/** * Constructor. * * @param inTable saved table as read */ public CodecTable(StarTable inTable) { /* Sort out table parameters. */ codecParamMap_ = new HashMap<String, DescribedValue>(); List<DescribedValue> dataParamList = new ArrayList<DescribedValue>(); for (Iterator it = inTable.getParameters().iterator(); it.hasNext(); ) { DescribedValue param = (DescribedValue) it.next(); String utype = param.getInfo().getUtype(); if (isCodecUtype(utype)) { codecParamMap_.put(utype, param); } else { dataParamList.add(param); } } /* Sort out table columns. */ codecIcolMap_ = new HashMap<String, Integer>(); IntList dataIcolList = new IntList(); for (int icol = 0; icol < inTable.getColumnCount(); icol++) { ColumnInfo info = inTable.getColumnInfo(icol); String utype = info.getUtype(); if (isCodecUtype(utype)) { codecIcolMap_.put(utype, icol); } else { dataIcolList.add(icol); } } int[] dataColMap = dataIcolList.toIntArray(); /* Construct a table containing only the data items. */ dataTable_ = new MetaCopyStarTable(new ColumnPermutedStarTable(inTable, dataColMap, true)); dataTable_.getParameters().clear(); dataTable_.getParameters().addAll(dataParamList); }
/** * Constructs the DataLink Parameters from an URL string containing a VOTable with DataLink * information The VOTABLE must contain only Datalink info! ????? or? * * @throws IOException */ public DataLinkParams(String dataLinksrc) throws IOException { id_source = null; request = null; accessURL = null; contentType = null; service = new ArrayList<DataLinkService>(); DataLinkService thisService = new DataLinkService(); URL dataLinkURL = new URL(dataLinksrc); DataSource datsrc = new URLDataSource(dataLinkURL); StarTable starTable = new VOTableBuilder().makeStarTable(datsrc, true, StoragePolicy.getDefaultPolicy()); int ncol = starTable.getColumnCount(); for (int k = 0; k < ncol; k++) { ColumnInfo colInfo = starTable.getColumnInfo(k); // String utype = colInfo.getUtype(); String name = colInfo.getName(); if (name != null) thisService.addParam(name, (String) starTable.getCell(0, k)); // if ( utype != null ) { // utype = utype.toLowerCase(); // if ( utype.endsWith( "datalink.accessurl" ) ) { // thisService.addParam("accessURL", (String) starTable.getCell(0, k)); // } // if ( utype.endsWith( "datalink.contenttype" ) ) { // thisService.addParam("contentType", (String) starTable.getCell(0, k)); // } } service.add(thisService); }
public void writeData(DataOutput strm) throws IOException { /* Work out the length of each row in bytes. */ int rowBytes = 0; int ncol = table.getColumnCount(); for (int icol = 0; icol < ncol; icol++) { ColumnWriter writer = colWriters[icol]; if (writer != null) { rowBytes += writer.getLength(); } } /* Write the data cells, delegating the item in each column to * the writer that knows how to handle it. */ long nWritten = 0L; RowSequence rseq = table.getRowSequence(); try { while (rseq.next()) { Object[] row = rseq.getRow(); for (int icol = 0; icol < ncol; icol++) { ColumnWriter writer = colWriters[icol]; if (writer != null) { writer.writeValue(strm, row[icol]); } } nWritten += rowBytes; } } finally { rseq.close(); } /* Write padding. */ int extra = (int) (nWritten % (long) 2880); if (extra > 0) { strm.write(new byte[2880 - extra]); } }
/** * @param ra - in degrees * @param dec - in degrees * @param angularWidthAlongRAAxis - width along RA axis * @param angularWidthAlongDecAxis - width along DEC axis * @param otherConstraints - map of UCDKey -> Value. Only images whose column UCDs match the * values are selected * @return array of fits image urls * @throws Exception - */ public String[] fetchFitsImages( double ra, double dec, double angularWidthAlongRAAxis, double angularWidthAlongDecAxis, Map<String, Object> otherConstraints) throws MalformedURLException, SAXException, IOException, NoValidResultsResourceFoundException, SiaQueryFailedException { // TODO: Need to take a call on the otherConstraints argument String modurl = url + "&FORMAT=image/fits"; modurl += "&POS=" + ra + "," + dec; modurl += "&SIZE=" + angularWidthAlongRAAxis + "," + angularWidthAlongDecAxis; URL siaUrl = new URL(modurl); logger.info("Connecting to SIA URL: " + siaUrl); String interestedImageFormat = "image/fits"; ArrayList<String> imageUrls = new ArrayList<String>(); VOElement votable = new VOElementFactory().makeVOElement(siaUrl); NodeList resources = votable.getElementsByTagName("RESOURCE"); // check for a "results" resource with of sia votable resu int resInd = 0; for (; resInd < resources.getLength(); resInd++) { VOElement resource = (VOElement) resources.item(resInd); if (SIAP_RESOURCE_TYPE_VALUE_RESULTS.equals(resource.getAttribute("type"))) { break; } } if (resInd == resources.getLength()) { throw new NoValidResultsResourceFoundException(); } else { String queryStatus = null; String queryStatusDescription = null; // check query status VOElement resource = (VOElement) resources.item(resInd); NodeList infos = resource.getElementsByTagName("INFO"); for (int infoInd = 0; infoInd < infos.getLength(); infoInd++) { VOElement info = (VOElement) infos.item(infoInd); String name = info.getAttribute("name"); if (name.equals(QUERY_STATUS)) { queryStatus = info.getAttribute("value"); queryStatusDescription = info.getNodeValue(); } } // if query successful.equalsIgnoreCase() if (!queryStatus.equals(QUERY_STATUS_VALUE_OK)) { throw new SiaQueryFailedException(queryStatusDescription); } // handle the table VOElement[] tables = resource.getChildrenByName("TABLE"); if (tables.length > 0) { // take the first table and look for URLs in it. TableElement tableElement = (TableElement) tables[0]; // create star-table StarTable table = new VOStarTable(tableElement); // ideally its mandatory to have RA_UCD, DEC_UCD, NAXES_UCD, // NAXIS_UCD, FORMAT_UCD, SCALE_UCD in each row but we will not // check for those as of now. int formatColIndex = -1; int urlColIndex = -1; int otherConstraintsSize = (otherConstraints != null) ? otherConstraints.size() : 0; HashMap<String, Integer> otherConstraintsIndices = new HashMap<String, Integer>(); for (int colInd = 0; colInd < table.getColumnCount(); colInd++) { ColumnInfo colInfo = table.getColumnInfo(colInd); if (colInfo.getUCD().equalsIgnoreCase(FORMAT_UCD)) { formatColIndex = colInd; } else if (colInfo.getUCD().equalsIgnoreCase(ACCESS_REF_UCD)) { urlColIndex = colInd; } if (otherConstraintsSize > 0) { Iterator<String> keyIte = otherConstraints.keySet().iterator(); while (keyIte.hasNext()) { String key = keyIte.next(); if (key.equalsIgnoreCase(colInfo.getUCD())) { otherConstraintsIndices.put(key, colInd); } } } } for (int rowInd = 0; rowInd < table.getRowCount(); rowInd++) { Object[] cells = table.getRow(rowInd); // looking for only FITS images or JPG images .. .. if (interestedImageFormat.equalsIgnoreCase((String) cells[formatColIndex])) { Iterator<String> keyIte = otherConstraintsIndices.keySet().iterator(); boolean allConstraintsPassed = true; while (keyIte.hasNext()) { String key = keyIte.next(); int keyInd = otherConstraintsIndices.get(key); if (!cells[keyInd].equals(otherConstraints.get(key))) { allConstraintsPassed = false; break; } } if (allConstraintsPassed) { imageUrls.add((String) cells[urlColIndex]); } } } } return imageUrls.toArray(new String[] {}); } }
/** * Configures this serializer for use with a given table and column writer factory. Should be * called before this object is ready for use; in a constructor would be a good place. Calls * {@link #createColumnWriter}. * * @param table table to be written */ final void init(StarTable table) throws IOException { if (this.table != null) { throw new IllegalStateException("Table already initialised"); } this.table = table; /* Get table dimensions (though we may need to calculate the row * count directly later. */ int ncol = table.getColumnCount(); long nrow = table.getRowCount(); /* Store column infos. */ colInfos = Tables.getColumnInfos(table); /* Work out column shapes, and check if any are unknown (variable * last dimension). */ boolean hasVarShapes = false; boolean checkForNullableInts = false; int[][] shapes = new int[ncol][]; int[] maxChars = new int[ncol]; int[] maxElements = new int[ncol]; long[] totalElements = new long[ncol]; boolean[] useCols = new boolean[ncol]; boolean[] varShapes = new boolean[ncol]; boolean[] varChars = new boolean[ncol]; boolean[] varElementChars = new boolean[ncol]; boolean[] mayHaveNullableInts = new boolean[ncol]; Arrays.fill(useCols, true); boolean[] hasNulls = new boolean[ncol]; for (int icol = 0; icol < ncol; icol++) { ColumnInfo colinfo = colInfos[icol]; Class clazz = colinfo.getContentClass(); if (clazz.isArray()) { shapes[icol] = (int[]) colinfo.getShape().clone(); int[] shape = shapes[icol]; if (shape[shape.length - 1] < 0) { varShapes[icol] = true; hasVarShapes = true; } else { int nel = shape.length > 0 ? 1 : 0; for (int id = 0; id < shape.length; id++) { nel *= shape[id]; } assert nel >= 0; maxElements[icol] = nel; } if (clazz.getComponentType().equals(String.class)) { maxChars[icol] = colinfo.getElementSize(); if (maxChars[icol] <= 0) { varElementChars[icol] = true; hasVarShapes = true; } } } else if (clazz.equals(String.class)) { maxChars[icol] = colinfo.getElementSize(); if (maxChars[icol] <= 0) { varChars[icol] = true; hasVarShapes = true; } } else if (colinfo.isNullable() && (clazz == Byte.class || clazz == Short.class || clazz == Integer.class || clazz == Long.class)) { mayHaveNullableInts[icol] = true; /* Only set the flag which forces a first pass if we need * to work out whether nulls actually exist. If the * aux datum giving a null value exists we will use it in * any case, so finding out whether there are in fact null * values by scanning the data is not necessary. */ if (colinfo.getAuxDatumValue(Tables.NULL_VALUE_INFO, Number.class) != null) { hasNulls[icol] = true; } else { checkForNullableInts = true; } } } /* If necessary, make a first pass through the table data to * find out the maximum size of variable length fields and the length * of the table. */ if (hasVarShapes || checkForNullableInts || nrow < 0) { StringBuffer sbuf = new StringBuffer("First pass needed: "); if (hasVarShapes) { sbuf.append("(variable array shapes) "); } if (checkForNullableInts) { sbuf.append("(nullable ints) "); } if (nrow < 0) { sbuf.append("(unknown row count) "); } logger.config(sbuf.toString()); nrow = 0L; /* Get the maximum dimensions. */ RowSequence rseq = table.getRowSequence(); try { while (rseq.next()) { nrow++; for (int icol = 0; icol < ncol; icol++) { if (useCols[icol] && (varShapes[icol] || varChars[icol] || varElementChars[icol] || (mayHaveNullableInts[icol] && !hasNulls[icol]))) { Object cell = rseq.getCell(icol); if (cell == null) { if (mayHaveNullableInts[icol]) { hasNulls[icol] = true; } } else { if (varChars[icol]) { int leng = ((String) cell).length(); maxChars[icol] = Math.max(maxChars[icol], leng); } else if (varElementChars[icol]) { String[] svals = (String[]) cell; for (int i = 0; i < svals.length; i++) { maxChars[icol] = Math.max(maxChars[icol], svals[i].length()); } } if (varShapes[icol]) { int nel = Array.getLength(cell); maxElements[icol] = Math.max(maxElements[icol], nel); totalElements[icol] += nel; } } } } } } finally { rseq.close(); } /* In the case of variable string lengths and no non-null data * in any of the cells, maxChars could still be set negative. * Fix that here. */ for (int icol = 0; icol < ncol; icol++) { if (maxChars[icol] < 0) { maxChars[icol] = 0; } } /* Furthermore, zero length strings are probably a bad idea * for FITS output. Make sure that all output strings have * a length of at least 1. */ for (int icol = 0; icol < ncol; icol++) { if (maxChars[icol] == 0) { maxChars[icol] = 1; } } /* Work out the actual shapes for columns which have variable ones, * based on the shapes that we encountered in the rows. */ if (hasVarShapes) { for (int icol = 0; icol < ncol; icol++) { if (useCols[icol]) { if (varShapes[icol]) { int[] shape = shapes[icol]; int ndim = shape.length; assert shape[ndim - 1] <= 0; int nel = 1; for (int i = 0; i < ndim - 1; i++) { nel *= shape[i]; } shape[ndim - 1] = Math.max(1, (maxElements[icol] + nel - 1) / nel); } } } } } /* Store the row count, which we must have got by now. */ assert nrow >= 0; rowCount = nrow; /* We now have all the information we need about the table. * Construct and store a custom writer for each column which * knows about the characteristics of the column and how to * write values to the stream. For columns which can't be * written in FITS format store a null in the writers array * and log a message. */ colWriters = new ColumnWriter[ncol]; int rbytes = 0; for (int icol = 0; icol < ncol; icol++) { if (useCols[icol]) { ColumnInfo cinfo = colInfos[icol]; ColumnWriter writer = createColumnWriter( cinfo, shapes[icol], varShapes[icol], maxChars[icol], maxElements[icol], totalElements[icol], mayHaveNullableInts[icol] && hasNulls[icol]); if (writer == null) { logger.warning( "Ignoring column " + cinfo.getName() + " - don't know how to write to FITS"); } colWriters[icol] = writer; } } }
public Header getHeader() throws HeaderCardException { /* Work out the dimensions in columns and bytes of the table. */ int rowLength = 0; int nUseCol = 0; int ncol = table.getColumnCount(); for (int icol = 0; icol < ncol; icol++) { ColumnWriter writer = colWriters[icol]; if (writer != null) { nUseCol++; rowLength += writer.getLength(); } } /* Prepare a FITS header block. */ Header hdr = new Header(); /* Add HDU layout metadata. */ hdr.addValue("XTENSION", "BINTABLE", "binary table extension"); hdr.addValue("BITPIX", 8, "8-bit bytes"); hdr.addValue("NAXIS", 2, "2-dimensional table"); hdr.addValue("NAXIS1", rowLength, "width of table in bytes"); hdr.addValue("NAXIS2", rowCount, "number of rows in table"); hdr.addValue("PCOUNT", 0, "size of special data area"); hdr.addValue("GCOUNT", 1, "one data group"); hdr.addValue("TFIELDS", nUseCol, "number of columns"); /* Add EXTNAME record containing table name. */ String tname = table.getName(); if (tname != null && tname.trim().length() > 0) { FitsConstants.addTrimmedValue(hdr, "EXTNAME", tname, "table name"); } /* Add HDU metadata describing columns. */ int jcol = 0; for (int icol = 0; icol < ncol; icol++) { ColumnWriter colwriter = colWriters[icol]; if (colwriter != null) { jcol++; String forcol = " for column " + jcol; ColumnInfo colinfo = colInfos[icol]; /* Name. */ String name = colinfo.getName(); if (name != null && name.trim().length() > 0) { FitsConstants.addTrimmedValue(hdr, "TTYPE" + jcol, name, "label" + forcol); } /* Format. */ String form = colwriter.getFormat(); hdr.addValue("TFORM" + jcol, form, "format" + forcol); /* Units. */ String unit = colinfo.getUnitString(); if (unit != null && unit.trim().length() > 0) { FitsConstants.addTrimmedValue(hdr, "TUNIT" + jcol, unit, "units" + forcol); } /* Blank. */ Number bad = colwriter.getBadNumber(); if (bad != null) { hdr.addValue("TNULL" + jcol, bad.longValue(), "blank value" + forcol); } /* Shape. */ int[] dims = colwriter.getDims(); if (dims != null && dims.length > 1) { StringBuffer sbuf = new StringBuffer(); for (int i = 0; i < dims.length; i++) { sbuf.append(i == 0 ? '(' : ','); sbuf.append(dims[i]); } sbuf.append(')'); hdr.addValue("TDIM" + jcol, sbuf.toString(), "dimensions" + forcol); } /* Scaling. */ double zero = colwriter.getZero(); double scale = colwriter.getScale(); if (zero != 0.0) { hdr.addValue("TZERO" + jcol, zero, "base" + forcol); } if (scale != 1.0) { hdr.addValue("TSCALE" + jcol, scale, "factor" + forcol); } /* Comment (non-standard). */ String comm = colinfo.getDescription(); if (comm != null && comm.trim().length() > 0) { try { hdr.addValue("TCOMM" + jcol, comm, null); } catch (HeaderCardException e) { // never mind. } } /* UCD (non-standard). */ String ucd = colinfo.getUCD(); if (ucd != null && ucd.trim().length() > 0 && ucd.length() < 68) { try { hdr.addValue("TUCD" + jcol, ucd, null); } catch (HeaderCardException e) { // never mind. } } /* Utype (non-standard). */ String utype = colinfo.getUtype(); if (utype != null && utype.trim().length() > 0 && utype.trim().length() < 68) { try { hdr.addValue("TUTYP" + jcol, utype, null); } catch (HeaderCardException e) { // never mind. } } } } return hdr; }