niu/bioformats-imageinfo
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update bio-formats version to 6.14.0.

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This commit is contained in:
Yoshihiro OKUMURA
2023-07-13 13:50:25 +09:00
parent 705e7f7e7d
commit 4c581052ab
7 changed files with 64 additions and 30 deletions
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5
src/main/assembly/assembly.xml
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@@ -1,5 +1,6 @@
<?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"
<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>
@@ -32,4 +33,4 @@
<outputDirectory>lib</outputDirectory>
</dependencySet>
</dependencySets>
</assembly>
</assembly>

14
src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java
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@@ -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";
}

24
src/main/java/jp/riken/neurodata/tools/BioFormatsImageThumbnail.java
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@@ -27,7 +27,7 @@ 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;
@@ -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 different with requrested dimension.
// 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);
@@ -86,8 +86,8 @@ 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();
if (param.canWriteCompressed()) {
@@ -97,7 +97,7 @@ public class BioFormatsImageThumbnail {
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);
}
@@ -107,8 +107,8 @@ public class BioFormatsImageThumbnail {
protected static byte[] getPngByteArray(final BufferedImage image) 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("png").next();
final ImageWriteParam param = writer.getDefaultWriteParam();
if (param.canWriteCompressed()) {
@@ -118,7 +118,7 @@ public class BioFormatsImageThumbnail {
writer.setOutput(ios);
writer.write(null, new IIOImage(image, null, null), param);
writer.dispose();
ret = baos.toByteArray();
ret = bos.toByteArray();
} catch (final IOException e) {
throw new BioFormatsImageException(e);
}
@@ -133,7 +133,7 @@ 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);
@@ -178,12 +178,12 @@ public class BioFormatsImageThumbnail {
// 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);
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.
// perform auto scaling if 16bit or gray scale thumbnail image.
ret = AWTImageTools.autoscale(ret);
}
} catch (final Throwable t) {