first commit.
This commit is contained in:
commit
5c39e9d57f
74
.gitignore
vendored
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74
.gitignore
vendored
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@ -0,0 +1,74 @@
|
||||
# Created by https://www.toptal.com/developers/gitignore/api/java,maven,visualstudiocode
|
||||
# Edit at https://www.toptal.com/developers/gitignore?templates=java,maven,visualstudiocode
|
||||
|
||||
### Java ###
|
||||
# Compiled class file
|
||||
*.class
|
||||
|
||||
# Log file
|
||||
*.log
|
||||
|
||||
# BlueJ files
|
||||
*.ctxt
|
||||
|
||||
# Mobile Tools for Java (J2ME)
|
||||
.mtj.tmp/
|
||||
|
||||
# Package Files #
|
||||
*.jar
|
||||
*.war
|
||||
*.nar
|
||||
*.ear
|
||||
*.zip
|
||||
*.tar.gz
|
||||
*.rar
|
||||
|
||||
# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
|
||||
hs_err_pid*
|
||||
replay_pid*
|
||||
|
||||
### Maven ###
|
||||
target/
|
||||
pom.xml.tag
|
||||
pom.xml.releaseBackup
|
||||
pom.xml.versionsBackup
|
||||
pom.xml.next
|
||||
release.properties
|
||||
dependency-reduced-pom.xml
|
||||
buildNumber.properties
|
||||
.mvn/timing.properties
|
||||
# https://github.com/takari/maven-wrapper#usage-without-binary-jar
|
||||
.mvn/wrapper/maven-wrapper.jar
|
||||
|
||||
# Eclipse m2e generated files
|
||||
# Eclipse Core
|
||||
.project
|
||||
# JDT-specific (Eclipse Java Development Tools)
|
||||
.classpath
|
||||
|
||||
### VisualStudioCode ###
|
||||
.vscode/*
|
||||
!.vscode/settings.json
|
||||
!.vscode/tasks.json
|
||||
!.vscode/launch.json
|
||||
!.vscode/extensions.json
|
||||
!.vscode/*.code-snippets
|
||||
|
||||
# Local History for Visual Studio Code
|
||||
.history/
|
||||
|
||||
# Built Visual Studio Code Extensions
|
||||
*.vsix
|
||||
|
||||
### VisualStudioCode Patch ###
|
||||
# Ignore all local history of files
|
||||
.history
|
||||
.ionide
|
||||
|
||||
# Support for Project snippet scope
|
||||
.vscode/*.code-snippets
|
||||
|
||||
# Ignore code-workspaces
|
||||
*.code-workspace
|
||||
|
||||
# End of https://www.toptal.com/developers/gitignore/api/java,maven,visualstudiocode
|
||||
41
README.md
Normal file
41
README.md
Normal file
@ -0,0 +1,41 @@
|
||||
# BioFormatsImageInfo
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||||
Metadata extraction tool based on Bio-Formats
|
||||
|
||||
### Compile
|
||||
```shell
|
||||
mvn compile
|
||||
```
|
||||
|
||||
### run
|
||||
```shell
|
||||
mvn exec:java -Dexec.mainClass=jp.riken.neurodata.tools.BioFormatsImageInfo -Dexec.args="'[path to image file]'"
|
||||
```
|
||||
|
||||
### make jar package
|
||||
```shell
|
||||
mvn package
|
||||
```
|
||||
|
||||
### run by jar
|
||||
```shell
|
||||
java -jar target\bioformats-imageinfo-1.0.0.jar [path to image file]
|
||||
```
|
||||
|
||||
### run by class
|
||||
```java
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
import jp.riken.neurodata.tools.BioFormatsImageInfo;
|
||||
import jp.riken.neurodata.tools.BioFormatsException;
|
||||
|
||||
String path = "[path to image file]";
|
||||
String format = "";
|
||||
Map<String, Object> metadata = new LinkedHashMap<String, Object>();
|
||||
|
||||
try {
|
||||
format = BioFormatsImageInfo.readMetadata(path, metadata));
|
||||
} catch (BioFormatsImageException e) {
|
||||
// error occured
|
||||
e.printStackTrace();
|
||||
}
|
||||
```
|
||||
114
pom.xml
Normal file
114
pom.xml
Normal file
@ -0,0 +1,114 @@
|
||||
<?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">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<groupId>jp.riken.neurodata.tools.BioFormatsImageInfo</groupId>
|
||||
<artifactId>bioformats-imageinfo</artifactId>
|
||||
<version>1.0.0</version>
|
||||
|
||||
<name>bioformats-imageinfo</name>
|
||||
<url>https://neurodata.riken.jp</url>
|
||||
|
||||
<properties>
|
||||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
||||
<maven.compiler.source>1.8</maven.compiler.source>
|
||||
<maven.compiler.target>1.8</maven.compiler.target>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>ome</groupId>
|
||||
<artifactId>bioformats_package</artifactId>
|
||||
<version>6.10.0</version>
|
||||
<type>pom</type>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-dependency-plugin</artifactId>
|
||||
<version>3.3.0</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>copy-dependencies</id>
|
||||
<phase>prepare-package</phase>
|
||||
<goals>
|
||||
<goal>copy-dependencies</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<outputDirectory>${project.build.directory}/libs</outputDirectory>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-jar-plugin</artifactId>
|
||||
<version>3.2.2</version>
|
||||
<configuration>
|
||||
<archive>
|
||||
<manifest>
|
||||
<addClasspath>true</addClasspath>
|
||||
<classpathPrefix>libs/</classpathPrefix>
|
||||
<mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</mainClass>
|
||||
</manifest>
|
||||
</archive>
|
||||
</configuration>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<version>3.4.1</version>
|
||||
<configuration>
|
||||
<descriptorRefs>
|
||||
<descriptorRef>jar-with-dependencies</descriptorRef>
|
||||
</descriptorRefs>
|
||||
<archive>
|
||||
<manifest>
|
||||
<mainClass>jp.riken.neurodata.tools.BioFormatsImageInfo</mainClass>
|
||||
</manifest>
|
||||
</archive>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>make-assembly</id>
|
||||
<phase>package</phase>
|
||||
<goals>
|
||||
<goal>single</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
|
||||
<pluginRepositories>
|
||||
<pluginRepository>
|
||||
<id>central</id>
|
||||
<name>Central Repository</name>
|
||||
<url>https://repo.maven.apache.org/maven2</url>
|
||||
<layout>default</layout>
|
||||
</pluginRepository>
|
||||
</pluginRepositories>
|
||||
<repositories>
|
||||
<repository>
|
||||
<id>central</id>
|
||||
<name>Central Repository</name>
|
||||
<url>https://repo.maven.apache.org/maven2</url>
|
||||
</repository>
|
||||
<repository>
|
||||
<id>unidata.releases</id>
|
||||
<url>https://artifacts.unidata.ucar.edu/content/repositories/unidata-releases</url>
|
||||
<snapshots><enabled>false</enabled></snapshots>
|
||||
</repository>
|
||||
<repository>
|
||||
<id>ome</id>
|
||||
<name>OME Artifactory</name>
|
||||
<url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
|
||||
</repository>
|
||||
</repositories>
|
||||
|
||||
</project>
|
||||
@ -0,0 +1,12 @@
|
||||
package jp.riken.neurodata.tools;
|
||||
|
||||
public class BioFormatsImageException extends Exception {
|
||||
|
||||
public BioFormatsImageException(String message) {
|
||||
super(message);
|
||||
}
|
||||
|
||||
public BioFormatsImageException(Throwable cause) {
|
||||
super(cause.getMessage());
|
||||
}
|
||||
}
|
||||
273
src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java
Normal file
273
src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java
Normal file
@ -0,0 +1,273 @@
|
||||
package jp.riken.neurodata.tools;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Hashtable;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import org.apache.commons.io.FilenameUtils;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import loci.common.DebugTools;
|
||||
import loci.formats.FormatException;
|
||||
import loci.formats.FormatTools;
|
||||
import loci.formats.IFormatReader;
|
||||
import loci.formats.ImageReader;
|
||||
import loci.formats.MetadataTools;
|
||||
import loci.formats.Modulo;
|
||||
import loci.formats.meta.MetadataRetrieve;
|
||||
import loci.formats.meta.MetadataStore;
|
||||
import loci.formats.tools.ImageInfo;
|
||||
|
||||
public class BioFormatsImageInfo {
|
||||
|
||||
protected static Map<String, Object> readImages(IFormatReader reader) throws FormatException, IOException {
|
||||
Map<String, Object> metadata = new LinkedHashMap<String, Object>();
|
||||
|
||||
// read basic metadata
|
||||
int seriesCount = reader.getSeriesCount();
|
||||
metadata.put("count", seriesCount);
|
||||
MetadataStore ms = reader.getMetadataStore();
|
||||
MetadataRetrieve mr = ms instanceof MetadataRetrieve ? (MetadataRetrieve) ms : null;
|
||||
for (int j = 0; j < seriesCount; j++) {
|
||||
reader.setSeries(j);
|
||||
Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
|
||||
|
||||
// read basic metadata for series #j
|
||||
int imageCount = reader.getImageCount();
|
||||
int resolutionCount = reader.getResolutionCount();
|
||||
|
||||
// output basic metadata for series #i
|
||||
String seriesName = mr == null ? null : mr.getImageName(j);
|
||||
if (seriesName != null) {
|
||||
seriesMetadata.put("name", seriesName);
|
||||
}
|
||||
|
||||
// resolutions
|
||||
if (resolutionCount > 1) {
|
||||
Map<String, Object> resolutionsMetadata = new LinkedHashMap<String, Object>();
|
||||
resolutionsMetadata.put("count", resolutionCount);
|
||||
for (int i = 0; i < resolutionCount; i++) {
|
||||
reader.setResolution(i);
|
||||
resolutionsMetadata.put(String.format("resolution[%d]", i),
|
||||
makeRectangle(reader.getSizeX(), reader.getSizeY()));
|
||||
}
|
||||
seriesMetadata.put("resolutions", resolutionsMetadata);
|
||||
reader.setResolution(0);
|
||||
}
|
||||
|
||||
seriesMetadata.put("imageCount", imageCount);
|
||||
seriesMetadata.put("RGB", new Object[] { reader.isRGB(), reader.getRGBChannelCount() });
|
||||
seriesMetadata.put("interleaved", reader.isInterleaved());
|
||||
|
||||
// indexed
|
||||
{
|
||||
List<Object> indexed = new ArrayList<Object>();
|
||||
indexed.add(reader.isIndexed());
|
||||
indexed.add(String.format("%b color", !reader.isFalseColor()));
|
||||
byte[][] table8 = reader.get8BitLookupTable();
|
||||
if (table8 != null) {
|
||||
indexed.add(
|
||||
String.format("8-bit LUT: %d x %s", table8.length, table8[0] == null ? "null" : "" + table8[0].length));
|
||||
}
|
||||
short[][] table16 = reader.get16BitLookupTable();
|
||||
if (table16 != null) {
|
||||
indexed.add(String.format("16-bit LUT: %d x %s", table16.length,
|
||||
table16[0] == null ? "null" : "" + table16[0].length));
|
||||
}
|
||||
seriesMetadata.put("indexed", indexed);
|
||||
}
|
||||
|
||||
seriesMetadata.put("sizeX", reader.getSizeX());
|
||||
seriesMetadata.put("sizeY", reader.getSizeY());
|
||||
int sizeZ = reader.getSizeZ();
|
||||
seriesMetadata.put("sizeZ", makeDimension(sizeZ, sizeZ, reader.getModuloZ()));
|
||||
seriesMetadata.put("sizeC", makeDimension(reader.getSizeC(), reader.getEffectiveSizeC(), reader.getModuloC()));
|
||||
int sizeT = reader.getSizeT();
|
||||
seriesMetadata.put("sizeT", makeDimension(sizeT, sizeT, reader.getModuloT()));
|
||||
seriesMetadata.put("tileSize", makeRectangle(reader.getOptimalTileWidth(), reader.getOptimalTileHeight()));
|
||||
seriesMetadata.put("thumbnailSize", makeRectangle(reader.getThumbSizeX(), reader.getThumbSizeY()));
|
||||
seriesMetadata.put("endianness", reader.isLittleEndian() ? "little" : "big");
|
||||
seriesMetadata.put("dimensionOrder",
|
||||
new String[] { reader.getDimensionOrder(), reader.isOrderCertain() ? "certain" : "uncertain" });
|
||||
seriesMetadata.put("pixelType", FormatTools.getPixelTypeString(reader.getPixelType()));
|
||||
seriesMetadata.put("validBitsPerPixel", reader.getBitsPerPixel());
|
||||
seriesMetadata.put("metadataComplete", reader.isMetadataComplete());
|
||||
seriesMetadata.put("thumbnailSeries", reader.isThumbnailSeries());
|
||||
|
||||
// plane
|
||||
{
|
||||
int[] indices;
|
||||
if (imageCount > 6) {
|
||||
int q = imageCount / 2;
|
||||
indices = new int[] { 0, q - 2, q - 1, q, q + 1, q + 2, imageCount - 1 };
|
||||
} else if (imageCount > 2) {
|
||||
indices = new int[] { 0, imageCount / 2, imageCount - 1 };
|
||||
} else if (imageCount > 1) {
|
||||
indices = new int[] { 0, 1 };
|
||||
} else {
|
||||
indices = new int[] { 0 };
|
||||
}
|
||||
int[][] zct = new int[indices.length][];
|
||||
int[] indices2 = new int[indices.length];
|
||||
for (int i = 0; i < indices.length; i++) {
|
||||
zct[i] = reader.getZCTCoords(indices[i]);
|
||||
indices2[i] = reader.getIndex(zct[i][0], zct[i][1], zct[i][2]);
|
||||
Map<String, Object> planeMetadata = new LinkedHashMap<String, Object>();
|
||||
planeMetadata.put("Z", zct[i][0]);
|
||||
planeMetadata.put("C", zct[i][1]);
|
||||
planeMetadata.put("T", zct[i][2]);
|
||||
if (indices[i] != indices2[i]) {
|
||||
planeMetadata.put("[mismatch]", indices2[i]);
|
||||
}
|
||||
seriesMetadata.put(String.format("plane[%d]", indices[i]), planeMetadata);
|
||||
}
|
||||
}
|
||||
metadata.put(String.format("series[%d]", j), seriesMetadata);
|
||||
}
|
||||
|
||||
return metadata;
|
||||
}
|
||||
|
||||
protected static Map<String, Object> readAnnotations(IFormatReader reader) {
|
||||
Map<String, Object> metadata = new LinkedHashMap<String, Object>();
|
||||
// global metadata
|
||||
Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata();
|
||||
for (String key : MetadataTools.keys(globalMetadata)) {
|
||||
metadata.put(key, globalMetadata.get(key));
|
||||
}
|
||||
// original metadata
|
||||
int seriesCount = reader.getSeriesCount();
|
||||
for (int j = 0; j < seriesCount; j++) {
|
||||
reader.setSeries(j);
|
||||
Hashtable<String, Object> seriesMagedata = reader.getSeriesMetadata();
|
||||
if (!seriesMagedata.isEmpty()) {
|
||||
Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
|
||||
String[] keys = MetadataTools.keys(seriesMagedata);
|
||||
for (int i = 0; i < keys.length; i++) {
|
||||
seriesMetadata.put(keys[i], seriesMagedata.get(keys[i]));
|
||||
}
|
||||
metadata.put(String.format("series[%d]", j), seriesMetadata);
|
||||
}
|
||||
}
|
||||
|
||||
return metadata;
|
||||
}
|
||||
|
||||
protected static Object makeDimension(int size, int effSize, Modulo modulo) {
|
||||
int mLength = modulo.length();
|
||||
if (size == effSize && mLength == 1) {
|
||||
return size;
|
||||
}
|
||||
List<Object> ret = new ArrayList<Object>();
|
||||
ret.add(size);
|
||||
if (size != effSize) {
|
||||
ret.add(String.format("(effectively %d)", effSize));
|
||||
}
|
||||
if (mLength != 1) {
|
||||
ret.add(String.format("(%d %s x %d %s)", size / mLength, modulo.parentType, mLength, modulo.type));
|
||||
}
|
||||
|
||||
return ret;
|
||||
}
|
||||
|
||||
protected static LinkedHashMap<String, Object> makeRectangle(int width, int height) {
|
||||
LinkedHashMap<String, Object> ret = new LinkedHashMap<String, Object>();
|
||||
ret.put("width", width);
|
||||
ret.put("height", height);
|
||||
return ret;
|
||||
}
|
||||
|
||||
protected static String getJsonString(Map<String, Object> map) {
|
||||
ObjectMapper mapper = new ObjectMapper();
|
||||
String json = null;
|
||||
try {
|
||||
json = mapper.writeValueAsString(map);
|
||||
// json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
|
||||
} catch (Exception e) {
|
||||
// return "null" if conversion error occured
|
||||
json = "null";
|
||||
}
|
||||
|
||||
return json;
|
||||
}
|
||||
|
||||
public static String readMetadata(String path, Map<String, Object> metadata) throws BioFormatsImageException {
|
||||
if (FilenameUtils.getExtension(path).toLowerCase().equals("zip")) {
|
||||
// ignore if file is zip archive
|
||||
throw new BioFormatsImageException("Zip is not supported");
|
||||
}
|
||||
String format = "";
|
||||
ImageInfo info = new ImageInfo();
|
||||
IFormatReader reader = new ImageReader();
|
||||
try {
|
||||
// info.parseArgs(new String[] { path, "-nopix", "-noflat", "-omexml" });
|
||||
info.parseArgs(new String[] { path, "-nopix", "-noflat" });
|
||||
info.setReader(reader);
|
||||
info.mapLocation();
|
||||
info.configureReaderPreInit();
|
||||
|
||||
// initialize reader
|
||||
reader.setId(path);
|
||||
format = reader.getFormat();
|
||||
info.configureReaderPostInit();
|
||||
info.checkWarnings();
|
||||
// info.printOMEXML();
|
||||
// info.readCoreMetadata();
|
||||
metadata.put("images", readImages(reader));
|
||||
info.initPreMinMaxValues();
|
||||
reader.setSeries(0);
|
||||
reader.setResolution(0);
|
||||
// info.printGlobalMetadata();
|
||||
// info.printOriginalMetadata();
|
||||
metadata.put("annotations", readAnnotations(reader));
|
||||
} catch (Exception e) {
|
||||
throw new BioFormatsImageException(e);
|
||||
} finally {
|
||||
if (reader != null) {
|
||||
try {
|
||||
reader.close();
|
||||
} catch (IOException e) {
|
||||
throw new BioFormatsImageException(e);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return format;
|
||||
}
|
||||
|
||||
// -- Main method --
|
||||
public static void main(String[] args) {
|
||||
boolean status = true;
|
||||
String message = "";
|
||||
String format = "";
|
||||
Map<String, Object> metadata = new LinkedHashMap<String, Object>();
|
||||
if (args.length != 1) {
|
||||
status = false;
|
||||
message = "filename argument required";
|
||||
} else {
|
||||
try {
|
||||
DebugTools.enableLogging("ERROR");
|
||||
format = readMetadata(args[0], metadata);
|
||||
} catch (BioFormatsImageException e) {
|
||||
status = false;
|
||||
metadata.clear();
|
||||
message = e.getMessage();
|
||||
}
|
||||
}
|
||||
|
||||
Map<String, Object> results = new LinkedHashMap<String, Object>();
|
||||
results.put("status", status);
|
||||
results.put("message", message);
|
||||
results.put("format", format);
|
||||
results.put("metadata", metadata.isEmpty() ? null : metadata);
|
||||
System.out.println(getJsonString(results));
|
||||
|
||||
if (!status) {
|
||||
System.exit(1);
|
||||
}
|
||||
}
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user