niu/bioformats-imageinfo
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perform autoscaling if floating point thumbnail found.

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This commit is contained in:
Yoshihiro OKUMURA 2022-10-12 13:54:42 +09:00
parent 4ea2dc7110
commit 0df492ff14
1 changed files with 15 additions and 3 deletions
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18
src/main/java/jp/riken/neurodata/tools/BioFormatsImageThumbnail.java
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@ -21,7 +21,9 @@ import javax.imageio.stream.ImageOutputStream;
import loci.common.DebugTools; import loci.common.DebugTools;
import loci.formats.FormatException; import loci.formats.FormatException;
import loci.formats.FormatTools;
import loci.formats.ImageReader; import loci.formats.ImageReader;
import loci.formats.gui.AWTImageTools;
import loci.formats.gui.BufferedImageReader; import loci.formats.gui.BufferedImageReader;
public class BioFormatsImageThumbnail { public class BioFormatsImageThumbnail {
@ -89,8 +91,10 @@ public class BioFormatsImageThumbnail {
final ImageOutputStream ios = ImageIO.createImageOutputStream(baos);) { final ImageOutputStream ios = ImageIO.createImageOutputStream(baos);) {
final ImageWriter writer = ImageIO.getImageWritersByFormatName("jpeg").next(); final ImageWriter writer = ImageIO.getImageWritersByFormatName("jpeg").next();
final ImageWriteParam param = writer.getDefaultWriteParam(); final ImageWriteParam param = writer.getDefaultWriteParam();
param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT); if (param.canWriteCompressed()) {
param.setCompressionQuality(quality); param.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
param.setCompressionQuality(quality);
}
writer.setOutput(ios); writer.setOutput(ios);
writer.write(null, new IIOImage(removeAlphaChannel(image, matColor), null, null), param); writer.write(null, new IIOImage(removeAlphaChannel(image, matColor), null, null), param);
writer.dispose(); writer.dispose();
@ -166,12 +170,19 @@ public class BioFormatsImageThumbnail {
} }
} }
reader.setSeries(series); 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("series count: " + seriesCount);
// System.out.println("image count: " + reader.getImageCount()); // System.out.println("image count: " + reader.getImageCount());
// System.out.println("resolution: " + reader.getResolutionCount()); // System.out.println("resolution: " + reader.getResolutionCount());
// System.out.println("thubmail series: " + series); // System.out.println("thubmail series: " + series);
ret = reader.openThumbImage(no); ret = reader.openThumbImage(no);
if (!FormatTools.isFloatingPoint(reader.getPixelType())) {
// auto scalling floating point thumbnail.
ret = AWTImageTools.autoscale(ret);
}
} catch (final Throwable t) { } catch (final Throwable t) {
for (Throwable e = t; e != null; e = e.getCause()) { for (Throwable e = t; e != null; e = e.getCause()) {
if (t instanceof OutOfMemoryError) { if (t instanceof OutOfMemoryError) {
@ -252,6 +263,7 @@ public class BioFormatsImageThumbnail {
System.out.println(dataUri); System.out.println(dataUri);
// saveFile(dataUri, "/var/tmp/thumbnail." + format); // saveFile(dataUri, "/var/tmp/thumbnail." + format);
} catch (final Throwable t) { } catch (final Throwable t) {
// t.printStackTrace();
System.out.println(t.getMessage()); System.out.println(t.getMessage());
System.exit(1); System.exit(1);
} }