private static DicomDataset Decode(
DicomDataset oldDataset,
DicomTransferSyntax outSyntax,
IDicomCodec codec,
DicomCodecParams parameters)
{
if (codec == null)
{
throw new DicomCodecException("Decoding dataset with transfer syntax: {0} is not supported.",
oldDataset.InternalTransferSyntax);
}
var oldPixelData = DicomPixelData.Create(oldDataset);
var newDataset = oldDataset.Clone();
newDataset.InternalTransferSyntax = outSyntax;
var newPixelData = DicomPixelData.Create(newDataset, true);
codec.Decode(oldPixelData, newPixelData, parameters);
ProcessOverlays(oldDataset, newDataset);
newDataset.RecalculateGroupLengths(false);
return(newDataset);
}
private static DicomDataset Decode(
DicomDataset oldDataset,
DicomTransferSyntax outSyntax,
IDicomCodec codec,
DicomCodecParams parameters)
{
if (codec == null)
{
throw new DicomCodecException("Decoding dataset with transfer syntax: {0} is not supported. See here to get help resolving the reason: https://github.com/fo-dicom/fo-dicom/wiki/Native-codecs-on-.NET",
oldDataset.InternalTransferSyntax);
}
var oldPixelData = DicomPixelData.Create(oldDataset);
var newDataset = oldDataset.Clone();
newDataset.InternalTransferSyntax = outSyntax;
var newPixelData = DicomPixelData.Create(newDataset, true);
codec.Decode(oldPixelData, newPixelData, parameters);
ProcessOverlays(oldDataset, newDataset);
newDataset.RecalculateGroupLengths(false);
return(newDataset);
}
static public unsafe void GetAverageValue(this DicomDataset original, IDicomCodec codec, out double average, out double dispersion, out ushort min, out ushort max)
{
DicomDataset dataset = new DicomDataset();
original.CopyTo(dataset);
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
DicomPixelData pixelDataSource = DicomPixelData.Create(original, false);
codec.Decode(pixelDataSource, pixelData, new DicomJpegParams {
});
GetAverageValue(dataset, out average, out dispersion, out min, out max);
}
private DicomDataset Decode(DicomDataset oldDataset, DicomTransferSyntax outSyntax, IDicomCodec codec, DicomCodecParams parameters)
{
DicomPixelData oldPixelData = DicomPixelData.Create(oldDataset, false);
DicomDataset newDataset = oldDataset.Clone();
newDataset.InternalTransferSyntax = outSyntax;
DicomPixelData newPixelData = DicomPixelData.Create(newDataset, true);
codec.Decode(oldPixelData, newPixelData, parameters);
return(newDataset);
}
static public DicomDataset Uncompress(this DicomDataset original, IDicomCodec codec)
{
DicomDataset dataset = new DicomDataset();
original.CopyTo(dataset);
DicomPixelData pixelData = DicomPixelData.Create(dataset, true);
DicomPixelData pixelDataSource = DicomPixelData.Create(original, false);
codec.Decode(pixelDataSource, pixelData, new DicomJpeg2000Params {
});
return(dataset);
}
private static DicomDataset Decode(
DicomDataset oldDataset,
DicomTransferSyntax outSyntax,
IDicomCodec codec,
DicomCodecParams parameters)
{
var oldPixelData = DicomPixelData.Create(oldDataset, false);
var newDataset = oldDataset.Clone();
newDataset.InternalTransferSyntax = outSyntax;
var newPixelData = DicomPixelData.Create(newDataset, true);
codec.Decode(oldPixelData, newPixelData, parameters);
ProcessOverlays(oldDataset, newDataset);
newDataset.RecalculateGroupLengths(false);
return(newDataset);
}
private DicomDataset Decode(DicomDataset oldDataset, DicomTransferSyntax outSyntax, IDicomCodec codec, DicomCodecParams parameters) {
DicomPixelData oldPixelData = DicomPixelData.Create(oldDataset, false);
DicomDataset newDataset = oldDataset.Clone();
newDataset.InternalTransferSyntax = outSyntax;
DicomPixelData newPixelData = DicomPixelData.Create(newDataset, true);
codec.Decode(oldPixelData, newPixelData, parameters);
ProcessOverlays(oldDataset, newDataset);
newDataset.RecalculateGroupLengths(false);
return newDataset;
}
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)
{
Platform.Log(LogLevel.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);
}
DicomAttribute 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);
var rawPixelData = (byte[])pixelData.Values;
//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(rawPixelData, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
var newHighBit = (ushort)(pd.HighBit - pd.LowBit);
Platform.Log(LogLevel.Debug, "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(rawPixelData, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
Platform.Log(LogLevel.Debug, "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.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.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 attribute) && !attribute.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)
{
Platform.Log(LogLevel.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);
}
}
DicomAttribute 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.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.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 attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
}
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
}
}
}
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)
{
Platform.Log(LogLevel.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);
}
DicomAttribute 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.");
}
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(DataSet);
DicomCompressedPixelData fragments = new DicomCompressedPixelData(pd);
// Set before compression, the codecs need it.
fragments.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.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.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 attribute) && !attribute.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)
{
Platform.Log(LogLevel.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);
}
}
DicomAttribute 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.");
}
DicomCompressedPixelData fragments = new DicomCompressedPixelData(DataSet);
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(fragments);
codec.Decode(fragments, pd, parameters);
pd.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.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.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 attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
}
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
}
}
}