/**
* Read a DICOM image input format file encoded in a compressed transfer syntax and extract the
* compressed bitstreams into a file for each frame.
*
* <p>The output file will be named with the specified prefix to which will be appended a 6 digit
* zero padded frame number starting from 1, followed by an appropriate file name extension for
* the transfer syntax.
*
* @param arg two parameters, the inputFile, the outputFile prefix
*/
public static void main(String arg[]) {
try {
if (arg.length == 2) {
DecimalFormat sixDigitZeroPaddedFormat = new DecimalFormat("000000");
AttributeList list = new AttributeList();
list.setDecompressPixelData(false);
list.read(arg[0]);
String fileNameExtension = getFileNameExtensionForCompressedPixelData(list);
OtherByteAttributeMultipleCompressedFrames aPixelData =
(OtherByteAttributeMultipleCompressedFrames) (list.getPixelData());
byte[][] frames = aPixelData.getFrames();
for (int f = 0; f < frames.length; ++f) {
String outputFilename =
arg[1] + sixDigitZeroPaddedFormat.format(f + 1) + "." + fileNameExtension;
System.err.println("Writing " + outputFilename);
FileOutputStream o = new FileOutputStream(outputFilename);
o.write(frames[f]);
o.close();
}
} else {
System.err.println("Error: Incorrect number of arguments");
System.err.println("Usage: UnencapsulateCompressedPixelData inputFile outputFilePrefix");
System.exit(1);
}
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Generate commomn attributes for converted images.
*
* <p>Does NOT add ManufacturerModelName ... that should be added by caller.
*
* <p>Does NOT call
* CodingSchemeIdentification.replaceCodingSchemeIdentificationSequenceWithCodingSchemesUsedInAttributeList
* ... that should be done by caller.
*
* @param list
* @param patientName
* @param patientID
* @param studyID
* @param seriesNumber
* @param instanceNumber
* @param modality may be null
* @param sopClass may be null
* @throws DicomException
* @throws NumberFormatException
*/
public static void generateCommonAttributes(
AttributeList list,
String patientName,
String patientID,
String studyID,
String seriesNumber,
String instanceNumber,
String modality,
String sopClass)
throws DicomException {
UIDGenerator u = new UIDGenerator();
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SOPInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SeriesInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.StudyInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.FrameOfReferenceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.PatientName);
a.addValue(patientName);
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.PatientID);
a.addValue(patientID);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.PatientBirthDate);
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.PatientSex);
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.StudyID);
a.addValue(studyID);
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.ReferringPhysicianName);
a.addValue("^^^^");
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.AccessionNumber);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.SeriesNumber);
a.addValue(seriesNumber);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.InstanceNumber);
a.addValue(instanceNumber);
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.Manufacturer);
a.addValue("PixelMed");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.DeviceSerialNumber);
a.addValue(new java.rmi.dgc.VMID().toString());
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.SoftwareVersions);
a.addValue(VersionAndConstants.getBuildDate());
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.PatientOrientation);
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.BurnedInAnnotation);
a.addValue("NO");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.RecognizableVisualFeatures);
a.addValue("NO");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.ContentQualification);
a.addValue("RESEARCH");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.LossyImageCompression);
a.addValue("00");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.PositionReferenceIndicator);
list.put(a);
}
{
java.util.Date currentDateTime = new java.util.Date();
String currentDate = new java.text.SimpleDateFormat("yyyyMMdd").format(currentDateTime);
String currentTime = new java.text.SimpleDateFormat("HHmmss.SSS").format(currentDateTime);
{
Attribute a = new DateAttribute(TagFromName.StudyDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.StudyTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.SeriesDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.SeriesTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.ContentDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.ContentTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.InstanceCreationDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.InstanceCreationTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.TimezoneOffsetFromUTC);
a.addValue(DateTimeAttribute.getTimeZone(java.util.TimeZone.getDefault(), currentDateTime));
list.put(a);
}
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.InstanceCreatorUID);
a.addValue(VersionAndConstants.instanceCreatorUID);
list.put(a);
}
int numberOfFrames =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.NumberOfFrames, 1);
int samplesPerPixel =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.SamplesPerPixel, 1);
if (sopClass == null) {
// if modality were not null, could actually attempt to guess SOP Class based on modality here
// :(
sopClass = SOPClass.SecondaryCaptureImageStorage;
if (numberOfFrames > 1) {
if (samplesPerPixel == 1) {
int bitsAllocated =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.BitsAllocated, 1);
if (bitsAllocated == 8) {
sopClass = SOPClass.MultiframeGrayscaleByteSecondaryCaptureImageStorage;
} else if (bitsAllocated == 16) {
sopClass = SOPClass.MultiframeGrayscaleWordSecondaryCaptureImageStorage;
} else {
Attribute aPixelData = list.getPixelData();
if (aPixelData instanceof OtherFloatAttribute
|| aPixelData instanceof OtherDoubleAttribute) {
sopClass = SOPClass.ParametricMapStorage;
}
}
} else if (samplesPerPixel == 3) {
sopClass = SOPClass.MultiframeTrueColorSecondaryCaptureImageStorage;
}
}
}
if (sopClass.equals(SOPClass.ParametricMapStorage)) {
addParametricMapFrameTypeSharedFunctionalGroup(list);
{
Attribute a = new CodeStringAttribute(TagFromName.ContentLabel);
a.addValue("LABEL1");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.ContentDescription);
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.ContentCreatorName);
list.put(a);
}
}
if (SOPClass.isEnhancedMultiframeImageStorage(sopClass)) {
if (samplesPerPixel == 1) {
double windowWidth =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.WindowWidth, 0);
if (windowWidth > 0) {
double windowCenter =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.WindowCenter, 0);
String voiLUTFunction =
Attribute.getSingleStringValueOrDefault(list, TagFromName.VOILUTFunction, "LINEAR");
FunctionalGroupUtilities.generateVOILUTFunctionalGroup(
list, numberOfFrames, windowWidth, windowCenter, voiLUTFunction);
list.remove(TagFromName.WindowCenter);
list.remove(TagFromName.WindowWidth);
list.remove(TagFromName.VOILUTFunction);
}
}
double rescaleSlope =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.RescaleSlope, 0);
if (rescaleSlope > 0) {
double rescaleIntercept =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.RescaleIntercept, 0);
String rescaleType =
Attribute.getSingleStringValueOrDefault(list, TagFromName.RescaleType, "US");
FunctionalGroupUtilities.generatePixelValueTransformationFunctionalGroup(
list, numberOfFrames, rescaleSlope, rescaleIntercept, rescaleType);
list.remove(TagFromName.RescaleSlope);
list.remove(TagFromName.RescaleIntercept);
list.remove(TagFromName.RescaleType);
}
// four values required
{
Attribute a = new CodeStringAttribute(TagFromName.ImageType);
a.addValue("DERIVED");
a.addValue("PRIMARY");
a.addValue("");
a.addValue("");
list.put(a);
}
} else {
// two values will usually do
{
Attribute a = new CodeStringAttribute(TagFromName.ImageType);
a.addValue("DERIVED");
a.addValue("PRIMARY");
list.put(a);
}
}
if (SOPClass.isMultiframeSecondaryCaptureImageStorage(sopClass)) {
if (list.get(TagFromName.PerFrameFunctionalGroupsSequence) != null) {
{
AttributeTagAttribute a = new AttributeTagAttribute(TagFromName.FrameIncrementPointer);
a.addValue(TagFromName.PerFrameFunctionalGroupsSequence);
list.put(a);
}
} else {
if (numberOfFrames > 1) {
{
AttributeTagAttribute a = new AttributeTagAttribute(TagFromName.FrameIncrementPointer);
a.addValue(TagFromName.PageNumberVector);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.PageNumberVector);
for (int page = 1; page <= numberOfFrames; ++page) {
a.addValue(page);
}
list.put(a);
}
}
}
}
System.err.println(
"CommonConvertedAttributeGeneration.generateCommonAttributes(): SOP Class = " + sopClass);
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SOPClassUID);
a.addValue(sopClass);
list.put(a);
}
if (SOPClass.isSecondaryCaptureImageStorage(sopClass)) {
{
Attribute a = new CodeStringAttribute(TagFromName.ConversionType);
a.addValue("WSD");
list.put(a);
}
}
if (modality == null) {
// could actually attempt to guess modality based on SOP Class here :(
modality = "OT";
}
{
Attribute a = new CodeStringAttribute(TagFromName.Modality);
a.addValue(modality);
list.put(a);
}
{
Attribute a = new SequenceAttribute(TagFromName.AcquisitionContextSequence);
list.put(a);
}
}