From 15f668f42fff45e7f3843a8827be6fbd4a1f143c Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Fri, 25 Jan 2013 09:42:05 +0000
Subject: [PATCH] SP-452 BIS-297 Add reading color depth to image readers
SVN: 28193
---
.../cisd/imagereaders/IImageReader.java | 9 +++
.../bioformats/BioFormatsImageUtils.java | 34 ++++++++++-
.../DefaultBioformatsImageReader.java | 7 +++
.../imagereaders/ij/ImageJReaderLibrary.java | 12 ++++
.../imageio/ImageIOReaderLibrary.java | 14 +++++
.../imagereaders/jai/DefaultImageReader.java | 16 ++++++
.../BioFormatsReaderLibraryTest.java | 25 +++++++--
.../ij/ImageJReaderLibraryTest.java | 22 +++++---
.../imageio/ImageIOReaderLibraryTest.java | 25 ++++++---
.../jai/DefaultImageReaderTest.java | 56 ++++++++++++-------
10 files changed, 177 insertions(+), 43 deletions(-)
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReader.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReader.java
index 4922fdf2d56..4825a972229 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReader.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReader.java
@@ -132,4 +132,13 @@ public interface IImageReader
* @return dimensions of the image
*/
public Dimension readDimensions(IRandomAccessFile handle, ImageID imageID);
+
+ /**
+ * Reads image color depth
+ *
+ * @param handle the image file as {@link IRandomAccessFile}
+ * @param imageID the ID of the image to be read
+ * @return the size of the color component
+ */
+ public Integer readColorDepth(IRandomAccessFile handle, ImageID imageID);
}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
index b440211a8eb..ce3817be9da 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
@@ -346,14 +346,44 @@ final class BioFormatsImageUtils
}
}
+ static Integer readImageColorDepth(IFormatReader reader, IRandomAccess handle, ImageID imageID)
+ throws IOExceptionUnchecked, IllegalArgumentException
+ {
+ // Add to static map.
+ String handleId = generateHandleId(reader, imageID);
+ Location.mapFile(handleId, handle);
+ try
+ {
+ // This does the actual parsing.
+ reader.setId(handleId);
+ reader.setSeries(imageID.getSeriesIndex());
+ int depth = reader.getBitsPerPixel();
+ reader.close();
+ return depth;
+ } catch (FormatException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ } finally
+ {
+ // Remove from static map.
+ Location.mapFile(handleId, null);
+ }
+ }
+
public static String generateHandleId(IFormatHandler formatHandler, ImageID imageId)
{
String id = UUID.randomUUID().toString() + "." + formatHandler.getSuffixes()[0];
- if (imageId != null && imageId.getFileName() != null && (imageId.getFileName().endsWith(".c01") || imageId.getFileName().endsWith("C01"))) {
+ if (imageId != null
+ && imageId.getFileName() != null
+ && (imageId.getFileName().endsWith(".c01") || imageId.getFileName().endsWith("C01")))
+ {
id = imageId.getFileName();
}
return id;
-
+
}
private static void nullSafeAddAll(HashMap<String, Object> accumulator,
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/DefaultBioformatsImageReader.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/DefaultBioformatsImageReader.java
index aebbbd348af..1c550871696 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/DefaultBioformatsImageReader.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/DefaultBioformatsImageReader.java
@@ -100,4 +100,11 @@ class DefaultBioformatsImageReader extends AbstractMetaDataAwareImageReader
IRandomAccess input = new BioFormatsRandomAccessAdapter(handle);
return BioFormatsImageUtils.readImageDimensions(formatReader, input, imageID);
}
+
+ @Override
+ public Integer readColorDepth(IRandomAccessFile handle, ImageID imageID)
+ {
+ IRandomAccess input = new BioFormatsRandomAccessAdapter(handle);
+ return BioFormatsImageUtils.readImageColorDepth(formatReader, input, imageID);
+ }
}
\ No newline at end of file
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/ij/ImageJReaderLibrary.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/ij/ImageJReaderLibrary.java
index 2d9c4fe0e9b..16dc8220bb4 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/ij/ImageJReaderLibrary.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/ij/ImageJReaderLibrary.java
@@ -81,6 +81,18 @@ public class ImageJReaderLibrary implements IImageReaderLibrary
}
return new Dimension(imagePlus.getWidth(), imagePlus.getHeight());
}
+
+ @Override
+ public Integer readColorDepth(IRandomAccessFile handle, ImageID imageID)
+ {
+ AdapterIInputStreamToInputStream is = new AdapterIInputStreamToInputStream(handle);
+ ImagePlus imagePlus = new Opener().openTiff(is, "");
+ if (imagePlus == null)
+ {
+ throw new IllegalStateException("Cannot open the image file with ImageJ.");
+ }
+ return imagePlus.getBytesPerPixel();
+ }
};
private BufferedImage createBufferedImageOfSameType(ImagePlus imagePlus)
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/imageio/ImageIOReaderLibrary.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/imageio/ImageIOReaderLibrary.java
index bb97dccbec7..7f3188aa35e 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/imageio/ImageIOReaderLibrary.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/imageio/ImageIOReaderLibrary.java
@@ -133,6 +133,20 @@ public class ImageIOReaderLibrary implements IImageReaderLibrary
}
}
+ @Override
+ public Integer readColorDepth(IRandomAccessFile handle, ImageID imageID)
+ {
+ try
+ {
+ ImageInputStream imageInput = adaptHandle(handle);
+ ioReader.setInput(imageInput);
+ return ioReader.read(0).getColorModel().getPixelSize();
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
private ImageInputStream adaptHandle(IRandomAccessFile handle)
{
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/jai/DefaultImageReader.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/jai/DefaultImageReader.java
index 9dc38e05eb8..e8cee39ffad 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/jai/DefaultImageReader.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/jai/DefaultImageReader.java
@@ -110,4 +110,20 @@ class DefaultImageReader extends AbstractImageReader
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
}
+
+ @Override
+ public Integer readColorDepth(IRandomAccessFile handle, ImageID imageID)
+ {
+ try
+ {
+ InputStream input = new AdapterIInputStreamToInputStream(handle);
+ ImageDecoder decoder = ImageCodec.createImageDecoder(getName(), input, null);
+ RenderedImage renderedImage =
+ decoder.decodeAsRenderedImage(imageID.getTimeSeriesIndex());
+ return renderedImage.getColorModel().getPixelSize();
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
}
\ No newline at end of file
diff --git a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsReaderLibraryTest.java b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsReaderLibraryTest.java
index 0c05d60e645..148162e4429 100644
--- a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsReaderLibraryTest.java
+++ b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsReaderLibraryTest.java
@@ -18,10 +18,13 @@ package ch.systemsx.cisd.imagereaders.bioformats;
import java.awt.image.BufferedImage;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.RandomAccessFile;
import java.util.List;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.base.io.RandomAccessFileImpl;
import ch.systemsx.cisd.imagereaders.IImageReader;
import ch.systemsx.cisd.imagereaders.ImageID;
import ch.systemsx.cisd.imagereaders.ImageReaderTestCase;
@@ -32,22 +35,36 @@ import ch.systemsx.cisd.imagereaders.ImageReaderTestCase;
public class BioFormatsReaderLibraryTest extends ImageReaderTestCase
{
@Test
- public void testTIFF()
+ public void testTIFF() throws FileNotFoundException
{
BioFormatsReaderLibrary library = new BioFormatsReaderLibrary();
String libraryName = library.getName();
File imageFile = getImageFileForLibrary(libraryName, "multi-page.tif");
IImageReader reader = library.tryGetReaderForFile(imageFile.getPath());
-
+
List<ImageID> imageIDs = reader.getImageIDs(imageFile);
assertEquals("[0-0-0-0, 0-1-0-0]", imageIDs.toString());
-
+
BufferedImage image0 = reader.readImage(imageFile, imageIDs.get(0), null);
assertEquals(459, image0.getWidth());
assertEquals(435, image0.getHeight());
-
+
BufferedImage image1 = reader.readImage(imageFile, imageIDs.get(1), null);
assertEquals(459, image1.getWidth());
assertEquals(435, image1.getHeight());
+
+ int depth =
+ reader.readColorDepth(
+ new RandomAccessFileImpl(new RandomAccessFile(imageFile, "r")),
+ imageIDs.get(0));
+
+ assertEquals(8, depth);
+
+ depth =
+ reader.readColorDepth(
+ new RandomAccessFileImpl(new RandomAccessFile(imageFile, "r")),
+ imageIDs.get(1));
+
+ assertEquals(8, depth);
}
}
diff --git a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/ij/ImageJReaderLibraryTest.java b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/ij/ImageJReaderLibraryTest.java
index 1f46395a0eb..b072fca79f5 100644
--- a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/ij/ImageJReaderLibraryTest.java
+++ b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/ij/ImageJReaderLibraryTest.java
@@ -18,40 +18,46 @@ package ch.systemsx.cisd.imagereaders.ij;
import java.awt.image.BufferedImage;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.RandomAccessFile;
import java.util.List;
import java.util.Map;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.base.io.RandomAccessFileImpl;
import ch.systemsx.cisd.imagereaders.IImageReader;
import ch.systemsx.cisd.imagereaders.ImageID;
import ch.systemsx.cisd.imagereaders.ImageReaderTestCase;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ImageJReaderLibraryTest extends ImageReaderTestCase
{
@Test
- public void testMultiPageTIFF()
+ public void testMultiPageTIFF() throws FileNotFoundException
{
ImageJReaderLibrary library = new ImageJReaderLibrary();
String libraryName = library.getName();
File imageFile = getImageFileForLibrary(libraryName, "multi-page.tif");
IImageReader reader = library.tryGetReaderForFile(imageFile.getPath());
-
+
List<ImageID> imageIDs = reader.getImageIDs(imageFile);
assertEquals("[0-0-0-0]", imageIDs.toString());
-
+
Map<String, Object> metaData = reader.readMetaData(imageFile, imageIDs.get(0), null);
assertEquals(0, metaData.size());
-
+
BufferedImage image0 = reader.readImage(imageFile, imageIDs.get(0), null);
assertEquals(459, image0.getWidth());
assertEquals(435, image0.getHeight());
- }
-
+ int depth =
+ reader.readColorDepth(
+ new RandomAccessFileImpl(new RandomAccessFile(imageFile, "r")),
+ imageIDs.get(0));
+
+ assertEquals(4, depth);
+ }
}
diff --git a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/imageio/ImageIOReaderLibraryTest.java b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/imageio/ImageIOReaderLibraryTest.java
index f8db8dc1626..8e08fdb70e7 100644
--- a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/imageio/ImageIOReaderLibraryTest.java
+++ b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/imageio/ImageIOReaderLibraryTest.java
@@ -18,19 +18,19 @@ package ch.systemsx.cisd.imagereaders.imageio;
import java.awt.image.BufferedImage;
import java.io.File;
+import java.io.RandomAccessFile;
import java.util.List;
import java.util.Map;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.base.io.RandomAccessFileImpl;
import ch.systemsx.cisd.imagereaders.IImageReader;
import ch.systemsx.cisd.imagereaders.ImageID;
import ch.systemsx.cisd.imagereaders.ImageReaderTestCase;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ImageIOReaderLibraryTest extends ImageReaderTestCase
@@ -40,14 +40,14 @@ public class ImageIOReaderLibraryTest extends ImageReaderTestCase
{
return new Object[][]
{
- { "pond.bmp" },
- { "pond.gif" },
- { "pond.jpg" },
- { "pond.png" } };
+ { "pond.bmp", 24 },
+ { "pond.gif", 8 },
+ { "pond.jpg", 24 },
+ { "pond.png", 24 } };
}
@Test(dataProvider = "image-files")
- public void testSingleImageExamples(String imageFileName) throws Exception
+ public void testSingleImageExamples(String imageFileName, int expectedDepth) throws Exception
{
ImageIOReaderLibrary library = new ImageIOReaderLibrary();
String libraryName = library.getName();
@@ -56,12 +56,19 @@ public class ImageIOReaderLibraryTest extends ImageReaderTestCase
List<ImageID> imageIDs = reader.getImageIDs(imageFile);
assertEquals("[0-0-0-0]", imageIDs.toString());
-
+
Map<String, Object> metaData = reader.readMetaData(imageFile, imageIDs.get(0), null);
assertEquals(0, metaData.size());
-
+
BufferedImage image = reader.readImage(imageFile, imageIDs.get(0), null);
assertEquals(512, image.getWidth());
assertEquals(384, image.getHeight());
+
+ int depth =
+ reader.readColorDepth(
+ new RandomAccessFileImpl(new RandomAccessFile(imageFile, "r")),
+ imageIDs.get(0));
+
+ assertEquals(expectedDepth, depth);
}
}
diff --git a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/jai/DefaultImageReaderTest.java b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/jai/DefaultImageReaderTest.java
index 95d37057c88..8fde5b9deff 100644
--- a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/jai/DefaultImageReaderTest.java
+++ b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/jai/DefaultImageReaderTest.java
@@ -18,77 +18,93 @@ package ch.systemsx.cisd.imagereaders.jai;
import java.awt.image.BufferedImage;
import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.RandomAccessFile;
import java.util.List;
import java.util.Map;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.base.io.RandomAccessFileImpl;
import ch.systemsx.cisd.imagereaders.IImageReader;
import ch.systemsx.cisd.imagereaders.ImageID;
import ch.systemsx.cisd.imagereaders.ImageReaderTestCase;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class DefaultImageReaderTest extends ImageReaderTestCase
{
@Test
- public void testMultiPageTIFF()
+ public void testMultiPageTIFF() throws FileNotFoundException
{
JAIReaderLibrary library = new JAIReaderLibrary();
String libraryName = library.getName();
File imageFile = getImageFileForLibrary(libraryName, "multi-page.tif");
IImageReader reader = library.tryGetReaderForFile(imageFile.getPath());
-
+
List<ImageID> imageIDs = reader.getImageIDs(imageFile);
assertEquals("[0-0-0-0, 0-1-0-0]", imageIDs.toString());
-
+
Map<String, Object> metaData = reader.readMetaData(imageFile, imageIDs.get(0), null);
assertEquals(0, metaData.size());
-
+
BufferedImage image0 = reader.readImage(imageFile, imageIDs.get(0), null);
assertEquals(459, image0.getWidth());
assertEquals(435, image0.getHeight());
-
+
BufferedImage image1 = reader.readImage(imageFile, imageIDs.get(1), null);
assertEquals(460, image1.getWidth());
assertEquals(437, image1.getHeight());
+
+ int depth =
+ reader.readColorDepth(
+ new RandomAccessFileImpl(new RandomAccessFile(imageFile, "r")),
+ imageIDs.get(0));
+
+ assertEquals(24, depth);
}
-
+
@DataProvider(name = "image-files")
public Object[][] librariesToTest()
{
return new Object[][]
{
- { "pond.bmp" },
- { "pond.gif" },
- { "pond.jpg" },
- { "pond.png" },
- { "pond.pgm" },
- { "pond.tif" },
- { "pond.ppm" } };
+ { "pond.bmp", 24 },
+ { "pond.gif", 8 },
+ { "pond.jpg", 24 },
+ { "pond.png", 24 },
+ { "pond.pgm", 8 },
+ { "pond.tif", 24 },
+ { "pond.ppm", 24 } };
}
@Test(dataProvider = "image-files")
- public void testSingleImageExamples(String imageFileName)
+ public void testSingleImageExamples(String imageFileName, int expectedDepth)
+ throws FileNotFoundException
{
JAIReaderLibrary library = new JAIReaderLibrary();
String libraryName = library.getName();
File imageFile = getImageFileForLibrary(libraryName, imageFileName);
IImageReader reader = library.tryGetReaderForFile(imageFile.getPath());
-
+
List<ImageID> imageIDs = reader.getImageIDs(imageFile);
assertEquals("[0-0-0-0]", imageIDs.toString());
-
+
Map<String, Object> metaData = reader.readMetaData(imageFile, imageIDs.get(0), null);
assertEquals(0, metaData.size());
-
+
BufferedImage image = reader.readImage(imageFile, imageIDs.get(0), null);
assertEquals(512, image.getWidth());
assertEquals(384, image.getHeight());
+
+ int depth =
+ reader.readColorDepth(
+ new RandomAccessFileImpl(new RandomAccessFile(imageFile, "r")),
+ imageIDs.get(0));
+
+ assertEquals(expectedDepth, depth);
}
-
+
}
--
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