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