ijfx.core.workflow.WorkflowIOTest.java Source code

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Here is the source code for ijfx.core.workflow.WorkflowIOTest.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.workflow;

import com.fasterxml.jackson.databind.ObjectMapper;
import ijfx.core.IjfxTest;
import ijfx.core.batch.BatchService;
import ijfx.core.datamodel.DefaultInterval;
import ijfx.core.datamodel.LongInterval;
import ijfx.core.image.ChannelSettings;
import ijfx.core.image.DefaultChannelSettings;
import ijfx.plugins.projection.MedianProjection;
import ijfx.plugins.projection.Projection;
import java.io.File;
import java.io.IOException;
import net.imagej.axis.Axes;
import net.imagej.axis.AxisType;
import net.imagej.lut.LUTService;
import net.imagej.plugins.commands.imglib.GaussianBlur;
import net.imglib2.display.ColorTable;
import net.imglib2.display.ColorTable16;
import net.imglib2.display.ColorTable8;
import org.junit.Assert;
import org.junit.Test;
import org.scijava.plugin.Parameter;

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

    @Parameter
    BatchService batchService;

    @Parameter
    WorkflowIOService workflowIOService;

    @Parameter
    LUTService lutService;

    @Test
    public void channelSettings() throws IOException {

        ChannelSettings channelSettings = new DefaultChannelSettings()
                .addSetting("GFP", 200, 400, new ColorTable8()).addSetting("mCherry", 100, 300, new ColorTable16());

        File tmpFile = File.createTempFile("channelsettings", ".json");

        ObjectMapper mapper = workflowIOService.getObjectMapper();

        mapper.writeValue(tmpFile, channelSettings);

        displayFile(tmpFile);

        ChannelSettings loaded = mapper.readValue(tmpFile, ChannelSettings.class);

        Assert.assertNotNull(loaded);

        Assert.assertEquals("same number of channels", channelSettings.getChannelCount(), loaded.getChannelCount());
        Assert.assertEquals("same channels", channelSettings.get(0).getChannelMin(), loaded.get(0).getChannelMin(),
                0.0);

        System.out.println("Testing color tables...");

        for (int i = 0; i != channelSettings.getChannelCount(); i++) {

            ColorTable c1 = channelSettings.get(i).getColorTable();
            ColorTable c2 = loaded.get(i).getColorTable();

            Assert.assertEquals("Channel length " + (i + 1), c1.getLength(), c2.getLength());
            for (int j = 0; j != c1.getLength(); j++) {
                Assert.assertEquals(String.format("Byte from channel %d / %d", i, j), c1.get(0, j), c2.get(0, j));
            }
        }

        //Assert.assertEquals("same colot table byes", channelSettings.get(0).getColorTable().);
    }

    @Test
    public void longInterval() throws IOException {

        LongInterval interval = new DefaultInterval(2, 10, 0, 20);

        File tmpFile = File.createTempFile("longinterval", ".json");

        ObjectMapper mapper = workflowIOService.getObjectMapper();

        mapper.writeValue(tmpFile, interval);

        displayFile(tmpFile);

        LongInterval loaded = mapper.readValue(tmpFile, LongInterval.class);

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

        Assert.assertEquals("interval equals", loaded, interval);

    }

    @Test
    public void testWorkflowSaving() throws Exception {

        Workflow workflow = batchService.builder().addStep(GaussianBlur.class, "data", new File("hello.txt"))
                .addStep(GaussianBlur.class, "sigma", 3.0)
                //.addStep(GaussianBlur.class, "sigma", 3.0)
                .addStep(Projection.class, "projectionMethod", new MedianProjection(), "axisType", Axes.CHANNEL)
                .getWorkflow();

        File tmpFile = File.createTempFile("testIjfx", ".json");

        workflowIOService.saveWorkflow(workflow, tmpFile);

        System.out.println(org.apache.commons.io.FileUtils.readFileToString(tmpFile));

        Workflow loadedWorkflow = workflowIOService.loadWorkflow(tmpFile);

        Assert.assertEquals("workflow size", workflow.getStepList().size(), loadedWorkflow.getStepList().size());
        Assert.assertEquals("workflow params", workflow.getStepList().get(1).getParameters().get("sigma"),
                loadedWorkflow.getStepList().get(1).getParameters().get("sigma"));
        Assert.assertEquals("exotic parameter types", MedianProjection.class,
                workflow.getStepList().get(2).getParameters().get("projectionMethod").getClass());

        Assert.assertEquals("exotic parameter types", Axes.CHANNEL,
                workflow.getStepList().get(2).getParameters().get("axisType"));

    }

}