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 26b7a9062be5e42c2332bb24261c159e6f758e67..2a022062940184da6d426067465f85e021de0329 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
@@ -316,7 +316,8 @@ public class ImageUtil
{
assert (imageLibraryReaderNameOrNull == null || imageLibraryNameOrNull != null) : "if image reader "
+ "is specified then library name should be specified as well";
- ImageID imageID = parseImageID(imageIdOrNull);
+ ImageID imageID = parseImageID(imageIdOrNull, contentNode);
+
if (imageLibraryNameOrNull != null && imageLibraryReaderNameOrNull != null)
{
IImageReader reader =
@@ -353,7 +354,8 @@ public class ImageUtil
{
assert (imageLibraryReaderNameOrNull == null || imageLibraryNameOrNull != null) : "if image reader "
+ "is specified then library name should be specified as well";
- ImageID imageID = parseImageID(imageIdOrNull);
+ ImageID imageID = parseImageID(imageIdOrNull, contentNode);
+
if (imageLibraryNameOrNull != null && imageLibraryReaderNameOrNull != null)
{
IImageReader reader =
@@ -538,9 +540,16 @@ public class ImageUtil
* Parses specified string representation of an {@link ImageID}. If the argument is
* <code>null</code> {@link ImageID#NULL} will be returned.
*/
- public static ImageID parseImageID(String imageIdOrNull)
+ public static ImageID parseImageID(String imageIdOrNull, IHierarchicalContentNode contentNode)
{
- return imageIdOrNull == null ? ImageID.NULL : ImageID.parse(imageIdOrNull);
+ ImageID id = imageIdOrNull == null ? ImageID.NULL : ImageID.parse(imageIdOrNull);
+ try
+ {
+ id.setFileName(contentNode.getFile().getCanonicalPath());
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ return id;
}
private static BufferedImage loadImageGuessingLibrary(IHierarchicalContentNode contentNode,
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/ImageID.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/ImageID.java
index 5f80e0e4f11ce58910ab1706374a09123b00ecc3..07dc099c9da22805149cd47f0911b6c73ef562c9 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/ImageID.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/ImageID.java
@@ -49,6 +49,15 @@ public class ImageID
private final int focalPlaneIndex;
private final int colorChannelIndex;
private final String id;
+ private String filename;
+
+ public void setFileName(String f) {
+ this.filename = f;
+ }
+
+ public String getFileName() {
+ return this.filename;
+ }
/**
* Creates an instance for the specified series index, time series (or T) index, focal plane (or
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
index c20323f7123e2d4bc31e78f7273ad676defcec7c..b440211a8eb67bf045b31d35599cdb09cdca7d7c 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
@@ -153,7 +153,7 @@ final class BioFormatsImageUtils
static List<ImageID> listImageIDs(IFormatReader reader, IRandomAccess handle)
{
- String handleId = generateHandleId(reader);
+ String handleId = generateHandleId(reader, null);
// Add to static map.
Location.mapFile(handleId, handle);
try
@@ -200,7 +200,8 @@ final class BioFormatsImageUtils
static BufferedImage readImage(IFormatReader reader, IRandomAccess handle, ImageID imageID)
throws IOExceptionUnchecked, IllegalArgumentException
{
- String handleId = generateHandleId(reader);
+ String handleId = generateHandleId(reader, imageID);
+
// Add to static map.
Location.mapFile(handleId, handle);
try
@@ -243,7 +244,7 @@ final class BioFormatsImageUtils
ImageID imageID)
{
// Add to static map.
- String handleId = generateHandleId(reader);
+ String handleId = generateHandleId(reader, imageID);
Location.mapFile(handleId, handle);
try
@@ -284,7 +285,8 @@ final class BioFormatsImageUtils
IllegalArgumentException
{
// Add to static map.
- String handleId = generateHandleId(reader);
+ String handleId = generateHandleId(reader, imageID);
+
Location.mapFile(handleId, handle);
try
{
@@ -320,7 +322,7 @@ final class BioFormatsImageUtils
throws IOExceptionUnchecked, IllegalArgumentException
{
// Add to static map.
- String handleId = generateHandleId(reader);
+ String handleId = generateHandleId(reader, imageID);
Location.mapFile(handleId, handle);
try
{
@@ -344,9 +346,14 @@ final class BioFormatsImageUtils
}
}
- public static String generateHandleId(IFormatHandler formatHandler)
+ public static String generateHandleId(IFormatHandler formatHandler, ImageID imageId)
{
- return UUID.randomUUID().toString() + "." + formatHandler.getSuffixes()[0];
+ String id = UUID.randomUUID().toString() + "." + formatHandler.getSuffixes()[0];
+ if (imageId != null && imageId.getFileName() != null && (imageId.getFileName().endsWith(".c01") || imageId.getFileName().endsWith("C01"))) {
+ id = imageId.getFileName();
+ }
+ return id;
+
}
private static void nullSafeAddAll(HashMap<String, Object> accumulator,
diff --git a/screening/source/core-plugins/cellomics/1/dss/drop-boxes/cellomics-dropbox/cellomics-dropbox.py b/screening/source/core-plugins/cellomics/1/dss/drop-boxes/cellomics-dropbox/cellomics-dropbox.py
new file mode 100644
index 0000000000000000000000000000000000000000..5b49af47e342064aae4b9790a718b86fbac9905d
--- /dev/null
+++ b/screening/source/core-plugins/cellomics/1/dss/drop-boxes/cellomics-dropbox/cellomics-dropbox.py
@@ -0,0 +1,91 @@
+import os
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import ImageMetadata
+from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
+
+SPACE_CODE = "TEST"
+PROJECT_CODE = "TEST-PROJECT"
+PROJECT_ID = "/%(SPACE_CODE)s/%(PROJECT_CODE)s" % vars()
+EXPERIMENT_CODE = "DEMO-EXP-HCS"
+EXPERIMENT_ID = "/%(SPACE_CODE)s/%(PROJECT_CODE)s/%(EXPERIMENT_CODE)s" % vars()
+
+PLATE_CODE = "PLATE1"
+PLATE_ID = "/%(SPACE_CODE)s/%(PLATE_CODE)s" % vars()
+PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
+PLATE_GEOMETRY = "384_WELLS_16X24"
+
+
+def create_space_if_needed(transaction):
+ space = transaction.getSpace(SPACE_CODE)
+ if None == space:
+ space = transaction.createNewSpace(SPACE_CODE, None)
+ space.setDescription("A demo space")
+
+def create_project_if_needed(transaction):
+ project = transaction.getProject(PROJECT_ID)
+ if None == project:
+ create_space_if_needed(transaction)
+ project = transaction.createNewProject(PROJECT_ID)
+ project.setDescription("A demo project")
+
+def create_experiment_if_needed(transaction):
+ """ Get the specified experiment or register it if necessary """
+ exp = transaction.getExperiment(EXPERIMENT_ID)
+ if None == exp:
+ create_project_if_needed(transaction)
+ print 'Creating new experiment : ' + EXPERIMENT_ID
+ exp = transaction.createNewExperiment(EXPERIMENT_ID, 'SIRNA_HCS')
+ exp.setPropertyValue("DESCRIPTION", "A sample experiment")
+
+ return exp
+
+def create_plate_if_needed(transaction):
+ """ Get the specified sample or register it if necessary """
+
+ samp = transaction.getSample(PLATE_ID)
+
+ if None == samp:
+ exp = create_experiment_if_needed(transaction)
+ samp = transaction.createNewSample(PLATE_ID, 'PLATE')
+ samp.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, PLATE_GEOMETRY)
+ samp.setExperiment(exp)
+
+ return samp
+
+
+class MyImageDataSetConfig(SimpleImageDataConfig):
+ def extractImageMetadata(self, imagePath):
+
+ basename = os.path.splitext(imagePath)[0]
+ value = basename.split("_")[2]
+ plate = basename.split("_")[1]
+ well = value[0:3]
+ tile = value[4:6]
+ tile = int(tile) + 1
+ channelCode = value[6:8]
+
+ image_tokens = ImageMetadata()
+ image_tokens.well = well
+ try:
+ image_tokens.tileNumber = int(tile)
+ except ValueError:
+ raise Exception("Cannot parse field number from '" + tile + "' in '" + basename + "' file name.")
+
+ image_tokens.channelCode = channelCode
+ return image_tokens
+
+ def getTileGeometry(self, imageTokens, maxTileNumber):
+ return Geometry.createFromRowColDimensions(maxTileNumber / 3, 3)
+
+if incoming.isDirectory():
+ imageDataset = MyImageDataSetConfig()
+ imageDataset.setRawImageDatasetType()
+ #imageDataset.setGenerateThumbnails(True)
+ imageDataset.setPlate(SPACE_CODE, PLATE_CODE)
+ imageDataset.setImageLibrary('BioFormats', 'CellomicsReader##SINGLE_IMAGE')
+ registrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
+ transaction = service.transaction(incoming, factory)
+ plate = create_plate_if_needed(transaction)
+ dataset = transaction.createNewDataSet(registrationDetails);
+ dataset.setSample(plate)
+ transaction.moveFile(incoming.getPath(), dataset);
diff --git a/screening/source/core-plugins/cellomics/1/dss/drop-boxes/cellomics-dropbox/plugin.properties b/screening/source/core-plugins/cellomics/1/dss/drop-boxes/cellomics-dropbox/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..a5305fc2e44669a2f84983a23fa7d4260149dcd2
--- /dev/null
+++ b/screening/source/core-plugins/cellomics/1/dss/drop-boxes/cellomics-dropbox/plugin.properties
@@ -0,0 +1,13 @@
+#
+# Drop box for cellomics data sets
+#
+# Variables:
+# incoming-root-dir
+# Path to the directory which contains incoming directories for drop boxes.
+incoming-dir = ${incoming-root-dir}/incoming-cellomics
+incoming-data-completeness-condition = auto-detection
+top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler
+script-path = cellomics-dropbox.py
+storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+storage-processor.data-source = imaging-db
+storage-processor.define-channels-per-experiment = false
\ No newline at end of file
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 28d8e5bc85add1991ee7059e70f63b44a5cf2dd3..0a2f2d102752a6a1dd07b883684e4dae78863bdd 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
@@ -203,7 +203,7 @@ abstract public class SimpleImageDataConfig
private boolean isMeasured = false;
private String[] recognizedImageExtensions = new String[]
- { "tiff", "tif", "png", "gif", "jpg", "jpeg" };
+ { "tiff", "tif", "png", "gif", "jpg", "jpeg", "c01" };
private List<IThumbnailsConfiguration> imagePyramid = new ArrayList<IThumbnailsConfiguration>();
@@ -348,7 +348,7 @@ abstract public class SimpleImageDataConfig
/**
* Only files with these extensions will be recognized as images (e.g. ["jpg", "png"]).<br>
- * By default it is set to [ "tiff", "tif", "png", "gif", "jpg", "jpeg" ].
+ * By default it is set to [ "tiff", "tif", "png", "gif", "jpg", "jpeg", "c01" ].
*/
public void setRecognizedImageExtensions(String[] recognizedImageExtensions)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
index 0b3b43ea9dadaa92d2d937c946473b5ca984bd9b..6fa62bb2c3d84741a1b77a427ec24b5e4f606f67 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
@@ -263,7 +263,10 @@ public class SimpleImageDataSetRegistrator
if (readerOrNull != null)
{
// NOTE: ugly side effect which is used later on
- imageLibraryInfoOrNull.setReaderName(readerOrNull.getName());
+ // if (null == imageLibraryInfoOrNull.getReaderName())
+ // {
+ imageLibraryInfoOrNull.setReaderName(readerOrNull.getName());
+ // }
} else
{
throw ConfigurationFailureException.fromTemplate(