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 7502c46aff9e7f090aac6b80586fdeb5eef1719d..4922fdf2d56fe9508f950b68a8a00edc4bacff74 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReader.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReader.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.imagereaders;
+import java.awt.Dimension;
import java.awt.image.BufferedImage;
import java.io.File;
import java.util.List;
@@ -41,12 +42,12 @@ public interface IImageReader
* Return the name of the reader.
*/
public String getName();
-
+
/**
* Returns a list of IDs uniquely identifying all images in the specified file.
*/
public List<ImageID> getImageIDs(File file) throws IOExceptionUnchecked;
-
+
/**
* Returns a list of IDs uniquely identifying all images in the specified byte array.
*/
@@ -56,7 +57,7 @@ public interface IImageReader
* Returns a list of IDs uniquely identifying all images in the specified handle.
*/
public List<ImageID> getImageIDs(IRandomAccessFile handle) throws IOExceptionUnchecked;
-
+
/**
* Reads a {@link BufferedImage} from a {@link File}.
*
@@ -64,7 +65,8 @@ public interface IImageReader
* @param imageID the ID of the image to be read
* @param params read parameters
*/
- public BufferedImage readImage(File file, ImageID imageID, IReadParams params) throws IOExceptionUnchecked;
+ public BufferedImage readImage(File file, ImageID imageID, IReadParams params)
+ throws IOExceptionUnchecked;
/**
* Reads a {@link BufferedImage} from a byte array.
@@ -119,7 +121,15 @@ public interface IImageReader
* @param imageID the ID of the image to be read
* @param params read parameters
*/
- public Map<String, Object> readMetaData(IRandomAccessFile handle, ImageID imageID, IReadParams params)
- throws IOExceptionUnchecked;
+ public Map<String, Object> readMetaData(IRandomAccessFile handle, ImageID imageID,
+ IReadParams params) throws IOExceptionUnchecked;
+ /**
+ * Reads image dimensions (width and height).
+ *
+ * @param handle the image file as {@link IRandomAccessFile}
+ * @param imageID the ID of the image to be read
+ * @return dimensions of the image
+ */
+ public Dimension readDimensions(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 362631914698bf23ef74bf54eef21e0e793a500d..c20323f7123e2d4bc31e78f7273ad676defcec7c 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
@@ -20,6 +20,7 @@ import ij.ImagePlus;
import ij.ImageStack;
import ij.process.ImageProcessor;
+import java.awt.Dimension;
import java.awt.image.BufferedImage;
import java.io.IOException;
import java.util.ArrayList;
@@ -149,7 +150,7 @@ final class BioFormatsImageUtils
{
return reader.getClass().getSimpleName();
}
-
+
static List<ImageID> listImageIDs(IFormatReader reader, IRandomAccess handle)
{
String handleId = generateHandleId(reader);
@@ -196,8 +197,8 @@ final class BioFormatsImageUtils
*
* @throws IOExceptionUnchecked If access to <var>handle</var> fails.
*/
- static BufferedImage readImage(IFormatReader reader,
- IRandomAccess handle, ImageID imageID) throws IOExceptionUnchecked, IllegalArgumentException
+ static BufferedImage readImage(IFormatReader reader, IRandomAccess handle, ImageID imageID)
+ throws IOExceptionUnchecked, IllegalArgumentException
{
String handleId = generateHandleId(reader);
// Add to static map.
@@ -235,7 +236,7 @@ final class BioFormatsImageUtils
/**
* Returns the metadata of the image file represented by <var>handle</var>.
*
- * @param imageID
+ * @param imageID
* @throws IOExceptionUnchecked If access to <var>handle</var> fails.
*/
public static Map<String, Object> readMetadata(IFormatReader reader, IRandomAccess handle,
@@ -268,7 +269,6 @@ final class BioFormatsImageUtils
}
}
-
/**
* An utility method that uses bio-formats reader to read an image and ImageJ to do a basic
* intensity rescaling.
@@ -295,7 +295,8 @@ final class BioFormatsImageUtils
int height = reader.getSizeY();
final ImageStack stack = new ImageStack(width, height);
int imageIndex = calculateImageIndex(reader, imageID);
- final ImageProcessor ip = BioFormatsImageProcessor.openProcessor(reader, imageIndex, channel);
+ final ImageProcessor ip =
+ BioFormatsImageProcessor.openProcessor(reader, imageIndex, channel);
stack.addSlice("", ip);
final ImagePlus imp = new ImagePlus(handleId, stack);
@@ -315,6 +316,34 @@ final class BioFormatsImageUtils
}
}
+ static Dimension readImageDimensions(IFormatReader reader, IRandomAccess handle, ImageID imageID)
+ throws IOExceptionUnchecked, IllegalArgumentException
+ {
+ // Add to static map.
+ String handleId = generateHandleId(reader);
+ Location.mapFile(handleId, handle);
+ try
+ {
+ // This does the actual parsing.
+ reader.setId(handleId);
+ reader.setSeries(imageID.getSeriesIndex());
+ int width = reader.getSizeX();
+ int height = reader.getSizeY();
+ reader.close();
+ return new Dimension(width, height);
+ } 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)
{
return UUID.randomUUID().toString() + "." + formatHandler.getSuffixes()[0];
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 b87e6334dd6e21db1f5e0f9c7a77dd93f66ca38d..c0d745d1eda12e7dddc25bd45c8520e283ece5ca 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
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.imagereaders.bioformats;
+import java.awt.Dimension;
import java.awt.image.BufferedImage;
import java.util.List;
import java.util.Map;
@@ -91,4 +92,10 @@ class DefaultBioformatsImageReader extends AbstractMetaDataAwareImageReader
IRandomAccess input = new BioFormatsRandomAccessAdapter(handle);
return BioFormatsImageUtils.readMetadata(formatReader, input, imageID);
}
+
+ public Dimension readDimensions(IRandomAccessFile handle, ImageID imageID)
+ {
+ IRandomAccess input = new BioFormatsRandomAccessAdapter(handle);
+ return BioFormatsImageUtils.readImageDimensions(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 165b0d53ccbc21b26b26be8635a5ff8877a1830c..64ed38cdf46b622f6cc30b94132e754030c1aae5 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
@@ -21,6 +21,7 @@ import ij.io.Opener;
import ij.process.ImageProcessor;
import ij.process.ShortProcessor;
+import java.awt.Dimension;
import java.awt.Graphics2D;
import java.awt.image.BufferedImage;
import java.util.Arrays;
@@ -67,6 +68,17 @@ public class ImageJReaderLibrary implements IImageReaderLibrary
}
return createBufferedImageOfSameType(imagePlus);
}
+
+ public Dimension readDimensions(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 new Dimension(imagePlus.getWidth(), imagePlus.getHeight());
+ }
};
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 13e53309e578b2a978173b4b777676270af08683..f39fa4d7879fc125957ea28ea04976702ed93879 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
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.imagereaders.imageio;
+import java.awt.Dimension;
import java.awt.image.BufferedImage;
import java.io.IOException;
import java.io.InputStream;
@@ -113,6 +114,19 @@ public class ImageIOReaderLibrary implements IImageReaderLibrary
}
}
+ public Dimension readDimensions(IRandomAccessFile handle, ImageID imageID)
+ {
+ try
+ {
+ ImageInputStream imageInput = adaptHandle(handle);
+ ioReader.setInput(imageInput);
+ return new Dimension(ioReader.getWidth(0), ioReader.getHeight(0));
+ } 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 1894f6febfbd1ca694070b6392c62540d2483501..e7140c9cab1821172bf40a3afb324fb6d87092e9 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
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.imagereaders.jai;
+import java.awt.Dimension;
import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
import java.io.IOException;
@@ -92,4 +93,19 @@ class DefaultImageReader extends AbstractImageReader
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
}
+
+ public Dimension readDimensions(IRandomAccessFile handle, ImageID imageID)
+ {
+ try
+ {
+ InputStream input = new AdapterIInputStreamToInputStream(handle);
+ ImageDecoder decoder = ImageCodec.createImageDecoder(getName(), input, null);
+ RenderedImage renderedImage =
+ decoder.decodeAsRenderedImage(imageID.getTimeSeriesIndex());
+ return new Dimension(renderedImage.getWidth(), renderedImage.getHeight());
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
}
\ No newline at end of file