    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, null);
    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                return copyMetadata(metadata, null);
    313        }
    314
    315        /**
    316         * Copy metadata. If oMetadata is not null, then copy from that when it has the corresponding items
    317         * @since 2.1.2
    318         * @param metadata
    319         * @param oMetadata can be null
    320         * @return
    321         */
    322        protected static ConcurrentMap<Class<? extends MetadataType>, List<MetadataType>> copyMetadata(Map<Class<? extends MetadataType>, List<MetadataType>> metadata, Map<Class<? extends MetadataType>, List<MetadataType>> oMetadata) {
    323                if (metadata == null)
    324                        return null;
    325
    326                ConcurrentHashMap<Class<? extends MetadataType>, List<MetadataType>> map = new ConcurrentHashMap<Class<? extends MetadataType>, List<MetadataType>>();
    327
    328                for (Class<? extends MetadataType> c : metadata.keySet()) {
    329                        List<MetadataType> l = metadata.get(c);
    330                        if (!l.isEmpty() && oMetadata != null && oMetadata.containsKey(c)) { // only override when not empty
    331                                l = oMetadata.get(c);
    332                        }
    333                        List<MetadataType> nl = new ArrayList<MetadataType>(l.size());
    334                        map.put(c, nl);
    335                        for (MetadataType m : l) {
    336                                nl.add(m.clone());
    337                        }
    338                }
    339                return map;
    340        }
    341
    342        interface MetadatasetAnnotationOperation {
    343                /**
    344                 * Process value of given field
    345                 * <p>
    346                 * When the field is not a container then the returned value
    347                 * may replace the old value
    348                 * @param f given field
    349                 * @param o value of field
    350                 * @return transformed field
    351                 */
    352                Object processField(Field f, Object o);
    353
    354                /**
    355                 * @return annotated class
    356                 */
    357                Class<? extends Annotation> getAnnClass();
    358
    359                /**
    360                 * @param axis
    361                 * @return number of dimensions to insert or remove
    362                 */
    363                int change(int axis);
    364
    365                /**
    366                 *
    367                 * @return rank or -1 to match
    368                 */
    369                int getNewRank();
    370
    371                /**
    372                 * Run on given lazy dataset
    373                 * @param lz
    374                 * @return
    375                 */
    376                ILazyDataset run(ILazyDataset lz);
    377        }
    378
    379        class MdsSlice implements MetadatasetAnnotationOperation {
    380                private boolean asView;
    381                private int[] start;
    382                private int[] stop;
    383                private int[] step;
    384                private int[] oShape;
    385                private long oSize;
    386
    387                public MdsSlice(boolean asView, final int[] start, final int[] stop, final int[] step, final int[] oShape) {
    388                        this.asView = asView;
    389                        this.start = start;
    390                        this.stop = stop;
    391                        this.step = step;
    392                        this.oShape = oShape;
    393                        oSize = ShapeUtils.calcLongSize(oShape);
    394                }
    395
    396                @Override
    397                public Object processField(Field field, Object o) {
    398                        return o;
    399                }
    400
    401                @Override
    402                public Class<? extends Annotation> getAnnClass() {
    403                        return Sliceable.class;
    404                }
    405
    406                @Override
    407                public int change(int axis) {
    408                        return 0;
    409                }
    410
    411                @Override
    412                public int getNewRank() {
    413                        return -1;
    414                }
    415
    416                @Override
    417                public ILazyDataset run(ILazyDataset lz) {
    418                        int rank = lz.getRank();
    419                        if (start.length != rank) {
    420                                throw new IllegalArgumentException("Slice dimensions do not match dataset!");
    421                        }
    422
    423                        int[] shape = lz.getShape();
    424                        int[] stt;
    425                        int[] stp;
    426                        int[] ste;
    427                        if (lz.getSize() == oSize) {
    428                                stt = start;
    429                                stp = stop;
    430                                ste = step;
    431                        } else {
    432                                stt = start.clone();
    433                                stp = stop.clone();
    434                                ste = step.clone();
    435                                for (int i = 0; i < rank; i++) {
    436                                        if (shape[i] >= oShape[i]) continue;
    437                                        if (shape[i] == 1) {
    438                                                stt[i] = 0;
    439                                                stp[i] = 1;
    440                                                ste[i] = 1;
    441                                        } else {
    442                                                throw new IllegalArgumentException("Sliceable dataset has invalid size!");
    443                                        }
    444                                }
    445                        }
    446
    447                        if (asView || (lz instanceof IDataset))
    448                                return lz.getSliceView(stt, stp, ste);
    449                        try {
    450                                return lz.getSlice(stt, stp, ste);
    451                        } catch (DatasetException e) {
    452                                logger.error("Could not slice dataset in metadata", e);
    453                                return null;
    454                        }
    455                }
    456        }
    457
    458        class MdsReshape implements MetadatasetAnnotationOperation {
    459                private boolean matchRank;
    460                private int[] oldShape;
    461                private int[] newShape;
    462                boolean onesOnly;
    463                int[] differences;
    464
    465                /*
    466                 * if only ones then record differences (insertions and deletions)
    467                 *
    468                 * if shape changing, find broadcasted dimensions and disallow
    469                 * merging that include those dimensions
    470                 */
    471                public MdsReshape(final int[] oldShape, final int[] newShape) {
    472                        this.oldShape = oldShape;
    473                        this.newShape = newShape;
    474                        differences = null;
    475                }
    476
    477                @Override
    478                public Object processField(Field field, Object o) {
    479                        Annotation a = field.getAnnotation(Reshapeable.class);
    480                        if (a != null) { // cannot be null
    481                                matchRank = ((Reshapeable) a).matchRank();
    482                        }
    483                        return o;
    484                }
    485
    486                @Override
    487                public Class<? extends Annotation> getAnnClass() {
    488                        return Reshapeable.class;
    489                }
    490
    491                @Override
    492                public int change(int axis) {
    493                        if (matchRank) {
    494                                if (differences == null)
    495                                        init();
    496
    497                                if (onesOnly) {
    498                                        return differences[axis];
    499                                }
    500                                throw new UnsupportedOperationException("TODO support other shape operations");
    501                        }
    502                        return 0;
    503                }
    504
    505                @Override
    506                public int getNewRank() {
    507                        return matchRank ? newShape.length : -1;
    508                }
    509
    510                private void init() {
    511                        int or = oldShape.length - 1;
    512                        int nr = newShape.length - 1;
    513                        if (or < 0 || nr < 0) { // zero-rank shapes
    514                                onesOnly = true;
    515                                differences = new int[1];
    516                                differences[0] = or < 0 ? nr + 1 : or + 1;
    517                                return;
    518                        }
    519                        int ob = 0;
    520                        int nb = 0;
    521                        onesOnly = true;
    522                        do {
    523                                while (oldShape[ob] == 1 && ob < or) {
    524                                        ob++; // next non-unit dimension
    525                                }
    526                                while (newShape[nb] == 1 && nb < nr) {
    527                                        nb++;
    528                                }
    529                                if (oldShape[ob++] != newShape[nb++]) {
    530                                        onesOnly = false;
    531                                        break;
    532                                }
    533                        } while (ob <= or && nb <= nr);
    534
    535                        ob = 0;
    536                        nb = 0;
    537                        differences = new int[or + 2];
    538                        if (onesOnly) {
    539                                // work out unit dimensions removed from or add to old
    540                                int j = 0;
    541                                do {
    542                                        if (oldShape[ob] != 1 && newShape[nb] != 1) {
    543                                                ob++;
    544                                                nb++;
    545                                        } else {
    546                                                while (oldShape[ob] == 1 && ob < or) {
    547                                                        ob++;
    548                                                        differences[j]--;
    549                                                }
    550                                                while (newShape[nb] == 1 && nb < nr) {
    551                                                        nb++;
    552                                                        differences[j]++;
    553                                                }
    554                                        }
    555                                        j++;
    556                                } while (ob <= or && nb <= nr && j <= or);
    557                                while (ob <= or && oldShape[ob] == 1) {
    558                                        ob++;
    559                                        differences[j]--;
    560                                }
    561                                while (nb <= nr && newShape[nb] == 1) {
    562                                        nb++;
    563                                        differences[j]++;
    564                                }
    565                        } else {
    566                                if (matchRank) {
    567                                        logger.error("Combining dimensions is currently not supported");
    568                                        throw new IllegalArgumentException("Combining dimensions is currently not supported");
    569                                }
    570                                // work out mapping: contiguous dimensions can be grouped or split
    571                                while (ob <= or && nb <= nr) {
    572                                        int ol = oldShape[ob];
    573                                        while (ol == 1 && ol <= or) {
    574                                                ob++;
    575                                                ol = oldShape[ob];
    576                                        }
    577                                        int oe = ob + 1;
    578                                        int nl = newShape[nb];
    579                                        while (nl == 1 && nl <= nr) {
    580                                                nb++;
    581                                                nl = newShape[nb];
    582                                        }
    583                                        int ne = nb + 1;
    584                                        if (ol < nl) {
    585                                                differences[ob] = 1;
    586                                                do { // case where new shape combines several dimensions into one dimension
    587                                                        if (oe == (or + 1)) {
    588                                                                break;
    589                                                        }
    590                                                        differences[oe] = 1;
    591                                                        ol *= oldShape[oe++];
    592                                                } while (ol < nl);
    593                                                differences[oe - 1] = oe - ob; // signal end with difference
    594                                                if (nl != ol) {
    595                                                        logger.error("Single dimension is incompatible with subshape");
    596                                                        throw new IllegalArgumentException("Single dimension is incompatible with subshape");
    597                                                }
    598                                        } else if (ol > nl) {
    599                                                do { // case where new shape spreads single dimension over several dimensions
    600                                                        if (ne == (nr + 1)) {
    601                                                                break;
    602                                                        }
    603                                                        nl *= newShape[ne++];
    604                                                } while (nl < ol);
    605                                                if (nl != ol) {
    606                                                        logger.error("Subshape is incompatible with single dimension");
    607                                                        throw new IllegalArgumentException("Subshape is incompatible with single dimension");
    608                                                }
    609
    610                                        }
    611
    612                                        ob = oe;
    613                                        nb = ne;
    614                                }
    615
    616                        }
    617                }
    618
    619                @Override
    620                public ILazyDataset run(ILazyDataset lz) {
    621                        if (differences == null)
    622                                init();
    623
    624                        int[] lshape = lz.getShape();
    625                        if (Arrays.equals(newShape, lshape)) {
    626                                return lz;
    627                        }
    628                        int or = lz.getRank();
    629                        int nr = newShape.length;
    630                        int[] nshape = new int[nr];
    631                        Arrays.fill(nshape, 1);
    632                        if (onesOnly) {
    633                                // ignore omit removed dimensions
    634                                for (int i = 0, si = 0, di = 0; i < (or+1) && si <= or && di < nr; i++) {
    635                                        int c = differences[i];
    636                                        if (c == 0) {
    637                                                nshape[di++] = lshape[si++];
    638                                        } else if (c > 0) {
    639                                                while (c-- > 0 && di < nr) {
    640                                                        di++;
    641                                                }
    642                                        } else if (c < 0) {
    643                                                si -= c; // remove dimensions by skipping forward in source array
    644                                        }
    645                                }
    646                        } else {
    647                                boolean[] broadcast = new boolean[or];
    648                                for (int ob = 0; ob < or; ob++) {
    649                                        broadcast[ob] = oldShape[ob] != 1 && lshape[ob] == 1;
    650                                }
    651                                int osize = lz.getSize();
    652
    653                                // cannot do 3x5x... to 15x... if metadata is broadcasting (i.e. 1x5x...)
    654                                int ob = 0;
    655                                int nsize = 1;
    656                                for (int i = 0; i < nr; i++) {
    657                                        if (ob < or && broadcast[ob]) {
    658                                                if (differences[ob] != 0) {
    659                                                        logger.error("Metadata contains a broadcast axis which cannot be reshaped");
    660                                                        throw new IllegalArgumentException("Metadata contains a broadcast axis which cannot be reshaped");
    661                                                }
    662                                        } else {
    663                                                nshape[i] = nsize < osize ? newShape[i] : 1;
    664                                        }
    665                                        nsize *= nshape[i];
    666                                        ob++;
    667                                }
    668                        }
    669
    670                        ILazyDataset nlz = lz.getSliceView();
    671                        if (lz instanceof Dataset) {
    672                                nlz = ((Dataset) lz).reshape(nshape);
    673                        } else {
    674                                nlz = lz.getSliceView();
    675                                nlz.setShape(nshape);
    676                        }
    677                        return nlz;
    678                }
    679        }
    680
    681        class MdsTranspose implements MetadatasetAnnotationOperation {
    682                int[] map;
    683
    684                public MdsTranspose(final int[] axesMap) {
    685                        map = axesMap;
    686                }
    687
    688                @SuppressWarnings({ "rawtypes", "unchecked" })
    689                @Override
    690                public Object processField(Field f, Object o) {
    691                        // reorder arrays and lists according the axes map
    692                        if (o.getClass().isArray()) {
    693                                int l = Array.getLength(o);
    694                                if (l == map.length) {
    695                                        Object narray = Array.newInstance(o.getClass().getComponentType(), l);
    696                                        for (int i = 0; i < l; i++) {
    697                                                Array.set(narray, i, Array.get(o, map[i]));
    698                                        }
    699                                        for (int i = 0; i < l; i++) {
    700                                                Array.set(o, i, Array.get(narray, i));
    701                                        }
    702                                }
    703                        } else if (o instanceof List<?>) {
    704                                List list = (List) o;
    705                                int l = list.size();
    706                                if (l == map.length) {
    707                                        Object narray = Array.newInstance(o.getClass().getComponentType(), l);
    708                                        for (int i = 0; i < l; i++) {
    709                                                Array.set(narray, i, list.get(map[i]));
    710                                        }
    711                                        list.clear();
    712                                        for (int i = 0; i < l; i++) {
    713                                                list.add(Array.get(narray, i));
    714                                        }
    715                                }
    716                        }
    717                        return o;
    718                }
    719
    720                @Override
    721                public Class<? extends Annotation> getAnnClass() {
    722                        return Transposable.class;
    723                }
    724
    725                @Override
    726                public int change(int axis) {
    727                        return 0;
    728                }
    729
    730                @Override
    731                public int getNewRank() {
    732                        return -1;
    733                }
    734
    735                @Override
    736                public ILazyDataset run(ILazyDataset lz) {
    737                        return lz.getTransposedView(map);
    738                }
    739        }
    740
    741        class MdsDirty implements MetadatasetAnnotationOperation {
    742
    743                @Override
    744                public Object processField(Field f, Object o) {
    745                        // throw exception if not boolean???
    746                        Class<?> t = f.getType();
    747                        if (t.equals(boolean.class) || t.equals(Boolean.class)) {
    748                                if (o.equals(false)) {
    749                                        o = true;
    750                                }
    751                        }
    752                        return o;
    753                }
    754
    755                @Override
    756                public Class<? extends Annotation> getAnnClass() {
    757                        return Dirtiable.class;
    758                }
    759
    760                @Override
    761                public int change(int axis) {
    762                        return 0;
    763                }
    764
    765                @Override
    766                public int getNewRank() {
    767                        return -1;
    768                }
    769
    770                @Override
    771                public ILazyDataset run(ILazyDataset lz) {
    772                        return lz;
    773                }
    774        }
    775
    776        /**
    777         * Slice all datasets in metadata that are annotated by @Sliceable. Call this on the new sliced
    778         * dataset after cloning the metadata
    779         * @param asView if true then just a view
    780         * @param slice
    781         */
    782        protected void sliceMetadata(boolean asView, final SliceND slice) {
    783                processAnnotatedMetadata(new MdsSlice(asView, slice.getStart(), slice.getStop(), slice.getStep(), slice.getSourceShape()), true);
    784        }
    785
    786        /**
    787         * Reshape all datasets in metadata that are annotated by @Reshapeable. Call this when squeezing
    788         * or setting the shape
    789         *
    790         * @param newShape
    791         */
    792        protected void reshapeMetadata(final int[] oldShape, final int[] newShape) {
    793                processAnnotatedMetadata(new MdsReshape(oldShape, newShape), true);
    794        }
    795
    796        /**
    797         * Transpose all datasets in metadata that are annotated by @Transposable. Call this on the transposed
    798         * dataset after cloning the metadata
    799         * @param axesMap
    800         */
    801        protected void transposeMetadata(final int[] axesMap) {
    802                processAnnotatedMetadata(new MdsTranspose(axesMap), true);
    803        }
    804
    805        /**
    806         * Dirty metadata that are annotated by @Dirtiable. Call this when the dataset has been modified
    807         * @since 2.0
    808         */
    809        protected void dirtyMetadata() {
    810                processAnnotatedMetadata(new MdsDirty(), true);
    811        }
    812
    813        @SuppressWarnings("unchecked")
    814        private void processAnnotatedMetadata(MetadatasetAnnotationOperation op, boolean throwException) {
    815                if (metadata == null)
    816                        return;
    817
    818                for (Class<? extends MetadataType> c : metadata.keySet()) {
    819                        for (MetadataType m : metadata.get(c)) {
    820                                if (m == null)
    821                                        continue;
    822
    823                                Class<? extends MetadataType> mc = m.getClass();
    824                                do { // iterate over super-classes
    825                                        processClass(op, m, mc, throwException);
    826                                        Class<?> sclazz = mc.getSuperclass();
    827                                        if (!MetadataType.class.isAssignableFrom(sclazz))
    828                                                break;
    829                                        mc = (Class<? extends MetadataType>) sclazz;
    830                                } while (true);
    831                        }
    832                }
    833        }
    834
    835        @SuppressWarnings({ "unchecked", "rawtypes" })
    836        private static void processClass(MetadatasetAnnotationOperation op, MetadataType m, Class<? extends MetadataType> mc, boolean throwException) {
    837                for (Field f : mc.getDeclaredFields()) {
    838                        if (!f.isAnnotationPresent(op.getAnnClass()))
    839                                continue;
    840
    841                        try {
    842                                f.setAccessible(true);
    843                                Object o = f.get(m);
    844                                if (o == null)
    845                                        continue;
    846
    847                                Object no = op.processField(f, o);
    848                                if (no != o) {
    849                                        f.set(m, no);
    850                                        continue;
    851                                }
    852                                Object r = null;
    853                                if (o instanceof ILazyDataset) {
    854                                        try {
    855                                                f.set(m, op.run((ILazyDataset) o));
    856                                        } catch (Exception e) {
    857                                                logger.error("Problem processing " + o, e);
    858                                                if (!catchExceptions)
    859                                                        throw e;
    860                                        }
    861                                } else if (o.getClass().isArray()) {
    862                                        int l = Array.getLength(o);
    863                                        if (l <= 0)
    864                                                continue;
    865
    866                                        for (int i = 0; r == null && i < l; i++) {
    867                                                r = Array.get(o, i);
    868                                        }
    869                                        int n = op.getNewRank();
    870                                        if (r == null) {
    871                                                if (n < 0 || n != l) { // all nulls be need to match rank as necessary
    872                                                        f.set(m, Array.newInstance(o.getClass().getComponentType(), n < 0 ? l : n));
    873                                                }
    874                                                continue;
    875                                        }
    876                                        if (n < 0)
    877                                                n = l;
    878                                        Object narray = Array.newInstance(r.getClass(), n);
    879                                        for (int i = 0, si = 0, di = 0; di < n && si < l; i++) {
    880                                                int c = op.change(i);
    881                                                if (c == 0) {
    882                                                        Array.set(narray, di++, processObject(op, Array.get(o, si++)));
    883                                                } else if (c > 0) {
    884                                                        di += c; // add nulls by skipping forward in destination array
    885                                                } else if (c < 0) {
    886                                                        si -= c; // remove dimensions by skipping forward in source array
    887                                                }
    888                                        }
    889                                        if (n == l) {
    890                                                for (int i = 0; i < l; i++) {
    891                                                        Array.set(o, i, Array.get(narray, i));
    892                                                }
    893                                        } else {
    894                                                f.set(m, narray);
    895                                        }
    896                                } else if (o instanceof List<?>) {
    897                                        List list = (List) o;
    898                                        int l = list.size();
    899                                        if (l <= 0)
    900                                                continue;
    901
    902                                        for (int i = 0; r == null && i < l; i++) {
    903                                                r = list.get(i);
    904                                        }
    905                                        int n = op.getNewRank();
    906                                        if (r == null) {
    907                                                if (n < 0 || n != l) { // all nulls be need to match rank as necessary
    908                                                        list.clear();
    909                                                        for (int i = 0, imax = n < 0 ? l : n; i < imax; i++) {
    910                                                                list.add(null);
    911                                                        }
    912                                                }
    913                                                continue;
    914                                        }
    915
    916                                        if (n < 0)
    917                                                n = l;
    918                                        Object narray = Array.newInstance(r.getClass(), n);
    919                                        for (int i = 0, si = 0, di = 0; i < l && si < l; i++) {
    920                                                int c = op.change(i);
    921                                                if (c == 0) {
    922                                                        Array.set(narray, di++, processObject(op, list.get(si++)));
    923                                                } else if (c > 0) {
    924                                                        di += c; // add nulls by skipping forward in destination array
    925                                                } else if (c < 0) {
    926                                                        si -= c; // remove dimensions by skipping forward in source array
    927                                                }
    928                                        }
    929                                        list.clear();
    930                                        for (int i = 0; i < n; i++) {
    931                                                list.add(Array.get(narray, i));
    932                                        }
    933                                } else if (o instanceof Map<?,?>) {
    934                                        Map map = (Map) o;
    935                                        for (Object k : map.keySet()) {
    936                                                map.put(k, processObject(op, map.get(k)));
    937                                        }
    938                                }
    939                        } catch (Exception e) {
    940                                logger.error("Problem occurred when processing metadata of class {}: {}", mc.getCanonicalName(), e);
    941                                if (throwException)
    942                                        throw new RuntimeException(e);
    943                        }
    944                }
    945        }
    946
    947        @SuppressWarnings({ "unchecked", "rawtypes" })
    948        private static Object processObject(MetadatasetAnnotationOperation op, Object o) throws Exception {
    949                if (o == null)
    950                        return o;
    951
    952                if (o instanceof ILazyDataset) {
    953                        try {
    954                                return op.run((ILazyDataset) o);
    955                        } catch (Exception e) {
    956                                logger.error("Problem processing " + o, e);
    957                                if (!catchExceptions)
    958                                        throw e;
    959                        }
    960                } else if (o.getClass().isArray()) {
    961                        int l = Array.getLength(o);
    962                        for (int i = 0; i < l; i++) {
    963                                Array.set(o, i, processObject(op, Array.get(o, i)));
    964                        }
    965                } else if (o instanceof List<?>) {
    966                        List list = (List) o;
    967                        for (int i = 0, imax = list.size(); i < imax; i++) {
    968                                list.set(i, processObject(op, list.get(i)));
    969                        }
    970                } else if (o instanceof Map<?,?>) {
    971                        Map map = (Map) o;
    972                        for (Object k : map.keySet()) {
    973                                map.put(k, processObject(op, map.get(k)));
    974                        }
    975                }
    976                return o;
    977        }
    978
    979        protected void restoreMetadata(Map<Class<? extends MetadataType>, List<MetadataType>> oldMetadata) {
    980                for (Class<? extends MetadataType> mc : oldMetadata.keySet()) {
    981                        metadata.put(mc, oldMetadata.get(mc));
    982                }
    983        }
    984
    985        protected ILazyDataset createFromSerializable(Serializable blob, boolean keepLazy) {
    986                ILazyDataset d = null;
    987                if (blob instanceof ILazyDataset) {
    988                        d = (ILazyDataset) blob;
    989                        if (d instanceof IDataset) {
    990                                Dataset ed = DatasetUtils.convertToDataset((IDataset) d);
    991                                int is = ed.getElementsPerItem();
    992                                if (is != 1 && is != getElementsPerItem()) {
    993                                        throw new IllegalArgumentException("Dataset has incompatible number of elements with this dataset");
    994                                }
    995                                d = ed.cast(is == 1 ? Dataset.FLOAT64 : Dataset.ARRAYFLOAT64);
    996                        } else if (!keepLazy) {
    997                                final int is = getElementsPerItem();
    998                                try {
    999                                        d = DatasetUtils.cast(d.getSlice(), is == 1 ? Dataset.FLOAT64 : Dataset.ARRAYFLOAT64);
    1000                                } catch (DatasetException e) {
    1001                                        logger.error("Could not get data from lazy dataset", e);
    1002                                        return null;
    1003                                }
    1004                        }
    1005                } else {
    1006                        final int is = getElementsPerItem();
    1007                        if (is == 1) {
    1008                                d = DatasetFactory.createFromObject(DoubleDataset.class, blob);
    1009                        } else {
    1010                                try {
    1011                                        d = DatasetFactory.createFromObject(is, CompoundDoubleDataset.class, blob);
    1012                                } catch (IllegalArgumentException e) { // if only single value supplied try again
    1013                                        d = DatasetFactory.createFromObject(DoubleDataset.class, blob);
    1014                                }
    1015                        }
    1016                        if (d.getSize() == getSize() && !Arrays.equals(d.getShape(), shape)) {
    1017                                d.setShape(shape.clone());
    1018                        }
    1019                }
    1020                List<int[]> s = BroadcastUtils.broadcastShapesToMax(shape, d.getShape());
    1021                d.setShape(s.get(0));
    1022
    1023                return d;
    1024        }
    1025
    1026        @Override
    1027        public void setErrors(Serializable errors) {
    1028                if (shape == null) {
    1029                        throw new IllegalArgumentException("Cannot set errors for null dataset");
    1030                }
    1031                if (errors == null) {
    1032                        clearMetadata(ErrorMetadata.class);
    1033                        return;
    1034                }
    1035                if (errors == this) {
    1036                        logger.warn("Ignoring setting error to itself as this will lead to infinite recursion");
    1037                        return;
    1038                }
    1039
    1040                ILazyDataset errorData = createFromSerializable(errors, true);
    1041
    1042                ErrorMetadata emd = getErrorMetadata();
    1043                if (emd == null) {
    1044                        try {
    1045                                emd = MetadataFactory.createMetadata(ErrorMetadata.class);
    1046                                setMetadata(emd);
    1047                        } catch (MetadataException me) {
    1048                                logger.error("Could not create metadata", me);
    1049                        }
    1050                }
    1051                emd.setError(errorData);
    1052        }
    1053
    1054        protected ErrorMetadata getErrorMetadata() {
    1055                try {
    1056                        List<ErrorMetadata> el = getMetadata(ErrorMetadata.class);
    1057                        if (el != null && !el.isEmpty()) {
    1058                                 return el.get(0);
    1059                        }
    1060                } catch (Exception e) {
    1061                }
    1062                return null;
    1063        }
    1064
    1065        @Override
    1066        public ILazyDataset getErrors() {
    1067                ErrorMetadata emd = getErrorMetadata();
    1068                return emd == null ? null : emd.getError();
    1069        }
    1070
    1071        @Override
    1072        public boolean hasErrors() {
    1073                return LazyDatasetBase.this.getErrors() != null;
    1074        }
    1075
    1076        /**
    1077         * Check permutation axes
    1078         * @param shape
    1079         * @param axes
    1080         * @return cleaned up axes or null if trivial
    1081         */
    1082        public static int[] checkPermutatedAxes(int[] shape, int... axes) {
    1083                int rank = shape == null ? 0 : shape.length;
    1084
    1085                if (axes == null || axes.length == 0) {
    1086                        axes = new int[rank];
    1087                        for (int i = 0; i < rank; i++) {
    1088                                axes[i] = rank - 1 - i;
    1089                        }
    1090                }
    1091
    1092                if (axes.length != rank) {
    1093                        logger.error("axis permutation has length {} that does not match dataset's rank {}", axes.length, rank);
    1094                        throw new IllegalArgumentException("axis permutation does not match shape of dataset");
    1095                }
    1096
    1097                // check all permutation values are within bounds
    1098                for (int i = 0; i < rank; i++) {
    1099                        axes[i] = ShapeUtils.checkAxis(rank, axes[i]);
    1100                }
    1101
    1102                // check for a valid permutation (is this an unnecessary restriction?)
    1103                int[] perm = axes.clone();
    1104                Arrays.sort(perm);
    1105
    1106                for (int i = 0; i < rank; i++) {
    1107                        if (perm[i] != i) {
    1108                                logger.error("axis permutation is not valid: it does not contain complete set of axes");
    1109                                throw new IllegalArgumentException("axis permutation does not contain complete set of axes");
    1110                        }
    1111                }
    1112
    1113                if (Arrays.equals(axes, perm))
    1114                        return null; // signal identity or trivial permutation
    1115
    1116                return axes;
    1117        }
    1118}