ijfx.core.io.ExplorableIOTest.java Source code

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Here is the source code for ijfx.core.io.ExplorableIOTest.java

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/*
This file is part of ImageJ FX.
    
ImageJ FX 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.
    
ImageJ FX 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 ImageJ FX.  If not, see <http://www.gnu.org/licenses/>. 
    
 Copyright 2015,2016 Cyril MONGIS, Michael Knop
       
 */
package ijfx.core.io;

import com.fasterxml.jackson.databind.ObjectMapper;
import ijfx.core.IjfxTest;
import ijfx.core.metadata.MetaData;
import ijfx.core.overlay.OverlayStatService;
import ijfx.core.overlay.io.PolygonOverlayBuilder;
import ijfx.core.segmentation.DefaultSegmentedObject;
import ijfx.core.segmentation.SegmentedObjectExplorerWrapper;
import ijfx.explorer.ExplorableList;
import ijfx.explorer.core.FolderManagerService;
import ijfx.explorer.datamodel.DefaultTag;
import ijfx.explorer.datamodel.Explorable;
import ijfx.explorer.datamodel.Tag;
import ijfx.explorer.datamodel.Taggable;
import ijfx.explorer.datamodel.wrappers.PlaneMetaDataSetWrapper;
import java.io.File;
import java.io.IOException;
import java.util.Collection;
import java.util.List;
import java.util.stream.Collectors;
import mongis.utils.task.ProgressHandler;
import net.imagej.overlay.PolygonOverlay;
import org.apache.commons.io.FileUtils;
import org.junit.Assert;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import org.junit.Test;
import org.scijava.plugin.Parameter;
import ijfx.explorer.ExplorerViewService;

/**
 *
 * @author cyril
 */
public class ExplorableIOTest extends IjfxTest {

    @Parameter
    ExplorableIOService explorableIOService;

    @Parameter
    OverlayStatService overlayStatsService;

    @Parameter
    ExplorerViewService explorerService;

    @Parameter
    FolderManagerService folderManagerService;

    static final File TEST_DIRECTORY = new File("src/test/resources/dataset");

    @Test
    public void contextNotNull() {
        Assert.assertNotNull(getContext());
    }

    @Test
    public void saveTag() throws IOException {
        File tmpFile = File.createTempFile("tag", ".json");
        Tag tag = new DefaultTag("hello");
        explorableIOService.getJsonMapper().writeValue(tmpFile, tag);

        Tag loaded = explorableIOService.getJsonMapper().readValue(tmpFile, Tag.class);
        displayFile(tmpFile);
        Assert.assertEquals(tag, loaded);

    }

    @Test
    public void saveSegmentedObject() throws IOException {

        System.out.println("### Creating tmp file");

        File tmpFile = File.createTempFile("saveSegmentedObject", ExplorableIOService.DB_EXTENSION);

        DefaultSegmentedObject original = new DefaultSegmentedObject();
        PolygonOverlay polygon = new PolygonOverlayBuilder(getContext()).addVertex(0, 0).addVertex(10, 10)
                .addVertex(5, 3).addVertex(1, 5)

                .build();
        polygon.setName("hello");
        original.setOverlay(polygon);
        original.addTag(new DefaultTag("hello"));
        original.getMetaDataSet().merge(overlayStatsService.getShapeStatisticsAsMap(polygon));

        SegmentedObjectExplorerWrapper wrapper = new SegmentedObjectExplorerWrapper(original);

        explorableIOService.saveOne(wrapper, tmpFile);

        displayFile(tmpFile);

        SegmentedObjectExplorerWrapper loaded = (SegmentedObjectExplorerWrapper) explorableIOService
                .loadOne(tmpFile);

        Assert.assertNotNull("taggable not null", loaded);

        Assert.assertEquals("type", original.getMetaDataSet().getType(), loaded.getMetaDataSet().getType());

        assertTrue("taggable instanceof DefaultSegmentedObject",
                loaded instanceof ijfx.core.segmentation.SegmentedObjectExplorerWrapper);
        assertEquals("overlay name", original.getOverlay().getName(),
                loaded.getWrappedTaggable().getOverlay().getName());

    }

    @Test
    public void saveFolder() throws Exception {

    }

    private int contentHash(Collection<? extends Taggable> set) {

        return set.stream().map(Taggable::getMetaDataSet).mapToInt(ExplorableList::contentHash).sum();

    }

    @Test
    public void saveFileMetaData() throws IOException {
        List<Explorable> initial = explorerService.indexDirectory(ProgressHandler.NONE, TEST_DIRECTORY)
                .collect(Collectors.toList());

        File tmpFile = File.createTempFile("saveSegmentedObject", ExplorableIOService.DB_EXTENSION);

        explorableIOService.saveAll(initial, tmpFile);

        displayFile(tmpFile);

        List<? extends Explorable> loaded = explorableIOService.loadAll(tmpFile);

        assertNotNull("List not null", loaded);

        assertTrue("List of the same size", initial.size() == loaded.size());

        System.out.println(initial.get(0).getMetaDataSet());
        System.out.println(loaded.get(0).getMetaDataSet());
        assertEquals("Same metadata", initial.get(0).getMetaDataSet().get(MetaData.ABSOLUTE_PATH),
                loaded.get(0).getMetaDataSet().get(MetaData.ABSOLUTE_PATH));

        Assert.assertNotNull("dataset", loaded.get(0).getDataset());

    }

    protected ObjectMapper getMapper() {
        return explorableIOService.getJsonMapper();
    }

    @Test
    public void savePlaneMetaData() throws IOException {

        File tmpFile = File.createTempFile("planes", ExplorableIOService.DB_EXTENSION);

        List<Explorable> planes = explorerService.indexDirectory(ProgressHandler.NONE, TEST_DIRECTORY)
                .map(exp -> folderManagerService.extractPlanes(exp)).flatMap(exp -> exp)
                .collect(Collectors.toList());
        ;

        explorableIOService.saveAll(planes, tmpFile);

        displayFile(tmpFile);

        List<? extends Explorable> loaded = explorableIOService.loadAll(tmpFile);

        Assert.assertTrue("Loading success", loaded != null && loaded.size() == planes.size());
        Assert.assertTrue("Loads the right type", loaded.get(0) instanceof PlaneMetaDataSetWrapper);
        Assert.assertNotNull("Loads with context injection", loaded.get(0).getDataset());
    }

}