From 156530d1b8bd5857713e56f5eb78df1e6dfba8ba Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Thu, 10 Feb 2011 14:09:18 +0000
Subject: [PATCH] LMS-2027 configure machine load during thumbnails generation
and quality of the thumbnails from the python dropbox
SVN: 19881
---
.../dss/generic/shared/utils/ImageUtil.java | 12 ++++---
.../etl/AbstractImageStorageProcessor.java | 22 ++++++------
.../dss/etl/Hdf5ThumbnailGenerator.java | 36 +++++++++++--------
.../dto/api/v1/ThumbnailsStorageFormat.java | 24 +++++++++++--
.../server/images/ImageChannelsUtils.java | 24 +++++++------
.../server/images/dto/RequestedImageSize.java | 14 ++++++++
6 files changed, 89 insertions(+), 43 deletions(-)
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 9a1f18c3cde..d8f2b1673dd 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
@@ -265,7 +265,7 @@ public class ImageUtil
*/
public static BufferedImage createThumbnail(BufferedImage image, int maxWidth, int maxHeight)
{
- return rescale(image, maxWidth, maxHeight, true);
+ return rescale(image, maxWidth, maxHeight, true, false);
}
/**
@@ -277,9 +277,11 @@ public class ImageUtil
* @param maxHeight Maximum height of the result image.
* @param enlargeIfNecessary if false and the image has smaller width and height than the
* specified limit, then the image is not changed.
+ * @param highQuality if true thumbnails will be of higher quality, but rescaling will take
+ * longer (BICUBIC rescaling will be used instead of BILINEAR).
*/
public static BufferedImage rescale(BufferedImage image, int maxWidth, int maxHeight,
- boolean enlargeIfNecessary)
+ boolean enlargeIfNecessary, boolean highQuality)
{
int width = image.getWidth();
int height = image.getHeight();
@@ -306,8 +308,10 @@ public class ImageUtil
: BufferedImage.TYPE_INT_RGB;
BufferedImage thumbnail = new BufferedImage(thumbnailWidth, thumbnailHeight, imageType);
Graphics2D graphics2D = thumbnail.createGraphics();
- graphics2D.setRenderingHint(RenderingHints.KEY_INTERPOLATION,
- RenderingHints.VALUE_INTERPOLATION_BILINEAR);
+ Object renderingHint =
+ highQuality ? RenderingHints.VALUE_INTERPOLATION_BICUBIC
+ : RenderingHints.VALUE_INTERPOLATION_BILINEAR;
+ graphics2D.setRenderingHint(RenderingHints.KEY_INTERPOLATION, renderingHint);
graphics2D.drawImage(image, 0, 0, thumbnailWidth, thumbnailHeight, null);
return thumbnail;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
index 64b210b939c..3200f364013 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
@@ -412,13 +412,11 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
if (thumbnailsStorageFormatOrNull != null)
{
Hdf5Container container = new Hdf5Container(thumbnailsFile);
- container.runWriterClient(
- thumbnailsStorageFormatOrNull.isStoreCompressed(),
- new Hdf5ThumbnailGenerator(plateImages, imagesInStoreFolder,
- thumbnailsStorageFormatOrNull.getMaxWidth(),
- thumbnailsStorageFormatOrNull.getMaxHeight(),
- relativeThumbnailFilePath, thumbnailsStorageFormatOrNull
- .getAllowedMachineLoadDuringGeneration(), operationLog));
+ container
+ .runWriterClient(thumbnailsStorageFormatOrNull.isStoreCompressed(),
+ new Hdf5ThumbnailGenerator(plateImages, imagesInStoreFolder,
+ thumbnailsStorageFormatOrNull, relativeThumbnailFilePath,
+ operationLog));
}
}
@@ -625,7 +623,8 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
{
checkParameters(incomingDataSetDirectory, storedDataDirectory);
- final File originalDataFile = tryGetProprietaryData(storedDataDirectory);
+ final File originalDataFile =
+ tryGetProprietaryData(storedDataDirectory);
if (originalDataFile == null)
{
// nothing has been stored in the file system yet,
@@ -639,9 +638,10 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
moveFileToDirectory(originalDataFile, incomingDirectory);
if (operationLog.isInfoEnabled())
{
- operationLog.info(String.format(
- "Directory '%s' has moved to incoming directory '%s'.", originalDataFile,
- incomingDirectory.getAbsolutePath()));
+ operationLog
+ .info(String
+ .format("Storage operation rollback: directory '%s' has moved to incoming directory '%s'.",
+ originalDataFile, incomingDirectory.getAbsolutePath()));
}
} catch (final EnvironmentFailureException ex)
{
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 cc979c75d6a..098222c0cee 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
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.etlserver.hdf5.Hdf5Container.IHdf5WriterClient;
import ch.systemsx.cisd.hdf5.IHDF5SimpleWriter;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
/**
@@ -44,41 +45,39 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
private final File imagesInStoreFolder;
- private final int thumbnailMaxWidth;
-
- private final int thumbnailMaxHeight;
+ private final ThumbnailsStorageFormat thumbnailsStorageFormat;
private final String relativeThumbnailFilePath;
- private final int allowedMachineLoadDuringGeneration;
-
private final Logger operationLog;
Hdf5ThumbnailGenerator(List<AcquiredSingleImage> plateImages, File imagesInStoreFolder,
- int thumbnailMaxWidth, int thumbnailMaxHeight, String relativeThumbnailFilePath,
- int allowedMachineLoadDuringGeneration, Logger operationLog)
+ ThumbnailsStorageFormat thumbnailsStorageFormat, String relativeThumbnailFilePath,
+ Logger operationLog)
{
this.plateImages = plateImages;
this.imagesInStoreFolder = imagesInStoreFolder;
- this.thumbnailMaxWidth = thumbnailMaxWidth;
- this.thumbnailMaxHeight = thumbnailMaxHeight;
+ this.thumbnailsStorageFormat = thumbnailsStorageFormat;
this.relativeThumbnailFilePath = relativeThumbnailFilePath;
- this.allowedMachineLoadDuringGeneration = allowedMachineLoadDuringGeneration;
this.operationLog = operationLog;
}
private Status generateThumbnail(IHDF5SimpleWriter writer, AcquiredSingleImage plateImage)
{
+ long start = System.currentTimeMillis();
RelativeImageReference imageReference = plateImage.getImageReference();
String imagePath = imageReference.getRelativeImagePath();
File img = new File(imagesInStoreFolder, imagePath);
BufferedImage image = ImageUtil.loadImage(img);
BufferedImage thumbnail =
- ImageUtil.rescale(image, thumbnailMaxWidth, thumbnailMaxHeight, false);
+ ImageUtil.rescale(image, thumbnailsStorageFormat.getMaxWidth(),
+ thumbnailsStorageFormat.getMaxHeight(), false,
+ thumbnailsStorageFormat.isHighQuality());
ByteArrayOutputStream output = new ByteArrayOutputStream();
try
{
ImageIO.write(thumbnail, "png", output);
+
String thumbnailPath = replaceExtensionToPng(imagePath);
String path =
@@ -88,10 +87,16 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
byte[] byteArray = output.toByteArray();
if (operationLog.isDebugEnabled())
{
- operationLog.debug("thumbnail " + thumbnailPath + " (" + byteArray.length
- + " bytes)");
+ long now = System.currentTimeMillis();
+ operationLog.debug(Thread.currentThread().getName() + " thumbnail " + thumbnailPath
+ + " (" + byteArray.length + " bytes) generated in " + (now - start)
+ + " msec");
+ }
+
+ synchronized (writer)
+ {
+ writer.writeByteArray(thumbnailPath, byteArray);
}
- writer.writeByteArray(thumbnailPath, byteArray);
} catch (IOException ex)
{
return Status.createError(ex.getMessage());
@@ -126,6 +131,7 @@ class Hdf5ThumbnailGenerator implements IHdf5WriterClient
public void runWithSimpleWriter(IHDF5SimpleWriter writer)
{
ParallelizedExecutor.process(plateImages, createThumbnailGenerator(writer),
- allowedMachineLoadDuringGeneration, 100, 1);
+ thumbnailsStorageFormat.getAllowedMachineLoadDuringGeneration(), 100,
+ "Thumbnails generation", 1);
}
}
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 a3f7671a5ce..990a3b6f4de 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
@@ -37,7 +37,9 @@ public class ThumbnailsStorageFormat
private boolean storeCompressed = DEFAULT_COMPRESS_THUMBNAILS;
- private int allowedMachineLoadDuringGeneration = 1;
+ private double allowedMachineLoadDuringGeneration = 1;
+
+ private boolean highQuality = false;
/**
* Creates empty object which instructs that the thumbnails should be generated with default
@@ -62,11 +64,18 @@ public class ThumbnailsStorageFormat
return storeCompressed;
}
- public int getAllowedMachineLoadDuringGeneration()
+ public double getAllowedMachineLoadDuringGeneration()
{
return allowedMachineLoadDuringGeneration;
}
+ public boolean isHighQuality()
+ {
+ return highQuality;
+ }
+
+ // --- setters ---
+
/** Sets the maximum width of a thumbnail. */
public void setMaxWidth(int maxWidth)
{
@@ -89,8 +98,17 @@ public class ThumbnailsStorageFormat
* The number of threads which will be used during thumbnails generation will be equal to number
* of processor cores * machineLoad.
*/
- public void setAllowedMachineLoadDuringGeneration(int machineLoad)
+ public void setAllowedMachineLoadDuringGeneration(double machineLoad)
{
this.allowedMachineLoadDuringGeneration = machineLoad;
}
+
+ /**
+ * Set to true if you want your thumbnails to be of higher quality. In such a case thumbnails
+ * generation during dataset registration will take longer. Recommended for overlay images.
+ */
+ public void setHighQuality(boolean highQuality)
+ {
+ this.highQuality = highQuality;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
index 6b22e8228d4..8c2f35c3390 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
@@ -143,9 +143,9 @@ public class ImageChannelsUtils
return calculateSingleImages(imageContents);
}
- private static RequestedImageSize getSize(BufferedImage img)
+ private static RequestedImageSize getSize(BufferedImage img, boolean highQuality)
{
- return new RequestedImageSize(new Size(img.getWidth(), img.getHeight()), true);
+ return new RequestedImageSize(new Size(img.getWidth(), img.getHeight()), true, highQuality);
}
private static RequestedImageSize calcOverlaySize(BufferedImage imageOrNull,
@@ -155,15 +155,19 @@ public class ImageChannelsUtils
{
// thumbnais are not used, so use the original size even if it does not match
return RequestedImageSize.createOriginal();
- }
- if (imageOrNull != null)
- {
- // all overlays have to be of the same size as the basic image
- return getSize(imageOrNull);
} else
{
- // if there is no basic image yet, enlarging too small images is not necessary
- return new RequestedImageSize(thumbnailSizeOrNull, false);
+ // we want higher quality only if thumbnail overlays are generated
+ boolean highQuality = true;
+ if (imageOrNull != null)
+ {
+ // all overlays have to be of the same size as the basic image
+ return getSize(imageOrNull, highQuality);
+ } else
+ {
+ // if there is no basic image yet, enlarging too small images is not necessary
+ return new RequestedImageSize(thumbnailSizeOrNull, false, highQuality);
+ }
}
}
@@ -444,7 +448,7 @@ public class ImageChannelsUtils
start = operationLog.isDebugEnabled() ? System.currentTimeMillis() : 0;
image =
ImageUtil.rescale(image, size.getWidth(), size.getHeight(),
- requestedSize.enlargeIfNecessary());
+ requestedSize.enlargeIfNecessary(), requestedSize.isHighQualityRescalingRequired());
if (operationLog.isDebugEnabled())
{
operationLog.debug("Create thumbnail: " + (System.currentTimeMillis() - start));
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/RequestedImageSize.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/RequestedImageSize.java
index d986b3fad51..5e80e921a14 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/RequestedImageSize.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/RequestedImageSize.java
@@ -36,10 +36,19 @@ public class RequestedImageSize extends AbstractHashable
private final boolean enlargeIfNecessary;
+ private final boolean highQualityRescalingRequired;
+
public RequestedImageSize(Size thumbnailSizeOrNull, boolean enlargeIfNecessary)
+ {
+ this(thumbnailSizeOrNull, enlargeIfNecessary, false);
+ }
+
+ public RequestedImageSize(Size thumbnailSizeOrNull, boolean enlargeIfNecessary,
+ boolean highQualityRescalingRequired)
{
this.thumbnailSizeOrNull = thumbnailSizeOrNull;
this.enlargeIfNecessary = enlargeIfNecessary;
+ this.highQualityRescalingRequired = highQualityRescalingRequired;
}
/** original size if null */
@@ -58,6 +67,11 @@ public class RequestedImageSize extends AbstractHashable
return enlargeIfNecessary;
}
+ public boolean isHighQualityRescalingRequired()
+ {
+ return highQualityRescalingRequired;
+ }
+
@Override
public String toString()
{
--
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