public Attributes parseAttributesWithLazyBulkData(Association as, File file) throws IOException { DicomInputStream in = null; try { in = new DicomInputStream(file); in.setIncludeBulkData(IncludeBulkData.URI); return in.readDataset(-1, -1); } catch (IOException e) { LOG.warn(as + ": Failed to decode dataset:", e); throw new DicomServiceException(Status.CannotUnderstand); } finally { in.close(); } }
protected DicomDirReader(File file, String mode) throws IOException { this.file = file; this.raf = new RandomAccessFile(file, mode); try { this.in = new DicomInputStream(new RAFInputStreamAdapter(raf)); this.fmi = in.readFileMetaInformation(); this.fsInfo = in.readDataset(-1, Tag.DirectoryRecordSequence); if (in.tag() != Tag.DirectoryRecordSequence) throw new IOException("Missing Directory Record Sequence"); } catch (IOException e) { SafeClose.close(raf); throw e; } }
public void parse(DicomInputStream dis) throws IOException { dis.setIncludeBulkData(includeBulkData); dis.setBulkDataDescriptor(bulkDataDescriptor); dis.setBulkDataDirectory(blkDirectory); dis.setBulkDataFilePrefix(blkFilePrefix); dis.setBulkDataFileSuffix(blkFileSuffix); dis.setConcatenateBulkDataFiles(catBlkFiles); JsonGenerator jsonGen = createGenerator(System.out); JSONWriter jsonWriter = new JSONWriter(jsonGen); dis.setDicomInputHandler(jsonWriter); dis.readDataset(-1, -1); jsonGen.flush(); }
public void parse(DicomInputStream dis) throws IOException { dis.setIncludeBulkData(includeBulkData); dis.setBulkDataDescriptor(bulkDataDescriptor); dis.setBulkDataDirectory(blkDirectory); dis.setBulkDataFilePrefix(blkFilePrefix); dis.setBulkDataFileSuffix(blkFileSuffix); dis.setConcatenateBulkDataFiles(catBlkFiles); dataset = dis.readDataset(-1, -1); fmi = dis.getFileMetaInformation(); bulkDataFiles = dis.getBulkDataFiles(); }
public void parse(DicomInputStream dis) throws IOException { dis.setDicomInputHandler(this); dis.readDataset(-1, -1); }
private static Attributes parse(File file) throws IOException { DicomInputStream in = new DicomInputStream(file); try { in.setIncludeBulkData(IncludeBulkData.NO); return in.readDataset(-1, Tag.PixelData); } finally { SafeClose.close(in); } }
@Override public Attributes readDataset(String tsuid) throws IOException { DicomInputStream in = new DicomInputStream(this, tsuid); try { return in.readDataset(-1, -1); } finally { SafeClose.close(in); } }
private void loadDcmDocuments() throws Exception { Path testPath = xdsi.resolve(testPfn); Utility.isValidPfn("test doc", testPath, PfnType.FILE, "r"); din = new DicomInputStream(testPath.toFile()); testAttr = din.readDataset(-1, Tag.PixelData); din.close(); din = null; Path stdPath = xdsi.resolve(stdPfn); Utility.isValidPfn("std doc", stdPath, PfnType.FILE, "r"); din = new DicomInputStream(stdPath.toFile()); stdAttr = din.readDataset(-1, Tag.PixelData); din.close(); din = null; }
DicomInputStream in = null; try { in = new DicomInputStream(f); in.setIncludeBulkData(IncludeBulkData.NO); Attributes fmi = in.readFileMetaInformation(); long dsPos = in.getPosition(); Attributes ds = in.readDataset(-1, Tag.PixelData); if (fmi == null || !fmi.containsValue(Tag.TransferSyntaxUID) || !fmi.containsValue(Tag.MediaStorageSOPClassUID) || !fmi.containsValue(Tag.MediaStorageSOPInstanceUID)) fmi = ds.createFileMetaInformation(in.getTransferSyntax()); boolean b = scb.dicomFile(f, fmi, dsPos, ds); if (printout)System.out.print(b ? '.' : 'I');
Attributes fmi = dis.readFileMetaInformation(); Attributes ds = dis.readDataset(-1, Tag.PixelData); if (dis.tag() == Tag.PixelData) { imageDescriptor = new ImageDescriptor(ds); pixelDataVR = dis.vr(); pixelDataLength = dis.length(); if (pixelDataLength == -1) epdiis = new EncapsulatedPixelDataImageInputStream(dis, imageDescriptor); } else { try { dis.readAttributes(ds, -1, -1); } catch (EOFException e) {}; DicomInputStream dis = new DicomInputStream(new ImageInputStreamAdapter(iis)); dis.setIncludeBulkData(IncludeBulkData.URI); dis.setBulkDataDescriptor(BulkDataDescriptor.PIXELDATA); dis.setURI("java:iis"); // avoid copy of pixeldata to temporary file Attributes fmi = dis.readFileMetaInformation(); Attributes ds = dis.readDataset(-1, Tag.PixelData); if( dis.tag() == Tag.PixelData ) { imageDescriptor = new ImageDescriptor(ds); pixelDataVR = dis.vr(); pixelDataLength = dis.length(); } else { try { dis.readAttributes(ds, -1, -1); } catch (EOFException e) {};
@SuppressWarnings("unchecked") public static void main(String[] args) { try { CommandLine cl = parseComandLine(args); Dcm2Json main = new Dcm2Json(); main.setIndent(cl.hasOption("I")); configureBulkdata(main, cl); String fname = fname(cl.getArgList()); if (fname.equals("-")) { main.parse(new DicomInputStream(System.in)); } else { DicomInputStream dis = new DicomInputStream(new File(fname)); try { main.parse(dis); } finally { dis.close(); } } } catch (ParseException e) { System.err.println("dcm2xml: " + e.getMessage()); System.err.println(rb.getString("try")); System.exit(2); } catch (Exception e) { System.err.println("dcm2xml: " + e.getMessage()); e.printStackTrace(); System.exit(2); } }
public int extract(File file) throws IOException { Attributes src; DicomInputStream dis = new DicomInputStream(file); try { dis.setIncludeBulkData(IncludeBulkData.URI); src = dis.readDataset(-1, -1); } finally { SafeClose.close(dis); } Attributes fmi = dis.getFileMetaInformation(); if (frames == null) { int n = src.getInt(Tag.NumberOfFrames, 1); for (int frame = 0; frame < n; ++frame) extract(file, fmi, src, frame); return n; } else { for (int frame : frames) extract(file, fmi, src, frame); return frames.length; } }
dis = new DicomInputStream(new ImageInputStreamAdapter(iis)); dis.setIncludeBulkData(IncludeBulkData.URI); dis.setBulkDataDescriptor(DicomCodec.BULKDATA_DESCRIPTOR); dis.setURI(uri.toString()); Attributes fmi = dis.readFileMetaInformation(); Attributes ds = dis.readDataset(-1, -1); if (fmi == null) { fmi = ds.createFileMetaInformation(dis.getTransferSyntax()); tsuid = dis.getTransferSyntax(); numberOfFrame = ds.getInt(Tag.NumberOfFrames, 1); hasPixel = ds.getInt(Tag.BitsStored, ds.getInt(Tag.BitsAllocated, 0)) > 0;
String tsuid = null; Attributes dataset; dis = new DicomInputStream(in); try { dis.setIncludeBulkData(IncludeBulkData.URI); dataset = dis.readDataset(-1, -1); tsuid = dis.getTransferSyntax(); } finally { dis.close(); SafeClose.close(dos); if (dis != null) { List<File> blkFiles = dis.getBulkDataFiles(); if (blkFiles != null) { for (File file : blkFiles) {
din = new DicomInputStream(srcFile); Attributes meta = din.readFileMetaInformation(); Attributes dataSet = din.readDataset(-1, -1); String oldSeriesId = dataSet.getString(Tag.SeriesInstanceUID, ""); if (seriesIds.containsKey(oldSeriesId) == false) {
public Transcoder(InputStream in, String tsuid) throws IOException { this(new DicomInputStream(in, tsuid)); }
protected DataWriter createDataWriter(T inst, String tsuid) throws Exception { DicomInputStream in = new DicomInputStream(inst.getFile()); in.readFileMetaInformation(); return new InputStreamDataWriter(in); }
DicomInputStream dis = new DicomInputStream(fis); DicomObject obj = dis.readDicomObject(); for (int tag : TAGS) dis.close(); writeDicomFile(obj, fileOutput); } catch (Exception e) {
private Attributes readCommand() throws IOException { DicomInputStream in = new DicomInputStream(this, UID.ImplicitVRLittleEndian); try { return in.readCommand(); } finally { SafeClose.close(in); } }
DicomInputStream in = null; try { in = new DicomInputStream(file); return in.readDicomObject(); } catch (IOException e) { exit(e.getMessage());