private static void TestRightAlignSigned(byte[] testValues, int bitsStored, int highBit, sbyte[] expectedValues)
{
Assert.IsTrue(DicomUncompressedPixelData.ZeroUnusedBits(testValues, bitsStored, highBit));
Assert.IsTrue(DicomUncompressedPixelData.RightAlign(testValues, bitsStored, highBit));
Assert.AreEqual(expectedValues, DicomSignedToSigned(testValues, highBit - DicomPixelData.GetLowBit(bitsStored, highBit)));
}
public void TestRightAlign_BitsStored16_NoOp()
{
var testValues = new ushort[] { 65535, 32767 };
var expectedValues = (ushort[])testValues.Clone();
Assert.IsFalse(DicomUncompressedPixelData.RightAlign(expectedValues, 16, 15));
Assert.AreEqual(testValues, expectedValues);
}
public void TestRightAlign_BitsStored8_NoOp()
{
var testValues = new byte[] { 128, 255 };
var expectedValues = (byte[])testValues.Clone();
Assert.IsFalse(DicomUncompressedPixelData.RightAlign(expectedValues, 8, 7));
Assert.AreEqual(expectedValues, testValues);
}
public void TestRightAlign_BitsStored7_NoOp()
{
// 64, 127
// 0\1000000, 0\1111111
var testValues = new byte[] { 64, 127 };
var expectedValues = (byte[])testValues.Clone();
Assert.IsFalse(DicomUncompressedPixelData.RightAlign(testValues, 7, 6));
Assert.AreEqual(expectedValues, testValues);
}
public void TestRightAlign_BitsStored15_NoOp()
{
// Actual: 32767, 21845, 10922 (with extra bit at left=43690)
// Test: 0\111111111111111, 0\101010101010101, 1\010101010101010
// Expected: 32767, 21845, 10922
var testValues = new ushort[] { 32767, 21845, 43690 };
var expectedValues = new ushort[] { 32767, 21845, 10922 };
Assert.IsTrue(DicomUncompressedPixelData.ZeroUnusedBits(testValues, 15, 14));
Assert.IsFalse(DicomUncompressedPixelData.RightAlign(testValues, 16, 15));
Assert.AreEqual(expectedValues, testValues);
}
private void SetupEncapsulatedImageWithIconSequence(DicomFile file, bool encapsulateIconPixelData)
{
var codec = new NullDicomCodec();
DicomAttributeCollection dataSet = file.DataSet;
SetupSecondaryCapture(dataSet);
SetupMetaInfo(file);
file.TransferSyntax = TransferSyntax.ImplicitVrLittleEndian;
file.ChangeTransferSyntax(codec.CodecTransferSyntax);
// explicitly create the icon sequence as either encapsulated or native, so that we are not depending on correct behaviour elsewhere...
CreateIconImageSequence(dataSet);
if (encapsulateIconPixelData)
{
var dataset = ((DicomAttributeSQ)dataSet[DicomTags.IconImageSequence])[0];
var pixelData = dataset[DicomTags.PixelData];
var pd = new DicomUncompressedPixelData(dataset);
using (var pixelStream = ((DicomAttributeBinary)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);
pd.HighBit = newHighBit; //correct high bit after right-aligning.
dataset[DicomTags.HighBit].SetUInt16(0, newHighBit);
}
DicomUncompressedPixelData.ZeroUnusedBits(pixelStream, pd.BitsAllocated, pd.BitsStored, pd.HighBit);
}
// Set transfer syntax before compression, the codecs need it.
var fragments = new DicomCompressedPixelData(pd)
{
TransferSyntax = codec.CodecTransferSyntax
};
codec.Encode(pd, fragments, null);
fragments.UpdateAttributeCollection(dataset);
}
}
private static void TestRightAlign(ref ushort[] testValues, int bitsStored, int highBit, bool asBytes, bool asOpposingEndian)
{
if (!asBytes)
{
if (asOpposingEndian)
{
var opposingEndian = (ByteBuffer.LocalMachineEndian == Endian.Big) ? Endian.Little : Endian.Big;
ByteConverter.SwapBytes(testValues);
Assert.IsTrue(DicomUncompressedPixelData.ZeroUnusedBits(testValues, bitsStored, highBit, opposingEndian));
Assert.IsTrue(DicomUncompressedPixelData.RightAlign(testValues, bitsStored, highBit, opposingEndian));
ByteConverter.SwapBytes(testValues);
}
else
{
Assert.IsTrue(DicomUncompressedPixelData.ZeroUnusedBits(testValues, bitsStored, highBit));
Assert.IsTrue(DicomUncompressedPixelData.RightAlign(testValues, bitsStored, highBit));
}
}
else
{
if (asOpposingEndian)
{
ByteConverter.SwapBytes(testValues);
var testValuesBytes = ByteConverter.ToByteArray(testValues);
var opposingEndian = (ByteBuffer.LocalMachineEndian == Endian.Big) ? Endian.Little : Endian.Big;
Assert.IsTrue(DicomUncompressedPixelData.ZeroUnusedBits(testValuesBytes, 16, bitsStored, highBit, opposingEndian));
Assert.IsTrue(DicomUncompressedPixelData.RightAlign(testValuesBytes, 16, bitsStored, highBit, opposingEndian));
testValues = ByteConverter.ToUInt16Array(testValuesBytes);
ByteConverter.SwapBytes(testValues);
}
else
{
var testValuesBytes = ByteConverter.ToByteArray(testValues);
Assert.IsTrue(DicomUncompressedPixelData.ZeroUnusedBits(testValuesBytes, 16, bitsStored, highBit));
Assert.IsTrue(DicomUncompressedPixelData.RightAlign(testValuesBytes, 16, bitsStored, highBit));
testValues = ByteConverter.ToUInt16Array(testValuesBytes);
}
}
}
public static bool Compare(DicomPixelData pixels1, DicomPixelData pixels2, out string failureDescription)
{
failureDescription = string.Empty;
if (pixels1.BitsAllocated != pixels2.BitsAllocated)
{
failureDescription = String.Format("Tag (7fe0,0010) Pixel Data: Bits Allocated varies: {0} , {1}", pixels1.BitsAllocated, pixels2.BitsAllocated);
return(false);
}
if (pixels1.BitsStored != pixels2.BitsStored)
{
failureDescription = String.Format("Tag (7fe0,0010) Pixel Data: Bits Stored varies: {0} , {1}", pixels1.BitsStored, pixels2.BitsStored);
return(false);
}
if (pixels1.ImageHeight != pixels2.ImageHeight)
{
failureDescription = String.Format("Tag (7fe0,0010) Pixel Data: Rows varies: {0} , {1}", pixels1.ImageHeight, pixels2.ImageHeight);
return(false);
}
if (pixels1.ImageWidth != pixels2.ImageWidth)
{
failureDescription = String.Format("Tag (7fe0,0010) Pixel Data: Columns varies: {0} , {1}", pixels1.ImageWidth, pixels2.ImageWidth);
return(false);
}
if (pixels1.SamplesPerPixel != pixels2.SamplesPerPixel)
{
failureDescription = String.Format("Tag (7fe0,0010) Pixel Data: Samples per pixel varies: {0} , {1}", pixels1.SamplesPerPixel, pixels2.SamplesPerPixel);
return(false);
}
if (pixels1.NumberOfFrames != pixels2.NumberOfFrames)
{
failureDescription = String.Format("Tag (7fe0,0010) Pixel Data: Number of frames varies: {0} , {1}", pixels1.NumberOfFrames, pixels2.NumberOfFrames);
return(false);
}
long pixelsVarying = 0;
long totalVariation = 0;
int pixels = pixels1.ImageHeight * pixels1.ImageWidth * pixels1.SamplesPerPixel;
if (pixels1.BitsAllocated == 8)
{
for (int frame = 0; frame < pixels1.NumberOfFrames; frame++)
{
byte[] pixel1 = pixels1.GetFrame(frame);
byte[] pixel2 = pixels2.GetFrame(frame);
if (pixels1.HighBit != pixels2.HighBit)
{
// Justify the pixel, if needed
if (DicomUncompressedPixelData.RightAlign(pixel1, pixels1.BitsAllocated, pixels1.BitsStored,
pixels1.HighBit))
{
//pixels1.HighBit = (ushort)(pixels1.BitsStored - 1);
DicomUncompressedPixelData.ZeroUnusedBits(pixel1, pixels1.BitsAllocated, pixels1.BitsStored,
pixels1.BitsStored - 1);
}
if (DicomUncompressedPixelData.RightAlign(pixel2, pixels2.BitsAllocated, pixels2.BitsStored,
pixels2.HighBit))
{
//pixels2.HighBit = (ushort)(pixels2.BitsStored - 1);
DicomUncompressedPixelData.ZeroUnusedBits(pixel2, pixels2.BitsAllocated, pixels2.BitsStored,
pixels2.BitsStored - 1);
}
}
int[] intPixels1 = pixels1.IsSigned
? Convert8BitSigned(pixel1, pixels, (DicomUncompressedPixelData)pixels1)
: Convert8BitUnsigned(pixel1, pixels, (DicomUncompressedPixelData)pixels1);
int[] intPixels2 = pixels2.IsSigned
? Convert8BitSigned(pixel2, pixels, (DicomUncompressedPixelData)pixels2)
: Convert8BitUnsigned(pixel2, pixels, (DicomUncompressedPixelData)pixels2);
for (int i = 0; i < pixels; i++)
{
if (intPixels1[i] != intPixels2[i])
{
pixelsVarying++;
totalVariation += Math.Abs(intPixels1[i] - intPixels2[i]);
}
}
}
if (pixelsVarying > 0)
{
failureDescription = String.Format(
"Tag (7fe0,0010) Pixel Data: {0} of {1} pixels varying, average difference: {2}",
pixelsVarying, pixels * pixels1.NumberOfFrames, totalVariation / pixelsVarying);
return(false);
}
}
else
{
for (int frame = 0; frame < pixels1.NumberOfFrames; frame++)
{
byte[] pixel1 = pixels1.GetFrame(frame);
byte[] pixel2 = pixels2.GetFrame(frame);
if (pixels1.HighBit != pixels2.HighBit)
{
// Justify the pixel, if needed
if (DicomUncompressedPixelData.RightAlign(pixel1, pixels1.BitsAllocated, pixels1.BitsStored,
pixels1.HighBit))
{
//pixels1.HighBit = (ushort) (pixels1.BitsStored - 1);
DicomUncompressedPixelData.ZeroUnusedBits(pixel1, pixels1.BitsAllocated, pixels1.BitsStored,
pixels1.BitsStored - 1);
}
if (DicomUncompressedPixelData.RightAlign(pixel2, pixels2.BitsAllocated, pixels2.BitsStored,
pixels2.HighBit))
{
//pixels2.HighBit = (ushort)(pixels2.BitsStored - 1);
DicomUncompressedPixelData.ZeroUnusedBits(pixel2, pixels2.BitsAllocated, pixels2.BitsStored,
pixels2.BitsStored - 1);
}
}
int[] intPixels1 = pixels1.IsSigned
? Convert16BitSigned(pixel1, pixels, (DicomUncompressedPixelData)pixels1)
: Convert16BitUnsigned(pixel1, pixels, (DicomUncompressedPixelData)pixels1);
int[] intPixels2 = pixels2.IsSigned
? Convert16BitSigned(pixel2, pixels, (DicomUncompressedPixelData)pixels2)
: Convert16BitUnsigned(pixel2, pixels, (DicomUncompressedPixelData)pixels2);
for (int i = 0; i < pixels; i++)
{
if (intPixels1[i] != intPixels2[i])
{
pixelsVarying++;
totalVariation += Math.Abs(intPixels1[i] - intPixels2[i]);
}
}
}
if (pixelsVarying > 0)
{
failureDescription = String.Format("Tag (7fe0,0010) Pixel Data: {0} of {1} pixels varying, average difference: {2}", pixelsVarying, pixels, totalVariation / pixelsVarying);
return(false);
}
}
return(true);
}
private static void TestRightAlign(byte[] testValues, int bitsStored, int highBit, byte[] expectedValues)
{
Assert.IsTrue(DicomUncompressedPixelData.ZeroUnusedBits(testValues, bitsStored, highBit));
Assert.IsTrue(DicomUncompressedPixelData.RightAlign(testValues, bitsStored, highBit));
Assert.AreEqual(expectedValues, testValues); //Expected values in hex
}
public void Go()
{
string[] files = BuildFileList();
var args = new SelectFolderDialogCreationArgs
{
Path = GetDirectoryOfFirstPath(),
AllowCreateNewFolder = true,
Prompt = "Select output folder"
};
var result = base.Context.DesktopWindow.ShowSelectFolderDialogBox(args);
if (result.Action != DialogBoxAction.Ok)
{
return;
}
try
{
foreach (string file in files)
{
DicomFile dicomFile = new DicomFile(file);
dicomFile.Load();
if (dicomFile.TransferSyntax.Encapsulated)
{
continue;
}
DicomAttribute attribute;
if (!dicomFile.DataSet.TryGetAttribute(DicomTags.PixelData, out attribute))
{
continue;
}
new OverlayPlaneModuleIod(dicomFile.DataSet).ExtractEmbeddedOverlays();
var rawPixelData = (byte[])attribute.Values;
DicomPixelData pd = new DicomUncompressedPixelData(dicomFile);
if (DicomUncompressedPixelData.ZeroUnusedBits(rawPixelData, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
Platform.Log(LogLevel.Info, "Zeroed some unused bits.");
}
if (DicomUncompressedPixelData.RightAlign(rawPixelData, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
var newHighBit = (ushort)(pd.HighBit - pd.LowBit);
Platform.Log(LogLevel.Info, "Right aligned pixel data (High Bit: {0}->{1}).", pd.HighBit, newHighBit);
pd.HighBit = newHighBit; //correct high bit after right-aligning.
dicomFile.DataSet[DicomTags.HighBit].SetUInt16(0, newHighBit);
}
string sourceFileName = System.IO.Path.GetFileNameWithoutExtension(file);
string fileName = System.IO.Path.Combine(result.FileName, sourceFileName);
fileName += ".fixed-pixeldata.dcm";
dicomFile.Save(fileName);
}
}
catch (Exception e)
{
ExceptionHandler.Report(e, Context.DesktopWindow);
}
}
