From bacd6ebbba6bba584d5ece44955419226f6d2b6b Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 5 Jan 2012 09:16:06 +0000
Subject: [PATCH] LMS-2735 feed imaging database with original image size
SVN: 24092
---
.../dss/etl/AbsoluteImageReference.java | 38 ++++-------
.../dss/etl/Hdf5ThumbnailGenerator.java | 10 +--
.../etl/ImageSizeFeedingMaintenanceTask.java | 8 +--
.../dss/etl/PlateStorageProcessor.java | 20 +++++-
.../systemsx/cisd/openbis/dss/etl/Utils.java | 64 +++++++++++++++++++
.../dto/api/impl/ImageDataSetInformation.java | 28 ++++++++
.../etl/jython/JythonPlateDataSetHandler.java | 23 +++++++
7 files changed, 152 insertions(+), 39 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Utils.java
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 95d90d19c98..0a2e1eb7e82 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
@@ -16,7 +16,6 @@
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;
@@ -24,7 +23,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
@@ -101,37 +100,22 @@ public class AbsoluteImageReference extends AbstractImageReference
{
if (image == null)
{
- image = loadUnchangedImage(contentNode, tryGetImageID(), imageLibraryOrNull);
+ image = Utils.loadUnchangedImage(contentNode, tryGetImageID(), imageLibraryOrNull);
}
return image;
}
-
- static BufferedImage loadUnchangedImage(IHierarchicalContentNode contentNode,
- String imageIdOrNull, ImageLibraryInfo imageLibraryOrNull)
- {
- String imageLibraryNameOrNull = null;
- String imageLibraryReaderNameOrNull = null;
- if (imageLibraryOrNull != null)
- {
- imageLibraryNameOrNull = imageLibraryOrNull.getName();
- imageLibraryReaderNameOrNull = imageLibraryOrNull.getReaderName();
- }
- return ImageUtil.loadUnchangedImage(contentNode, imageIdOrNull, imageLibraryNameOrNull,
- imageLibraryReaderNameOrNull, null);
- }
-
- static Dimension loadUnchangedImageDimension(IHierarchicalContentNode contentNode,
- String imageIdOrNull, ImageLibraryInfo imageLibraryOrNull)
+
+ /**
+ * Returns the image size. Preferred method if only image size is needed because only the
+ * header of an image file might be read to get the size.
+ */
+ public Size getUnchangedImageSize()
{
- String imageLibraryNameOrNull = null;
- String imageLibraryReaderNameOrNull = null;
- if (imageLibraryOrNull != null)
+ if (image != null)
{
- imageLibraryNameOrNull = imageLibraryOrNull.getName();
- imageLibraryReaderNameOrNull = imageLibraryOrNull.getReaderName();
+ return new Size(image.getWidth(), image.getHeight());
}
- return ImageUtil.loadUnchangedImageDimension(contentNode, imageIdOrNull,
- imageLibraryNameOrNull, imageLibraryReaderNameOrNull);
+ return Utils.loadUnchangedImageSize(contentNode, tryGetImageID(), imageLibraryOrNull);
}
public RequestedImageSize getRequestedSize()
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 178a122e75f..432fe5f1c1c 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
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.dss.etl;
-import java.awt.Dimension;
import java.awt.image.BufferedImage;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
@@ -52,6 +51,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageIdentifier;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageStorageConfiguraton;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
/**
@@ -234,7 +234,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
if (thumbnailsStorageFormat.getZoomLevel() != null)
{
- Dimension originalSize = loadUnchangedImageDimension(imageFile, null);
+ Size originalSize = loadUnchangedImageDimension(imageFile, null);
double zoomLevel = thumbnailsStorageFormat.getZoomLevel();
width = (int) Math.round(zoomLevel * originalSize.getWidth());
height = (int) Math.round(zoomLevel * originalSize.getHeight());
@@ -288,13 +288,13 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
private BufferedImage loadUnchangedImage(File imageFile, String imageIdOrNull)
{
- return AbsoluteImageReference.loadUnchangedImage(new FileBasedContentNode(imageFile),
+ return Utils.loadUnchangedImage(new FileBasedContentNode(imageFile),
imageIdOrNull, imageLibraryOrNull);
}
- private Dimension loadUnchangedImageDimension(File imageFile, String imageIdOrNull)
+ private Size loadUnchangedImageDimension(File imageFile, String imageIdOrNull)
{
- return AbsoluteImageReference.loadUnchangedImageDimension(new FileBasedContentNode(
+ return Utils.loadUnchangedImageSize(new FileBasedContentNode(
imageFile), imageIdOrNull, imageLibraryOrNull);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTask.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTask.java
index f46add68789..6d397da18b1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTask.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTask.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.dss.etl;
-import java.awt.image.BufferedImage;
import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
@@ -38,6 +37,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
@@ -183,9 +183,9 @@ public class ImageSizeFeedingMaintenanceTask implements IDataStoreLockingMainten
{
return null;
}
- BufferedImage unchangedImage = image.getUnchangedImage();
- int width = unchangedImage.getWidth();
- int height = unchangedImage.getHeight();
+ Size size = image.getUnchangedImageSize();
+ int width = size.getWidth();
+ int height = size.getHeight();
dao.addImageZoomLevel(new ImgImageZoomLevelDTO(dataSetCode, original, "", width, height,
null, null, dataSetId));
return (original ? "Original" : "Thumbnail") + " size " + width + "x" + height
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
index a9149c31a1d..ce7fa2ea346 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageDatasetInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageZoomLevel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat.FileFormat;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -164,21 +165,34 @@ public final class PlateStorageProcessor extends AbstractImageStorageProcessor
super(containerDatasetPermId, originalDataset);
this.imageZoomLevels = createZoomLevels(originalDataset, thumbnailsInfosOrNull);
}
+
+ private static Integer nullifyIfZero(int value)
+ {
+ return value == 0 ? null : value;
+ }
private static List<ImageZoomLevel> createZoomLevels(DataSetInformation originalDataset,
ThumbnailsInfo thumbnailsInfosOrNull)
{
List<ImageZoomLevel> zoomLevels = new ArrayList<ImageZoomLevel>();
-
+ Integer width = null;
+ Integer height = null;
+ if (originalDataset instanceof ImageDataSetInformation)
+ {
+ ImageDataSetInformation imageDataSet = (ImageDataSetInformation) originalDataset;
+ width = nullifyIfZero(imageDataSet.getMaximumImageWidth());
+ height = nullifyIfZero(imageDataSet.getMaximumImageHeight());
+ }
ImageZoomLevel originalZoomLevel =
new ImageZoomLevel(originalDataset.getDataSetCode(), true,
- StringUtils.EMPTY_STRING, null, null, null, null);
+ StringUtils.EMPTY_STRING, width, height, null, null);
zoomLevels.add(originalZoomLevel);
if (thumbnailsInfosOrNull != null)
{
for (String permId : thumbnailsInfosOrNull.getThumbnailPhysicalDatasetsPermIds())
{
- Integer width = null, height = null;
+ width = null;
+ height = null;
Size dimension = thumbnailsInfosOrNull.tryGetDimension(permId);
if (dimension != null)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Utils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Utils.java
new file mode 100644
index 00000000000..71c4afcefae
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Utils.java
@@ -0,0 +1,64 @@
+/*
+ * Copyright 2012 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;
+
+import java.awt.Dimension;
+import java.awt.image.BufferedImage;
+
+import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+
+/**
+ * Collection of helper functions.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class Utils
+{
+
+ public static BufferedImage loadUnchangedImage(IHierarchicalContentNode contentNode,
+ String imageIdOrNull, ImageLibraryInfo imageLibraryOrNull)
+ {
+ String imageLibraryNameOrNull = null;
+ String imageLibraryReaderNameOrNull = null;
+ if (imageLibraryOrNull != null)
+ {
+ imageLibraryNameOrNull = imageLibraryOrNull.getName();
+ imageLibraryReaderNameOrNull = imageLibraryOrNull.getReaderName();
+ }
+ return ImageUtil.loadUnchangedImage(contentNode, imageIdOrNull, imageLibraryNameOrNull,
+ imageLibraryReaderNameOrNull, null);
+ }
+
+ public static Size loadUnchangedImageSize(IHierarchicalContentNode contentNode,
+ String imageIdOrNull, ImageLibraryInfo imageLibraryOrNull)
+ {
+ String imageLibraryNameOrNull = null;
+ String imageLibraryReaderNameOrNull = null;
+ if (imageLibraryOrNull != null)
+ {
+ imageLibraryNameOrNull = imageLibraryOrNull.getName();
+ imageLibraryReaderNameOrNull = imageLibraryOrNull.getReaderName();
+ }
+ Dimension dimension = ImageUtil.loadUnchangedImageDimension(contentNode, imageIdOrNull,
+ imageLibraryNameOrNull, imageLibraryReaderNameOrNull);
+ return new Size(dimension.width, dimension.height);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
index 3505d444113..803eac5ebb0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
@@ -45,6 +45,10 @@ public class ImageDataSetInformation extends BasicDataSetInformation
private ThumbnailsInfo thumbnailsInfos;
private String containerDatasetPermId;
+
+ private int maximumImageWidth;
+
+ private int maximumImageHeight;
public File getIncomingDirectory()
{
@@ -100,6 +104,26 @@ public class ImageDataSetInformation extends BasicDataSetInformation
// -------
+ public int getMaximumImageWidth()
+ {
+ return maximumImageWidth;
+ }
+
+ public void setMaximumImageWidth(int maximumImageWidth)
+ {
+ this.maximumImageWidth = maximumImageWidth;
+ }
+
+ public int getMaximumImageHeight()
+ {
+ return maximumImageHeight;
+ }
+
+ public void setMaximumImageHeight(int maximumImageHeight)
+ {
+ this.maximumImageHeight = maximumImageHeight;
+ }
+
@Override
public String toString()
{
@@ -107,6 +131,10 @@ public class ImageDataSetInformation extends BasicDataSetInformation
appendNameAndObject(buffer, "images structure", imageDataSetStructure);
appendNameAndObject(buffer, "container dataset", containerDatasetPermId);
appendNameAndObject(buffer, "original dataset", this.getDataSetCode());
+ if (maximumImageHeight > 0 && maximumImageWidth > 0)
+ {
+ appendNameAndObject(buffer, "bounding box", maximumImageWidth + "x" + maximumImageHeight);
+ }
if (getThumbnailsInfos() != null)
{
appendNameAndObject(buffer, "thumbnail", getThumbnailsInfos());
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 624149f0b2e..e83294278d9 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
@@ -18,6 +18,7 @@ import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.io.FileBasedContentNode;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
@@ -33,6 +34,8 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTra
import ch.systemsx.cisd.openbis.dss.Constants;
import ch.systemsx.cisd.openbis.dss.etl.Hdf5ThumbnailGenerator;
import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
+import ch.systemsx.cisd.openbis.dss.etl.Utils;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
@@ -445,6 +448,7 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
}
imageDataSetInformation.setThumbnailsInfo(thumbnailsInfo);
}
+ calculateBoundingBox(imageDataSetInformation, imageDataSetStructure, incomingDirectory);
// create main dataset (with original images)
@SuppressWarnings("unchecked")
DataSet<ImageDataSetInformation> mainDataset =
@@ -469,6 +473,25 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
return containerDataset;
}
+ private void calculateBoundingBox(ImageDataSetInformation imageDataSetInformation,
+ ImageDataSetStructure imageDataSetStructure, File incomingDirectory)
+ {
+ ImageLibraryInfo imageLibrary =
+ imageDataSetStructure.getImageStorageConfiguraton().tryGetImageLibrary();
+ List<ImageFileInfo> images = imageDataSetStructure.getImages();
+ for (ImageFileInfo imageFileInfo : images)
+ {
+ File file = new File(incomingDirectory, imageFileInfo.getImageRelativePath());
+ Size size =
+ Utils.loadUnchangedImageSize(new FileBasedContentNode(file), null,
+ imageLibrary);
+ imageDataSetInformation.setMaximumImageWidth(Math.max(
+ imageDataSetInformation.getMaximumImageWidth(), size.getWidth()));
+ imageDataSetInformation.setMaximumImageHeight(Math.max(
+ imageDataSetInformation.getMaximumImageHeight(), size.getHeight()));
+ }
+ }
+
private File prependOriginalDirectory(String directoryPath)
{
return new File(originalDirName + File.separator + directoryPath);
--
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