...
 
Commits (2)
...@@ -7,7 +7,7 @@ ...@@ -7,7 +7,7 @@
<groupId>mosaic</groupId> <groupId>mosaic</groupId>
<artifactId>MosaicSuite</artifactId> <artifactId>MosaicSuite</artifactId>
<packaging>jar</packaging> <packaging>jar</packaging>
<version>1.0.16</version> <version>1.0.17</version>
<description>Package contains image processing algorithms developed in MOSAIC Group</description> <description>Package contains image processing algorithms developed in MOSAIC Group</description>
<url>http://mosaic.mpi-cbg.de/?q=downloads/imageJ</url> <url>http://mosaic.mpi-cbg.de/?q=downloads/imageJ</url>
<inceptionYear>2010</inceptionYear> <inceptionYear>2010</inceptionYear>
......
...@@ -31,7 +31,7 @@ public class ShellCommand { ...@@ -31,7 +31,7 @@ public class ShellCommand {
// we can use bash // we can use bash
return new String[] { "bash", "-c", cmd }; return new String[] { "bash", "-c", cmd };
} }
return new String[] { "cmd", cmd }; return new String[] { "cmd /C", cmd };
} }
/** /**
......
...@@ -69,6 +69,8 @@ public class BregmanGLM_Batch implements Segmentation { ...@@ -69,6 +69,8 @@ public class BregmanGLM_Batch implements Segmentation {
if (iIsMacro) { if (iIsMacro) {
aArgs = Macro.getOptions(); aArgs = Macro.getOptions();
} }
if (aArgs == null) aArgs = "";
logger.info("Input options: [" + aArgs + "]"); logger.info("Input options: [" + aArgs + "]");
iParameters = readConfiguration(aArgs); iParameters = readConfiguration(aArgs);
iParameters.nthreads = readNumberOfThreads(aArgs); iParameters.nthreads = readNumberOfThreads(aArgs);
...@@ -294,11 +296,11 @@ public class BregmanGLM_Batch implements Segmentation { ...@@ -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); RScript.makeRScript(aOutputSavePath, aObjectsDataFile, aObjectsColocFile, aImagesDataFile, aChannelPairs, iParameters.nbimages, iParameters.groupnames, iParameters.ch1, iParameters.ch2);
// Try to run the R script // Try to run the R script
try { try {
logger.debug("================ RSCRIPT BEGIN ===================="); logger.info("================ RSCRIPT BEGIN ====================");
String command = "cd " + aOutputSavePath + "; Rscript " + aOutputSavePath + File.separator + RScript.ScriptName; String command = "cd " + aOutputSavePath + "; Rscript " + aOutputSavePath + File.separator + RScript.ScriptName;
logger.debug("Command: [" + command + "]"); logger.info("Command: [" + command + "]");
ShellCommand.exeCmdString(command); ShellCommand.exeCmdString(command);
logger.debug("================ RSCRIPT END ===================="); logger.info("================ RSCRIPT END ====================");
} }
catch (final IOException e) { catch (final IOException e) {
e.printStackTrace(); e.printStackTrace();
......