update README.md to reflect new features, usage instructions, and supported formats

.vscode/settings.json

@@ -8,7 +8,7 @@
     },
     // Extensions - Code Spell Checker
     "cSpell.ignoreWords": ["endianness", "noflat", "nopix", "omexml"],
-    "cSpell.words": ["bioformats", "imageinfo", "neurodata", "riken"],
+    "cSpell.words": ["appassembler", "bioformats", "codehaus", "imageinfo", "neurodata", "riken", "unidata"],
     // Extentions - Prettier
     "prettier.printWidth": 120,
     "prettier.singleQuote": true,

README.md

@@ -1,32 +1,96 @@
 # BioFormatsImageInfo
 
-Metadata extraction tool based on Bio-Formats
+[![Maven](https://img.shields.io/badge/Java-1.8+-blue.svg)](https://www.oracle.com/java/)
+[![Bio-Formats](https://img.shields.io/badge/Bio--Formats-8.3.0-green.svg)](https://www.openmicroscopy.org/bio-formats/)
 
-## make package
+BioFormatsImageInfo is a metadata extraction and thumbnail generation tool for biomedical images, based on the [Bio-Formats](https://www.openmicroscopy.org/bio-formats/) library. It supports over 150 image formats and can be used both as a command-line tool and as a Java library.
+
+## Features
+
+-   **Wide Format Support**: Leverages Bio-Formats' extensive format support
+-   **Metadata Extraction**: Outputs detailed image information in JSON format
+-   **Thumbnail Generation**: Creates high-quality thumbnail images
+-   **Command-Line Ready**: Suitable for batch processing and scripting
+-   **Library Integration**: Can be embedded into Java applications
+
+## Requirements
+
+-   Java 1.8 or higher
+-   Maven 3.0 or higher (for building)
+
+## Installation & Build
+
+Clone and build the project:
 
 ```shell
+git clone [repository-url]
+cd bioformats-imageinfo
 mvn package
 ```
 
-## run
+After the build completes, the following files will be generated:
+
+-   `target/dist/` - Executable distribution
+-   `target/bioformats-imageinfo-1.2.6.jar` - Standard JAR file
+-   `target/bioformats-imageinfo-1.2.6-jar-with-dependencies.jar` - Fat JAR with dependencies
+
+## Usage
+
+### Command Line Execution
+
+#### Using Executable Script (Recommended)
 
 ```shell
-./target/dist/bin/bioformats-imageinfo "[path to image file]"
+./target/dist/bin/bioformats-imageinfo [OPTION] [path to image file]
 ```
 
-### run by jar
+#### Running from JAR File
 
 ```shell
-java -jar ./target/dist/lib/bioformats-imageinfo-1.2.2.jar "[path to image file]"
+java -jar ./target/dist/lib/bioformats-imageinfo-1.2.6.jar [OPTION] [path to image file]
 ```
 
-### run by fat jar
+#### Running from Fat JAR
 
 ```shell
-java -jar ./target/bioformats-imageinfo-1.2.2-jar-with-dependencies.jar "[path to image file]"
+java -jar ./target/bioformats-imageinfo-1.2.6-jar-with-dependencies.jar [OPTION] [path to image file]
 ```
 
-## library usage
+### Options
+
+| Option | Description                          |
+| ------ | ------------------------------------ |
+| `-M`   | Output metadata in JSON format       |
+| `-T`   | Generate and output thumbnail images |
+
+### Usage Examples
+
+```shell
+# Extract metadata
+./target/dist/bin/bioformats-imageinfo -M sample.tif
+
+# Generate thumbnail
+./target/dist/bin/bioformats-imageinfo -T sample.tif
+
+# Output both metadata and thumbnail
+./target/dist/bin/bioformats-imageinfo -M -T sample.tif
+```
+
+## Library Usage
+
+Example of using as a library in Java applications:
+
+### Adding Dependencies
+
+```xml
+<dependency>
+    <groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
+    <artifactId>bioformats-imageinfo</artifactId>
+    <version>1.2.6</version>
+</dependency>
+```
+
+### Sample Code
 
 ```java
 import java.util.LinkedHashMap;
@@ -35,16 +99,89 @@ import jp.riken.neurodata.tools.BioFormatsImageInfo;
 import jp.riken.neurodata.tools.BioFormatsImageException;
 import jp.riken.neurodata.tools.BioFormatsImageThumbnail;
 
-String path = "[path to image file]";
+// Path to image file
+String path = "path/to/your/image.tif";
 String format = "";
-Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+Map<String, Object> metadata = new LinkedHashMap<>();
-Map<String, Object> thumbnail = new LinkedHashMap<String, Object>();
+Map<String, Object> thumbnail = new LinkedHashMap<>();
 
 try {
-  format = BioFormatsImageInfo.readMetadata(path, metadata);
+    // Read metadata
-  BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
+    format = BioFormatsImageInfo.readMetadata(path, metadata);
+
+    // Generate thumbnail
+    BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
+
+    // Use results
+    System.out.println("Image format: " + format);
+    System.out.println("Metadata: " + metadata);
+    System.out.println("Thumbnail info: " + thumbnail);
+
 } catch (BioFormatsImageException e) {
-  // error occurred
+    // Error handling
-  e.printStackTrace();
+    System.err.println("Error occurred while processing image: " + e.getMessage());
+    e.printStackTrace();
 }
 ```
+
+## Supported Image Formats
+
+As this tool uses the Bio-Formats library, it supports a wide variety of biomedical image formats including:
+
+-   **Microscopy Images**: LSM, CZI, ND2, OIB, OIF, LIF, etc.
+-   **Common Images**: TIFF, JPEG, PNG, BMP, etc.
+-   **Medical Images**: DICOM
+-   **Others**: Over 150 formats
+
+For detailed format support information, please refer to the [Bio-Formats official website](https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html).
+
+## Output Formats
+
+### Metadata Output
+
+-   Structured metadata in JSON format
+-   Image size, pixel information, acquisition conditions, etc.
+-   Detailed information for each series
+
+### Thumbnail Output
+
+-   Thumbnail images in JPEG format
+-   Base64 encoding support for embedding
+-   Adjustable quality (default: 85%)
+
+## License
+
+Please refer to the `LICENSE.txt` file for the license of this project.
+
+## Development & Contribution
+
+Developed by the Neuroinformatics Unit, RIKEN Center for Brain Science. Contributions are welcome via pull requests or issues on the repository.
+
+-   **Developer**: Neuroinformatics Unit, RIKEN Center for Brain Science
+-   **Project URL**: https://neurodata.riken.jp
+
+## Troubleshooting
+
+### Common Issues
+
+1. **Out of Memory Error**
+
+    ```shell
+    java -Xmx4g -jar bioformats-imageinfo-1.2.6-jar-with-dependencies.jar -M image.tif
+    ```
+
+2. **Processing Large Files**
+
+    - Disable Bio-Formats debug mode to improve processing speed
+    - Adjust JVM heap size as needed
+
+3. **Format Support**
+    - For unsupported formats, check the latest Bio-Formats version for support status
+
+### Log Output Configuration
+
+When detailed logs are needed:
+
+```shell
+java -Dloci.common.DebugTools.enableLogging=true -jar bioformats-imageinfo-1.2.6-jar-with-dependencies.jar -M image.tif
+```

pom.xml

@@ -5,17 +5,18 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
   <artifactId>bioformats-imageinfo</artifactId>
-  <version>1.2.2</version>
+  <version>1.2.6</version>
 
   <name>bioformats-imageinfo</name>
   <url>https://neurodata.riken.jp</url>
 
   <properties>
-    <bio-formats.version>7.1.0</bio-formats.version>
+    <bio-formats.version>8.3.0</bio-formats.version>
     <bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
 
-    <maven.compiler.source>1.8</maven.compiler.source>
+    <java.version>1.8</java.version>
-    <maven.compiler.target>1.8</maven.compiler.target>
+    <maven.compiler.source>${java.version}</maven.compiler.source>
+    <maven.compiler.target>${java.version}</maven.compiler.target>
 
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
@@ -39,7 +40,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-enforcer-plugin</artifactId>
-        <version>3.4.1</version>
+        <version>3.6.2</version>
         <executions>
           <execution>
             <id>enforce-maven</id>
@@ -49,7 +50,7 @@
             <configuration>
               <rules>
                 <requireMavenVersion>
-                  <version>3.2.5</version>
+                  <version>3.6.3</version>
                 </requireMavenVersion>
               </rules>
             </configuration>
@@ -59,7 +60,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-dependency-plugin</artifactId>
-        <version>3.6.1</version>
+        <version>3.9.0</version>
         <executions>
           <execution>
             <id>copy-dependencies</id>
@@ -76,7 +77,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-jar-plugin</artifactId>
-        <version>3.3.0</version>
+        <version>3.4.2</version>
         <configuration>
           <archive>
             <manifest>
@@ -113,7 +114,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-assembly-plugin</artifactId>
-        <version>3.6.0</version>
+        <version>3.7.1</version>
         <configuration>
           <descriptorRefs>
             <descriptorRef>jar-with-dependencies</descriptorRef>
@@ -140,7 +141,7 @@
       <plugin>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-maven</artifactId>
-        <version>9.0.9</version>
+        <version>12.1.8</version>
         <executions>
           <execution>
             <goals>
@@ -156,7 +157,6 @@
     <pluginRepository>
       <id>central</id>
       <name>Central Repository</name>
-      <!-- <url>https://repo.maven.apache.org/maven2</url> -->
       <url>https://repo1.maven.org/maven2/</url>
       <layout>default</layout>
     </pluginRepository>
@@ -166,7 +166,6 @@
     <repository>
       <id>central</id>
       <name>Central Repository</name>
-      <!-- <url>https://repo.maven.apache.org/maven2</url> -->
       <url>https://repo1.maven.org/maven2/</url>
     </repository>
     <repository>
@@ -176,7 +175,8 @@
     </repository>
     <repository>
       <id>unidata.releases</id>
-      <url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases</url>
+      <name>Unidata Releases</name>
+      <url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases/</url>
     </repository>
   </repositories>
 

src/main/java/jp/riken/neurodata/tools/BioFormatsImageException.java

@@ -6,7 +6,7 @@ public class BioFormatsImageException extends Exception {
         super(message);
     }
 
-    public BioFormatsImageException(Throwable cause) {
+    public BioFormatsImageException(Exception cause) {
         super(cause.getMessage());
     }
 }

src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java

@@ -2,7 +2,7 @@ package jp.riken.neurodata.tools;
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -16,7 +16,6 @@ import loci.formats.FormatException;
 import loci.formats.FormatTools;
 import loci.formats.IFormatReader;
 import loci.formats.ImageReader;
-import loci.formats.MetadataTools;
 import loci.formats.Modulo;
 import loci.formats.meta.MetadataRetrieve;
 import loci.formats.meta.MetadataStore;
@@ -25,7 +24,7 @@ import loci.formats.tools.ImageInfo;
 public class BioFormatsImageInfo {
 
     protected static Map<String, Object> readImages(final IFormatReader reader) throws FormatException, IOException {
-        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+        final Map<String, Object> metadata = new LinkedHashMap<>();
 
         // read basic metadata
         final int seriesCount = reader.getSeriesCount();
@@ -35,7 +34,7 @@ public class BioFormatsImageInfo {
 
             // read basic metadata for series #j
             reader.setSeries(j);
-            final Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
+            final Map<String, Object> seriesMetadata = new LinkedHashMap<>();
 
             final int imageCount = reader.getImageCount();
             final int resolutionCount = reader.getResolutionCount();
@@ -46,7 +45,7 @@ public class BioFormatsImageInfo {
 
             // resolutions
             if (resolutionCount > 1) {
-                final Map<String, Object> resolutionsMetadata = new LinkedHashMap<String, Object>();
+                final Map<String, Object> resolutionsMetadata = new LinkedHashMap<>();
                 for (int i = 0; i < resolutionCount; i++) {
                     reader.setResolution(i);
                     resolutionsMetadata.put(String.format("resolution[%d]", i),
@@ -62,7 +61,7 @@ public class BioFormatsImageInfo {
 
             // indexed
             {
-                final List<Object> indexed = new ArrayList<Object>();
+                final List<Object> indexed = new ArrayList<>();
                 indexed.add(reader.isIndexed());
                 indexed.add(String.format("%b color", !reader.isFalseColor()));
                 final byte[][] table8 = reader.get8BitLookupTable();
@@ -115,7 +114,7 @@ public class BioFormatsImageInfo {
                 for (int i = 0; i < indices.length; i++) {
                     zct[i] = reader.getZCTCoords(indices[i]);
                     indices2[i] = reader.getIndex(zct[i][0], zct[i][1], zct[i][2]);
-                    final Map<String, Object> planeMetadata = new LinkedHashMap<String, Object>();
+                    final Map<String, Object> planeMetadata = new LinkedHashMap<>();
                     planeMetadata.put("Z", zct[i][0]);
                     planeMetadata.put("C", zct[i][1]);
                     planeMetadata.put("T", zct[i][2]);
@@ -132,22 +131,21 @@ public class BioFormatsImageInfo {
     }
 
     protected static Map<String, Object> readAnnotations(final IFormatReader reader) {
-        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+        final Map<String, Object> metadata = new LinkedHashMap<>();
         // global metadata
-        final Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata();
+        final HashMap<String, Object> globalMetadata = new HashMap<>(reader.getGlobalMetadata());
-        for (String key : MetadataTools.keys(globalMetadata)) {
+        for (Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
-            metadata.put(key, globalMetadata.get(key));
+            metadata.put(entry.getKey(), entry.getValue());
         }
         // original metadata
         final int seriesCount = reader.getSeriesCount();
         for (int j = 0; j < seriesCount; j++) {
             reader.setSeries(j);
-            final Hashtable<String, Object> seriesMetadata = reader.getSeriesMetadata();
+            final HashMap<String, Object> seriesMetadata = new HashMap<>(reader.getSeriesMetadata());
             if (!seriesMetadata.isEmpty()) {
-                final Map<String, Object> originalMetadata = new LinkedHashMap<String, Object>();
+                final Map<String, Object> originalMetadata = new LinkedHashMap<>();
-                final String[] keys = MetadataTools.keys(seriesMetadata);
+                for (Map.Entry<String, Object> entry : seriesMetadata.entrySet()) {
-                for (int i = 0; i < keys.length; i++) {
+                    originalMetadata.put(entry.getKey(), entry.getValue());
-                    originalMetadata.put(keys[i], seriesMetadata.get(keys[i]));
                 }
                 metadata.put(String.format("series[%d]", j), originalMetadata);
             }
@@ -161,7 +159,7 @@ public class BioFormatsImageInfo {
         if (size == effSize && mLength == 1) {
             return size;
         }
-        final List<Object> ret = new ArrayList<Object>();
+        final List<Object> ret = new ArrayList<>();
         ret.add(size);
         if (size != effSize) {
             ret.add(String.format("(effectively %d)", effSize));
@@ -174,7 +172,7 @@ public class BioFormatsImageInfo {
     }
 
     protected static Map<String, Object> makeRectangle(final int width, final int height) {
-        final Map<String, Object> ret = new LinkedHashMap<String, Object>();
+        final Map<String, Object> ret = new LinkedHashMap<>();
         ret.put("width", width);
         ret.put("height", height);
 
@@ -185,9 +183,8 @@ public class BioFormatsImageInfo {
         final ObjectMapper mapper = new ObjectMapper();
         String json = null;
         try {
-            // json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
             json = mapper.writeValueAsString(map);
-        } catch (final Throwable e) {
+        } catch (final Exception e) {
             // return "null" if conversion error occurred
             json = "null";
         }
@@ -197,15 +194,13 @@ public class BioFormatsImageInfo {
 
     public static String readMetadata(final String path, final Map<String, Object> metadata)
             throws BioFormatsImageException {
-        if (FilenameUtils.getExtension(path).toLowerCase().equals("zip")) {
+        if (FilenameUtils.getExtension(path).equalsIgnoreCase("zip")) {
             // ignore if file is zip archive
             throw new BioFormatsImageException("Zip is not supported");
         }
         String format = "";
         final ImageInfo info = new ImageInfo();
-        final IFormatReader reader = new ImageReader();
+        try (final IFormatReader reader = new ImageReader()) {
-        try {
-            // info.parseArgs(new String[] { path, "-nopix", "-noflat", "-omexml" });
             info.parseArgs(new String[] { path, "-nopix", "-noflat" });
             info.setReader(reader);
             info.mapLocation();
@@ -216,28 +211,17 @@ public class BioFormatsImageInfo {
             format = reader.getFormat();
             info.configureReaderPostInit();
             info.checkWarnings();
-            // info.printOMEXML();
-            // info.readCoreMetadata();
             metadata.put("images", readImages(reader));
             info.initPreMinMaxValues();
             reader.setSeries(0);
             reader.setResolution(0);
-            // info.printGlobalMetadata();
+
-            // info.printOriginalMetadata();
             final Map<String, Object> annotations = readAnnotations(reader);
             if (!annotations.isEmpty()) {
                 metadata.put("annotations", annotations);
             }
-        } catch (final Throwable e) {
+        } catch (final Exception e) {
             throw new BioFormatsImageException(e);
-        } finally {
-            if (reader != null) {
-                try {
-                    reader.close();
-                } catch (final IOException e) {
-                    throw new BioFormatsImageException(e);
-                }
-            }
         }
 
         return format;
@@ -248,26 +232,43 @@ public class BioFormatsImageInfo {
         boolean status = true;
         String message = "";
         String format = "";
-        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+        boolean metadataON = true;
-        final Map<String, Object> thumbnail = new LinkedHashMap<String, Object>();
+        boolean thumbnailON = true;
-        if (args.length != 1) {
+        String path = "";
-            status = false;
+        final Map<String, Object> metadata = new LinkedHashMap<>();
-            message = "filename argument required";
+        final Map<String, Object> thumbnail = new LinkedHashMap<>();
+        if (args.length == 1) {
+            path = args[0];
+        } else if (args.length == 2) {
+            if (args[0].startsWith("-")) {
+                metadataON = args[0].toUpperCase().contains("M");
+                thumbnailON = args[0].toUpperCase().contains("T");
+            }
+            path = args[1];
         } else {
-            final String path = args[0];
+            status = false;
+            message = "invalid parameters";
+            message += "\nUsage ./target/dist/bin/bioformats-imageinfo \"[OPTION]\" \"[path to image file]\"";
+            message += "\n-M output metadata\n-T output thumbnail";
+        }
+        if (status) {
             try {
                 DebugTools.enableLogging("OFF");
-                format = readMetadata(path, metadata);
+                if (metadataON) {
-                BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
+                    format = readMetadata(path, metadata);
-            } catch (Throwable t) {
+                }
+                if (thumbnailON) {
+                    BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
+                }
+            } catch (final Exception e) {
                 status = false;
-                message = t.getMessage();
+                message = e.getMessage();
                 metadata.clear();
                 thumbnail.clear();
             }
         }
 
-        final Map<String, Object> results = new LinkedHashMap<String, Object>();
+        final Map<String, Object> results = new LinkedHashMap<>();
         results.put("status", status);
         results.put("message", message);
         results.put("format", format);

src/main/java/jp/riken/neurodata/tools/BioFormatsImageThumbnail.java

@@ -47,8 +47,8 @@ public class BioFormatsImageThumbnail {
         Image resizeImage = image;
         if (scale != 1.0) {
             // resize image if dimension is different with requested dimension.
-            resizeWidth = (int) (scale * (double) imageWidth);
+            resizeWidth = (int) (scale * imageWidth);
-            resizeHeight = (int) (scale * (double) imageHeight);
+            resizeHeight = (int) (scale * imageHeight);
             resizeImage = image.getScaledInstance(resizeWidth, resizeHeight, Image.SCALE_AREA_AVERAGING);
         }
         final int type = hasAlpha ? BufferedImage.TYPE_INT_ARGB : BufferedImage.TYPE_INT_RGB;
@@ -57,10 +57,6 @@ public class BioFormatsImageThumbnail {
         final Color c = new Color(image.getRGB(0, 0), hasAlpha);
         final int offsetX = (width - resizeWidth) / 2;
         final int offsetY = (height - resizeHeight) / 2;
-        // System.out.println("original:" + imageWidth + "," + imageHeight);
-        // System.out.println("resize:" + resizeWidth + "," + resizeHeight);
-        // System.out.println("target:" + width + "," + height);
-        // System.out.println("offset:" + offsetX + "," + offsetY);
         g.setColor(c);
         g.fillRect(0, 0, width, height);
         g.drawImage(resizeImage, offsetX, offsetY, resizeWidth, resizeHeight, null);
@@ -141,26 +137,18 @@ public class BioFormatsImageThumbnail {
         if (bytes.length == 0) {
             throw new BioFormatsImageException("Failed to convert to " + mimeType + " format");
         }
-        final String dataUri = "data:" + mimeType + ";base64," + Base64.getEncoder().encodeToString(bytes);
 
-        return dataUri;
+        return "data:" + mimeType + ";base64," + Base64.getEncoder().encodeToString(bytes);
     }
 
     public static BufferedImage getImageFromBioFormatsFile(final String path) throws BioFormatsImageException {
         BufferedImage ret = null;
-        final BufferedImageReader reader = new BufferedImageReader(new ImageReader());
+        try (final BufferedImageReader reader = new BufferedImageReader(new ImageReader())) {
-        reader.setFlattenedResolutions(false);
+            reader.setFlattenedResolutions(false);
-        reader.setNormalized(true);
+            reader.setNormalized(true);
-        reader.setOriginalMetadataPopulated(false);
+            reader.setOriginalMetadataPopulated(false);
-        reader.setMetadataFiltered(true);
+            reader.setMetadataFiltered(true);
-        try {
             reader.setId(path);
-        } catch (FormatException | IOException e) {
-            throw new BioFormatsImageException("unsupported file: " + path);
-        } catch (Throwable t) {
-            throw new BioFormatsImageException(t);
-        }
-        try {
             int series = 0;
             final int seriesCount = reader.getSeriesCount();
             for (int i = 0; i < seriesCount; i++) {
@@ -175,10 +163,7 @@ public class BioFormatsImageThumbnail {
             final int t = reader.getSizeT() / 2; // middle of frames
             final int c = 0; // first channel
             final int no = reader.getIndex(z, c, t);
-            // System.out.println("series count: " + seriesCount);
+
-            // System.out.println("image count: " + reader.getImageCount());
-            // System.out.println("resolution: " + reader.getResolutionCount());
-            // System.out.println("thumbnail series: " + series);
             ret = reader.openThumbImage(no);
             final boolean is16bit = reader.getBitsPerPixel() > 8;
             final boolean isGrayScale = ret.getSampleModel().getNumBands() == 1;
@@ -186,19 +171,12 @@ public class BioFormatsImageThumbnail {
                 // perform auto scaling if 16bit or gray scale thumbnail image.
                 ret = AWTImageTools.autoscale(ret);
             }
-        } catch (final Throwable t) {
+        } catch (final OutOfMemoryError e) {
-            for (Throwable e = t; e != null; e = e.getCause()) {
+            throw new BioFormatsImageException("out of memory");
-                if (e instanceof OutOfMemoryError) {
+        } catch (final FormatException | IOException e) {
-                    throw new BioFormatsImageException("out of memory");
+            throw new BioFormatsImageException("unsupported file: " + path);
-                }
+        } catch (final Exception e) {
-            }
+            throw new BioFormatsImageException(e);
-            throw new BioFormatsImageException(t);
-        } finally {
-            try {
-                reader.close();
-            } catch (final IOException e) {
-                throw new BioFormatsImageException(e);
-            }
         }
 
         return ret;
@@ -222,7 +200,7 @@ public class BioFormatsImageThumbnail {
         if (!matcher.find()) {
             throw new BioFormatsImageException("Unsupported data URI format");
         }
-        final byte[] bytes = matcher.group(2) == "utf8" ? matcher.group(3).getBytes()
+        final byte[] bytes = "utf8".equals(matcher.group(2)) ? matcher.group(3).getBytes()
                 : Base64.getDecoder().decode(matcher.group(3));
         try (final FileOutputStream fos = new FileOutputStream(path);) {
             fos.write(bytes);
@@ -243,7 +221,7 @@ public class BioFormatsImageThumbnail {
             thumbnail.put("height", height);
             thumbnail.put("mimeType", mimeType);
             thumbnail.put("url", dataUri);
-        } catch (final Throwable t) {
+        } catch (final Exception e) {
             // ignore
             ret = false;
         }
@@ -261,13 +239,12 @@ public class BioFormatsImageThumbnail {
             DebugTools.enableLogging("OFF");
             BufferedImage image = getImageFromBioFormatsFile(path);
             final String format = image.getColorModel().hasAlpha() ? "png" : "jpeg";
-            // image = resize(image, 160, 160);
             final String dataUri = getDataUri(image, "image/" + format);
             System.out.println(dataUri);
-            // saveFile(dataUri, "/var/tmp/thumbnail." + format);
+            saveFile(dataUri, "/var/tmp/thumbnail." + format);
-        } catch (final Throwable t) {
+        } catch (final Exception e) {
-            // t.printStackTrace();
+            e.printStackTrace();
-            System.out.println(t.getMessage());
+            System.out.println(e.getMessage());
             System.exit(1);
         }
     }