update bio-formats version to 8.2.0.

.vscode/extensions.json

@@ -1,8 +1,9 @@
 {
     "recommendations": [
-        "vscjava.vscode-java-pack",
         "esbenp.prettier-vscode",
         "mosapride.zenkaku",
-        "streetsidesoftware.code-spell-checker"
+        "redhat.fabric8-analytics",
+        "streetsidesoftware.code-spell-checker",
+        "vscjava.vscode-java-pack"
     ]
 }

.vscode/settings.json

@@ -1,17 +1,18 @@
 {
     "editor.formatOnSave": true,
     "editor.codeActionsOnSave": {
-        "source.organizeImports": true
+        "source.organizeImports": "explicit"
     },
     "[jsonc]": {
         "editor.defaultFormatter": "esbenp.prettier-vscode"
     },
     // Extensions - Code Spell Checker
     "cSpell.ignoreWords": ["endianness", "noflat", "nopix", "omexml"],
-    "cSpell.words": ["bioformats", "imageinfo", "neurodata", "riken"],
+    "cSpell.words": ["appassembler", "bioformats", "codehaus", "imageinfo", "neurodata", "riken", "unidata"],
     // Extentions - Prettier
     "prettier.printWidth": 120,
     "prettier.singleQuote": true,
     "prettier.tabWidth": 4,
-    "java.configuration.updateBuildConfiguration": "interactive"
+    "java.configuration.updateBuildConfiguration": "interactive",
+    "java.compile.nullAnalysis.mode": "automatic"
 }

README.md

@@ -2,31 +2,38 @@
 
 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]"
+./target/dist/bin/bioformats-imageinfo "[OPTION]" "[path to image file]"
 ```
 
 ### run by jar
 
 ```shell
-java -jar ./target/dist/lib/bioformats-imageinfo-1.1.4.jar "[path to image file]"
+java -jar ./target/dist/lib/bioformats-imageinfo-1.2.5.jar "[OPTION]" "[path to image file]"
 ```
 
 ### run by fat jar
 
 ```shell
-java -jar ./target/bioformats-imageinfo-1.1.4-jar-with-dependencies.jar "[path to image file]"
+java -jar ./target/bioformats-imageinfo-1.2.5-jar-with-dependencies.jar "[OPTION]" "[path to image file]"
 ```
 
-### library usage
+### OPTION
+
+```shell
+-M output metadata
+-T output thumbnail
+```
+
+## library usage
 
 ```java
 import java.util.LinkedHashMap;

pom.xml

@@ -5,13 +5,13 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
   <artifactId>bioformats-imageinfo</artifactId>
-  <version>1.1.4</version>
+  <version>1.2.5</version>
 
   <name>bioformats-imageinfo</name>
   <url>https://neurodata.riken.jp</url>
 
   <properties>
-    <bio-formats.version>6.14.0</bio-formats.version>
+    <bio-formats.version>8.2.0</bio-formats.version>
     <bioformats-imageinfo.mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</bioformats-imageinfo.mainClass>
 
     <maven.compiler.source>1.8</maven.compiler.source>
@@ -30,7 +30,7 @@
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-nop</artifactId>
-      <version>1.7.30</version>
+      <version>2.0.9</version>
     </dependency>
   </dependencies>
 
@@ -39,7 +39,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-enforcer-plugin</artifactId>
-        <version>3.3.0</version>
+        <version>3.5.0</version>
         <executions>
           <execution>
             <id>enforce-maven</id>
@@ -59,7 +59,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-dependency-plugin</artifactId>
-        <version>3.6.0</version>
+        <version>3.8.1</version>
         <executions>
           <execution>
             <id>copy-dependencies</id>
@@ -76,7 +76,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-jar-plugin</artifactId>
-        <version>3.3.0</version>
+        <version>3.4.2</version>
         <configuration>
           <archive>
             <manifest>
@@ -113,7 +113,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-assembly-plugin</artifactId>
-        <version>3.6.0</version>
+        <version>3.7.1</version>
         <configuration>
           <descriptorRefs>
             <descriptorRef>jar-with-dependencies</descriptorRef>
@@ -140,7 +140,7 @@
       <plugin>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-maven</artifactId>
-        <version>8.3.1</version>
+        <version>12.1.3</version>
         <executions>
           <execution>
             <goals>
@@ -156,7 +156,6 @@
     <pluginRepository>
       <id>central</id>
       <name>Central Repository</name>
-      <!-- <url>https://repo.maven.apache.org/maven2</url> -->
       <url>https://repo1.maven.org/maven2/</url>
       <layout>default</layout>
     </pluginRepository>
@@ -166,7 +165,6 @@
     <repository>
       <id>central</id>
       <name>Central Repository</name>
-      <!-- <url>https://repo.maven.apache.org/maven2</url> -->
       <url>https://repo1.maven.org/maven2/</url>
     </repository>
     <repository>

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

@@ -6,7 +6,7 @@ public class BioFormatsImageException extends Exception {
         super(message);
     }
 
-    public BioFormatsImageException(Throwable cause) {
+    public BioFormatsImageException(Exception cause) {
         super(cause.getMessage());
     }
 }

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

@@ -2,7 +2,7 @@ package jp.riken.neurodata.tools;
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -16,7 +16,6 @@ import loci.formats.FormatException;
 import loci.formats.FormatTools;
 import loci.formats.IFormatReader;
 import loci.formats.ImageReader;
-import loci.formats.MetadataTools;
 import loci.formats.Modulo;
 import loci.formats.meta.MetadataRetrieve;
 import loci.formats.meta.MetadataStore;
@@ -25,7 +24,7 @@ import loci.formats.tools.ImageInfo;
 public class BioFormatsImageInfo {
 
     protected static Map<String, Object> readImages(final IFormatReader reader) throws FormatException, IOException {
-        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+        final Map<String, Object> metadata = new LinkedHashMap<>();
 
         // read basic metadata
         final int seriesCount = reader.getSeriesCount();
@@ -35,7 +34,7 @@ public class BioFormatsImageInfo {
 
             // read basic metadata for series #j
             reader.setSeries(j);
-            final Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
+            final Map<String, Object> seriesMetadata = new LinkedHashMap<>();
 
             final int imageCount = reader.getImageCount();
             final int resolutionCount = reader.getResolutionCount();
@@ -46,7 +45,7 @@ public class BioFormatsImageInfo {
 
             // resolutions
             if (resolutionCount > 1) {
-                final Map<String, Object> resolutionsMetadata = new LinkedHashMap<String, Object>();
+                final Map<String, Object> resolutionsMetadata = new LinkedHashMap<>();
                 for (int i = 0; i < resolutionCount; i++) {
                     reader.setResolution(i);
                     resolutionsMetadata.put(String.format("resolution[%d]", i),
@@ -62,7 +61,7 @@ public class BioFormatsImageInfo {
 
             // indexed
             {
-                final List<Object> indexed = new ArrayList<Object>();
+                final List<Object> indexed = new ArrayList<>();
                 indexed.add(reader.isIndexed());
                 indexed.add(String.format("%b color", !reader.isFalseColor()));
                 final byte[][] table8 = reader.get8BitLookupTable();
@@ -115,7 +114,7 @@ public class BioFormatsImageInfo {
                 for (int i = 0; i < indices.length; i++) {
                     zct[i] = reader.getZCTCoords(indices[i]);
                     indices2[i] = reader.getIndex(zct[i][0], zct[i][1], zct[i][2]);
-                    final Map<String, Object> planeMetadata = new LinkedHashMap<String, Object>();
+                    final Map<String, Object> planeMetadata = new LinkedHashMap<>();
                     planeMetadata.put("Z", zct[i][0]);
                     planeMetadata.put("C", zct[i][1]);
                     planeMetadata.put("T", zct[i][2]);
@@ -132,22 +131,21 @@ public class BioFormatsImageInfo {
     }
 
     protected static Map<String, Object> readAnnotations(final IFormatReader reader) {
-        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
+        final Map<String, Object> metadata = new LinkedHashMap<>();
         // global metadata
-        final Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata();
-        for (String key : MetadataTools.keys(globalMetadata)) {
-            metadata.put(key, globalMetadata.get(key));
+        final HashMap<String, Object> globalMetadata = new HashMap<>(reader.getGlobalMetadata());
+        for (Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
+            metadata.put(entry.getKey(), entry.getValue());
         }
         // original metadata
         final int seriesCount = reader.getSeriesCount();
         for (int j = 0; j < seriesCount; j++) {
             reader.setSeries(j);
-            final Hashtable<String, Object> seriesMetadata = reader.getSeriesMetadata();
+            final HashMap<String, Object> seriesMetadata = new HashMap<>(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++) {
-                    originalMetadata.put(keys[i], seriesMetadata.get(keys[i]));
+                final Map<String, Object> originalMetadata = new LinkedHashMap<>();
+                for (Map.Entry<String, Object> entry : seriesMetadata.entrySet()) {
+                    originalMetadata.put(entry.getKey(), entry.getValue());
                 }
                 metadata.put(String.format("series[%d]", j), originalMetadata);
             }
@@ -161,7 +159,7 @@ public class BioFormatsImageInfo {
         if (size == effSize && mLength == 1) {
             return size;
         }
-        final List<Object> ret = new ArrayList<Object>();
+        final List<Object> ret = new ArrayList<>();
         ret.add(size);
         if (size != effSize) {
             ret.add(String.format("(effectively %d)", effSize));
@@ -174,7 +172,7 @@ public class BioFormatsImageInfo {
     }
 
     protected static Map<String, Object> makeRectangle(final int width, final int height) {
-        final Map<String, Object> ret = new LinkedHashMap<String, Object>();
+        final Map<String, Object> ret = new LinkedHashMap<>();
         ret.put("width", width);
         ret.put("height", height);
 
@@ -185,9 +183,8 @@ public class BioFormatsImageInfo {
         final ObjectMapper mapper = new ObjectMapper();
         String json = null;
         try {
-            // json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
             json = mapper.writeValueAsString(map);
-        } catch (final Throwable e) {
+        } catch (final Exception e) {
             // return "null" if conversion error occurred
             json = "null";
         }
@@ -197,15 +194,13 @@ public class BioFormatsImageInfo {
 
     public static String readMetadata(final String path, final Map<String, Object> metadata)
             throws BioFormatsImageException {
-        if (FilenameUtils.getExtension(path).toLowerCase().equals("zip")) {
+        if (FilenameUtils.getExtension(path).equalsIgnoreCase("zip")) {
             // ignore if file is zip archive
             throw new BioFormatsImageException("Zip is not supported");
         }
         String format = "";
         final ImageInfo info = new ImageInfo();
-        final IFormatReader reader = new ImageReader();
-        try {
-            // info.parseArgs(new String[] { path, "-nopix", "-noflat", "-omexml" });
+        try (final IFormatReader reader = new ImageReader()) {
             info.parseArgs(new String[] { path, "-nopix", "-noflat" });
             info.setReader(reader);
             info.mapLocation();
@@ -216,28 +211,17 @@ public class BioFormatsImageInfo {
             format = reader.getFormat();
             info.configureReaderPostInit();
             info.checkWarnings();
-            // info.printOMEXML();
-            // info.readCoreMetadata();
             metadata.put("images", readImages(reader));
             info.initPreMinMaxValues();
             reader.setSeries(0);
             reader.setResolution(0);
-            // info.printGlobalMetadata();
-            // info.printOriginalMetadata();
+
             final Map<String, Object> annotations = readAnnotations(reader);
             if (!annotations.isEmpty()) {
                 metadata.put("annotations", annotations);
             }
-        } catch (final Throwable e) {
+        } catch (final Exception e) {
             throw new BioFormatsImageException(e);
-        } finally {
-            if (reader != null) {
-                try {
-                    reader.close();
-                } catch (final IOException e) {
-                    throw new BioFormatsImageException(e);
-                }
-            }
         }
 
         return format;
@@ -248,26 +232,43 @@ public class BioFormatsImageInfo {
         boolean status = true;
         String message = "";
         String format = "";
-        final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
-        final Map<String, Object> thumbnail = new LinkedHashMap<String, Object>();
-        if (args.length != 1) {
-            status = false;
-            message = "filename argument required";
+        boolean metadataON = true;
+        boolean thumbnailON = true;
+        String path = "";
+        final Map<String, Object> metadata = new LinkedHashMap<>();
+        final Map<String, Object> thumbnail = new LinkedHashMap<>();
+        if (args.length == 1) {
+            path = args[0];
+        } else if (args.length == 2) {
+            if (args[0].startsWith("-")) {
+                metadataON = args[0].toUpperCase().contains("M");
+                thumbnailON = args[0].toUpperCase().contains("T");
+            }
+            path = args[1];
         } else {
-            final String path = args[0];
+            status = false;
+            message = "invalid parameters";
+            message += "\nUsage ./target/dist/bin/bioformats-imageinfo \"[OPTION]\" \"[path to image file]\"";
+            message += "\n-M output metadata\n-T output thumbnail";
+        }
+        if (status) {
             try {
                 DebugTools.enableLogging("OFF");
+                if (metadataON) {
                     format = readMetadata(path, metadata);
+                }
+                if (thumbnailON) {
                     BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
-            } catch (Throwable t) {
+                }
+            } catch (final Exception e) {
                 status = false;
-                message = t.getMessage();
+                message = e.getMessage();
                 metadata.clear();
                 thumbnail.clear();
             }
         }
 
-        final Map<String, Object> results = new LinkedHashMap<String, Object>();
+        final Map<String, Object> results = new LinkedHashMap<>();
         results.put("status", status);
         results.put("message", message);
         results.put("format", format);

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

@@ -47,8 +47,8 @@ public class BioFormatsImageThumbnail {
         Image resizeImage = image;
         if (scale != 1.0) {
             // resize image if dimension is different with requested dimension.
-            resizeWidth = (int) (scale * (double) imageWidth);
-            resizeHeight = (int) (scale * (double) imageHeight);
+            resizeWidth = (int) (scale * imageWidth);
+            resizeHeight = (int) (scale * imageHeight);
             resizeImage = image.getScaledInstance(resizeWidth, resizeHeight, Image.SCALE_AREA_AVERAGING);
         }
         final int type = hasAlpha ? BufferedImage.TYPE_INT_ARGB : BufferedImage.TYPE_INT_RGB;
@@ -57,10 +57,6 @@ public class BioFormatsImageThumbnail {
         final Color c = new Color(image.getRGB(0, 0), hasAlpha);
         final int offsetX = (width - resizeWidth) / 2;
         final int offsetY = (height - resizeHeight) / 2;
-        // System.out.println("original:" + imageWidth + "," + imageHeight);
-        // System.out.println("resize:" + resizeWidth + "," + resizeHeight);
-        // System.out.println("target:" + width + "," + height);
-        // System.out.println("offset:" + offsetX + "," + offsetY);
         g.setColor(c);
         g.fillRect(0, 0, width, height);
         g.drawImage(resizeImage, offsetX, offsetY, resizeWidth, resizeHeight, null);
@@ -141,26 +137,18 @@ public class BioFormatsImageThumbnail {
         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;
+        return "data:" + mimeType + ";base64," + Base64.getEncoder().encodeToString(bytes);
     }
 
     public static BufferedImage getImageFromBioFormatsFile(final String path) throws BioFormatsImageException {
         BufferedImage ret = null;
-        final BufferedImageReader reader = new BufferedImageReader(new ImageReader());
+        try (final BufferedImageReader reader = new BufferedImageReader(new ImageReader())) {
             reader.setFlattenedResolutions(false);
             reader.setNormalized(true);
             reader.setOriginalMetadataPopulated(false);
             reader.setMetadataFiltered(true);
-        try {
             reader.setId(path);
-        } catch (FormatException | IOException e) {
-            throw new BioFormatsImageException("unsupported file: " + path);
-        } catch (Throwable t) {
-            throw new BioFormatsImageException(t);
-        }
-        try {
             int series = 0;
             final int seriesCount = reader.getSeriesCount();
             for (int i = 0; i < seriesCount; i++) {
@@ -175,10 +163,7 @@ public class BioFormatsImageThumbnail {
             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("thumbnail series: " + series);
+
             ret = reader.openThumbImage(no);
             final boolean is16bit = reader.getBitsPerPixel() > 8;
             final boolean isGrayScale = ret.getSampleModel().getNumBands() == 1;
@@ -186,20 +171,13 @@ public class BioFormatsImageThumbnail {
                 // 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) {
+        } catch (final OutOfMemoryError e) {
             throw new BioFormatsImageException("out of memory");
-                }
-            }
-            throw new BioFormatsImageException(t);
-        } finally {
-            try {
-                reader.close();
-            } catch (final IOException e) {
+        } catch (final FormatException | IOException e) {
+            throw new BioFormatsImageException("unsupported file: " + path);
+        } catch (final Exception e) {
             throw new BioFormatsImageException(e);
         }
-        }
 
         return ret;
     }
@@ -222,7 +200,7 @@ public class BioFormatsImageThumbnail {
         if (!matcher.find()) {
             throw new BioFormatsImageException("Unsupported data URI format");
         }
-        final byte[] bytes = matcher.group(2) == "utf8" ? matcher.group(3).getBytes()
+        final byte[] bytes = "utf8".equals(matcher.group(2)) ? matcher.group(3).getBytes()
                 : Base64.getDecoder().decode(matcher.group(3));
         try (final FileOutputStream fos = new FileOutputStream(path);) {
             fos.write(bytes);
@@ -243,7 +221,7 @@ public class BioFormatsImageThumbnail {
             thumbnail.put("height", height);
             thumbnail.put("mimeType", mimeType);
             thumbnail.put("url", dataUri);
-        } catch (final Throwable t) {
+        } catch (final Exception e) {
             // ignore
             ret = false;
         }
@@ -261,13 +239,12 @@ public class BioFormatsImageThumbnail {
             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 Throwable t) {
-            // t.printStackTrace();
-            System.out.println(t.getMessage());
+            saveFile(dataUri, "/var/tmp/thumbnail." + format);
+        } catch (final Exception e) {
+            e.printStackTrace();
+            System.out.println(e.getMessage());
             System.exit(1);
         }
     }