/**
* Imports a DICOM file.
*
* <p>The FileDTO object refers to an existing DICOM file (This method does NOT check this file!)
* and the Dataset object holds the meta data for database.
*
* <p>
*
* @param fileDTO Refers the DICOM file.
* @param ds Dataset with metadata for database.
* @param last last file to import
*/
public void importFile(FileDTO fileDTO, Dataset ds, String prevseriuid, boolean last)
throws Exception {
Storage store = getStorage();
String seriud = ds.getString(Tags.SeriesInstanceUID);
if (prevseriuid != null && !prevseriuid.equals(seriud)) {
SeriesStored seriesStored = store.makeSeriesStored(prevseriuid);
if (seriesStored != null) {
log.debug("Send SeriesStoredNotification - series changed");
scp.doAfterSeriesIsStored(store, null, seriesStored);
}
}
String cuid = ds.getString(Tags.SOPClassUID);
String iuid = ds.getString(Tags.SOPInstanceUID);
FileMetaInfo fmi =
DcmObjectFactory.getInstance().newFileMetaInfo(cuid, iuid, fileDTO.getFileTsuid());
ds.setFileMetaInfo(fmi);
String fsPath = fileDTO.getDirectoryPath();
String filePath = fileDTO.getFilePath();
File f = FileUtils.toFile(fsPath, filePath);
// Modified by [email protected] on 01.09.2009
// In case the file is not stored in file system but somewhere else
// scp.updateDB(store, ds, fileDTO.getFileSystemPk(), filePath, f.length(),
// fileDTO.getFileMd5(), true);
scp.updateDB(
store,
ds,
fileDTO.getFileSystemPk(),
filePath,
fileDTO.getFileSize(),
fileDTO.getFileMd5(),
true);
if (last) {
SeriesStored seriesStored = store.makeSeriesStored(seriud);
if (seriesStored != null) {
scp.doAfterSeriesIsStored(store, null, seriesStored);
}
}
}
/**
* 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());
}
}