mirror of
https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2026-08-11 20:50:41 +02:00
rework of the plugin to work with the "latest" hdf5 version - its quite a hack
This commit is contained in:
-28
@@ -1,28 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="src" output="target/classes" path="src/main/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="src" output="target/test-classes" path="src/test/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry including="**/*.java" kind="src" path="src/main/resources"/>
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<classpathentry including="**/*.java" kind="src" path="src/test/resources"/>
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<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="output" path="target/classes"/>
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</classpath>
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@@ -4,3 +4,4 @@ imagej.hdf5.iml
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/target
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.gradle
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build
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out/
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@@ -1,29 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<projectDescription>
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<name>ch.psi.imagej.hdf5</name>
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<comment></comment>
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<projects>
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</projects>
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<buildSpec>
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<buildCommand>
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<name>org.eclipse.jdt.core.javabuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.m2e.core.maven2Builder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>ch.acanda.eclipse.pmd.builder.PMDBuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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</buildSpec>
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<natures>
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<nature>org.eclipse.jdt.core.javanature</nature>
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<nature>org.eclipse.m2e.core.maven2Nature</nature>
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<nature>ch.acanda.eclipse.pmd.builder.PMDNature</nature>
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</natures>
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</projectDescription>
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@@ -1,3 +0,0 @@
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eclipse.preferences.version=1
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encoding//src/main/java=UTF-8
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encoding//src/test/java=UTF-8
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@@ -1,5 +0,0 @@
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eclipse.preferences.version=1
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
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org.eclipse.jdt.core.compiler.compliance=1.7
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org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
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org.eclipse.jdt.core.compiler.source=1.7
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@@ -1,4 +0,0 @@
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activeProfiles=
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eclipse.preferences.version=1
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resolveWorkspaceProjects=true
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version=1
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+23
-15
@@ -2,7 +2,7 @@ apply plugin: 'java'
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//apply plugin: 'maven'
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group = 'ch.psi'
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version = '0.12.0'
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version = '0.13.0'
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description = """"""
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@@ -10,10 +10,13 @@ sourceCompatibility = 1.8
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targetCompatibility = 1.8
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repositories {
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mavenCentral()
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maven { url "http://artifacts.psi.ch/artifactory/libs-releases" }
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mavenCentral()
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maven { url "http://artifacts.psi.ch/artifactory/libs-releases" }
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maven { url "http://maven.imagej.net/content/repositories/public/" }
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flatDir {
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dirs 'lib'
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}
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}
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// define a provided scope
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@@ -24,14 +27,20 @@ configurations {
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dependencies {
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compile group: 'hdf5', name: 'hdf', version:'2.10.0'
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compile group: 'hdf5', name: 'hdfobj', version:'2.10.0'
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compile group: 'hdf5', name: 'hdf5', version:'2.10.0'
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compile group: 'hdf5', name: 'hdf5obj', version:'2.10.0'
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compile group: 'org.slf4j', name: 'slf4j-api', version:'1.7.6'
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testCompile group: 'junit', name: 'junit', version:'4.11'
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compile name: 'sis-jhdf5-19.04.0'
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compile name: 'sis-base-18.09.0'
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compile name: 'commons-io-2.6'
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// compile name: 'sis-base-18.09.0'
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// compile group: 'cisd', name: 'jhdf5', version: '14.12.6'
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// compile group: 'hdf5', name: 'hdf', version:'2.10.0'
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// compile group: 'hdf5', name: 'hdfobj', version:'2.10.0'
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// compile group: 'hdf5', name: 'hdf5', version:'2.10.0'
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// compile group: 'hdf5', name: 'hdf5obj', version:'2.10.0'
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compile group: 'org.slf4j', name: 'slf4j-api', version: '1.7.6'
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testCompile group: 'junit', name: 'junit', version: '4.11'
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provided group: 'net.imagej', name: 'ij', version:'1.53e'
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provided group: 'net.imagej', name: 'ij', version: '1.53e'
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}
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task fatJar(type: Jar) {
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@@ -41,12 +50,11 @@ task fatJar(type: Jar) {
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// 'Main-Class': 'ch.psi.caview.CaView'
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// }
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archiveBaseName = 'HDF5_Viewer'
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from { (configurations.compile- configurations.provided).collect { it.isDirectory() ? it : zipTree(it) } }
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from { (configurations.compile - configurations.provided).collect { it.isDirectory() ? it : zipTree(it) } }
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with jar
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// { exclude group: "net.imagej", name:'ij'}
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}
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//
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//task distributionZip(type: Zip, dependsOn: [jar]) {
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//task distributionZip(type: Zip, dependsOn: [fatJar]) {
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// baseName "${project.group}-jhdf5"
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//
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// from('targets/dist') {
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@@ -1,77 +0,0 @@
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>ch.psi</groupId>
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<artifactId>imagej.hdf5</artifactId>
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<version>0.12.0</version>
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<dependencies>
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<dependency>
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<groupId>gov.nih.imagej</groupId>
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<artifactId>imagej</artifactId>
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<version>1.46</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>hdf5</groupId>
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<artifactId>hdf</artifactId>
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<version>2.10.0</version>
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</dependency>
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<dependency>
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<groupId>hdf5</groupId>
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<artifactId>hdfobj</artifactId>
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<version>2.10.0</version>
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</dependency>
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<dependency>
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<groupId>hdf5</groupId>
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<artifactId>hdf5</artifactId>
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<version>2.10.0</version>
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</dependency>
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<dependency>
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<groupId>hdf5</groupId>
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<artifactId>hdf5obj</artifactId>
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<version>2.10.0</version>
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</dependency>
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<!-- The HDF5 libraries -->
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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<version>1.7.6</version>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.11</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<plugin>
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<artifactId>maven-compiler-plugin</artifactId>
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<version>2.3.2</version>
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<configuration>
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<encoding>UTF-8</encoding>
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<source>1.7</source>
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<target>1.7</target>
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</configuration>
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</plugin>
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<plugin>
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<artifactId>maven-assembly-plugin</artifactId>
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<version>2.4</version>
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<configuration>
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<finalName>HDF5_Viewer-${pom.version}</finalName>
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<appendAssemblyId>false</appendAssemblyId>
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<archive />
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<descriptors>
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<descriptor>src/main/assembly/assembly_jar.xml</descriptor>
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<descriptor>src/main/assembly/assembly.xml</descriptor>
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</descriptors>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>
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@@ -1,44 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<settings xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd" xmlns="http://maven.apache.org/SETTINGS/1.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<profiles>
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<profile>
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<repositories>
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<repository>
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<snapshots>
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<enabled>false</enabled>
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</snapshots>
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<id>central</id>
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<name>libs-releases</name>
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<url>http://artifacts.psi.ch/artifactory/libs-releases</url>
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</repository>
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<repository>
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<snapshots />
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<id>snapshots</id>
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<name>libs-snapshots</name>
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<url>http://artifacts.psi.ch/artifactory/libs-snapshots</url>
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</repository>
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</repositories>
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<pluginRepositories>
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<pluginRepository>
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<snapshots>
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<enabled>false</enabled>
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</snapshots>
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<id>central</id>
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<name>libs-releases</name>
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<url>http://artifacts.psi.ch/artifactory/libs-releases</url>
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</pluginRepository>
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<pluginRepository>
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<snapshots />
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<id>snapshots</id>
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<name>libs-releases</name>
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<url>http://artifacts.psi.ch/artifactory/libs-releases</url>
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</pluginRepository>
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</pluginRepositories>
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<id>artifactory</id>
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</profile>
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</profiles>
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<activeProfiles>
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<activeProfile>artifactory</activeProfile>
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</activeProfiles>
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</settings>
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@@ -3,7 +3,7 @@ package ch.psi.imagej.hdf5;
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import java.util.ArrayList;
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import java.util.List;
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import ncsa.hdf.object.Dataset;
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import hdf.object.Dataset;
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public class DatasetSelection {
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@@ -1,5 +1,9 @@
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package ch.psi.imagej.hdf5;
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import hdf.hdf5lib.exceptions.HDF5Exception;
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import hdf.object.Dataset;
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import hdf.object.Datatype;
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import hdf.object.h5.H5File;
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import ij.IJ;
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import ij.ImagePlus;
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import ij.CompositeImage;
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@@ -14,10 +18,6 @@ import java.util.*;
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import java.util.logging.Level;
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import java.util.logging.Logger;
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import ncsa.hdf.object.*;
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import ncsa.hdf.object.h5.*;
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import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
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public class HDF5Reader implements PlugIn {
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private static final Logger logger = Logger.getLogger(HDF5Reader.class.getName());
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@@ -139,7 +139,7 @@ public class HDF5Reader implements PlugIn {
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int numberOfDimensions = var.getRank();
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long[] dimensions= var.getDims();
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logger.info("Reading dataset: " + datasetName + " Dimensions: " + numberOfDimensions + " Type: " + datatype.getDatatypeDescription());
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logger.info("Reading dataset: " + datasetName + " Dimensions: " + numberOfDimensions + " Type: " + datatype.getDescription());
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// Read dataset
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@@ -11,40 +11,40 @@ import java.util.regex.Pattern;
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import javax.swing.tree.DefaultMutableTreeNode;
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import ncsa.hdf.object.Attribute;
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import ncsa.hdf.object.Dataset;
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import ncsa.hdf.object.FileFormat;
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import ncsa.hdf.object.Group;
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import ncsa.hdf.object.HObject;
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import ncsa.hdf.object.h5.H5File;
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import hdf.object.Attribute;
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import hdf.object.Dataset;
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import hdf.object.FileFormat;
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import hdf.object.Group;
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import hdf.object.HObject;
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import hdf.object.h5.H5File;
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public class HDF5Utilities {
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private static final Logger logger = Logger.getLogger(HDF5Utilities.class.getName());
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|
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/**
|
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* Get attributes from object
|
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* @param object Object to retrieve the attributes from
|
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* @return Map of attributes or null if an error occurred while retrieving the attributes or the passed object is null
|
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*/
|
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public static Map<String,Attribute> getAttributes(HObject object) {
|
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Objects.requireNonNull(object);
|
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|
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Map<String, Attribute> attributes = new HashMap<>();
|
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try{
|
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for(Object m: object.getMetadata()){
|
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if(m instanceof Attribute){
|
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attributes.put(((Attribute) m).getName(), (Attribute) m);
|
||||
}
|
||||
}
|
||||
}
|
||||
catch(Exception e){
|
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logger.warning("Unable to retrieve metadata from object");
|
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return null;
|
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}
|
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|
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return attributes;
|
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}
|
||||
// /**
|
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// * Get attributes from object
|
||||
// * @param object Object to retrieve the attributes from
|
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// * @return Map of attributes or null if an error occurred while retrieving the attributes or the passed object is null
|
||||
// */
|
||||
// public static Map<String,Attribute> getAttributes(HObject object) {
|
||||
// Objects.requireNonNull(object);
|
||||
//
|
||||
// Map<String, Attribute> attributes = new HashMap<>();
|
||||
// try{
|
||||
// for(Object m: object.getMetadata()){
|
||||
// if(m instanceof Attribute){
|
||||
// attributes.put(((Attribute) m).getName(), (Attribute) m);
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
// catch(Exception e){
|
||||
// logger.warning("Unable to retrieve metadata from object");
|
||||
// return null;
|
||||
// }
|
||||
//
|
||||
// return attributes;
|
||||
// }
|
||||
|
||||
|
||||
/**
|
||||
@@ -85,7 +85,7 @@ public class HDF5Utilities {
|
||||
* @return
|
||||
*/
|
||||
public static Group createGroup( FileFormat file, String groupName) {
|
||||
return createGroup(file, (Group) ((DefaultMutableTreeNode) file.getRootNode()).getUserObject(), groupName);
|
||||
return createGroup(file, (Group) file.getRootObject(), groupName);
|
||||
}
|
||||
|
||||
/**
|
||||
@@ -100,7 +100,7 @@ public class HDF5Utilities {
|
||||
Objects.requireNonNull(groupName);
|
||||
|
||||
if (group == null){
|
||||
group = (Group) ((DefaultMutableTreeNode) file.getRootNode()).getUserObject();
|
||||
group = (Group) file.getRootObject();
|
||||
}
|
||||
|
||||
Group ngroup = group;
|
||||
@@ -130,7 +130,7 @@ public class HDF5Utilities {
|
||||
* @return
|
||||
*/
|
||||
public static List<Dataset> getDatasets(H5File file) {
|
||||
Group rootNode = (Group) ((javax.swing.tree.DefaultMutableTreeNode) file.getRootNode()).getUserObject();
|
||||
Group rootNode = (Group) file.getRootObject();
|
||||
List<Dataset> datasets = getDatasets(rootNode);
|
||||
return datasets;
|
||||
}
|
||||
|
||||
@@ -1,6 +1,12 @@
|
||||
package ch.psi.imagej.hdf5;
|
||||
|
||||
|
||||
import hdf.object.Dataset;
|
||||
import hdf.object.Datatype;
|
||||
import hdf.object.FileFormat;
|
||||
import hdf.object.Group;
|
||||
import hdf.object.h5.H5Datatype;
|
||||
import hdf.object.h5.H5File;
|
||||
import ij.*;
|
||||
import ij.io.*;
|
||||
import ij.plugin.filter.PlugInFilter;
|
||||
@@ -10,9 +16,9 @@ import ij.gui.*;
|
||||
import java.util.logging.Level;
|
||||
import java.util.logging.Logger;
|
||||
|
||||
import ncsa.hdf.object.*; // the common object package
|
||||
import ncsa.hdf.object.h5.*; // the HDF5 implementation
|
||||
import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
|
||||
//import hdf.object.*; // the common object package
|
||||
//import hdf.object.h5.*; // the HDF5 implementation
|
||||
import hdf.hdf5lib.exceptions.HDF5Exception;
|
||||
|
||||
public class HDF5Writer implements PlugInFilter {
|
||||
|
||||
@@ -60,18 +66,22 @@ public class HDF5Writer implements PlugInFilter {
|
||||
int imgColorType = imp.getType();
|
||||
|
||||
Datatype type = null;
|
||||
if (imgColorType == ImagePlus.GRAY8) {
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY8");
|
||||
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.GRAY16) {
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY16");
|
||||
type = new H5Datatype(Datatype.CLASS_INTEGER, 2, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.GRAY32) {
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY32");
|
||||
type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
|
||||
} else if (imgColorType == ImagePlus.COLOR_RGB) {
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: COLOR_RGB");
|
||||
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
try {
|
||||
if (imgColorType == ImagePlus.GRAY8) {
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY8");
|
||||
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.GRAY16) {
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY16");
|
||||
type = new H5Datatype(Datatype.CLASS_INTEGER, 2, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.GRAY32) {
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY32");
|
||||
type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
|
||||
} else if (imgColorType == ImagePlus.COLOR_RGB) {
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: COLOR_RGB");
|
||||
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
}
|
||||
} catch (Exception e){
|
||||
throw new RuntimeException("Unable to create dataset", e);
|
||||
}
|
||||
|
||||
if (imp.getOpenAsHyperStack() || imp.isHyperStack()) {
|
||||
|
||||
@@ -14,7 +14,7 @@ import javax.swing.JPanel;
|
||||
import javax.swing.JScrollPane;
|
||||
import javax.swing.ScrollPaneConstants;
|
||||
|
||||
import ncsa.hdf.object.Dataset;
|
||||
import hdf.object.Dataset;
|
||||
import javax.swing.JTextField;
|
||||
import java.awt.FlowLayout;
|
||||
|
||||
|
||||
@@ -3,8 +3,8 @@ package ch.psi.imagej.hdf5;
|
||||
import java.util.logging.Level;
|
||||
import java.util.logging.Logger;
|
||||
|
||||
import ncsa.hdf.object.Dataset;
|
||||
import ncsa.hdf.object.h5.H5File;
|
||||
import hdf.object.Dataset;
|
||||
import hdf.object.h5.H5File;
|
||||
import ij.ImageStack;
|
||||
import ij.process.ByteProcessor;
|
||||
import ij.process.ColorProcessor;
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,445 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
/**
|
||||
* A CompoundDS is a dataset with compound datatype.
|
||||
* <p>
|
||||
* A compound datatype is an aggregation of one or more datatypes. Each member
|
||||
* of a compound type has a name which is unique within that type, and a
|
||||
* datatype of that member in a compound datum. Compound datatypes can be nested,
|
||||
* i.e. members of a compound datatype can be some other compound datatype.
|
||||
* <p>
|
||||
* For more details on compound datatypes,
|
||||
* see <b> <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a> </b>
|
||||
* <p>
|
||||
* Since Java cannot handle C-structured compound data, data in a compound dataset
|
||||
* is loaded in to an Java List. Each element of the list is a data array that
|
||||
* corresponds to a compound field. The data is read/written by compound field.
|
||||
* <p>
|
||||
* For example, if compound dataset "comp" has the following nested structure,
|
||||
* and member datatypes
|
||||
*
|
||||
* <pre>
|
||||
* comp --> m01 (int)
|
||||
* comp --> m02 (float)
|
||||
* comp --> nest1 --> m11 (char)
|
||||
* comp --> nest1 --> m12 (String)
|
||||
* comp --> nest1 --> nest2 --> m21 (long)
|
||||
* comp --> nest1 --> nest2 --> m22 (double)
|
||||
* </pre>
|
||||
*
|
||||
* The data object is a Java list of six arrays: {int[], float[], char[],
|
||||
* Stirng[], long[] and double[]}.
|
||||
*
|
||||
*
|
||||
* @version 1.1 9/4/2007
|
||||
* @author Peter X. Cao
|
||||
*/
|
||||
public abstract class CompoundDS extends Dataset implements CompoundDataFormat {
|
||||
private static final long serialVersionUID = -4880399929644095662L;
|
||||
|
||||
private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(CompoundDS.class);
|
||||
|
||||
/**
|
||||
* A single character to separate the names of nested compound fields. An
|
||||
* extended ASCII character, 0x95, is used to avoid common characters in
|
||||
* compound names.
|
||||
*/
|
||||
public static final String SEPARATOR = "\u0095";
|
||||
|
||||
/**
|
||||
* The number of members of the compound dataset.
|
||||
*/
|
||||
protected int numberOfMembers;
|
||||
|
||||
/**
|
||||
* The names of members of the compound dataset.
|
||||
*/
|
||||
protected String[] memberNames;
|
||||
|
||||
/**
|
||||
* Returns array containing the total number of elements of the members of
|
||||
* this compound dataset.
|
||||
* <p>
|
||||
* For example, a compound dataset COMP has members of A, B and C as
|
||||
*
|
||||
* <pre>
|
||||
* COMP {
|
||||
* int A;
|
||||
* float B[5];
|
||||
* double C[2][3];
|
||||
* }
|
||||
* </pre>
|
||||
*
|
||||
* memberOrders is an integer array of {1, 5, 6} to indicate that member A
|
||||
* has one element, member B has 5 elements, and member C has 6 elements.
|
||||
*/
|
||||
protected int[] memberOrders;
|
||||
|
||||
/**
|
||||
* The dimension sizes of each member.
|
||||
* <p>
|
||||
* The i-th element of the Object[] is an integer array (int[]) that
|
||||
* contains the dimension sizes of the i-th member.
|
||||
*/
|
||||
protected transient Object[] memberDims;
|
||||
|
||||
/**
|
||||
* The datatypes of compound members.
|
||||
*/
|
||||
protected Datatype[] memberTypes;
|
||||
|
||||
/**
|
||||
* The array to store flags to indicate if a member of this compound
|
||||
* dataset is selected for read/write.
|
||||
* <p>
|
||||
* If a member is selected, the read/write will perform on the member.
|
||||
* Applications such as HDFView will only display the selected members of
|
||||
* the compound dataset.
|
||||
*
|
||||
* <pre>
|
||||
* For example, if a compound dataset has four members
|
||||
* String[] memberNames = {"X", "Y", "Z", "TIME"};
|
||||
* and
|
||||
* boolean[] isMemberSelected = {true, false, false, true};
|
||||
* members "X" and "TIME" are selected for read and write.
|
||||
* </pre>
|
||||
*/
|
||||
protected boolean[] isMemberSelected;
|
||||
|
||||
/**
|
||||
* Constructs a CompoundDS object with the given file, dataset name and path.
|
||||
* <p>
|
||||
* The dataset object represents an existing dataset in the file. For
|
||||
* example, new H5CompoundDS(file, "dset1", "/g0/") constructs a dataset
|
||||
* object that corresponds to the dataset, "dset1", at group "/g0/".
|
||||
* <p>
|
||||
* This object is usually constructed at FileFormat.open(), which loads the
|
||||
* file structure and object information into memory. It is rarely used
|
||||
* elsewhere.
|
||||
*
|
||||
* @param theFile
|
||||
* the file that contains the dataset.
|
||||
* @param dsName
|
||||
* the name of the CompoundDS, e.g. "compDS".
|
||||
* @param dsPath
|
||||
* the full path of the CompoundDS, e.g. "/g1".
|
||||
*/
|
||||
public CompoundDS(FileFormat theFile, String dsName, String dsPath) {
|
||||
this(theFile, dsName, dsPath, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* @deprecated Not for public use in the future.<br>
|
||||
* Using {@link #CompoundDS(FileFormat, String, String)}
|
||||
*
|
||||
* @param theFile
|
||||
* the file that contains the dataset.
|
||||
* @param dsName
|
||||
* the name of the CompoundDS, e.g. "compDS".
|
||||
* @param dsPath
|
||||
* the full path of the CompoundDS, e.g. "/g1".
|
||||
* @param oid
|
||||
* the oid of the CompoundDS.
|
||||
*/
|
||||
@Deprecated
|
||||
public CompoundDS(FileFormat theFile, String dsName, String dsPath, long[] oid) {
|
||||
super(theFile, dsName, dsPath, oid);
|
||||
|
||||
numberOfMembers = 0;
|
||||
memberNames = null;
|
||||
isMemberSelected = null;
|
||||
memberTypes = null;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the number of members of the compound dataset.
|
||||
*
|
||||
* @return the number of members of the compound dataset.
|
||||
*/
|
||||
@Override
|
||||
public final int getMemberCount() {
|
||||
return numberOfMembers;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the number of selected members of the compound dataset.
|
||||
*
|
||||
* Selected members are the compound fields which are selected for
|
||||
* read/write.
|
||||
* <p>
|
||||
* For example, in a compound datatype of {int A, float B, char[] C},
|
||||
* users can choose to retrieve only {A, C} from the dataset. In this
|
||||
* case, getSelectedMemberCount() returns two.
|
||||
*
|
||||
* @return the number of selected members.
|
||||
*/
|
||||
@Override
|
||||
public final int getSelectedMemberCount() {
|
||||
int count = 0;
|
||||
|
||||
if (isMemberSelected != null) {
|
||||
for (int i = 0; i < isMemberSelected.length; i++) {
|
||||
if (isMemberSelected[i]) {
|
||||
count++;
|
||||
}
|
||||
}
|
||||
}
|
||||
log.trace("count of selected members={}", count);
|
||||
|
||||
return count;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the names of the members of the compound dataset. The names of
|
||||
* compound members are stored in an array of Strings.
|
||||
* <p>
|
||||
* For example, for a compound datatype of {int A, float B, char[] C}
|
||||
* getMemberNames() returns ["A", "B", "C"}.
|
||||
*
|
||||
* @return the names of compound members.
|
||||
*/
|
||||
@Override
|
||||
public final String[] getMemberNames() {
|
||||
return memberNames;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns an array of the names of the selected members of the compound dataset.
|
||||
*
|
||||
* @return an array of the names of the selected members of the compound dataset.
|
||||
*/
|
||||
public final String[] getSelectedMemberNames() {
|
||||
if (isMemberSelected == null) {
|
||||
log.debug("getSelectedMemberNames(): isMemberSelected array is null");
|
||||
log.trace("getSelectedMemberNames(): finish");
|
||||
return memberNames;
|
||||
}
|
||||
|
||||
int idx = 0;
|
||||
String[] names = new String[getSelectedMemberCount()];
|
||||
for (int i = 0; i < isMemberSelected.length; i++) {
|
||||
if (isMemberSelected[i]) {
|
||||
names[idx++] = memberNames[i];
|
||||
}
|
||||
}
|
||||
|
||||
return names;
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if a member of the compound dataset is selected for read/write.
|
||||
*
|
||||
* @param idx
|
||||
* the index of compound member.
|
||||
*
|
||||
* @return true if the i-th memeber is selected; otherwise returns false.
|
||||
*/
|
||||
@Override
|
||||
public final boolean isMemberSelected(int idx) {
|
||||
if ((isMemberSelected != null) && (isMemberSelected.length > idx)) {
|
||||
return isMemberSelected[idx];
|
||||
}
|
||||
else {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Selects the i-th member for read/write.
|
||||
*
|
||||
* @param idx
|
||||
* the index of compound member.
|
||||
*/
|
||||
@Override
|
||||
public final void selectMember(int idx) {
|
||||
if ((isMemberSelected != null) && (isMemberSelected.length > idx)) {
|
||||
isMemberSelected[idx] = true;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Selects/deselects all members.
|
||||
*
|
||||
* @param selectAll
|
||||
* The indicator to select or deselect all members. If true, all
|
||||
* members are selected for read/write. If false, no member is
|
||||
* selected for read/write.
|
||||
*/
|
||||
@Override
|
||||
public final void setAllMemberSelection(boolean selectAll) {
|
||||
if (isMemberSelected == null) {
|
||||
return;
|
||||
}
|
||||
|
||||
for (int i = 0; i < isMemberSelected.length; i++) {
|
||||
isMemberSelected[i] = selectAll;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns array containing the total number of elements of the members of
|
||||
* the compound dataset.
|
||||
* <p>
|
||||
* For example, a compound dataset COMP has members of A, B and C as
|
||||
*
|
||||
* <pre>
|
||||
* COMP {
|
||||
* int A;
|
||||
* float B[5];
|
||||
* double C[2][3];
|
||||
* }
|
||||
* </pre>
|
||||
*
|
||||
* getMemberOrders() will return an integer array of {1, 5, 6} to indicate
|
||||
* that member A has one element, member B has 5 elements, and member C has
|
||||
* 6 elements.
|
||||
*
|
||||
* @return the array containing the total number of elements of the members
|
||||
* of compound.
|
||||
*/
|
||||
@Override
|
||||
public final int[] getMemberOrders() {
|
||||
return memberOrders;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns array containing the total number of elements of the selected
|
||||
* members of the compound dataset.
|
||||
*
|
||||
* <p>
|
||||
* For example, a compound dataset COMP has members of A, B and C as
|
||||
*
|
||||
* <pre>
|
||||
* COMP {
|
||||
* int A;
|
||||
* float B[5];
|
||||
* double C[2][3];
|
||||
* }
|
||||
* </pre>
|
||||
*
|
||||
* If A and B are selected, getSelectedMemberOrders() returns an array of
|
||||
* {1, 5}
|
||||
*
|
||||
* @return array containing the total number of elements of the selected
|
||||
* members of compound.
|
||||
*/
|
||||
@Override
|
||||
public final int[] getSelectedMemberOrders() {
|
||||
log.trace("getSelectedMemberOrders(): start");
|
||||
|
||||
if (isMemberSelected == null) {
|
||||
log.debug("getSelectedMemberOrders(): isMemberSelected array is null");
|
||||
log.trace("getSelectedMemberOrders(): finish");
|
||||
return memberOrders;
|
||||
}
|
||||
|
||||
int idx = 0;
|
||||
int[] orders = new int[getSelectedMemberCount()];
|
||||
for (int i = 0; i < isMemberSelected.length; i++) {
|
||||
if (isMemberSelected[i]) {
|
||||
orders[idx++] = memberOrders[i];
|
||||
}
|
||||
}
|
||||
|
||||
log.trace("getSelectedMemberOrders(): finish");
|
||||
|
||||
return orders;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the dimension sizes of the i-th member.
|
||||
* <p>
|
||||
* For example, a compound dataset COMP has members of A, B and C as
|
||||
*
|
||||
* <pre>
|
||||
* COMP {
|
||||
* int A;
|
||||
* float B[5];
|
||||
* double C[2][3];
|
||||
* }
|
||||
* </pre>
|
||||
*
|
||||
* getMemberDims(2) returns an array of {2, 3}, while getMemberDims(1)
|
||||
* returns an array of {5}, and getMemberDims(0) returns null.
|
||||
*
|
||||
* @param i the i-th member
|
||||
*
|
||||
* @return the dimension sizes of the i-th member, null if the compound
|
||||
* member is not an array.
|
||||
*/
|
||||
@Override
|
||||
public final int[] getMemberDims(int i) {
|
||||
if (memberDims == null) {
|
||||
return null;
|
||||
}
|
||||
return (int[]) memberDims[i];
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns an array of datatype objects of compound members.
|
||||
* <p>
|
||||
* Each member of a compound dataset has its own datatype. The datatype of a
|
||||
* member can be atomic or other compound datatype (nested compound).
|
||||
* Sub-classes set up the datatype objects at init().
|
||||
* <p>
|
||||
*
|
||||
* @return the array of datatype objects of the compound members.
|
||||
*/
|
||||
@Override
|
||||
public final Datatype[] getMemberTypes() {
|
||||
return memberTypes;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns an array of datatype objects of selected compound members.
|
||||
*
|
||||
* @return an array of datatype objects of selected compound members.
|
||||
*/
|
||||
@Override
|
||||
public final Datatype[] getSelectedMemberTypes() {
|
||||
log.trace("getSelectedMemberTypes(): start");
|
||||
|
||||
if (isMemberSelected == null) {
|
||||
log.debug("getSelectedMemberTypes(): isMemberSelected array is null");
|
||||
log.trace("getSelectedMemberTypes(): finish");
|
||||
return memberTypes;
|
||||
}
|
||||
|
||||
int idx = 0;
|
||||
Datatype[] types = new Datatype[getSelectedMemberCount()];
|
||||
for (int i = 0; i < isMemberSelected.length; i++) {
|
||||
if (isMemberSelected[i]) {
|
||||
types[idx++] = memberTypes[i];
|
||||
}
|
||||
}
|
||||
|
||||
log.trace("getSelectedMemberTypes(): finish");
|
||||
|
||||
return types;
|
||||
}
|
||||
|
||||
/**
|
||||
* @deprecated Not implemented for compound dataset.
|
||||
*/
|
||||
@Deprecated
|
||||
@Override
|
||||
public Dataset copy(Group pgroup, String name, long[] dims, Object data)
|
||||
throws Exception {
|
||||
throw new UnsupportedOperationException(
|
||||
"Writing a subset of a compound dataset to a new dataset is not implemented.");
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,184 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
/**
|
||||
* An interface that provides general operations for data with a Compound
|
||||
* datatype. For example, getting the names, dataspaces or datatypes of the
|
||||
* members of the Compound datatype.
|
||||
* <p>
|
||||
*
|
||||
* @see hdf.object.HObject
|
||||
*
|
||||
* @version 1.0 5/3/2018
|
||||
* @author Jordan T. Henderson
|
||||
*/
|
||||
public interface CompoundDataFormat extends DataFormat {
|
||||
|
||||
/**
|
||||
* Returns the number of members of the compound data object.
|
||||
*
|
||||
* @return the number of members of the compound data object.
|
||||
*/
|
||||
public abstract int getMemberCount();
|
||||
|
||||
/**
|
||||
* Returns the number of selected members of the compound data object.
|
||||
*
|
||||
* Selected members are the compound fields which are selected for read/write.
|
||||
* <p>
|
||||
* For example, in a compound datatype of {int A, float B, char[] C}, users can
|
||||
* choose to retrieve only {A, C} from the data object. In this case,
|
||||
* getSelectedMemberCount() returns two.
|
||||
*
|
||||
* @return the number of selected members.
|
||||
*/
|
||||
public abstract int getSelectedMemberCount();
|
||||
|
||||
/**
|
||||
* Returns the names of the members of the compound data object. The names of
|
||||
* compound members are stored in an array of Strings.
|
||||
* <p>
|
||||
* For example, for a compound datatype of {int A, float B, char[] C}
|
||||
* getMemberNames() returns ["A", "B", "C"}.
|
||||
*
|
||||
* @return the names of compound members.
|
||||
*/
|
||||
public abstract String[] getMemberNames();
|
||||
|
||||
/**
|
||||
* Returns an array of the names of the selected compound members.
|
||||
*
|
||||
* @return an array of the names of the selected compound members.
|
||||
*/
|
||||
public abstract String[] getSelectedMemberNames();
|
||||
|
||||
/**
|
||||
* Checks if a member of the compound data object is selected for read/write.
|
||||
*
|
||||
* @param idx
|
||||
* the index of compound member.
|
||||
*
|
||||
* @return true if the i-th memeber is selected; otherwise returns false.
|
||||
*/
|
||||
public abstract boolean isMemberSelected(int idx);
|
||||
|
||||
/**
|
||||
* Selects the i-th member for read/write.
|
||||
*
|
||||
* @param idx
|
||||
* the index of compound member.
|
||||
*/
|
||||
public abstract void selectMember(int idx);
|
||||
|
||||
/**
|
||||
* Selects/deselects all members.
|
||||
*
|
||||
* @param selectAll
|
||||
* The indicator to select or deselect all members. If true, all
|
||||
* members are selected for read/write. If false, no member is
|
||||
* selected for read/write.
|
||||
*/
|
||||
public abstract void setAllMemberSelection(boolean selectAll);
|
||||
|
||||
/**
|
||||
* Returns array containing the total number of elements of the members of the
|
||||
* compound data object.
|
||||
* <p>
|
||||
* For example, a compound dataset COMP has members of A, B and C as
|
||||
*
|
||||
* <pre>
|
||||
* COMP {
|
||||
* int A;
|
||||
* float B[5];
|
||||
* double C[2][3];
|
||||
* }
|
||||
* </pre>
|
||||
*
|
||||
* getMemberOrders() will return an integer array of {1, 5, 6} to indicate that
|
||||
* member A has one element, member B has 5 elements, and member C has 6
|
||||
* elements.
|
||||
*
|
||||
* @return the array containing the total number of elements of the members of
|
||||
* the compound data object.
|
||||
*/
|
||||
public abstract int[] getMemberOrders();
|
||||
|
||||
/**
|
||||
* Returns array containing the total number of elements of the selected members
|
||||
* of the compound data object.
|
||||
*
|
||||
* <p>
|
||||
* For example, a compound dataset COMP has members of A, B and C as
|
||||
*
|
||||
* <pre>
|
||||
* COMP {
|
||||
* int A;
|
||||
* float B[5];
|
||||
* double C[2][3];
|
||||
* }
|
||||
* </pre>
|
||||
*
|
||||
* If A and B are selected, getSelectedMemberOrders() returns an array of {1, 5}
|
||||
*
|
||||
* @return array containing the total number of elements of the selected members
|
||||
* of the compound data object.
|
||||
*/
|
||||
public abstract int[] getSelectedMemberOrders();
|
||||
|
||||
/**
|
||||
* Returns the dimension sizes of the i-th member.
|
||||
* <p>
|
||||
* For example, a compound dataset COMP has members of A, B and C as
|
||||
*
|
||||
* <pre>
|
||||
* COMP {
|
||||
* int A;
|
||||
* float B[5];
|
||||
* double C[2][3];
|
||||
* }
|
||||
* </pre>
|
||||
*
|
||||
* getMemberDims(2) returns an array of {2, 3}, while getMemberDims(1) returns
|
||||
* an array of {5}, and getMemberDims(0) returns null.
|
||||
*
|
||||
* @param i
|
||||
* the i-th member
|
||||
*
|
||||
* @return the dimension sizes of the i-th member, null if the compound member
|
||||
* is not an array.
|
||||
*/
|
||||
public abstract int[] getMemberDims(int i);
|
||||
|
||||
/**
|
||||
* Returns an array of datatype objects of the compound members.
|
||||
* <p>
|
||||
* Each member of a compound data object has its own datatype. The datatype of a
|
||||
* member can be atomic or other compound datatype (nested compound). The
|
||||
* datatype objects are setup at init().
|
||||
* <p>
|
||||
*
|
||||
* @return the array of datatype objects of the compound members.
|
||||
*/
|
||||
public abstract Datatype[] getMemberTypes();
|
||||
|
||||
/**
|
||||
* Returns an array of datatype objects of the selected compound members.
|
||||
*
|
||||
* @return an array of datatype objects of the selected compound members.
|
||||
*/
|
||||
public abstract Datatype[] getSelectedMemberTypes();
|
||||
|
||||
}
|
||||
@@ -0,0 +1,366 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
/**
|
||||
* An interface that provides general I/O operations for object data. For
|
||||
* example, reading data content from the file into memory or writing data
|
||||
* content from memory into the file.
|
||||
* <p>
|
||||
*
|
||||
* @see hdf.object.HObject
|
||||
*
|
||||
* @version 1.0 4/2/2018
|
||||
* @author Jordan T. Henderson
|
||||
*/
|
||||
public interface DataFormat {
|
||||
public abstract boolean isInited();
|
||||
|
||||
public abstract void init();
|
||||
|
||||
/**
|
||||
* Retrieves the object's data from the file.
|
||||
*
|
||||
* @return the object's data.
|
||||
*
|
||||
* @throws Exception
|
||||
* if the data can not be retrieved
|
||||
*/
|
||||
public abstract Object getData() throws Exception, OutOfMemoryError;
|
||||
|
||||
/**
|
||||
*
|
||||
*
|
||||
* @param data
|
||||
* the data to write.
|
||||
*/
|
||||
public abstract void setData(Object data);
|
||||
|
||||
/**
|
||||
* Clears the current data buffer in memory and forces the next read() to load
|
||||
* the data from file.
|
||||
* <p>
|
||||
* The function read() loads data from file into memory only if the data is not
|
||||
* read. If data is already in memory, read() just returns the memory buffer.
|
||||
* Sometimes we want to force read() to re-read data from file. For example,
|
||||
* when the selection is changed, we need to re-read the data.
|
||||
*
|
||||
* @see #getData()
|
||||
* @see #read()
|
||||
*/
|
||||
public abstract void clearData();
|
||||
|
||||
/**
|
||||
* Reads the data from file.
|
||||
* <p>
|
||||
* read() reads the data from file to a memory buffer and returns the memory
|
||||
* buffer. The dataset object does not hold the memory buffer. To store the
|
||||
* memory buffer in the dataset object, one must call getData().
|
||||
* <p>
|
||||
* By default, the whole dataset is read into memory. Users can also select
|
||||
* a subset to read. Subsetting is done in an implicit way.
|
||||
*
|
||||
* @return the data read from file.
|
||||
*
|
||||
* @see #getData()
|
||||
*
|
||||
* @throws Exception
|
||||
* if object can not be read
|
||||
* @throws OutOfMemoryError
|
||||
* if memory is exhausted
|
||||
*/
|
||||
public abstract Object read() throws Exception, OutOfMemoryError;
|
||||
|
||||
/**
|
||||
* Writes a memory buffer to the object in the file.
|
||||
*
|
||||
* @param buf
|
||||
* the data to write
|
||||
*
|
||||
* @throws Exception
|
||||
* if data can not be written
|
||||
*/
|
||||
public abstract void write(Object buf) throws Exception;
|
||||
|
||||
/**
|
||||
* Writes the current memory buffer to the object in the file.
|
||||
*
|
||||
* @throws Exception
|
||||
* if data can not be written
|
||||
*/
|
||||
public abstract void write() throws Exception;
|
||||
|
||||
/**
|
||||
* Converts the data values of this data object to appropriate Java integers if
|
||||
* they are unsigned integers.
|
||||
*
|
||||
* @see hdf.object.Dataset#convertToUnsignedC(Object)
|
||||
* @see hdf.object.Dataset#convertFromUnsignedC(Object, Object)
|
||||
*
|
||||
* @return the converted data buffer.
|
||||
*/
|
||||
public Object convertFromUnsignedC();
|
||||
|
||||
/**
|
||||
* Converts Java integer data values of this data object back to unsigned C-type
|
||||
* integer data if they are unsigned integers.
|
||||
*
|
||||
* @see hdf.object.Dataset#convertToUnsignedC(Object)
|
||||
* @see hdf.object.Dataset#convertToUnsignedC(Object, Object)
|
||||
*
|
||||
* @return the converted data buffer.
|
||||
*/
|
||||
public Object convertToUnsignedC();
|
||||
|
||||
/**
|
||||
* Returns the fill values for the data object.
|
||||
*
|
||||
* @return the fill values for the data object.
|
||||
*/
|
||||
public abstract Object getFillValue();
|
||||
|
||||
/**
|
||||
* Returns the datatype of the data object.
|
||||
*
|
||||
* @return the datatype of the data object.
|
||||
*/
|
||||
public abstract Datatype getDatatype();
|
||||
|
||||
/**
|
||||
* Returns the rank (number of dimensions) of the data object. It returns a
|
||||
* negative number if it failed to retrieve the dimension information from
|
||||
* the file.
|
||||
*
|
||||
* @return the number of dimensions of the data object.
|
||||
*/
|
||||
public abstract int getRank();
|
||||
|
||||
/**
|
||||
* Returns the array that contains the dimension sizes of the data value of
|
||||
* the data object. It returns null if it failed to retrieve the dimension
|
||||
* information from the file.
|
||||
*
|
||||
* @return the dimension sizes of the data object.
|
||||
*/
|
||||
public abstract long[] getDims();
|
||||
|
||||
|
||||
/****************************************************************
|
||||
* * The following four definitions are used for data subsetting. * *
|
||||
****************************************************************/
|
||||
|
||||
/**
|
||||
* Returns the dimension sizes of the selected subset.
|
||||
* <p>
|
||||
* The SelectedDims is the number of data points of the selected subset.
|
||||
* Applications can use this array to change the size of selected subset.
|
||||
*
|
||||
* The selected size must be less than or equal to the current dimension size.
|
||||
* Combined with the starting position, selected sizes and stride, the subset of
|
||||
* a rectangle selection is fully defined.
|
||||
* <p>
|
||||
* For example, if a 4 X 5 dataset is as follows:
|
||||
*
|
||||
* <pre>
|
||||
* 0, 1, 2, 3, 4
|
||||
* 10, 11, 12, 13, 14
|
||||
* 20, 21, 22, 23, 24
|
||||
* 30, 31, 32, 33, 34
|
||||
* long[] dims = {4, 5};
|
||||
* long[] startDims = {1, 2};
|
||||
* long[] selectedDims = {3, 3};
|
||||
* long[] selectedStride = {1, 1};
|
||||
* then the following subset is selected by the startDims and selectedDims
|
||||
* 12, 13, 14
|
||||
* 22, 23, 24
|
||||
* 32, 33, 34
|
||||
* </pre>
|
||||
*
|
||||
* @return the dimension sizes of the selected subset.
|
||||
*/
|
||||
public abstract long[] getSelectedDims();
|
||||
|
||||
/**
|
||||
* Returns the starting position of a selected subset.
|
||||
* <p>
|
||||
* Applications can use this array to change the starting position of a
|
||||
* selection. Combined with the selected dimensions, selected sizes and stride,
|
||||
* the subset of a rectangle selection is fully defined.
|
||||
* <p>
|
||||
* For example, if a 4 X 5 dataset is as follows:
|
||||
*
|
||||
* <pre>
|
||||
* 0, 1, 2, 3, 4
|
||||
* 10, 11, 12, 13, 14
|
||||
* 20, 21, 22, 23, 24
|
||||
* 30, 31, 32, 33, 34
|
||||
* long[] dims = {4, 5};
|
||||
* long[] startDims = {1, 2};
|
||||
* long[] selectedDims = {3, 3};
|
||||
* long[] selectedStride = {1, 1};
|
||||
* then the following subset is selected by the startDims and selectedDims
|
||||
* 12, 13, 14
|
||||
* 22, 23, 24
|
||||
* 32, 33, 34
|
||||
* </pre>
|
||||
*
|
||||
* @return the starting position of a selected subset.
|
||||
*/
|
||||
public abstract long[] getStartDims();
|
||||
|
||||
/**
|
||||
* Returns the selectedStride of the selected dataset.
|
||||
* <p>
|
||||
* Applications can use this array to change how many elements to move in each
|
||||
* dimension.
|
||||
*
|
||||
* Combined with the starting position and selected sizes, the subset of a
|
||||
* rectangle selection is defined.
|
||||
* <p>
|
||||
* For example, if a 4 X 5 dataset is as follows:
|
||||
*
|
||||
* <pre>
|
||||
* 0, 1, 2, 3, 4
|
||||
* 10, 11, 12, 13, 14
|
||||
* 20, 21, 22, 23, 24
|
||||
* 30, 31, 32, 33, 34
|
||||
* long[] dims = {4, 5};
|
||||
* long[] startDims = {0, 0};
|
||||
* long[] selectedDims = {2, 2};
|
||||
* long[] selectedStride = {2, 3};
|
||||
* then the following subset is selected by the startDims and selectedDims
|
||||
* 0, 3
|
||||
* 20, 23
|
||||
* </pre>
|
||||
*
|
||||
* @return the selectedStride of the selected dataset.
|
||||
*/
|
||||
public abstract long[] getStride();
|
||||
|
||||
/**
|
||||
* Returns the indices of display order.
|
||||
* <p>
|
||||
*
|
||||
* selectedIndex[] is provided for two purposes:
|
||||
* <OL>
|
||||
* <LI>selectedIndex[] is used to indicate the order of dimensions for display.
|
||||
* selectedIndex[0] is for the row, selectedIndex[1] is for the column and
|
||||
* selectedIndex[2] for the depth.
|
||||
* <p>
|
||||
* For example, for a four dimension dataset, if selectedIndex[] = {1, 2, 3},
|
||||
* then dim[1] is selected as row index, dim[2] is selected as column index and
|
||||
* dim[3] is selected as depth index.
|
||||
* <LI>selectedIndex[] is also used to select dimensions for display for
|
||||
* datasets with three or more dimensions. We assume that applications such as
|
||||
* HDFView can only display data values up to three dimensions (2D
|
||||
* spreadsheet/image with a third dimension which the 2D spreadsheet/image is
|
||||
* selected from). For datasets with more than three dimensions, we need
|
||||
* selectedIndex[] to tell applications which three dimensions are chosen for
|
||||
* display. <br>
|
||||
* For example, for a four dimension dataset, if selectedIndex[] = {1, 2, 3},
|
||||
* then dim[1] is selected as row index, dim[2] is selected as column index and
|
||||
* dim[3] is selected as depth index. dim[0] is not selected. Its location is
|
||||
* fixed at 0 by default.
|
||||
* </OL>
|
||||
*
|
||||
* @return the array of the indices of display order.
|
||||
*/
|
||||
public int[] getSelectedIndex();
|
||||
|
||||
/**************************************************************************
|
||||
* * The following two definitions are used primarily for GUI applications. * *
|
||||
**************************************************************************/
|
||||
|
||||
/**
|
||||
* Returns the dimension size of the vertical axis.
|
||||
*
|
||||
* <p>
|
||||
* This function is used by GUI applications such as HDFView. GUI applications
|
||||
* display a dataset in a 2D table or 2D image. The display order is specified
|
||||
* by the index array of selectedIndex as follow:
|
||||
* <dl>
|
||||
* <dt>selectedIndex[0] -- height</dt>
|
||||
* <dd>The vertical axis</dd>
|
||||
* <dt>selectedIndex[1] -- width</dt>
|
||||
* <dd>The horizontal axis</dd>
|
||||
* <dt>selectedIndex[2] -- depth</dt>
|
||||
* <dd>The depth axis is used for 3 or more dimensional datasets.</dd>
|
||||
* </dl>
|
||||
* Applications can use getSelectedIndex() to access and change the display
|
||||
* order. For example, in a 2D dataset of 200x50 (dim0=200, dim1=50), the
|
||||
* following code will set the height=200 and width=50.
|
||||
*
|
||||
* <pre>
|
||||
* int[] selectedIndex = dataset.getSelectedIndex();
|
||||
* selectedIndex[0] = 0;
|
||||
* selectedIndex[1] = 1;
|
||||
* </pre>
|
||||
*
|
||||
* @see #getSelectedIndex()
|
||||
* @see #getWidth()
|
||||
*
|
||||
* @return the size of dimension of the vertical axis.
|
||||
*/
|
||||
public long getHeight();
|
||||
|
||||
/**
|
||||
* Returns the dimension size of the horizontal axis.
|
||||
*
|
||||
* <p>
|
||||
* This function is used by GUI applications such as HDFView. GUI applications
|
||||
* display a dataset in 2D Table or 2D Image. The display order is specified by
|
||||
* the index array of selectedIndex as follow:
|
||||
* <dl>
|
||||
* <dt>selectedIndex[0] -- height</dt>
|
||||
* <dd>The vertical axis</dd>
|
||||
* <dt>selectedIndex[1] -- width</dt>
|
||||
* <dd>The horizontal axis</dd>
|
||||
* <dt>selectedIndex[2] -- depth</dt>
|
||||
* <dd>The depth axis, which is used for 3 or more dimension datasets.</dd>
|
||||
* </dl>
|
||||
* Applications can use getSelectedIndex() to access and change the display
|
||||
* order. For example, in a 2D dataset of 200x50 (dim0=200, dim1=50), the
|
||||
* following code will set the height=200 and width=100.
|
||||
*
|
||||
* <pre>
|
||||
* int[] selectedIndex = dataset.getSelectedIndex();
|
||||
* selectedIndex[0] = 0;
|
||||
* selectedIndex[1] = 1;
|
||||
* </pre>
|
||||
*
|
||||
* @see #getSelectedIndex()
|
||||
* @see #getHeight()
|
||||
*
|
||||
* @return the size of dimension of the horizontal axis.
|
||||
*/
|
||||
public long getWidth();
|
||||
|
||||
/**
|
||||
* Returns the string representation of compression information.
|
||||
* <p>
|
||||
* For example, "SZIP: Pixels per block = 8: H5Z_FILTER_CONFIG_DECODE_ENABLED".
|
||||
*
|
||||
* @return the string representation of compression information.
|
||||
*/
|
||||
public abstract String getCompression();
|
||||
|
||||
/**
|
||||
* Get runtime Class of the original data buffer if converted.
|
||||
*
|
||||
* @return the Class of the original data buffer
|
||||
*/
|
||||
@SuppressWarnings("rawtypes")
|
||||
public abstract Class getOriginalClass();
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,933 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Map.Entry;
|
||||
|
||||
/**
|
||||
* Datatype is an abstract class that defines datatype characteristics and APIs for a data type.
|
||||
* <p>
|
||||
* A datatype has four basic characteristics: class, size, byte order and sign. These
|
||||
* characteristics are defined in the
|
||||
* <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>.
|
||||
* <p>
|
||||
* These characteristics apply to all the sub-classes. The sub-classes may have different ways to
|
||||
* describe a datatype. We here define the <strong> native datatype</strong> to the datatype used by
|
||||
* the sub-class. For example, H5Datatype uses a datatype identifier (hid_t) to specify a datatype.
|
||||
* NC2Datatype uses ucar.nc2.DataType object to describe its datatype. "Native" here is different
|
||||
* from the "native" definition in the HDF5 library.
|
||||
* <p>
|
||||
* Two functions, createNative() and fromNative(), are defined to convert the general
|
||||
* characteristics to/from the native datatype. Sub-classes must implement these functions so that
|
||||
* the conversion will be done correctly. The values of the CLASS member are not identical to HDF5
|
||||
* values for a datatype class.
|
||||
* <p>
|
||||
*
|
||||
* @version 1.1 9/4/2007
|
||||
* @author Peter X. Cao
|
||||
*/
|
||||
public abstract class Datatype extends HObject implements MetaDataContainer {
|
||||
|
||||
private static final long serialVersionUID = -581324710549963177L;
|
||||
|
||||
private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(Datatype.class);
|
||||
|
||||
/**
|
||||
* The default definition for datatype size, order, and sign.
|
||||
*/
|
||||
public static final int NATIVE = -1;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_NO_CLASS = -1;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_INTEGER = 0;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_FLOAT = 1;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_CHAR = 2;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_STRING = 3;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_BITFIELD = 4;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_OPAQUE = 5;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_COMPOUND = 6;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_REFERENCE = 7;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_ENUM = 8;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_VLEN = 9;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_ARRAY = 10;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int CLASS_TIME = 11;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int ORDER_LE = 0;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int ORDER_BE = 1;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int ORDER_VAX = 2;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int ORDER_NONE = 3;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int SIGN_NONE = 0;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int SIGN_2 = 1;
|
||||
|
||||
/**
|
||||
* See <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*/
|
||||
public static final int NSGN = 2;
|
||||
|
||||
protected String datatypeDescription = null;
|
||||
|
||||
/**
|
||||
* The class of the datatype.
|
||||
*/
|
||||
protected int datatypeClass;
|
||||
|
||||
/**
|
||||
* The size (in bytes) of the datatype.
|
||||
*/
|
||||
protected long datatypeSize;
|
||||
|
||||
/**
|
||||
* The byte order of the datatype. Valid values are ORDER_LE, ORDER_BE, and
|
||||
* ORDER_VAX.
|
||||
*/
|
||||
protected int datatypeOrder;
|
||||
|
||||
/**
|
||||
* The sign of the datatype.
|
||||
*/
|
||||
protected int datatypeSign;
|
||||
|
||||
/**
|
||||
* The base datatype of this datatype (null if this datatype is atomic).
|
||||
*/
|
||||
protected Datatype baseType;
|
||||
|
||||
/**
|
||||
* The dimensions of the ARRAY element of an ARRAY datatype.
|
||||
*/
|
||||
protected long[] arrayDims;
|
||||
|
||||
/**
|
||||
* Determines whether this datatype is a variable-length type.
|
||||
*/
|
||||
protected boolean isVLEN = false;
|
||||
protected boolean isVariableStr = false;
|
||||
|
||||
/**
|
||||
* The (name, value) pairs of enum members.
|
||||
*/
|
||||
protected Map<String, String> enumMembers;
|
||||
|
||||
/**
|
||||
* The list of names of members of a compound Datatype.
|
||||
*/
|
||||
protected List<String> compoundMemberNames;
|
||||
|
||||
/**
|
||||
* The list of types of members of a compound Datatype.
|
||||
*/
|
||||
protected List<Datatype> compoundMemberTypes;
|
||||
|
||||
/**
|
||||
* The list of offsets of members of a compound Datatype.
|
||||
*/
|
||||
protected List<Long> compoundMemberOffsets;
|
||||
|
||||
/**
|
||||
* Constructs a named datatype with a given file, name and path.
|
||||
*
|
||||
* @param theFile
|
||||
* the HDF file.
|
||||
* @param typeName
|
||||
* the name of the datatype, e.g "12-bit Integer".
|
||||
* @param typePath
|
||||
* the full group path of the datatype, e.g. "/datatypes/".
|
||||
*/
|
||||
public Datatype(FileFormat theFile, String typeName, String typePath) {
|
||||
this(theFile, typeName, typePath, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* @deprecated Not for public use in the future.<br>
|
||||
* Using {@link #Datatype(FileFormat, String, String)}
|
||||
*
|
||||
* @param theFile
|
||||
* the HDF file.
|
||||
* @param typeName
|
||||
* the name of the datatype, e.g "12-bit Integer".
|
||||
* @param typePath
|
||||
* the full group path of the datatype, e.g. "/datatypes/".
|
||||
* @param oid
|
||||
* the oidof the datatype.
|
||||
*/
|
||||
@Deprecated
|
||||
public Datatype(FileFormat theFile, String typeName, String typePath, long[] oid) {
|
||||
super(theFile, typeName, typePath, oid);
|
||||
}
|
||||
|
||||
/**
|
||||
* Constructs a Datatype with specified class, size, byte order and sign.
|
||||
* <p>
|
||||
* The following is a list of a few examples of Datatype.
|
||||
* <ol>
|
||||
* <li>to create unsigned native integer<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_INTEGER, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
* <li>to create 16-bit signed integer with big endian<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_INTEGER, 2, Datatype.ORDER_BE, Datatype.NATIVE);
|
||||
* <li>to create native float<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, Datatype.NATIVE);
|
||||
* <li>to create 64-bit double<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, Datatype.NATIVE);
|
||||
* </ol>
|
||||
*
|
||||
* @param tclass
|
||||
* the class of the datatype, e.g. CLASS_INTEGER, CLASS_FLOAT and etc.
|
||||
* @param tsize
|
||||
* the size of the datatype in bytes, e.g. for a 32-bit integer, the size is 4.
|
||||
* Valid values are NATIVE or a positive value.
|
||||
* @param torder
|
||||
* the byte order of the datatype. Valid values are ORDER_LE, ORDER_BE, ORDER_VAX,
|
||||
* ORDER_NONE and NATIVE.
|
||||
* @param tsign
|
||||
* the sign of the datatype. Valid values are SIGN_NONE, SIGN_2 and NATIVE.
|
||||
*
|
||||
* @throws Exception
|
||||
* if there is an error
|
||||
*/
|
||||
public Datatype(int tclass, int tsize, int torder, int tsign) throws Exception {
|
||||
this(tclass, tsize, torder, tsign, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Constructs a Datatype with specified class, size, byte order and sign.
|
||||
* <p>
|
||||
* The following is a list of a few examples of Datatype.
|
||||
* <ol>
|
||||
* <li>to create unsigned native integer<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_INTEGER, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
* <li>to create 16-bit signed integer with big endian<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_INTEGER, 2, Datatype.ORDER_BE, Datatype.NATIVE);
|
||||
* <li>to create native float<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, Datatype.NATIVE);
|
||||
* <li>to create 64-bit double<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, Datatype.NATIVE);
|
||||
* </ol>
|
||||
*
|
||||
* @param tclass
|
||||
* the class of the datatype, e.g. CLASS_INTEGER, CLASS_FLOAT and
|
||||
* etc.
|
||||
* @param tsize
|
||||
* the size of the datatype in bytes, e.g. for a 32-bit integer,
|
||||
* the size is 4.
|
||||
* Valid values are NATIVE or a positive value.
|
||||
* @param torder
|
||||
* the byte order of the datatype. Valid values are ORDER_LE,
|
||||
* ORDER_BE, ORDER_VAX, ORDER_NONE and NATIVE.
|
||||
* @param tsign
|
||||
* the sign of the datatype. Valid values are SIGN_NONE, SIGN_2 and NATIVE.
|
||||
* @param tbase
|
||||
* the base datatype of the new datatype
|
||||
*
|
||||
* @throws Exception
|
||||
* if there is an error
|
||||
*/
|
||||
public Datatype(int tclass, int tsize, int torder, int tsign, Datatype tbase) throws Exception {
|
||||
this(tclass, tsize, torder, tsign, tbase, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Constructs a Datatype with specified class, size, byte order and sign.
|
||||
* <p>
|
||||
* The following is a list of a few examples of Datatype.
|
||||
* <ol>
|
||||
* <li>to create unsigned native integer<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_INTEGER, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
* <li>to create 16-bit signed integer with big endian<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_INTEGER, 2, Datatype.ORDER_BE, Datatype.NATIVE);
|
||||
* <li>to create native float<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, Datatype.NATIVE);
|
||||
* <li>to create 64-bit double<br>
|
||||
* Datatype type = new Dataype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, Datatype.NATIVE);
|
||||
* </ol>
|
||||
*
|
||||
* @param tclass
|
||||
* the class of the datatype, e.g. CLASS_INTEGER, CLASS_FLOAT and etc.
|
||||
* @param tsize
|
||||
* the size of the datatype in bytes, e.g. for a 32-bit integer, the size is 4.
|
||||
* Valid values are NATIVE or a positive value.
|
||||
* @param torder
|
||||
* the byte order of the datatype. Valid values are ORDER_LE, ORDER_BE, ORDER_VAX,
|
||||
* ORDER_NONE and NATIVE.
|
||||
* @param tsign
|
||||
* the sign of the datatype. Valid values are SIGN_NONE, SIGN_2 and NATIVE.
|
||||
* @param tbase
|
||||
* the base datatype of the new datatype
|
||||
* @param pbase
|
||||
* the parent datatype of the new datatype
|
||||
*
|
||||
* @throws Exception
|
||||
* if there is an error
|
||||
*/
|
||||
public Datatype(int tclass, int tsize, int torder, int tsign, Datatype tbase, Datatype pbase) throws Exception {
|
||||
if ((tsize == 0) || (tsize < 0 && tsize != NATIVE))
|
||||
throw new Exception("invalid datatype size - " + tsize);
|
||||
if ((torder != ORDER_LE) && (torder != ORDER_BE) && (torder != ORDER_VAX)
|
||||
&& (torder != ORDER_NONE) && (torder != NATIVE))
|
||||
throw new Exception("invalid datatype order - " + torder);
|
||||
if ((tsign != SIGN_NONE) && (tsign != SIGN_2) && (tsign != NATIVE))
|
||||
throw new Exception("invalid datatype sign - " + tsign);
|
||||
|
||||
datatypeClass = tclass;
|
||||
datatypeSize = tsize;
|
||||
datatypeOrder = torder;
|
||||
datatypeSign = tsign;
|
||||
enumMembers = null;
|
||||
baseType = tbase;
|
||||
arrayDims = null;
|
||||
isVariableStr = (datatypeClass == Datatype.CLASS_STRING) && (tsize < 0);
|
||||
isVLEN = (datatypeClass == Datatype.CLASS_VLEN) || isVariableStr;
|
||||
|
||||
compoundMemberNames = new ArrayList<>();
|
||||
compoundMemberTypes = new ArrayList<>();
|
||||
compoundMemberOffsets = new ArrayList<>();
|
||||
|
||||
log.trace("datatypeClass={} datatypeSize={} datatypeOrder={} datatypeSign={} baseType={}",
|
||||
datatypeClass, datatypeSize, datatypeOrder, datatypeSign, baseType);
|
||||
}
|
||||
|
||||
/**
|
||||
* Constructs a Datatype with a given native datatype identifier.
|
||||
* <p>
|
||||
* For example, if the datatype identifier is a 32-bit unsigned integer created from HDF5,
|
||||
*
|
||||
* <pre>
|
||||
* long tid = H5.H5Tcopy(HDF5Constants.H5T_NATIVE_UNINT32);
|
||||
* Datatype dtype = new Datatype(tid);
|
||||
* </pre>
|
||||
*
|
||||
* will construct a datatype equivalent to new Datatype(CLASS_INTEGER, 4, NATIVE, SIGN_NONE);
|
||||
*
|
||||
* @see #fromNative(long tid)
|
||||
* @param tid
|
||||
* the native datatype identifier.
|
||||
*
|
||||
* @throws Exception
|
||||
* if there is an error
|
||||
*/
|
||||
public Datatype(long tid) throws Exception {
|
||||
this(tid, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Constructs a Datatype with a given native datatype identifier.
|
||||
* <p>
|
||||
* For example, if the datatype identifier is a 32-bit unsigned integer created from HDF5,
|
||||
*
|
||||
* <pre>
|
||||
* long tid = H5.H5Tcopy(HDF5Constants.H5T_NATIVE_UNINT32);
|
||||
* Datatype dtype = new Datatype(tid);
|
||||
* </pre>
|
||||
*
|
||||
* will construct a datatype equivalent to new Datatype(CLASS_INTEGER, 4, NATIVE, SIGN_NONE);
|
||||
*
|
||||
* @see #fromNative(long tid)
|
||||
* @param tid
|
||||
* the native datatype identifier.
|
||||
* @param pbase
|
||||
* the parent datatype of the new datatype
|
||||
*
|
||||
* @throws Exception
|
||||
* if there is an error
|
||||
*/
|
||||
public Datatype(long tid, Datatype pbase) throws Exception {
|
||||
this(CLASS_NO_CLASS, NATIVE, NATIVE, NATIVE, null, pbase);
|
||||
}
|
||||
|
||||
/**
|
||||
* Opens access to this named datatype. Sub-classes must replace this default implementation. For
|
||||
* example, in H5Datatype, open() function H5.H5Topen(loc_id, name) to get the datatype identifier.
|
||||
*
|
||||
* @return the datatype identifier if successful; otherwise returns negative value.
|
||||
*/
|
||||
@Override
|
||||
public long open() {
|
||||
return -1;
|
||||
}
|
||||
|
||||
/**
|
||||
* Closes a datatype identifier.
|
||||
* <p>
|
||||
* Sub-classes must replace this default implementation.
|
||||
*
|
||||
* @param id
|
||||
* the datatype identifier to close.
|
||||
*/
|
||||
@Override
|
||||
public abstract void close(long id);
|
||||
|
||||
/**
|
||||
* Returns the class of the datatype. Valid values are:
|
||||
* <ul>
|
||||
* <li>CLASS_NO_CLASS
|
||||
* <li>CLASS_INTEGER
|
||||
* <li>CLASS_FLOAT
|
||||
* <li>CLASS_CHAR
|
||||
* <li>CLASS_STRING
|
||||
* <li>CLASS_BITFIELD
|
||||
* <li>CLASS_OPAQUE
|
||||
* <li>CLASS_COMPOUND
|
||||
* <li>CLASS_REFERENCE
|
||||
* <li>CLASS_ENUM
|
||||
* <li>CLASS_VLEN
|
||||
* <li>CLASS_ARRAY
|
||||
* </ul>
|
||||
*
|
||||
* @return the class of the datatype.
|
||||
*/
|
||||
public int getDatatypeClass() {
|
||||
return datatypeClass;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the size of the datatype in bytes. For example, for a 32-bit
|
||||
* integer, the size is 4 (bytes).
|
||||
*
|
||||
* @return the size of the datatype.
|
||||
*/
|
||||
public long getDatatypeSize() {
|
||||
return datatypeSize;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the byte order of the datatype. Valid values are
|
||||
* <ul>
|
||||
* <li>ORDER_LE
|
||||
* <li>ORDER_BE
|
||||
* <li>ORDER_VAX
|
||||
* <li>ORDER_NONE
|
||||
* </ul>
|
||||
*
|
||||
* @return the byte order of the datatype.
|
||||
*/
|
||||
public int getDatatypeOrder() {
|
||||
return datatypeOrder;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the sign (SIGN_NONE, SIGN_2) of an integer datatype.
|
||||
*
|
||||
* @return the sign of the datatype.
|
||||
*/
|
||||
public int getDatatypeSign() {
|
||||
return datatypeSign;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the base datatype for this datatype.
|
||||
* <p>
|
||||
* For example, in a dataset of type ARRAY of integer, the datatype of the dataset is ARRAY. The
|
||||
* datatype of the base type is integer.
|
||||
*
|
||||
* @return the datatype of the contained basetype.
|
||||
*/
|
||||
public Datatype getDatatypeBase() {
|
||||
return baseType;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the (key, value) pairs of enum members for enum datatype.
|
||||
* <p>
|
||||
* For Example,
|
||||
* <dl>
|
||||
* <dt>setEnumMembers("-40=lowTemp, 90=highTemp")</dt>
|
||||
* <dd>sets the key of enum member lowTemp to -40 and highTemp to 90.</dd>
|
||||
* <dt>setEnumMembers("lowTemp, highTemp")</dt>
|
||||
* <dd>sets enum members to defaults, i.e. 0=lowTemp and 1=highTemp</dd>
|
||||
* <dt>setEnumMembers("10=lowTemp, highTemp")</dt>
|
||||
* <dd>sets enum member lowTemp to 10 and highTemp to 11.</dd>
|
||||
* </dl>
|
||||
*
|
||||
* @param enumStr
|
||||
* the (key, value) pairs of enum members
|
||||
*/
|
||||
public final void setEnumMembers(String enumStr) {
|
||||
log.trace("setEnumMembers: is_enum enum_members={}", enumStr);
|
||||
enumMembers = new HashMap<>();
|
||||
String[] entries = enumStr.split(",");
|
||||
for (String entry : entries) {
|
||||
String[] keyValue = entry.split("=");
|
||||
enumMembers.put(keyValue[0].trim(), keyValue[1].trim());
|
||||
if (log.isTraceEnabled())
|
||||
log.trace("setEnumMembers: is_enum value={} name={}", keyValue[0].trim(), keyValue[1].trim());
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the Map<String,String> pairs of enum members for enum datatype.
|
||||
*
|
||||
* @return enumStr Map<String,String%gt; pairs of enum members
|
||||
*/
|
||||
public final Map<String, String> getEnumMembers() {
|
||||
if (enumMembers == null) {
|
||||
enumMembers = new HashMap<>();
|
||||
enumMembers.put("1", "0");
|
||||
enumMembers.put("2", "1");
|
||||
}
|
||||
|
||||
return enumMembers;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the HashMap pairs of enum members for enum datatype.
|
||||
* <p>
|
||||
* For Example,
|
||||
* <dl>
|
||||
* <dt>getEnumMembersAsString()</dt>
|
||||
* <dd>returns "10=lowTemp, 40=highTemp"</dd>
|
||||
* </dl>
|
||||
*
|
||||
* @return enumStr the (key, value) pairs of enum members
|
||||
*/
|
||||
@SuppressWarnings("rawtypes")
|
||||
public final String getEnumMembersAsString() {
|
||||
if (enumMembers == null) {
|
||||
enumMembers = new HashMap<>();
|
||||
enumMembers.put("1", "0");
|
||||
enumMembers.put("2", "1");
|
||||
}
|
||||
|
||||
StringBuilder enumStr = new StringBuilder();
|
||||
Iterator<Entry<String, String>> entries = enumMembers.entrySet().iterator();
|
||||
int i = enumMembers.size();
|
||||
while (entries.hasNext()) {
|
||||
Entry thisEntry = entries.next();
|
||||
enumStr.append((String) thisEntry.getKey())
|
||||
.append("=")
|
||||
.append((String) thisEntry.getValue());
|
||||
|
||||
i--;
|
||||
if (i > 0)
|
||||
enumStr.append(", ");
|
||||
}
|
||||
return enumStr.toString();
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the dimensions of an Array Datatype.
|
||||
*
|
||||
* @return dims the dimensions of the Array Datatype
|
||||
*/
|
||||
public final long[] getArrayDims() {
|
||||
return arrayDims;
|
||||
}
|
||||
|
||||
public final List<String> getCompoundMemberNames() {
|
||||
return compoundMemberNames;
|
||||
}
|
||||
|
||||
public final List<Datatype> getCompoundMemberTypes() {
|
||||
return compoundMemberTypes;
|
||||
}
|
||||
|
||||
/**
|
||||
* Converts the datatype object to a native datatype.
|
||||
*
|
||||
* Subclasses must implement it so that this datatype will be converted accordingly. Use close() to
|
||||
* close the native identifier; otherwise, the datatype will be left open.
|
||||
* <p>
|
||||
* For example, a HDF5 datatype created from<br>
|
||||
*
|
||||
* <pre>
|
||||
* H5Dataype dtype = new H5Datatype(CLASS_INTEGER, 4, NATIVE, SIGN_NONE);
|
||||
* int tid = dtype.createNative();
|
||||
* </pre>
|
||||
*
|
||||
* The "tid" will be the HDF5 datatype id of a 64-bit unsigned integer, which is equivalent to
|
||||
*
|
||||
* <pre>
|
||||
* int tid = H5.H5Tcopy(HDF5Constants.H5T_NATIVE_UNINT32);
|
||||
* </pre>
|
||||
*
|
||||
* @return the identifier of the native datatype.
|
||||
*/
|
||||
public abstract long createNative();
|
||||
|
||||
/**
|
||||
* Set datatype characteristics (class, size, byte order and sign) from a given datatype identifier.
|
||||
* <p>
|
||||
* Sub-classes must implement it so that this datatype will be converted accordingly.
|
||||
* <p>
|
||||
* For example, if the type identifier is a 64-bit unsigned integer created from HDF5,
|
||||
*
|
||||
* <pre>
|
||||
* H5Datatype dtype = new H5Datatype();
|
||||
* dtype.fromNative(HDF5Constants.H5T_NATIVE_UNINT32);
|
||||
* </pre>
|
||||
*
|
||||
* Where dtype is equivalent to <br>
|
||||
* new H5Datatype(CLASS_INTEGER, 4, NATIVE, SIGN_NONE);
|
||||
*
|
||||
* @param nativeID
|
||||
* the datatype identifier.
|
||||
*/
|
||||
public abstract void fromNative(long nativeID);
|
||||
|
||||
/**
|
||||
* Returns a short text description of this datatype.
|
||||
*
|
||||
* @return a short text description of this datatype
|
||||
*/
|
||||
public String getDescription() {
|
||||
log.trace("getDescription(): start");
|
||||
|
||||
if (datatypeDescription != null) {
|
||||
log.trace("getDescription(): finish");
|
||||
return datatypeDescription;
|
||||
}
|
||||
|
||||
StringBuilder description = new StringBuilder();
|
||||
|
||||
switch (datatypeClass) {
|
||||
case CLASS_CHAR:
|
||||
description.append("8-bit ").append((isUnsigned() ? "unsigned " : "")).append("integer");
|
||||
break;
|
||||
case CLASS_INTEGER:
|
||||
if (datatypeSize == NATIVE)
|
||||
description.append("native ").append((isUnsigned() ? "unsigned " : "")).append("integer");
|
||||
else
|
||||
description.append(String.valueOf(datatypeSize * 8)).append("-bit ")
|
||||
.append((isUnsigned() ? "unsigned " : "")).append("integer");
|
||||
break;
|
||||
case CLASS_FLOAT:
|
||||
if (datatypeSize == NATIVE)
|
||||
description.append("native floating-point");
|
||||
else
|
||||
description.append(String.valueOf(datatypeSize * 8)).append("-bit floating-point");
|
||||
break;
|
||||
case CLASS_STRING:
|
||||
description.append("String");
|
||||
break;
|
||||
case CLASS_REFERENCE:
|
||||
description.append("Object reference");
|
||||
break;
|
||||
case CLASS_OPAQUE:
|
||||
if (datatypeSize == NATIVE)
|
||||
description.append("native opaque");
|
||||
else
|
||||
description.append(String.valueOf(datatypeSize * 8)).append("-bit opaque");
|
||||
break;
|
||||
case CLASS_BITFIELD:
|
||||
if (datatypeSize == NATIVE)
|
||||
description.append("native bitfield");
|
||||
else
|
||||
description.append(String.valueOf(datatypeSize * 8)).append("-bit bitfield");
|
||||
break;
|
||||
case CLASS_ENUM:
|
||||
if (datatypeSize == NATIVE)
|
||||
description.append("native enum");
|
||||
else
|
||||
description.append(String.valueOf(datatypeSize * 8)).append("-bit enum");
|
||||
break;
|
||||
case CLASS_ARRAY:
|
||||
description.append("Array");
|
||||
|
||||
if (arrayDims != null) {
|
||||
description.append(" [");
|
||||
for (int i = 0; i < arrayDims.length; i++) {
|
||||
description.append(arrayDims[i]);
|
||||
if (i < arrayDims.length - 1)
|
||||
description.append(" x ");
|
||||
}
|
||||
description.append("]");
|
||||
}
|
||||
|
||||
break;
|
||||
case CLASS_COMPOUND:
|
||||
description.append("Compound");
|
||||
break;
|
||||
case CLASS_VLEN:
|
||||
description.append("Variable-length");
|
||||
break;
|
||||
default:
|
||||
description.append("Unknown");
|
||||
break;
|
||||
}
|
||||
|
||||
if (baseType != null) {
|
||||
description.append(" of " + baseType.getDescription());
|
||||
}
|
||||
|
||||
log.trace("getDescription(): finish");
|
||||
return description.toString();
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is unsigned.
|
||||
*
|
||||
* @return true if the datatype is unsigned;
|
||||
* otherwise, returns false.
|
||||
*/
|
||||
public boolean isUnsigned() {
|
||||
if (baseType != null)
|
||||
return baseType.isUnsigned();
|
||||
else {
|
||||
if (isCompound()) {
|
||||
if ((compoundMemberTypes != null) && !compoundMemberTypes.isEmpty()) {
|
||||
boolean allMembersUnsigned = true;
|
||||
|
||||
Iterator<Datatype> cmpdTypeListIT = compoundMemberTypes.iterator();
|
||||
while (cmpdTypeListIT.hasNext()) {
|
||||
Datatype next = cmpdTypeListIT.next();
|
||||
|
||||
allMembersUnsigned = allMembersUnsigned && next.isUnsigned();
|
||||
}
|
||||
|
||||
return allMembersUnsigned;
|
||||
}
|
||||
else {
|
||||
log.debug("isUnsigned(): compoundMemberTypes is null");
|
||||
return false;
|
||||
}
|
||||
}
|
||||
else {
|
||||
return (datatypeSign == Datatype.SIGN_NONE);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public abstract boolean isText();
|
||||
|
||||
/**
|
||||
* Checks if this datatype is an integer type.
|
||||
*
|
||||
* @return true if the datatype is integer; false otherwise
|
||||
*/
|
||||
public boolean isInteger() {
|
||||
return (datatypeClass == Datatype.CLASS_INTEGER);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a floating-point type.
|
||||
*
|
||||
* @return true if the datatype is floating-point; false otherwise
|
||||
*/
|
||||
public boolean isFloat() {
|
||||
return (datatypeClass == Datatype.CLASS_FLOAT);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a variable-length string type.
|
||||
*
|
||||
* @return true if the datatype is variable-length string; false otherwise
|
||||
*/
|
||||
public boolean isVarStr() {
|
||||
return isVariableStr;
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a variable-length type.
|
||||
*
|
||||
* @return true if the datatype is variable-length; false otherwise
|
||||
*/
|
||||
public boolean isVLEN() {
|
||||
return isVLEN;
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is an compound type.
|
||||
*
|
||||
* @return true if the datatype is compound; false otherwise
|
||||
*/
|
||||
public boolean isCompound() {
|
||||
return (datatypeClass == Datatype.CLASS_COMPOUND);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is an array type.
|
||||
*
|
||||
* @return true if the datatype is array; false otherwise
|
||||
*/
|
||||
public boolean isArray() {
|
||||
return (datatypeClass == Datatype.CLASS_ARRAY);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a string type.
|
||||
*
|
||||
* @return true if the datatype is string; false otherwise
|
||||
*/
|
||||
public boolean isString() {
|
||||
return (datatypeClass == Datatype.CLASS_STRING);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a character type.
|
||||
*
|
||||
* @return true if the datatype is character; false otherwise
|
||||
*/
|
||||
public boolean isChar() {
|
||||
return (datatypeClass == Datatype.CLASS_CHAR);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a reference type.
|
||||
*
|
||||
* @return true if the datatype is reference; false otherwise
|
||||
*/
|
||||
public boolean isRef() {
|
||||
return (datatypeClass == Datatype.CLASS_REFERENCE);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a enum type.
|
||||
*
|
||||
* @return true if the datatype is enum; false otherwise
|
||||
*/
|
||||
public boolean isEnum() {
|
||||
return (datatypeClass == Datatype.CLASS_ENUM);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a opaque type.
|
||||
*
|
||||
* @return true if the datatype is opaque; false otherwise
|
||||
*/
|
||||
public boolean isOpaque() {
|
||||
return (datatypeClass == Datatype.CLASS_OPAQUE);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if this datatype is a bitfield type.
|
||||
*
|
||||
* @return true if the datatype is bitfield; false otherwise
|
||||
*/
|
||||
public boolean isBitField() {
|
||||
return (datatypeClass == Datatype.CLASS_BITFIELD);
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#getMetadata()
|
||||
*/
|
||||
@Override
|
||||
@SuppressWarnings("rawtypes")
|
||||
public List getMetadata() throws Exception {
|
||||
return null;
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#writeMetadata(java.lang.Object)
|
||||
*/
|
||||
@Override
|
||||
public void writeMetadata(Object info) throws Exception {
|
||||
throw new UnsupportedOperationException("Unsupported operation. Subclasses must implement Datatype:writeMetadata.");
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#removeMetadata(java.lang.Object)
|
||||
*/
|
||||
@Override
|
||||
public void removeMetadata(Object info) throws Exception {
|
||||
throw new UnsupportedOperationException("Unsupported operation. Subclasses must implement Datatype:removeMetadata.");
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#updateMetadata(java.lang.Object)
|
||||
*/
|
||||
@Override
|
||||
public void updateMetadata(Object info) throws Exception {
|
||||
throw new UnsupportedOperationException("Unsupported operation. Subclasses must implement Datatype:updateMetadata.");
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return getDescription();
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,326 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
import java.util.Iterator;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
import java.util.Queue;
|
||||
import java.util.Stack;
|
||||
import java.util.Vector;
|
||||
|
||||
/**
|
||||
* Group is an abstract class. Current implementing classes are the H4Group and
|
||||
* H5Group. This class includes general information of a group object such as
|
||||
* members of a group and common operations on groups.
|
||||
* <p>
|
||||
* Members of a group may include other groups, datasets or links.
|
||||
*
|
||||
* @version 1.1 9/4/2007
|
||||
* @author Peter X. Cao
|
||||
*/
|
||||
public abstract class Group extends HObject implements MetaDataContainer {
|
||||
|
||||
private static final long serialVersionUID = 3913174542591568052L;
|
||||
|
||||
/**
|
||||
* The list of members (Groups and Datasets) of this group in memory.
|
||||
*/
|
||||
private List<HObject> memberList;
|
||||
|
||||
/**
|
||||
* The parent group where this group is located. The parent of the root
|
||||
* group is null.
|
||||
*/
|
||||
protected Group parent;
|
||||
|
||||
/**
|
||||
* Total number of members of this group in file.
|
||||
*/
|
||||
protected int nMembersInFile;
|
||||
|
||||
public static final int LINK_TYPE_HARD = 0;
|
||||
|
||||
public static final int LINK_TYPE_SOFT = 1;
|
||||
|
||||
public static final int LINK_TYPE_EXTERNAL = 64;
|
||||
|
||||
public static final int CRT_ORDER_TRACKED = 1;
|
||||
|
||||
public static final int CRT_ORDER_INDEXED = 2;
|
||||
|
||||
|
||||
/**
|
||||
* Constructs an instance of the group with specific name, path and parent
|
||||
* group. An HDF data object must have a name. The path is the group path
|
||||
* starting from the root. The parent group is the group where this group is
|
||||
* located.
|
||||
* <p>
|
||||
* For example, in H5Group(h5file, "grp", "/groups/", pgroup), "grp" is the
|
||||
* name of the group, "/groups/" is the group path of the group, and pgroup
|
||||
* is the group where "grp" is located.
|
||||
*
|
||||
* @param theFile
|
||||
* the file containing the group.
|
||||
* @param grpName
|
||||
* the name of this group, e.g. "grp01".
|
||||
* @param grpPath
|
||||
* the full path of this group, e.g. "/groups/".
|
||||
* @param grpParent
|
||||
* the parent of this group.
|
||||
*/
|
||||
public Group(FileFormat theFile, String grpName, String grpPath, Group grpParent) {
|
||||
this(theFile, grpName, grpPath, grpParent, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* @deprecated Not for public use in the future.<br>
|
||||
* Using {@link #Group(FileFormat, String, String, Group)}
|
||||
*
|
||||
* @param theFile
|
||||
* the file containing the group.
|
||||
* @param grpName
|
||||
* the name of this group, e.g. "grp01".
|
||||
* @param grpPath
|
||||
* the full path of this group, e.g. "/groups/".
|
||||
* @param grpParent
|
||||
* the parent of this group.
|
||||
* @param oid
|
||||
* the oid of this group.
|
||||
*/
|
||||
@Deprecated
|
||||
public Group(FileFormat theFile, String grpName, String grpPath, Group grpParent, long[] oid) {
|
||||
super(theFile, grpName, grpPath, oid);
|
||||
|
||||
this.parent = grpParent;
|
||||
}
|
||||
|
||||
/**
|
||||
* Clears up member list and other resources in memory for the group. Since
|
||||
* the destructor will clear memory space, the function is usually not
|
||||
* needed.
|
||||
*/
|
||||
public void clear() {
|
||||
if (memberList != null) {
|
||||
((Vector<HObject>) memberList).setSize(0);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds an object to the member list of this group in memory.
|
||||
*
|
||||
* @param object
|
||||
* the HObject to be added to the member list.
|
||||
*/
|
||||
public void addToMemberList(HObject object) {
|
||||
if (memberList == null) {
|
||||
int size = Math.min(getNumberOfMembersInFile(), this
|
||||
.getFileFormat().getMaxMembers());
|
||||
memberList = new Vector<>(size + 5);
|
||||
}
|
||||
|
||||
if ((object != null) && !memberList.contains(object)) {
|
||||
memberList.add(object);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Removes an object from the member list of this group in memory.
|
||||
*
|
||||
* @param object
|
||||
* the HObject (Group or Dataset) to be removed from the member
|
||||
* list.
|
||||
*/
|
||||
public void removeFromMemberList(HObject object) {
|
||||
if (memberList != null) {
|
||||
memberList.remove(object);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the list of members of this group. The list is an java.util.List
|
||||
* containing HObjects.
|
||||
*
|
||||
* @return the list of members of this group.
|
||||
*/
|
||||
public List<HObject> getMemberList() {
|
||||
FileFormat theFile = this.getFileFormat();
|
||||
|
||||
if ((memberList == null) && (theFile != null)) {
|
||||
int size = Math.min(getNumberOfMembersInFile(), this.getFileFormat().getMaxMembers());
|
||||
memberList = new Vector<>(size + 5); // avoid infinite loop search for groups without members
|
||||
|
||||
// find the memberList from the file by checking the group path and
|
||||
// name. group may be created out of the structure tree
|
||||
// (H4/5File.loadTree()).
|
||||
if (theFile.getFID() < 0) {
|
||||
try {
|
||||
theFile.open();
|
||||
} // load the file structure;
|
||||
catch (Exception ex) {
|
||||
;
|
||||
}
|
||||
}
|
||||
|
||||
HObject root = theFile.getRootObject();
|
||||
if (root == null) return memberList;
|
||||
|
||||
Iterator<HObject> it = ((Group) root).depthFirstMemberList().iterator();
|
||||
Group g = null;
|
||||
Object uObj = null;
|
||||
while (it.hasNext()) {
|
||||
uObj = it.next();
|
||||
|
||||
if (uObj instanceof Group) {
|
||||
g = (Group) uObj;
|
||||
if (g.getPath() != null) // add this check to get rid of null exception
|
||||
{
|
||||
if ((this.isRoot() && g.isRoot())
|
||||
|| (this.getPath().equals(g.getPath()) &&
|
||||
g.getName().endsWith(this.getName()))) {
|
||||
memberList = g.getMemberList();
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return memberList;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the members of this Group in breadth-first order.
|
||||
*/
|
||||
public List<HObject> breadthFirstMemberList() {
|
||||
Vector<HObject> members = new Vector<>();
|
||||
Queue<HObject> queue = new LinkedList<>();
|
||||
HObject currentObj = this;
|
||||
|
||||
queue.addAll(((Group) currentObj).getMemberList());
|
||||
|
||||
while(!queue.isEmpty()) {
|
||||
currentObj = queue.remove();
|
||||
members.add(currentObj);
|
||||
|
||||
if(currentObj instanceof Group && ((Group) currentObj).getNumberOfMembersInFile() > 0) {
|
||||
queue.addAll(((Group) currentObj).getMemberList());
|
||||
}
|
||||
}
|
||||
|
||||
return members;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return the members of this Group in depth-first order.
|
||||
*/
|
||||
public List<HObject> depthFirstMemberList() {
|
||||
Vector<HObject> members = new Vector<>();
|
||||
Stack<HObject> stack = new Stack<>();
|
||||
HObject currentObj = this;
|
||||
|
||||
// Push elements onto the stack in reverse order
|
||||
List<HObject> list = ((Group) currentObj).getMemberList();
|
||||
for(int i = list.size() - 1; i >= 0; i--) {
|
||||
stack.push(list.get(i));
|
||||
}
|
||||
|
||||
while(!stack.empty()) {
|
||||
currentObj = stack.pop();
|
||||
members.add(currentObj);
|
||||
|
||||
if(currentObj instanceof Group && ((Group) currentObj).getNumberOfMembersInFile() > 0) {
|
||||
list = ((Group) currentObj).getMemberList();
|
||||
for(int i = list.size() - 1; i >= 0; i--) {
|
||||
stack.push(list.get(i));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return members;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the name of the group.
|
||||
* <p>
|
||||
* setName (String newName) changes the name of the group in memory and
|
||||
* file.
|
||||
* <p>
|
||||
* setName() updates the path in memory for all the objects that are under
|
||||
* the group with the new name.
|
||||
*
|
||||
* @param newName
|
||||
* The new name of the group.
|
||||
*
|
||||
* @throws Exception if the name can not be set
|
||||
*/
|
||||
@Override
|
||||
public void setName(String newName) throws Exception {
|
||||
super.setName(newName);
|
||||
|
||||
if (memberList != null) {
|
||||
int n = memberList.size();
|
||||
HObject theObj = null;
|
||||
for (int i = 0; i < n; i++) {
|
||||
theObj = memberList.get(i);
|
||||
theObj.setPath(this.getPath() + newName + HObject.SEPARATOR);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/** @return the parent group. */
|
||||
public final Group getParent() {
|
||||
return parent;
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if it is a root group.
|
||||
*
|
||||
* @return true if the group is a root group; otherwise, returns false.
|
||||
*/
|
||||
public final boolean isRoot() {
|
||||
return (parent == null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the total number of members of this group in file.
|
||||
*
|
||||
* Current Java applications such as HDFView cannot handle files with large
|
||||
* numbers of objects (1,000,000 or more objects) due to JVM memory
|
||||
* limitation. The max_members is used so that applications such as HDFView
|
||||
* will load up to <i>max_members</i> number of objects. If the number of
|
||||
* objects in file is larger than <i>max_members</i>, only
|
||||
* <i>max_members</i> are loaded in memory.
|
||||
* <p>
|
||||
* getNumberOfMembersInFile() returns the number of objects in this group.
|
||||
* The number of objects in memory is obtained by getMemberList().size().
|
||||
*
|
||||
* @return Total number of members of this group in the file.
|
||||
*/
|
||||
public int getNumberOfMembersInFile() {
|
||||
return nMembersInFile;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the HObject at the specified index in this Group's member list.
|
||||
* @param idx The index of the HObject to get.
|
||||
* @return The HObject at the specified index.
|
||||
*/
|
||||
public HObject getMember(int idx) {
|
||||
if(memberList.size() <= 0 || idx >= memberList.size()) return null;
|
||||
|
||||
return memberList.get(idx);
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,562 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
/**
|
||||
* The HObject class is the root class of all the HDF data objects. Every data
|
||||
* class has HObject as a superclass. All objects implement the methods of this
|
||||
* class. The following is the inherited structure of HDF Objects.
|
||||
*
|
||||
* <pre>
|
||||
* HObject
|
||||
* __________________________|________________________________
|
||||
* | | |
|
||||
* Group Dataset Datatype
|
||||
* | _________|___________ |
|
||||
* | | | |
|
||||
* | ScalarDS CompoundDS |
|
||||
* | | | |
|
||||
* ---------------------Implementing classes such as-------------------------
|
||||
* ____|____ _____|______ _____|_____ _____|_____
|
||||
* | | | | | | | |
|
||||
* H5Group H4Group H5ScalarDS H4ScalarDS H5CompDS H4CompDS H5Datatype H4Datatype
|
||||
*
|
||||
* </pre>
|
||||
*
|
||||
* All HDF4 and HDF5 data objects are inherited from HObject. At the top level
|
||||
* of the hierarchy, both HDF4 and HDF5 have the same super-classes, such as
|
||||
* Group and Dataset. At the bottom level of the hierarchy, HDF4 and HDF5
|
||||
* objects have their own implementation, such as H5Group, H5ScalarDS,
|
||||
* H5CompoundDS, and H5Datatype.
|
||||
* <p>
|
||||
* <b>Warning: HDF4 and HDF5 may have multiple links to the same object. Data
|
||||
* objects in this model do not deal with multiple links. Users may create
|
||||
* duplicate copies of the same data object with different paths. Applications
|
||||
* should check the OID of the data object to avoid duplicate copies of the same
|
||||
* object.</b>
|
||||
* <p>
|
||||
* HDF4 objects are uniquely identified by the OID (tag_id, ref_id) pair. The
|
||||
* ref_id is the object reference count. The tag_id is a pre-defined number to
|
||||
* identify the type of object. For example, DFTAG_RI is for raster image,
|
||||
* DFTAG_SD is for scientific dataset, and DFTAG_VG is for Vgroup.
|
||||
* <p>
|
||||
* HDF5 objects are uniquely identified by the OID containing just the object
|
||||
* reference. The OID is usually obtained by H5Rcreate(). The following example
|
||||
* shows how to retrieve an object ID from a file:
|
||||
*
|
||||
* <pre>
|
||||
* // retrieve the object ID
|
||||
* try {
|
||||
* byte[] ref_buf = H5.H5Rcreate(h5file.getFID(), this.getFullName(), HDF5Constants.H5R_OBJECT, -1);
|
||||
* long[] oid = new long[1];
|
||||
* oid[0] = HDFNativeData.byteToLong(ref_buf, 0);
|
||||
* } catch (Exception ex) {
|
||||
* }
|
||||
* </pre>
|
||||
*
|
||||
* @version 2.0 4/2/2018
|
||||
* @author Peter X. Cao, Jordan T. Henderson
|
||||
* @see <a href="DataFormat.html">hdf.object.DataFormat</a>
|
||||
*/
|
||||
public abstract class HObject implements Serializable {
|
||||
|
||||
/**
|
||||
* The serialVersionUID is a universal version identifier for a Serializable
|
||||
* class. Deserialization uses this number to ensure that a loaded class
|
||||
* corresponds exactly to a serialized object. For details, see
|
||||
* http://java.sun.com/j2se/1.5.0/docs/api/java/io/Serializable.html
|
||||
*/
|
||||
private static final long serialVersionUID = -1723666708199882519L;
|
||||
|
||||
private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(HObject.class);
|
||||
|
||||
/**
|
||||
* The separator of object path, i.e. "/".
|
||||
*/
|
||||
public static final String SEPARATOR = "/";
|
||||
|
||||
/**
|
||||
* The full path of the file that contains the object.
|
||||
*/
|
||||
private String filename;
|
||||
|
||||
/**
|
||||
* The file which contains the object
|
||||
*/
|
||||
protected final FileFormat fileFormat;
|
||||
|
||||
/**
|
||||
* The name of the data object. The root group has its default name, a
|
||||
* slash. The name can be changed except the root group.
|
||||
*/
|
||||
private String name;
|
||||
|
||||
/**
|
||||
* The full path of the data object. The full path always starts with the
|
||||
* root, a slash. The path cannot be changed. Also, a path must be ended with a
|
||||
* slash. For example, /arrays/ints/
|
||||
*/
|
||||
private String path;
|
||||
|
||||
/** The full name of the data object, i.e. "path + name" */
|
||||
private String fullName;
|
||||
|
||||
/**
|
||||
* Array of long integer storing unique identifier for the object.
|
||||
* <p>
|
||||
* HDF4 objects are uniquely identified by a (tag_id, ref_id) pair. i.e.
|
||||
* oid[0] = tag, oid[1] = ref_id.<br>
|
||||
* HDF5 objects are uniquely identified by an object reference. i.e.
|
||||
* oid[0] = obj_id.
|
||||
*/
|
||||
protected long[] oid;
|
||||
|
||||
/**
|
||||
* The name of the Target Object that is being linked to.
|
||||
*/
|
||||
protected String linkTargetObjName;
|
||||
|
||||
/**
|
||||
* Number of attributes attached to the object.
|
||||
*/
|
||||
// protected int nAttributes = -1;
|
||||
|
||||
/**
|
||||
* Constructs an instance of a data object without name and path.
|
||||
*/
|
||||
public HObject() {
|
||||
this(null, null, null, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Constructs an instance of a data object with specific name and path.
|
||||
* <p>
|
||||
* For example, in H5ScalarDS(h5file, "dset", "/arrays"), "dset" is the name
|
||||
* of the dataset, "/arrays" is the group path of the dataset.
|
||||
*
|
||||
* @param theFile
|
||||
* the file that contains the data object.
|
||||
* @param theName
|
||||
* the name of the data object, e.g. "dset".
|
||||
* @param thePath
|
||||
* the group path of the data object, e.g. "/arrays".
|
||||
*/
|
||||
public HObject(FileFormat theFile, String theName, String thePath) {
|
||||
this(theFile, theName, thePath, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Constructs an instance of a data object with specific name and path.
|
||||
* <p>
|
||||
* For example, in H5ScalarDS(h5file, "dset", "/arrays"), "dset" is the name
|
||||
* of the dataset, "/arrays" is the group path of the dataset.
|
||||
*
|
||||
* @param theFile
|
||||
* the file that contains the data object.
|
||||
* @param theName
|
||||
* the name of the data object, e.g. "dset".
|
||||
* @param thePath
|
||||
* the group path of the data object, e.g. "/arrays".
|
||||
* @param oid
|
||||
* the ids of the data object.
|
||||
*/
|
||||
@Deprecated
|
||||
public HObject(FileFormat theFile, String theName, String thePath, long[] oid) {
|
||||
this.fileFormat = theFile;
|
||||
this.oid = oid;
|
||||
|
||||
if (fileFormat != null) {
|
||||
this.filename = fileFormat.getFilePath();
|
||||
}
|
||||
else {
|
||||
this.filename = null;
|
||||
}
|
||||
|
||||
// file name is packed in the full path
|
||||
if ((theName == null) && (thePath != null)) {
|
||||
if (thePath.equals(SEPARATOR)) {
|
||||
theName = SEPARATOR;
|
||||
thePath = null;
|
||||
}
|
||||
else {
|
||||
// the path must starts with "/"
|
||||
if (!thePath.startsWith(HObject.SEPARATOR)) {
|
||||
thePath = HObject.SEPARATOR + thePath;
|
||||
}
|
||||
|
||||
// get rid of the last "/"
|
||||
if (thePath.endsWith(HObject.SEPARATOR)) {
|
||||
thePath = thePath.substring(0, thePath.length() - 1);
|
||||
}
|
||||
|
||||
// separate the name and the path
|
||||
theName = thePath.substring(thePath.lastIndexOf(SEPARATOR) + 1);
|
||||
thePath = thePath.substring(0, thePath.lastIndexOf(SEPARATOR));
|
||||
}
|
||||
}
|
||||
else if ((theName != null) && (thePath == null) && (theName.indexOf(SEPARATOR) >= 0)) {
|
||||
if (theName.equals(SEPARATOR)) {
|
||||
theName = SEPARATOR;
|
||||
thePath = null;
|
||||
}
|
||||
else {
|
||||
// the full name must starts with "/"
|
||||
if (!theName.startsWith(SEPARATOR)) {
|
||||
theName = SEPARATOR + theName;
|
||||
}
|
||||
|
||||
// the fullname must not end with "/"
|
||||
int n = theName.length();
|
||||
if (theName.endsWith(SEPARATOR)) {
|
||||
theName = theName.substring(0, n - 1);
|
||||
}
|
||||
|
||||
int idx = theName.lastIndexOf(SEPARATOR);
|
||||
if (idx < 0) {
|
||||
thePath = SEPARATOR;
|
||||
}
|
||||
else {
|
||||
thePath = theName.substring(0, idx);
|
||||
theName = theName.substring(idx + 1);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// the path must start and end with "/"
|
||||
if (thePath != null) {
|
||||
thePath = thePath.replaceAll("//", "/");
|
||||
if (!thePath.endsWith(SEPARATOR)) {
|
||||
thePath += SEPARATOR;
|
||||
}
|
||||
}
|
||||
|
||||
this.name = theName;
|
||||
this.path = thePath;
|
||||
|
||||
log.trace("name={} path={}", this.name, this.path);
|
||||
|
||||
if (thePath != null) {
|
||||
this.fullName = thePath + theName;
|
||||
}
|
||||
else {
|
||||
if (theName == null) {
|
||||
this.fullName = "/";
|
||||
}
|
||||
else if (theName.startsWith("/")) {
|
||||
this.fullName = theName;
|
||||
}
|
||||
else {
|
||||
if (this instanceof Attribute)
|
||||
this.fullName = theName;
|
||||
else
|
||||
this.fullName = "/" + theName;
|
||||
}
|
||||
}
|
||||
|
||||
log.trace("fullName={}", this.fullName);
|
||||
}
|
||||
|
||||
/**
|
||||
* Print out debug information
|
||||
* <p>
|
||||
*
|
||||
* @param msg
|
||||
* the debug message to print
|
||||
*/
|
||||
protected final void debug(Object msg) {
|
||||
System.out.println("*** " + this.getClass().getName() + ": " + msg);
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the name of the file that contains this data object.
|
||||
* <p>
|
||||
* The file name is necessary because the file of this data object is
|
||||
* uniquely identified when multiple files are opened by an application at
|
||||
* the same time.
|
||||
*
|
||||
* @return The full path (path + name) of the file.
|
||||
*/
|
||||
public final String getFile() {
|
||||
return filename;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the name of the object. For example, "Raster Image #2".
|
||||
*
|
||||
* @return The name of the object.
|
||||
*/
|
||||
public final String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the name of the target object that is linked to.
|
||||
*
|
||||
* @return The name of the object that is linked to.
|
||||
*/
|
||||
public final String getLinkTargetObjName() {
|
||||
return linkTargetObjName;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the name of the target object that is linked to.
|
||||
*
|
||||
* @param targetObjName
|
||||
* The new name of the object.
|
||||
*/
|
||||
public final void setLinkTargetObjName(String targetObjName) {
|
||||
linkTargetObjName = targetObjName;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the full name (group path + object name) of the object. For
|
||||
* example, "/Images/Raster Image #2"
|
||||
*
|
||||
* @return The full name (group path + object name) of the object.
|
||||
*/
|
||||
public final String getFullName() {
|
||||
return fullName;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the group path of the object. For example, "/Images".
|
||||
*
|
||||
* @return The group path of the object.
|
||||
*/
|
||||
public final String getPath() {
|
||||
return path;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the name of the object.
|
||||
*
|
||||
* setName (String newName) changes the name of the object in the file.
|
||||
*
|
||||
* @param newName
|
||||
* The new name of the object.
|
||||
*
|
||||
* @throws Exception if name is root or contains separator
|
||||
*/
|
||||
public void setName(String newName) throws Exception {
|
||||
if (newName != null) {
|
||||
if (newName.equals(HObject.SEPARATOR)) {
|
||||
throw new IllegalArgumentException("The new name cannot be the root");
|
||||
}
|
||||
|
||||
if (newName.startsWith(HObject.SEPARATOR)) {
|
||||
newName = newName.substring(1);
|
||||
}
|
||||
|
||||
if (newName.endsWith(HObject.SEPARATOR)) {
|
||||
newName = newName.substring(0, newName.length() - 2);
|
||||
}
|
||||
|
||||
if (newName.contains(HObject.SEPARATOR)) {
|
||||
throw new IllegalArgumentException("The new name contains the SEPARATOR character: " + HObject.SEPARATOR);
|
||||
}
|
||||
}
|
||||
|
||||
name = newName;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the path of the object.
|
||||
* <p>
|
||||
* setPath() is needed to change the path for an object when the name of a
|
||||
* group containing the object is changed by setName(). The path of the
|
||||
* object in memory under this group should be updated to the new path to
|
||||
* the group. Unlike setName(), setPath() does not change anything in file.
|
||||
*
|
||||
* @param newPath
|
||||
* The new path of the object.
|
||||
*
|
||||
* @throws Exception if a failure occurred
|
||||
*/
|
||||
public void setPath(String newPath) throws Exception {
|
||||
if (newPath == null) {
|
||||
newPath = "/";
|
||||
}
|
||||
|
||||
path = newPath;
|
||||
}
|
||||
|
||||
/**
|
||||
* Opens an existing object such as a dataset or group for access.
|
||||
*
|
||||
* The return value is an object identifier obtained by implementing classes
|
||||
* such as H5.H5Dopen(). This function is needed to allow other objects to
|
||||
* be able to access the object. For instance, H5File class uses the open()
|
||||
* function to obtain object identifier for copyAttributes(long src_id, long
|
||||
* dst_id) and other purposes. The open() function should be used in pair
|
||||
* with close(long) function.
|
||||
*
|
||||
* @see HObject#close(long)
|
||||
*
|
||||
* @return the object identifier if successful; otherwise returns a negative
|
||||
* value.
|
||||
*/
|
||||
public abstract long open();
|
||||
|
||||
/**
|
||||
* Closes access to the object.
|
||||
* <p>
|
||||
* Sub-classes must implement this interface because different data objects
|
||||
* have their own ways of how the data resources are closed.
|
||||
* <p>
|
||||
* For example, H5Group.close() calls the hdf.hdf5lib.H5.H5Gclose()
|
||||
* method and closes the group resource specified by the group id.
|
||||
*
|
||||
* @param id
|
||||
* The object identifier.
|
||||
*/
|
||||
public abstract void close(long id);
|
||||
|
||||
/**
|
||||
* Returns the file identifier of of the file containing the object.
|
||||
*
|
||||
* @return the file identifier of of the file containing the object.
|
||||
*/
|
||||
public final long getFID() {
|
||||
if (fileFormat != null) {
|
||||
return fileFormat.getFID();
|
||||
}
|
||||
else {
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the file that contains the object.
|
||||
*
|
||||
* @return The file that contains the object.
|
||||
*/
|
||||
public final FileFormat getFileFormat() {
|
||||
return fileFormat;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns a cloned copy of the object identifier.
|
||||
* <p>
|
||||
* The object OID cannot be modified once it is created. getOID() clones the object OID to ensure
|
||||
* the object OID cannot be modified outside of this class.
|
||||
*
|
||||
* @return the cloned copy of the object OID.
|
||||
*/
|
||||
public final long[] getOID() {
|
||||
if (oid == null) {
|
||||
return null;
|
||||
}
|
||||
|
||||
return oid.clone();
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks if the OID of the object is the same as the given object identifier within the same file.
|
||||
* <p>
|
||||
* HDF4 and HDF5 data objects are identified by their unique OIDs. A data object in a file may have
|
||||
* multiple logical names , which are represented in a graph structure as separate objects.
|
||||
* <p>
|
||||
* The HObject.equalsOID(long[] theID) can be used to check if two data objects with different names
|
||||
* are pointed to the same object within the same file.
|
||||
*
|
||||
* @param theID
|
||||
* The list object identifiers.
|
||||
*
|
||||
* @return true if the ID of the object equals the given OID; otherwise, returns false.
|
||||
*/
|
||||
public final boolean equalsOID(long[] theID) {
|
||||
if ((theID == null) || (oid == null)) {
|
||||
return false;
|
||||
}
|
||||
|
||||
int n1 = theID.length;
|
||||
int n2 = oid.length;
|
||||
|
||||
if (n1 == 0 || n2 == 0) {
|
||||
return false;
|
||||
}
|
||||
|
||||
int n = Math.min(n1, n2);
|
||||
boolean isMatched = (theID[0] == oid[0]);
|
||||
|
||||
for (int i = 1; isMatched && (i < n); i++) {
|
||||
isMatched = (theID[i] == oid[i]);
|
||||
}
|
||||
|
||||
return isMatched;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the name of the object.
|
||||
* <p>
|
||||
* This method overwrites the toString() method in the Java Object class
|
||||
* (the root class of all Java objects) so that it returns the name of the
|
||||
* HObject instead of the name of the class.
|
||||
* <p>
|
||||
* For example, toString() returns "Raster Image #2" instead of
|
||||
* "hdf.object.h4.H4SDS".
|
||||
*
|
||||
* @return The name of the object.
|
||||
*/
|
||||
@Override
|
||||
public String toString() {
|
||||
if (this instanceof Group) {
|
||||
if (((Group) this).isRoot() && this.getFileFormat() != null) return this.getFileFormat().getName();
|
||||
}
|
||||
|
||||
if (name != null) return name;
|
||||
|
||||
return super.toString();
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns whether this HObject is equal to the specified HObject by comparing their OIDs.
|
||||
*
|
||||
* @param obj
|
||||
* The object
|
||||
*
|
||||
* @return true if the object is equal by OID
|
||||
*/
|
||||
public boolean equals(HObject obj) {
|
||||
// Cast down to Object to avoid infinite recursion
|
||||
if (this.equals((Object) obj))
|
||||
return true;
|
||||
|
||||
// comparing the state of OID with
|
||||
// the state of 'this' OID.
|
||||
return this.equalsOID(obj.getOID());
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean equals(Object obj) {
|
||||
if (obj == null)
|
||||
return false;
|
||||
|
||||
// checking if both the object references are
|
||||
// referring to the same object.
|
||||
if (this == obj)
|
||||
return true;
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int hashCode() {
|
||||
// We are returning the OID as a hashcode value.
|
||||
return (int) oid[0];
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,91 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* An interface that provides general I/O operations for object metadata
|
||||
* attached to an object. For example, reading metadata content from the file
|
||||
* into memory or writing metadata content from memory into the file.
|
||||
* <p>
|
||||
*
|
||||
* @see HObject
|
||||
*
|
||||
* @version 2.0 4/2/2018
|
||||
* @author Peter X. Cao, Jordan T. Henderson
|
||||
*/
|
||||
@SuppressWarnings("rawtypes")
|
||||
public interface MetaDataContainer {
|
||||
/**
|
||||
* Retrieves the object's metadata, such as attributes, from the file.
|
||||
* <p>
|
||||
* Metadata, such as attributes, is stored in a List.
|
||||
*
|
||||
* @return the list of metadata objects.
|
||||
*
|
||||
* @throws Exception
|
||||
* if the metadata can not be retrieved
|
||||
*/
|
||||
public abstract List getMetadata() throws Exception;
|
||||
|
||||
/**
|
||||
* Writes a specific piece of metadata (such as an attribute) into the file.
|
||||
*
|
||||
* If an HDF(4&5) attribute exists in the file, this method updates its
|
||||
* value. If the attribute does not exist in the file, it creates the
|
||||
* attribute in the file and attaches it to the object. It will fail to
|
||||
* write a new attribute to the object where an attribute with the same name
|
||||
* already exists. To update the value of an existing attribute in the file,
|
||||
* one needs to get the instance of the attribute by getMetadata(), change
|
||||
* its values, then use writeMetadata() to write the value.
|
||||
*
|
||||
* @param metadata
|
||||
* the metadata to write.
|
||||
*
|
||||
* @throws Exception
|
||||
* if the metadata can not be written
|
||||
*/
|
||||
public abstract void writeMetadata(Object metadata) throws Exception;
|
||||
|
||||
/**
|
||||
* Deletes an existing piece of metadata from this object.
|
||||
*
|
||||
* @param metadata
|
||||
* the metadata to delete.
|
||||
*
|
||||
* @throws Exception
|
||||
* if the metadata can not be removed
|
||||
*/
|
||||
public abstract void removeMetadata(Object metadata) throws Exception;
|
||||
|
||||
/**
|
||||
* Updates an existing piece of metadata attached to this object.
|
||||
*
|
||||
* @param metadata
|
||||
* the metadata to update.
|
||||
*
|
||||
* @throws Exception
|
||||
* if the metadata can not be updated
|
||||
*/
|
||||
public abstract void updateMetadata(Object metadata) throws Exception;
|
||||
|
||||
/**
|
||||
* Check if the object has any attributes attached.
|
||||
*
|
||||
* @return true if it has any attributes, false otherwise.
|
||||
*/
|
||||
public abstract boolean hasAttribute();
|
||||
}
|
||||
@@ -0,0 +1,450 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import java.util.Vector;
|
||||
|
||||
/**
|
||||
* A scalar dataset is a multiple dimension array of scalar points. The Datatype of a scalar dataset must be an atomic
|
||||
* datatype. Common datatypes of scalar datasets include char, byte, short, int, long, float, double and string.
|
||||
* <p>
|
||||
* A ScalarDS can be an image or spreadsheet data. ScalarDS defines methods to deal with both images and
|
||||
* spreadsheets.
|
||||
* <p>
|
||||
* ScalarDS is an abstract class. Current implementing classes are the H4SDS, H5GRImage and H5ScalarDS.
|
||||
*
|
||||
* @version 1.1 9/4/2007
|
||||
* @author Peter X. Cao
|
||||
*/
|
||||
public abstract class ScalarDS extends Dataset {
|
||||
private static final long serialVersionUID = 8925371455928203981L;
|
||||
|
||||
private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(ScalarDS.class);
|
||||
|
||||
/************************************************************
|
||||
* The following constant strings are copied from *
|
||||
* https://support.hdfgroup.org/HDF5/doc/ADGuide/ImageSpec.html *
|
||||
* to make the definition consistent with the image specs. *
|
||||
************************************************************/
|
||||
|
||||
/**
|
||||
* Indicates that the pixel RGB values are contiguous.
|
||||
*/
|
||||
public static final int INTERLACE_PIXEL = 0;
|
||||
|
||||
/** Indicates that each pixel component of RGB is stored as a scan line. */
|
||||
public static final int INTERLACE_LINE = 1;
|
||||
|
||||
/** Indicates that each pixel component of RGB is stored as a plane. */
|
||||
public static final int INTERLACE_PLANE = 2;
|
||||
|
||||
/**
|
||||
* The interlace mode of the stored raster image data. Valid values are INTERLACE_PIXEL, INTERLACE_LINE and
|
||||
* INTERLACE_PLANE.
|
||||
*/
|
||||
protected int interlace;
|
||||
|
||||
/**
|
||||
* The min-max range of image data values. For example, [0, 255] indicates the min is 0, and the max is 255.
|
||||
*/
|
||||
protected double[] imageDataRange;
|
||||
|
||||
/**
|
||||
* The indexed RGB color model with 256 colors.
|
||||
* <p>
|
||||
* The palette values are stored in a two-dimensional byte array and arrange by color components of red, green and
|
||||
* blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue
|
||||
* components respectively.
|
||||
*/
|
||||
protected byte[][] palette;
|
||||
|
||||
/**
|
||||
* True if this dataset is an image.
|
||||
*/
|
||||
protected boolean isImage;
|
||||
|
||||
/**
|
||||
* True if this dataset is a true color image.
|
||||
*/
|
||||
protected boolean isTrueColor;
|
||||
|
||||
/**
|
||||
* True if this dataset is ASCII text.
|
||||
*/
|
||||
protected boolean isText;
|
||||
|
||||
/**
|
||||
* Flag to indicate is the original unsigned C data is converted.
|
||||
*/
|
||||
protected boolean unsignedConverted;
|
||||
|
||||
/** The fill value of the dataset. */
|
||||
protected Object fillValue = null;
|
||||
|
||||
private List<Number> filteredImageValues;
|
||||
|
||||
/** Flag to indicate if the dataset is displayed as an image. */
|
||||
protected boolean isImageDisplay;
|
||||
|
||||
/**
|
||||
* Flag to indicate if the dataset is displayed as an image with default order of dimensions.
|
||||
*/
|
||||
protected boolean isDefaultImageOrder;
|
||||
|
||||
/**
|
||||
* Flag to indicate if the FillValue is converted from unsigned C.
|
||||
*/
|
||||
public boolean isFillValueConverted;
|
||||
|
||||
/**
|
||||
* Constructs an instance of a ScalarDS with specific name and path. An HDF data object must have a name. The path
|
||||
* is the group path starting from the root.
|
||||
* <p>
|
||||
* For example, in H5ScalarDS(h5file, "dset", "/arrays/"), "dset" is the name of the dataset, "/arrays" is the group
|
||||
* path of the dataset.
|
||||
*
|
||||
* @param theFile
|
||||
* the file that contains the data object.
|
||||
* @param theName
|
||||
* the name of the data object, e.g. "dset".
|
||||
* @param thePath
|
||||
* the full path of the data object, e.g. "/arrays/".
|
||||
*/
|
||||
public ScalarDS(FileFormat theFile, String theName, String thePath) {
|
||||
this(theFile, theName, thePath, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* @deprecated Not for public use in the future.<br>
|
||||
* Using {@link #ScalarDS(FileFormat, String, String)}
|
||||
*
|
||||
* @param theFile
|
||||
* the file that contains the data object.
|
||||
* @param theName
|
||||
* the name of the data object, e.g. "dset".
|
||||
* @param thePath
|
||||
* the full path of the data object, e.g. "/arrays/".
|
||||
* @param oid
|
||||
* the v of the data object.
|
||||
*/
|
||||
@Deprecated
|
||||
public ScalarDS(FileFormat theFile, String theName, String thePath, long[] oid) {
|
||||
super(theFile, theName, thePath, oid);
|
||||
|
||||
palette = null;
|
||||
isImage = false;
|
||||
isTrueColor = false;
|
||||
isText = false;
|
||||
interlace = -1;
|
||||
imageDataRange = null;
|
||||
isImageDisplay = false;
|
||||
isDefaultImageOrder = true;
|
||||
isFillValueConverted = false;
|
||||
filteredImageValues = new Vector<>();
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.Dataset#clearData()
|
||||
*/
|
||||
@Override
|
||||
public void clearData() {
|
||||
super.clearData();
|
||||
unsignedConverted = false;
|
||||
}
|
||||
|
||||
/**
|
||||
* Converts the data values of this dataset to appropriate Java integer if they are unsigned integers.
|
||||
*
|
||||
* @see Dataset#convertToUnsignedC(Object)
|
||||
* @see Dataset#convertFromUnsignedC(Object, Object)
|
||||
*
|
||||
* @return the converted data buffer.
|
||||
*/
|
||||
@Override
|
||||
public Object convertFromUnsignedC() {
|
||||
log.trace("convertFromUnsignedC(): start");
|
||||
// keep a copy of original buffer and the converted buffer
|
||||
// so that they can be reused later to save memory
|
||||
log.trace("convertFromUnsignedC(): unsigned={}", getDatatype().isUnsigned());
|
||||
if ((data != null) && getDatatype().isUnsigned() && !unsignedConverted) {
|
||||
log.trace("convertFromUnsignedC(): convert");
|
||||
originalBuf = data;
|
||||
convertedBuf = convertFromUnsignedC(originalBuf, convertedBuf);
|
||||
data = convertedBuf;
|
||||
unsignedConverted = true;
|
||||
|
||||
if (fillValue != null) {
|
||||
if (!isFillValueConverted) {
|
||||
fillValue = convertFromUnsignedC(fillValue, null);
|
||||
isFillValueConverted = true;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
log.trace("convertFromUnsignedC(): finish");
|
||||
return data;
|
||||
}
|
||||
|
||||
/**
|
||||
* Converts Java integer data of this dataset back to unsigned C-type integer data if they are unsigned integers.
|
||||
*
|
||||
* @see Dataset#convertToUnsignedC(Object)
|
||||
* @see Dataset#convertToUnsignedC(Object, Object)
|
||||
* @see #convertFromUnsignedC(Object data_in)
|
||||
*
|
||||
* @return the converted data buffer.
|
||||
*/
|
||||
@Override
|
||||
public Object convertToUnsignedC() {
|
||||
log.trace("convertToUnsignedC(): start");
|
||||
// keep a copy of original buffer and the converted buffer
|
||||
// so that they can be reused later to save memory
|
||||
log.trace("convertToUnsignedC(): unsigned={}", getDatatype().isUnsigned());
|
||||
if ((data != null) && getDatatype().isUnsigned()) {
|
||||
log.trace("convertToUnsignedC(): convert");
|
||||
convertedBuf = data;
|
||||
originalBuf = convertToUnsignedC(convertedBuf, originalBuf);
|
||||
data = originalBuf;
|
||||
}
|
||||
|
||||
log.trace("convertToUnsignedC(): finish");
|
||||
return data;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the palette of this scalar dataset or null if palette does not exist.
|
||||
* <p>
|
||||
* A Scalar dataset can be displayed as spreadsheet data or an image. When a scalar dataset is displayed as an
|
||||
* image, the palette or color table may be needed to translate a pixel value to color components (for example, red,
|
||||
* green, and blue). Some scalar datasets have no palette and some datasets have one or more than one palettes. If
|
||||
* an associated palette exists but is not loaded, this interface retrieves the palette from the file and returns the
|
||||
* palette. If the palette is loaded, it returns the palette. It returns null if there is no palette associated with
|
||||
* the dataset.
|
||||
* <p>
|
||||
* Current implementation only supports palette model of indexed RGB with 256 colors. Other models such as
|
||||
* YUV", "CMY", "CMYK", "YCbCr", "HSV will be supported in the future.
|
||||
* <p>
|
||||
* The palette values are stored in a two-dimensional byte array and are arranges by color components of red, green and
|
||||
* blue. palette[][] = byte[3][256], where, palette[0][], palette[1][] and palette[2][] are the red, green and blue
|
||||
* components respectively.
|
||||
* <p>
|
||||
* Sub-classes have to implement this interface. HDF4 and HDF5 images use different libraries to retrieve the
|
||||
* associated palette.
|
||||
*
|
||||
* @return the 2D palette byte array.
|
||||
*/
|
||||
public abstract byte[][] getPalette();
|
||||
|
||||
/**
|
||||
* Sets the palette for this dataset.
|
||||
*
|
||||
* @param pal
|
||||
* the 2D palette byte array.
|
||||
*/
|
||||
public final void setPalette(byte[][] pal) {
|
||||
palette = pal;
|
||||
}
|
||||
|
||||
/**
|
||||
* Reads a specific image palette from file.
|
||||
* <p>
|
||||
* A scalar dataset may have multiple palettes attached to it. readPalette(int idx) returns a specific palette
|
||||
* identified by its index.
|
||||
*
|
||||
* @param idx
|
||||
* the index of the palette to read.
|
||||
*
|
||||
* @return the image palette
|
||||
*/
|
||||
public abstract byte[][] readPalette(int idx);
|
||||
|
||||
/**
|
||||
* Get the name of a specific image palette from file.
|
||||
* <p>
|
||||
* A scalar dataset may have multiple palettes attached to it. getPaletteName(int idx) returns the name of a
|
||||
* specific palette identified by its index.
|
||||
*
|
||||
* @param idx
|
||||
* the index of the palette to retrieve the name.
|
||||
*
|
||||
* @return The name of the palette
|
||||
*/
|
||||
public String getPaletteName(int idx) {
|
||||
String paletteName = "Default ";
|
||||
if (idx != 0)
|
||||
paletteName = "Default " + idx;
|
||||
return paletteName;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the byte array of palette refs.
|
||||
* <p>
|
||||
* A palette reference is an object reference that points to the palette dataset.
|
||||
* <p>
|
||||
* For example, Dataset "Iceberg" has an attribute of object reference "Palette". The arrtibute "Palette" has value
|
||||
* "2538" that is the object reference of the palette data set "Iceberg Palette".
|
||||
*
|
||||
* @return null if there is no palette attribute attached to this dataset.
|
||||
*/
|
||||
public abstract byte[] getPaletteRefs();
|
||||
|
||||
/**
|
||||
* Returns true if this dataset is an image.
|
||||
* <p>
|
||||
* For all Images, they must have an attribute called "CLASS". The value of this attribute is "IMAGE". For more
|
||||
* details, read <a href="https://support.hdfgroup.org/HDF5/doc/ADGuide/ImageSpec.html"> HDF5 Image and Palette Specification</a>
|
||||
*
|
||||
* @return true if the dataset is an image; otherwise, returns false.
|
||||
*/
|
||||
public final boolean isImage() {
|
||||
return isImage;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns true if this dataset is displayed as an image.
|
||||
* <p>
|
||||
* A ScalarDS can be displayed as an image or a spreadsheet in a table.
|
||||
*
|
||||
* @return true if this dataset is displayed as an image; otherwise, returns false.
|
||||
*/
|
||||
public final boolean isImageDisplay() {
|
||||
|
||||
return isImageDisplay;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns true if this dataset is displayed as an image with default image order.
|
||||
* <p>
|
||||
* A ScalarDS can be displayed as an image with different orders of dimensions.
|
||||
*
|
||||
* @return true if this dataset is displayed as an image with default image order; otherwise, returns false.
|
||||
*/
|
||||
public final boolean isDefaultImageOrder() {
|
||||
return isDefaultImageOrder;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the flag to display the dataset as an image.
|
||||
*
|
||||
* @param b
|
||||
* if b is true, display the dataset as an image
|
||||
*/
|
||||
public final void setIsImageDisplay(boolean b) {
|
||||
isImageDisplay = b;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the flag to indicate this dataset is an image.
|
||||
*
|
||||
* @param b
|
||||
* if b is true, the dataset is an image.
|
||||
*/
|
||||
public final void setIsImage(boolean b) {
|
||||
isImage = b;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets data range for an image.
|
||||
*
|
||||
* @param min
|
||||
* the data range start.
|
||||
* @param max
|
||||
* the data range end.
|
||||
*/
|
||||
public final void setImageDataRange(double min, double max) {
|
||||
if (max <= min)
|
||||
return;
|
||||
|
||||
if (imageDataRange == null)
|
||||
imageDataRange = new double[2];
|
||||
|
||||
imageDataRange[0] = min;
|
||||
imageDataRange[1] = max;
|
||||
}
|
||||
|
||||
/**
|
||||
* Add a value that will be filtered out in an image.
|
||||
*
|
||||
* @param x
|
||||
* value to be filtered
|
||||
*/
|
||||
public void addFilteredImageValue(Number x) {
|
||||
Iterator<Number> it = filteredImageValues.iterator();
|
||||
while (it.hasNext()) {
|
||||
if (it.next().toString().equals(x.toString()))
|
||||
return;
|
||||
}
|
||||
|
||||
filteredImageValues.add(x);
|
||||
}
|
||||
|
||||
/**
|
||||
* Get a list of values that will be filtered out in an image.
|
||||
*
|
||||
* @return the list of Image values
|
||||
*/
|
||||
public List<Number> getFilteredImageValues() {
|
||||
return filteredImageValues;
|
||||
}
|
||||
|
||||
/**
|
||||
* @return true if this dataset is a true color image.
|
||||
*
|
||||
*/
|
||||
|
||||
public final boolean isTrueColor() {
|
||||
return isTrueColor;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the interlace mode of a true color image (RGB).
|
||||
*
|
||||
* Valid values:
|
||||
*
|
||||
* <pre>
|
||||
* INTERLACE_PIXEL -- RGB components are contiguous, i.e. rgb, rgb, rgb, ...
|
||||
* INTERLACE_LINE -- each RGB component is stored as a scan line
|
||||
* INTERLACE_PLANE -- each RGB component is stored as a plane
|
||||
* </pre>
|
||||
*
|
||||
* @return the interlace mode of a true color image (RGB).
|
||||
*/
|
||||
public final int getInterlace() {
|
||||
return interlace;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the (min, max) pair of image data range.
|
||||
*
|
||||
* @return the (min, max) pair of image data range.
|
||||
*/
|
||||
public double[] getImageDataRange() {
|
||||
return imageDataRange;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the fill values for the dataset.
|
||||
*
|
||||
* @return the fill values for the dataset.
|
||||
*/
|
||||
@Override
|
||||
public final Object getFillValue() {
|
||||
return fillValue;
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,48 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object;
|
||||
|
||||
public final class Utils {
|
||||
private Utils() {
|
||||
throw new IllegalStateException("Utility class");
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieves the Java Runtime Class of the given Object. B = byte array, S = short array, I = int
|
||||
* array, J = long array, F = float array, D = double array, L = class or interface
|
||||
*
|
||||
* @param o
|
||||
* the Object to determine the Runtime Class of
|
||||
* @return the Java Runtime Class of the given Object.
|
||||
*/
|
||||
public static char getJavaObjectRuntimeClass(Object o) {
|
||||
if (o == null)
|
||||
return ' ';
|
||||
|
||||
String cName = o.getClass().getName();
|
||||
|
||||
if (cName.equals("java.lang.String") || cName.equals("java.util.Vector")
|
||||
|| cName.equals("java.util.Arrays$ArrayList") || cName.equals("java.util.ArrayList"))
|
||||
return 'L';
|
||||
|
||||
int cIndex = cName.lastIndexOf('[');
|
||||
if (cIndex >= 0) {
|
||||
return cName.charAt(cIndex + 1);
|
||||
}
|
||||
|
||||
return ' ';
|
||||
}
|
||||
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,506 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object.h5;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Vector;
|
||||
|
||||
import hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
import hdf.hdf5lib.HDFNativeData;
|
||||
import hdf.hdf5lib.exceptions.HDF5Exception;
|
||||
import hdf.hdf5lib.structs.H5G_info_t;
|
||||
import hdf.hdf5lib.structs.H5O_info_t;
|
||||
import hdf.object.Attribute;
|
||||
import hdf.object.FileFormat;
|
||||
import hdf.object.Group;
|
||||
import hdf.object.HObject;
|
||||
|
||||
/**
|
||||
* An H5Group object represents an existing HDF5 group in file.
|
||||
* <p>
|
||||
* In HDF5, every object has at least one name. An HDF5 group is used to store a
|
||||
* set of the names together in one place, i.e. a group. The general structure
|
||||
* of a group is similar to that of the UNIX file system in that the group may
|
||||
* contain references to other groups or data objects just as the UNIX directory
|
||||
* may contain sub-directories or files.
|
||||
* <p>
|
||||
* For more information on HDF5 Groups,
|
||||
*
|
||||
* <a href="https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html">HDF5 User's Guide</a>
|
||||
*
|
||||
* @version 1.1 9/4/2007
|
||||
* @author Peter X. Cao
|
||||
*/
|
||||
public class H5Group extends Group {
|
||||
|
||||
private static final long serialVersionUID = -951164512330444150L;
|
||||
|
||||
private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(H5Group.class);
|
||||
|
||||
/**
|
||||
* The list of attributes of this data object. Members of the list are
|
||||
* instance of Attribute.
|
||||
*/
|
||||
@SuppressWarnings("rawtypes")
|
||||
protected List attributeList;
|
||||
|
||||
private int nAttributes = -1;
|
||||
|
||||
private H5O_info_t obj_info;
|
||||
|
||||
/**
|
||||
* Constructs an HDF5 group with specific name, path, and parent.
|
||||
*
|
||||
* @param theFile
|
||||
* the file which containing the group.
|
||||
* @param name
|
||||
* the name of this group, e.g. "grp01".
|
||||
* @param path
|
||||
* the full path of this group, e.g. "/groups/".
|
||||
* @param parent
|
||||
* the parent of this group.
|
||||
*/
|
||||
public H5Group(FileFormat theFile, String name, String path, Group parent) {
|
||||
this(theFile, name, path, parent, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* @deprecated Not for public use in the future.<br>
|
||||
* Using {@link #H5Group(FileFormat, String, String, Group)}
|
||||
*
|
||||
* @param theFile
|
||||
* the file which containing the group.
|
||||
* @param name
|
||||
* the name of this group, e.g. "grp01".
|
||||
* @param path
|
||||
* the full path of this group, e.g. "/groups/".
|
||||
* @param parent
|
||||
* the parent of this group.
|
||||
* @param oid
|
||||
* the oid of this group.
|
||||
*/
|
||||
@Deprecated
|
||||
public H5Group(FileFormat theFile, String name, String path, Group parent, long[] oid) {
|
||||
super(theFile, name, path, parent, oid);
|
||||
nMembersInFile = -1;
|
||||
obj_info = new H5O_info_t(-1L, -1L, 0, 0, -1L, 0L, 0L, 0L, 0L, null, null, null);
|
||||
|
||||
if ((oid == null) && (theFile != null)) {
|
||||
// retrieve the object ID
|
||||
try {
|
||||
byte[] ref_buf = H5.H5Rcreate(theFile.getFID(), this.getFullName(), HDF5Constants.H5R_OBJECT, -1);
|
||||
this.oid = new long[1];
|
||||
this.oid[0] = HDFNativeData.byteToLong(ref_buf, 0);
|
||||
}
|
||||
catch (Exception ex) {
|
||||
this.oid = new long[1];
|
||||
this.oid[0] = 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#hasAttribute()
|
||||
*/
|
||||
@Override
|
||||
public boolean hasAttribute() {
|
||||
obj_info.num_attrs = nAttributes;
|
||||
|
||||
if (obj_info.num_attrs < 0) {
|
||||
long gid = open();
|
||||
if (gid > 0) {
|
||||
try {
|
||||
obj_info = H5.H5Oget_info(gid);
|
||||
|
||||
}
|
||||
catch (Exception ex) {
|
||||
obj_info.num_attrs = 0;
|
||||
}
|
||||
close(gid);
|
||||
}
|
||||
}
|
||||
|
||||
log.trace("hasAttribute(): nAttributes={}", obj_info.num_attrs);
|
||||
|
||||
return (obj_info.num_attrs > 0);
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.Group#getNumberOfMembersInFile()
|
||||
*/
|
||||
@Override
|
||||
public int getNumberOfMembersInFile() {
|
||||
if (nMembersInFile < 0) {
|
||||
long gid = open();
|
||||
if (gid > 0) {
|
||||
try {
|
||||
H5G_info_t group_info = null;
|
||||
group_info = H5.H5Gget_info(gid);
|
||||
nMembersInFile = (int) group_info.nlinks;
|
||||
}
|
||||
catch (Exception ex) {
|
||||
nMembersInFile = 0;
|
||||
}
|
||||
close(gid);
|
||||
}
|
||||
}
|
||||
return nMembersInFile;
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.Group#clear()
|
||||
*/
|
||||
@SuppressWarnings("rawtypes")
|
||||
@Override
|
||||
public void clear() {
|
||||
super.clear();
|
||||
|
||||
if (attributeList != null) {
|
||||
((Vector) attributeList).setSize(0);
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#getMetadata()
|
||||
*/
|
||||
@Override
|
||||
@SuppressWarnings("rawtypes")
|
||||
public List getMetadata() throws HDF5Exception {
|
||||
return this.getMetadata(fileFormat.getIndexType(null), fileFormat.getIndexOrder(null));
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#getMetadata(int...)
|
||||
*/
|
||||
@SuppressWarnings("rawtypes")
|
||||
public List getMetadata(int... attrPropList) throws HDF5Exception {
|
||||
log.trace("getMetadata(): start");
|
||||
if (attributeList == null) {
|
||||
log.trace("getMetadata(): get attributeList");
|
||||
|
||||
int indxType = fileFormat.getIndexType(null);
|
||||
int order = fileFormat.getIndexOrder(null);
|
||||
|
||||
if (attrPropList.length > 0) {
|
||||
indxType = attrPropList[0];
|
||||
if (attrPropList.length > 1) {
|
||||
order = attrPropList[1];
|
||||
}
|
||||
}
|
||||
try {
|
||||
attributeList = H5File.getAttribute(this, indxType, order);
|
||||
}
|
||||
catch (Exception ex) {
|
||||
log.debug("getMetadata(): H5File.getAttribute failure: ", ex);
|
||||
}
|
||||
}
|
||||
|
||||
try {
|
||||
if (!this.isRoot()) this.linkTargetObjName = H5File.getLinkTargetName(this);
|
||||
}
|
||||
catch (Exception ex) {
|
||||
log.debug("getMetadata(): getLinkTargetName failure: ", ex);
|
||||
}
|
||||
|
||||
log.trace("getMetadata(): finish");
|
||||
return attributeList;
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#writeMetadata(java.lang.Object)
|
||||
*/
|
||||
@Override
|
||||
@SuppressWarnings("unchecked")
|
||||
public void writeMetadata(Object info) throws Exception {
|
||||
log.trace("writeMetadata(): start");
|
||||
// only attribute metadata is supported.
|
||||
if (!(info instanceof Attribute)) {
|
||||
log.debug("writeMetadata(): Object not an Attribute");
|
||||
log.trace("writeMetadata(): finish");
|
||||
return;
|
||||
}
|
||||
|
||||
boolean attrExisted = false;
|
||||
Attribute attr = (Attribute) info;
|
||||
log.trace("writeMetadata(): {}", attr.getName());
|
||||
|
||||
if (attributeList == null) {
|
||||
this.getMetadata();
|
||||
}
|
||||
|
||||
if (attributeList != null) attrExisted = attributeList.contains(attr);
|
||||
|
||||
getFileFormat().writeAttribute(this, attr, attrExisted);
|
||||
// add the new attribute into attribute list
|
||||
if (!attrExisted) {
|
||||
attributeList.add(attr);
|
||||
nAttributes = attributeList.size();
|
||||
}
|
||||
log.trace("writeMetadata(): finish");
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#removeMetadata(java.lang.Object)
|
||||
*/
|
||||
@Override
|
||||
@SuppressWarnings("rawtypes")
|
||||
public void removeMetadata(Object info) throws HDF5Exception {
|
||||
log.trace("removeMetadata(): start");
|
||||
// only attribute metadata is supported.
|
||||
if (!(info instanceof Attribute)) {
|
||||
log.debug("removeMetadata(): Object not an Attribute");
|
||||
log.trace("removeMetadata(): finish");
|
||||
return;
|
||||
}
|
||||
|
||||
Attribute attr = (Attribute) info;
|
||||
log.trace("removeMetadata(): {}", attr.getName());
|
||||
long gid = open();
|
||||
if(gid >= 0) {
|
||||
try {
|
||||
H5.H5Adelete(gid, attr.getName());
|
||||
List attrList = getMetadata();
|
||||
attrList.remove(attr);
|
||||
nAttributes = attributeList.size();
|
||||
}
|
||||
finally {
|
||||
close(gid);
|
||||
}
|
||||
}
|
||||
else {
|
||||
log.debug("removeMetadata(): failed to open group");
|
||||
}
|
||||
|
||||
log.trace("removeMetadata(): finish");
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.DataFormat#updateMetadata(java.lang.Object)
|
||||
*/
|
||||
@Override
|
||||
public void updateMetadata(Object info) throws HDF5Exception {
|
||||
log.trace("updateMetadata(): start");
|
||||
// only attribute metadata is supported.
|
||||
if (!(info instanceof Attribute)) {
|
||||
log.debug("updateMetadata(): Object not an Attribute");
|
||||
log.trace("updateMetadata(): finish");
|
||||
return;
|
||||
}
|
||||
|
||||
nAttributes = -1;
|
||||
log.trace("updateMetadata(): finish");
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.HObject#open()
|
||||
*/
|
||||
@Override
|
||||
public long open() {
|
||||
log.trace("open(): start");
|
||||
long gid = -1;
|
||||
|
||||
try {
|
||||
if (isRoot()) {
|
||||
gid = H5.H5Gopen(getFID(), SEPARATOR, HDF5Constants.H5P_DEFAULT);
|
||||
}
|
||||
else {
|
||||
gid = H5.H5Gopen(getFID(), getPath() + getName(), HDF5Constants.H5P_DEFAULT);
|
||||
}
|
||||
|
||||
}
|
||||
catch (HDF5Exception ex) {
|
||||
gid = -1;
|
||||
}
|
||||
|
||||
log.trace("open(): finish");
|
||||
return gid;
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.HObject#close(int)
|
||||
*/
|
||||
@Override
|
||||
public void close(long gid) {
|
||||
try {
|
||||
H5.H5Gclose(gid);
|
||||
}
|
||||
catch (HDF5Exception ex) {
|
||||
log.debug("close(): H5Gclose(gid {}): ", gid, ex);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates a new group with a name in a group and with the group creation
|
||||
* properties specified in gplist.
|
||||
* <p>
|
||||
* The gplist contains a sequence of group creation property list
|
||||
* identifiers, lcpl, gcpl, gapl. It allows the user to create a group with
|
||||
* group creation properties. It will close the group creation properties
|
||||
* specified in gplist.
|
||||
*
|
||||
* @see H5#H5Gcreate(long, String, long, long, long) for the
|
||||
* order of property list identifiers.
|
||||
*
|
||||
* @param name
|
||||
* The name of a new group.
|
||||
* @param pgroup
|
||||
* The parent group object.
|
||||
* @param gplist
|
||||
* The group creation properties, in which the order of the
|
||||
* properties conforms the HDF5 library API, H5Gcreate(), i.e.
|
||||
* lcpl, gcpl and gapl, where
|
||||
* <ul>
|
||||
* <li>lcpl : Property list for link creation <li>gcpl : Property
|
||||
* list for group creation <li>gapl : Property list for group
|
||||
* access
|
||||
* </ul>
|
||||
*
|
||||
* @return The new group if successful; otherwise returns null.
|
||||
*
|
||||
* @throws Exception if there is a failure.
|
||||
*/
|
||||
public static H5Group create(String name, Group pgroup, long... gplist) throws Exception {
|
||||
log.trace("create(): start");
|
||||
H5Group group = null;
|
||||
String fullPath = null;
|
||||
long lcpl = HDF5Constants.H5P_DEFAULT;
|
||||
long gcpl = HDF5Constants.H5P_DEFAULT;
|
||||
long gapl = HDF5Constants.H5P_DEFAULT;
|
||||
|
||||
if (gplist.length > 0) {
|
||||
lcpl = gplist[0];
|
||||
if (gplist.length > 1) {
|
||||
gcpl = gplist[1];
|
||||
if (gplist.length > 2) gapl = gplist[2];
|
||||
}
|
||||
}
|
||||
|
||||
if ((name == null) || (pgroup == null)) {
|
||||
log.debug("create(): one or more parameters are null");
|
||||
log.trace("create(): finish");
|
||||
System.err.println("(name == null) || (pgroup == null)");
|
||||
return null;
|
||||
}
|
||||
|
||||
H5File file = (H5File) pgroup.getFileFormat();
|
||||
|
||||
if (file == null) {
|
||||
log.debug("create(): Parent Group FileFormat is null");
|
||||
log.trace("create(): finish");
|
||||
System.err.println("Could not get file that contains object");
|
||||
return null;
|
||||
}
|
||||
|
||||
String path = HObject.SEPARATOR;
|
||||
if (!pgroup.isRoot()) {
|
||||
path = pgroup.getPath() + pgroup.getName() + HObject.SEPARATOR;
|
||||
if (name.endsWith("/")) {
|
||||
name = name.substring(0, name.length() - 1);
|
||||
}
|
||||
int idx = name.lastIndexOf('/');
|
||||
if (idx >= 0) {
|
||||
name = name.substring(idx + 1);
|
||||
}
|
||||
}
|
||||
|
||||
fullPath = path + name;
|
||||
|
||||
// create a new group and add it to the parent node
|
||||
long gid = H5.H5Gcreate(file.open(), fullPath, lcpl, gcpl, gapl);
|
||||
try {
|
||||
H5.H5Gclose(gid);
|
||||
}
|
||||
catch (Exception ex) {
|
||||
log.debug("create(): H5Gcreate {} H5Gclose(gid {}) failure: ", fullPath, gid, ex);
|
||||
}
|
||||
|
||||
byte[] ref_buf = H5.H5Rcreate(file.open(), fullPath, HDF5Constants.H5R_OBJECT, -1);
|
||||
long l = HDFNativeData.byteToLong(ref_buf, 0);
|
||||
long[] oid = { l };
|
||||
|
||||
group = new H5Group(file, name, path, pgroup, oid);
|
||||
|
||||
if (group != null) {
|
||||
pgroup.addToMemberList(group);
|
||||
}
|
||||
|
||||
if (gcpl > 0) {
|
||||
try {
|
||||
H5.H5Pclose(gcpl);
|
||||
}
|
||||
catch (final Exception ex) {
|
||||
log.debug("create(): create prop H5Pclose(gcpl {}) failure: ", gcpl, ex);
|
||||
}
|
||||
}
|
||||
|
||||
log.trace("create(): finish");
|
||||
return group;
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.HObject#setName(java.lang.String)
|
||||
*/
|
||||
@Override
|
||||
public void setName(String newName) throws Exception {
|
||||
H5File.renameObject(this, newName);
|
||||
super.setName(newName);
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.HObject#setPath(java.lang.String)
|
||||
*/
|
||||
@SuppressWarnings("rawtypes")
|
||||
@Override
|
||||
public void setPath(String newPath) throws Exception {
|
||||
super.setPath(newPath);
|
||||
|
||||
List members = this.getMemberList();
|
||||
if (members == null) {
|
||||
return;
|
||||
}
|
||||
|
||||
int n = members.size();
|
||||
HObject obj = null;
|
||||
for (int i = 0; i < n; i++) {
|
||||
obj = (HObject) members.get(i);
|
||||
obj.setPath(getPath() + getName() + HObject.SEPARATOR);
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,112 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object.h5;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import hdf.hdf5lib.structs.H5O_info_t;
|
||||
import hdf.object.FileFormat;
|
||||
import hdf.object.HObject;
|
||||
import hdf.object.MetaDataContainer;
|
||||
|
||||
/**
|
||||
* An H5Link object represents an existing HDF5 object in file.
|
||||
* <p>
|
||||
* H5Link object is an HDF5 object that is either a soft or an external link to
|
||||
* an object in a file that does not exist. The type of the object is unknown.
|
||||
* Once the object being linked to is created, and the type is known, then
|
||||
* H5link object will change its type.
|
||||
*
|
||||
* @version 2.7.2 7/6/2010
|
||||
* @author Nidhi Gupta
|
||||
*/
|
||||
|
||||
public class H5Link extends HObject implements MetaDataContainer {
|
||||
private static final long serialVersionUID = -8137277460521594367L;
|
||||
|
||||
@SuppressWarnings("unused")
|
||||
private H5O_info_t obj_info;
|
||||
|
||||
/**
|
||||
* Constructs an HDF5 link with specific name, path, and parent.
|
||||
*
|
||||
* @param theFile
|
||||
* the file which containing the link.
|
||||
* @param name
|
||||
* the name of this link, e.g. "link1".
|
||||
* @param path
|
||||
* the full path of this link, e.g. "/groups/".
|
||||
*/
|
||||
public H5Link(FileFormat theFile, String name, String path) {
|
||||
this (theFile, name, path, null);
|
||||
}
|
||||
|
||||
@SuppressWarnings("deprecation")
|
||||
public H5Link(FileFormat theFile, String theName, String thePath,
|
||||
long[] oid) {
|
||||
super(theFile, theName, thePath, oid);
|
||||
|
||||
obj_info = new H5O_info_t(-1L, -1L, -1, 0, -1L, 0L, 0L, 0L, 0L, null,null,null);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void close(long id) {
|
||||
}
|
||||
|
||||
@Override
|
||||
public long open() {
|
||||
return 0;
|
||||
}
|
||||
|
||||
@SuppressWarnings("rawtypes")
|
||||
public List getMetadata() throws Exception {
|
||||
|
||||
try{
|
||||
this.linkTargetObjName= H5File.getLinkTargetName(this);
|
||||
}catch(Exception ex){
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
|
||||
public boolean hasAttribute() {
|
||||
return false;
|
||||
}
|
||||
|
||||
public void removeMetadata(Object info) throws Exception {
|
||||
}
|
||||
|
||||
public void writeMetadata(Object info) throws Exception {
|
||||
}
|
||||
|
||||
public void updateMetadata(Object info) throws Exception {
|
||||
}
|
||||
|
||||
@SuppressWarnings("rawtypes")
|
||||
public List getMetadata(int... attrPropList) throws Exception {
|
||||
return null;
|
||||
}
|
||||
|
||||
/*
|
||||
* (non-Javadoc)
|
||||
*
|
||||
* @see hdf.object.HObject#setName(java.lang.String)
|
||||
*/
|
||||
@Override
|
||||
public void setName(String newName) throws Exception {
|
||||
H5File.renameObject(this, newName);
|
||||
super.setName(newName);
|
||||
}
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,135 @@
|
||||
/*****************************************************************************
|
||||
* Copyright by The HDF Group. *
|
||||
* Copyright by the Board of Trustees of the University of Illinois. *
|
||||
* All rights reserved. *
|
||||
* *
|
||||
* This file is part of the HDF Java Products distribution. *
|
||||
* The full copyright notice, including terms governing use, modification, *
|
||||
* and redistribution, is contained in the files COPYING and Copyright.html. *
|
||||
* COPYING can be found at the root of the source code distribution tree. *
|
||||
* Or, see https://support.hdfgroup.org/products/licenses.html *
|
||||
* If you do not have access to either file, you may request a copy from *
|
||||
* help@hdfgroup.org. *
|
||||
****************************************************************************/
|
||||
|
||||
package hdf.object.h5;
|
||||
|
||||
import hdf.hdf5lib.H5;
|
||||
import hdf.hdf5lib.HDF5Constants;
|
||||
import hdf.hdf5lib.exceptions.HDF5Exception;
|
||||
|
||||
public final class H5Utils {
|
||||
|
||||
private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(H5Utils.class);
|
||||
|
||||
/**
|
||||
* Set up a hyperslab selection within a dataset.
|
||||
*
|
||||
* @param did
|
||||
* IN dataset ID
|
||||
* @param dsetDims
|
||||
* IN dimensions
|
||||
* @param startDims
|
||||
* IN start dimensions
|
||||
* @param selectedStride
|
||||
* IN selected stride values
|
||||
* @param selectedDims
|
||||
* IN selected dimensions
|
||||
* @param spaceIDs
|
||||
* IN/OUT memory and file space IDs -- spaceIDs[0]=mspace, spaceIDs[1]=fspace
|
||||
*
|
||||
* @return total number of data points selected
|
||||
*
|
||||
* @throws HDF5Exception
|
||||
* If there is an error at the HDF5 library level.
|
||||
*/
|
||||
public static final long selectHyperslab(long did, long[] dsetDims, long[] startDims, long[] selectedStride,
|
||||
long[] selectedDims, long[] spaceIDs) throws HDF5Exception {
|
||||
log.trace("selectHyperslab(): start");
|
||||
|
||||
if (dsetDims == null) {
|
||||
log.debug("selectHyperslab(): dsetDims is null");
|
||||
return -1;
|
||||
}
|
||||
|
||||
int rank = dsetDims.length;
|
||||
if ((startDims != null) && (startDims.length != rank)) {
|
||||
log.debug("selectHyperslab(): startDims rank didn't match dsetDims rank");
|
||||
return -1;
|
||||
}
|
||||
if ((selectedStride != null) && (selectedStride.length != rank)) {
|
||||
log.debug("selectHyperslab(): selectedStride rank didn't match startDims rank");
|
||||
return -1;
|
||||
}
|
||||
if ((selectedDims != null) && (selectedDims.length != rank)) {
|
||||
log.debug("selectHyperslab(): selectedDims rank didn't match startDims rank");
|
||||
return -1;
|
||||
}
|
||||
|
||||
long lsize = 1;
|
||||
|
||||
boolean isAllSelected = true;
|
||||
for (int i = 0; i < rank; i++) {
|
||||
if (selectedDims != null) {
|
||||
lsize *= selectedDims[i];
|
||||
if (selectedDims[i] < dsetDims[i]) {
|
||||
isAllSelected = false;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
log.trace("selectHyperslab(): isAllSelected={}", isAllSelected);
|
||||
|
||||
if (isAllSelected) {
|
||||
spaceIDs[0] = HDF5Constants.H5S_ALL;
|
||||
spaceIDs[1] = HDF5Constants.H5S_ALL;
|
||||
}
|
||||
else {
|
||||
spaceIDs[1] = H5.H5Dget_space(did);
|
||||
|
||||
// When a 1D dataspace is used for a chunked dataset, reading is very slow.
|
||||
//
|
||||
// It is a known problem within the HDF5 library.
|
||||
// mspace = H5.H5Screate_simple(1, lsize, null);
|
||||
spaceIDs[0] = H5.H5Screate_simple(rank, selectedDims, null);
|
||||
H5.H5Sselect_hyperslab(spaceIDs[1], HDF5Constants.H5S_SELECT_SET, startDims, selectedStride, selectedDims, null);
|
||||
}
|
||||
|
||||
log.trace("selectHyperslab(): finish");
|
||||
|
||||
return lsize;
|
||||
}
|
||||
|
||||
public static final long getTotalSelectedSpacePoints(long did, long[] dsetDims, long[] startDims,
|
||||
long[] selectedStride, long[] selectedDims, long[] spaceIDs) throws HDF5Exception {
|
||||
long totalSelectedSpacePoints = selectHyperslab(did, dsetDims, startDims, selectedStride, selectedDims, spaceIDs);
|
||||
|
||||
log.trace("getTotalSelectedSpacePoints(): selected {} points in dataset's dataspace", totalSelectedSpacePoints);
|
||||
|
||||
if (totalSelectedSpacePoints == 0) {
|
||||
log.debug("getTotalSelectedSpacePoints(): No data to read. Dataset or selected subset is empty.");
|
||||
log.trace("getTotalSelectedSpacePoints(): finish");
|
||||
throw new HDF5Exception("No data to read.\nEither the dataset or the selected subset is empty.");
|
||||
}
|
||||
|
||||
if (totalSelectedSpacePoints < Integer.MIN_VALUE || totalSelectedSpacePoints > Integer.MAX_VALUE) {
|
||||
log.debug("getTotalSelectedSpacePoints(): totalSelectedSpacePoints outside valid Java int range; unsafe cast");
|
||||
log.trace("getTotalSelectedSpacePoints(): finish");
|
||||
throw new HDF5Exception("Invalid int size");
|
||||
}
|
||||
|
||||
if (log.isDebugEnabled()) {
|
||||
// check is storage space is allocated
|
||||
try {
|
||||
long ssize = H5.H5Dget_storage_size(did);
|
||||
log.trace("getTotalSelectedSpacePoints(): Storage space allocated = {} bytes", ssize);
|
||||
}
|
||||
catch (Exception ex) {
|
||||
log.debug("getTotalSelectedSpacePoints(): check if storage space is allocated:", ex);
|
||||
}
|
||||
}
|
||||
|
||||
return totalSelectedSpacePoints;
|
||||
}
|
||||
|
||||
}
|
||||
Reference in New Issue
Block a user