use ImageWriter to export to png image.

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-1.1.1.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-1.1.1-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>1.1.1</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

@@ -68,7 +68,8 @@ public class BioFormatsImageInfo {
                 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));
+                            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) {
@@ -82,7 +83,8 @@ public class BioFormatsImageInfo {
             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()));
+            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()));
@@ -269,8 +271,8 @@ public class BioFormatsImageInfo {
         results.put("status", status);
         results.put("message", message);
         results.put("format", format);
-    results.put("thumbnail", thumbnail.isEmpty() ? null : thumbnail);
         results.put("metadata", metadata.isEmpty() ? null : metadata);
+        results.put("thumbnail", thumbnail.isEmpty() ? null : thumbnail);
         System.out.println(getJsonString(results));
 
         if (!status) {

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

@@ -4,7 +4,6 @@ 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;
@@ -31,7 +30,7 @@ public class BioFormatsImageThumbnail {
     protected static final int BACKGROUND_COLOR = 0x000000;
     protected static final double MAXIMUM_SCALE = 2.0;
 
-    protected static BufferedImage resize(final BufferedImage image, final int width, final int height) {
+    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();
@@ -46,7 +45,7 @@ public class BioFormatsImageThumbnail {
         int resizeHeight = imageHeight;
         Image resizeImage = image;
         if (scale != 1.0) {
-            // resize image if dimension is larger than maximum dimention.
+            // 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);
@@ -105,12 +104,14 @@ public class BioFormatsImageThumbnail {
 
     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();
+        try (final ByteArrayOutputStream baos = new ByteArrayOutputStream();
+                final ImageOutputStream ios = ImageIO.createImageOutputStream(baos);) {
+            final ImageWriter writer = ImageIO.getImageWritersByFormatName("png").next();
+            final ImageWriteParam param = writer.getDefaultWriteParam();
+            param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
+            writer.setOutput(ios);
+            writer.write(null, new IIOImage(image, null, null), param);
+            writer.dispose();
             ret = baos.toByteArray();
         } catch (final IOException e) {
             throw new BioFormatsImageException(e);
@@ -131,6 +132,9 @@ public class BioFormatsImageThumbnail {
             default:
                 throw new BioFormatsImageException("Unsupported image format: " + mimeType);
         }
+        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;
@@ -149,12 +153,21 @@ public class BioFormatsImageThumbnail {
             throw new BioFormatsImageException("unsupported file: " + path);
         }
         try {
-            final int series = 0;
+            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: " + reader.getSeriesCount());
+            // System.out.println("series count: " + seriesCount);
             // System.out.println("image count: " + reader.getImageCount());
             // System.out.println("resolution: " + reader.getResolutionCount());
-            reader.setSeries(series);
+            // System.out.println("thubmail series: " + series);
             ret = reader.openThumbImage(no);
         } catch (final Throwable e) {
             for (Throwable t = e; t != null; t = t.getCause()) {
@@ -233,8 +246,8 @@ public class BioFormatsImageThumbnail {
             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);
+            System.out.println(dataUri);
+            // saveFile(dataUri, "/var/tmp/thumbnail." + format);
         } catch (final BioFormatsImageException e) {
             System.out.println(e.getMessage());
             System.exit(1);