diff --git a/datastore_server/build/build.xml b/datastore_server/build/build.xml
index 91a4beee0ad60b245caf3d9b346536b1e1068517..b46645777998e7a3e799f86178ffa0840b4a6365 100644
--- a/datastore_server/build/build.xml
+++ b/datastore_server/build/build.xml
@@ -103,6 +103,11 @@
<include name="server/*.jar" />
</fileset>
</copy>
+ <copy todir="${dist.datastore_server.lib}">
+ <fileset dir="${lib}/cisd-image_readers">
+ <include name="*.jar" />
+ </fileset>
+ </copy>
<copy file="${lib}/cisd-base/cisd-base.jar" todir="${dist.datastore_server.lib}" />
<copy file="${lib}/cisd-args4j/cisd-args4j.jar" todir="${dist.datastore_server.lib}" />
<copy file="${lib}/cifex/cifex.jar" todir="${dist.datastore_server.lib}" />
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
index d9a180432d511adef451381a11b974e0f898b577..12ad535539b1d9c44144f2538cda001166bafab9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtil.java
@@ -16,16 +16,15 @@
package ch.systemsx.cisd.openbis.dss.generic.shared.utils;
-import ij.io.Opener;
+import static ch.systemsx.cisd.common.utilities.DataTypeUtil.GIF_FILE;
+import static ch.systemsx.cisd.common.utilities.DataTypeUtil.JPEG_FILE;
+import static ch.systemsx.cisd.common.utilities.DataTypeUtil.PNG_FILE;
+import static ch.systemsx.cisd.common.utilities.DataTypeUtil.TIFF_FILE;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
-import java.awt.image.Raster;
-import java.io.BufferedInputStream;
import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
@@ -33,18 +32,17 @@ import java.util.HashSet;
import java.util.Map;
import java.util.Set;
-import javax.imageio.ImageIO;
+import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-
-import com.sun.media.jai.codec.ImageCodec;
-import com.sun.media.jai.codec.ImageDecoder;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.base.io.IRandomAccessFile;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.common.utilities.DataTypeUtil;
+import ch.systemsx.cisd.imagereaders.IImageReader;
+import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
+import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
+import ch.systemsx.cisd.imagereaders.TiffReadParams;
/**
* Utility function on images.
@@ -58,42 +56,35 @@ public class ImageUtil
private static interface ImageLoader
{
- public BufferedImage load(InputStream inputStream);
+ public BufferedImage load(IRandomAccessFile raf);
- public BufferedImage load(InputStream inputStream, int page);
+ public BufferedImage load(IRandomAccessFile raf, int page);
}
private static final class TiffImageLoader implements ImageLoader
{
- static final ImageLoader INSTANCE = new TiffImageLoader();
-
- public BufferedImage load(InputStream inputStream)
+ public BufferedImage load(IRandomAccessFile handle)
{
- return load(inputStream, 0);
+ return load(handle, 0);
}
- private final static int MAX_READ_AHEAD = 30000000;
+ // TODO KE : ask if anyone remembers what is this ?!
+ // private final static int MAX_READ_AHEAD = 30000000;
- public BufferedImage load(InputStream inputStream, int page)
+ public BufferedImage load(IRandomAccessFile handle, int page)
{
- inputStream.mark(MAX_READ_AHEAD);
+ // inputStream.mark(MAX_READ_AHEAD);
try
{
- return loadJavaAdvancedImagingTiff(inputStream, page, false);
+ return loadJavaAdvancedImagingTiff(handle, page, false);
} catch (RuntimeException ex)
{
if (page == 0)
{
- try
- {
- inputStream.reset();
- } catch (IOException ex1)
- {
- throw ex;
- }
- // There are some TIFF files which cannot be opened by JIA, try ImageJ
+ handle.seek(0);
+ // There are some TIFF files which cannot be opened by JAI, try ImageJ
// instead...
- return loadWithImageJ(inputStream);
+ return loadWithImageJ(handle);
} else
{
throw ex;
@@ -101,9 +92,12 @@ public class ImageUtil
}
}
- private BufferedImage loadWithImageJ(InputStream inputStream)
+ private BufferedImage loadWithImageJ(IRandomAccessFile handle)
{
- return new Opener().openTiff(inputStream, "").getBufferedImage();
+ IImageReader imageReader =
+ ImageReaderFactory.tryGetReader(ImageReaderConstants.IMAGEJ_LIBRARY, "tiff");
+ return imageReader.readImage(handle, null);
+
}
}
@@ -114,55 +108,57 @@ public class ImageUtil
* appropriate buffered imaged type will be used, otherwise the image will be
* converted to 24 bits RGB. Useful if access to original pixel values is needed.
*/
- public static BufferedImage loadJavaAdvancedImagingTiff(InputStream inputStream,
+ public static BufferedImage loadJavaAdvancedImagingTiff(IRandomAccessFile handle,
Integer pageOrNull, boolean allow16BitGrayscaleModel)
throws EnvironmentFailureException
{
+ IImageReader imageReader =
+ ImageReaderFactory.tryGetReader(ImageReaderConstants.JAI_LIBRARY, "tiff");
+ if (imageReader == null)
+ {
+ throw EnvironmentFailureException
+ .fromTemplate("Cannot find JAI image decoder for TIFF files.");
+ }
+
int page = getPageNumber(pageOrNull);
- final ImageDecoder dec = ImageCodec.createImageDecoder("tiff", inputStream, null);
- Raster raster;
+ TiffReadParams readParams = new TiffReadParams(page);
+ readParams.setAllow16BitGrayscaleModel(allow16BitGrayscaleModel);
try
{
- raster = dec.decodeAsRaster(page);
- } catch (IOException ex)
+ return imageReader.readImage(handle, readParams);
+ } catch (Exception ex)
{
throw EnvironmentFailureException.fromTemplate("Cannot decode image.", ex);
}
- int bufferType = findBestImageBufferType(raster, allow16BitGrayscaleModel);
- final BufferedImage image =
- new BufferedImage(raster.getWidth(), raster.getHeight(), bufferType);
- image.setData(raster);
- return image;
- }
-
- private static int findBestImageBufferType(Raster raster, boolean allow16BitGrayscaleModel)
- {
- boolean is16BitGrayscale =
- raster.getNumBands() == 1 && raster.getSampleModel().getSampleSize()[0] == 16;
- return is16BitGrayscale && allow16BitGrayscaleModel ? BufferedImage.TYPE_USHORT_GRAY
- : BufferedImage.TYPE_INT_RGB;
}
private static final class JavaImageLoader implements ImageLoader
{
- static final ImageLoader INSTANCE = new JavaImageLoader();
+ private final String fileType;
- public BufferedImage load(InputStream inputStream)
+ JavaImageLoader(String fileType)
{
- try
- {
- return ImageIO.read(inputStream);
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
+ this.fileType = fileType;
}
- public BufferedImage load(InputStream inputStream, int page)
+ public BufferedImage load(IRandomAccessFile handle)
+ {
+ return load(handle, 0);
+ }
+
+ public BufferedImage load(IRandomAccessFile handle, int page)
{
if (page == 0)
{
- return load(inputStream);
+ IImageReader imageReader =
+ ImageReaderFactory.tryGetReader(ImageReaderConstants.IMAGEIO_LIBRARY,
+ fileType);
+ if (imageReader == null)
+ {
+ throw EnvironmentFailureException.fromTemplate(
+ "Cannot find ImageIO reader for file type '%s'", fileType);
+ }
+ return imageReader.readImage(handle, null);
} else
{
throw new UnsupportedOperationException();
@@ -175,10 +171,10 @@ public class ImageUtil
static
{
- imageLoaders.put(DataTypeUtil.GIF_FILE, JavaImageLoader.INSTANCE);
- imageLoaders.put(DataTypeUtil.JPEG_FILE, JavaImageLoader.INSTANCE);
- imageLoaders.put(DataTypeUtil.PNG_FILE, JavaImageLoader.INSTANCE);
- imageLoaders.put(DataTypeUtil.TIFF_FILE, TiffImageLoader.INSTANCE);
+ imageLoaders.put(GIF_FILE, new JavaImageLoader(GIF_FILE));
+ imageLoaders.put(JPEG_FILE, new JavaImageLoader(JPEG_FILE));
+ imageLoaders.put(PNG_FILE, new JavaImageLoader(PNG_FILE));
+ imageLoaders.put(TIFF_FILE, new TiffImageLoader());
}
/**
@@ -190,18 +186,8 @@ public class ImageUtil
public static boolean isImageFile(File file)
{
String fileName = file.getName();
- String fileType = tryGetFileExtension(fileName);
- return fileType != null && FILE_TYPES.contains(fileType);
- }
-
- private static String tryGetFileExtension(String name)
- {
- int lastIndexOfDot = name.lastIndexOf('.');
- if (lastIndexOfDot < 0)
- {
- return null;
- }
- return name.substring(lastIndexOfDot + 1).toLowerCase();
+ String fileType = FilenameUtils.getExtension(fileName);
+ return fileType != null && FILE_TYPES.contains(fileType.toLowerCase());
}
/**
@@ -228,13 +214,9 @@ public class ImageUtil
public static BufferedImage loadImage(IContent content, Integer pageOrNull)
{
int page = getPageNumber(pageOrNull);
- InputStream markSupportingInputStream = content.getInputStream();
- if (markSupportingInputStream.markSupported() == false)
- {
- markSupportingInputStream = new BufferedInputStream(markSupportingInputStream);
- }
- String fileType = DataTypeUtil.tryToFigureOutFileTypeOf(markSupportingInputStream);
- return loadImage(markSupportingInputStream, fileType, page);
+ IRandomAccessFile handle = content.getReadOnlyRandomAccessFile();
+ String fileType = DataTypeUtil.tryToFigureOutFileTypeOf(handle);
+ return loadImage(handle, fileType, page);
}
private static int getPageNumber(Integer pageOrNull)
@@ -243,14 +225,14 @@ public class ImageUtil
}
/**
- * Loads the specified <var>page</var> from the image from the tiven </var>inputStream</var>.
+ * Loads the specified <var>page</var> from the image from the given </var>handle</var>.
* Supported images formats are GIF, JPG, PNG, and TIFF. The input stream will be closed after
* loading. Note that only for TIFF files a <var>page</var> other than 0 may be specified.
*
* @throws IllegalArgumentException if the input stream doesn't start with a magic number
* identifying supported image format.
*/
- private static BufferedImage loadImage(InputStream inputStream, String fileType, int page)
+ private static BufferedImage loadImage(IRandomAccessFile handle, String fileType, int page)
{
try
{
@@ -268,10 +250,10 @@ public class ImageUtil
throw new IllegalArgumentException("Unable to load image of file type '" + fileType
+ "'.");
}
- return imageLoader.load(inputStream, page);
+ return imageLoader.load(handle, page);
} finally
{
- IOUtils.closeQuietly(inputStream);
+ closeQuietly(handle);
}
}
@@ -350,4 +332,16 @@ public class ImageUtil
graphics2D.drawImage(image, 0, 0, thumbnailWidth, thumbnailHeight, null);
return thumbnail;
}
+
+ private static void closeQuietly(IRandomAccessFile handle)
+ {
+ try
+ {
+ handle.close();
+ } catch (Exception ex)
+ {
+ // keep quiet
+ }
+ }
+
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
index 05dda6c326bf2085a22a357536008ed9869be63a..ff2ebf020401b129fd1b3a6b4cca7fa13837acf6 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
@@ -18,27 +18,27 @@ package ch.systemsx.cisd.openbis.dss.generic.shared.utils;
import java.awt.image.BufferedImage;
import java.io.File;
-import java.io.IOException;
import java.io.InputStream;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.io.IContent;
+import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
+import ch.systemsx.cisd.imagereaders.ImageReadersTestHelper;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ImageUtilTest extends AssertJUnit
{
private static class MockIContent implements IContent
{
- final MockInputStream is = new MockInputStream();
+ final MockRandomAccessFile is = new MockRandomAccessFile();
public String tryGetName()
{
@@ -57,39 +57,41 @@ public class ImageUtilTest extends AssertJUnit
public IRandomAccessFile getReadOnlyRandomAccessFile()
{
- throw new UnsupportedOperationException();
+ return is;
}
public InputStream getInputStream()
{
- return is;
+ throw new UnsupportedOperationException();
}
}
- private static class MockInputStream extends InputStream
+ private static class MockRandomAccessFile extends ByteBufferRandomAccessFile
{
- boolean closeInvoked;
-
- @Override
- public void close() throws IOException
+ public MockRandomAccessFile()
{
- closeInvoked = true;
+ super(1);
}
+
+ boolean closeInvoked;
@Override
- public int read() throws IOException
+ public void close()
{
- return 0;
+ closeInvoked = true;
}
}
private File dir;
@BeforeMethod
- public void setUp()
+ public void setUp() throws Exception
{
dir = new File("../datastore_server/resource/test-data/ImageUtilTest");
+ ImageReadersTestHelper.setUpLibraries(ImageReaderConstants.IMAGEIO_LIBRARY,
+ ImageReaderConstants.JAI_LIBRARY, ImageReaderConstants.IMAGEJ_LIBRARY);
+
}
@Test
@@ -119,7 +121,7 @@ public class ImageUtilTest extends AssertJUnit
assertImageSize(805, 1023, loadImageByFile("tiff-example.tiff"));
assertImageSize(805, 1023, loadImageByInputStream("tiff-example.tiff"));
}
-
+
@Test
public void testCreateThumbnail()
{
diff --git a/screening/.classpath b/screening/.classpath
index 314d7bc3a608d1dfee5cf1486f3d9996ce55d894..4f2e3b0b2b03f3700ac90f06e62839ed566becec 100644
--- a/screening/.classpath
+++ b/screening/.classpath
@@ -2,7 +2,6 @@
<classpath>
<classpathentry kind="src" path="source/java"/>
<classpathentry kind="src" path="sourceTest/java"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
<classpathentry combineaccessrules="false" kind="src" path="/common"/>
<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
@@ -48,5 +47,8 @@
<classpathentry kind="lib" path="/libraries/jython/jython.jar" sourcepath="/libraries/jython/src.zip"/>
<classpathentry kind="lib" path="/libraries/hibernate/hibernate3.jar" sourcepath="/libraries/hibernate/src.zip"/>
<classpathentry kind="lib" path="/libraries/bioformats/bioformats.jar" sourcepath="/libraries/bioformats/bioformats_src.zip"/>
+ <classpathentry kind="lib" path="/libraries/cisd-image_readers/cisd-image_readers-bioformats.jar"/>
+ <classpathentry kind="lib" path="/libraries/cisd-image_readers/cisd-image_readers.jar"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
</classpath>
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java
index 86171607e97f2174c21137bf661012243fc8cb3e..7ceca090b970beb9a65cdc0ea929628c3b61043e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java
@@ -19,22 +19,17 @@ package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.TreeSet;
-import loci.formats.IFormatReader;
-import loci.formats.ImageReader;
-import loci.formats.gui.BufferedImageReader;
-import loci.formats.in.DefaultMetadataOptions;
-import loci.formats.in.MetadataLevel;
-import loci.formats.in.MetadataOptions;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.imagereaders.IImageReader;
+import ch.systemsx.cisd.imagereaders.IMetaDataAwareImageReader;
+import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
+import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
/**
@@ -49,26 +44,13 @@ public class ImageMetadataExtractor
public static Map<String, Object> extractMetadata(File imageFile)
{
- HashMap<String, Object> result = new HashMap<String, Object>();
- // initialize the reader
- IFormatReader reader = new BufferedImageReader(new ImageReader());
- MetadataOptions metaOptions = new DefaultMetadataOptions(MetadataLevel.ALL);
- reader.setMetadataOptions(metaOptions);
+ IImageReader imageReader =
+ ImageReaderFactory.tryGetImageReaderForFile(
+ ImageReaderConstants.BIOFORMATS_LIBRARY,
+ imageFile.getAbsolutePath());
- try
- {
- reader.setId(imageFile.getAbsolutePath());
- nullSafeAddAll(result, reader.getGlobalMetadata());
- nullSafeAddAll(result, reader.getSeriesMetadata());
- } catch (Exception ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- close(reader);
- }
-
- return result;
+ IMetaDataAwareImageReader metaDataReader = (IMetaDataAwareImageReader) imageReader;
+ return metaDataReader.readMetaData(imageFile, null);
}
/**
@@ -98,27 +80,6 @@ public class ImageMetadataExtractor
return result;
}
- private static void nullSafeAddAll(HashMap<String, Object> accumulator,
- Hashtable<String, Object> toAdd)
- {
- if (toAdd != null)
- {
- accumulator.putAll(toAdd);
- }
-
- }
-
- private static void close(IFormatReader reader)
- {
- try
- {
- reader.close();
- } catch (Exception ex)
- {
- // do not throw exception
- }
- }
-
private static Location extractLocation(Map<String, Object> metadata, List<Number> xCoords,
List<Number> yCoords)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
index 297f35dc6dff8959fa4391536e34daf164cbb923..3c6240fe532e7bd96a4833c457c21a271795bfef 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
@@ -162,8 +162,8 @@ public class DynamixWellBrightnessEqualizerProcessingPlugin extends
ImgImageEnrichedDTO image)
{
IContent content = contentRepository.getContent(image.getFilePath());
- return ImageUtil.loadJavaAdvancedImagingTiff(content.getInputStream(), image.getPage(),
- true);
+ return ImageUtil.loadJavaAdvancedImagingTiff(content.getReadOnlyRandomAccessFile(),
+ image.getPage(), true);
}
private static IImageTransformerFactoryProvider createImageTransformerFactoryProvider(
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java
index cc52ffe1cc9227bdaaafb4b0ceb5138117e0491b..1c4d9824b5fb39b65c46dc2e21f001aecdd9c3bd 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractorTest.java
@@ -16,11 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl.biozentrum;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
import java.util.HashMap;
-import java.util.List;
import java.util.Map;
import org.testng.AssertJUnit;
@@ -33,112 +29,6 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
*/
public class ImageMetadataExtractorTest extends AssertJUnit
{
-
- public final String FILE_NAME =
- "./sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/demo.tif";
-
- @Test
- public void testMetaDataExtraction() throws Exception
- {
- File imageFile = new File(FILE_NAME);
- Map<String, Object> metaData = ImageMetadataExtractor.extractMetadata(imageFile);
- List<String> sortedKeys = new ArrayList<String>(metaData.keySet());
- Collections.sort(sortedKeys);
-
- StringBuilder output = new StringBuilder();
- for (String key : sortedKeys)
- {
- Object value = metaData.get(key);
- output.append(key + ": " + value);
- output.append("\n");
- }
-
- assertEquals(
- "<prop id=\"Description\" type=\"string\" value=\"Experiment base name:ME20101116METADATA03&#13;&#10;Experiment set:ME20101116METADATA03&#13;&#10;Plate Screen&#13;&#10;Exposure: 10 ms&#13;&#10;Binning: 1 x 1&#13;&#10;Region: 1392 x 1040, offset at (0, 0)&#13;&#10;Acquired from Photometrics&#13;&#10;Subtract: Off&#13;&#10;Shading: Off&#13;&#10;Digitizer: 20 MHz&#13;&#10;Gain: Gain 1 (1x)&#13;&#10;Camera Shutter: Always Open&#13;&#10;Clear Count: 2&#13;&#10;Clear Mode: CLEAR PRE SEQUENCE&#13;&#10;Frames to Average: 1&#13;&#10;Trigger Mode: Normal (TIMED)&#13;&#10;Temperature: -29.95&#13;&#10;\">\n"
- + "<prop id=\"stage-label\" type=\"string\" value=\"F09: Site 1\">\n"
- + "ApplicationName: MetaMorph\n"
- + "ApplicationVersion: 3.1.0.79\n"
- + "Binning: 1 x 1\n"
- + "BitsPerSample: 16\n"
- + "Camera Bit Depth: 12\n"
- + "Camera Shutter: Always Open\n"
- + "Clear Count: 2\n"
- + "Clear Mode: CLEAR PRE SEQUENCE\n"
- + "Compression: Uncompressed\n"
- + "DateTime: 20101121 16:52:52.986\n"
- + "Digitizer: 20 MHz\n"
- + "Experiment base name: ME20101116METADATA03\n"
- + "Experiment set: ME20101116METADATA03\n"
- + "Exposure: 10 ms\n"
- + "Frames to Average: 1\n"
- + "Gain: Gain 1 (1x)\n"
- + "ImageLength: 1040\n"
- + "ImageWidth: 1392\n"
- + "ImageXpress Micro Filter Cube: Texas Red\n"
- + "ImageXpress Micro Objective: 10X S Fluor\n"
- + "ImageXpress Micro Shutter: Closed\n"
- + "Laser focus score: 36.4006\n"
- + "MetaDataPhotometricInterpretation: Monochrome\n"
- + "MetaDataVersion: 1\n"
- + "NewSubfileType: 2\n"
- + "NumberOfChannels: 1\n"
- + "PhotometricInterpretation: BlackIsZero\n"
- + "Region: 1392 x 1040, offset at (0, 0)\n"
- + "SamplesPerPixel: 1\n"
- + "Shading: Off\n"
- + "Software: MetaSeries\n"
- + "Subtract: Off\n"
- + "Temperature: -29.95\n"
- + "Trigger Mode: Normal (TIMED)\n"
- + "X position for position #1: 73296.5\n"
- + "Y position for position #1: 25554.2\n"
- + "_IllumSetting_: Cy3\n"
- + "_MagNA_: 0.5\n"
- + "_MagRI_: 1\n"
- + "_MagSetting_: 10X S Fluor\n"
- + "acquisition-time-local: 20101121 16:52:52.986\n"
- + "autoscale-max-percent: 0\n"
- + "autoscale-min-percent: 0\n"
- + "autoscale-state: off\n"
- + "bits-per-pixel: 16\n"
- + "camera-binning-x: 1\n"
- + "camera-binning-y: 1\n"
- + "camera-chip-offset-x: 0\n"
- + "camera-chip-offset-y: 0\n"
- + "gamma: 1\n"
- + "gray-calibration-curve-fit-algorithm: 4\n"
- + "gray-calibration-max: -1\n"
- + "gray-calibration-min: -1\n"
- + "gray-calibration-units: \n"
- + "gray-calibration-values: \n"
- + "image-name: Cy3\n"
- + "look-up-table-name: Set By Wavelength\n"
- + "look-up-table-type: by-wavelength\n"
- + "modification-time-local: 20101121 16:52:53.50\n"
- + "number-of-planes: 1\n"
- + "photonegative-mode: off\n"
- + "pixel-size-x: 1392\n"
- + "pixel-size-y: 1040\n"
- + "plane-guid: {70EAFB69-A568-464E-9EE2-4479767F96EF}\n"
- + "plane-type: plane\n"
- + "scale-max: 1058\n"
- + "scale-min: 96\n"
- + "spatial-calibration-state: on\n"
- + "spatial-calibration-units: um\n"
- + "spatial-calibration-x: 0.645\n"
- + "spatial-calibration-y: 0.645\n"
- + "stage-label: F09 : Site 1\n"
- + "stage-position-x: 73296.5\n"
- + "stage-position-y: 25554.2\n"
- + "threshold-color: 4080ff\n"
- + "threshold-high: 65535\n"
- + "threshold-low: 0\n"
- + "threshold-state: ThresholdOff\n"
- + "timestamp 0: 2010-11-21T16:52:52\n"
- + "wavelength: 624\n" + "z-position: 11145.7\n" + "zoom-percent: 50\n",
- output.toString());
- }
-
@Test
public void testTileMapping() throws Exception
{
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/demo.tif b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/demo.tif
deleted file mode 100644
index b8290408d1d313b80c144fa74baab7eb31eacaab..0000000000000000000000000000000000000000
Binary files a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/demo.tif and /dev/null differ
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index cbba754fbb7f453825a9443fbe4aca3712a0ac48..412db84bbd1252ea129d09ea16952721f7e5268f 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -60,7 +60,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize
import ch.systemsx.cisd.openbis.dss.generic.shared.Constants;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProviderTestWrapper;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.DssSessionAuthorizationHolder;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
@@ -152,7 +152,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
{
DssSessionAuthorizationHolder.setAuthorizer(new DatasetSessionAuthorizer());
final StaticListableBeanFactory applicationContext = new StaticListableBeanFactory();
- ServiceProvider.setBeanFactory(applicationContext);
+ ServiceProviderTestWrapper.setApplicationContext(applicationContext);
context = new Mockery();
service = context.mock(IEncapsulatedOpenBISService.class);
applicationContext.addBean("openBIS-service", service);
@@ -209,9 +209,10 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
return identifier;
}
- @AfterMethod
+ @AfterMethod(alwaysRun = true)
public final void tearDown()
{
+ ServiceProviderTestWrapper.restoreApplicationContext();
// 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();