LMS-2147 example program for Sanofi to fetch images with the API

SVN: 20511

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/LoadImagesScreeningClientApiTest.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.plugin.screening.client.api.v1;
+
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.log4j.PropertyConfigurator;
+
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+
+/**
+ * A test class which shows how to use API to load images.
+ * 
+ * @author Tomasz Pylak
+ */
+public class LoadImagesScreeningClientApiTest
+{
+    public static void main(String[] args) throws IOException
+    {
+        if (args.length != 3)
+        {
+            System.err.println("Usage: <user> <password> <openbis-server-url>");
+            System.err.println("Example parameters: test-user my-password http://localhost:8888");
+            System.exit(1);
+            return;
+        }
+        configureLogging();
+
+        String userId = args[0];
+        String userPassword = args[1];
+        String serverUrl = args[2];
+
+        print(String.format("Connecting to the server '%s' as a user '%s.", serverUrl, userId));
+        IScreeningOpenbisServiceFacade facade =
+                ScreeningOpenbisServiceFacadeFactory.tryCreate(userId, userPassword, serverUrl);
+        if (facade == null)
+        {
+            System.err.println("Authentication failed: check the user name and password.");
+            System.exit(1);
+            return;
+        }
+
+        // Another way: PlateIdentifier.createFromAugmentedCode("/SPACE_CODE/MY_PLATE_CODE")
+        // PlateIdentifier plate = new PlateIdentifier("MY_PLATE_CODE", "SPACE_CODE", null);
+        PlateIdentifier plate = new PlateIdentifier("PLATE-2-A", "TEST", null);
+        List<ImageDatasetReference> imageDatasets =
+                facade.listRawImageDatasets(Arrays.asList(plate));
+        if (imageDatasets.size() == 0)
+        {
+            System.err.println("No image datasets connected to plate " + plate);
+            System.exit(1);
+        }
+        // take the first image dataset
+        ImageDatasetReference imageDataset = imageDatasets.get(0);
+        // You could get to know more about the image dataset metadata with:
+        // facade.listImageMetadata(imageDataset);
+        // Here we will make some assumptions.
+
+        // Note: first tile has number 0
+        int tile = 0;
+        String channel = "DAPI";
+        // Note: first well 1 has coordinates (1,1)
+        int row = 1;
+        int column = 3;
+        WellPosition well = new WellPosition(row, column);
+        PlateImageReference imageRef = new PlateImageReference(tile, channel, well, imageDataset);
+        loadImage(facade, imageRef);
+
+        facade.logout();
+    }
+
+    private static File createImageFile(PlateImageReference imageRef)
+    {
+        File dir = new File(imageRef.getDatasetCode());
+        dir.mkdir();
+        return new File(dir, createImageFileName(imageRef));
+    }
+
+    /**
+     * @throws IOException when reading images from the server or writing them to the files fails
+     */
+    private static void loadImage(IScreeningOpenbisServiceFacade facade,
+            PlateImageReference imageReference) throws IOException
+    {
+        File imageOutputFile = createImageFile(imageReference);
+        final OutputStream out = new BufferedOutputStream(new FileOutputStream(imageOutputFile));
+        try
+        {
+            facade.loadImages(Arrays.asList(imageReference), new IImageOutputStreamProvider()
+                {
+                    public OutputStream getOutputStream(PlateImageReference imageRef)
+                            throws IOException
+                    {
+                        return out;
+                    }
+                });
+        } finally
+        {
+            out.close();
+        }
+    }
+
+    private static void print(String msg)
+    {
+        System.out.println(new Date() + "\t" + msg);
+    }
+
+    private static String createImageFileName(PlateImageReference image)
+    {
+        WellPosition well = image.getWellPosition();
+        return "img_row" + well.getWellRow() + "_col" + well.getWellColumn() + "_"
+                + image.getChannel() + "_tile" + image.getTile() + ".png";
+    }
+
+    private static void configureLogging()
+    {
+        Properties props = new Properties();
+        props.put("log4j.appender.STDOUT", "org.apache.log4j.ConsoleAppender");
+        props.put("log4j.appender.STDOUT.layout", "org.apache.log4j.PatternLayout");
+        props.put("log4j.appender.STDOUT.layout.ConversionPattern", "%d %-5p [%t] %c - %m%n");
+        props.put("log4j.rootLogger", "INFO, STDOUT");
+        PropertyConfigurator.configure(props);
+    }
+}