update depending bio-formats version to 6.10.1.

README.md

@@ -13,12 +13,12 @@ mvn package
 
 ### run by jar
 ```shell
-java -jar ./target/dist/lib/bioformats-imageinfo-1.0.0.jar "[path to image file]"
+java -jar ./target/dist/lib/bioformats-imageinfo-1.1.0.jar "[path to image file]"
 ```
 
 ### run by fat jar
 ```shell
-java -jar ./target/bioformats-imageinfo-1.0.0-jar-with-dependencies.jar "[path to image file]"
+java -jar ./target/bioformats-imageinfo-1.1.0-jar-with-dependencies.jar "[path to image file]"
 ```
 
 ### library usage
@@ -26,14 +26,17 @@ java -jar ./target/bioformats-imageinfo-1.0.0-jar-with-dependencies.jar "[path t
 import java.util.LinkedHashMap;
 import java.util.Map;
 import jp.riken.neurodata.tools.BioFormatsImageInfo;
-import jp.riken.neurodata.tools.BioFormatsException;
+import jp.riken.neurodata.tools.BioFormatsImageException;
+import jp.riken.neurodata.tools.BioFormatsImageThumbnail;
 
 String path = "[path to image file]";
 String format = "";
 Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+Map<String, Object> thumbnail = new LinkedHashMap<String, Object>();
 
 try {
   format = BioFormatsImageInfo.readMetadata(path, metadata);
+  BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
 } catch (BioFormatsImageException e) {
   // error occurred
   e.printStackTrace();

pom.xml

@@ -5,13 +5,13 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
   <artifactId>bioformats-imageinfo</artifactId>
-  <version>1.0.0</version>
+  <version>1.1.0</version>
 
   <name>bioformats-imageinfo</name>
   <url>https://neurodata.riken.jp</url>
 
   <properties>
-    <bio-formats.version>6.10.0</bio-formats.version>
+    <bio-formats.version>6.10.1</bio-formats.version>
     <bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
 
     <maven.compiler.source>1.8</maven.compiler.source>

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

@@ -24,250 +24,259 @@ import loci.formats.tools.ImageInfo;
 
 public class BioFormatsImageInfo {
 
-  protected static Map<String, Object> readImages(IFormatReader reader) throws FormatException, IOException {
+    protected static Map<String, Object> readImages(final IFormatReader reader) throws FormatException, IOException {
-    Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
 
-    // read basic metadata
+        // read basic metadata
-    int seriesCount = reader.getSeriesCount();
+        final int seriesCount = reader.getSeriesCount();
-    MetadataStore ms = reader.getMetadataStore();
+        final MetadataStore ms = reader.getMetadataStore();
-    MetadataRetrieve mr = ms instanceof MetadataRetrieve ? (MetadataRetrieve) ms : null;
+        final MetadataRetrieve mr = ms instanceof MetadataRetrieve ? (MetadataRetrieve) ms : null;
-    for (int j = 0; j < seriesCount; j++) {
+        for (int j = 0; j < seriesCount; j++) {
 
-      // read basic metadata for series #j
+            // read basic metadata for series #j
-      reader.setSeries(j);
+            reader.setSeries(j);
-      Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
+            final Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
 
-      int imageCount = reader.getImageCount();
+            final int imageCount = reader.getImageCount();
-      int resolutionCount = reader.getResolutionCount();
+            final int resolutionCount = reader.getResolutionCount();
-      String seriesName = mr == null ? null : mr.getImageName(j);
+            final String seriesName = mr == null ? null : mr.getImageName(j);
-      if (seriesName != null) {
+            if (seriesName != null) {
-        seriesMetadata.put("name", seriesName);
+                seriesMetadata.put("name", seriesName);
-      }
+            }
 
-      // resolutions
+            // resolutions
-      if (resolutionCount > 1) {
+            if (resolutionCount > 1) {
-        Map<String, Object> resolutionsMetadata = new LinkedHashMap<String, Object>();
+                final Map<String, Object> resolutionsMetadata = new LinkedHashMap<String, Object>();
-        for (int i = 0; i < resolutionCount; i++) {
+                for (int i = 0; i < resolutionCount; i++) {
-          reader.setResolution(i);
+                    reader.setResolution(i);
-          resolutionsMetadata.put(String.format("resolution[%d]", i),
+                    resolutionsMetadata.put(String.format("resolution[%d]", i),
-              makeRectangle(reader.getSizeX(), reader.getSizeY()));
+                            makeRectangle(reader.getSizeX(), reader.getSizeY()));
+                }
+                seriesMetadata.put("resolutions", resolutionsMetadata);
+                reader.setResolution(0);
+            }
+
+            seriesMetadata.put("imageCount", imageCount);
+            seriesMetadata.put("RGB", new Object[] { reader.isRGB(), reader.getRGBChannelCount() });
+            seriesMetadata.put("interleaved", reader.isInterleaved());
+
+            // indexed
+            {
+                final List<Object> indexed = new ArrayList<Object>();
+                indexed.add(reader.isIndexed());
+                indexed.add(String.format("%b color", !reader.isFalseColor()));
+                final byte[][] table8 = reader.get8BitLookupTable();
+                if (table8 != null) {
+                    indexed.add(
+                            String.format("8-bit LUT: %d x %s", table8.length,
+                                    table8[0] == null ? "null" : "" + table8[0].length));
+                }
+                final short[][] table16 = reader.get16BitLookupTable();
+                if (table16 != null) {
+                    indexed.add(String.format("16-bit LUT: %d x %s", table16.length,
+                            table16[0] == null ? "null" : "" + table16[0].length));
+                }
+                seriesMetadata.put("indexed", indexed);
+            }
+
+            seriesMetadata.put("sizeX", reader.getSizeX());
+            seriesMetadata.put("sizeY", reader.getSizeY());
+            final int sizeZ = reader.getSizeZ();
+            seriesMetadata.put("sizeZ", makeDimension(sizeZ, sizeZ, reader.getModuloZ()));
+            seriesMetadata.put("sizeC",
+                    makeDimension(reader.getSizeC(), reader.getEffectiveSizeC(), reader.getModuloC()));
+            final int sizeT = reader.getSizeT();
+            seriesMetadata.put("sizeT", makeDimension(sizeT, sizeT, reader.getModuloT()));
+            seriesMetadata.put("tileSize", makeRectangle(reader.getOptimalTileWidth(), reader.getOptimalTileHeight()));
+            seriesMetadata.put("thumbnailSize", makeRectangle(reader.getThumbSizeX(), reader.getThumbSizeY()));
+            seriesMetadata.put("endianness", reader.isLittleEndian() ? "little" : "big");
+            seriesMetadata.put("dimensionOrder",
+                    new String[] { reader.getDimensionOrder(), reader.isOrderCertain() ? "certain" : "uncertain" });
+            seriesMetadata.put("pixelType", FormatTools.getPixelTypeString(reader.getPixelType()));
+            seriesMetadata.put("validBitsPerPixel", reader.getBitsPerPixel());
+            seriesMetadata.put("metadataComplete", reader.isMetadataComplete());
+            seriesMetadata.put("thumbnailSeries", reader.isThumbnailSeries());
+
+            // plane
+            {
+                final int[] indices;
+                if (imageCount > 6) {
+                    int q = imageCount / 2;
+                    indices = new int[] { 0, q - 2, q - 1, q, q + 1, q + 2, imageCount - 1 };
+                } else if (imageCount > 2) {
+                    indices = new int[] { 0, imageCount / 2, imageCount - 1 };
+                } else if (imageCount > 1) {
+                    indices = new int[] { 0, 1 };
+                } else {
+                    indices = new int[] { 0 };
+                }
+                final int[][] zct = new int[indices.length][];
+                final int[] indices2 = new int[indices.length];
+                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>();
+                    planeMetadata.put("Z", zct[i][0]);
+                    planeMetadata.put("C", zct[i][1]);
+                    planeMetadata.put("T", zct[i][2]);
+                    if (indices[i] != indices2[i]) {
+                        planeMetadata.put("[mismatch]", indices2[i]);
+                    }
+                    seriesMetadata.put(String.format("plane[%d]", indices[i]), planeMetadata);
+                }
+            }
+            metadata.put(String.format("series[%d]", j), seriesMetadata);
         }
-        seriesMetadata.put("resolutions", resolutionsMetadata);
-        reader.setResolution(0);
-      }
 
-      seriesMetadata.put("imageCount", imageCount);
+        return metadata;
-      seriesMetadata.put("RGB", new Object[] { reader.isRGB(), reader.getRGBChannelCount() });
+    }
-      seriesMetadata.put("interleaved", reader.isInterleaved());
 
-      // indexed
+    protected static Map<String, Object> readAnnotations(final IFormatReader reader) {
-      {
+        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
-        List<Object> indexed = new ArrayList<Object>();
+        // global metadata
-        indexed.add(reader.isIndexed());
+        final Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata();
-        indexed.add(String.format("%b color", !reader.isFalseColor()));
+        for (String key : MetadataTools.keys(globalMetadata)) {
-        byte[][] table8 = reader.get8BitLookupTable();
+            metadata.put(key, globalMetadata.get(key));
-        if (table8 != null) {
-          indexed.add(
-              String.format("8-bit LUT: %d x %s", table8.length, table8[0] == null ? "null" : "" + table8[0].length));
         }
-        short[][] table16 = reader.get16BitLookupTable();
+        // original metadata
-        if (table16 != null) {
+        final int seriesCount = reader.getSeriesCount();
-          indexed.add(String.format("16-bit LUT: %d x %s", table16.length,
+        for (int j = 0; j < seriesCount; j++) {
-              table16[0] == null ? "null" : "" + table16[0].length));
+            reader.setSeries(j);
+            final Hashtable<String, Object> seriesMagedata = reader.getSeriesMetadata();
+            if (!seriesMagedata.isEmpty()) {
+                final Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
+                final String[] keys = MetadataTools.keys(seriesMagedata);
+                for (int i = 0; i < keys.length; i++) {
+                    seriesMetadata.put(keys[i], seriesMagedata.get(keys[i]));
+                }
+                metadata.put(String.format("series[%d]", j), seriesMetadata);
+            }
         }
-        seriesMetadata.put("indexed", indexed);
-      }
 
-      seriesMetadata.put("sizeX", reader.getSizeX());
+        return metadata;
-      seriesMetadata.put("sizeY", reader.getSizeY());
+    }
-      int sizeZ = reader.getSizeZ();
-      seriesMetadata.put("sizeZ", makeDimension(sizeZ, sizeZ, reader.getModuloZ()));
-      seriesMetadata.put("sizeC", makeDimension(reader.getSizeC(), reader.getEffectiveSizeC(), reader.getModuloC()));
-      int sizeT = reader.getSizeT();
-      seriesMetadata.put("sizeT", makeDimension(sizeT, sizeT, reader.getModuloT()));
-      seriesMetadata.put("tileSize", makeRectangle(reader.getOptimalTileWidth(), reader.getOptimalTileHeight()));
-      seriesMetadata.put("thumbnailSize", makeRectangle(reader.getThumbSizeX(), reader.getThumbSizeY()));
-      seriesMetadata.put("endianness", reader.isLittleEndian() ? "little" : "big");
-      seriesMetadata.put("dimensionOrder",
-          new String[] { reader.getDimensionOrder(), reader.isOrderCertain() ? "certain" : "uncertain" });
-      seriesMetadata.put("pixelType", FormatTools.getPixelTypeString(reader.getPixelType()));
-      seriesMetadata.put("validBitsPerPixel", reader.getBitsPerPixel());
-      seriesMetadata.put("metadataComplete", reader.isMetadataComplete());
-      seriesMetadata.put("thumbnailSeries", reader.isThumbnailSeries());
 
-      // plane
+    protected static Object makeDimension(final int size, final int effSize, final Modulo modulo) {
-      {
+        final int mLength = modulo.length();
-        int[] indices;
+        if (size == effSize && mLength == 1) {
-        if (imageCount > 6) {
+            return size;
-          int q = imageCount / 2;
-          indices = new int[] { 0, q - 2, q - 1, q, q + 1, q + 2, imageCount - 1 };
-        } else if (imageCount > 2) {
-          indices = new int[] { 0, imageCount / 2, imageCount - 1 };
-        } else if (imageCount > 1) {
-          indices = new int[] { 0, 1 };
-        } else {
-          indices = new int[] { 0 };
         }
-        int[][] zct = new int[indices.length][];
+        final List<Object> ret = new ArrayList<Object>();
-        int[] indices2 = new int[indices.length];
+        ret.add(size);
-        for (int i = 0; i < indices.length; i++) {
+        if (size != effSize) {
-          zct[i] = reader.getZCTCoords(indices[i]);
+            ret.add(String.format("(effectively %d)", effSize));
-          indices2[i] = reader.getIndex(zct[i][0], zct[i][1], zct[i][2]);
-          Map<String, Object> planeMetadata = new LinkedHashMap<String, Object>();
-          planeMetadata.put("Z", zct[i][0]);
-          planeMetadata.put("C", zct[i][1]);
-          planeMetadata.put("T", zct[i][2]);
-          if (indices[i] != indices2[i]) {
-            planeMetadata.put("[mismatch]", indices2[i]);
-          }
-          seriesMetadata.put(String.format("plane[%d]", indices[i]), planeMetadata);
         }
-      }
+        if (mLength != 1) {
-      metadata.put(String.format("series[%d]", j), seriesMetadata);
+            ret.add(String.format("(%d %s x %d %s)", size / mLength, modulo.parentType, mLength, modulo.type));
-    }
-
-    return metadata;
-  }
-
-  protected static Map<String, Object> readAnnotations(IFormatReader reader) {
-    Map<String, Object> metadata = new LinkedHashMap<String, Object>();
-    // global metadata
-    Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata();
-    for (String key : MetadataTools.keys(globalMetadata)) {
-      metadata.put(key, globalMetadata.get(key));
-    }
-    // original metadata
-    int seriesCount = reader.getSeriesCount();
-    for (int j = 0; j < seriesCount; j++) {
-      reader.setSeries(j);
-      Hashtable<String, Object> seriesMagedata = reader.getSeriesMetadata();
-      if (!seriesMagedata.isEmpty()) {
-        Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
-        String[] keys = MetadataTools.keys(seriesMagedata);
-        for (int i = 0; i < keys.length; i++) {
-          seriesMetadata.put(keys[i], seriesMagedata.get(keys[i]));
         }
-        metadata.put(String.format("series[%d]", j), seriesMetadata);
+
-      }
+        return ret;
     }
 
-    return metadata;
+    protected static Map<String, Object> makeRectangle(final int width, final int height) {
-  }
+        final Map<String, Object> ret = new LinkedHashMap<String, Object>();
+        ret.put("width", width);
+        ret.put("height", height);
 
-  protected static Object makeDimension(int size, int effSize, Modulo modulo) {
+        return ret;
-    int mLength = modulo.length();
-    if (size == effSize && mLength == 1) {
-      return size;
-    }
-    List<Object> ret = new ArrayList<Object>();
-    ret.add(size);
-    if (size != effSize) {
-      ret.add(String.format("(effectively %d)", effSize));
-    }
-    if (mLength != 1) {
-      ret.add(String.format("(%d %s x %d %s)", size / mLength, modulo.parentType, mLength, modulo.type));
     }
 
-    return ret;
+    protected static String getJsonString(final Map<String, Object> map) {
-  }
+        final ObjectMapper mapper = new ObjectMapper();
-
+        String json = null;
-  protected static Map<String, Object> makeRectangle(int width, int height) {
-    Map<String, Object> ret = new LinkedHashMap<String, Object>();
-    ret.put("width", width);
-    ret.put("height", height);
-    return ret;
-  }
-
-  protected static String getJsonString(Map<String, Object> map) {
-    ObjectMapper mapper = new ObjectMapper();
-    String json = null;
-    try {
-      // json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
-      json = mapper.writeValueAsString(map);
-    } catch (Exception e) {
-      // return "null" if conversion error occured
-      json = "null";
-    }
-
-    return json;
-  }
-
-  public static String readMetadata(String path, Map<String, Object> metadata) throws BioFormatsImageException {
-    if (FilenameUtils.getExtension(path).toLowerCase().equals("zip")) {
-      // ignore if file is zip archive
-      throw new BioFormatsImageException("Zip is not supported");
-    }
-    String format = "";
-    ImageInfo info = new ImageInfo();
-    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();
-      info.configureReaderPreInit();
-
-      // initialize reader
-      reader.setId(path);
-      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();
-      Map<String, Object> annotations = readAnnotations(reader);
-      if (!annotations.isEmpty()) {
-        metadata.put("annotations", annotations);
-      }
-    } catch (Exception e) {
-      throw new BioFormatsImageException(e);
-    } finally {
-      if (reader != null) {
         try {
-          reader.close();
+            // json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
-        } catch (IOException e) {
+            json = mapper.writeValueAsString(map);
-          throw new BioFormatsImageException(e);
+        } catch (final Throwable e) {
+            // return "null" if conversion error occured
+            json = "null";
         }
-      }
+
+        return json;
     }
 
-    return format;
+    public static String readMetadata(final String path, final Map<String, Object> metadata)
-  }
+            throws BioFormatsImageException {
+        if (FilenameUtils.getExtension(path).toLowerCase().equals("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 {
+            // info.parseArgs(new String[] { path, "-nopix", "-noflat", "-omexml" });
+            info.parseArgs(new String[] { path, "-nopix", "-noflat" });
+            info.setReader(reader);
+            info.mapLocation();
+            info.configureReaderPreInit();
 
-  // -- Main method --
+            // initialize reader
-  public static void main(String[] args) {
+            reader.setId(path);
-    boolean status = true;
+            format = reader.getFormat();
-    String message = "";
+            info.configureReaderPostInit();
-    String format = "";
+            info.checkWarnings();
-    Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+            // info.printOMEXML();
-    if (args.length != 1) {
+            // info.readCoreMetadata();
-      status = false;
+            metadata.put("images", readImages(reader));
-      message = "filename argument required";
+            info.initPreMinMaxValues();
-    } else {
+            reader.setSeries(0);
-      try {
+            reader.setResolution(0);
-        DebugTools.enableLogging("ERROR");
+            // info.printGlobalMetadata();
-        format = readMetadata(args[0], metadata);
+            // info.printOriginalMetadata();
-      } catch (BioFormatsImageException e) {
+            final Map<String, Object> annotations = readAnnotations(reader);
-        status = false;
+            if (!annotations.isEmpty()) {
-        metadata.clear();
+                metadata.put("annotations", annotations);
-        message = e.getMessage();
+            }
-      }
+        } catch (final Throwable e) {
+            throw new BioFormatsImageException(e);
+        } finally {
+            if (reader != null) {
+                try {
+                    reader.close();
+                } catch (final IOException e) {
+                    throw new BioFormatsImageException(e);
+                }
+            }
+        }
+
+        return format;
     }
 
-    Map<String, Object> results = new LinkedHashMap<String, Object>();
+    // -- Main method --
-    results.put("status", status);
+    public static void main(final String[] args) {
-    results.put("message", message);
+        boolean status = true;
-    results.put("format", format);
+        String message = "";
-    results.put("metadata", metadata.isEmpty() ? null : metadata);
+        String format = "";
-    System.out.println(getJsonString(results));
+        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+        final Map<String, Object> thumbnail = new LinkedHashMap<String, Object>();
+        if (args.length != 1) {
+            status = false;
+            message = "filename argument required";
+        } else {
+            final String path = args[0];
+            try {
+                DebugTools.enableLogging("ERROR");
+                format = readMetadata(path, metadata);
+                BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
+            } catch (BioFormatsImageException e) {
+                status = false;
+                message = e.getMessage();
+                metadata.clear();
+                thumbnail.clear();
+            }
+        }
 
-    if (!status) {
+        final Map<String, Object> results = new LinkedHashMap<String, Object>();
-      System.exit(1);
+        results.put("status", status);
+        results.put("message", message);
+        results.put("format", format);
+        results.put("metadata", metadata.isEmpty() ? null : metadata);
+        results.put("thumbnail", thumbnail.isEmpty() ? null : thumbnail);
+        System.out.println(getJsonString(results));
+
+        if (!status) {
+            System.exit(1);
+        }
     }
-  }
 }

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

@@ -0,0 +1,252 @@
+package jp.riken.neurodata.tools;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.image.BufferedImage;
+import java.io.BufferedOutputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Base64;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.imageio.IIOImage;
+import javax.imageio.ImageIO;
+import javax.imageio.ImageWriteParam;
+import javax.imageio.ImageWriter;
+import javax.imageio.stream.ImageOutputStream;
+
+import loci.common.DebugTools;
+import loci.formats.FormatException;
+import loci.formats.ImageReader;
+import loci.formats.gui.BufferedImageReader;
+
+public class BioFormatsImageThumbnail {
+
+    protected static final float JPEG_QUORITY = 0.85f;
+    protected static final int BACKGROUND_COLOR = 0x000000;
+    protected static final double MAXIMUM_SCALE = 2.0;
+
+    public static BufferedImage resize(final BufferedImage image, final int width, final int height) {
+        final boolean hasAlpha = image.getColorModel().hasAlpha();
+        final int imageWidth = image.getWidth();
+        final int imageHeight = image.getHeight();
+        final double scaleWidth = (double) width / (double) imageWidth;
+        final double scaleHeight = (double) height / (double) imageHeight;
+        double scale = Math.min(scaleWidth, scaleHeight);
+        if (scale > MAXIMUM_SCALE) {
+            // limit scalling size to maximum scale
+            scale = MAXIMUM_SCALE;
+        }
+        int resizeWidth = imageWidth;
+        int resizeHeight = imageHeight;
+        Image resizeImage = image;
+        if (scale != 1.0) {
+            // resize image if dimension is different with requrested dimension.
+            resizeWidth = (int) (scale * (double) imageWidth);
+            resizeHeight = (int) (scale * (double) imageHeight);
+            resizeImage = image.getScaledInstance(resizeWidth, resizeHeight, Image.SCALE_AREA_AVERAGING);
+        }
+        final int type = hasAlpha ? BufferedImage.TYPE_INT_ARGB : BufferedImage.TYPE_INT_RGB;
+        final BufferedImage ret = new BufferedImage(width, height, type);
+        final Graphics2D g = ret.createGraphics();
+        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);
+        g.dispose();
+
+        return ret;
+    }
+
+    protected static BufferedImage removeAlphaChannel(final BufferedImage image, final int matColor) {
+        if (!image.getColorModel().hasAlpha()) {
+            return image;
+        }
+        final BufferedImage ret = new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_INT_RGB);
+        final Graphics2D g = ret.createGraphics();
+        g.setColor(new Color(matColor, false));
+        g.fillRect(0, 0, image.getWidth(), image.getHeight());
+        g.drawImage(image, 0, 0, null);
+        g.dispose();
+
+        return ret;
+    }
+
+    protected static byte[] getJpegByteArray(final BufferedImage image, final float quality, final int matColor)
+            throws BioFormatsImageException {
+        byte[] ret = null;
+        try (final ByteArrayOutputStream baos = new ByteArrayOutputStream();
+                final ImageOutputStream ios = ImageIO.createImageOutputStream(baos);) {
+            final ImageWriter writer = ImageIO.getImageWritersByFormatName("jpeg").next();
+            final ImageWriteParam param = writer.getDefaultWriteParam();
+            param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
+            param.setCompressionQuality(quality);
+            writer.setOutput(ios);
+            writer.write(null, new IIOImage(removeAlphaChannel(image, matColor), null, null), param);
+            writer.dispose();
+            ret = baos.toByteArray();
+        } catch (final IOException e) {
+            throw new BioFormatsImageException(e);
+        }
+
+        return ret;
+    }
+
+    protected static byte[] getPngByteArray(final BufferedImage image) throws BioFormatsImageException {
+        byte[] ret = null;
+        try (ByteArrayOutputStream baos = new ByteArrayOutputStream();
+                BufferedOutputStream bos = new BufferedOutputStream(baos);) {
+            image.flush();
+            ImageIO.write(image, "png", bos);
+            bos.flush();
+            bos.close();
+            ret = baos.toByteArray();
+        } catch (final IOException e) {
+            throw new BioFormatsImageException(e);
+        }
+
+        return ret;
+    }
+
+    public static String getDataUri(final BufferedImage image, final String mimeType) throws BioFormatsImageException {
+        byte[] bytes = null;
+        switch (mimeType) {
+            case "image/png":
+                bytes = getPngByteArray(image);
+                break;
+            case "image/jpeg":
+                bytes = getJpegByteArray(image, JPEG_QUORITY, BACKGROUND_COLOR);
+                break;
+            default:
+                throw new BioFormatsImageException("Unsupported image format: " + mimeType);
+        }
+        final String dataUri = "data:" + mimeType + ";base64," + Base64.getEncoder().encodeToString(bytes);
+
+        return dataUri;
+    }
+
+    public static BufferedImage getImageFromBioFormatsFile(final String path) throws BioFormatsImageException {
+        BufferedImage ret = null;
+        final BufferedImageReader reader = new BufferedImageReader(new ImageReader());
+        reader.setFlattenedResolutions(false);
+        reader.setNormalized(true);
+        reader.setOriginalMetadataPopulated(false);
+        reader.setMetadataFiltered(true);
+        try {
+            reader.setId(path);
+        } catch (FormatException | IOException e) {
+            throw new BioFormatsImageException("unsupported file: " + path);
+        }
+        try {
+            int series = 0;
+            final int seriesCount = reader.getSeriesCount();
+            for (int i = 0; i < seriesCount; i++) {
+                reader.setSeries(i);
+                if (reader.isThumbnailSeries()) {
+                    series = i;
+                    break;
+                }
+            }
+            reader.setSeries(series);
+            final int no = 0;
+            // System.out.println("series count: " + seriesCount);
+            // System.out.println("image count: " + reader.getImageCount());
+            // System.out.println("resolution: " + reader.getResolutionCount());
+            // System.out.println("thubmail series: " + series);
+            ret = reader.openThumbImage(no);
+        } catch (final Throwable e) {
+            for (Throwable t = e; t != null; t = t.getCause()) {
+                if (t instanceof OutOfMemoryError) {
+                    throw new BioFormatsImageException("out of memory");
+                }
+            }
+            throw new BioFormatsImageException(e);
+        } finally {
+            try {
+                reader.close();
+            } catch (final IOException e) {
+                throw new BioFormatsImageException(e);
+            }
+        }
+
+        return ret;
+    }
+
+    public static BufferedImage getImageFromFile(final String path) throws BioFormatsImageException {
+        BufferedImage ret = null;
+        final File file = new File(path);
+        try {
+            ret = ImageIO.read(file);
+        } catch (final IOException e) {
+            throw new BioFormatsImageException(e);
+        }
+
+        return ret;
+    }
+
+    public static void saveFile(final String dataUri, final String path) throws BioFormatsImageException {
+        final Pattern pattern = Pattern.compile("^data:(image/[^;]+);(base64|utf8),(.*)$", Pattern.MULTILINE);
+        final Matcher matcher = pattern.matcher(dataUri);
+        if (!matcher.find()) {
+            throw new BioFormatsImageException("Unsupported data URI format");
+        }
+        final byte[] bytes = matcher.group(2) == "utf8" ? matcher.group(3).getBytes()
+                : Base64.getDecoder().decode(matcher.group(3));
+        try (final FileOutputStream fos = new FileOutputStream(path);) {
+            fos.write(bytes);
+        } catch (final IOException e) {
+            throw new BioFormatsImageException(e);
+        }
+    }
+
+    public static boolean readThumbnail(final String path, final Map<String, Object> thumbnail) {
+        boolean ret = true;
+        try {
+            final BufferedImage image = getImageFromBioFormatsFile(path);
+            final int width = image.getWidth();
+            final int height = image.getHeight();
+            final String mimeType = image.getColorModel().hasAlpha() ? "image/png" : "image/jpeg";
+            final String dataUri = getDataUri(image, mimeType);
+            thumbnail.put("width", width);
+            thumbnail.put("height", height);
+            thumbnail.put("mimeType", mimeType);
+            thumbnail.put("url", dataUri);
+        } catch (final BioFormatsImageException e) {
+            // ignore
+            ret = false;
+        }
+
+        return ret;
+    }
+
+    public static void main(final String[] args) throws BioFormatsImageException {
+        if (args.length != 1) {
+            System.out.println("filename argument required");
+            System.exit(1);
+        }
+        final String path = args[0];
+        try {
+            DebugTools.enableLogging("ERROR");
+            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);
+        } catch (final BioFormatsImageException e) {
+            System.out.println(e.getMessage());
+            System.exit(1);
+        }
+    }
+}