public void setIncludeBulkData(DicomInputStream.IncludeBulkData includeBulkData) { dis.setIncludeBulkData(includeBulkData); }
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); } }
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); } }
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); } }
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 protected DataWriter createDataWriter(InstanceLocator inst, String tsuid) throws IOException { Attributes attrs; DicomInputStream in = new DicomInputStream(inst.getFile()); try { if (withoutBulkData) { in.setIncludeBulkData(IncludeBulkData.NO); attrs = in.readDataset(-1, Tag.PixelData); } else { in.setIncludeBulkData(IncludeBulkData.URI); attrs = in.readDataset(-1, -1); } } finally { SafeClose.close(in); } if (delayCStore > 0) try { Thread.sleep(delayCStore); } catch (InterruptedException ignore) {} return new DataWriterAdapter(attrs); }
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(); } }
@Override protected DataWriter createDataWriter(InstanceLocator inst, String tsuid) throws IOException { Attributes attrs; DicomInputStream in = new DicomInputStream(inst.getFile()); try { if (withoutBulkData) { in.setIncludeBulkData(IncludeBulkData.NO); attrs = in.readDataset(-1, Tag.PixelData); } else { in.setIncludeBulkData(IncludeBulkData.URI); attrs = in.readDataset(-1, -1); } } finally { SafeClose.close(in); } if (delayCStore > 0) try { Thread.sleep(delayCStore); } catch (InterruptedException ignore) {} return new DataWriterAdapter(attrs); }
private char processFile(File file) { try { Attributes dataset; try (DicomInputStream is = new DicomInputStream(file)) { is.setIncludeBulkData(DicomInputStream.IncludeBulkData.URI); dataset = is.readDataset(-1, -1); } VR.Holder vr = new VR.Holder(); Object value = dataset.getValue(Tag.PixelData, vr); if ((value instanceof BulkData) && vr.vr == VR.OW) { try (RandomAccessFile raf = new RandomAccessFile(file, "rw")) { toggleEndian(raf, (BulkData) value); } updated++; return '.'; } skipped++; return value == null ? 'p' : (value instanceof BulkData) ? 'b' : 'c'; } catch (IOException e) { System.err.println("Failed to update " + file + ':'); e.printStackTrace(System.err); failed++; } return 'E'; }
public void parse(DicomInputStream dis) throws IOException, TransformerConfigurationException { dis.setIncludeBulkData(includeBulkData); dis.setBulkDataDescriptor(bulkDataDescriptor); dis.setBulkDataDirectory(blkDirectory); dis.setBulkDataFilePrefix(blkFilePrefix); dis.setBulkDataFileSuffix(blkFileSuffix); dis.setConcatenateBulkDataFiles(catBlkFiles); TransformerHandler th = getTransformerHandler(); Transformer t = th.getTransformer(); t.setOutputProperty(OutputKeys.INDENT, indent ? "yes" : "no"); t.setOutputProperty(OutputKeys.VERSION, xmlVersion); th.setResult(new StreamResult(System.out)); SAXWriter saxWriter = new SAXWriter(th); saxWriter.setIncludeKeyword(includeKeyword); saxWriter.setIncludeNamespaceDeclaration(includeNamespaceDeclaration); dis.setDicomInputHandler(saxWriter); dis.readDataset(-1, -1); }
public void parse(DicomInputStream dis) throws IOException, TransformerConfigurationException { dis.setIncludeBulkData(includeBulkData); dis.setBulkDataDescriptor(bulkDataDescriptor); dis.setBulkDataDirectory(blkDirectory); dis.setBulkDataFilePrefix(blkFilePrefix); dis.setBulkDataFileSuffix(blkFileSuffix); dis.setConcatenateBulkDataFiles(catBlkFiles); TransformerHandler th = getTransformerHandler(); Transformer t = th.getTransformer(); t.setOutputProperty(OutputKeys.INDENT, indent ? "yes" : "no"); t.setOutputProperty(OutputKeys.VERSION, xmlVersion); th.setResult(new StreamResult(System.out)); SAXWriter saxWriter = new SAXWriter(th); saxWriter.setIncludeKeyword(includeKeyword); saxWriter.setIncludeNamespaceDeclaration(includeNamespaceDeclaration); dis.setDicomInputHandler(saxWriter); dis.readDataset(-1, -1); }
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.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.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 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; } }
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; } }
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 transcode(File src, File dest) throws IOException { Attributes fmi; Attributes dataset; try (DicomInputStream dis = new DicomInputStream(src)) { dis.setIncludeBulkData(IncludeBulkData.URI); fmi = dis.readFileMetaInformation(); dataset = dis.readDataset(-1, -1); } deidentifier.deidentify(dataset); if (fmi != null) fmi = dataset.createFileMetaInformation(fmi.getString(Tag.TransferSyntaxUID)); try (DicomOutputStream dos = new DicomOutputStream(dest)) { dos.setEncodingOptions(encOpts); dos.writeDataset(fmi, dataset); } }
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 transcode(File src, File dest) throws IOException { Attributes fmi; Attributes dataset; try (DicomInputStream dis = new DicomInputStream(src)) { dis.setIncludeBulkData(IncludeBulkData.URI); fmi = dis.readFileMetaInformation(); dataset = dis.readDataset(-1, -1); } deidentifier.deidentify(dataset); if (fmi != null) fmi = dataset.createFileMetaInformation(fmi.getString(Tag.TransferSyntaxUID)); try (DicomOutputStream dos = new DicomOutputStream(dest)) { dos.setEncodingOptions(encOpts); dos.writeDataset(fmi, dataset); } }