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

Introduction

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

Prototype

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

Source Link

Document

Converts an array of primitive booleans to objects.

Usage

From source file:ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl.java

private void scoreOutliers(Geeq gq, DoubleMatrix<BioAssay, BioAssay> cormat) {
    double score;
    boolean hasCorrMat = true;
    boolean hasNaNs = false;
    boolean outliers = true;

    if (cormat == null || cormat.rows() == 0) {
        hasCorrMat = false;//from  ww w  .  j av  a2s . c o m
    } else {
        // Check if cormat has NaNs (diagonal is not checked, but there really should not be NaNs on the diagonal)
        Double[] doubleArray = ArrayUtils.toObject(this.getLowerTriangle(cormat.getRawMatrix()));
        List<Double> list = new ArrayList<>(Arrays.asList(doubleArray));
        hasNaNs = list.contains(Double.NaN);

        outliers = outlierDetectionService.identifyOutliersByMedianCorrelation(cormat).size() > 0;
    }

    score = outliers ? GeeqServiceImpl.N_10 : GeeqServiceImpl.P_10; //
    gq.setCorrMatIssues((byte) (!hasCorrMat ? 1 : hasNaNs ? 2 : 0));
    gq.setqScoreOutliers(score);
}

---

From source file:ubic.gemma.persistence.service.expression.experiment.GeeqServiceImpl.java

private double[] getLowerTriCormat(DoubleMatrix<BioAssay, BioAssay> cormat) {
    if (cormat == null || cormat.rows() == 0) {
        return new double[] {};
    }/*  www  .j  ava 2 s. co m*/
    double[] corTri = this.getLowerTriangle(cormat.getRawMatrix());

    // We have to remove NaNs, some cormats have them (we notify user about this in the outlier score)
    // this is not very efficient, but the DoubleMatrix does not have a method to get an array of Doubles (not doubles)
    Double[] doubleArray = ArrayUtils.toObject(corTri);
    List<Double> list = new ArrayList<>(Arrays.asList(doubleArray));
    //noinspection StatementWithEmptyBody // because java standard libraries suck, we have to iterate like this to remove all NaNs, not just the first one.
    while (list.remove(Double.NaN)) {
    }

    return ArrayUtils.toPrimitive(list.toArray(new Double[0]));
}

---

From source file:uk.ac.diamond.scisoft.analysis.rcp.inspector.InspectionTab.java

private void pushImages(final IMonitor monitor, final Slice[] slices, final int[] order) {
    // work out slicing result
    final int[] shape = dataset.getShape();

    //      System.err.printf("Shape: %s; slicing: [%s]; order: %s\n", Arrays.toString(shape), Slice.createString(slices), Arrays.toString(order));

    int rank = shape.length;
    int ns = slices.length;
    // dimensions for iterating over (order.length == slices.length)
    int ids = ns > 3 ? 2 : 1;

    final List<Integer> gridDimNumber = new ArrayList<Integer>();
    final int[] gridShape = new int[ids];
    for (int i = 0; i < ids; i++) {
        // After dimension reordering, first two dimensions should be an image size
        // followed by grid dimensions
        int o = order[i + 2];
        gridDimNumber.add(o);// w  ww .j  ava 2s.com
        gridShape[i] = slices[o].getNumSteps();
    }

    try {
        //         System.err.printf("Grid: %s\n", Arrays.toString(gridShape));
        if (ids == 1) {
            SDAPlotter.setupNewImageGrid(explorerName, gridShape[0]);
        } else {
            SDAPlotter.setupNewImageGrid(explorerName, gridShape[1], gridShape[0]);
        }
    } catch (Exception e) {
        logger.warn("Problem with setting up image explorer", e);
    }

    // use position iterator ignoring first set of slicing axes
    int[] start = new int[rank];
    int[] stop = new int[rank];
    int[] step = new int[rank];
    Slice.convertFromSlice(slices, shape, start, stop, step);

    List<Integer> ignoreAxesList = new ArrayList<Integer>(Arrays.asList(ArrayUtils.toObject(order)));
    ignoreAxesList.removeAll(gridDimNumber);
    int[] ignoreAxes = ArrayUtils.toPrimitive(ignoreAxesList.toArray(new Integer[0]));
    PositionIterator it = new PositionIterator(shape, start.clone(), stop.clone(), step, ignoreAxes);
    int[] pos = it.getPos();

    int dimGridX = gridDimNumber.get(0);
    int gridX0 = start[dimGridX];
    int dimGridY = (ids == 1) ? -1 : gridDimNumber.get(1);
    int gridY0 = (ids == 1) ? -1 : start[dimGridY];

    try {
        setInspectionRunning();
        boolean memoryOK = true;
        while (!memoryOK || it.hasNext()) { // short-cut iteration when low on memory
            try {
                for (int i = 0; i < ids; i++) {
                    int o = gridDimNumber.get(i);
                    int b = pos[o];
                    start[o] = b;
                    stop[o] = b + 1;
                }
                Dataset slicedData = sliceData(monitor, start, stop, step);
                if (slicedData == null)
                    return;
                //               System.err.printf("Pos %s; start %s; stop %s; step %s; ", Arrays.toString(pos), Arrays.toString(start), Arrays.toString(stop), Arrays.toString(step));
                //               System.err.printf("Shape %s\n", Arrays.toString(slicedData.getShape()));

                Dataset reorderedData = slicedData.getTransposedView(order);

                reorderedData.setName(slicedData.getName());
                reorderedData.squeeze();
                if (reorderedData.getSize() < 1)
                    return;

                reorderedData.setName(dataset.getName() + Arrays.toString(pos));
                if (!canContinueInspection()) {
                    return;
                }

                if (explorer.isStopped()) {
                    stopInspection();
                    return;
                }

                if (ids == 1) {
                    SDAPlotter.plotImageToGrid(explorerName, reorderedData, true);
                } else {
                    int gridX = pos[dimGridX] - gridX0;
                    int gridY = pos[dimGridY] - gridY0;
                    SDAPlotter.plotImageToGrid(explorerName, reorderedData, gridX, gridY, true);
                }

                if (!memoryOK)
                    logger.warn("... memory reduction successful");
                memoryOK = true;
            } catch (OutOfMemoryError e) {
                if (!memoryOK) // only allow one GC per slice
                    throw e;
                memoryOK = false;
                logger.warn("Ran out of memory: attempting to reduce memory used...");
                System.gc();
                // try again after memory reduction
            }
        }
    } catch (Exception e) {
        logger.warn("Problem with sending data to image explorer", e);
    } finally {
        stopInspection();
    }
}

---

From source file:uk.ac.diamond.scisoft.analysis.rpc.flattening.helpers.GuiBeanHelper.java

/**
 * We know the intended type, so in many cases we can upgrade from flattened to the expected type e.g. Object[] to
 * List<Object>.//ww w .j a  v  a2s  . c o m
 * 
 * @param params
 * @param valueObj
 * @return upgraded valueObj, or the original if it matches
 */
private Serializable unflattenParam(GuiParameters params, Serializable valueObj) {
    Class<?> clazz = params.getStorageClass();
    if (clazz.isInstance(valueObj)) {
        return valueObj;
    } else if (clazz.equals(List.class)) {
        return new ArrayList<Object>(Arrays.asList((Object[]) valueObj));
    } else if (clazz.equals(Integer[].class)) {
        return ArrayUtils.toObject((int[]) valueObj);
    } else if (clazz.equals(GuiPlotMode.class)) {
        return GuiPlotMode.valueOf((String) valueObj);
    } else if (clazz.equals(UUID.class)) {
        return UUID.fromString(valueObj.toString());
    }
    return valueObj;
}

---

From source file:uk.ac.diamond.scisoft.ncd.actors.NcdNexusTreeTransformer.java

private void writeNxsFile(String filePath, List<DataMessageComponent> cache, DataMessageComponent comp)
        throws NullPointerException, HDF5Exception {

    final List<IDataset> sets = MessageUtils.getDatasets(cache);
    Dataset data = (Dataset) sets.get(0);

    // add frame dimension
    int[] newShape = ArrayUtils.addAll(new int[] { 1, 1 }, data.getShape());
    data = data.reshape(newShape);//  w  w  w .  j  a  va 2 s.  c o  m

    int fapl = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
    H5.H5Pset_fclose_degree(fapl, HDF5Constants.H5F_CLOSE_STRONG);
    int nxsfile_handle = H5.H5Fcreate(filePath, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, fapl);
    H5.H5Pclose(fapl);
    int[] libversion = new int[3];
    H5.H5get_libversion(libversion);
    putattr(nxsfile_handle, "HDF5_version", StringUtils.join(ArrayUtils.toObject(libversion), "."));
    putattr(nxsfile_handle, "file_name", filePath);

    Date date = new Date();
    SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ");
    String dt = format.format(date);
    putattr(nxsfile_handle, "file_time", dt);

    int entry_group_id = makegroup(nxsfile_handle, "entry1", "NXentry");

    int instrument_group_id = makegroup(entry_group_id, "instrument", "NXinstrument");
    int detector_group_id = makegroup(instrument_group_id, detector, "NXdetector");

    int datatype = -1;
    if (data instanceof ShortDataset) {
        datatype = HDF5Constants.H5T_NATIVE_SHORT;
    } else if (data instanceof IntegerDataset) {
        datatype = HDF5Constants.H5T_NATIVE_INT;
    } else if (data instanceof LongDataset) {
        datatype = HDF5Constants.H5T_NATIVE_LONG;
    } else if (data instanceof FloatDataset) {
        datatype = HDF5Constants.H5T_NATIVE_FLOAT;
    } else if (data instanceof DoubleDataset) {
        datatype = HDF5Constants.H5T_NATIVE_DOUBLE;
    }

    int input_data_id = makedata(detector_group_id, "data", datatype, data);
    putattr(input_data_id, "signal", 1);
    putattr(input_data_id, "units", "counts");
    make_sas_type(detector_group_id);

    int link_group_id = makegroup(entry_group_id, detector, "NXdata");
    H5.H5Lcreate_hard(detector_group_id, "./data", link_group_id, "./data", HDF5Constants.H5P_DEFAULT,
            HDF5Constants.H5P_DEFAULT);

    H5.H5Dclose(input_data_id);
    H5.H5Gclose(detector_group_id);
    H5.H5Gclose(instrument_group_id);
    H5.H5Gclose(link_group_id);
    H5.H5Gclose(entry_group_id);
    H5.H5Fclose(nxsfile_handle);
}

---

From source file:uk.ac.diamond.scisoft.ncd.core.utils.NcdDataUtils.java

/**
 * Method for generating all combination of elements supplied in the input array
 * //from w  ww. j av a2 s.c om
 * @param input
 *          Array containing arrays of elements.
 *          Resulting combinations will pick single element from every input array. 
 * @return
 *          Array containing all combinations of the input elements with only one element
 *          picked from every input array at a time.
 */
public static ArrayList<int[]> generateCombinations(final ArrayList<int[]> input) {
    ArrayList<int[]> result = new ArrayList<int[]>();
    @SuppressWarnings("unchecked")
    ArrayList<int[]> tmpInput = (ArrayList<int[]>) input.clone();
    int[] first = tmpInput.remove(0);
    for (int i = 0; i < first.length; i++) {
        if (!tmpInput.isEmpty()) {
            ArrayList<int[]> recursive = generateCombinations(tmpInput);
            for (int j = 0; j < recursive.size(); j++) {
                ArrayList<Integer> tmp = new ArrayList<Integer>();
                tmp.add(first[i]);
                tmp.addAll(Arrays.asList(ArrayUtils.toObject(recursive.get(j))));
                result.add(ArrayUtils.toPrimitive(tmp.toArray(new Integer[] {})));
            }
        } else {
            ArrayList<Integer> tmp = new ArrayList<Integer>();
            tmp.add(first[i]);
            result.add(ArrayUtils.toPrimitive(tmp.toArray(new Integer[] {})));
        }
    }
    return result;
}

---

From source file:uk.ac.diamond.scisoft.ncd.passerelle.actors.service.DataReductionServiceImpl.java

private String createResultsFile(IDataReductionContext context, String inputfileName, String inputfilePath,
        String prefix) {/*from  w  ww  . j  av  a2 s .c  o  m*/

    String datetime = generateDateTimeStamp();
    String detNames = "_" + ((context.isEnableWaxs()) ? context.getWaxsDetectorName() : "")
            + ((context.isEnableSaxs()) ? context.getSaxsDetectorName() : "") + "_";
    final String filename = context.getWorkingDir() + File.separator + prefix + "_"
            + FilenameUtils.getBaseName(inputfileName) + detNames + datetime + ".nxs";

    int fid = -1;
    int entry_id = -1;
    try {
        int fapl = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
        H5.H5Pset_fclose_degree(fapl, HDF5Constants.H5F_CLOSE_WEAK);
        fid = H5.H5Fcreate(filename, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, fapl);
        H5.H5Pclose(fapl);

        int[] libversion = new int[3];
        H5.H5get_libversion(libversion);
        putattr(fid, "HDF5_version", StringUtils.join(ArrayUtils.toObject(libversion), "."));
        putattr(fid, "file_name", filename);

        Date date = new Date();
        SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ");
        String dt = format.format(date);
        putattr(fid, "file_time", dt);

        entry_id = NcdNexusUtils.makegroup(fid, "entry1", Nexus.ENTRY);

        final String calibration = context.getCalibrationName();
        if (calibration != null) {
            int calib_id = NcdNexusUtils.makegroup(entry_id, calibration, Nexus.DATA);
            H5.H5Lcreate_external(inputfilePath, "/entry1/" + calibration + "/data", calib_id, "data",
                    HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            H5.H5Gclose(calib_id);
        }

        writeNCDMetadata(entry_id, inputfilePath);

        createInstrumentNode(entry_id, inputfilePath);

        if (context.isEnableWaxs()) {
            createDetectorNode(context.getWaxsDetectorName(), entry_id, inputfilePath);
        }

        if (context.isEnableSaxs()) {
            createDetectorNode(context.getSaxsDetectorName(), entry_id, inputfilePath);
        }

    } catch (HDF5Exception e) {
        throw new RuntimeException("Failed to create results NeXus file", e);
    } catch (URISyntaxException e) {
        throw new RuntimeException("Invalind NeXus link path in the input data file", e);
    } finally {
        try {
            NcdNexusUtils.closeH5id(entry_id);
        } catch (Exception e2) {
            logger.error("Failed to close entry group in the NeXus results file", e2);
        } finally {
            try {
                NcdNexusUtils.closeH5id(fid);
            } catch (Exception e3) {
                logger.error("Failed to close reference id of the NeXus results file", e3);
            }
        }
    }
    return filename;
}

---

From source file:uk.ac.diamond.scisoft.xpdf.operations.XPDFAzimuthalIntegrationOperation.java

@Override
protected OperationData process(IDataset input, IMonitor monitor) throws OperationException {

    // get the XPDF metadata
    XPDFMetadata xMeta = input.getFirstMetadata(XPDFMetadata.class);

    // create the Operation that will do the processing
    AzimuthalPixelIntegrationOperation<XPDFAzimuthalIntegrationInternalModel> internalOperation = new AzimuthalPixelIntegrationOperation<XPDFAzimuthalIntegrationInternalModel>();

    // create the fake model that will supply the parameters to the internal Operation
    XPDFAzimuthalIntegrationInternalModel internalModel = new XPDFAzimuthalIntegrationInternalModel(
            model.getAzimuthalRange(), model.getRadialRange(), model.isPixelSplitting(),
            model.getNumberOfBins());// w  ww  . j  a  v a2s.  c o  m

    internalOperation.setModel(internalModel);

    // Resize the data to be more like it was in the execute() method
    SliceFromSeriesMetadata ssm = getSliceSeriesMetadata(input);
    // Get the dimensions in the original data
    int[] dataDims = ssm.getDataDimensions();
    int maxDimension = Collections.max(Arrays.asList(ArrayUtils.toObject(dataDims)));
    int[] newShape = new int[maxDimension + 1];
    int[] oldShape = input.getShape();
    // All elements of the new shape are 1
    Arrays.fill(newShape, 1);
    // except those that are in the data
    for (int dim = 0; dim < oldShape.length; dim++)
        newShape[dataDims[dim]] = oldShape[dim];

    IDataset reshapedInput = input.clone();
    // The reshaped data is now (hopefully) the same shape as input was in this.execute()
    reshapedInput.resize(newShape);

    OperationData output = internalOperation.execute(reshapedInput, monitor);

    // Set the axis coordinate to q
    if (xMeta != null) {
        xMeta.getSample().getTrace().setAxisAngle(false);
    }

    output.getData().addMetadata(xMeta);

    return output;

    //      OperationData superResult = super.process(input, monitor);
    //
    //      // The downstream processing relies on metadata to tell if the axis is 2 or q
    //      if (xMeta != null) {
    //         
    //         if (model.getAxisType() != XAxis.ANGLE)
    //            xMeta.getSample().getTrace().setAxisAngle(false);
    //      
    //         superResult.getData().setMetadata(xMeta);
    //      }
    //      return superResult;
}

---

From source file:uk.ac.diamond.scisoft.xpdf.views.SampleParametersTest.java

@Test
public void testSetGetDimensions() {
    testSetGetComposition();/*from   www  . j a  v  a 2 s . c o m*/
    cap.setShape("cylinder");
    double[] dims = new double[] { 0.15, 0.16 };
    cap.setDimensions(dims);
    assertEquals("New dimensions not set/got correctly", Arrays.asList(ArrayUtils.toObject(dims)),
            Arrays.asList(ArrayUtils.toObject(cap.getDimensions())));
}

---

From source file:uk.gov.gchq.gaffer.sketches.datasketches.sampling.function.aggregate.ReservoirLongUnionAggregatorTest.java

@Test
public void testAggregate() {
    final ReservoirLongsUnionAggregator unionAggregator = new ReservoirLongsUnionAggregator();
    unionAggregator.init();//from w w  w .j a v  a  2s. c  om

    unionAggregator._aggregate(union1);
    ReservoirLongsSketch currentState = unionAggregator._state().getResult();
    assertEquals(3L, currentState.getN());
    assertEquals(3, currentState.getNumSamples());
    // As less items have been added than the capacity, the sample should exactly match what was added.
    Set<Long> samples = new HashSet<>(Arrays.asList(ArrayUtils.toObject(currentState.getSamples())));
    Set<Long> expectedSamples = new HashSet<>();
    expectedSamples.add(1L);
    expectedSamples.add(2L);
    expectedSamples.add(3L);
    assertEquals(expectedSamples, samples);

    unionAggregator._aggregate(union2);
    currentState = unionAggregator._state().getResult();
    assertEquals(99L, currentState.getN());
    assertEquals(20L, currentState.getNumSamples());
    // As more items have been added than the capacity, we can't know exactly what items will be present
    // in the sample but we can check that they are all from the set of things we added.
    samples = new HashSet<>(Arrays.asList(ArrayUtils.toObject(currentState.getSamples())));
    for (long l = 4L; l < 100; l++) {
        expectedSamples.add(l);
    }
    assertTrue(expectedSamples.containsAll(samples));
}

---

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