niu/bioformats-imageinfo
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fixed some warnings.

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This commit is contained in:
Yoshihiro OKUMURA
2025-07-01 17:27:57 +09:00
parent 0b3938c13f
commit 2946707155
3 changed files with 48 additions and 87 deletions
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2
src/main/java/jp/riken/neurodata/tools/BioFormatsImageException.java
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@ -6,7 +6,7 @@ public class BioFormatsImageException extends Exception {
super(message); super(message);
} }
public BioFormatsImageException(Throwable cause) { public BioFormatsImageException(Exception cause) {
super(cause.getMessage()); super(cause.getMessage());
} }
} }

68
src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java
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@ -2,7 +2,7 @@ package jp.riken.neurodata.tools;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Hashtable; import java.util.HashMap;
import java.util.LinkedHashMap; import java.util.LinkedHashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
@ -16,7 +16,6 @@ import loci.formats.FormatException;
import loci.formats.FormatTools; import loci.formats.FormatTools;
import loci.formats.IFormatReader; import loci.formats.IFormatReader;
import loci.formats.ImageReader; import loci.formats.ImageReader;
import loci.formats.MetadataTools;
import loci.formats.Modulo; import loci.formats.Modulo;
import loci.formats.meta.MetadataRetrieve; import loci.formats.meta.MetadataRetrieve;
import loci.formats.meta.MetadataStore; import loci.formats.meta.MetadataStore;
@ -25,7 +24,7 @@ import loci.formats.tools.ImageInfo;
public class BioFormatsImageInfo { public class BioFormatsImageInfo {
protected static Map<String, Object> readImages(final IFormatReader reader) throws FormatException, IOException { 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 // read basic metadata
final int seriesCount = reader.getSeriesCount(); final int seriesCount = reader.getSeriesCount();
@ -35,7 +34,7 @@ public class BioFormatsImageInfo {
// read basic metadata for series #j // read basic metadata for series #j
reader.setSeries(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 imageCount = reader.getImageCount();
final int resolutionCount = reader.getResolutionCount(); final int resolutionCount = reader.getResolutionCount();
@ -46,7 +45,7 @@ public class BioFormatsImageInfo {
// resolutions // resolutions
if (resolutionCount > 1) { 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++) { for (int i = 0; i < resolutionCount; i++) {
reader.setResolution(i); reader.setResolution(i);
resolutionsMetadata.put(String.format("resolution[%d]", i), resolutionsMetadata.put(String.format("resolution[%d]", i),
@ -62,7 +61,7 @@ public class BioFormatsImageInfo {
// indexed // indexed
{ {
final List<Object> indexed = new ArrayList<Object>(); final List<Object> indexed = new ArrayList<>();
indexed.add(reader.isIndexed()); indexed.add(reader.isIndexed());
indexed.add(String.format("%b color", !reader.isFalseColor())); indexed.add(String.format("%b color", !reader.isFalseColor()));
final byte[][] table8 = reader.get8BitLookupTable(); final byte[][] table8 = reader.get8BitLookupTable();
@ -115,7 +114,7 @@ public class BioFormatsImageInfo {
for (int i = 0; i < indices.length; i++) { for (int i = 0; i < indices.length; i++) {
zct[i] = reader.getZCTCoords(indices[i]); zct[i] = reader.getZCTCoords(indices[i]);
indices2[i] = reader.getIndex(zct[i][0], zct[i][1], zct[i][2]); 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("Z", zct[i][0]);
planeMetadata.put("C", zct[i][1]); planeMetadata.put("C", zct[i][1]);
planeMetadata.put("T", zct[i][2]); planeMetadata.put("T", zct[i][2]);
@ -132,22 +131,21 @@ public class BioFormatsImageInfo {
} }
protected static Map<String, Object> readAnnotations(final IFormatReader reader) { 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 // global metadata
final Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata(); final HashMap<String, Object> globalMetadata = new HashMap<>(reader.getGlobalMetadata());
for (String key : MetadataTools.keys(globalMetadata)) { for (Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
metadata.put(key, globalMetadata.get(key)); metadata.put(entry.getKey(), entry.getValue());
} }
// original metadata // original metadata
final int seriesCount = reader.getSeriesCount(); final int seriesCount = reader.getSeriesCount();
for (int j = 0; j < seriesCount; j++) { for (int j = 0; j < seriesCount; j++) {
reader.setSeries(j); reader.setSeries(j);
final Hashtable<String, Object> seriesMetadata = reader.getSeriesMetadata(); final HashMap<String, Object> seriesMetadata = new HashMap<>(reader.getSeriesMetadata());
if (!seriesMetadata.isEmpty()) { if (!seriesMetadata.isEmpty()) {
final Map<String, Object> originalMetadata = new LinkedHashMap<String, Object>(); final Map<String, Object> originalMetadata = new LinkedHashMap<>();
final String[] keys = MetadataTools.keys(seriesMetadata); for (Map.Entry<String, Object> entry : seriesMetadata.entrySet()) {
for (int i = 0; i < keys.length; i++) { originalMetadata.put(entry.getKey(), entry.getValue());
originalMetadata.put(keys[i], seriesMetadata.get(keys[i]));
} }
metadata.put(String.format("series[%d]", j), originalMetadata); metadata.put(String.format("series[%d]", j), originalMetadata);
} }
@ -161,7 +159,7 @@ public class BioFormatsImageInfo {
if (size == effSize && mLength == 1) { if (size == effSize && mLength == 1) {
return size; return size;
} }
final List<Object> ret = new ArrayList<Object>(); final List<Object> ret = new ArrayList<>();
ret.add(size); ret.add(size);
if (size != effSize) { if (size != effSize) {
ret.add(String.format("(effectively %d)", 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) { 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("width", width);
ret.put("height", height); ret.put("height", height);
@ -185,9 +183,8 @@ public class BioFormatsImageInfo {
final ObjectMapper mapper = new ObjectMapper(); final ObjectMapper mapper = new ObjectMapper();
String json = null; String json = null;
try { try {
// json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
json = mapper.writeValueAsString(map); json = mapper.writeValueAsString(map);
} catch (final Throwable e) { } catch (final Exception e) {
// return "null" if conversion error occurred // return "null" if conversion error occurred
json = "null"; json = "null";
} }
@ -197,15 +194,13 @@ public class BioFormatsImageInfo {
public static String readMetadata(final String path, final Map<String, Object> metadata) public static String readMetadata(final String path, final Map<String, Object> metadata)
throws BioFormatsImageException { throws BioFormatsImageException {
if (FilenameUtils.getExtension(path).toLowerCase().equals("zip")) { if (FilenameUtils.getExtension(path).equalsIgnoreCase("zip")) {
// ignore if file is zip archive // ignore if file is zip archive
throw new BioFormatsImageException("Zip is not supported"); throw new BioFormatsImageException("Zip is not supported");
} }
String format = ""; String format = "";
final ImageInfo info = new ImageInfo(); final ImageInfo info = new ImageInfo();
final IFormatReader reader = new ImageReader(); try (final IFormatReader reader = new ImageReader()) {
try {
// info.parseArgs(new String[] { path, "-nopix", "-noflat", "-omexml" });
info.parseArgs(new String[] { path, "-nopix", "-noflat" }); info.parseArgs(new String[] { path, "-nopix", "-noflat" });
info.setReader(reader); info.setReader(reader);
info.mapLocation(); info.mapLocation();
@ -216,28 +211,17 @@ public class BioFormatsImageInfo {
format = reader.getFormat(); format = reader.getFormat();
info.configureReaderPostInit(); info.configureReaderPostInit();
info.checkWarnings(); info.checkWarnings();
// info.printOMEXML();
// info.readCoreMetadata();
metadata.put("images", readImages(reader)); metadata.put("images", readImages(reader));
info.initPreMinMaxValues(); info.initPreMinMaxValues();
reader.setSeries(0); reader.setSeries(0);
reader.setResolution(0); reader.setResolution(0);
// info.printGlobalMetadata();
// info.printOriginalMetadata();
final Map<String, Object> annotations = readAnnotations(reader); final Map<String, Object> annotations = readAnnotations(reader);
if (!annotations.isEmpty()) { if (!annotations.isEmpty()) {
metadata.put("annotations", annotations); metadata.put("annotations", annotations);
} }
} catch (final Throwable e) { } catch (final Exception e) {
throw new BioFormatsImageException(e); throw new BioFormatsImageException(e);
} finally {
if (reader != null) {
try {
reader.close();
} catch (final IOException e) {
throw new BioFormatsImageException(e);
}
}
} }
return format; return format;
@ -251,8 +235,8 @@ public class BioFormatsImageInfo {
boolean metadataON = true; boolean metadataON = true;
boolean thumbnailON = true; boolean thumbnailON = true;
String path = ""; String path = "";
final Map<String, Object> metadata = new LinkedHashMap<String, Object>(); final Map<String, Object> metadata = new LinkedHashMap<>();
final Map<String, Object> thumbnail = new LinkedHashMap<String, Object>(); final Map<String, Object> thumbnail = new LinkedHashMap<>();
if (args.length == 1) { if (args.length == 1) {
path = args[0]; path = args[0];
} else if (args.length == 2) { } else if (args.length == 2) {
@ -276,15 +260,15 @@ public class BioFormatsImageInfo {
if (thumbnailON) { if (thumbnailON) {
BioFormatsImageThumbnail.readThumbnail(path, thumbnail); BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
} }
} catch (Throwable t) { } catch (final Exception e) {
status = false; status = false;
message = t.getMessage(); message = e.getMessage();
metadata.clear(); metadata.clear();
thumbnail.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("status", status);
results.put("message", message); results.put("message", message);
results.put("format", format); results.put("format", format);

65
src/main/java/jp/riken/neurodata/tools/BioFormatsImageThumbnail.java
View File

@ -47,8 +47,8 @@ public class BioFormatsImageThumbnail {
Image resizeImage = image; Image resizeImage = image;
if (scale != 1.0) { if (scale != 1.0) {
// resize image if dimension is different with requested dimension. // resize image if dimension is different with requested dimension.
resizeWidth = (int) (scale * (double) imageWidth); resizeWidth = (int) (scale * imageWidth);
resizeHeight = (int) (scale * (double) imageHeight); resizeHeight = (int) (scale * imageHeight);
resizeImage = image.getScaledInstance(resizeWidth, resizeHeight, Image.SCALE_AREA_AVERAGING); resizeImage = image.getScaledInstance(resizeWidth, resizeHeight, Image.SCALE_AREA_AVERAGING);
} }
final int type = hasAlpha ? BufferedImage.TYPE_INT_ARGB : BufferedImage.TYPE_INT_RGB; 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 Color c = new Color(image.getRGB(0, 0), hasAlpha);
final int offsetX = (width - resizeWidth) / 2; final int offsetX = (width - resizeWidth) / 2;
final int offsetY = (height - resizeHeight) / 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.setColor(c);
g.fillRect(0, 0, width, height); g.fillRect(0, 0, width, height);
g.drawImage(resizeImage, offsetX, offsetY, resizeWidth, resizeHeight, null); g.drawImage(resizeImage, offsetX, offsetY, resizeWidth, resizeHeight, null);
@ -141,26 +137,18 @@ public class BioFormatsImageThumbnail {
if (bytes.length == 0) { if (bytes.length == 0) {
throw new BioFormatsImageException("Failed to convert to " + mimeType + " format"); 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 { public static BufferedImage getImageFromBioFormatsFile(final String path) throws BioFormatsImageException {
BufferedImage ret = null; BufferedImage ret = null;
final BufferedImageReader reader = new BufferedImageReader(new ImageReader()); try (final BufferedImageReader reader = new BufferedImageReader(new ImageReader())) {
reader.setFlattenedResolutions(false); reader.setFlattenedResolutions(false);
reader.setNormalized(true); reader.setNormalized(true);
reader.setOriginalMetadataPopulated(false); reader.setOriginalMetadataPopulated(false);
reader.setMetadataFiltered(true); reader.setMetadataFiltered(true);
try {
reader.setId(path); reader.setId(path);
} catch (FormatException | IOException e) {
throw new BioFormatsImageException("unsupported file: " + path);
} catch (Throwable t) {
throw new BioFormatsImageException(t);
}
try {
int series = 0; int series = 0;
final int seriesCount = reader.getSeriesCount(); final int seriesCount = reader.getSeriesCount();
for (int i = 0; i < seriesCount; i++) { 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 t = reader.getSizeT() / 2; // middle of frames
final int c = 0; // first channel final int c = 0; // first channel
final int no = reader.getIndex(z, c, t); 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); ret = reader.openThumbImage(no);
final boolean is16bit = reader.getBitsPerPixel() > 8; final boolean is16bit = reader.getBitsPerPixel() > 8;
final boolean isGrayScale = ret.getSampleModel().getNumBands() == 1; final boolean isGrayScale = ret.getSampleModel().getNumBands() == 1;
@ -186,19 +171,12 @@ public class BioFormatsImageThumbnail {
// perform auto scaling if 16bit or gray scale thumbnail image. // perform auto scaling if 16bit or gray scale thumbnail image.
ret = AWTImageTools.autoscale(ret); ret = AWTImageTools.autoscale(ret);
} }
} catch (final Throwable t) { } catch (final OutOfMemoryError e) {
for (Throwable e = t; e != null; e = e.getCause()) { throw new BioFormatsImageException("out of memory");
if (e instanceof OutOfMemoryError) { } catch (final FormatException | IOException e) {
throw new BioFormatsImageException("out of memory"); throw new BioFormatsImageException("unsupported file: " + path);
} } catch (final Exception e) {
} throw new BioFormatsImageException(e);
throw new BioFormatsImageException(t);
} finally {
try {
reader.close();
} catch (final IOException e) {
throw new BioFormatsImageException(e);
}
} }
return ret; return ret;
@ -222,7 +200,7 @@ public class BioFormatsImageThumbnail {
if (!matcher.find()) { if (!matcher.find()) {
throw new BioFormatsImageException("Unsupported data URI format"); 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)); : Base64.getDecoder().decode(matcher.group(3));
try (final FileOutputStream fos = new FileOutputStream(path);) { try (final FileOutputStream fos = new FileOutputStream(path);) {
fos.write(bytes); fos.write(bytes);
@ -243,7 +221,7 @@ public class BioFormatsImageThumbnail {
thumbnail.put("height", height); thumbnail.put("height", height);
thumbnail.put("mimeType", mimeType); thumbnail.put("mimeType", mimeType);
thumbnail.put("url", dataUri); thumbnail.put("url", dataUri);
} catch (final Throwable t) { } catch (final Exception e) {
// ignore // ignore
ret = false; ret = false;
} }
@ -261,13 +239,12 @@ public class BioFormatsImageThumbnail {
DebugTools.enableLogging("OFF"); DebugTools.enableLogging("OFF");
BufferedImage image = getImageFromBioFormatsFile(path); BufferedImage image = getImageFromBioFormatsFile(path);
final String format = image.getColorModel().hasAlpha() ? "png" : "jpeg"; final String format = image.getColorModel().hasAlpha() ? "png" : "jpeg";
// image = resize(image, 160, 160);
final String dataUri = getDataUri(image, "image/" + format); final String dataUri = getDataUri(image, "image/" + format);
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 Exception e) {
// t.printStackTrace(); e.printStackTrace();
System.out.println(t.getMessage()); System.out.println(e.getMessage());
System.exit(1); System.exit(1);
} }
} }