Java tutorial
/* * $Id$ * * Copyright 2009 Glencoe Software, Inc. All rights reserved. * Use is subject to license terms supplied in LICENSE.txt */ package ome.services.blitz.impl; import java.awt.Color; import java.awt.Point; import java.awt.image.BufferedImage; import java.io.ByteArrayInputStream; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import javax.imageio.ImageIO; import ome.api.IQuery; import ome.api.IUpdate; import ome.model.IObject; import ome.model.core.OriginalFile; import ome.parameters.Filter; import ome.services.blitz.util.BlitzExecutor; import ome.services.blitz.util.BlitzOnly; import ome.services.blitz.util.ServiceFactoryAware; import ome.services.roi.GeomTool; import ome.services.throttling.Adapter; import ome.services.util.Executor.SimpleWork; import ome.system.ServiceFactory; import ome.tools.hibernate.QueryBuilder; import ome.util.SqlAction; import omero.ServerError; import omero.api.AMD_IRoi_findByImage; import omero.api.AMD_IRoi_findByPlane; import omero.api.AMD_IRoi_findByRoi; import omero.api.AMD_IRoi_getMeasuredRois; import omero.api.AMD_IRoi_getMeasuredRoisMap; import omero.api.AMD_IRoi_getPoints; import omero.api.AMD_IRoi_getRoiMeasurements; import omero.api.AMD_IRoi_getRoiStats; import omero.api.AMD_IRoi_getShapeStats; import omero.api.AMD_IRoi_getShapeStatsList; import omero.api.AMD_IRoi_getTable; import omero.api.AMD_IRoi_uploadMask; import omero.api.RoiOptions; import omero.api.RoiResult; import omero.api._IRoiOperations; import omero.constants.namespaces.NSMEASUREMENT; import omero.model.OriginalFileI; import omero.model.Roi; import omero.model.Shape; import omero.util.IceMapper; import org.apache.commons.collections.MultiMap; import org.apache.commons.collections.map.MultiValueMap; import org.hibernate.Query; import org.hibernate.Session; import org.springframework.transaction.annotation.Transactional; import Ice.Current; /** * implementation of the IRoi service interface. * * @since Beta4.1 */ public class RoiI extends AbstractAmdServant implements _IRoiOperations, ServiceFactoryAware, BlitzOnly { protected ServiceFactoryI factory; protected final GeomTool geomTool; protected final SqlAction sql; public RoiI(BlitzExecutor be, GeomTool geomTool, SqlAction sql) { super(null, be); this.geomTool = geomTool; this.sql = sql; } public void setServiceFactory(ServiceFactoryI sf) { this.factory = sf; } // ~ Service methods // ========================================================================= public void findByImage_async(AMD_IRoi_findByImage __cb, final long imageId, final RoiOptions opts, Current __current) throws ServerError { final IceMapper mapper = new RoiResultMapper(opts); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "findByImage", imageId, opts) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { boolean ns = false; if (opts != null) if (opts.namespace != null) ns = true; if (ns) { List<Map<String, Object>> mapList = sql.roiByImageAndNs(imageId, opts.namespace.getValue()); List<Long> idList = new ArrayList<Long>(); for (Map<String, Object> idMap : mapList) idList.add((Long) idMap.get("id")); if (idList.size() == 0) return new ArrayList(); String hqlQuery = "select distinct r from Roi r join " + "r.image i join fetch r.shapes where r.id in (:ids)"; hqlQuery = hqlQuery + " order by r.id"; Query q = session.createQuery(hqlQuery); q.setParameterList("ids", idList); return q.list(); } else { String queryString = "select distinct r from Roi r join r.image i " + "join fetch r.shapes where i.id = :id"; queryString = queryString + " order by r.id"; Query q = session.createQuery(queryString); q.setParameter("id", imageId); return q.list(); } } })); } public void findByRoi_async(AMD_IRoi_findByRoi __cb, final long roiId, final RoiOptions opts, Current __current) throws ServerError { final IceMapper mapper = new RoiResultMapper(opts); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "findByRoi", roiId) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { RoiQueryBuilder qb = new RoiQueryBuilder(Arrays.asList(roiId)); return qb.query(session).list(); } })); } public void findByPlane_async(AMD_IRoi_findByPlane __cb, final long imageId, final int z, final int t, RoiOptions opts, Current __current) throws ServerError { final IceMapper mapper = new RoiResultMapper(opts); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "findByPlane", imageId, z, t) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { Query q = session.createQuery( "select distinct r from Roi r " + "join fetch r.shapes s where r.id = :id " + "and ( s.theZ is null or s.theZ = :z ) " + "and ( s.theT is null or s.theT = :t ) " + "order by r.id"); q.setParameter("id", imageId); q.setParameter("z", z); q.setParameter("t", t); return q.list(); } })); } public void getPoints_async(AMD_IRoi_getPoints __cb, final long shapeId, Current __current) throws ServerError { final IceMapper mapper = new IceMapper(IceMapper.UNMAPPED); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "getPoints", shapeId) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { return geomTool.getPoints(shapeId, session); } })); } public void getShapeStats_async(AMD_IRoi_getShapeStats __cb, final long shapeId, Current __current) throws ServerError { final IceMapper mapper = new IceMapper(IceMapper.UNMAPPED); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "getShapeStats", shapeId) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { return geomTool.getStats(Arrays.asList(shapeId)).perShape[0]; } })); } public void getShapeStatsList_async(AMD_IRoi_getShapeStatsList __cb, final List<Long> shapeIdList, Current __current) throws ServerError { final IceMapper mapper = new IceMapper(IceMapper.UNMAPPED); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "getShapeStatsList", shapeIdList) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { return Arrays.asList(geomTool.getStats(shapeIdList).perShape); } })); } public void getRoiStats_async(AMD_IRoi_getRoiStats __cb, final long roiId, Current __current) throws ServerError { final IceMapper mapper = new IceMapper(IceMapper.UNMAPPED); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "getRoiStats", roiId) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { List<Long> shapesInRoi = sql.getShapeIds(roiId); return geomTool.getStats(shapesInRoi); } })); } // Measurement results. // ========================================================================= public void getRoiMeasurements_async(AMD_IRoi_getRoiMeasurements __cb, final long imageId, final RoiOptions opts, Current __current) throws ServerError { final IceMapper mapper = new IceMapper(IceMapper.FILTERABLE_COLLECTION); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "getRoiMeasurements", imageId) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { QueryBuilder qb = new QueryBuilder(); qb.select("distinct fa"); qb.from("Image", "i"); qb.append(", Roi roi "); qb.join("roi.annotationLinks", "rlinks", false, false); qb.join("rlinks.child", "rfa", false, false); qb.join("i.wellSamples", "ws", false, false); qb.join("ws.well", "well", false, false); qb.join("well.plate", "plate", false, false); qb.join("plate.annotationLinks", "links", false, false); qb.join("links.child", "fa", false, false); qb.where(); qb.and("fa.ns = '" + NSMEASUREMENT.value + "'"); qb.and("rfa.id = fa.id"); qb.and("i.id = :id"); qb.and("i.id = roi.image"); qb.param("id", imageId); qb.filter("fa", filter(opts)); return qb.query(session).list(); } })); } protected List<ome.model.roi.Roi> loadMeasuredRois(Session session, long imageId, long annotationId) { Query q = session.createQuery("select distinct r from Roi r join r.image i " + "join fetch r.shapes join i.wellSamples ws join ws.well well " + "join well.plate plate join plate.annotationLinks links " + "join links.child a where a.id = :aid and i.id = :iid " + "order by r.id"); q.setParameter("iid", imageId); q.setParameter("aid", annotationId); return q.list(); } public void getMeasuredRoisMap_async(AMD_IRoi_getMeasuredRoisMap __cb, final long imageId, final List<Long> annotationIds, RoiOptions opts, Current __current) throws ServerError { final IceMapper mapper = new IceMapper(new RoiResultMapReturnMapper(opts)); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "getMeasuredRoisMap", imageId, annotationIds) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { if (annotationIds == null) { return null; } Map<Long, List<ome.model.roi.Roi>> rv = new HashMap<Long, List<ome.model.roi.Roi>>(); for (Long annotationId : annotationIds) { rv.put(annotationId, loadMeasuredRois(session, imageId, annotationId)); } return rv; } })); } public void getMeasuredRois_async(AMD_IRoi_getMeasuredRois __cb, final long imageId, final long annotationId, final RoiOptions opts, Current __current) throws ServerError { final IceMapper mapper = new RoiResultMapper(opts); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "getMeasuredRois", imageId, annotationId) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { return loadMeasuredRois(session, imageId, annotationId); } })); } public void getTable_async(AMD_IRoi_getTable __cb, final long annotationId, final Current __current) throws ServerError { final IceMapper mapper = new IceMapper(IceMapper.UNMAPPED); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "getTable", annotationId) { @Transactional(readOnly = true) public Object doWork(Session session, ServiceFactory sf) { QueryBuilder qb = new QueryBuilder(); qb.select("f"); qb.from("FileAnnotation", "fa"); qb.join("fa.file", "f", false, false); qb.where(); qb.and("fa.id = :id"); qb.param("id", annotationId); OriginalFile file = (OriginalFile) qb.query(session).uniqueResult(); if (file == null) { throw new ome.conditions.ApiUsageException("No such file annotation: " + annotationId); } try { return factory.sharedResources(__current) .openTable(new OriginalFileI(file.getId(), false)); } catch (ServerError e) { throw new RuntimeException(e); } } })); } class MaskClass { Set<Point> points; int colour; Point min, max; int width; int height; MaskClass(int value) { points = new HashSet<Point>(); colour = value; } public Color getColour() { return new Color(colour); } public byte[] asBytes() throws IOException { byte[] data = new byte[(int) Math.ceil((double) width * (double) height / 8.0)]; int offset = 0; for (int y = min.y; y < max.y + 1; y++) { for (int x = min.x; x < max.x + 1; x++) { if (points.contains(new Point(x, y))) setBit(data, offset, 1); else setBit(data, offset, 0); offset++; } } return data; } public void add(Point p) { if (points.size() == 0) { min = new Point(p); max = new Point(p); } else { min.x = Math.min(p.x, min.x); min.y = Math.min(p.y, min.y); max.x = Math.max(p.x, max.x); max.y = Math.max(p.y, max.y); } width = max.x - min.x + 1; height = max.y - min.y + 1; points.add(p); } public ome.model.roi.Mask asMaskI(int z, int t) throws IOException { ome.model.roi.Mask mask = new ome.model.roi.Mask(); mask.setX((double) min.x); mask.setY((double) min.y); mask.setWidth((double) width); mask.setHeight((double) height); mask.setLocked(true); mask.setTheT(t); mask.setTheZ(z); byte[] theseBytes; theseBytes = this.asBytes(); mask.setBytes(theseBytes); return mask; } /** * Set the bit value in a byte array at position bit to be the value * value. * @param data See above. * @param bit See above. * @param val See above. */ private void setBit(byte[] data, int bit, int val) { int bytePosition = bit / 8; int bitPosition = 7 - bit % 8; data[bytePosition] = (byte) ((byte) (data[bytePosition] & (~(byte) (0x1 << bitPosition))) | (byte) (val << bitPosition)); } /** * Set the bit value in a byte array at position bit to be the value * value. * @param data See above. * @param bit See above. * @param val See above. */ private byte getBit(byte[] data, int bit) { int bytePosition = bit / 8; int bitPosition = 7 - bit % 8; return (byte) ((byte) (data[bytePosition] & (0x1 << bitPosition)) != 0 ? (byte) 1 : (byte) 0); } } @SuppressWarnings("unchecked") private <T extends IObject> T safeReverse(Object o, IceMapper mapper) { try { return (T) mapper.reverse(o); } catch (Exception e) { throw new RuntimeException("Failed to safely reverse: " + o); } } public void uploadMask_async(final AMD_IRoi_uploadMask __cb, final long imageId, final int z, final int t, final byte[] bytes, final Current __current) throws ServerError { final IceMapper mapper = new IceMapper(IceMapper.VOID); runnableCall(__current, new Adapter(__cb, __current, mapper, factory.getExecutor(), factory.principal, new SimpleWork(this, "uploadMask", bytes) { @Transactional(readOnly = false) public Object doWork(Session session, ServiceFactory sf) { IUpdate update = sf.getUpdateService(); ome.model.core.Image image; ome.model.roi.Roi roi; ByteArrayInputStream s = new ByteArrayInputStream(bytes); IQuery query = sf.getQueryService(); IObject o = query.findByQuery( "from Image as i left outer join " + "fetch i.pixels as p where i.id = " + imageId, null); try { image = (ome.model.core.Image) o; BufferedImage inputImage = ImageIO.read(s); Map<Integer, MaskClass> map = new HashMap<Integer, MaskClass>(); MaskClass mask; int value; for (int x = 0; x < inputImage.getWidth(); x++) for (int y = 0; y < inputImage.getHeight(); y++) { value = inputImage.getRGB(x, y); if (value == Color.black.getRGB()) continue; if (!map.containsKey(value)) { mask = new MaskClass(value); map.put(value, mask); } else mask = map.get(value); mask.add(new Point(x, y)); } Iterator<Integer> maskIterator = map.keySet().iterator(); while (maskIterator.hasNext()) { int colour = maskIterator.next(); mask = map.get(colour); roi = new ome.model.roi.Roi(); roi.setImage(image); ome.model.roi.Mask toSaveMask = mask.asMaskI(z, t); roi.addShape(toSaveMask); ome.model.roi.Roi newROI = update.saveAndReturnObject(roi); } return null; } catch (Exception e) { __cb.ice_exception(e); } return null; } })); } // Helpers // ========================================================================= private Filter filter(RoiOptions opts) { Filter f = new Filter(); if (opts != null) { if (opts.userId != null) { f.owner(opts.userId.getValue()); } if (opts.groupId != null) { f.group(opts.groupId.getValue()); } Integer offset = null; Integer limit = null; if (opts.offset != null) { offset = opts.offset.getValue(); } if (opts.limit != null) { limit = opts.limit.getValue(); } if (offset != null || limit != null) { f.page(offset, limit); } } return f; } private static class RoiQueryBuilder extends QueryBuilder { RoiQueryBuilder(List<Long> roiIds) { this.paramList("ids", roiIds); this.select("distinct r"); this.from("Roi", "r"); this.join("r.shapes", "s", false, true); this.where(); } @Override public Query query(Session session) { this.and("r.id in (:ids)"); this.append("order by r.id"); return super.query(session); } } public static class RoiResultMapper extends IceMapper { public RoiResultMapper(RoiOptions opts) { super(new RoiResultReturnMapper(opts)); } } public static class RoiResultReturnMapper implements IceMapper.ReturnMapping { private final RoiOptions opts; public RoiResultReturnMapper(RoiOptions opts) { this.opts = opts; } @SuppressWarnings("unchecked") public Object mapReturnValue(IceMapper mapper, Object value) throws Ice.UserException { RoiResult result = new RoiResult(); result.opts = opts; if (value == null) { result.rois = Collections.emptyList(); result.byZ = Collections.emptyMap(); result.byT = Collections.emptyMap(); result.byG = Collections.emptyMap(); result.groups = Collections.emptyMap(); return result; // EARLY EXIT } List<Roi> rois = (List<Roi>) IceMapper.FILTERABLE_COLLECTION.mapReturnValue(mapper, value); result.rois = rois; MultiMap byZ = new MultiValueMap(); MultiMap byT = new MultiValueMap(); MultiMap byG = new MultiValueMap(); for (Roi roi : rois) { omero.model.RoiI roii = (omero.model.RoiI) roi; Iterator<Shape> it = roii.iterateShapes(); while (it.hasNext()) { Shape shape = it.next(); if (shape == null) { continue; } if (shape.getTheT() != null) { byT.put(shape.getTheT().getValue(), shape); } else { byT.put(-1, shape); } if (shape.getTheZ() != null) { byZ.put(shape.getTheZ().getValue(), shape); } else { byZ.put(-1, shape); } if (shape.getG() != null) { byG.put(shape.getG().getValue(), shape); } else { byG.put("", shape); } } result.byG = byG; result.byZ = byZ; result.byT = byT; } return result; } } public static class RoiResultMapReturnMapper implements IceMapper.ReturnMapping { private final RoiOptions opts; public RoiResultMapReturnMapper(RoiOptions opts) { this.opts = opts; } @SuppressWarnings("unchecked") public Object mapReturnValue(IceMapper mapper, Object value) throws Ice.UserException { Map<Long, RoiResult> rv = new HashMap<Long, RoiResult>(); Map<Long, List<ome.model.roi.Roi>> iv = (Map<Long, List<ome.model.roi.Roi>>) value; RoiResultMapper m = new RoiResultMapper(opts); for (Map.Entry<Long, List<ome.model.roi.Roi>> entry : iv.entrySet()) { rv.put(entry.getKey(), (RoiResult) m.mapReturnValue(entry.getValue())); } return rv; } } private class NamespaceKeywords { public String[] namespaces; public String[][] keywords; } }