001/*-
002 *******************************************************************************
003 * Copyright (c) 2011, 2016 Diamond Light Source Ltd.
004 * All rights reserved. This program and the accompanying materials
005 * are made available under the terms of the Eclipse Public License v1.0
006 * which accompanies this distribution, and is available at
007 * http://www.eclipse.org/legal/epl-v10.html
008 *
009 * Contributors:
010 *    Peter Chang - initial API and implementation and/or initial documentation
011 *******************************************************************************/
012
013package org.eclipse.january.dataset;
014
015import java.io.Serializable;
016import java.lang.annotation.Annotation;
017import java.lang.reflect.Array;
018import java.lang.reflect.Field;
019import java.util.ArrayList;
020import java.util.Arrays;
021import java.util.Collection;
022import java.util.concurrent.ConcurrentMap;
023import java.util.concurrent.ConcurrentHashMap;
024import java.util.List;
025import java.util.Map;
026
027import org.eclipse.january.DatasetException;
028import org.eclipse.january.MetadataException;
029import org.eclipse.january.metadata.Dirtiable;
030import org.eclipse.january.metadata.ErrorMetadata;
031import org.eclipse.january.metadata.IMetadata;
032import org.eclipse.january.metadata.MetadataFactory;
033import org.eclipse.january.metadata.MetadataType;
034import org.eclipse.january.metadata.Reshapeable;
035import org.eclipse.january.metadata.Sliceable;
036import org.eclipse.january.metadata.Transposable;
037import org.slf4j.Logger;
038import org.slf4j.LoggerFactory;
039
040/**
041 * Common base for both lazy and normal dataset implementations
042 */
043public abstract class LazyDatasetBase implements ILazyDataset, Serializable {
044
045        private static final long serialVersionUID = 767926846438976050L;
046
047        protected static final Logger logger = LoggerFactory.getLogger(LazyDatasetBase.class);
048
049        protected static boolean catchExceptions;
050
051        static {
052                /**
053                 * Boolean to set to true if running jython scripts that utilise ScisoftPy in IDE
054                 */
055                try {
056                        catchExceptions = Boolean.getBoolean("run.in.eclipse");
057                } catch (SecurityException e) {
058                        // set a default for when the security manager does not allow access to the requested key
059                        catchExceptions = false;
060                }
061        }
062
063        transient private boolean dirty = true; // indicate dirty state of metadata
064        protected String name = "";
065
066        /**
067         * The shape or dimensions of the dataset
068         */
069        protected int[] shape;
070
071        protected ConcurrentMap<Class<? extends MetadataType>, List<MetadataType>> metadata = null;
072
073        /**
074         * @return type of dataset item
075         */
076        abstract public int getDType();
077
078        @Override
079        public Class<?> getElementClass() {
080                return DTypeUtils.getElementClass(getDType());
081        }
082
083        @Override
084        public LazyDatasetBase clone() {
085                return null;
086        }
087
088        @Override
089        public boolean equals(Object obj) {
090                if (this == obj) {
091                        return true;
092                }
093                if (obj == null) {
094                        return false;
095                }
096                if (!getClass().equals(obj.getClass())) {
097                        return false;
098                }
099        
100                LazyDatasetBase other = (LazyDatasetBase) obj;
101                if (getDType() != other.getDType()) {
102                        return false;
103                }
104                if (getElementsPerItem() != other.getElementsPerItem()) {
105                        return false;
106                }
107                if (!Arrays.equals(shape, other.shape)) {
108                        return false;
109                }
110                return true;
111        }
112
113        @Override
114        public int hashCode() {
115                int hash = getDType() * 17 + getElementsPerItem();
116                int rank = shape.length;
117                for (int i = 0; i < rank; i++) {
118                        hash = hash*17 + shape[i];
119                }
120                return hash;
121        }
122
123        @Override
124        public String getName() {
125                return name;
126        }
127
128        @Override
129        public void setName(String name) {
130                this.name = name;
131        }
132
133        @Override
134        public int[] getShape() {
135                return shape.clone();
136        }
137
138        @Override
139        public int getRank() {
140                return shape.length;
141        }
142
143        /**
144         * This method allows anything that dirties the dataset to clear various metadata values
145         * so that the other methods can work correctly.
146         * @since 2.1
147         */
148        public void setDirty() {
149                dirty = true;
150        }
151
152        /**
153         * Find first sub-interface of (or class that directly implements) MetadataType
154         * @param clazz
155         * @return sub-interface
156         * @exception IllegalArgumentException when given class is {@link MetadataType} or an anonymous sub-class of it
157         */
158        @SuppressWarnings("unchecked")
159        public static Class<? extends MetadataType> findMetadataTypeSubInterfaces(Class<? extends MetadataType> clazz) {
160                if (clazz.equals(MetadataType.class)) {
161                        throw new IllegalArgumentException("Cannot accept MetadataType");
162                }
163
164                if (clazz.isInterface()) {
165                        return clazz;
166                }
167
168                if (clazz.isAnonymousClass()) { // special case
169                        Class<?> s = clazz.getSuperclass();
170                        if (!s.equals(Object.class)) {
171                                // only use super class if it is not an anonymous class of an interface
172                                clazz = (Class<? extends MetadataType>) s;
173                        }
174                }
175
176                for (Class<?> c : clazz.getInterfaces()) {
177                        if (c.equals(MetadataType.class)) {
178                                if (clazz.isAnonymousClass()) {
179                                        throw new IllegalArgumentException("Cannot accept anonymous subclasses of MetadataType");
180                                }
181                                return clazz;
182                        }
183                        if (MetadataType.class.isAssignableFrom(c)) {
184                                return (Class<? extends MetadataType>) c;
185                        }
186                }
187
188                Class<?> c = clazz.getSuperclass(); // Naughty: someone has sub-classed a metadata class
189                if (c != null) {
190                        return findMetadataTypeSubInterfaces((Class<? extends MetadataType>) c);
191                }
192
193                logger.error("Somehow the search for metadata type interface ended in a bad place");
194                assert false; // should not be able to get here!!!
195                return null;
196        }
197
198        @Override
199        public void setMetadata(MetadataType metadata) {
200                addMetadata(metadata, true);
201        }
202
203        @Override
204        public void addMetadata(MetadataType metadata) {
205                addMetadata(metadata, false);
206        }
207
208        private synchronized void addMetadata(MetadataType metadata, boolean clear) {
209                if (metadata == null)
210                        return;
211
212                if (this.metadata == null) {
213                        this.metadata = new ConcurrentHashMap<Class<? extends MetadataType>, List<MetadataType>>();
214                }
215
216                Class<? extends MetadataType> clazz = findMetadataTypeSubInterfaces(metadata.getClass());
217                if (!this.metadata.containsKey(clazz)) {
218                        this.metadata.put(clazz, new ArrayList<MetadataType>());
219                } else if (clear) {
220                        this.metadata.get(clazz).clear();
221                }
222                this.metadata.get(clazz).add(metadata);
223
224                // add for special case of sub-interfaces of IMetadata
225                if (!IMetadata.class.equals(clazz) && IMetadata.class.isAssignableFrom(clazz)) {
226                        clazz = IMetadata.class;
227                        if (!this.metadata.containsKey(clazz)) {
228                                this.metadata.put(clazz, new ArrayList<MetadataType>());
229                        } else if (clear) {
230                                this.metadata.get(clazz).clear();
231                        }
232                        this.metadata.get(clazz).add(metadata);
233                }
234        }
235
236        @Override
237        @Deprecated
238        public synchronized IMetadata getMetadata() {
239                return getFirstMetadata(IMetadata.class);
240        }
241
242        @SuppressWarnings("unchecked")
243        @Override
244        public synchronized <S extends MetadataType, T extends S> List<S> getMetadata(Class<T> clazz) throws MetadataException {
245                if (metadata == null) {
246                        dirty = false;
247                        return null;
248                }
249
250                if (dirty) {
251                        dirtyMetadata();
252                        dirty = false;
253                }
254
255                if (clazz == null) {
256                        List<S> all = new ArrayList<S>();
257                        for (Class<? extends MetadataType> c : metadata.keySet()) {
258                                all.addAll((Collection<S>) metadata.get(c));
259                        }
260                        return all;
261                }
262
263                return (List<S>) metadata.get(findMetadataTypeSubInterfaces(clazz));
264        }
265
266        @Override
267        public synchronized <S extends MetadataType, T extends S> S getFirstMetadata(Class<T> clazz) {
268                try {
269                        List<S> ml = getMetadata(clazz);
270                        if (ml == null) {
271                                return null;
272                        }
273                        for (S t : ml) {
274                                if (clazz.isInstance(t)) {
275                                        return t;
276                                }
277                        }
278                } catch (Exception e) {
279                        logger.error("Get metadata failed!",e);
280                }
281
282                return null;
283        }
284
285        @Override
286        public synchronized void clearMetadata(Class<? extends MetadataType> clazz) {
287                if (metadata == null)
288                        return;
289
290                if (clazz == null) {
291                        metadata.clear();
292                        return;
293                }
294
295                List<MetadataType> list = metadata.get(findMetadataTypeSubInterfaces(clazz));
296                if( list != null) {
297                        list.clear();
298                }
299        }
300
301        /**
302         * @since 2.0
303         */
304        protected synchronized ConcurrentMap<Class<? extends MetadataType>, List<MetadataType>> copyMetadata() {
305                return copyMetadata(metadata);
306        }
307
308        /**
309         * @since 2.0
310         */
311        protected static ConcurrentMap<Class<? extends MetadataType>, List<MetadataType>> copyMetadata(Map<Class<? extends MetadataType>, List<MetadataType>> metadata) {
312                if (metadata == null)
313                        return null;
314
315                ConcurrentHashMap<Class<? extends MetadataType>, List<MetadataType>> map = new ConcurrentHashMap<Class<? extends MetadataType>, List<MetadataType>>();
316
317                for (Class<? extends MetadataType> c : metadata.keySet()) {
318                        List<MetadataType> l = metadata.get(c);
319                        List<MetadataType> nl = new ArrayList<MetadataType>(l.size());
320                        map.put(c, nl);
321                        for (MetadataType m : l) {
322                                nl.add(m.clone());
323                        }
324                }
325                return map;
326        }
327
328        interface MetadatasetAnnotationOperation {
329                /**
330                 * Process value of given field
331                 * <p>
332                 * When the field is not a container then the returned value
333                 * may replace the old value
334                 * @param f given field
335                 * @param o value of field
336                 * @return transformed field
337                 */
338                Object processField(Field f, Object o);
339
340                /**
341                 * @return annotated class
342                 */
343                Class<? extends Annotation> getAnnClass();
344
345                /**
346                 * @param axis
347                 * @return number of dimensions to insert or remove
348                 */
349                int change(int axis);
350
351                /**
352                 * 
353                 * @return rank or -1 to match
354                 */
355                int getNewRank();
356
357                /**
358                 * Run on given lazy dataset
359                 * @param lz
360                 * @return 
361                 */
362                ILazyDataset run(ILazyDataset lz);
363        }
364
365        class MdsSlice implements MetadatasetAnnotationOperation {
366                private boolean asView;
367                private int[] start;
368                private int[] stop;
369                private int[] step;
370                private int[] oShape;
371                private long oSize;
372
373                public MdsSlice(boolean asView, final int[] start, final int[] stop, final int[] step, final int[] oShape) {
374                        this.asView = asView;
375                        this.start = start;
376                        this.stop = stop;
377                        this.step = step;
378                        this.oShape = oShape;
379                        oSize = ShapeUtils.calcLongSize(oShape);
380                }
381
382                @Override
383                public Object processField(Field field, Object o) {
384                        return o;
385                }
386
387                @Override
388                public Class<? extends Annotation> getAnnClass() {
389                        return Sliceable.class;
390                }
391
392                @Override
393                public int change(int axis) {
394                        return 0;
395                }
396
397                @Override
398                public int getNewRank() {
399                        return -1;
400                }
401
402                @Override
403                public ILazyDataset run(ILazyDataset lz) {
404                        int rank = lz.getRank();
405                        if (start.length != rank) {
406                                throw new IllegalArgumentException("Slice dimensions do not match dataset!");
407                        }
408
409                        int[] shape = lz.getShape();
410                        int[] stt;
411                        int[] stp;
412                        int[] ste;
413                        if (lz.getSize() == oSize) {
414                                stt = start;
415                                stp = stop;
416                                ste = step;
417                        } else {
418                                stt = start.clone();
419                                stp = stop.clone();
420                                ste = step.clone();
421                                for (int i = 0; i < rank; i++) {
422                                        if (shape[i] >= oShape[i]) continue;
423                                        if (shape[i] == 1) {
424                                                stt[i] = 0;
425                                                stp[i] = 1;
426                                                ste[i] = 1;
427                                        } else {
428                                                throw new IllegalArgumentException("Sliceable dataset has invalid size!");
429                                        }
430                                }
431                        }
432
433                        if (asView || (lz instanceof IDataset))
434                                return lz.getSliceView(stt, stp, ste);
435                        try {
436                                return lz.getSlice(stt, stp, ste);
437                        } catch (DatasetException e) {
438                                logger.error("Could not slice dataset in metadata", e);
439                                return null;
440                        }
441                }
442        }
443
444        class MdsReshape implements MetadatasetAnnotationOperation {
445                private boolean matchRank;
446                private int[] oldShape;
447                private int[] newShape;
448                boolean onesOnly;
449                int[] differences;
450
451                /*
452                 * if only ones then record differences (insertions and deletions)
453                 * 
454                 * if shape changing, find broadcasted dimensions and disallow
455                 * merging that include those dimensions
456                 */
457                public MdsReshape(final int[] oldShape, final int[] newShape) {
458                        this.oldShape = oldShape;
459                        this.newShape = newShape;
460                        differences = null;
461                }
462
463                @Override
464                public Object processField(Field field, Object o) {
465                        Annotation a = field.getAnnotation(Reshapeable.class);
466                        if (a != null) { // cannot be null
467                                matchRank = ((Reshapeable) a).matchRank();
468                        }
469                        return o;
470                }
471
472                @Override
473                public Class<? extends Annotation> getAnnClass() {
474                        return Reshapeable.class;
475                }
476
477                @Override
478                public int change(int axis) {
479                        if (matchRank) {
480                                if (differences == null)
481                                        init();
482
483                                if (onesOnly) {
484                                        return differences[axis];
485                                }
486                                throw new UnsupportedOperationException("TODO support other shape operations");
487                        }
488                        return 0;
489                }
490
491                @Override
492                public int getNewRank() {
493                        return matchRank ? newShape.length : -1;
494                }
495
496                private void init() {
497                        int or = oldShape.length - 1;
498                        int nr = newShape.length - 1;
499                        if (or < 0 || nr < 0) { // zero-rank shapes
500                                onesOnly = true;
501                                differences = new int[1];
502                                differences[0] = or < 0 ? nr + 1 : or + 1;
503                                return;
504                        }
505                        int ob = 0;
506                        int nb = 0;
507                        onesOnly = true;
508                        do {
509                                while (oldShape[ob] == 1 && ob < or) {
510                                        ob++; // next non-unit dimension
511                                }
512                                while (newShape[nb] == 1 && nb < nr) {
513                                        nb++;
514                                }
515                                if (oldShape[ob++] != newShape[nb++]) {
516                                        onesOnly = false;
517                                        break;
518                                }
519                        } while (ob <= or && nb <= nr);
520
521                        ob = 0;
522                        nb = 0;
523                        differences = new int[or + 2];
524                        if (onesOnly) {
525                                // work out unit dimensions removed from or add to old
526                                int j = 0;
527                                do {
528                                        if (oldShape[ob] != 1 && newShape[nb] != 1) {
529                                                ob++;
530                                                nb++;
531                                        } else {
532                                                while (oldShape[ob] == 1 && ob < or) {
533                                                        ob++;
534                                                        differences[j]--;
535                                                }
536                                                while (newShape[nb] == 1 && nb < nr) {
537                                                        nb++;
538                                                        differences[j]++;
539                                                }
540                                        }
541                                        j++;
542                                } while (ob <= or && nb <= nr && j <= or);
543                                while (ob <= or && oldShape[ob] == 1) {
544                                        ob++;
545                                        differences[j]--;
546                                }
547                                while (nb <= nr && newShape[nb] == 1) {
548                                        nb++;
549                                        differences[j]++;
550                                }
551                        } else {
552                                if (matchRank) {
553                                        logger.error("Combining dimensions is currently not supported");
554                                        throw new IllegalArgumentException("Combining dimensions is currently not supported");
555                                }
556                                // work out mapping: contiguous dimensions can be grouped or split
557                                while (ob <= or && nb <= nr) {
558                                        int ol = oldShape[ob];
559                                        while (ol == 1 && ol <= or) {
560                                                ob++;
561                                                ol = oldShape[ob];
562                                        }
563                                        int oe = ob + 1;
564                                        int nl = newShape[nb];
565                                        while (nl == 1 && nl <= nr) {
566                                                nb++;
567                                                nl = newShape[nb];
568                                        }
569                                        int ne = nb + 1;
570                                        if (ol < nl) {
571                                                differences[ob] = 1;
572                                                do { // case where new shape combines several dimensions into one dimension
573                                                        if (oe == (or + 1)) {
574                                                                break;
575                                                        }
576                                                        differences[oe] = 1;
577                                                        ol *= oldShape[oe++];
578                                                } while (ol < nl);
579                                                differences[oe - 1] = oe - ob; // signal end with difference
580                                                if (nl != ol) {
581                                                        logger.error("Single dimension is incompatible with subshape");
582                                                        throw new IllegalArgumentException("Single dimension is incompatible with subshape");
583                                                }
584                                        } else if (ol > nl) {
585                                                do { // case where new shape spreads single dimension over several dimensions
586                                                        if (ne == (nr + 1)) {
587                                                                break;
588                                                        }
589                                                        nl *= newShape[ne++];
590                                                } while (nl < ol);
591                                                if (nl != ol) {
592                                                        logger.error("Subshape is incompatible with single dimension");
593                                                        throw new IllegalArgumentException("Subshape is incompatible with single dimension");
594                                                }
595
596                                        }
597
598                                        ob = oe;
599                                        nb = ne;
600                                }
601
602                        }
603                }
604
605                @Override
606                public ILazyDataset run(ILazyDataset lz) {
607                        if (differences == null)
608                                init();
609
610                        int[] lshape = lz.getShape();
611                        if (Arrays.equals(newShape, lshape)) {
612                                return lz;
613                        }
614                        int or = lz.getRank();
615                        int nr = newShape.length;
616                        int[] nshape = new int[nr];
617                        Arrays.fill(nshape, 1);
618                        if (onesOnly) {
619                                // ignore omit removed dimensions
620                                for (int i = 0, si = 0, di = 0; i < (or+1) && si <= or && di < nr; i++) {
621                                        int c = differences[i];
622                                        if (c == 0) {
623                                                nshape[di++] = lshape[si++];
624                                        } else if (c > 0) {
625                                                while (c-- > 0 && di < nr) {
626                                                        di++;
627                                                }
628                                        } else if (c < 0) {
629                                                si -= c; // remove dimensions by skipping forward in source array
630                                        }
631                                }
632                        } else {
633                                boolean[] broadcast = new boolean[or];
634                                for (int ob = 0; ob < or; ob++) {
635                                        broadcast[ob] = oldShape[ob] != 1 && lshape[ob] == 1;
636                                }
637                                int osize = lz.getSize();
638
639                                // cannot do 3x5x... to 15x... if metadata is broadcasting (i.e. 1x5x...)
640                                int ob = 0;
641                                int nsize = 1;
642                                for (int i = 0; i < nr; i++) {
643                                        if (ob < or && broadcast[ob]) {
644                                                if (differences[ob] != 0) {
645                                                        logger.error("Metadata contains a broadcast axis which cannot be reshaped");
646                                                        throw new IllegalArgumentException("Metadata contains a broadcast axis which cannot be reshaped");
647                                                }
648                                        } else {
649                                                nshape[i] = nsize < osize ? newShape[i] : 1;
650                                        }
651                                        nsize *= nshape[i];
652                                        ob++;
653                                }
654                        }
655
656                        ILazyDataset nlz = lz.getSliceView();
657                        if (lz instanceof Dataset) {
658                                nlz = ((Dataset) lz).reshape(nshape);
659                        } else {
660                                nlz = lz.getSliceView();
661                                nlz.setShape(nshape);
662                        }
663                        return nlz;
664                }
665        }
666
667        class MdsTranspose implements MetadatasetAnnotationOperation {
668                int[] map;
669
670                public MdsTranspose(final int[] axesMap) {
671                        map = axesMap;
672                }
673
674                @SuppressWarnings({ "rawtypes", "unchecked" })
675                @Override
676                public Object processField(Field f, Object o) {
677                        // reorder arrays and lists according the axes map
678                        if (o.getClass().isArray()) {
679                                int l = Array.getLength(o);
680                                if (l == map.length) {
681                                        Object narray = Array.newInstance(o.getClass().getComponentType(), l);
682                                        for (int i = 0; i < l; i++) {
683                                                Array.set(narray, i, Array.get(o, map[i]));
684                                        }
685                                        for (int i = 0; i < l; i++) {
686                                                Array.set(o, i, Array.get(narray, i));
687                                        }
688                                }
689                        } else if (o instanceof List<?>) {
690                                List list = (List) o;
691                                int l = list.size();
692                                if (l == map.length) {
693                                        Object narray = Array.newInstance(o.getClass().getComponentType(), l);
694                                        for (int i = 0; i < l; i++) {
695                                                Array.set(narray, i, list.get(map[i]));
696                                        }
697                                        list.clear();
698                                        for (int i = 0; i < l; i++) {
699                                                list.add(Array.get(narray, i));
700                                        }
701                                }
702                        }
703                        return o;
704                }
705
706                @Override
707                public Class<? extends Annotation> getAnnClass() {
708                        return Transposable.class;
709                }
710
711                @Override
712                public int change(int axis) {
713                        return 0;
714                }
715
716                @Override
717                public int getNewRank() {
718                        return -1;
719                }
720
721                @Override
722                public ILazyDataset run(ILazyDataset lz) {
723                        return lz.getTransposedView(map);
724                }
725        }
726
727        class MdsDirty implements MetadatasetAnnotationOperation {
728
729                @Override
730                public Object processField(Field f, Object o) {
731                        // throw exception if not boolean???
732                        Class<?> t = f.getType();
733                        if (t.equals(boolean.class) || t.equals(Boolean.class)) {
734                                if (o.equals(false)) {
735                                        o = true;
736                                }
737                        }
738                        return o;
739                }
740
741                @Override
742                public Class<? extends Annotation> getAnnClass() {
743                        return Dirtiable.class;
744                }
745
746                @Override
747                public int change(int axis) {
748                        return 0;
749                }
750
751                @Override
752                public int getNewRank() {
753                        return -1;
754                }
755
756                @Override
757                public ILazyDataset run(ILazyDataset lz) {
758                        return lz;
759                }
760        }
761
762        /**
763         * Slice all datasets in metadata that are annotated by @Sliceable. Call this on the new sliced
764         * dataset after cloning the metadata
765         * @param asView if true then just a view
766         * @param slice
767         */
768        protected void sliceMetadata(boolean asView, final SliceND slice) {
769                processAnnotatedMetadata(new MdsSlice(asView, slice.getStart(), slice.getStop(), slice.getStep(), slice.getSourceShape()), true);
770        }
771
772        /**
773         * Reshape all datasets in metadata that are annotated by @Reshapeable. Call this when squeezing
774         * or setting the shape
775         * 
776         * @param newShape
777         */
778        protected void reshapeMetadata(final int[] oldShape, final int[] newShape) {
779                processAnnotatedMetadata(new MdsReshape(oldShape, newShape), true);
780        }
781
782        /**
783         * Transpose all datasets in metadata that are annotated by @Transposable. Call this on the transposed
784         * dataset after cloning the metadata
785         * @param axesMap
786         */
787        protected void transposeMetadata(final int[] axesMap) {
788                processAnnotatedMetadata(new MdsTranspose(axesMap), true);
789        }
790
791        /**
792         * Dirty metadata that are annotated by @Dirtiable. Call this when the dataset has been modified
793         * @since 2.0
794         */
795        protected void dirtyMetadata() {
796                processAnnotatedMetadata(new MdsDirty(), true);
797        }
798
799        @SuppressWarnings("unchecked")
800        private void processAnnotatedMetadata(MetadatasetAnnotationOperation op, boolean throwException) {
801                if (metadata == null)
802                        return;
803
804                for (Class<? extends MetadataType> c : metadata.keySet()) {
805                        for (MetadataType m : metadata.get(c)) {
806                                if (m == null)
807                                        continue;
808
809                                Class<? extends MetadataType> mc = m.getClass();
810                                do { // iterate over super-classes
811                                        processClass(op, m, mc, throwException);
812                                        Class<?> sclazz = mc.getSuperclass();
813                                        if (!MetadataType.class.isAssignableFrom(sclazz))
814                                                break;
815                                        mc = (Class<? extends MetadataType>) sclazz;
816                                } while (true);
817                        }
818                }
819        }
820
821        @SuppressWarnings({ "unchecked", "rawtypes" })
822        private static void processClass(MetadatasetAnnotationOperation op, MetadataType m, Class<? extends MetadataType> mc, boolean throwException) {
823                for (Field f : mc.getDeclaredFields()) {
824                        if (!f.isAnnotationPresent(op.getAnnClass()))
825                                continue;
826
827                        try {
828                                f.setAccessible(true);
829                                Object o = f.get(m);
830                                if (o == null)
831                                        continue;
832
833                                Object no = op.processField(f, o);
834                                if (no != o) {
835                                        f.set(m, no);
836                                        continue;
837                                }
838                                Object r = null;
839                                if (o instanceof ILazyDataset) {
840                                        try {
841                                                f.set(m, op.run((ILazyDataset) o));
842                                        } catch (Exception e) {
843                                                logger.error("Problem processing " + o, e);
844                                                if (!catchExceptions)
845                                                        throw e;
846                                        }
847                                } else if (o.getClass().isArray()) {
848                                        int l = Array.getLength(o);
849                                        if (l <= 0)
850                                                continue;
851
852                                        for (int i = 0; r == null && i < l; i++) {
853                                                r = Array.get(o, i);
854                                        }
855                                        int n = op.getNewRank();
856                                        if (r == null) {
857                                                if (n < 0 || n != l) { // all nulls be need to match rank as necessary
858                                                        f.set(m, Array.newInstance(o.getClass().getComponentType(), n < 0 ? l : n));
859                                                }
860                                                continue;
861                                        }
862                                        if (n < 0)
863                                                n = l;
864                                        Object narray = Array.newInstance(r.getClass(), n);
865                                        for (int i = 0, si = 0, di = 0; di < n && si < l; i++) {
866                                                int c = op.change(i);
867                                                if (c == 0) {
868                                                        Array.set(narray, di++, processObject(op, Array.get(o, si++)));
869                                                } else if (c > 0) {
870                                                        di += c; // add nulls by skipping forward in destination array
871                                                } else if (c < 0) {
872                                                        si -= c; // remove dimensions by skipping forward in source array
873                                                }
874                                        }
875                                        if (n == l) {
876                                                for (int i = 0; i < l; i++) {
877                                                        Array.set(o, i, Array.get(narray, i));
878                                                }
879                                        } else {
880                                                f.set(m, narray);
881                                        }
882                                } else if (o instanceof List<?>) {
883                                        List list = (List) o;
884                                        int l = list.size();
885                                        if (l <= 0)
886                                                continue;
887
888                                        for (int i = 0; r == null && i < l; i++) {
889                                                r = list.get(i);
890                                        }
891                                        int n = op.getNewRank();
892                                        if (r == null) {
893                                                if (n < 0 || n != l) { // all nulls be need to match rank as necessary
894                                                        list.clear();
895                                                        for (int i = 0, imax = n < 0 ? l : n; i < imax; i++) {
896                                                                list.add(null);
897                                                        }
898                                                }
899                                                continue;
900                                        }
901
902                                        if (n < 0)
903                                                n = l;
904                                        Object narray = Array.newInstance(r.getClass(), n);
905                                        for (int i = 0, si = 0, di = 0; i < l && si < l; i++) {
906                                                int c = op.change(i);
907                                                if (c == 0) {
908                                                        Array.set(narray, di++, processObject(op, list.get(si++)));
909                                                } else if (c > 0) {
910                                                        di += c; // add nulls by skipping forward in destination array
911                                                } else if (c < 0) {
912                                                        si -= c; // remove dimensions by skipping forward in source array
913                                                }
914                                        }
915                                        list.clear();
916                                        for (int i = 0; i < n; i++) {
917                                                list.add(Array.get(narray, i));
918                                        }
919                                } else if (o instanceof Map<?,?>) {
920                                        Map map = (Map) o;
921                                        for (Object k : map.keySet()) {
922                                                map.put(k, processObject(op, map.get(k)));
923                                        }
924                                }
925                        } catch (Exception e) {
926                                logger.error("Problem occurred when processing metadata of class {}: {}", mc.getCanonicalName(), e);
927                                if (throwException)
928                                        throw new RuntimeException(e);
929                        }
930                }
931        }
932
933        @SuppressWarnings({ "unchecked", "rawtypes" })
934        private static Object processObject(MetadatasetAnnotationOperation op, Object o) throws Exception {
935                if (o == null)
936                        return o;
937
938                if (o instanceof ILazyDataset) {
939                        try {
940                                return op.run((ILazyDataset) o);
941                        } catch (Exception e) {
942                                logger.error("Problem processing " + o, e);
943                                if (!catchExceptions)
944                                        throw e;
945                        }
946                } else if (o.getClass().isArray()) {
947                        int l = Array.getLength(o);
948                        for (int i = 0; i < l; i++) {
949                                Array.set(o, i, processObject(op, Array.get(o, i)));
950                        }
951                } else if (o instanceof List<?>) {
952                        List list = (List) o;
953                        for (int i = 0, imax = list.size(); i < imax; i++) {
954                                list.set(i, processObject(op, list.get(i)));
955                        }
956                } else if (o instanceof Map<?,?>) {
957                        Map map = (Map) o;
958                        for (Object k : map.keySet()) {
959                                map.put(k, processObject(op, map.get(k)));
960                        }
961                }
962                return o;
963        }
964
965        protected void restoreMetadata(Map<Class<? extends MetadataType>, List<MetadataType>> oldMetadata) {
966                for (Class<? extends MetadataType> mc : oldMetadata.keySet()) {
967                        metadata.put(mc, oldMetadata.get(mc));
968                }
969        }
970
971        protected ILazyDataset createFromSerializable(Serializable blob, boolean keepLazy) {
972                ILazyDataset d = null;
973                if (blob instanceof ILazyDataset) {
974                        d = (ILazyDataset) blob;
975                        if (d instanceof IDataset) {
976                                Dataset ed = DatasetUtils.convertToDataset((IDataset) d);
977                                int is = ed.getElementsPerItem();
978                                if (is != 1 && is != getElementsPerItem()) {
979                                        throw new IllegalArgumentException("Dataset has incompatible number of elements with this dataset");
980                                }
981                                d = ed.cast(is == 1 ? Dataset.FLOAT64 : Dataset.ARRAYFLOAT64);
982                        } else if (!keepLazy) {
983                                final int is = getElementsPerItem();
984                                try {
985                                        d = DatasetUtils.cast(d.getSlice(), is == 1 ? Dataset.FLOAT64 : Dataset.ARRAYFLOAT64);
986                                } catch (DatasetException e) {
987                                        logger.error("Could not get data from lazy dataset", e);
988                                        return null;
989                                }
990                        }
991                } else {
992                        final int is = getElementsPerItem();
993                        if (is == 1) {
994                                d = DatasetFactory.createFromObject(DoubleDataset.class, blob);
995                        } else {
996                                try {
997                                        d = DatasetFactory.createFromObject(is, CompoundDoubleDataset.class, blob);
998                                } catch (IllegalArgumentException e) { // if only single value supplied try again
999                                        d = DatasetFactory.createFromObject(DoubleDataset.class, blob);
1000                                }
1001                        }
1002                        if (d.getSize() == getSize() && !Arrays.equals(d.getShape(), shape)) {
1003                                d.setShape(shape.clone());
1004                        }
1005                }
1006                List<int[]> s = BroadcastUtils.broadcastShapesToMax(shape, d.getShape());
1007                d.setShape(s.get(0));
1008
1009                return d;
1010        }
1011
1012        @Override
1013        public void setErrors(Serializable errors) {
1014                if (shape == null) {
1015                        throw new IllegalArgumentException("Cannot set errors for null dataset");
1016                }
1017                if (errors == null) {
1018                        clearMetadata(ErrorMetadata.class);
1019                        return;
1020                }
1021                if (errors == this) {
1022                        logger.warn("Ignoring setting error to itself as this will lead to infinite recursion");
1023                        return;
1024                }
1025
1026                ILazyDataset errorData = createFromSerializable(errors, true);
1027
1028                ErrorMetadata emd = getErrorMetadata();
1029                if (emd == null) {
1030                        try {
1031                                emd = MetadataFactory.createMetadata(ErrorMetadata.class);
1032                                setMetadata(emd);
1033                        } catch (MetadataException me) {
1034                                logger.error("Could not create metadata", me);
1035                        }
1036                }
1037                emd.setError(errorData);
1038        }
1039
1040        protected ErrorMetadata getErrorMetadata() {
1041                try {
1042                        List<ErrorMetadata> el = getMetadata(ErrorMetadata.class);
1043                        if (el != null && !el.isEmpty()) {
1044                                 return el.get(0);
1045                        }
1046                } catch (Exception e) {
1047                }
1048                return null;
1049        }
1050
1051        @Override
1052        public ILazyDataset getErrors() {
1053                ErrorMetadata emd = getErrorMetadata();
1054                return emd == null ? null : emd.getError();
1055        }
1056
1057        @Override
1058        public boolean hasErrors() {
1059                return LazyDatasetBase.this.getErrors() != null;
1060        }
1061
1062        /**
1063         * Check permutation axes
1064         * @param shape
1065         * @param axes
1066         * @return cleaned up axes or null if trivial
1067         */
1068        public static int[] checkPermutatedAxes(int[] shape, int... axes) {
1069                int rank = shape == null ? 0 : shape.length;
1070
1071                if (axes == null || axes.length == 0) {
1072                        axes = new int[rank];
1073                        for (int i = 0; i < rank; i++) {
1074                                axes[i] = rank - 1 - i;
1075                        }
1076                }
1077
1078                if (axes.length != rank) {
1079                        logger.error("axis permutation has length {} that does not match dataset's rank {}", axes.length, rank);
1080                        throw new IllegalArgumentException("axis permutation does not match shape of dataset");
1081                }
1082        
1083                // check all permutation values are within bounds
1084                for (int i = 0; i < rank; i++) {
1085                        axes[i] = ShapeUtils.checkAxis(rank, axes[i]);
1086                }
1087        
1088                // check for a valid permutation (is this an unnecessary restriction?)
1089                int[] perm = axes.clone();
1090                Arrays.sort(perm);
1091
1092                for (int i = 0; i < rank; i++) {
1093                        if (perm[i] != i) {
1094                                logger.error("axis permutation is not valid: it does not contain complete set of axes");
1095                                throw new IllegalArgumentException("axis permutation does not contain complete set of axes");
1096                        }
1097                }
1098
1099                if (Arrays.equals(axes, perm))
1100                        return null; // signal identity or trivial permutation
1101
1102                return axes;
1103        }
1104}