diff --git a/screening/resource/test-data/ConvertToolImageTransformerTest/pond-transformed.png b/screening/resource/test-data/ConvertToolImageTransformerTest/pond-transformed.png
new file mode 100644
index 0000000000000000000000000000000000000000..6b41b07cde5e588e2bf182ee759e4d2b1967b131
Binary files /dev/null and b/screening/resource/test-data/ConvertToolImageTransformerTest/pond-transformed.png differ
diff --git a/screening/resource/test-data/ConvertToolImageTransformerTest/pond.png b/screening/resource/test-data/ConvertToolImageTransformerTest/pond.png
new file mode 100644
index 0000000000000000000000000000000000000000..21f8705bee636013b88b21ab151a1b148805039c
Binary files /dev/null and b/screening/resource/test-data/ConvertToolImageTransformerTest/pond.png differ
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
index 32d0e9b160ec38fffcf42953cefe8d3a89132fea..6bc57261a8affb2a6bc1c24a722846736619cf91 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
@@ -27,6 +27,7 @@ import java.util.Map.Entry;
import java.util.Set;
import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ImagingChannelsMap;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgAcquiredImageDTO;
@@ -55,12 +56,16 @@ abstract class AbstractImageDatasetUploader
private final RelativeImageReference thumbnailPathOrNull;
+ private final IImageTransformerFactory imageTransformerFactoryOrNull;
+
public AcquiredImageInStack(String channelCode, RelativeImageReference imageFilePath,
- RelativeImageReference thumbnailPathOrNull)
+ RelativeImageReference thumbnailPathOrNull,
+ IImageTransformerFactory imageTransformerFactoryOrNull)
{
this.channelCode = channelCode.toUpperCase();
this.imageFilePath = imageFilePath;
this.thumbnailPathOrNull = thumbnailPathOrNull;
+ this.imageTransformerFactoryOrNull = imageTransformerFactoryOrNull;
}
public String getChannelCode()
@@ -77,6 +82,11 @@ abstract class AbstractImageDatasetUploader
{
return thumbnailPathOrNull;
}
+
+ public IImageTransformerFactory getImageTransformerFactoryOrNull()
+ {
+ return imageTransformerFactoryOrNull;
+ }
}
protected static interface ISpotProvider
@@ -137,7 +147,7 @@ abstract class AbstractImageDatasetUploader
private static AcquiredImageInStack makeAcquiredImageInStack(AcquiredSingleImage image)
{
return new AcquiredImageInStack(image.getChannelCode(), image.getImageReference(),
- image.getThumbnailFilePathOrNull());
+ image.getThumbnailFilePathOrNull(), image.getImageTransformerFactoryOrNull());
}
private ImgChannelStackDTO makeStackDtoWithouId(AcquiredSingleImage image,
@@ -178,19 +188,22 @@ abstract class AbstractImageDatasetUploader
List<ImgAcquiredImageDTO> acquiredImageDTOs = imagesToCreate.getAcquiredImages();
for (AcquiredImageInStack image : images)
{
- long channelTechId = channelsMap.getChannelId(image.getChannelCode());
-
ImgImageDTO imageDTO = mkImageWithIdDTO(image.getImageFilePath());
- ImgImageDTO thumbnailDTO = tryMkImageWithIdDTO(image.getThumbnailPathOrNull());
- Long thumbnailId = thumbnailDTO == null ? null : thumbnailDTO.getId();
- ImgAcquiredImageDTO acquiredImage =
- mkAcquiredImage(stackId, channelTechId, imageDTO.getId(), thumbnailId);
-
imageDTOs.add(imageDTO);
+
+ ImgImageDTO thumbnailDTO = tryMkImageWithIdDTO(image.getThumbnailPathOrNull());
+ Long thumbnailId = null;
if (thumbnailDTO != null)
{
+ thumbnailId = thumbnailDTO.getId();
imageDTOs.add(thumbnailDTO);
}
+
+ long channelTechId = channelsMap.getChannelId(image.getChannelCode());
+ ImgAcquiredImageDTO acquiredImage =
+ mkAcquiredImage(stackId, channelTechId, imageDTO.getId(), thumbnailId,
+ image.getImageTransformerFactoryOrNull());
+
acquiredImageDTOs.add(acquiredImage);
}
}
@@ -220,13 +233,14 @@ abstract class AbstractImageDatasetUploader
}
private ImgAcquiredImageDTO mkAcquiredImage(long stackId, long channelTechId, long imageId,
- Long thumbnailId)
+ Long thumbnailId, IImageTransformerFactory transformerFactoryOrNull)
{
ImgAcquiredImageDTO acquiredImage = new ImgAcquiredImageDTO();
acquiredImage.setImageId(imageId);
acquiredImage.setThumbnailId(thumbnailId);
acquiredImage.setChannelStackId(stackId);
acquiredImage.setChannelId(channelTechId);
+ acquiredImage.setImageTransformerFactory(transformerFactoryOrNull);
return acquiredImage;
}
@@ -241,6 +255,7 @@ abstract class AbstractImageDatasetUploader
private ImgImageDTO mkImageWithIdDTO(RelativeImageReference imageReferenceOrNull)
{
+
ImgImageDTO dto =
new ImgImageDTO(dao.createImageId(), imageReferenceOrNull.getRelativeImagePath(),
imageReferenceOrNull.tryGetPage(),
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 299adf9efaecaa9f9aad5a68202bd34cce3d0990..087fe3425e75053c1f0d916fe0ea61366da423da 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
@@ -32,6 +32,7 @@ import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang.time.DurationFormatUtils;
import org.apache.log4j.Logger;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
@@ -640,6 +641,8 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
imageStorageConfiguraton = globalImageStorageConfiguraton;
}
+ setPerImageTransformationIfNeeded(images, imageStorageConfiguraton);
+
ImageFileExtractionResult extractionResult =
new ImageFileExtractionResult(images, invalidFiles, imageDataSetInfo.getChannels(),
tileGeometry, imageStorageConfiguraton.getStoreChannelsOnExperimentLevel());
@@ -682,6 +685,20 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
return ColorComponent.valueOf(channelColorComponent.name());
}
+ private void setPerImageTransformationIfNeeded(List<AcquiredSingleImage> images,
+ ImageStorageConfiguraton imageStorageConfiguraton)
+ {
+ if (imageStorageConfiguraton != null
+ && imageStorageConfiguraton.getImageTransformerFactory() != null)
+ {
+ IImageTransformerFactory imgTransformerFactory =
+ imageStorageConfiguraton.getImageTransformerFactory();
+ for (AcquiredSingleImage image : images) {
+ image.setImageTransformerFactoryOrNull(imgTransformerFactory);
+ }
+ }
+ }
+
protected IImageFileExtractor tryGetImageFileExtractor(File incomingDataSetDirectory)
{
return imageFileExtractorOrNull;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredSingleImage.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredSingleImage.java
index 745daa8167c6a7257d2d8db5fa7f9385309031a4..409583834d2cb8642e8b88dd1f9561154144c7af 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredSingleImage.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredSingleImage.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
@@ -45,6 +46,8 @@ public class AcquiredSingleImage extends AbstractHashable
private RelativeImageReference thumbnailFilePathOrNull;
+ private IImageTransformerFactory imageTransformerFactoryOrNull;
+
public AcquiredSingleImage(Location wellLocationOrNull, Location tileLocation,
String channelCode, Float timePointOrNull, Float depthOrNull, Integer seriesNumberOrNull,
RelativeImageReference imageFilePath)
@@ -128,4 +131,15 @@ public class AcquiredSingleImage extends AbstractHashable
{
this.seriesNumberOrNull = seriesNumber;
}
+
+ public IImageTransformerFactory getImageTransformerFactoryOrNull()
+ {
+ return imageTransformerFactoryOrNull;
+ }
+
+ public void setImageTransformerFactoryOrNull(
+ IImageTransformerFactory imageTransformerFactoryOrNull)
+ {
+ this.imageTransformerFactoryOrNull = imageTransformerFactoryOrNull;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformer.java
new file mode 100644
index 0000000000000000000000000000000000000000..8454cdc84353476110201c4e89bfa04d802b4fa8
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformer.java
@@ -0,0 +1,149 @@
+/*
+ * 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.biozentrum;
+
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.base.image.IImageTransformer;
+import ch.systemsx.cisd.base.utilities.OSUtilities;
+import ch.systemsx.cisd.common.concurrent.ConcurrencyUtilities;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+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.imagereaders.IImageReader;
+import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
+import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
+
+/**
+ * An {@link IImageTransformer} using the convert command line tool for transformations.
+ *
+ * @author Kaloyan Enimanev
+ */
+public class ConvertToolImageTransformer implements IImageTransformer
+{
+
+ private static final String PNG = "png";
+
+ private static final File convertUtilityOrNull = OSUtilities.findExecutable("convert");
+
+ private static final Logger machineLog = LogFactory.getLogger(LogCategory.MACHINE,
+ ConvertToolImageTransformer.class);
+
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ ConvertToolImageTransformer.class);
+
+ private final List<String> convertCliArguments;
+
+ ConvertToolImageTransformer(String arguments)
+ {
+ this.convertCliArguments = parseCommandArguments(arguments);
+ }
+
+ public BufferedImage transform(BufferedImage image)
+ {
+ File tmpFile = null;
+ try
+ {
+ // TODO KE: we should use the standard input to instead of a temporary file
+ tmpFile = createTempImageFile(image);
+ byte[] output = transform(tmpFile);
+ return toBufferedImage(output);
+ } catch (IOException ioex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ioex);
+ } finally
+ {
+ if (tmpFile != null)
+ {
+ tmpFile.delete();
+ }
+ }
+ }
+
+ private BufferedImage toBufferedImage(byte[] output) throws ConfigurationFailureException
+ {
+ IImageReader imageReader =
+ ImageReaderFactory.tryGetReader(ImageReaderConstants.IMAGEIO_LIBRARY, PNG);
+ if (imageReader == null)
+ {
+ throw new ConfigurationFailureException("No ImageIO image readers available");
+ }
+ return imageReader.readImage(output, null);
+ }
+
+ private byte[] transform(File imageFile) throws IOException
+ {
+ String filePath = imageFile.getAbsolutePath();
+
+ ProcessResult result =
+ ProcessExecutionHelper.run(getCommandLine(filePath), operationLog, machineLog,
+ ConcurrencyUtilities.NO_TIMEOUT,
+ ProcessIOStrategy.BINARY_DISCARD_STDERR_IO_STRATEGY, false);
+
+ if (result.isOK() == false)
+ {
+ System.err.println(result.getErrorOutput());
+ System.err.println(result.getOutput());
+ System.err.println(result.getCommandLine());
+ throw new IOException(String.format(
+ "Error calling 'convert' for image '%s'. Exit value: %d, I/O status: %s",
+ filePath, result.getExitValue(), result.getProcessIOResult().getStatus()));
+ } else
+ {
+ return result.getBinaryOutput();
+ }
+
+ }
+
+ private List<String> parseCommandArguments(String argsString)
+ {
+ String[] arguments = argsString.trim().split("\\s");
+ return Arrays.asList(arguments);
+ }
+
+ private List<String> getCommandLine(String filePath)
+ {
+ ArrayList<String> result = new ArrayList<String>();
+ result.add(convertUtilityOrNull.getPath());
+ result.addAll(convertCliArguments);
+ result.add(filePath);
+ result.add("png:-");
+ return result;
+ }
+
+ private File createTempImageFile(BufferedImage image) throws IOException
+ {
+ File tmpFile = File.createTempFile(getClass().getSimpleName(), PNG);
+ tmpFile.deleteOnExit();
+ ImageIO.write(image, PNG, tmpFile);
+ return tmpFile;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformerFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..8c2591ee481bbfd32f26c726ed8d4699f0862a95
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformerFactory.java
@@ -0,0 +1,43 @@
+/*
+ * 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.biozentrum;
+
+import ch.systemsx.cisd.base.image.IImageTransformer;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+
+/**
+ * A {@link IImageTransformerFactory} that constructs {@link ConvertToolImageTransformer} instances.
+ *
+ * @author Kaloyan Enimanev
+ */
+public class ConvertToolImageTransformerFactory implements IImageTransformerFactory
+{
+ private static final long serialVersionUID = 1L;
+
+ private final String convertCliArguments;
+
+ public ConvertToolImageTransformerFactory(String convertCliArguments)
+ {
+ this.convertCliArguments = convertCliArguments;
+ }
+
+ public IImageTransformer createTransformer()
+ {
+ return new ConvertToolImageTransformer(convertCliArguments);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
index 417eef63693ab7f65a2bf74e5e81a8d8357eed5e..abe4e2a8a478b23454086d224e924c706c569821 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
@@ -60,8 +60,8 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
+ "(?{1.id}, ?{1.filePath}, ?{1.page}, ?{1.colorComponentAsString})", batchUpdate = true)
public void addImages(List<ImgImageDTO> images);
- @Update(sql = "insert into ACQUIRED_IMAGES (IMG_ID, THUMBNAIL_ID, CHANNEL_STACK_ID, CHANNEL_ID) values "
- + "(?{1.imageId}, ?{1.thumbnailId}, ?{1.channelStackId}, ?{1.channelId})", batchUpdate = true)
+ @Update(sql = "insert into ACQUIRED_IMAGES (IMG_ID, THUMBNAIL_ID, CHANNEL_STACK_ID, CHANNEL_ID, IMAGE_TRANSFORMER_FACTORY) values "
+ + "(?{1.imageId}, ?{1.thumbnailId}, ?{1.channelStackId}, ?{1.channelId}, ?{1.serializedImageTransformerFactory})", batchUpdate = true)
public void addAcquiredImages(List<ImgAcquiredImageDTO> acquiredImages);
// inserts
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 5674ac8a2762653e5166efb2ff6971140a7412be..b0d1c4a644e8bc13c362a5baec2062d098e7ae88 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 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
/**
@@ -38,6 +39,11 @@ public class ImageStorageConfiguraton extends AbstractHashable
/** No preferences by default, each storage processor decides by its own if it is not set. */
private Boolean storeChannelsOnExperimentLevelOrNull = null;
+ /**
+ * an image transformation to be applied before the image is stored.
+ */
+ private IImageTransformerFactory imageTransformerFactoryOrNull;
+
/** Returns the default configuration. */
public static ImageStorageConfiguraton createDefault()
{
@@ -89,4 +95,17 @@ public class ImageStorageConfiguraton extends AbstractHashable
return storeChannelsOnExperimentLevelOrNull;
}
+ public IImageTransformerFactory getImageTransformerFactory()
+ {
+ return imageTransformerFactoryOrNull;
+ }
+
+ /**
+ * Allows for applying an image transformation before persisting an image in the store.
+ */
+ public void setImageTransformerFactory(IImageTransformerFactory transformerFactory)
+ {
+ this.imageTransformerFactoryOrNull = transformerFactory;
+ }
+
}
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 221dd019dedaa820316fb591a462b582f388983a..d866e4ad55e3ba70906ebdbc4ec07975b7447c5e 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
@@ -18,6 +18,9 @@ package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
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.biozentrum.ConvertToolImageTransformerFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -110,6 +113,8 @@ abstract public class SimpleImageDataConfig
private OriginalDataStorageFormat originalDataStorageFormat =
OriginalDataStorageFormat.UNCHANGED;
+ private String convertTransformationCliArgumentsOrNull;
+
// --- getters & setters ----------------------------------------------
public ImageStorageConfiguraton getImageStorageConfiguration()
@@ -130,6 +135,13 @@ abstract public class SimpleImageDataConfig
thumbnailsStorageFormat.setHighQuality(generateThumbnailsInHighQuality);
imageStorageConfiguraton.setThumbnailsStorageFormat(thumbnailsStorageFormat);
}
+ if (false == StringUtils.isBlank(convertTransformationCliArgumentsOrNull))
+ {
+ IImageTransformerFactory convertTransformerFactory =
+ new ConvertToolImageTransformerFactory(convertTransformationCliArgumentsOrNull);
+ imageStorageConfiguraton.setImageTransformerFactory(convertTransformerFactory);
+
+ }
return imageStorageConfiguraton;
}
@@ -321,4 +333,18 @@ abstract public class SimpleImageDataConfig
return isMeasured;
}
+ public String getConvertTransformationCliArguments()
+ {
+ return convertTransformationCliArgumentsOrNull;
+ }
+
+ /**
+ * Sets parameters for the 'convert' command line tool, which will be used to apply an image
+ * transformation before persisting the images in the data store.
+ */
+ public void setConvertTransformationCliArguments(String convertTransformationCliArguments)
+ {
+ this.convertTransformationCliArgumentsOrNull = convertTransformationCliArguments;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
index ca07053cf9304b6f8f1e252a1082e08fd1f00c97..f26648c429a4e0059b8435d5fecfaff4a7b3eb54 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
@@ -69,18 +69,18 @@ public class SimpleImageDataSetRegistrator
}
public static DataSetRegistrationDetails<ImageDataSetInformation> createImageDatasetDetails(
- SimpleImageDataConfig imageDataSet, File incoming,
+ SimpleImageDataConfig simpleImageConfig, File incoming,
IDataSetRegistrationDetailsFactory<ImageDataSetInformation> factory)
{
- return new SimpleImageDataSetRegistrator(imageDataSet).createImageDatasetDetails(incoming,
+ return new SimpleImageDataSetRegistrator(simpleImageConfig).createImageDatasetDetails(incoming,
factory);
}
- private final SimpleImageDataConfig imageDataSet;
+ private final SimpleImageDataConfig simpleImageConfig;
- private SimpleImageDataSetRegistrator(SimpleImageDataConfig imageDataSet)
+ private SimpleImageDataSetRegistrator(SimpleImageDataConfig simpleImageConfig)
{
- this.imageDataSet = imageDataSet;
+ this.simpleImageConfig = simpleImageConfig;
}
private DataSetRegistrationDetails<ImageDataSetInformation> createImageDatasetDetails(
@@ -101,7 +101,7 @@ public class SimpleImageDataSetRegistrator
private List<File> listImageFiles(final File incomingDirectory)
{
return FileOperations.getInstance().listFiles(incomingDirectory,
- imageDataSet.getRecognizedImageExtensions(), true);
+ simpleImageConfig.getRecognizedImageExtensions(), true);
}
/**
@@ -115,7 +115,7 @@ public class SimpleImageDataSetRegistrator
{
String imageRelativePath =
FileUtilities.getRelativeFile(incomingDirectory, new File(imageFile.getPath()));
- ImageMetadata imageTokens = imageDataSet.extractImageMetadata(imageRelativePath);
+ ImageMetadata imageTokens = simpleImageConfig.extractImageMetadata(imageRelativePath);
imageTokens.ensureValid();
imageTokensList.add(new ImageTokensWithPath(imageTokens, imageRelativePath));
}
@@ -124,7 +124,7 @@ public class SimpleImageDataSetRegistrator
throw UserFailureException.fromTemplate(
"Incoming directory '%s' contains no images with extensions %s!",
incomingDirectory.getPath(),
- CollectionUtils.abbreviate(imageDataSet.getRecognizedImageExtensions(), -1));
+ CollectionUtils.abbreviate(simpleImageConfig.getRecognizedImageExtensions(), -1));
}
return imageTokensList;
}
@@ -135,7 +135,7 @@ public class SimpleImageDataSetRegistrator
protected ImageFileInfo createImageInfo(ImageTokensWithPath imageTokens, Geometry tileGeometry)
{
Location tileCoords =
- imageDataSet.getTileCoordinates(imageTokens.getTileNumber(), tileGeometry);
+ simpleImageConfig.getTileCoordinates(imageTokens.getTileNumber(), tileGeometry);
ImageFileInfo img =
new ImageFileInfo(imageTokens.getChannelCode(), tileCoords.getRow(),
tileCoords.getColumn(), imageTokens.getImagePath());
@@ -172,7 +172,7 @@ public class SimpleImageDataSetRegistrator
List<Channel> channels = new ArrayList<Channel>();
for (String channelCode : channelCodes)
{
- channels.add(imageDataSet.createChannel(channelCode));
+ channels.add(simpleImageConfig.createChannel(channelCode));
}
return channels;
}
@@ -195,18 +195,18 @@ public class SimpleImageDataSetRegistrator
*/
protected void setImageDataset(File incoming, ImageDataSetInformation dataset)
{
- dataset.setDatasetTypeCode(imageDataSet.getDataSetType());
- dataset.setFileFormatCode(imageDataSet.getFileFormatType());
- dataset.setMeasured(imageDataSet.isMeasuredData());
+ dataset.setDatasetTypeCode(simpleImageConfig.getDataSetType());
+ dataset.setFileFormatCode(simpleImageConfig.getFileFormatType());
+ dataset.setMeasured(simpleImageConfig.isMeasuredData());
- String sampleCode = imageDataSet.getPlateCode();
- String spaceCode = imageDataSet.getPlateSpace();
+ String sampleCode = simpleImageConfig.getPlateCode();
+ String spaceCode = simpleImageConfig.getPlateSpace();
dataset.setSample(spaceCode, sampleCode);
dataset.setMeasured(true);
List<ImageTokensWithPath> imageTokensList = parseImageTokens(incoming);
int maxTileNumber = getMaxTileNumber(imageTokensList);
- Geometry tileGeometry = imageDataSet.getTileGeometry(imageTokensList, maxTileNumber);
+ Geometry tileGeometry = simpleImageConfig.getTileGeometry(imageTokensList, maxTileNumber);
List<ImageFileInfo> images = createImageInfos(imageTokensList, tileGeometry);
List<Channel> channels = getAvailableChannels(images);
@@ -214,16 +214,16 @@ public class SimpleImageDataSetRegistrator
dataset.setChannels(channels);
dataset.setTileGeometry(tileGeometry.getNumberOfRows(), tileGeometry.getNumberOfColumns());
- dataset.setImageStorageConfiguraton(imageDataSet.getImageStorageConfiguration());
+ dataset.setImageStorageConfiguraton(simpleImageConfig.getImageStorageConfiguration());
}
private <T extends DataSetInformation> void setRegistrationDetails(
DataSetRegistrationDetails<T> registrationDetails, T dataset)
{
registrationDetails.setDataSetInformation(dataset);
- registrationDetails.setFileFormatType(new FileFormatType(imageDataSet.getFileFormatType()));
- registrationDetails.setDataSetType(new DataSetType(imageDataSet.getDataSetType()));
- registrationDetails.setMeasuredData(imageDataSet.isMeasuredData());
+ registrationDetails.setFileFormatType(new FileFormatType(simpleImageConfig.getFileFormatType()));
+ registrationDetails.setDataSetType(new DataSetType(simpleImageConfig.getDataSetType()));
+ registrationDetails.setMeasuredData(simpleImageConfig.isMeasuredData());
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java
index 90944b759cfc4c2f1264b2f17894502a71036896..2d23bc7066217a202068a6cc8bdbc2c564e115ae 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractImageTransformerFactoryHolder.java
@@ -1,5 +1,6 @@
/*
* Copyright 2010 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.
@@ -25,7 +26,7 @@ import ch.systemsx.cisd.base.image.IImageTransformerFactory;
/**
* @author Franz-Josef Elmer
*/
-abstract class AbstractImageTransformerFactoryHolder extends AbstractImgIdentifiable
+public abstract class AbstractImageTransformerFactoryHolder extends AbstractImgIdentifiable
{
@ResultColumn("IMAGE_TRANSFORMER_FACTORY")
private byte[] serializedImageTransformerFactory;
@@ -40,7 +41,18 @@ abstract class AbstractImageTransformerFactoryHolder extends AbstractImgIdentifi
this.serializedImageTransformerFactory = serializedImageTransformerFactory;
}
- public IImageTransformerFactory tryGetImageTransformerFactory()
+ public final void setImageTransformerFactory(IImageTransformerFactory factory)
+ {
+ if (factory != null)
+ {
+ this.serializedImageTransformerFactory = SerializationUtils.serialize(factory);
+ } else
+ {
+ this.serializedImageTransformerFactory = null;
+ }
+ }
+
+ public final IImageTransformerFactory tryGetImageTransformerFactory()
{
if (serializedImageTransformerFactory == null)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageDTO.java
index 767a3d10a70b0c31ccfc7ab5b52fbc8ffc1905e0..448fd7ead8d8663db4d1da350ccdc127ccce756d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageDTO.java
@@ -21,7 +21,7 @@ import net.lemnik.eodsql.ResultColumn;
/**
* @author Tomasz Pylak
*/
-public class ImgAcquiredImageDTO extends AbstractImgIdentifiable
+public class ImgAcquiredImageDTO extends AbstractImageTransformerFactoryHolder
{
@ResultColumn("IMG_ID")
private long imageId;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformerTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..6104232c32139da7df2d3c53a3d1811095824422
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ConvertToolImageTransformerTest.java
@@ -0,0 +1,81 @@
+/*
+ * 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.biozentrum;
+
+import java.awt.image.BufferedImage;
+import java.awt.image.DataBuffer;
+import java.io.File;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.image.IImageTransformer;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class ConvertToolImageTransformerTest extends AssertJUnit
+{
+ private final String IMAGE_FOLDER = "./resource/test-data/" + getClass().getSimpleName();
+
+ private final String CONVERT_PARAMS =
+ " -contrast-stretch 0 -edge 1 -threshold 1 -transparent black ";
+
+ @Test
+ public void testTransformation()
+ {
+ BufferedImage templateImage = readImage("pond.png");
+ BufferedImage expected = readImage("pond-transformed.png");
+
+ BufferedImage transformationResult = createTransformer().transform(templateImage);
+
+ assertNotNull(transformationResult);
+ assertEqualImages(expected, transformationResult);
+
+ }
+
+ private IImageTransformer createTransformer()
+ {
+ ConvertToolImageTransformerFactory factory =
+ new ConvertToolImageTransformerFactory(CONVERT_PARAMS);
+ return factory.createTransformer();
+ }
+
+ private void assertEqualImages(BufferedImage expected, BufferedImage actual)
+ {
+ DataBuffer expectedDB = expected.getData().getDataBuffer();
+ DataBuffer actualDB = actual.getData().getDataBuffer();
+
+ String notEqualError = "Converted image not equal to expected result";
+ assertEquals(notEqualError, expectedDB.getSize(), actualDB.getSize());
+
+ for (int i = 0; i < expectedDB.getSize(); i++)
+ {
+ assertEquals(notEqualError, expectedDB.getElem(i), actualDB.getElem(i));
+
+ }
+
+ }
+
+ private BufferedImage readImage(String image)
+ {
+ File imageFile = new File(IMAGE_FOLDER, image);
+ return ImageUtil.loadImage(imageFile);
+ }
+
+}