diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
index 28502c54b29212f20f2e6ce902cebc7f1eb3a713..fcf3ed43780f4a651f44ea1251596239eb75872a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
@@ -295,7 +295,7 @@ abstract public class AbstractDatasetDownloadServlet extends HttpServlet
protected static final BufferedImage createThumbnail(IHierarchicalContentNode fileNode,
Size thumbnailSize)
{
- BufferedImage image = ImageUtil.loadImage(fileNode);
+ BufferedImage image = ImageUtil.loadImageForDisplay(fileNode);
return createThumbnail(image, thumbnailSize);
}
@@ -303,7 +303,7 @@ abstract public class AbstractDatasetDownloadServlet extends HttpServlet
{
int width = thumbnailSize.getWidth();
int height = thumbnailSize.getHeight();
- return ImageUtil.createThumbnail(image, width, height);
+ return ImageUtil.createThumbnailForDisplay(image, width, height);
}
// if display mode describes a thumbnail return its expected size
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 b1b09962833dbbc500870db6e8845393f6a05664..10abc68c5ae0f6bd111902cab13f63383dece687 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
@@ -24,6 +24,7 @@ import static ch.systemsx.cisd.common.utilities.DataTypeUtil.TIFF_FILE;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
+import java.awt.image.ColorModel;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.OutputStream;
@@ -47,6 +48,8 @@ import ar.com.hjg.pngj.PngWriter;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.image.IntensityRescaling;
+import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.common.io.hierarchical_content.HierarchicalNodeBasedContent;
@@ -57,7 +60,6 @@ import ch.systemsx.cisd.imagereaders.IReadParams;
import ch.systemsx.cisd.imagereaders.ImageID;
import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
-import ch.systemsx.cisd.imagereaders.ReadParams;
/**
* Utility function on images.
@@ -83,7 +85,7 @@ public class ImageUtil
handle.mark(MAX_READ_AHEAD);
try
{
- return loadJavaAdvancedImagingTiff(handle, imageID, false);
+ return loadJavaAdvancedImagingTiff(handle, imageID);
} catch (RuntimeException ex)
{
if (imageID.equals(ImageID.NULL))
@@ -110,13 +112,9 @@ public class ImageUtil
/**
* For experts only! Loads some kinds of TIFF images handled by JAI library.
- *
- * @param allow16BitGrayscaleModel if true and the image is 16 bit grayscale, then the
- * appropriate buffered imaged type will be used, otherwise the image will be
- * converted to 24 bits RGB. Useful if access to original pixel values is needed.
*/
public static BufferedImage loadJavaAdvancedImagingTiff(IRandomAccessFile handle,
- ImageID imageID, boolean allow16BitGrayscaleModel) throws EnvironmentFailureException
+ ImageID imageID) throws EnvironmentFailureException
{
IImageReader imageReader =
ImageReaderFactory.tryGetReader(ImageReaderConstants.JAI_LIBRARY, "tiff");
@@ -126,11 +124,9 @@ public class ImageUtil
.fromTemplate("Cannot find JAI image decoder for TIFF files.");
}
- ReadParams readParams = new ReadParams();
- readParams.setAllow16BitGrayscaleModel(allow16BitGrayscaleModel);
try
{
- return imageReader.readImage(handle, imageID, readParams);
+ return imageReader.readImage(handle, imageID, null);
} catch (Exception ex)
{
throw EnvironmentFailureException.fromTemplate("Cannot decode image.", ex);
@@ -194,11 +190,14 @@ public class ImageUtil
* 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 BufferedImage loadImage(IContent content, String imageIdOrNull,
+ public static BufferedImage loadUnchangedImage(IContent content, String imageIdOrNull,
String imageLibraryNameOrNull, String imageLibraryReaderNameOrNull, IReadParams params)
{
assert (imageLibraryReaderNameOrNull == null || imageLibraryNameOrNull != null) : "if image reader "
@@ -416,7 +415,7 @@ public class ImageUtil
@Private
static BufferedImage loadImage(IContent content)
{
- return loadImage(content, null, null, null, null);
+ return loadUnchangedImage(content, null, null, null, null);
}
/**
@@ -424,26 +423,54 @@ public class ImageUtil
*
* @throws IllegalArgumentException if the file isn't a valid image file.
*/
- public static BufferedImage loadImage(IHierarchicalContentNode fileNode)
+ public static BufferedImage loadImageForDisplay(IHierarchicalContentNode fileNode)
{
if (fileNode.exists() == false)
{
throw new IllegalArgumentException("File does not exist: " + fileNode.getRelativePath());
}
- return loadImage(new HierarchicalNodeBasedContent(fileNode));
+ BufferedImage result = loadImage(new HierarchicalNodeBasedContent(fileNode));
+ result = convertForDisplayIfNecessary(result);
+ return result;
}
/**
* Re-scales the image to be the biggest one which fits into a (0,0,maxWidth, maxHeight)
* rectangle. Preserves the aspect ratio. If the rectangle is bigger than the image does
- * nothing. Ignores alpha channel of the original image.
+ * nothing.
+ * <p>
+ * If the specified image uses grayscale with color depth larger then 8 bits, conversion to 8
+ * bits grayscale is done.
+ * </p>
*
* @param maxWidth Maximum width of the result image.
* @param maxHeight Maximum height of the result image.
*/
- public static BufferedImage createThumbnail(BufferedImage image, int maxWidth, int maxHeight)
+ public static BufferedImage createThumbnailForDisplay(BufferedImage image, int maxWidth,
+ int maxHeight)
+ {
+ BufferedImage result = rescale(image, maxWidth, maxHeight, true, false);
+ result = convertForDisplayIfNecessary(result);
+ return result;
+ }
+
+ /**
+ * If the specified image uses grayscale with color depth larger then 8 bits, conversion to 8
+ * bits grayscale is done. Otherwise the original image is returned.
+ */
+ public static BufferedImage convertForDisplayIfNecessary(BufferedImage image)
{
- return rescale(image, maxWidth, maxHeight, true, false);
+ ColorModel colorModel = image.getColorModel();
+ // is grayscale?
+ if (colorModel.getColorSpace().getNumComponents() == 1)
+ {
+ if (colorModel.getPixelSize() > 8)
+ {
+ Levels intensityRange = IntensityRescaling.computeLevels(image, 0);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, intensityRange);
+ }
+ }
+ return image;
}
/**
@@ -480,10 +507,7 @@ public class ImageUtil
int thumbnailWidth = (int) (scale * width + 0.5);
int thumbnailHeight = (int) (scale * height + 0.5);
- // preserve alpha channel if it was present before
- int imageType =
- image.getColorModel().hasAlpha() ? BufferedImage.TYPE_INT_ARGB
- : BufferedImage.TYPE_INT_RGB;
+ int imageType = image.getType();
BufferedImage thumbnail = new BufferedImage(thumbnailWidth, thumbnailHeight, imageType);
Graphics2D graphics2D = thumbnail.createGraphics();
Object renderingHint =
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
index ae4865d5369d9a47543874578d2c856f39fc27a7..49159712a497645324ae3649b03014f47b756936 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
@@ -128,8 +128,8 @@ public class ImageUtilTest extends AssertJUnit
public void testCreateThumbnail()
{
BufferedImage image = loadImageByFile("gif-example.gif");
- assertImageSize(79, 100, ImageUtil.createThumbnail(image, 200, 100));
- assertImageSize(100, 127, ImageUtil.createThumbnail(image, 100, 200));
+ assertImageSize(79, 100, ImageUtil.createThumbnailForDisplay(image, 200, 100));
+ assertImageSize(100, 127, ImageUtil.createThumbnailForDisplay(image, 100, 200));
}
@Test
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ThumbnailTiming.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ThumbnailTiming.java
index 9ebff8850e35dcd1469527c31888171c1a39b1b9..07c9f28131713496a42f6fd4ef849977f0cc8f41 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ThumbnailTiming.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ThumbnailTiming.java
@@ -43,7 +43,7 @@ public class ThumbnailTiming
BufferedImage image = ImageUtil.loadImage(file);
stopWatch.stop();
stopWatch.start("Convert");
- BufferedImage thumbnail = ImageUtil.createThumbnail(image, 120, 60);
+ BufferedImage thumbnail = ImageUtil.createThumbnailForDisplay(image, 120, 60);
stopWatch.stop();
stopWatch.start("Write");
try
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 507bc8cf4cbf53db4b7a605d0043ed6b21ebf275..8163116a76861b48a653d4d183cc224f7ac4221c 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
@@ -95,16 +95,16 @@ public class AbsoluteImageReference extends AbstractImageReference
}
}
- public BufferedImage getImage()
+ public BufferedImage getUnchangedImage()
{
if (image == null)
{
- image = loadImage(content, tryGetImageID(), imageLibraryOrNull);
+ image = loadUnchangedImage(content, tryGetImageID(), imageLibraryOrNull);
}
return image;
}
- static BufferedImage loadImage(IContent content, String imageIdOrNull,
+ static BufferedImage loadUnchangedImage(IContent content, String imageIdOrNull,
ImageLibraryInfo imageLibraryOrNull)
{
String imageLibraryNameOrNull = null;
@@ -114,7 +114,7 @@ public class AbsoluteImageReference extends AbstractImageReference
imageLibraryNameOrNull = imageLibraryOrNull.getName();
imageLibraryReaderNameOrNull = imageLibraryOrNull.getReaderName();
}
- return ImageUtil.loadImage(content, imageIdOrNull, imageLibraryNameOrNull,
+ return ImageUtil.loadUnchangedImage(content, imageIdOrNull, imageLibraryNameOrNull,
imageLibraryReaderNameOrNull, null);
}
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 bb018f9b2bda0fa57842afea16180e90c00e86e1..f3e8e45a8c45c92011ebb432b9bfcb8da5111ce8 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
@@ -201,8 +201,7 @@ class Hdf5ThumbnailGenerator implements IHDF5WriterClient
private BufferedImage loadImage(File imageFile, String imageIdOrNull)
{
- // NOTE 2011-04-20, Tomasz Pylak: support paged tiffs when generating thumbnails
- return AbsoluteImageReference.loadImage(new FileBasedContent(imageFile), imageIdOrNull,
+ return AbsoluteImageReference.loadUnchangedImage(new FileBasedContent(imageFile), imageIdOrNull,
imageLibraryOrNull);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
index 7fd1e6a062fcd0cfad90a5ba1642e2aa8d26a9dc..b9c9b8c825601b718f42cad6870b72738535e581 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -27,10 +28,12 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageTransformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
/**
* Helper class for retrieving and/or creating entities associated with the imaging database:
@@ -409,9 +412,33 @@ public class ImagingDatabaseHelper
ImgChannelDTO channelDTO = makeChannelDTO(channel, channelOwner);
long channelId = dao.addChannel(channelDTO);
channelDTO.setId(channelId);
+ saveChannelImageTransformations(channelId, channel.getAvailableTransformations());
return channelDTO;
}
+ private void saveChannelImageTransformations(long channelId,
+ ImageTransformation[] transformations)
+ {
+ if (transformations.length == 0)
+ {
+ return;
+ }
+ List<ImgImageTransformationDTO> transformationDTOs =
+ new ArrayList<ImgImageTransformationDTO>();
+ for (ImageTransformation transformation : transformations)
+ {
+ transformationDTOs.add(createTransformationDTO(transformation, channelId));
+ }
+ dao.addImageTransformations(transformationDTOs);
+ }
+
+ private ImgImageTransformationDTO createTransformationDTO(ImageTransformation tr,
+ long channelId)
+ {
+ return new ImgImageTransformationDTO(tr.getCode(), tr.getLabel(), tr.getDescription(),
+ tr.isEditable(), channelId, tr.getImageTransformerFactory());
+ }
+
private static ImgChannelDTO makeChannelDTO(Channel channel, ChannelOwner channelOwner)
{
ChannelColor channelColor = channel.tryGetChannelColor();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
index c1eb6f00962cf4db90fdc295ace4aa6ce7f34246..af00232405943884ebbc81fd2d2e35a40191a390 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
@@ -28,7 +28,7 @@ public class ImagingDatabaseVersionHolder implements IDatabaseVersionHolder
public String getDatabaseVersion()
{
- return "013"; // changed in S108
+ return "014"; // changed in S115
}
}
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 98ad698efd25155442c1e9c5e702562c66164f69..946d40f0b3e458731d65ce778ffd90b6c10a8a68 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
@@ -33,6 +33,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFe
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureVocabularyTermDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSpotDTO;
/**
@@ -69,8 +70,8 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
@Select("insert into EXPERIMENTS (PERM_ID) values (?{1}) returning ID")
public long addExperiment(String experimentPermId);
- @Select("insert into CHANNELS (LABEL, CODE, DESCRIPTION, WAVELENGTH, DS_ID, EXP_ID, COLOR) values "
- + "(?{1.label}, ?{1.code}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}, ?{1.dbChannelColor}) returning ID")
+ @Select("insert into CHANNELS (CODE, LABEL, DESCRIPTION, WAVELENGTH, DS_ID, EXP_ID, COLOR) values "
+ + "(?{1.code}, ?{1.label}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}, ?{1.dbChannelColor}) returning ID")
public long addChannel(ImgChannelDTO channel);
@Select("insert into CONTAINERS (PERM_ID, SPOTS_WIDTH, SPOTS_HEIGHT, EXPE_ID) values "
@@ -85,6 +86,13 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
+ "?{1.imageLibraryName}, ?{1.imageReaderName}) returning ID")
public long addDataset(ImgDatasetDTO dataset);
+ @Update(sql = "insert into IMAGE_TRANSFORMATIONS(CODE, LABEL, DESCRIPTION, IMAGE_TRANSFORMER_FACTORY, IS_EDITABLE, CHANNEL_ID) values "
+ + "(?{1.code}, ?{1.label}, ?{1.description}, ?{1.serializedImageTransformerFactory}, ?{1.isEditable}, ?{1.channelId})", batchUpdate = true)
+ public void addImageTransformations(List<ImgImageTransformationDTO> imageTransformations);
+
+ @Update(sql = "delete from IMAGE_TRANSFORMATIONS where CODE = ?{1} and CHANNEL_ID = ?{2}")
+ public void removeImageTransformation(String transformationCode, long channelId);
+
@Select("insert into SPOTS (X, Y, CONT_ID) values "
+ "(?{1.column}, ?{1.row}, ?{1.containerId}) returning ID")
public long addSpot(ImgSpotDTO spot);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
index 402a58583c8b888d3e266bc774201e9a4b43519d..28b691b58551846f8e6cd77fe8fc277567ebea4c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java
@@ -17,6 +17,9 @@
package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import java.awt.image.BufferedImage;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
import org.apache.commons.lang.StringUtils;
@@ -42,6 +45,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgCh
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
/**
* {@link HCSDatasetLoader} extension with code for handling images.
@@ -98,7 +102,7 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
}
AbsoluteImageReference imgRef =
createAbsoluteImageReference(imageDTO, channel, imageSize, thumbnailFetched);
- if (thumbnailFetched && isThumbnailsTooSmall(imageSize, imgRef.getImage()))
+ if (thumbnailFetched && isThumbnailsTooSmall(imageSize, imgRef.getUnchangedImage()))
{
imageDTO = tryGetOriginalImage(channel.getId(), channelStackReference, datasetId);
if (imageDTO != null)
@@ -143,11 +147,33 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
ImageTransfomationFactories imageTransfomationFactories = new ImageTransfomationFactories();
imageTransfomationFactories
.setForMergedChannels(tryGetImageTransformerFactoryForMergedChannels());
- imageTransfomationFactories.setForChannel(channel.tryGetImageTransformerFactory());
+
+ Map<String, IImageTransformerFactory> singleChannelMap =
+ getAvailableImageTransformationsForChannel(channel);
+ imageTransfomationFactories.setForChannel(singleChannelMap);
+
imageTransfomationFactories.setForImage(imageDTO.tryGetImageTransformerFactory());
return imageTransfomationFactories;
}
+ private Map<String, IImageTransformerFactory> getAvailableImageTransformationsForChannel(
+ ImgChannelDTO channel)
+ {
+ List<ImgImageTransformationDTO> availableImageTransformations =
+ availableImageTransformationsMap.get(channel.getId());
+ Map<String, IImageTransformerFactory> singleChannelMap =
+ new HashMap<String, IImageTransformerFactory>();
+ if (availableImageTransformations != null)
+ {
+ for (ImgImageTransformationDTO transformation : availableImageTransformations)
+ {
+ singleChannelMap.put(transformation.getCode(),
+ transformation.getImageTransformerFactory());
+ }
+ }
+ return singleChannelMap;
+ }
+
private IImageTransformerFactory tryGetImageTransformerFactoryForMergedChannels()
{
IImageTransformerFactory imageTransformerFactory = dataset.tryGetImageTransformerFactory();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
index 3a6aa9f26c661afaf8029fc3fc5d1546514ec10d..43caf51acac04c165122c4d6b98aed47fb8e098f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.dss.etl.dto;
+import java.util.Map;
+
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
/**
@@ -25,8 +27,8 @@ import ch.systemsx.cisd.base.image.IImageTransformerFactory;
*/
public class ImageTransfomationFactories
{
- // applied when a single channel is displayed
- private IImageTransformerFactory singleChannel;
+ // transformation with a specified code can be applied when a single channel is displayed
+ private Map<String/* transformation code */, IImageTransformerFactory> singleChannelMap;
// applied when all channels of the image are merged
private IImageTransformerFactory mergedChannels;
@@ -34,14 +36,24 @@ public class ImageTransfomationFactories
// individual transformation for the image
private IImageTransformerFactory image;
- public IImageTransformerFactory tryGetForChannel(boolean areChannelsMerged)
+ public IImageTransformerFactory tryGetForChannel(String transformationCodeOrNull)
+ {
+ if (transformationCodeOrNull == null)
+ {
+ return null;
+ }
+ return singleChannelMap.get(transformationCodeOrNull);
+ }
+
+ public IImageTransformerFactory tryGetForMerged()
{
- return areChannelsMerged ? mergedChannels : singleChannel;
+ return mergedChannels;
}
- public void setForChannel(IImageTransformerFactory transformerFactoryForChannel)
+ public void setForChannel(
+ Map<String/* transformation code */, IImageTransformerFactory> singleChannelMap)
{
- this.singleChannel = transformerFactoryForChannel;
+ this.singleChannelMap = singleChannelMap;
}
public void setForMergedChannels(IImageTransformerFactory transformerFactoryForMergedChannels)
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 10c6c9ac0aa0b95a0f27ebdf2c4f434c06035356..e2d4450e71e33806b1dd9091117482a567f34dca 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
@@ -24,6 +24,8 @@ 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.transformations.ConvertToolImageTransformerFactory;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformationBuffer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -34,14 +36,18 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst
*/
abstract public class SimpleImageDataConfig
{
- // --- one of the following two methods have to be overridden -----------------
+ // --- one of the following two methods has to be overridden -----------------
/**
- * Extracts tile number, channel code and well code for a given relative path to an image.
+ * Extracts tile number, channel code and well code for a given relative path to a single image.
+ * This method should overridden to deal with files containing single images. It is ignored if
+ * {@link #extractImagesMetadata(String, List)} is overridden as well.
* <p>
- * Will be called for each file found in the incoming directory which has the extension returned
- * by {@link #getRecognizedImageExtensions()}.
+ * It will be called for each file found in the incoming directory which has the extension
+ * returned by {@link #getRecognizedImageExtensions()}.
* </p>
+ * To deal with image containers (like multi-page TIFF files) override
+ * {@link #extractImagesMetadata(String, List)} instead, otherwise leave that method unchanged.
*/
public ImageMetadata extractImageMetadata(String imagePath)
{
@@ -50,12 +56,14 @@ abstract public class SimpleImageDataConfig
}
/**
- * Returns meta-data for each image contained in specified image file path. This method returns
- * just the {@link ImageMetadata} object returned by {@link #extractImageMetadata(String)}.
+ * Returns meta-data for each image in the specified image container. This method should
+ * overridden to deal with container images (like multi-page TIFF files).
* <p>
- * In case of a image container file format (like multi-page TIFF) this method should
- * overridden.
+ * This implementation returns the result of {@link #extractImageMetadata(String)} wrapped in an
+ * array, image identifiers are ignored.
+ * </p>
*
+ * @param imagePath path to the single image or container of many images
* @param imageIdentifiers Identifiers of all images contained in the image file.
*/
public ImageMetadata[] extractImagesMetadata(String imagePath,
@@ -103,13 +111,33 @@ abstract public class SimpleImageDataConfig
* <p>
* Creates channel description for a given code. Can be overridden in subclasses.
* </p>
- * By default rhe channel label will be equal to the code. Channel color returned by
+ * By default the channel label will be equal to the code. Channel color returned by
* {@link #getChannelColor(String)} will be used.
*/
public Channel createChannel(String channelCode)
{
- ChannelColor channelColor = getChannelColor(channelCode.toUpperCase());
- return new Channel(channelCode, channelCode, channelColor);
+ ChannelColor channelColor = getChannelColor(channelCode);
+ ImageTransformation[] availableTransformations =
+ getAvailableChannelTransformations(channelCode);
+ String label = channelCode;
+ String normalizedChannelCode = CodeNormalizer.normalize(channelCode);
+ Channel channel = new Channel(normalizedChannelCode, label, channelColor);
+ channel.setAvailableTransformations(availableTransformations);
+ return channel;
+ }
+
+ /**
+ * Sets available transformations which can be applied to images of the specified channel (on
+ * user's request).
+ * <p>
+ * Can be overridden in subclasses. The easiest way to create transformations is to use
+ * {@link ImageTransformationBuffer} class.
+ * <p>
+ * By default returns null.
+ */
+ public ImageTransformation[] getAvailableChannelTransformations(String channelCode)
+ {
+ return null;
}
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBuffer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBuffer.java
index 75edc13c1b6cf2bb88162f79d0b84f7b8989b84e..b63e6071c2506e5a2e7bdb98ccd735afddb1aca7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBuffer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/ImageTransformationBuffer.java
@@ -33,7 +33,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageTransformation;
*/
public class ImageTransformationBuffer
{
- private static final String PREDEFINED_TRANSFORMATIONS_CODE_PREFIX = "PREDEFINED_";
+ private static final String PREDEFINED_TRANSFORMATIONS_CODE_PREFIX = "_";
private final List<ImageTransformation> imageTransformations;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactory.java
index 27a0b7f970d7af7b6b3c1d8a2b6d87d0ec3f8dea..38c3aee6c83de4a8be39351c27b2189d01b4b0fd 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactory.java
@@ -80,7 +80,11 @@ class ImageGenerationDescriptionFactory
throw new UserFailureException(
"Neither channels nor segmentation objects have been specified!");
}
- return new ImageGenerationDescription(channelsToMerge, overlayChannels, sessionId,
+
+ String singleChannelTransformationCodeOrNull =
+ request.getParameter(ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM);
+ return new ImageGenerationDescription(channelsToMerge,
+ singleChannelTransformationCodeOrNull, overlayChannels, sessionId,
thumbnailSizeOrNull);
}
@@ -95,7 +99,7 @@ class ImageGenerationDescriptionFactory
{
String datasetCode = entry.getKey();
List<String> channels = entry.getValue();
- overlayChannels.add(new DatasetAcquiredImagesReference(datasetCode,
+ overlayChannels.add(DatasetAcquiredImagesReference.createForManyChannels(datasetCode,
channelStackReference, channels));
}
return overlayChannels;
@@ -143,17 +147,29 @@ class ImageGenerationDescriptionFactory
{
return null;
}
- List<String> channelsOrNull = null;
if (isMergedChannels == false)
{
- channelsOrNull = tryGetParams(request, ImageServletUrlParameters.CHANNEL_PARAM);
+ List<String> channelsOrNull =
+ tryGetParams(request, ImageServletUrlParameters.CHANNEL_PARAM);
if (channelsOrNull == null)
{
return null; // no channels to merge at all
}
+ if (channelsOrNull.size() > 1)
+ {
+ return DatasetAcquiredImagesReference.createForManyChannels(datasetCode,
+ channelStackReference, channelsOrNull);
+ } else
+ {
+ String channelCode = channelsOrNull.get(0);
+ return DatasetAcquiredImagesReference.createForSingleChannel(datasetCode,
+ channelStackReference, channelCode);
+ }
+ } else
+ {
+ return DatasetAcquiredImagesReference.createForMergedChannels(datasetCode,
+ channelStackReference);
}
- return new DatasetAcquiredImagesReference(datasetCode, channelStackReference,
- channelsOrNull);
}
private static boolean isMergedChannels(HttpServletRequest request)
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 4bef593d90d88f3833144d992085db663daf346b..5902a3a4dc78fe94ca865a6137ad2974b6356d08 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
@@ -21,15 +21,11 @@ import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
-import java.io.ByteArrayOutputStream;
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.rinn.restrictions.Private;
@@ -49,6 +45,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.ResponseContentStream;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageGenerationDescription;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageTransformationParams;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
@@ -109,7 +106,10 @@ public class ImageChannelsUtils
if (imageChannels != null)
{
RequestedImageSize imageSize = new RequestedImageSize(thumbnailSizeOrNull, false);
- image = calculateBufferedImage(imageChannels, datasetDirectoryProvider, imageSize);
+ image =
+ calculateBufferedImage(imageChannels,
+ params.tryGetSingleChannelTransformationCode(),
+ datasetDirectoryProvider, imageSize);
}
RequestedImageSize overlaySize = calcOverlaySize(image, thumbnailSizeOrNull);
@@ -147,7 +147,9 @@ public class ImageChannelsUtils
boolean mergeAllChannels = utils.isMergeAllChannels(imagesReference);
List<AbsoluteImageReference> imageContents =
utils.fetchImageContents(imagesReference, mergeAllChannels, true);
- return calculateSingleImages(imageContents, true, mergeAllChannels);
+ ImageTransformationParams transformationInfo =
+ new ImageTransformationParams(true, mergeAllChannels, null);
+ return calculateSingleImagesForDisplay(imageContents, transformationInfo);
}
private static RequestedImageSize getSize(BufferedImage img, boolean highQuality)
@@ -187,11 +189,19 @@ public class ImageChannelsUtils
private static BufferedImage calculateBufferedImage(
DatasetAcquiredImagesReference imageChannels,
+ String singleChannelTransformationCodeOrNull,
IDatasetDirectoryProvider datasetDirectoryProvider, RequestedImageSize imageSizeLimit)
{
ImageChannelsUtils imageChannelsUtils =
createImageChannelsUtils(imageChannels, datasetDirectoryProvider, imageSizeLimit);
- return imageChannelsUtils.calculateBufferedImage(imageChannels, true);
+
+ boolean useMergedChannelsTransformation =
+ imageChannelsUtils.isMergeAllChannels(imageChannels);
+ ImageTransformationParams transformationInfo =
+ new ImageTransformationParams(true, useMergedChannelsTransformation,
+ singleChannelTransformationCodeOrNull);
+
+ return imageChannelsUtils.calculateBufferedImage(imageChannels, transformationInfo);
}
private static ImageChannelsUtils createImageChannelsUtils(
@@ -205,50 +215,29 @@ public class ImageChannelsUtils
@Private
BufferedImage calculateBufferedImage(DatasetAcquiredImagesReference imageChannels,
- boolean transform)
+ ImageTransformationParams transformationInfo)
{
boolean mergeAllChannels = isMergeAllChannels(imageChannels);
List<AbsoluteImageReference> imageContents =
fetchImageContents(imageChannels, mergeAllChannels, false);
- return mergeChannels(imageContents, transform, mergeAllChannels);
+ return calculateBufferedImage(imageContents, transformationInfo);
}
- // Check if all exiting channels of the image should be merged (and not a single one or a
- // subset).
- // We want to treat the case where merged channels were requested in the same way as the case
- // where all channel names have been enumerated.
private boolean isMergeAllChannels(DatasetAcquiredImagesReference imageChannels)
{
- if (imageChannels.isMergeAllChannels())
- {
- return true;
- }
- List<String> wantedChannelCodes = imageChannels.getChannelCodes();
- List<String> allChannelsCodes = imageAccessor.getImageParameters().getChannelsCodes();
- if (allChannelsCodes.size() == 1)
- {
- return false; // there is only one channel in total, single channel transformation
- // should be used
- }
- for (String existingChannelCode : allChannelsCodes)
- {
- if (wantedChannelCodes.indexOf(existingChannelCode) == -1)
- {
- return false;
- }
- }
- return true;
+ return imageChannels.isMergeAllChannels(getAllChannelCodes());
}
/**
* @param skipNonExisting if true references to non-existing images are ignored, otherwise an
* exception is thrown
+ * @param mergeAllChannels true if all existing channel images should be merged
*/
private List<AbsoluteImageReference> fetchImageContents(
DatasetAcquiredImagesReference imagesReference, boolean mergeAllChannels,
boolean skipNonExisting)
{
- List<String> channelCodes = getChannelCodes(imagesReference);
+ List<String> channelCodes = imagesReference.getChannelCodes(getAllChannelCodes());
List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
for (String channelCode : channelCodes)
{
@@ -289,17 +278,6 @@ public class ImageChannelsUtils
return HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
}
- private List<String> getChannelCodes(DatasetAcquiredImagesReference imagesReference)
- {
- if (imagesReference.isMergeAllChannels())
- {
- return imageAccessor.getImageParameters().getChannelsCodes();
- } else
- {
- return imagesReference.getChannelCodes();
- }
- }
-
/**
* Returns content of the image which is representative for the given dataset.
*/
@@ -311,7 +289,9 @@ public class ImageChannelsUtils
List<AbsoluteImageReference> imageReferences =
new ImageChannelsUtils(imageAccessor, imageSizeLimitOrNull)
.getRepresentativeImageReferences(wellLocationOrNull);
- BufferedImage image = mergeChannels(imageReferences, true, true);
+ BufferedImage image =
+ calculateBufferedImage(imageReferences, new ImageTransformationParams(true, true,
+ null));
String name = createFileName(datasetCode, wellLocationOrNull, imageSizeLimitOrNull);
return createResponseContentStream(image, name);
}
@@ -344,15 +324,12 @@ public class ImageChannelsUtils
*/
public static IContent getImage(IImagingDatasetLoader imageAccessor,
ImageChannelStackReference channelStackReference, String chosenChannelCode,
- Size imageSizeLimitOrNull, boolean convertToPng)
+ Size imageSizeLimitOrNull, String singleChannelImageTransformationCodeOrNull,
+ boolean convertToPng, boolean transform)
{
- String datasetCode = imageAccessor.getImageParameters().getDatasetCode();
- boolean isMergedChannels =
- ScreeningConstants.MERGED_CHANNELS.equalsIgnoreCase(chosenChannelCode);
- List<String> channelCodes = isMergedChannels ? null : Arrays.asList(chosenChannelCode);
-
DatasetAcquiredImagesReference imagesReference =
- new DatasetAcquiredImagesReference(datasetCode, channelStackReference, channelCodes);
+ createDatasetAcquiredImagesReference(imageAccessor, channelStackReference,
+ chosenChannelCode);
ImageChannelsUtils imageChannelsUtils =
new ImageChannelsUtils(imageAccessor, imageSizeLimitOrNull);
@@ -365,38 +342,29 @@ public class ImageChannelsUtils
{
return rawContent;
}
- BufferedImage image = mergeChannels(imageContents, false, mergeAllChannels);
+ ImageTransformationParams transformationInfo =
+ new ImageTransformationParams(transform, mergeAllChannels,
+ singleChannelImageTransformationCodeOrNull);
+ BufferedImage image = calculateBufferedImage(imageContents, transformationInfo);
return createPngContent(image, null);
}
- /**
- * @return an image for the specified tile in the specified size and for the requested channel.
- */
- public static IContent getImage(IImagingDatasetLoader imageAccessor,
- ImageChannelStackReference channelStackReference, String chosenChannelCode,
- Size imageSizeLimitOrNull, boolean convertToPng, boolean transform)
+ private static DatasetAcquiredImagesReference createDatasetAcquiredImagesReference(
+ IImagingDatasetLoader imageAccessor, ImageChannelStackReference channelStackReference,
+ String chosenChannelCode)
{
String datasetCode = imageAccessor.getImageParameters().getDatasetCode();
boolean isMergedChannels =
ScreeningConstants.MERGED_CHANNELS.equalsIgnoreCase(chosenChannelCode);
- List<String> channelCodes = isMergedChannels ? null : Arrays.asList(chosenChannelCode);
-
- DatasetAcquiredImagesReference imagesReference =
- new DatasetAcquiredImagesReference(datasetCode, channelStackReference, channelCodes);
-
- ImageChannelsUtils imageChannelsUtils =
- new ImageChannelsUtils(imageAccessor, imageSizeLimitOrNull);
- boolean mergeAllChannels = imageChannelsUtils.isMergeAllChannels(imagesReference);
- List<AbsoluteImageReference> imageContents =
- imageChannelsUtils.fetchImageContents(imagesReference, mergeAllChannels, false);
-
- IContent rawContent = tryGetRawContent(convertToPng, imageContents);
- if (rawContent != null)
+ if (isMergedChannels)
{
- return rawContent;
+ return DatasetAcquiredImagesReference.createForMergedChannels(datasetCode,
+ channelStackReference);
+ } else
+ {
+ return DatasetAcquiredImagesReference.createForSingleChannel(datasetCode,
+ channelStackReference, chosenChannelCode);
}
- BufferedImage image = mergeChannels(imageContents, transform, mergeAllChannels);
- return createPngContent(image, null);
}
// optimization: if there is exactly one image reference, maybe its original raw content is the
@@ -417,7 +385,7 @@ public class ImageChannelsUtils
{
List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
- for (String chosenChannel : imageAccessor.getImageParameters().getChannelsCodes())
+ for (String chosenChannel : getAllChannelCodes())
{
AbsoluteImageReference image =
getRepresentativeImageReference(chosenChannel, wellLocationOrNull);
@@ -426,6 +394,11 @@ public class ImageChannelsUtils
return images;
}
+ private List<String> getAllChannelCodes()
+ {
+ return imageAccessor.getImageParameters().getChannelsCodes();
+ }
+
/**
* @throw {@link EnvironmentFailureException} when image does not exist
*/
@@ -451,18 +424,19 @@ public class ImageChannelsUtils
* @param useMergedChannelsTransformation sometimes we can have a single image which contain all
* channels merged. In this case a different transformation will be applied to it.
*/
- private static BufferedImage calculateAndTransformSingleImage(
- AbsoluteImageReference imageReference, boolean transform,
- boolean useMergedChannelsTransformation)
+ private static BufferedImage calculateAndTransformSingleImageForDisplay(
+ AbsoluteImageReference imageReference, ImageTransformationParams transformationInfo)
{
BufferedImage image = calculateSingleImage(imageReference);
- return transform(image, imageReference, transform, useMergedChannelsTransformation);
+ image = transform(image, imageReference, transformationInfo);
+ image = ImageUtil.convertForDisplayIfNecessary(image);
+ return image;
}
private static BufferedImage calculateSingleImage(AbsoluteImageReference imageReference)
{
long start = operationLog.isDebugEnabled() ? System.currentTimeMillis() : 0;
- BufferedImage image = imageReference.getImage();
+ BufferedImage image = imageReference.getUnchangedImage();
if (operationLog.isDebugEnabled())
{
operationLog.debug("Load original image: " + (System.currentTimeMillis() - start));
@@ -504,29 +478,51 @@ public class ImageChannelsUtils
* @param allChannelsMerged if true then we use one special transformation on the merged images
* instead of transforming every single image.
*/
- private static BufferedImage mergeChannels(List<AbsoluteImageReference> imageReferences,
- boolean transform, boolean allChannelsMerged)
+ private static BufferedImage calculateBufferedImage(
+ List<AbsoluteImageReference> imageReferences,
+ ImageTransformationParams transformationInfo)
{
AbsoluteImageReference singleImageReference = imageReferences.get(0);
if (imageReferences.size() == 1)
{
- return calculateAndTransformSingleImage(singleImageReference, transform,
- allChannelsMerged);
+ return calculateAndTransformSingleImageForDisplay(singleImageReference,
+ transformationInfo);
} else
{
- // We do not transform single images here.
- // The 'merged channels' transformation will be applied later.
- List<ImageWithReference> images =
- calculateSingleImages(imageReferences, false, allChannelsMerged);
- BufferedImage mergedImage = mergeImages(images);
- // NOTE: even if we are not merging all the channels but just few of them we use the
- // merged-channel transformation
- return transform(mergedImage, singleImageReference, transform, true);
+ return mergeChannels(imageReferences, transformationInfo, singleImageReference);
}
}
+ private static BufferedImage mergeChannels(List<AbsoluteImageReference> imageReferences,
+ ImageTransformationParams transformationInfo,
+ AbsoluteImageReference singleImageReference)
+ {
+ // We do not transform single images here.
+ // The 'merged channels' transformation will be applied later.
+ List<ImageWithReference> images = calculateSingleImagesForDisplay(imageReferences, null);
+ BufferedImage mergedImage = mergeImages(images);
+ // NOTE: even if we are not merging all the channels but just few of them we use the
+ // merged-channel transformation
+
+ // TODO 2011-09-13, Tomasz Pylak: it looks like we are applying image level
+ // transformation from a random single channel to merged images. Replace with following
+ // code after testing:
+
+ // if (transformationInfo.isApplyNonImageLevelTransformation())
+ // {
+ // IImageTransformerFactory transformationOrNull =
+ // singleImageReference.getImageTransfomationFactories().tryGetForMerged();
+ // mergedImage =
+ // applyImageTransformation(mergedImage, transformationOrNull);
+ // }
+ // return mergedImage;
+
+ return transform(mergedImage, singleImageReference,
+ transformationInfo.cloneAndSetUseMergedChannelsTransformation());
+ }
+
private static BufferedImage transform(BufferedImage image,
- AbsoluteImageReference imageReference, boolean transform, boolean allChannelsMerged)
+ AbsoluteImageReference imageReference, ImageTransformationParams transformationInfo)
{
BufferedImage resultImage = image;
ImageTransfomationFactories transfomations =
@@ -535,13 +531,21 @@ public class ImageChannelsUtils
// external image viewer
resultImage = applyImageTransformation(resultImage, transfomations.tryGetForImage());
- if (transform == false)
+ if (transformationInfo.isApplyNonImageLevelTransformation() == false)
{
return resultImage;
}
- IImageTransformerFactory channelLevelTransformation =
- transfomations.tryGetForChannel(allChannelsMerged);
- return applyImageTransformation(resultImage, channelLevelTransformation);
+ IImageTransformerFactory channelLevelTransformationOrNull;
+ if (transformationInfo.isUseMergedChannelsTransformation())
+ {
+ channelLevelTransformationOrNull = transfomations.tryGetForMerged();
+ } else
+ {
+ channelLevelTransformationOrNull =
+ transfomations.tryGetForChannel(transformationInfo
+ .tryGetSingleChannelTransformationCode());
+ }
+ return applyImageTransformation(resultImage, channelLevelTransformationOrNull);
}
private static BufferedImage applyImageTransformation(BufferedImage image,
@@ -577,24 +581,28 @@ public class ImageChannelsUtils
}
}
- /** @param useMergedChannelsTransformation used only if transformEachImage is true */
- private static List<ImageWithReference> calculateSingleImages(
- List<AbsoluteImageReference> imageReferences, boolean transformEachImage,
- boolean useMergedChannelsTransformation)
+ /**
+ * @param transformationInfoOrNull if null all transformations (including image-level) will be
+ * skipped
+ */
+ private static List<ImageWithReference> calculateSingleImagesForDisplay(
+ List<AbsoluteImageReference> imageReferences,
+ ImageTransformationParams transformationInfoOrNull)
{
List<ImageWithReference> images = new ArrayList<ImageWithReference>();
for (AbsoluteImageReference imageRef : imageReferences)
{
BufferedImage image;
- if (transformEachImage)
+ if (transformationInfoOrNull != null)
{
image =
- calculateAndTransformSingleImage(imageRef, true,
- useMergedChannelsTransformation);
+ calculateAndTransformSingleImageForDisplay(imageRef,
+ transformationInfoOrNull);
} else
{
+ // NOTE: here we skip image level transformations as well
image = calculateSingleImage(imageRef);
-
+ image = ImageUtil.convertForDisplayIfNecessary(image);
}
images.add(new ImageWithReference(image, imageRef));
}
@@ -636,11 +644,12 @@ public class ImageChannelsUtils
return (i1OrNull == null) ? (i2OrNull == null) : i1OrNull.equals(i2OrNull);
}
+ // this method always returns RGB images, even if the input was in grayscale
private static BufferedImage mergeImages(List<ImageWithReference> images)
{
assert images.size() > 1 : "more than 1 image expected, but found: " + images.size();
- BufferedImage newImage = createNewImage(images.get(0).getBufferedImage());
+ BufferedImage newImage = createNewRGBImage(images.get(0).getBufferedImage());
int width = newImage.getWidth();
int height = newImage.getHeight();
int colorBuffer[] = new int[4];
@@ -795,7 +804,7 @@ public class ImageChannelsUtils
private static BufferedImage transformToChannel(BufferedImage bufferedImage,
ColorComponent colorComponent)
{
- BufferedImage newImage = createNewImage(bufferedImage);
+ BufferedImage newImage = createNewRGBImage(bufferedImage);
int width = bufferedImage.getWidth();
int height = bufferedImage.getHeight();
for (int x = 0; x < width; x++)
@@ -803,7 +812,7 @@ public class ImageChannelsUtils
for (int y = 0; y < height; y++)
{
int rgb = bufferedImage.getRGB(x, y);
- int channelColor = getGrayscaleAsChannel(rgb, colorComponent);
+ int channelColor = extractSingleComponent(rgb, colorComponent);
newImage.setRGB(x, y, channelColor);
}
}
@@ -812,7 +821,7 @@ public class ImageChannelsUtils
// NOTE: drawing on this image will not preserve transparency - but we do not need it and the
// image is smaller
- private static BufferedImage createNewImage(RenderedImage bufferedImage)
+ private static BufferedImage createNewRGBImage(RenderedImage bufferedImage)
{
BufferedImage newImage =
new BufferedImage(bufferedImage.getWidth(), bufferedImage.getHeight(),
@@ -848,9 +857,9 @@ public class ImageChannelsUtils
}
}
- // we assume that the color was in a grayscale
- // we reset all ingredients besides the one which should be shown
- private static int getGrayscaleAsChannel(int rgb, ColorComponent colorComponent)
+ // We reset all ingredients besides the one which is specified by color component.
+ // The result is the rgb value with only one component which is non-zero.
+ private static int extractSingleComponent(int rgb, ColorComponent colorComponent)
{
return colorComponent.extractSingleComponent(rgb).getRGB();
}
@@ -866,10 +875,10 @@ public class ImageChannelsUtils
return new Color(rgb[0], rgb[1], rgb[2], rgb[3]).getRGB();
}
-
private static IContent createPngContent(BufferedImage image, String nameOrNull)
{
final byte[] output = ImageUtil.imageToPngFast(image);
return new ByteArrayBasedContent(output, nameOrNull);
}
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/DatasetAcquiredImagesReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/DatasetAcquiredImagesReference.java
index 10d3e10d786fa058913a412fd0fa2c2d15715116..4113176606cb05b9d0d3a051b19af3210ede4f2b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/DatasetAcquiredImagesReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/DatasetAcquiredImagesReference.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.generic.server.images.dto;
+import java.util.Arrays;
import java.util.List;
/**
@@ -29,10 +30,30 @@ public class DatasetAcquiredImagesReference
private final ImageChannelStackReference channelStackReference;
+ /** Can be null if merged channels are requested. */
private final List<String> channelCodesOrNull;
+ public static DatasetAcquiredImagesReference createForMergedChannels(String datasetCode,
+ ImageChannelStackReference channelStackReference)
+ {
+ return new DatasetAcquiredImagesReference(datasetCode, channelStackReference, null);
+ }
+
+ public static DatasetAcquiredImagesReference createForSingleChannel(String datasetCode,
+ ImageChannelStackReference channelStackReference, String channelCode)
+ {
+ return new DatasetAcquiredImagesReference(datasetCode, channelStackReference,
+ Arrays.asList(channelCode));
+ }
+
+ public static DatasetAcquiredImagesReference createForManyChannels(String datasetCode,
+ ImageChannelStackReference channelStackReference, List<String> channelCodes)
+ {
+ return new DatasetAcquiredImagesReference(datasetCode, channelStackReference, channelCodes);
+ }
+
/** @param channelCodesOrNull null if channels should be merged */
- public DatasetAcquiredImagesReference(String datasetCode,
+ private DatasetAcquiredImagesReference(String datasetCode,
ImageChannelStackReference channelStackReference, List<String> channelCodesOrNull)
{
assert datasetCode != null;
@@ -53,14 +74,42 @@ public class DatasetAcquiredImagesReference
return channelStackReference;
}
- public boolean isMergeAllChannels()
+ /**
+ * Check if all exiting channels of the image should be merged (and not a single one or a
+ * subset). We want to treat the case where merged channels were requested in the same way as
+ * the case where all channel names have been enumerated.
+ */
+ public boolean isMergeAllChannels(List<String> allChannelsCodes)
{
- return channelCodesOrNull == null;
+ if (channelCodesOrNull == null)
+ {
+ return true;
+ }
+ List<String> wantedChannelCodes = channelCodesOrNull;
+ if (allChannelsCodes.size() == 1)
+ {
+ return false; // there is only one channel in total, single channel transformation
+ // should be used
+ }
+ for (String existingChannelCode : allChannelsCodes)
+ {
+ if (wantedChannelCodes.indexOf(existingChannelCode) == -1)
+ {
+ return false;
+ }
+ }
+ return true;
}
- public List<String> getChannelCodes()
+ public List<String> getChannelCodes(List<String> allChannelsCodes)
{
- return channelCodesOrNull;
+ if (channelCodesOrNull == null)
+ {
+ return allChannelsCodes;
+ } else
+ {
+ return channelCodesOrNull;
+ }
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageGenerationDescription.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageGenerationDescription.java
index a397574ed0609ecf3ca79797f090c25df132dde8..959b93a38a5a2b3288cd22d5651c9f6bbcc30792 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageGenerationDescription.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageGenerationDescription.java
@@ -32,6 +32,8 @@ public class ImageGenerationDescription
{
private final DatasetAcquiredImagesReference imageChannelsOrNull;
+ private final String singleChannelTransformationCodeOrNull;
+
private final List<DatasetAcquiredImagesReference> overlayChannels;
private final String sessionId;
@@ -40,10 +42,12 @@ public class ImageGenerationDescription
private final Size thumbnailSizeOrNull;
public ImageGenerationDescription(DatasetAcquiredImagesReference imageChannelsOrNull,
+ String singleChannelTransformationCodeOrNull,
List<DatasetAcquiredImagesReference> overlayChannels, String sessionId,
Size thumbnailSizeOrNull)
{
this.imageChannelsOrNull = imageChannelsOrNull;
+ this.singleChannelTransformationCodeOrNull = singleChannelTransformationCodeOrNull;
this.overlayChannels = overlayChannels;
this.sessionId = sessionId;
this.thumbnailSizeOrNull = thumbnailSizeOrNull;
@@ -54,6 +58,11 @@ public class ImageGenerationDescription
return imageChannelsOrNull;
}
+ public String tryGetSingleChannelTransformationCode()
+ {
+ return singleChannelTransformationCodeOrNull;
+ }
+
public List<DatasetAcquiredImagesReference> getOverlayChannels()
{
return overlayChannels;
@@ -116,10 +125,17 @@ public class ImageGenerationDescription
private static void appendChannels(StringBuffer sb, DatasetAcquiredImagesReference imagesRef)
{
- for (String channel : imagesRef.getChannelCodes())
+ List<String> channelCodes = imagesRef.getChannelCodes(null);
+ if (channelCodes == null)
{
- sb.append("_");
- sb.append(channel);
+ sb.append("merged");
+ } else
+ {
+ for (String channel : channelCodes)
+ {
+ sb.append("_");
+ sb.append(channel);
+ }
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageTransformationParams.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageTransformationParams.java
new file mode 100644
index 0000000000000000000000000000000000000000..2cc933d370a8cc22799fd3b348ab59022ac53555
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/dto/ImageTransformationParams.java
@@ -0,0 +1,67 @@
+/*
+ * 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.generic.server.images.dto;
+
+/**
+ * Describes which image transformations should be applied. Note that image-level transformation is
+ * always applied for single channels.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageTransformationParams
+{
+ private final boolean applyNonImageLevelTransformation;
+
+ /** ignored if {@link #applyNonImageLevelTransformation} is false */
+ private final boolean useMergedChannelsTransformation;
+
+ /**
+ * ignored if {@link #applyNonImageLevelTransformation} is false or if
+ * {@link #useMergedChannelsTransformation} is false
+ */
+ private final String singleChannelTransformationCodeOrNull;
+
+ public ImageTransformationParams(boolean applyNonImageLevelTransformation,
+ boolean useMergedChannelsTransformation, String singleChannelTransformationCodeOrNull)
+ {
+ this.applyNonImageLevelTransformation = applyNonImageLevelTransformation;
+ this.useMergedChannelsTransformation = useMergedChannelsTransformation;
+ this.singleChannelTransformationCodeOrNull = singleChannelTransformationCodeOrNull;
+ }
+
+ public boolean isApplyNonImageLevelTransformation()
+ {
+ return applyNonImageLevelTransformation;
+ }
+
+ public boolean isUseMergedChannelsTransformation()
+ {
+ return useMergedChannelsTransformation;
+ }
+
+ public String tryGetSingleChannelTransformationCode()
+ {
+ return singleChannelTransformationCodeOrNull;
+ }
+
+ public ImageTransformationParams cloneAndSetUseMergedChannelsTransformation()
+ {
+ return new ImageTransformationParams(applyNonImageLevelTransformation, true,
+ singleChannelTransformationCodeOrNull);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ColorRangeCalculator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ColorRangeCalculator.java
index 61c80b2b2e8a285ac907fc7f8507883356b7ad4d..84be648d935c31d0e63f855d24e43943c3d3a436 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ColorRangeCalculator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ColorRangeCalculator.java
@@ -153,7 +153,6 @@ public class ColorRangeCalculator
}
ReadParams params = new ReadParams();
- params.setAllow16BitGrayscaleModel(true);
return reader.readImage(file, ImageID.NULL, params);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
index 944ecccc43086bd82de0a257eb6ba16ac04d119a..4842599c0c6126be2232d309522cd66cf16be775 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java
@@ -91,7 +91,7 @@ public class DynamixWellBrightnessEqualizerProcessingPlugin extends
{
IContent content = contentRepository.getContent(image.getFilePath());
return ImageUtil.loadJavaAdvancedImagingTiff(content.getReadOnlyRandomAccessFile(),
- ImageUtil.parseImageID(image.getImageID()), true);
+ ImageUtil.parseImageID(image.getImageID()));
}
private static IImageTransformerFactoryProvider createImageTransformerFactoryProvider(
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 2ccee7a932e492e658d5f06fe922005026593e02..97716ac006063cc0ebcc5ca94158389096575970 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -28,8 +28,6 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
-import net.lemnik.eodsql.QueryTool;
-
import org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
@@ -84,10 +82,11 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoa
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingTransformerDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.TransformerFactoryMapper;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
/**
* Implementation of the screening API interface using RPC. The instance will be created in spring
@@ -104,12 +103,6 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
*/
public static final int MINOR_VERSION = 8;
-
- static
- {
- QueryTool.getTypeMap().put(IImageTransformerFactory.class, new TransformerFactoryMapper());
- }
-
// this dao will hold one connection to the database
private IImagingReadonlyQueryDAO dao;
@@ -282,7 +275,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
imageAccessor.tryGetRepresentativeImage(channelCode, null, originalOrThumbnail);
if (image != null)
{
- return image.getImage();
+ return image.getUnchangedImage();
}
}
throw new IllegalStateException("Cannot find any image in a dataset: " + dataset);
@@ -298,7 +291,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
imageAccessor.tryGetRepresentativeThumbnail(channelCode, null);
if (image != null)
{
- return image.getImage();
+ return image.getUnchangedImage();
}
}
return null;
@@ -319,7 +312,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
col, row));
if (image != null)
{
- return image.getImage();
+ return image.getUnchangedImage();
}
}
}
@@ -343,7 +336,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
row), originalOrThumbnail);
if (image != null)
{
- return image.getImage();
+ return image.getUnchangedImage();
}
}
}
@@ -461,13 +454,13 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
boolean convertToPng)
{
- return loadImages(sessionToken, imageReferences, null, convertToPng);
+ return loadImages(sessionToken, imageReferences, null, null, convertToPng);
}
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
ImageSize thumbnailSizeOrNull)
{
- return loadImages(sessionToken, imageReferences, tryAsSize(thumbnailSizeOrNull), true);
+ return loadImages(sessionToken, imageReferences, tryAsSize(thumbnailSizeOrNull), null, true);
}
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
@@ -476,20 +469,24 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
final Map<String, IImagingDatasetLoader> imageLoadersMap =
getImageDatasetsMap(sessionToken, imageReferences);
return loadImages(imageReferences, tryAsSize(configuration.getDesiredImageSize()),
+ configuration.getSingleChannelImageTransformationCode(),
configuration.isDesiredImageFormatPng(),
configuration.isOpenBisImageTransformationApplied(), imageLoadersMap);
}
private InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences,
- final Size sizeOrNull, final boolean convertToPng)
+ final Size sizeOrNull, String singleChannelImageTransformationCodeOrNull,
+ final boolean convertToPng)
{
final Map<String, IImagingDatasetLoader> imageLoadersMap =
getImageDatasetsMap(sessionToken, imageReferences);
- return loadImages(imageReferences, sizeOrNull, convertToPng, false, imageLoadersMap);
+ return loadImages(imageReferences, sizeOrNull, singleChannelImageTransformationCodeOrNull,
+ convertToPng, false, imageLoadersMap);
}
private InputStream loadImages(List<PlateImageReference> imageReferences,
- final Size sizeOrNull, final boolean convertToPng, final boolean transform,
+ final Size sizeOrNull, final String singleChannelImageTransformationCodeOrNull,
+ final boolean convertToPng, final boolean transform,
final Map<String, IImagingDatasetLoader> imageLoadersMap)
{
final List<IContent> imageContents = new ArrayList<IContent>();
@@ -508,7 +505,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
public IContent getContent()
{
return tryGetImageContent(imageAccessor, channelStackRef, channelCode,
- sizeOrNull, convertToPng, transform);
+ sizeOrNull, singleChannelImageTransformationCodeOrNull,
+ convertToPng, transform);
}
}));
}
@@ -558,7 +556,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
new HashMap<String, IImagingDatasetLoader>();
imageLoadersMap.put(dataSetIdentifier.getDatasetCode(), imageAccessor);
- return loadImages(imageReferences, size, true, false, imageLoadersMap);
+ return loadImages(imageReferences, size, null, true, false, imageLoadersMap);
}
public InputStream loadThumbnailImages(String sessionToken,
@@ -590,7 +588,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
public IContent getContent()
{
return tryGetImageContent(imageAccessor, channelStackRef, channelCode,
- sizeOrNull, true, false);
+ sizeOrNull, null, true, false);
}
}));
}
@@ -720,6 +718,13 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
return ScreeningConstants.MERGED_CHANNELS.equals(channel);
}
+ static final String IMAGE_VIEWER_TRANSFORMATION_CODE = "_CUSTOM";
+
+ private static final String IMAGE_VIEWER_TRANSFORMATION_LABEL = "Custom";
+
+ private static final String IMAGE_VIEWER_TRANSFORMATION_DESCRIPTION =
+ "Custom image transformation defined with the Color Adjustment tool.";
+
private void saveImageTransformerFactoryForExperiment(long experimentId, String channel,
IImageTransformerFactory transformerFactory)
{
@@ -738,11 +743,36 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
operationLog.info("save image transformer factory " + transformerFactory
+ " for experiment " + experimentId + " and channel '" + channel + "'.");
}
- transformerDAO.saveTransformerFactoryForExperimentChannel(experimentId, channel,
- transformerFactory);
+ Long channelId = transformerDAO.getExperimentChannelId(experimentId, channel);
+ createOrUpdateImageViewerTransformation(channelId, transformerFactory);
+ }
+ }
+
+ private void createOrUpdateImageViewerTransformation(long channelId,
+ IImageTransformerFactory transformerFactory)
+ {
+ Long transformationIdOrNull =
+ transformerDAO.tryGetImageTransformationId(channelId,
+ IMAGE_VIEWER_TRANSFORMATION_CODE);
+ if (transformationIdOrNull == null)
+ {
+ transformerDAO.addImageTransformation(createImageViewerTransformation(channelId,
+ transformerFactory));
+ } else
+ {
+ transformerDAO
+ .updateImageTransformerFactory(transformationIdOrNull, transformerFactory);
}
}
+ private ImgImageTransformationDTO createImageViewerTransformation(long channelId,
+ IImageTransformerFactory transformerFactory)
+ {
+ return new ImgImageTransformationDTO(IMAGE_VIEWER_TRANSFORMATION_CODE,
+ IMAGE_VIEWER_TRANSFORMATION_LABEL, IMAGE_VIEWER_TRANSFORMATION_DESCRIPTION, true,
+ channelId, transformerFactory);
+ }
+
private void saveImageTransformerFactoryForDataset(long datasetId, String channel,
IImageTransformerFactory transformerFactory)
{
@@ -761,8 +791,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
operationLog.info("save image transformer factory " + transformerFactory
+ " for dataset " + datasetId + " and channel '" + channel + "'.");
}
- transformerDAO.saveTransformerFactoryForDatasetChannel(datasetId, channel,
- transformerFactory);
+ long channelId = transformerDAO.getDatasetChannelId(datasetId, channel);
+ createOrUpdateImageViewerTransformation(channelId, transformerFactory);
}
}
@@ -818,11 +848,22 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
return dataset.tryGetImageTransformerFactory();
} else
{
- return getDAO().tryGetChannelForDataset(dataset.getId(), channel)
- .tryGetImageTransformerFactory();
+ long channelId = getDAO().getDatasetChannelId(dataset.getId(), channel);
+ return tryGetImageViewerTransformation(channelId);
}
}
+ private IImageTransformerFactory tryGetImageViewerTransformation(long channelId)
+ {
+ ImgImageTransformationDTO transformation =
+ getDAO().tryGetImageTransformation(channelId, IMAGE_VIEWER_TRANSFORMATION_CODE);
+ if (transformation == null)
+ {
+ return null;
+ }
+ return transformation.getImageTransformerFactory();
+ }
+
private IImageTransformerFactory tryGetImageTransformerFactoryForExperiment(
String experimentPermID, String channel)
{
@@ -832,8 +873,11 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
.tryGetImageTransformerFactory();
} else
{
- return getDAO().tryGetChannelForExperimentPermId(experimentPermID, channel)
- .tryGetImageTransformerFactory();
+ ImgChannelDTO channelDTO =
+ getDAO().tryGetChannelForExperimentPermId(experimentPermID, channel);
+ assert channelDTO != null : String.format("No channel '%s' for experiment '%s'.",
+ channel, experimentPermID);
+ return tryGetImageViewerTransformation(channelDTO.getId());
}
}
@@ -982,12 +1026,14 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
private IContent tryGetImageContent(IImagingDatasetLoader imageAccessor,
final ImageChannelStackReference channelStackReference, String channelCode,
- Size thumbnailSizeOrNull, boolean convertToPng, boolean transform)
+ Size thumbnailSizeOrNull, String singleChannelImageTransformationCodeOrNull,
+ boolean convertToPng, boolean transform)
{
try
{
return ImageChannelsUtils.getImage(imageAccessor, channelStackReference, channelCode,
- thumbnailSizeOrNull, convertToPng, transform);
+ thumbnailSizeOrNull, singleChannelImageTransformationCodeOrNull, convertToPng,
+ transform);
} catch (EnvironmentFailureException e)
{
operationLog.error("Error reading image.", e);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/LoadImageConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/LoadImageConfiguration.java
index 769f472d0354472d75cfc5dab0c2b06740e31d8d..e27b7078e43058421c1c11cd23d58cd230a42558 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/LoadImageConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/LoadImageConfiguration.java
@@ -43,6 +43,8 @@ public class LoadImageConfiguration implements Serializable
private boolean openBisImageTransformationApplied = false;
+ private String singleChannelImageTransformationCodeOrNull = null;
+
/**
* The desired size of the image. Null if the original size is requested.
* <p>
@@ -93,7 +95,8 @@ public class LoadImageConfiguration implements Serializable
}
/**
- * Should the image transformation stored in openBIS be applied to the image?
+ * Should the image transformation stored in openBIS for a channel or merged channel be applied
+ * to the image?
*
* @return True if the image transformation should be applied; false if the original image
* should be returned.
@@ -104,7 +107,8 @@ public class LoadImageConfiguration implements Serializable
}
/**
- * Set whether the image transformation stored in openBIS should be applied.
+ * Set whether the image transformation stored in openBIS for a channel or merged channel should
+ * be applied.
*
* @param openBisImageTransformationApplied Pass in true if the transformation should be
* applied; false otherwise.
@@ -112,6 +116,34 @@ public class LoadImageConfiguration implements Serializable
public void setOpenBisImageTransformationApplied(boolean openBisImageTransformationApplied)
{
this.openBisImageTransformationApplied = openBisImageTransformationApplied;
+ if (openBisImageTransformationApplied && getSingleChannelImageTransformationCode() == null)
+ {
+ // for backward compatibility - apply Color Adjustment tool transformation
+ setSingleChannelImageTransformationCode("_CUSTOM");
+ }
+ }
+
+ /** Code of the transformation, which should be applied to the image. Can return null. */
+ public String getSingleChannelImageTransformationCode()
+ {
+ return singleChannelImageTransformationCodeOrNull;
+ }
+
+ /**
+ * Sets the code of the transformation, which should be applied to the image. This parameter
+ * will be ignored if {@link #isOpenBisImageTransformationApplied()} is false. To keep backward
+ * compatibility if {@link #isOpenBisImageTransformationApplied()} is true and no image
+ * transformation code is specified, then the transformation defined by the Color Adjustment
+ * tool will be applied.
+ * <p>
+ * Transformation has to be assigned (usually during dataset registration) to the channel which
+ * will be fetched. Note that such transformations can be channel-specific. If merged channels
+ * image will be requested or the transformation does not exist then untransformed image will be
+ * returned.
+ */
+ public void setSingleChannelImageTransformationCode(String transformationCodeOrNull)
+ {
+ this.singleChannelImageTransformationCodeOrNull = transformationCodeOrNull;
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
index 20e40fac3e176e2c354f02a7a813abc1db403637..97f2e0987e4b4b78d22099c434a757f555f0f3ff 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
@@ -20,10 +20,12 @@ import javax.sql.DataSource;
import net.lemnik.eodsql.QueryTool;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingTransformerDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.TransformerFactoryMapper;
/**
* Utility methods for DSS.
@@ -34,6 +36,11 @@ public class DssScreeningUtils
{
private static final IImagingReadonlyQueryDAO query = createQuery();
+ static
+ {
+ QueryTool.getTypeMap().put(IImageTransformerFactory.class, new TransformerFactoryMapper());
+ }
+
/**
* Returned query is reused and should NOT be closed.
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ExampleImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ExampleImageTransformerFactory.java
index 57253aea57ee33f622af4b9503a1ab7c4e72fc4a..4812ae65a19a6fd1c99d59c8c8d3df0141e4a42c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ExampleImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ExampleImageTransformerFactory.java
@@ -116,4 +116,35 @@ public class ExampleImageTransformerFactory implements IImageTransformerFactory
return getClass().getSimpleName() + "[" + colorPattern + "]";
}
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + brightnessDelta;
+ result = prime * result + ((colorPattern == null) ? 0 : colorPattern.hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ ExampleImageTransformerFactory other = (ExampleImageTransformerFactory) obj;
+ if (brightnessDelta != other.brightnessDelta)
+ return false;
+ if (colorPattern == null)
+ {
+ if (other.colorPattern != null)
+ return false;
+ } else if (!colorPattern.equals(other.colorPattern))
+ return false;
+ return true;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageReference.java
index 51115c7aab861bce9c99e6fda20a07252c3777c0..2bed12ee1400b19e6a3e22aeffe29b5d34b16975 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageReference.java
@@ -124,9 +124,11 @@ public class LogicalImageReference
return datastoreCode;
}
- public String getTransformerFactorySignatureOrNull(String channelCode)
+ public String tryGetTransformerFactorySignature(String channelCodeOrNull,
+ String transformationCode)
{
- return imageParameters.getTransformerFactorySignatureOrNull(channelCode);
+ return imageParameters.tryGetTransformerFactorySignature(channelCodeOrNull,
+ transformationCode);
}
public List<DatasetOverlayImagesReference> getOverlayDatasets()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/utils/ImageUrlUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/utils/ImageUrlUtils.java
index 529dc03ff109a24faddcbf1117c68cf1c704a174..91534478d3f5e17bcd6f547227517f17f5df229c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/utils/ImageUrlUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/utils/ImageUrlUtils.java
@@ -146,6 +146,12 @@ public class ImageUrlUtils
}
methodWithParameters.addParameter(ImageServletUrlParameters.TILE_ROW_PARAM, tileRow);
methodWithParameters.addParameter(ImageServletUrlParameters.TILE_COL_PARAM, tileCol);
+ if (channelReferences.tryGetImageTransformationCode() != null)
+ {
+ methodWithParameters.addParameter(
+ ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM,
+ channelReferences.tryGetImageTransformationCode());
+ }
addImageTransformerSignature(methodWithParameters, channelReferences);
String linkURLOrNull = createImageLinks ? methodWithParameters.toString() : null;
addThumbnailSize(methodWithParameters, width, height);
@@ -170,7 +176,14 @@ public class ImageUrlUtils
{
for (String channel : channels)
{
- String signature = images.getTransformerFactorySignatureOrNull(channel);
+ String channelOrNull = channel;
+ if (channelOrNull.equalsIgnoreCase(ScreeningConstants.MERGED_CHANNELS))
+ {
+ channelOrNull = null;
+ }
+ String signature =
+ images.tryGetTransformerFactorySignature(channelOrNull,
+ channelReferences.tryGetImageTransformationCode());
if (signature != null)
{
url.addParameter("transformerFactorySignature", signature);
@@ -203,7 +216,6 @@ public class ImageUrlUtils
methodWithParameters.addParameter(ImageServletUrlParameters.CHANNEL_PARAM, channel);
}
}
-
addOverlayParameters(channelReferences.getOverlayChannels(), methodWithParameters);
return methodWithParameters;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java
index e526f08518bae9d72dfd27492829742df86ab783..c3fd5d26526a66cc195801196bc392a859a145d3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
-import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
@@ -51,9 +50,9 @@ public class ImageChannel implements ISerializable
{
}
- // FIXME add List<ImageTransformationInfo> availableImageTransformations param
public ImageChannel(String code, String label, String description, Integer wavelength,
- ImageChannelColor channelColor)
+ ImageChannelColor channelColor,
+ List<ImageTransformationInfo> availableImageTransformations)
{
assert code != null;
// assert availableImageTransformations != null;
@@ -63,7 +62,7 @@ public class ImageChannel implements ISerializable
this.description = description;
this.wavelength = wavelength;
this.channelColor = channelColor;
- this.availableImageTransformations = new ArrayList<ImageTransformationInfo>();
+ this.availableImageTransformations = availableImageTransformations;
}
public String getCode()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
index c98e9a0bbaad8a61dc5ae1ad57484fe832ffa0ad..c00644bd8a0c0d420f465e8e2a50f2b0efd50ef9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
@@ -17,9 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
@@ -47,12 +45,11 @@ public class ImageDatasetParameters implements ISerializable
private List<ImageChannel> channels;
- private Map<String/* channel code */, String/* signature */> channelsTransformerFactorySignatures =
- new HashMap<String, String>();
-
// true if any well in the dataset has a time series (or depth stack) of images
private boolean isMultidimensional;
+ private String mergedChannelTransformerFactorySignatureOrNull;
+
public Integer tryGetRowsNum()
{
return rowsNumOrNull;
@@ -161,13 +158,39 @@ public class ImageDatasetParameters implements ISerializable
return channels;
}
- public void addTransformerFactorySignatureFor(String channelCode, String signatureOrNull)
+ /**
+ * @param channelCodeOrNull null for merged channels (transformationCode is ignored in that
+ * case)
+ */
+ public String tryGetTransformerFactorySignature(String channelCodeOrNull,
+ String transformationCode)
+ {
+ if (channelCodeOrNull == null)
+ {
+ return mergedChannelTransformerFactorySignatureOrNull;
+ }
+ List<ImageTransformationInfo> transformations =
+ getAvailableImageTransformationsFor(channelCodeOrNull);
+ for (ImageTransformationInfo transformation : transformations)
+ {
+ if (transformation.getCode().equalsIgnoreCase(transformationCode))
+ {
+ return transformation.getTransformationSignature();
+ }
+ }
+ return null;
+ }
+
+ public String tryGetMergedChannelTransformerFactorySignature()
{
- channelsTransformerFactorySignatures.put(channelCode, signatureOrNull);
+ return mergedChannelTransformerFactorySignatureOrNull;
}
- public String getTransformerFactorySignatureOrNull(String channelCode)
+ public void setMergedChannelTransformerFactorySignature(
+ String mergedChannelTransformerFactorySignatureOrNull)
{
- return channelsTransformerFactorySignatures.get(channelCode);
+ this.mergedChannelTransformerFactorySignatureOrNull =
+ mergedChannelTransformerFactorySignatureOrNull;
}
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageTransformationInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageTransformationInfo.java
index 625c47e1006d3fb53a407ed3dfa07ee850a4daa5..f1a4e3a326ea68d7f378d3fee2d2d19e7ed85dfe 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageTransformationInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageTransformationInfo.java
@@ -35,6 +35,8 @@ public class ImageTransformationInfo implements ISerializable
// can be null
private String description;
+ private String transformationSignature;
+
private boolean isDefault;
// GWT only
@@ -43,7 +45,8 @@ public class ImageTransformationInfo implements ISerializable
{
}
- public ImageTransformationInfo(String code, String label, String description, boolean isDefault)
+ public ImageTransformationInfo(String code, String label, String description,
+ String transformationSignature, boolean isDefault)
{
assert code != null : "code is null";
assert label != null : " label is null";
@@ -51,6 +54,7 @@ public class ImageTransformationInfo implements ISerializable
this.code = code;
this.label = label;
this.description = description;
+ this.transformationSignature = transformationSignature;
this.isDefault = isDefault;
}
@@ -69,8 +73,18 @@ public class ImageTransformationInfo implements ISerializable
return description;
}
+ public String getTransformationSignature()
+ {
+ return transformationSignature;
+ }
+
public boolean isDefault()
{
return isDefault;
}
+
+ public void setDefault(boolean isDefault)
+ {
+ this.isDefault = isDefault;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
index b404115ca6df2a288f1bb0e1abbadde5cd42d26c..4cbe2e1c84db7e45d23cccff0e42059d603d3c7d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
@@ -178,6 +178,8 @@ public class ScreeningConstants
public final static String WELL_COLUMN_PARAM = "wellCol";
+ public final static String SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM = "transformation";
+
// -- mandatory servlet parameters
public final static String DATASET_CODE_PARAM = "dataset";
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
index a127fd776492d681289777686c9e27e2da04c440..a3ec275036596569e74bb46521a87ce339c36e44 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
@@ -18,13 +18,17 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
+import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.utilities.MD5ChecksumCalculator;
+import ch.systemsx.cisd.openbis.generic.shared.basic.utils.GroupByMap;
+import ch.systemsx.cisd.openbis.generic.shared.basic.utils.IGroupKeyExtractor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStack;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageTransformationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
@@ -32,6 +36,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgCh
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
/**
* Helper class for easy handling of HCS image dataset standard structure with no code for handling
@@ -46,8 +51,6 @@ public class HCSDatasetLoader implements IImageDatasetLoader
protected final ImgDatasetDTO dataset;
- private final String mergedChannelTransformerFactorySignatureOrNull;
-
protected ImgContainerDTO containerOrNull;
protected ImgExperimentDTO experimentOrNull;
@@ -56,6 +59,10 @@ public class HCSDatasetLoader implements IImageDatasetLoader
protected List<ImgChannelDTO> channels;
+ protected Map<Long/* channel id */, List<ImgImageTransformationDTO>> availableImageTransformationsMap;
+
+ private final String mergedChannelTransformerFactorySignatureOrNull;
+
public HCSDatasetLoader(IImagingReadonlyQueryDAO query, String datasetPermId)
{
this.query = query;
@@ -80,6 +87,26 @@ public class HCSDatasetLoader implements IImageDatasetLoader
this.mergedChannelTransformerFactorySignatureOrNull =
tryGetImageTransformerFactorySignatureForMergedChannels();
this.channels = loadChannels();
+ this.availableImageTransformationsMap = loadAvailableImageTransformations();
+ }
+
+ private Map<Long, List<ImgImageTransformationDTO>> loadAvailableImageTransformations()
+ {
+ List<ImgImageTransformationDTO> imageTransformations =
+ query.listImageTransformationsByDatasetId(dataset.getId());
+ if (imageTransformations.size() == 0 && containerOrNull != null)
+ {
+ imageTransformations =
+ query.listImageTransformationsByExperimentId(containerOrNull.getExperimentId());
+ }
+ return GroupByMap.create(imageTransformations,
+ new IGroupKeyExtractor<Long, ImgImageTransformationDTO>()
+ {
+ public Long getKey(ImgImageTransformationDTO transformation)
+ {
+ return transformation.getChannelId();
+ }
+ }).getMap();
}
private List<ImgChannelDTO> loadChannels()
@@ -160,32 +187,69 @@ public class HCSDatasetLoader implements IImageDatasetLoader
params.setTileRowsNum(getDataset().getFieldNumberOfRows());
params.setTileColsNum(getDataset().getFieldNumberOfColumns());
params.setIsMultidimensional(dataset.getIsMultidimensional());
- params.addTransformerFactorySignatureFor(ScreeningConstants.MERGED_CHANNELS,
- mergedChannelTransformerFactorySignatureOrNull);
+ params.setMergedChannelTransformerFactorySignature(mergedChannelTransformerFactorySignatureOrNull);
+ params.setChannels(convertChannels());
+ return params;
+ }
+ private List<ImageChannel> convertChannels()
+ {
List<ImageChannel> convertedChannels = new ArrayList<ImageChannel>();
for (ImgChannelDTO channelDTO : channels)
{
ImageChannel channel = convert(channelDTO);
convertedChannels.add(channel);
-
- String transformationSignature =
- tryGetSignature(channelDTO.getSerializedImageTransformerFactory());
- params.addTransformerFactorySignatureFor(channelDTO.getCode(), transformationSignature);
}
- params.setChannels(convertedChannels);
- return params;
+ return convertedChannels;
}
- private static ImageChannel convert(ImgChannelDTO channelDTO)
+ private ImageChannel convert(ImgChannelDTO channelDTO)
{
ImageChannelColor imageChannelColor =
ImageChannelColor.valueOf(channelDTO.getDbChannelColor());
+ List<ImageTransformationInfo> availableImageTransformations =
+ convertTransformations(availableImageTransformationsMap.get(channelDTO.getId()));
return new ImageChannel(channelDTO.getCode(), channelDTO.getLabel(),
- channelDTO.getDescription(), channelDTO.getWavelength(), imageChannelColor);
+ channelDTO.getDescription(), channelDTO.getWavelength(), imageChannelColor,
+ availableImageTransformations);
+ }
+
+ private static List<ImageTransformationInfo> convertTransformations(
+ List<ImgImageTransformationDTO> transformationsOrNull)
+ {
+ if (transformationsOrNull == null)
+ {
+ return new ArrayList<ImageTransformationInfo>();
+ } else
+ {
+ List<ImageTransformationInfo> transformations =
+ CollectionUtils
+ .map(transformationsOrNull,
+ new CollectionUtils.ICollectionMappingFunction<ImageTransformationInfo, ImgImageTransformationDTO>()
+ {
+ public ImageTransformationInfo map(
+ ImgImageTransformationDTO transformation)
+ {
+ return convert(transformation);
+ }
+ });
+ if (transformations.size() > 0)
+ {
+ transformations.get(0).setDefault(true);
+ }
+ return transformations;
+ }
+ }
+
+ private static ImageTransformationInfo convert(ImgImageTransformationDTO transformation)
+ {
+ String transformationSignature =
+ tryGetSignature(transformation.getSerializedImageTransformerFactory());
+ return new ImageTransformationInfo(transformation.getCode(), transformation.getLabel(),
+ transformation.getDescription(), transformationSignature, false);
}
- private String tryGetSignature(byte[] bytesOrNull)
+ private static String tryGetSignature(byte[] bytesOrNull)
{
if (bytesOrNull == null)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
index 0f5fba7ee47f7877b185139eaffbfd9e122a8ac7..4501533d29ece9e23011bb60975f1bec2d10e99f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
@@ -176,16 +176,6 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
+ "where cs.ds_id = ?{1} and cs.spot_id is NULL")
public List<ImgChannelStackDTO> listSpotlessChannelStacks(long datasetId);
- @Select("select * from CHANNELS where DS_ID = ?{1} order by ID")
- public List<ImgChannelDTO> getChannelsByDatasetId(long datasetId);
-
- @Select("select * from CHANNELS where (DS_ID = ?{1}) and CODE = upper(?{2})")
- public ImgChannelDTO tryGetChannelForDataset(long datasetId, String chosenChannelCode);
-
- @Select("select count(*) > 0 from CHANNELS ch "
- + "join DATA_SETS d on ch.ds_id = d.id where d.PERM_ID = ?{1}")
- public boolean hasDatasetChannels(String datasetPermId);
-
// ---------------- Generic ---------------------------------
/** @return an image for the specified channel and channel stack or null */
@@ -221,7 +211,58 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
{ StringArrayMapper.class }, fetchSize = FETCH_SIZE)
public List<ImgDatasetDTO> listDatasetsByPermId(String... datasetPermIds);
- // ---------------- HCS - experiments, containers, channels ---------------------------------
+ // ------------ dataset and experiment channels
+
+ @Select("select * from CHANNELS where DS_ID = ?{1} order by ID")
+ public List<ImgChannelDTO> getChannelsByDatasetId(long datasetId);
+
+ @Select(sql = "select * from CHANNELS where EXP_ID = ?{1} order by ID", fetchSize = FETCH_SIZE)
+ public List<ImgChannelDTO> getChannelsByExperimentId(long experimentId);
+
+ @Select("select * from CHANNELS where (DS_ID = ?{1}) and CODE = upper(?{2})")
+ public ImgChannelDTO tryGetChannelForDataset(long datasetId, String channelCode);
+
+ @Select("select * from CHANNELS where (EXP_ID = ?{1}) and CODE = upper(?{2})")
+ public ImgChannelDTO tryGetChannelForExperiment(long experimentId, String channelCode);
+
+ @Select("select id from channels where ds_id = ?{1} and code = upper(?{2})")
+ public long getDatasetChannelId(long datasetId, String channelCode);
+
+ @Select("select id from channels where exp_id = ?{1} and code = upper(?{2})")
+ public long getExperimentChannelId(long experimentId, String channelCode);
+
+ @Select("select count(*) > 0 from CHANNELS ch "
+ + "join DATA_SETS d on ch.ds_id = d.id where d.PERM_ID = ?{1}")
+ public boolean hasDatasetChannels(String datasetPermId);
+
+ @Select("select * from channels where code = ?{2} and "
+ + "exp_id in (select id from experiments where perm_id = ?{1})")
+ public ImgChannelDTO tryGetChannelForExperimentPermId(String experimentPermId,
+ String channelCode);
+
+ // ----------- image transformations
+
+ @Select("select * from IMAGE_TRANSFORMATIONS tr where tr.channel_id = ?{1} order by tr.ID")
+ public List<ImgImageTransformationDTO> listImageTransformations(long channelId);
+
+ @Select("select id from image_transformations where channel_id = ?{1} and code = ?{2}")
+ public Long tryGetImageTransformationId(long channelId, String transformationCode);
+
+ @Select("select * from image_transformations where channel_id = ?{1} and code = ?{2}")
+ public ImgImageTransformationDTO tryGetImageTransformation(long channelId,
+ String transformationCode);
+
+ @Select("select tr.* from IMAGE_TRANSFORMATIONS tr "
+ + " join channels ch on tr.channel_id = ch.id "
+ + " where ch.ds_id = ?{1} order by tr.ID ")
+ public List<ImgImageTransformationDTO> listImageTransformationsByDatasetId(long datasetId);
+
+ @Select("select tr.* from IMAGE_TRANSFORMATIONS tr "
+ + " join channels ch on tr.channel_id = ch.id "
+ + " where ch.exp_id = ?{1} order by tr.ID ")
+ public List<ImgImageTransformationDTO> listImageTransformationsByExperimentId(long experimentId);
+
+ // ---------------- HCS - experiments, containers ---------------------------------
@Select("select * from EXPERIMENTS where PERM_ID = ?{1}")
public ImgExperimentDTO tryGetExperimentByPermId(String experimentPermId);
@@ -246,20 +287,9 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
+ "where cs.ds_id = ?{1} and s.x = ?{2} and s.y = ?{3}")
public List<ImgChannelStackDTO> listChannelStacks(long datasetId, int spotX, int spotY);
- @Select(sql = "select * from CHANNELS where EXP_ID = ?{1} order by ID", fetchSize = FETCH_SIZE)
- public List<ImgChannelDTO> getChannelsByExperimentId(long experimentId);
-
@Select("select * from SPOTS where cont_id = ?{1}")
public List<ImgSpotDTO> listSpots(long contId);
- @Select("select * from CHANNELS where (EXP_ID = ?{1}) and CODE = upper(?{2})")
- public ImgChannelDTO tryGetChannelForExperiment(long experimentId, String chosenChannelCode);
-
- @Select("select * from channels where code = ?{2} and "
- + "exp_id in (select id from experiments where perm_id = ?{1})")
- public ImgChannelDTO tryGetChannelForExperimentPermId(String experimentPermId,
- String chosenChannelCode);
-
// ---------------- HCS - feature vectors ---------------------------------
@Select(sql = "select * from FEATURE_DEFS where DS_ID = any(?{1})", parameterBindings =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java
index c9c45d9061666f7b934565fa8b501bb3c489789f..b30820274d76712a969eeeb530481175d194a3ca 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingTransformerDAO.java
@@ -23,9 +23,11 @@ import net.lemnik.eodsql.Update;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
/**
+ * Write operations on {@link IImageTransformerFactory} + all inherited read operations.
+ *
* @author Franz-Josef Elmer
*/
-public interface IImagingTransformerDAO extends TransactionQuery
+public interface IImagingTransformerDAO extends TransactionQuery, IImagingReadonlyQueryDAO
{
@Update(sql = "update experiments set image_transformer_factory = ?{2} where id = ?{1}", parameterBindings =
{ TransformerFactoryMapper.class, TypeMapper.class /* default */})
@@ -41,16 +43,12 @@ public interface IImagingTransformerDAO extends TransactionQuery
public void saveTransformerFactoryForImage(long acquiredImageId,
IImageTransformerFactory factory);
- @Update(sql = "update channels set image_transformer_factory = ?{3} "
- + "where code = ?{2} and exp_id = ?{1}", parameterBindings =
- { TransformerFactoryMapper.class, TypeMapper.class/* default */, TypeMapper.class /* default */})
- public void saveTransformerFactoryForExperimentChannel(long experimentId, String channel,
- IImageTransformerFactory factory);
+ @Update(sql = "insert into IMAGE_TRANSFORMATIONS(CODE, LABEL, DESCRIPTION, IMAGE_TRANSFORMER_FACTORY, IS_EDITABLE, CHANNEL_ID) values "
+ + "(?{1.code}, ?{1.label}, ?{1.description}, ?{1.serializedImageTransformerFactory}, ?{1.isEditable}, ?{1.channelId})")
+ public void addImageTransformation(ImgImageTransformationDTO imageTransformation);
- @Update(sql = "update channels set image_transformer_factory = ?{3} "
- + "where code = ?{2} and ds_id = ?{1}", parameterBindings =
- { TransformerFactoryMapper.class, TypeMapper.class/* default */, TypeMapper.class /* default */})
- public void saveTransformerFactoryForDatasetChannel(long datasetId, String channel,
+ @Update(sql = "update IMAGE_TRANSFORMATIONS set IMAGE_TRANSFORMER_FACTORY = ?{2} where id = ?{1}", parameterBindings =
+ { TransformerFactoryMapper.class, TypeMapper.class /* default */})
+ public void updateImageTransformerFactory(long imageTransformationId,
IImageTransformerFactory factory);
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
index ff2d9e6a57acf257e03c773daca8f9166cbd31ee..1c30c8fba51c8bbfc857e28eb89fe50db7c98069 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
@@ -24,7 +24,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelCo
/**
* @author Tomasz Pylak
*/
-public class ImgChannelDTO extends AbstractImageTransformerFactoryHolder
+public class ImgChannelDTO extends AbstractImgIdentifiable
{
@ResultColumn("CODE")
private String code;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageTransformationDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageTransformationDTO.java
new file mode 100644
index 0000000000000000000000000000000000000000..c609382d9c6b50fe005fe37c8852fd3083c7db00
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageTransformationDTO.java
@@ -0,0 +1,124 @@
+/*
+ * 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.plugin.screening.shared.imaging.dataaccess;
+
+import net.lemnik.eodsql.ResultColumn;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class ImgImageTransformationDTO extends AbstractImageTransformerFactoryHolder
+{
+ @ResultColumn("CODE")
+ private String code;
+
+ @ResultColumn("LABEL")
+ private String label;
+
+ @ResultColumn("DESCRIPTION")
+ private String descriptionOrNull;
+
+ @ResultColumn("IS_EDITABLE")
+ private boolean isEditable;
+
+ @ResultColumn("CHANNEL_ID")
+ private long channelId;
+
+ // EODSQL only
+ @SuppressWarnings("unused")
+ private ImgImageTransformationDTO()
+ {
+ // All Data-Object classes must have a default constructor.
+ }
+
+ public ImgImageTransformationDTO(String code, String label, String descriptionOrNull,
+ boolean isEditable, long channelId, IImageTransformerFactory imageTransformationFactory)
+ {
+ assert code != null : "code is null";
+ assert label != null : "label is null";
+ assert imageTransformationFactory != null : "transformationFactory is null";
+
+ this.code = CodeNormalizer.normalize(code);
+ this.label = label;
+ this.descriptionOrNull = descriptionOrNull;
+ this.isEditable = isEditable;
+ this.channelId = channelId;
+ setImageTransformerFactory(imageTransformationFactory);
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ public String getLabel()
+ {
+ return label;
+ }
+
+ public void setLabel(String label)
+ {
+ this.label = label;
+ }
+
+ /** Can be null. */
+ public String getDescription()
+ {
+ return descriptionOrNull;
+ }
+
+ public void setDescription(String descriptionOrNull)
+ {
+ this.descriptionOrNull = descriptionOrNull;
+ }
+
+ public boolean getIsEditable()
+ {
+ return isEditable;
+ }
+
+ public void setEditable(boolean isEditable)
+ {
+ this.isEditable = isEditable;
+ }
+
+ public long getChannelId()
+ {
+ return channelId;
+ }
+
+ public void setChannelId(long channelId)
+ {
+ this.channelId = channelId;
+ }
+
+ public final IImageTransformerFactory getImageTransformerFactory()
+ {
+ IImageTransformerFactory factory = super.tryGetImageTransformerFactory();
+ assert factory != null : "image factory is null";
+ return factory;
+ }
+
+}
diff --git a/screening/source/sql/imaging/postgresql/014/schema-014.sql b/screening/source/sql/imaging/postgresql/014/schema-014.sql
index 7b2517dd8b987a20d7c7658c90d7625199099e66..cb225d7d6cfefde5f37664d2172e7ba5ecedbc10 100644
--- a/screening/source/sql/imaging/postgresql/014/schema-014.sql
+++ b/screening/source/sql/imaging/postgresql/014/schema-014.sql
@@ -121,7 +121,7 @@ CREATE TABLE IMAGE_TRANSFORMATIONS (
CODE NAME NOT NULL,
LABEL NAME NOT NULL,
- DESCRIPTION DESCRIPTION,
+ DESCRIPTION character varying(1000),
IS_EDITABLE BOOLEAN_CHAR NOT NULL,
IMAGE_TRANSFORMER_FACTORY BYTEA NOT NULL,
diff --git a/screening/source/sql/imaging/postgresql/migration/migration-013-014.sql b/screening/source/sql/imaging/postgresql/migration/migration-013-014.sql
index 10d6b0ec12d22d3ef5c1aff5130a8db3d716b809..c15735ca9590e265c5e88ee60ca59f546a797d62 100644
--- a/screening/source/sql/imaging/postgresql/migration/migration-013-014.sql
+++ b/screening/source/sql/imaging/postgresql/migration/migration-013-014.sql
@@ -5,7 +5,7 @@ CREATE TABLE IMAGE_TRANSFORMATIONS (
CODE NAME NOT NULL,
LABEL NAME NOT NULL,
- DESCRIPTION DESCRIPTION,
+ DESCRIPTION character varying(1000),
IS_EDITABLE BOOLEAN_CHAR NOT NULL,
IMAGE_TRANSFORMER_FACTORY BYTEA NOT NULL,
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
index 37894657d9a7e940b00496ac6bcc93e327f00507..96bf69b4bbbea838e2b2cefb5c3e111e72ec24e7 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
@@ -30,7 +30,10 @@ import net.lemnik.eodsql.QueryTool;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.AbstractDBTest;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
@@ -41,6 +44,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgCo
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageEnrichedDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSpotDTO;
/**
@@ -53,6 +57,14 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSp
public class ImagingQueryDAOTest extends AbstractDBTest
{
+ private static final boolean IMAGE_TRANSFORMATION_IS_EDITABLE = false;
+
+ private static final String IMAGE_TRANSFORMATION_DESC = "tr_desc";
+
+ private static final String IMAGE_TRANSFORMATION_LABEL = "tr_label";
+
+ private static final String IMAGE_TRANSFORMATION_CODE = "tr_code";
+
private static final String CHANNEL_LABEL = "Channel Label";
private static final ImageChannelColor CHANNEL_COLOR = ImageChannelColor.RED;
@@ -216,8 +228,14 @@ public class ImagingQueryDAOTest extends AbstractDBTest
final long datasetId = addDataset(DS_PERM_ID, containerId);
final long spotId = addSpot(containerId);
final long datasetChannelId1 = addDatasetChannel(datasetId);
+ addImageTransformationsAndTestListing(datasetChannelId1);
+ testAddingAndRemovingImageTransformation(datasetChannelId1, DS_CHANNEL, datasetId, null);
+
assertTrue(dao.hasDatasetChannels(DS_PERM_ID));
final long experimentChannelId2 = addExperimentChannel(experimentId);
+ addImageTransformationsAndTestListing(experimentChannelId2);
+ testAddingAndRemovingImageTransformation(experimentChannelId2, EXP_CHANNEL, null,
+ experimentId);
testChannelMethods(experimentId, datasetId, datasetChannelId1, experimentChannelId2);
@@ -409,6 +427,125 @@ public class ImagingQueryDAOTest extends AbstractDBTest
return dao.addChannel(channel);
}
+ private void testAddingAndRemovingImageTransformation(long channelId, String channelCode,
+ Long datasetId, Long experimentId)
+ {
+ ImgImageTransformationDTO transformation = addImageTransformation(channelId, 312);
+
+ String transformationCode = transformation.getCode();
+ Long testedTransformationId =
+ tryGetTransformationIdForDatasetOrExperimentChannel(datasetId, experimentId,
+ transformationCode);
+ assertNotNull("Cannot get the transformation id back", testedTransformationId);
+
+ ImgImageTransformationDTO testedTransformation =
+ dao.tryGetImageTransformation(channelId, transformationCode);
+ assertNotNull(testedTransformation);
+ assertEquals(testedTransformationId.longValue(), testedTransformation.getId());
+
+ List<ImgImageTransformationDTO> allTransformations =
+ listImageTransformations(datasetId, experimentId);
+ assertEquals(1, allTransformations.size());
+ ImgImageTransformationDTO testedTransformationListed = allTransformations.get(0);
+ assertEquals("list transformations failed", testedTransformation,
+ testedTransformationListed);
+
+ // test removal of transformation
+ dao.removeImageTransformation(transformationCode, channelId);
+ testedTransformationId =
+ tryGetTransformationIdForDatasetOrExperimentChannel(datasetId, experimentId,
+ transformationCode);
+ assertNull(testedTransformationId);
+
+ }
+
+ private List<ImgImageTransformationDTO> listImageTransformations(Long datasetIdOrNull,
+ Long experimentIdOrNull)
+ {
+ if (datasetIdOrNull != null)
+ {
+ return dao.listImageTransformationsByDatasetId(datasetIdOrNull);
+ } else
+ {
+ assert experimentIdOrNull != null : "both dataset and exp id are null";
+ return dao.listImageTransformationsByExperimentId(experimentIdOrNull);
+ }
+ }
+
+ private Long tryGetTransformationIdForDatasetOrExperimentChannel(Long datasetId,
+ Long experimentId, String transformationCode)
+ {
+ long channelId = getChannelId(datasetId, experimentId);
+ return dao.tryGetImageTransformationId(channelId, transformationCode);
+ }
+
+ private long getChannelId(Long datasetIdOrNull, Long experimentIdOrNull)
+ {
+ if (datasetIdOrNull != null)
+ {
+ return dao.getDatasetChannelId(datasetIdOrNull, DS_CHANNEL);
+ } else
+ {
+ assert experimentIdOrNull != null : "both dataset and exp id are null";
+ return dao.getExperimentChannelId(experimentIdOrNull, EXP_CHANNEL);
+ }
+ }
+
+ private ImgImageTransformationDTO addImageTransformation(long channelId, long codeSuffix)
+ {
+ IImageTransformerFactory transformerFactory1 = new ExampleImageTransformerFactory(123);
+ ImgImageTransformationDTO transformation1 =
+ createImageTransformation(channelId, codeSuffix, transformerFactory1);
+ dao.addImageTransformations(Arrays.asList(transformation1));
+ return transformation1;
+ }
+
+ // adds two transformtion for the channel and tests that they are written correctly
+ private void addImageTransformationsAndTestListing(long channelId)
+ {
+ IImageTransformerFactory transformerFactory1 = new ExampleImageTransformerFactory(123);
+ ImgImageTransformationDTO transformation1 =
+ createImageTransformation(channelId, 0, transformerFactory1);
+ IImageTransformerFactory transformerFactory2 = new ExampleImageTransformerFactory(321);
+ ImgImageTransformationDTO transformation2 =
+ createImageTransformation(channelId, 1, transformerFactory2);
+
+ dao.addImageTransformations(Arrays.asList(transformation1, transformation2));
+
+ // read back and test
+
+ // listImageTransformations() test
+ List<ImgImageTransformationDTO> readTransformations =
+ dao.listImageTransformations(channelId);
+
+ assertEquals(2, readTransformations.size());
+ assertEquals(transformerFactory1, readTransformations.get(0)
+ .tryGetImageTransformerFactory());
+ assertEquals(transformerFactory2, readTransformations.get(1)
+ .tryGetImageTransformerFactory());
+
+ for (int i = 0; i < 2; i++)
+ {
+ ImgImageTransformationDTO readTransformation = readTransformations.get(i);
+ assertEquals(CodeNormalizer.normalize(IMAGE_TRANSFORMATION_CODE + i),
+ readTransformation.getCode());
+ assertEquals(IMAGE_TRANSFORMATION_LABEL, readTransformation.getLabel());
+ assertEquals(IMAGE_TRANSFORMATION_DESC, readTransformation.getDescription());
+ assertEquals(IMAGE_TRANSFORMATION_IS_EDITABLE, readTransformation.getIsEditable());
+ // clean the db
+ dao.removeImageTransformation(readTransformation.getCode(), channelId);
+
+ }
+ }
+
+ private ImgImageTransformationDTO createImageTransformation(long channelId, long codeSuffix,
+ IImageTransformerFactory transformerFactory)
+ {
+ return new ImgImageTransformationDTO(IMAGE_TRANSFORMATION_CODE + codeSuffix,
+ IMAGE_TRANSFORMATION_LABEL, IMAGE_TRANSFORMATION_DESC,
+ IMAGE_TRANSFORMATION_IS_EDITABLE, channelId, transformerFactory);
+ }
+
private long addExperimentChannel(long experimentId)
{
final ImgChannelDTO channel =
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactoryTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactoryTest.java
index fdf8afbc2708edea82d11d56be8e5eb821412127..1b38791510b341219d875ae45d9ed7a9ad84d469 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactoryTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/ImageGenerationDescriptionFactoryTest.java
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackR
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageGenerationDescription;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.generic.shared.ServletParamsParsingTestUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.ImageServletUrlParameters;
/**
* Tests of {@link ImageGenerationDescriptionFactory}.
@@ -62,7 +63,7 @@ public class ImageGenerationDescriptionFactoryTest extends ServletParamsParsingT
DatasetAcquiredImagesReference channelsToMerge = desc.tryGetImageChannels();
assertEquals(channelStackRef, channelsToMerge.getChannelStackReference());
- assertEquals(Arrays.asList("DAPI", "GFP"), channelsToMerge.getChannelCodes());
+ assertEquals(Arrays.asList("DAPI", "GFP"), channelsToMerge.getChannelCodes(null));
assertEquals(BASIC_DATASET_CODE, channelsToMerge.getDatasetCode());
List<DatasetAcquiredImagesReference> overlayChannels = desc.getOverlayChannels();
@@ -73,7 +74,7 @@ public class ImageGenerationDescriptionFactoryTest extends ServletParamsParsingT
DatasetAcquiredImagesReference firstChannel = overlayChannels.get(firstChannelIx);
assertEquals(channelStackRef, firstChannel.getChannelStackReference());
- assertEquals(Arrays.asList("X", "Y"), firstChannel.getChannelCodes());
+ assertEquals(Arrays.asList("X", "Y"), firstChannel.getChannelCodes(null));
assertEquals(firstOverlayDatasetCode, firstChannel.getDatasetCode());
DatasetAcquiredImagesReference secondChannel = overlayChannels.get(1 - firstChannelIx);
@@ -86,16 +87,21 @@ public class ImageGenerationDescriptionFactoryTest extends ServletParamsParsingT
Map<String, String[]> paramsMap = createBasicParamsMap();
addListParams(paramsMap, "dataset", BASIC_DATASET_CODE);
addListParams(paramsMap, "mergeChannels", "true");
+ String myImageTransformationCode = "make-darker";
+ addListParams(paramsMap,
+ ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM,
+ myImageTransformationCode);
+
addRequestParamsExpectations(paramsMap);
ImageGenerationDescription desc = ImageGenerationDescriptionFactory.create(request);
DatasetAcquiredImagesReference channelsToMerge = desc.tryGetImageChannels();
assertNotNull(channelsToMerge);
- assertNull(channelsToMerge.getChannelCodes());
- assertTrue(channelsToMerge.isMergeAllChannels());
+ assertNull(channelsToMerge.getChannelCodes(null));
+ assertTrue(channelsToMerge.isMergeAllChannels(null));
assertEquals(BASIC_DATASET_CODE, channelsToMerge.getDatasetCode());
-
+ assertEquals(myImageTransformationCode, desc.tryGetSingleChannelTransformationCode());
assertEquals(0, desc.getOverlayChannels().size());
}
@@ -120,7 +126,8 @@ public class ImageGenerationDescriptionFactoryTest extends ServletParamsParsingT
final Map<String, String[]> paramsMap = new HashMap<String, String[]>();
addSingleParams(paramsMap, "sessionID", "sessionXXX", "wellRow", "1", "wellCol", "4",
"tileRow", "7", "tileCol", "2", "mode", "thumbnail200x120", "channelStackId", null,
- "mergeChannels", null, "dataset", null);
+ "mergeChannels", null, "dataset", null,
+ ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM, null);
return paramsMap;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
index 69614af24fa68e4fba014e08b42fad28dc61d397..52983bd109def2c436ca3cd53887d9587615b563 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
@@ -20,7 +20,10 @@ import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
import org.apache.commons.io.IOUtils;
import org.jmock.Expectations;
@@ -44,12 +47,14 @@ import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageTransformationParams;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtilTest;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageTransformationInfo;
/**
* @author Franz-Josef Elmer
@@ -115,7 +120,8 @@ public class ImageChannelsUtilsTest extends AssertJUnit
try
{
- createImageChannelsUtils(null).calculateBufferedImage(imageRef, true);
+ createImageChannelsUtils(null).calculateBufferedImage(imageRef,
+ createSingleChannelTransformationParams());
fail("EnvironmentFailureException expected");
} catch (EnvironmentFailureException ex)
{
@@ -126,6 +132,11 @@ public class ImageChannelsUtilsTest extends AssertJUnit
context.assertIsSatisfied();
}
+ private ImageTransformationParams createSingleChannelTransformationParams()
+ {
+ return new ImageTransformationParams(true, false, null);
+ }
+
@Test
public void testGetTiffImage()
{
@@ -152,8 +163,8 @@ public class ImageChannelsUtilsTest extends AssertJUnit
prepareExpectations(absoluteImageReference, imageRef);
BufferedImage image =
- createImageChannelsUtils(thumbnailSizeOrNull)
- .calculateBufferedImage(imageRef, true);
+ createImageChannelsUtils(thumbnailSizeOrNull).calculateBufferedImage(imageRef,
+ createSingleChannelTransformationParams());
assertEquals(expectedImageContentDescription, getImageContentDescription(image));
context.assertIsSatisfied();
@@ -165,17 +176,17 @@ public class ImageChannelsUtilsTest extends AssertJUnit
context.checking(new Expectations()
{
{
- one(loader).getImageParameters();
+ allowing(loader).getImageParameters();
ImageDatasetParameters imgParams = new ImageDatasetParameters();
imgParams.setChannels(Arrays.asList(new ImageChannel(CHANNEL, CHANNEL, null,
- null, null)));
+ null, null, new ArrayList<ImageTransformationInfo>())));
will(returnValue(imgParams));
RequestedImageSize requestedSize =
absoluteImageReferenceOrNull == null ? RequestedImageSize
.createOriginal() : absoluteImageReferenceOrNull
.getRequestedSize();
- one(loader).tryGetImage(imageRef.getChannelCodes().get(0),
+ one(loader).tryGetImage(imageRef.getChannelCodes(null).get(0),
imageRef.getChannelStackReference(), requestedSize);
will(returnValue(absoluteImageReferenceOrNull));
}
@@ -187,8 +198,8 @@ public class ImageChannelsUtilsTest extends AssertJUnit
ImageChannelStackReference channelStackReference =
ImageChannelStackReference.createFromId(4711);
final DatasetAcquiredImagesReference imageRef =
- new DatasetAcquiredImagesReference(DATASET_CODE, channelStackReference,
- Arrays.asList(CHANNEL));
+ DatasetAcquiredImagesReference.createForSingleChannel(DATASET_CODE,
+ channelStackReference, CHANNEL);
return imageRef;
}
@@ -198,7 +209,10 @@ public class ImageChannelsUtilsTest extends AssertJUnit
final DatasetAcquiredImagesReference imageRef = createDatasetAcquiredImagesReference();
AbsoluteImageReference imgRef =
createAbsoluteImageReference("img1.gif", RequestedImageSize.createOriginal());
- imgRef.getImageTransfomationFactories().setForChannel(transformerFactory);
+ String transformationCode = "MY_TRANSFORMATION";
+ Map<String, IImageTransformerFactory> transformations =
+ createImageTransformationsMap(transformationCode, transformerFactory);
+ imgRef.getImageTransfomationFactories().setForChannel(transformations);
prepareExpectations(imgRef, imageRef);
context.checking(new Expectations()
@@ -209,13 +223,24 @@ public class ImageChannelsUtilsTest extends AssertJUnit
}
});
- BufferedImage image = createImageChannelsUtils(null).calculateBufferedImage(imageRef, true);
+ BufferedImage image =
+ createImageChannelsUtils(null).calculateBufferedImage(imageRef,
+ new ImageTransformationParams(true, false, transformationCode));
assertEquals("e00 f00 f00 e00\n" + "f00 c00 c00 f00\n" + "f00 c00 c00 f00\n"
+ "e00 f00 f00 e00\n", getImageContentDescription(image));
context.assertIsSatisfied();
}
+ private static Map<String, IImageTransformerFactory> createImageTransformationsMap(
+ String transformationCode, IImageTransformerFactory transformerFactory)
+ {
+ Map<String, IImageTransformerFactory> transformations =
+ new HashMap<String, IImageTransformerFactory>();
+ transformations.put(transformationCode, transformerFactory);
+ return transformations;
+ }
+
private static AbsoluteImageReference createAbsoluteImageReference(String fileName,
RequestedImageSize imageSize)
{
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 03df1842ff2cdd8bca9f8d79a57c316425fca010..1f6f50e8f46c06d92cba98124072b965c5e5e753 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -83,6 +83,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageTransformationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
@@ -94,6 +95,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgEx
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureVocabularyTermDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageTransformationDTO;
/**
* Test cases for the {@link DssServiceRpcScreening}.
@@ -175,8 +177,10 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
imageParameters.setTileRowsNum(1);
imageParameters.setTileColsNum(2);
imageParameters.setDatasetCode(DATASET_CODE);
- imageParameters.setChannels(Arrays.asList(new ImageChannel(CHANNEL_CODE, CHANNEL_CODE,
- null, null, null)));
+ ImageChannel imageChannel =
+ new ImageChannel(CHANNEL_CODE, CHANNEL_CODE, null, null, null,
+ new ArrayList<ImageTransformationInfo>());
+ imageParameters.setChannels(Arrays.asList(imageChannel));
context.checking(new Expectations()
{
{
@@ -395,9 +399,16 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
ImgChannelDTO channelDTO =
new ImgChannelDTO("dapi", null, null, new Long(42), null, "dapi",
ImageChannelColor.BLUE);
- channelDTO.setSerializedImageTransformerFactory(SerializationUtils
- .serialize(transformerFactory));
+ long channelId = 444;
+ channelDTO.setId(channelId);
will(returnValue(channelDTO));
+
+ one(dao).tryGetImageTransformation(channelId,
+ DssServiceRpcScreening.IMAGE_VIEWER_TRANSFORMATION_CODE);
+ ImgImageTransformationDTO transformationDTO =
+ new ImgImageTransformationDTO("tr_code", "tr_labal", null, true,
+ channelId, transformerFactory);
+ will(returnValue(transformationDTO));
}
});
@@ -494,8 +505,18 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
allowing(dao).hasDatasetChannels(DATASET_CODE);
will(returnValue(true));
- exactly(2).of(transformerDAO).saveTransformerFactoryForDatasetChannel(
- datasetId, channel, transformerFactory);
+ long channelId = 5;
+ long transactionId = 123;
+ exactly(2).of(transformerDAO).getDatasetChannelId(datasetId, channel);
+ will(returnValue(channelId));
+
+ exactly(2).of(transformerDAO).tryGetImageTransformationId(channelId,
+ DssServiceRpcScreening.IMAGE_VIEWER_TRANSFORMATION_CODE);
+
+ will(returnValue(transactionId));
+
+ exactly(2).of(transformerDAO).updateImageTransformerFactory(transactionId,
+ transformerFactory);
one(transformerDAO).commit();
}