public static int Main(string[] args)
{
string filename = args[0];
string outfilename = args[1];
using( var sfcts = FileChangeTransferSyntax.New() )
{
FileChangeTransferSyntax fcts = sfcts.__ref__();
//SimpleSubjectWatcher watcher = new SimpleSubjectWatcher(fcts, "FileChangeTransferSyntax");
gdcm.TransferSyntax ts = new TransferSyntax( TransferSyntax.TSType.JPEG2000 );
fcts.SetTransferSyntax( ts );
ImageCodec ic = fcts.GetCodec();
JPEG2000Codec jpeg2000 = JPEG2000Codec.Cast( ic );
jpeg2000.SetReversible( false );
jpeg2000.SetQuality(0, 55);
fcts.SetInputFileName( filename );
fcts.SetOutputFileName( outfilename );
if( !fcts.Change() )
{
return 1;
}
}
return 0;
}
/// <summary>
/// Read explicit VR little endian up to transfer syntax element and determines transfer syntax for rest of elements
/// </summary>
/// <param name="dr">the binary reader which is reading the DICOM object</param>
/// <param name="syntax">the transfer syntax of the DICOM file</param>
/// <returns>elements preceeding and including transfer syntax element</returns>
public static List<IDICOMElement> ReadFileMetadata(DICOMBinaryReader dr, ref TransferSyntax syntax)
{
var elements = new List<IDICOMElement>();
syntax = syntax != TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN
? syntax
: TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN;
while (dr.StreamPosition < dr.StreamLength)
{
long position = dr.StreamPosition;
if (TagReader.ReadLittleEndian(dr).Group == _metaGroup)
{
dr.StreamPosition = position;
IDICOMElement el = DICOMElementReader.ReadElementExplicitLittleEndian(dr);
Tag uid = TagHelper.TRANSFER_SYNTAX_UID;
if (el.Tag == uid)
{
syntax = TransferSyntaxHelper.GetSyntax(el);
}
elements.Add(el);
}
else
{
dr.StreamPosition = position;
break;
}
}
return elements;
}
public static int Main(string[] args)
{
string filename = args[0];
string outfilename = args[1];
using( var sfcts = FileChangeTransferSyntax.New() )
{
FileChangeTransferSyntax fcts = sfcts.__ref__();
//SimpleSubjectWatcher watcher = new SimpleSubjectWatcher(fcts, "FileChangeTransferSyntax");
gdcm.TransferSyntax ts = new TransferSyntax( TransferSyntax.TSType.JPEGLSNearLossless );
fcts.SetTransferSyntax( ts );
ImageCodec ic = fcts.GetCodec();
JPEGLSCodec jpegls = JPEGLSCodec.Cast( ic );
jpegls.SetLossless( false );
jpegls.SetLossyError( 2 );
fcts.SetInputFileName( filename );
fcts.SetOutputFileName( outfilename );
if( !fcts.Change() )
{
return 1;
}
}
return 0;
}
/// <summary>
/// Read explicit VR little endian up to transfer syntax element and determines transfer syntax for rest of elements
/// </summary>
/// <param name="dr">the binary reader which is reading the DICOM object</param>
/// <param name="syntax">the transfer syntax of the DICOM file</param>
/// <returns>elements preceeding and including transfer syntax element</returns>
private static List<IDICOMElement> ReadFileMetadata(DICOMBinaryReader dr, out TransferSyntax syntax)
{
List<IDICOMElement> elements = new List<IDICOMElement>();
syntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN;
while (dr.StreamPosition < dr.StreamLength)
{
long position = dr.StreamPosition;
if (TagReader.ReadLittleEndian(dr).Group == _MetaGroup)
{
dr.StreamPosition = position;
IDICOMElement el = DICOMElementReader.ReadElementExplicitLittleEndian(dr);
if (el.Tag.CompleteID == TagHelper.TRANSFER_SYNTAX_UID.CompleteID)
{
syntax = TransferSyntaxHelper.GetSyntax(el);
}
elements.Add(el);
}
else
{
dr.StreamPosition = position;
break;
}
}
return elements;
}
public static void SkipItemLittleEndian(DICOMBinaryReader dr, TransferSyntax syntax)
{
int length = LengthReader.ReadLittleEndian(VR.Null, dr.Skip(4));
if (length != -1)
{
dr.Skip(length);
}
else
{
if (syntax == TransferSyntax.EXPLICIT_VR_LITTLE_ENDIAN)
{
while (!IsEndOfSequenceItemLittleEndian(dr))
{
dr.StreamPosition -= 8;
DICOMElementReader.SkipElementExplicitLittleEndian(dr);
}
}
else
{
while (!IsEndOfSequenceItemLittleEndian(dr))
{
dr.StreamPosition -= 8;
DICOMElementReader.SkipElementImplicitLittleEndian(dr);
}
}
}
}
public static void LosslessImageTest(TransferSyntax syntax, DicomFile theFile)
{
if (File.Exists(theFile.Filename))
File.Delete(theFile.Filename);
DicomFile saveCopy = new DicomFile(theFile.Filename, theFile.MetaInfo.Copy(), theFile.DataSet.Copy());
theFile.ChangeTransferSyntax(syntax);
theFile.Save(DicomWriteOptions.ExplicitLengthSequence);
DicomFile newFile = new DicomFile(theFile.Filename);
newFile.Load(DicomReadOptions.Default);
newFile.ChangeTransferSyntax(saveCopy.TransferSyntax);
List<DicomAttributeComparisonResult> list = new List<DicomAttributeComparisonResult>();
bool result = newFile.DataSet.Equals(saveCopy.DataSet, ref list);
StringBuilder sb = new StringBuilder();
foreach (DicomAttributeComparisonResult compareResult in list)
sb.AppendFormat("Comparison Failure: {0}, ", compareResult.Details);
Assert.IsTrue(result,sb.ToString());
}
public static int Main(string[] args)
{
string filename = args[0];
string outfilename = args[1];
using( var sfcts = FileChangeTransferSyntax.New() )
{
FileChangeTransferSyntax fcts = sfcts.__ref__();
//SimpleSubjectWatcher watcher = new SimpleSubjectWatcher(fcts, "FileChangeTransferSyntax");
gdcm.TransferSyntax ts = new TransferSyntax( TransferSyntax.TSType.RLELossless );
fcts.SetTransferSyntax( ts );
ImageCodec ic = fcts.GetCodec();
RLECodec rle = RLECodec.Cast( ic );
// need to call at least one member func to check not NULL:
long val = rle.GetBufferLength();
System.Console.WriteLine( val ); // use val to remove a warning
fcts.SetInputFileName( filename );
fcts.SetOutputFileName( outfilename );
if( !fcts.Change() )
{
return 1;
}
}
return 0;
}
public void ChangeSyntax(TransferSyntax syntax)
{
try
{
if (!_dicomFile.TransferSyntax.Encapsulated)
{
// Check if Overlay is embedded in pixels
OverlayPlaneModuleIod overlayIod = new OverlayPlaneModuleIod(_dicomFile.DataSet);
for (int i = 0; i < 16; i++)
{
if (overlayIod.HasOverlayPlane(i))
{
OverlayPlane overlay = overlayIod[i];
if (overlay.OverlayData == null)
{
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(_dicomFile);
overlay.ConvertEmbeddedOverlay(pd);
}
}
}
}
else if (syntax.Encapsulated)
{
// Must decompress first.
_dicomFile.ChangeTransferSyntax(TransferSyntax.ExplicitVrLittleEndian);
}
_dicomFile.ChangeTransferSyntax(syntax);
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception compressing/decompressing DICOM file");
}
}
public DicomCompressCommand(DicomMessageBase file, TransferSyntax syntax, IDicomCodec codec, DicomCodecParameters parms)
: base("DICOM Compress Command", true)
{
_file = file;
_syntax = syntax;
_codec = codec;
_parms = parms;
}
public static DICOMObject ReadObject(byte[] objectBytes, TransferSyntax syntax)
{
List<IDICOMElement> elements;
using (DICOMBinaryReader dr = new DICOMBinaryReader(objectBytes))
{
elements = DICOMElementReader.ReadAllElements(dr, syntax);
}
return new DICOMObject(elements);
}
internal DicomPresContext(byte pcid, SopClass abstractSyntax, TransferSyntax transferSyntax, DicomPresContextResult result) {
_pcid = pcid;
_result = result;
_roles = DicomRoleSelection.Disabled;
_abstract = abstractSyntax;
if (abstractSyntax.Uid.Length == 0)
throw new DicomException("Invalid abstract syntax for presentation context, UID is zero length.");
_transfers = new List<TransferSyntax>();
_transfers.Add(transferSyntax);
}
public static int ReadIndefiniteLengthLittleEndian(DICOMBinaryReader dr, TransferSyntax syntax)
{
long startingPos = dr.StreamPosition;
while (!IsEndOfSequenceLittleEndian(dr))
{
dr.StreamPosition -= 8;
SequenceItemReader.SkipItemLittleEndian(dr, syntax);
}
return CalculateLength(dr, startingPos)-8;
}
/// <summary>
/// Reads the length from a series of bytes in a stream. The number of bytes is automatically determined from
/// VR.
/// </summary>
/// <param name="vr">the value representation of the element</param>
/// <param name="dr">the binary stream with a current position on the length parameter</param>
/// <param name="syntax">the transfer syntax of this element</param>
/// <returns></returns>
public static int Read(VR vr, DICOMBinaryReader dr, TransferSyntax syntax)
{
switch (syntax)
{
case TransferSyntax.EXPLICIT_VR_BIG_ENDIAN:
return ReadBigEndian(vr, dr);
default:
return ReadLittleEndian(vr, dr);
}
}
public static DICOMObject ReadObject(byte[] objectBytes, TransferSyntax syntax, out long bytesRead)
{
List<IDICOMElement> elements;
using (var dr = new DICOMBinaryReader(objectBytes))
{
elements = DICOMElementReader.ReadAllElements(dr, syntax);
bytesRead = dr.StreamPosition;
}
return new DICOMObject(elements);
}
/// <summary>
/// Reads the data from an element encoded in little endian byte order
/// </summary>
/// <param name="lengthToRead">the length of the data</param>
/// <param name="dr">the binary reader which is reading the DICOM object</param>
/// <returns>the data from this element</returns>
public static byte[] ReadLittleEndian(int lengthToRead, DICOMBinaryReader dr, TransferSyntax syntax)
{
if (lengthToRead != -1)
{
return dr.ReadBytes(lengthToRead);
}
int length = SequenceReader.ReadIndefiniteLengthLittleEndian(dr, syntax);
byte[] seqBytes = dr.ReadBytes(length);
dr.Skip(8);
return seqBytes;
}
/// <summary>
/// Reads a DICOM file from a byte array
/// </summary>
/// <param name="fileBytes">the bytes of the DICOM file</param>
/// <returns>a DICOM object containing all elements</returns>
public static DICOMObject Read(byte[] fileBytes, TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
TransferSyntax syntax = trySyntax; //Will keep if metadata doesn't exist
List<IDICOMElement> elements;
using (var dr = new DICOMBinaryReader(fileBytes))
{
DICOMPreambleReader.Read(dr);
List<IDICOMElement> metaElements = ReadFileMetadata(dr, ref syntax);
elements = metaElements.Concat(DICOMElementReader.ReadAllElements(dr, syntax)).ToList();
}
return new DICOMObject(elements);
}
/// <summary>
/// Reads a DICOM file from a path
/// </summary>
/// <param name="stream">the stream to the DICOM file</param>
/// <returns>a DICOM object containing all elements</returns>
public static DICOMObject Read(Stream stream,
TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
TransferSyntax syntax = trySyntax;
List<IDICOMElement> elements;
using (var dr = new DICOMBinaryReader(stream))
{
DICOMPreambleReader.Read(dr);
List<IDICOMElement> metaElements = ReadFileMetadata(dr, ref syntax);
elements = metaElements.Concat(DICOMElementReader.ReadAllElements(dr, syntax)).ToList();
}
return new DICOMObject(elements);
}
public static DICOMObject ReadBigEndian(DICOMBinaryReader dr, TransferSyntax syntax)
{
DICOMObject d;
int length = LengthReader.ReadLittleEndian(VR.Null, dr.Skip(4));
if (LengthReader.IsIndefinite(length))
{
d = ReadIndefiniteBigEndian(dr, syntax);
}
else
{
d = DICOMObjectReader.ReadObject(dr.ReadBytes(length), syntax);
}
return d;
}
/// <summary>
/// Asynchronously reads a DICOM file from a path
/// </summary>
/// <param name="filePath">the path to the DICOM file</param>
/// <returns>a DICOM object containing all elements</returns>
public static async Task<DICOMObject> ReadAsync(string filePath,
TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
return await Task.Run(() =>
{
TransferSyntax syntax = trySyntax;
List<IDICOMElement> elements;
using (var dr = new DICOMBinaryReader(filePath))
{
DICOMPreambleReader.Read(dr);
List<IDICOMElement> metaElements = ReadFileMetadata(dr, ref syntax);
elements = metaElements.Concat(DICOMElementReader.ReadAllElements(dr, syntax)).ToList();
}
return new DICOMObject(elements);
});
}
public void TestRegister()
{
const string uid = "1.2.3";
var registered = new TransferSyntax("a", "1.2.3", true, true, true, false, false, true);
TransferSyntax.RegisterTransferSyntax(registered);
Assert.IsTrue(TransferSyntax.TransferSyntaxes.Contains(registered));
var retrieved = TransferSyntax.GetTransferSyntax(uid);
Assert.AreEqual(uid, retrieved.UidString);
TransferSyntax.UnregisterTransferSyntax(registered);
Assert.IsFalse(TransferSyntax.TransferSyntaxes.Contains(registered));
TransferSyntax.UnregisterTransferSyntax(registered);
}
public static List<IDICOMElement> ReadAllElements(DICOMBinaryReader dr, TransferSyntax syntax)
{
List<IDICOMElement> elements;
switch (syntax)
{
case TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN:
elements = ReadAllElementsImplicitLittleEndian(dr);
break;
case TransferSyntax.EXPLICIT_VR_BIG_ENDIAN:
elements = ReadAllElementsExplicitBigEndian(dr);
break;
default:
elements = ReadAllElementsExplicitLittleEndian(dr);
break;
}
return elements;
}
public static List<DICOMObject> ReadItems(byte[] data, TransferSyntax syntax)
{
List<DICOMObject> objects = new List<DICOMObject>();
using (DICOMBinaryReader dr = new DICOMBinaryReader(data))
{
while (dr.StreamPosition < dr.StreamLength)
{
switch (syntax)
{
case TransferSyntax.EXPLICIT_VR_BIG_ENDIAN:
objects.Add(SequenceItemReader.ReadBigEndian(dr,syntax));
break;
default:
objects.Add(SequenceItemReader.ReadLittleEndian(dr,syntax));
break;
}
}
}
return objects;
}
public DicomCompressCommand(DicomMessageBase file, XmlDocument parms, bool failOnCodecException)
: base("DICOM Compress Command", true)
{
_file = file;
_failOnCodecException = failOnCodecException;
XmlElement element = parms.DocumentElement;
string syntax = element.Attributes["syntax"].Value;
_syntax = TransferSyntax.GetTransferSyntax(syntax);
if (_syntax == null)
{
string failureDescription =
String.Format("Invalid transfer syntax in compression command: {0}", element.Attributes["syntax"].Value);
Platform.Log(LogLevel.Error, "Error with input syntax: {0}", failureDescription);
throw new DicomCodecException(failureDescription);
}
IDicomCodecFactory[] codecs = DicomCodecRegistry.GetCodecFactories();
IDicomCodecFactory theCodecFactory = null;
foreach (IDicomCodecFactory codec in codecs)
if (codec.CodecTransferSyntax.Equals(_syntax))
{
theCodecFactory = codec;
break;
}
if (theCodecFactory == null)
{
string failureDescription = String.Format("Unable to find codec for compression: {0}", _syntax.Name);
Platform.Log(LogLevel.Error, "Error with compression input parameters: {0}", failureDescription);
throw new DicomCodecException(failureDescription);
}
_codec = theCodecFactory.GetDicomCodec();
_parms = theCodecFactory.GetCodecParameters(parms);
}
public void TestEquality()
{
// ReSharper disable ExpressionIsAlwaysNull
var ts0 = (TransferSyntax) null;
var tsA = new TransferSyntax("a", "1.2.3", true, true, true, false, false, true);
var tsA2 = new TransferSyntax("a2", "1.2.3", true, true, true, false, false, true);
var tsA3 = tsA;
var tsB = new TransferSyntax("b", "1.2.3.4", true, true, true, false, false, true);
Assert.IsTrue(null == ts0);
Assert.IsTrue(ts0 == null);
Assert.IsTrue(Equals(null, ts0));
Assert.IsTrue(Equals(ts0, null));
Assert.IsTrue(tsA == tsA2);
Assert.IsTrue(tsA2 == tsA);
Assert.IsTrue(Equals(tsA, tsA2));
Assert.IsTrue(Equals(tsA2, tsA));
Assert.IsTrue(tsA == tsA3);
Assert.IsTrue(tsA3 == tsA);
Assert.IsTrue(Equals(tsA, tsA3));
Assert.IsTrue(Equals(tsA3, tsA));
Assert.IsFalse(ts0 == tsA);
Assert.IsFalse(tsA == ts0);
Assert.IsFalse(Equals(ts0, tsA));
Assert.IsFalse(Equals(tsA, ts0));
Assert.IsFalse(tsA == tsB);
Assert.IsFalse(tsB == tsA);
Assert.IsFalse(Equals(tsA, tsB));
Assert.IsFalse(Equals(tsB, tsA));
// ReSharper restore ExpressionIsAlwaysNull
}
public void Read(RawPDU raw)
{
uint l = raw.Length;
raw.ReadUInt16("Version");
raw.SkipBytes("Reserved", 2);
_assoc.CalledAE = raw.ReadString("Called AE", 16);
_assoc.CallingAE = raw.ReadString("Calling AE", 16);
raw.SkipBytes("Reserved", 32);
l -= 2 + 2 + 16 + 16 + 32;
while (l > 0)
{
byte type = raw.ReadByte("Item-Type");
raw.SkipBytes("Reserved", 1);
ushort il = raw.ReadUInt16("Item-Length");
l -= 4 + (uint)il;
if (type == 0x10)
{
// Application Context
raw.SkipBytes("Application Context", il);
}
else
if (type == 0x20)
{
// Presentation Context
byte id = raw.ReadByte("Presentation Context ID");
raw.SkipBytes("Reserved", 3);
il -= 4;
while (il > 0)
{
byte pt = raw.ReadByte("Presentation Context Item-Type");
raw.SkipBytes("Reserved", 1);
ushort pl = raw.ReadUInt16("Presentation Context Item-Length");
string sx = raw.ReadString("Presentation Context Syntax UID", pl);
if (pt == 0x30)
{
SopClass sopClass = SopClass.GetSopClass(sx);
if (sopClass == null)
sopClass = new SopClass("Private SOP Class", sx, false);
_assoc.AddPresentationContext(id, sopClass);
}
else if (pt == 0x40)
{
TransferSyntax transferSyntax = TransferSyntax.GetTransferSyntax(sx);
if (transferSyntax == null)
transferSyntax = new TransferSyntax("Private Syntax", sx, true, false, true, false, false, false);
_assoc.AddTransferSyntax(id, transferSyntax);
}
il -= (ushort)(4 + pl);
}
}
else
if (type == 0x50)
{
// User Information
while (il > 0)
{
byte ut = raw.ReadByte("User Information Item-Type");
raw.SkipBytes("Reserved", 1);
ushort ul = raw.ReadUInt16("User Information Item-Length");
il -= (ushort)(4 + ul);
if (ut == 0x51)
{
_assoc.RemoteMaximumPduLength = raw.ReadUInt32("Max PDU Length");
}
else if (ut == 0x52)
{
_assoc.ImplementationClass = new DicomUid(raw.ReadString("Implementation Class UID", ul), "Implementation Class UID", UidType.Unknown);
}
else if (ut == 0x53)
{
_assoc.RemoteMaxOperationsInvoked = raw.ReadUInt16("Max Operations Invoked");
_assoc.RemoteMaxOperationsPerformed = raw.ReadUInt16("Max Operations Performed");
}
else if (ut == 0x55)
{
_assoc.ImplementationVersion = raw.ReadString("Implementation Version", ul);
}
else if (ut == 0x54)
{
raw.SkipBytes("SCU/SCP Role Selection", ul);
/*
ushort rsul = raw.ReadUInt16();
if ((rsul + 4) != ul) {
throw new DicomNetworkException("SCU/SCP role selection length (" + ul + " bytes) does not match uid length (" + rsul + " + 4 bytes)");
}
raw.ReadChars(rsul); // Abstract Syntax
raw.ReadByte(); // SCU role
raw.ReadByte(); // SCP role
*/
}
else
{
Platform.Log(LogLevel.Error, "Unhandled user item: 0x{0:x2} ({1} + 4 bytes)", ut, ul);
raw.SkipBytes("Unhandled User Item", ul);
}
}
}
}
}
/// <summary>
/// Constructor.
/// </summary>
/// <param name="dicomFile"></param>
public StorageInstance(DicomFile dicomFile)
{
_dicomFile = dicomFile;
string sopClassInFile = _dicomFile.DataSet[DicomTags.SopClassUid].ToString();
if (!sopClassInFile.Equals(_dicomFile.SopClass.Uid))
{
Platform.Log(LogLevel.Warn, "SOP Class in Meta Info ({0}) does not match SOP Class in DataSet ({1})",
_dicomFile.SopClass.Uid, sopClassInFile);
_sopClass = SopClass.GetSopClass(sopClassInFile);
if (_sopClass == null)
{
Platform.Log(LogLevel.Warn, "Unknown SOP Class in dataset, reverting to meta info: {0}", sopClassInFile);
_sopClass = _dicomFile.SopClass;
}
}
else
_sopClass = _dicomFile.SopClass;
_syntax = _dicomFile.TransferSyntax;
SopInstanceUid = _dicomFile.MediaStorageSopInstanceUid;
_filename = dicomFile.Filename;
StudyInstanceUid = _dicomFile.DataSet[DicomTags.StudyInstanceUid].GetString(0, string.Empty);
SeriesInstanceUid = _dicomFile.DataSet[DicomTags.SeriesInstanceUid].GetString(0, string.Empty);
PatientsName = _dicomFile.DataSet[DicomTags.PatientsName].GetString(0, string.Empty);
PatientId = _dicomFile.DataSet[DicomTags.PatientId].GetString(0, string.Empty);
_infoLoaded = true;
}
/// <summary>
/// Load enough information from the file to allow negotiation of the association.
/// </summary>
public void LoadInfo()
{
if (_infoLoaded)
return;
DicomFile theFile = new DicomFile(_filename);
theFile.Load(DicomTags.RelatedGeneralSopClassUid, DicomReadOptions.Default);
string sopClassInFile = theFile.DataSet[DicomTags.SopClassUid].ToString();
if (!sopClassInFile.Equals(theFile.SopClass.Uid))
{
Platform.Log(LogLevel.Warn, "SOP Class in Meta Info ({0}) does not match SOP Class in DataSet ({1})",
theFile.SopClass.Uid, sopClassInFile);
_sopClass = SopClass.GetSopClass(sopClassInFile);
if (_sopClass == null)
{
Platform.Log(LogLevel.Warn,"Unknown SOP Class in dataset, reverting to meta info: {0}", sopClassInFile);
_sopClass = theFile.SopClass;
}
}
else
_sopClass = theFile.SopClass;
_syntax = theFile.TransferSyntax;
SopInstanceUid = theFile.MediaStorageSopInstanceUid;
MetaInfoFileLength = theFile.MetaInfoFileLength;
_infoLoaded = true;
}
internal override void WriteData(SwappableBinaryWriter bw, ILogger logger, TransferSyntax transferSyntax)
{
// Make sure to follow the UID rules
bw.Write(Uid.UidToBytes(this.data));
}
protected override void OnExecute(CommandProcessor theProcessor, IUpdateContext updateContext)
{
// Check if the File is the same syntax as the
TransferSyntax fileSyntax = _file.TransferSyntax;
TransferSyntax dbSyntax = TransferSyntax.GetTransferSyntax(_location.TransferSyntaxUid);
// Check if the syntaxes match the location
if ((!fileSyntax.Encapsulated && !dbSyntax.Encapsulated) ||
(fileSyntax.LosslessCompressed && dbSyntax.LosslessCompressed) ||
(fileSyntax.LossyCompressed && dbSyntax.LossyCompressed))
{
// no changes necessary, just return;
return;
}
// Select the Server Transfer Syntax
var syntaxCriteria = new ServerTransferSyntaxSelectCriteria();
var syntaxBroker = updateContext.GetBroker <IServerTransferSyntaxEntityBroker>();
syntaxCriteria.Uid.EqualTo(fileSyntax.UidString);
ServerTransferSyntax serverSyntax = syntaxBroker.FindOne(syntaxCriteria);
if (serverSyntax == null)
{
Platform.Log(LogLevel.Error, "Unable to load ServerTransferSyntax for {0}. Unable to update study status.", fileSyntax.Name);
return;
}
// Get the FilesystemStudyStorage update broker ready
var filesystemStudyStorageEntityBroker = updateContext.GetBroker <IFilesystemStudyStorageEntityBroker>();
var filesystemStorageUpdate = new FilesystemStudyStorageUpdateColumns();
var filesystemStorageCritiera = new FilesystemStudyStorageSelectCriteria();
filesystemStorageUpdate.ServerTransferSyntaxKey = serverSyntax.Key;
filesystemStorageCritiera.StudyStorageKey.EqualTo(_location.Key);
// Get the StudyStorage update broker ready
var studyStorageBroker =
updateContext.GetBroker <IStudyStorageEntityBroker>();
var studyStorageUpdate = new StudyStorageUpdateColumns();
StudyStatusEnum statusEnum = _location.StudyStatusEnum;
if (fileSyntax.LossyCompressed)
{
studyStorageUpdate.StudyStatusEnum = statusEnum = StudyStatusEnum.OnlineLossy;
}
else if (fileSyntax.LosslessCompressed)
{
studyStorageUpdate.StudyStatusEnum = statusEnum = StudyStatusEnum.OnlineLossless;
}
studyStorageUpdate.LastAccessedTime = Platform.Time;
if (!filesystemStudyStorageEntityBroker.Update(filesystemStorageCritiera, filesystemStorageUpdate))
{
Platform.Log(LogLevel.Error, "Unable to update FilesystemQueue row: Study {0}, Server Entity {1}",
_location.StudyInstanceUid, _location.ServerPartitionKey);
}
else if (!studyStorageBroker.Update(_location.GetKey(), studyStorageUpdate))
{
Platform.Log(LogLevel.Error, "Unable to update StudyStorage row: Study {0}, Server Entity {1}",
_location.StudyInstanceUid, _location.ServerPartitionKey);
}
else
{
// Update the location, so the next time we come in here, we don't try and update the database
// for another sop in the study.
_location.StudyStatusEnum = statusEnum;
_location.TransferSyntaxUid = fileSyntax.UidString;
_location.ServerTransferSyntaxKey = serverSyntax.Key;
}
}
void IDicomServerHandler.OnReceiveRequestMessage(DicomServer server, ServerAssociationParameters association, byte presentationID, DicomMessage message)
{
if (message.CommandField == DicomCommandField.CEchoRequest)
{
server.SendCEchoResponse(presentationID, message.MessageId, DicomStatuses.Success);
return;
}
String studyInstanceUid = null;
String seriesInstanceUid = null;
DicomUid sopInstanceUid;
String patientName = null;
bool ok = message.DataSet[DicomTags.SopInstanceUid].TryGetUid(0, out sopInstanceUid);
if (ok)
{
ok = message.DataSet[DicomTags.SeriesInstanceUid].TryGetString(0, out seriesInstanceUid);
}
if (ok)
{
ok = message.DataSet[DicomTags.StudyInstanceUid].TryGetString(0, out studyInstanceUid);
}
if (ok)
{
ok = message.DataSet[DicomTags.PatientsName].TryGetString(0, out patientName);
}
if (!ok)
{
Platform.Log(LogLevel.Error, "Unable to retrieve UIDs from request message, sending failure status.");
server.SendCStoreResponse(presentationID, message.MessageId, sopInstanceUid.UID,
DicomStatuses.ProcessingFailure);
return;
}
TransferSyntax syntax = association.GetPresentationContext(presentationID).AcceptedTransferSyntax;
if (List)
{
Platform.Log(LogLevel.Info, message.Dump());
}
if (Bitbucket)
{
Platform.Log(LogLevel.Info, "Received SOP Instance: {0} for patient {1} in syntax {2}", sopInstanceUid,
patientName, syntax.Name);
server.SendCStoreResponse(presentationID, message.MessageId,
sopInstanceUid.UID,
DicomStatuses.Success);
return;
}
if (!Directory.Exists(StorageLocation))
{
Directory.CreateDirectory(StorageLocation);
}
var path = new StringBuilder();
path.AppendFormat("{0}{1}{2}{3}{4}", StorageLocation, Path.DirectorySeparatorChar,
studyInstanceUid, Path.DirectorySeparatorChar, seriesInstanceUid);
Directory.CreateDirectory(path.ToString());
path.AppendFormat("{0}{1}.dcm", Path.DirectorySeparatorChar, sopInstanceUid.UID);
var dicomFile = new DicomFile(message, path.ToString())
{
TransferSyntaxUid = syntax.UidString,
MediaStorageSopInstanceUid = sopInstanceUid.UID,
ImplementationClassUid = DicomImplementation.ClassUID.UID,
ImplementationVersionName = DicomImplementation.Version,
SourceApplicationEntityTitle = association.CallingAE,
MediaStorageSopClassUid = message.SopClass.Uid
};
dicomFile.Save(DicomWriteOptions.None);
Platform.Log(LogLevel.Info, "Received SOP Instance: {0} for patient {1} in syntax {2}", sopInstanceUid,
patientName, syntax.Name);
server.SendCStoreResponse(presentationID, message.MessageId,
sopInstanceUid.UID,
DicomStatuses.Success);
}
private static DICOMObject GetDataObject(List <PDataTF> pDatas, TransferSyntax syntax)
{
byte[] dicomBytes = DIMSEReader.MergePDataTFData(pDatas);
return(DIMSEReader.CreateDICOMObject(dicomBytes, syntax));
}
/// <summary>
/// Creates a new DICOM nested data set instance from specified
/// DICOM output stream using specified transfer syntax.
/// </summary>
public NestedDataSet(Stream stream, TransferSyntax transferSyntax) :
base(stream, transferSyntax)
{
}
internal override uint ParseData(SwappableBinaryReader br, ILogger logger, uint length, TransferSyntax transferSyntax)
{
//reuse setter
Data = System.Text.Encoding.ASCII.GetString(br.ReadBytes((int)length));
return(length);
}
public void Read(RawPDU raw)
{
uint l = raw.Length;
raw.ReadUInt16("Version");
raw.SkipBytes("Reserved", 2);
raw.SkipBytes("Reserved", 16);
raw.SkipBytes("Reserved", 16);
raw.SkipBytes("Reserved", 32);
l -= 68;
while (l > 0)
{
byte type = raw.ReadByte("Item-Type");
l -= 1;
if (type == 0x10)
{
// Application Context
raw.SkipBytes("Reserved", 1);
ushort c = raw.ReadUInt16("Item-Length");
raw.SkipBytes("Value", (int)c);
l -= 3 + (uint)c;
}
else
if (type == 0x21)
{
// Presentation Context
raw.ReadByte("Reserved");
ushort pl = raw.ReadUInt16("Presentation Context Item-Length");
byte id = raw.ReadByte("Presentation Context ID");
raw.ReadByte("Reserved");
byte res = raw.ReadByte("Presentation Context Result/Reason");
raw.ReadByte("Reserved");
l -= (uint)pl + 3;
pl -= 4;
// Presentation Context Transfer Syntax
raw.ReadByte("Presentation Context Item-Type (0x40)");
raw.ReadByte("Reserved");
ushort tl = raw.ReadUInt16("Presentation Context Item-Length");
string tx = raw.ReadString("Presentation Context Syntax UID", tl);
pl -= (ushort)(tl + 4);
_assoc.SetPresentationContextResult(id, (DicomPresContextResult)res);
TransferSyntax acceptedSyntax = TransferSyntax.GetTransferSyntax(tx);
if (acceptedSyntax != null)
{
_assoc.SetAcceptedTransferSyntax(id, acceptedSyntax);
}
else
{
_assoc.GetPresentationContext(id).ClearTransfers();
}
}
else
if (type == 0x50)
{
// User Information
raw.ReadByte("Reserved");
ushort il = raw.ReadUInt16("User Information Item-Length");
l -= (uint)(il + 3);
while (il > 0)
{
byte ut = raw.ReadByte("User Item-Type");
raw.ReadByte("Reserved");
ushort ul = raw.ReadUInt16("User Item-Length");
il -= (ushort)(ul + 4);
if (ut == 0x51)
{
_assoc.RemoteMaximumPduLength = raw.ReadUInt32("Max PDU Length");
}
else if (ut == 0x52)
{
_assoc.ImplementationClass = DicomUids.Lookup(raw.ReadString("Implementation Class UID", ul));
}
else if (ut == 0x55)
{
_assoc.ImplementationVersion = raw.ReadString("Implementation Version", ul);
}
else
{
raw.SkipBytes("User Item Value", (int)ul);
}
}
}
else
{
raw.SkipBytes("Reserved", 1);
ushort il = raw.ReadUInt16("User Item-Length");
raw.SkipBytes("Unknown User Item", il);
l -= (uint)(il + 3);
}
}
}
internal override uint ParseData(SwappableBinaryReader br, ILogger logger, uint length, TransferSyntax transferSyntax)
{
//Covered by PS 3.5, Chapter 7.5 (pg. 42-45)
bool encapImage = (Tag == DICOMTags.PixelData);
bool done = false;
uint count = 0;
while (!done)
{
//If explicit length, see if we're done
if (length != 0xFFFFFFFF && count >= length)
{
done = true;
continue;
}
ushort grp = br.ReadUInt16();
ushort elem = br.ReadUInt16();
uint len = br.ReadUInt32();
count += 8;
//Sometimes there's retarded files that are msb swapped inside of sequences outside of the transfer syntax
bool needMoreSwap = (grp == 0xFEFF);
if (needMoreSwap)
{
//Swap the reader for now, then swap back after the sqitem
br.ToggleSwapped();
//still have to swap the stuff we've already read by hand tho
grp = MSBSwapper.SwapW(grp);
elem = MSBSwapper.SwapW(elem);
len = MSBSwapper.SwapDW(len);
}
if (grp == 0xFFFE && elem == 0xE000)
{
//Normal element, parse it out.
SQItem item = new SQItem(this);
count += item.ParseStream(br, logger, transferSyntax, len, encapImage);
Items.Add(item);
}
else if (grp == 0xFFFE && elem == 0xE0DD)
{
//End element
//In case there's garbage in there, read the length bytes
br.ReadBytes((int)len);
count += len;
done = true;
}
else
{
throw new NotImplementedException();
}
//toggle back in case it's just one SQItem that's hosed
if (needMoreSwap)
{
br.ToggleSwapped();
}
}
return(count);
}
public void Read(RawPDU raw)
{
uint l = raw.Length;
raw.ReadUInt16("Version");
raw.SkipBytes("Reserved", 2);
_assoc.CalledAE = raw.ReadString("Called AE", 16);
_assoc.CallingAE = raw.ReadString("Calling AE", 16);
raw.SkipBytes("Reserved", 32);
l -= 2 + 2 + 16 + 16 + 32;
while (l > 0)
{
byte type = raw.ReadByte("Item-Type");
raw.SkipBytes("Reserved", 1);
ushort il = raw.ReadUInt16("Item-Length");
l -= 4 + (uint)il;
if (type == 0x10)
{
// Application Context
raw.SkipBytes("Application Context", il);
}
else
if (type == 0x20)
{
// Presentation Context
byte id = raw.ReadByte("Presentation Context ID");
raw.SkipBytes("Reserved", 3);
il -= 4;
while (il > 0)
{
byte pt = raw.ReadByte("Presentation Context Item-Type");
raw.SkipBytes("Reserved", 1);
ushort pl = raw.ReadUInt16("Presentation Context Item-Length");
string sx = raw.ReadString("Presentation Context Syntax UID", pl);
if (pt == 0x30)
{
SopClass sopClass = SopClass.GetSopClass(sx);
if (sopClass == null)
{
sopClass = new SopClass("Private SOP Class", sx, false);
}
_assoc.AddPresentationContext(id, sopClass);
}
else if (pt == 0x40)
{
TransferSyntax transferSyntax = TransferSyntax.GetTransferSyntax(sx);
if (transferSyntax == null)
{
transferSyntax = new TransferSyntax("Private Syntax", sx, true, false, true, false, false, false);
}
_assoc.AddTransferSyntax(id, transferSyntax);
}
il -= (ushort)(4 + pl);
}
}
else
if (type == 0x50)
{
// User Information
while (il > 0)
{
byte ut = raw.ReadByte("User Information Item-Type");
raw.SkipBytes("Reserved", 1);
ushort ul = raw.ReadUInt16("User Information Item-Length");
il -= (ushort)(4 + ul);
if (ut == 0x51)
{
_assoc.RemoteMaximumPduLength = raw.ReadUInt32("Max PDU Length");
}
else if (ut == 0x52)
{
_assoc.ImplementationClass = new DicomUid(raw.ReadString("Implementation Class UID", ul), "Implementation Class UID", UidType.Unknown);
}
else if (ut == 0x53)
{
_assoc.MaxOperationsInvoked = raw.ReadUInt16("Max Operations Invoked");
_assoc.MaxOperationsPerformed = raw.ReadUInt16("Max Operations Performed");
}
else if (ut == 0x55)
{
_assoc.ImplementationVersion = raw.ReadString("Implementation Version", ul);
}
else if (ut == 0x54)
{
raw.SkipBytes("SCU/SCP Role Selection", ul);
/*
* ushort rsul = raw.ReadUInt16();
* if ((rsul + 4) != ul) {
* throw new DicomNetworkException("SCU/SCP role selection length (" + ul + " bytes) does not match uid length (" + rsul + " + 4 bytes)");
* }
* raw.ReadChars(rsul); // Abstract Syntax
* raw.ReadByte(); // SCU role
* raw.ReadByte(); // SCP role
*/
}
else
{
Platform.Log(LogLevel.Error, "Unhandled user item: 0x{0:x2} ({1} + 4 bytes)", ut, ul);
raw.SkipBytes("Unhandled User Item", ul);
}
}
}
}
}
public static DICOMObject ReadObject(DICOMBinaryReader dr, TransferSyntax syntax)
{
List <IDICOMElement> elements = DICOMElementReader.ReadAllElements(dr, syntax);
return(new DICOMObject(elements));
}
public static DICOMObject ReadObject(byte[] objectBytes, TransferSyntax syntax)
{
long bytesRead;
return(ReadObject(objectBytes, syntax, out bytesRead));
}
/// <summary>
/// Reads a DICOM file from a byte array
/// </summary>
/// <param name="file">the bytes of the DICOM file</param>
/// <param name="trySyntax">the transfer syntax to use in case there is no metadata explicitly included</param>
/// <returns></returns>
public static DICOMObject Read(byte[] file, TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
return(DICOMFileReader.Read(file, trySyntax));
}
public static int Main(string[] args)
{
if (args.Length < 2)
{
System.Console.WriteLine(" input.dcm output.dcm");
return(1);
}
string filename = args[0];
string outfilename = args[1];
ImageReader reader = new ImageReader();
reader.SetFileName(filename);
if (!reader.Read())
{
System.Console.WriteLine("Could not read: " + filename);
return(1);
}
// The output of gdcm::Reader is a gdcm::File
File file = reader.GetFile();
// the dataset is the the set of element we are interested in:
DataSet ds = file.GetDataSet();
Image image = reader.GetImage();
//image.Print( cout );
ImageChangeTransferSyntax change = new ImageChangeTransferSyntax();
TransferSyntax targetts = new TransferSyntax(TransferSyntax.TSType.JPEGBaselineProcess1);
change.SetTransferSyntax(targetts);
// Setup our JPEGCodec, warning it should be compatible with JPEGBaselineProcess1
JPEGCodec jpegcodec = new JPEGCodec();
if (!jpegcodec.CanCode(targetts))
{
System.Console.WriteLine("Something went really wrong, JPEGCodec cannot handle JPEGBaselineProcess1");
return(1);
}
jpegcodec.SetLossless(false);
jpegcodec.SetQuality(50); // poor quality !
change.SetUserCodec(jpegcodec); // specify the codec to use to the ImageChangeTransferSyntax
change.SetInput(image);
bool b = change.Change();
if (!b)
{
System.Console.WriteLine("Could not change the Transfer Syntax");
return(1);
}
ImageWriter writer = new ImageWriter();
writer.SetImage((gdcm.Image)change.GetOutput());
writer.SetFile(reader.GetFile());
writer.SetFileName(outfilename);
if (!writer.Write())
{
System.Console.WriteLine("Could not write: " + outfilename);
return(1);
}
return(0);
}
internal override void WriteData(SwappableBinaryWriter bw, ILogger logger, TransferSyntax transferSyntax)
{
bw.Write(data);
}
/// <summary>
/// Checks for a storage location for the study in the database, and creates a new location
/// in the database if it doesn't exist.
/// </summary>
/// <param name="partition">The partition where the study is being sent to</param>
/// <param name="created"></param>
/// <param name="studyDate"></param>
/// <param name="studyInstanceUid"></param>
/// <param name="syntax"></param>
/// <param name="updateContext">The update context to create the study on</param>
/// <returns>A <see cref="StudyStorageLocation"/> instance.</returns>
public StudyStorageLocation GetOrCreateWritableStudyStorageLocation(string studyInstanceUid, string studyDate, TransferSyntax syntax, IUpdateContext updateContext, ServerPartition partition, out bool created)
{
created = false;
StudyStorageLocation location;
try
{
GetWritableStudyStorageLocation(partition.Key, studyInstanceUid, StudyRestore.True,
StudyCache.True, out location);
return(location);
}
catch (StudyNotFoundException)
{
}
FilesystemSelector selector = new FilesystemSelector(Instance);
ServerFilesystemInfo filesystem = selector.SelectFilesystem();
if (filesystem == null)
{
throw new NoWritableFilesystemException();
}
IInsertStudyStorage locInsert = updateContext.GetBroker <IInsertStudyStorage>();
InsertStudyStorageParameters insertParms = new InsertStudyStorageParameters
{
ServerPartitionKey = partition.GetKey(),
StudyInstanceUid = studyInstanceUid,
Folder =
ResolveStorageFolder(partition.Key, studyInstanceUid, studyDate,
updateContext, false
/* set to false for optimization because we are sure it's not in the system */),
FilesystemKey = filesystem.Filesystem.GetKey(),
QueueStudyStateEnum = QueueStudyStateEnum.Idle
};
if (syntax.LosslessCompressed)
{
insertParms.TransferSyntaxUid = syntax.UidString;
insertParms.StudyStatusEnum = StudyStatusEnum.OnlineLossless;
}
else if (syntax.LossyCompressed)
{
insertParms.TransferSyntaxUid = syntax.UidString;
insertParms.StudyStatusEnum = StudyStatusEnum.OnlineLossy;
}
else
{
insertParms.TransferSyntaxUid = syntax.UidString;
insertParms.StudyStatusEnum = StudyStatusEnum.Online;
}
location = locInsert.FindOne(insertParms);
created = true;
return(location);
}
/// <summary>
/// Used to add a supported transfer syntax.
/// </summary>
/// <param name="syntax">The transfer syntax supproted by the SOP Class.</param>
public void AddSyntax(TransferSyntax syntax)
{
SyntaxList.Add(syntax);
}
internal override uint ParseData(SwappableBinaryReader br, ILogger logger, uint length, TransferSyntax transferSyntax)
{
if (length < 2)
{
//busted...
data = (ushort)0;
br.ReadBytes((int)length);
}
else if (length == 2)
{
data = br.ReadUInt16();
}
else if (length > 2)
{
uint readBytes = 0;
DataDictionaryElement elemCheck = DataDictionary.LookupElement(this.Tag);
if (elemCheck == null || elemCheck.VMMax > 1)
{
//Unknown VM or VM goes to > 1
data = new ushort[length / 2];
for (int i = 0; i < length / 2; i++)
{
((ushort[])data)[i] = br.ReadUInt16();
}
readBytes = (length / 2) * 2;
}
else
{
//VM of 1 -- force to single data point
data = br.ReadUInt16();
readBytes = 2;
}
if (length - readBytes > 0)
{
br.ReadBytes((int)(length - readBytes));
}
}
return(length);
}
internal abstract ByteBuffer GetByteBuffer(TransferSyntax syntax, String specificCharacterSet);
public DicomReadStatus Read(DicomTag stopAtTag, DicomReadOptions options)
{
if (stopAtTag == null)
{
stopAtTag = new DicomTag(0xFFFFFFFF, "Bogus Tag", "BogusTag", DicomVr.UNvr, false, 1, 1, false);
}
// Counters:
// _remain - bytes remaining in stream
// _bytes - estimates bytes to end of dataset
// _read - number of bytes read from stream
try
{
BytesNeeded = 0;
_remain = _stream.Length - _stream.Position;
while (_remain > 0)
{
if (_inGroup2 && BytesRead >= _endGroup2)
{
_inGroup2 = false;
// Only change if we're still reading the meta info
if (Dataset.StartTagValue < DicomTags.TransferSyntaxUid)
{
TransferSyntax group2Syntax =
TransferSyntax.GetTransferSyntax(
Dataset[DicomTags.TransferSyntaxUid].GetString(0, String.Empty));
if (group2Syntax == null)
{
throw new DicomException("Unsupported transfer syntax in group 2 elements");
}
TransferSyntax = group2Syntax;
}
}
uint tagValue;
if (LastTagRead == null)
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_pos = _stream.Position;
ushort g = _reader.ReadUInt16();
ushort e = _reader.ReadUInt16();
tagValue = DicomTag.GetTagValue(g, e);
if (DicomTag.IsPrivateGroup(g) && e > 0x00ff)
{
SaveTagRead = LastTagRead = DicomTagDictionary.GetDicomTag(g, e) ??
new DicomTag((uint)g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
else
{
if (e == 0x0000)
{
SaveTagRead = LastTagRead = new DicomTag((uint)g << 16 | e, "Group Length", "GroupLength", DicomVr.ULvr, false, 1, 1, false);
}
else
{
SaveTagRead = LastTagRead = DicomTagDictionary.GetDicomTag(g, e) ??
new DicomTag((uint)g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
}
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
else
{
tagValue = LastTagRead.TagValue;
}
if ((tagValue >= stopAtTag.TagValue) &&
(_sqrs.Count == 0)) // only exit in root message when after stop tag
{
if (_inGroup2 && tagValue > 0x0002FFFF)
{
if (_endGroup2 != BytesRead - 4)
{
LogAdapter.Logger.Info("File Meta Info Length, {0}, not equal to actual bytes read in file, {1}, overwriting length.",
EndGroupTwo, BytesRead - 4);
_endGroup2 = BytesRead - 4;
}
_inGroup2 = false;
}
EncounteredStopTag = true;
return(DicomReadStatus.Success);
}
bool twoByteLength;
if (_vr == null)
{
if (_syntax.ExplicitVr)
{
if (LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem)
{
_vr = DicomVr.NONE;
twoByteLength = _vr.Is16BitLengthField;
}
else
{
if (_remain < 2)
{
return(NeedMoreData(2));
}
string vr = new string(_reader.ReadChars(2));
_vr = DicomVr.GetVR(vr);
twoByteLength = _vr.Is16BitLengthField;
_remain -= 2;
BytesEstimated += 2;
BytesRead += 2;
if (LastTagRead.VR.Equals(DicomVr.UNvr))
{
LastTagRead = new DicomTag(LastTagRead.TagValue, "Private Tag", "PrivateTag", _vr, false, 1, uint.MaxValue, false);
if (vr.Equals("??"))
{
twoByteLength = true;
}
}
else if (!LastTagRead.VR.Equals(_vr))
{
if (!vr.Equals(" "))
{
DicomTag tag =
new DicomTag(LastTagRead.TagValue, LastTagRead.Name, LastTagRead.VariableName, _vr, LastTagRead.MultiVR,
LastTagRead.VMLow, LastTagRead.VMHigh,
LastTagRead.Retired);
LastTagRead = tag;
; // TODO, log something
}
}
}
}
else
{
_vr = LastTagRead.VR;
twoByteLength = _vr.Is16BitLengthField;
}
if (_vr == DicomVr.UNvr)
{
if (LastTagRead.IsPrivate)
{
if (LastTagRead.Element <= 0x00ff && LastTagRead.Element >= 0x0010)
{
// Reset the tag with the right VR and a more descriptive name.
LastTagRead = new DicomTag(LastTagRead.TagValue, "Private Creator Code", "PrivateCreatorCode", DicomVr.LOvr, false, 1, uint.MaxValue, false);
// private creator id
// Only set the VR to LO for Implicit VR, if we do it for
// Explicit VR syntaxes, we would incorrectly read the tag
// length below.
if (!_syntax.ExplicitVr)
{
_vr = DicomVr.LOvr;
}
}
else if (_stream.CanSeek && Flags.IsSet(options, DicomReadOptions.AllowSeekingForContext))
{
// attempt to identify private sequence by checking if the tag has
// an undefined length
long pos = _stream.Position;
int bytesToCheck = _syntax.ExplicitVr ? 6 : 4;
if (_remain >= bytesToCheck)
{
if (_syntax.ExplicitVr)
{
_reader.ReadUInt16();
}
uint l = _reader.ReadUInt32();
if (l == UndefinedLength)
{
_vr = DicomVr.SQvr;
}
}
_stream.Position = pos;
}
}
}
}
else
{
twoByteLength = _vr.Is16BitLengthField;
}
// Read the value length
if (_len == UndefinedLength)
{
if (_syntax.ExplicitVr)
{
if (LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem)
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_len = _reader.ReadUInt32();
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
else
{
if (twoByteLength)
{
if (_remain < 2)
{
return(NeedMoreData(2));
}
_len = _reader.ReadUInt16();
_remain -= 2;
BytesEstimated += 2;
BytesRead += 2;
}
else
{
if (_remain < 6)
{
return(NeedMoreData(6));
}
_reader.ReadByte();
_reader.ReadByte();
_len = _reader.ReadUInt32();
_remain -= 6;
BytesEstimated += 6;
BytesRead += 6;
}
}
}
else
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_len = _reader.ReadUInt32();
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
if ((_len != UndefinedLength) &&
!_vr.Equals(DicomVr.SQvr) &&
!(LastTagRead.Equals(DicomTag.Item) &&
_fragment == null))
{
BytesEstimated += _len;
}
}
// If we have a private creator code, set the VR to LO, because
// that is what it is. We must do this after we read the length
// so that the 32 bit length is read properly.
if ((LastTagRead.IsPrivate) &&
(_vr.Equals(DicomVr.UNvr)) &&
(LastTagRead.Element <= 0x00ff))
{
_vr = DicomVr.LOvr;
}
if (_fragment != null)
{
// In the middle of parsing pixels
if (LastTagRead == DicomTag.Item)
{
if (_remain < _len)
{
return(NeedMoreData(_remain - _len));
}
if (Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences) &&
_fragment.HasOffsetTable)
{
FileReference reference = new FileReference(StreamOpener, _stream.Position, _len, _endian, DicomVr.OBvr);
DicomFragment fragment = new DicomFragment(reference);
_fragment.AddFragment(fragment);
if (_stream.CanSeek)
{
_stream.Seek(_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
}
else
{
ByteBuffer data = new ByteBuffer(_endian, _len);
data.CopyFrom(_stream, (int)_len);
if (!_fragment.HasOffsetTable)
{
_fragment.SetOffsetTable(data);
}
else
{
DicomFragment fragment = new DicomFragment(data);
_fragment.AddFragment(fragment);
}
}
_remain -= _len;
BytesRead += _len;
}
else if (LastTagRead == DicomTag.SequenceDelimitationItem)
{
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomDataset ds = rec.Current;
ds[_fragment.Tag] = _fragment;
if (rec.Curlen != UndefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
Dataset[_fragment.Tag] = _fragment;
}
_fragment = null;
}
else
{
LogAdapter.Logger.Error("Encountered unexpected tag in stream: {0}", LastTagRead.ToString());
// unexpected tag
return(DicomReadStatus.UnknownError);
}
}
else if (_sqrs.Count > 0 &&
(LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem))
{
SequenceRecord rec = _sqrs.Peek();
if (LastTagRead.Equals(DicomTag.Item))
{
if (_len != UndefinedLength)
{
if (_len > _remain)
{
return(NeedMoreData(_remain - _len));
}
}
DicomSequenceItem ds;
if (rec.Tag.TagValue.Equals(DicomTags.DirectoryRecordSequence))
{
DirectoryRecordSequenceItem dr = new DirectoryRecordSequenceItem
{
Offset = (uint)_pos
};
ds = dr;
}
else
{
ds = new DicomSequenceItem();
}
rec.Current = ds;
if (rec.Tag.VR.Equals(DicomVr.UNvr))
{
DicomTag tag = new DicomTag(rec.Tag.TagValue, rec.Tag.Name,
rec.Tag.VariableName, DicomVr.SQvr, rec.Tag.MultiVR, rec.Tag.VMLow,
rec.Tag.VMHigh, rec.Tag.Retired);
rec.Parent[tag].AddSequenceItem(ds);
}
else
{
rec.Parent[rec.Tag].AddSequenceItem(ds);
}
// Specific character set is inherited, save it. It will be overwritten
// if a new value of the tag is encountered in the sequence.
rec.Current.SpecificCharacterSet = rec.Parent.SpecificCharacterSet;
// save the sequence length
rec.Curpos = _pos + 8;
rec.Curlen = _len;
_sqrs.Pop();
_sqrs.Push(rec);
if (_len != UndefinedLength)
{
ByteBuffer data = new ByteBuffer(_endian, _len);
data.CopyFrom(_stream, (int)_len);
data.Stream.Position = 0;
_remain -= _len;
BytesRead += _len;
DicomStreamReader idsr = new DicomStreamReader(data.Stream)
{
Dataset = ds,
TransferSyntax = rec.Tag.VR.Equals(DicomVr.UNvr)
? TransferSyntax.ImplicitVrLittleEndian
: _syntax,
StreamOpener = StreamOpener
};
DicomReadStatus stat = idsr.Read(null, options & ~DicomReadOptions.StorePixelDataReferences);
if (stat != DicomReadStatus.Success)
{
LogAdapter.Logger.Error("Unexpected parsing error ({0}) when reading sequence attribute: {1}.", stat, rec.Tag.ToString());
return(stat);
}
}
}
else if (LastTagRead == DicomTag.ItemDelimitationItem)
{
}
else if (LastTagRead == DicomTag.SequenceDelimitationItem)
{
SequenceRecord rec2 = _sqrs.Pop();
if (rec2.Current == null)
{
rec2.Parent[rec.Tag].SetNullValue();
}
}
if (rec.Len != UndefinedLength)
{
long end = rec.Pos + 8 + rec.Len;
if (_syntax.ExplicitVr)
{
end += 2 + 2;
}
if (_stream.Position >= end)
{
_sqrs.Pop();
}
}
}
else
{
if (_len == UndefinedLength)
{
if (_vr.Equals(DicomVr.UNvr))
{
if (!_syntax.ExplicitVr)
{
_vr = DicomVr.SQvr;
LastTagRead = LastTagRead.IsPrivate
? new DicomTag(LastTagRead.TagValue, "Private Tag", "PrivateTag", DicomVr.SQvr, false, 1, uint.MaxValue, false)
: new DicomTag(LastTagRead.TagValue, "Unknown Tag", "UnknownTag", DicomVr.SQvr, false, 1, uint.MaxValue, false);
}
else
{
// To handle this case, we'd have to add a new mechanism to transition the parser to implicit VR parsing,
// and then return back to implicit once the parsing of the SQ is complete.
LogAdapter.Logger.Error(
"Encountered unknown tag {0}, encoded as undefined length in an Explicit VR transfer syntax at offset {1}. Unable to parse.",
LastTagRead, _stream.Position);
return(DicomReadStatus.UnknownError);
}
}
if (_vr.Equals(DicomVr.SQvr))
{
SequenceRecord rec = new SequenceRecord
{
Parent = _sqrs.Count > 0
? _sqrs.Peek().Current
: Dataset,
Current = null,
Tag = LastTagRead,
Len = UndefinedLength
};
_sqrs.Push(rec);
}
else
{
_fragment = new DicomFragmentSequence(LastTagRead);
}
}
else
{
if (_vr.Equals(DicomVr.SQvr))
{
if (_len == 0)
{
DicomDataset ds;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
ds = rec.Current;
}
else
{
ds = Dataset;
}
ds[LastTagRead].SetNullValue();
}
else
{
SequenceRecord rec = new SequenceRecord
{
Len = _len,
Pos = _pos,
Tag = LastTagRead,
Parent = _sqrs.Count > 0
? _sqrs.Peek().Current
: Dataset
};
_sqrs.Push(rec);
}
}
else
{
if (_remain < _len)
{
return(NeedMoreData(_len - _remain));
}
if ((LastTagRead.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.DoNotStorePixelDataInDataSet))
{
// Skip PixelData !!
if (_stream.CanSeek)
{
_stream.Seek((int)_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
_remain -= _len;
BytesRead += _len;
}
else if ((LastTagRead.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences))
{
var reference = new FileReference(StreamOpener, _stream.Position, _len, _endian, LastTagRead.VR);
if (_stream.CanSeek)
{
_stream.Seek((int)_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
DicomElement elem;
if (LastTagRead.VR.Equals(DicomVr.OWvr))
{
elem = new DicomElementOw(LastTagRead, reference);
}
else if (LastTagRead.VR.Equals(DicomVr.OBvr))
{
elem = new DicomElementOb(LastTagRead, reference);
}
else if (LastTagRead.VR.Equals(DicomVr.ODvr))
{
elem = new DicomElementOD(LastTagRead, reference);
}
else
{
elem = new DicomElementOf(LastTagRead, reference);
}
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomDataset ds = rec.Current;
ds[LastTagRead] = elem;
if (rec.Curlen != UndefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
Dataset[LastTagRead] = elem;
}
_remain -= _len;
BytesRead += _len;
}
else
{
ByteBuffer bb = new ByteBuffer(_len);
// If the tag is impacted by specific character set,
// set the encoding properly.
if (LastTagRead.VR.SpecificCharacterSet)
{
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
bb.SpecificCharacterSet = rec.Current.SpecificCharacterSet;
}
else
{
bb.SpecificCharacterSet = Dataset.SpecificCharacterSet;
}
}
if (LastTagRead.VR.Equals(DicomVr.UNvr) &&
!SaveTagRead.VR.Equals(DicomVr.UNvr) &&
!SaveTagRead.VR.Equals(DicomVr.SQvr) &&
Flags.IsSet(options, DicomReadOptions.UseDictionaryForExplicitUN))
{
LastTagRead = SaveTagRead;
bb.Endian = Endian.Little;
}
else
{
bb.Endian = _endian;
}
bb.CopyFrom(_stream, (int)_len);
DicomElement elem = LastTagRead.CreateDicomAttribute(bb);
_remain -= _len;
BytesRead += _len;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomDataset ds = rec.Current;
if (elem.Tag.TagValue == DicomTags.SpecificCharacterSet)
{
ds.SpecificCharacterSet = elem.ToString();
}
if (LastTagRead.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
{
ds[LastTagRead] = elem;
}
}
else
{
ds[LastTagRead] = elem;
}
if (rec.Curlen != UndefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
if (LastTagRead.TagValue == DicomTags.FileMetaInformationGroupLength)
{
// Save the end of the group 2 elements, so that we can automatically
// check and change our transfer syntax when needed.
_inGroup2 = true;
uint group2Len;
elem.TryGetUInt32(0, out group2Len);
_endGroup2 = BytesRead + group2Len;
}
else if (LastTagRead.TagValue == DicomTags.SpecificCharacterSet)
{
Dataset.SpecificCharacterSet = elem.ToString();
}
if (LastTagRead.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
{
Dataset[LastTagRead] = elem;
}
}
else
{
Dataset[LastTagRead] = elem;
}
}
}
}
}
}
LastTagRead = null;
_vr = null;
_len = UndefinedLength;
}
return(DicomReadStatus.Success);
}
catch (EndOfStreamException e)
{
// should never happen
LogAdapter.Logger.Error("Unexpected exception when reading file: {0}", e.ToString());
return(DicomReadStatus.UnknownError);
}
}
/// <summary>
/// Reads a DICOM file from a path
/// </summary>
/// <param name="filePath">the path to the file</param>
/// <param name="trySyntax">the transfer syntax to use in case there is no metadata explicitly included</param>
/// <returns>the DICOM Object</returns>
/// <example>
///<code>
///var dcm = DICOMObject.Read("mydcm.dcm");
///</code>
///</example>
public static DICOMObject Read(string filePath,
TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
return(DICOMFileReader.Read(filePath, trySyntax));
}
public MimeTypeProcessorOutput Process(ImageStreamingContext context)
{
Platform.CheckForNullReference(context, "context");
DicomPixelData pd = context.PixelData;
MimeTypeProcessorOutput output = new MimeTypeProcessorOutput();
int frame = context.FrameNumber;
if (context.FrameNumber < 0)
{
throw new WADOException(HttpStatusCode.BadRequest, String.Format("Requested FrameNumber {0} cannot be negative.", frame));
}
else if (frame >= pd.NumberOfFrames)
{
throw new WADOException(HttpStatusCode.BadRequest, String.Format("Requested FrameNumber {0} exceeds the number of frames in the image.", frame));
}
output.ContentType = OutputMimeType;
PixelDataLoader loader = new PixelDataLoader(context);
output.Output = loader.ReadFrame(frame);
output.IsLast = (pd.NumberOfFrames == frame + 1);
// note: the transfer syntax of the returned pixel data may not be the same as that in the original image.
// In the future, the clients may specify different transfer syntaxes which may mean the compressed image must be decompressed or vice versa.
TransferSyntax transferSyntax = pd.TransferSyntax;
output.IsCompressed = transferSyntax.LosslessCompressed || transferSyntax.LossyCompressed;
#region Special Code
// Note: this block of code inject special header fields to assist the clients handling the images
// For eg, the
if (output.IsLast)
{
context.Response.Headers.Add("IsLast", "true");
}
if (output.IsCompressed)
{
// Fields that can be used by the web clients to decompress the compressed images streamed by the server.
context.Response.Headers.Add("Compressed", "true");
context.Response.Headers.Add("TransferSyntaxUid", pd.TransferSyntax.UidString);
context.Response.Headers.Add("BitsAllocated", pd.BitsAllocated.ToString());
context.Response.Headers.Add("BitsStored", pd.BitsStored.ToString());
context.Response.Headers.Add("DerivationDescription", pd.DerivationDescription);
context.Response.Headers.Add("HighBit", pd.HighBit.ToString());
context.Response.Headers.Add("ImageHeight", pd.ImageHeight.ToString());
context.Response.Headers.Add("ImageWidth", pd.ImageWidth.ToString());
context.Response.Headers.Add("LossyImageCompression", pd.LossyImageCompression);
context.Response.Headers.Add("LossyImageCompressionMethod", pd.LossyImageCompressionMethod);
context.Response.Headers.Add("LossyImageCompressionRatio", pd.LossyImageCompressionRatio.ToString());
context.Response.Headers.Add("NumberOfFrames", pd.NumberOfFrames.ToString());
context.Response.Headers.Add("PhotometricInterpretation", pd.PhotometricInterpretation);
context.Response.Headers.Add("PixelRepresentation", pd.PixelRepresentation.ToString());
context.Response.Headers.Add("PlanarConfiguration", pd.PlanarConfiguration.ToString());
context.Response.Headers.Add("SamplesPerPixel", pd.SamplesPerPixel.ToString());
}
#endregion
if (Platform.IsLogLevelEnabled(LogLevel.Debug))
{
Platform.Log(LogLevel.Debug, "Streaming {0} pixel data: {1} x {2} x {3} , {4} bits [{5} KB] ({6})",
output.IsCompressed ? "compressed" : "uncompressed",
pd.ImageHeight,
pd.ImageWidth,
pd.SamplesPerPixel,
pd.BitsStored,
output.Output.Length / 1024,
pd.TransferSyntax.Name);
}
return(output);
}
public static void LosslessImageTestWithBitsAllocatedConversion(TransferSyntax syntax, DicomFile theFile)
{
if (File.Exists(theFile.Filename))
{
File.Delete(theFile.Filename);
}
DicomFile saveCopy = new DicomFile(theFile.Filename, theFile.MetaInfo.Copy(), theFile.DataSet.Copy());
theFile.ChangeTransferSyntax(syntax);
theFile.Save(DicomWriteOptions.ExplicitLengthSequence);
DicomFile newFile = new DicomFile(theFile.Filename);
newFile.Load(DicomReadOptions.Default);
newFile.ChangeTransferSyntax(saveCopy.TransferSyntax);
string failureDescription;
var newPd = DicomPixelData.CreateFrom(newFile);
var oldPd = DicomPixelData.CreateFrom(saveCopy);
bool result = Compare(newPd, oldPd, out failureDescription);
Assert.IsFalse(result, failureDescription);
Assert.IsFalse(newFile.DataSet.Equals(saveCopy.DataSet));
DicomAttributeCollection newDataSet = newFile.DataSet.Copy(true, true, true);
DicomAttributeCollection oldDataSet = theFile.DataSet.Copy(true, true, true);
oldDataSet.RemoveAttribute(DicomTags.BitsAllocated);
newDataSet.RemoveAttribute(DicomTags.BitsAllocated);
oldDataSet.RemoveAttribute(DicomTags.PixelData);
newDataSet.RemoveAttribute(DicomTags.PixelData);
var results = new List <DicomAttributeComparisonResult>();
bool check = oldDataSet.Equals(newDataSet, ref results);
Assert.IsTrue(check, results.Count > 0 ? CollectionUtils.FirstElement(results).Details : string.Empty);
for (int i = 0; i < oldPd.NumberOfFrames; i++)
{
var frame = oldPd.GetFrame(i);
var convertedFrame = DicomUncompressedPixelData.ToggleBitDepth(frame, frame.Length,
oldPd.UncompressedFrameSize,
oldPd.BitsStored, oldPd.BitsAllocated);
var newFrame = newPd.GetFrame(i);
int pixelsVarying = 0;
decimal totalVariation = 0.0m;
for (int j = 0; j < convertedFrame.Length; j++)
{
if (convertedFrame[j] != newFrame[j])
{
pixelsVarying++;
totalVariation += Math.Abs(convertedFrame[i] - newFrame[i]);
}
}
if (pixelsVarying > 0)
{
Assert.Fail(String.Format(
"Tag (7fe0,0010) Pixel Data: {0} of {1} pixels varying, average difference: {2}",
pixelsVarying, convertedFrame.Length, totalVariation / pixelsVarying));
}
}
}
/// <summary>
/// Do the restore.
/// </summary>
/// <param name="queueItem">The queue item to restore.</param>
public void Run(RestoreQueue queueItem)
{
using (var context = new RestoreProcessorContext(queueItem))
{
try
{
// Load up related classes.
using (IReadContext readContext = _hsmArchive.PersistentStore.OpenReadContext())
{
_archiveStudyStorage = ArchiveStudyStorage.Load(readContext, queueItem.ArchiveStudyStorageKey);
_serverSyntax = ServerTransferSyntax.Load(readContext, _archiveStudyStorage.ServerTransferSyntaxKey);
_syntax = TransferSyntax.GetTransferSyntax(_serverSyntax.Uid);
var parms = new StudyStorageLocationQueryParameters
{
StudyStorageKey = queueItem.StudyStorageKey
};
var broker = readContext.GetBroker <IQueryStudyStorageLocation>();
_location = broker.FindOne(parms);
if (_location == null)
{
_studyStorage = StudyStorage.Load(readContext, queueItem.StudyStorageKey);
if (_studyStorage == null)
{
DateTime scheduleTime = Platform.Time.AddMinutes(5);
Platform.Log(LogLevel.Error, "Unable to find storage location, rescheduling restore request to {0}",
scheduleTime);
queueItem.FailureDescription = "Unable to find storage location, rescheduling request.";
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Pending, scheduleTime);
return;
}
}
}
if (_location == null)
{
Platform.Log(LogLevel.Info, "Starting restore of nearline study: {0}",
_studyStorage.StudyInstanceUid);
// Get the zip file path from the xml data in the ArchiveStudyStorage entry
// Also store the "StudyFolder" for use below
string studyFolder;
string zipFile = GetZipFileName(out studyFolder);
// Do a test read of the zip file. If it succeeds, the file is available, if it
// fails, we just set back to pending and recheck.
if (!CanReadZip(zipFile, queueItem))
{
return;
}
RestoreNearlineStudy(queueItem, zipFile, studyFolder);
}
else
{
Platform.Log(LogLevel.Info, "Starting restore of online study: {0}", _location.StudyInstanceUid);
// Get the zip file path from the xml data in the ArchiveStudyStorage entry
// Also store the "StudyFolder" for use below
string studyFolder;
string zipFile = GetZipFileName(out studyFolder);
// Do a test read of the zip file. If it succeeds, the file is available, if it
// fails, we just set back to pending and recheck.
if (!CanReadZip(zipFile, queueItem))
{
return;
}
RestoreOnlineStudy(queueItem, zipFile, _location.GetStudyPath());
}
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception processing restore request for {0} on archive {1}",
_studyStorage == null ? (_location == null ? string.Empty : _location.StudyInstanceUid) : _studyStorage.StudyInstanceUid,
_hsmArchive.PartitionArchive.Description);
queueItem.FailureDescription = e.Message;
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
}
}
public static void ExpectedFailureTest(TransferSyntax syntax, DicomFile theFile)
{
try
{
theFile.ChangeTransferSyntax(syntax);
}
catch (DicomCodecUnsupportedSopException)
{
return;
}
Assert.IsTrue(false, "Unexpected successfull compression of object.");
}
public void ChangeTransferSyntax(TransferSyntax newTransferSyntax)
{
ChangeTransferSyntax(newTransferSyntax, null, null);
}
public void ChangeTransferSyntax(TransferSyntax newTransferSyntax, IDicomCodec inputCodec, DicomCodecParameters inputParameters)
{
IDicomCodec codec = inputCodec;
DicomCodecParameters parameters = inputParameters;
if (newTransferSyntax.Encapsulated && TransferSyntax.Encapsulated)
{
throw new DicomCodecException("Source and destination transfer syntaxes encapsulated");
}
if (newTransferSyntax.Encapsulated)
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(newTransferSyntax);
if (codec == null)
{
LogAdapter.Logger.Error("Unable to get registered codec for {0}", newTransferSyntax);
throw new DicomCodecException("No registered codec for: " + newTransferSyntax.Name);
}
}
if (parameters == null)
{
parameters = DicomCodecRegistry.GetCodecParameters(newTransferSyntax, DataSet);
}
DicomElement pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
{
throw new DicomCodecException("Sop pixel data has no valid value and cannot be compressed.");
}
new OverlayPlaneModuleIod(DataSet).ExtractEmbeddedOverlays();
var pd = new DicomUncompressedPixelData(DataSet);
using (var pixelStream = ((DicomElementBinary)pixelData).AsStream())
{
//Before compression, make the pixel data more "typical", so it's harder to mess up the codecs.
//NOTE: Could combine mask and align into one method so we're not iterating twice, but I prefer having the methods separate.
if (DicomUncompressedPixelData.RightAlign(pixelStream, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
var newHighBit = (ushort)(pd.HighBit - pd.LowBit);
LogAdapter.Logger.Warn("Right aligned pixel data (High Bit: {0}->{1}).", pd.HighBit, newHighBit);
pd.HighBit = newHighBit; //correct high bit after right-aligning.
DataSet[DicomTags.HighBit].SetUInt16(0, newHighBit);
}
if (DicomUncompressedPixelData.ZeroUnusedBits(pixelStream, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
LogAdapter.Logger.Warn("Zeroed some unused bits before compression.");
}
}
// Set transfer syntax before compression, the codecs need it.
var fragments = new DicomCompressedPixelData(pd)
{
TransferSyntax = newTransferSyntax
};
codec.Encode(pd, fragments, parameters);
fragments.UpdateMessage(this);
//TODO: should we validate the number of frames in the compressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
{
throw new DicomCodecException("Sop has no pixel data after compression.");
}
}
else
{
//A bit cheap, but check for basic image attributes - if any exist
// and are non-empty, there should probably be pixel data too.
DicomElement element;
if (DataSet.TryGetAttribute(DicomTags.Rows, out element) && !element.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
}
if (DataSet.TryGetAttribute(DicomTags.Columns, out element) && !element.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
}
TransferSyntax = newTransferSyntax;
}
}
else
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(TransferSyntax);
if (codec == null)
{
LogAdapter.Logger.Error("Unable to get registered codec for {0}", TransferSyntax);
throw new DicomCodecException("No registered codec for: " + TransferSyntax.Name);
}
if (parameters == null)
{
parameters = DicomCodecRegistry.GetCodecParameters(TransferSyntax, DataSet);
}
}
DicomElement pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
{
throw new DicomCodecException("Sop pixel data has no valid value and cannot be decompressed.");
}
var fragments = new DicomCompressedPixelData(DataSet);
var pd = new DicomUncompressedPixelData(fragments);
codec.Decode(fragments, pd, parameters);
pd.TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
pd.UpdateMessage(this);
//TODO: should we validate the number of frames in the decompressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
{
throw new DicomCodecException("Sop has no pixel data after decompression.");
}
}
else
{
//NOTE: doing this for consistency, really.
DicomElement element;
if (DataSet.TryGetAttribute(DicomTags.Rows, out element) && !element.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
}
if (DataSet.TryGetAttribute(DicomTags.Columns, out element) && !element.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
}
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
}
}
}
/// <summary>
/// Gets the <see cref="TransferSyntax"/>es of the available <see cref="IDicomCodecFactory"/> implementations.
/// </summary>
public static TransferSyntax[] GetCodecTransferSyntaxes()
{
TransferSyntax[] syntaxes = new TransferSyntax[_dictionary.Count];
_dictionary.Keys.CopyTo(syntaxes, 0);
return(syntaxes);
}
public StorageInstance(DicomMessage msg)
{
_sopClass = msg.SopClass;
_syntax = msg.TransferSyntax;
SopInstanceUid = msg.DataSet[DicomTags.SopInstanceUid].GetString(0, string.Empty);
StudyInstanceUid = msg.DataSet[DicomTags.StudyInstanceUid].GetString(0, string.Empty);
SeriesInstanceUid = msg.DataSet[DicomTags.SeriesInstanceUid].GetString(0, string.Empty);
PatientsName = msg.DataSet[DicomTags.PatientsName].GetString(0, string.Empty);
PatientId = msg.DataSet[DicomTags.PatientId].GetString(0, string.Empty);
_infoLoaded = true;
}
/// <summary>
/// Generates a concrete element class from the VR, tag, data and syntax. Also directs the appropriate data
/// interpretation.
/// </summary>
/// <param name="tag">the tag of the element to be generated</param>
/// <param name="vr">the VR of the element to be generated</param>
/// <param name="data">the raw data to be procesed (byte array)</param>
/// <param name="syntax">the transfer syntax by which to interepret the data</param>
/// <returns>a concrete DICOM element that uses the interface IDICOMElement</returns>
public static IDICOMElement GenerateElement(Tag tag, VR vr, object data, TransferSyntax syntax, StringEncoding enc)
{
//HANDLE NUMBERS
if (syntax == TransferSyntax.EXPLICIT_VR_BIG_ENDIAN)
{
switch (vr)
{
case VR.AttributeTag:
return(new AttributeTag(tag, BigEndianReader.ReadTag(data as byte[])));
case VR.FloatingPointDouble:
return(new FloatingPointDouble(tag, BigEndianReader.ReadDoublePrecision(data as byte[])));
case VR.FloatingPointSingle:
return(new FloatingPointSingle(tag, BigEndianReader.ReadSinglePrecision(data as byte[])));
case VR.SignedLong:
return(new SignedLong(tag, BigEndianReader.ReadSignedLong(data as byte[])));
case VR.SignedShort:
return(new SignedShort(tag, BigEndianReader.ReadSignedShort(data as byte[])));
case VR.UnsignedLong:
return(new UnsignedLong(tag, BigEndianReader.ReadUnsignedLong(data as byte[])));
case VR.UnsignedShort:
return(new UnsignedShort(tag, BigEndianReader.ReadUnsignedShort(data as byte[])));
}
}
else
{
switch (vr)
{
case VR.AttributeTag:
return(new AttributeTag(tag, LittleEndianReader.ReadTag(data as byte[])));
case VR.FloatingPointDouble:
return(new FloatingPointDouble(tag, LittleEndianReader.ReadDoublePrecision(data as byte[])));
case VR.FloatingPointSingle:
return(new FloatingPointSingle(tag, LittleEndianReader.ReadSinglePrecision(data as byte[])));
case VR.SignedLong:
return(new SignedLong(tag, LittleEndianReader.ReadSignedLong(data as byte[])));
case VR.SignedShort:
return(new SignedShort(tag, LittleEndianReader.ReadSignedShort(data as byte[])));
case VR.UnsignedLong:
return(new UnsignedLong(tag, LittleEndianReader.ReadUnsignedLong(data as byte[])));
case VR.UnsignedShort:
return(new UnsignedShort(tag, LittleEndianReader.ReadUnsignedShort(data as byte[])));
}
}
//HANDLE ALL OTHERS
switch (vr)
{
//HANDLE STRINGS
case VR.AgeString:
case VR.ApplicationEntity:
case VR.CodeString:
case VR.Date:
case VR.DateTime:
case VR.DecimalString:
case VR.IntegerString:
case VR.LongString:
case VR.LongText:
case VR.PersonName:
case VR.ShortString:
case VR.ShortText:
case VR.Time:
case VR.UnlimitedCharacter:
case VR.UnlimitedText:
case VR.UniversalResourceId:
case VR.UniqueIdentifier:
return(ReadString(vr, tag, data, enc));
//HANDLE BYTE DATA
case VR.Sequence:
return(new Sequence {
Tag = tag, Items = SequenceReader.ReadItems(data as byte[], syntax, enc)
});
case VR.OtherByteString:
return(new OtherByteString(tag, data as byte[]));
case VR.OtherFloatString:
return(new OtherFloatString(tag, data as byte[]));
case VR.OtherWordString:
return(new OtherWordString(tag, data as byte[]));
case VR.OtherDoubleString:
return(new OtherDoubleString(tag, data as byte[]));
case VR.OtherLongString:
return(new OtherLongString(tag, data as byte[]));
default:
var unk = new Unknown(tag, data as byte[]);
unk.TransferSyntax = syntax;
return(unk);
}
}
public DicomWriteStatus Write(TransferSyntax syntax, DicomAttributeCollection dataset, DicomWriteOptions options)
{
TransferSyntax = syntax;
foreach (DicomAttribute item in dataset)
{
if (item.IsEmpty)
continue;
if (item.Tag.Element == 0x0000)
continue;
if (Flags.IsSet(options, DicomWriteOptions.CalculateGroupLengths)
&& item.Tag.Group != _group)
{
_group = item.Tag.Group;
_writer.Write((ushort) _group);
_writer.Write((ushort) 0x0000);
if (_syntax.ExplicitVr)
{
_writer.Write((byte) 'U');
_writer.Write((byte) 'L');
_writer.Write((ushort) 4);
}
else
{
_writer.Write((uint) 4);
}
_writer.Write((uint) dataset.CalculateGroupWriteLength(_group, _syntax, options));
}
_writer.Write((ushort) item.Tag.Group);
_writer.Write((ushort) item.Tag.Element);
if (_syntax.ExplicitVr)
{
_writer.Write((byte) item.Tag.VR.Name[0]);
_writer.Write((byte) item.Tag.VR.Name[1]);
}
if (item is DicomAttributeSQ)
{
var sq = item as DicomAttributeSQ;
if (_syntax.ExplicitVr)
_writer.Write((ushort) 0x0000);
if (Flags.IsSet(options, DicomWriteOptions.DigitalSignatureMacEncoding))
{
// length field is not written when generating digital signature MAC
}
else if (Flags.IsSet(options, DicomWriteOptions.ExplicitLengthSequence))
{
int hl = _syntax.ExplicitVr ? 12 : 8;
_writer.Write((uint) sq.CalculateWriteLength(_syntax, options & ~DicomWriteOptions.CalculateGroupLengths) - (uint) hl);
}
else
{
_writer.Write((uint) _undefinedLength);
}
foreach (DicomSequenceItem ids in (DicomSequenceItem[]) sq.Values)
{
_writer.Write((ushort) DicomTag.Item.Group);
_writer.Write((ushort) DicomTag.Item.Element);
if (Flags.IsSet(options, DicomWriteOptions.DigitalSignatureMacEncoding))
{
// length field is not written when generating digital signature MAC
}
else if (Flags.IsSet(options, DicomWriteOptions.ExplicitLengthSequenceItem))
{
_writer.Write((uint) ids.CalculateWriteLength(_syntax, options & ~DicomWriteOptions.CalculateGroupLengths));
}
else
{
_writer.Write((uint) _undefinedLength);
}
Write(TransferSyntax, ids, options & ~DicomWriteOptions.CalculateGroupLengths);
if (!Flags.IsSet(options, DicomWriteOptions.ExplicitLengthSequenceItem)
&& !Flags.IsSet(options, DicomWriteOptions.DigitalSignatureMacEncoding))
{
_writer.Write((ushort) DicomTag.ItemDelimitationItem.Group);
_writer.Write((ushort) DicomTag.ItemDelimitationItem.Element);
_writer.Write((uint) 0x00000000);
}
}
if (Flags.IsSet(options, DicomWriteOptions.DigitalSignatureMacEncoding))
{
_writer.Write((ushort) DicomTag.SequenceDelimitationItem.Group);
_writer.Write((ushort) DicomTag.SequenceDelimitationItem.Element);
}
else if (!Flags.IsSet(options, DicomWriteOptions.ExplicitLengthSequence))
{
_writer.Write((ushort) DicomTag.SequenceDelimitationItem.Group);
_writer.Write((ushort) DicomTag.SequenceDelimitationItem.Element);
_writer.Write((uint) 0x00000000);
}
}
else if (item is DicomFragmentSequence)
{
var fs = item as DicomFragmentSequence;
if (_syntax.ExplicitVr)
_writer.Write((ushort) 0x0000);
if (Flags.IsSet(options, DicomWriteOptions.DigitalSignatureMacEncoding))
{
// length field is not written when generating digital signature MAC
}
else
{
_writer.Write((uint) _undefinedLength);
}
_writer.Write((ushort) DicomTag.Item.Group);
_writer.Write((ushort) DicomTag.Item.Element);
if (Flags.IsSet(options, DicomWriteOptions.DigitalSignatureMacEncoding))
{
// length field is not written when generating digital signature MAC
if (fs.HasOffsetTable) fs.OffsetTableBuffer.CopyTo(_writer);
}
else if (Flags.IsSet(options, DicomWriteOptions.WriteFragmentOffsetTable) && fs.HasOffsetTable)
{
_writer.Write((uint) fs.OffsetTableBuffer.Length);
fs.OffsetTableBuffer.CopyTo(_writer);
}
else
{
_writer.Write((uint) 0x00000000);
}
foreach (DicomFragment bb in fs.Fragments)
{
_writer.Write((ushort) DicomTag.Item.Group);
_writer.Write((ushort) DicomTag.Item.Element);
if (Flags.IsSet(options, DicomWriteOptions.DigitalSignatureMacEncoding))
{
// length field is not written when generating digital signature MAC
}
else
{
_writer.Write((uint) bb.Length);
}
bb.GetByteBuffer(_syntax).CopyTo(_writer);
}
if (Flags.IsSet(options, DicomWriteOptions.DigitalSignatureMacEncoding))
{
_writer.Write((ushort) DicomTag.SequenceDelimitationItem.Group);
_writer.Write((ushort) DicomTag.SequenceDelimitationItem.Element);
}
else
{
_writer.Write((ushort) DicomTag.SequenceDelimitationItem.Group);
_writer.Write((ushort) DicomTag.SequenceDelimitationItem.Element);
_writer.Write((uint) 0x00000000);
}
}
else
{
DicomAttribute de = item;
ByteBuffer theData = de.GetByteBuffer(_syntax, dataset.SpecificCharacterSet);
if (_syntax.ExplicitVr)
{
if (de.Tag.VR.Is16BitLengthField)
{
// #10890: Can't encode the value length if the length of the data exceeds max value for a 16-bit field
if (theData.Length > ushort.MaxValue - 1 /* must be even length so max allowed = 65534 */)
throw new DicomDataException(string.Format(
"Value for {0} exceeds maximum stream length allowed for a {1} VR attribute encoded using {2}",
de.Tag, de.Tag.VR, _syntax));
_writer.Write((ushort) theData.Length);
}
else
{
_writer.Write((ushort) 0x0000);
_writer.Write((uint) theData.Length);
}
}
else
{
_writer.Write((uint) theData.Length);
}
if (theData.Length > 0)
theData.CopyTo(_writer);
}
}
return DicomWriteStatus.Success;
}
internal override uint ParseData(SwappableBinaryReader br, ILogger logger, uint length, TransferSyntax transferSyntax)
{
if (length < 4)
{
data = 0;
br.ReadBytes((int)length);
}
else
{
data = br.ReadInt32();
if (length > 4)
{
br.ReadBytes((int)length - 4);
}
}
return(length);
}
public InstanceXml(XmlNode instanceNode, DicomAttributeCollection baseCollection)
{
InstanceXmlDicomAttributeCollection thisCollection = new InstanceXmlDicomAttributeCollection();
_collection = thisCollection;
_collection.ValidateVrValues = false;
_collection.ValidateVrLengths = false;
if (baseCollection != null)
{
AddExcludedTagsFromBase(baseCollection);
_baseCollectionEnumerator = baseCollection.GetEnumerator();
if (!_baseCollectionEnumerator.MoveNext())
{
_baseCollectionEnumerator = null;
}
}
if (!instanceNode.HasChildNodes)
{
return;
}
_instanceXmlEnumerator = instanceNode.ChildNodes.GetEnumerator();
if (!_instanceXmlEnumerator.MoveNext())
{
_instanceXmlEnumerator = null;
}
if (instanceNode.Attributes["UID"] != null)
{
_sopInstanceUid = instanceNode.Attributes["UID"].Value;
}
if (instanceNode.Attributes["SourceAETitle"] != null)
{
_sourceAETitle = XmlUnescapeString(instanceNode.Attributes["SourceAETitle"].Value);
}
if (instanceNode.Attributes["SopClassUID"] != null)
{
_sopClass = SopClass.GetSopClass(instanceNode.Attributes["SopClassUID"].Value);
}
_transferSyntax = instanceNode.Attributes["TransferSyntaxUID"] != null
? TransferSyntax.GetTransferSyntax(instanceNode.Attributes["TransferSyntaxUID"].Value)
: TransferSyntax.ExplicitVrLittleEndian;
if (instanceNode.Attributes["SourceFileName"] != null)
{
_sourceFileName = instanceNode.Attributes["SourceFileName"].Value;
}
if (instanceNode.Attributes["FileSize"] != null)
{
long.TryParse(instanceNode.Attributes["FileSize"].Value, out _fileSize);
}
// This should never happen
if (_sopClass == null)
{
_sopClass = SopClass.GetSopClass(Collection[DicomTags.SopClassUid].GetString(0, String.Empty));
}
}
/// <summary>
/// Reads a DICOM file from a path
/// </summary>
/// <param name="filePath">the path to the file</param>
/// <param name="trySyntax">the transfer syntax to use in case there is no metadata explicitly included</param>
/// <returns>the DICOM Object</returns>
/// <example>
///<code>
///var dcm = DICOMObject.Read("mydcm.dcm");
///</code>
///</example>
public static async Task <DICOMObject> ReadAsync(string filePath,
TransferSyntax trySyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN)
{
return(await DICOMFileReader.ReadAsync(filePath, trySyntax));
}
