au.com.nicta.ct.solution.export.concrete.CtImagesCoordinatesExportProcess.java Source code

Introduction

Here is the source code for au.com.nicta.ct.solution.export.concrete.CtImagesCoordinatesExportProcess.java

Source

// ====================================================================================================================
// Copyright (c) 2013, National ICT Australia Ltd and The Walter and Eliza Hall Institute of Medical Research.
// All rights reserved.
//
// This software and source code is made available under a GPL v2 licence.
// The terms of the licence can be read here: http://www.gnu.org/licenses/gpl-2.0.txt
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
// INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
// ====================================================================================================================

package au.com.nicta.ct.solution.export.concrete;

import au.com.nicta.ct.db.CtManualFlush;
import au.com.nicta.ct.db.CtSession;
import au.com.nicta.ct.db.hibernate.CtImagesCoordinates;
import au.com.nicta.ct.db.hibernate.CtSolutions;
import au.com.nicta.ct.solution.export.CtDefaultExportProcess;
import au.com.nicta.ct.solution.export.CtExportCSV;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.hibernate.Query;
import org.hibernate.Session;

/**
 * Coordinates of every image, CSV. Also a complete unique list of image PKs.
 * @author davidjr
 */
public class CtImagesCoordinatesExportProcess extends CtDefaultExportProcess {

    CtExportCSV ecsv = new CtExportCSV();

    public String getName() {
        return "Image coordinates (.csv)";
    }

    public String apply(CtSolutions sol, String filePath) {

        ecsv.clear();
        ecsv.addHeader(getFields());

        Session s = CtSession.Current();
        CtManualFlush mf = new CtManualFlush(s);

        Query q = s.createQuery(" SELECT ctIC" + " FROM CtImagesCoordinates as ctIC");

        List<CtImagesCoordinates> l = (List<CtImagesCoordinates>) q.list();

        int currentExperiment = sol.getCtExperiments().getPkExperiment();
        for (CtImagesCoordinates ic : l) {
            // skip if not in current experiment
            if (ic.getCtImages().getCtExperiments().getPkExperiment() != currentExperiment) {
                continue;
            }

            ArrayList<String> fields = new ArrayList<String>();

            fields.add(String.valueOf(ic.getPkImageCoordinate()));
            fields.add(String.valueOf(ic.getCtImages().getPkImage()));
            fields.add(String.valueOf(ic.getCtImages().getUri()));
            fields.add(String.valueOf(ic.getCtCoordinates().getCtCoordinatesTypes().getName()));
            fields.add(String.valueOf(ic.getCtCoordinates().getValue()));
            fields.add(String.valueOf(ic.getCtCoordinates().getName()));

            ecsv.addRow(fields);
        }

        mf.restore();

        String result = ecsv.write(filePath);
        return result;
    }

    public Collection<String> getFields() {
        ArrayList<String> fields = new ArrayList<String>();

        fields.add("pk_image_coordinate");
        fields.add("pk_image");
        fields.add("image_uri");
        fields.add("coordinate_type");
        fields.add("coordinate_value");
        fields.add("coordinate_name");

        return fields;
    }

}