LMS-1870 Making inner class Size an outer class. First tests for ImageChannelsUtilsTest.

SVN: 18639

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java

@@ -47,6 +47,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.common.logging.LogCategory;
 import ch.systemsx.cisd.common.logging.LogFactory;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
@@ -376,29 +377,6 @@ abstract public class AbstractDatasetDownloadServlet extends HttpServlet
         }
     }
 
-    public static final class Size
-    {
-        private final int width;
-
-        private final int height;
-
-        public Size(int width, int height)
-        {
-            this.width = width;
-            this.height = height;
-        }
-
-        public int getWidth()
-        {
-            return width;
-        }
-
-        public int getHeight()
-        {
-            return height;
-        }
-    }
-
     protected final File createDataSetRootDirectory(String dataSetCode, HttpSession session)
     {
         DatabaseInstance databaseInstance = getDatabaseInstance(session);

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java

@@ -42,6 +42,7 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.common.filesystem.FileUtilities;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
 
 /**

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/Size.java

+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.shared.dto;
+
+public final class Size
+{
+    private final int width;
+
+    private final int height;
+
+    public Size(int width, int height)
+    {
+        this.width = width;
+        this.height = height;
+    }
+
+    public int getWidth()
+    {
+        return width;
+    }
+
+    public int getHeight()
+    {
+        return height;
+    }
+}
\ No newline at end of file

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java

@@ -18,7 +18,7 @@ package ch.systemsx.cisd.openbis.dss.etl;
 
 import ch.systemsx.cisd.base.image.IImageTransformerFactory;
 import ch.systemsx.cisd.common.io.IContent;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
 
 /**

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java

@@ -16,8 +16,8 @@
 
 package ch.systemsx.cisd.openbis.dss.etl;
 
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
 
 /**

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java

@@ -22,9 +22,9 @@ import ch.systemsx.cisd.common.io.IContent;
 import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
 import ch.systemsx.cisd.openbis.dss.etl.IContentRepository;
 import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference.LocationImageChannelStackReference;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.HCSDatasetLoader;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;

screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java

@@ -37,7 +37,7 @@ import ch.systemsx.cisd.common.logging.LogCategory;
 import ch.systemsx.cisd.common.logging.LogFactory;
 import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
 import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
 

screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/TileImageReference.java

@@ -16,7 +16,7 @@
 
 package ch.systemsx.cisd.openbis.dss.generic.server.images;
 
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
 
 /**
@@ -45,28 +45,59 @@ public class TileImageReference
         return sessionId;
     }
 
+    public final void setSessionId(String sessionId)
+    {
+        this.sessionId = sessionId;
+    }
+    
     public String getDatasetCode()
     {
         return datasetCode;
     }
 
+    public final void setDatasetCode(String datasetCode)
+    {
+        this.datasetCode = datasetCode;
+    }
+    
     public Size tryGetThumbnailSize()
     {
         return thumbnailSizeOrNull;
     }
+    
+    public final void setThumbnailSizeOrNull(Size thumbnailSizeOrNull)
+    {
+        this.thumbnailSizeOrNull = thumbnailSizeOrNull;
+    }
 
     public boolean isMergeAllChannels()
     {
         return mergeAllChannels;
     }
 
+    public final void setMergeAllChannels(boolean mergeAllChannels)
+    {
+        this.mergeAllChannels = mergeAllChannels;
+    }
+    
     public String getChannel()
     {
         return channel;
     }
 
+    public final void setChannel(String channel)
+    {
+        this.channel = channel;
+    }
+    
     public ImageChannelStackReference getChannelStack()
     {
         return channelStackReference;
     }
+    
+    public final void setChannelStack(ImageChannelStackReference channelStackReference)
+    {
+        this.channelStackReference = channelStackReference;
+    }
+    
 }
\ No newline at end of file

screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java

@@ -41,12 +41,12 @@ import ch.systemsx.cisd.common.io.IContent;
 import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
 import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
 import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
-import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
 import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDssServiceRpc;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
 import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
 import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreeningInternal;

screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java

+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.server.images;
+
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+
+import org.apache.commons.io.IOUtils;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.base.image.IImageTransformer;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.io.ByteArrayBasedContent;
+import ch.systemsx.cisd.common.io.FileBasedContent;
+import ch.systemsx.cisd.common.io.IContent;
+import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ImageChannelsUtilsTest extends AssertJUnit
+{
+    private static final String SESSION_ID = "session-42";
+    private static final String DATASET_CODE = "dataset-123";
+
+    private static final String CHANNEL = "GFP";
+
+    private static final IImageTransformer TRANSFORMER = new IImageTransformer()
+        {
+            public BufferedImage transform(BufferedImage image)
+            {
+                int width = image.getWidth();
+                int height = image.getHeight();
+                BufferedImage output = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+                for (int x = 0; x < width; x++)
+                {
+                    for (int y = 0; y < height; y++)
+                    {
+                        int rgb = image.getRGB(x, y);
+                        output.setRGB(x, y, (rgb & 0xff) << 16);
+                    }
+                }
+                return output;
+            }
+        };
+
+    private Mockery context;
+    private IHCSImageDatasetLoader loader;
+    private File imageFolder;
+    private IImageTransformerFactory transformerFactory;
+
+    @BeforeMethod
+    public void setUp()
+    {
+        context = new Mockery();
+        loader = context.mock(IHCSImageDatasetLoader.class);
+        transformerFactory = context.mock(IImageTransformerFactory.class);
+        
+        imageFolder = new File("../screening/sourceTest/java/" + getClass().getPackage().getName().replace('.', '/'));
+    }
+    
+    @AfterMethod
+    public void tearDown()
+    {
+        // The following line of code should also be called at the end of each test method.
+        // Otherwise one do not known which test failed.
+        context.assertIsSatisfied();
+    }
+    
+    @Test
+    public void testGetUnkownImage()
+    {
+        final TileImageReference imageRef = new TileImageReference();
+        imageRef.setChannel(CHANNEL);
+        imageRef.setDatasetCode(DATASET_CODE);
+        imageRef.setSessionId(SESSION_ID);
+        imageRef.setChannelStack(ImageChannelStackReference.createFromId(4711));
+        context.checking(new Expectations()
+            {
+                {
+                    one(loader)
+                            .tryGetImage(imageRef.getChannel(), imageRef.getChannelStack(), null);
+                    will(returnValue(null));
+                }
+            });
+
+        try
+        {
+            ImageChannelsUtils.getImage(loader, imageRef);
+            fail("EnvironmentFailureException expected");
+        } catch (EnvironmentFailureException ex)
+        {
+            assertEquals("No image found for channel stack "
+                    + "ImageChannelStackReference{locationRefOrNull=<null>,idRefOrNull=4711} "
+                    + "and channel GFP", ex.getMessage());
+        }
+
+        context.assertIsSatisfied();
+    }
+    
+    @Test
+    public void testGetTiffImage()
+    {
+        final TileImageReference imageRef = new TileImageReference();
+        imageRef.setChannel(CHANNEL);
+        imageRef.setDatasetCode(DATASET_CODE);
+        imageRef.setSessionId(SESSION_ID);
+        imageRef.setChannelStack(ImageChannelStackReference.createFromId(4711));
+        context.checking(new Expectations()
+            {
+                {
+                    one(loader)
+                            .tryGetImage(imageRef.getChannel(), imageRef.getChannelStack(), null);
+                    will(returnValue(new AbsoluteImageReference(
+                            image("img1.tiff"), "id42", null, null, null)));
+                }
+            });
+        
+        IContent image = ImageChannelsUtils.getImage(loader, imageRef);
+        assertEquals(getImageContentDescription(image("img1.png")), getImageContentDescription(image));
+        
+        context.assertIsSatisfied();
+    }
+    
+    @Test
+    public void testGetJpegImageAsPngThumbnail()
+    {
+        final TileImageReference imageRef = new TileImageReference();
+        imageRef.setChannel(CHANNEL);
+        imageRef.setDatasetCode(DATASET_CODE);
+        imageRef.setSessionId(SESSION_ID);
+        imageRef.setChannelStack(ImageChannelStackReference.createFromId(4711));
+        context.checking(new Expectations()
+            {
+                {
+                    one(loader)
+                            .tryGetImage(imageRef.getChannel(), imageRef.getChannelStack(), null);
+                    will(returnValue(new AbsoluteImageReference(image("img1.jpg"), "id42", null,
+                            null, new Size(4, 2))));
+                }
+            });
+
+        IContent image = ImageChannelsUtils.getImage(loader, imageRef);
+        assertPNG(image);
+        assertEquals("c4dce6 c5dce4\nc3dbe5 c4dbe3\n", getImageContentDescription(image));
+        
+        context.assertIsSatisfied();
+    }
+    
+    @Test
+    public void testGetTransformedImage()
+    {
+        final TileImageReference imageRef = new TileImageReference();
+        imageRef.setChannel(CHANNEL);
+        imageRef.setDatasetCode(DATASET_CODE);
+        imageRef.setSessionId(SESSION_ID);
+        imageRef.setChannelStack(ImageChannelStackReference.createFromId(4711));
+        context.checking(new Expectations()
+            {
+                {
+                    one(loader)
+                            .tryGetImage(imageRef.getChannel(), imageRef.getChannelStack(), null);
+                    AbsoluteImageReference imgRef =
+                            new AbsoluteImageReference(image("img1.gif"), "id42", null, null,
+                                    null);
+                    imgRef.setTransformerFactory(transformerFactory);
+                    will(returnValue(imgRef));
+                    
+                    one(transformerFactory).createTransformer();
+                    will(returnValue(TRANSFORMER));
+                }
+            });
+        
+        IContent image = ImageChannelsUtils.getImage(loader, imageRef);
+        assertPNG(image);
+        assertEquals("e50000 f00000 f00000 e40000\n" + "f20000 cf0000 cf0000 f00000\n"
+                + "f00000 cf0000 cf0000 f00000\n" + "e50000 f00000 f00000 e50000\n",
+                getImageContentDescription(image));
+        
+        context.assertIsSatisfied();
+    }
+
+    public void assertPNG(IContent image)
+    {
+        InputStream inputStream = image.getInputStream();
+        try
+        {
+            byte[] signature = new byte[3];
+            inputStream.read(); // skip first byte
+            inputStream.read(signature);
+            inputStream.close();
+            assertEquals("PNG", new String(signature));
+        } catch (IOException ex)
+        {
+            throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+        } finally
+        {
+            IOUtils.closeQuietly(inputStream);
+        }
+    }
+    
+    private IContent image(String fileName)
+    {
+        return new FileBasedContent(new File(imageFolder, fileName));
+    }
+    
+    private String getImageContentDescription(IContent image)
+    {
+        BufferedImage bufferedImage = ImageUtil.loadImage(image.getInputStream());
+        int width = bufferedImage.getWidth();
+        int height = bufferedImage.getHeight();
+        StringBuilder builder = new StringBuilder();
+        for (int j = 0; j < height; j++)
+        {
+            for (int i = 0; i < width; i++)
+            {
+                int pixel = bufferedImage.getRGB(i, j);
+                if (i > 0)
+                {
+                    builder.append(' ');
+                }
+                builder.append(Integer.toHexString(pixel).substring(2));
+            }
+            builder.append('\n');
+        }
+        return builder.toString();
+    }
+}