diff --git a/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java b/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
index 209e2ab5a9090b5597b904bf3a237e2a95834b13..d15f37f59f868d624dcb1573fdc0622c3ab2770c 100644
--- a/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
+++ b/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
@@ -200,12 +200,16 @@ public class IntensityRescaling
int[][] pixelData = pixels.getPixelData();
for (Channel channel : channels)
{
- int[] channelPixelData = pixelData[channel.getBand()];
- for (int i = 0; i < channelPixelData.length; i++)
+ int band = channel.getBand();
+ if (band < pixelData.length)
{
- histogramArray[channelPixelData[i]]++;
+ int[] channelPixelData = pixelData[band];
+ for (int i = 0; i < channelPixelData.length; i++)
+ {
+ histogramArray[channelPixelData[i]]++;
+ }
+ histogram.pixelCount += channelPixelData.length;
}
- histogram.pixelCount += channelPixelData.length;
}
}
@@ -332,6 +336,11 @@ public class IntensityRescaling
}
}
+
+ public static interface IImageToPixelsConverter
+ {
+ public Pixels convert(BufferedImage image);
+ }
/**
* Computes the levels (black point and white point) of the given <var>histogram</var> for the
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/test/ImageDebugViewer.java b/common/sourceTest/java/ch/systemsx/cisd/common/test/ImageDebugViewer.java
index 63c6cde1ca5d42ede50eb4b461a9c3993157d220..8f2e6cf7e2b1e339af3a147af4dc00f3e173b0eb 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/test/ImageDebugViewer.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/test/ImageDebugViewer.java
@@ -157,7 +157,7 @@ public class ImageDebugViewer
System.out.println("\\_________ " + title);
}
- private static String tryGetTypeAsString(BufferedImage image)
+ public static String tryGetTypeAsString(BufferedImage image)
{
int type = image.getType();
return type >= 0 && type < IMAGE_TYPES.length ? IMAGE_TYPES[type] : null;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
index ea06230a93d4c07ca3edf8655405d1da5999937d..7ae7cb8df0aff1571b7e144dc10e6cbd4d3c5302 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
@@ -39,6 +39,7 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.image.IntensityRescaling.IImageToPixelsConverter;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
@@ -254,17 +255,18 @@ abstract public class AbstractDatasetDownloadServlet extends HttpServlet
}
protected static final BufferedImage createThumbnail(IHierarchicalContentNode fileNode,
- Size thumbnailSize)
+ Size thumbnailSize, IImageToPixelsConverter converterOrNull)
{
- BufferedImage image = ImageUtil.loadImageForDisplay(fileNode);
- return createThumbnail(image, thumbnailSize);
+ BufferedImage image = ImageUtil.loadImageForDisplay(fileNode, converterOrNull);
+ return createThumbnail(image, thumbnailSize, converterOrNull);
}
- protected static final BufferedImage createThumbnail(BufferedImage image, Size thumbnailSize)
+ protected static final BufferedImage createThumbnail(BufferedImage image, Size thumbnailSize,
+ IImageToPixelsConverter converterOrNull)
{
int width = thumbnailSize.getWidth();
int height = thumbnailSize.getHeight();
- return ImageUtil.createThumbnailForDisplay(image, width, height);
+ return ImageUtil.createThumbnailForDisplay(image, width, height, converterOrNull);
}
// if display mode describes a thumbnail return its expected size
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java
index 1067e55249207085299201e213d8d9d7009482b4..b9e7166af414431118bf5db8ac8d70ff3969e7c8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServlet.java
@@ -495,7 +495,7 @@ public class DatasetDownloadServlet extends AbstractDatasetDownloadServlet
Size thumbnailSize = tryAsThumbnailDisplayMode(displayMode);
if (thumbnailSize != null)
{
- BufferedImage image = createThumbnail(fileNode, thumbnailSize);
+ BufferedImage image = createThumbnail(fileNode, thumbnailSize, null);
infoPostfix = " as a thumbnail.";
responseStream = createResponseContentStream(image, fileNode.getName());
} else
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 7b323ec843837b1399267b5bfc4ac0bb4f51af16..cdcdae98a699e3e69751c6bf59ac3b3a9f6c5d81 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
@@ -20,6 +20,7 @@ import java.awt.Dimension;
import java.awt.Graphics2D;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
+import java.awt.image.ColorModel;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
@@ -52,6 +53,7 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.image.ImageHistogram;
import ch.systemsx.cisd.common.image.IntensityRescaling;
import ch.systemsx.cisd.common.image.IntensityRescaling.Channel;
+import ch.systemsx.cisd.common.image.IntensityRescaling.IImageToPixelsConverter;
import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
import ch.systemsx.cisd.common.image.IntensityRescaling.Pixels;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -881,7 +883,8 @@ public class ImageUtil
*
* @throws IllegalArgumentException if the file isn't a valid image file.
*/
- public static BufferedImage loadImageForDisplay(IHierarchicalContentNode contentNode)
+ public static BufferedImage loadImageForDisplay(IHierarchicalContentNode contentNode,
+ IImageToPixelsConverter converterOrNull)
{
if (contentNode.exists() == false)
{
@@ -889,7 +892,7 @@ public class ImageUtil
+ contentNode.getRelativePath());
}
BufferedImage result = loadImage(contentNode);
- result = convertForDisplayIfNecessary(result, null);
+ result = convertForDisplayIfNecessary(result, null, converterOrNull);
return result;
}
@@ -906,37 +909,91 @@ public class ImageUtil
* @param maxHeight Maximum height of the result image.
*/
public static BufferedImage createThumbnailForDisplay(BufferedImage image, int maxWidth,
- int maxHeight)
+ int maxHeight, IImageToPixelsConverter converterOrNull)
{
- BufferedImage result = rescale(image, maxWidth, maxHeight, true, false);
- result = convertForDisplayIfNecessary(result, null);
+ BufferedImage result = rescale(image, maxWidth, maxHeight, true, false, converterOrNull);
+ result = convertForDisplayIfNecessary(result, null, converterOrNull);
return result;
}
/**
* If the specified image uses grayscale with color depth larger then 8 bits, conversion to 8
* bits grayscale is done. Otherwise the original image is returned.
+ * <p>
+ * Conversion is done by intensity rescaling (with outlier cutoff specified by <code>threshold</code>)
+ * because the actual resolution is often not know because getMaxNumberOfBitsPerComponent() might
+ * return 16 even tough the resolution is only 12.
*/
- public static BufferedImage convertForDisplayIfNecessary(BufferedImage image, Float threshold)
+ private static BufferedImage convertForDisplayIfNecessary(BufferedImage image, Float threshold,
+ IImageToPixelsConverter converterOrNull)
+ {
+ Channel channel = getRepresentativeChannelIfEffectiveGrayAndMoreThan8Bit(image);
+ if (channel != null)
+ {
+ Pixels pixels = converterOrNull == null ? new Pixels(image) : converterOrNull.convert(image);
+ Levels intensityRange = IntensityRescaling.computeLevels(pixels,
+ threshold == null ? DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR : threshold, channel);
+ convertToGray(pixels);
+ BufferedImage result =
+ IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, intensityRange, Channel.values());
+ return result;
+ }
+ return image;
+ }
+
+ private static void convertToGray(Pixels pixels)
{
- if (isGrayscale(image))
+ int[][] pixelData = pixels.getPixelData();
+ if (pixelData.length > 1)
{
- if (image.getColorModel().getPixelSize() > 8)
+ for (int i = 0, n = pixelData[0].length; i < n; i++)
{
- Pixels pixels = new Pixels(image);
- Levels intensityRange = IntensityRescaling.computeLevels(pixels,
- threshold == null ? DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR : threshold, Channel.RED);
- BufferedImage result =
- IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, intensityRange, Channel.RED);
- return result;
+ int max = 0;
+ for (int c = 0; c < pixelData.length; c++)
+ {
+ max = Math.max(max, pixelData[c][i]);
+ }
+ for (int c = 0; c < pixelData.length; c++)
+ {
+ pixelData[c][i] = max;
+ }
}
}
- return image;
}
- private static boolean isGrayscale(BufferedImage image)
+ private static Channel getRepresentativeChannelIfEffectiveGrayAndMoreThan8Bit(BufferedImage image)
+ {
+ if (getMaxNumberOfBitsPerComponent(image) <= 8)
+ {
+ return null;
+ }
+ ColorModel colorModel = image.getColorModel();
+ if (image.getType() != BufferedImage.TYPE_CUSTOM)
+ {
+ return colorModel.getNumColorComponents() == 1 ? Channel.RED : null;
+ }
+ return getRepresentativeChannelIfEffectiveGray(image);
+ }
+
+ /**
+ * Returns the maximum bit resolution of the specified image. It returns the maximum of the array
+ * returned by {@link ColorModel#getComponentSize()}. If not defined (which should be only the case
+ * for Index16ColorModel of the BioFormats library) {@link ColorModel#getPixelSize()} is returned.
+ */
+ public static int getMaxNumberOfBitsPerComponent(BufferedImage image)
{
- return image.getColorModel().getColorSpace().getNumComponents() == 1;
+ ColorModel colorModel = image.getColorModel();
+ int[] componentSize = colorModel.getComponentSize();
+ if (componentSize == null)
+ {
+ return colorModel.getPixelSize();
+ }
+ int max = 0;
+ for (int size : componentSize)
+ {
+ max = Math.max(max, size);
+ }
+ return max;
}
/**
@@ -953,13 +1010,12 @@ public class ImageUtil
checkIfChannelIsUsed(histogramsByChannels, numberOfPixels, Channel.RED, imageHistogram.getRedHistogram());
checkIfChannelIsUsed(histogramsByChannels, numberOfPixels, Channel.GREEN, imageHistogram.getGreenHistogram());
checkIfChannelIsUsed(histogramsByChannels, numberOfPixels, Channel.BLUE, imageHistogram.getBlueHistogram());
- List<Entry<Channel, int[]>> usedChannels = new ArrayList<Map.Entry<Channel,int[]>>(histogramsByChannels.entrySet());
- if (usedChannels.isEmpty())
+ if (histogramsByChannels.isEmpty())
{
return Channel.RED; // Black image is a gray image, doesn't matter which channel to return.
}
- Entry<Channel, int[]> representativeChannel = usedChannels.get(0);
- int[] representativeHistogram = representativeChannel.getValue();
+ List<Entry<Channel, int[]>> usedChannels = new ArrayList<Map.Entry<Channel,int[]>>(histogramsByChannels.entrySet());
+ int[] representativeHistogram = usedChannels.get(0).getValue();
for (int i = 1; i < usedChannels.size(); i++)
{
int[] histogram = usedChannels.get(i).getValue();
@@ -971,7 +1027,7 @@ public class ImageUtil
}
}
}
- return representativeChannel.getKey();
+ return usedChannels.get(0).getKey();
}
private static void checkIfChannelIsUsed(Map<Channel, int[]> usedChannels, int numberOfPixels, Channel channel, int[] histogram)
@@ -993,9 +1049,10 @@ public class ImageUtil
* specified limit, then the image is not changed.
* @param highQuality8Bit if true thumbnails will be of higher quality, but rescaling will take
* longer and the image will be converted to 8 bit.
+ * @param converterOrNull
*/
public static BufferedImage rescale(BufferedImage image, int maxWidth, int maxHeight,
- boolean enlargeIfNecessary, boolean highQuality8Bit)
+ boolean enlargeIfNecessary, boolean highQuality8Bit, IImageToPixelsConverter converterOrNull)
{
int width = image.getWidth();
int height = image.getHeight();
@@ -1028,7 +1085,7 @@ public class ImageUtil
// WORKAROUND: non-default interpolations do not work well with 16 bit grayscale images.
// We have to rescale colors to 8 bit here, otherwise the result will contain only few
// colors.
- imageToRescale = convertForDisplayIfNecessary(imageToRescale, 0f);
+ imageToRescale = convertForDisplayIfNecessary(imageToRescale, 0f, converterOrNull);
}
graphics2D.drawImage(imageToRescale, 0, 0, thumbnailWidth, thumbnailHeight, null);
graphics2D.dispose();
@@ -1064,7 +1121,7 @@ public class ImageUtil
} else if (imageType == BufferedImage.TYPE_BYTE_INDEXED)
{
imageType = BufferedImage.TYPE_INT_RGB;
- } else
+ } else
{
imageType = isTransparent ? BufferedImage.TYPE_INT_ARGB : BufferedImage.TYPE_INT_RGB;
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
index 16f8790de14065579de07ca0a400bf3417f67da2..d1aeb542ed1f92b714b0a9bf6c9f0c04daffbab3 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ImageUtilTest.java
@@ -195,8 +195,8 @@ public class ImageUtilTest extends AssertJUnit
public void testCreateThumbnail()
{
BufferedImage image = loadImageByFile("gif-example.gif");
- assertImageSize(79, 100, ImageUtil.createThumbnailForDisplay(image, 200, 100));
- assertImageSize(100, 127, ImageUtil.createThumbnailForDisplay(image, 100, 200));
+ assertImageSize(79, 100, ImageUtil.createThumbnailForDisplay(image, 200, 100, null));
+ assertImageSize(100, 127, ImageUtil.createThumbnailForDisplay(image, 100, 200, null));
}
@Test
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ThumbnailTiming.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ThumbnailTiming.java
index c9398b194fb451bf03f9f99ea67f7b77bf52946e..1206c96e505a3361bd7f239d394b4c96a486972e 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ThumbnailTiming.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/ThumbnailTiming.java
@@ -45,7 +45,7 @@ public class ThumbnailTiming
BufferedImage image = ImageUtil.loadImage(file);
stopWatch.stop();
stopWatch.start("Convert");
- BufferedImage thumbnail = ImageUtil.createThumbnailForDisplay(image, 120, 60);
+ BufferedImage thumbnail = ImageUtil.createThumbnailForDisplay(image, 120, 60, null);
stopWatch.stop();
stopWatch.start("Write");
try
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new file mode 100644
index 0000000000000000000000000000000000000000..48035210735d6717cd3ed57ad9e9690ab6776e71
Binary files /dev/null and b/screening/resource/test-data/Simple16BitImageDropboxTest/PLATE-16-BIT/PLATE-16-BIT_A01_06_GFP.png differ
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
index 39d4e54d68d72f7ae77e902bfecff5ec6016d623..8d108164ed632db04c806acbb846e57811eadd43 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
@@ -143,8 +143,7 @@ public class AbsoluteImageReference extends AbstractImageReference
{
return image.getColorModel().getPixelSize();
}
- return Utils.loadUnchangedImageColorDepth(contentNode, channelCodeOrNull,
- imageLibraryOrNull);
+ return Utils.loadUnchangedImageColorDepth(contentNode, tryGetImageID(), imageLibraryOrNull);
}
public RequestedImageSize getRequestedSize()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
index b0e4a87b87101bf25a1da56e0868e6820382cb84..9e15f914f4c7b9137897a520c99d1b7a8ec00be7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java
@@ -65,6 +65,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformat
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
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.dss.shared.DssScreeningUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
@@ -444,7 +445,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
}
boolean highQuality = thumbnailsStorageFormat.isHighQuality();
- BufferedImage rescaledImage = ImageUtil.rescale(image, widht, height, false, highQuality);
+ BufferedImage rescaledImage = ImageUtil.rescale(image, widht, height, false, highQuality, DssScreeningUtils.CONVERTER);
final List<ThumbnailData> thumbnails = new ArrayList<ThumbnailData>();
for (String channelCode : getChannelsToProcess(imageFileInfo.getChannelCode()))
@@ -475,26 +476,14 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
private BufferedImage applyTransformationsChain(BufferedImage image,
ColorComponent colorComponent, IImageTransformer transformer)
{
- return applyTransformationIfNeeded(extractSingleChannelIfNeeded(image, colorComponent),
- transformer);
+ BufferedImage extractedChannelImage = ImageChannelsUtils.extractChannel(image, colorComponent);
+ return applyTransformationIfNeeded(extractedChannelImage, transformer);
}
private BufferedImage applyTransformationsChain(BufferedImage image, String channelCode,
ColorComponent colorComponent)
{
- return applyTransformationsChain(image, colorComponent,
- tryCreateImageTransformer(channelCode));
- }
-
- private static BufferedImage extractSingleChannelIfNeeded(BufferedImage image,
- ColorComponent colorComponent)
- {
- if (colorComponent != null)
- {
- return ImageChannelsUtils.transformToChannel(image, colorComponent);
- }
-
- return image;
+ return applyTransformationsChain(image, colorComponent, tryCreateImageTransformer(channelCode));
}
private static BufferedImage applyTransformationIfNeeded(BufferedImage image,
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 73c5bdeb110911aca96c950bd099997dd7f3da5e..dc8c8d5784515aa01342fb274a42c7aef4c7c61c 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
@@ -31,9 +31,11 @@ import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.base.image.IImageTransformer;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.image.ImageHistogram;
import ch.systemsx.cisd.common.image.IntensityRescaling;
import ch.systemsx.cisd.common.image.IntensityRescaling.Channel;
import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
+import ch.systemsx.cisd.common.image.IntensityRescaling.PixelHistogram;
import ch.systemsx.cisd.common.image.IntensityRescaling.Pixels;
import ch.systemsx.cisd.common.image.MixColors;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -394,86 +396,54 @@ public class ImageChannelsUtils
AbsoluteImageReference imageReference, ImageTransformationParams transformationInfo,
Float threshold)
{
- BufferedImage image = calculateSingleImage(imageReference);
- image = transform(image, imageReference, transformationInfo);
- image = ImageUtil.convertForDisplayIfNecessary(image, threshold);
- image = convertTo8Bit(image);
- Channel channel = ImageUtil.getRepresentativeChannelIfEffectiveGray(image);
- if (channel != null)
- {
- final ChannelColorRGB channelColor = imageReference.getChannelColor();
- image = transformColor(image, createColorTransformation(channel, channelColor));
- }
+ BufferedImage image = imageReference.getUnchangedImage();
+ image = rescaleIfNot8Bit(image, threshold);
+ image = resize(image, imageReference.getRequestedSize());
+ image = extractChannel(image, imageReference.tryGetColorComponent());
+ image = transform(image, imageReference, transformationInfo, threshold);
+ image = transformGrayToColor(image, imageReference.getChannelColor());
return image;
}
-
- private static BufferedImage calculateSingleImage(AbsoluteImageReference imageReference)
- {
- long start = operationLog.isDebugEnabled() ? System.currentTimeMillis() : 0;
- BufferedImage image = imageReference.getUnchangedImage();
-
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug("Load original image: " + (System.currentTimeMillis() - start));
- }
-
- // resized the image if necessary
- RequestedImageSize requestedSize = imageReference.getRequestedSize();
- Size size = requestedSize.tryGetThumbnailSize();
- if (size != null)
+ private static BufferedImage rescaleIfNot8Bit(BufferedImage image, Float threshold)
+ {
+ if (ImageUtil.getMaxNumberOfBitsPerComponent(image) <= 8)
{
- start = operationLog.isDebugEnabled() ? System.currentTimeMillis() : 0;
- boolean enlarge = requestedSize.enlargeIfNecessary();
- boolean highQuality8Bit = requestedSize.isHighQualityRescalingRequired();
- image = ImageUtil.rescale(image, size.getWidth(), size.getHeight(), enlarge, highQuality8Bit);
- if (highQuality8Bit == false)
- {
- image = ImageUtil.convertForDisplayIfNecessary(image, null);
- }
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug("Create thumbnail: " + (System.currentTimeMillis() - start));
- }
+ return image;
}
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ float thresholdValue = getThresholdValue(threshold);
+ Levels levels = IntensityRescaling.computeLevels(pixels, thresholdValue, Channel.values());
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.values());
+ }
- // choose color component if necessary
- final ColorComponent colorComponentOrNull = imageReference.tryGetColorComponent();
- if (colorComponentOrNull != null)
- {
- start = operationLog.isDebugEnabled() ? System.currentTimeMillis() : 0;
- image = transformToChannel(image, colorComponentOrNull);
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug("Select single channel: " + (System.currentTimeMillis() - start));
- }
- }
- return image;
+ private static float getThresholdValue(Float threshold)
+ {
+ return threshold == null ? ImageUtil.DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR : threshold;
}
- private static BufferedImage convertTo8Bit(BufferedImage image)
+ private static BufferedImage transformGrayToColor(BufferedImage image, final ChannelColorRGB channelColor)
{
- Pixels pixels = DssScreeningUtils.createPixels(image);
- int[][] pixelData = pixels.getPixelData();
- int maxIntensity = 0;
- for (int[] colorChannelPixels : pixelData)
+ Channel channel = ImageUtil.getRepresentativeChannelIfEffectiveGray(image);
+ if (channel == null)
{
- for (int intensity : colorChannelPixels)
- {
- if (intensity > maxIntensity)
- {
- maxIntensity = intensity;
- }
- }
+ return image;
}
- if (maxIntensity < 256)
+ return transformColor(image, createColorTransformation(channel, channelColor));
+ }
+
+ private static BufferedImage resize(BufferedImage image, RequestedImageSize requestedSize)
+ {
+ Size size = requestedSize.tryGetThumbnailSize();
+ if (size == null)
{
return image;
}
- Levels levels = new Levels(0, maxIntensity < 4096 ? 4096 : 1 << 16);
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.values());
+ boolean enlarge = requestedSize.enlargeIfNecessary();
+ boolean highQuality8Bit = requestedSize.isHighQualityRescalingRequired();
+ return ImageUtil.rescale(image, size.getWidth(), size.getHeight(), enlarge, highQuality8Bit, DssScreeningUtils.CONVERTER);
}
-
+
private static IColorTransformation createColorTransformation(final Channel channel, final ChannelColorRGB channelColor)
{
return new IColorTransformation()
@@ -516,29 +486,19 @@ public class ImageChannelsUtils
ImageTransformationParams transformationInfo,
IImageTransformerFactory mergedChannelTransformationOrNull)
{
- // We do not transform single images here.
- IImageCalculator calculator = createCalculator(transformationInfo);
- List<ImageWithReference> images = calculateSingleImages(imageReferences, calculator);
- for (int i = 0; i < images.size(); i++)
+ assert transformationInfo != null;
+ List<ImageWithReference> images = new ArrayList<ImageWithReference>();
+ for (AbsoluteImageReference imageReference : imageReferences)
{
- ImageWithReference imageWithReference = images.get(i);
- BufferedImage image = imageWithReference.getBufferedImage();
- AbsoluteImageReference imageReference = imageWithReference.getReference();
- Channel channel = ImageUtil.getRepresentativeChannelIfEffectiveGray(image);
- if (channel != null)
- {
- final ChannelColorRGB channelColor = imageReference.getChannelColor();
- image = transformColor(image, createColorTransformation(channel, channelColor));
- imageWithReference.setImage(image);
- }
+ images.add(new ImageWithReference(imageReference.getUnchangedImage(), imageReference));
}
-
+ calculateImagesForMerging(images, transformationInfo);
BufferedImage mergedImage = mergeImages(images);
// non-user transformation - apply color range fix after mixing
Map<String, String> transMap = transformationInfo.tryGetTransformationCodeForChannels();
IImageTransformerFactory channelTransformation = mergedChannelTransformationOrNull;
- if ((transMap == null || transMap.size() == 0) && channelTransformation == null)
+ if ((transMap == null || transMap.isEmpty()) && channelTransformation == null)
{
Levels levels = IntensityRescaling.computeLevels(DssScreeningUtils.createPixels(mergedImage), 30);
int minLevel = levels.getMinLevel();
@@ -555,33 +515,37 @@ public class ImageChannelsUtils
return mergedImage;
}
- private static IImageCalculator createCalculator(final ImageTransformationParams transformationInfo)
+ private static void calculateImagesForMerging(List<ImageWithReference> images, ImageTransformationParams transformationInfo)
{
- return new IImageCalculator()
- {
- @Override
- public BufferedImage create(AbsoluteImageReference imageContent)
- {
- boolean applyNonImageLevelTransformation = false;
- String transformationCode = null;
- if (transformationInfo != null)
- {
- String channelCode = imageContent.tryGetChannelCode();
- transformationCode = transformationInfo.tryGetTransformationCodeForChannel(channelCode);
- if (transformationCode != null)
- {
- applyNonImageLevelTransformation = transformationInfo.isApplyNonImageLevelTransformation();
- }
- }
- ImageTransformationParams info = new ImageTransformationParams(applyNonImageLevelTransformation,
- false, transformationCode, null);
- return calculateAndTransformSingleImageForDisplay(imageContent, info, null);
- }
- };
+ for (ImageWithReference imageWithReference : images)
+ {
+ BufferedImage image = imageWithReference.getBufferedImage();
+ AbsoluteImageReference imageReference = imageWithReference.getReference();
+ image = rescaleIfNot8Bit(image, 0f);
+ image = resize(image, imageReference.getRequestedSize());
+ image = transformForChannel(image, imageReference, transformationInfo);
+ image = transformGrayToColor(image, imageReference.getChannelColor());
+ imageWithReference.setImage(image);
+ }
+ }
+
+ private static BufferedImage transformForChannel(BufferedImage image, AbsoluteImageReference imageReference,
+ ImageTransformationParams transformationInfo)
+ {
+ String channelCode = imageReference.tryGetChannelCode();
+ String transformationCode = transformationInfo.tryGetTransformationCodeForChannel(channelCode);
+ boolean applyNonImageLevelTransformation = false;
+ if (transformationCode != null)
+ {
+ applyNonImageLevelTransformation = transformationInfo.isApplyNonImageLevelTransformation();
+ }
+ ImageTransformationParams info
+ = new ImageTransformationParams(applyNonImageLevelTransformation, false, transformationCode, null);
+ return transform(image, imageReference, info, 0f);
}
private static BufferedImage transform(BufferedImage image,
- AbsoluteImageReference imageReference, ImageTransformationParams transformationInfo)
+ AbsoluteImageReference imageReference, ImageTransformationParams transformationInfo, Float threshold)
{
BufferedImage resultImage = image;
ImageTransfomationFactories transformations = imageReference.getImageTransformationFactories();
@@ -615,7 +579,7 @@ public class ImageChannelsUtils
if (channelLevelTransformationOrNull == null)
{
channelLevelTransformationOrNull = new AutoRescaleIntensityImageTransformerFactory(
- ImageUtil.DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR);
+ getThresholdValue(threshold));
}
}
return applyImageTransformation(resultImage, channelLevelTransformationOrNull);
@@ -629,8 +593,8 @@ public class ImageChannelsUtils
return image;
}
IImageTransformer transformer = transformerFactoryOrNull.createTransformer();
- BufferedImage transformImage = transformer.transform(image);
- return transformImage;
+ BufferedImage transformedImage = transformer.transform(image);
+ return transformedImage;
}
private static List<ImageWithReference> calculateSingleImages(List<AbsoluteImageReference> imageContents,
@@ -771,8 +735,12 @@ public class ImageChannelsUtils
/**
* Transforms the given <var>bufferedImage</var> by selecting a single channel from it.
*/
- public static BufferedImage transformToChannel(BufferedImage bufferedImage, final ColorComponent colorComponent)
+ public static BufferedImage extractChannel(BufferedImage bufferedImage, final ColorComponent colorComponent)
{
+ if (colorComponent == null)
+ {
+ return bufferedImage;
+ }
return transformColor(bufferedImage, new IColorTransformation()
{
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
index 02fb8c36342a62f8629a3713d1bdd5eec1cc47c1..f1e6389489e7becbdb1196b3406dc2b5e39ab9f7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
@@ -25,6 +25,7 @@ import loci.formats.gui.Index16ColorModel;
import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.common.image.IntensityRescaling.IImageToPixelsConverter;
import ch.systemsx.cisd.common.image.IntensityRescaling.Pixels;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -39,6 +40,15 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.Trans
*/
public class DssScreeningUtils
{
+ public static final IImageToPixelsConverter CONVERTER = new IImageToPixelsConverter()
+ {
+ @Override
+ public Pixels convert(BufferedImage image)
+ {
+ return createPixels(image);
+ }
+ };
+
private static IImagingReadonlyQueryDAO query;
static
@@ -82,7 +92,7 @@ public class DssScreeningUtils
ScreeningConstants.IMAGING_DATA_SOURCE);
return QueryTool.getQuery(dataSource, IImagingTransformerDAO.class);
}
-
+
/**
* Creates {@link Pixels} wrapper object for the specified image which can also handle
* 16bit index color models. Such color models are used when reading Nikon microscopy
@@ -116,5 +126,4 @@ public class DssScreeningUtils
}
};
}
-
}
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 9f7a3988de02caac79e3e6475e950f6a6b63b200..149865111cdd22577b48258d1414624cf5097a1c 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
@@ -49,6 +49,8 @@ class MicroscopySingleDatasetConfig(SimpleImageContainerDataConfig):
# Disable thumbnail generation by ImageMagick
self.setUseImageMagicToGenerateThumbnails(False)
+
+ self.setGenerateHighQuality8BitThumbnails(True)
# Enable thumbnail generation
self.setGenerateThumbnails(True)
@@ -89,7 +91,7 @@ class MicroscopySingleDatasetConfig(SimpleImageContainerDataConfig):
name = "No name"
# Return the color
- return Channel(channelCode, name)
+ return Channel(channelCode, name, self._getChannelColorRGB(channelCode))
def extractImagesMetadata(self, imagePath, imageIdentifiers):
@@ -143,7 +145,7 @@ class MicroscopySingleDatasetConfig(SimpleImageContainerDataConfig):
return metaData
- def getChannelColorRGB(self, channelCode):
+ def _getChannelColorRGB(self, channelCode):
"""Returns a ChannelColorRGB instantiated with the RGB color components
extracted from the file by the MetadataReader.
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 132e6918a6b1acdb14c489a95c84d7479909d028..7c3cbd869e617a5606e1801dd7fbb2b979d6d6dd 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
@@ -98,6 +98,15 @@ public class MicroscopyImageDropboxTest extends AbstractImageDropboxTestCase
imageChecker.check(new File(getTestDataFolder(), "C1_512x512.png"),
new ImageLoader(dataSet, sessionToken).microscopy().channel("SERIES-0_CHANNEL-1")
.mode("thumbnail512x512"));
+ imageChecker.check(new File(getTestDataFolder(), "C2_Default.png"),
+ new ImageLoader(dataSet, sessionToken).microscopy().channel("SERIES-0_CHANNEL-2")
+ .mode("thumbnail480x480"));
+ imageChecker.check(new File(getTestDataFolder(), "C2_256x256.png"),
+ new ImageLoader(dataSet, sessionToken).microscopy().channel("SERIES-0_CHANNEL-2")
+ .mode("thumbnail256x256"));
+ imageChecker.check(new File(getTestDataFolder(), "C2_512x512.png"),
+ new ImageLoader(dataSet, sessionToken).microscopy().channel("SERIES-0_CHANNEL-2")
+ .mode("thumbnail512x512"));
imageChecker.check(new File(getTestDataFolder(), "C01_Default.png"),
new ImageLoader(dataSet, sessionToken).microscopy().channel("SERIES-0_CHANNEL-0")
.channel("SERIES-0_CHANNEL-1").mode("thumbnail480x480"));
@@ -107,9 +116,9 @@ public class MicroscopyImageDropboxTest extends AbstractImageDropboxTestCase
imageChecker.check(new File(getTestDataFolder(), "C01_512x512.png"),
new ImageLoader(dataSet, sessionToken).microscopy().channel("SERIES-0_CHANNEL-0")
.channel("SERIES-0_CHANNEL-1").mode("thumbnail512x512"));
- imageChecker.check(new File(getTestDataFolder(), "Merged_256x256_C0_0_20_C4_2_15.png"),
- new ImageLoader(dataSet, sessionToken).microscopy().rescaling("SERIES-0_CHANNEL-0", 0, 20)
- .rescaling("SERIES-0_CHANNEL-4", 2, 15).mode("thumbnail256x256"));
+ 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"));
imageChecker.assertNoFailures();
}