldn't you have done this more easily using other, non-VO tools?", to which the honest answer is "no, probably not". It is true that the ERO selection and the generation of the various figures above plotting attributes against each other, etc, could have been readily produced in IDL, say, but we have used a lot of different data sets in this exercise, and an IDL programmer would have had to have figured out the data formats and structures of each before being able to load them: the level of interoperability between data sources present in this first generation of VO tools is already a boon to astronomical research.

One thing that is clear from this exercise is that there are a number of non-astronomical tools available which could prove very valuable for the exploration of the multi-dimensional datasets of attributes produced by cross-matching different astronomical catalogues. We barely scratched the surface of what can be done with general data mining packages, such as Weka, and these are likely to become important as the VO develops, and it is crucial that the VO infrastructure supports their use; for example, through the availability of the XSLT transformations needed to convert VOTable into their specific data formats, so that such tools can be readily use as part of a VO data analysis workflow. It was clear, however, even from our brief foray into their use, that such tools cannot be regarded as black boxes, to be used blindly on any astronomical dataset. We found that we did not obtain very enlightening results from running Weka and CViz simply because we had not thought properly about what data to give them, while, at a more general level, we would have to understand the myriad algorithms and options offered by such tools before we could start to use them effectively.

Our exercise did identify a number of gaps in the current prototype VO toolkit:


Appendix: TOPCAT a beta release table viewer, editor and plotter



Acknowledgement:
Bob Mann gratefully acknowledges the award of a Professeur invité position at the Université Louis Pasteur, Strasbourg during the period within which this work was undertaken.