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779bac69
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Marc NICOLAS
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package fr.ias.sitools.resources.spectrofits;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import org.restlet.data.MediaType;
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import org.restlet.ext.json.JsonRepresentation;
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import org.restlet.ext.wadl.MethodInfo;
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import org.restlet.representation.Representation;
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import org.restlet.representation.Variant;
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import org.restlet.resource.Get;
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import fr.cnes.sitools.common.exception.SitoolsException;
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import fr.cnes.sitools.common.resource.SitoolsParameterizedResource;
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import fr.cnes.sitools.dataset.DataSetApplication;
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import fr.cnes.sitools.dataset.database.DatabaseRequestFactory;
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import fr.cnes.sitools.dataset.database.DatabaseRequestParameters;
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import fr.cnes.sitools.dataset.database.common.DataSetExplorerUtil;
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import fr.cnes.sitools.plugins.resources.model.ResourceParameter;
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import fr.cnes.sitools.resources.order.utils.OrderResourceUtils;
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import fr.cnes.sitools.dataset.database.DatabaseRequest;
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import fr.cnes.sitools.datasource.jdbc.model.AttributeValue;
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import fr.cnes.sitools.datasource.jdbc.model.Record;
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import nom.tam.fits.*;
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import org.json.JSONArray;
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import org.json.JSONException;
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import org.json.JSONObject;
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public class GetFitsDataSpectro extends SitoolsParameterizedResource {
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@Override
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public void sitoolsDescribe() {
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setName("GetFitsDataSpectro");
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setDescription("Get cube fits file data");
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}
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@Override
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public void doInit() {
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super.doInit();
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}
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@Get
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public Representation getCsv() {
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return execute();
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}
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@Override
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protected void describeGet(MethodInfo info) {
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this.addInfo(info);
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info.setIdentifier("retrieve records and extract data and metadata from fits file");
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info.setDocumentation("Method to get the data and metadata from a fits file");
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addStandardGetRequestInfo(info);
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DataSetExplorerUtil.addDatasetExplorerGetRequestInfo(info);
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DataSetApplication application = (DataSetApplication) getApplication();
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DataSetExplorerUtil.addDatasetExplorerGetFilterInfo(info, application.getFilterChained());
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addStandardResponseInfo(info);
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addStandardInternalServerErrorInfo(info);
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}
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@Override
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protected Representation head(Variant variant) {
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Representation repr = super.head();
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repr.setMediaType(MediaType.APPLICATION_JSON);
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return repr;
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}
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private Representation execute() {
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Representation repr = null;
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DataSetApplication datasetApp = (DataSetApplication) getApplication();
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DataSetExplorerUtil dsExplorerUtil = new DataSetExplorerUtil(datasetApp, getRequest(), getContext());
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if (datasetApp.getConverterChained() != null) {
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datasetApp.getConverterChained().getContext().getAttributes().put("REQUEST", getRequest());
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}
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DatabaseRequestParameters params = dsExplorerUtil.getDatabaseParams();
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DatabaseRequest databaseRequest = DatabaseRequestFactory.getDatabaseRequest(params);
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if (params.getDistinct()) {
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try {
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databaseRequest.createDistinctRequest();
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}
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catch (SitoolsException e) {
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e.printStackTrace();
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}
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} else {
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try {
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databaseRequest.createRequest();
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}
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catch (SitoolsException e) {
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e.printStackTrace();
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}
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}
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ResourceParameter urlName = this.getModel().getParameterByName("colUrl");
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int hdu = Integer.parseInt(this.getModel().getParameterByName("hduCube").getValue());
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String waveLocation = this.getModel().getParameterByName("wave").getValue();
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if (databaseRequest != null) {
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try {
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databaseRequest.nextResult();
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Record rec = databaseRequest.getRecord();
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AttributeValue attributeValueURL = OrderResourceUtils.getInParam(urlName, rec);
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if (attributeValueURL.getValue() != null){
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String filePath = (String) attributeValueURL.getValue();
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try {
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Fits fits = new Fits(filePath);
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FitsFactory.setUseHierarch(true);
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Header.setLongStringsEnabled(true);
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JSONObject jSON = new JSONObject();
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int waveHDU = -1;
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int nberHDUs = fits.size();
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System.out.println("Number of HDUs: "+nberHDUs);
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jSON.put("HDUs", nberHDUs);
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System.out.println("Getting Headers...");
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List<String> headers = new ArrayList<String>(nberHDUs);
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List<List<List<String>>> headersList = new ArrayList<List<List<String>>>(nberHDUs);
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for (int i=0;i<nberHDUs;i++){
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Header header = fits.getHDU(i).getHeader();
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int nbreCards = header.getNumberOfCards();
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String headerStr = "";
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HashMap<String,String> mapHierarch = new HashMap<String,String>();
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for (int j=0; j<nbreCards; j++){
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String cardStr = header.getCard(j);
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if (cardStr.matches("HIERARCH\\s.*\\s(META.*)\\s*=\\s*(.*)")) {
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Pattern p = Pattern.compile("HIERARCH\\s.*\\s(META.*)\\s*=\\s*(.*)");
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Matcher m = p.matcher(cardStr);
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if (m.find()) {
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mapHierarch.put(m.group(1), m.group(2));
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}
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}
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headerStr = headerStr+cardStr+"<br>";
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}
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List<List<String>> cardList = new ArrayList<List<String>>(nbreCards);
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for (int j=0; j<nbreCards; j++){
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List<String> keyValueComment = new ArrayList<String>(nbreCards);
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HeaderCard card = header.findCard(header.getKey(j));
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if ( card!=null ) {
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if (mapHierarch.containsKey(card.getKey())) {
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keyValueComment.add( "HIERARCH "+mapHierarch.get(card.getKey()) );
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}
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else {
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keyValueComment.add(card.getKey());
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}
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keyValueComment.add(card.getValue());
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if ( card.getKey().contains("EXTNAME") && card.getValue().contains("ImageIndex") ) {
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System.out.println("ImageIndex in HDU "+i);
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waveHDU=i;
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}
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String commentCard = card.getComment();
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if (commentCard!=null) {
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if (commentCard.contains("&")) {
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commentCard = commentCard.substring(0, commentCard.length()-1);
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int jTmp = j;
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while(header.getCard(jTmp+1).startsWith("COMMENT")){
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String commentCardNext = header.getCard(jTmp+1);
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if (commentCardNext.contains("&")) { commentCardNext = commentCardNext.substring(0, commentCardNext.length()-1); }
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commentCard += commentCardNext.split("COMMENT ")[1];
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jTmp++;
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}
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keyValueComment.add(commentCard);
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}
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else { keyValueComment.add(commentCard); }
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} else {keyValueComment.add("");}
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cardList.add(keyValueComment);
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}
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}
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headersList.add(cardList);
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headers.add(headerStr);
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}
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jSON.put("HEADERSGRID", headersList);
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System.out.println("Headers - Done !");
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System.out.println("Getting Wave...");
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int hhdduu = -1;
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for (int i=0;i<nberHDUs;i++){
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Header header = fits.getHDU(i).getHeader();
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String a = header.findKey("CDELT3");
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if(a != null){
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System.out.println("CDELT3 find in "+i);
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hhdduu = i;
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}else{
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System.out.println("CDELT3 not found in "+i);
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}
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}
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if(hhdduu != -1){
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System.out.println("... from WCS");
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double naxis3 = fits.getHDU(hdu).getHeader().getDoubleValue("NAXIS3");
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double crval3 = fits.getHDU(hdu).getHeader().getDoubleValue("CRVAL3");
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double cdelt3 = fits.getHDU(hdu).getHeader().getDoubleValue("CDELT3");
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System.out.println(naxis3+" "+crval3+" "+cdelt3);
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float[] wave = new float[(int)naxis3];
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for (int i = 0 ; i < wave.length; i++) { wave[i] = (float) (crval3 + i * cdelt3); }
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jSON.put("WAVE", wave);
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}else {
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System.out.println("not from WCS");
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if (waveHDU!=-1) {
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System.out.println("No wave data in the cube WCS - Using wave array from ImageIndex HDU table");
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TableHDU cols = (TableHDU) fits.getHDU(waveHDU);
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double[] waveD = (double[]) cols.getColumn(0);
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float[] wave = new float[waveD.length];
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for (int i = 0 ; i < waveD.length; i++) { wave[i] = (float) waveD[i]; }
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jSON.put("WAVE", wave);
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} else {
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System.out.println("No wave data in the cube WCS - Using wave array from specific HDU table - "+waveLocation);
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if (waveLocation.matches("(\\d+)-(\\d+)")){
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int waveTable = Integer.parseInt(waveLocation.split("-")[0]);
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int waveColumn = Integer.parseInt(waveLocation.split("-")[1]);
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TableHDU cols = (TableHDU) fits.getHDU(waveTable);
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double[] waveD = (double[]) cols.getColumn(waveColumn);
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float[] wave = new float[waveD.length];
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for (int i = 0 ; i < waveD.length; i++) { wave[i] = (float) waveD[i]; }
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jSON.put("WAVE", wave);
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} else {
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System.out.println("No wave data in "+waveLocation);
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}
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}
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}
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System.out.println(" Wave - Done !");
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System.out.println("Getting Cube Data...");
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for (int m=1; m<=2; m++) {
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jSON.put("NAXIS"+m, fits.getHDU(hdu).getHeader().getDoubleValue("NAXIS"+m));
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jSON.put("CRPIX"+m, fits.getHDU(hdu).getHeader().getDoubleValue("CRPIX"+m));
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jSON.put("CRVAL"+m, fits.getHDU(hdu).getHeader().getDoubleValue("CRVAL"+m));
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jSON.put("CDELT"+m, fits.getHDU(hdu).getHeader().getDoubleValue("CDELT"+m));
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jSON.put("CTYPE"+m, fits.getHDU(hdu).getHeader().getStringValue("CTYPE"+m));
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}
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jSON.put("NAXIS3", fits.getHDU(hdu).getHeader().getDoubleValue("NAXIS3"));
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jSON.put("INFO_QTTY", fits.getHDU(hdu).getHeader().getStringValue("INFO____") );
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jSON.put("UNIT_QTTY", fits.getHDU(hdu).getHeader().getStringValue("QTTY____") );
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jSON.put("INFO_WAVE", fits.getHDU(hdu).getHeader().getStringValue("CTYPE3") );
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jSON.put("UNIT_WAVE", fits.getHDU(hdu).getHeader().getStringValue("CUNIT3") );
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double[][][] cubeFits = ((double[][][]) fits.getHDU(hdu).getData().getData());
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int naxis1 = cubeFits[0][0].length;
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int naxis2 = cubeFits[0].length;
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int naxis3 = cubeFits.length;
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List<List<List<Float>>> cube3DL = new ArrayList<List<List<Float>>>(naxis1);
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for (int x=0;x<naxis1;x++){
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List<List<Float>> list2 = new ArrayList<List<Float>>(naxis2);
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for (int y=0;y<naxis2;y++){
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List<Float> list3 = new ArrayList<Float>(naxis3);
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for (int z=0;z<naxis3;z++){
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if (cubeFits[z][y][x] != Double.NaN ) { list3.add( (float) cubeFits[z][y][x] ); }
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else { list3.add(null); }
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}
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list2.add(list3);
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}
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cube3DL.add(list2);
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}
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|
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JSONArray cubeJL= new JSONArray(cube3DL.toString());
|
370 |
|
|
jSON.put("SPECTRUM", cubeJL);
|
371 |
|
|
|
372 |
|
|
System.out.println(" Cube - Done !");
|
373 |
|
|
|
374 |
|
|
repr = new JsonRepresentation(jSON);
|
375 |
|
|
|
376 |
|
|
|
377 |
|
|
}
|
378 |
|
|
catch (FitsException e) {
|
379 |
|
|
|
380 |
|
|
e.printStackTrace();
|
381 |
|
|
}
|
382 |
|
|
catch (IOException e) {
|
383 |
|
|
|
384 |
|
|
e.printStackTrace();
|
385 |
|
|
}
|
386 |
|
|
|
387 |
|
|
catch (JSONException e) {
|
388 |
|
|
|
389 |
|
|
e.printStackTrace();
|
390 |
|
|
}
|
391 |
|
|
|
392 |
|
|
}
|
393 |
|
|
databaseRequest.close();
|
394 |
|
|
|
395 |
|
|
}
|
396 |
|
|
catch (SitoolsException e) {
|
397 |
|
|
|
398 |
|
|
e.printStackTrace();
|
399 |
|
|
}
|
400 |
|
|
|
401 |
|
|
}
|
402 |
|
|
|
403 |
|
|
return repr;
|
404 |
|
|
|
405 |
|
|
}
|
406 |
|
|
|
407 |
|
|
} |