/** * Organize all the data required for anonymization. * * @param cmds the complete set of scripts. * @param lkup the local lookup table. * @param inDS the input dataset. * @param outDS the dataset to be modified */ public DICOMAnonymizerContext( Properties cmds, Properties lkup, IntegerTable intTable, Dataset inDS, Dataset outDS) { this.cmds = cmds; this.lkup = lkup; this.intTable = intTable; this.inDS = inDS; this.inFMI = inDS.getFileMetaInfo(); this.outDS = outDS; // Build the index of private groups pgIndex = new PrivateGroupsIndex(inDS); // Make a table to hold locally defined names for private elements privateElementNames = new Hashtable<String, Integer>(); // Set up the booleans to handle the global cases rpg = (cmds.getProperty("remove.privategroups") != null); rue = (cmds.getProperty("remove.unspecifiedelements") != null); rol = (cmds.getProperty("remove.overlays") != null); rc = (cmds.getProperty("remove.curves") != null); kspe = (cmds.getProperty("keep.safeprivateelements") != null); // Set up the keepGroups and the script Hashtable LinkedList<String> list = new LinkedList<String>(); scriptTable = new Hashtable<Integer, String>(); for (Enumeration it = cmds.keys(); it.hasMoreElements(); ) { String key = (String) it.nextElement(); if (key.startsWith("set.[")) { int k = findClosingBracket(key, 4); if (k > 0) { int tag = getElementTag(key.substring(5, k)); if (tag != 0) { // Store the script Integer tagInteger = new Integer(tag); scriptTable.put(tagInteger, cmds.getProperty(key)); // If this is a private group element with a name, index the name. if ((tag & 0x10000) != 0) { String name = key.substring(k + 1).trim(); if (!name.equals("")) privateElementNames.put(name, tagInteger); } } } } else if (key.startsWith("keep.group")) { list.add(key.substring("keep.group".length()).trim()); } } // Convert the list to an int[] Iterator<String> iter = list.iterator(); keepGroups = new int[list.size()]; for (int i = 0; i < keepGroups.length; i++) { try { keepGroups[i] = Integer.parseInt(iter.next(), 16) << 16; } catch (Exception ex) { keepGroups[i] = 0; } } Arrays.sort(keepGroups); inStack = new LinkedList<Dataset>(); outStack = new LinkedList<Dataset>(); }
/** * Convert an image to RGB. * * @param inFile the file to convert. * @param outFile the output file, which may be same as inFile. * @return the static status result */ public static AnonymizerStatus convert(File inFile, File outFile) { long fileLength = inFile.length(); logger.debug("Entering DICOMPaletteImageConverter.convert"); logger.debug("File length = " + fileLength); BufferedInputStream in = null; BufferedOutputStream out = null; File tempFile = null; byte[] buffer = new byte[4096]; try { // Check that this is a known format. in = new BufferedInputStream(new FileInputStream(inFile)); DcmParser parser = pFact.newDcmParser(in); FileFormat fileFormat = parser.detectFileFormat(); if (fileFormat == null) { throw new IOException("Unrecognized file format: " + inFile); } // Get the dataset (excluding pixels) and leave the input stream open Dataset dataset = oFact.newDataset(); parser.setDcmHandler(dataset.getDcmHandler()); parser.parseDcmFile(fileFormat, Tags.PixelData); // Make sure this is an image if (parser.getReadTag() != Tags.PixelData) { close(in); return AnonymizerStatus.SKIP(inFile, "Not an image"); } // Get the required parameters and make sure they are okay int numberOfFrames = getInt(dataset, Tags.NumberOfFrames, 1); int rows = getInt(dataset, Tags.Rows, 0); int columns = getInt(dataset, Tags.Columns, 0); String photometricInterpretation = getString(dataset, Tags.PhotometricInterpretation, ""); if ((rows == 0) || (columns == 0)) { close(in); return AnonymizerStatus.SKIP(inFile, "Unable to get the rows and columns"); } if (!photometricInterpretation.equals("PALETTE COLOR")) { close(in); return AnonymizerStatus.SKIP( inFile, "Unsupported PhotometricInterpretation: " + photometricInterpretation); } if (parser.getReadTag() != Tags.PixelData) { close(in); return AnonymizerStatus.SKIP(inFile, "No pixels"); } // Get the encoding and set the parameters DcmDecodeParam fileParam = parser.getDcmDecodeParam(); String fileEncodingUID = UIDs.ImplicitVRLittleEndian; FileMetaInfo fmi = dataset.getFileMetaInfo(); if (fmi != null) fileEncodingUID = fmi.getTransferSyntaxUID(); boolean isBigEndian = fileEncodingUID.equals(UIDs.ExplicitVRBigEndian); String encodingUID = UIDs.ExplicitVRLittleEndian; DcmEncodeParam encoding = (DcmEncodeParam) DcmDecodeParam.valueOf(encodingUID); boolean swap = (fileParam.byteOrder != encoding.byteOrder); if (encoding.encapsulated) { logger.debug("Encapsulated pixel data found"); close(in); return AnonymizerStatus.SKIP(inFile, "Encapsulated pixel data not supported"); } // Get the LUTs LUT red = new LUT( dataset.getInts(Tags.RedPaletteColorLUTDescriptor), dataset.getInts(Tags.RedPaletteColorLUTData)); LUT green = new LUT( dataset.getInts(Tags.GreenPaletteColorLUTDescriptor), dataset.getInts(Tags.GreenPaletteColorLUTData)); LUT blue = new LUT( dataset.getInts(Tags.BluePaletteColorLUTDescriptor), dataset.getInts(Tags.BluePaletteColorLUTData)); // Set the PlanarConfiguration to 0 dataset.putUS(Tags.PlanarConfiguration, 0); // Set the PhotometricInterpretation to RGB dataset.putCS(Tags.PhotometricInterpretation, "RGB"); // Set the pixel parameters dataset.putUS(Tags.SamplesPerPixel, 3); dataset.putUS(Tags.BitsAllocated, 8); dataset.putUS(Tags.BitsStored, 8); dataset.putUS(Tags.HighBit, 7); // Remove the lookup tables and their descriptors dataset.remove(Tags.RedPaletteColorLUTDescriptor); dataset.remove(Tags.GreenPaletteColorLUTDescriptor); dataset.remove(Tags.BluePaletteColorLUTDescriptor); dataset.remove(Tags.RedPaletteColorLUTData); dataset.remove(Tags.GreenPaletteColorLUTData); dataset.remove(Tags.BluePaletteColorLUTData); // Save the dataset to a temporary file, and rename at the end. File tempDir = outFile.getParentFile(); tempFile = File.createTempFile("DCMtemp-", ".anon", tempDir); out = new BufferedOutputStream(new FileOutputStream(tempFile)); // Create and write the metainfo for the encoding we are using fmi = oFact.newFileMetaInfo(dataset, encodingUID); dataset.setFileMetaInfo(fmi); fmi.write(out); // Write the dataset as far as was parsed dataset.writeDataset(out, encoding); // Process the pixels int nPixels = numberOfFrames * rows * columns; int nPixelBytes = nPixels * 3 /*samplesPerPixel*/; int pad = nPixelBytes & 1; dataset.writeHeader(out, encoding, parser.getReadTag(), VRs.OB, nPixelBytes + pad); int pd; int b1, b2; int bytesPerFrame = rows * columns * 2; byte[] frameBytes = new byte[bytesPerFrame]; for (int frame = 0; frame < numberOfFrames; frame++) { if (in.read(frameBytes, 0, frameBytes.length) != bytesPerFrame) throw new Exception("End of File"); for (int p = 0; p < bytesPerFrame; ) { b1 = frameBytes[p++]; b2 = frameBytes[p++]; if (!swap) { pd = ((b2 & 0xff) << 8) | (b1 & 0xff); } else { pd = ((b1 & 0xff) << 8) | (b2 & 0xff); } out.write(red.get(pd)); out.write(green.get(pd)); out.write(blue.get(pd)); } } if (pad != 0) out.write(0); logger.debug("Finished writing the pixels"); // Skip everything after the pixels out.flush(); out.close(); in.close(); outFile.delete(); tempFile.renameTo(outFile); return AnonymizerStatus.OK(outFile, ""); } catch (Exception e) { logger.debug("Exception while processing image.", e); // Close the input stream if it actually got opened. close(in); // Close the output stream if it actually got opened, // and delete the tempFile in case it is still there. try { if (out != null) { out.close(); tempFile.delete(); } } catch (Exception ex) { logger.warn("Unable to close the output stream."); } // Quarantine the object return AnonymizerStatus.QUARANTINE(inFile, e.getMessage()); } }