Java tutorial
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(By way * of non-limiting example, you will not contribute any code obtained by you under the GNU General Public License or other * so-called "reciprocal" license.) *******************************************************************************/ package edu.stanford.epad.epadws.processing.pipeline.task; import java.io.BufferedReader; import java.io.File; import java.io.FileWriter; import java.io.InputStream; import java.io.InputStreamReader; import org.apache.commons.io.IOUtils; import edu.stanford.epad.common.util.EPADConfig; import edu.stanford.epad.common.util.EPADFileUtils; import edu.stanford.epad.common.util.EPADLogger; /** * @author amsnyder */ public class DicomHeadersTask implements Runnable { private static final EPADLogger logger = EPADLogger.getInstance(); private final String seriesUID; private final File dicomInputFile; private final File outputFile; public DicomHeadersTask(String seriesUID, File dicomInputFile, File outputFile) { this.seriesUID = seriesUID; this.dicomInputFile = dicomInputFile; this.outputFile = outputFile; } @Override public void run() { Thread.currentThread().setPriority(Thread.MIN_PRIORITY); // Let interactive thread run sooner FileWriter tagFileWriter = null; InputStream is = null; InputStreamReader isr = null; BufferedReader br = null; Process process = null; try { String[] command = { "./dcm2txt", "-w", "250", "-l", "250", dicomInputFile.getAbsolutePath() }; ProcessBuilder processBuilder = new ProcessBuilder(command); String dicomBinDir = EPADConfig.getEPADWebServerDICOMScriptsDir() + "bin/"; File script = new File(dicomBinDir, "dcm2txt"); if (!script.exists()) dicomBinDir = EPADConfig.getEPADWebServerDICOMBinDir(); script = new File(dicomBinDir, "dcm2txt"); // Java 6 - Runtime.getRuntime().exec("chmod u+x "+script.getAbsolutePath()); script.setExecutable(true); processBuilder.directory(new File(dicomBinDir)); process = processBuilder.start(); process.getOutputStream(); is = process.getInputStream(); isr = new InputStreamReader(is); br = new BufferedReader(isr); String line; StringBuilder sb = new StringBuilder(); StringBuilder log = new StringBuilder(); while ((line = br.readLine()) != null) { sb.append(line).append("\n"); log.append("./dcm2txt: " + line).append("\n"); } try { process.waitFor(); } catch (InterruptedException e) { logger.info(log.toString()); logger.warning("Couldn't get tags for series " + seriesUID + "; dicom=" + dicomInputFile.getAbsolutePath() + " tagFile:" + outputFile.getAbsolutePath(), e); } EPADFileUtils.createDirsAndFile(outputFile); File tagFile = outputFile; tagFileWriter = new FileWriter(tagFile); tagFileWriter.write(sb.toString()); } catch (Exception e) { logger.warning("DicomHeadersTask failed to create DICOM tags for series " + seriesUID + " dicom FIle:" + dicomInputFile.getAbsolutePath() + " : " + outputFile.getAbsolutePath(), e); } catch (OutOfMemoryError oome) { logger.warning("DicomHeadersTask for series " + seriesUID + " out of memory: ", oome); } finally { IOUtils.closeQuietly(tagFileWriter); IOUtils.closeQuietly(br); if (process != null) process.destroy(); } } }