update bio-formats version to 7.0.0.

.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+    "recommendations": [
+        "vscjava.vscode-java-pack",
+        "esbenp.prettier-vscode",
+        "mosapride.zenkaku",
+        "streetsidesoftware.code-spell-checker"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,17 @@
+{
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+        "source.organizeImports": true
+    },
+    "[jsonc]": {
+        "editor.defaultFormatter": "esbenp.prettier-vscode"
+    },
+    // Extensions - Code Spell Checker
+    "cSpell.ignoreWords": ["endianness", "noflat", "nopix", "omexml"],
+    "cSpell.words": ["bioformats", "imageinfo", "neurodata", "riken"],
+    // Extentions - Prettier
+    "prettier.printWidth": 120,
+    "prettier.singleQuote": true,
+    "prettier.tabWidth": 4,
+    "java.configuration.updateBuildConfiguration": "interactive"
+}

README.md

@@ -1,39 +1,48 @@
 # BioFormatsImageInfo
+
 Metadata extraction tool based on Bio-Formats
 
-### make package
+## make package
+
 ```shell
 mvn package
 ```
 
-### run
+## run
+
 ```shell
 ./target/dist/bin/bioformats-imageinfo "[path to image file]"
 ```
 
 ### 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-1.2.0.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-1.2.0-jar-with-dependencies.jar "[path to image file]"
 ```
 
-### library usage
+## library usage
+
 ```java
 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 +1,17 @@
 <?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"
+<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>1.2.0</version>
 
   <name>bioformats-imageinfo</name>
   <url>https://neurodata.riken.jp</url>
 
   <properties>
-    <bio-formats.version>6.10.0</bio-formats.version>
+    <bio-formats.version>7.0.0</bio-formats.version>
     <bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
 
     <maven.compiler.source>1.8</maven.compiler.source>
@@ -27,14 +27,39 @@
       <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>3.6.0</version>
         <executions>
           <execution>
             <id>copy-dependencies</id>
@@ -44,59 +69,35 @@
             </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 +110,37 @@
           </execution>
         </executions>
       </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <version>3.6.0</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>8.4.0</version>
         <executions>
           <execution>
             <goals>
@@ -128,15 +156,18 @@
     <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 +1,36 @@
+<?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

@@ -142,14 +142,14 @@ public class BioFormatsImageInfo {
         final int seriesCount = reader.getSeriesCount();
         for (int j = 0; j < seriesCount; j++) {
             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);
+            final Hashtable<String, Object> seriesMetadata = reader.getSeriesMetadata();
+            if (!seriesMetadata.isEmpty()) {
+                final Map<String, Object> originalMetadata = new LinkedHashMap<String, Object>();
+                final String[] keys = MetadataTools.keys(seriesMetadata);
                 for (int i = 0; i < keys.length; i++) {
-                    seriesMetadata.put(keys[i], seriesMagedata.get(keys[i]));
+                    originalMetadata.put(keys[i], seriesMetadata.get(keys[i]));
                 }
-                metadata.put(String.format("series[%d]", j), seriesMetadata);
+                metadata.put(String.format("series[%d]", j), originalMetadata);
             }
         }
 
@@ -188,7 +188,7 @@ public class BioFormatsImageInfo {
             // json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
             json = mapper.writeValueAsString(map);
         } catch (final Throwable e) {
-            // return "null" if conversion error occured
+            // return "null" if conversion error occurred
             json = "null";
         }
 
@@ -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;
@@ -23,15 +22,16 @@ 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 {
 
-    protected static final float JPEG_QUORITY = 0.85f;
+    protected static final float JPEG_QUALITY = 0.85f;
     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();
@@ -39,14 +39,14 @@ public class BioFormatsImageThumbnail {
         final double scaleHeight = (double) height / (double) imageHeight;
         double scale = Math.min(scaleWidth, scaleHeight);
         if (scale > MAXIMUM_SCALE) {
-            // limit scalling size to maximum scale
+            // limit scaling 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 larger than maximum dimention.
+            // resize image if dimension is different with requested dimension.
             resizeWidth = (int) (scale * (double) imageWidth);
             resizeHeight = (int) (scale * (double) imageHeight);
             resizeImage = image.getScaledInstance(resizeWidth, resizeHeight, Image.SCALE_AREA_AVERAGING);
@@ -86,16 +86,18 @@ public class BioFormatsImageThumbnail {
     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);) {
+        try (final ByteArrayOutputStream bos = new ByteArrayOutputStream();
+                final ImageOutputStream ios = ImageIO.createImageOutputStream(bos);) {
             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();
-            ret = baos.toByteArray();
+            ret = bos.toByteArray();
         } catch (final IOException e) {
             throw new BioFormatsImageException(e);
         }
@@ -105,13 +107,18 @@ 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();
-            ret = baos.toByteArray();
+        try (final ByteArrayOutputStream bos = new ByteArrayOutputStream();
+                final ImageOutputStream ios = ImageIO.createImageOutputStream(bos);) {
+            final ImageWriter writer = ImageIO.getImageWritersByFormatName("png").next();
+            final ImageWriteParam param = writer.getDefaultWriteParam();
+            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();
+            ret = bos.toByteArray();
         } catch (final IOException e) {
             throw new BioFormatsImageException(e);
         }
@@ -126,11 +133,14 @@ public class BioFormatsImageThumbnail {
                 bytes = getPngByteArray(image);
                 break;
             case "image/jpeg":
-                bytes = getJpegByteArray(image, JPEG_QUORITY, BACKGROUND_COLOR);
+                bytes = getJpegByteArray(image, JPEG_QUALITY, BACKGROUND_COLOR);
                 break;
             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);
+            // System.out.println("thumbnail 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 scaling 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) {
-            System.out.println(e.getMessage());
+            System.out.println(dataUri);
+            // saveFile(dataUri, "/var/tmp/thumbnail." + format);
+        } catch (final Throwable t) {
+            // t.printStackTrace();
+            System.out.println(t.getMessage());
             System.exit(1);
         }
     }