diff --git a/image_readers/.classpath b/image_readers/.classpath
index 6b6fea16a4ad237fad666553337f3e01e626f4a8..2cb8df3f38db4a6e209d3f17dd67788c39657687 100644
--- a/image_readers/.classpath
+++ b/image_readers/.classpath
@@ -1,6 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="source/java"/>
+ <classpathentry kind="src" path="sourceTest/java"/>
<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
<classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
<classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
@@ -12,5 +13,8 @@
<classpathentry kind="lib" path="/libraries/slf4j/log4j12/slf4j-log4j12.jar" sourcepath="/libraries/slf4j/log4j12/src.jar"/>
<classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.launching.macosx.MacOSXType/JVM 1.6"/>
+ <classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/common"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/image_readers/source/java/META-INF/services/ch.systemsx.cisd.imagereaders.IImageReaderLibrary b/image_readers/source/java/META-INF/services/ch.systemsx.cisd.imagereaders.IImageReaderLibrary
new file mode 100644
index 0000000000000000000000000000000000000000..0d171e0c047de3ccf9d70f3f8a1d592ec5481ae8
--- /dev/null
+++ b/image_readers/source/java/META-INF/services/ch.systemsx.cisd.imagereaders.IImageReaderLibrary
@@ -0,0 +1 @@
+ch.systemsx.cisd.imagereaders.bioformats.BioFormatsReaderLibrary
\ No newline at end of file
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/AbstractImageReader.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/AbstractImageReader.java
new file mode 100644
index 0000000000000000000000000000000000000000..108838052fedacfb2c3f35e40580fc6200cdb21d
--- /dev/null
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/AbstractImageReader.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.imagereaders;
+
+import java.awt.image.BufferedImage;
+import java.io.File;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+import ch.systemsx.cisd.base.io.ByteBufferRandomAccessFile;
+import ch.systemsx.cisd.base.io.IRandomAccessFile;
+import ch.systemsx.cisd.base.io.RandomAccessFileImpl;
+
+/**
+ * A convenience abstract class to be extended by {@link IImageReader} implementations.
+ *
+ * @author Kaloyan Enimanev
+ */
+public abstract class AbstractImageReader implements IImageReader
+{
+ private final String libraryName;
+
+ private final String readerName;
+
+ public AbstractImageReader(String libraryName, String readerName)
+ {
+ this.libraryName = libraryName;
+ this.readerName = readerName;
+ }
+
+ @Override
+ public String getLibraryName()
+ {
+ return libraryName;
+ }
+
+ @Override
+ public String getName()
+ {
+ return readerName;
+ }
+
+ @Override
+ public BufferedImage readImage(File file, int page) throws IOExceptionUnchecked
+ {
+ IRandomAccessFile raf = new RandomAccessFileImpl(file, "r");
+ return readImage(raf, page);
+ }
+
+ @Override
+ public BufferedImage readImage(byte[] bytes, int page)
+ {
+ IRandomAccessFile raf = new ByteBufferRandomAccessFile(bytes);
+ return readImage(raf, page);
+ }
+
+}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/Constants.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/Constants.java
new file mode 100644
index 0000000000000000000000000000000000000000..c126ebacd232a3fa1b04d8572e5b66eefb0e6612
--- /dev/null
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/Constants.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.imagereaders;
+
+/**
+ * Constants to be used when working with the image readers API.
+ *
+ * @author Kaloyan Enimanev
+ */
+public final class Constants
+{
+
+ public static final String BIOFORMATS_LIBRARY = "BioFormats";
+
+ public static final String BIOFORMATS_RESCALING_LIBRARY = "bioformats-rescaling";
+
+ public static final String JAI_LIBRARY = "JAI";
+}
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 5bfcaeb0f491848cd3652f83b604eaae86e36fef..aed420edb7738ab7ad1e426cc1af21f13f8f729c 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReader.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReader.java
@@ -23,18 +23,45 @@ import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
/**
+ * {@link IImageReader} can read images in a particular format (e.g. TIFF, JPG, GIF etc.). To obtain
+ * the correct {@link IImageReader} instance use the API of {@link ImageReaderFactory}.
+ *
* @author Bernd Rinn
*/
public interface IImageReader
{
+ /**
+ * Return the name of the library for this reader.
+ */
public String getLibraryName();
+ /**
+ * Return the name of the reader.
+ */
public String getName();
+ /**
+ * Reads a {@link BufferedImage} from a {@link File}.
+ *
+ * @param file the image file
+ * @param page specified the image page to be read (in case of multiple pages)
+ */
public BufferedImage readImage(File file, int page) throws IOExceptionUnchecked;
- public BufferedImage readImage(String filename, IRandomAccessFile handle, int page)
- throws IOExceptionUnchecked;
+ /**
+ * Reads a {@link BufferedImage} from a byte array.
+ *
+ * @param bytes the image file as a byte array
+ * @param page specified the image page to be read (in case of multiple pages)
+ */
+ public BufferedImage readImage(byte[] bytes, int page);
- public BufferedImage readImage(String filename, byte[] bytes, int page);
+ /**
+ * Reads a {@link BufferedImage} from a handle.
+ *
+ * @param handle the image file as {@link IRandomAccessFile}
+ * @param page specified the image page to be read (in case of multiple pages)
+ */
+ public BufferedImage readImage(IRandomAccessFile handle, int page)
+ throws IOExceptionUnchecked;
}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReaderLibrary.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReaderLibrary.java
index 6eb42df6c460f24dafee0e91f0d26fdc15126ff0..10580e48b21017eb4983c63420f7263fdf36cb98 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReaderLibrary.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/IImageReaderLibrary.java
@@ -25,12 +25,30 @@ import java.util.List;
*/
public interface IImageReaderLibrary
{
+ /**
+ * Return library name.
+ */
public String getName();
+ /**
+ * Return a collection with the names of the image readers available in the library.
+ */
public List<String> getReaderNames();
+ /**
+ * Returns an {@link IImageReader} for a specified name. Can return <code>null</code> if no
+ * reader with the specified name is available.
+ */
public IImageReader tryGetReader(String readerName);
-
+
+ /**
+ * Tries to find a suitable reader for a specified <var>fileName</var>. May return
+ * <code>null</code> if no suitable reader is found.
+ * <p>
+ * The behavior of this method may vary across libraries. For example, some image libraries can
+ * use the suffix of <var>fileName</var> to find the right reader, while others might attempt to
+ * open the file and apply heuristics on its content to determine the appropriate reader.
+ */
public IImageReader tryGetReaderForFile(String fileName);
}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/ImageReaderFactory.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/ImageReaderFactory.java
index 0043a792cb47b7867f050f984f1622f7ceacae55..7b452274a117aeaefe444b68133364b30be724c6 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/ImageReaderFactory.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/ImageReaderFactory.java
@@ -16,16 +16,60 @@
package ch.systemsx.cisd.imagereaders;
+import java.util.Iterator;
import java.util.ServiceLoader;
/**
* A factory for image readers.
* <p>
* Uses {@link ServiceLoader}s underneath to find out about the available libraries and readers.
- *
+ *
* @author Bernd Rinn
+ * @author Kaloyan Enimanev
*/
public class ImageReaderFactory
{
+ private static final ServiceLoader<IImageReaderLibrary> libraryServiceLoader = ServiceLoader
+ .load(IImageReaderLibrary.class);
+
+ /**
+ * Returns an {@link IImageReader} for specified library name and reader name. Can return
+ * <code>null</code> if no matching reader is found.
+ */
+ public static IImageReader tryGetReader(String libraryName, String readerName)
+ {
+ IImageReaderLibrary library = tryGetLibrary(libraryName);
+ return (library == null) ? null : library.tryGetReader(readerName);
+ }
+
+ /**
+ * Tries to find a suitable reader in a library for a specified <var>fileName</var>. May return
+ * <code>null</code> if no suitable reader is found.
+ * <p>
+ * The behavior of this method may vary across libraries. For example, some image libraries can
+ * use the suffix of <var>fileName</var> to find the right reader, while others might attempt to
+ * open the file and apply heuristics on its content to determine the appropriate reader.
+ */
+ public static IImageReader tryGetImageReaderForFile(String libraryName, String fileName)
+ {
+ IImageReaderLibrary library = tryGetLibrary(libraryName);
+ return (library == null) ? null : library.tryGetReaderForFile(fileName);
+ }
+
+ private static IImageReaderLibrary tryGetLibrary(String libraryName)
+ throws IllegalArgumentException
+ {
+ Iterator<IImageReaderLibrary> iterator = libraryServiceLoader.iterator();
+ while (iterator.hasNext())
+ {
+ IImageReaderLibrary library = iterator.next();
+ if (library.getName().equals(libraryName))
+ {
+ return library;
+ }
+ }
+ return null;
+ }
+
}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/AbstractBioFormatsReaderLibrary.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/AbstractBioFormatsReaderLibrary.java
new file mode 100644
index 0000000000000000000000000000000000000000..7fa6d87c41076cbb2b9558977784ed8080d1c93d
--- /dev/null
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/AbstractBioFormatsReaderLibrary.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.imagereaders.bioformats;
+
+import java.util.List;
+
+import loci.formats.IFormatReader;
+
+import ch.systemsx.cisd.imagereaders.IImageReader;
+import ch.systemsx.cisd.imagereaders.IImageReaderLibrary;
+
+/**
+ * {@link IImageReaderLibrary} for BioFormats readers with intensity rescaling.
+ *
+ * @author Kaloyan Enimanev
+ */
+abstract class AbstractBioFormatsReaderLibrary implements IImageReaderLibrary
+{
+
+ /**
+ * Adapt a BioFormats {@link IFormatReader} to {@link IImageReader}.
+ *
+ * @param formatReader this parameter is guaranteed to be non-null.
+ */
+ protected abstract IImageReader adaptFormatReader(final IFormatReader formatReader);
+
+
+ @Override
+ public List<String> getReaderNames()
+ {
+ return BioFormatsImageUtils.getReaderNames();
+ }
+
+ @Override
+ public IImageReader tryGetReader(String readerName)
+ {
+ final IFormatReader formatReaderOrNull = BioFormatsImageUtils.tryFindReaderByName(readerName);
+ return tryAdaptFormatReader(formatReaderOrNull);
+ }
+
+ @Override
+ public IImageReader tryGetReaderForFile(String fileName)
+ {
+ IFormatReader formatReaderOrNull = BioFormatsImageUtils.tryFindReaderForFile(fileName);
+ return tryAdaptFormatReader(formatReaderOrNull);
+ }
+
+ /**
+ * Delegate the wrapping of non-null readers to an abstract method.
+ */
+ protected IImageReader tryAdaptFormatReader(final IFormatReader formatReaderOrNull)
+ {
+ return (formatReaderOrNull == null) ? null : adaptFormatReader(formatReaderOrNull);
+ }
+
+}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJUtils.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJUtils.java
deleted file mode 100644
index a63b0353abfeb9c9b58eb1bc824b2fa2b39a96c5..0000000000000000000000000000000000000000
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJUtils.java
+++ /dev/null
@@ -1,146 +0,0 @@
-/*
- * Copyright 2011 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.imagereaders.bioformats;
-
-import ij.ImagePlus;
-import ij.ImageStack;
-import ij.process.ImageProcessor;
-
-import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.IOException;
-
-import loci.common.ByteArrayHandle;
-import loci.common.IRandomAccess;
-import loci.common.Location;
-import loci.common.NIOFileHandle;
-import loci.formats.FormatException;
-import loci.formats.IFormatReader;
-
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
-import ch.systemsx.cisd.base.io.IRandomAccessFile;
-
-/**
- * A utility class to use bio-formats readers to read images and ImageJ to do a basic intensity
- * rescaling.
- *
- * @author Bernd Rinn
- */
-public final class BioFormatsImageJUtils
-{
-
- /**
- * Returns the image <var>filename</var> represented by <var>bytes</var> as
- * {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- public static BufferedImage readAndTransformImage(String filename, byte[] bytes, int page,
- int channel) throws IOExceptionUnchecked, IllegalArgumentException
- {
- return readAndTransformImage(filename, new ByteArrayHandle(bytes), page, channel);
- }
-
- /**
- * Returns the image <var>file</var> represented by <var>handle</var> as {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>file</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- public static BufferedImage readAndTransformImage(File file, int page, int channel)
- throws IOExceptionUnchecked, IllegalArgumentException
- {
- try
- {
- return readAndTransformImage(file.getPath(), new NIOFileHandle(file, "r"), page,
- channel);
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- /**
- * Returns the image <var>filename</var> represented by <var>handle</var> as
- * {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- public static BufferedImage readAndTransformImage(String filename, IRandomAccessFile handle,
- int page, int channel) throws IOExceptionUnchecked, IllegalArgumentException
- {
- return readAndTransformImage(filename, new BioFormatsRandomAccessAdapter(handle), page,
- channel);
- }
-
- /**
- * Returns the image <var>filename</var> represented by <var>handle</var> as
- * {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- private static BufferedImage readAndTransformImage(String filename, IRandomAccess handle,
- int page, int channel) throws IOExceptionUnchecked, IllegalArgumentException
- {
- // Add to static map.
- Location.mapFile(filename, handle);
- try
- {
- final IFormatReader reader = BioFormatsImageUtils.findReaderForFile(filename);
- // This does the actual parsing.
- reader.setId(filename);
- int width = reader.getSizeX();
- int height = reader.getSizeY();
- final ImageStack stack = new ImageStack(width, height);
- final ImageProcessor ip = BioFormatsImageProcessor.openProcessor(reader, page, channel);
- stack.addSlice("", ip);
- final ImagePlus imp = new ImagePlus(filename, stack);
-
- final BufferedImage image = imp.getBufferedImage();
- reader.close();
- return image;
- } catch (FormatException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- // Remove from static map.
- Location.mapFile(filename, null);
- }
- }
-
- private BioFormatsImageJUtils()
- {
- // Not to be instantiated.
- }
-
-}
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 1e532d5649b48fefaa604b69270af7ab9de518b0..3c811c973d65a3732b1c74fcc883fb468a49bd27 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
@@ -16,16 +16,19 @@
package ch.systemsx.cisd.imagereaders.bioformats;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.process.ImageProcessor;
+
import java.awt.image.BufferedImage;
-import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
+import java.util.UUID;
-import loci.common.ByteArrayHandle;
import loci.common.IRandomAccess;
import loci.common.Location;
-import loci.common.NIOFileHandle;
import loci.formats.FormatException;
import loci.formats.IFormatReader;
import loci.formats.ImageReader;
@@ -33,43 +36,30 @@ import loci.formats.gui.BufferedImageReader;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
-import ch.systemsx.cisd.base.io.IRandomAccessFile;
/**
* A utility class to use bio-formats to read images.
*
* @author Bernd Rinn
*/
-public final class BioFormatsImageUtils
+final class BioFormatsImageUtils
{
- private final static List<IFormatReader> readers = new ArrayList<IFormatReader>();
+ private final static List<IFormatReader> readers;
static
{
- final Class<? extends IFormatReader>[] classes =
- ImageReader.getDefaultReaderClasses().getClasses();
- for (int i = 0; i < classes.length; i++)
- {
- IFormatReader reader = null;
- try
- {
- reader = classes[i].newInstance();
- } catch (IllegalAccessException exc)
- {
- } catch (InstantiationException exc)
- {
- }
- if (reader == null)
- {
- continue;
- }
- readers.add(reader);
- }
+ IFormatReader[] formatReaders = new ImageReader().getReaders();
+ readers = Arrays.asList(formatReaders);
}
- public static IFormatReader tryFindReaderForFile(String fileName) throws IOException,
- IllegalArgumentException
+ /**
+ * Tries to find a suitable reader for the file specified with <var>fileName</var>. May return
+ * <code>null</code> if no suitable reader is found.
+ * <p>
+ * Note that the suffix of <var>fileName</var> is used to find the right reader.
+ */
+ public static IFormatReader tryFindReaderForFile(String fileName)
{
for (IFormatReader r : readers)
{
@@ -81,19 +71,10 @@ public final class BioFormatsImageUtils
return null;
}
- public static IFormatReader findReaderForFile(String fileName) throws IOException,
- IllegalArgumentException
- {
- final IFormatReader readerOrNull = tryFindReaderForFile(fileName);
- if (readerOrNull == null)
- {
- throw new IllegalArgumentException("Cannot find reader.");
- } else
- {
- return readerOrNull;
- }
- }
-
+ /**
+ * Return an {@link IFormatReader} for a specified name. May return <code>null</code> if no
+ * corresponding reader is found.
+ */
public static IFormatReader tryFindReaderByName(String readerName)
throws IllegalArgumentException
{
@@ -108,147 +89,44 @@ public final class BioFormatsImageUtils
}
- public static IFormatReader findReaderByName(String readerName) throws IllegalArgumentException
- {
- final IFormatReader readerOrNull = tryFindReaderByName(readerName);
- if (readerOrNull == null)
- {
- throw new IllegalArgumentException("Cannot find reader.");
- } else
- {
- return readerOrNull;
- }
-
- }
-
+ /**
+ * Return a list with the names of all known readers.
+ */
public static List<String> getReaderNames()
{
final List<String> readerNames = new ArrayList<String>(readers.size());
for (IFormatReader reader : readers)
{
- readerNames.add(reader.getClass().getSimpleName());
+ String readerName = getReaderName(reader);
+ readerNames.add(readerName);
}
return readerNames;
}
/**
- * Returns all images of the image <var>filename</var> represented by <var>bytes</var> as
- * {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- public static BufferedImage[] readImages(String filename, byte[] bytes)
- throws IOExceptionUnchecked, IllegalArgumentException
- {
- return readImages(filename, new ByteArrayHandle(bytes));
- }
-
- /**
- * Returns the image <var>filename</var> represented by <var>bytes</var> as
- * {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- public static BufferedImage readImage(String filename, byte[] bytes, int page)
- throws IOExceptionUnchecked, IllegalArgumentException
- {
- return readImage(filename, new ByteArrayHandle(bytes), page);
- }
-
- /**
- * Returns all images of the image file given by <var>file</var> as {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>file</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- public static BufferedImage[] readImages(File file) throws IOExceptionUnchecked,
- IllegalArgumentException
- {
- NIOFileHandle handle = null;
- try
- {
- handle = new NIOFileHandle(file, "r");
- return readImages(file.getPath(), handle);
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- if (handle != null)
- {
- try
- {
- handle.close();
- } catch (IOException ex)
- {
- // Silence.
- }
- }
- }
- }
-
- /**
- * Returns the image <var>file</var> represented by <var>handle</var> as {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>file</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
+ * Return the name of a {@link IFormatReader}.
*/
- public static BufferedImage readImage(File file, int page) throws IOExceptionUnchecked,
- IllegalArgumentException
+ public static String getReaderName(IFormatReader reader)
{
- try
- {
- return readImage(file.getPath(), new NIOFileHandle(file, "r"), page);
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
+ return reader.getClass().getSimpleName();
}
/**
* Returns the image <var>page</var> of the image file given by <var>filename</var> represented
* by <var>handle</var> as {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
*
* @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
*/
- public static BufferedImage readImage(String filename, IRandomAccessFile handle, int page)
- throws IOExceptionUnchecked, IllegalArgumentException
- {
- return readImage(filename, new BioFormatsRandomAccessAdapter(handle), page);
- }
-
- /**
- * Returns the image <var>page</var> of the image file given by <var>filename</var> represented
- * by <var>handle</var> as {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
- *
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- private static BufferedImage readImage(String filename, IRandomAccess handle, int page)
- throws IOExceptionUnchecked, IllegalArgumentException
+ static BufferedImage readImage(IFormatReader reader,
+ IRandomAccess handle, int page) throws IOExceptionUnchecked, IllegalArgumentException
{
+ String handleId = generateHandleId();
// Add to static map.
- Location.mapFile(filename, handle);
+ Location.mapFile(handleId, handle);
try
{
- final IFormatReader reader = findReaderForFile(filename);
// This does the actual parsing.
- reader.setId(filename);
+ reader.setId(handleId);
final BufferedImageReader biReader =
BufferedImageReader.makeBufferedImageReader(reader);
final BufferedImage image = biReader.openImage(page);
@@ -263,32 +141,39 @@ public final class BioFormatsImageUtils
} finally
{
// Remove from static map.
- Location.mapFile(filename, null);
+ Location.mapFile(handleId, null);
}
}
/**
- * Returns the image <var>page</var> of the image file given by <var>filename</var> represented
- * by <var>handle</var> as {@link BufferedImage}.
+ * An utility method that uses bio-formats reader to read an image and ImageJ to do a basic
+ * intensity rescaling.
* <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
+ * Returns the image <var>filename</var> represented by <var>handle</var> as
+ * {@link BufferedImage}.
*
* @throws IOExceptionUnchecked If access to <var>handle</var> fails.
* @throws IllegalArgumentException If no suitable reader can be found.
*/
- static BufferedImage readImage(IFormatReader formatReader, String filename,
- IRandomAccess handle, int page) throws IOExceptionUnchecked, IllegalArgumentException
+ static BufferedImage readImageWithIntensityRescaling(IFormatReader reader,
+ IRandomAccess handle, int page, int channel) throws IOExceptionUnchecked,
+ IllegalArgumentException
{
// Add to static map.
- Location.mapFile(filename, handle);
+ String handleId = generateHandleId();
+ Location.mapFile(handleId, handle);
try
{
- final IFormatReader reader = findReaderForFile(filename);
// This does the actual parsing.
- reader.setId(filename);
- final BufferedImageReader biReader =
- BufferedImageReader.makeBufferedImageReader(reader);
- final BufferedImage image = biReader.openImage(page);
+ reader.setId(handleId);
+ int width = reader.getSizeX();
+ int height = reader.getSizeY();
+ final ImageStack stack = new ImageStack(width, height);
+ final ImageProcessor ip = BioFormatsImageProcessor.openProcessor(reader, page, channel);
+ stack.addSlice("", ip);
+ final ImagePlus imp = new ImagePlus(handleId, stack);
+
+ final BufferedImage image = imp.getBufferedImage();
reader.close();
return image;
} catch (FormatException ex)
@@ -300,71 +185,13 @@ public final class BioFormatsImageUtils
} finally
{
// Remove from static map.
- Location.mapFile(filename, null);
+ Location.mapFile(handleId, null);
}
}
- /**
- * Returns all images of the image file given by <var>filename</var> represented by
- * <var>handle</var> as {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
- *
- * @param filename The name of the image, suffix used to determine the reader
- * @param handle The handle of the content of the file, may be used to determine the reader as
- * well. Will <i>not</i> be closed!
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- public static BufferedImage[] readImages(String filename, IRandomAccessFile handle)
- throws IOExceptionUnchecked, IllegalArgumentException
+ public static String generateHandleId()
{
- return readImages(filename, new BioFormatsRandomAccessAdapter(handle));
- }
-
- /**
- * Returns all images of the image file given by <var>filename</var> represented by
- * <var>handle</var> as {@link BufferedImage}.
- * <p>
- * Note that the suffix of <var>filename</var> is used to find the right reader.
- *
- * @param filename The name of the image, suffix used to determine the reader
- * @param handle The handle of the content of the file, may be used to determine the reader as
- * well. Will <i>not</i> be closed!
- * @throws IOExceptionUnchecked If access to <var>handle</var> fails.
- * @throws IllegalArgumentException If no suitable reader can be found.
- */
- private static BufferedImage[] readImages(String filename, IRandomAccess handle)
- throws IOExceptionUnchecked, IllegalArgumentException
- {
- BufferedImage[] images = null;
- // Add to static map.
- Location.mapFile(filename, handle);
- try
- {
- final IFormatReader reader = findReaderForFile(filename);
- // This does the actual parsing.
- reader.setId(filename);
- final BufferedImageReader biReader =
- BufferedImageReader.makeBufferedImageReader(reader);
- images = new BufferedImage[biReader.getImageCount()];
- for (int i = 0; i < images.length; ++i)
- {
- images[i] = biReader.openImage(i);
- }
- reader.close();
- return images;
- } catch (FormatException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- // Remove from static map.
- Location.mapFile(filename, null);
- }
+ return UUID.randomUUID().toString();
}
private BioFormatsImageUtils()
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsRandomAccessAdapter.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsRandomAccessAdapter.java
index 2952746965724b452e5c554170e11fbb9c9c0920..57fdabf2d3f216b58d19c1bdf2eeae9eefc2cea3 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsRandomAccessAdapter.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsRandomAccessAdapter.java
@@ -51,17 +51,6 @@ final class BioFormatsRandomAccessAdapter implements IRandomAccess
}
}
- public int read() throws IOException
- {
- try
- {
- return randomAccessFile.read();
- } catch (IOExceptionUnchecked ex)
- {
- throw ex.getCause();
- }
- }
-
@Override
public int read(byte[] b) throws IOException
{
@@ -122,17 +111,6 @@ final class BioFormatsRandomAccessAdapter implements IRandomAccess
}
}
- public void setLength(long newLength) throws IOException
- {
- try
- {
- randomAccessFile.setLength(newLength);
- } catch (IOExceptionUnchecked ex)
- {
- throw ex.getCause();
- }
- }
-
@Override
public void readFully(byte[] b) throws IOException
{
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsReaderLibrary.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsReaderLibrary.java
index f9508f17cccd889d995d382c8a3c297a95a28d58..04e6bc4daf19a2b6ee53b824e6a0a6f9f57dbec0 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsReaderLibrary.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsReaderLibrary.java
@@ -17,90 +17,43 @@
package ch.systemsx.cisd.imagereaders.bioformats;
import java.awt.image.BufferedImage;
-import java.io.File;
-import java.util.List;
+import loci.common.IRandomAccess;
import loci.formats.IFormatReader;
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.base.io.IRandomAccessFile;
+import ch.systemsx.cisd.imagereaders.AbstractImageReader;
+import ch.systemsx.cisd.imagereaders.Constants;
import ch.systemsx.cisd.imagereaders.IImageReader;
-import ch.systemsx.cisd.imagereaders.IImageReaderLibrary;
/**
- *
- *
* @author Bernd Rinn
*/
-public class BioFormatsReaderLibrary implements IImageReaderLibrary
+public class BioFormatsReaderLibrary extends AbstractBioFormatsReaderLibrary
{
@Override
public String getName()
{
- return "bioformats";
- }
-
- @Override
- public List<String> getReaderNames()
- {
- return BioFormatsImageUtils.getReaderNames();
+ return Constants.BIOFORMATS_LIBRARY;
}
@Override
- public IImageReader tryGetReader(String readerName)
+ protected IImageReader adaptFormatReader(final IFormatReader formatReader)
{
- final IFormatReader formatReaderOrNull = BioFormatsImageUtils.tryFindReaderByName(readerName);
- if (formatReaderOrNull == null)
- {
- return null;
- } else
- {
- return new IImageReader()
+ final String libraryName = getName();
+ final String readerName = BioFormatsImageUtils.getReaderName(formatReader);
+
+ return new AbstractImageReader(libraryName, readerName)
+ {
+ @Override
+ public BufferedImage readImage(IRandomAccessFile handle, int page)
+ throws IOExceptionUnchecked
{
-
- @Override
- public BufferedImage readImage(String filename, byte[] bytes, int page)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public BufferedImage readImage(String filename, IRandomAccessFile handle, int page)
- throws IOExceptionUnchecked
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public BufferedImage readImage(File file, int page) throws IOExceptionUnchecked
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public String getName()
- {
- return formatReaderOrNull.getClass().getSimpleName();
- }
-
- @Override
- public String getLibraryName()
- {
- return BioFormatsReaderLibrary.this.getName();
- }
- };
- }
+ IRandomAccess input = new BioFormatsRandomAccessAdapter(handle);
+ return BioFormatsImageUtils.readImage(formatReader, input, page);
+ }
+ };
}
-
- @Override
- public IImageReader tryGetReaderForFile(String fileName)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsRescalingReaderLibrary.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsRescalingReaderLibrary.java
new file mode 100644
index 0000000000000000000000000000000000000000..976c65ac804de4be7f3de7287888d7b0a05c6183
--- /dev/null
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsRescalingReaderLibrary.java
@@ -0,0 +1,64 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.imagereaders.bioformats;
+
+import java.awt.image.BufferedImage;
+
+import loci.common.IRandomAccess;
+import loci.formats.IFormatReader;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+import ch.systemsx.cisd.base.io.IRandomAccessFile;
+import ch.systemsx.cisd.imagereaders.AbstractImageReader;
+import ch.systemsx.cisd.imagereaders.Constants;
+import ch.systemsx.cisd.imagereaders.IImageReader;
+import ch.systemsx.cisd.imagereaders.IImageReaderLibrary;
+
+/**
+ * {@link IImageReaderLibrary} for bioformat readers with intensity rescaling.
+ *
+ * @author Kaloyan Enimanev
+ */
+public class BioFormatsRescalingReaderLibrary extends AbstractBioFormatsReaderLibrary
+{
+
+ @Override
+ public String getName()
+ {
+ return Constants.BIOFORMATS_RESCALING_LIBRARY;
+ }
+
+ @Override
+ protected IImageReader adaptFormatReader(final IFormatReader formatReader)
+ {
+ final String libraryName = getName();
+ final String readerName = BioFormatsImageUtils.getReaderName(formatReader);
+
+ return new AbstractImageReader(libraryName, readerName)
+ {
+ @Override
+ public BufferedImage readImage(IRandomAccessFile handle, int page)
+ throws IOExceptionUnchecked
+ {
+ IRandomAccess input = new BioFormatsRandomAccessAdapter(handle);
+ // TODO KE: Is 0 a sensible default for channel ?
+ return BioFormatsImageUtils.readImageWithIntensityRescaling(formatReader,
+ input, page, 0);
+ }
+ };
+ }
+}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/MetaDataExtraction.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/MetaDataExtraction.java
deleted file mode 100644
index 37a241e82b94a2896230392a20180b47bdb187ad..0000000000000000000000000000000000000000
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/MetaDataExtraction.java
+++ /dev/null
@@ -1,458 +0,0 @@
-//
-// MetaDataExtraction.java
-//
-
-/*
- OME Bio-Formats package for reading and converting biological file formats.
- Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
-
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
- */
-
-package ch.systemsx.cisd.imagereaders.bioformats;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.regex.Pattern;
-
-import loci.common.DebugTools;
-import loci.common.services.DependencyException;
-import loci.common.services.ServiceException;
-import loci.common.services.ServiceFactory;
-import loci.common.xml.XMLTools;
-import loci.formats.FormatException;
-import loci.formats.IFormatReader;
-import loci.formats.ImageReader;
-import loci.formats.MetadataTools;
-import loci.formats.MissingLibraryException;
-import loci.formats.gui.BufferedImageReader;
-import loci.formats.in.DefaultMetadataOptions;
-import loci.formats.in.MetadataLevel;
-import loci.formats.in.MetadataOptions;
-import loci.formats.in.OMETiffReader;
-import loci.formats.meta.MetadataRetrieve;
-import loci.formats.meta.MetadataStore;
-import loci.formats.services.OMEXMLService;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- *
- */
-public class MetaDataExtraction
-{
-
- // -- Constants --
-
- private static final Logger LOGGER = LoggerFactory.getLogger(MetaDataExtraction.class);
-
- // -- Fields --
-
- private String directory = null;
-
- private String filePattern = ".*";
-
- private String fileName = null;
-
- private String pathName = null;
-
- private boolean doOriginal = false;
-
- private boolean doGlobal = false;
-
- private boolean doCSV = false;
-
- private boolean doOMEXML = false;
-
- private String omexmlVersion = null;
-
- private Hashtable<String, Object> vCSVKeyToKeyMapping;
-
- private Hashtable<String, Object> vCSVMetaData;
-
- private String[] vCSVKeys;
-
- private String[] vCSVMetaKeys;
-
- private IFormatReader reader;
-
- private IFormatReader baseReader;
-
- // -- MetaDataExtraction methods --
-
- public boolean parseArgs(String[] args)
- {
- directory = null;
- filePattern = ".*";
- fileName = null;
- pathName = null;
- doOriginal = false;
- doGlobal = false;
- doCSV = false;
- doOMEXML = false;
- omexmlVersion = null;
- if (args == null)
- {
- return false;
- }
- for (int i = 0; i < args.length; i++)
- {
- if (args[i].length() == 0)
- {
- continue;
- }
- if (args[i].startsWith("-"))
- {
- if (args[i].equals("-csv"))
- {
- doCSV = true;
- } else if (args[i].equals("-original"))
- {
- doOriginal = true;
- } else if (args[i].equals("-global"))
- {
- doGlobal = true;
- } else if (args[i].equals("-omexml"))
- {
- doOMEXML = true;
- } else if (args[i].equals("-xmlversion"))
- {
- omexmlVersion = args[++i];
- } else if (args[i].equals("-directory"))
- {
- directory = args[++i];
- } else if (args[i].equals("-pattern"))
- {
- filePattern = args[++i];
- } else if (args[i].equals("-help") || args[i].equals("--help"))
- {
- printUsage();
- return false;
- } else
- {
- LOGGER.error("Found unknown command flag: '{}' exiting.", args[i]);
- return false;
- }
- } else
- {
- LOGGER.error("Found unknown argument: '{}' exiting.", args[i]);
- return false;
- }
- }
- return true;
- }
-
- public void printUsage()
- {
- String[] s =
- {
- "To test read a file, run:",
- " MetaDataExtraction -directory <directory> -pattern <pattern> [-omexml] [-csv]",
- " [-original] [-global]", "",
- " -directory: the directory with image file(s) to read",
- " -pattern: regular expression for file names to read",
- " -original: print original metadata (unformatted)",
- " -global: print global metadata (unformatted)",
- " -csv: print metadata in CSV format",
- " -omexml: print metadata in OME-XML format", "" };
- for (int i = 0; i < s.length; i++)
- {
- LOGGER.error(s[i]);
- }
- }
-
- public void printGlobalMetadata()
- {
- Hashtable<String, Object> meta = reader.getGlobalMetadata();
- String[] vOriginalMetaKeys = MetadataTools.keys(meta);
- for (String key : vOriginalMetaKeys)
- {
- System.out.println(key + ": " + meta.get(key));
- }
- }
-
- public void printOriginalMetadata()
- {
- Hashtable<String, Object> meta = reader.getSeriesMetadata();
- String[] vOriginalMetaKeys = MetadataTools.keys(meta);
- for (int i = 0; i < vOriginalMetaKeys.length; i++)
- {
- System.out.println(vOriginalMetaKeys[i] + ": " + meta.get(vOriginalMetaKeys[i]));
- }
- }
-
- public void initCSVMetadata()
- {
- vCSVKeyToKeyMapping = new Hashtable<String, Object>();
- vCSVKeyToKeyMapping.put("ApplicationName", "ApplicationName");
- vCSVKeyToKeyMapping.put("ApplicationVersion", "ApplicationVersion");
- vCSVKeyToKeyMapping.put("Camera Bit Depth", "Camera Bit Depth");
- vCSVKeyToKeyMapping.put("Experiment base name", "Experiment base name");
- vCSVKeyToKeyMapping.put("Experiment set", "Experiment set");
- vCSVKeyToKeyMapping.put("Exposure", "ExposureTime");
- vCSVKeyToKeyMapping.put("Frames to Average", "Frames to Average");
- vCSVKeyToKeyMapping.put("Gain", "Gain");
- vCSVKeyToKeyMapping.put("ImageXpress Micro Filter Cube", "ImageXpress Micro Filter Cube");
- vCSVKeyToKeyMapping.put("ImageXpress Micro Objective", "ImageXpress Micro Objective");
- vCSVKeyToKeyMapping.put("Laser focus score", "Laser focus score");
- vCSVKeyToKeyMapping.put("Shading", "Shading");
- vCSVKeyToKeyMapping.put("Subtract", "Subtract");
- vCSVKeyToKeyMapping.put("Temperature", "Temperature");
- // vCSVKeyToKeyMapping.put("_IllumSetting_", "_IllumSetting_");
- // vCSVKeyToKeyMapping.put("_MagSetting_", "_MagSetting_");
- vCSVKeyToKeyMapping.put("acquisition-time-local", "AcquiredDate");
- vCSVKeyToKeyMapping.put("camera-binning-x", "camera-binning-x");
- vCSVKeyToKeyMapping.put("camera-binning-y", "camera-binning-y");
- vCSVKeyToKeyMapping.put("camera-chip-offset-x", "camera-chip-offset-x");
- vCSVKeyToKeyMapping.put("camera-chip-offset-y", "camera-chip-offset-y");
- vCSVKeyToKeyMapping.put("gamma", "gamma");
- vCSVKeyToKeyMapping.put("number-of-planes", "SizeZ");
- vCSVKeyToKeyMapping.put("pixel-size-x", "SizeX");
- vCSVKeyToKeyMapping.put("pixel-size-y", "SizeY");
- vCSVKeyToKeyMapping.put("spatial-calibration-state", "spatial-calibration-state");
- vCSVKeyToKeyMapping.put("spatial-calibration-units", "spatial-calibration-units");
- vCSVKeyToKeyMapping.put("spatial-calibration-x", "PhysicalSizeX");
- vCSVKeyToKeyMapping.put("spatial-calibration-y", "PhysicalSizeY");
- vCSVKeyToKeyMapping.put("stage-label", "stage-label");
- vCSVKeyToKeyMapping.put("stage-position-x", "PositionX");
- vCSVKeyToKeyMapping.put("stage-position-y", "PositionY");
- vCSVKeyToKeyMapping.put("z-position", "PositionZ");
- vCSVKeyToKeyMapping.put("wavelength", "wavelength");
- vCSVKeys = MetadataTools.keys(vCSVKeyToKeyMapping);
-
- vCSVMetaData = new Hashtable<String, Object>();
- for (int i = 0; i < vCSVKeys.length; i++)
- {
- String vCSVMappedKey = "" + vCSVKeyToKeyMapping.get(vCSVKeys[i]);
- String vOriginalMetaValue = "-";
- vCSVMetaData.put(vCSVMappedKey, vOriginalMetaValue);
- }
- vCSVMetaKeys = MetadataTools.keys(vCSVMetaData);
- }
-
- public void printCSVHeader()
- {
- System.out.print("\"" + "Filename" + "\",");
- for (int i = 0; i < vCSVMetaKeys.length; i++)
- {
- System.out.print("\"" + vCSVMetaKeys[i] + "\",");
- }
- System.out.println("");
- }
-
- public void printCSVMetadata()
- {
- Hashtable<String, Object> vOriginalMetaData = reader.getSeriesMetadata();
- // String[] vOriginalMetaKeys = MetadataTools.keys(vOriginalMetaData);
-
- vCSVMetaData = new Hashtable<String, Object>();
- for (int i = 0; i < vCSVKeys.length; i++)
- {
- String vCSVMappedKey = "" + vCSVKeyToKeyMapping.get(vCSVKeys[i]);
- String vOriginalMetaValue;
- if (vOriginalMetaData.containsKey(vCSVKeys[i]))
- {
- vOriginalMetaValue = "" + vOriginalMetaData.get(vCSVKeys[i]);
- } else
- {
- vOriginalMetaValue = "-";
- }
- vCSVMetaData.put(vCSVMappedKey, vOriginalMetaValue);
- }
-
- // Print the CSV output
- System.out.print("\"" + fileName + "\",");
- for (int i = 0; i < vCSVMetaKeys.length; i++)
- {
- System.out.print("\"" + vCSVMetaData.get(vCSVMetaKeys[i]) + "\",");
- }
- System.out.println("");
- }
-
- public void printOMEXML() throws MissingLibraryException, ServiceException
- {
- MetadataStore ms = reader.getMetadataStore();
-
- if (baseReader instanceof ImageReader)
- {
- baseReader = ((ImageReader) baseReader).getReader();
- }
- if (baseReader instanceof OMETiffReader)
- {
- ms = ((OMETiffReader) baseReader).getMetadataStoreForDisplay();
- }
-
- OMEXMLService service;
- try
- {
- ServiceFactory factory = new ServiceFactory();
- service = factory.getInstance(OMEXMLService.class);
- } catch (DependencyException de)
- {
- throw new MissingLibraryException(OMETiffReader.NO_OME_XML_MSG, de);
- }
- if (ms instanceof MetadataRetrieve)
- {
- String xml = service.getOMEXML((MetadataRetrieve) ms);
- if (service.validateOMEXML(xml))
- {
- System.out.print(XMLTools.indentXML(xml, true));
- } else
- {
- LOGGER.error("Could not validate OME-XML.");
- }
- } else
- {
- LOGGER.error("The metadata could not be converted to OME-XML.");
- if (omexmlVersion == null)
- {
- LOGGER.error("The OME-XML Java library is probably not available.");
- } else
- {
- LOGGER.error("{} is probably not a legal schema version.", omexmlVersion);
- }
- }
- }
-
- /**
- * A utility method for reading a file from the command line, and displaying the results in a
- * simple display.
- */
- public boolean testRead(String[] args) throws FormatException, ServiceException, IOException
- {
- // DebugTools.enableLogging("INFO");
- DebugTools.enableLogging("ERROR");
- boolean validArgs = parseArgs(args);
- if (validArgs == false)
- {
- return false;
- }
- if (directory == null)
- {
- printUsage();
- return false;
- }
- Pattern vPattern = Pattern.compile(filePattern, Pattern.CASE_INSENSITIVE);
-
- // initialize required structures
- boolean shownCSVHeader = false;
- if (doCSV)
- {
- initCSVMetadata();
- }
-
- // initialize the reader
- baseReader = new ImageReader();
- reader = new BufferedImageReader(baseReader);
-
- MetadataOptions metaOptions = new DefaultMetadataOptions(MetadataLevel.ALL);
-
- if (doOMEXML)
- {
- reader.setOriginalMetadataPopulated(true);
- try
- {
- ServiceFactory factory = new ServiceFactory();
- OMEXMLService service = factory.getInstance(OMEXMLService.class);
- reader.setMetadataStore(service.createOMEXMLMetadata(null, omexmlVersion));
- } catch (DependencyException de)
- {
- throw new MissingLibraryException(OMETiffReader.NO_OME_XML_MSG, de);
- } catch (ServiceException se)
- {
- throw new FormatException(se);
- }
- }
-
- // Get a sorted directory listing
- File directoryObject = new File(directory);
- pathName = directoryObject.getAbsolutePath();
- String[] directoryObjectEntries = directoryObject.list();
- Arrays.sort(directoryObjectEntries);
-
- // Iterate over the available files
- for (int vFileIdx = 0; vFileIdx < directoryObjectEntries.length; vFileIdx++)
- {
- File directoryObjectEntry = new File(directoryObjectEntries[vFileIdx]);
- if (directoryObjectEntry.isDirectory())
- {
- continue;
- }
-
- fileName = directoryObjectEntry.getName();
-
- boolean vMatches = vPattern.matcher(fileName).matches();
- if (vMatches == false)
- {
- continue;
- }
-
- // System.out.println("Found " + vFileIdx + ": " + FileName + ": " + vMatches);
-
- reader.close();
- reader.setMetadataOptions(metaOptions);
-
- // initialize reader
- try
- {
- // mapLocation();
- reader.setId(pathName + "/" + fileName);
-
- // read format-specific metadata table
- if (doOriginal)
- {
- printOriginalMetadata();
- }
- if (doGlobal)
- {
- printGlobalMetadata();
- }
- if (doCSV)
- {
- if (shownCSVHeader == false)
- {
- printCSVHeader();
- shownCSVHeader = true;
- }
- printCSVMetadata();
- }
- if (doOMEXML)
- {
- printOMEXML();
- }
- } catch (FormatException e)
- {
- } catch (IOException e)
- {
- }
- }
-
- return true;
- }
-
- // -- Main method --
-
- public static void main(String[] args) throws Exception
- {
- if (new MetaDataExtraction().testRead(args) == false)
- {
- System.exit(1);
- }
- }
-
-}
diff --git a/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/ImageReaderFactoryTest.java b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/ImageReaderFactoryTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..00982caaba469db5f453ac40523ab3b9c28c037f
--- /dev/null
+++ b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/ImageReaderFactoryTest.java
@@ -0,0 +1,85 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.imagereaders;
+
+import static ch.systemsx.cisd.imagereaders.Constants.BIOFORMATS_LIBRARY;
+
+import java.awt.image.BufferedImage;
+import java.io.File;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+
+/**
+ * Unit test for {@link ImageReaderFactory}.
+ *
+ * @author Kaloyan Enimanev
+ */
+public class ImageReaderFactoryTest extends AssertJUnit
+{
+ private static final String IMAGES_DIR = "./sourceTest/resources/images/";
+
+ @Test
+ public void testBioFormatReaders()
+ {
+ assertImageReadable(BIOFORMATS_LIBRARY, getResourceFile("demo.tif"));
+ assertImageReadable(BIOFORMATS_LIBRARY, getResourceFile("annapolis.jpg"));
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public void testGetInvalidLibrary()
+ {
+ assertImageReadable("Invalid_library", getResourceFile("demo.tif"));
+ }
+
+ @Test(expectedExceptions = IOExceptionUnchecked.class)
+ public void testReadNonExistingFile()
+ {
+ final String invalidName = "invalid_file_path.jpg";
+ final File invalidFile = new File(invalidName);
+
+ IImageReader reader =
+ ImageReaderFactory.tryGetImageReaderForFile(BIOFORMATS_LIBRARY, invalidName);
+ reader.readImage(invalidFile, 0);
+ }
+
+ private void assertImageReadable(String libraryName, File file)
+ {
+ IImageReader reader =
+ ImageReaderFactory.tryGetImageReaderForFile(libraryName, file.getAbsolutePath());
+ assertNotNull("Reader should not have NULL name", reader.getName());
+ assertEquals(libraryName, reader.getLibraryName());
+
+ String error =
+ String.format("Cannot find appropriate reader for file '%s' " + "in library '%s'",
+ libraryName, file.getAbsolutePath());
+ assertNotNull(error, reader);
+
+ BufferedImage image = reader.readImage(file, 0);
+ assertNotNull("Read image should not be null", image);
+ assertTrue("Image should have non-negative height", image.getHeight() > 0);
+ assertTrue("Image should have non-negative width", image.getWidth() > 0);
+ }
+
+ private File getResourceFile(String name)
+ {
+ return new File(IMAGES_DIR, name);
+ }
+
+}
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJImageViewer.java b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJImageViewer.java
similarity index 77%
rename from image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJImageViewer.java
rename to image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJImageViewer.java
index d7d346db879800ce404057a36725c4b782fafa8f..861129118bbd618fd5e9709e45781dd44e465c79 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJImageViewer.java
+++ b/image_readers/sourceTest/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageJImageViewer.java
@@ -19,15 +19,19 @@ package ch.systemsx.cisd.imagereaders.bioformats;
import java.awt.Frame;
import java.awt.image.BufferedImage;
import java.awt.image.RenderedImage;
+import java.io.File;
import javax.media.jai.widget.ScrollingImagePanel;
import org.apache.log4j.BasicConfigurator;
-import ch.systemsx.cisd.base.io.RandomAccessFileImpl;
+import ch.systemsx.cisd.imagereaders.Constants;
+import ch.systemsx.cisd.imagereaders.IImageReader;
+import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
/**
* An image viewer that uses BioFormats for reading and ImageJ for intensity rescaling.
+ * <p>
*
* @author Bernd Rinn
*/
@@ -54,9 +58,14 @@ public class BioFormatsImageJImageViewer
System.exit(1);
}
BasicConfigurator.configure();
- final BufferedImage image =
- BioFormatsImageJUtils.readAndTransformImage(args[0], new RandomAccessFileImpl(
- args[0], "r"), 0, 0);
+
+ final String fileName = args[0];
+ IImageReader imageReader =
+ ImageReaderFactory.tryGetImageReaderForFile(Constants.BIOFORMATS_RESCALING_LIBRARY,
+ fileName);
+
+ File file = new File(fileName);
+ final BufferedImage image = imageReader.readImage(file, 0);
showImage(image);
}
}
diff --git a/image_readers/sourceTest/resources/images/annapolis.jpg b/image_readers/sourceTest/resources/images/annapolis.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..61bc6775f0f6394f8e684338df416f7d1732d64f
Binary files /dev/null and b/image_readers/sourceTest/resources/images/annapolis.jpg differ
diff --git a/image_readers/sourceTest/resources/images/demo.tif b/image_readers/sourceTest/resources/images/demo.tif
new file mode 100644
index 0000000000000000000000000000000000000000..b8290408d1d313b80c144fa74baab7eb31eacaab
Binary files /dev/null and b/image_readers/sourceTest/resources/images/demo.tif differ