update bio-formats version to 6.12.0.

README.md

@@ -13,12 +13,12 @@ mvn package
 
 ### run by jar
 ```shell
-java -jar ./target/dist/lib/bioformats-imageinfo-1.1.1.jar "[path to image file]"
+java -jar ./target/dist/lib/bioformats-imageinfo-1.1.3.jar "[path to image file]"
 ```
 
 ### run by fat jar
 ```shell
-java -jar ./target/bioformats-imageinfo-1.1.1-jar-with-dependencies.jar "[path to image file]"
+java -jar ./target/bioformats-imageinfo-1.1.3-jar-with-dependencies.jar "[path to image file]"
 ```
 
 ### library usage

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>1.1.1</version>
+  <version>1.1.3</version>
 
   <name>bioformats-imageinfo</name>
   <url>https://neurodata.riken.jp</url>
 
   <properties>
-    <bio-formats.version>6.10.1</bio-formats.version>
+    <bio-formats.version>6.12.0</bio-formats.version>
     <bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
 
     <maven.compiler.source>1.8</maven.compiler.source>
@@ -27,14 +25,39 @@
       <artifactId>bio-formats-tools</artifactId>
       <version>${bio-formats.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.slf4j</groupId>
+      <artifactId>slf4j-nop</artifactId>
+      <version>1.7.30</version>
+    </dependency>
   </dependencies>
 
   <build>
     <plugins>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-dependency-plugin</artifactId>
+        <artifactId>maven-enforcer-plugin</artifactId>
         <version>3.3.0</version>
+        <executions>
+          <execution>
+            <id>enforce-maven</id>
+            <goals>
+              <goal>enforce</goal>
+            </goals>
+            <configuration>
+              <rules>
+                <requireMavenVersion>
+                  <version>3.2.5</version>
+                </requireMavenVersion>
+              </rules>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-dependency-plugin</artifactId>
+        <version>3.5.0</version>
         <executions>
           <execution>
             <id>copy-dependencies</id>
@@ -44,59 +67,35 @@
             </goals>
             <configuration>
               <overWriteIfNewer>true</overWriteIfNewer>
-           </configuration>
+            </configuration>
           </execution>
         </executions>
       </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-jar-plugin</artifactId>
-        <version>3.2.2</version>
+        <version>3.3.0</version>
         <configuration>
           <archive>
             <manifest>
               <addClasspath>true</addClasspath>
-	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
+              <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
             </manifest>
           </archive>
         </configuration>
       </plugin>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-assembly-plugin</artifactId>
-	<version>3.4.1</version>
-        <configuration>
-          <descriptorRefs>
-            <descriptorRef>jar-with-dependencies</descriptorRef>
-          </descriptorRefs>
-          <archive>
-            <manifest>
-	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
-            </manifest>
-          </archive>
-        </configuration>
-        <executions>
-          <execution>
-            <id>make-assembly</id>
-            <phase>package</phase>
-            <goals>
-              <goal>single</goal>
-            </goals>
-          </execution>
-        </executions>
-      </plugin>
       <plugin>
         <groupId>org.codehaus.mojo</groupId>
         <artifactId>appassembler-maven-plugin</artifactId>
-        <version>1.10</version>
+        <version>2.1.0</version>
         <configuration>
           <assembleDirectory>${project.build.directory}/dist</assembleDirectory>
-	  <repositoryLayout>flat</repositoryLayout>
-	  <repositoryName>lib</repositoryName>
+          <repositoryLayout>flat</repositoryLayout>
+          <repositoryName>lib</repositoryName>
           <programs>
             <program>
-	      <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
-	      <id>${project.name}</id>
+              <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
+              <id>${project.name}</id>
             </program>
           </programs>
         </configuration>
@@ -109,10 +108,37 @@
           </execution>
         </executions>
       </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <version>3.5.0</version>
+        <configuration>
+          <descriptorRefs>
+            <descriptorRef>jar-with-dependencies</descriptorRef>
+          </descriptorRefs>
+          <archive>
+            <manifest>
+              <mainClass>${bioformats-imageinfo.mainClass}</mainClass>
+            </manifest>
+          </archive>
+          <descriptors>
+            <descriptor>src/main/assembly/assembly.xml</descriptor>
+          </descriptors>
+        </configuration>
+        <executions>
+          <execution>
+            <id>make-assembly</id>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
       <plugin>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-maven</artifactId>
-        <version>7.1.1</version>
+        <version>8.2.1</version>
         <executions>
           <execution>
             <goals>
@@ -128,15 +154,18 @@
     <pluginRepository>
       <id>central</id>
       <name>Central Repository</name>
-      <url>https://repo.maven.apache.org/maven2</url>
+      <!-- <url>https://repo.maven.apache.org/maven2</url> -->
+      <url>https://repo1.maven.org/maven2/</url>
       <layout>default</layout>
     </pluginRepository>
   </pluginRepositories>
+
   <repositories>
     <repository>
       <id>central</id>
       <name>Central Repository</name>
-      <url>https://repo.maven.apache.org/maven2</url>
+      <!-- <url>https://repo.maven.apache.org/maven2</url> -->
+      <url>https://repo1.maven.org/maven2/</url>
     </repository>
     <repository>
       <id>ome</id>

src/main/assembly/assembly.xml

@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+  <id>bin</id>
+  <formats>
+    <format>tar.gz</format>
+    <format>tar.bz2</format>
+    <format>zip</format>
+  </formats>
+  <fileSets>
+    <fileSet>
+      <directory>target/dist/bin</directory>
+      <outputDirectory>bin</outputDirectory>
+      <excludes>
+        <exclude>*.bat</exclude>
+      </excludes>
+      <directoryMode>0755</directoryMode>
+      <fileMode>0755</fileMode>
+    </fileSet>
+    <fileSet>
+      <directory>target/dist/bin</directory>
+      <outputDirectory>bin</outputDirectory>
+      <includes>
+        <include>*.bat</include>
+      </includes>
+      <directoryMode>0755</directoryMode>
+      <fileMode>0644</fileMode>
+    </fileSet>
+  </fileSets>
+  <dependencySets>
+    <dependencySet>
+      <outputDirectory>lib</outputDirectory>
+    </dependencySet>
+  </dependencySets>
+</assembly>

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

@@ -22,6 +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 {
@@ -89,8 +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);
-            param.setCompressionQuality(quality);
+            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();
@@ -108,7 +111,10 @@ public class BioFormatsImageThumbnail {
                 final ImageOutputStream ios = ImageIO.createImageOutputStream(baos);) {
             final ImageWriter writer = ImageIO.getImageWritersByFormatName("png").next();
             final ImageWriteParam param = writer.getDefaultWriteParam();
-            param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
+            if (param.canWriteCompressed()) {
+                param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
+                param.setCompressionQuality(0.0f);
+            }
             writer.setOutput(ios);
             writer.write(null, new IIOImage(image, null, null), param);
             writer.dispose();
@@ -151,6 +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;
@@ -163,19 +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) {
-            for (Throwable t = e; t != null; t = t.getCause()) {
-                if (t instanceof OutOfMemoryError) {
+            final boolean is16bit = reader.getBitsPerPixel() > 8;
+            final boolean isGrayScale = ret.getSampleModel().getNumBands() == 1;
+            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();
@@ -226,7 +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;
         }
@@ -234,22 +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) {
-            System.out.println(e.getMessage());
+        } catch (final Throwable t) {
+            // t.printStackTrace();
+            System.out.println(t.getMessage());
             System.exit(1);
         }
     }