disable logging.

README.md

@@ -13,12 +13,12 @@ mvn package
 
 ### run by jar
 ```shell
-java -jar ./target/dist/lib/bioformats-imageinfo-1.1.0.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-1.1.0-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

pom.xml

@@ -1,11 +1,9 @@
 <?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>1.1.0</version>
+  <version>1.1.2</version>
 
   <name>bioformats-imageinfo</name>
   <url>https://neurodata.riken.jp</url>
@@ -44,7 +42,7 @@
             </goals>
             <configuration>
               <overWriteIfNewer>true</overWriteIfNewer>
-           </configuration>
+            </configuration>
           </execution>
         </executions>
       </plugin>
@@ -56,7 +54,7 @@
           <archive>
             <manifest>
               <addClasspath>true</addClasspath>
-	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
+              <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
             </manifest>
           </archive>
         </configuration>
@@ -64,14 +62,14 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-assembly-plugin</artifactId>
-	<version>3.4.1</version>
+        <version>3.4.1</version>
         <configuration>
           <descriptorRefs>
             <descriptorRef>jar-with-dependencies</descriptorRef>
           </descriptorRefs>
           <archive>
             <manifest>
-	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
+              <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
             </manifest>
           </archive>
         </configuration>
@@ -91,12 +89,12 @@
         <version>1.10</version>
         <configuration>
           <assembleDirectory>${project.build.directory}/dist</assembleDirectory>
-	  <repositoryLayout>flat</repositoryLayout>
+          <repositoryLayout>flat</repositoryLayout>
-	  <repositoryName>lib</repositoryName>
+          <repositoryName>lib</repositoryName>
           <programs>
             <program>
-	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
+              <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
-	      <id>${project.name}</id>
+              <id>${project.name}</id>
             </program>
           </programs>
         </configuration>
@@ -132,6 +130,7 @@
       <layout>default</layout>
     </pluginRepository>
   </pluginRepositories>
+
   <repositories>
     <repository>
       <id>central</id>

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

@@ -256,12 +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();
             }

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 {
@@ -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();
-            param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
+            if (param.canWriteCompressed()) {
-            param.setCompressionQuality(quality);
+                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;
@@ -147,6 +157,8 @@ public class BioFormatsImageThumbnail {
             reader.setId(path);
         } catch (FormatException | IOException e) {
             throw new BioFormatsImageException("unsupported file: " + path);
+        } catch (Throwable t) {
+            throw new BioFormatsImageException(t);
         }
         try {
             int series = 0;
@@ -159,19 +171,28 @@ public class BioFormatsImageThumbnail {
                 }
             }
             reader.setSeries(series);
-            final int no = 0;
+            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());
             // 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();
@@ -222,7 +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;
         }
@@ -230,22 +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);
             // 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);
         }
     }