Implemented option to hide image when opening

Readme.md

@@ -99,6 +99,8 @@ To create an all in one zip file for installation in a ImageJ installation use:
 
 The zip file contains an all in one jar as well as the required native libraries for Windows, Linux and Mac OS X.
 
+Note: to be able to build the package you need to have access to the PSI artifact server. Therefore this only works within the PSI networks and if you have a certain maven configuration. An example Maven settings.xml that you can copy to `~/.m2/settings.xml` is located [here](settings.xml).
+
 # Acknowledgements
 This project was inspired by the ImageJ HDF Plugin of Matthias Schlachter Chair of Pattern Recognition and Image Processing, University of Freiburg, Germany ( https://code.google.com/p/imagej-hdf ) . 
 It is a complete rewrite of the code with the focus on efficiency and maintainability

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ch.psi</groupId>
 	<artifactId>imagej.hdf5</artifactId>
-	<version>0.11.0</version>
+	<version>0.12.0</version>
 
 	<dependencies>
 		<dependency>

settings.xml

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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"
+          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <profiles>
+        <profile>
+            <repositories>
+                <repository>
+                    <snapshots>
+                        <enabled>false</enabled>
+                    </snapshots>
+                    <id>central</id>
+                    <name>libs-releases</name>
+                    <url>http://artifacts.psi.ch/artifactory/libs-releases</url>
+                </repository>
+                <repository>
+                    <snapshots />
+                    <id>snapshots</id>
+                    <name>libs-snapshots</name>
+                    <url>http://artifacts.psi.ch/artifactory/libs-snapshots</url>
+                </repository>
+            </repositories>
+            <pluginRepositories>
+                <pluginRepository>
+                    <snapshots>
+                        <enabled>false</enabled>
+                    </snapshots>
+                    <id>central</id>
+                    <name>libs-releases</name>
+                    <url>http://artifacts.psi.ch/artifactory/libs-releases</url>
+                </pluginRepository>
+                <pluginRepository>
+                    <snapshots />
+                    <id>snapshots</id>
+                    <name>libs-releases</name>
+                    <url>http://artifacts.psi.ch/artifactory/libs-releases</url>
+                </pluginRepository>
+            </pluginRepositories>
+            <id>artifactory</id>
+        </profile>
+    </profiles>
+    <activeProfiles>
+        <activeProfile>artifactory</activeProfile>
+    </activeProfiles>
+</settings>

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

@@ -46,7 +46,12 @@ public class HDF5Reader implements PlugIn {
 	 * dataset=/your/path/to/dataset
 	 *
 	 */
+
 	public ImageStack open(String arg, boolean interactive, String filename, String nameOfDataset, boolean virtualstack) {
+		return open(arg, interactive, filename, nameOfDataset, virtualstack, true);
+	}
+
+	public ImageStack open(String arg, boolean interactive, String filename, String nameOfDataset, boolean virtualstack, boolean showImage) {
 
 //		Map arguments = HDF5Reader.parseArguments(arg);
 
@@ -118,7 +123,9 @@ public class HDF5Reader implements PlugIn {
 				
 				ImagePlus imp = new ImagePlus(filename, stack);
 				imp.resetDisplayRange();
-				imp.show();
+				if(showImage) {
+					imp.show();
+				}
 
 				stacks.add(stack);
 				return stack; // TODO should return stacks instead of stack
@@ -166,7 +173,9 @@ public class HDF5Reader implements PlugIn {
 					imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
 					imp.setOpenAsHyperStack(true);
 					imp.resetDisplayRange();
-					imp.show();
+					if(showImage) {
+						imp.show();
+					}
 					
 				} else if (numberOfDimensions == 4 && dimensions[3] == 3) {
 					logger.info("3D RGB Image");
@@ -194,7 +203,9 @@ public class HDF5Reader implements PlugIn {
 					imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
 					imp.setOpenAsHyperStack(true);
 					imp.resetDisplayRange();
-					imp.show();
+					if(showImage) {
+						imp.show();
+					}
 					
 				} else if (numberOfDimensions == 4) {
 					logger.info("4D Image (HyperVolume)");
@@ -224,7 +235,9 @@ public class HDF5Reader implements PlugIn {
 					imp.setDimensions(1, (int) dimensions[1], (int) dimensions[0]);
 					imp.setOpenAsHyperStack(true);
 					imp.resetDisplayRange();
-					imp.show();
+					if(showImage) {
+						imp.show();
+					}
 					
 				} else if (numberOfDimensions == 3 && dimensions[2] == 3) {
 					logger.info("2D RGB Image");
@@ -247,7 +260,9 @@ public class HDF5Reader implements PlugIn {
 					imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
 					imp.setOpenAsHyperStack(true);
 					imp.resetDisplayRange();
-					imp.show();
+					if(showImage) {
+						imp.show();
+					}
 					
 				} else if (numberOfDimensions == 3) {
 					logger.info("3D Image");
@@ -322,7 +337,9 @@ public class HDF5Reader implements PlugIn {
 					stacks.add(stack);
 					ImagePlus imp = new ImagePlusHDF5(filename + " " + datasetName, stack);
 					imp.resetDisplayRange();
-					imp.show();
+					if(showImage) {
+						imp.show();
+					}
 					
 				} else if (numberOfDimensions == 2) {
 					logger.info("2D Image");
@@ -335,7 +352,9 @@ public class HDF5Reader implements PlugIn {
 					
 					ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
 					imp.resetDisplayRange();
-					imp.show();
+					if(showImage) {
+						imp.show();
+					}
 					
 				} else {
 					IJ.showStatus("Variable Dimension " + numberOfDimensions + " not supported");