public static void verifyMD5(File file, String originalMd5) throws Exception {
log.info("M-READ file:" + file);
MessageDigest md = MessageDigest.getInstance("MD5");
BufferedInputStream in = new BufferedInputStream(new FileInputStream(file));
DigestInputStream dis = new DigestInputStream(in, md);
try {
DcmParser parser = DcmParserFactory.getInstance().newDcmParser(dis);
parser.parseDcmFile(FileFormat.DICOM_FILE, Tags.PixelData);
if ((parser.getReadTag() & 0xFFFFFFFFL) >= Tags.PixelData) {
if (parser.getReadLength() == -1) {
while (parser.parseHeader() == Tags.Item) {
readOut(parser.getInputStream(), parser.getReadLength());
}
}
readOut(parser.getInputStream(), parser.getReadLength());
parser.parseDataset(parser.getDcmDecodeParam(), -1);
}
} finally {
try {
dis.close();
} catch (IOException ignore) {
}
}
byte[] md5 = md.digest();
if (!Arrays.equals(md5, MD5.toBytes(originalMd5))) {
log.error(
"MD5 for "
+ file.getAbsolutePath()
+ " is different that expected. Has the file been changed or corrupted?");
throw new IllegalStateException("MD5 mismatch");
}
}
public static boolean equalsPixelData(File f1, File f2) throws IOException {
InputStream in1 = new BufferedInputStream(new FileInputStream(f1));
try {
InputStream in2 = new BufferedInputStream(new FileInputStream(f2));
try {
Dataset attrs = DcmObjectFactory.getInstance().newDataset();
DcmParserFactory pf = DcmParserFactory.getInstance();
DcmParser p1 = pf.newDcmParser(in1);
DcmParser p2 = pf.newDcmParser(in2);
p1.setDcmHandler(attrs.getDcmHandler());
p1.parseDcmFile(FileFormat.DICOM_FILE, Tags.PixelData);
p2.parseDcmFile(FileFormat.DICOM_FILE, Tags.PixelData);
int samples = attrs.getInt(Tags.SamplesPerPixel, 1);
int frames = attrs.getInt(Tags.NumberOfFrames, 1);
int rows = attrs.getInt(Tags.Rows, 1);
int columns = attrs.getInt(Tags.Columns, 1);
int bitsAlloc = attrs.getInt(Tags.BitsAllocated, 8);
int bitsStored = attrs.getInt(Tags.BitsStored, bitsAlloc);
int frameLength = rows * columns * samples * bitsAlloc / 8;
int pixelDataLength = frameLength * frames;
if (pixelDataLength > p1.getReadLength() || pixelDataLength > p2.getReadLength()) {
return false;
}
byte[] b1 = new byte[BUFFER_SIZE];
byte[] b2 = new byte[BUFFER_SIZE];
int[] mask = {0xff, 0xff};
int len, len2;
if (bitsAlloc == 16 && bitsStored < 16) {
mask[p1.getDcmDecodeParam().byteOrder == ByteOrder.LITTLE_ENDIAN ? 1 : 0] =
0xff >>> (16 - bitsStored);
}
int pos = 0;
while (pos < pixelDataLength) {
len = in1.read(b1, 0, Math.min(pixelDataLength - pos, BUFFER_SIZE));
if (len < 0) // EOF
return false;
int off = 0;
while (off < len) {
off += len2 = in2.read(b2, off, len - off);
if (len2 < 0) // EOF
return false;
}
for (int i = 0; i < len; i++, pos++)
if (((b1[i] - b2[i]) & mask[pos & 1]) != 0) return false;
}
return true;
} finally {
in2.close();
}
} finally {
in1.close();
}
}
/**
* 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());
}
}