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 18455e27d6e43148ec32634c5f593f3134e53885..867effcf27ba32ba93ec118ed9feb56c673d1573 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
@@ -21,6 +21,7 @@ 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.Dimension;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
@@ -83,6 +84,8 @@ public class ImageUtil
private static interface ImageLoader
{
public BufferedImage load(IRandomAccessFile raf, ImageID imageID);
+
+ public Dimension readDimension(IRandomAccessFile handle, ImageID imageID);
}
private static final class TiffImageLoader implements ImageLoader
@@ -115,6 +118,33 @@ public class ImageUtil
}
}
}
+
+ public Dimension readDimension(IRandomAccessFile handle, ImageID imageID)
+ {
+ handle.mark(MAX_READ_AHEAD);
+ try
+ {
+ return loadDimensionWithBioFormats(handle, imageID);
+ } catch (RuntimeException ex1)
+ {
+ try
+ {
+ return loadDimensionJavaAdvancedImagingTiff(handle, imageID);
+ } catch (RuntimeException ex2)
+ {
+ if (imageID.equals(ImageID.NULL))
+ {
+ handle.reset();
+ // There are some TIFF files which cannot be opened by JAI, try ImageJ
+ // instead...
+ return loadDimensionWithImageJ(handle);
+ } else
+ {
+ throw ex2;
+ }
+ }
+ }
+ }
}
private static BufferedImage loadWithImageJ(IRandomAccessFile handle)
@@ -122,12 +152,24 @@ public class ImageUtil
return loadWithLibrary(handle, ImageID.NULL, ImageReaderConstants.IMAGEJ_LIBRARY, "tiff");
}
+ private static Dimension loadDimensionWithImageJ(IRandomAccessFile handle)
+ {
+ return loadDimensionWithLibrary(handle, ImageID.NULL, ImageReaderConstants.IMAGEJ_LIBRARY,
+ "tiff");
+ }
+
private static BufferedImage loadWithBioFormats(IRandomAccessFile handle, ImageID imageID)
{
return loadWithLibrary(handle, imageID, ImageReaderConstants.BIOFORMATS_LIBRARY,
"TiffDelegateReader");
}
+ private static Dimension loadDimensionWithBioFormats(IRandomAccessFile handle, ImageID imageID)
+ {
+ return loadDimensionWithLibrary(handle, imageID, ImageReaderConstants.BIOFORMATS_LIBRARY,
+ "TiffDelegateReader");
+ }
+
/**
* For experts only! Loads some kinds of TIFF images handled by JAI library.
*/
@@ -137,6 +179,15 @@ public class ImageUtil
return loadWithLibrary(handle, imageID, ImageReaderConstants.JAI_LIBRARY, "tiff");
}
+ /**
+ * For experts only! Loads some kinds of TIFF images handled by JAI library.
+ */
+ public static Dimension loadDimensionJavaAdvancedImagingTiff(IRandomAccessFile handle,
+ ImageID imageID) throws EnvironmentFailureException
+ {
+ return loadDimensionWithLibrary(handle, imageID, ImageReaderConstants.JAI_LIBRARY, "tiff");
+ }
+
private static BufferedImage loadWithLibrary(IRandomAccessFile handle, ImageID imageIDOrNull,
String libraryName, String readerName)
{
@@ -156,6 +207,25 @@ public class ImageUtil
}
}
+ private static Dimension loadDimensionWithLibrary(IRandomAccessFile handle,
+ ImageID imageIDOrNull, String libraryName, String readerName)
+ {
+ operationLog.debug("Load tiff image using " + libraryName);
+ IImageReader imageReader = ImageReaderFactory.tryGetReader(libraryName, readerName);
+ if (imageReader == null)
+ {
+ throw new IllegalStateException(String.format(
+ "There is no reader '%s' in image library '%s'.", readerName, libraryName));
+ }
+ try
+ {
+ return imageReader.readDimensions(handle, imageIDOrNull);
+ } catch (Exception ex)
+ {
+ throw EnvironmentFailureException.fromTemplate("Cannot decode image.", ex);
+ }
+ }
+
private static final class JavaImageLoader implements ImageLoader
{
private final String fileType;
@@ -184,6 +254,24 @@ public class ImageUtil
}
}
+ public Dimension readDimension(IRandomAccessFile handle, ImageID imageID)
+ {
+ if (imageID.equals(ImageID.NULL))
+ {
+ 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.readDimensions(handle, imageID);
+ } else
+ {
+ throw new UnsupportedOperationException();
+ }
+ }
}
private static final Map<String, ImageLoader> imageLoaders = new HashMap<String, ImageLoader>();
@@ -247,6 +335,43 @@ public class ImageUtil
return loadImageGuessingLibrary(contentNode, imageID);
}
+ /**
+ * Loads the image specified by <var>imageIdOrNull</var> from the given </var>inputStream</var>.
+ * Supported images formats are GIF, JPG, PNG, and TIFF. The input stream will be closed after
+ * loading.
+ * <p>
+ * Note that the original color depth will be kept, so e.g. 12 or 16 bit grayscale images will
+ * not be converted to RGB.
+ *
+ * @throws IllegalArgumentException if the input stream doesn't start with a magic number
+ * identifying supported image format.
+ */
+ public static Dimension loadUnchangedImageDimension(IHierarchicalContentNode contentNode,
+ String imageIdOrNull, String imageLibraryNameOrNull, String imageLibraryReaderNameOrNull)
+ {
+ assert (imageLibraryReaderNameOrNull == null || imageLibraryNameOrNull != null) : "if image reader "
+ + "is specified then library name should be specified as well";
+ ImageID imageID = parseImageID(imageIdOrNull);
+ if (imageLibraryNameOrNull != null && imageLibraryReaderNameOrNull != null)
+ {
+ IImageReader reader =
+ ImageReaderFactory.tryGetReader(imageLibraryNameOrNull,
+ imageLibraryReaderNameOrNull);
+ if (reader != null)
+ {
+ IRandomAccessFile handle = contentNode.getFileContent();
+ try
+ {
+ return reader.readDimensions(handle, imageID);
+ } finally
+ {
+ closeQuietly(handle);
+ }
+ }
+ }
+ return loadImageDimensionGuessingLibrary(contentNode, imageID);
+ }
+
/**
* Converts the given <var>image</var> to a PNG image. Uses fast parameters for the filter and
* deflate level (no filter and no deflation).
@@ -412,6 +537,14 @@ public class ImageUtil
return loadImageGuessingLibrary(handle, fileType, imageID);
}
+ private static Dimension loadImageDimensionGuessingLibrary(
+ IHierarchicalContentNode contentNode, ImageID imageID)
+ {
+ IRandomAccessFile handle = contentNode.getFileContent();
+ String fileType = DataTypeUtil.tryToFigureOutFileTypeOf(handle);
+ return loadImageDimensionGuessingLibrary(handle, fileType, imageID);
+ }
+
/**
* Loads the image specified by <var>imageID</var> from the image from the given
* </var>handle</var>. Supported images formats are GIF, JPG, PNG, and TIFF. The input stream
@@ -443,6 +576,29 @@ public class ImageUtil
}
}
+ private static Dimension loadImageDimensionGuessingLibrary(IRandomAccessFile handle,
+ String fileType, ImageID imageID)
+ {
+ try
+ {
+ if (fileType == null)
+ {
+ throw new IllegalArgumentException(
+ "File type of an image input stream couldn't be determined.");
+ }
+ ImageLoader imageLoader = imageLoaders.get(fileType);
+ if (imageLoader == null)
+ {
+ throw new IllegalArgumentException("Unable to load image of file type '" + fileType
+ + "'.");
+ }
+ return imageLoader.readDimension(handle, imageID);
+ } finally
+ {
+ closeQuietly(handle);
+ }
+ }
+
/**
* Only for tests
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
index c653eea86c63c9189b96c71d4fae1b619fbb26fc..95d90d19c9804a433f8ba3717bd8b8a1a55740bc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
+import java.awt.Dimension;
import java.awt.image.BufferedImage;
import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
@@ -119,6 +120,20 @@ public class AbsoluteImageReference extends AbstractImageReference
imageLibraryReaderNameOrNull, null);
}
+ static Dimension loadUnchangedImageDimension(IHierarchicalContentNode contentNode,
+ String imageIdOrNull, ImageLibraryInfo imageLibraryOrNull)
+ {
+ String imageLibraryNameOrNull = null;
+ String imageLibraryReaderNameOrNull = null;
+ if (imageLibraryOrNull != null)
+ {
+ imageLibraryNameOrNull = imageLibraryOrNull.getName();
+ imageLibraryReaderNameOrNull = imageLibraryOrNull.getReaderName();
+ }
+ return ImageUtil.loadUnchangedImageDimension(contentNode, imageIdOrNull,
+ imageLibraryNameOrNull, imageLibraryReaderNameOrNull);
+ }
+
public RequestedImageSize getRequestedSize()
{
return imageSize;
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 b30e716206c37dfbea79c32f4657a714b0ce344d..f3145f15c3af77f014aa659e739b142817c038a7 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
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
+import java.awt.Dimension;
import java.awt.image.BufferedImage;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
@@ -43,8 +44,8 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
import ch.systemsx.cisd.common.process.ProcessIOStrategy;
import ch.systemsx.cisd.common.process.ProcessResult;
-import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailFilePaths;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageStorageConfiguraton;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
@@ -68,10 +69,10 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
*/
public static ThumbnailFilePaths tryGenerateThumbnails(List<RelativeImageFile> images,
File imagesParentDirectory, String thumbnailFilePath,
- ImageStorageConfiguraton imageStorageConfiguraton, String thumbnailPhysicalDatasetPermId)
+ ImageStorageConfiguraton imageStorageConfiguraton,
+ String thumbnailPhysicalDatasetPermId,
+ ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
{
- ThumbnailsStorageFormat thumbnailsStorageFormatOrNull =
- imageStorageConfiguraton.getThumbnailsStorageFormat();
if (thumbnailsStorageFormatOrNull != null)
{
ThumbnailFilePaths thumbnailPaths =
@@ -211,6 +212,19 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
String size =
thumbnailsStorageFormat.getMaxWidth() + "x"
+ thumbnailsStorageFormat.getMaxHeight();
+
+ if (thumbnailsStorageFormat.getZoomLevel() != null)
+ {
+ Dimension originalSize = loadUnchangedImageDimension(imageFile, null);
+ long x =
+ (int) Math.round(thumbnailsStorageFormat.getZoomLevel()
+ * originalSize.getWidth());
+ long y =
+ (int) Math.round(thumbnailsStorageFormat.getZoomLevel()
+ * originalSize.getHeight());
+ size = x + "x" + y;
+ }
+
String imageFilePath = imageFile.getPath();
List<String> params = new ArrayList<String>();
params.addAll(Arrays.asList(convertUtilityOrNull.getPath(), imageFilePath, "-scale", size));
@@ -239,9 +253,17 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
ByteArrayOutputStream bufferOutputStream) throws IOException
{
BufferedImage image = loadUnchangedImage(imageFile, imageIdOrNull);
+
+ long x = thumbnailsStorageFormat.getMaxWidth();
+ long y = thumbnailsStorageFormat.getMaxHeight();
+ if (thumbnailsStorageFormat.getZoomLevel() != null)
+ {
+ x = Math.round(thumbnailsStorageFormat.getZoomLevel() * image.getWidth());
+ y = Math.round(thumbnailsStorageFormat.getZoomLevel() * image.getHeight());
+ }
+
BufferedImage thumbnail =
- ImageUtil.rescale(image, thumbnailsStorageFormat.getMaxWidth(),
- thumbnailsStorageFormat.getMaxHeight(), false,
+ ImageUtil.rescale(image, (int) x, (int) y, false,
thumbnailsStorageFormat.isHighQuality());
ImageUtil.writeImageToPng(thumbnail, bufferOutputStream);
return bufferOutputStream.toByteArray();
@@ -253,6 +275,12 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
imageIdOrNull, imageLibraryOrNull);
}
+ private Dimension loadUnchangedImageDimension(File imageFile, String imageIdOrNull)
+ {
+ return AbsoluteImageReference.loadUnchangedImageDimension(new FileBasedContentNode(
+ imageFile), imageIdOrNull, imageLibraryOrNull);
+ }
+
private Status createStatus(String thumbnailPath, IOException ex)
{
logger.warn("Retriable error when creating thumbnail '" + thumbnailPath + "'", ex);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetStructure.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetStructure.java
index 2c48a25dda81c409043b1f4dfbf7e320910199ba..21b727cda33b1832b3f1bcd48f938338cec59b36 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetStructure.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetStructure.java
@@ -79,7 +79,7 @@ public class ImageDataSetStructure
public boolean areThumbnailsGenerated()
{
- return getImageStorageConfiguraton().getThumbnailsStorageFormat() != null;
+ return getImageStorageConfiguraton().getThumbnailsStorageFormat().size() > 0;
}
// ------ setters
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
index 9625dc3fc1969b74daca684862b6811b826e3aba..2b964329b07a3f2b4746689d463b1ed45e5426d7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+import java.util.ArrayList;
+import java.util.List;
+
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
@@ -40,7 +43,8 @@ public class ImageStorageConfiguraton extends AbstractHashable
// --- State ----------
/** No thumbnails are generated by default. */
- private ThumbnailsStorageFormat thumbnailsStorageFormatOrNull = null;
+ private List<ThumbnailsStorageFormat> thumbnailsStorageFormatsList =
+ new ArrayList<ThumbnailsStorageFormat>();
private OriginalDataStorageFormat originalDataStorageFormat =
OriginalDataStorageFormat.UNCHANGED;
@@ -62,15 +66,28 @@ public class ImageStorageConfiguraton extends AbstractHashable
// --- Getters & Setters ----------
/** @return null if no thumbnails should be generated */
- public ThumbnailsStorageFormat getThumbnailsStorageFormat()
+ public List<ThumbnailsStorageFormat> getThumbnailsStorageFormat()
{
- return thumbnailsStorageFormatOrNull;
+ return thumbnailsStorageFormatsList;
}
- /** Set to null if no thumbnails should be generated */
+ /** Set to null if no thumbnails should be generated. Overrides previous thumbnails settings. */
public void setThumbnailsStorageFormat(ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
{
- this.thumbnailsStorageFormatOrNull = thumbnailsStorageFormatOrNull;
+ thumbnailsStorageFormatsList.clear();
+ addThumbnailsStorageFormat(thumbnailsStorageFormatOrNull);
+
+ }
+
+ /**
+ * Adds new thumbnails setting to the list
+ */
+ public void addThumbnailsStorageFormat(ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
+ {
+ if (thumbnailsStorageFormatOrNull != null)
+ {
+ thumbnailsStorageFormatsList.add(thumbnailsStorageFormatOrNull);
+ }
}
/**
@@ -79,7 +96,8 @@ public class ImageStorageConfiguraton extends AbstractHashable
*/
public void switchOnThumbnailsGeneration()
{
- this.thumbnailsStorageFormatOrNull = new ThumbnailsStorageFormat();
+ thumbnailsStorageFormatsList.clear();
+ thumbnailsStorageFormatsList.add(new ThumbnailsStorageFormat());
}
public OriginalDataStorageFormat getOriginalDataStorageFormat()
@@ -143,9 +161,12 @@ public class ImageStorageConfiguraton extends AbstractHashable
appendNameAndObject(buffer, "original data storage format",
originalDataStorageFormat.toString());
}
- if (thumbnailsStorageFormatOrNull != null)
+ if (thumbnailsStorageFormatsList.size() > 0)
{
- appendNameAndObject(buffer, "thumbnails", thumbnailsStorageFormatOrNull.toString());
+ for (ThumbnailsStorageFormat thumbnailsStorageFormat : thumbnailsStorageFormatsList)
+ {
+ appendNameAndObject(buffer, "thumbnails", thumbnailsStorageFormat.toString());
+ }
}
if (storeChannelsOnExperimentLevelOrNull != null)
{
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 e58045e06e8e6ef33498f55cde1279f8a90fc847..5d9b274d0aa2d350fd06c0f0ef541476df2cf245 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 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
@@ -23,6 +24,9 @@ import java.util.List;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails.DefaultThumbnailsConfiguration;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails.IThumbnailsConfiguration;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails.ZoomLevelBasedThumbnailsConfiguration;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ConvertToolImageTransformerFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformationBuffer;
@@ -200,7 +204,8 @@ abstract public class SimpleImageDataConfig
private String[] recognizedImageExtensions = new String[]
{ "tiff", "tif", "png", "gif", "jpg", "jpeg" };
- private boolean generateThumbnails = false;
+ private List<IThumbnailsConfiguration> thumbnailsPyramid =
+ new ArrayList<IThumbnailsConfiguration>();
private int maxThumbnailWidthAndHeight = 256;
@@ -244,17 +249,10 @@ abstract public class SimpleImageDataConfig
imageStorageConfiguraton
.setStoreChannelsOnExperimentLevel(isStoreChannelsOnExperimentLevel());
imageStorageConfiguraton.setOriginalDataStorageFormat(getOriginalDataStorageFormat());
- if (isGenerateThumbnails())
+ for (IThumbnailsConfiguration thumbnailsConfiguration : thumbnailsPyramid)
{
- ThumbnailsStorageFormat thumbnailsStorageFormat = new ThumbnailsStorageFormat();
- thumbnailsStorageFormat
- .setAllowedMachineLoadDuringGeneration(getAllowedMachineLoadDuringThumbnailsGeneration());
- thumbnailsStorageFormat.setMaxWidth(getMaxThumbnailWidthAndHeight());
- thumbnailsStorageFormat.setMaxHeight(getMaxThumbnailWidthAndHeight());
- thumbnailsStorageFormat.setGenerateWithImageMagic(generateThumbnailsWithImageMagic);
- thumbnailsStorageFormat.setImageMagicParams(thumbnailsGenerationImageMagicParams);
- thumbnailsStorageFormat.setHighQuality(generateThumbnailsIn8BitHighQuality);
- imageStorageConfiguraton.setThumbnailsStorageFormat(thumbnailsStorageFormat);
+ imageStorageConfiguraton.addThumbnailsStorageFormat(thumbnailsConfiguration
+ .getThumbnailsStorageFormat(this));
}
if (false == StringUtils.isBlank(convertTransformationCliArgumentsOrNull))
{
@@ -284,7 +282,7 @@ abstract public class SimpleImageDataConfig
public boolean isGenerateThumbnails()
{
- return generateThumbnails;
+ return thumbnailsPyramid.size() > 0;
}
public int getMaxThumbnailWidthAndHeight()
@@ -358,7 +356,22 @@ abstract public class SimpleImageDataConfig
/** should thumbnails be generated? False by default. */
public void setGenerateThumbnails(boolean generateThumbnails)
{
- this.generateThumbnails = generateThumbnails;
+ thumbnailsPyramid.clear();
+ thumbnailsPyramid.add(new DefaultThumbnailsConfiguration());
+ }
+
+ public void setGenerateThumbnailsPyramid(double[] zoomLevels)
+ {
+ if (zoomLevels == null)
+ {
+ thumbnailsPyramid.clear();
+ } else
+ {
+ for (double zoomLevel : zoomLevels)
+ {
+ thumbnailsPyramid.add(new ZoomLevelBasedThumbnailsConfiguration(zoomLevel));
+ }
+ }
}
/** the maximal width and height of the generated thumbnails */
@@ -391,6 +404,11 @@ abstract public class SimpleImageDataConfig
this.generateThumbnailsWithImageMagic = generateWithImageMagic;
}
+ public boolean getGenerateThumbnailsWithImageMagic()
+ {
+ return generateThumbnailsWithImageMagic;
+ }
+
/**
* Sets additional parameters which should be passed to ImageMagic 'convert' utility when it is
* used to generate thumbnails.
@@ -403,6 +421,11 @@ abstract public class SimpleImageDataConfig
this.thumbnailsGenerationImageMagicParams = Arrays.asList(imageMagicParams);
}
+ public List<String> getThumbnailsGenerationImageMagicParams()
+ {
+ return thumbnailsGenerationImageMagicParams;
+ }
+
/**
* If true and thumbnails generation is switched on, thumbnails will be generated with high
* quality.
@@ -416,6 +439,11 @@ abstract public class SimpleImageDataConfig
this.generateThumbnailsIn8BitHighQuality = highQualityThumbnails;
}
+ public boolean getGenerateThumbnailsIn8BitHighQuality()
+ {
+ return generateThumbnailsIn8BitHighQuality;
+ }
+
/**
* See {@link #setGenerateHighQuality8BitThumbnails}.
*
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 2b11cceba9f51a07ba1eb971f9dff17428247f46..736b1f09fa668866fbfb2b2b2b3529621a0ca862 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
@@ -20,6 +20,7 @@ import java.util.Collections;
import java.util.List;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.dss.Constants;
/**
* Configuration parameters which describe how thumbnails should be generated.
@@ -40,6 +41,8 @@ public class ThumbnailsStorageFormat extends AbstractHashable
private int maxHeight = DEFAULT_THUMBNAIL_MAX_SIZE;
+ private Double zoomLevel = null;
+
private boolean storeCompressed = DEFAULT_COMPRESS_THUMBNAILS;
private double allowedMachineLoadDuringGeneration = 1;
@@ -50,6 +53,8 @@ public class ThumbnailsStorageFormat extends AbstractHashable
private List<String> imageMagicParams = Collections.emptyList();
+ private String thumbnailsFileName;
+
/**
* 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).
@@ -153,4 +158,24 @@ public class ThumbnailsStorageFormat extends AbstractHashable
this.imageMagicParams = imageMagicParams;
}
+ public Double getZoomLevel()
+ {
+ return zoomLevel;
+ }
+
+ public void setZoomLevel(Double zoomLevel)
+ {
+ this.zoomLevel = zoomLevel;
+ }
+
+ public String getThumbnailsFileName()
+ {
+ return thumbnailsFileName == null ? Constants.HDF5_CONTAINER_THUMBNAILS_FILE_NAME
+ : thumbnailsFileName;
+ }
+
+ public void setThumbnailsFileName(String thumbnailsFileName)
+ {
+ this.thumbnailsFileName = thumbnailsFileName;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/AbstractThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/AbstractThumbnailsConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..2f1987fa810375d5e49a857be21087f4d7915020
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/AbstractThumbnailsConfiguration.java
@@ -0,0 +1,25 @@
+/*
+ * Copyright 2011 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.etl.dto.api.v1.thumbnails;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public abstract class AbstractThumbnailsConfiguration implements IThumbnailsConfiguration
+{
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/DefaultThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/DefaultThumbnailsConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..4088edbaa9978632c3514f8752d493a9f18cd1e8
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/DefaultThumbnailsConfiguration.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright 2011 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.etl.dto.api.v1.thumbnails;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class DefaultThumbnailsConfiguration extends AbstractThumbnailsConfiguration
+{
+ public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config)
+ {
+ ThumbnailsStorageFormat thumbnailsStorageFormat = new ThumbnailsStorageFormat();
+ thumbnailsStorageFormat.setAllowedMachineLoadDuringGeneration(config
+ .getAllowedMachineLoadDuringThumbnailsGeneration());
+ thumbnailsStorageFormat.setMaxWidth(config.getMaxThumbnailWidthAndHeight());
+ thumbnailsStorageFormat.setMaxHeight(config.getMaxThumbnailWidthAndHeight());
+ thumbnailsStorageFormat.setGenerateWithImageMagic(config
+ .getGenerateThumbnailsWithImageMagic());
+ thumbnailsStorageFormat.setImageMagicParams(config
+ .getThumbnailsGenerationImageMagicParams());
+ thumbnailsStorageFormat.setHighQuality(config.getGenerateThumbnailsIn8BitHighQuality());
+ return thumbnailsStorageFormat;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/IThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/IThumbnailsConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..411cb80eb4f2138f52e1f4dec6d6c6bd468f914a
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/IThumbnailsConfiguration.java
@@ -0,0 +1,28 @@
+/*
+ * Copyright 2011 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.etl.dto.api.v1.thumbnails;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public interface IThumbnailsConfiguration
+{
+ public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config);
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java
new file mode 100644
index 0000000000000000000000000000000000000000..64657150acf9accb81515fbbc87835fca7bb62c6
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/thumbnails/ZoomLevelBasedThumbnailsConfiguration.java
@@ -0,0 +1,49 @@
+/*
+ * Copyright 2011 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.etl.dto.api.v1.thumbnails;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ZoomLevelBasedThumbnailsConfiguration extends AbstractThumbnailsConfiguration
+{
+ private double zoomLevel;
+
+ public ZoomLevelBasedThumbnailsConfiguration(double zoomLevel)
+ {
+ this.zoomLevel = zoomLevel;
+ }
+
+ public ThumbnailsStorageFormat getThumbnailsStorageFormat(SimpleImageDataConfig config)
+ {
+ ThumbnailsStorageFormat thumbnailsStorageFormat = new ThumbnailsStorageFormat();
+ thumbnailsStorageFormat.setAllowedMachineLoadDuringGeneration(config
+ .getAllowedMachineLoadDuringThumbnailsGeneration());
+ thumbnailsStorageFormat.setZoomLevel(zoomLevel);
+ thumbnailsStorageFormat.setThumbnailsFileName(String.format("thumbnails_%.0f%%.h5",
+ zoomLevel * 100.0));
+ thumbnailsStorageFormat.setGenerateWithImageMagic(config
+ .getGenerateThumbnailsWithImageMagic());
+ thumbnailsStorageFormat.setImageMagicParams(config
+ .getThumbnailsGenerationImageMagicParams());
+ thumbnailsStorageFormat.setHighQuality(config.getGenerateThumbnailsIn8BitHighQuality());
+ return thumbnailsStorageFormat;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
index db29ded27713fd02364cd66084fbfaba935d3bd3..1054c30c7d3a6477ba585444499b89a7763a2f88 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImagingDataSetRegistrationTr
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImagingDatasetFactory;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorParser;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -419,17 +420,25 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
List<String> containedDataSetCodes = new ArrayList<String>();
// create thumbnails dataset if needed
- IDataSet thumbnailDatasetOrNull = null;
+ List<IDataSet> thumbnailDatasets = new ArrayList<IDataSet>();
boolean generateThumbnails = imageDataSetStructure.areThumbnailsGenerated();
if (generateThumbnails)
{
- thumbnailDatasetOrNull = createThumbnailDataset();
+ List<ThumbnailsStorageFormat> thumbnailsStorageFormatList =
+ imageDataSetStructure.getImageStorageConfiguraton()
+ .getThumbnailsStorageFormat();
- ThumbnailFilePaths thumbnailPaths =
- generateThumbnails(imageDataSetStructure, incomingDirectory,
- thumbnailDatasetOrNull);
- imageDataSetInformation.setThumbnailFilePaths(thumbnailPaths);
- containedDataSetCodes.add(thumbnailDatasetOrNull.getDataSetCode());
+ for (ThumbnailsStorageFormat thumbnailsStorageFormat : thumbnailsStorageFormatList)
+ {
+ IDataSet thumbnailDataset = createThumbnailDataset();
+ thumbnailDatasets.add(thumbnailDataset);
+
+ ThumbnailFilePaths thumbnailPaths =
+ generateThumbnails(imageDataSetStructure, incomingDirectory,
+ thumbnailDataset, thumbnailsStorageFormat);
+ imageDataSetInformation.setThumbnailFilePaths(thumbnailPaths);
+ containedDataSetCodes.add(thumbnailDataset.getDataSetCode());
+ }
}
// create main dataset (with original images)
@SuppressWarnings("unchecked")
@@ -438,18 +447,17 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
.createNewDataSet(imageRegistrationDetails);
containedDataSetCodes.add(mainDataset.getDataSetCode());
- if (thumbnailDatasetOrNull != null)
+ for (IDataSet thumbnailDataset : thumbnailDatasets)
{
- setSameDatasetOwner(mainDataset, thumbnailDatasetOrNull);
+ setSameDatasetOwner(mainDataset, thumbnailDataset);
}
-
ImageContainerDataSet containerDataset =
createImageContainerDataset(mainDataset, imageDataSetInformation,
containedDataSetCodes);
containerDataset.setOriginalDataset(mainDataset);
- if (thumbnailDatasetOrNull != null)
+ for (IDataSet thumbnailDataset : thumbnailDatasets)
{
- containerDataset.setThumbnailDatasets(Arrays.asList(thumbnailDatasetOrNull));
+ containerDataset.setThumbnailDatasets(Arrays.asList(thumbnailDataset));
}
imageDataSetInformation.setContainerDatasetPermId(containerDataset.getDataSetCode());
@@ -462,16 +470,27 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
}
private ThumbnailFilePaths generateThumbnails(ImageDataSetStructure imageDataSetStructure,
- File incomingDirectory, IDataSet thumbnailDataset)
+ File incomingDirectory, IDataSet thumbnailDataset,
+ ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
{
- String thumbnailFile =
- createNewFile(thumbnailDataset, Constants.HDF5_CONTAINER_THUMBNAILS_FILE_NAME);
+ String thumbnailFile;
+ if (thumbnailsStorageFormatOrNull == null)
+ {
+ thumbnailFile =
+ createNewFile(thumbnailDataset,
+ Constants.HDF5_CONTAINER_THUMBNAILS_FILE_NAME);
+ } else
+ {
+ thumbnailFile =
+ createNewFile(thumbnailDataset,
+ thumbnailsStorageFormatOrNull.getThumbnailsFileName());
+ }
List<RelativeImageFile> images = asRelativeImageFile(imageDataSetStructure.getImages());
ThumbnailFilePaths thumbnailPaths =
Hdf5ThumbnailGenerator.tryGenerateThumbnails(images, incomingDirectory,
thumbnailFile, imageDataSetStructure.getImageStorageConfiguraton(),
- thumbnailDataset.getDataSetCode());
+ thumbnailDataset.getDataSetCode(), thumbnailsStorageFormatOrNull);
return thumbnailPaths;
}