From 5f8e95e446c1a489f0d98c6b1a753e94e1383524 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 10 Apr 2012 11:48:25 +0000
Subject: [PATCH] LMS-2875 Initial test
SVN: 24845
---
.../bPLATE_wA1_s1_cRGB.png | Bin 0 -> 13062 bytes
.../data-set-handler.py | 150 +++++++++++++++++
.../etl/AbstractImageStorageProcessor.java | 7 +-
.../TransformedImageRepresentationsTest.java | 158 ++++++++++++++++++
4 files changed, 311 insertions(+), 4 deletions(-)
create mode 100644 screening/resource/test-data/TransformedImageRepresentationsTest/TRANSFORMED-THUMB-PLATE/bPLATE_wA1_s1_cRGB.png
create mode 100644 screening/resource/test-data/TransformedImageRepresentationsTest/data-set-handler.py
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/TransformedImageRepresentationsTest.java
diff --git a/screening/resource/test-data/TransformedImageRepresentationsTest/TRANSFORMED-THUMB-PLATE/bPLATE_wA1_s1_cRGB.png b/screening/resource/test-data/TransformedImageRepresentationsTest/TRANSFORMED-THUMB-PLATE/bPLATE_wA1_s1_cRGB.png
new file mode 100644
index 0000000000000000000000000000000000000000..ec584cf9b80a7c13bfb5a06c9a043bd67b806618
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diff --git a/screening/resource/test-data/TransformedImageRepresentationsTest/data-set-handler.py b/screening/resource/test-data/TransformedImageRepresentationsTest/data-set-handler.py
new file mode 100644
index 00000000000..74db9b21d85
--- /dev/null
+++ b/screening/resource/test-data/TransformedImageRepresentationsTest/data-set-handler.py
@@ -0,0 +1,150 @@
+#!/usr/bin/env python
+
+PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
+PLATE_GEOMETRY = "384_WELLS_16X24"
+
+"""
+An Jython dropbox for importing HCS image datasets for use by the TransformedImageRepresentationsTest
+
+The folder loaded to the dropbox folder should have the same name as the plate that the data will be attached to.
+"""
+
+import os
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig, ImageMetadata, Location, Channel, ChannelColor, ChannelColorComponent
+from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations import ImageTransformationBuffer
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.thumbnails import ResolutionBasedThumbnailsConfiguration
+
+
+class ImageDataSetFlexible(SimpleImageDataConfig):
+ def extractImageMetadata(self, imagePath):
+ """
+ Extracts tile number, channel code and well code for a given relative path to an image.
+ Will be called for each file found in the incoming directory which has the allowed image extension.
+
+ Example file name: bDZ01-1A_wD17_s3_z123_t321_cGFP
+ Returns:
+ ImageMetadata
+ """
+ image_tokens = ImageMetadata()
+
+ basename = os.path.splitext(imagePath)[0]
+ #
+ token_dict = {}
+ for token in basename.split("_"):
+ token_dict[token[:1]] = token[1:]
+
+ image_tokens.well = token_dict["w"]
+ fieldText = token_dict["s"]
+ try:
+ image_tokens.tileNumber = int(fieldText)
+ except ValueError:
+ raise Exception("Cannot parse field number from '" + fieldText + "' in '" + basename + "' file name.")
+
+ image_tokens.channelCode = token_dict["c"]
+ return image_tokens
+
+ def getTileGeometry(self, imageTokens, maxTileNumber):
+ """
+ Overrides the default implementation which returns (1, maxTileNumber) geometry.
+
+ Calculates the width and height of the matrix of tiles (a.k.a. fields or sides) in the well.
+
+ Parameter imageMetadataList: a list of metadata for each encountered image
+ Parameter maxTileNumber: the biggest tile number among all encountered images
+ Returns:
+ Geometry
+ """
+ return Geometry.createFromRowColDimensions(1, 1);
+
+ def getTileCoordinates(self, tileNumber, tileGeometry):
+ """
+ Overrides the default implementation which does the same thing (to demonstrate how this can be done).
+
+ For a given tile number and tiles geometry returns (x,y) which describes where the tile is
+ located on the well.
+
+ Parameter tileNumber: number of the tile
+ Parameter tileGeometry: the geometry of the well matrix
+ Returns:
+ Location
+ """
+ columns = tileGeometry.getWidth()
+ row = ((tileNumber - 1) / columns) + 1
+ col = ((tileNumber - 1) % columns) + 1
+ return Location(row, col)
+
+
+def getAvailableChannelTransformations():
+ """
+ Create a collection of transformations that are applicable to the image
+ """
+ transforms = ImageTransformationBuffer()
+ transforms.appendImageMagicConvert("-edge 1", "Edge detection")
+ transforms.appendImageMagicConvert("-radial-blur 30", "Radial Blur")
+ transforms.appendImageMagicConvert("-blur 3x.7 -solarize 50% -level 50%,0", "Fuzzy")
+ transforms.appendImageMagicConvert("-shade 0x45", "3D 1")
+ transforms.appendImageMagicConvert("-shade 90x60", "3D 2")
+ transforms.appendImageMagicConvert("-blur 0x3 -shade 120x45 -normalize", "3D 3")
+ transforms.appendImageMagicConvert("-motion-blur 0x12+45", "Motion Blur")
+ transforms.appendImageMagicConvert("-fft -delete 1 -auto-level -evaluate log 100000", "FFT")
+
+ return transforms.getTransformations()
+
+def create_experiment(tr):
+ space = tr.createNewSpace("TEST", "etlserver")
+ project = tr.createNewProject("/TEST/TEST-PROJECT")
+ expid = "/TEST/TEST-PROJECT/TRANSFORMED_THUMBNAILS_EXP"
+
+ exp = tr.createNewExperiment(expid, 'SIRNA_HCS')
+ exp.setPropertyValue("DESCRIPTION", "Test experiment")
+
+ return exp
+
+def create_plate(tr, experiment, plateCode):
+ plateId = "/TEST/" + plateCode
+ plate = tr.createNewSample(plateId, 'PLATE')
+ plate.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, PLATE_GEOMETRY)
+ plate.setExperiment(experiment)
+
+ wellA1 = tr.createNewSample(plate.getSampleIdentifier() + ":A1", "SIRNA_WELL")
+ wellA1.setContainer(plate)
+
+ wellA2 = tr.createNewSample(plate.getSampleIdentifier() + ":A2", "SIRNA_WELL")
+ wellA2.setContainer(plate)
+
+ return plate
+
+
+if incoming.isDirectory():
+ tr = service.transaction()
+ experiment = create_experiment(tr)
+ plate = create_plate(tr, experiment, 'TRANSFORMED-THUMB-PLATE')
+ tr.commit()
+
+
+ imageDataset = ImageDataSetFlexible()
+ imageDataset.setRawImageDatasetType()
+ imageDataset.setPlate("TEST", 'TRANSFORMED-THUMB-PLATE')
+ transforms = getAvailableChannelTransformations()
+ # We want thumbnails generarted for the following resolutions, and they should be JPEG and have the
+ # Radial Blur transform applied
+ for resolution in ['64x64', '128x128', '256x256']:
+ representation = imageDataset.addGeneratedImageRepresentationWithResolution(resolution)
+ for channel in ["DAPI", "GFP", "Cy5"]:
+ representation.setTransformation(channel, transforms[1].getCode())
+ storageFormat = representation.getThumbnailsStorageFormat(imageDataset)
+ storageFormat.setFileFormat('JPEG')
+
+ imageRegistrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
+ datasetInfo = imageRegistrationDetails.getDataSetInformation()
+ channels = [ Channel(code, code) for code in ["DAPI", "GFP", "Cy5"]]
+ colorComponents = [ ChannelColorComponent.BLUE, ChannelColorComponent.GREEN, ChannelColorComponent.RED]
+
+ # Add transforms to the channels
+ for channel in channels:
+ channel.setAvailableTransformations(transforms)
+
+ datasetInfo.setChannels(channels, colorComponents)
+
+ factory.registerImageDataset(imageRegistrationDetails, incoming, service)
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 c639f8cbf66..67099adfe53 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
@@ -665,10 +665,9 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
ImageDataSetStructure imageDataSetStructure = dataSetInformation.getImageDataSetStructure();
if (imageDataSetStructure.isValid() == false)
{
- throw ConfigurationFailureException
- .fromTemplate("Invalid image dataset info object, check if your jython script fills all the required fields. "
- + "Or maybe the recognized files extensions is set incorrectly? Dataset: "
- + imageDataSetStructure);
+ throw new ConfigurationFailureException("Invalid image dataset info object, check if your jython script fills all the required fields. "
+ + "Or maybe the recognized files extensions is set incorrectly? Dataset: "
+ + imageDataSetStructure);
}
Geometry tileGeometry =
new Geometry(imageDataSetStructure.getTileRowsNumber(),
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/TransformedImageRepresentationsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/TransformedImageRepresentationsTest.java
new file mode 100644
index 00000000000..4e2310cdfbb
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/TransformedImageRepresentationsTest.java
@@ -0,0 +1,158 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.screening.systemtests;
+
+import static ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil.OPENBIS_DSS_SYSTEM_PROPERTIES_PREFIX;
+
+import java.awt.Dimension;
+import java.awt.Point;
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+
+import org.apache.commons.io.FileUtils;
+import org.springframework.mock.web.MockHttpServletRequest;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.servlet.SpringRequestContextProvider;
+import ch.systemsx.cisd.etlserver.DefaultStorageProcessor;
+import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor;
+import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientService;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+@Test(groups =
+ { "slow", "systemtest" })
+public class TransformedImageRepresentationsTest extends AbstractScreeningSystemTestCase
+{
+ private MockHttpServletRequest request;
+
+ private String sessionToken;
+
+ private IScreeningClientService screeningClientService;
+
+ private IScreeningApiServer screeningServer;
+
+ private IScreeningOpenbisServiceFacade screeningFacade;
+
+ @Override
+ protected void setUpTestThread()
+ {
+ setUpTestThread(JythonPlateDataSetHandler.class, PlateStorageProcessor.class,
+ getTestDataFolder() + "data-set-handler.py");
+
+ System.setProperty(OPENBIS_DSS_SYSTEM_PROPERTIES_PREFIX
+ + "dss-system-test-thread.storage-processor.processor", DefaultStorageProcessor.class.getName());
+ System.setProperty(OPENBIS_DSS_SYSTEM_PROPERTIES_PREFIX
+ + "dss-system-test-thread.storage-processor.data-source", "imaging-db");
+ }
+
+ @BeforeMethod
+ public void setUp() throws Exception
+ {
+ screeningClientService =
+ (IScreeningClientService) applicationContext
+ .getBean(ResourceNames.SCREENING_PLUGIN_SERVICE);
+ request = new MockHttpServletRequest();
+ ((SpringRequestContextProvider) applicationContext.getBean("request-context-provider"))
+ .setRequest(request);
+ Object bean = applicationContext.getBean(ResourceNames.SCREENING_PLUGIN_SERVER);
+ screeningServer = (IScreeningApiServer) bean;
+ sessionToken = screeningClientService.tryToLogin("admin", "a").getSessionID();
+ screeningFacade = ScreeningOpenbisServiceFacade.tryCreateForTest(sessionToken, "http://localhost:" + SYSTEM_TEST_CASE_SERVER_PORT, screeningServer);
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ File[] files = getIncomingDirectory().listFiles();
+ for (File file : files)
+ {
+ FileUtilities.deleteRecursively(file);
+ }
+ }
+
+ @Test
+ public void testTransformedThumbnails() throws Exception
+ {
+ dropAnExampleDataSet();
+ // The components of the plate identifier come from the dropbox code
+ // (resource/test-data/TransformedImageRepresentationsTest/data-set-handler.py)
+ PlateIdentifier plate = new PlateIdentifier("TRANSFORMED-THUMB-PLATE", "TEST", null);
+ List<ImageDatasetReference> imageDataSets = screeningFacade.listRawImageDatasets(Arrays.asList(plate));
+ List<DatasetImageRepresentationFormats> representationFormats = screeningFacade.listAvailableImageRepresentationFormats(imageDataSets);
+ assertEquals(1, representationFormats.size());
+ List<ImageRepresentationFormat> formats = representationFormats.get(0).getImageRepresentationFormats();
+
+ HashSet<Dimension> expectedResolutions = new HashSet<Dimension>();
+ expectedResolutions.addAll(Arrays.asList(new Dimension(64, 64), new Dimension(128, 128), new Dimension(256, 256), new Dimension(512, 512)));
+ for (ImageRepresentationFormat format : formats)
+ {
+ Dimension resolution = new Dimension(format.getWidth(), format.getHeight());
+ // Make sure the resolution we specified was found
+ assertTrue("" + resolution + " was not expected", expectedResolutions.remove(resolution));
+ }
+ assertEquals(0, expectedResolutions.size());
+
+ System.err.println(representationFormats);
+ }
+
+ private void dropAnExampleDataSet() throws IOException, Exception
+ {
+ File exampleDataSet = createTestDataContents();
+ moveFileToIncoming(exampleDataSet);
+ waitUntilDataSetImported();
+ }
+
+ private File createTestDataContents() throws IOException
+ {
+ File dest = new File(workingDirectory, "test-data");
+ dest.mkdirs();
+ File src = new File(getTestDataFolder(), "TRANSFORMED-THUMB-PLATE");
+
+ // Copy the test data set to the location for processing
+ FileUtils.copyDirectory(src, dest);
+ return dest;
+ }
+
+ private String getTestDataFolder()
+ {
+ return "../screening/resource/test-data/" + getClass().getSimpleName() + "/";
+ }
+
+ @Override
+ protected int dataSetImportWaitDurationInSeconds()
+ {
+ return 60;
+ }
+
+}
--
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