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.common.dicom; import java.awt.image.BufferedImage; import java.awt.image.Raster; import java.io.File; import java.io.IOException; import javax.imageio.ImageIO; import javax.imageio.stream.FileImageInputStream; import org.apache.commons.io.IOUtils; import org.dcm4che2.data.DicomObject; import org.dcm4che2.data.Tag; import org.dcm4che2.imageio.plugins.dcm.DicomImageReadParam; import org.dcm4che2.imageioimpl.plugins.dcm.DicomImageReader; import org.dcm4che2.imageioimpl.plugins.dcm.DicomImageReaderSpi; import org.dcm4che2.io.DicomInputStream; import org.dcm4che2.io.StopTagInputHandler; import com.pixelmed.display.ConsumerFormatImageMaker; import edu.stanford.epad.common.util.EPADLogger; /** * Read a DICOM instance and generate a variety of other formats that can be used to create files. * * @author Bradley Ross * @see edu.stanford.aim.proxy.servlet.files.GetJpeg * @see RasterProcessor * * Class extracted from https://bmir-gforge.stanford.edu/svn/dirac/trunk/ePAD/ePAD-2012/DicomInterface to remove * dependency. */ public class DicomReader { private static final EPADLogger log = EPADLogger.getInstance(); protected final File dicomFile; static { ImageIO.scanForPlugins(); } public DicomReader(File dicomFile) { this.dicomFile = dicomFile; } /** * Generate a buffered image using the parameters in the file. * * @param frameValue frame number * @return image * @throws IOException */ public BufferedImage getImage(int frameValue) throws IOException { FileImageInputStream fis = null; BufferedImage image; try { fis = new FileImageInputStream(dicomFile); DicomImageReader codec = (DicomImageReader) new DicomImageReaderSpi().createReaderInstance(); codec.setInput(fis); DicomImageReadParam param = (DicomImageReadParam) codec.getDefaultReadParam(); image = codec.read(frameValue, param); } finally { if (fis != null) fis.close(); } return image; } /** * Generate a buffered image with the high order bits of PixelData in the red channel and low order bits in the green * channel. * * @return image * @throws IOException */ public BufferedImage getPackedImage() throws IOException { return getPackedImage(0); } /** * Generate a buffered image with the high order bits of PixelData in the red channel and low order bits in the green * channel. * * @param frameValue frame number * @return image * @throws IOException */ public BufferedImage getPackedImage(int frameValue) throws IOException { FileImageInputStream fis = null; DicomInputStream dis = null; BufferedImage packedImage = null; try { StopTagInputHandler stop = new StopTagInputHandler(Tag.PixelData); log.info("" + Thread.currentThread().getId() + " Opening Dicom:" + dicomFile.getName()); dis = new DicomInputStream(dicomFile); dis.setHandler(stop); DicomObject object = dis.readDicomObject(); RasterProcessor rasterProcessor = new RasterProcessor(object); dis.close(); fis = new FileImageInputStream(dicomFile); DicomImageReader codec = (DicomImageReader) new DicomImageReaderSpi().createReaderInstance(); codec.setInput(fis); DicomImageReadParam param = (DicomImageReadParam) codec.getDefaultReadParam(); Raster raster = codec.readRaster(frameValue, param); packedImage = rasterProcessor.buildPng(raster); } finally { IOUtils.closeQuietly(dis); if (fis != null) fis.close(); log.info("" + Thread.currentThread().getId() + " Closed"); } return packedImage; } // See http://forums.dcm4che.org/jiveforums/message.jspa?messageID=21407 for various ways of reading a DICOM file. public static String getPatientName(File dicomFile) throws IOException { DicomInputStream dis = null; String patientName = null; try { log.info("" + Thread.currentThread().getId() + " Opening Dicom:" + dicomFile.getName()); dis = new DicomInputStream(dicomFile); dis.setHandler(new StopTagInputHandler(Tag.PixelData)); DicomObject dicomObject = dis.readDicomObject(); patientName = dicomObject.getString(Tag.PatientName); } finally { IOUtils.closeQuietly(dis); log.info("" + Thread.currentThread().getId() + " Closed"); } return patientName; } public static String getPatientID(File dicomFile) throws IOException { DicomInputStream dis = null; String patientID = null; try { log.info("" + Thread.currentThread().getId() + " Opening Dicom:" + dicomFile.getName()); dis = new DicomInputStream(dicomFile); dis.setHandler(new StopTagInputHandler(Tag.PixelData)); DicomObject dicomObject = dis.readDicomObject(); patientID = dicomObject.getString(Tag.PatientID); } finally { IOUtils.closeQuietly(dis); log.info("" + Thread.currentThread().getId() + " Closed"); } return patientID; } public static String getStudyIUID(File dicomFile) throws IOException { DicomInputStream dis = null; String studyIUID = null; try { log.info("" + Thread.currentThread().getId() + " Opening Dicom:" + dicomFile.getName()); dis = new DicomInputStream(dicomFile); dis.setHandler(new StopTagInputHandler(Tag.PixelData)); DicomObject dicomObject = dis.readDicomObject(); studyIUID = dicomObject.getString(Tag.StudyInstanceUID); } finally { IOUtils.closeQuietly(dis); log.info("" + Thread.currentThread().getId() + " Closed"); } return studyIUID; } public static DicomObject getDicomObject(File dicomFile) throws IOException { DicomInputStream dis = null; try { log.info("" + Thread.currentThread().getId() + " Opening Dicom:" + dicomFile.getName()); dis = new DicomInputStream(dicomFile); dis.setHandler(new StopTagInputHandler(Tag.PixelData)); return dis.readDicomObject(); } catch (Exception e) { log.warning("Error in reading dicom object " + e.getMessage()); return null; } finally { IOUtils.closeQuietly(dis); log.info("" + Thread.currentThread().getId() + " Closed"); } } public static String getModality(File dicomFile) throws IOException { DicomInputStream dis = null; String modality = null; try { log.info("" + Thread.currentThread().getId() + " Opening Dicom:" + dicomFile.getName()); dis = new DicomInputStream(dicomFile); dis.setHandler(new StopTagInputHandler(Tag.PixelData)); DicomObject dicomObject = dis.readDicomObject(); modality = dicomObject.getString(Tag.Modality); } finally { IOUtils.closeQuietly(dis); log.info("" + Thread.currentThread().getId() + " Closed"); } return modality; } /* * Copied from dcmche forums (appears to be same as above method) */ // public void dcmconvpng2(int index, File pngFile) throws Exception{ // ImageIO.scanForPlugins(); // Iterator<ImageReader> iter = ImageIO.getImageReadersByFormatName("dicom"); // if (!iter.hasNext()) // throw new Exception("Dicom Reader not found"); // ImageReader readers = iter.next();//next item // DicomImageReadParam param = (DicomImageReadParam) readers.getDefaultReadParam();//return DicomImageReadParam // // Adjust the values of Rows and Columns in it and add a Pixel Data attribute with the byte array from the DataBuffer of the scaled Raster // // ImageInputStream iis = ImageIO.createImageInputStream(dicomFile); // // readers.setInput(iis, true);//sets the input source to use the given ImageInputSteam or other Object // // BufferedImage myPngImage = readers.read(index, param); //read dicom // OutputStream output = new BufferedOutputStream(new FileOutputStream(pngFile)); //BufferedOuput permit make file // try { // PNGEncodeParam.RGB param2 = new PNGEncodeParam.RGB(); // ImageEncoder enc = ImageCodec.createImageEncoder("PNG", output,param2); // enc.encode( myPngImage); // } // finally { // output.close(); // } // } /* * Pixelmed library */ public void dcmconvpng3(int index, File pngFile) throws Exception { ConsumerFormatImageMaker.convertFileToEightBitImage(dicomFile.getAbsolutePath(), pngFile.getAbsolutePath(), "png", index); } }