diff --git a/screening/resource/test-data/MicroscopyImageDropboxTest/maximum_intensity_projection.png b/screening/resource/test-data/MicroscopyImageDropboxTest/maximum_intensity_projection.png
new file mode 100644
index 0000000000000000000000000000000000000000..1b83f88d594ae05c37b0eecbc9d791f9d61e0c07
Binary files /dev/null and b/screening/resource/test-data/MicroscopyImageDropboxTest/maximum_intensity_projection.png differ
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IImageGenerationAlgorithm.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IImageGenerationAlgorithm.java
index cb88f88cf9b95491f3bb38cb8b395cff2d802200..859c6f77766d22291be50d1a47dcd65047b9b6cf 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IImageGenerationAlgorithm.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/IImageGenerationAlgorithm.java
@@ -4,7 +4,6 @@ import java.awt.image.BufferedImage;
import java.util.List;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetStructure;
/**
* Algorithm for creating a representative thumbnails.
@@ -14,9 +13,9 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetStructure;
public interface IImageGenerationAlgorithm
{
/**
- * Creates thumbnails for the specified data set info and structure.
+ * Creates thumbnails for the specified data set info.
*/
- public List<BufferedImage> generateImages(ImageDataSetInformation information, ImageDataSetStructure structure);
+ public List<BufferedImage> generateImages(ImageDataSetInformation information);
/**
* Returns the code of the data set to be registered containing these representative thumbnails.
@@ -25,7 +24,7 @@ public interface IImageGenerationAlgorithm
/**
* Returns the thumbnail file name for the specified index. The index specifies the corresponding
- * image returned by {@link #generateImages(ImageDataSetInformation, ImageDataSetStructure)}.
+ * image returned by {@link #generateImages(ImageDataSetInformation)}.
* Note, all file names generated by this method have to different.
*/
public String getImageFileName(int index);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/EmptyImageCreationAlgorithm.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/EmptyImageCreationAlgorithm.java
index 9f036dea2745158698e3a280142f80451676c55d..5b5c8e530c7299627f15d9ca9d106660a8a3906e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/EmptyImageCreationAlgorithm.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/EmptyImageCreationAlgorithm.java
@@ -20,7 +20,7 @@ public class EmptyImageCreationAlgorithm implements IImageGenerationAlgorithm, S
}
@Override
- public List<BufferedImage> generateImages(ImageDataSetInformation information, ImageDataSetStructure structure)
+ public List<BufferedImage> generateImages(ImageDataSetInformation information)
{
return Collections.emptyList();
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithm.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithm.java
index 263b75669cbb4cae3c8b50a42f1ede89ffac8f17..cb33ecbbf555399a3f54efbc0164e8c656b1fb49 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithm.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithm.java
@@ -6,17 +6,45 @@ import java.awt.image.BufferedImage;
import java.io.File;
import java.io.Serializable;
import java.util.Collections;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode;
import ch.systemsx.cisd.openbis.dss.etl.Utils;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.IImageGenerationAlgorithm;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
+/**
+ * Implementation of {@link IImageGenerationAlgorithm} which generates from a bunch of images
+ * a representative image where at each pixel the brightest pixel from the images are taken.
+ *
+ * @author Antti Luomi
+ * @author Franz-Josef Elmer
+ */
public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGenerationAlgorithm, Serializable
{
+ private static final class ChannelAndColorComponent
+ {
+ private Channel channel;
+ private ColorComponent colorComponent;
+
+ ChannelAndColorComponent(Channel channel, ColorComponent colorComponent)
+ {
+ this.channel = channel;
+ this.colorComponent = colorComponent;
+ }
+ }
+
+ public static final String DEFAULT_FILE_NAME = "maximum_intensity_projection.png";
+
private static final long serialVersionUID = IServer.VERSION;
private transient BufferedImage result = null;
@@ -29,18 +57,38 @@ public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGene
private int height;
- public MaximumIntensityProjectionGenerationAlgorithm(String dataSetTypeCode) {
+ /**
+ * Creates an instance for the specified data set type. The generated image will have the same size as
+ * the original images. The file name will be <code>maximum_intensity_projection.png</code>.
+ */
+ public MaximumIntensityProjectionGenerationAlgorithm(String dataSetTypeCode)
+ {
this(dataSetTypeCode, 0, 0);
}
- public MaximumIntensityProjectionGenerationAlgorithm(String dataSetTypeCode, String filename) {
+
+ /**
+ * Creates an instance for the specified data set type and file name.
+ * The generated image will have the same size as the original images.
+ */
+ public MaximumIntensityProjectionGenerationAlgorithm(String dataSetTypeCode, String filename)
+ {
this(dataSetTypeCode, 0, 0, filename);
}
-
- public MaximumIntensityProjectionGenerationAlgorithm(String dataSetTypeCode, int width, int height) {
- this(dataSetTypeCode, width, height, "maximum_intensity_projection");
+
+ /**
+ * Creates an instance for the specified data set type and specified image size.
+ * The file name will be <code>maximum_intensity_projection.png</code>.
+ */
+ public MaximumIntensityProjectionGenerationAlgorithm(String dataSetTypeCode, int width, int height)
+ {
+ this(dataSetTypeCode, width, height, DEFAULT_FILE_NAME);
}
- public MaximumIntensityProjectionGenerationAlgorithm(String dataSetTypeCode, int width, int height, String filename) {
+ /**
+ * Creates an instance for the specified data set type, specified image size and specified file name.
+ */
+ public MaximumIntensityProjectionGenerationAlgorithm(String dataSetTypeCode, int width, int height, String filename)
+ {
this.dataSetTypeCode = dataSetTypeCode;
this.width = width;
this.height = height;
@@ -52,86 +100,136 @@ public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGene
{
return dataSetTypeCode;
}
-
+
@Override
- public List<BufferedImage> generateImages(ImageDataSetInformation information, ImageDataSetStructure structure)
+ public List<BufferedImage> generateImages(ImageDataSetInformation information)
{
+ ImageDataSetStructure structure = information.getImageDataSetStructure();
ImageLibraryInfo library = structure.getImageStorageConfiguraton().tryGetImageLibrary();
List<ImageFileInfo> images = structure.getImages();
+ Map<String, ChannelAndColorComponent> channelsByCode = getChannelsByCode(structure);
+ File incomingDirectory = information.getIncomingDirectory();
int maxIntensity = 0;
- for (ImageFileInfo image: images) {
- String imagePath = image.getImageRelativePath();
- if (image.tryGetTimepoint() == null || image.tryGetTimepoint() != 0) {
+ for (ImageFileInfo imageFileInfo : images)
+ {
+ if (imageToBeIgnored(imageFileInfo))
+ {
continue;
}
- BufferedImage imageData = Utils.loadUnchangedImage(new FileBasedContentNode(new File(
- information.getIncomingDirectory(), imagePath)), image.tryGetUniqueStringIdentifier(), library);
- maxIntensity = addImage(imageData);
+ String imagePath = imageFileInfo.getImageRelativePath();
+ ChannelAndColorComponent channelAndColorComponent = channelsByCode.get(imageFileInfo.getChannelCode());
+ String identifier = imageFileInfo.tryGetUniqueStringIdentifier();
+ BufferedImage image = loadImage(incomingDirectory, imagePath, identifier, library);
+ image = ImageChannelsUtils.rescaleIfNot8Bit(image, 0f);
+ image = ImageChannelsUtils.extractChannel(image, channelAndColorComponent.colorComponent);
+ image = ImageChannelsUtils.transformGrayToColor(image, channelAndColorComponent.channel.tryGetChannelColor());
+ maxIntensity = addImage(image);
}
-
- if (result == null) {
+
+ if (result == null)
+ {
return Collections.emptyList();
- } else {
- for (int y=0; y<result.getHeight(); y++) {
- for (int x=0; x<result.getWidth(); x++) {
+ } else
+ {
+ for (int y = 0; y < result.getHeight(); y++)
+ {
+ for (int x = 0; x < result.getWidth(); x++)
+ {
result.setRGB(x, y, adjust(result.getRGB(x, y), maxIntensity));
}
}
- if (width > 0 && height > 0) {
+ if (width > 0 && height > 0)
+ {
BufferedImage scaled = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
AffineTransform at = new AffineTransform();
- at.scale((double)width / (double)result.getWidth(), (double)height / (double)result.getHeight());
+ at.scale((double) width / (double) result.getWidth(), (double) height / (double) result.getHeight());
AffineTransformOp scaleOp = new AffineTransformOp(at, AffineTransformOp.TYPE_BILINEAR);
- result = scaleOp.filter(result, scaled);
+ result = scaleOp.filter(result, scaled);
}
-
+
return Collections.singletonList(result);
}
+ }
+ @Private BufferedImage loadImage(File incomingDirectory, String imagePath, String identifier, ImageLibraryInfo library)
+ {
+ File file = new File(incomingDirectory, imagePath);
+ return Utils.loadUnchangedImage(new FileBasedContentNode(file), identifier, library);
}
- private int adjust(int rgb, int maxIntensity)
+ /**
+ * Returns <code>true</code> if the specified image should be ignored. Can be overridden.
+ */
+ protected boolean imageToBeIgnored(ImageFileInfo image)
{
- if (maxIntensity > 255) {
- maxIntensity = 255;
+ return image.tryGetTimepoint() == null || image.tryGetTimepoint() != 0;
+ }
+
+ private Map<String, ChannelAndColorComponent> getChannelsByCode(ImageDataSetStructure structure)
+ {
+ Map<String, ChannelAndColorComponent> channelsByCode = new HashMap<String, ChannelAndColorComponent>();
+ List<Channel> channels = structure.getChannels();
+ for (int i = 0; i < channels.size(); i++)
+ {
+ Channel channel = channels.get(i);
+ ColorComponent colorComponent = tryGetColorComponent(structure, i);
+ channelsByCode.put(channel.getCode(), new ChannelAndColorComponent(channel, colorComponent));
+ }
+ return channelsByCode;
+ }
+
+ private ColorComponent tryGetColorComponent(ImageDataSetStructure structure, int i)
+ {
+ List<ChannelColorComponent> channelColorComponents = structure.getChannelColorComponents();
+ if (channelColorComponents == null || channelColorComponents.isEmpty())
+ {
+ return null;
}
- int r = new Double( ((double)getRed(rgb)) / ((double)maxIntensity) * 255).intValue();
- int g = new Double( ((double)getGreen(rgb)) / ((double)maxIntensity) * 255).intValue();
- int b = new Double( ((double)getBlue(rgb)) / ((double)maxIntensity) * 255).intValue();
-
+ return ChannelColorComponent.getColorComponent(channelColorComponents.get(i));
+ }
+
+ private int adjust(int rgb, int maximumIntensity)
+ {
+ int maxIntensity = Math.min(255, maximumIntensity);
+ int r = rescale(getRed(rgb), maxIntensity);
+ int g = rescale(getGreen(rgb), maxIntensity);
+ int b = rescale(getBlue(rgb), maxIntensity);
return (r << 16) + (g << 8) + b;
-
}
-
+
+ private int rescale(int intensity, int maxIntensity)
+ {
+ return (intensity * 255 + maxIntensity / 2) / maxIntensity;
+ }
private int addImage(BufferedImage image)
{
- if (result == null) {
- result = new BufferedImage(image.getWidth(),image.getHeight(), BufferedImage.TYPE_INT_RGB);
- for (int y=0; y<image.getHeight(); y++) {
- for (int x=0; x<image.getWidth(); x++) {
- image.setRGB(x,y, 0);
+ int w = image.getWidth();
+ int h = image.getHeight();
+ if (result == null)
+ {
+ result = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB);
+ for (int y = 0; y < h; y++)
+ {
+ for (int x = 0; x < w; x++)
+ {
+ result.setRGB(x, y, 0);
}
}
}
int maxIntensity = 0;
- for (int y=0; y<image.getHeight(); y++) {
- for (int x=0; x<image.getWidth(); x++) {
- int rgb1 = result.getRGB(x,y);
- int rgb2 = image.getRGB(x,y);
-
+ for (int y = 0; y < h; y++)
+ {
+ for (int x = 0; x < w; x++)
+ {
+ int rgb1 = result.getRGB(x, y);
+ int rgb2 = image.getRGB(x, y);
+
int intensity1 = intensity(rgb1);
int intensity2 = intensity(rgb2);
-
- if (intensity1 > maxIntensity) {
- maxIntensity = intensity1;
- }
-
- if (intensity2 > maxIntensity) {
- maxIntensity = intensity2;
- }
-
- result.setRGB(x,y, intensity1 > intensity2 ? rgb1 : rgb2);
+ maxIntensity = Math.max(Math.max(maxIntensity, intensity1), intensity2);
+
+ result.setRGB(x, y, intensity1 > intensity2 ? rgb1 : rgb2);
}
}
return maxIntensity;
@@ -142,22 +240,19 @@ public class MaximumIntensityProjectionGenerationAlgorithm implements IImageGene
double r = getRed(rgb);
double g = getGreen(rgb);
double b = getBlue(rgb);
- return new Double(Math.sqrt(r*r + g*g + b*b)).intValue();
+ return new Double(Math.sqrt(r * r + g * g + b * b)).intValue();
}
-
private int getBlue(int rgb)
{
return rgb & 0xff;
}
-
private int getGreen(int rgb)
{
return (rgb >> 8) & 0xff;
}
-
private int getRed(int rgb)
{
return (rgb >> 16) & 0xff;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
index 5a3f323c815056edd0c2660caaee16ed6910328f..2c08e93145687af3afb409799a7deef8201ddf06 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
@@ -347,8 +347,8 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
containedDataSetCodes.add(mainDataset.getDataSetCode());
- createRepresentativeThumbnailByImageGenerationAlgorithm(imageDataSetInformation, imageDataSetStructure,
- containedDataSetCodes, thumbnailDatasets);
+ createRepresentativeThumbnailByImageGenerationAlgorithm(imageDataSetInformation, containedDataSetCodes,
+ thumbnailDatasets);
for (IDataSet thumbnailDataset : thumbnailDatasets)
{
@@ -366,14 +366,14 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
}
private void createRepresentativeThumbnailByImageGenerationAlgorithm(ImageDataSetInformation imageDataSetInformation,
- ImageDataSetStructure imageDataSetStructure, List<String> containedDataSetCodes, List<IDataSet> thumbnailDatasets)
+ List<String> containedDataSetCodes, List<IDataSet> thumbnailDatasets)
{
IImageGenerationAlgorithm algorithm = imageDataSetInformation.getImageGenerationAlgorithm();
if (algorithm == null)
{
return;
}
- List<BufferedImage> images = algorithm.generateImages(imageDataSetInformation, imageDataSetStructure);
+ List<BufferedImage> images = algorithm.generateImages(imageDataSetInformation);
if (images.size() > 0) {
IDataSet representative = createNewDataSet(algorithm.getDataSetTypeCode());
for (int i = 0; i < images.size(); i++)
diff --git a/screening/sourceTest/core-plugins/MicroscopyImageDropboxTest/1/dss/drop-boxes/MicroscopyImageDropboxTest-drop-box/MicroscopySingleDatasetConfig.py b/screening/sourceTest/core-plugins/MicroscopyImageDropboxTest/1/dss/drop-boxes/MicroscopyImageDropboxTest-drop-box/MicroscopySingleDatasetConfig.py
index 149865111cdd22577b48258d1414624cf5097a1c..7dfb4ce3f3dff6bae92f34ecfea045d6006b10d7 100644
--- a/screening/sourceTest/core-plugins/MicroscopyImageDropboxTest/1/dss/drop-boxes/MicroscopyImageDropboxTest-drop-box/MicroscopySingleDatasetConfig.py
+++ b/screening/sourceTest/core-plugins/MicroscopyImageDropboxTest/1/dss/drop-boxes/MicroscopyImageDropboxTest-drop-box/MicroscopySingleDatasetConfig.py
@@ -13,6 +13,13 @@ from ch.systemsx.cisd.openbis.dss.etl.dto.api import ImageMetadata
from ch.systemsx.cisd.openbis.dss.etl.dto.api import OriginalDataStorageFormat
from ch.systemsx.cisd.openbis.dss.etl.dto.api import ChannelColorRGB
from ch.systemsx.cisd.openbis.dss.etl.dto.api import Channel
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.impl import MaximumIntensityProjectionGenerationAlgorithm;
+
+class TestAlgorithm(MaximumIntensityProjectionGenerationAlgorithm):
+ def __init__(self):
+ MaximumIntensityProjectionGenerationAlgorithm.__init__(self, 'MICROSCOPY_REPRESENTATIVE_IMG')
+ def imageToBeIgnored(self, imageFileInfo):
+ return False
class MicroscopySingleDatasetConfig(SimpleImageContainerDataConfig):
"""Image data configuration class for multi datasets image files."""
@@ -60,6 +67,7 @@ class MicroscopySingleDatasetConfig(SimpleImageContainerDataConfig):
# Set the dataset type
self.setDataSetType("MICROSCOPY_IMG")
+ self.setImageGenerationAlgorithm(TestAlgorithm())
def createChannel(self, channelCode):
"""Create a channel from the channelCode with the name as read from
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithmTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithmTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c2d5ec5c9ff9897877c632cf76f41243cbdc273e
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/MaximumIntensityProjectionGenerationAlgorithmTest.java
@@ -0,0 +1,207 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * 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.dto.api.impl;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.image.ImageHistogram;
+import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageStorageConfiguraton;
+
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Friend(toClasses = MaximumIntensityProjectionGenerationAlgorithm.class)
+public class MaximumIntensityProjectionGenerationAlgorithmTest extends AbstractFileSystemTestCase
+{
+ private static final class ImageBuilder
+ {
+ private BufferedImage image;
+ private Graphics graphics;
+
+ ImageBuilder(int imageType)
+ {
+ image = new BufferedImage(10, 6, BufferedImage.TYPE_INT_RGB);
+ graphics = image.getGraphics();
+ }
+
+ BufferedImage getImage()
+ {
+ return image;
+ }
+
+ ImageBuilder rect(int x, int y, int width, int height, Color color)
+ {
+ graphics.setColor(color);
+ graphics.fillRect(x, y, width, height);
+ return this;
+ }
+ }
+
+ private static final class MaximumIntensityProjectionGenerationAlgorithmWithMockedLoading
+ extends MaximumIntensityProjectionGenerationAlgorithm
+ {
+ private static final long serialVersionUID = 1L;
+
+ private final List<String> recorder = new ArrayList<String>();
+
+ private final Map<String, BufferedImage> images;
+
+ private final Set<String> imagesToIgnore;
+
+ public MaximumIntensityProjectionGenerationAlgorithmWithMockedLoading(String dataSetTypeCode,
+ int width, int height, String filename, Map<String, BufferedImage> images, String... imagesToIgnore)
+ {
+ super(dataSetTypeCode, width, height, filename);
+ this.images = images;
+ this.imagesToIgnore = new HashSet<String>(Arrays.asList(imagesToIgnore));
+ }
+
+ @Override
+ BufferedImage loadImage(File incomingDirectory, String imagePath, String identifier, ImageLibraryInfo library)
+ {
+ recorder.add(incomingDirectory.getName() + "/" + imagePath + ": " + identifier + " [" + library + "]");
+ BufferedImage bufferedImage = images.get(identifier);
+ assertNotNull("image " + identifier, bufferedImage);
+ return bufferedImage;
+ }
+
+ @Override
+ protected boolean imageToBeIgnored(ImageFileInfo image)
+ {
+ return imagesToIgnore.contains(image.tryGetUniqueStringIdentifier());
+ }
+ }
+
+ private Map<String, BufferedImage> images;
+ private ImageDataSetInformation information;
+ private ImageDataSetStructure structure;
+
+ @BeforeMethod
+ public void createImages()
+ {
+ images = new LinkedHashMap<String, BufferedImage>();
+ images.put("i1", new ImageBuilder(BufferedImage.TYPE_INT_RGB)
+ .rect(1, 0, 3, 2, new Color(255, 128, 128))
+ .rect(5, 4, 3, 2, new Color(80, 255, 128)).getImage());
+ images.put("i2", new ImageBuilder(BufferedImage.TYPE_USHORT_GRAY)
+ .rect(2, 1, 5, 4, new Color(100, 100, 100)).getImage());
+ images.put("i3", new ImageBuilder(BufferedImage.TYPE_USHORT_GRAY)
+ .rect(3, 2, 5, 4, new Color(30, 30, 30)).getImage());
+ information = new ImageDataSetInformation();
+ information.setIncomingDirectory(new File(workingDirectory, "incoming"));
+ structure = new ImageDataSetStructure();
+ information.setImageDataSetStructure(structure);
+ ImageStorageConfiguraton imageStorageConfiguraton = new ImageStorageConfiguraton();
+ imageStorageConfiguraton.setImageLibrary(new ImageLibraryInfo("lib", "reader"));
+ structure.setImageStorageConfiguraton(imageStorageConfiguraton);
+ Set<String> keySet = images.keySet();
+ List<ImageFileInfo> imageFileInfos = new ArrayList<ImageFileInfo>();
+ for (String key : keySet)
+ {
+ ImageFileInfo fileInfo = new ImageFileInfo("C" + key.toUpperCase(), 1, 1, "images/" + key + ".png");
+ fileInfo.setUniqueImageIdentifier(key);
+ imageFileInfos.add(fileInfo);
+ }
+ structure.setImages(imageFileInfos);
+ }
+
+ @Test
+ public void test8BitColorImageAnd16BitGrayImage()
+ {
+
+ MaximumIntensityProjectionGenerationAlgorithmWithMockedLoading generationAlgorithm
+ = new MaximumIntensityProjectionGenerationAlgorithmWithMockedLoading("ABC", 10, 6, "r.png", images, "i3");
+ assertEquals("ABC", generationAlgorithm.getDataSetTypeCode());
+ assertEquals("r.png", generationAlgorithm.getImageFileName(0));
+ Channel channel1 = new Channel("CI1", "i1", new ChannelColorRGB(200, 100, 80));
+ Channel channel2 = new Channel("CI2", "i2", new ChannelColorRGB(0, 120, 180));
+ structure.setChannels(Arrays.asList(channel1, channel2));
+
+ List<BufferedImage> generatedImages = generationAlgorithm.generateImages(information);
+
+ assertEquals("[incoming/images/i1.png: i1 [lib (reader: reader)], "
+ + "incoming/images/i2.png: i2 [lib (reader: reader)]]", generationAlgorithm.recorder.toString());
+
+ ImageHistogram histogram = ImageHistogram.calculateHistogram(generatedImages.get(0));
+ assertEquals("[0=48, 80=6, 255=6]", renderHistogram(histogram.getRedHistogram()));
+ assertEquals("[0=32, 47=16, 128=6, 255=6]", renderHistogram(histogram.getGreenHistogram()));
+ assertEquals("[0=32, 71=16, 128=12]", renderHistogram(histogram.getBlueHistogram()));
+ assertEquals(1, generatedImages.size());
+ }
+
+ @Test
+ public void testTwo16BitGrayImages()
+ {
+
+ MaximumIntensityProjectionGenerationAlgorithmWithMockedLoading generationAlgorithm
+ = new MaximumIntensityProjectionGenerationAlgorithmWithMockedLoading("ABC", 10, 6, "r.png", images, "i1");
+ Channel channel1 = new Channel("CI2", "i2", new ChannelColorRGB(200, 100, 80));
+ Channel channel2 = new Channel("CI3", "i3", new ChannelColorRGB(0, 120, 180));
+ structure.setChannels(Arrays.asList(channel1, channel2));
+
+ List<BufferedImage> generatedImages = generationAlgorithm.generateImages(information);
+
+ assertEquals("[incoming/images/i2.png: i2 [lib (reader: reader)], "
+ + "incoming/images/i3.png: i3 [lib (reader: reader)]]", generationAlgorithm.recorder.toString());
+
+ ImageHistogram histogram = ImageHistogram.calculateHistogram(generatedImages.get(0));
+ assertEquals("[0=40, 216=20]", renderHistogram(histogram.getRedHistogram()));
+ assertEquals("[0=32, 39=8, 108=20]", renderHistogram(histogram.getGreenHistogram()));
+ assertEquals("[0=32, 58=8, 86=20]", renderHistogram(histogram.getBlueHistogram()));
+ assertEquals(1, generatedImages.size());
+ }
+
+ private String renderHistogram(int[] histogram)
+ {
+ StringBuilder builder = new StringBuilder();
+ for (int i = 0; i < histogram.length; i++)
+ {
+ int value = histogram[i];
+ if (value > 0)
+ {
+ if (builder.length() > 0)
+ {
+ builder.append(", ");
+ }
+ builder.append(i).append("=").append(value);
+ }
+ }
+ return "[" + builder.toString() + "]";
+ }
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractScreeningSystemTestCase.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractScreeningSystemTestCase.java
index 57436c6d52100d5a8f0a47d3813ab339d4c9498a..8270cb500045290516fca04fe521c80663c6f1ce 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractScreeningSystemTestCase.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AbstractScreeningSystemTestCase.java
@@ -94,12 +94,17 @@ public abstract class AbstractScreeningSystemTestCase extends SystemTestCase
}
+ private static interface IImageLoader
+ {
+ public BufferedImage load();
+
+ }
/**
* Helper class to load an image from the image download servlet.
*
* @author Franz-Josef Elmer
*/
- protected static final class ImageLoader
+ protected static final class ImageLoader implements IImageLoader
{
private final URLMethodWithParameters url;
private final List<String> channels = new ArrayList<String>();
@@ -120,6 +125,7 @@ public abstract class AbstractScreeningSystemTestCase extends SystemTestCase
url.addParameter(ImageServletUrlParameters.DATASET_CODE_PARAM, dataSet.getCode());
}
+ @Override
public BufferedImage load()
{
try
@@ -241,7 +247,7 @@ public abstract class AbstractScreeningSystemTestCase extends SystemTestCase
}
/**
- * Asserts no failures occurred for all invocations of {@link #check(File, ImageLoader)}.
+ * Asserts no failures occurred for all invocations of {@link #check(File, IImageLoader)}.
* Otherwise an {@link AssertionError} is thrown.
*/
public void assertNoFailures()
@@ -253,11 +259,39 @@ public abstract class AbstractScreeningSystemTestCase extends SystemTestCase
}
}
+ /**
+ * Checks that the specified reference image is equals to the image loaded from the specified file
+ * in the specified data set.
+ */
+ public void check(File referenceImage, final String sessionToken, final AbstractExternalData dataSet,
+ final String pathInDataSet)
+ {
+ check(referenceImage, new IImageLoader()
+ {
+
+ @Override
+ public BufferedImage load()
+ {
+ URLMethodWithParameters url = new URLMethodWithParameters(dataSet.getDataStore().getHostUrl()
+ + "/datastore_server/" + dataSet.getCode() + "/" + pathInDataSet);
+ url.addParameter(Utils.SESSION_ID_PARAM, sessionToken);
+ url.addParameter("mode", "simpleHtml");
+ try
+ {
+ return ImageIO.read(new URL(url.toString()));
+ } catch (Exception ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+ });
+ }
+
/**
* Checks that the specified reference image is equals to the image loaded by the specified image loader.
* A report is created in case of a failure.
*/
- public void check(File referenceImage, ImageLoader imageLoader)
+ public void check(File referenceImage, IImageLoader imageLoader)
{
FailureReport report = new FailureReport(referenceImage);
try
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/MicroscopyImageDropboxTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/MicroscopyImageDropboxTest.java
index 7c3cbd869e617a5606e1801dd7fbb2b979d6d6dd..a0cdbadaddce386320f76c2e56e82f3cfcc59eee 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/MicroscopyImageDropboxTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/MicroscopyImageDropboxTest.java
@@ -22,6 +22,7 @@ import java.util.Collections;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.MaximumIntensityProjectionGenerationAlgorithm;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
@@ -67,6 +68,9 @@ public class MicroscopyImageDropboxTest extends AbstractImageDropboxTestCase
dataSetType = new DataSetType("MICROSCOPY_IMG_OVERVIEW");
dataSetType.setDataSetKind(DataSetKind.PHYSICAL);
registerDataSetType(commonServer, dataSetType);
+ dataSetType = new DataSetType("MICROSCOPY_REPRESENTATIVE_IMG");
+ dataSetType.setDataSetKind(DataSetKind.PHYSICAL);
+ registerDataSetType(commonServer, dataSetType);
dataSetType = new DataSetType("MICROSCOPY_IMG_CONTAINER");
dataSetType.setDataSetKind(DataSetKind.CONTAINER);
registerDataSetType(commonServer, dataSetType);
@@ -119,6 +123,8 @@ public class MicroscopyImageDropboxTest extends AbstractImageDropboxTestCase
imageChecker.check(new File(getTestDataFolder(), "Merged_256x256_C0_0_200_C4_150_300.png"),
new ImageLoader(dataSet, sessionToken).microscopy().rescaling("SERIES-0_CHANNEL-0", 0, 200)
.rescaling("SERIES-0_CHANNEL-4", 150, 300).mode("thumbnail256x256"));
+ String pathInDataSet = MaximumIntensityProjectionGenerationAlgorithm.DEFAULT_FILE_NAME;
+ imageChecker.check(new File(getTestDataFolder(), pathInDataSet), sessionToken, dataSet, pathInDataSet);
imageChecker.assertNoFailures();
}