Cleanup HDF5Config

pom.xml

@@ -39,6 +39,13 @@
 			<artifactId>slf4j-api</artifactId>
 			<version>1.7.6</version>
 		</dependency>
+		
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.11</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<build>

src/main/java/ch/psi/imagej/hdf5/HDF5Config.java

@@ -12,30 +12,21 @@ public class HDF5Config implements PlugIn {
 	
 	private static final Logger logger = Logger.getLogger(HDF5Config.class.getName());
 
-	public static String GROUP_VARS_BY_NAME = "HDF5.groupVarsByName";
+	private static final String GROUP_VARS_BY_NAME = "HDF5.groupVarsByName";
-	public static String SHOW_UNMATCHED_DATASET_NAMES = "HDF5.showUnmatchedDataSetNames";
+	private static final String SHOW_UNMATCHED_DATASET_NAMES = "HDF5.showUnmatchedDataSetNames";
-	public static String GROUP_VARS_BY_NAME_FORMAT_GROUP = "HDF5.groupVarsByNameFormatGroup";
+	private static final String GROUP_VARS_BY_NAME_FORMAT_GROUP = "HDF5.groupVarsByNameFormatGroup";
-	public static String GROUP_VARS_BY_NAME_FORMAT = "HDF5.groupVarsByNameFormat";
+	private static final String GROUP_VARS_BY_NAME_FORMAT = "HDF5.groupVarsByNameFormat";
-	public static String DOLLAR_REGEXP_FOR_GROUPING = "HDF5.dollarRegexpForGrouping";
+	private static final String DOLLAR_REGEXP_FOR_GROUPING = "HDF5.dollarRegexpForGrouping";
+	
+	// Getting preference or default values
+	private boolean groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, true);
+	private boolean showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, true);
+	private String groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, "/hints");
+	private String groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, "/t$T/channel$C");
+	private String dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, "[0-9]+");
+	
 	
 	public void run(String arg) {
-		// set default values
-		setDefaultsIfNoValueExists();
-		// read ImageJ Preferences
-		boolean groupVarsByName = Boolean.getBoolean(getDefaultValue(GROUP_VARS_BY_NAME));
-		groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName);
-
-		boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue(SHOW_UNMATCHED_DATASET_NAMES));
-		showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
-
-		String groupVarsByNameFormatGroup = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT_GROUP);
-		groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
-
-		String groupVarsByNameFormat = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT);
-		groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
-
-		String dollarRegexpForGrouping = getDefaultValue(DOLLAR_REGEXP_FOR_GROUPING);
-		dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
 		
 		GenericDialog configDiag = new GenericDialog("HDF5 Preferences");
 		configDiag.addMessage("Reader:");
@@ -43,45 +34,19 @@ public class HDF5Config implements PlugIn {
 		configDiag.addCheckbox("Show unmatched data set names in a separate list", showUnmatchedDataSetNames);
 		configDiag.addStringField("HDF5 group containing pattern " + "for data set grouping: ", groupVarsByNameFormatGroup, 15);
 		configDiag.addStringField("Pattern for grouping (if no attributes" + " are found): ", groupVarsByNameFormat, 15);
-		// configDiag.addStringField("$ regexp (ignored because only numbers" +
-		// " work right now): ",
-		// dollarRegexpForGrouping,15);
-		configDiag.addMessage("Writer:");
 		
-		String yesLabel = "Save";
-		String noLabel = "Reset";
-		configDiag.enableYesNoCancel(yesLabel, noLabel);
 		configDiag.showDialog();
 
 		if (configDiag.wasCanceled()) {
-			// do nothing
 			return;
 		}
-		if (!configDiag.wasOKed()) {
-			// reset button was pressed
-			logger.info("reset button was pressed");
-			// reset all and return a new dialog
-			configDiag.setVisible(false);
-			this.run(arg);
-			return;
-		}
-		// get parameters check if they are correct
 
+		// Get parameters check if they are correct
 		groupVarsByName = configDiag.getNextBoolean();
-		logger.info("groupVarsByName: " + Boolean.toString(groupVarsByName));
-
 		showUnmatchedDataSetNames = configDiag.getNextBoolean();
-		logger.info("showUnmatchedDataSetNames: " + Boolean.toString(showUnmatchedDataSetNames));
-
 		groupVarsByNameFormatGroup = configDiag.getNextString();
-		logger.info("groupVarsByNameFormatGroup: " + groupVarsByNameFormatGroup);
-
 		groupVarsByNameFormat = configDiag.getNextString();
-		logger.info("groupVarsByNameFormat: " + groupVarsByNameFormat);
 
-		// dollarRegexpForGrouping = configDiag.getNextString();
-		// logger.info("dollarRegexpForGrouping: " +
-		// dollarRegexpForGrouping);
 		
 		try {
 			String[] formatTokens = HDF5GroupedVarnames.parseFormatString(groupVarsByNameFormat, dollarRegexpForGrouping);
@@ -97,62 +62,32 @@ public class HDF5Config implements PlugIn {
 			this.run(arg);
 			return;
 		}
+		
 		logger.info("Saving...");
 
-		// all OK and "Save" was pressed, so save it...
+		// All OK and "Save" was pressed, so save it...
 		Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName);
 		Prefs.set(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
 		Prefs.set(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
 		Prefs.set(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
-		//
-		// ignore the $ regexp for now, because only numbers work
-		//
 		Prefs.set(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
 
 	}
 
-	public static void setDefaultsIfNoValueExists() {
-		boolean groupVarsByName = Boolean.getBoolean(getDefaultValue(GROUP_VARS_BY_NAME));
-		groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName);
-		Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName);
 
-		boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue(SHOW_UNMATCHED_DATASET_NAMES));
+	public boolean isGroupVarsByName() {
-		showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
+		return groupVarsByName;
-		Prefs.set(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
-
-		String groupVarsByNameFormatGroup = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT_GROUP);
-		groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
-		Prefs.set(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
-
-		String groupVarsByNameFormat = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT);
-		groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
-		Prefs.set(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
-
-		String dollarRegexpForGrouping = getDefaultValue(DOLLAR_REGEXP_FOR_GROUPING);
-		dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
-		Prefs.set(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
 	}
-
+	public boolean isShowUnmatchedDataSetNames() {
-	public static String getDefaultValue(String key) {
+		return showUnmatchedDataSetNames;
-		if (key.equals(GROUP_VARS_BY_NAME)) {
+	}
-			boolean groupVarsByName = true; // default
+	public String getGroupVarsByNameFormatGroup() {
-			return Boolean.toString(groupVarsByName);
-		} else if (key.equals(SHOW_UNMATCHED_DATASET_NAMES)) {
-			boolean showUnmatchedDataSetNames = true; // default
-			return Boolean.toString(showUnmatchedDataSetNames);
-		} else if (key.equals(GROUP_VARS_BY_NAME_FORMAT_GROUP)) {
-			String groupVarsByNameFormatGroup = "/hints"; // default
 		return groupVarsByNameFormatGroup;
-		} else if (key.equals(GROUP_VARS_BY_NAME_FORMAT)) {
+	}
-			String groupVarsByNameFormat = "/t$T/channel$C"; // default
+	public String getGroupVarsByNameFormat() {
 		return groupVarsByNameFormat;
-		} else if (key.equals(DOLLAR_REGEXP_FOR_GROUPING)) {
+	}
-			String dollarRegexpForGrouping = "[0-9]+"; // default
+	public String getDollarRegexpForGrouping() {
 		return dollarRegexpForGrouping;
-		} else {
-			logger.info("No default value for key: " + key);
-			return null;
 	}
-	}
-
 }

src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java

@@ -21,7 +21,6 @@ package ch.psi.imagej.hdf5;
  */
 
 import ij.IJ;
-import ij.Prefs;
 import ij.ImagePlus;
 import ij.CompositeImage;
 import ij.ImageStack;
@@ -100,14 +99,12 @@ public class HDF5Reader implements PlugIn {
 			/*-------------------------------------------------------------------
 			 *  read HDF5_Config prefs
 			 *-------------------------------------------------------------------*/
-			boolean groupVarsByName = Boolean.getBoolean(HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME));
+			HDF5Config config = new HDF5Config();
-			groupVarsByName = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME, groupVarsByName);
+			boolean groupVarsByName = config.isGroupVarsByName();
+			boolean showUnmatchedDataSetNames = config.isShowUnmatchedDataSetNames();
+			String groupVarsByNameFormatGroup = config.getGroupVarsByNameFormatGroup();
+			String dollarRegexpForGrouping = config.getDollarRegexpForGrouping();
 
-			boolean showUnmatchedDataSetNames = Boolean.getBoolean(HDF5Config.getDefaultValue(HDF5Config.SHOW_UNMATCHED_DATASET_NAMES));
-			showUnmatchedDataSetNames = Prefs.get(HDF5Config.SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
-
-			String groupVarsByNameFormatGroup = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT_GROUP);
-			groupVarsByNameFormatGroup = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
 			
 			// TODO: try to read attribute containing format String
 			String groupVarsByNameFormat = null;
@@ -159,17 +156,14 @@ public class HDF5Reader implements PlugIn {
 					logger.info("File has format string for grouping: " + groupVarsByNameFormat);
 				} else {
 					logger.info("File has no format string for grouping" + ", using default");
-					groupVarsByNameFormat = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT);
+					groupVarsByNameFormat = config.getGroupVarsByNameFormat();
-					groupVarsByNameFormat = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
 				}
 			} catch (Exception e) {
 				logger.info("Error occured read format string " + "for grouping, using default");
-				groupVarsByNameFormat = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT);
+				groupVarsByNameFormat = config.getGroupVarsByNameFormat();
-				groupVarsByNameFormat = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
 			}
 
-			String dollarRegexpForGrouping = HDF5Config.getDefaultValue(HDF5Config.DOLLAR_REGEXP_FOR_GROUPING);
+			
-			dollarRegexpForGrouping = Prefs.get(HDF5Config.DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
 
 			/*-------------------------------------------------------------------
 			 *  init the frame and channel ranges

src/test/java/ch/psi/imagej/hdf5/HDF5ConfigTest.java

@@ -0,0 +1,50 @@
+/**
+ * 
+ * Copyright 2014 Paul Scherrer Institute. All rights reserved.
+ * 
+ * This code is free software: you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ * 
+ * This code is distributed in the hope that it will be useful, but without any
+ * warranty; without even the implied warranty of merchantability or fitness for
+ * a particular purpose. See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this code. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+package ch.psi.imagej.hdf5;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * 
+ */
+public class HDF5ConfigTest {
+
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@Before
+	public void setUp() throws Exception {
+	}
+
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@After
+	public void tearDown() throws Exception {
+	}
+
+	@Test
+	public void test() {
+		HDF5Config config = new HDF5Config();
+		config.run("");
+	}
+
+}