ShapeProcessor.java example

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openmicroscopy-master
/*
 * ome.formats.model.ShapeProcessor
 *
 *------------------------------------------------------------------------------
 *  Copyright (C) 2006-2008 University of Dundee. All rights reserved.
 *
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License along
 *  with this program; if not, write to the Free Software Foundation, Inc.,
 *  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 *
 *------------------------------------------------------------------------------
 */

package ome.formats.model;

import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;

import ome.formats.Index;
import omero.metadatastore.IObjectContainer;
import omero.model.Ellipse;
import omero.model.IObject;
import omero.model.Line;
import omero.model.Mask;
import omero.model.Path;
import omero.model.Point;
import omero.model.Polygon;
import omero.model.Polyline;
import omero.model.Rectangle;
import omero.model.Roi;
import omero.model.Label;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Processes the shapes of a IObjectContainerStore and ensures
 * that the ROI containers are present.
 *
 * @author Chris Allan <callan at blackcat dot ca>
 *
 */
public class ShapeProcessor implements ModelProcessor {

  /** Logger for this class */
  private Logger log = LoggerFactory.getLogger(ShapeProcessor.class);

  /** Exhaustive list of ROI types. */
  private static final List<Class<? extends IObject>> SHAPE_TYPES =
      new ArrayList<Class<? extends IObject>>();

  static {
    SHAPE_TYPES.add(Line.class);
    SHAPE_TYPES.add(Rectangle.class);
    SHAPE_TYPES.add(Mask.class);
    SHAPE_TYPES.add(Ellipse.class);
    SHAPE_TYPES.add(Point.class);
    SHAPE_TYPES.add(Polyline.class);
    SHAPE_TYPES.add(Path.class);
    SHAPE_TYPES.add(Label.class);
    // XXX: Unused OME-XML type
    SHAPE_TYPES.add(Polygon.class);
  }

  /**
   * Processes the OMERO client side metadata store.
   * @param store OMERO metadata store to process.
   * @throws ModelException If there is an error during processing.
   */
  public void process(IObjectContainerStore store) throws ModelException {
    for (Class<? extends IObject> klass : SHAPE_TYPES) {
      List<IObjectContainer> containers =
        store.getIObjectContainers(klass);
      for (IObjectContainer container : containers) {
        Integer roiIndex = container.indexes.get(Index.ROI_INDEX.getValue());
        LinkedHashMap<Index, Integer> indexes =
            new LinkedHashMap<Index, Integer>();
        indexes.put(Index.ROI_INDEX, roiIndex);
        // Creates an ROI if one doesn't exist
        store.getIObjectContainer(Roi.class, indexes);
      }
    }
  }
}