From 764e680d7cd1ab07ca21bc7b27935afff75ce110 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 22 Sep 2014 13:47:26 +0000
Subject: [PATCH] SSDM-773: Handle 12-bit microscopy images correctly in order
to allow useful user defined transformation.
SVN: 32471
---
.../cisd/common/image/ImageHistogram.java | 3 +-
.../cisd/common/image/IntensityRescaling.java | 179 +++++++-----------
.../common/image/IntensityRescalingTest.java | 26 ++-
.../dss/generic/shared/utils/ImageUtil.java | 2 +-
...scaleIntensityImageTransformerFactory.java | 34 +---
.../BitShiftingImageTransformerFactory.java | 7 +-
...IntensityRangeImageTransformerFactory.java | 13 +-
...scaleIntensityImageTransformerFactory.java | 31 +--
.../BitShiftingImageTransformerFactory.java | 5 +-
...IntensityRangeImageTransformerFactory.java | 7 +-
.../v1/SimpleImageDataSetRegistrator.java | 3 +-
.../v2/SimpleImageDataSetRegistrator.java | 3 +-
.../server/images/ImageChannelsUtils.java | 33 +++-
.../openbis/dss/shared/DssScreeningUtils.java | 45 ++++-
14 files changed, 209 insertions(+), 182 deletions(-)
diff --git a/common/source/java/ch/systemsx/cisd/common/image/ImageHistogram.java b/common/source/java/ch/systemsx/cisd/common/image/ImageHistogram.java
index 6d3be675bf5..295cc480ca3 100644
--- a/common/source/java/ch/systemsx/cisd/common/image/ImageHistogram.java
+++ b/common/source/java/ch/systemsx/cisd/common/image/ImageHistogram.java
@@ -299,8 +299,7 @@ public class ImageHistogram
}
}
-
- private boolean isGray()
+ public boolean isGray()
{
for (int i = 0; i < redCounters.length; i++)
{
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 d819acb75da..209e2ab5a90 100644
--- a/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
+++ b/common/source/java/ch/systemsx/cisd/common/image/IntensityRescaling.java
@@ -123,60 +123,6 @@ public class IntensityRescaling
}
}
- private static int getGrayIntensity(BufferedImage image, int x, int y)
- {
- return image.getRaster().getSample(x, y, 0);
- }
-
- private static int getBitShiftLowerThanThreshold(int[] b0, float pixels, float threshold)
- {
- int shift = b0.length - 1;
- while (shift >= 0 && (b0[shift] / pixels) < threshold)
- {
- --shift;
- }
- return shift + 1;
- }
-
- /**
- * Computes the number of significant bits in an image, minus 8. A bit position is considered
- * significant if only a small fraction (given by <var>threshold</var> of all pixels has a value
- * of 1 in this bit position.
- * <p>
- * For example, if the image is 16-bit and only uses 10-bits, this method will return 2.
- *
- * @param image The image to compute the bits for.
- * @param threshold The threshold of pixels (divided by the total number of pixels) that can be
- * '1' in bit position so that the bit-position is still consider insignificant. A
- * typical value will be 0.001f (one per-mill).
- * @return The number of significant bits of the intensity minus 8.
- */
- public static int computeBitShift(BufferedImage image, float threshold)
- {
- if (isNotGrayscale(image))
- {
- throw new IllegalArgumentException(
- "computeBitShift() is only applicable to gray scale images.");
- }
- float pixels = image.getWidth() * image.getHeight();
- final int[] b0 = new int[image.getColorModel().getPixelSize() - 8];
- for (int y = 0; y < image.getHeight(); ++y)
- {
- for (int x = 0; x < image.getWidth(); ++x)
- {
- final int intensity = getGrayIntensity(image, x, y);
- for (int b = 0; b < b0.length; ++b)
- {
- if (((intensity >>> (b + 8)) & 1) == 1)
- {
- ++b0[b];
- }
- }
- }
- }
- return getBitShiftLowerThanThreshold(b0, pixels, threshold);
- }
-
/** @return true if the specified image in not in grayscale */
public static boolean isNotGrayscale(BufferedImage image)
{
@@ -216,22 +162,6 @@ public class IntensityRescaling
return channels;
}
- /**
- * Performs an intensity rescaling on a gray-scale image by shifting all intensities so that
- * only significant bits are kept. A bit position is considered significant if only a small
- * fraction (given by <var>threshold</var> of all pixels has a value of 1 in this bit position.
- *
- * @param image The original n-bit gray-scale image (n>8).
- * @param threshold The threshold of pixels (divided by the total number of pixels) that can be
- * '1' in bit position so that the bit-position is still consider insignificant. A
- * typical value will be 0.001f (one per-mill).
- * @return The rescaled 8-bit gray-scale image.
- */
- public static BufferedImage rescaleIntensityBitShiftTo8Bits(BufferedImage image, float threshold)
- {
- return rescaleIntensityBitShiftTo8Bits(image, computeBitShift(image, threshold));
- }
-
/**
* Performs an intensity rescaling on a gray-scale image by shifting all intensities by
* <var>shiftBits</var> bits.
@@ -240,13 +170,7 @@ public class IntensityRescaling
* @param shiftBits The number of bits to shift the image by.
* @return The rescaled 8-bit gray-scale image.
*/
- public static BufferedImage rescaleIntensityBitShiftTo8Bits(BufferedImage image, int shiftBits)
- {
- return rescaleIntensityBitShiftTo8Bits(new Pixels(image), shiftBits);
- }
-
- /** See {@link #rescaleIntensityBitShiftTo8Bits(BufferedImage, int)}. */
- private static BufferedImage rescaleIntensityBitShiftTo8Bits(Pixels image, int shiftBits)
+ public static BufferedImage rescaleIntensityBitShiftTo8Bits(Pixels image, int shiftBits)
{
final BufferedImage rescaledImage =
new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_BYTE_GRAY);
@@ -268,25 +192,15 @@ public class IntensityRescaling
/**
* Process <var>image</var> and add its pixels to the <var>histogram</var>. Calling this method
* multiple times with the same <var>histogram</var> accumulates the histogram for all images.
- *
- * @param image a gray scale image (will not be checked)
*/
- public static void addToLevelStats(PixelHistogram histogram, BufferedImage image)
- {
- Pixels pixels = new Pixels(image);
- addToLevelStats(histogram, pixels);
- }
-
- /**
- * Process <var>image</var> and add its pixels to the <var>histogram</var>. Calling this method
- * multiple times with the same <var>histogram</var> accumulates the histogram for all images.
- */
- private static void addToLevelStats(PixelHistogram histogram, Pixels pixels)
+ public static void addToLevelStats(PixelHistogram histogram, Pixels pixels, Channel... channels)
{
+ assert channels.length > 0 : "No channels specified.";
int[] histogramArray = histogram.getHistogram();
int[][] pixelData = pixels.getPixelData();
- for (int[] channelPixelData : pixelData)
+ for (Channel channel : channels)
{
+ int[] channelPixelData = pixelData[channel.getBand()];
for (int i = 0; i < channelPixelData.length; i++)
{
histogramArray[channelPixelData[i]]++;
@@ -313,18 +227,35 @@ public class IntensityRescaling
width = image.getWidth();
height = image.getHeight();
ColorModel colorModel = image.getColorModel();
- pixelData = new int[colorModel.getNumColorComponents()][width * height];
+ int numColorComponents = colorModel.getNumColorComponents();
+ pixelData = new int[numColorComponents][width * height];
WritableRaster raster = image.getRaster();
int numberOfBands = raster.getNumBands();
- if (colorModel instanceof IndexColorModel == false && numberOfBands >= pixelData.length)
+ int[][] colorIndexMap = null;
+ if (numColorComponents == 3 && numberOfBands == 1)
+ {
+ colorIndexMap = tryCreateColorIndexMap(colorModel);
+ }
+ if (numberOfBands >= pixelData.length || colorIndexMap != null)
{
- for (int band = 0; band < pixelData.length; band++)
+ for (int band = 0, n = Math.min(numberOfBands, pixelData.length); band < n; band++)
{
raster.getSamples(0, 0, width, height, band, pixelData[band]);
}
+ if (colorIndexMap != null)
+ {
+ for (int i = 0; i < pixelData[0].length; i++)
+ {
+ int index = pixelData[0][i];
+ for (int c = 0; c < 3; c++)
+ {
+ pixelData[c][i] = colorIndexMap[c][index];
+ }
+ }
+ }
} else
{
- // In case of an IndexColorModel or
+ // In case of the color model isn't a recognized index color model and
// number of bands is less then number of color components
// we can not use the fast method
for (int y = 0; y < height; y++)
@@ -342,6 +273,46 @@ public class IntensityRescaling
}
}
+ /**
+ * Creates the index color map from the specified color model. The result is an array
+ * of three integer arrays. The first/second/third array is the red/green/blue index to color map.
+ * <p>
+ * This method only handles {@link IndexColorModel} for 8bit indicies. To handle other
+ * index color models (like loci.formats.gui.Index16ColorModel from the BioFormats library) this
+ * method should be overwritten.
+ *
+ * @return <code>null</code> if the color model isn't a known index color model.
+ *
+ */
+ protected int[][] tryCreateColorIndexMap(ColorModel colorModel)
+ {
+ if (colorModel instanceof IndexColorModel == false)
+ {
+ return null;
+ }
+ IndexColorModel indexColorModel = (IndexColorModel) colorModel;
+ int mapSize = indexColorModel.getMapSize();
+ byte[] blues = new byte[mapSize];
+ indexColorModel.getBlues(blues);
+ byte[] greens = new byte[mapSize];
+ indexColorModel.getGreens(greens);
+ byte[] reds = new byte[mapSize];
+ indexColorModel.getReds(reds);
+ int[][] result = new int[3][mapSize];
+ copyTo(reds, result[0]);
+ copyTo(greens, result[1]);
+ copyTo(blues, result[2]);
+ return result;
+ }
+
+ private void copyTo(byte[] bytes, int[] integers)
+ {
+ for (int i = 0; i < bytes.length; i++)
+ {
+ integers[i] = bytes[i] & 0xff;
+ }
+ }
+
/** @return all the pixels of the image */
public int[][] getPixelData()
{
@@ -410,18 +381,17 @@ public class IntensityRescaling
}
/**
- * Calculates levels for the specified image. It starts with a threshold 0.01 (i.e. cut-off of points
+ * Calculates levels for the specified pixels. It starts with a threshold 0.01 (i.e. cut-off of points
* to be too light or dark). If the number of levels is less than the specified minimum the threshold
* is reduced by a factor 10 and the levels are calculated again. This iteration is continue until
* either the number of levels is large enough or the threshold is below 10<sup>-5</sup>.
*/
- public static Levels computeLevels(BufferedImage image, int minimumNumberOfLevels)
+ public static Levels computeLevels(Pixels pixels, int minimumNumberOfLevels)
{
- Pixels pixels = new Pixels(image);
Levels levels = null;
for (float threshold = 0.01f; threshold > 1e-5; threshold /= 10)
{
- levels = computeLevels(pixels, threshold);
+ levels = computeLevels(pixels, threshold, Channel.values());
if (levels.getMaxLevel() - levels.getMinLevel() > minimumNumberOfLevels)
{
break;
@@ -439,10 +409,11 @@ public class IntensityRescaling
* @param image a gray scale image (will not be checked).
* @return The levels of the <var>histogram</var> for the <var>treshold</var>.
*/
- public static Levels computeLevels(Pixels image, float threshold)
+ public static Levels computeLevels(Pixels image, float threshold, Channel...channels)
{
+ assert channels.length > 0 : "No channels specified.";
final PixelHistogram stats = new PixelHistogram();
- addToLevelStats(stats, image);
+ addToLevelStats(stats, image, channels);
return computeLevels(stats, threshold);
}
@@ -450,14 +421,10 @@ public class IntensityRescaling
* Computes an intensity rescaled image from the given <var>image</var>, using the black point
* and white point as defined by <var>levels</var>.
*/
- public static BufferedImage rescaleIntensityLevelTo8Bits(BufferedImage image, Levels levels)
- {
- return rescaleIntensityLevelTo8Bits(new Pixels(image), levels, Channel.values());
- }
-
public static BufferedImage rescaleIntensityLevelTo8Bits(Pixels pixels, Levels levels,
Channel... channels)
{
+ assert channels.length > 0 : "No channels specified.";
final int width = pixels.getWidth();
final int height = pixels.getHeight();
int[][] pixelData = pixels.getPixelData();
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/image/IntensityRescalingTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/image/IntensityRescalingTest.java
index 2170cc31265..c835c10d590 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/image/IntensityRescalingTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/image/IntensityRescalingTest.java
@@ -21,6 +21,7 @@ import static org.testng.AssertJUnit.assertEquals;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.image.BufferedImage;
+import java.awt.image.ColorModel;
import org.testng.annotations.Test;
@@ -103,7 +104,8 @@ public class IntensityRescalingTest
graphics.setColor(Color.PINK);
graphics.fillRect(1, 1, 4, 3);
- BufferedImage rescaledImage = IntensityRescaling.rescaleIntensityLevelTo8Bits(image, new Levels(75, 190));
+ BufferedImage rescaledImage = IntensityRescaling.rescaleIntensityLevelTo8Bits(new Pixels(image),
+ new Levels(75, 190), Channel.values());
ImageHistogram histogram = ImageHistogram.calculateHistogram(rescaledImage);
@@ -112,6 +114,28 @@ public class IntensityRescalingTest
assertEquals("[0=18, 222=12]", renderHistogram(histogram.getBlueHistogram()));
}
+ @Test
+ public void testRescaleIntensityLevelForAnIndexColorModel()
+ {
+ BufferedImage image = new BufferedImage(6, 5, BufferedImage.TYPE_BYTE_INDEXED);
+ ColorModel colorModel = image.getColorModel();
+ assertEquals("IndexColorModel", colorModel.getClass().getSimpleName());
+ Graphics graphics = image.getGraphics();
+ graphics.setColor(Color.ORANGE);
+ graphics.fillRect(0, 0, 4, 3);
+ graphics.setColor(Color.PINK);
+ graphics.fillRect(1, 1, 4, 3);
+
+ BufferedImage rescaledImage = IntensityRescaling.rescaleIntensityLevelTo8Bits(new Pixels(image),
+ new Levels(75, 190), Channel.values());
+
+ ImageHistogram histogram = ImageHistogram.calculateHistogram(rescaledImage);
+
+ assertEquals("[0=12, 255=18]", renderHistogram(histogram.getRedHistogram()));
+ assertEquals("[0=12, 173=12, 255=6]", renderHistogram(histogram.getGreenHistogram()));
+ assertEquals("[0=18, 173=12]", renderHistogram(histogram.getBlueHistogram()));
+ }
+
@Test
public void testRescaleIntensityLevelTo8BitsForGrayExample()
{
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 2fe24534b3f..18a674cac83 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
@@ -925,7 +925,7 @@ public class ImageUtil
{
Pixels pixels = new Pixels(image);
Levels intensityRange = IntensityRescaling.computeLevels(pixels,
- threshold == null ? DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR : threshold);
+ threshold == null ? DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR : threshold, Channel.RED);
BufferedImage result =
IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, intensityRange, Channel.RED);
return result;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/AutoRescaleIntensityImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/AutoRescaleIntensityImageTransformerFactory.java
index 771daec22aa..d81dcd2bdb1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/AutoRescaleIntensityImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/AutoRescaleIntensityImageTransformerFactory.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations;
import java.awt.image.BufferedImage;
-import java.awt.image.WritableRaster;
import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.base.image.IImageTransformer;
@@ -27,11 +26,12 @@ import ch.systemsx.cisd.common.image.IntensityRescaling.Channel;
import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
import ch.systemsx.cisd.common.image.IntensityRescaling.Pixels;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
/**
* Transformation performed by
- * {@link IntensityRescaling#rescaleIntensityLevelTo8Bits(BufferedImage, Levels)} where levels are
- * computed automatically by {@link IntensityRescaling#computeLevels(Pixels, float)}.
+ * {@link IntensityRescaling#rescaleIntensityLevelTo8Bits(Pixels, Levels, Channel...)} where levels are
+ * computed automatically by {@link IntensityRescaling#computeLevels(Pixels, float, Channel...)}.
* <p>
* Warning: The serialized version of this class can be stored in the database for each image.
* Moving this class to a different package or changing it in a backward incompatible way would make
@@ -66,32 +66,14 @@ public class AutoRescaleIntensityImageTransformerFactory implements IImageTransf
{
return image;
}
- Pixels grayScaleImage = toGrayScale(image, channel);
- Levels levels = IntensityRescaling.computeLevels(grayScaleImage, threshold);
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ Levels levels = IntensityRescaling.computeLevels(pixels, threshold, channel);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.values());
}
- Pixels pixels = new Pixels(image);
- Levels levels = IntensityRescaling.computeLevels(pixels, threshold);
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ Levels levels = IntensityRescaling.computeLevels(pixels, threshold, Channel.RED);
return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.RED);
}
};
}
-
- private Pixels toGrayScale(BufferedImage image, Channel channel)
- {
- BufferedImage gray =
- new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_BYTE_GRAY);
- WritableRaster raster = gray.getRaster();
-
- for (int y = 0; y < image.getHeight(); y++)
- {
- for (int x = 0; x < image.getWidth(); x++)
- {
- int value = (image.getRGB(x, y) >> channel.getShift()) & 0xff;
- raster.setPixel(x, y, new int[]
- { value });
- }
- }
- return new Pixels(gray);
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/BitShiftingImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/BitShiftingImageTransformerFactory.java
index 5917b60a0cc..e828fc8f24c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/BitShiftingImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/BitShiftingImageTransformerFactory.java
@@ -6,10 +6,12 @@ import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.base.image.IImageTransformer;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.image.IntensityRescaling;
+import ch.systemsx.cisd.common.image.IntensityRescaling.Pixels;
+import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
/**
* Transformation performed by
- * {@link IntensityRescaling#rescaleIntensityBitShiftTo8Bits(java.awt.image.BufferedImage, int)}
+ * {@link IntensityRescaling#rescaleIntensityBitShiftTo8Bits(Pixels, int)}
* <p>
* Warning: The serialized version of this class can be stored in the database for each image.
* Moving this class to a different package or changing it in a backward incompatible way would make
@@ -41,7 +43,8 @@ final class BitShiftingImageTransformerFactory implements IImageTransformerFacto
{
return image;
}
- return IntensityRescaling.rescaleIntensityBitShiftTo8Bits(image, shiftBits);
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ return IntensityRescaling.rescaleIntensityBitShiftTo8Bits(pixels, shiftBits);
}
};
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/IntensityRangeImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/IntensityRangeImageTransformerFactory.java
index 502d5ccdc05..832dcc05b92 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/IntensityRangeImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/transformations/IntensityRangeImageTransformerFactory.java
@@ -26,9 +26,10 @@ 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.Pixels;
+import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
/**
- * Transformation performed by {@link IntensityRescaling#rescaleIntensityLevelTo8Bits(BufferedImage, Levels)}.
+ * Transformation performed by {@link IntensityRescaling#rescaleIntensityLevelTo8Bits(Pixels, Levels, Channel...)}.
* <p>
* Warning: The serialized version of this class can be stored in the database for each image. Moving this class to a different package or changing it
* in a backward incompatible way would make all the saved transformations invalid.
@@ -71,15 +72,17 @@ public class IntensityRangeImageTransformerFactory implements IImageTransformerF
Levels levels = new Levels(blackPointIntensity, whitePointIntensity);
if (IntensityRescaling.isNotGrayscale(image))
{
+ Pixels pixels = DssScreeningUtils.createPixels(image);
EnumSet<Channel> channels = IntensityRescaling.getUsedRgbChannels(image);
if (channels.size() != 1)
{
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.values());
}
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(new Pixels(image), levels,
- channels.iterator().next());
+ Channel channel = channels.iterator().next();
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, channel);
}
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.values());
}
};
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/AutoRescaleIntensityImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/AutoRescaleIntensityImageTransformerFactory.java
index 83b2000e3cc..61fa01749a7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/AutoRescaleIntensityImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/AutoRescaleIntensityImageTransformerFactory.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations;
import java.awt.image.BufferedImage;
-import java.awt.image.WritableRaster;
import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.base.image.IImageTransformer;
@@ -27,6 +26,7 @@ import ch.systemsx.cisd.common.image.IntensityRescaling.Channel;
import ch.systemsx.cisd.common.image.IntensityRescaling.Levels;
import ch.systemsx.cisd.common.image.IntensityRescaling.Pixels;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
/**
* This class is obsolete, and should not be used. Use
@@ -62,33 +62,14 @@ public class AutoRescaleIntensityImageTransformerFactory implements IImageTransf
{
return image;
}
- Pixels grayScaleImage = toGrayScale(image, channel);
- Levels levels = IntensityRescaling.computeLevels(grayScaleImage, threshold);
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ Levels levels = IntensityRescaling.computeLevels(pixels, threshold, channel);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.values());
}
- Pixels pixels = new Pixels(image);
- Levels levels = IntensityRescaling.computeLevels(pixels, threshold);
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ Levels levels = IntensityRescaling.computeLevels(pixels, threshold, Channel.RED);
return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.RED);
}
};
}
-
- private Pixels toGrayScale(BufferedImage image, Channel channel)
- {
- BufferedImage gray =
- new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_BYTE_GRAY);
- WritableRaster raster = gray.getRaster();
-
- for (int y = 0; y < image.getHeight(); y++)
- {
- for (int x = 0; x < image.getWidth(); x++)
- {
- int value = (image.getRGB(x, y) >> channel.getShift()) & 0xff;
- raster.setPixel(x, y, new int[]
- { value });
- }
- }
- return new Pixels(gray);
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/BitShiftingImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/BitShiftingImageTransformerFactory.java
index 0ac8971dade..637943f2ee6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/BitShiftingImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/BitShiftingImageTransformerFactory.java
@@ -6,6 +6,8 @@ import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.base.image.IImageTransformer;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.image.IntensityRescaling;
+import ch.systemsx.cisd.common.image.IntensityRescaling.Pixels;
+import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
/**
* This class is obsolete, and should not be used. Use {@link ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ConvertToolImageTransformer}
@@ -38,7 +40,8 @@ final class BitShiftingImageTransformerFactory implements IImageTransformerFacto
{
return image;
}
- return IntensityRescaling.rescaleIntensityBitShiftTo8Bits(image, shiftBits);
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ return IntensityRescaling.rescaleIntensityBitShiftTo8Bits(pixels, shiftBits);
}
};
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/IntensityRangeImageTransformerFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/IntensityRangeImageTransformerFactory.java
index 56d775f1927..677849d5319 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/IntensityRangeImageTransformerFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/transformations/IntensityRangeImageTransformerFactory.java
@@ -26,6 +26,7 @@ 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.Pixels;
+import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
/**
* This class is obsolete, and should not be used. Use
@@ -76,12 +77,14 @@ public class IntensityRangeImageTransformerFactory implements IImageTransformerF
} else
{
Levels levels = new Levels(blackPointIntensity, whitePointIntensity);
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(new Pixels(image), levels,
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels,
channels.iterator().next());
}
}
Levels levels = new Levels(blackPointIntensity, whitePointIntensity);
- return IntensityRescaling.rescaleIntensityLevelTo8Bits(image, levels);
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.values());
}
};
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/SimpleImageDataSetRegistrator.java
index 79406de96f3..79e8b93e8d5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/SimpleImageDataSetRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v1/SimpleImageDataSetRegistrator.java
@@ -602,7 +602,8 @@ public class SimpleImageDataSetRegistrator
imageFile.getPath()));
return null;
}
- IntensityRescaling.addToLevelStats(histogram, image);
+ IntensityRescaling.addToLevelStats(histogram, DssScreeningUtils.createPixels(image),
+ ch.systemsx.cisd.common.image.IntensityRescaling.Channel.RED);
}
}
return IntensityRescaling.computeLevels(histogram, threshold);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/SimpleImageDataSetRegistrator.java
index c3cada40072..b6737bb912a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/SimpleImageDataSetRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/SimpleImageDataSetRegistrator.java
@@ -610,7 +610,8 @@ public class SimpleImageDataSetRegistrator
imageFile.getPath()));
return null;
}
- IntensityRescaling.addToLevelStats(histogram, image);
+ IntensityRescaling.addToLevelStats(histogram, DssScreeningUtils.createPixels(image),
+ ch.systemsx.cisd.common.image.IntensityRescaling.Channel.RED);
}
} catch (Exception ex)
{
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 f7a853d70d9..73c5bdeb110 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
@@ -61,6 +61,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
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.generic.shared.dto.OpenBISSessionHolder;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -396,6 +397,7 @@ public class ImageChannelsUtils
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)
{
@@ -448,7 +450,30 @@ public class ImageChannelsUtils
}
return image;
}
-
+
+ private static BufferedImage convertTo8Bit(BufferedImage image)
+ {
+ Pixels pixels = DssScreeningUtils.createPixels(image);
+ int[][] pixelData = pixels.getPixelData();
+ int maxIntensity = 0;
+ for (int[] colorChannelPixels : pixelData)
+ {
+ for (int intensity : colorChannelPixels)
+ {
+ if (intensity > maxIntensity)
+ {
+ maxIntensity = intensity;
+ }
+ }
+ }
+ if (maxIntensity < 256)
+ {
+ return image;
+ }
+ Levels levels = new Levels(0, maxIntensity < 4096 ? 4096 : 1 << 16);
+ return IntensityRescaling.rescaleIntensityLevelTo8Bits(pixels, levels, Channel.values());
+ }
+
private static IColorTransformation createColorTransformation(final Channel channel, final ChannelColorRGB channelColor)
{
return new IColorTransformation()
@@ -515,7 +540,7 @@ public class ImageChannelsUtils
IImageTransformerFactory channelTransformation = mergedChannelTransformationOrNull;
if ((transMap == null || transMap.size() == 0) && channelTransformation == null)
{
- Levels levels = IntensityRescaling.computeLevels(mergedImage, 30);
+ Levels levels = IntensityRescaling.computeLevels(DssScreeningUtils.createPixels(mergedImage), 30);
int minLevel = levels.getMinLevel();
int maxLevel = levels.getMaxLevel();
channelTransformation = new IntensityRangeImageTransformerFactory(minLevel, maxLevel);
@@ -593,7 +618,6 @@ public class ImageChannelsUtils
ImageUtil.DEFAULT_IMAGE_OPTIMAL_RESCALING_FACTOR);
}
}
-
return applyImageTransformation(resultImage, channelLevelTransformationOrNull);
}
@@ -763,7 +787,7 @@ public class ImageChannelsUtils
public static BufferedImage transformColor(BufferedImage bufferedImage, IColorTransformation transformation)
{
- Pixels pixels = new Pixels(bufferedImage);
+ Pixels pixels = DssScreeningUtils.createPixels(bufferedImage);
int width = pixels.getWidth();
int height = pixels.getHeight();
int[][] pixelData = pixels.getPixelData();
@@ -791,5 +815,4 @@ public class ImageChannelsUtils
final byte[] output = ImageUtil.imageToPngFast(image);
return new ByteArrayBasedContentNode(output, nameOrNull);
}
-
}
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 97f2e0987e4..0b901e63473 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
@@ -16,11 +16,16 @@
package ch.systemsx.cisd.openbis.dss.shared;
+import java.awt.image.BufferedImage;
+import java.awt.image.ColorModel;
+
import javax.sql.DataSource;
+import loci.formats.gui.Index16ColorModel;
import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+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;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
@@ -50,8 +55,7 @@ public class DssScreeningUtils
}
/**
- * Creates a DAO based on imaging database specified in DSS service.properties by data source
- * {@link ScreeningConstants#IMAGING_DATA_SOURCE}.
+ * Creates a DAO based on imaging database specified in DSS service.properties by data source {@link ScreeningConstants#IMAGING_DATA_SOURCE}.
* <p>
* Returned query is reused and should not be closed.
* </p>
@@ -65,8 +69,7 @@ public class DssScreeningUtils
}
/**
- * Creates a new query each time when it is called. Returned query should be closed after all
- * operations are done.
+ * Creates a new query each time when it is called. Returned query should be closed after all operations are done.
*/
public static IImagingTransformerDAO createImagingTransformerDAO()
{
@@ -76,4 +79,38 @@ public class DssScreeningUtils
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
+ * image files with ND2Reader of BioFormats.
+ */
+ public static Pixels createPixels(BufferedImage image)
+ {
+ return new Pixels(image)
+ {
+ @Override
+ protected int[][] tryCreateColorIndexMap(ColorModel colorModel)
+ {
+ int[][] indexMap = super.tryCreateColorIndexMap(colorModel);
+ if (indexMap == null && colorModel instanceof Index16ColorModel)
+ {
+ Index16ColorModel indexColorModel = (Index16ColorModel) colorModel;
+ indexMap = new int[3][1 << 16];
+ copyTo(indexColorModel.getReds(), indexMap[0]);
+ copyTo(indexColorModel.getGreens(), indexMap[1]);
+ copyTo(indexColorModel.getBlues(), indexMap[2]);
+ }
+ return indexMap;
+ }
+
+ private void copyTo(short[] shorts, int[] integers)
+ {
+ for (int i = 0; i < shorts.length; i++)
+ {
+ integers[i] = shorts[i] & 0xffff;
+ }
+ }
+ };
+ }
+
}
--
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