From 0df492ff14771bf21e4a9ae89dd7a66d3b5f7bdf Mon Sep 17 00:00:00 2001
From: Yoshihiro OKUMURA <orrisroot@gmail.com>
Date: Wed, 12 Oct 2022 13:54:42 +0900
Subject: [PATCH] perform autoscaling if floating point thumbnail found.

---
 .../tools/BioFormatsImageThumbnail.java        | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/src/main/java/jp/riken/neurodata/tools/BioFormatsImageThumbnail.java b/src/main/java/jp/riken/neurodata/tools/BioFormatsImageThumbnail.java
index 0b7b5be..e3a9014 100644
--- a/src/main/java/jp/riken/neurodata/tools/BioFormatsImageThumbnail.java
+++ b/src/main/java/jp/riken/neurodata/tools/BioFormatsImageThumbnail.java
@@ -21,7 +21,9 @@ import javax.imageio.stream.ImageOutputStream;
 
 import loci.common.DebugTools;
 import loci.formats.FormatException;
+import loci.formats.FormatTools;
 import loci.formats.ImageReader;
+import loci.formats.gui.AWTImageTools;
 import loci.formats.gui.BufferedImageReader;
 
 public class BioFormatsImageThumbnail {
@@ -89,8 +91,10 @@ 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();
@@ -166,12 +170,19 @@ 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);
+            if (!FormatTools.isFloatingPoint(reader.getPixelType())) {
+                // auto scalling floating point thumbnail.
+                ret = AWTImageTools.autoscale(ret);
+            }
         } catch (final Throwable t) {
             for (Throwable e = t; e != null; e = e.getCause()) {
                 if (t instanceof OutOfMemoryError) {
@@ -252,6 +263,7 @@ public class BioFormatsImageThumbnail {
             System.out.println(dataUri);
             // saveFile(dataUri, "/var/tmp/thumbnail." + format);
         } catch (final Throwable t) {
+            // t.printStackTrace();
             System.out.println(t.getMessage());
             System.exit(1);
         }