OpenBISScreeningML.java

    {
        return loadRawImages(plate, row, col, channels, createSingleTileIterator(tile));
    }

    /**
     * Has the same effect as {@link #loadImages(String, int, int, int, String[])}, but instead of
     * loading raw images loads their segmentation results if available.
     * 
     * @param objectNames The names of the segmentation objects to get the images for
     */
    public static Object[][][] loadSegmentationImages(String plate, int row, int col,
            final int tile, String[] objectNames)
    {
        return loadSegmentationImages(plate, row, col, objectNames, createSingleTileIterator(tile));
    }

    private static ITileNumberIterable createSingleTileIterator(final int tile)
    {
        return new ITileNumberIterable()
            {
                public void setMaximumNumberOfTiles(int numberOfTiles)
                {
                    if (tile >= numberOfTiles)
                    {
                        throw new IllegalArgumentException("Tile number " + tile
                                + " is not less than number of tiles " + numberOfTiles + ".");
                    }
                }

                public int getMaximumNumberOfTiles()
                {
                    return 1;
                }

                public Iterator<Integer> iterator()
                {
                    return new Iterator<Integer>()
                        {
                            private boolean delivered;

                            public boolean hasNext()
                            {
                                return delivered == false;
                            }

                            public Integer next()
                            {
                                delivered = true;
                                return tile;
                            }

                            public void remove()
                            {
                                throw new UnsupportedOperationException();
                            }
                        };
                }
            };
    }

    /**
     * Lists all segmentation objects for the <var>plate</var>.
     * <p>
     * Matlab example:
     * 
     * <pre>
     * % Get the segmentation objects of plate P005 in space SPACE.
     * segmentationObjects = OpenBISScreeningML.listSegmentationObjects('/SPACE/P005');
     * % How many segmentation objects do we have?
     * length(segmentationObjects)
     * % What is the name of segmentation objects 1?
     * segmentationObjects(1)
     * </pre>
     * 
     * @param plate augmented code of the plate
     * @return Each row contains information about one segmentation object. Currently the only
     *         information available is the segmentation object name.
     */
    public static Object[][] listSegmentationObjects(String plate)
    {
        checkLoggedIn();
        Plate plateId = getPlate(plate);
        final List<ImageDatasetReference> imageDatasets = listSegmentationImageDatasets(plateId);
        if (imageDatasets.isEmpty())
        {
            return new Object[0][];
        }
        return extractChannels(imageDatasets.get(0));
    }

    private static Object[][] extractChannels(ImageDatasetReference imageDatasetReference)
    {
        final List<ImageDatasetMetadata> meta =
                openbis.listImageMetadata(Arrays.asList(imageDatasetReference));
        if (meta.isEmpty())
        {
            return new Object[0][];
        }
        final List<String> channels = getChannelCodes(meta);
        Object[][] result = new Object[channels.size()][1];
        for (int i = 0; i < result.length; ++i)
        {
            result[i][0] = channels.get(i);
        }
        return result;
    }

    private static Object[][][] loadRawImages(String plate, int row, int col, String[] channels,
            ITileNumberIterable tileNumberIterable)
    {
        checkLoggedIn();
        final Plate plateId = getPlate(plate);
        final List<ImageDatasetReference> imageDatasets = listRawImageDatasets(plateId);
        return loadImages(plateId, imageDatasets, row, col, channels, tileNumberIterable);
    }

    private static Object[][][] loadSegmentationImages(String plate, int row, int col,
            String[] channels, ITileNumberIterable tileNumberIterable)
    {
        checkLoggedIn();
        final Plate plateId = getPlate(plate);
        final List<ImageDatasetReference> imageDatasets = listSegmentationImageDatasets(plateId);
        return loadImages(plateId, imageDatasets, row, col, channels, tileNumberIterable);
    }

    private static Object[][][] loadImages(Plate plate, List<ImageDatasetReference> imageDatasets,
            int row, int col, String[] channels, ITileNumberIterable tileNumberIterable)
    {
        final List<ImageDatasetMetadata> meta = openbis.listImageMetadata(imageDatasets);
        if (meta.isEmpty())
        {
            return new Object[][][]
                { new Object[0][], new Object[0][] };
        }
        final List<String> imageChannels;
        if (channels == null || channels.length == 0)
        {
            imageChannels = getChannelCodes(meta);
        } else
        {
            imageChannels = Arrays.asList(channels);
        }
        final List<ImageReferenceAndFile> imageReferencesAndFiles =
                new ArrayList<ImageReferenceAndFile>(imageDatasets.size());
        final Object[][][] result = new Object[2][][];
        tileNumberIterable.setMaximumNumberOfTiles(meta.get(0).getNumberOfTiles());
        int numberOfTiles = tileNumberIterable.getMaximumNumberOfTiles();
        result[0] = new Object[imageDatasets.size() * imageChannels.size() * numberOfTiles][1];
        result[1] = new Object[imageDatasets.size() * imageChannels.size() * numberOfTiles][15];
        int dsIdx = 0;
        int resultIdx = 0;
        for (ImageDatasetReference ds : imageDatasets)
        {
            for (String channel : imageChannels)
            {
                for (Integer tile : tileNumberIterable)
                {
                    final PlateImageReference ref =
                            new PlateImageReference(row, col, tile, channel, ds);
                    final File imageFile = createImageFileName(plate, ref);
                    imageReferencesAndFiles.add(new ImageReferenceAndFile(ref, imageFile));
                    result[0][resultIdx][0] = imageFile.getPath();
                    PlateIdentifier plateIdentifier = ds.getPlate();
                    ExperimentIdentifier expIdentifier = ds.getExperimentIdentifier();
                    final Object[] annotations =
                            new Object[]
                                { channel, tile,
                                        createPlateWellDescription(plateIdentifier, row, col),
                                        plateIdentifier.getAugmentedCode(),
                                        plateIdentifier.getPermId(),
                                        plateIdentifier.tryGetSpaceCode(),
                                        plateIdentifier.getPlateCode(), row, col,
                                        expIdentifier.getAugmentedCode(),
                                        expIdentifier.getPermId(), expIdentifier.getSpaceCode(),
                                        expIdentifier.getProjectCode(),
                                        expIdentifier.getExperimentCode(), ds.getPermId(), };
                    System.arraycopy(annotations, 0, result[1][resultIdx], 0, annotations.length);
                    resultIdx++;
                }
            }
            dsIdx++;
        }
        try
        {
            loadImages(imageReferencesAndFiles);
        } catch (IOException ex)
        {
            throw new RuntimeException(ex);
        }
        return result;
    }

    private static List<ImageDatasetReference> listRawImageDatasets(final Plate plateId)
    {
        return openbis.listRawImageDatasets(Arrays.asList(plateId));
    }

    private static List<ImageDatasetReference> listSegmentationImageDatasets(final Plate plateId)
    {
        return openbis.listSegmentationImageDatasets(Arrays.asList(plateId));
    }

    /**
     * Saves images for a given list of image references (given by data set code, well position,
     * channel and tile) and files.
     * 
     * @throws IOException when reading images from the server or writing them to the files fails
     */
    private static void loadImages(List<ImageReferenceAndFile> imageReferencesAndFiles)
            throws IOException
    {
        List<PlateImageReference> imageReferences = new ArrayList<PlateImageReference>();
        final Map<PlateImageReference, ImageReferenceAndFile> imageRefToFileMap =
                new HashMap<PlateImageReference, ImageReferenceAndFile>();
        for (ImageReferenceAndFile imageReferenceAndFile : imageReferencesAndFiles)
        {
            PlateImageReference imageReference = imageReferenceAndFile.getImageReference();
            File file = loadedImages.get(imageReference);
            if (file == null)
            {
                imageReferences.add(imageReference);
                imageRefToFileMap.put(imageReference, imageReferenceAndFile);
            }
        }
        try
        {
            openbis.loadImages(imageReferences, new IImageOutputStreamProvider()
                {
                    public OutputStream getOutputStream(PlateImageReference imageReference)
                            throws IOException
                    {
                        return imageRefToFileMap.get(imageReference).open();
                    }
                }, false);
        } finally
        {
            Collection<ImageReferenceAndFile> values = imageRefToFileMap.values();
            for (ImageReferenceAndFile imageReferenceAndFile : values)
            {
                imageReferenceAndFile.close();
                PlateImageReference imageReference = imageReferenceAndFile.getImageReference();
                loadedImages.put(imageReference, imageReferenceAndFile.getImageFile());
            }
        }
    }

    private static File createImageFileName(Plate plate, PlateImageReference image)
    {
        final WellPosition well = image.getWellPosition();
        File imageDir = new File(temporarySessionDir, "images");
        imageDir.mkdirs();
        final File f =
                new File(imageDir, "img_" + plate.getPlateCode() + "_" + image.getDatasetCode()
                        + "_row" + well.getWellRow() + "_col" + well.getWellColumn() + "_"
                        + image.getChannel() + "_tile" + image.getTile() + ".tiff");
        f.deleteOnExit();
        return f;
    }

    //
    // Feature matrix
    //

    /**
     * Returns the feature matrix of all features for all locations in <var>experiment</var> (a
     * location is one well position in one feature vector data set) connected to <var>gene</var> in
     * <code>[0]</code>, location annotations in <code>[1]</code> and feature annotation in
     * <code>[2]</code>.
     * <p>
     * Matlab example:
     * 
     * <pre>
     * % Get feature matrix for experiment /SPACE/PROJ/MYEXP for locations connected to GENENAME
     * fmatrix = OpenBISScreeningML.getFeatureMatrix('/SPACE/PROJ/MYEXP', 'GENENAME');
     * % Get the feature vector for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,:,2,3)
     * % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,4,:,3)
     * % Get code of the fourth feature (assuming that there are at least 4 features)
     * fmatrix(3,4)
     * % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(2,2,3,:)
     * </pre>
     * 
     * @param experiment The augmented experiment code
     * @param gene The gene code (stored as material code in openBIS, usually it is gene id)
     * @return a four dimensional matrix. The first dimension denotes the type in the following
     *         order: <code>{feature matrix, annotations per location, feature codes}</code>. The
     *         other dimensions depend on the value of the first dimension:
     *         <ol>
     *         <li>feature matrix: 2. dimension is feature vector, 3. dimension is location number,
     *         4. dimension is data set number. If for a particular location and a particular data
     *         set the corresponding feature value does not exists <code>NaN</code> will be returned. 
     *         <li>annotations: 2. dimension is location number, 3. dimension is data set number, 4.
     *         dimension is location annotations in the following order: <code>{plate well
     *         description, plate augmented code, plate perm id, plate space code, plate code, row,
     *         column, experiment augmented code, experiment perm id, experiment space code,
     *         experiment project code, experiment code, data set code}</code> 
     *         <li>feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
     *         dimension are meaningless (i.e. they have length one) 
     *         </ol>
     */
    public static Object[][][] getFeatureMatrix(String experiment, String gene)
    {
        return getFeatureMatrix(experiment, gene, (String[]) null);
    }

    /**
     * Returns the feature matrix of the specified features for all locations in
     * <var>experiment</var> (a location is one well position in one feature vector data set) in
     * <var>experiment</var> connected to <var>gene</var> in <code>[0]</code>, location annotations
     * in <code>[1]</code> and feature annotation in <code>[2]</code>.
     * <p>
     * Matlab example:
     * 
     * <pre>
     * % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE3 for 
     * % experiment /SPACE/PROJ/MYEXP for locations connected to GENENAME
     * fmatrix = OpenBISScreeningML.getFeatureMatrix('/SPACE/PROJ/MYEXP', 'GENENAME', ('FEATURE1','FEATURE2','FEATURE3'));
     * % Get the feature vector for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,:,2,3)
     * % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,4,:,3)
     * % Get code of the fourth feature (assuming that there are at least 4 features)
     * fmatrix(3,4)
     * % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(2,2,3,:)
     * </pre>
     * 
     * @param experiment The augmented experiment code
     * @param gene The gene code (stored as material code in openBIS, usually it is gene id)
     * @param features The names of the features to contain the feature matrix
     * @return a four dimensional matrix. The first dimension denotes the type in the following
     *         order: <code>{feature matrix, annotations per location, feature codes}</code>. The
     *         other dimensions depend on the value of the first dimension:
     *         <ol>
     *         <li>feature matrix: 2. dimension is feature vector, 3. dimension is location number,
     *         4. dimension is data set number. If for a particular location and a particular data
     *         set the corresponding feature value does not exists <code>NaN</code> will be returned. 
     *         <li>annotations: 2. dimension is location number, 3. dimension is data set number, 4.
     *         dimension is location annotations in the following order: <code>{plate well
     *         description, plate augmented code, plate perm id, plate space code, plate code, row,
     *         column, experiment augmented code, experiment perm id, experiment space code,
     *         experiment project code, experiment code, data set code}</code> 
     *         <li>feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
     *         dimension are meaningless (i.e. they have length one) 
     *         </ol>
     */
    public static Object[][][][] getFeatureMatrix(String experiment, String gene, String[] features)
    {
        checkLoggedIn();
        final ExperimentIdentifier experimentId = experimentCodeToExperimentMap.get(experiment);
        if (experimentId == null)
        {
            throw new RuntimeException("No experiment with that code found.");
        }
        final List<Plate> experimentPlates = experimentToPlateMap.get(experiment);
        if (experimentPlates == null || experimentPlates.isEmpty())
        {
            return new Object[][][][]
                { new Object[0][][], new Object[0][][], new Object[0][][] };
        }
        final List<FeatureVectorWithDescription> featureVectors =
                openbis.loadFeaturesForPlateWells(experimentId, new MaterialIdentifier(
                        MaterialTypeIdentifier.GENE, gene),
                        (features == null) ? null : Arrays.asList(features));
        return getFeatureMatrix(featureVectors);
    }
    
    /**
     * Returns the feature matrix of all features for all locations (a location is one well position
     * in one feature vector data set) connected to <var>gene</var> in <code>[0]</code>, location
     * annotations in <code>[1]</code> and feature annotation in <code>[2]</code>.
     * <p>
     * Matlab example:
     * 
     * <pre>
     * % Get feature matrix for GENENAME
     * fmatrix = OpenBISScreeningML.getFeatureMatrix('GENENAME');
     * % Get the feature vector for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,:,2,3)
     * % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,4,:,3)
     * % Get code of the fourth feature (assuming that there are at least 4 features)
     * fmatrix(3,4)
     * % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(2,2,3,:)
     * </pre>
     * 
     * @param gene The gene code (stored as material code in openBIS, usually it is gene id)
     * @return a four dimensional matrix. The first dimension denotes the type in the following
     *         order: <code>{feature matrix, annotations per location, feature codes}</code>. The
     *         other dimensions depend on the value of the first dimension:
     *         <ol>
     *         <li>feature matrix: 2. dimension is feature vector, 3. dimension is location number,
     *         4. dimension is data set number. If for a particular location and a particular data
     *         set the corresponding feature value does not exists <code>NaN</code> will be returned. 
     *         <li>annotations: 2. dimension is location number, 3. dimension is data set number, 4.
     *         dimension is location annotations in the following order: <code>{plate well
     *         description, plate augmented code, plate perm id, plate space code, plate code, row,
     *         column, experiment augmented code, experiment perm id, experiment space code,
     *         experiment project code, experiment code, data set code}</code> 
     *         <li>feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
     *         dimension are meaningless (i.e. they have length one) 
     *         </ol>
     */
    public static Object[][][][] getFeatureMatrix(String gene)
    {
        return getFeatureMatrix(gene, (String[]) null);
    }

    /**
     * Returns the feature matrix of the specified features for all locations (a location is one
     * well position in one feature vector data set) in <var>experiment</var> connected to
     * <var>gene</var> in <code>[0]</code>, location annotations in <code>[1]</code> and feature
     * annotation in <code>[2]</code>.
     * <p>
     * Matlab example:
     * 
     * <pre>
     * % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE3 for GENENAME
     * fmatrix = OpenBISScreeningML.getFeatureMatrix('GENENAME', ('FEATURE1','FEATURE2','FEATURE3'));
     * % Get the feature vector for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,:,2,3)
     * % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,4,:,3)
     * % Get code of the fourth feature (assuming that there are at least 4 features)
     * fmatrix(3,4)
     * % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(2,2,3,:)
     * </pre>
     * 
     * @param gene The gene code (stored as material code in openBIS, usually it is gene id)
     * @param features The names of the features to contain the feature matrix
     * @return a four dimensional matrix. The first dimension denotes the type in the following
     *         order: <code>{feature matrix, annotations per location, feature codes}</code>. The
     *         other dimensions depend on the value of the first dimension:
     *         <ol>
     *         <li>feature matrix: 2. dimension is feature vector, 3. dimension is location number,
     *         4. dimension is data set number. If for a particular location and a particular data
     *         set the corresponding feature value does not exists <code>NaN</code> will be returned. 
     *         <li>annotations: 2. dimension is location number, 3. dimension is data set number, 4.
     *         dimension is location annotations in the following order: <code>{plate well
     *         description, plate augmented code, plate perm id, plate space code, plate code, row,
     *         column, experiment augmented code, experiment perm id, experiment space code,
     *         experiment project code, experiment code, data set code}</code> 
     *         <li>feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
     *         dimension are meaningless (i.e. they have length one) 
     *         </ol>
     */
    public static Object[][][][] getFeatureMatrix(String gene, String[] features)
    {
        checkLoggedIn();
        final List<FeatureVectorWithDescription> featureVectors =
                openbis.loadFeaturesForPlateWells(new MaterialIdentifier(
                        MaterialTypeIdentifier.GENE, gene),
                        (features == null) ? null : Arrays.asList(features));
        return getFeatureMatrix(featureVectors);
    }

    private static Object[][][][] getFeatureMatrix(
            final List<FeatureVectorWithDescription> featureVectors)
    {
        final Object[][][][] result = new Object[3][][][];
        if (featureVectors.isEmpty())
        {
            return result;
        }
        List<String> featureCodes = getFeatureCodes(featureVectors);
        Map<String, Integer> featureCodeToIndexMap = new HashMap<String, Integer>();
        result[2] = new Object[featureCodes.size()][1][1];
        for (int i = 0; i < featureCodes.size(); ++i)
        {
            String code = featureCodes.get(i);
            result[2][i][0][0] = code;
            featureCodeToIndexMap.put(code, i);
        }
        IndexSet<String> dataSetCodes = new IndexSet<String>();
        IndexSet<WellPosition> wellPositions = new IndexSet<WellPosition>();
        for (FeatureVectorWithDescription featureVector : featureVectors)
        {
            WellPosition wellPosition = featureVector.getWellPosition();
            wellPositions.add(wellPosition);
            dataSetCodes.add(featureVector.getDatasetWellReference().getDatasetCode());
        }
        result[0] =
                new Object[featureCodes.size()][wellPositions.size()][dataSetCodes.size()];
        result[1] = new Object[wellPositions.size()][dataSetCodes.size()][13];
        for (FeatureVectorWithDescription vector : featureVectors)
        {
            WellPosition wellPosition = vector.getWellPosition();
            int wellIndex = wellPositions.getIndex(wellPosition);
            int[] featureIndexes = createFeatureIndexes(vector, featureCodeToIndexMap);
            FeatureVectorDatasetWellReference dataSetRef = vector.getDatasetWellReference();
            int dataSetIndex = dataSetCodes.getIndex(dataSetRef.getDatasetCode());
            copyFeatureValuesInto(result, wellIndex, dataSetIndex, featureIndexes, vector);
            copyAnnotationsInto(result, wellIndex, dataSetIndex, dataSetRef, vector);
        }
        return replaceFeatureNullValuesByNaN(result);
    }

    /**
     * Returns the feature matrix of all available features for all locations (a location is one
     * well position in one feature vector data set) of all feature vector data sets of the given
     * <var>plate</var> in <code>[0]</code>, location annotations in <code>[1]</code> and feature
     * annotation in <code>[2]</code>.
     * <p>
     * Matlab example:
     * <pre>
     * % Get feature matrix for PLATECODE
     * fmatrix = OpenBISScreeningML.getFeatureMatrixForPlate('PLATECODE');
     * % Get the feature vector for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,:,2,3)
     * % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,4,:,3)
     * % Get code of the fourth feature (assuming that there are at least 4 features)
     * fmatrix(3,4)
     * % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(2,2,3,:)
     * </pre>
     * 
     * @param plate augmented code of the plate for which features should be loaded
     * @return a four dimensional matrix. The first dimension denotes the type in the following
     *         order: <code>{feature matrix, annotations per location, feature codes}</code>. The
     *         other dimensions depend on the value of the first dimension:
     *         <ol>
     *         <li>feature matrix: 2. dimension is feature vector, 3. dimension is location number,
     *         4. dimension is data set number. If for a particular location and a particular data
     *         set the corresponding feature value does not exists <code>NaN</code> will be returned. 
     *         <li>annotations: 2. dimension is location number, 3. dimension is data set number, 4.
     *         dimension is location annotations in the following order: <code>{plate well
     *         description, plate augmented code, plate perm id, plate space code, plate code, row,
     *         column, experiment augmented code, experiment perm id, experiment space code,
     *         experiment project code, experiment code, data set code}</code> 
     *         <li>feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
     *         dimension are meaningless (i.e. they have length one) 
     *         </ol>
     */
    public static Object[][][][] getFeatureMatrixForPlate(String plate)
    {
        return getFeatureMatrixForPlate(plate, (String[]) null);
    }

    /**
     * Returns the feature matrix of the specified features for all locations (a location is one
     * well position in one feature vector data set) of all feature vector data sets of the given
     * <var>plate</var> in <code>[0]</code>, location annotations in <code>[1]</code> and feature
     * annotation in <code>[2]</code>.
     * <p>
     * Matlab example:
     * <pre>
     * % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE3 for PLATECODE
     * fmatrix = OpenBISScreeningML.getFeatureMatrixForPlate('PLATECODE', ('FEATURE1','FEATURE2','FEATURE3'));
     * % Get the feature vector for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,:,2,3)
     * % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(1,4,:,3)
     * % Get code of the fourth feature (assuming that there are at least 4 features)
     * fmatrix(3,4)
     * % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
     * % of third data set (assuming that there are at least three data sets)
     * fmatrix(2,2,3,:)
     * </pre>
     * 
     * @param plate augmented code of the plate for which features should be loaded
     * @param features The codes of the features to contain the feature matrix. 
     *         Unknown feature codes will be ignored.
     * @return a four dimensional matrix. The first dimension denotes the type in the following
     *         order: <code>{feature matrix, annotations per location, feature codes}</code>. The
     *         other dimensions depend on the value of the first dimension:
     *         <ol>
     *         <li>feature matrix: 2. dimension is feature vector, 3. dimension is location number,
     *         4. dimension is data set number. If for a particular location and a particular data
     *         set the corresponding feature value does not exists <code>NaN</code> will be returned. 
     *         <li>annotations: 2. dimension is location number, 3. dimension is data set number, 4.
     *         dimension is location annotations in the following order: <code>{plate well
     *         description, plate augmented code, plate perm id, plate space code, plate code, row,
     *         column, experiment augmented code, experiment perm id, experiment space code,
     *         experiment project code, experiment code, data set code}</code> 
     *         <li>feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4.
     *         dimension are meaningless (i.e. they have length one) 
     *         </ol>
     */
    public static Object[][][][] getFeatureMatrixForPlate(String plate, String[] features)
    {
        checkLoggedIn();
        final List<FeatureVectorDataset> dataSets =
                openbis.loadFeaturesForPlates(
                        Arrays.asList(PlateIdentifier.createFromAugmentedCode(plate)),
                        (features == null) ? null : Arrays.asList(features));
        final Object[][][][] result = new Object[3][][][];
        if (dataSets.isEmpty())
        {
            return result;
        }
        List<String> featureCodes = getFeatureCodes(dataSets);
        Map<String, Integer> featureCodeToIndexMap = new HashMap<String, Integer>();
        result[2] = new Object[featureCodes.size()][1][1];
        for (int i = 0; i < featureCodes.size(); ++i)
        {
            String code = featureCodes.get(i);
            result[2][i][0][0] = code;
            featureCodeToIndexMap.put(code, i);
        }
        IndexSet<WellPosition> wellPositions = new IndexSet<WellPosition>();
        for (FeatureVectorDataset dataSet : dataSets)
        {
            List<FeatureVector> featureVectors = dataSet.getFeatureVectors();
            for (FeatureVector featureVector : featureVectors)
            {
                WellPosition wellPosition = featureVector.getWellPosition();
                wellPositions.add(wellPosition);
            }
        }
        int numberOfDataSets = dataSets.size();
        result[0] =
                new Object[featureCodes.size()][wellPositions.size()][numberOfDataSets];
        result[1] = new Object[wellPositions.size()][numberOfDataSets][13];
        for (int dataSetIndex = 0; dataSetIndex < numberOfDataSets; dataSetIndex++)
        {
            FeatureVectorDataset dataSet = dataSets.get(dataSetIndex);
            FeatureVectorDatasetReference dataSetRef = dataSet.getDataset();
            int[] featureIndexes = createFeatureIndexes(dataSet, featureCodeToIndexMap);
            for (FeatureVector vector : dataSet.getFeatureVectors())
            {
                WellPosition wellPosition = vector.getWellPosition();
                int wellIndex = wellPositions.getIndex(wellPosition);
                copyFeatureValuesInto(result, wellIndex, dataSetIndex, featureIndexes, vector);
                copyAnnotationsInto(result, wellIndex, dataSetIndex, dataSetRef, vector);
            }
        }
        return replaceFeatureNullValuesByNaN(result);
    }

    private static Object[][][][] replaceFeatureNullValuesByNaN(final Object[][][][] result)
    {
        Double nan = Double.NaN;
        for (int i = 0; i < result[0].length; i++)
        {
            Object[][] r0i = result[0][i];
            for (int j = 0; j < r0i.length; j++)
            {
                Object[] r0ij = r0i[j];
                for (int k = 0; k < r0ij.length; k++)
                {
                    if (r0ij[k] == null)
                    {
                        r0ij[k] = nan;
                    }
                }
            }
        }
        return result;
    }

    private static int[] createFeatureIndexes(IFeatureCodesProvider dataSet,
            Map<String, Integer> featureCodeToIndexMap)
    {
        List<String> codes = dataSet.getFeatureCodes();
        int[] featureIndexes = new int[codes.size()];
        for (int i = 0; i < featureIndexes.length; i++)
        {
            featureIndexes[i] = featureCodeToIndexMap.get(codes.get(i));
        }
        return featureIndexes;
    }

    private static void copyFeatureValuesInto(final Object[][][][] result, int wellIndex,
            int dataSetIndex, int[] featureIndexes, FeatureVector vector)
    {
        List<Object> valueObjects = vector.getValueObjects();
        for (int i = 0, n = valueObjects.size(); i < n; i++)
        {
            int featureIndex = featureIndexes[i];
            try
            {
                Object[][] f = result[0][featureIndex];
                Object[] d = f[wellIndex];
                d[dataSetIndex] = valueObjects.get(i);
                
            } catch (Exception ex)
            {
                throw new RuntimeException(featureIndex+"."+wellIndex+"."+dataSetIndex, ex);
            }
        }
    }

    private static void copyAnnotationsInto(final Object[][][][] result, int wellIndex,
            int dataSetIndex, FeatureVectorDatasetReference dataSetRef, FeatureVector vector)
    {
        Object[] annotations =
                new Object[]
                    { createPlateWellDescription(dataSetRef.getPlate(), vector),
                            dataSetRef.getPlate().getAugmentedCode(),
                            dataSetRef.getPlate().getPermId(),
                            dataSetRef.getPlate().tryGetSpaceCode(),
                            dataSetRef.getPlate().getPlateCode(),
                            vector.getWellPosition().getWellRow(),
                            vector.getWellPosition().getWellColumn(),
                            dataSetRef.getExperimentIdentifier().getAugmentedCode(),
                            dataSetRef.getExperimentIdentifier().getPermId(),
                            dataSetRef.getExperimentIdentifier().getSpaceCode(),
                            dataSetRef.getExperimentIdentifier().getProjectCode(),
                            dataSetRef.getExperimentIdentifier().getExperimentCode(),
                            dataSetRef.getDatasetCode(), };
        System.arraycopy(annotations, 0, result[1][wellIndex][dataSetIndex], 0, annotations.length);
    }
    
    private static List<String> getFeatureCodes(List<? extends IFeatureCodesProvider> dataSets)
    {
        Set<String> codes = new HashSet<String>();
        for (IFeatureCodesProvider featureVectorDataset : dataSets)
        {
            codes.addAll(featureVectorDataset.getFeatureCodes());
        }
        List<String> result = new ArrayList<String>(codes);
        Collections.sort(result);
        return result;
    }

    /**
     * Returns the gene mapping for the given <var>plateCodes</var> in <code>[0]</code> and location
     * annotations in <code>[1]</code>.
     * <p>
     * One row in the matrix corresponds to one well.
     * <p>
     * Matlab example:
     * 
     * <pre>
     * % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE for PLATECODE
     * genes = getGeneMappingForPlate('PLATECODE');
     * % Get the plate well location description of the 10th wells
     * loc2 = genes(2,10,1)
     * % Get the gene ids that are in the 10th well
     * geneIds = genes(1,10,:)
     * </pre>
     * 
     * @param platesCodes The augmented codes of the plates to get the mapping for
     * @return <code>{ gene ids, annotations per well }</code> where <code>gene ids</code> can be 0,
     *         1 or more gene ids. <code>annotations per location</code> contain:
     *         <p>
     *         <code>{ plate well description, plate augmented code, plate perm id,
     *         plate space code, plate code, row, column }</code>
     */
    public static Object[][][] getGeneMappingForPlates(String[] platesCodes)
    {
        checkLoggedIn();
        final List<PlateWellMaterialMapping> mappingList =
                openbis.listPlateMaterialMapping(toPlates(platesCodes), MaterialTypeIdentifier.GENE);
        int size = 0;
        for (PlateWellMaterialMapping mapping : mappingList)
        {
            size +=
                    mapping.getPlateGeometry().getNumberOfRows()
                            * mapping.getPlateGeometry().getNumberOfColumns();
        }
        final Object[][][] result = new Object[2][size][];
        int resultIdx = 0;
        for (PlateWellMaterialMapping mapping : mappingList)
        {
            for (int row = 1; row <= mapping.getPlateGeometry().getNumberOfRows(); ++row)
            {
                for (int col = 1; col <= mapping.getPlateGeometry().getNumberOfColumns(); ++col)
                {
                    final List<MaterialIdentifier> genes = mapping.getMaterialsForWell(row, col);
                    result[0][resultIdx] = new Object[genes.size()];
                    for (int i = 0; i < genes.size(); ++i)
                    {
                        result[0][resultIdx][i] = genes.get(i).getMaterialCode();
                    }
                    final PlateIdentifier plate = mapping.getPlateIdentifier();
                    result[1][resultIdx] =
                            new Object[]
                                { createPlateWellDescription(plate, row, col),
                                        plate.getAugmentedCode(), plate.getPermId(),
                                        plate.tryGetSpaceCode(), plate.getPlateCode(), row, col, };
                    ++resultIdx;
                }
            }
        }
        return result;
    }

    //
    // Helper methods
    //

    private static List<PlateIdentifier> toPlates(String[] augmentedPlateCodes)
    {
        final List<PlateIdentifier> result =
                new ArrayList<PlateIdentifier>(augmentedPlateCodes.length);
        for (String plateCode : augmentedPlateCodes)
        {
            result.add(PlateIdentifier.createFromAugmentedCode(plateCode));
        }
        return result;
    }

    private static Plate getPlate(String augmentedPlateCode)
    {
        Plate plateIdentifier = plateCodeToPlateMap.get(augmentedPlateCode);
        if (plateIdentifier == null)
        {
            throw new RuntimeException("No plate with that code '" + augmentedPlateCode
                    + "' found.");
        }
        return plateIdentifier;
    }

    private static String createPlateWellDescription(PlateIdentifier p, FeatureVector f)
    {
        return createPlateWellDescription(p, f.getWellPosition().getWellRow(), f.getWellPosition()
                .getWellColumn());
    }

    private static String createPlateWellDescription(PlateIdentifier p, int row, int col)
    {
        return p.getPlateCode() + ":" + translateRowNumberIntoLetterCode(row) + col;
    }

    /**
     * Translates a row number into letter code. Thus, 1 -> A, 2 -> B, 26 -> Z, 27 -> AA, 28 -> AB,
     * etc.
     */
    private static String translateRowNumberIntoLetterCode(int rowNumber)
    {
        int rowIndex = rowNumber - 1;
        String code = "";
        while (rowIndex >= 0)
        {
            code = (char) (rowIndex % 26 + 'A') + code;
            rowIndex = rowIndex / 26 - 1;
        }
        return code;
    }

    private static void checkLoggedIn()
    {
        if (openbis == null)
        {
            if (Login.OPENBIS_TOKEN_FILE.exists())
            {
                BufferedReader br = null;
                try
                {
                    br = new BufferedReader(new FileReader(Login.OPENBIS_TOKEN_FILE));
                    final String token = br.readLine();
                    br.close();
                    br = new BufferedReader(new FileReader(Login.OPENBIS_SERVER_URL_FILE));
                    final String serverUrl = br.readLine();
                    br.close();
                    br = null;
                    IScreeningOpenbisServiceFacade facade =
                            facadeFactory.tryToCreate(token, serverUrl);
                    if (facade == null)
                    {
                        throw new RuntimeException("Login failed.");
                    }
                    init(facade);
                } catch (IOException ex)
                {
                    if (openbis == null)
                    {
                        throw new RuntimeException("Login failed.", ex);
                    }
                } finally
                {
                    if (br != null)
                    {
                        try
                        {
                            br.close();
                        } catch (IOException ex)
                        {
                            // Silence this.
                        }
                    }
                }
            }
            if (openbis == null)
            {
                throw new RuntimeException("Not logged in.");
            }
        }
    }
}