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adapted for DataLink support
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added handling of Echelle Spectra
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@mmpcn
mmpcn committed Feb 27, 2014
1 parent c7e19fd commit 4f2b0ad
Showing 1 changed file with 117 additions and 5 deletions.
122 changes: 117 additions & 5 deletions splat/src/main/uk/ac/starlink/splat/data/SpecDataFactory.java
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Expand Up @@ -115,6 +115,10 @@ public class SpecDataFactory

/** VOTable SED source, XXX not yet a proper type */
public final static int SED = 8;

/** VOTable Datalink source */
public final static int DATALINK = 9;


/**
* Short descriptions of each type.
Expand Down Expand Up @@ -276,6 +280,7 @@ public SpecData get( String specspec, int type )
}
}
break;
case DATALINK:
case TABLE: {
impl = makeTableSpecDataImpl( specspec );

Expand Down Expand Up @@ -1203,7 +1208,11 @@ public SpecData[] reprocessTo1D( SpecData specData, int method,
results = collapseSpecData( specData, specDims );
}
else if ( method == EXTRACT ) {
results = extractSpecData( specData, specDims );
String testEchelle = specData.getProperty("WAT0_001");
if (! testEchelle.isEmpty() && testEchelle.contains("system=multispec")) {
results = extractEchelleSpecData( specData, specDims );
} else
results = extractSpecData( specData, specDims );
}

// Purge any spectra with BAD limits.
Expand Down Expand Up @@ -1330,6 +1339,101 @@ private SpecData[] extractSpecData( SpecData specData, SpecDims specDims )
}
return results;
}

/**
* Create a set of new 1D SpecData instances from IRAF Echelle FITS format by extracting each line of a
* 2D or 3D implementation along the dispersion axis and applying the defined parameters.
*/
private SpecData[] extractEchelleSpecData( SpecData specData, SpecDims specDims )
throws SplatException
{
SpecData[] results = null;
int dispax = specDims.getDispAxis( true );
int[] dims = specDims.getSigDims();

if ( dims.length == 2 ) {
// Simple 2D data.
if ( dispax == 1 ) {
results = new SpecData[dims[0]];
}
else {
results = new SpecData[dims[1]];
}

boolean moreinfo=true;

ArrayList<String> specline = new ArrayList<String>();
String specParams = "";
int specindex=1;
for (int i=1; moreinfo ;i++) {
String property= "WAT2_"+ String.format("%03d", i); // think of a better algorithm!!!
String propline = specData.getProperty(property); // Problem: getProperty always removes tailing empty spaces

logger.info("propline1 "+propline+"<\n");
if (! propline.isEmpty()) {
propline=specParams.concat(propline);
logger.info("propline2 "+propline+"<\n");
int specstart = propline.indexOf(" spec"+specindex);
if (specstart != -1) {
if (i > 1 ) { // do not do this at the first line
specParams = propline.substring(0, specstart -1);
specline.add(specParams);
}
specParams = propline.substring(specstart +1);
specindex++;
} else {
specParams = propline;
}

} else {
moreinfo = false;
if (specParams != null)
specline.add(specParams);
}
}

logger.info("results "+results+ "count "+specline.size()+"\n");
for ( int i = 0; i < results.length; i++ ) {

logger.info(specline.get(i)+"\n");
int ind1 = specline.get(i).indexOf('"');
if (ind1 < specline.get(i).length()-1)
ind1+=1;
// int ind2 = specline.get(i).indexOf('"', ind1)-1;
String sparamstr = specline.get(i).substring(ind1 );
String [] sparams = sparamstr.split(" ");
SpecDataImpl newImpl = null;
try {
newImpl = new ExtractedSpecDataImpl( specData, specDims, i , Integer.parseInt(sparams[2]),
Double.parseDouble(sparams[3]), Double.parseDouble(sparams[4]), Double.parseDouble(sparams[6]));
results[i] = new SpecData( newImpl );
}
catch (Exception e) {
logger.info(i+ "- " + e.getMessage());
results[i]=null;
e.printStackTrace();
}

}
}
else {
int stepaxis = specDims.getSelectAxis( true );
int otheraxis = specDims.getFreeAxis( true );
int steplength = dims[stepaxis];
int otherlength = dims[otheraxis];

results = new SpecData[steplength*otherlength];
int count = 0;
for ( int j = 0; j < otherlength; j++ ) {
for ( int i = 0; i < steplength; i++ ) {
SpecDataImpl newImpl =
new ExtractedSpecDataImpl( specData, specDims, i, j );
results[count++] = new SpecData( newImpl );
}
}
}
return results;
}

/**
* Process a SED (IVOA spectral data model) XML file and extract all the
Expand Down Expand Up @@ -1370,16 +1474,18 @@ public SpecData[] expandXMLSED( String specspec )
tagName = child[j].getTagName();
if ( "TABLE".equals( tagName ) ) {
utype = child[j].getAttribute( "utype" );
if ( "sed:Segment".equals( utype ) ) {
String sname = child[j].getAttribute("name");
// if ( "sed:Segment".equals( utype ) ) { // we try this also for multiple spectra in a VOTable which do not have this utype (i.E. echelle spectra)
try {
table = new VOStarTable( (TableElement) child[j] );
specData = new SpecData( new TableSpecDataImpl(table) );
specData.setShortName(specData.getShortName() + " " + child[j].getAttribute("name"));
specList.add( specData );
}
catch (Exception e) {
throw new SplatException( e );
}
}
// }
}
}
}
Expand Down Expand Up @@ -1417,7 +1523,7 @@ public SpecData[] expandFITSSED( String specspec, int nspec )
* int constants defined in SpecDataFactory). Note we use the full MIME
* types and the SSAP shorthand versions (fits, votable, xml).
*/
public int mimeToSPLATType( String type )
public static int mimeToSPLATType( String type )
{
int stype = SpecDataFactory.DEFAULT;
String simpleType = type.toLowerCase();
Expand Down Expand Up @@ -1446,10 +1552,16 @@ else if ( simpleType.startsWith( "application/x-votable+xml" ) ||
simpleType.equals( "text/xml;x-votable" ) ||
simpleType.startsWith( "text/x-votable+xml" ) ||
simpleType.equals( "xml" ) ) {

// VOTABLE containing DataLink information
if (simpleType.contains("content=datalink"))
stype = SpecDataFactory.DATALINK;
else
// VOTable spectrum, open as a table. Is really the SSAP native
// XML representation so could an SED? In which case this might be
// better as SpecDataFactory.SED, we'll see.
stype = SpecDataFactory.TABLE;
// stype = SpecDataFactory.TABLE;
stype = SpecDataFactory.SED;
}
else if ( simpleType.startsWith( "spectrum/votable" ) ||
simpleType.equals( "votable" ) ) {
Expand Down

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