    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.annotation.Annotation;
    017import java.lang.reflect.Array;
    018import java.lang.reflect.Field;
    019import java.util.ArrayList;
    020import java.util.Arrays;
    021import java.util.Collection;
    022import java.util.concurrent.ConcurrentMap;
    023import java.util.concurrent.ConcurrentHashMap;
    024import java.util.List;
    025import java.util.Map;
    026
    027import org.eclipse.january.DatasetException;
    028import org.eclipse.january.MetadataException;
    029import org.eclipse.january.metadata.Dirtiable;
    030import org.eclipse.january.metadata.ErrorMetadata;
    031import org.eclipse.january.metadata.IMetadata;
    032import org.eclipse.january.metadata.MetadataFactory;
    033import org.eclipse.january.metadata.MetadataType;
    034import org.eclipse.january.metadata.Reshapeable;
    035import org.eclipse.january.metadata.Sliceable;
    036import org.eclipse.january.metadata.Transposable;
    037import org.slf4j.Logger;
    038import org.slf4j.LoggerFactory;
    039
    040/**
    041 * Common base for both lazy and normal dataset implementations
    042 */
    043public abstract class LazyDatasetBase implements ILazyDataset, Serializable {
    044
    045        private static final long serialVersionUID = 767926846438976050L;
    046
    047        protected static final Logger logger = LoggerFactory.getLogger(LazyDatasetBase.class);
    048
    049        protected static boolean catchExceptions;
    050
    051        static {
    052                /**
    053                 * Boolean to set to true if running jython scripts that utilise ScisoftPy in IDE
    054                 */
    055                try {
    056                        catchExceptions = Boolean.getBoolean("run.in.eclipse");
    057                } catch (SecurityException e) {
    058                        // set a default for when the security manager does not allow access to the requested key
    059                        catchExceptions = false;
    060                }
    061        }
    062
    063        transient private boolean dirty = true; // indicate dirty state of metadata
    064        protected String name = "";
    065
    066        /**
    067         * The shape or dimensions of the dataset
    068         */
    069        protected int[] shape;
    070
    071        protected ConcurrentMap<Class<? extends MetadataType>, List<MetadataType>> metadata = null;
    072
    073        /**
    074         * @return type of dataset item
    075         */
    076        abstract public int getDType();
    077
    078        @Override
    079        public Class<?> getElementClass() {
    080                return DTypeUtils.getElementClass(getDType());
    081        }
    082
    083        @Override
    084        public LazyDatasetBase clone() {
    085                return null;
    086        }
    087
    088        @Override
    089        public boolean equals(Object obj) {
    090                if (this == obj) {
    091                        return true;
    092                }
    093                if (obj == null) {
    094                        return false;
    095                }
    096                if (!getClass().equals(obj.getClass())) {
    097                        return false;
    098                }
    099
    100                LazyDatasetBase other = (LazyDatasetBase) obj;
    101                if (getDType() != other.getDType()) {
    102                        return false;
    103                }
    104                if (getElementsPerItem() != other.getElementsPerItem()) {
    105                        return false;
    106                }
    107                if (!Arrays.equals(shape, other.shape)) {
    108                        return false;
    109                }
    110                return true;
    111        }
    112
    113        @Override
    114        public int hashCode() {
    115                int hash = getDType() * 17 + getElementsPerItem();
    116                int rank = shape.length;
    117                for (int i = 0; i < rank; i++) {
    118                        hash = hash*17 + shape[i];
    119                }
    120                return hash;
    121        }
    122
    123        @Override
    124        public String getName() {
    125                return name;
    126        }
    127
    128        @Override
    129        public void setName(String name) {
    130                this.name = name;
    131        }
    132
    133        @Override
    134        public int[] getShape() {
    135                return shape.clone();
    136        }
    137
    138        @Override
    139        public int getRank() {
    140                return shape.length;
    141        }
    142
    143        /**
    144         * This method allows anything that dirties the dataset to clear various metadata values
    145         * so that the other methods can work correctly.
    146         * @since 2.1
    147         */
    148        public void setDirty() {
    149                dirty = true;
    150        }
    151
    152        /**
    153         * Find first sub-interface of (or class that directly implements) MetadataType
    154         * @param clazz
    155         * @return sub-interface
    156         * @exception IllegalArgumentException when given class is {@link MetadataType} or an anonymous sub-class of it
    157         */
    158        @SuppressWarnings("unchecked")
    159        public static Class<? extends MetadataType> findMetadataTypeSubInterfaces(Class<? extends MetadataType> clazz) {
    160                if (clazz.equals(MetadataType.class)) {
    161                        throw new IllegalArgumentException("Cannot accept MetadataType");
    162                }
    163
    164                if (clazz.isInterface()) {
    165                        return clazz;
    166                }
    167
    168                if (clazz.isAnonymousClass()) { // special case
    169                        Class<?> s = clazz.getSuperclass();
    170                        if (!s.equals(Object.class)) {
    171                                // only use super class if it is not an anonymous class of an interface
    172                                clazz = (Class<? extends MetadataType>) s;
    173                        }
    174                }
    175
    176                for (Class<?> c : clazz.getInterfaces()) {
    177                        if (c.equals(MetadataType.class)) {
    178                                if (clazz.isAnonymousClass()) {
    179                                        throw new IllegalArgumentException("Cannot accept anonymous subclasses of MetadataType");
    180                                }
    181                                return clazz;
    182                        }
    183                        if (MetadataType.class.isAssignableFrom(c)) {
    184                                return (Class<? extends MetadataType>) c;
    185                        }
    186                }
    187
    188                Class<?> c = clazz.getSuperclass(); // Naughty: someone has sub-classed a metadata class
    189                if (c != null) {
    190                        return findMetadataTypeSubInterfaces((Class<? extends MetadataType>) c);
    191                }
    192
    193                logger.error("Somehow the search for metadata type interface ended in a bad place");
    194                assert false; // should not be able to get here!!!
    195                return null;
    196        }
    197
    198        @Override
    199        public void setMetadata(MetadataType metadata) {
    200                addMetadata(metadata, true);
    201        }
    202
    203        @Override
    204        public void addMetadata(MetadataType metadata) {
    205                addMetadata(metadata, false);
    206        }
    207
    208        private synchronized void addMetadata(MetadataType metadata, boolean clear) {
    209                if (metadata == null)
    210                        return;
    211
    212                if (this.metadata == null) {
    213                        this.metadata = new ConcurrentHashMap<Class<? extends MetadataType>, List<MetadataType>>();
    214                }
    215
    216                Class<? extends MetadataType> clazz = findMetadataTypeSubInterfaces(metadata.getClass());
    217                if (!this.metadata.containsKey(clazz)) {
    218                        this.metadata.put(clazz, new ArrayList<MetadataType>());
    219                } else if (clear) {
    220                        this.metadata.get(clazz).clear();
    221                }
    222                this.metadata.get(clazz).add(metadata);
    223
    224                // add for special case of sub-interfaces of IMetadata
    225                if (!IMetadata.class.equals(clazz) && IMetadata.class.isAssignableFrom(clazz)) {
    226                        clazz = IMetadata.class;
    227                        if (!this.metadata.containsKey(clazz)) {
    228                                this.metadata.put(clazz, new ArrayList<MetadataType>());
    229                        } else if (clear) {
    230                                this.metadata.get(clazz).clear();
    231                        }
    232                        this.metadata.get(clazz).add(metadata);
    233                }
    234        }
    235
    236        @Override
    237        @Deprecated
    238        public synchronized IMetadata getMetadata() {
    239                return getFirstMetadata(IMetadata.class);
    240        }
    241
    242        @SuppressWarnings("unchecked")
    243        @Override
    244        public synchronized <S extends MetadataType, T extends S> List<S> getMetadata(Class<T> clazz) throws MetadataException {
    245                if (metadata == null) {
    246                        dirty = false;
    247                        return null;
    248                }
    249
    250                if (dirty) {
    251                        dirtyMetadata();
    252                        dirty = false;
    253                }
    254
    255                if (clazz == null) {
    256                        List<S> all = new ArrayList<S>();
    257                        for (Class<? extends MetadataType> c : metadata.keySet()) {
    258                                all.addAll((Collection<S>) metadata.get(c));
    259                        }
    260                        return all;
    261                }
    262
    263                return (List<S>) metadata.get(findMetadataTypeSubInterfaces(clazz));
    264        }
    265
    266        @Override
    267        public synchronized <S extends MetadataType, T extends S> S getFirstMetadata(Class<T> clazz) {
    268                try {
    269                        List<S> ml = getMetadata(clazz);
    270                        if (ml == null) {
    271                                return null;
    272                        }
    273                        for (S t : ml) {
    274                                if (clazz.isInstance(t)) {
    275                                        return t;
    276                                }
    277                        }
    278                } catch (Exception e) {
    279                        logger.error("Get metadata failed!",e);
    280                }
    281
    282                return null;
    283        }
    284
    285        @Override
    286        public synchronized void clearMetadata(Class<? extends MetadataType> clazz) {
    287                if (metadata == null)
    288                        return;
    289
    290                if (clazz == null) {
    291                        metadata.clear();
    292                        return;
    293                }
    294
    295                List<MetadataType> list = metadata.get(findMetadataTypeSubInterfaces(clazz));
    296                if( list != null) {
    297                        list.clear();
    298                }
    299        }
    300
    301        /**
    302         * @since 2.0
    303         */
    304        protected synchronized ConcurrentMap<Class<? extends MetadataType>, List<MetadataType>> copyMetadata() {
    305                return copyMetadata(metadata);
    306        }
    307
    308        /**
    309         * @since 2.0
    310         */
    311        protected static ConcurrentMap<Class<? extends MetadataType>, List<MetadataType>> copyMetadata(Map<Class<? extends MetadataType>, List<MetadataType>> metadata) {
    312                if (metadata == null)
    313                        return null;
    314
    315                ConcurrentHashMap<Class<? extends MetadataType>, List<MetadataType>> map = new ConcurrentHashMap<Class<? extends MetadataType>, List<MetadataType>>();
    316
    317                for (Class<? extends MetadataType> c : metadata.keySet()) {
    318                        List<MetadataType> l = metadata.get(c);
    319                        List<MetadataType> nl = new ArrayList<MetadataType>(l.size());
    320                        map.put(c, nl);
    321                        for (MetadataType m : l) {
    322                                nl.add(m.clone());
    323                        }
    324                }
    325                return map;
    326        }
    327
    328        interface MetadatasetAnnotationOperation {
    329                /**
    330                 * Process value of given field
    331                 * <p>
    332                 * When the field is not a container then the returned value
    333                 * may replace the old value
    334                 * @param f given field
    335                 * @param o value of field
    336                 * @return transformed field
    337                 */
    338                Object processField(Field f, Object o);
    339
    340                /**
    341                 * @return annotated class
    342                 */
    343                Class<? extends Annotation> getAnnClass();
    344
    345                /**
    346                 * @param axis
    347                 * @return number of dimensions to insert or remove
    348                 */
    349                int change(int axis);
    350
    351                /**
    352                 *
    353                 * @return rank or -1 to match
    354                 */
    355                int getNewRank();
    356
    357                /**
    358                 * Run on given lazy dataset
    359                 * @param lz
    360                 * @return
    361                 */
    362                ILazyDataset run(ILazyDataset lz);
    363        }
    364
    365        class MdsSlice implements MetadatasetAnnotationOperation {
    366                private boolean asView;
    367                private int[] start;
    368                private int[] stop;
    369                private int[] step;
    370                private int[] oShape;
    371                private long oSize;
    372
    373                public MdsSlice(boolean asView, final int[] start, final int[] stop, final int[] step, final int[] oShape) {
    374                        this.asView = asView;
    375                        this.start = start;
    376                        this.stop = stop;
    377                        this.step = step;
    378                        this.oShape = oShape;
    379                        oSize = ShapeUtils.calcLongSize(oShape);
    380                }
    381
    382                @Override
    383                public Object processField(Field field, Object o) {
    384                        return o;
    385                }
    386
    387                @Override
    388                public Class<? extends Annotation> getAnnClass() {
    389                        return Sliceable.class;
    390                }
    391
    392                @Override
    393                public int change(int axis) {
    394                        return 0;
    395                }
    396
    397                @Override
    398                public int getNewRank() {
    399                        return -1;
    400                }
    401
    402                @Override
    403                public ILazyDataset run(ILazyDataset lz) {
    404                        int rank = lz.getRank();
    405                        if (start.length != rank) {
    406                                throw new IllegalArgumentException("Slice dimensions do not match dataset!");
    407                        }
    408
    409                        int[] shape = lz.getShape();
    410                        int[] stt;
    411                        int[] stp;
    412                        int[] ste;
    413                        if (lz.getSize() == oSize) {
    414                                stt = start;
    415                                stp = stop;
    416                                ste = step;
    417                        } else {
    418                                stt = start.clone();
    419                                stp = stop.clone();
    420                                ste = step.clone();
    421                                for (int i = 0; i < rank; i++) {
    422                                        if (shape[i] >= oShape[i]) continue;
    423                                        if (shape[i] == 1) {
    424                                                stt[i] = 0;
    425                                                stp[i] = 1;
    426                                                ste[1] = 1;
    427                                        } else {
    428                                                throw new IllegalArgumentException("Sliceable dataset has invalid size!");
    429                                        }
    430                                }
    431                        }
    432
    433                        if (asView || (lz instanceof IDataset))
    434                                return lz.getSliceView(stt, stp, ste);
    435                        try {
    436                                return lz.getSlice(stt, stp, ste);
    437                        } catch (DatasetException e) {
    438                                logger.error("Could not slice dataset in metadata", e);
    439                                return null;
    440                        }
    441                }
    442        }
    443
    444        class MdsReshape implements MetadatasetAnnotationOperation {
    445                private boolean matchRank;
    446                private int[] oldShape;
    447                private int[] newShape;
    448                boolean onesOnly;
    449                int[] differences;
    450
    451                /*
    452                 * if only ones then record differences (insertions and deletions)
    453                 *
    454                 * if shape changing, find broadcasted dimensions and disallow
    455                 * merging that include those dimensions
    456                 */
    457                public MdsReshape(final int[] oldShape, final int[] newShape) {
    458                        this.oldShape = oldShape;
    459                        this.newShape = newShape;
    460                        differences = null;
    461                }
    462
    463                @Override
    464                public Object processField(Field field, Object o) {
    465                        Annotation a = field.getAnnotation(Reshapeable.class);
    466                        if (a != null) { // cannot be null
    467                                matchRank = ((Reshapeable) a).matchRank();
    468                        }
    469                        return o;
    470                }
    471
    472                @Override
    473                public Class<? extends Annotation> getAnnClass() {
    474                        return Reshapeable.class;
    475                }
    476
    477                @Override
    478                public int change(int axis) {
    479                        if (matchRank) {
    480                                if (differences == null)
    481                                        init();
    482
    483                                if (onesOnly) {
    484                                        return differences[axis];
    485                                }
    486                                throw new UnsupportedOperationException("TODO support other shape operations");
    487                        }
    488                        return 0;
    489                }
    490
    491                @Override
    492                public int getNewRank() {
    493                        return matchRank ? newShape.length : -1;
    494                }
    495
    496                private void init() {
    497                        int or = oldShape.length - 1;
    498                        int nr = newShape.length - 1;
    499                        if (or < 0 || nr < 0) { // zero-rank shapes
    500                                onesOnly = true;
    501                                differences = new int[1];
    502                                differences[0] = or < 0 ? nr + 1 : or + 1;
    503                                return;
    504                        }
    505                        int ob = 0;
    506                        int nb = 0;
    507                        onesOnly = true;
    508                        do {
    509                                while (oldShape[ob] == 1 && ob < or) {
    510                                        ob++; // next non-unit dimension
    511                                }
    512                                while (newShape[nb] == 1 && nb < nr) {
    513                                        nb++;
    514                                }
    515                                if (oldShape[ob++] != newShape[nb++]) {
    516                                        onesOnly = false;
    517                                        break;
    518                                }
    519                        } while (ob <= or && nb <= nr);
    520
    521                        ob = 0;
    522                        nb = 0;
    523                        differences = new int[or + 2];
    524                        if (onesOnly) {
    525                                // work out unit dimensions removed from or add to old
    526                                int j = 0;
    527                                do {
    528                                        if (oldShape[ob] != 1 && newShape[nb] != 1) {
    529                                                ob++;
    530                                                nb++;
    531                                        } else {
    532                                                while (oldShape[ob] == 1 && ob < or) {
    533                                                        ob++;
    534                                                        differences[j]--;
    535                                                }
    536                                                while (newShape[nb] == 1 && nb < nr) {
    537                                                        nb++;
    538                                                        differences[j]++;
    539                                                }
    540                                        }
    541                                        j++;
    542                                } while (ob <= or && nb <= nr && j <= or);
    543                                while (ob <= or && oldShape[ob] == 1) {
    544                                        ob++;
    545                                        differences[j]--;
    546                                }
    547                                while (nb <= nr && newShape[nb] == 1) {
    548                                        nb++;
    549                                        differences[j]++;
    550                                }
    551                        } else {
    552                                if (matchRank) {
    553                                        logger.error("Combining dimensions is currently not supported");
    554                                        throw new IllegalArgumentException("Combining dimensions is currently not supported");
    555                                }
    556                                // work out mapping: contiguous dimensions can be grouped or split
    557                                while (ob <= or && nb <= nr) {
    558                                        int ol = oldShape[ob];
    559                                        while (ol == 1 && ol <= or) {
    560                                                ob++;
    561                                                ol = oldShape[ob];
    562                                        }
    563                                        int oe = ob + 1;
    564                                        int nl = newShape[nb];
    565                                        while (nl == 1 && nl <= nr) {
    566                                                nb++;
    567                                                nl = newShape[nb];
    568                                        }
    569                                        int ne = nb + 1;
    570                                        if (ol < nl) {
    571                                                differences[ob] = 1;
    572                                                do { // case where new shape combines several dimensions into one dimension
    573                                                        if (oe == (or + 1)) {
    574                                                                break;
    575                                                        }
    576                                                        differences[oe] = 1;
    577                                                        ol *= oldShape[oe++];
    578                                                } while (ol < nl);
    579                                                differences[oe - 1] = oe - ob; // signal end with difference
    580                                                if (nl != ol) {
    581                                                        logger.error("Single dimension is incompatible with subshape");
    582                                                        throw new IllegalArgumentException("Single dimension is incompatible with subshape");
    583                                                }
    584                                        } else if (ol > nl) {
    585                                                do { // case where new shape spreads single dimension over several dimensions
    586                                                        if (ne == (nr + 1)) {
    587                                                                break;
    588                                                        }
    589                                                        nl *= newShape[ne++];
    590                                                } while (nl < ol);
    591                                                if (nl != ol) {
    592                                                        logger.error("Subshape is incompatible with single dimension");
    593                                                        throw new IllegalArgumentException("Subshape is incompatible with single dimension");
    594                                                }
    595
    596                                        }
    597
    598                                        ob = oe;
    599                                        nb = ne;
    600                                }
    601
    602                        }
    603                }
    604
    605                @Override
    606                public ILazyDataset run(ILazyDataset lz) {
    607                        if (differences == null)
    608                                init();
    609
    610                        int[] lshape = lz.getShape();
    611                        if (Arrays.equals(newShape, lshape)) {
    612                                return lz;
    613                        }
    614                        int or = lz.getRank();
    615                        int nr = newShape.length;
    616                        int[] nshape = new int[nr];
    617                        Arrays.fill(nshape, 1);
    618                        if (onesOnly) {
    619                                // ignore omit removed dimensions
    620                                for (int i = 0, si = 0, di = 0; i < (or+1) && si <= or && di < nr; i++) {
    621                                        int c = differences[i];
    622                                        if (c == 0) {
    623                                                nshape[di++] = lshape[si++];
    624                                        } else if (c > 0) {
    625                                                while (c-- > 0 && di < nr) {
    626                                                        di++;
    627                                                }
    628                                        } else if (c < 0) {
    629                                                si -= c; // remove dimensions by skipping forward in source array
    630                                        }
    631                                }
    632                        } else {
    633                                boolean[] broadcast = new boolean[or];
    634                                for (int ob = 0; ob < or; ob++) {
    635                                        broadcast[ob] = oldShape[ob] != 1 && lshape[ob] == 1;
    636                                }
    637                                int osize = lz.getSize();
    638
    639                                // cannot do 3x5x... to 15x... if metadata is broadcasting (i.e. 1x5x...)
    640                                int ob = 0;
    641                                int nsize = 1;
    642                                for (int i = 0; i < nr; i++) {
    643                                        if (ob < or && broadcast[ob]) {
    644                                                if (differences[ob] != 0) {
    645                                                        logger.error("Metadata contains a broadcast axis which cannot be reshaped");
    646                                                        throw new IllegalArgumentException("Metadata contains a broadcast axis which cannot be reshaped");
    647                                                }
    648                                        } else {
    649                                                nshape[i] = nsize < osize ? newShape[i] : 1;
    650                                        }
    651                                        nsize *= nshape[i];
    652                                        ob++;
    653                                }
    654                        }
    655
    656                        ILazyDataset nlz = lz.getSliceView();
    657                        if (lz instanceof Dataset) {
    658                                nlz = ((Dataset) lz).reshape(nshape);
    659                        } else {
    660                                nlz = lz.getSliceView();
    661                                nlz.setShape(nshape);
    662                        }
    663                        return nlz;
    664                }
    665        }
    666
    667        class MdsTranspose implements MetadatasetAnnotationOperation {
    668                int[] map;
    669
    670                public MdsTranspose(final int[] axesMap) {
    671                        map = axesMap;
    672                }
    673
    674                @SuppressWarnings({ "rawtypes", "unchecked" })
    675                @Override
    676                public Object processField(Field f, Object o) {
    677                        // reorder arrays and lists according the axes map
    678                        if (o.getClass().isArray()) {
    679                                int l = Array.getLength(o);
    680                                if (l == map.length) {
    681                                        Object narray = Array.newInstance(o.getClass().getComponentType(), l);
    682                                        for (int i = 0; i < l; i++) {
    683                                                Array.set(narray, i, Array.get(o, map[i]));
    684                                        }
    685                                        for (int i = 0; i < l; i++) {
    686                                                Array.set(o, i, Array.get(narray, i));
    687                                        }
    688                                }
    689                        } else if (o instanceof List<?>) {
    690                                List list = (List) o;
    691                                int l = list.size();
    692                                if (l == map.length) {
    693                                        Object narray = Array.newInstance(o.getClass().getComponentType(), l);
    694                                        for (int i = 0; i < l; i++) {
    695                                                Array.set(narray, i, list.get(map[i]));
    696                                        }
    697                                        list.clear();
    698                                        for (int i = 0; i < l; i++) {
    699                                                list.add(Array.get(narray, i));
    700                                        }
    701                                }
    702                        }
    703                        return o;
    704                }
    705
    706                @Override
    707                public Class<? extends Annotation> getAnnClass() {
    708                        return Transposable.class;
    709                }
    710
    711                @Override
    712                public int change(int axis) {
    713                        return 0;
    714                }
    715
    716                @Override
    717                public int getNewRank() {
    718                        return -1;
    719                }
    720
    721                @Override
    722                public ILazyDataset run(ILazyDataset lz) {
    723                        return lz.getTransposedView(map);
    724                }
    725        }
    726
    727        class MdsDirty implements MetadatasetAnnotationOperation {
    728
    729                @Override
    730                public Object processField(Field f, Object o) {
    731                        // throw exception if not boolean???
    732                        Class<?> t = f.getType();
    733                        if (t.equals(boolean.class) || t.equals(Boolean.class)) {
    734                                if (o.equals(false)) {
    735                                        o = true;
    736                                }
    737                        }
    738                        return o;
    739                }
    740
    741                @Override
    742                public Class<? extends Annotation> getAnnClass() {
    743                        return Dirtiable.class;
    744                }
    745
    746                @Override
    747                public int change(int axis) {
    748                        return 0;
    749                }
    750
    751                @Override
    752                public int getNewRank() {
    753                        return -1;
    754                }
    755
    756                @Override
    757                public ILazyDataset run(ILazyDataset lz) {
    758                        return lz;
    759                }
    760        }
    761
    762        /**
    763         * Slice all datasets in metadata that are annotated by @Sliceable. Call this on the new sliced
    764         * dataset after cloning the metadata
    765         * @param asView if true then just a view
    766         * @param slice
    767         */
    768        protected void sliceMetadata(boolean asView, final SliceND slice) {
    769                processAnnotatedMetadata(new MdsSlice(asView, slice.getStart(), slice.getStop(), slice.getStep(), slice.getSourceShape()), true);
    770        }
    771
    772        /**
    773         * Reshape all datasets in metadata that are annotated by @Reshapeable. Call this when squeezing
    774         * or setting the shape
    775         *
    776         * @param newShape
    777         */
    778        protected void reshapeMetadata(final int[] oldShape, final int[] newShape) {
    779                processAnnotatedMetadata(new MdsReshape(oldShape, newShape), true);
    780        }
    781
    782        /**
    783         * Transpose all datasets in metadata that are annotated by @Transposable. Call this on the transposed
    784         * dataset after cloning the metadata
    785         * @param axesMap
    786         */
    787        protected void transposeMetadata(final int[] axesMap) {
    788                processAnnotatedMetadata(new MdsTranspose(axesMap), true);
    789        }
    790
    791        /**
    792         * Dirty metadata that are annotated by @Dirtiable. Call this when the dataset has been modified
    793         * @since 2.0
    794         */
    795        protected void dirtyMetadata() {
    796                processAnnotatedMetadata(new MdsDirty(), true);
    797        }
    798
    799        @SuppressWarnings("unchecked")
    800        private void processAnnotatedMetadata(MetadatasetAnnotationOperation op, boolean throwException) {
    801                if (metadata == null)
    802                        return;
    803
    804                for (Class<? extends MetadataType> c : metadata.keySet()) {
    805                        for (MetadataType m : metadata.get(c)) {
    806                                if (m == null)
    807                                        continue;
    808
    809                                Class<? extends MetadataType> mc = m.getClass();
    810                                do { // iterate over super-classes
    811                                        processClass(op, m, mc, throwException);
    812                                        Class<?> sclazz = mc.getSuperclass();
    813                                        if (!MetadataType.class.isAssignableFrom(sclazz))
    814                                                break;
    815                                        mc = (Class<? extends MetadataType>) sclazz;
    816                                } while (true);
    817                        }
    818                }
    819        }
    820
    821        @SuppressWarnings({ "unchecked", "rawtypes" })
    822        private static void processClass(MetadatasetAnnotationOperation op, MetadataType m, Class<? extends MetadataType> mc, boolean throwException) {
    823                for (Field f : mc.getDeclaredFields()) {
    824                        if (!f.isAnnotationPresent(op.getAnnClass()))
    825                                continue;
    826
    827                        try {
    828                                f.setAccessible(true);
    829                                Object o = f.get(m);
    830                                if (o == null)
    831                                        continue;
    832
    833                                Object no = op.processField(f, o);
    834                                if (no != o) {
    835                                        f.set(m, no);
    836                                        continue;
    837                                }
    838                                Object r = null;
    839                                if (o instanceof ILazyDataset) {
    840                                        try {
    841                                                f.set(m, op.run((ILazyDataset) o));
    842                                        } catch (Exception e) {
    843                                                logger.error("Problem processing " + o, e);
    844                                                if (!catchExceptions)
    845                                                        throw e;
    846                                        }
    847                                } else if (o.getClass().isArray()) {
    848                                        int l = Array.getLength(o);
    849                                        if (l <= 0)
    850                                                continue;
    851
    852                                        for (int i = 0; r == null && i < l; i++) {
    853                                                r = Array.get(o, i);
    854                                        }
    855                                        int n = op.getNewRank();
    856                                        if (r == null) {
    857                                                if (n < 0 || n != l) { // all nulls be need to match rank as necessary
    858                                                        f.set(m, Array.newInstance(o.getClass().getComponentType(), n < 0 ? l : n));
    859                                                }
    860                                                continue;
    861                                        }
    862                                        if (n < 0)
    863                                                n = l;
    864                                        Object narray = Array.newInstance(r.getClass(), n);
    865                                        for (int i = 0, si = 0, di = 0; di < n && si < l; i++) {
    866                                                int c = op.change(i);
    867                                                if (c == 0) {
    868                                                        Array.set(narray, di++, processObject(op, Array.get(o, si++)));
    869                                                } else if (c > 0) {
    870                                                        di += c; // add nulls by skipping forward in destination array
    871                                                } else if (c < 0) {
    872                                                        si -= c; // remove dimensions by skipping forward in source array
    873                                                }
    874                                        }
    875                                        if (n == l) {
    876                                                for (int i = 0; i < l; i++) {
    877                                                        Array.set(o, i, Array.get(narray, i));
    878                                                }
    879                                        } else {
    880                                                f.set(m, narray);
    881                                        }
    882                                } else if (o instanceof List<?>) {
    883                                        List list = (List) o;
    884                                        int l = list.size();
    885                                        if (l <= 0)
    886                                                continue;
    887
    888                                        for (int i = 0; r == null && i < l; i++) {
    889                                                r = list.get(i);
    890                                        }
    891                                        int n = op.getNewRank();
    892                                        if (r == null) {
    893                                                if (n < 0 || n != l) { // all nulls be need to match rank as necessary
    894                                                        list.clear();
    895                                                        for (int i = 0, imax = n < 0 ? l : n; i < imax; i++) {
    896                                                                list.add(null);
    897                                                        }
    898                                                }
    899                                                continue;
    900                                        }
    901
    902                                        if (n < 0)
    903                                                n = l;
    904                                        Object narray = Array.newInstance(r.getClass(), n);
    905                                        for (int i = 0, si = 0, di = 0; i < l && si < l; i++) {
    906                                                int c = op.change(i);
    907                                                if (c == 0) {
    908                                                        Array.set(narray, di++, processObject(op, list.get(si++)));
    909                                                } else if (c > 0) {
    910                                                        di += c; // add nulls by skipping forward in destination array
    911                                                } else if (c < 0) {
    912                                                        si -= c; // remove dimensions by skipping forward in source array
    913                                                }
    914                                        }
    915                                        list.clear();
    916                                        for (int i = 0; i < n; i++) {
    917                                                list.add(Array.get(narray, i));
    918                                        }
    919                                } else if (o instanceof Map<?,?>) {
    920                                        Map map = (Map) o;
    921                                        for (Object k : map.keySet()) {
    922                                                map.put(k, processObject(op, map.get(k)));
    923                                        }
    924                                }
    925                        } catch (Exception e) {
    926                                logger.error("Problem occurred when processing metadata of class {}: {}", mc.getCanonicalName(), e);
    927                                if (throwException)
    928                                        throw new RuntimeException(e);
    929                        }
    930                }
    931        }
    932
    933        @SuppressWarnings({ "unchecked", "rawtypes" })
    934        private static Object processObject(MetadatasetAnnotationOperation op, Object o) throws Exception {
    935                if (o == null)
    936                        return o;
    937
    938                if (o instanceof ILazyDataset) {
    939                        try {
    940                                return op.run((ILazyDataset) o);
    941                        } catch (Exception e) {
    942                                logger.error("Problem processing " + o, e);
    943                                if (!catchExceptions)
    944                                        throw e;
    945                        }
    946                } else if (o.getClass().isArray()) {
    947                        int l = Array.getLength(o);
    948                        for (int i = 0; i < l; i++) {
    949                                Array.set(o, i, processObject(op, Array.get(o, i)));
    950                        }
    951                } else if (o instanceof List<?>) {
    952                        List list = (List) o;
    953                        for (int i = 0, imax = list.size(); i < imax; i++) {
    954                                list.set(i, processObject(op, list.get(i)));
    955                        }
    956                } else if (o instanceof Map<?,?>) {
    957                        Map map = (Map) o;
    958                        for (Object k : map.keySet()) {
    959                                map.put(k, processObject(op, map.get(k)));
    960                        }
    961                }
    962                return o;
    963        }
    964
    965        protected void restoreMetadata(Map<Class<? extends MetadataType>, List<MetadataType>> oldMetadata) {
    966                for (Class<? extends MetadataType> mc : oldMetadata.keySet()) {
    967                        metadata.put(mc, oldMetadata.get(mc));
    968                }
    969        }
    970
    971        protected ILazyDataset createFromSerializable(Serializable blob, boolean keepLazy) {
    972                ILazyDataset d = null;
    973                if (blob instanceof ILazyDataset) {
    974                        d = (ILazyDataset) blob;
    975                        if (d instanceof IDataset) {
    976                                Dataset ed = DatasetUtils.convertToDataset((IDataset) d);
    977                                int is = ed.getElementsPerItem();
    978                                if (is != 1 && is != getElementsPerItem()) {
    979                                        throw new IllegalArgumentException("Dataset has incompatible number of elements with this dataset");
    980                                }
    981                                d = ed.cast(is == 1 ? Dataset.FLOAT64 : Dataset.ARRAYFLOAT64);
    982                        } else if (!keepLazy) {
    983                                final int is = getElementsPerItem();
    984                                try {
    985                                        d = DatasetUtils.cast(d.getSlice(), is == 1 ? Dataset.FLOAT64 : Dataset.ARRAYFLOAT64);
    986                                } catch (DatasetException e) {
    987                                        logger.error("Could not get data from lazy dataset", e);
    988                                        return null;
    989                                }
    990                        }
    991                } else {
    992                        final int is = getElementsPerItem();
    993                        if (is == 1) {
    994                                d = DatasetFactory.createFromObject(DoubleDataset.class, blob);
    995                        } else {
    996                                try {
    997                                        d = DatasetFactory.createFromObject(is, CompoundDoubleDataset.class, blob);
    998                                } catch (IllegalArgumentException e) { // if only single value supplied try again
    999                                        d = DatasetFactory.createFromObject(DoubleDataset.class, blob);
    1000                                }
    1001                        }
    1002                        if (d.getSize() == getSize() && !Arrays.equals(d.getShape(), shape)) {
    1003                                d.setShape(shape.clone());
    1004                        }
    1005                }
    1006                List<int[]> s = BroadcastUtils.broadcastShapesToMax(shape, d.getShape());
    1007                d.setShape(s.get(0));
    1008
    1009                return d;
    1010        }
    1011
    1012        @Override
    1013        public void setErrors(Serializable errors) {
    1014                if (shape == null) {
    1015                        throw new IllegalArgumentException("Cannot set errors for null dataset");
    1016                }
    1017                if (errors == null) {
    1018                        clearMetadata(ErrorMetadata.class);
    1019                        return;
    1020                }
    1021                if (errors == this) {
    1022                        logger.warn("Ignoring setting error to itself as this will lead to infinite recursion");
    1023                        return;
    1024                }
    1025
    1026                ILazyDataset errorData = createFromSerializable(errors, true);
    1027
    1028                ErrorMetadata emd = getErrorMetadata();
    1029                if (emd == null) {
    1030                        try {
    1031                                emd = MetadataFactory.createMetadata(ErrorMetadata.class);
    1032                                setMetadata(emd);
    1033                        } catch (MetadataException me) {
    1034                                logger.error("Could not create metadata", me);
    1035                        }
    1036                }
    1037                emd.setError(errorData);
    1038        }
    1039
    1040        protected ErrorMetadata getErrorMetadata() {
    1041                try {
    1042                        List<ErrorMetadata> el = getMetadata(ErrorMetadata.class);
    1043                        if (el != null && !el.isEmpty()) {
    1044                                 return el.get(0);
    1045                        }
    1046                } catch (Exception e) {
    1047                }
    1048                return null;
    1049        }
    1050
    1051        @Override
    1052        public ILazyDataset getErrors() {
    1053                ErrorMetadata emd = getErrorMetadata();
    1054                return emd == null ? null : emd.getError();
    1055        }
    1056
    1057        @Override
    1058        public boolean hasErrors() {
    1059                return LazyDatasetBase.this.getErrors() != null;
    1060        }
    1061
    1062        /**
    1063         * Check permutation axes
    1064         * @param shape
    1065         * @param axes
    1066         * @return cleaned up axes or null if trivial
    1067         */
    1068        public static int[] checkPermutatedAxes(int[] shape, int... axes) {
    1069                int rank = shape == null ? 0 : shape.length;
    1070
    1071                if (axes == null || axes.length == 0) {
    1072                        axes = new int[rank];
    1073                        for (int i = 0; i < rank; i++) {
    1074                                axes[i] = rank - 1 - i;
    1075                        }
    1076                }
    1077
    1078                if (axes.length != rank) {
    1079                        logger.error("axis permutation has length {} that does not match dataset's rank {}", axes.length, rank);
    1080                        throw new IllegalArgumentException("axis permutation does not match shape of dataset");
    1081                }
    1082
    1083                // check all permutation values are within bounds
    1084                for (int i = 0; i < rank; i++) {
    1085                        axes[i] = ShapeUtils.checkAxis(rank, axes[i]);
    1086                }
    1087
    1088                // check for a valid permutation (is this an unnecessary restriction?)
    1089                int[] perm = axes.clone();
    1090                Arrays.sort(perm);
    1091
    1092                for (int i = 0; i < rank; i++) {
    1093                        if (perm[i] != i) {
    1094                                logger.error("axis permutation is not valid: it does not contain complete set of axes");
    1095                                throw new IllegalArgumentException("axis permutation does not contain complete set of axes");
    1096                        }
    1097                }
    1098
    1099                if (Arrays.equals(axes, perm))
    1100                        return null; // signal identity or trivial permutation
    1101
    1102                return axes;
    1103        }
    1104}