Attemp to use plugin options

Readme.md

@@ -1,4 +1,4 @@
-# Overview
+ # Overview
 
 ImageJ plugin for reading and writing HDF5 files.
 
@@ -79,6 +79,11 @@ cd <FIJI_HOME>
 Starting with Java 8 just the LD_LIBRARY_PATH variable need to be set. For MacOSX it is export `DYLD_LIBRARY_PATH=lib/mac64/:$DYLD_LIBRARY_PATH`.
 
 # Development
+
+To be able to run the tests and plugin from within the following arguments need to be passed:
+
+![RunSettings](RunSettings.png)
+
 To create an all in one zip file for installation in a ImageJ installation use: 
 `mvn clean compile assembly:assembly`
 

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

@@ -10,7 +10,10 @@ import ij.plugin.PlugIn;
 
 import java.io.File;
 import java.lang.reflect.Array;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -28,14 +31,24 @@ public class HDF5Reader implements PlugIn {
 	 */
 	public static void main(String[] args){
 		HDF5Reader r = new HDF5Reader();
-		r.run("");
+		r.run("path=/Users/ebner/Desktop/ open=A8_d_400N030_.h5");
+//		IJ.run("HDF5...", "/Users/ebner/Desktop/A8_d_400N030_.h5");
 	}
 	
 	/**
 	 * Main function plugin
+	 * arg is a space separated list of arguments that can be passed to the run method.
+	 * arg looks something like this: "para1=value1 para2=value2 ....."
+	 *
+	 * Supported arguments for arg:
+	 * open=<path>
+	 * dataset=/your/path/to/dataset
+	 *
 	 */
 	public void run(String arg) {
 
+		Map arguments = HDF5Reader.parseArguments(arg);
+
 		OpenDialog od = new OpenDialog("Open HDF5 ...", arg);
 
 		
@@ -58,7 +71,19 @@ public class HDF5Reader implements PlugIn {
 			file.open();
 
 			List<Dataset> datasets = HDF5Utilities.getDatasets(file);
-			DatasetSelection selectedDatasets = selectDatasets(datasets);
+
+			DatasetSelection selectedDatasets = null;
+			if(arguments.containsKey("dataset")){
+				logger.info("Using automatic selection");
+				selectedDatasets = selectDatasets(datasets, arguments);
+			}
+			else{
+				logger.info("Using manual selection");
+				// Manual selection of the dataset and other parameters via a dialog
+				selectedDatasets = selectDatasets(datasets);
+			}
+
+
 			// TODO to be removed - Workaround virtual stack - keep HDF5 file open at the end 
 			close=!selectedDatasets.isVirtualStack();
 
@@ -353,6 +378,41 @@ public class HDF5Reader implements PlugIn {
 		return selectedDatasets;
 	}
 
+	private DatasetSelection selectDatasets(List<Dataset> datasets, Map<String,String> arguments) throws HDF5Exception {
+
+		GenericDialog gd = new GenericDialog("Variable Name Selection");
+		gd.addMessage("Please select variables to be loaded.\n");
+
+		SelectionPanel panel = new SelectionPanel(datasets);
+
+		gd = new GenericDialog("Variable Name Selection");
+		gd.add(panel);
+		gd.addMessage("");
+		gd.pack();
+		gd.showDialog();
+
+		DatasetSelection selectedDatasets = new DatasetSelection();
+		for(Dataset dataset: datasets){
+			if(dataset.getFullName().equals(arguments.get("dataset"))){
+				selectedDatasets.getDatasets().add(dataset);
+				break; // we only support one selection for the time being
+			}
+		}
+
+//		selectedDatasets.setGroup(panel.groupValues());
+//		selectedDatasets.setSlice(panel.getSlice());
+//		selectedDatasets.setModulo(panel.getModulo());
+
+		if(arguments.containsKey("virtualstack") && arguments.get("virtualstack").equalsIgnoreCase("false")){
+			selectedDatasets.setVirtualStack(false);
+		}
+		else{
+			selectedDatasets.setVirtualStack(true);
+		}
+
+		return selectedDatasets;
+	}
+
 
 	/**
 	 * Add slice to image stack
@@ -433,4 +493,22 @@ public class HDF5Reader implements PlugIn {
 		stack.addSlice(null, g);
 		stack.addSlice(null, b);
 	}
+
+	public static Map<String,String> parseArguments(String arg){
+
+		/// ImageJ arguments look something like this: "para1=value1 para2=value2 ....."
+		Map<String,String> map = new HashMap<>();
+		arg = arg.trim();
+		for(String argument: arg.split("\\s+")){
+			String[] entry = argument.split("=");
+			if(entry.length==2) {
+				map.put(entry[0], entry[1]);
+			}
+			else{
+				// ignore
+				logger.warning("Cannot parse argument " + argument + " - Ignore");
+			}
+		}
+		return map;
+	}
 }

src/test/java/ch/psi/imagej/hdf5/HDF5ReaderTest.java

@@ -0,0 +1,22 @@
+package ch.psi.imagej.hdf5;
+
+import org.junit.Test;
+
+import java.util.Map;
+
+import static org.junit.Assert.*;
+
+/**
+ *
+ */
+public class HDF5ReaderTest {
+    @Test
+    public void parseArguments() throws Exception {
+
+        Map map = HDF5Reader.parseArguments("para1=value1 para2=value2  PARA=VAL");
+        assertTrue(map.get("para1").equals("value1"));
+        assertTrue(map.get("para2").equals("value2"));
+        assertTrue(map.get("PARA").equals("VAL"));
+    }
+
+}

src/test/java/ch/psi/imagej/hdf5/HDF5UtilitiesTest.java

@@ -2,6 +2,7 @@ package ch.psi.imagej.hdf5;
 
 import static org.junit.Assert.*;
 
+import ij.IJ;
 import org.junit.Test;
 
 public class HDF5UtilitiesTest {
@@ -22,4 +23,14 @@ public class HDF5UtilitiesTest {
 		assertEquals(gdescriptor, "three");
 	}
 
+
+	@Test
+	public void testOpen() {
+		IJ.run("HDF5...");
+		String descriptor = "/test/one/two/three";
+		String gdescriptor = HDF5Utilities.getDatasetName(descriptor);
+		System.out.println(gdescriptor);
+		assertEquals(gdescriptor, "three");
+	}
+
 }