diff --git a/screening/dist/etc/service.properties b/screening/dist/etc/service.properties
index 6901f3595d13c171207ad897f6baf6c5f358c055..0fa1001749a7d6ae2541b6a062bd0170b6c5a521 100644
--- a/screening/dist/etc/service.properties
+++ b/screening/dist/etc/service.properties
@@ -137,6 +137,23 @@ tabular-data-graph-servlet.properties-file = etc/tabular-data-graph.properties
screening-dss-api-exporter-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.DssScreeningApiServlet
screening-dss-api-exporter-servlet.path = /rmi-datastore-server-screening-api-v1/*
+# ---------------------------------------------------------------------------
+# image overview plugins configuration
+# ---------------------------------------------------------------------------
+
+# Comma separated names of image overview plugins.
+# Each plugin should have configuration properties prefixed with its name.
+# Generic properties for each <plugin> include:
+# <plugin>.class - Fully qualified plugin class name (mandatory).
+# <plugin>.default - If true all data set types not handled by other plugins should be handled
+# by the plugin (default = false).
+# <plugin>.dataset-types - Comma separated list of data set types handled by the plugin
+# (optional and ignored if default is true, otherwise mandatory).
+overview-plugins = microscopy-image-overview
+
+microscopy-image-overview.class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet
+microscopy-image-overview.dataset-types = MICROSCOPY_IMAGE
+
# ---------------------------------------------------------------------------
maintenance-plugins=data-set-clean-up
@@ -289,3 +306,51 @@ image-analysis-results.storage-processor.ignore-comments = true
image-analysis-results.storage-processor.well-name-row = row
image-analysis-results.storage-processor.well-name-col = col
image-analysis-results.storage-processor.well-name-col-is-alphanum = true
+
+# --- Example configuration of a dropbox for images which are not connected to wells on the plate
+
+# The directory to watch for incoming data.
+#microscopy-dropbox.incoming-dir = ${incoming-root-dir}/incoming-microscopy
+#microscopy-dropbox.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+#microscopy-dropbox.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+#microscopy-dropbox.data-set-info-extractor.entity-separator = .
+#microscopy-dropbox.data-set-info-extractor.index-of-sample-code = 0
+#microscopy-dropbox.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+#microscopy-dropbox.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+#microscopy-dropbox.type-extractor.file-format-type = TIFF
+#microscopy-dropbox.type-extractor.locator-type = RELATIVE_LOCATION
+#microscopy-dropbox.type-extractor.data-set-type = MICROSCOPY_IMAGE
+#microscopy-dropbox.type-extractor.is-measured = true
+
+#microscopy-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyStorageProcessor
+#microscopy-dropbox.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyImageFileExtractor
+#microscopy-dropbox.storage-processor.data-source = imaging-db
+#microscopy-dropbox.storage-processor.channel-names = BLUE, GREEN, RED
+#microscopy-dropbox.storage-processor.well_geometry = 2x3
+#microscopy-dropbox.storage-processor.tile_mapping = 1,2,3;4,5,6
+
+# --- Microscopy dropbox with a series of images with any names ---------------------------
+
+# The directory to watch for incoming data.
+#microscopy-series-dropbox.incoming-dir = ${incoming-root-dir}/incoming-microscopy-series
+#microscopy-series-dropbox.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+#microscopy-series-dropbox.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+#microscopy-series-dropbox.data-set-info-extractor.entity-separator = .
+#microscopy-series-dropbox.data-set-info-extractor.index-of-sample-code = 0
+#microscopy-series-dropbox.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+#microscopy-series-dropbox.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+#microscopy-series-dropbox.type-extractor.file-format-type = TIFF
+#microscopy-series-dropbox.type-extractor.locator-type = RELATIVE_LOCATION
+#microscopy-series-dropbox.type-extractor.data-set-type = MICROSCOPY_IMAGE
+#microscopy-series-dropbox.type-extractor.is-measured = true
+
+#microscopy-series-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyBlackboxSeriesStorageProcessor
+#microscopy-series-dropbox.storage-processor.data-source = imaging-db
diff --git a/screening/dist/server/web-client.properties b/screening/dist/server/web-client.properties
index ae923f04e69c29cb0d43c19d4a9a148ce9e89f94..58d0637fdfd83c1fc2c81cea5e0cade6bb87c6f5 100644
--- a/screening/dist/server/web-client.properties
+++ b/screening/dist/server/web-client.properties
@@ -3,6 +3,12 @@
#
#default-view-mode = SIMPLE
+# (optional) List of data set types for which there should be an image overview shown in dataset tables.
+# If not specified image overview will not be shown for any datasets
+# even if some overview plugins have been configured.
+#
+data-set-types-with-image-overview = MICROSCOPY_IMAGE
+
# Configuration of entity (experiment, sample, data set, material) detail views.
# Allows to hide chosen sections.
#
@@ -19,6 +25,7 @@
# data-set-parents-section
# data-set-children-section
# plate-layout-dataset-section
+# logical-image-dataset-section (valid only for microscopy datasets)
# query-section
# generic_experiment_viewer
# data-sets-section
@@ -35,11 +42,12 @@
# data-sets-section
# attachment-section
# query-section
+# logical-image-well-section (valid only for HCS well samples)
# generic_material_viewer
# plate-locations-material-section
# query-section
#
-detail-views = plate-or-well-view, image-data-view, image-analysis-data-view
+detail-views = plate-or-well-view, image-data-view, image-analysis-data-view, microscopy-dataset-view
#experiment-view.view = generic_experiment_viewer
#experiment-view.types = SIRNA_HCS
@@ -61,5 +69,11 @@ image-analysis-data-view.hide-sections = data-set-parents-section, data-set-chil
image-analysis-data-view.hide-smart-view = true
image-analysis-data-view.hide-file-view = true
+microscopy-dataset-view.view = generic_dataset_viewer
+microscopy-dataset-view.types = MICROSCOPY_IMAGE
+microscopy-dataset-view.hide-sections = data-set-children-section, data-set-parents-section
+microscopy-dataset-view.hide-smart-view = false
+microscopy-dataset-view.hide-file-view = true
+
technologies = screening
-#screening.image-viewer-enabled = true
+screening.image-viewer-enabled = true
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
index 6350058ffff0664af20d1013f50ae5e598486f21..32d0e9b160ec38fffcf42953cefe8d3a89132fea 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
@@ -17,12 +17,16 @@
package ch.systemsx.cisd.openbis.dss.etl;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ImagingChannelsMap;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgAcquiredImageDTO;
@@ -105,10 +109,23 @@ abstract class AbstractImageDatasetUploader
stackImages.add(makeAcquiredImageInStack(image));
map.put(stackDTO, stackImages);
}
- setChannelStackIds(map.keySet());
+ Set<ImgChannelStackDTO> channelStacks = map.keySet();
+ setChannelStackIds(channelStacks);
+ setChannelStackRepresentatives(channelStacks);
return map;
}
+ private void setChannelStackRepresentatives(Set<ImgChannelStackDTO> channelStacks)
+ {
+ Set<ImgChannelStackDTO> representatives =
+ ChannelStackRepresentativesOracle.calculateRepresentatives(channelStacks);
+ for (ImgChannelStackDTO channelStack : channelStacks)
+ {
+ boolean isRepresentative = representatives.contains(channelStack);
+ channelStack.setRepresentative(isRepresentative);
+ }
+ }
+
private void setChannelStackIds(Set<ImgChannelStackDTO> channelStacks)
{
for (ImgChannelStackDTO channelStack : channelStacks)
@@ -129,7 +146,8 @@ abstract class AbstractImageDatasetUploader
Long spotId = spotProvider.tryGetSpotId(image);
int dummyId = 0;
return new ImgChannelStackDTO(dummyId, image.getTileRow(), image.getTileColumn(),
- datasetId, spotId, image.tryGetTimePoint(), image.tryGetDepth());
+ datasetId, spotId, image.tryGetTimePoint(), image.tryGetDepth(),
+ image.tryGetSeriesNumber(), false);
}
private void createImages(Map<ImgChannelStackDTO, List<AcquiredImageInStack>> stackImagesMap,
@@ -229,4 +247,86 @@ abstract class AbstractImageDatasetUploader
imageReferenceOrNull.tryGetColorComponent());
return dto;
}
+
+ @Private
+ static final class ChannelStackRepresentativesOracle
+ {
+ /**
+ * For all images of one spot chooses the 'smallest' element as an representative. If there
+ * are no spots than the smallest element of all specified images is chosen.
+ */
+ public static Set<ImgChannelStackDTO> calculateRepresentatives(
+ Set<ImgChannelStackDTO> images)
+ {
+ Map<Long/* spot or null */, List<ImgChannelStackDTO>> mapBySpot =
+ createMapBySpot(images);
+ Comparator<? super ImgChannelStackDTO> spotChannelStacksComparator =
+ createChannelStacksComparator();
+ for (List<ImgChannelStackDTO> spotChannelStacks : mapBySpot.values())
+ {
+ Collections.sort(spotChannelStacks, spotChannelStacksComparator);
+ }
+
+ Set<ImgChannelStackDTO> representatives = new HashSet<ImgChannelStackDTO>();
+ for (List<ImgChannelStackDTO> spotChannelStacks : mapBySpot.values())
+ {
+ representatives.add(spotChannelStacks.get(0));
+ }
+ return representatives;
+ }
+
+ private static Comparator<? super ImgChannelStackDTO> createChannelStacksComparator()
+ {
+ return new Comparator<ImgChannelStackDTO>()
+ {
+ public int compare(ImgChannelStackDTO o1, ImgChannelStackDTO o2)
+ {
+ int cmp = compareNullable(o1.getRow(), o2.getRow());
+ if (cmp != 0)
+ return cmp;
+ cmp = compareNullable(o1.getColumn(), o2.getColumn());
+ if (cmp != 0)
+ return cmp;
+ cmp = compareNullable(o1.getT(), o2.getT());
+ if (cmp != 0)
+ return cmp;
+ cmp = compareNullable(o1.getZ(), o2.getZ());
+ if (cmp != 0)
+ return cmp;
+ cmp = compareNullable(o1.getSeriesNumber(), o2.getSeriesNumber());
+ return cmp;
+ }
+
+ private <T extends Comparable<T>> int compareNullable(T v1OrNull, T v2OrNull)
+ {
+ if (v1OrNull == null)
+ {
+ return v2OrNull == null ? 0 : -1;
+ } else
+ {
+ return v2OrNull == null ? 1 : v1OrNull.compareTo(v2OrNull);
+ }
+ }
+ };
+ }
+
+ private static Map<Long/* spot or null */, List<ImgChannelStackDTO>> createMapBySpot(
+ Set<ImgChannelStackDTO> channelStacks)
+ {
+ Map<Long, List<ImgChannelStackDTO>> mapBySpot =
+ new HashMap<Long, List<ImgChannelStackDTO>>();
+ for (ImgChannelStackDTO channelStack : channelStacks)
+ {
+ Long spotId = channelStack.getSpotId();
+ List<ImgChannelStackDTO> spotChannelStacks = mapBySpot.get(spotId);
+ if (spotChannelStacks == null)
+ {
+ spotChannelStacks = new ArrayList<ImgChannelStackDTO>();
+ }
+ spotChannelStacks.add(channelStack);
+ mapBySpot.put(spotId, spotChannelStacks);
+ }
+ return mapBySpot;
+ }
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
index 90ff5dcebaafc6d2ab5242a45c784604583eb039..572255e05ab8f1bd9f0c0d72fdc96c35d00cf795 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
@@ -96,12 +96,21 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
protected final Geometry wellGeometry;
- protected AbstractImageFileExtractor(final Properties properties)
+ protected AbstractImageFileExtractor(Properties properties)
{
- this.channelDescriptions = tryExtractChannelDescriptions(properties);
+ this(extractChannelDescriptions(properties), getWellGeometry(properties), properties);
+ }
+
+ protected AbstractImageFileExtractor(List<ChannelDescription> channelDescriptions,
+ Geometry wellGeometry, Properties properties)
+ {
+ assert wellGeometry != null : "wel geometry is null";
+ assert channelDescriptions != null : "channelDescriptions is null";
+
+ this.channelDescriptions = channelDescriptions;
+ this.wellGeometry = wellGeometry;
this.channelColorComponentsOrNull = tryGetChannelComponents(properties);
checkChannelsAndColorComponents();
- this.wellGeometry = getWellGeometry(properties);
this.tileMapperOrNull =
TileMapper.tryCreate(properties.getProperty(TILE_MAPPING_PROPERTY), wellGeometry);
}
@@ -252,7 +261,7 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
return channels;
}
- protected final static List<ChannelDescription> tryExtractChannelDescriptions(
+ protected final static List<ChannelDescription> extractChannelDescriptions(
final Properties properties)
{
return PlateStorageProcessor.extractChannelDescriptions(properties);
@@ -289,7 +298,7 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
colorComponentOrNull);
return new AcquiredSingleImage(imageInfo.tryGetWellLocation(), imageInfo.getTileLocation(),
imageInfo.getChannelCode(), imageInfo.tryGetTimepoint(), imageInfo.tryGetDepth(),
- relativeImageRef);
+ imageInfo.tryGetSeriesNumber(), relativeImageRef);
}
protected static Integer tryAsInt(String valueOrNull)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
index e2dc3e06eb01982c271aac3a7ef9eaa229435930..506221fdea355304766a11ceee86ce2227a07dbd 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
@@ -184,28 +184,42 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor
// ---
public AbstractImageStorageProcessor(final Properties properties)
+ {
+ this(getMandatorySpotGeometry(properties), extractChannelDescriptions(properties),
+ tryCreateImageExtractor(properties), properties);
+ }
+
+ protected AbstractImageStorageProcessor(Geometry spotGeometry,
+ List<ChannelDescription> channelDescriptions, IImageFileExtractor imageFileExtractor,
+ Properties properties)
{
super(properties);
- String spotGeometryText = getMandatoryProperty(SPOT_GEOMETRY_PROPERTY);
- this.spotGeometry = Geometry.createFromString(spotGeometryText);
- channelDescriptions = extractChannelDescriptions(properties);
- thumbnailMaxWidth =
+ this.spotGeometry = spotGeometry;
+ this.channelDescriptions = channelDescriptions;
+ this.imageFileExtractor = imageFileExtractor;
+ this.thumbnailMaxWidth =
PropertyUtils.getInt(properties, THUMBNAIL_MAX_WIDTH_PROPERTY,
DEFAULT_THUMBNAIL_MAX_WIDTH);
- thumbnailMaxHeight =
+ this.thumbnailMaxHeight =
PropertyUtils.getInt(properties, THUMBNAIL_MAX_HEIGHT_PROPERTY,
DEFAULT_THUMBNAIL_MAX_HEIGHT);
- generateThumbnails =
+ this.generateThumbnails =
PropertyUtils.getBoolean(properties, GENERATE_THUMBNAILS_PROPERTY, false);
- areThumbnailsCompressed =
+ this.areThumbnailsCompressed =
PropertyUtils.getBoolean(properties, COMPRESS_THUMBNAILS_PROPERTY, false);
- originalDataStorageFormat = getOriginalDataStorageFormat(properties);
+ this.originalDataStorageFormat = getOriginalDataStorageFormat(properties);
- this.imageFileExtractor = tryCreateImageExtractor(properties);
this.dataSource = ServiceProvider.getDataSourceProvider().getDataSource(properties);
this.currentTransaction = null;
}
+ private static Geometry getMandatorySpotGeometry(Properties properties)
+ {
+ String spotGeometryText =
+ PropertyUtils.getMandatoryProperty(properties, SPOT_GEOMETRY_PROPERTY);
+ return Geometry.createFromString(spotGeometryText);
+ }
+
private static IImageFileExtractor tryCreateImageExtractor(final Properties properties)
{
String fileExtractorClass = PropertyUtils.getProperty(properties, FILE_EXTRACTOR_PROPERTY);
@@ -720,7 +734,8 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor
{
for (AcquiredSingleImage image : images)
{
- if (image.tryGetTimePoint() != null || image.tryGetDepth() != null)
+ if (image.tryGetTimePoint() != null || image.tryGetDepth() != null
+ || image.tryGetSeriesNumber() != null)
{
return true;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredSingleImage.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredSingleImage.java
index 2bc1f80f4298c632a98515a4ceac32b28f51def5..745daa8167c6a7257d2d8db5fa7f9385309031a4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredSingleImage.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredSingleImage.java
@@ -37,13 +37,16 @@ public class AcquiredSingleImage extends AbstractHashable
// can be null
private final Float timePointOrNull, depthOrNull;
+ // can be null
+ private Integer seriesNumberOrNull;
+
private final RelativeImageReference imageFilePath; // relative to the original dataset
// directory
private RelativeImageReference thumbnailFilePathOrNull;
public AcquiredSingleImage(Location wellLocationOrNull, Location tileLocation,
- String channelCode, Float timePointOrNull, Float depthOrNull,
+ String channelCode, Float timePointOrNull, Float depthOrNull, Integer seriesNumberOrNull,
RelativeImageReference imageFilePath)
{
this.wellLocationOrNull = wellLocationOrNull;
@@ -51,9 +54,15 @@ public class AcquiredSingleImage extends AbstractHashable
this.channelCode = channelCode.toUpperCase();
this.timePointOrNull = timePointOrNull;
this.depthOrNull = depthOrNull;
+ this.seriesNumberOrNull = seriesNumberOrNull;
this.imageFilePath = imageFilePath;
}
+ public Location tryGetWellLocation()
+ {
+ return wellLocationOrNull;
+ }
+
/** Valid only in HCS case, do not call this method for microscopy images. */
public int getWellRow()
{
@@ -103,9 +112,20 @@ public class AcquiredSingleImage extends AbstractHashable
return thumbnailFilePathOrNull;
}
+ public Integer tryGetSeriesNumber()
+ {
+ return seriesNumberOrNull;
+ }
+
+ // ---- setters
+
public final void setThumbnailFilePathOrNull(RelativeImageReference thumbnailFilePathOrNull)
{
this.thumbnailFilePathOrNull = thumbnailFilePathOrNull;
}
+ public void setSeriesNumber(int seriesNumber)
+ {
+ this.seriesNumberOrNull = seriesNumber;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
index 43a590c245855954cba063d4e5ca8e9f1a58ae3c..05ebadacd74581458d29732fb4e6f2258c51ee70 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
@@ -23,11 +23,7 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
-import org.apache.log4j.Logger;
-
import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimension;
@@ -42,9 +38,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimension;
*/
public final class HCSImageCheckList
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- HCSImageCheckList.class);
-
private final Map<FullLocation, Check> imageMap;
public HCSImageCheckList(final List<String> channelCodes, final PlateDimension plateGeometry,
@@ -95,16 +88,12 @@ public final class HCSImageCheckList
}
Float timepointOrNull = image.tryGetTimePoint();
Float depthOrNull = image.tryGetDepth();
- if (check.isCheckedOff(timepointOrNull, depthOrNull))
+ Integer seriesNumberOrNull = image.tryGetSeriesNumber();
+ if (check.isCheckedOff(timepointOrNull, depthOrNull, seriesNumberOrNull))
{
throw new IllegalArgumentException("Image already handled: " + image);
}
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug("Checking location " + location
- + (timepointOrNull == null ? "" : " timepoint " + timepointOrNull));
- }
- check.checkOff(timepointOrNull, depthOrNull);
+ check.checkOff(timepointOrNull, depthOrNull, seriesNumberOrNull);
}
private static FullLocation createLocation(AcquiredSingleImage image)
@@ -118,7 +107,7 @@ public final class HCSImageCheckList
final List<FullLocation> fullLocations = new ArrayList<FullLocation>();
for (final Map.Entry<FullLocation, Check> entry : imageMap.entrySet())
{
- if (entry.getValue().isCheckedOff(null, null) == false)
+ if (entry.getValue().isCheckedOff(null, null, null) == false)
{
fullLocations.add(entry.getKey());
}
@@ -136,10 +125,13 @@ public final class HCSImageCheckList
private final Float depthOrNull;
- public CheckDimension(Float timeOrNull, Float depthOrNull)
+ private final Integer seriesNumberOrNull;
+
+ public CheckDimension(Float timeOrNull, Float depthOrNull, Integer seriesNumberOrNull)
{
this.timeOrNull = timeOrNull;
this.depthOrNull = depthOrNull;
+ this.seriesNumberOrNull = seriesNumberOrNull;
}
@Override
@@ -149,6 +141,9 @@ public final class HCSImageCheckList
int result = 1;
result = prime * result + ((depthOrNull == null) ? 0 : depthOrNull.hashCode());
result = prime * result + ((timeOrNull == null) ? 0 : timeOrNull.hashCode());
+ result =
+ prime * result
+ + ((seriesNumberOrNull == null) ? 0 : seriesNumberOrNull.hashCode());
return result;
}
@@ -174,6 +169,12 @@ public final class HCSImageCheckList
return false;
} else if (!timeOrNull.equals(other.timeOrNull))
return false;
+ if (seriesNumberOrNull == null)
+ {
+ if (other.seriesNumberOrNull != null)
+ return false;
+ } else if (!seriesNumberOrNull.equals(other.seriesNumberOrNull))
+ return false;
return true;
}
}
@@ -184,18 +185,19 @@ public final class HCSImageCheckList
private final Set<CheckDimension> dimensions = new HashSet<CheckDimension>();
- final void checkOff(Float timepointOrNull, Float depthOrNull)
+ final void checkOff(Float timepointOrNull, Float depthOrNull, Integer seriesNumberOrNull)
{
- dimensions.add(new CheckDimension(timepointOrNull, depthOrNull));
+ dimensions.add(new CheckDimension(timepointOrNull, depthOrNull, seriesNumberOrNull));
checkedOff = true;
}
- final boolean isCheckedOff(Float timepointOrNull, Float depthOrNull)
+ final boolean isCheckedOff(Float timepointOrNull, Float depthOrNull,
+ Integer seriesNumberOrNull)
{
CheckDimension dim = null;
- if (timepointOrNull != null || depthOrNull != null)
+ if (timepointOrNull != null || depthOrNull != null || seriesNumberOrNull != null)
{
- dim = new CheckDimension(timepointOrNull, depthOrNull);
+ dim = new CheckDimension(timepointOrNull, depthOrNull, seriesNumberOrNull);
}
return checkedOff && (dim == null || dimensions.contains(dim));
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
index b02502a15e9034811c2812843a17f7052c82b92c..adcaf45b70636e3f0f67a5751f21e613728caaa2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
@@ -172,9 +172,10 @@ public class HCSImageFileExtractor extends AbstractImageFileExtractor
Float timepointOrNull = tryAsFloat(unparsedInfo.getTimepointToken());
Float depthOrNull = tryAsFloat(unparsedInfo.getDepthToken());
+ Integer seriesNumberOrNull = tryAsInt(unparsedInfo.getSeriesNumberToken());
String imageRelativePath = getRelativeImagePath(incomingDataSetDirectory, imageFile);
return new ImageFileInfo(wellLocation, channelCode, tileLocation, imageRelativePath,
- timepointOrNull, depthOrNull);
+ timepointOrNull, depthOrNull, seriesNumberOrNull);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
index 0fcc5948895a954df41e0fdac9f07094da8f9cc4..79a3ed836795619744c63b18e13c7178b473e94b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
+import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IImageDatasetLoader;
@@ -34,4 +35,16 @@ public interface IImagingDatasetLoader extends IImageDatasetLoader
*/
AbsoluteImageReference tryGetImage(String chosenChannelCode,
ImageChannelStackReference channelStackReference, Size thumbnailSizeOrNull);
+
+ /**
+ * Finds representative image of this dataset in a given channel.
+ *
+ * @param channelCode channel code for which representative image is requested
+ * @param wellLocationOrNull if not null the returned images are restricted to one well.
+ * Otherwise the dataset is assumed to have no container and spots.
+ * @param thumbnailSizeOrNull if not null the thumbnail in th especified size will be returned.
+ */
+ AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
+ Location wellLocationOrNull, Size thumbnailSizeOrNull);
+
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyBlackboxSeriesStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyBlackboxSeriesStorageProcessor.java
new file mode 100644
index 0000000000000000000000000000000000000000..c0ea63d0ab1963fdb3179767e0ebb0143f89060c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyBlackboxSeriesStorageProcessor.java
@@ -0,0 +1,137 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.etl;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Properties;
+
+import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
+
+/**
+ * Storage processor which stores microscopy images in a special-purpose imaging database. Image
+ * files do not have to adhere to any naming convention, it's assumed that there is exactly one
+ * tile, one channel, no time or depth dimensions. Images are sorted lexicographically and
+ * subsequent series numbers are assigned to them.
+ * <p>
+ * In this storage processor one can set neither well geometry, channels nor image file extractor.<br>
+ * See {@link AbstractImageStorageProcessor} documentation to check how to configure thumbnails
+ * generation.
+ *
+ * @author Tomasz Pylak
+ */
+public class MicroscopyBlackboxSeriesStorageProcessor extends AbstractImageStorageProcessor
+{
+ private static final String DEFAULT_CHANNEL_CODE = "DEFAULT";
+
+ private static final String DEFAULT_CHANNEL_LABEL = "Default";
+
+ private static final Location DEFAULT_TILE = new Location(1, 1);
+
+ private static final Geometry DEFAULT_WELL_GEOMETRY = new Geometry(1, 1);
+
+ private static final List<ChannelDescription> DEFAULT_CHANNELS = Arrays
+ .asList(new ChannelDescription(DEFAULT_CHANNEL_CODE, DEFAULT_CHANNEL_LABEL));
+
+ public MicroscopyBlackboxSeriesStorageProcessor(Properties properties)
+ {
+ super(DEFAULT_WELL_GEOMETRY, DEFAULT_CHANNELS, new BlackboxSeriesImageFileExtractor(
+ properties), properties);
+ }
+
+ private static class BlackboxSeriesImageFileExtractor extends AbstractImageFileExtractor
+ {
+ protected BlackboxSeriesImageFileExtractor(Properties properties)
+ {
+ super(DEFAULT_CHANNELS, DEFAULT_WELL_GEOMETRY, properties);
+ }
+
+ @Override
+ protected ImageFileInfo tryExtractImageInfo(File imageFile, File incomingDataSetDirectory,
+ SampleIdentifier datasetSample)
+ {
+ String imageRelativePath = getRelativeImagePath(incomingDataSetDirectory, imageFile);
+ // we postpone assigning series numbers until all images are extracted
+ return new ImageFileInfo(null, DEFAULT_CHANNEL_CODE, DEFAULT_TILE, imageRelativePath,
+ null, null, null);
+ }
+ }
+
+ @Override
+ protected void storeInDatabase(IImagingQueryDAO dao, DataSetInformation dataSetInformation,
+ ImageFileExtractionResult extractedImages)
+ {
+ List<AcquiredSingleImage> images = extractedImages.getImages();
+ setSeriesNumber(images);
+ MicroscopyImageDatasetInfo dataset =
+ createMicroscopyImageDatasetInfo(dataSetInformation, images);
+
+ MicroscopyImageDatasetUploader.upload(dao, dataset, images, extractedImages.getChannels());
+ }
+
+ private void setSeriesNumber(List<AcquiredSingleImage> images)
+ {
+ Collections.sort(images, createPathComparator());
+ int seriesNumber = 1;
+ for (AcquiredSingleImage image : images)
+ {
+ image.setSeriesNumber(seriesNumber++);
+ }
+ }
+
+ private Comparator<AcquiredSingleImage> createPathComparator()
+ {
+ return new Comparator<AcquiredSingleImage>()
+ {
+ public int compare(AcquiredSingleImage o1, AcquiredSingleImage o2)
+ {
+ return getPath(o1).compareTo(getPath(o2));
+ }
+
+ private String getPath(AcquiredSingleImage o1)
+ {
+ return o1.getImageReference().getRelativeImagePath();
+ }
+ };
+ }
+
+ private MicroscopyImageDatasetInfo createMicroscopyImageDatasetInfo(
+ DataSetInformation dataSetInformation, List<AcquiredSingleImage> images)
+ {
+ boolean hasImageSeries = hasImageSeries(images);
+ return new MicroscopyImageDatasetInfo(dataSetInformation.getDataSetCode(),
+ spotGeometry.getRows(), spotGeometry.getColumns(), hasImageSeries);
+ }
+
+ @Override
+ protected void validateImages(DataSetInformation dataSetInformation, IMailClient mailClient,
+ File incomingDataSetDirectory, ImageFileExtractionResult extractionResult)
+ {
+ // do nothing - for now we do not have good examples of real data
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
index c908f2c3fdef402d9021c3191a898a590ac5420c..d1bf1fbe627d09410a820772924bec9f990a2be6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
@@ -74,10 +74,11 @@ public class MicroscopyImageFileExtractor extends AbstractImageFileExtractor
Float timepointOrNull = tryAsFloat(unparsedInfo.getTimepointToken());
Float depthOrNull = tryAsFloat(unparsedInfo.getDepthToken());
+ Integer seriesNumberOrNull = tryAsInt(unparsedInfo.getSeriesNumberToken());
String imageRelativePath = getRelativeImagePath(incomingDataSetDirectory, imageFile);
return new ImageFileInfo(null, channelCode, tileLocation, imageRelativePath,
- timepointOrNull, depthOrNull);
+ timepointOrNull, depthOrNull, seriesNumberOrNull);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
index 85caba84f479cb6aa811068e125b80e3190bd3aa..d02e7bad0743067a656803dbc5e6b215f73be5e4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
@@ -97,7 +97,7 @@ public final class PlateStorageProcessor extends AbstractImageStorageProcessor
String channelCode = getChannelCodeOrLabel(channelCodes, channel);
AcquiredSingleImage imageDesc =
new AcquiredSingleImage(wellLocation, tileLocation, channelCode, null, null,
- new RelativeImageReference(imageRelativePath, null, null));
+ null, new RelativeImageReference(imageRelativePath, null, null));
images.add(imageDesc);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/UnparsedImageFileInfoLexer.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/UnparsedImageFileInfoLexer.java
index f32bcbc8b68a80322c1b9fc00f867b1fafe0ee62..f7b3521f22c7c305310ada602ebea8d9de4c6c09 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/UnparsedImageFileInfoLexer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/UnparsedImageFileInfoLexer.java
@@ -59,6 +59,8 @@ public class UnparsedImageFileInfoLexer
private static final char TIME_MARKER = 't';
+ private static final char SERIES_NUMBER_MARKER = 'n';
+
public static UnparsedImageFileInfo tryExtractHCSImageFileInfo(File imageFile,
File incomingDataSetPath)
{
@@ -107,6 +109,7 @@ public class UnparsedImageFileInfoLexer
final String channelToken = tokensMap.get(CHANNEL_MARKER);
final String timepointToken = tokensMap.get(TIME_MARKER);
final String depthToken = tokensMap.get(DEPTH_MARKER);
+ final String seriesNumberToken = tokensMap.get(SERIES_NUMBER_MARKER);
UnparsedImageFileInfo info = new UnparsedImageFileInfo();
info.setWellLocationToken(wellLocationToken);
@@ -114,6 +117,7 @@ public class UnparsedImageFileInfoLexer
info.setChannelToken(channelToken);
info.setTimepointToken(timepointToken);
info.setDepthToken(depthToken);
+ info.setSeriesNumberToken(seriesNumberToken);
return info;
}
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 2932b505145f24ace96cbb3c4b98e805f7516a04..417eef63693ab7f65a2bf74e5e81a8d8357eed5e 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
@@ -52,8 +52,8 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
// batch updates
- @Update(sql = "insert into CHANNEL_STACKS (ID, X, Y, Z_in_M, T_in_SEC, DS_ID, SPOT_ID) values "
- + "(?{1.id}, ?{1.column}, ?{1.row}, ?{1.z}, ?{1.t}, ?{1.datasetId}, ?{1.spotId})", batchUpdate = true)
+ @Update(sql = "insert into CHANNEL_STACKS (ID, X, Y, Z_in_M, T_in_SEC, SERIES_NUMBER, IS_REPRESENTATIVE, DS_ID, SPOT_ID) values "
+ + "(?{1.id}, ?{1.column}, ?{1.row}, ?{1.z}, ?{1.t}, ?{1.seriesNumber}, ?{1.isRepresentative}, ?{1.datasetId}, ?{1.spotId})", batchUpdate = true)
public void addChannelStacks(List<ImgChannelStackDTO> channelStacks);
@Update(sql = "insert into IMAGES (ID, PATH, PAGE, COLOR) values "
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 7dca0ee839fc05a3126beabc4e111fb18d5f8bd7..29740923cde967e380561200d7ab2be63caa4241 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
@@ -80,16 +80,23 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
{
return null;
}
+ AbsoluteImageReference imgRef =
+ createAbsoluteImageReference(imageDTO, channel, thumbnailSizeOrNull);
+
+ return imgRef;
+ }
+
+ private AbsoluteImageReference createAbsoluteImageReference(ImgImageDTO imageDTO,
+ ImgChannelDTO channel, Size thumbnailSizeOrNull)
+ {
String path = imageDTO.getFilePath();
IContent content = contentRepository.getContent(path);
ColorComponent colorComponent = imageDTO.getColorComponent();
AbsoluteImageReference imgRef =
new AbsoluteImageReference(content, path, imageDTO.getPage(), colorComponent,
thumbnailSizeOrNull);
-
- imgRef.setTransformerFactory(channel.getImageTransformerFactory());
imgRef.setTransformerFactoryForMergedChannels(tryGetImageTransformerFactoryForMergedChannels());
-
+ imgRef.setTransformerFactory(channel.getImageTransformerFactory());
return imgRef;
}
@@ -205,4 +212,54 @@ public class ImagingDatasetLoader extends HCSDatasetLoader implements IImagingDa
return query.tryGetThumbnail(channelId, channelStackId, datasetId);
}
}
+
+ private ImgImageDTO tryGetRepresentativeImageDTO(long channelId, Location wellLocationOrNull,
+ boolean thumbnailWanted)
+ {
+ long datasetId = dataset.getId();
+ ImgImageDTO image = null;
+ if (wellLocationOrNull == null)
+ {
+ if (thumbnailWanted)
+ {
+ image = query.tryGetMicroscopyRepresentativeThumbnail(datasetId, channelId);
+ }
+ if (image == null)
+ {
+ image = query.tryGetMicroscopyRepresentativeImage(datasetId, channelId);
+ }
+ } else
+ {
+ if (thumbnailWanted)
+ {
+ image =
+ query.tryGetHCSRepresentativeThumbnail(datasetId, wellLocationOrNull,
+ channelId);
+ }
+ if (image == null)
+ {
+ image =
+ query.tryGetHCSRepresentativeImage(datasetId, wellLocationOrNull, channelId);
+ }
+ }
+ return image;
+ }
+
+ public AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
+ Location wellLocationOrNull, Size thumbnailSizeOrNull)
+ {
+ ImgChannelDTO channel = tryLoadChannel(channelCode);
+ if (channel == null)
+ {
+ return null;
+ }
+ ImgImageDTO imageDTO =
+ tryGetRepresentativeImageDTO(channel.getId(), wellLocationOrNull,
+ thumbnailSizeOrNull != null);
+ if (imageDTO == null)
+ {
+ return null;
+ }
+ return createAbsoluteImageReference(imageDTO, channel, thumbnailSizeOrNull);
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageFileInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageFileInfo.java
index 12ff5b1cac3cf08d9527d3943417a023a2860449..d4dfb34702d9d7ccabdbf6318ccb32a5e7799bf5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageFileInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageFileInfo.java
@@ -21,8 +21,10 @@ public final class ImageFileInfo
private final Float depthOrNull;
+ private final Integer seriesNumber;
+
public ImageFileInfo(Location wellLocationOrNull, String channelCode, Location tileLocation,
- String imageRelativePath, Float timepointOrNull, Float depthOrNull)
+ String imageRelativePath, Float timepointOrNull, Float depthOrNull, Integer seriesNumber)
{
assert channelCode != null;
assert tileLocation != null;
@@ -34,6 +36,7 @@ public final class ImageFileInfo
this.imageRelativePath = imageRelativePath;
this.timepointOrNull = timepointOrNull;
this.depthOrNull = depthOrNull;
+ this.seriesNumber = seriesNumber;
}
public Location tryGetWellLocation()
@@ -66,6 +69,11 @@ public final class ImageFileInfo
return depthOrNull;
}
+ public Integer tryGetSeriesNumber()
+ {
+ return seriesNumber;
+ }
+
public void setChannelCode(String channelCode)
{
this.channelCode = channelCode;
@@ -76,7 +84,8 @@ public final class ImageFileInfo
{
return "ImageFileInfo [well=" + wellLocationOrNull + ", tile=" + tileLocation
+ ", channel=" + channelCode + ", path=" + imageRelativePath + ", timepoint="
- + timepointOrNull + ", depth=" + depthOrNull + "]";
+ + timepointOrNull + ", depth=" + depthOrNull + ", seriesNumber=" + seriesNumber
+ + "]";
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/UnparsedImageFileInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/UnparsedImageFileInfo.java
index df02548da37b63d90c25dd03f385d7b9bd437bff..bb02be652e00e63c79d3fd606f79945b5a67ccfc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/UnparsedImageFileInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/UnparsedImageFileInfo.java
@@ -23,6 +23,9 @@ public class UnparsedImageFileInfo extends AbstractHashable
// can be null
private String depthToken;
+ // can be null
+ private String seriesNumberToken;
+
/** can be null */
public String getWellLocationToken()
{
@@ -75,4 +78,14 @@ public class UnparsedImageFileInfo extends AbstractHashable
{
this.depthToken = depthToken;
}
+
+ public String getSeriesNumberToken()
+ {
+ return seriesNumberToken;
+ }
+
+ public void setSeriesNumberToken(String seriesNumberToken)
+ {
+ this.seriesNumberToken = seriesNumberToken;
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
index 3802e195bcbce39dc9eaadb64636fdf7936684d3..53f6afcace0eb4bb69dd4b13ba2d8110919541ba 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
@@ -84,7 +84,7 @@ public class HCSImageFileExtractor extends AbstractImageFileExtractor
String imageRelativePath = getRelativeImagePath(incomingDataSetDirectory, imageFile);
return new ImageFileInfo(asLocation(wellLocation), channelCode, tileLocation,
- imageRelativePath, timepoint, null);
+ imageRelativePath, timepoint, null, null);
}
private long getSecondsFromFirstMeasurement(File imageFile, String[] tokens)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
index 96e91344f5a5718b6478b6e6807357e833c9263f..a97bc7d6a3844dfe4cf73af71c1fc5743005dbf6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
@@ -18,26 +18,36 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.File;
import java.io.IOException;
+import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.io.IContent;
-import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
-import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.images.TileImageReference;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ImageResolutionKind;
/**
- * Allows to download screening images in a chosen size for a specified channels or with all
+ * Allows to:<br>
+ * - download screening and microscopy images in a chosen size for a specified channels or with all
* channels merged.<br>
- * Assumes that originally there is one image for each channel and no image with all the channels
- * merged exist.
+ * - fetch representative microscopy dataset image
*
* @author Tomasz Pylak
*/
-public class MergingImagesDownloadServlet extends AbstractImagesDownloadServlet
+public class MergingImagesDownloadServlet extends AbstractImagesDownloadServlet implements
+ IDatasetImageOverviewPlugin
{
private static final long serialVersionUID = 1L;
+ /** Used to construct {@link IDatasetImageOverviewPlugin}. */
+ public MergingImagesDownloadServlet(Properties pluginProperties)
+ {
+ }
+
+ public MergingImagesDownloadServlet()
+ {
+ }
+
/**
* @throws EnvironmentFailureException if image does not exist
**/
@@ -45,10 +55,28 @@ public class MergingImagesDownloadServlet extends AbstractImagesDownloadServlet
protected final ResponseContentStream createImageResponse(TileImageReference params,
File datasetRoot, String datasetCode) throws IOException, EnvironmentFailureException
{
- IImagingDatasetLoader imageAccessor =
- HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
- IContent image = ImageChannelsUtils.getImage(imageAccessor, params);
- return ResponseContentStream.create(image.getInputStream(), image.getSize(),
- ImageChannelsUtils.IMAGES_CONTENT_TYPE, image.tryGetName());
+ return ImageChannelsUtils.getImageStream(datasetRoot, datasetCode, params);
+ }
+
+ private static final Size DEFAULT_THUMBNAIL_SIZE = new Size(200, 120);
+
+ /** Provides overview of microscopy datasets. */
+ public ResponseContentStream createImageOverview(String datasetCode, String datasetTypeCode,
+ File datasetRoot, ImageResolutionKind resolution)
+ {
+ Size thumbnailSize = tryGetThumbnailSize(resolution);
+ return ImageChannelsUtils.getRepresentativeImageStream(datasetRoot, datasetCode, null,
+ thumbnailSize);
+ }
+
+ private static Size tryGetThumbnailSize(ImageResolutionKind resolution)
+ {
+ if (resolution == ImageResolutionKind.NORMAL)
+ {
+ return null;
+ } else
+ {
+ return DEFAULT_THUMBNAIL_SIZE;
+ }
}
}
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 cc6a31b01b566aa23f3a09561b70d01413c981c9..7d395c6cea76325f1695296bdbb479db8d9715db 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
@@ -20,6 +20,7 @@ import java.awt.Color;
import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
import java.io.ByteArrayOutputStream;
+import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
@@ -29,14 +30,18 @@ import javax.imageio.ImageIO;
import org.apache.log4j.Logger;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.io.ByteArrayBasedContent;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
+import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.generic.server.ResponseContentStream;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -56,16 +61,46 @@ public class ImageChannelsUtils
// MIME type of the images which are produced by this class
public static final String IMAGES_CONTENT_TYPE = "image/png";
-
/**
* Returns content of image for the specified tile in the specified size and for the requested
* channel or with all channels merged.
*/
- public static IContent getImage(IImagingDatasetLoader imageAccessor, TileImageReference params)
+ public static ResponseContentStream getImageStream(File datasetRoot, String datasetCode,
+ TileImageReference params)
+ {
+ IImagingDatasetLoader imageAccessor =
+ HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
+ IContent image = getImage(imageAccessor, params);
+ return asResponseContentStream(image);
+ }
+
+ /**
+ * Returns content of the image which is representative for the given dataset.
+ */
+ public static ResponseContentStream getRepresentativeImageStream(File datasetRoot,
+ String datasetCode, Location wellLocationOrNull, Size thumbnailSizeOrNull)
+ {
+ IImagingDatasetLoader imageAccessor =
+ HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
+ List<AbsoluteImageReference> imageReferences =
+ getRepresentativeImageReferences(imageAccessor, wellLocationOrNull,
+ thumbnailSizeOrNull);
+ IContent imageContent = mergeAllChannels(imageReferences, true, true);
+ return asResponseContentStream(imageContent);
+ }
+
+ private static ResponseContentStream asResponseContentStream(IContent image)
+ {
+ return ResponseContentStream.create(image.getInputStream(), image.getSize(),
+ ImageChannelsUtils.IMAGES_CONTENT_TYPE, image.tryGetName());
+ }
+
+ @Private
+ static IContent getImage(IImagingDatasetLoader imageAccessor, TileImageReference params)
{
return getImage(imageAccessor, params, true, true);
}
-
+
private static IContent getImage(IImagingDatasetLoader imageAccessor,
TileImageReference params, boolean transform, boolean convertToPng)
{
@@ -93,10 +128,48 @@ public class ImageChannelsUtils
tileImageReference.setChannelStack(channelStackReference);
tileImageReference.setChannel(chosenChannelCode);
tileImageReference.setThumbnailSizeOrNull(thumbnailSizeOrNull);
- tileImageReference.setMergeAllChannels(ScreeningConstants.MERGED_CHANNELS.equalsIgnoreCase(chosenChannelCode));
+ tileImageReference.setMergeAllChannels(ScreeningConstants.MERGED_CHANNELS
+ .equalsIgnoreCase(chosenChannelCode));
return getImage(imageAccessor, tileImageReference, false, convertToPng);
}
+ private static List<AbsoluteImageReference> getRepresentativeImageReferences(
+ IImagingDatasetLoader imageAccessor, Location wellLocationOrNull,
+ Size thumbnailSizeOrNull)
+ {
+ List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
+
+ for (String chosenChannel : imageAccessor.getImageParameters().getChannelsCodes())
+ {
+ AbsoluteImageReference image =
+ getRepresentativeImageReference(imageAccessor, chosenChannel,
+ wellLocationOrNull, thumbnailSizeOrNull);
+ images.add(image);
+ }
+ return images;
+ }
+
+ /**
+ * @throw {@link EnvironmentFailureException} when image does not exist
+ */
+ private static AbsoluteImageReference getRepresentativeImageReference(
+ IImagingDatasetLoader imageAccessor, String channelCode, Location wellLocationOrNull,
+ Size thumbnailSizeOrNull)
+ {
+ AbsoluteImageReference image =
+ imageAccessor.tryGetRepresentativeImage(channelCode, wellLocationOrNull,
+ thumbnailSizeOrNull);
+ if (image != null)
+ {
+ return image;
+ } else
+ {
+ throw EnvironmentFailureException.fromTemplate("No representative "
+ + (thumbnailSizeOrNull != null ? "thumbnail" : "image")
+ + " found for well %s and channel %s", wellLocationOrNull, channelCode);
+ }
+ }
+
private static List<AbsoluteImageReference> getImageReferences(
IImagingDatasetLoader imageAccessor, TileImageReference params)
{
@@ -128,7 +201,8 @@ public class ImageChannelsUtils
final IContent content;
if (convertToPng || imageReference.tryGetColorComponent() != null)
{
- final BufferedImage image = transform(calculateSingleImage(imageReference), transformerFactoryOrNull);
+ final BufferedImage image =
+ transform(calculateSingleImage(imageReference), transformerFactoryOrNull);
long start = operationLog.isDebugEnabled() ? System.currentTimeMillis() : 0;
content = createPngContent(image, imageReference.getContent().tryGetName());
@@ -181,7 +255,8 @@ public class ImageChannelsUtils
image = transformToChannel(image, colorComponentOrNull);
if (operationLog.isDebugEnabled())
{
- operationLog.debug("Select single channel: " + (System.currentTimeMillis() - start));
+ operationLog
+ .debug("Select single channel: " + (System.currentTimeMillis() - start));
}
}
return image;
@@ -199,7 +274,8 @@ public class ImageChannelsUtils
return image;
}
- private static IContent mergeAllChannels(List<AbsoluteImageReference> imageReferences, boolean transform, boolean convertToPng)
+ private static IContent mergeAllChannels(List<AbsoluteImageReference> imageReferences,
+ boolean transform, boolean convertToPng)
{
AbsoluteImageReference allChannelsImageReference =
tryCreateAllChannelsImageReference(imageReferences);
@@ -215,13 +291,15 @@ public class ImageChannelsUtils
{
List<BufferedImage> images = calculateSingleImages(imageReferences);
BufferedImage mergedImage = mergeChannels(images);
- IImageTransformerFactory transformerFactory = transform ?
- imageReferences.get(0).getTransformerFactoryForMergedChannels() : null;
+ IImageTransformerFactory transformerFactory =
+ transform ? imageReferences.get(0).getTransformerFactoryForMergedChannels()
+ : null;
return createPngContent(transform(mergedImage, transformerFactory), null);
}
}
-
- private static BufferedImage transform(BufferedImage input, IImageTransformerFactory factoryOrNull)
+
+ private static BufferedImage transform(BufferedImage input,
+ IImageTransformerFactory factoryOrNull)
{
if (factoryOrNull == null)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewer.java
index 11561437dcd598bfa97a6e4aee6f1924363f747a..2ca9e031b6c8e050630985d4db2e71c8d5e93116 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewer.java
@@ -17,9 +17,10 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import java.util.Map;
-import java.util.Map.Entry;
+import java.util.Set;
import java.util.TreeMap;
import com.extjs.gxt.ui.client.event.Events;
@@ -40,23 +41,203 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelSt
class LogicalImageSeriesViewer
{
+ static class ImageSeriesPoint implements Comparable<ImageSeriesPoint>
+ {
+ private final Float tOrNull, zOrNull;
+
+ private final Integer seriesNumberOrNull;
+
+ public ImageSeriesPoint(ImageChannelStack stack)
+ {
+ this.tOrNull = stack.tryGetTimepoint();
+ this.zOrNull = stack.tryGetDepth();
+ this.seriesNumberOrNull = stack.tryGetSeriesNumber();
+ }
+
+ public ImageSeriesPoint(Float tOrNull, Float zOrNull, Integer seriesNumberOrNull)
+ {
+ this.tOrNull = tOrNull;
+ this.zOrNull = zOrNull;
+ this.seriesNumberOrNull = seriesNumberOrNull;
+ }
+
+ public String getLabel()
+ {
+ String desc = "";
+ if (tOrNull != null)
+ {
+ if (desc.length() > 0)
+ {
+ desc += ". ";
+ }
+ desc += "Time: " + tOrNull + " sec";
+ }
+ if (zOrNull != null)
+ {
+ if (desc.length() > 0)
+ {
+ desc += ". ";
+ }
+ desc += "Depth: " + zOrNull;
+ }
+ if (seriesNumberOrNull != null)
+ {
+ if (desc.length() > 0)
+ {
+ desc += ". ";
+ }
+ desc += "Series: " + seriesNumberOrNull;
+ }
+ return desc;
+ }
+
+ public int compareTo(ImageSeriesPoint o)
+ {
+ int cmp;
+ cmp = compareNullable(seriesNumberOrNull, o.seriesNumberOrNull);
+ if (cmp != 0)
+ return cmp;
+ cmp = compareNullable(tOrNull, o.tOrNull);
+ if (cmp != 0)
+ return cmp;
+ return compareNullable(zOrNull, o.zOrNull);
+ }
+
+ private static <T extends Comparable<T>> int compareNullable(T v1OrNull, T v2OrNull)
+ {
+ if (v1OrNull == null)
+ {
+ return v2OrNull == null ? 0 : -1;
+ } else
+ {
+ return v2OrNull == null ? 1 : v1OrNull.compareTo(v2OrNull);
+ }
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result =
+ prime * result
+ + ((seriesNumberOrNull == null) ? 0 : seriesNumberOrNull.hashCode());
+ result = prime * result + ((tOrNull == null) ? 0 : tOrNull.hashCode());
+ result = prime * result + ((zOrNull == null) ? 0 : zOrNull.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;
+ ImageSeriesPoint other = (ImageSeriesPoint) obj;
+ if (seriesNumberOrNull == null)
+ {
+ if (other.seriesNumberOrNull != null)
+ return false;
+ } else if (!seriesNumberOrNull.equals(other.seriesNumberOrNull))
+ return false;
+ if (tOrNull == null)
+ {
+ if (other.tOrNull != null)
+ return false;
+ } else if (!tOrNull.equals(other.tOrNull))
+ return false;
+ if (zOrNull == null)
+ {
+ if (other.zOrNull != null)
+ return false;
+ } else if (!zOrNull.equals(other.zOrNull))
+ return false;
+ return true;
+ }
+ }
+
+ static class LogicalImageSeriesViewerModel
+ {
+ private final List<ImageSeriesPoint> sortedPoints;
+
+ private final List<List<ImageChannelStack>> sortedChannelStackSeriesPoints;
+
+ public LogicalImageSeriesViewerModel(List<ImageChannelStack> channelStackImages)
+ {
+ Map<ImageSeriesPoint, List<ImageChannelStack>> channelStackImagesBySeries =
+ groupImagesBySeries(channelStackImages);
+ this.sortedPoints = sortPoints(channelStackImagesBySeries.keySet());
+ this.sortedChannelStackSeriesPoints =
+ getSortedSeries(channelStackImagesBySeries, sortedPoints);
+ }
+
+ private static Map<ImageSeriesPoint, List<ImageChannelStack>> groupImagesBySeries(
+ List<ImageChannelStack> channelStackImages)
+ {
+ Map<ImageSeriesPoint, List<ImageChannelStack>> result =
+ new TreeMap<ImageSeriesPoint, List<ImageChannelStack>>();
+ for (ImageChannelStack ref : channelStackImages)
+ {
+ ImageSeriesPoint point = new ImageSeriesPoint(ref);
+ List<ImageChannelStack> imageReferences = result.get(point);
+ if (imageReferences == null)
+ {
+ imageReferences = new ArrayList<ImageChannelStack>();
+ result.put(point, imageReferences);
+ }
+ imageReferences.add(ref);
+ }
+ return result;
+ }
+
+ public List<ImageSeriesPoint> getSortedPoints()
+ {
+ return sortedPoints;
+ }
+
+ public List<List<ImageChannelStack>> getSortedChannelStackSeriesPoints()
+ {
+ return sortedChannelStackSeriesPoints;
+ }
+ }
+
public static LayoutContainer create(String sessionId,
List<ImageChannelStack> channelStackImages, LogicalImageReference images,
String channel, int imageWidth, int imageHeight)
{
- Map<Float, List<ImageChannelStack>> channelStackImagesByTimepoint =
- groupImagesByTimepoint(channelStackImages);
-
+ LogicalImageSeriesViewerModel model = new LogicalImageSeriesViewerModel(channelStackImages);
List<LayoutContainer> frames =
- createTimepointFrames(channelStackImagesByTimepoint, images, channel, sessionId,
- imageWidth, imageHeight);
+ createTimepointFrames(model.getSortedChannelStackSeriesPoints(), images, channel,
+ sessionId, imageWidth, imageHeight);
+
+ return createMoviePlayer(frames, model.getSortedPoints());
+ }
- Float[] timepoints = channelStackImagesByTimepoint.keySet().toArray(new Float[0]);
- return createMoviePlayer(frames, timepoints);
+ private static List<List<ImageChannelStack>> getSortedSeries(
+ Map<ImageSeriesPoint, List<ImageChannelStack>> channelStackImagesBySeries,
+ List<ImageSeriesPoint> sortedPoints)
+ {
+ List<List<ImageChannelStack>> sortedSeries = new ArrayList<List<ImageChannelStack>>();
+ for (ImageSeriesPoint point : sortedPoints)
+ {
+ List<ImageChannelStack> series = channelStackImagesBySeries.get(point);
+ sortedSeries.add(series);
+ }
+ return sortedSeries;
+ }
+
+ private static List<ImageSeriesPoint> sortPoints(Set<ImageSeriesPoint> points)
+ {
+ ArrayList<ImageSeriesPoint> pointsList = new ArrayList<ImageSeriesPoint>(points);
+ Collections.sort(pointsList);
+ return pointsList;
}
private static LayoutContainer createMoviePlayer(final List<LayoutContainer> frames,
- final Float[] timepoints)
+ final List<ImageSeriesPoint> sortedPoints)
{
final LayoutContainer mainContainer = new LayoutContainer();
addAll(mainContainer, frames);
@@ -73,29 +254,33 @@ class LogicalImageSeriesViewer
}
frames.get(newValue - 1).show();
mainContainer.remove(mainContainer.getItem(0));
- mainContainer.insert(new Label(createTimepointLabel(timepoints, newValue)), 0);
+ mainContainer
+ .insert(new Label(createTimepointLabel(sortedPoints, newValue)), 0);
mainContainer.layout();
}
});
mainContainer.insert(slider, 0);
- mainContainer.insert(new Label(createTimepointLabel(timepoints, 1)), 0);
+ mainContainer.insert(new Label(createTimepointLabel(sortedPoints, 1)), 0);
slider.setValue(1);
return mainContainer;
}
+ /**
+ * @param sortedChannelStackSeriesPoints - one element on the list are all tiles for a fixed
+ * series point
+ */
private static List<LayoutContainer> createTimepointFrames(
- Map<Float, List<ImageChannelStack>> channelStackImagesByTimepoint,
+ List<List<ImageChannelStack>> sortedChannelStackSeriesPoints,
LogicalImageReference images, String channel, String sessionId, int imageWidth,
int imageHeight)
{
final List<LayoutContainer> frames = new ArrayList<LayoutContainer>();
int counter = 0;
- for (Entry<Float, List<ImageChannelStack>> entry : channelStackImagesByTimepoint.entrySet())
+ for (List<ImageChannelStack> seriesPointStacks : sortedChannelStackSeriesPoints)
{
- List<ImageChannelStack> imageReferences = entry.getValue();
final LayoutContainer container =
- createTilesGridForTimepoint(imageReferences, images, channel, sessionId,
+ createTilesGridForTimepoint(seriesPointStacks, images, channel, sessionId,
imageWidth, imageHeight);
frames.add(container);
if (counter > 0)
@@ -116,14 +301,14 @@ class LogicalImageSeriesViewer
}
private static LayoutContainer createTilesGridForTimepoint(
- List<ImageChannelStack> channelStackReferences, LogicalImageReference images,
+ List<ImageChannelStack> seriesPointStacks, LogicalImageReference images,
String channel, String sessionId, int imageWidth, int imageHeight)
{
final LayoutContainer container =
new LayoutContainer(new TableLayout(images.getTileColsNum()));
ImageChannelStack[/* tileRow */][/* tileCol */] tilesMap =
- createTilesMap(channelStackReferences, images);
+ createTilesMap(seriesPointStacks, images);
for (int row = 1; row <= images.getTileRowsNum(); row++)
{
for (int col = 1; col <= images.getTileColsNum(); col++)
@@ -163,29 +348,12 @@ class LogicalImageSeriesViewer
container.add(dummy);
}
- private static String createTimepointLabel(Float[] timepoints, int sequenceNumber)
- {
- Float timepoint = timepoints[sequenceNumber - 1];
- int numberOfSequences = timepoints.length;
- return "Timepoint: " + timepoint + "sec (" + sequenceNumber + "/" + numberOfSequences + ")";
- }
-
- private static Map<Float, List<ImageChannelStack>> groupImagesByTimepoint(
- List<ImageChannelStack> channelStackImages)
+ private static String createTimepointLabel(List<ImageSeriesPoint> sortedPoints,
+ int sequenceNumber)
{
- Map<Float, List<ImageChannelStack>> result = new TreeMap<Float, List<ImageChannelStack>>();
- for (ImageChannelStack ref : channelStackImages)
- {
- Float t = ref.tryGetTimepoint();
- List<ImageChannelStack> imageReferences = result.get(t);
- if (imageReferences == null)
- {
- imageReferences = new ArrayList<ImageChannelStack>();
- result.put(t, imageReferences);
- }
- imageReferences.add(ref);
- }
- return result;
+ ImageSeriesPoint point = sortedPoints.get(sequenceNumber - 1);
+ int numberOfSequences = sortedPoints.size();
+ return point.getLabel() + " (" + sequenceNumber + "/" + numberOfSequences + ")";
}
private static final Slider createTimepointsSlider(int maxValue, Listener<SliderEvent> listener)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelStack.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelStack.java
index 0a403091cb834b667bbeb2791e9ba2a9cea22b88..6b97736df150047c66e99563221a567ad5aef39d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelStack.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelStack.java
@@ -37,6 +37,8 @@ public class ImageChannelStack implements ISerializable
private Float tOrNull, zOrNull;
+ private Integer seriesNumberOrNull;
+
// GWT only
@SuppressWarnings("unused")
private ImageChannelStack()
@@ -44,13 +46,14 @@ public class ImageChannelStack implements ISerializable
}
public ImageChannelStack(long channelStackTechId, int tileRow, int tileCol, Float tOrNull,
- Float zOrNull)
+ Float zOrNull, Integer seriesNumberOrNull)
{
this.channelStackTechId = channelStackTechId;
this.tileRow = tileRow;
this.tileCol = tileCol;
this.tOrNull = tOrNull;
this.zOrNull = zOrNull;
+ this.seriesNumberOrNull = seriesNumberOrNull;
}
public long getChannelStackTechId()
@@ -78,6 +81,11 @@ public class ImageChannelStack implements ISerializable
return zOrNull;
}
+ public Integer tryGetSeriesNumber()
+ {
+ return seriesNumberOrNull;
+ }
+
@Override
public String toString()
{
@@ -90,7 +98,10 @@ public class ImageChannelStack implements ISerializable
{
desc += ", z=" + zOrNull;
}
-
+ if (seriesNumberOrNull != null)
+ {
+ desc += ", series=" + seriesNumberOrNull;
+ }
return "channelStack=" + channelStackTechId + ", tile[" + tileRow + "," + tileCol + "]"
+ desc;
}
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 68e1df0c4d892c4defbb6b35a29e4fb0e96679d2..d0e56ba874790e79073f953a00c381c8c79d729d 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
@@ -144,7 +144,7 @@ public class HCSDatasetLoader implements IImageDatasetLoader
private static ImageChannelStack convert(ImgChannelStackDTO stack)
{
return new ImageChannelStack(stack.getId(), stack.getRow(), stack.getColumn(),
- stack.getT(), stack.getZ());
+ stack.getT(), stack.getZ(), stack.getSeriesNumber());
}
public ImageDatasetParameters getImageParameters()
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 79194a2867df09b5a5401f811161faacfc5e506b..c9084979a196da6fcc1eaf6d4c4b17d335c80942 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
@@ -54,13 +54,35 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
// joins
+ "ACQUIRED_IMAGES.CHANNEL_STACK_ID = CHANNEL_STACKS.ID ";
- // FIXME 2010-12-10, Tomasz Pylak: uncomment when we are able to show a representative image
+ public static final String SQL_HCS_IMAGE_REPRESENTATIVE =
+ "select i.* from CHANNEL_STACKS, SPOTS, ACQUIRED_IMAGES, IMAGES as i "
+ + "where "
+ + "CHANNEL_STACKS.is_representative = 'T' and "
+ + "CHANNEL_STACKS.DS_ID = ?{1} and "
+ + "ACQUIRED_IMAGES.channel_id = ?{3} and "
+ + "SPOTS.x = ?{2.x} and SPOTS.y = ?{2.y} and "
+ // joins
+ + "ACQUIRED_IMAGES.CHANNEL_STACK_ID = CHANNEL_STACKS.ID and "
+ + "CHANNEL_STACKS.SPOT_ID = SPOTS.ID ";
+
+ public static final String SQL_MICROSCOPY_IMAGE_REPRESENTATIVE =
+ "select i.* from CHANNEL_STACKS, ACQUIRED_IMAGES, IMAGES as i "
+ + "where "
+ + "CHANNEL_STACKS.is_representative = 'T' and "
+ + "CHANNEL_STACKS.DS_ID = ?{1} and "
+ + "ACQUIRED_IMAGES.channel_id = ?{2} and "
+ // joins
+ + "ACQUIRED_IMAGES.CHANNEL_STACK_ID = CHANNEL_STACKS.ID ";
+
+ // TODO 2010-12-10, Tomasz Pylak: uncomment when we are able to show a representative image
public static final String SQL_NO_MULTIDIMENTIONAL_DATA_COND =
" order by CHANNEL_STACKS.T_in_SEC, CHANNEL_STACKS.Z_in_M limit 1";
// " and CHANNEL_STACKS.T_in_SEC IS NULL "
// + " and CHANNEL_STACKS.Z_in_M IS NULL ";
+ // ---------------- HCS ---------------------------------
+
/**
* @return an HCS image for the specified chanel, well and tile. If many images (e.g. for
* different timepoints or depths) exist, null is returned.
@@ -79,6 +101,24 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
public ImgImageDTO tryGetHCSThumbnail(long channelId, long datasetId, Location tileLocation,
Location wellLocation);
+ /**
+ * @return an representative HCS image for the specified dataset and well. Returns null if there
+ * are no images at all for the specified well.
+ */
+ @Select(SQL_HCS_IMAGE_REPRESENTATIVE + " and ACQUIRED_IMAGES.IMG_ID = i.ID ")
+ public ImgImageDTO tryGetHCSRepresentativeImage(long datasetId, Location wellLocation,
+ long channelId);
+
+ /**
+ * @return an representative HCS thumbnail for the specified dataset and well. Returns null if
+ * there are no images at all for the specified well.
+ */
+ @Select(SQL_HCS_IMAGE_REPRESENTATIVE + " and ACQUIRED_IMAGES.THUMBNAIL_ID = i.ID ")
+ public ImgImageDTO tryGetHCSRepresentativeThumbnail(long datasetId, Location wellLocation,
+ long channelId);
+
+ // ---------------- Microscopy ---------------------------------
+
/**
* @return an microscopy image for the specified channel and tile. If many images (e.g. for
* different timepoints or depths) exist, null is returned.
@@ -96,6 +136,33 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
public ImgImageDTO tryGetMicroscopyThumbnail(long channelId, long datasetId,
Location tileLocation);
+ /**
+ * @return an representative microscopy image for the specified dataset.
+ */
+ @Select(SQL_MICROSCOPY_IMAGE_REPRESENTATIVE + " and ACQUIRED_IMAGES.IMG_ID = i.ID ")
+ public ImgImageDTO tryGetMicroscopyRepresentativeImage(long datasetId, long channelId);
+
+ /**
+ * @return an representative microscopy thumbnail for the specified dataset. Can be null if
+ * thumbnail has not been generated.
+ */
+ @Select(SQL_MICROSCOPY_IMAGE_REPRESENTATIVE + " and ACQUIRED_IMAGES.THUMBNAIL_ID = i.ID ")
+ public ImgImageDTO tryGetMicroscopyRepresentativeThumbnail(long datasetId, long channelId);
+
+ // ---------------- Microscopy - channels ---------------------------------
+
+ @Select("select cs.* from CHANNEL_STACKS cs "
+ + "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);
+
+ // ---------------- Generic ---------------------------------
+
/** @return an image for the specified channel and channel stack or null */
@Select("select i.* from IMAGES as i "
+ "join ACQUIRED_IMAGES on ACQUIRED_IMAGES.IMG_ID = i.ID "
@@ -120,6 +187,11 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
// simple getters
+ @Select("select * from DATA_SETS where PERM_ID = ?{1}")
+ public ImgDatasetDTO tryGetDatasetByPermId(String datasetPermId);
+
+ // ---------------- HCS - experiments, containers, channels ---------------------------------
+
@Select("select * from EXPERIMENTS where PERM_ID = ?{1}")
public ImgExperimentDTO tryGetExperimentByPermId(String experimentPermId);
@@ -129,9 +201,6 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
@Select("select ID from CONTAINERS where PERM_ID = ?{1}")
public Long tryGetContainerIdPermId(String containerPermId);
- @Select("select * from DATA_SETS where PERM_ID = ?{1}")
- public ImgDatasetDTO tryGetDatasetByPermId(String datasetPermId);
-
@Select("select * from CONTAINERS where ID = ?{1}")
public ImgContainerDTO getContainerById(long containerId);
@@ -142,19 +211,22 @@ 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("select cs.* from CHANNEL_STACKS cs "
- + "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(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("select * from FEATURE_DEFS where DS_ID = ?{1}")
public List<ImgFeatureDefDTO> listFeatureDefsByDataSetId(long dataSetId);
@@ -166,15 +238,4 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
@Select(sql = "select * from FEATURE_VALUES where FD_ID = ?{1.id} order by T_in_SEC, Z_in_M", resultSetBinding = FeatureVectorDataObjectBinding.class)
public List<ImgFeatureValuesDTO> getFeatureValues(ImgFeatureDefDTO featureDef);
- @Select("select * from CHANNELS where (EXP_ID = ?{1}) and CODE = upper(?{2})")
- public ImgChannelDTO tryGetChannelForExperiment(long experimentId, String chosenChannelCode);
-
- @Select("select * from CHANNELS where (DS_ID = ?{1}) and CODE = upper(?{2})")
- public ImgChannelDTO tryGetChannelForDataset(long datasetId, 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);
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
index f262b732a3f21c4f1ae93225f8353e83a75a3898..eb973b183d0a88850fd86c4bc6c6bf1431452573 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
@@ -47,12 +47,18 @@ public class ImgChannelStackDTO
@ResultColumn("T_in_SEC")
private Float t;
+ @ResultColumn("SERIES_NUMBER")
+ private Integer seriesNumber;
+
@ResultColumn("DS_ID")
private long datasetId;
@ResultColumn("SPOT_ID")
private Long spotId;
+ @ResultColumn("IS_REPRESENTATIVE")
+ private boolean isRepresentative;
+
@SuppressWarnings("unused")
private ImgChannelStackDTO()
{
@@ -60,7 +66,7 @@ public class ImgChannelStackDTO
}
public ImgChannelStackDTO(long id, int row, int column, long datasetId, Long spotIdOrNull,
- Float tOrNull, Float zOrNull)
+ Float tOrNull, Float zOrNull, Integer seriesNumber, boolean isRepresentative)
{
this.id = id;
this.row = row;
@@ -69,6 +75,8 @@ public class ImgChannelStackDTO
this.spotId = spotIdOrNull;
this.t = tOrNull;
this.z = zOrNull;
+ this.seriesNumber = seriesNumber;
+ this.isRepresentative = isRepresentative;
}
public long getId()
@@ -111,6 +119,16 @@ public class ImgChannelStackDTO
this.t = t;
}
+ public Integer getSeriesNumber()
+ {
+ return seriesNumber;
+ }
+
+ public void setSeriesNumber(Integer seriesNumber)
+ {
+ this.seriesNumber = seriesNumber;
+ }
+
public long getDatasetId()
{
return datasetId;
@@ -132,10 +150,21 @@ public class ImgChannelStackDTO
this.spotId = spotId;
}
+ public boolean getIsRepresentative()
+ {
+ return isRepresentative;
+ }
+
+ public void setRepresentative(boolean isRepresentative)
+ {
+ this.isRepresentative = isRepresentative;
+ }
+
@Override
// use all fields besides id
public int hashCode()
{
+ // NOTE: isRepresentative field is derived and can be skipped
final int prime = 31;
int result = 1;
result = prime * result + (int) (datasetId ^ (datasetId >>> 32));
@@ -144,6 +173,7 @@ public class ImgChannelStackDTO
result = prime * result + ((spotId == null) ? 0 : spotId.hashCode());
result = prime * result + ((t == null) ? 0 : t.hashCode());
result = prime * result + ((z == null) ? 0 : z.hashCode());
+ result = prime * result + ((seriesNumber == null) ? 0 : seriesNumber.hashCode());
return result;
}
@@ -151,6 +181,7 @@ public class ImgChannelStackDTO
// use all fields besides id
public boolean equals(Object obj)
{
+ // NOTE: isRepresentative field is derived and can be skipped
if (obj == null)
return false;
if (this == obj)
@@ -192,6 +223,12 @@ public class ImgChannelStackDTO
return false;
} else if (!z.equals(other.z))
return false;
+ if (seriesNumber == null)
+ {
+ if (other.seriesNumber != null)
+ return false;
+ } else if (!seriesNumber.equals(other.seriesNumber))
+ return false;
return true;
}
diff --git a/screening/source/sql/postgresql/009/schema-009.sql b/screening/source/sql/postgresql/009/schema-009.sql
index 834d82dbf0e26750adc8b42c6e639e5271d78010..a94fe7dceadada7ec33792d554f474255de81770 100644
--- a/screening/source/sql/postgresql/009/schema-009.sql
+++ b/screening/source/sql/postgresql/009/schema-009.sql
@@ -112,13 +112,9 @@ CREATE TABLE CHANNEL_STACKS (
X INTEGER,
Y INTEGER,
-- We use the fixed dimension meters here.
- -- Not null only if SERIES_NUMBER is null.
Z_in_M REAL,
-- We use the fixed dimension seconds here.
- -- Not null only if SERIES_NUMBER is null.
T_in_SEC REAL,
- -- not null if and only if t and z are null
- -- TODO: write constraint which checks this
SERIES_NUMBER INTEGER,
-- For all channel stacks of a well (HCS) or image dataset (microscopy) there should be exactly
diff --git a/screening/source/sql/postgresql/migration/migration-008-009.sql b/screening/source/sql/postgresql/migration/migration-008-009.sql
index 65f164222760cf2fb165b6b12aada8366b1f59d2..54d146739b65a4115b32e4e70ad2b102c6ce879b 100644
--- a/screening/source/sql/postgresql/migration/migration-008-009.sql
+++ b/screening/source/sql/postgresql/migration/migration-008-009.sql
@@ -33,3 +33,11 @@ $$ LANGUAGE 'plpgsql';
CREATE TRIGGER CHANNEL_STACKS_CHECK BEFORE INSERT OR UPDATE ON CHANNEL_STACKS
FOR EACH ROW EXECUTE PROCEDURE CHANNEL_STACKS_CHECK();
+--- for each spot set exactly one representative channel_stacks record (with minimal id) ---------
+
+update channel_stacks as cs
+ set cs.is_representative = 'T'
+ where cs.id in (select min(cs.id)
+ from channel_stacks cs
+ join spots on spots.id = cs.spot_id
+ group by spots.id)
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagesRepresentativesOracleTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagesRepresentativesOracleTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..1b77f1efa8dd03f7b117b4314c2ab0e7cd3c1472
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImagesRepresentativesOracleTest.java
@@ -0,0 +1,79 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.etl;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.openbis.dss.etl.AbstractImageDatasetUploader.ChannelStackRepresentativesOracle;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelStackDTO;
+
+/**
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses = ChannelStackRepresentativesOracle.class)
+public class ImagesRepresentativesOracleTest extends AssertJUnit
+{
+ @Test
+ public void testWithSpots()
+ {
+ ImgChannelStackDTO img1 = createStack(2, 2, 2L, 1f, 1f);
+ ImgChannelStackDTO img2 = createStack(1, 1, 1L, 200f, 200f);
+ ImgChannelStackDTO img3 = createStack(1, 1, 1L, 1f, 1f);
+
+ Set<ImgChannelStackDTO> representatives = calculateRepresentatives(img1, img2, img3);
+ assertTrue(representatives.contains(img1));
+ assertFalse(representatives.contains(img2));
+ assertTrue(representatives.contains(img3));
+ }
+
+ private Set<ImgChannelStackDTO> calculateRepresentatives(ImgChannelStackDTO... stacks)
+ {
+ Set<ImgChannelStackDTO> stacksSet = new HashSet<ImgChannelStackDTO>();
+ for (ImgChannelStackDTO stack : stacks)
+ {
+ stacksSet.add(stack);
+ }
+ Set<ImgChannelStackDTO> representatives =
+ ChannelStackRepresentativesOracle.calculateRepresentatives(stacksSet);
+ return representatives;
+ }
+
+ @Test
+ public void testWithoutSpots()
+ {
+ ImgChannelStackDTO img1 = createStack(2, 2, null, 1f, 1f);
+ ImgChannelStackDTO img2 = createStack(1, 1, null, 200f, 200f);
+ ImgChannelStackDTO img3 = createStack(1, 1, null, 1f, 1f);
+
+ Set<ImgChannelStackDTO> representatives = calculateRepresentatives(img1, img2, img3);
+ assertFalse(representatives.contains(img1));
+ assertFalse(representatives.contains(img2));
+ assertTrue(representatives.contains(img3));
+ }
+
+ private ImgChannelStackDTO createStack(int row, int column, Long spotIdOrNull, Float tOrNull,
+ Float zOrNull)
+ {
+ return new ImgChannelStackDTO(0L, row, column, 0L, spotIdOrNull, tOrNull, zOrNull, null,
+ false);
+ }
+}
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 1994fed759163733b9c37ac79facc1f14e66d66b..f12cfbaf16820089276f1f8d63fca3ef059478e2 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
@@ -129,12 +129,20 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals(MICROSCOPY_IMAGE_PATH1, image1.getFilePath());
assertEquals(ColorComponent.BLUE, image1.getColorComponent());
+ ImgImageDTO representativeImage =
+ dao.tryGetMicroscopyRepresentativeImage(datasetId, channelId);
+ assertEquals(image1, representativeImage);
+
ImgImageDTO image1bis = dao.tryGetImage(channelId, channelStackId, datasetId);
assertEquals(image1, image1bis);
ImgImageDTO thumbnail1 = dao.tryGetMicroscopyThumbnail(channelId, datasetId, tileLocation);
assertEquals(image1, thumbnail1);
+ ImgImageDTO representativeThumbnail =
+ dao.tryGetMicroscopyRepresentativeThumbnail(datasetId, channelId);
+ assertEquals(image1, representativeThumbnail);
+
ImgImageDTO thumbnail1bis = dao.tryGetThumbnail(channelId, channelStackId, datasetId);
assertEquals(thumbnail1, thumbnail1bis);
}
@@ -249,6 +257,10 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals(PATH1, image1.getFilePath());
assertEquals(ColorComponent.BLUE, image1.getColorComponent());
+ ImgImageDTO representativeImage =
+ dao.tryGetHCSRepresentativeImage(datasetId, wellLocation, channelId1);
+ assertEquals(image1, representativeImage);
+
ImgImageDTO image1bis = dao.tryGetImage(channelId1, channelStackId, datasetId);
assertEquals(image1, image1bis);
@@ -256,6 +268,10 @@ public class ImagingQueryDAOTest extends AbstractDBTest
dao.tryGetHCSThumbnail(channelId1, datasetId, tileLocation, wellLocation);
assertEquals(image1, thumbnail1);
+ ImgImageDTO representativeThumbnail =
+ dao.tryGetHCSRepresentativeThumbnail(datasetId, wellLocation, channelId1);
+ assertEquals(thumbnail1, representativeThumbnail);
+
ImgImageDTO thumbnail1bis = dao.tryGetThumbnail(channelId1, channelStackId, datasetId);
assertEquals(thumbnail1, thumbnail1bis);
@@ -379,7 +395,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
{
final ImgChannelStackDTO channelStack =
new ImgChannelStackDTO(dao.createChannelStackId(), Y_TILE_ROW, X_TILE_COLUMN,
- datasetId, spotIdOrNull, timeOrNull, depthOrNull);
+ datasetId, spotIdOrNull, timeOrNull, depthOrNull, null, true);
dao.addChannelStacks(Arrays.asList(channelStack));
return channelStack.getId();
}
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 8b4e89434c1c60d29bb8c51f05c425d6b305720f..d1cd52963926070df64b0d7f5d473942d0b1b74a 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
@@ -29,6 +29,7 @@ import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.image.IImageTransformer;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
@@ -43,6 +44,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
/**
* @author Franz-Josef Elmer
*/
+@Friend(toClasses = ImageChannelsUtils.class)
public class ImageChannelsUtilsTest extends AssertJUnit
{
public static final File TEST_IMAGE_FOLDER = new File("../screening/sourceTest/java/"
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewerModelTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewerModelTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..04fc91d9732325bbf35a58248ebdf764a45eb229
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageSeriesViewerModelTest.java
@@ -0,0 +1,86 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * 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.client.web.client.application.detailviewers;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.LogicalImageSeriesViewer.ImageSeriesPoint;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.LogicalImageSeriesViewer.LogicalImageSeriesViewerModel;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStack;
+
+/**
+ * Unit tests of {@link LogicalImageSeriesViewerModel}.
+ *
+ * @author Tomasz Pylak
+ */
+public class LogicalImageSeriesViewerModelTest extends AssertJUnit
+{
+
+ @Test
+ public void testModel()
+ {
+ Float times[] = new Float[]
+ { 3.4f, null, 1.2f, 6.6f };
+ Float depths[] = new Float[]
+ { 66.6f, 33.4f, null, 11.2f };
+ Integer series[] = new Integer[]
+ { 1, 2, 3, null };
+
+ LogicalImageSeriesViewerModel model = createModel(times, depths, series);
+
+ List<ImageSeriesPoint> sortedPoints = model.getSortedPoints();
+ ImageSeriesPoint firstPoint = new ImageSeriesPoint(null, null, null);
+ assertEquals(firstPoint, sortedPoints.get(0));
+ ImageSeriesPoint lastPoint = new ImageSeriesPoint(6.6f, 66.6f, 3);
+ assertEquals(lastPoint, sortedPoints.get(sortedPoints.size() - 1));
+
+ List<List<ImageChannelStack>> stackSeriesPoints = model.getSortedChannelStackSeriesPoints();
+ List<ImageChannelStack> firstList = stackSeriesPoints.get(0);
+ assertEquals(firstPoint, new ImageSeriesPoint(firstList.get(0)));
+
+ List<ImageChannelStack> lastList = stackSeriesPoints.get(stackSeriesPoints.size() - 1);
+ assertEquals(lastPoint, new ImageSeriesPoint(lastList.get(0)));
+ }
+
+ private LogicalImageSeriesViewerModel createModel(Float[] times, Float[] depths,
+ Integer[] series)
+ {
+ List<ImageChannelStack> stacks = new ArrayList<ImageChannelStack>();
+ for (int time = 0; time < times.length; time++)
+ {
+ for (int depth = 0; depth < depths.length; depth++)
+ {
+ for (int seriesNum = 0; seriesNum < series.length; seriesNum++)
+ {
+ stacks.add(mkStack(1, 1, times[time], depths[depth], series[seriesNum]));
+ stacks.add(mkStack(2, 2, times[time], depths[depth], series[seriesNum]));
+ }
+ }
+ }
+ return new LogicalImageSeriesViewerModel(stacks);
+ }
+
+ private static ImageChannelStack mkStack(int row, int col, Float tOrNull, Float zOrNull,
+ Integer seriesNumberOrNull)
+ {
+ return new ImageChannelStack(0, row, col, tOrNull, zOrNull, seriesNumberOrNull);
+ }
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTOTest.java
index 0748606ef44f2bb63652cc6dc8a0453ed157f59f..fb1e839134b01802e56ea1e4b89e368d336e1378 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTOTest.java
@@ -54,7 +54,7 @@ public class ImgChannelStackDTOTest
private ImgChannelStackDTO createStackChannel(Long spotId)
{
- return new ImgChannelStackDTO(0, 1, 1, 1, spotId, 123F, null);
+ return new ImgChannelStackDTO(0, 1, 1, 1, spotId, 123F, null, null, false);
}
}