Commit 57ac32c0 authored by gonciarz's avatar gonciarz

Version 1.0.17

parent 8a11b267
......@@ -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>
......
......@@ -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 };
}
/**
......
......@@ -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();
......
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