Example usage for org.apache.commons.lang ArrayUtils toPrimitive

List of usage examples for org.apache.commons.lang ArrayUtils toPrimitive

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Introduction

In this page you can find the example usage for org.apache.commons.lang ArrayUtils toPrimitive.

Prototype

public static boolean[] toPrimitive(Boolean[] array)

Source Link

Document

Converts an array of object Booleans to primitives.

Usage

From source file:org.apache.hadoop.mapred.NetCDFInputFormatPrunerByFileIndex.java

private NetCDFInfo getNetCDFInfo(Path file, FileSystem fs, JobConf job) {
    //traverse header and return chunk start and size arrays
    NetCDFInfo result = new NetCDFInfo();//library call

    NetcdfFile ncFile;//from w  ww. j  a  v  a2  s.c om
    Variable v;
    Variable time;
    Variable lat;
    Variable lon;
    ncFile = null;
    try {
        //if( file == null ){
        //System.out.println( "[SAMAN] NetCDFInputFormat.getNetCDFInfo  file is null" );
        //LOG.info( "[SAMAN] NetCDFInputFormat.getNetCDFInfo  file is null" );
        //}else{
        //System.out.println( "[SAMAN] NetCDFInputFormat.getNetCDFInfo file is " + file.toString() );
        //LOG.info( "[SAMAN] NetCDFInputFormat.getNetCDFInfo  file is null" );
        //}
        ncFile = NetcdfDataset.openFile(file.toString(), null);
        List<Variable> vs = ncFile.getVariables();
        for (int i = 0; i < vs.size(); i++) {
            System.out.println("[SAMAN][NetCDFInputFormatPrunerByFileIndex][getNetCDFInfo] variable is: "
                    + vs.get(i).getName());
        }

        v = ncFile.findVariable("rsut");
        time = ncFile.findVariable("time");
        lat = ncFile.findVariable("lat");
        lon = ncFile.findVariable("lon");

        //List<Variable> vs = ncFile.getVariables();
        //v = vs.get(vs.size()-1);

        //LOG.info("Variable is "+ v.getFullName());
        result.fileSize = ncFile.vfileSize;
        result.recStart = ncFile.vrecStart;
        Long[] metaArray = v.reallyReadMeta().toArray(new Long[(int) (ncFile.vnumRecs)]);
        result.chunkStarts = ArrayUtils.toPrimitive(metaArray);
        //result.chunkSizes = nc.chunkSizes;
        result.numRecs = ncFile.vnumRecs;
        result.recSize = ncFile.vrecSize;
        result.smallRecSize = ncFile.vsmallRecSize;
        result.timeLength = (int) (time.getSize());
        result.latLength = (int) (lat.getSize());
        result.lonLength = (int) (lon.getSize());
        //result.shape = v.shape;

    } catch (Exception e)

    {
        LOG.info("Bad... " + e);
        e.printStackTrace();
        e.printStackTrace(System.out);
        System.out.println("Bad... \n");
    }
    try {
        if (ncFile != null)
            ncFile.close();
    } catch (Exception e) {
        LOG.info("Bad2... " + e);
        System.out.println("Bad2... " + e);
    }

    return result;
}

From source file:org.apache.hadoop.mapred.NetCDFInputFormatPrunerByFileIndexMultiFileTwoDimensions.java

private NetCDFInfo getNetCDFInfo(Path file, FileSystem fs, JobConf job) {
    //traverse header and return chunk start and size arrays
    result = new NetCDFInfo();//library call

    NetcdfFile ncFile;/*from  w ww .  j  a  va 2 s  .co  m*/
    Variable v;
    Variable time;
    Variable lat;
    Variable lon;
    ncFile = null;
    try {
        //if( file == null ){
        //System.out.println( "[SAMAN] NetCDFInputFormat.getNetCDFInfo  file is null" );
        //LOG.info( "[SAMAN] NetCDFInputFormat.getNetCDFInfo  file is null" );
        //}else{
        //System.out.println( "[SAMAN] NetCDFInputFormat.getNetCDFInfo file is " + file.toString() );
        //LOG.info( "[SAMAN] NetCDFInputFormat.getNetCDFInfo  file is null" );
        //}
        ncFile = NetcdfDataset.openFile(file.toString(), null);

        v = ncFile.findVariable("rsut");
        time = ncFile.findVariable("time");
        lat = ncFile.findVariable("lat");
        lon = ncFile.findVariable("lon");

        //List<Variable> vs = ncFile.getVariables();
        //v = vs.get(vs.size()-1);

        //LOG.info("Variable is "+ v.getFullName());
        result.fileSize = ncFile.vfileSize;
        result.recStart = ncFile.vrecStart;
        Long[] metaArray = v.reallyReadMeta().toArray(new Long[(int) (ncFile.vnumRecs)]);
        result.chunkStarts = ArrayUtils.toPrimitive(metaArray);
        //result.chunkSizes = nc.chunkSizes;
        result.numRecs = ncFile.vnumRecs;
        result.recSize = ncFile.vrecSize;
        result.smallRecSize = ncFile.vsmallRecSize;
        result.timeLength = (int) (time.getSize());
        result.latLength = (int) (lat.getSize());
        result.lonLength = (int) (lon.getSize());
        //result.shape = v.shape;

    } catch (Exception e)

    {
        LOG.info("Bad... " + e);
        System.out.println("Bad... " + e);
    }
    try {
        if (ncFile != null)
            ncFile.close();
    } catch (Exception e) {
        LOG.info("Bad2... " + e);
        System.out.println("Bad2... " + e);
    }

    return result;
}

From source file:org.apache.solr.handler.AnalysisRequestHandlerTestBase.java

protected void assertToken(NamedList token, TokenInfo info) {
    assertEquals(info.getText(), token.get("text"));
    if (info.getRawText() != null) {
        assertEquals(info.getRawText(), token.get("raw_text"));
    }//from   w w w  .j a v  a 2 s  .  c o m
    assertEquals(info.getType(), token.get("type"));
    assertEquals(new Integer(info.getStart()), token.get("start"));
    assertEquals(new Integer(info.getEnd()), token.get("end"));
    assertEquals(new Integer(info.getPosition()), token.get("position"));
    assertArrayEquals(info.getPositionHistory(),
            ArrayUtils.toPrimitive((Integer[]) token.get("positionHistory")));
    if (info.isMatch()) {
        assertEquals(Boolean.TRUE, token.get("match"));
    }
    if (info.getPayload() != null) {
        assertEquals(info.getPayload(), token.get("payload"));
    }
}

From source file:org.apache.sysml.runtime.transform.BinAgent.java

public BinAgent(JSONObject parsedSpec, String[] colnames, int clen, boolean colsOnly)
        throws JSONException, IOException {
    super(null, clen);
    if (!parsedSpec.containsKey(TfUtils.TXMETHOD_BIN))
        return;/* w  w  w .ja va  2 s.  co m*/

    if (colsOnly) {
        List<Integer> collist = TfMetaUtils.parseBinningColIDs(parsedSpec, colnames);
        initColList(ArrayUtils.toPrimitive(collist.toArray(new Integer[0])));
    } else {
        JSONObject obj = (JSONObject) parsedSpec.get(TfUtils.TXMETHOD_BIN);
        JSONArray attrs = (JSONArray) obj.get(TfUtils.JSON_ATTRS);
        JSONArray nbins = (JSONArray) obj.get(TfUtils.JSON_NBINS);
        initColList(attrs);

        _numBins = new int[attrs.size()];
        for (int i = 0; i < _numBins.length; i++)
            _numBins[i] = UtilFunctions.toInt(nbins.get(i));

        // initialize internal transformation metadata
        _min = new double[_colList.length];
        Arrays.fill(_min, Double.MAX_VALUE);
        _max = new double[_colList.length];
        Arrays.fill(_max, -Double.MAX_VALUE);

        _binWidths = new double[_colList.length];
    }
}

From source file:org.apache.sysml.runtime.transform.decode.DecoderFactory.java

@SuppressWarnings("unchecked")
public static Decoder createDecoder(String spec, String[] colnames, ValueType[] schema, FrameBlock meta)
        throws DMLRuntimeException {
    Decoder decoder = null;/* w  w w  .j  ava  2 s .c  o  m*/

    try {
        //parse transform specification
        JSONObject jSpec = new JSONObject(spec);
        List<Decoder> ldecoders = new ArrayList<Decoder>();

        //create decoders 'recode', 'dummy' and 'pass-through'
        List<Integer> rcIDs = Arrays.asList(
                ArrayUtils.toObject(TfMetaUtils.parseJsonIDList(jSpec, colnames, TfUtils.TXMETHOD_RECODE)));
        List<Integer> dcIDs = Arrays.asList(
                ArrayUtils.toObject(TfMetaUtils.parseJsonIDList(jSpec, colnames, TfUtils.TXMETHOD_DUMMYCODE)));
        rcIDs = new ArrayList<Integer>(CollectionUtils.union(rcIDs, dcIDs));
        List<Integer> ptIDs = new ArrayList<Integer>(
                CollectionUtils.subtract(UtilFunctions.getSequenceList(1, meta.getNumColumns(), 1), rcIDs));

        //create default schema if unspecified (with double columns for pass-through)
        if (schema == null) {
            schema = UtilFunctions.nCopies(meta.getNumColumns(), ValueType.STRING);
            for (Integer col : ptIDs)
                schema[col - 1] = ValueType.DOUBLE;
        }

        if (!dcIDs.isEmpty()) {
            ldecoders.add(new DecoderDummycode(schema, ArrayUtils.toPrimitive(dcIDs.toArray(new Integer[0]))));
        }
        if (!rcIDs.isEmpty()) {
            ldecoders.add(new DecoderRecode(schema, !dcIDs.isEmpty(),
                    ArrayUtils.toPrimitive(rcIDs.toArray(new Integer[0]))));
        }
        if (!ptIDs.isEmpty()) {
            ldecoders.add(new DecoderPassThrough(schema, ArrayUtils.toPrimitive(ptIDs.toArray(new Integer[0])),
                    ArrayUtils.toPrimitive(dcIDs.toArray(new Integer[0]))));
        }

        //create composite decoder of all created decoders
        //and initialize with given meta data (recode, dummy, bin)
        decoder = new DecoderComposite(schema, ldecoders);
        if (meta != null)
            decoder.initMetaData(meta);
    } catch (Exception ex) {
        throw new DMLRuntimeException(ex);
    }

    return decoder;
}

From source file:org.apache.sysml.runtime.transform.encode.EncoderBin.java

public EncoderBin(JSONObject parsedSpec, String[] colnames, int clen, boolean colsOnly)
        throws JSONException, IOException {
    super(null, clen);
    if (!parsedSpec.containsKey(TfUtils.TXMETHOD_BIN))
        return;/*from   ww w.java2s .c  o m*/

    if (colsOnly) {
        List<Integer> collist = TfMetaUtils.parseBinningColIDs(parsedSpec, colnames);
        initColList(ArrayUtils.toPrimitive(collist.toArray(new Integer[0])));
    } else {
        JSONObject obj = (JSONObject) parsedSpec.get(TfUtils.TXMETHOD_BIN);
        JSONArray attrs = (JSONArray) obj.get(TfUtils.JSON_ATTRS);
        JSONArray nbins = (JSONArray) obj.get(TfUtils.JSON_NBINS);
        initColList(attrs);

        _numBins = new int[attrs.size()];
        for (int i = 0; i < _numBins.length; i++)
            _numBins[i] = UtilFunctions.toInt(nbins.get(i));

        // initialize internal transformation metadata
        _min = new double[_colList.length];
        Arrays.fill(_min, Double.POSITIVE_INFINITY);
        _max = new double[_colList.length];
        Arrays.fill(_max, Double.NEGATIVE_INFINITY);
    }
}

From source file:org.apache.sysml.runtime.transform.encode.EncoderFactory.java

@SuppressWarnings("unchecked")
public static Encoder createEncoder(String spec, String[] colnames, ValueType[] schema, FrameBlock meta)
        throws DMLRuntimeException {
    Encoder encoder = null;//from   ww w  .  j  av  a 2 s  .  c  o  m
    int clen = schema.length;

    try {
        //parse transform specification
        JSONObject jSpec = new JSONObject(spec);
        List<Encoder> lencoders = new ArrayList<Encoder>();

        //prepare basic id lists (recode, dummycode, pass-through)
        //note: any dummycode column requires recode as preparation
        List<Integer> rcIDs = Arrays.asList(
                ArrayUtils.toObject(TfMetaUtils.parseJsonIDList(jSpec, colnames, TfUtils.TXMETHOD_RECODE)));
        List<Integer> dcIDs = Arrays.asList(
                ArrayUtils.toObject(TfMetaUtils.parseJsonIDList(jSpec, colnames, TfUtils.TXMETHOD_DUMMYCODE)));
        rcIDs = new ArrayList<Integer>(CollectionUtils.union(rcIDs, dcIDs));
        List<Integer> binIDs = TfMetaUtils.parseBinningColIDs(jSpec, colnames);
        List<Integer> ptIDs = new ArrayList<Integer>(CollectionUtils
                .subtract(CollectionUtils.subtract(UtilFunctions.getSequenceList(1, clen, 1), rcIDs), binIDs));
        List<Integer> oIDs = Arrays.asList(
                ArrayUtils.toObject(TfMetaUtils.parseJsonIDList(jSpec, colnames, TfUtils.TXMETHOD_OMIT)));
        List<Integer> mvIDs = Arrays.asList(ArrayUtils
                .toObject(TfMetaUtils.parseJsonObjectIDList(jSpec, colnames, TfUtils.TXMETHOD_IMPUTE)));

        //create individual encoders
        if (!rcIDs.isEmpty()) {
            RecodeAgent ra = new RecodeAgent(jSpec, colnames, clen);
            ra.setColList(ArrayUtils.toPrimitive(rcIDs.toArray(new Integer[0])));
            lencoders.add(ra);
        }
        if (!ptIDs.isEmpty())
            lencoders.add(new EncoderPassThrough(ArrayUtils.toPrimitive(ptIDs.toArray(new Integer[0])), clen));
        if (!dcIDs.isEmpty())
            lencoders.add(new DummycodeAgent(jSpec, colnames, schema.length));
        if (!binIDs.isEmpty())
            lencoders.add(new BinAgent(jSpec, colnames, schema.length, true));
        if (!oIDs.isEmpty())
            lencoders.add(new OmitAgent(jSpec, colnames, schema.length));
        if (!mvIDs.isEmpty()) {
            MVImputeAgent ma = new MVImputeAgent(jSpec, colnames, schema.length);
            ma.initRecodeIDList(rcIDs);
            lencoders.add(ma);
        }

        //create composite decoder of all created encoders
        //and initialize meta data (recode, dummy, bin, mv)
        encoder = new EncoderComposite(lencoders);
        if (meta != null)
            encoder.initMetaData(meta);
    } catch (Exception ex) {
        throw new DMLRuntimeException(ex);
    }

    return encoder;
}

From source file:org.broad.igv.data.GenomeSummaryDataTest.java

/**
 * Build GenomeSummaryData from sorted (by chromosome and start position) set of features
 * @param genome/*from w ww .ja  v a  2s . c  o  m*/
 * @param trackId
 * @param features
 * @return
 */
private GenomeSummaryData buildGenomeSummaryData(Genome genome, String trackId, Iterable<BasicFeature> features,
        double scale) {
    GenomeSummaryData genomeSummaryData = new GenomeSummaryData(genome, new String[] { trackId });
    if (scale > 0) {
        genomeSummaryData.setScale(scale);
    }

    List<Integer> startLocations = new ArrayList<Integer>();
    List<Float> data = new ArrayList<Float>();
    String lastChr = null;

    for (BasicFeature feature : features) {
        String chr = feature.getChr();
        //Finish off last chromosome
        if (lastChr != null && !chr.equals(lastChr)) {
            Map<String, float[]> dMap = new HashMap<String, float[]>();
            dMap.put(trackId, ArrayUtils.toPrimitive(data.toArray(new Float[data.size()])));
            genomeSummaryData.addData(lastChr,
                    ArrayUtils.toPrimitive(startLocations.toArray(new Integer[startLocations.size()])), dMap);
            startLocations.clear();
            data.clear();
        }

        startLocations.add(feature.getStart());
        data.add(feature.getScore());

        lastChr = chr;
    }

    Map<String, float[]> dMap = new HashMap<String, float[]>();
    dMap.put(trackId, ArrayUtils.toPrimitive(data.toArray(new Float[data.size()])));
    genomeSummaryData.addData(lastChr,
            ArrayUtils.toPrimitive(startLocations.toArray(new Integer[startLocations.size()])), dMap);

    return genomeSummaryData;
}

From source file:org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcTestBuilder.java

public VariantContext makeACTest(final List<Integer> ACs, final int nNonInformative, final int nonTypePL) {
    return makeACTest(ArrayUtils.toPrimitive(ACs.toArray(new Integer[] {})), nNonInformative, nonTypePL);
}

From source file:org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationUnitTest.java

private List<Genotype> toGenotypes(final List<List<Integer>> PLsPerSample) {
    final List<Allele> nocall = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
    final List<Genotype> genotypes = new ArrayList<Genotype>(PLsPerSample.size());

    for (final List<Integer> PLs : PLsPerSample) {
        final int[] pls = ArrayUtils.toPrimitive(PLs.toArray(new Integer[3]));
        final int min = MathUtils.arrayMin(pls);
        for (int i = 0; i < pls.length; i++)
            pls[i] -= min;// ww w . j  a  v  a2  s.co  m
        genotypes.add(makePL(nocall, pls));
    }

    return genotypes;
}