diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
index 55047abcba110225a13611a44845531911947d39..92c905842030f52d36d1d155f302721c1b0172ca 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
@@ -20,7 +20,9 @@ import java.awt.image.BufferedImage;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.List;
import javax.imageio.ImageIO;
@@ -29,6 +31,7 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.base.utilities.OSUtilities;
import ch.systemsx.cisd.common.concurrent.ConcurrencyUtilities;
+import ch.systemsx.cisd.common.concurrent.FailureRecord;
import ch.systemsx.cisd.common.concurrent.ITaskExecutor;
import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor;
import ch.systemsx.cisd.common.exceptions.Status;
@@ -141,8 +144,8 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
return newImagePath;
}
- private byte[] generateThumbnail(ByteArrayOutputStream bufferOutputStream, File img, String imageIdOrNull)
- throws IOException
+ private byte[] generateThumbnail(ByteArrayOutputStream bufferOutputStream, File img,
+ String imageIdOrNull) throws IOException
{
byte[] byteArray;
if (thumbnailsStorageFormat.isGenerateWithImageMagic())
@@ -161,9 +164,16 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
thumbnailsStorageFormat.getMaxWidth() + "x"
+ thumbnailsStorageFormat.getMaxHeight();
String imageFilePath = imageFile.getPath();
+ List<String> params = new ArrayList<String>();
+ params.addAll(Arrays.asList(convertUtilityOrNull.getPath(), imageFilePath, "-scale", size));
+ List<String> additionalParams = thumbnailsStorageFormat.getImageMagicParams();
+ if (additionalParams != null)
+ {
+ params.addAll(additionalParams);
+ }
+ params.add("png:-");
final ProcessResult result =
- ProcessExecutionHelper.run(Arrays.asList(convertUtilityOrNull.getPath(),
- imageFilePath, "-scale", size, "png:-"), operationLog, machineLog,
+ ProcessExecutionHelper.run(params, operationLog, machineLog,
ConcurrencyUtilities.NO_TIMEOUT,
ProcessIOStrategy.BINARY_DISCARD_STDERR_IO_STRATEGY, false);
if (result.isOK() == false)
@@ -177,8 +187,8 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
}
}
- private byte[] generateThumbnailInternally(File imageFile,
- String imageIdOrNull, ByteArrayOutputStream bufferOutputStream) throws IOException
+ private byte[] generateThumbnailInternally(File imageFile, String imageIdOrNull,
+ ByteArrayOutputStream bufferOutputStream) throws IOException
{
BufferedImage image = loadImage(imageFile, imageIdOrNull);
BufferedImage thumbnail =
@@ -231,8 +241,16 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
public void runWithSimpleWriter(IHDF5SimpleWriter writer)
{
- ParallelizedExecutor.process(plateImages, createThumbnailGenerator(writer),
- thumbnailsStorageFormat.getAllowedMachineLoadDuringGeneration(), 100,
- "Thumbnails generation", MAX_RETRY_OF_FAILED_GENERATION);
+ Collection<FailureRecord<AcquiredSingleImage>> errors =
+ ParallelizedExecutor.process(plateImages, createThumbnailGenerator(writer),
+ thumbnailsStorageFormat.getAllowedMachineLoadDuringGeneration(), 100,
+ "Thumbnails generation", MAX_RETRY_OF_FAILED_GENERATION);
+ if (errors.size() > 0)
+ {
+ throw new IllegalStateException(
+ String.format(
+ "There were errors when generating %d thumbnails, the whole thumbnails generation process fails.",
+ errors.size()));
+ }
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
index 9a58eb515ad07b1df078e52adbf8bde6e59f5ae7..ee1ba7dfb08fa1b4920d13700cf73d1c052ef357 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+import java.util.Arrays;
+import java.util.Collections;
import java.util.List;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
@@ -52,7 +54,7 @@ abstract public class SimpleImageDataConfig
* just the {@link ImageMetadata} object returned by {@link #extractImageMetadata(String)}.
* <p>
* In case of a image container file format (like multi-page TIFF) this method should
- * overridden.
+ * overridden.
*
* @param imageIdentifiers Identifiers of all images contained in the image file.
*/
@@ -142,7 +144,9 @@ abstract public class SimpleImageDataConfig
private int maxThumbnailWidthAndHeight = 256;
- private boolean generateThumbnailsWithImageMagic = false;
+ private boolean generateThumbnailsWithImageMagic = true;
+
+ private List<String> thumbnailsGenerationImageMagicParams = Collections.emptyList();
private boolean generateThumbnailsInHighQuality = false;
@@ -176,6 +180,7 @@ abstract public class SimpleImageDataConfig
thumbnailsStorageFormat.setMaxWidth(getMaxThumbnailWidthAndHeight());
thumbnailsStorageFormat.setMaxHeight(getMaxThumbnailWidthAndHeight());
thumbnailsStorageFormat.setGenerateWithImageMagic(generateThumbnailsWithImageMagic);
+ thumbnailsStorageFormat.setImageMagicParams(thumbnailsGenerationImageMagicParams);
thumbnailsStorageFormat.setHighQuality(generateThumbnailsInHighQuality);
imageStorageConfiguraton.setThumbnailsStorageFormat(thumbnailsStorageFormat);
}
@@ -284,14 +289,30 @@ abstract public class SimpleImageDataConfig
}
/**
- * if true ImageMagic 'convert' utility will be used to generate thumbnails. It should be
- * installed and accessible.
+ * Decides if ImageMagic 'convert' utility will be used to generate thumbnails. True by default.
+ * <p>
+ * The tool should be installed and accessible, otherwise set this option to false and set
+ * {@link #setAllowedMachineLoadDuringThumbnailsGeneration(double)} to
+ * 1/numberOfYourProcessorCores. Internal library will be used to generate thumbnails, but it is
+ * not able to generate thumbnails in parallel.
*/
public void setUseImageMagicToGenerateThumbnails(boolean generateWithImageMagic)
{
this.generateThumbnailsWithImageMagic = generateWithImageMagic;
}
+ /**
+ * Sets additional parameters which should be passed to ImageMagic 'convert' utility when it is
+ * used to generate thumbnails.
+ * <p>
+ * Example: pass "-contrast-stretch 2%" to discard 2% of brightest and darkest pixels in the
+ * thumbnails.
+ */
+ public void setThumbnailsGenerationImageMagicParams(String[] imageMagicParams)
+ {
+ this.thumbnailsGenerationImageMagicParams = Arrays.asList(imageMagicParams);
+ }
+
/**
* if true and thumbnails generation is switched on, thumbnails will be generated with high
* quality.
@@ -356,7 +377,7 @@ abstract public class SimpleImageDataConfig
{
this.imageLibraryInfoOrNull = new ImageLibraryInfo(imageLibraryName, readerName);
}
-
+
/**
* Sets the image library to be used for reading images. Available libraries are: IJ, ImageIO,
* JAI, and BioFormats. The first image file is used to determine the actual reader. Note, that
@@ -366,7 +387,7 @@ abstract public class SimpleImageDataConfig
{
this.imageLibraryInfoOrNull = new ImageLibraryInfo(imageLibraryName);
}
-
+
// --- predefined image dataset types
/**
@@ -445,7 +466,7 @@ abstract public class SimpleImageDataConfig
{
return isMeasured;
}
-
+
public boolean isMicroscopyData()
{
return isMicroscopy;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
index d1fe0f3b7b331ac1c1e27647164ce262161443f7..0bd681c6cb8564974edf8b66a7b953235ad9213e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+import java.util.Collections;
+import java.util.List;
+
import ch.systemsx.cisd.common.utilities.AbstractHashable;
/**
@@ -45,6 +48,8 @@ public class ThumbnailsStorageFormat extends AbstractHashable
private boolean generateWithImageMagic = false;
+ private List<String> imageMagicParams = Collections.emptyList();
+
/**
* Creates empty object which instructs that the thumbnails should be generated with default
* settings. Use setters to change default behaviour (you will probably not have to).
@@ -83,6 +88,11 @@ public class ThumbnailsStorageFormat extends AbstractHashable
return generateWithImageMagic;
}
+ public List<String> getImageMagicParams()
+ {
+ return imageMagicParams;
+ }
+
// --- setters ---
/** Sets the maximum width of a thumbnail. */
@@ -124,12 +134,23 @@ public class ThumbnailsStorageFormat extends AbstractHashable
/**
* if true ImageMagic 'convert' utility should be installed and will be used to generate
* thumbnails. <br>
- * Note: if image library has been specified to handle the images, it will be ignored for
- * thumbnails generation if convert is supposed to be used.
+ * Note: if images should be handled with a specific image library, it will be ignored for
+ * thumbnails generation if 'convert' is supposed to be used. Make sure that 'convert' can deal
+ * with your images in such a case.
*/
public void setGenerateWithImageMagic(boolean generateWithImageMagic)
{
this.generateWithImageMagic = generateWithImageMagic;
}
+ /**
+ * Sets additional parameters which should be passed to ImageMagic 'convert' utility when it is
+ * used to generate thumbnails. Example: pass "-contrast-stretch 2%" to discard 2% of brightest
+ * and darkest pixels in the thumbnails.
+ */
+ public void setImageMagicParams(List<String> imageMagicParams)
+ {
+ this.imageMagicParams = imageMagicParams;
+ }
+
}