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.File; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStream; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Map; import java.util.Set; import javax.imageio.ImageIO; import org.apache.commons.io.IOUtils; import edu.stanford.epad.common.dicom.DICOMFileDescription; import edu.stanford.epad.common.dicom.DicomReader; import edu.stanford.epad.common.util.EPADConfig; import edu.stanford.epad.common.util.EPADFileUtils; import edu.stanford.epad.common.util.EPADLogger; import edu.stanford.epad.common.util.EventMessageCodes; import edu.stanford.epad.dtos.PNGFileProcessingStatus; import edu.stanford.epad.dtos.SeriesProcessingStatus; import edu.stanford.epad.dtos.TaskStatus; import edu.stanford.epad.epadws.dcm4chee.Dcm4CheeDatabaseUtils; import edu.stanford.epad.epadws.epaddb.EpadDatabase; import edu.stanford.epad.epadws.epaddb.EpadDatabaseOperations; import edu.stanford.epad.epadws.service.DefaultEpadProjectOperations; import edu.stanford.epad.epadws.service.EpadProjectOperations; import edu.stanford.epad.epadws.service.UserProjectService; public class SingleFrameDICOMPngGeneratorTask implements GeneratorTask { private static final EPADLogger log = EPADLogger.getInstance(); private final String patientName; private final String studyUID; private final String seriesUID; private final String imageUID; private final int instanceNumber; private final File dicomFile; private final File pngFile; static public Set imagesBeingProcessed = Collections.synchronizedSet(new HashSet()); public SingleFrameDICOMPngGeneratorTask(String patientName, DICOMFileDescription dicomFileDescription, File dicomFile, File pngFile) { this.patientName = patientName; this.studyUID = dicomFileDescription.studyUID; this.seriesUID = dicomFileDescription.seriesUID; this.imageUID = dicomFileDescription.imageUID; this.instanceNumber = dicomFileDescription.instanceNumber; this.dicomFile = dicomFile; this.pngFile = pngFile; } @Override public String getSeriesUID() { return this.seriesUID; } @Override public void run() { Thread.currentThread().setPriority(Thread.MIN_PRIORITY); // Let interactive thread run sooner if (imagesBeingProcessed.contains(imageUID)) { log.info("Image " + imageUID + " already being processed"); return; } generatePNGs(); } private void generatePNGs() { EpadDatabaseOperations epadDatabaseOperations = EpadDatabase.getInstance().getEPADDatabaseOperations(); EpadProjectOperations projectOperations = DefaultEpadProjectOperations.getInstance(); File inputDICOMFile = dicomFile; File outputPNGFile = pngFile; Map<String, String> epadFilesRow = new HashMap<String, String>(); OutputStream outputPNGStream = null; String pngPath = pngFile.getAbsolutePath(); try { imagesBeingProcessed.add(imageUID); String username = null; String projectID = EPADConfig.xnatUploadProjectID; if (UserProjectService.pendingUploads.containsKey(studyUID)) { username = UserProjectService.pendingUploads.get(studyUID); if (username != null && username.indexOf(":") != -1) { projectID = username.substring(username.indexOf(":") + 1); username = username.substring(0, username.indexOf(":")); } if (username != null) { epadDatabaseOperations.insertEpadEvent(username, EventMessageCodes.STUDY_PROCESSED, "", "", "", patientName, "", "", "Study:" + studyUID, projectID, "", "", "", false); UserProjectService.pendingUploads.remove(studyUID); } } projectOperations.updateUserTaskStatus(username, TaskStatus.TASK_DICOM_PNG_GEN, seriesUID, "Generating PNGs, instance:" + instanceNumber, null, null); DicomReader instance = new DicomReader(inputDICOMFile); String pngFilePath = outputPNGFile.getAbsolutePath(); outputPNGFile = new File(pngFilePath); EPADFileUtils.createDirsAndFile(outputPNGFile); try { outputPNGStream = new FileOutputStream(outputPNGFile); ImageIO.write(instance.getPackedImage(), "png", outputPNGStream); outputPNGStream.close(); } catch (Exception x) { // Try second method using pixelmed library log.warning("dcm4che failed to create PNG for instance " + instanceNumber + " in series " + seriesUID + " for patient " + patientName + ", trying pixelmed", x); outputPNGFile.delete(); instance.dcmconvpng3(0, outputPNGFile); } epadFilesRow = Dcm4CheeDatabaseUtils.createEPadFilesRowData(outputPNGFile.getAbsolutePath(), outputPNGFile.length(), imageUID); log.info("PNG of size " + getFileSize(epadFilesRow) + " generated for instance " + instanceNumber + " in series " + seriesUID + ", study " + studyUID + " for patient " + patientName); epadDatabaseOperations.updateEpadFileRow(epadFilesRow.get("file_path"), PNGFileProcessingStatus.DONE, getFileSize(epadFilesRow), ""); } catch (FileNotFoundException e) { log.warning("Failed to create PNG for instance " + instanceNumber + " in series " + seriesUID + " for patient " + patientName, e); //use outputPNGFile.getAbsolutePath() instead of epadFilesRow.get("file_path"). returns null if exception occured before createEPadFilesRowData epadDatabaseOperations.updateEpadFileRow(pngPath, PNGFileProcessingStatus.ERROR, 0, "DICOM file not found."); epadDatabaseOperations.updateOrInsertSeries(seriesUID, SeriesProcessingStatus.ERROR); } catch (IOException e) { log.warning("Failed to create PNG for instance " + instanceNumber + " in series " + seriesUID + " for patient " + patientName, e); epadDatabaseOperations.updateEpadFileRow(pngPath, PNGFileProcessingStatus.ERROR, 0, "IO Error: " + e.getMessage()); epadDatabaseOperations.updateOrInsertSeries(seriesUID, SeriesProcessingStatus.ERROR); } catch (Throwable t) { log.warning("Failed to create PNG for instance " + instanceNumber + " in series " + seriesUID + " for patient " + patientName, t); epadDatabaseOperations.updateEpadFileRow(pngPath, PNGFileProcessingStatus.ERROR, 0, "General Exception: " + t.getMessage()); epadDatabaseOperations.updateOrInsertSeries(seriesUID, SeriesProcessingStatus.ERROR); } finally { imagesBeingProcessed.remove(imageUID); IOUtils.closeQuietly(outputPNGStream); if (inputDICOMFile.getName().endsWith(".tmp")) { inputDICOMFile.delete(); } } } @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append("PngGeneratorTask[").append(" in=").append(dicomFile); sb.append(" out=").append(pngFile).append("]"); return sb.toString(); } @Override public File getDICOMFile() { return dicomFile; } @Override public String getTagFilePath() { return pngFile.getAbsolutePath().replaceAll("\\.png", ".tag"); } @Override public String getTaskType() { return "Png"; } private int getFileSize(Map<String, String> epadFilesTable) { try { String fileSize = epadFilesTable.get("file_size"); return Integer.parseInt(fileSize); } catch (Exception e) { log.warning("Warning: failed to get file", e); return 0; } } }