disable logging.

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-1.1.2.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-1.1.2-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

@@ -1,17 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
   <artifactId>bioformats-imageinfo</artifactId>
-  <version>1.0.0</version>
+  <version>1.1.2</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>
@@ -132,6 +130,7 @@
       <layout>default</layout>
     </pluginRepository>
   </pluginRepositories>
+
   <repositories>
     <repository>
       <id>central</id>

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()));
@@ -254,12 +256,12 @@ public class BioFormatsImageInfo {
         } else {
             final String path = args[0];
             try {
-        DebugTools.enableLogging("ERROR");
+                DebugTools.enableLogging("OFF");
                 format = readMetadata(path, metadata);
                 BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
-      } catch (BioFormatsImageException e) {
+            } catch (Throwable t) {
                 status = false;
-        message = e.getMessage();
+                message = t.getMessage();
                 metadata.clear();
                 thumbnail.clear();
             }
@@ -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;
@@ -23,6 +22,7 @@ import javax.imageio.stream.ImageOutputStream;
 import loci.common.DebugTools;
 import loci.formats.FormatException;
 import loci.formats.ImageReader;
+import loci.formats.gui.AWTImageTools;
 import loci.formats.gui.BufferedImageReader;
 
 public class BioFormatsImageThumbnail {
@@ -31,7 +31,7 @@ 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 +46,7 @@ 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);
@@ -90,8 +90,10 @@ public class BioFormatsImageThumbnail {
                 final ImageOutputStream ios = ImageIO.createImageOutputStream(baos);) {
             final ImageWriter writer = ImageIO.getImageWritersByFormatName("jpeg").next();
             final ImageWriteParam param = writer.getDefaultWriteParam();
+            if (param.canWriteCompressed()) {
                 param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
                 param.setCompressionQuality(quality);
+            }
             writer.setOutput(ios);
             writer.write(null, new IIOImage(removeAlphaChannel(image, matColor), null, null), param);
             writer.dispose();
@@ -105,12 +107,17 @@ public class BioFormatsImageThumbnail {
 
     protected static byte[] getPngByteArray(final BufferedImage image) throws BioFormatsImageException {
         byte[] ret = null;
-        try (ByteArrayOutputStream baos = new ByteArrayOutputStream();
+        try (final ByteArrayOutputStream baos = new ByteArrayOutputStream();
-                BufferedOutputStream bos = new BufferedOutputStream(baos);) {
+                final ImageOutputStream ios = ImageIO.createImageOutputStream(baos);) {
-            image.flush();
+            final ImageWriter writer = ImageIO.getImageWritersByFormatName("png").next();
-            ImageIO.write(image, "png", bos);
+            final ImageWriteParam param = writer.getDefaultWriteParam();
-            bos.flush();
+            if (param.canWriteCompressed()) {
-            bos.close();
+                param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
+                param.setCompressionQuality(0.0f);
+            }
+            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 +138,9 @@ 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;
@@ -147,22 +157,42 @@ public class BioFormatsImageThumbnail {
             reader.setId(path);
         } catch (FormatException | IOException e) {
             throw new BioFormatsImageException("unsupported file: " + path);
+        } catch (Throwable t) {
+            throw new BioFormatsImageException(t);
         }
         try {
-            final int series = 0;
+            int series = 0;
-            final int no = 0;
+            final int seriesCount = reader.getSeriesCount();
-            // System.out.println("series count: " + reader.getSeriesCount());
+            for (int i = 0; i < seriesCount; i++) {
+                reader.setSeries(i);
+                if (reader.isThumbnailSeries()) {
+                    series = i;
+                    break;
+                }
+            }
+            reader.setSeries(series);
+            final int z = reader.getSizeZ() / 2; // middle of slices
+            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());
-            reader.setSeries(series);
+            // System.out.println("thubmail series: " + series);
             ret = reader.openThumbImage(no);
-        } catch (final Throwable e) {
+            final boolean is16bit = reader.getBitsPerPixel() > 8;
-            for (Throwable t = e; t != null; t = t.getCause()) {
+            final boolean isGrayScale = ret.getSampleModel().getNumBands() == 1;
-                if (t instanceof OutOfMemoryError) {
+            if (is16bit || isGrayScale) {
+                // perform auto scalling if 16bit or gray scale thumbnail image.
+                ret = AWTImageTools.autoscale(ret);
+            }
+        } catch (final Throwable t) {
+            for (Throwable e = t; e != null; e = e.getCause()) {
+                if (e instanceof OutOfMemoryError) {
                     throw new BioFormatsImageException("out of memory");
                 }
             }
-            throw new BioFormatsImageException(e);
+            throw new BioFormatsImageException(t);
         } finally {
             try {
                 reader.close();
@@ -213,7 +243,7 @@ public class BioFormatsImageThumbnail {
             thumbnail.put("height", height);
             thumbnail.put("mimeType", mimeType);
             thumbnail.put("url", dataUri);
-        } catch (final BioFormatsImageException e) {
+        } catch (final Throwable t) {
             // ignore
             ret = false;
         }
@@ -221,22 +251,23 @@ public class BioFormatsImageThumbnail {
         return ret;
     }
 
-    public static void main(final String[] args) throws BioFormatsImageException {
+    public static void main(final String[] args) {
         if (args.length != 1) {
             System.out.println("filename argument required");
             System.exit(1);
         }
         final String path = args[0];
         try {
-            DebugTools.enableLogging("ERROR");
+            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);
+            System.out.println(dataUri);
-            saveFile(dataUri, "/var/tmp/thumbnail." + format);
+            // saveFile(dataUri, "/var/tmp/thumbnail." + format);
-        } catch (final BioFormatsImageException e) {
+        } catch (final Throwable t) {
-            System.out.println(e.getMessage());
+            // t.printStackTrace();
+            System.out.println(t.getMessage());
             System.exit(1);
         }
     }