tango.plugin.filter.PreFilterSequence.java Source code

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Here is the source code for tango.plugin.filter.PreFilterSequence.java

Source

package tango.plugin.filter;

import com.mongodb.BasicDBList;
import com.mongodb.BasicDBObject;
import tango.dataStructure.Experiment;
import mcib3d.utils.exceptionPrinter;
import ij.IJ;
import ij.ImagePlus;
import mcib3d.image3d.ImageHandler;
import java.util.ArrayList;
import tango.dataStructure.InputImages;
import tango.gui.Core;
import tango.parameter.Parameter;
import tango.plugin.PluginFactory;

/**
 *
 **
 * /**
 * Copyright (C) 2012 Jean Ollion
 *
 *
 *
 * This file is part of tango
 *
 * tango 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 3 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, see <http://www.gnu.org/licenses/>.
 *
 * @author Jean Ollion
 */
public class PreFilterSequence {
    // TODO pour alleger la memoire : les prefilters prennent en argument une image tampon vide
    ArrayList<PreFilter> filters;

    public PreFilterSequence(BasicDBObject settings, int nbCPUs, boolean verbose) {
        if (settings == null || !settings.containsField("preFilters"))
            return;
        BasicDBList prefilters = (BasicDBList) settings.get("preFilters");
        filters = new ArrayList<PreFilter>(prefilters.size());
        for (int i = 0; i < prefilters.size(); i++) {
            //IJ.log(i+"");
            Object o = prefilters.get(i);
            if (o != null) {
                BasicDBObject data = (BasicDBObject) o;
                //IJ.log("preFilter:"+data);
                if (!data.getBoolean("isActivated", true)) {
                    filters.add(new DummyPreFilter());
                    continue;
                }
                PreFilter f = PluginFactory.getPreFilter(data.getString("method"));
                if (f != null) {
                    //IJ.log("preFilter loaded:"+f.getId());
                    Parameter[] parameters = f.getParameters();
                    for (Parameter p : parameters)
                        p.dbGet(data);
                    filters.add(f);
                    f.setMultithread(nbCPUs);
                    f.setVerbose(verbose);
                }
            }
        }
    }

    public ImageHandler run(int currentStructureIdx, ImageHandler in, InputImages images) {
        ImageHandler currentImage = in;
        if (isEmpty())
            return in;
        while (!filters.isEmpty()) {

            currentImage = filters.remove(0).runPreFilter(currentStructureIdx, currentImage, images);

            currentImage.setScale(in);
            currentImage.setOffset(in);
        }
        currentImage.setTitle(in.getTitle() + "::preFiltered");
        return currentImage;
    }

    public void test(int currentStructureIdx, ImageHandler in, InputImages images, int step, boolean onlyStep) {
        ImageHandler currentImage = in;
        if (isEmpty() || step > filters.size())
            return;
        int idx = 0;
        while (!filters.isEmpty()) {
            PreFilter f = filters.remove(0);
            if (step == idx) {
                if (!onlyStep)
                    currentImage.showDuplicate("Image Before selected Step");
                images.setVerbose(true);
                f.setVerbose(true);
            } else {
                if (onlyStep) {
                    idx++;
                    continue;
                }
                images.setVerbose(false);
                f.setVerbose(false);
            }

            currentImage = f.runPreFilter(currentStructureIdx, currentImage, images);
            currentImage.setScale(in);
            currentImage.setOffset(in);
            if (step == idx) {
                currentImage.showDuplicate("Image After selected Step");
                images.setVerbose(false);
                return;
            }
            idx++;
        }
    }

    public boolean isEmpty() {
        return (filters == null || filters.isEmpty());
    }
}