Merge branch 'master' into develop

pom.xml

@@ -7,7 +7,7 @@
     <groupId>mosaic</groupId>
     <artifactId>MosaicSuite</artifactId>
     <packaging>jar</packaging>
-    <version>1.0.16</version>
+    <version>1.0.17</version>
     <description>Package contains image processing algorithms developed in MOSAIC Group</description>
     <url>http://mosaic.mpi-cbg.de/?q=downloads/imageJ</url>
     <inceptionYear>2010</inceptionYear>

src/main/java/mosaic/core/utils/ShellCommand.java

@@ -31,7 +31,7 @@ public class ShellCommand {
             // we can use bash
             return new String[] { "bash", "-c", cmd };
         }
-        return new String[] { "cmd", cmd };
+        return new String[] { "cmd /C", cmd };
     }
 
     /**

src/main/java/mosaic/plugins/BregmanGLM_Batch.java

@@ -69,6 +69,8 @@ public class BregmanGLM_Batch implements Segmentation {
         if (iIsMacro) {
             aArgs = Macro.getOptions();
         }
+        if (aArgs == null) aArgs = "";
+        
         logger.info("Input options: [" + aArgs + "]");
         iParameters = readConfiguration(aArgs);
         iParameters.nthreads = readNumberOfThreads(aArgs);
@@ -294,11 +296,11 @@ public class BregmanGLM_Batch implements Segmentation {
                 RScript.makeRScript(aOutputSavePath, aObjectsDataFile, aObjectsColocFile, aImagesDataFile, aChannelPairs, iParameters.nbimages, iParameters.groupnames, iParameters.ch1, iParameters.ch2);
                 // Try to run the R script
                 try {
-                    logger.debug("================ RSCRIPT BEGIN ====================");
+                    logger.info("================ RSCRIPT BEGIN ====================");
                     String command = "cd " + aOutputSavePath + "; Rscript " + aOutputSavePath + File.separator + RScript.ScriptName;
-                    logger.debug("Command: [" + command + "]");
+                    logger.info("Command: [" + command + "]");
                     ShellCommand.exeCmdString(command);
-                    logger.debug("================ RSCRIPT END ====================");
+                    logger.info("================ RSCRIPT END ====================");
                 }
                 catch (final IOException e) {
                     e.printStackTrace();