    001/*-
    002 *******************************************************************************
    003 * Copyright (c) 2011, 2016 Diamond Light Source Ltd.
    004 * All rights reserved. This program and the accompanying materials
    005 * are made available under the terms of the Eclipse Public License v1.0
    006 * which accompanies this distribution, and is available at
    007 * http://www.eclipse.org/legal/epl-v10.html
    008 *
    009 * Contributors:
    010 *    Peter Chang - initial API and implementation and/or initial documentation
    011 *******************************************************************************/
    012
    013package org.eclipse.january.dataset;
    014
    015import java.io.Serializable;
    016import java.lang.reflect.Array;
    017import java.text.Format;
    018import java.util.Arrays;
    019import java.util.List;
    020
    021import org.eclipse.january.DatasetException;
    022import org.eclipse.january.IMonitor;
    023import org.eclipse.january.MetadataException;
    024import org.eclipse.january.metadata.ErrorMetadata;
    025import org.eclipse.january.metadata.MetadataFactory;
    026import org.eclipse.january.metadata.StatisticsMetadata;
    027import org.eclipse.january.metadata.internal.ErrorMetadataImpl;
    028import org.eclipse.january.metadata.internal.StatisticsMetadataImpl;
    029import org.slf4j.Logger;
    030import org.slf4j.LoggerFactory;
    031
    032/**
    033 * Generic container class for data
    034 * <p>
    035 * Each subclass has an array of primitive types, elements of this array are grouped or
    036 * compounded to make items
    037 * <p>
    038 * Data items can be boolean, integer, float, complex float, vector float, etc
    039 */
    040public abstract class AbstractDataset extends LazyDatasetBase implements Dataset {
    041        // pin UID to base class
    042        private static final long serialVersionUID = Dataset.serialVersionUID;
    043
    044        private static final Logger logger = LoggerFactory.getLogger(AbstractDataset.class);
    045
    046        protected int size; // number of items
    047
    048        transient protected AbstractDataset base; // is null when not a view
    049        protected int[] stride; // can be null for row-major, contiguous datasets
    050        protected int offset;
    051
    052        /**
    053         * The data itself, held in a 1D array, but the object will wrap it to appear as possessing as many dimensions as
    054         * wanted
    055         */
    056        protected Serializable odata = null;
    057
    058        /**
    059         * Set aliased data as base data
    060         */
    061        abstract protected void setData();
    062
    063        /**
    064         * Constructor required for serialisation.
    065         */
    066        public AbstractDataset() {
    067        }
    068
    069        @Override
    070        public synchronized Dataset synchronizedCopy() {
    071                return clone();
    072        }
    073
    074        @Override
    075        public Class<?> getElementClass() {
    076                return InterfaceUtils.getElementClass(getClass());
    077        }
    078
    079        @Override
    080        public int getDType() {
    081                return DTypeUtils.getDType(getClass());
    082        }
    083
    084        @Override
    085        public int hashCode() {
    086                return getStats().getHash(shape);
    087        }
    088
    089        @Override
    090        abstract public AbstractDataset clone();
    091
    092        protected Format stringFormat = null;
    093
    094        @Override
    095        public void setStringFormat(Format format) {
    096                stringFormat = format;
    097        }
    098
    099        @Override
    100        public Dataset copy(final int dtype) {
    101                return copy(DTypeUtils.getInterface(dtype));
    102        }
    103
    104        @Override
    105        public <T extends Dataset> T copy(Class<T> clazz) {
    106                return DatasetUtils.copy(clazz, this);
    107        }
    108
    109        @Override
    110        public Dataset cast(final int dtype) {
    111                return cast(DTypeUtils.getInterface(dtype));
    112        }
    113
    114        @SuppressWarnings("unchecked")
    115        @Override
    116        public <T extends Dataset> T cast(Class<T> clazz) {
    117                if (clazz.isInstance(this)) {
    118                        return (T) this;
    119                }
    120                return DatasetUtils.cast(clazz, this);
    121        }
    122
    123        @SuppressWarnings("unchecked")
    124        @Override
    125        public <T extends Dataset> T cast(final int isize, Class<T> clazz, final boolean repeat) {
    126                if (clazz.isInstance(this) && getElementsPerItem() == isize) {
    127                        return (T) this;
    128                }
    129                return DatasetUtils.cast(isize, clazz, this, repeat);
    130        }
    131
    132        @Override
    133        public Dataset cast(final boolean repeat, final int dtype, final int isize) {
    134                return cast(isize, DTypeUtils.getInterface(dtype), repeat);
    135        }
    136
    137        @Override
    138        abstract public AbstractDataset getView(boolean deepCopyMetadata);
    139
    140        /**
    141         * Copy fields from original to view
    142         * @param orig original
    143         * @param view destination
    144         * @param clone if true, then clone everything but bulk data
    145         * @param cloneMetadata if true, clone metadata
    146         */
    147        protected static void copyToView(Dataset orig, AbstractDataset view, boolean clone, boolean cloneMetadata) {
    148                view.name = orig.getName();
    149                view.size = orig.getSize();
    150                view.odata = orig.getBuffer();
    151                view.offset = orig.getOffset();
    152                AbstractDataset a = orig instanceof AbstractDataset ? (AbstractDataset) orig : null;
    153                view.base = a == null ? null : a.base;
    154
    155                int[] s = a == null ? null : a.stride;
    156                if (clone) {
    157                        view.shape = orig.getShapeRef() == null ? null : orig.getShape();
    158                        view.stride = s == null ? null : s.clone();
    159                } else {
    160                        view.shape = orig.getShapeRef();
    161                        view.stride = s;
    162                }
    163
    164                view.metadata = getMetadataMap(orig, cloneMetadata);
    165                Class<? extends Dataset> oc = InterfaceUtils.findSubInterface(orig.getClass());
    166                Class<? extends Dataset> vc = InterfaceUtils.findSubInterface(view.getClass());
    167                if (!oc.equals(vc)) {
    168                        view.setDirty();
    169                }
    170        }
    171
    172        @Override
    173        public IntegerDataset getIndices() {
    174                final IntegerDataset ret = DatasetUtils.indices(shape);
    175                if (getName() != null) {
    176                        ret.setName("Indices of " + getName());
    177                }
    178                return ret;
    179        }
    180
    181        @Override
    182        public Dataset getTransposedView(int... axes) {
    183                axes = checkPermutatedAxes(shape, axes);
    184
    185                AbstractDataset t = getView(true);
    186                if (axes == null || getRank() == 1)
    187                        return t;
    188
    189                int rank = shape.length;
    190                int[] tstride = new int[rank];
    191                int[] toffset = new int[1];
    192                int[] nshape = createStrides(new SliceND(shape), this, tstride, toffset);
    193                int[] nstride = new int[rank];
    194                for (int i = 0; i < rank; i++) {
    195                        final int ax = axes[i];
    196                        nstride[i] = tstride[ax];
    197                        nshape[i] = shape[ax];
    198                }
    199                t.shape = nshape;
    200                t.stride = nstride;
    201                t.offset = toffset[0];
    202                t.base = this;
    203                t.setDirty();
    204                t.transposeMetadata(axes);
    205                return t;
    206        }
    207
    208        @Override
    209        public Dataset transpose(int... axes) {
    210                Dataset t = getTransposedView(axes);
    211                return t == null ? clone() : t.clone();
    212        }
    213
    214        @Override
    215        public Dataset swapAxes(int axis1, int axis2) {
    216                int rank = shape.length;
    217                axis1 = ShapeUtils.checkAxis(rank, axis1);
    218                axis2 = ShapeUtils.checkAxis(rank, axis2);
    219
    220                if (rank == 1 || axis1 == axis2) {
    221                        return this;
    222                }
    223
    224                int[] axes = new int[rank];
    225                for (int i = 0; i < rank; i++) {
    226                        axes[i] = i;
    227                }
    228
    229                axes[axis1] = axis2;
    230                axes[axis2] = axis1;
    231                return getTransposedView(axes);
    232        }
    233
    234        boolean isContiguous() {
    235                if (stride == null)
    236                        return true;
    237
    238                if (offset != 0)
    239                        return false;
    240
    241                int s = getElementsPerItem();
    242                for (int j = getRank() - 1; j >= 0; j--) {
    243                        if (stride[j] != s) {
    244                                return false;
    245                        }
    246                        s *= shape[j];
    247                }
    248
    249                return true;
    250        }
    251
    252        @Override
    253        public Dataset flatten() {
    254                if (!isContiguous()) { // need to make a copy if not contiguous
    255                        return clone().flatten();
    256                }
    257                return reshape(size);
    258        }
    259
    260        /**
    261         * Fill dataset from object at depth dimension
    262         * @param obj fill value
    263         * @param depth dimension
    264         * @param pos position
    265         */
    266        protected void fillData(Object obj, final int depth, final int[] pos) {
    267                if (obj == null) {
    268                        Class<?> c = InterfaceUtils.getElementClass(getClass());
    269                        if (Float.class.equals(c)) {
    270                                set(Float.NaN, pos);
    271                        } else if (Float.class.equals(c)) {
    272                                set(Double.NaN, pos);
    273                        }
    274                        return;
    275                }
    276
    277                Class<?> clazz = obj.getClass();
    278                if (obj instanceof List<?>) {
    279                        List<?> jl = (List<?>) obj;
    280                        int l = jl.size();
    281                        for (int i = 0; i < l; i++) {
    282                                Object lo = jl.get(i);
    283                                fillData(lo, depth + 1, pos);
    284                                pos[depth]++;
    285                        }
    286                        pos[depth] = 0;
    287                } else if (clazz.isArray()) {
    288                        int l = Array.getLength(obj);
    289                        if (clazz.equals(odata.getClass())) {
    290                                System.arraycopy(obj, 0, odata, get1DIndex(pos), l);
    291                        } else if (clazz.getComponentType().isPrimitive()) {
    292                                for (int i = 0; i < l; i++) {
    293                                        set(Array.get(obj, i), pos);
    294                                        pos[depth]++;
    295                                }
    296                                pos[depth] = 0;
    297                        } else {
    298                                for (int i = 0; i < l; i++) {
    299                                        fillData(Array.get(obj, i), depth + 1, pos);
    300                                        pos[depth]++;
    301                                }
    302                                pos[depth] = 0;
    303                        }
    304                } else if (obj instanceof IDataset) {
    305                        boolean[] a = new boolean[shape.length];
    306                        Arrays.fill(a, depth, a.length, true);
    307                        setSlice(obj, getSliceIteratorFromAxes(pos, a));
    308                } else {
    309                        set(obj, pos);
    310                }
    311        }
    312
    313        @Override
    314        public IndexIterator getIterator(final boolean withPosition) {
    315                if (stride != null) {
    316                        return base.getSize() == 1  ? (withPosition ? new PositionIterator(offset, shape) :
    317                                new SingleItemIterator(offset, size)) : new StrideIterator(shape, stride, offset);
    318                }
    319                if (shape == null) {
    320                        return new NullIterator();
    321                }
    322
    323                return withPosition ? new ContiguousIteratorWithPosition(shape, size) : new ContiguousIterator(size);
    324        }
    325
    326        @Override
    327        public IndexIterator getIterator() {
    328                return getIterator(false);
    329        }
    330
    331        @Override
    332        public PositionIterator getPositionIterator(final int... axes) {
    333                return new PositionIterator(shape, axes);
    334        }
    335
    336        @Override
    337        public IndexIterator getSliceIterator(final int[] start, final int[] stop, final int[] step) {
    338                return internalGetSliceIterator(new SliceND(shape, start, stop, step));
    339        }
    340
    341        /**
    342         * @param slice an n-D slice
    343         * @return an slice iterator that operates like an IndexIterator
    344         */
    345        public IndexIterator getSliceIterator(SliceND slice) {
    346                checkSliceND(slice);
    347                return internalGetSliceIterator(slice);
    348        }
    349
    350        /**
    351         * @param slice an n-D slice
    352         * @return an slice iterator that operates like an IndexIterator
    353         */
    354        protected IndexIterator internalGetSliceIterator(SliceND slice) {
    355                if (ShapeUtils.calcLongSize(slice.getShape()) == 0) {
    356                        return new NullIterator(shape, slice.getShape());
    357                }
    358                if (stride != null) {
    359                        return new StrideIterator(getElementsPerItem(), shape, stride, offset, slice);
    360                }
    361                return new SliceIterator(shape, size, slice);
    362        }
    363
    364        @Override
    365        public SliceIterator getSliceIteratorFromAxes(final int[] pos, boolean[] axes) {
    366                int rank = shape.length;
    367                int[] start;
    368                int[] stop = new int[rank];
    369                int[] step = new int[rank];
    370
    371                if (pos == null) {
    372                        start = new int[rank];
    373                } else if (pos.length == rank) {
    374                        start = pos.clone();
    375                } else {
    376                        throw new IllegalArgumentException("pos array length is not equal to rank of dataset");
    377                }
    378                if (axes == null) {
    379                        axes = new boolean[rank];
    380                        Arrays.fill(axes, true);
    381                } else if (axes.length != rank) {
    382                        throw new IllegalArgumentException("axes array length is not equal to rank of dataset");
    383                }
    384
    385                for (int i = 0; i < rank; i++) {
    386                        if (axes[i]) {
    387                                stop[i] = shape[i];
    388                        } else {
    389                                stop[i] = start[i] + 1;
    390                        }
    391                        step[i] = 1;
    392                }
    393                return (SliceIterator) getSliceIterator(start, stop, step);
    394        }
    395
    396        @Override
    397        public BooleanIterator getBooleanIterator(Dataset choice) {
    398                return getBooleanIterator(choice, true);
    399        }
    400
    401        @Override
    402        public BooleanIterator getBooleanIterator(Dataset choice, boolean value) {
    403                return BooleanIterator.createIterator(value, this, choice, this);
    404        }
    405
    406        @Override
    407        public Dataset getByBoolean(Dataset selection) {
    408                checkCompatibility(selection);
    409
    410                final int length = ((Number) selection.sum()).intValue();
    411                final int is = getElementsPerItem();
    412                Dataset r = DatasetFactory.zeros(is, getClass(), length);
    413                BooleanIterator biter = getBooleanIterator(selection);
    414
    415                int i = 0;
    416                while (biter.hasNext()) {
    417                        r.setObjectAbs(i, getObjectAbs(biter.index));
    418                        i += is;
    419                }
    420                return r;
    421        }
    422
    423        @Override
    424        public Dataset getBy1DIndex(IntegerDataset index) {
    425                final int is = getElementsPerItem();
    426                final Dataset r = DatasetFactory.zeros(is, getClass(), index.getShapeRef());
    427                final IntegerIterator iter = new IntegerIterator(index, size, is);
    428
    429                int i = 0;
    430                while (iter.hasNext()) {
    431                        r.setObjectAbs(i, getObjectAbs(iter.index));
    432                        i += is;
    433                }
    434                return r;
    435        }
    436
    437        @Override
    438        public Dataset getByIndexes(final Object... indexes) {
    439                final IntegersIterator iter = new IntegersIterator(shape, indexes);
    440                final int is = getElementsPerItem();
    441                final Dataset r = DatasetFactory.zeros(is, getClass(), iter.getShape());
    442
    443                final int[] pos = iter.getPos();
    444                int i = 0;
    445                while (iter.hasNext()) {
    446                        r.setObjectAbs(i, getObject(pos));
    447                        i += is;
    448                }
    449                return r;
    450        }
    451
    452        @Override
    453        public boolean hasFloatingPointElements() {
    454                Class<?> cls = getElementClass();
    455                return cls == Float.class || cls == Double.class;
    456        }
    457
    458        @Override
    459        public int getElementsPerItem() {
    460                return InterfaceUtils.getElementsPerItem(getClass());
    461        }
    462
    463        @Override
    464        public int getItemBytes() {
    465                return InterfaceUtils.getItemBytes(getElementsPerItem(), getClass());
    466        }
    467
    468        @Override
    469        public int getSize() {
    470                return size;
    471        }
    472
    473        @Override
    474        public int[] getShape() {
    475                // make a copy of the dimensions data, and put that out
    476                if (shape == null) {
    477                        logger.warn("Shape is null!!!");
    478                        return new int[] {};
    479                }
    480                return shape.clone();
    481        }
    482
    483        @Override
    484        public int getRank() {
    485                return shape == null ? 0 : shape.length;
    486        }
    487
    488        @Override
    489        public int getNbytes() {
    490                return getSize() * getItemBytes();
    491        }
    492
    493        /**
    494         * Check for -1 placeholder in shape and replace if necessary
    495         * @param shape to use
    496         * @param size expected size
    497         */
    498        private void checkShape(int[] shape, int size) {
    499                if (shape == null) {
    500                        if (size == 0) {
    501                                return;
    502                        }
    503                        logger.error("New shape must not be null for nonzero-sized dataset");
    504                        throw new IllegalArgumentException("New shape must not be null for nonzero-sized dataset");
    505                }
    506                int rank = shape.length;
    507                int found = -1;
    508                int nsize = 1;
    509                for (int i = 0; i < rank; i++) {
    510                        int d = shape[i];
    511                        if (d == -1) {
    512                                if (found == -1) {
    513                                        found = i;
    514                                } else {
    515                                        logger.error("Can only have one -1 placeholder in shape");
    516                                        throw new IllegalArgumentException("Can only have one -1 placeholder in shape");
    517                                }
    518                        } else {
    519                                nsize *= d;
    520                        }
    521                }
    522                if (found >= 0) {
    523                        shape[found] = size/nsize;
    524                } else if (nsize != size && !(rank == 0 && size == 0)) {
    525                        logger.error("New shape is not same size as old shape");
    526                        throw new IllegalArgumentException("New size is not same as the old size. Old size is "+size+" new size is "+nsize+" and shape is "+Arrays.toString(shape));
    527                }
    528        }
    529
    530        @Override
    531        public void setShape(final int... shape) {
    532                int[] nshape = shape == null ? null : shape.clone();
    533                checkShape(nshape, size);
    534                if (Arrays.equals(this.shape, nshape)) {
    535                        return;
    536                }
    537
    538                if (stride != null) {
    539                        // the only compatible shapes are ones where new dimensions are factors of old dimensions
    540                        // or are combined adjacent old dimensions
    541                        int[] oshape = this.shape;
    542                        int orank = oshape.length;
    543                        int nrank = nshape.length;
    544                        int diff = nrank - orank;
    545                        int[] nstride = new int[nrank];
    546                        boolean ones = true;
    547                        // work forwards for broadcasting cases
    548                        for (int i = 0, j = 0; i < orank || j < nrank;) {
    549                                if (j >= diff && i < orank && j < nrank && oshape[i] == nshape[j]) {
    550                                        nstride[j++] = stride[i++];
    551                                } else if (j < nrank && nshape[j] == 1) {
    552                                        nstride[j++] = 0;
    553                                } else if (i < orank && oshape[i] == 1) {
    554                                        i++;
    555                                } else {
    556                                        if (j < nrank)
    557                                                j++;
    558                                        if (i < orank)
    559                                                i++;
    560                                        ones = false;
    561                                }
    562                        }
    563                        if (!ones) { // not just ones differ in shapes
    564                                int[] ostride = stride;
    565                                int ob = 0;
    566                                int oe = 1;
    567                                int nb = 0;
    568                                int ne = 1;
    569                                while (ob < orank && nb < nrank) {
    570                                        int ol = oshape[ob];
    571                                        int nl = nshape[nb];
    572
    573                                        if (nl < ol) { // find group of shape dimensions that form common size
    574                                                do { // case where new shape spreads single dimension over several dimensions
    575                                                        if (ne == nrank) {
    576                                                                break;
    577                                                        }
    578                                                        nl *= nshape[ne++];
    579                                                } while (nl < ol);
    580                                                if (nl != ol) {
    581                                                        logger.error("Subshape is incompatible with single dimension");
    582                                                        throw new IllegalArgumentException("Subshape is incompatible with single dimension");
    583                                                }
    584                                                int on = ne - 1;
    585                                                while (nshape[on] == 1) {
    586                                                        on--;
    587                                                }
    588
    589                                                nstride[on] = ostride[ob];
    590                                                for (int n = on - 1; n >= nb; n--) {
    591                                                        if (nshape[n] == 1)
    592                                                                continue;
    593
    594                                                        nstride[n] = nshape[on] * nstride[on];
    595                                                        on = n;
    596                                                }
    597                                        } else if (ol < nl) {
    598                                                do { // case where new shape combines several dimensions into one dimension
    599                                                        if (oe == orank) {
    600                                                                break;
    601                                                        }
    602                                                        ol *= oshape[oe++];
    603                                                } while (ol < nl);
    604                                                if (nl != ol) {
    605                                                        logger.error("Single dimension is incompatible with subshape");
    606                                                        throw new IllegalArgumentException("Single dimension is incompatible with subshape");
    607                                                }
    608
    609                                                int oo = oe - 1;
    610                                                while (oshape[oo] == 1) {
    611                                                        oo--;
    612                                                }
    613                                                int os = ostride[oo];
    614                                                for (int o = oo - 1; o >= ob; o--) {
    615                                                        if (oshape[o] == 1)
    616                                                                continue;
    617                                                        if (ostride[o] != oshape[oo] * ostride[oo]) {
    618                                                                logger.error("Subshape cannot be a non-contiguous view");
    619                                                                throw new IllegalArgumentException("Subshape cannot be a non-contiguous view");
    620                                                        }
    621                                                        oo = o;
    622                                                }
    623                                                nstride[nb] = os;
    624                                        } else {
    625                                                nstride[nb] = ostride[ob];
    626                                        }
    627
    628                                        ob = oe++;
    629                                        nb = ne++;
    630                                }
    631                        }
    632
    633                        stride = nstride;
    634                }
    635
    636                setDirty();
    637                if (this.shape != null && metadata != null) {
    638                        reshapeMetadata(this.shape, nshape);
    639                }
    640                this.shape = nshape;
    641        }
    642
    643        @Override
    644        public int[] getShapeRef() {
    645                return shape;
    646        }
    647
    648        @Override
    649        public int getOffset() {
    650                return offset;
    651        }
    652
    653        @Override
    654        public int[] getStrides() {
    655                return stride;
    656        }
    657
    658        @Override
    659        public Serializable getBuffer() {
    660                return odata;
    661        }
    662
    663        @Override
    664        public void overrideInternal(Serializable buffer, int... shape) {
    665                if (buffer != null) {
    666                        odata = buffer;
    667                        setData();
    668                        setDirty();
    669                }
    670
    671                if (shape != null) {
    672                        this.shape = shape.clone();
    673                        size = ShapeUtils.calcSize(this.shape);
    674                }
    675        }
    676
    677        /**
    678         * Create a stride array from dataset
    679         * @param a dataset
    680         * @param offset output offset
    681         * @return new strides
    682         */
    683        public static int[] createStrides(Dataset a, final int[] offset) {
    684                return createStrides(a.getElementsPerItem(), a.getShapeRef(), a.getStrides(), a.getOffset(), offset);
    685        }
    686
    687        /**
    688         * Create a stride array from dataset
    689         * @param isize item size
    690         * @param shape to use
    691         * @param oStride original stride
    692         * @param oOffset original offset (only used if there is an original stride)
    693         * @param offset output offset
    694         * @return new strides
    695         */
    696        public static int[] createStrides(final int isize, final int[] shape, final int[] oStride, final int oOffset, final int[] offset) {
    697                int rank = shape.length;
    698                final int[] stride;
    699                if (oStride == null) {
    700                        offset[0] = 0;
    701                        stride = new int[rank];
    702                        int s = isize;
    703                        for (int j = rank - 1; j >= 0; j--) {
    704                                stride[j] = s;
    705                                s *= shape[j];
    706                        }
    707                } else {
    708                        offset[0] = oOffset;
    709                        stride = oStride.clone();
    710                }
    711                return stride;
    712        }
    713
    714        /**
    715         * Create a stride array from slice information and a dataset
    716         * @param slice an n-D slice
    717         * @param a dataset
    718         * @param stride output stride
    719         * @param offset output offset
    720         * @return new shape
    721         */
    722        public static int[] createStrides(final SliceND slice, final Dataset a, final int[] stride, final int[] offset) {
    723                return createStrides(slice, a.getElementsPerItem(), a.getShapeRef(), a.getStrides(), a.getOffset(), stride, offset);
    724        }
    725
    726        /**
    727         * Create a stride array from slice and dataset information
    728         * @param slice an n-D slice
    729         * @param isize item size
    730         * @param shape to use
    731         * @param oStride original stride
    732         * @param oOffset original offset (only used if there is an original stride)
    733         * @param stride output stride
    734         * @param offset output offset
    735         * @return new shape
    736         */
    737        public static int[] createStrides(final SliceND slice, final int isize, final int[] shape, final int[] oStride, final int oOffset, final int[] stride, final int[] offset) {
    738                int[] lstart = slice.getStart();
    739                int[] lstep = slice.getStep();
    740                int[] newShape = slice.getShape();
    741                int rank = shape.length;
    742
    743                if (oStride == null) {
    744                        int s = isize;
    745                        offset[0] = 0;
    746                        for (int j = rank - 1; j >= 0; j--) {
    747                                stride[j] = s * lstep[j];
    748                                offset[0] += s * lstart[j];
    749                                s *= shape[j];
    750                        }
    751                } else {
    752                        offset[0] = oOffset;
    753                        for (int j = 0; j < rank; j++) {
    754                                int s = oStride[j];
    755                                stride[j] = lstep[j] * s;
    756                                offset[0] += lstart[j] * s;
    757                        }
    758                }
    759
    760                return newShape;
    761        }
    762
    763        @Override
    764        public Dataset getBroadcastView(int... broadcastShape) {
    765                AbstractDataset view = getView(true);
    766
    767                if (!Arrays.equals(shape, broadcastShape)) {
    768                        List<int[]> nShapes = BroadcastUtils.broadcastShapesToMax(broadcastShape, shape);
    769                        view.setShape(nShapes.get(0));
    770                        view.stride = BroadcastUtils.createBroadcastStrides(view, broadcastShape);
    771                        view.base = this;
    772                        view.shape = broadcastShape.clone();
    773                        view.size = ShapeUtils.calcSize(broadcastShape);
    774                        if (view.name == null || view.name.isEmpty()) {
    775                                view.name = "Broadcast from " + Arrays.toString(shape);
    776                        } else {
    777                                view.name = "Broadcast of " + view.name + " from " + Arrays.toString(shape);
    778                        }
    779                }
    780                return view;
    781        }
    782
    783        @Override
    784        public Dataset getSliceView(final int[] start, final int[] stop, final int[] step) {
    785                return internalGetSliceView(new SliceND(shape, start, stop, step));
    786        }
    787
    788        @Override
    789        public Dataset getSliceView(Slice... slice) {
    790                if (slice == null || slice.length == 0) {
    791                        return getView(true);
    792                }
    793
    794                return internalGetSliceView(new SliceND(shape, slice));
    795        }
    796
    797        /**
    798         * Get a slice of the dataset. The returned dataset is a view on a selection of items
    799         * @param slice an n-D slice
    800         * @return slice view
    801         */
    802        @Override
    803        public Dataset getSliceView(SliceND slice) {
    804                checkSliceND(slice);
    805                return internalGetSliceView(slice);
    806        }
    807
    808        private Dataset internalGetSliceView(SliceND slice) {
    809                if (slice.isAll()) {
    810                        return getView(true);
    811                }
    812
    813                final int rank = shape.length;
    814                int[] sStride = new int[rank];
    815                int[] sOffset = new int[1];
    816
    817                int[] sShape = createStrides(slice, this, sStride, sOffset);
    818
    819                AbstractDataset s = getView(false);
    820                s.shape = sShape;
    821                s.size = ShapeUtils.calcSize(sShape);
    822                s.stride = sStride;
    823                s.offset = sOffset[0];
    824                s.base = this;
    825
    826                s.metadata = copyMetadata();
    827                s.sliceMetadata(true, slice);
    828
    829                s.setDirty();
    830                s.setName(name + BLOCK_OPEN + slice + BLOCK_CLOSE);
    831
    832                return s;
    833        }
    834
    835        /**
    836         * Get flattened view index of given position
    837         * @param pos
    838         *            the integer array specifying the n-D position
    839         * @return the index on the flattened dataset
    840         */
    841        private int getFlat1DIndex(final int[] pos) {
    842                final int imax = pos.length;
    843                if (imax == 0) {
    844                        return 0;
    845                }
    846
    847                return get1DIndexFromShape(pos);
    848        }
    849
    850        /**
    851         * @return index of first element
    852         * @since 2.0
    853         */
    854        protected int getFirst1DIndex() {
    855                if (shape == null) {
    856                        throw new IllegalArgumentException("Cannot find an index from a null shape");
    857                }
    858                return stride == null ? 0 : offset;
    859        }
    860
    861        @Override
    862        public int get1DIndex(final int... n) {
    863                if (n.length == 0 && shape.length == 0)
    864                        return offset;
    865
    866                return stride == null ? get1DIndexFromShape(n) : get1DIndexFromStrides(n);
    867        }
    868
    869        private static void throwAIOOBException(int i, int s, int d) {
    870                throw new ArrayIndexOutOfBoundsException("Index (" + i + ") out of range [-" + s + "," + s
    871                                + "] in dimension " + d);
    872        }
    873
    874        /**
    875         * @param i position in first dimension
    876         * @return the index on the data array corresponding to that location
    877         */
    878        protected int get1DIndex(int i) {
    879                if (shape == null) {
    880                        throw new IllegalArgumentException("Cannot find an index from a null shape");
    881                }
    882                if (shape.length > 1) {
    883                        logger.error("This dataset is not 1D but was addressed as such");
    884                        throw new UnsupportedOperationException("This dataset is not 1D but was addressed as such");
    885                }
    886                if (i < 0) {
    887                        i += shape[0];
    888                }
    889                if (i < 0 || i >= shape[0]) {
    890                        throwAIOOBException(i, shape[0], 0);
    891                }
    892                return stride == null ? i : i*stride[0] + offset;
    893        }
    894
    895        /**
    896         * @param i position in first dimension
    897         * @param j position in second dimension
    898         * @return the index on the data array corresponding to that location
    899         */
    900        protected int get1DIndex(int i, int j) {
    901                if (shape == null) {
    902                        throw new IllegalArgumentException("Cannot find an index from a null shape");
    903                }
    904                if (shape.length != 2) {
    905                        logger.error("This dataset is not 2D but was addressed as such");
    906                        throw new UnsupportedOperationException("This dataset is not 2D but was addressed as such");
    907                }
    908                if (i < 0) {
    909                        i += shape[0];
    910                }
    911                if (i < 0 || i >= shape[0]) {
    912                        throwAIOOBException(i, shape[0], 0);
    913                }
    914                if (j < 0) {
    915                        j += shape[1];
    916                }
    917                if (j < 0 || j >= shape[1]) {
    918                        throwAIOOBException(i, shape[1], 1);
    919                }
    920                return stride == null ? i*shape[1] + j : i*stride[0] + j*stride[1] + offset;
    921        }
    922
    923        protected int get1DIndexFromShape(final int[] n) {
    924                return get1DIndexFromShape(shape, n);
    925        }
    926
    927        protected static int get1DIndexFromShape(final int[] shape, final int[] n) {
    928                if (shape == null) {
    929                        throw new IllegalArgumentException("Cannot find an index from a null shape");
    930                }
    931                final int rank = shape.length;
    932                if (rank != n.length) {
    933                        String errMsg = String.format("Number of position values must be equal to rank of %d", rank);
    934                        logger.error(errMsg);
    935                        throw new IllegalArgumentException(errMsg);
    936                }
    937                int index = 0;
    938                for (int i = 0; i < rank; i++) {
    939                        final int si = shape[i];
    940                        int ni = n[i];
    941                        if (ni < 0) {
    942                                ni += si;
    943                        }
    944                        if (ni < 0 || ni >= si) {
    945                                throwAIOOBException(ni, si, i);
    946                        }
    947                        index = index * si + ni;
    948                }
    949
    950                return index;
    951        }
    952
    953        private int get1DIndexFromStrides(final int[] n) {
    954                return get1DIndexFromStrides(shape, stride, offset, n);
    955        }
    956
    957        private static int get1DIndexFromStrides(final int[] shape, final int[] stride, final int offset, final int[] n) {
    958                if (shape == null) {
    959                        throw new IllegalArgumentException("Cannot find an index from a null shape");
    960                }
    961                final int rank = shape.length;
    962                if (rank != n.length) {
    963                        String errMsg = String.format("Number of position values must be equal to rank of %d", rank);
    964                        logger.error(errMsg);
    965                        throw new IllegalArgumentException(errMsg);
    966                }
    967                int index = offset;
    968                for (int i = 0; i < rank; i++) {
    969                        final int st = stride[i];
    970                        if (st != 0) { // not broadcasted
    971                                final int si = shape[i];
    972                                int ni = n[i];
    973                                if (ni < 0) {
    974                                        ni += si;
    975                                }
    976                                if (ni < 0 || ni >= si) {
    977                                        throwAIOOBException(ni, si, i);
    978                                }
    979                                index += st * ni;
    980                        }
    981                }
    982                return index;
    983        }
    984
    985        @Override
    986        public int[] getNDPosition(final int n) {
    987                if (isIndexInRange(n)) {
    988                        throw new IllegalArgumentException("Index provided " + n
    989                                        + "is larger then the size of the containing array");
    990                }
    991
    992                return stride == null ? ShapeUtils.getNDPositionFromShape(n, shape) : getNDPositionFromStrides(n);
    993        }
    994
    995        private boolean isIndexInRange(final int n) {
    996                if (stride == null) {
    997                        return n >= size;
    998                }
    999                return n >= getBufferLength();
    1000        }
    1001
    1002        /**
    1003         * @return entire buffer length
    1004         */
    1005        abstract protected int getBufferLength();
    1006
    1007        private int[] getNDPositionFromStrides(int n) {
    1008                n -= offset;
    1009                int rank = shape.length;
    1010                if (rank == 1) {
    1011                        return new int[] { n / stride[0] };
    1012                }
    1013
    1014                int[] output = new int[rank];
    1015                int i = 0;
    1016                while (i != n) { // TODO find more efficient way than this exhaustive search
    1017                        int j = rank - 1;
    1018                        for (; j >= 0; j--) {
    1019                                output[j]++;
    1020                                i += stride[j];
    1021                                if (output[j] >= shape[j]) {
    1022                                        output[j] = 0;
    1023                                        i -= shape[j] * stride[j];
    1024                                } else {
    1025                                        break;
    1026                                }
    1027                        }
    1028                        if (j == -1) {
    1029                                logger.error("Index was not found in this strided dataset");
    1030                                throw new IllegalArgumentException("Index was not found in this strided dataset");
    1031                        }
    1032                }
    1033
    1034                return output;
    1035        }
    1036
    1037        @Override
    1038        public int checkAxis(int axis) {
    1039                return ShapeUtils.checkAxis(shape.length, axis);
    1040        }
    1041
    1042        @Deprecated
    1043        protected static int checkAxis(int rank, int axis) {
    1044                return ShapeUtils.checkAxis(rank, axis);
    1045        }
    1046
    1047        protected static final char BLOCK_OPEN = '[';
    1048        protected static final char BLOCK_CLOSE = ']';
    1049
    1050        @Override
    1051        public String toString() {
    1052                final int rank = shape == null ? 0 : shape.length;
    1053                final StringBuilder out = new StringBuilder();
    1054
    1055                if (InterfaceUtils.isElemental(getClass())) {
    1056                        out.append("Dataset ");
    1057                } else {
    1058                        out.append("Compound dataset (");
    1059                        out.append(getElementsPerItem());
    1060                        out.append(") ");
    1061                }
    1062
    1063                if (name != null && name.length() > 0) {
    1064                        out.append("'");
    1065                        out.append(name);
    1066                        out.append("' has shape ");
    1067                } else {
    1068                        out.append("shape is ");
    1069                }
    1070
    1071                out.append(BLOCK_OPEN);
    1072                if (rank > 0) {
    1073                        out.append(shape[0]);
    1074                }
    1075                for (int i = 1; i < rank; i++) {
    1076                        out.append(", " + shape[i]);
    1077                }
    1078                out.append(BLOCK_CLOSE);
    1079                return out.toString();
    1080        }
    1081
    1082        @Override
    1083        public String toString(boolean showData) {
    1084                if (!showData) {
    1085                        return toString();
    1086                }
    1087
    1088                if (size == 0) {
    1089                        return "[]";
    1090                }
    1091
    1092                final int rank = shape == null ? 0 : shape.length;
    1093                final StringBuilder out = new StringBuilder();
    1094
    1095                if (rank > 0) {
    1096                        int[] pos = new int[rank];
    1097                        final StringBuilder lead = new StringBuilder();
    1098                        printBlocks(out, lead, 0, pos);
    1099                } else {
    1100                        out.append(getString());
    1101                }
    1102                return out.toString();
    1103        }
    1104
    1105        /**
    1106         * Limit to strings output via the toString() method
    1107         */
    1108        private static int maxStringLength = 120;
    1109
    1110        /**
    1111         * Set maximum line length for toString() method
    1112         * @param maxLineLength limit on length of line
    1113         */
    1114        public static void setMaxLineLength(int maxLineLength) {
    1115                maxStringLength = maxLineLength;
    1116        }
    1117
    1118        /**
    1119         * @return maximum line length for toString() method
    1120         */
    1121        public static int getMaxLineLength() {
    1122                return maxStringLength;
    1123        }
    1124
    1125        /**
    1126         * Limit to number of sub-blocks output via the toString() method
    1127         */
    1128        private static final int MAX_SUBBLOCKS = 6;
    1129
    1130        private final static String SEPARATOR = ",";
    1131        private final static String SPACE = " ";
    1132        private final static String ELLIPSIS = "...";
    1133        private final static String NEWLINE = "\n";
    1134
    1135        /**
    1136         * Make a line of output for last dimension of dataset
    1137         * @param end
    1138         * @param start
    1139         * @return line
    1140         */
    1141        private StringBuilder makeLine(final int end, final int[] start) {
    1142                StringBuilder line = new StringBuilder();
    1143                final int[] pos;
    1144                if (end >= start.length) {
    1145                        pos = Arrays.copyOf(start, end + 1);
    1146                } else {
    1147                        pos = start;
    1148                }
    1149                pos[end] = 0;
    1150                line.append(BLOCK_OPEN);
    1151                line.append(getString(pos));
    1152
    1153                final int length = shape[end];
    1154
    1155                // trim elements printed if length exceed estimate of maximum elements
    1156                int excess = length - maxStringLength / 3; // space + number + separator
    1157                int midIndex = -1;
    1158                if (excess > 0) {
    1159                        int index = (length - excess) / 2;
    1160                        for (int y = 1; y < index; y++) {
    1161                                line.append(SEPARATOR + SPACE);
    1162                                pos[end] = y;
    1163                                line.append(getString(pos));
    1164                        }
    1165                        midIndex = line.length() + 2;
    1166                        index = (length + excess) / 2;
    1167                        for (int y = index; y < length; y++) {
    1168                                line.append(SEPARATOR + SPACE);
    1169                                pos[end] = y;
    1170                                line.append(getString(pos));
    1171                        }
    1172                } else {
    1173                        for (int y = 1; y < length; y++) {
    1174                                line.append(SEPARATOR + SPACE);
    1175                                pos[end] = y;
    1176                                line.append(getString(pos));
    1177                        }
    1178                }
    1179                line.append(BLOCK_CLOSE);
    1180
    1181                // trim string down to limit
    1182                int lineLength = line.length();
    1183                excess = lineLength - maxStringLength - ELLIPSIS.length() - 1;
    1184                if (excess > 0) {
    1185                        int index = (lineLength - excess) / 2;
    1186                        if (midIndex > 0 && index > midIndex) {
    1187                                index = midIndex;
    1188                        } else {
    1189                                index = line.lastIndexOf(SEPARATOR, index) + 2;
    1190                        }
    1191                        StringBuilder out = new StringBuilder(line.subSequence(0, index));
    1192                        out.append(ELLIPSIS + SEPARATOR);
    1193                        index = (lineLength + excess) / 2;
    1194                        if (midIndex > 0 && index <= midIndex) {
    1195                                index = midIndex - 1;
    1196                        } else {
    1197                                index = line.indexOf(SEPARATOR, index) + 1;
    1198                        }
    1199                        out.append(line.subSequence(index, lineLength));
    1200                        return out;
    1201                } else if (midIndex > 0) { // add ellipsis
    1202                        StringBuilder out = new StringBuilder(line.subSequence(0, midIndex));
    1203                        out.append(ELLIPSIS + SEPARATOR + SPACE);
    1204                        out.append(line.subSequence(midIndex, lineLength));
    1205                        return out;
    1206                }
    1207
    1208                return line;
    1209        }
    1210
    1211        /**
    1212         * recursive method to print blocks
    1213         */
    1214        private void printBlocks(final StringBuilder out, final StringBuilder lead, final int level, final int[] pos) {
    1215                if (out.length() > 0) {
    1216                        char last = out.charAt(out.length() - 1);
    1217                        if (last != BLOCK_OPEN) {
    1218                                out.append(lead);
    1219                        }
    1220                }
    1221                final int end = getRank() - 1;
    1222                if (level != end) {
    1223                        out.append(BLOCK_OPEN);
    1224                        int length = shape[level];
    1225
    1226                        // first sub-block
    1227                        pos[level] = 0;
    1228                        StringBuilder newlead = new StringBuilder(lead);
    1229                        newlead.append(SPACE);
    1230                        printBlocks(out, newlead, level + 1, pos);
    1231                        if (length < 2) { // escape
    1232                                out.append(BLOCK_CLOSE);
    1233                                return;
    1234                        }
    1235
    1236                        out.append(SEPARATOR + NEWLINE);
    1237                        for (int i = level + 1; i < end; i++) {
    1238                                out.append(NEWLINE);
    1239                        }
    1240
    1241                        // middle sub-blocks
    1242                        if (length < MAX_SUBBLOCKS) {
    1243                                for (int x = 1; x < length - 1; x++) {
    1244                                        pos[level] = x;
    1245                                        printBlocks(out, newlead, level + 1, pos);
    1246                                        if (end <= level + 1) {
    1247                                                out.append(SEPARATOR + NEWLINE);
    1248                                        } else {
    1249                                                out.append(SEPARATOR + NEWLINE + NEWLINE);
    1250                                        }
    1251                                }
    1252                        } else {
    1253                                final int excess = length - MAX_SUBBLOCKS;
    1254                                int xmax = (length - excess) / 2;
    1255                                for (int x = 1; x < xmax; x++) {
    1256                                        pos[level] = x;
    1257                                        printBlocks(out, newlead, level + 1, pos);
    1258                                        if (end <= level + 1) {
    1259                                                out.append(SEPARATOR + NEWLINE);
    1260                                        } else {
    1261                                                out.append(SEPARATOR + NEWLINE + NEWLINE);
    1262                                        }
    1263                                }
    1264                                out.append(newlead);
    1265                                out.append(ELLIPSIS + SEPARATOR + NEWLINE);
    1266                                xmax = (length + excess) / 2;
    1267                                for (int x = xmax; x < length - 1; x++) {
    1268                                        pos[level] = x;
    1269                                        printBlocks(out, newlead, level + 1, pos);
    1270                                        if (end <= level + 1) {
    1271                                                out.append(SEPARATOR + NEWLINE);
    1272                                        } else {
    1273                                                out.append(SEPARATOR + NEWLINE + NEWLINE);
    1274                                        }
    1275                                }
    1276                        }
    1277
    1278                        // last sub-block
    1279                        pos[level] = length - 1;
    1280                        printBlocks(out, newlead, level + 1, pos);
    1281                        out.append(BLOCK_CLOSE);
    1282                } else {
    1283                        out.append(makeLine(end, pos));
    1284                }
    1285        }
    1286
    1287        @Override
    1288        public Dataset squeezeEnds() {
    1289                return squeeze(true);
    1290        }
    1291
    1292        @Override
    1293        public Dataset squeeze() {
    1294                return squeeze(false);
    1295        }
    1296
    1297        @Override
    1298        public Dataset squeeze(boolean onlyFromEnds) {
    1299                final int[] tshape = ShapeUtils.squeezeShape(shape, onlyFromEnds);
    1300                final int[] oshape = shape;
    1301                if (stride == null) {
    1302                        shape = tshape;
    1303                } else {
    1304                        int rank = shape.length;
    1305                        int trank = tshape.length;
    1306                        if (trank < rank) {
    1307                                int[] tstride = new int[tshape.length];
    1308                                if (onlyFromEnds) {
    1309                                        for (int i = 0; i < rank; i++) {
    1310                                                if (shape[i] != 1) {
    1311                                                        for (int k = 0; k < trank; k++) {
    1312                                                                tstride[k] = stride[i++];
    1313                                                        }
    1314                                                        break;
    1315                                                }
    1316                                        }
    1317                                } else {
    1318                                        int t = 0;
    1319                                        for (int i = 0; i < rank; i++) {
    1320                                                if (shape[i] != 1) {
    1321                                                        tstride[t++] = stride[i];
    1322                                                }
    1323                                        }
    1324                                }
    1325                                shape = tshape;
    1326                                stride = tstride;
    1327                        }
    1328                }
    1329
    1330                setDirty();
    1331                reshapeMetadata(oshape, shape);
    1332                return this;
    1333        }
    1334
    1335        @Override
    1336        public boolean isCompatibleWith(final ILazyDataset g) {
    1337                return ShapeUtils.areShapesCompatible(shape, g.getShape());
    1338        }
    1339
    1340        @Override
    1341        public void checkCompatibility(final ILazyDataset g) throws IllegalArgumentException {
    1342                ShapeUtils.checkCompatibility(this, g);
    1343        }
    1344
    1345        @Override
    1346        public Dataset reshape(final int... shape) {
    1347                Dataset a;
    1348                try {
    1349                        a = getView(true);
    1350                        a.setShape(shape);
    1351                } catch (IllegalArgumentException e) {
    1352                        a = clone();
    1353                        a.setShape(shape);
    1354                }
    1355                return a;
    1356        }
    1357
    1358        /**
    1359         * @param start begin
    1360         * @param stop exclusive end
    1361         * @param step number to skip
    1362         * @return number of steps to take
    1363         */
    1364        protected static int calcSteps(final double start, final double stop, final double step) {
    1365                return Math.max(0, (int) Math.ceil((stop - start) / step));
    1366        }
    1367
    1368        @Override
    1369        public boolean isComplex() {
    1370                return false;
    1371        }
    1372
    1373        @Override
    1374        public Dataset getRealPart() {
    1375                return this;
    1376        }
    1377
    1378        @Override
    1379        public Dataset getRealView() {
    1380                return getView(true);
    1381        }
    1382
    1383        @Override
    1384        public Dataset getSlice(final int[] start, final int[] stop, final int[] step) {
    1385                return internalGetSlice(new SliceND(shape, start, stop, step));
    1386        }
    1387
    1388        @Override
    1389        public Dataset getSlice(Slice... slice) {
    1390                return internalGetSlice(new SliceND(shape, slice));
    1391        }
    1392
    1393        @Override
    1394        public Dataset getSlice(IMonitor monitor, Slice... slice) {
    1395                return getSlice(slice);
    1396        }
    1397
    1398        @Override
    1399        public Dataset getSlice(IMonitor monitor, SliceND slice) {
    1400                return getSlice(slice);
    1401        }
    1402
    1403        @Override
    1404        public Dataset getSlice(IMonitor monitor, int[] start, int[] stop, int[] step) {
    1405                return getSlice(start, stop, step);
    1406        }
    1407
    1408        /**
    1409         * Get a slice of the dataset. The returned dataset is a copied selection of items
    1410         * @param slice an n-D slice
    1411         * @return The dataset of the sliced data
    1412         */
    1413        @Override
    1414        public Dataset getSlice(final SliceND slice) {
    1415                checkSliceND(slice);
    1416                return internalGetSlice(slice);
    1417        }
    1418
    1419        private Dataset internalGetSlice(final SliceND slice) {
    1420                SliceIterator it = (SliceIterator) internalGetSliceIterator(slice);
    1421                AbstractDataset s = getSlice(it);
    1422                s.metadata = copyMetadata();
    1423                s.setDirty();
    1424                s.sliceMetadata(true, slice);
    1425                return s;
    1426        }
    1427
    1428        /**
    1429         * Get a slice of the dataset. The returned dataset is a copied selection of items
    1430         *
    1431         * @param iterator Slice iterator
    1432         * @return The dataset of the sliced data
    1433         */
    1434        abstract public AbstractDataset getSlice(final SliceIterator iterator);
    1435
    1436        @Override
    1437        public Dataset setSlice(final Object obj, final SliceND slice) {
    1438                checkSliceND(slice);
    1439                return internalSetSlice(obj, slice);
    1440        }
    1441
    1442        private Dataset internalSetSlice(final Object obj, final SliceND slice) {
    1443                Dataset ds;
    1444                if (obj instanceof Dataset) {
    1445                        ds = (Dataset) obj;
    1446                } else if (obj instanceof IDataset) {
    1447                        ds = DatasetUtils.convertToDataset((IDataset) obj);
    1448                } else {
    1449                        Class<? extends Dataset> dClass = getClass();
    1450                        if (!BooleanDataset.class.equals(dClass)) {
    1451                                dClass = InterfaceUtils.getLargestInterface(this);
    1452                        }
    1453                        ds = DatasetFactory.createFromObject(getElementsPerItem(), dClass, obj);
    1454                }
    1455
    1456                return setSlicedView(getSliceView(slice), ds);
    1457        }
    1458
    1459        @Override
    1460        public Dataset setSlice(final Object obj, final int[] start, final int[] stop, final int[] step) {
    1461                return internalSetSlice(obj, new SliceND(shape, start, stop, step));
    1462        }
    1463
    1464        /**
    1465         * Set a view of current dataset to given dataset with broadcasting
    1466         * @param view destination
    1467         * @param d source of data
    1468         * @return this dataset
    1469         */
    1470        abstract Dataset setSlicedView(Dataset view, Dataset d);
    1471
    1472        @Override
    1473        public Dataset setSlice(Object obj, Slice... slice) {
    1474                if (slice == null || slice.length == 0) {
    1475                        return internalSetSlice(obj, new SliceND(shape));
    1476                }
    1477                return internalSetSlice(obj, new SliceND(shape, slice));
    1478        }
    1479
    1480        @Override
    1481        public boolean all() {
    1482                return Comparisons.allTrue(this);
    1483        }
    1484
    1485        @Override
    1486        public BooleanDataset all(final int axis) {
    1487                return Comparisons.allTrue(this, axis);
    1488        }
    1489
    1490        @Override
    1491        public boolean any() {
    1492                return Comparisons.anyTrue(this);
    1493        }
    1494
    1495        @Override
    1496        public BooleanDataset any(final int axis) {
    1497                return Comparisons.anyTrue(this, axis);
    1498        }
    1499
    1500        @Override
    1501        public Dataset ifloorDivide(final Object o) {
    1502                return idivide(o).ifloor();
    1503        }
    1504
    1505        @Override
    1506        public double residual(final Object o) {
    1507                return residual(o, null, false);
    1508        }
    1509
    1510        @Override
    1511        public double residual(final Object o, boolean ignoreNaNs) {
    1512                return residual(o, null, ignoreNaNs);
    1513        }
    1514
    1515        /**
    1516         * @return statistics
    1517         * @since 2.0
    1518         */
    1519        @SuppressWarnings("unchecked")
    1520        protected StatisticsMetadata<Number> getStats() {
    1521                StatisticsMetadata<Number> md = getFirstMetadata(StatisticsMetadata.class);
    1522                if (md == null || md.isDirty(this)) {
    1523                        md = new StatisticsMetadataImpl<Number>();
    1524                        md.initialize(this);
    1525                        setMetadata(md);
    1526                }
    1527                return md;
    1528        }
    1529
    1530        /**
    1531         * @return statistics
    1532         * @since 2.0
    1533         */
    1534        @SuppressWarnings("unchecked")
    1535        protected StatisticsMetadata<String> getStringStats() {
    1536                StatisticsMetadata<String> md = getFirstMetadata(StatisticsMetadata.class);
    1537                if (md == null || md.isDirty(this)) {
    1538                        md = new StatisticsMetadataImpl<String>();
    1539                        md.initialize(this);
    1540                        setMetadata(md);
    1541                }
    1542                return md;
    1543        }
    1544
    1545        @Override
    1546        public Number max(boolean... ignoreInvalids) {
    1547                return getStats().getMaximum(ignoreInvalids);
    1548        }
    1549
    1550        @Override
    1551        public Dataset max(int axis, boolean... ignoreInvalids) {
    1552                return getStats().getMaximum(axis, ignoreInvalids);
    1553        }
    1554
    1555        @Override
    1556        public Dataset max(int[] axes, boolean... ignoreInvalids) {
    1557                return getStats().getMaximum(axes, ignoreInvalids);
    1558        }
    1559
    1560        @Override
    1561        public Number min(boolean... ignoreInvalids) {
    1562                return getStats().getMinimum(ignoreInvalids);
    1563        }
    1564
    1565        @Override
    1566        public Dataset min(int axis, boolean... ignoreInvalids) {
    1567                return getStats().getMinimum(axis, ignoreInvalids);
    1568        }
    1569
    1570        @Override
    1571        public Dataset min(int[] axes, boolean... ignoreInvalids) {
    1572                return getStats().getMinimum(axes, ignoreInvalids);
    1573        }
    1574
    1575        @Override
    1576        public int argMax(boolean... ignoreInvalids) {
    1577                return getFlat1DIndex(maxPos(ignoreInvalids));
    1578        }
    1579
    1580        /**
    1581         * @since 2.0
    1582         */
    1583        @Override
    1584        public IntegerDataset argMax(int axis, boolean... ignoreInvalids) {
    1585                return (IntegerDataset) getStats().getArgMaximum(axis, ignoreInvalids);
    1586        }
    1587
    1588        @Override
    1589        public int argMin(boolean... ignoreInvalids) {
    1590                return getFlat1DIndex(minPos(ignoreInvalids));
    1591        }
    1592
    1593        /**
    1594         * @since 2.0
    1595         */
    1596        @Override
    1597        public IntegerDataset argMin(int axis, boolean... ignoreInvalids) {
    1598                return (IntegerDataset) getStats().getArgMinimum(axis, ignoreInvalids);
    1599        }
    1600
    1601        @Override
    1602        public Number peakToPeak(boolean... ignoreInvalids) {
    1603                return InterfaceUtils.fromDoubleToBiggestNumber(getClass(), max(ignoreInvalids).doubleValue() - min(ignoreInvalids).doubleValue());
    1604        }
    1605
    1606        @Override
    1607        public Dataset peakToPeak(int axis,  boolean... ignoreInvalids) {
    1608                return Maths.subtract(max(axis, ignoreInvalids), min(axis, ignoreInvalids));
    1609        }
    1610
    1611        @Override
    1612        public Dataset peakToPeak(int[] axes,  boolean... ignoreInvalids) {
    1613                return Maths.subtract(max(axes, ignoreInvalids), min(axes, ignoreInvalids));
    1614        }
    1615
    1616        @Override
    1617        public long count(boolean... ignoreInvalids) {
    1618                return getStats().getCount(ignoreInvalids);
    1619        }
    1620
    1621        @Override
    1622        public Dataset count(int axis, boolean... ignoreInvalids) {
    1623                return getStats().getCount(axis, ignoreInvalids);
    1624        }
    1625
    1626        @Override
    1627        public Dataset count(int[] axes, boolean... ignoreInvalids) {
    1628                return getStats().getCount(axes, ignoreInvalids);
    1629        }
    1630
    1631        @Override
    1632        public Object sum(boolean... ignoreInvalids) {
    1633                return InterfaceUtils.toBiggestNumber(getClass(), getStats().getSum(ignoreInvalids));
    1634        }
    1635
    1636        @Override
    1637        public Dataset sum(int axis, boolean... ignoreInvalids) {
    1638                return getStats().getSum(axis, ignoreInvalids);
    1639        }
    1640
    1641        @Override
    1642        public Dataset sum(int[] axes, boolean... ignoreInvalids) {
    1643                return getStats().getSum(axes, ignoreInvalids);
    1644        }
    1645
    1646        @Override
    1647        public Object product(boolean... ignoreInvalids) {
    1648                return Stats.product(this, ignoreInvalids);
    1649        }
    1650
    1651        @Override
    1652        public Dataset product(int axis, boolean... ignoreInvalids) {
    1653                return Stats.product(this, axis, ignoreInvalids);
    1654        }
    1655
    1656        @Override
    1657        public Dataset product(int[] axes, boolean... ignoreInvalids) {
    1658                return Stats.product(this, axes, ignoreInvalids);
    1659        }
    1660
    1661        @Override
    1662        public Object mean(boolean... ignoreInvalids) {
    1663                return getStats().getMean(ignoreInvalids);
    1664        }
    1665
    1666        @Override
    1667        public Dataset mean(int axis, boolean... ignoreInvalids) {
    1668                return getStats().getMean(axis, ignoreInvalids);
    1669        }
    1670
    1671        @Override
    1672        public Dataset mean(int[] axes, boolean... ignoreInvalids) {
    1673                return getStats().getMean(axes, ignoreInvalids);
    1674        }
    1675
    1676        @Override
    1677        public double variance() {
    1678                return variance(false);
    1679        }
    1680
    1681        @Override
    1682        public double variance(boolean isWholePopulation, boolean... ignoreInvalids) {
    1683                return getStats().getVariance(isWholePopulation, ignoreInvalids);
    1684        }
    1685
    1686        @Override
    1687        public Dataset variance(int axis) {
    1688                return getStats().getVariance(axis, false);
    1689        }
    1690
    1691        @Override
    1692        public Dataset variance(int[] axes) {
    1693                return getStats().getVariance(axes, false);
    1694        }
    1695
    1696        @Override
    1697        public Dataset variance(int axis, boolean isWholePopulation, boolean... ignoreInvalids) {
    1698                return getStats().getVariance(axis, isWholePopulation, ignoreInvalids);
    1699        }
    1700
    1701        @Override
    1702        public Dataset variance(int[] axes, boolean isWholePopulation, boolean... ignoreInvalids) {
    1703                return getStats().getVariance(axes, isWholePopulation, ignoreInvalids);
    1704        }
    1705
    1706        @Override
    1707        public double stdDeviation() {
    1708                return Math.sqrt(variance());
    1709        }
    1710
    1711        @Override
    1712        public double stdDeviation(boolean isWholePopulation, boolean... ignoreInvalids) {
    1713                return Math.sqrt(variance(isWholePopulation, ignoreInvalids));
    1714        }
    1715
    1716        @Override
    1717        public Dataset stdDeviation(int axis) {
    1718                return Maths.sqrt(variance(axis, false));
    1719        }
    1720
    1721        @Override
    1722        public Dataset stdDeviation(int[] axes) {
    1723                return Maths.sqrt(variance(axes, false));
    1724        }
    1725
    1726        @Override
    1727        public Dataset stdDeviation(int axis, boolean isWholePopulation, boolean... ignoreInvalids) {
    1728                return Maths.sqrt(variance(axis, isWholePopulation, ignoreInvalids));
    1729        }
    1730
    1731        @Override
    1732        public Dataset stdDeviation(int[] axes, boolean isWholePopulation, boolean... ignoreInvalids) {
    1733                return Maths.sqrt(variance(axes, isWholePopulation, ignoreInvalids));
    1734        }
    1735
    1736        @Override
    1737        public double rootMeanSquare(boolean... ignoreInvalids) {
    1738                StatisticsMetadata<Number> stats = getStats();
    1739                final double mean = stats.getMean(ignoreInvalids).doubleValue();
    1740                final double var = stats.getVariance(true, ignoreInvalids);
    1741                return Math.sqrt(var + mean * mean);
    1742        }
    1743
    1744        @Override
    1745        public Dataset rootMeanSquare(int axis, boolean... ignoreInvalids) {
    1746                StatisticsMetadata<Number> stats = getStats();
    1747                Dataset v = stats.getVariance(axis, true, ignoreInvalids);
    1748                Dataset m = stats.getMean(axis, ignoreInvalids);
    1749                Dataset result = Maths.multiply(m, m);
    1750                return Maths.sqrt(result.iadd(v));
    1751        }
    1752
    1753        @Override
    1754        public Dataset rootMeanSquare(int[] axes, boolean... ignoreInvalids) {
    1755                StatisticsMetadata<Number> stats = getStats();
    1756                Dataset v = stats.getVariance(axes, true, ignoreInvalids);
    1757                Dataset m = stats.getMean(axes, ignoreInvalids);
    1758                Dataset result = Maths.multiply(m, m);
    1759                return Maths.sqrt(result.iadd(v));
    1760        }
    1761
    1762        /**
    1763         * Set item from compatible dataset in a direct and speedy way. Remember to setDirty afterwards.
    1764         *
    1765         * @param dindex destination index
    1766         * @param sindex source index
    1767         * @param src
    1768         *            is the source data buffer
    1769         */
    1770        protected abstract void setItemDirect(final int dindex, final int sindex, final Object src);
    1771
    1772        /**
    1773         * @return error broadcasted to current shape
    1774         */
    1775        private Dataset getBroadcastedInternalError() {
    1776                if (shape == null) {
    1777                        throw new IllegalArgumentException("Cannot get error for null dataset");
    1778                }
    1779                ILazyDataset led = super.getErrors();
    1780                if (led == null)
    1781                        return null;
    1782
    1783                Dataset ed = null;
    1784                try {
    1785                        ed = DatasetUtils.sliceAndConvertLazyDataset(led);
    1786                } catch (DatasetException e) {
    1787                        logger.error("Could not get data from lazy dataset", e);
    1788                }
    1789                if (led != ed) {
    1790                        setErrors(ed); // set back
    1791                }
    1792
    1793                return ed.getBroadcastView(shape);
    1794        }
    1795
    1796        @Override
    1797        public Dataset getErrors() {
    1798                Dataset ed = getBroadcastedInternalError();
    1799                if (ed == null)
    1800                        return null;
    1801
    1802                return ed;
    1803        }
    1804
    1805        @Override
    1806        public double getError() {
    1807                Dataset ed = getBroadcastedInternalError();
    1808                if (ed == null)
    1809                        return 0;
    1810
    1811                return ed.getDouble();
    1812        }
    1813
    1814        @Override
    1815        public double getError(final int i) {
    1816                Dataset ed = getBroadcastedInternalError();
    1817                if (ed == null)
    1818                        return 0;
    1819
    1820                return ed.getDouble(i);
    1821        }
    1822
    1823        @Override
    1824        public double getError(final int i, final int j) {
    1825                Dataset ed = getBroadcastedInternalError();
    1826                if (ed == null)
    1827                        return 0;
    1828
    1829                return ed.getDouble(i, j);
    1830        }
    1831
    1832        @Override
    1833        public double getError(int... pos) {
    1834                Dataset ed = getBroadcastedInternalError();
    1835                if (ed == null)
    1836                        return 0;
    1837
    1838                return ed.getDouble(pos);
    1839        }
    1840
    1841        @Override
    1842        public double[] getErrorArray(final int i) {
    1843                Dataset ed = getBroadcastedInternalError();
    1844                if (ed == null)
    1845                        return null;
    1846
    1847                return new double[] {getError(i)};
    1848        }
    1849
    1850        @Override
    1851        public double[] getErrorArray(final int i, final int j) {
    1852                Dataset ed = getBroadcastedInternalError();
    1853                if (ed == null)
    1854                        return null;
    1855
    1856                return new double[] {getError(i, j)};
    1857        }
    1858
    1859        @Override
    1860        public double[] getErrorArray(int... pos) {
    1861                Dataset ed = getBroadcastedInternalError();
    1862                if (ed == null)
    1863                        return null;
    1864
    1865                return new double[] {getError(pos)};
    1866        }
    1867
    1868        protected Dataset getInternalSquaredError() {
    1869                Dataset sed = getErrorBuffer().getBroadcastView(shape);
    1870                return sed;
    1871        }
    1872
    1873        @Override
    1874        public Dataset getErrorBuffer() {
    1875                ErrorMetadata emd = getErrorMetadata();
    1876                if (emd == null)
    1877                        return null;
    1878
    1879                if (!(emd instanceof ErrorMetadataImpl)) {
    1880                        ILazyDataset led = emd.getError();
    1881                        Dataset ed;
    1882                        try {
    1883                                ed = DatasetUtils.sliceAndConvertLazyDataset(led);
    1884                                emd = MetadataFactory.createMetadata(ErrorMetadata.class);
    1885                                setMetadata(emd);
    1886                                emd.setError(ed);
    1887                        } catch (MetadataException me) {
    1888                                logger.error("Could not create metadata", me);
    1889                        } catch (DatasetException e) {
    1890                                logger.error("Could not get data from lazy dataset", e);
    1891                        }
    1892                }
    1893
    1894                return ((ErrorMetadataImpl) emd).getSquaredError();
    1895        }
    1896
    1897        /**
    1898         * Set a copy of the buffer that backs the (squared) error data
    1899         * @param buffer can be null, anything that can be used to create a DoubleDataset or CompoundDoubleDataset
    1900         */
    1901        @Override
    1902        public void setErrorBuffer(Serializable buffer) {
    1903                if (shape == null) {
    1904                        throw new IllegalArgumentException("Cannot set error buffer for null dataset");
    1905                }
    1906                if (buffer == null) {
    1907                        clearMetadata(ErrorMetadata.class);
    1908                        return;
    1909                }
    1910
    1911                IDataset d = (IDataset) createFromSerializable(buffer, false);
    1912                ErrorMetadata emd = getErrorMetadata();
    1913                if (!(emd instanceof ErrorMetadataImpl)) {
    1914                        try {
    1915                                emd = MetadataFactory.createMetadata(ErrorMetadata.class);
    1916                                setMetadata(emd);
    1917                        } catch (MetadataException me) {
    1918                                logger.error("Could not create metadata", me);
    1919                        }
    1920                }
    1921                ((ErrorMetadataImpl) emd).setSquaredError(d);
    1922        }
    1923}