Changed to using streams to load.

#4
h5jan · Dec 19, 2019 · 40e2a6b · 40e2a6b
1 parent 5868ef5
commit 40e2a6b
Show file tree

Hide file tree

Showing 16 changed files with 241 additions and 256 deletions.
diff --git a/build.gradle b/build.gradle
@@ -22,8 +22,6 @@ apply plugin: 'java'
 apply plugin: 'jacoco'
 apply plugin: 'eclipse'
 apply plugin: 'idea'
-apply plugin: 'findbugs'
-apply plugin: 'pmd'
 apply plugin: 'checkstyle'
 
 // We aspire one day to be part of Eclipse January.
@@ -33,10 +31,10 @@ group 'io.github.h5jan'
 description = "h5jan-core"
 
 // To sign, enter the gradle command 'gradle(w) sign'
-defaultTasks 'compileJava', 'classes', 'jar', 'sourceJar', 'compileTestJava', 'processTestResources', 'testClasses', 'findbugsMain', 'pmdMain', 'test'
+defaultTasks 'compileJava', 'javadoc', 'enunciate', 'check', 'compileTestJava', 'processTestResources', 'test', 'jar'
 
 ext {
-	baseVersion = "0.5.0"
+	baseVersion = "0.6.0"
     if (project.hasProperty('version')) {
 		baseVersionNum = version
     }
@@ -152,18 +150,6 @@ repositories {
     }
 }
 
-
-findbugs {
-    ignoreFailures = true
-    sourceSets = [sourceSets.main]
-    reportsDir = file("$project.buildDir/reports/findbugs")
-    effort = "max"
-}
-
-pmd {
-    ignoreFailures = true
-}
-
 /**
  The Suites are for local testing, gradle can file other unit tests
  see https://docs.gradle.org/current/dsl/org.gradle.api.tasks.testing.Test.html
@@ -198,6 +184,9 @@ dependencies {
 	// https://mvnrepository.com/artifact/commons-beanutils/commons-beanutils
     compile group: 'commons-beanutils', name: 'commons-beanutils', version: '1.9.4'
 
+	// https://mvnrepository.com/artifact/org.apache.commons/commons-csv
+	compile group: 'org.apache.commons', name: 'commons-csv', version: '1.7'
+
 	// https://mvnrepository.com/artifact/tec.units/indriya/1.0  Units  BSD License
 	implementation group: 'tec.units', name: 'indriya', version: '1.0'
 
@@ -270,17 +259,17 @@ publishing {
 			    }
 			}// create the signed artifacts
 
-			project.tasks.signArchives.signatureFiles.each {
-			    artifact(it) {
-			        def matcher = it.file =~ /-(sources|javadoc)\.jar\.asc$/
-			        if (matcher.find()) {
-			            classifier = matcher.group(1)
-			        } else {
-			            classifier = null
-			        }
-			        extension = 'jar.asc'
-			    }
-			}
+			//project.tasks.signArchives.signatureFiles.each {
+			//    artifact(it) {
+			//        def matcher = it.file =~ /-(sources|javadoc)\.jar\.asc$/
+			//        if (matcher.find()) {
+			//            classifier = matcher.group(1)
+			//        } else {
+			//            classifier = null
+			//        }
+			//        extension = 'jar.asc'
+			//    }
+			//}
         }	
     }
 

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.4.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.0.1-bin.zip
diff --git a/...o/github/h5jan/io/AbstractFileLoader.java → ...github/h5jan/io/AbstractStreamLoader.java b/...o/github/h5jan/io/AbstractFileLoader.java → ...github/h5jan/io/AbstractStreamLoader.java
@@ -9,25 +9,19 @@
 
 package io.github.h5jan.io;
 
-import java.io.File;
 import java.io.IOException;
 
-import org.eclipse.january.DatasetException;
 import org.eclipse.january.IMonitor;
 import org.eclipse.january.dataset.Dataset;
-import org.eclipse.january.dataset.DatasetUtils;
 import org.eclipse.january.dataset.IDataset;
-import org.eclipse.january.dataset.ILazyDataset;
 import org.eclipse.january.dataset.LazyDataset;
 import org.eclipse.january.dataset.SliceND;
 import org.eclipse.january.io.ILazyLoader;
 
-import io.github.h5jan.core.DataFrame;
-
 /**
  * A class which can be extended when implementing IFileLoader
  */
-abstract class AbstractFileLoader implements IFileLoader {
+abstract class AbstractStreamLoader implements IStreamLoader {
 
 	/** 
 	 * Name prefix for an image dataset (should be followed by two digits, starting with 01)
@@ -54,90 +48,47 @@ abstract class AbstractFileLoader implements IFileLoader {
 	 */
 	protected static final String FILEPATH_DATASET_SEPARATOR = ":";
 
-	protected File file = null;
-
-	protected void setFile(final File file) {
-		this.file = file;
-	}
-
-	protected Configuration configuration = null;
 
-	protected void setConfiguration(final Configuration configuration) {
-		this.configuration = configuration;
-	}
-
-	protected class LazyLoaderStub implements ILazyLoader {
+	protected abstract class LazyLoaderStub implements ILazyLoader {
 
 		public static final long serialVersionUID = 5057544213374303912L;
-		private IFileLoader loader;
+		private IStreamLoader loader;
 		private String name;
 
 		public LazyLoaderStub() {
 			loader = null;
 			name = null;
 		}
 
-		public LazyLoaderStub(IFileLoader loader) {
+		public LazyLoaderStub(IStreamLoader loader) {
 			this(loader, null);
 		}
 
 		/**
 		 * @param loader
 		 * @param name dataset name in data holder (can be null to signify first dataset)
 		 */
-		public LazyLoaderStub(IFileLoader loader, String name) {
+		public LazyLoaderStub(IStreamLoader loader, String name) {
 			this.loader = loader;
 			this.name = name;
 		}
 
-		public IFileLoader getLoader() {
+		public IStreamLoader getLoader() {
 			return loader;
 		}
 
-		@Override
-		public IDataset getDataset(IMonitor mon, SliceND slice) throws IOException {
-
-			if (loader == null) {
-				return null;
-			}
-
-			try {
-				DataFrame holder = load(file, configuration, mon);
-				if (holder != null) {
-					ILazyDataset lazy = name == null ? holder.get(0) : holder.get(name);
-					if (lazy != null) {
-						IDataset data = lazy.getSlice();
-						return DatasetUtils.convertToDataset(data).getSliceView(slice);
-					}
-				} 
-
-				holder = loader.load(file, configuration, mon);
-				ILazyDataset lazy = name == null ? holder.get(0) : holder.get(name);
-				return lazy.getSlice().getSliceView(slice);
-
-			} catch (DatasetException de) {
-				throw new IOException(de);
-			}
-		}
-
+		public abstract IDataset getDataset(IMonitor mon, SliceND slice) throws IOException;
+
 		@Override
 		public boolean isFileReadable() {
-			return file.canRead();
+			return true;
 		}
 	}
 
 	protected LazyDataset createLazyDataset(LazyLoaderStub l, String dName, Class<? extends Dataset> clazz, int... shape) {
 		return new LazyDataset(l, dName, clazz, shape);
 	}
 
-	protected LazyDataset createLazyDataset(IFileLoader loader, String dName, Class<? extends Dataset> clazz, int... shape) {
-		return createLazyDataset(loader, dName, dName, clazz, shape);
-	}
-
-	protected LazyDataset createLazyDataset(IFileLoader loader, String dName, String dhName, Class<? extends Dataset> clazz, int... shape) {
-		return new LazyDataset(new LazyLoaderStub(loader, dhName), dName, clazz, shape);
-	}
-
 	/**
 	 * @param mon
 	 * @return false if cancelled

diff --git a/src/main/java/io/github/h5jan/io/Configuration.java b/src/main/java/io/github/h5jan/io/Configuration.java
@@ -10,9 +10,12 @@
  *******************************************************************************/
 package io.github.h5jan.io;
 
+import java.io.File;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.apache.commons.io.FilenameUtils;
+
 /**
  * A class to hold common dataset loading configurations.
  * 
@@ -24,17 +27,23 @@ public interface Configuration extends Map<String, Object> {
 	/**
 	 * No conf
 	 */
-	public static final Configuration DEFAULT = new ConfigurationImpl();
+	public static Configuration createDefault() {
+		return new ConfigurationImpl();
+	}
 
 	/**
 	 * Grey scale conf.
 	 */
-	public static final Configuration GREYSCALE = concrete("asGrey", Boolean.TRUE);
+	public static Configuration createGreyScale() { 
+		return concrete("asGrey", Boolean.TRUE);
+	}
 
 	/**
 	 * Keep pixel width
 	 */
-	public static final Configuration KEEPWIDTH = concrete("keepBitWidth", Boolean.TRUE);
+	public static Configuration createKeepWidth() {
+	    return concrete("keepBitWidth", Boolean.TRUE);
+	}
 
 	/**
 	 * Create any configuration with key value pairs
@@ -45,16 +54,42 @@ public static Configuration concrete(Object... values) {
 		return new ConfigurationImpl(values);
 	}
 
+	/**
+	 * Align from name and type
+	 * @param fileName - file name
+	 * @param fileType - file type
+	 * @param numBits - number of bits
+	 * @param asUnsigned - signed or unsigned.
+	 * @return configuration
+	 */
 	public static Configuration image(String fileName, String fileType, int numBits, boolean asUnsigned) {
 		return new ConfigurationImpl("fileName", fileName,
 									"fileType", fileType,
 									"numBits", numBits,
 									"asUnsigned", asUnsigned);
 	}
+
+	/**
+	 * Align from file.
+	 * @param file - file 
+	 * @param numBits - number of bits
+	 * @param asUnsigned - signed or unsigned.
+	 * @return configuration
+	 */
+	public static Configuration image(File file, int numBits, boolean asUnsigned) {
+		Configuration ret = new ConfigurationImpl("numBits", numBits,
+									"asUnsigned", asUnsigned);
+		ret.align(file);
+		return ret;
+	}
 
 	public default String getFileName() {
 		return (String)get("fileName");
 	}
+
+	public default String getFilePath() {
+		return (String)get("filePath");
+	}
 
 	public default String getFileType() {
 		return (String)get("fileType");
@@ -67,6 +102,17 @@ public default int getNumBits() {
 	public default boolean getAsUnsigned() {
 		return (Boolean)get("asUnsigned");
 	}
+
+	public default void align(File file) {
+		if (!containsKey("fileName")) put("fileName", file.getName());
+		if (!containsKey("filePath")) put("filePath", file.getAbsolutePath());
+		if (!containsKey("fileType")) {
+			String ext = FilenameUtils.getBaseName(file.getName());
+			if (ext!=null) {
+				 put("fileType", ext.toUpperCase());
+			}
+		}
+	}
 }
 
 class ConfigurationImpl extends HashMap<String,Object> implements Configuration {