disable logging.

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-1.1.2.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-1.1.2-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>1.1.1</version>
+  <version>1.1.2</version>
 
   <name>bioformats-imageinfo</name>
   <url>https://neurodata.riken.jp</url>
@@ -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

@@ -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();
+            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();
+            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);
         }
     }