/// <summary>
/// 将Dicom目录转化为NiFTI格式
/// </summary>
/// <param name="dicomPath">Dicom目录</param>
/// <returns>转化成功之后的.nii.gz文件</returns>
private string ConvetDicom2NiFTI(string dicomPath)
{
///TODO 吴昌霖继续完成
SimpleITK.ReadImage(dicomPath);
string niFTIFilePath = "";
return(niFTIFilePath);
/* private static string[] GetFile(String filepath)
* {
* string[] file = null;
* file = Directory.GetFiles(filepath);
* return file;
* }
* public static void Main(string[] args)
* {
* var vs = new VectorString();
* String[] dir = GetFile("C:/Users/dell/Desktop/d2n/T1");
* int time = 0;
* foreach (String fileName in dir)
* {
* if (fileName.EndsWith(".dcm"))
* {
* string str = dir.GetValue(time).ToString();
* vs.Add(str);
* Console.WriteLine(str + "已经添加");
* time++;
*
* }
* else {
* time++;
* }
* }
* time = 0; ;
* ImageSeriesReader isr = new ImageSeriesReader();
* isr.SetFileNames(vs);
* //String strr = vs.ToString();
* //Console.WriteLine(strr);
* Image img = SimpleITK.ReadImage(vs);
* //ImageSeriesWriter isw = new ImageSeriesWriter();
* // isw.SetFileNames(vs);
* //bool isTransport = isw.GetUseCompression();
* //Console.WriteLine(isTransport);
* //Console.ReadLine();
* ImageFileWriter isw = new ImageFileWriter();
* //
* isw.SetFileName("C:/Users/dell/Desktop/d2n/dcm2nii.nii.gz");
* isw.Execute(img);
*
* }
* }
* } */
}
private Color[] LoadNIFTIFile()
{
Color[] colors;
Image input = SimpleITK.ReadImage("/home/josher/Dropbox/UnityResources/2016.11.29.Brain.Tumor.in.Unity3D/Data/MRI_After_Surgery/AX_T1_3D_MPRAGE_NAVIGATION.nii.gz");
MinimumMaximumImageFilter filter = new MinimumMaximumImageFilter();
filter.Execute(input);
uint max = (uint)filter.GetMaximum();
uint min = (uint)filter.GetMinimum();
size[0] = input.GetWidth();
size[1] = input.GetHeight();
size[2] = input.GetDepth();
size2p [0] = ClosestPowOfTwo(size [0]);
size2p [1] = ClosestPowOfTwo(size [1]);
size2p [2] = ClosestPowOfTwo(size [2]);
//data = new float[size [0], size [1], size [2]];
colors = new Color[size2p[0] * size2p[1] * size2p[2]];
Color color = Color.black;
for (uint x = 0; x < size2p[0]; x++)
{
for (uint y = 0; y < size2p[1]; y++)
{
for (uint z = 0; z < size2p[2]; z++)
{
float temp = (float)input.GetPixelAsInt16(new VectorUInt32(new uint[] { x *size[0] / size2p[0], y *size[1] / size2p[1], z *size[2] / size2p[2] }));
// if(temp ==-1.0f) {
// temp=1100.0f;
// }
//data [x, y, z] = (temp-min)/(max-min);
color.a = (temp - min) / (max - min);
colors[x + y * size2p[0] + z * size2p[0] * size2p[1]] = color;
}
}
}
return(colors);
}
public static int[] fGetDatasetLength()
{
Class.manageImg managerView = HttpContext.Current.Session["managerView"] as Class.manageImg;
String sPath = managerView.sCurrentImageFolder[0];
String[] sFilenames;
if (sPath == null)
{
throw new ArgumentException("path variable in manageImg is not specified!");
}
else
{
sFilenames = (System.IO.Directory.EnumerateFiles(sPath, "*.*", SearchOption.AllDirectories).Where(s => Constant.lsExtensions.Any(e => s.EndsWith(e)))).ToArray();
int[] iSize = new int[] { 0, 0, 0 };
// get dataset length and set hiddenfield
itk.simple.Image itkImage = SimpleITK.ReadImage(sFilenames[0]); // Es wird nur das erste Listenelement ausgelesen?
VectorUInt32 UInt32Size = itkImage.GetSize();
iSize[0] = unchecked ((int)UInt32Size[0]);
iSize[1] = unchecked ((int)UInt32Size[1]);
iSize[2] = unchecked ((int)UInt32Size[2]);
return(iSize);
}
}
static void Main(string[] args)
{
if (args.Length < 8)
{
Console.WriteLine("Missing Parameters ");
Console.WriteLine("Usage: " + System.AppDomain.CurrentDomain.FriendlyName +
"inputImage initialModel outputImage cannyThreshold " +
"cannyVariance advectionWeight initialModelIsovalue maximumIterations ");
return;
}
string inputFilename = args[0];
string initialModelFilename = args[1];
string outputFilename = args[2];
double cannyThreshold = double.Parse(args[3], CultureInfo.InvariantCulture);
double cannyVariance = double.Parse(args[4], CultureInfo.InvariantCulture);
double advectionWeight = double.Parse(args[5], CultureInfo.InvariantCulture);
double intialModelIsovalue = double.Parse(args[6], CultureInfo.InvariantCulture);
uint maxIterations = uint.Parse(args[7], CultureInfo.InvariantCulture);
// Read input image
SitkImage inputImage = SimpleITK.ReadImage(inputFilename, PixelId.sitkFloat32);
SitkImage initialModel = SimpleITK.ReadImage(initialModelFilename, PixelId.sitkFloat32);
// The input image will be processed with a few iterations of
// feature-preserving diffusion. We create a filter and set the
// appropriate parameters.
GradientAnisotropicDiffusionImageFilter diffusion = new GradientAnisotropicDiffusionImageFilter();
diffusion.SetConductanceParameter(1.0);
diffusion.SetTimeStep(0.125);
diffusion.SetNumberOfIterations(5);
SitkImage diffusedImage = diffusion.Execute(inputImage);
// As with the other ITK level set segmentation filters, the terms of the
// CannySegmentationLevelSetImageFilter level set equation can be
// weighted by scalars. For this application we will modify the relative
// weight of the advection term. The propagation and curvature term weights
// are set to their defaults of 0 and 1, respectively.
CannySegmentationLevelSetImageFilter cannySegmentation = new CannySegmentationLevelSetImageFilter();
cannySegmentation.SetAdvectionScaling(advectionWeight);
cannySegmentation.SetCurvatureScaling(1.0);
cannySegmentation.SetPropagationScaling(0.0);
// The maximum number of iterations is specified from the command line.
// It may not be desirable in some applications to run the filter to
// convergence. Only a few iterations may be required.
cannySegmentation.SetMaximumRMSError(0.01);
cannySegmentation.SetNumberOfIterations(maxIterations);
// There are two important parameters in the
// CannySegmentationLevelSetImageFilter to control the behavior of the
// Canny edge detection. The variance parameter controls the
// amount of Gaussian smoothing on the input image. The threshold
// parameter indicates the lowest allowed value in the output image.
// Thresholding is used to suppress Canny edges whose gradient magnitudes
// fall below a certain value.
cannySegmentation.SetThreshold(cannyThreshold);
cannySegmentation.SetVariance(cannyVariance);
// Finally, it is very important to specify the isovalue of the surface in
// the initial model input image. In a binary image, for example, the
// isosurface is found midway between the foreground and background values.
cannySegmentation.SetIsoSurfaceValue(intialModelIsovalue);
SitkImage output = cannySegmentation.Execute(initialModel, diffusedImage);
BinaryThresholdImageFilter thresholder = new BinaryThresholdImageFilter();
thresholder.SetUpperThreshold(10.0);
thresholder.SetLowerThreshold(0.0);
thresholder.SetOutsideValue(0);
thresholder.SetInsideValue(255);
output = thresholder.Execute(output);
output = SimpleITK.Cast(output, PixelIDValueEnum.sitkUInt8);
SimpleITK.WriteImage(output, outputFilename);
// Print out some useful information
Console.WriteLine("");
Console.WriteLine("Max. no. iterations: {0}", cannySegmentation.GetNumberOfIterations());
Console.WriteLine("Max. RMS error: {0}", cannySegmentation.GetMaximumRMSError());
Console.WriteLine("");
Console.WriteLine("No. elpased iterations: {0}", cannySegmentation.GetElapsedIterations());
Console.WriteLine("RMS change: {0}", cannySegmentation.GetRMSChange());
}
/*! Constructor, fills most of the attributes of the DICOMSeries class.
* \note This does some heavy file/directory parsing to determine the files which are part of
* this series and their order. This is why the DICOMSeries should be constructed in a
* background thread and then passed to the main thread. */
public DICOMSeries(string directory, string seriesUID)
{
// Get the file names for the series:
filenames = ImageSeriesReader.GetGDCMSeriesFileNames(directory, seriesUID);
if (filenames.Count <= 0)
{
throw(new System.Exception("No files found for series " + seriesUID + "."));
}
this.seriesUID = seriesUID;
// Load the first slice in volume to get meta information:
firstSlice = SimpleITK.ReadImage(filenames[0]);
VectorDouble o1 = firstSlice.GetOrigin();
if (o1.Count < 3)
{
throw(new System.Exception("Invalid origins found in first image."));
}
origin = new Vector3((float)o1 [0], (float)o1 [1], (float)o1 [2]);
numberOfSlices = filenames.Count;
// Offset between two adjacent slices. If only one slice is present,
// this defaults to zero.
Vector3 sliceOffset = Vector3.zero;
// If we have more than one slice, also load the last slice to be able to determine the slice spacing:
if (filenames.Count > 1)
{
lastSlice = SimpleITK.ReadImage(filenames[filenames.Count - 1]);
// Get the origins of the two images:
VectorDouble o2 = lastSlice.GetOrigin();
if (o2.Count < 3)
{
throw(new System.Exception("Invalid origins found in last image."));
}
Vector3 lastOrigin = new Vector3((float)o2 [0], (float)o2 [1], (float)o2 [2]);
// Calculate offset between two adjacent slices (assuming all neighbours are the same distance apart):
// Note: I expect sliceOffset.x and sliceOffset.y to be zero most of the time.
// Using a Vector just for completeness.
sliceOffset = (lastOrigin - origin) / (filenames.Count - 1);
}
// Load the direction cosines:
// ITK stores the direction cosines in a matrix with row-major-ordering. The weird indexing is because
// we need the first and second column (0,3,6 for X and 1,4,7 for Y)
VectorDouble direction = firstSlice.GetDirection();
if (direction.Count < 6)
{
throw(new System.Exception("Invalid direction cosines found in images."));
}
directionCosineX = new Vector3((float)direction [0], (float)direction [3], (float)direction [6]);
directionCosineY = new Vector3((float)direction [1], (float)direction [4], (float)direction [7]);
sliceNormal = Vector3.Cross(directionCosineX, directionCosineY);
// Calculate the which direction the normal is facing to determine the orienation (Transverse,
// Coronal or Saggital).
float absX = Mathf.Abs(sliceNormal.x);
float absY = Mathf.Abs(sliceNormal.y);
float absZ = Mathf.Abs(sliceNormal.z);
if (absX > absY && absX > absZ)
{
sliceOrientation = SliceOrientation.Saggital;
}
else if (absY > absX && absY > absZ)
{
sliceOrientation = SliceOrientation.Coronal;
}
else if (absZ > absX && absZ > absY)
{
sliceOrientation = SliceOrientation.Transverse;
}
else
{
sliceOrientation = SliceOrientation.Unknown;
}
// Load the direction cosines:
// NOTE: It seems that the the first value is the spacing between rows (i.e. y direction),
// the second value is the spacing between columns (i.e. x direction).
// I was not able to verify this so far, since all test dicoms we had have the same spacing in
// x and y direction...
VectorDouble spacing = firstSlice.GetSpacing();
if (spacing.Count < 2)
{
throw(new System.Exception("Invalid pixel spacing found in images."));
}
pixelSpacing = new Vector2((float)spacing [1], (float)spacing [0]);
// Set up the transformation matrix:
Matrix4x4 transformMatrix = new Matrix4x4();
// Column 1:
transformMatrix [0, 0] = directionCosineX.x * pixelSpacing.x;
transformMatrix [1, 0] = directionCosineX.y * pixelSpacing.x;
transformMatrix [2, 0] = directionCosineX.z * pixelSpacing.x;
transformMatrix [3, 0] = 0f;
// Column 2:
transformMatrix [0, 1] = directionCosineY.x * pixelSpacing.y;
transformMatrix [1, 1] = directionCosineY.y * pixelSpacing.y;
transformMatrix [2, 1] = directionCosineY.z * pixelSpacing.y;
transformMatrix [3, 1] = 0f;
// Column 3:
transformMatrix [0, 2] = sliceOffset.x;
transformMatrix [1, 2] = sliceOffset.y;
transformMatrix [2, 2] = sliceOffset.z;
transformMatrix [3, 2] = 0f;
// Column 4:
transformMatrix [0, 3] = origin.x;
transformMatrix [1, 3] = origin.y;
transformMatrix [2, 3] = origin.z;
transformMatrix [3, 3] = 1f;
// Convert to a the left-hand-side coordinate system which Unity uses:
Matrix4x4 rightHandToLeftHand = new Matrix4x4();
rightHandToLeftHand [0, 0] = 1f;
rightHandToLeftHand [1, 1] = 1f;
rightHandToLeftHand [2, 2] = -1f;
rightHandToLeftHand [3, 3] = 1f;
pixelToPatient = rightHandToLeftHand * transformMatrix;
// Inverse transformation:
patientToPixel = pixelToPatient.inverse;
// Read the minimum and maximum values which are stored in this image:
minPixelValue = UInt16.MinValue;
maxPixelValue = UInt16.MaxValue;
foundMinMaxPixelValues = false;
try {
minPixelValue = Int32.Parse(firstSlice.GetMetaData("0028|0106"));
maxPixelValue = Int32.Parse(firstSlice.GetMetaData("0028|0107"));
foundMinMaxPixelValues = true;
} catch {
}
}
public void ProcessRequest(HttpContext context)
{
// image ID, brightness and contrast value
Int32 iID, iBVal, iRot, iNoFiles;
Double dCVal;
String sPath;
// response type
context.Response.ContentType = "image/png";
// get and convert image parameters
if (context.Request.QueryString["NqC3ke"] != null) // ID
{
iID = Convert.ToInt32(context.Request.QueryString["NqC3ke"]);
}
else
{
throw new ArgumentException("No image id specified");
}
if (context.Request.QueryString["tXt9X3"] != null) // brightness
{
iBVal = Convert.ToInt32(context.Request.QueryString["tXt9X3"]);
}
else
{
throw new ArgumentException("No image brightness specified");
}
if (context.Request.QueryString["XwjRGm"] != null) // contrast
{
dCVal = Convert.ToDouble(context.Request.QueryString["XwjRGm"]);
}
else
{
throw new ArgumentException("No image contrast specified");
}
if (context.Request.QueryString["WkYTCe"] != null) // path
{
string obscuredPath = Convert.ToString(context.Request.QueryString["WkYTCe"]);
string unobscuredPath = "";
// old obfuscation
//for (int z = 0; z < obscuredPath.Length; z++)
//{
// int add = Constant.ceasarOdd;
// if (z % 2 == 0)
// {
// add = Constant.ceasarEven;
// }
// char c = (char)(obscuredPath[z] - add);
// unobscuredPath += c.ToString();
//}
// new obfuscation
string allowedChars = Constant.allowedCharacters;
for (int p = 0; p < obscuredPath.Length; p++)
{
for (int c = 0; c < allowedChars.Length; c++)
{
if (obscuredPath[p] == allowedChars[c])
{ // character is allowed
int add = Constant.ceasarOdd;
if (p % 2 == 0)
{
add = Constant.ceasarEven;
}
// remove unneccessary loops
add = add % (allowedChars.Length - 1);
int shift = c - add;
if (shift > (allowedChars.Length - 1))
{
shift = shift - (allowedChars.Length - 1);
}
else if ((shift) < 0)
{
shift = shift + (allowedChars.Length - 1);
}
char character = allowedChars[shift];
unobscuredPath += character.ToString();
break;
}
}
}
//Debug.Print("deobfuscation\t\t" + obscuredPath + " -> " + unobscuredPath);
sPath = unobscuredPath;
}
else
{
sPath = "";
}
if (context.Request.QueryString["Hsfke2"] != null) // rotate
{
iRot = Convert.ToInt32(context.Request.QueryString["Hsfke2"]);
}
else
{
iRot = 0;
}
if (context.Request.QueryString["yAR8st"] != null) // length
{
iNoFiles = Convert.ToInt32(context.Request.QueryString["yAR8st"]);
}
else
{
iNoFiles = 1;
}
// load image in byte array "bmVal"
//var bOld = false;
byte[] bmVal;
int iWidth;
int iHeight;
int iDepth;
itk.simple.Image itkImage;
if (!File.Exists(sPath))
{
// file was not found
}
try
{
itkImage = SimpleITK.ReadImage(sPath, PixelIDValueEnum.sitkFloat32);
}
catch (System.StackOverflowException)
{
itk.simple.ImageFileReader reader = new itk.simple.ImageFileReader();
reader.SetFileName(sPath);
itkImage = reader.Execute();
}
// get image direction
var iDir = itkImage.GetDirection();
// get spacing
VectorDouble dSpacing = itkImage.GetSpacing();
// get size and number of dimension
VectorUInt32 iSize = itkImage.GetSize();
int len = 1;
for (int iDim = 0; iDim < itkImage.GetDimension(); iDim++)
{
len *= (int)iSize[iDim];
}
iWidth = unchecked ((int)iSize[0]);
iHeight = unchecked ((int)iSize[1]);
iDepth = unchecked ((int)iSize[2]);
// convert mm->dpi
float fResolutionX = System.Convert.ToSingle(System.Convert.ToDouble(iWidth) * 25.4 / dSpacing[0]);
float fResolutionY = System.Convert.ToSingle(System.Convert.ToDouble(iHeight) * 25.4 / dSpacing[1]);
// 2D image size
int iLength = iWidth * iHeight;
// copy buffer to new array
IntPtr ipBuffer = itkImage.GetBufferAsFloat();
float[] fArray = new float[iLength];
// no negative indices
if (iID < 0)
{
iID = 0;
}
// multiple DICOM files
int iOffset = 0;
if (iNoFiles > 1)
{
if (iID >= (iNoFiles - 1))
{
iID = iNoFiles - 1;
}
iOffset = 0;
}
else if (iNoFiles == 1)
{
// one DICOM file
if (iDepth == 1)
{
iID = 1;
iOffset = 0;
}
// one 3D MHD file
else if (iDepth > 1)
{
if (iID > (iDepth - 1))
{
iID = iDepth - 1;
}
iOffset = (iID - 1) * iLength;
}
}
// new pointer to data (due to offset)
Marshal.Copy(new IntPtr(ipBuffer.ToInt64() + sizeof(float) * iOffset), fArray, 0, iLength);
// convert floating point to 8 bit integer values - range:0 - 255
float fMax = fArray.Max();
float fMin = fArray.Min();
bmVal = new byte[iWidth * iHeight];
for (int iI = 0; iI < iLength; iI++)
{
var tmp = (float)(((fArray[iI] - fMin) / (fMax - fMin) * 255) + iBVal) * (float)dCVal;
if (tmp > 255)
{
tmp = 255;
}
if (tmp < 0)
{
tmp = 0;
}
bmVal[iI] = (byte)tmp;
}
Bitmap bmOutput = fCreateBitmap(bmVal, new int[] { iWidth, iHeight }, new float[] { fResolutionX, fResolutionY });
// rotate image and flip in X direction due to different image orientation convention
// corrects *.mhd orientation
List <String> lsExtensions = new List <String> {
".mhd", ".MHD"
};
foreach (var ext in lsExtensions)
{
if (sPath.EndsWith(ext))
{ // *.mhd files have a different orientation (compared to *.ima)
bmOutput.RotateFlip(RotateFlipType.Rotate90FlipNone);
}
}
switch (iRot)
{
case 0:
bmOutput.RotateFlip(RotateFlipType.RotateNoneFlipX);
break;
case 90:
bmOutput.RotateFlip(RotateFlipType.Rotate90FlipX);
break;
case 180:
bmOutput.RotateFlip(RotateFlipType.Rotate180FlipX);
break;
case 270:
bmOutput.RotateFlip(RotateFlipType.Rotate270FlipX);
break;
default:
break;
}
// save new image to response stream
bmOutput.Save(context.Response.OutputStream, ImageFormat.Png);
bmOutput.Dispose();
}
// Use this for initialization
void Start()
{
Image input = SimpleITK.ReadImage("/home/josher/UnityProjects/Read_Niftis/Assets/Ax_SWI.nii.gz");
}
/*! Loads a single file and creates an array of colors from the pixels.
* The array of colors can later be used to generate a texture, see getTexture2D() */
private void loadImageData(int slice)
{
VectorString fileNames = seriesInfo.filenames;
// Read the DICOM image:
Image image = SimpleITK.ReadImage(fileNames[slice]);
origTexWidth = (int)image.GetWidth();
origTexHeight = (int)image.GetHeight();
//int origTexDepth = (int)image.GetDepth ();
texWidth = Mathf.NextPowerOfTwo((int)image.GetWidth());
texHeight = Mathf.NextPowerOfTwo((int)image.GetHeight());
texDepth = 1;
colors = new Color32[texWidth * texHeight];
int intercept = 0;
int slope = 1;
try {
intercept = Int32.Parse(image.GetMetaData("0028|1052"));
slope = Int32.Parse(image.GetMetaData("0028|1053"));
} catch {
}
if (image.GetDimension() != 2 && image.GetDimension() != 3)
{
throw(new System.Exception("Only 2D and 3D images are currently supported. Dimensions of image: " + image.GetDimension()));
}
Int64 min = int.MaxValue;
Int64 max = int.MinValue;
// Copy the image into a colors array:
IntPtr bufferPtr;
UInt32 numberOfPixels = image.GetWidth() * image.GetHeight();
if (image.GetPixelID() == PixelIDValueEnum.sitkUInt16)
{
bufferPtr = image.GetBufferAsUInt16();
Int16[] colorsTmp = new Int16[numberOfPixels];
Marshal.Copy(bufferPtr, colorsTmp, 0, (int)numberOfPixels);
int index = 0;
//for (UInt32 z = 0; z < texDepth; z++) {
for (UInt32 y = 0; y < texHeight; y++)
{
for (UInt32 x = 0; x < texWidth; x++)
{
if (x < origTexWidth && y < origTexHeight) // && z < origTexDepth )
{
UInt16 pixelValue = (UInt16)((colorsTmp [index] - intercept) / slope);
colors [x + y * texWidth] = F2C(pixelValue);
if (pixelValue > max)
{
max = pixelValue;
}
if (pixelValue < min)
{
min = pixelValue;
}
index++;
}
}
}
}
else if (image.GetPixelID() == PixelIDValueEnum.sitkInt16)
{
bufferPtr = image.GetBufferAsInt16();
Int16[] colorsTmp = new Int16[numberOfPixels];
Marshal.Copy(bufferPtr, colorsTmp, 0, (int)numberOfPixels);
int index = 0;
//for (UInt32 z = 0; z < texDepth; z++) {
for (UInt32 y = 0; y < texHeight; y++)
{
for (UInt32 x = 0; x < texWidth; x++)
{
if (x < origTexWidth && y < origTexHeight) // && z < origTexDepth )
{
UInt16 pixelValue = (UInt16)((colorsTmp [index] - intercept) / slope);
colors [x + y * texWidth] = F2C(pixelValue);
if (pixelValue > max)
{
max = pixelValue;
}
if (pixelValue < min)
{
min = pixelValue;
}
index++;
}
}
}
}
else if (image.GetPixelID() == PixelIDValueEnum.sitkInt32)
{
bufferPtr = image.GetBufferAsInt32();
Int32[] colorsTmp = new Int32[numberOfPixels];
Marshal.Copy(bufferPtr, colorsTmp, 0, (int)numberOfPixels);
int index = 0;
//for (UInt32 z = 0; z < texDepth; z++) {
for (UInt32 y = 0; y < texHeight; y++)
{
for (UInt32 x = 0; x < texWidth; x++)
{
if (x < origTexWidth && y < origTexHeight) // && z < origTexDepth )
{
UInt32 pixelValue = (UInt32)((colorsTmp [index] - intercept) / slope);
colors [x + y * texWidth] = F2C(pixelValue);
if (pixelValue > max)
{
max = (Int64)pixelValue;
}
if (pixelValue < min)
{
min = (Int64)pixelValue;
}
index++;
}
}
}
}
else
{
throw(new System.Exception("Unsupported pixel format: " + image.GetPixelID()));
}
// If the DICOM header did not contain info about the minimum/maximum values and no one
// has manually set them yet, set the min/max values found for this slice:
if (!seriesInfo.foundMinMaxPixelValues)
{
seriesInfo.setMinMaxPixelValues((int)min, (int)max);
}
// Make the loaded image accessable from elsewhere:
this.image = image;
}
static void Main(string[] args)
{
if (args.Length < 9)
{
Console.WriteLine("Missing Parameters ");
Console.WriteLine("Usage: " + System.AppDomain.CurrentDomain.FriendlyName +
" inputImage outputImage seedX seedY " +
" Sigma SigmoidAlpha SigmoidBeta TimeThreshold");
return;
}
string inputFilename = args[0];
string outputFilename = args[1];
uint[] seedPosition = { Convert.ToUInt32(args[2]), Convert.ToUInt32(args[3]), 0 };
double sigma = double.Parse(args[4], CultureInfo.InvariantCulture);
double alpha = double.Parse(args[5], CultureInfo.InvariantCulture);;
double beta = double.Parse(args[6], CultureInfo.InvariantCulture);
double timeThreshold = double.Parse(args[7], CultureInfo.InvariantCulture);
double stoppingTime = double.Parse(args[8], CultureInfo.InvariantCulture);
// Read input image
SitkImage inputImage = SimpleITK.ReadImage(inputFilename, PixelIDValueEnum.sitkFloat32);
// The input image will be processed with a few iterations of
// feature-preserving diffusion. We create a filter and set the
// appropriate parameters.
CurvatureAnisotropicDiffusionImageFilter smoothing = new CurvatureAnisotropicDiffusionImageFilter();
smoothing.SetTimeStep(0.125);
smoothing.SetNumberOfIterations(5);
smoothing.SetConductanceParameter(9.0);
SitkImage smoothingOutput = smoothing.Execute(inputImage);
SitkImage gradientMagnitudeOutput = SimpleITK.GradientMagnitudeRecursiveGaussian(smoothingOutput, sigma);
SitkImage sigmoidOutput = SimpleITK.Sigmoid(gradientMagnitudeOutput, alpha, beta, 1.0, 0.0);
FastMarchingImageFilter fastMarching = new FastMarchingImageFilter();
//VectorUIntList trialPoints; Add trialPoints into list if using multiple seeds. Here we only use one seedpoint
VectorUInt32 trialPoint = new VectorUInt32(3);
trialPoint.Add(seedPosition[0]);
trialPoint.Add(seedPosition[1]);
trialPoint.Add(seedPosition[2]);
fastMarching.AddTrialPoint(trialPoint);
// Since the front representing the contour will propagate continuously
// over time, it is desirable to stop the process once a certain time has
// been reached. This allows us to save computation time under the
// assumption that the region of interest has already been computed. The
// value for stopping the process is defined with the method
// SetStoppingValue(). In principle, the stopping value should be a
// little bit higher than the threshold value.
fastMarching.SetStoppingValue(stoppingTime);
SitkImage fastmarchingOutput = fastMarching.Execute(sigmoidOutput);
BinaryThresholdImageFilter thresholder = new BinaryThresholdImageFilter();
thresholder.SetLowerThreshold(0.0);
thresholder.SetUpperThreshold(timeThreshold);
thresholder.SetOutsideValue(0);
thresholder.SetInsideValue(255);
SitkImage result = thresholder.Execute(fastmarchingOutput);
SimpleITK.WriteImage(result, outputFilename);
}
public DICOM2D(DICOMSeries seriesInfo, int slice) : base(seriesInfo)
{
dimensions = 2;
slice = Mathf.Clamp(slice, 0, seriesInfo.filenames.Count - 1);
this.slice = slice;
VectorString fileNames = seriesInfo.filenames;
// Read the DICOM image:
image = SimpleITK.ReadImage(fileNames[slice]);
loadImageData(image);
VectorDouble o1 = image.GetOrigin();
if (o1.Count < 3)
{
throw(new System.Exception("Invalid origins found in first image."));
}
origin = new Vector3((float)o1 [0], (float)o1 [1], (float)o1 [2]);
// Load the direction cosines:
// ITK stores the direction cosines in a matrix with row-major-ordering. The weird indexing is because
// we need the first and second column (0,3,6 for X and 1,4,7 for Y)
VectorDouble direction = image.GetDirection();
if (direction.Count < 6)
{
throw(new System.Exception("Invalid direction cosines found in images."));
}
directionCosineX = new Vector3((float)direction [0], (float)direction [3], (float)direction [6]);
directionCosineY = new Vector3((float)direction [1], (float)direction [4], (float)direction [7]);
sliceNormal = Vector3.Cross(directionCosineX, directionCosineY);
// Calculate which direction the normal is facing to determine the orienation (Transverse,
// Coronal or Saggital).
float absX = Mathf.Abs(sliceNormal.x);
float absY = Mathf.Abs(sliceNormal.y);
float absZ = Mathf.Abs(sliceNormal.z);
if (absX > absY && absX > absZ)
{
sliceOrientation = SliceOrientation.Saggital;
}
else if (absY > absX && absY > absZ)
{
sliceOrientation = SliceOrientation.Coronal;
}
else if (absZ > absX && absZ > absY)
{
sliceOrientation = SliceOrientation.Transverse;
}
else
{
sliceOrientation = SliceOrientation.Unknown;
}
// Load the pixel spacing:
// NOTE: It seems that the the first value is the spacing between rows (i.e. y direction),
// the second value is the spacing between columns (i.e. x direction).
// I was not able to verify this so far, since all test dicoms we had have the same spacing in
// x and y direction...
VectorDouble spacing = image.GetSpacing();
if (spacing.Count < 2)
{
throw(new System.Exception("Invalid pixel spacing found in images."));
}
pixelSpacing = new Vector2((float)spacing [1], (float)spacing [0]);
// Generate the transformation matrices which can later be used to translate pixels to
// 3D positions and vice versa.
setupTransformationMatrices();
}
static void Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("Usage: SimpleGaussian <input>");
return;
}
// Read input image
itk.simple.Image input = SimpleITK.ReadImage(args[0]);
// Cast to we know the the pixel type
input = SimpleITK.Cast(input, PixelId.sitkFloat32);
// calculate the number of pixels
VectorUInt32 size = input.GetSize();
int len = 1;
for (int dim = 0; dim < input.GetDimension(); dim++)
{
len *= (int)size[dim];
}
IntPtr buffer = input.GetBufferAsFloat();
// Note: C# also has a GetConstBufferAs... methods which do not
// implicitly call MakeUnique.
// There are two ways to access the buffer:
// (1) Access the underlying buffer as a pointer in an "unsafe" block
// (note that in C# "unsafe" simply means that the compiler can not
// perform full type checking), and requires the -unsafe compiler flag
// unsafe {
// float* bufferPtr = (float*)buffer.ToPointer();
// // Now the byte pointer can be accessed as per Brad's email
// // (of course this example is only a 2d single channel image):
// // This is a 1-D array but can be access as a 3-D. Given an
// // image of size [xS,yS,zS], you can access the image at
// // index [x,y,z] as you wish by image[x+y*xS+z*xS*yS],
// // so x is the fastest axis and z is the slowest.
// for (int j = 0; j < size[1]; j++) {
// for (int i = 0; i < size[0]; i++) {
// float pixel = bufferPtr[i + j*size[1]];
// // Do something with pixel here
// }
// }
// }
// (2) Copy the buffer to a "safe" array (i.e. a fully typed array)
// (note that this means memory is duplicated)
float[] bufferAsArray = new float[len]; // Allocates new memory the size of input
Marshal.Copy(buffer, bufferAsArray, 0, len);
double total = 0.0;
for (int j = 0; j < size[1]; j++)
{
for (int i = 0; i < size[0]; i++)
{
float pixel = bufferAsArray[i + j * size[1]];
total += pixel;
}
}
Console.WriteLine("Pixel value total: {0}", total);
}
static void Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("Usage: inputImage outputImage");
return;
}
string inputFilename = args[0];
string outputFilename = args[1];
// Read input image
SitkImage input = SimpleITK.ReadImage(inputFilename);
// Cast so we know the the pixel type
input = SimpleITK.Cast(input, PixelId.sitkFloat32);
// calculate the number of pixels
VectorUInt32 size = input.GetSize();
int len = 1;
for (int dim = 0; dim < input.GetDimension(); dim++)
{
len *= (int)size[dim];
}
IntPtr buffer = input.GetBufferAsFloat();
// There are two ways to access the buffer:
// (1) Access the underlying buffer as a pointer in an "unsafe" block
// (note that in C# "unsafe" simply means that the compiler can not
// perform full type checking), and requires the -unsafe compiler flag
// unsafe {
// float* bufferPtr = (float*)buffer.ToPointer();
// // Now the byte pointer can be accessed as per Brad's email
// // (of course this example is only a 2d single channel image):
// // This is a 1-D array but can be access as a 3-D. Given an
// // image of size [xS,yS,zS], you can access the image at
// // index [x,y,z] as you wish by image[x+y*xS+z*xS*yS],
// // so x is the fastest axis and z is the slowest.
// for (int j = 0; j < size[1]; j++) {
// for (int i = 0; i < size[0]; i++) {
// float pixel = bufferPtr[i + j*size[1]];
// // Do something with pixel here
// }
// }
// }
// (2) Copy the buffer to a "safe" array (i.e. a fully typed array)
// (note that this means memory is duplicated)
float[] bufferAsArray = new float[len]; // Allocates new memory the size of input
Marshal.Copy(buffer, bufferAsArray, 0, len);
double total = 0.0;
for (int j = 0; j < size[1]; j++)
{
for (int i = 0; i < size[0]; i++)
{
float pixel = bufferAsArray[i + j * size[1]];
total += pixel;
}
}
Console.WriteLine("Pixel value total: {0}", total);
// Set buffer of new SimpleITK Image from managed array.
// bufferAsArray could also have come from a bmp,png,etc...
uint width = input.GetWidth();
uint height = input.GetHeight();
SitkImage outImage = new SitkImage(width, height, PixelId.sitkFloat32);
IntPtr outImageBuffer = outImage.GetBufferAsFloat();
Marshal.Copy(bufferAsArray, 0, outImageBuffer, (int)(size[0] * size[1]));
//
// Write out the resulting file
//
outImage = SimpleITK.RescaleIntensity(outImage, 0, 255);
outImage = SimpleITK.Cast(outImage, PixelId.sitkUInt8);
SimpleITK.WriteImage(outImage, outputFilename);
}
static void Main(string[] args)
{
if (args.Length < 6)
{
Console.WriteLine("Missing Parameters ");
Console.WriteLine("Usage: " + System.AppDomain.CurrentDomain.FriendlyName +
" inputImage outputImage" +
" lowerThreshold upperThreshold seedX seedY [seed2X seed2Y ... ]");
return;
}
string inputFilename = args[0];
string outputFilename = args[1];
double lowerThreshold = double.Parse(args[2], CultureInfo.InvariantCulture);
double upperThreshold = double.Parse(args[3], CultureInfo.InvariantCulture);
//
// Read the image
//
SitkImage inputImage = SimpleITK.ReadImage(inputFilename, PixelIDValueEnum.sitkFloat32);
//
// Blur using CurvatureFlowImageFilter
//
CurvatureFlowImageFilter blurFilter = new sitk.CurvatureFlowImageFilter();
blurFilter.SetNumberOfIterations(5);
blurFilter.SetTimeStep(0.125);
inputImage = blurFilter.Execute(inputImage);
//
// Set up ConnectedThresholdImageFilter for segmentation
//
ConnectedThresholdImageFilter segmentationFilter = new sitk.ConnectedThresholdImageFilter();
segmentationFilter.SetLower(lowerThreshold);
segmentationFilter.SetUpper(upperThreshold);
segmentationFilter.SetReplaceValue(255);
for (uint i = 4; i + 1 < args.Length; i += 2)
{
VectorUInt32 seed = new VectorUInt32(new uint[] { Convert.ToUInt32(args[i]), Convert.ToUInt32(args[i + 1]), 0 });
segmentationFilter.AddSeed(seed);
Console.WriteLine("Adding a seed at: ");
for (int j = 0; j + 1 < seed.Count; j++)
{
Console.WriteLine(seed[j] + " ");
}
}
SitkImage outImage = segmentationFilter.Execute(inputImage);
//
// Write out the resulting file
//
SimpleITK.WriteImage(outImage, outputFilename);
return;
}
public static string getListOfPackageImage(int index)
{
Class.manageImg managerView = HttpContext.Current.Session["managerView"] as Class.manageImg;
managerView.currentPageIndex = index;
HttpContext.Current.Session["managerView"] = managerView;
ViewImage_ that = HttpContext.Current.Session["viewImage"] as ViewImage_;
that.updateReference(index);
// set default values
managerView.allImages[index][0].getUnlabelled = new int[] { -1, -1 };
managerView.allImages[index][0].getPercentage = "-";
if (managerView.tc.ActiveLearning) // when active learning is enabled, check if threshold is reached
{
if (DataAccess.DataAccessTestCase.checkThreshold(managerView))
{
return("alert('Active learning procedure has been executed, page index will be reset'); setTimeout(function(){ Reset=true; }, 3000);");
}
}
if (index >= 0 && index <= managerView.iNGroups)
{
managerView.sCurrentImageFolder = new List <String>(managerView.allImages[index].Count);
for (var i = 0; i < managerView.allImages[index].Count; i++)
{
managerView.sCurrentImageFolder.Add(null);
managerView.sCurrentImageFolder[i] = managerView.tc.dbPath + "\\" + managerView.allImages[index][i].Path.Replace('/', '\\'); //- Martin
}
// get the labelscales
for (int i = 0; i < managerView.allImages[index].Count; i++)
{
if (managerView.tc.DiskreteScale)
{
managerView.allImages[index][i].LableDiscrete = DataAccessTestCase.GetDiscreteLabel(managerView.IDUser, managerView.allImages[index][i].IdGroupImage);//pcw
}
else
{
managerView.allImages[index][i].LableContinuous = DataAccessTestCase.GetLableContinuous(managerView.allImages[index][i].IdGroupImage, managerView.IDUser, managerView.allImages[index][i].TypeScaleContinuous);//pcw
}
}
List <String> sPath = managerView.sCurrentImageFolder;
if (sPath == null)
{
throw new ArgumentException("path variable in manageImg is not specified!");
}
else
{
// get paths and dimension of every individual image
for (int i = 0; i < managerView.allImages[index].Count; i++)
{
managerView.allImages[index][i].imagePaths = (System.IO.Directory.EnumerateFiles(sPath[i], "*.*", SearchOption.AllDirectories).Where(s => Constant.lsExtensions.Any(e => s.EndsWith(e)))).ToArray();
Array.Sort(managerView.allImages[index][i].imagePaths);
int[] iSize = new int[] { 0, 0, 0 };
string pfad = managerView.allImages[index][i].imagePaths[0];
itk.simple.Image itkImage = SimpleITK.ReadImage(pfad); // bei DICOM werden nur die Dimensionen des ersten Bildes ausgelesen, diese sind bei den anderen Schichten identisch
VectorUInt32 UInt32Size = itkImage.GetSize();
iSize[0] = unchecked ((int)UInt32Size[0]);
iSize[1] = unchecked ((int)UInt32Size[1]);
if (managerView.allImages[index][i].imagePaths.Length > 1)// for DICOM files
{
iSize[2] = managerView.allImages[index][i].imagePaths.Length;
}
else if (managerView.allImages[index][i].imagePaths.Length == 1)//
{
iSize[2] = unchecked ((int)UInt32Size[2]);
iSize[2]--;
}
managerView.allImages[index][i].imageDimensions = iSize;
}
}
// get index of the next/previous page with not completely labelled images
try {
managerView.allImages[index][0].getNumOfPages = managerView.allImages.Count();
managerView.allImages[index][0].getUnlabelled = getUnlabelled(index);
managerView.allImages[index][0].getPercentage = getCurrPercentage();
}catch (ArgumentOutOfRangeException ex) {
return("alert('An error occurred while trying to load the image package, please contact the administrator');");
}
//Obfuscate image paths
for (int c = 0; c < managerView.allImages[index].Count; c++)
{
for (int z = 0; z < managerView.allImages[index][c].imagePaths.Length; z++)
{
managerView.allImages[index][c].imagePaths[z] = obfuscate(managerView.allImages[index][c].imagePaths[z]);
}
}
// put the array in the JSON format
var json = new JavaScriptSerializer().Serialize(managerView.allImages[index]);
return(json);
//return managerView.allImages[index];
}
else
{
return(null);
}
}
/*! Constructor, fills most of the attributes of the DICOMSeries class.
* \note This does some heavy file/directory parsing to determine the files which are part of
* this series and their order. This is why the DICOMSeries should be constructed in a
* background thread and then passed to the main thread. */
public DICOMSeries(string directory, string seriesUID)
{
Debug.Log("Loading Meta Data for Series: " + seriesUID);
// Get the file names for the series:
filenames = ImageSeriesReader.GetGDCMSeriesFileNames(directory, seriesUID);
if (filenames.Count <= 0)
{
throw(new System.Exception("No files found for series " + seriesUID + "."));
}
this.seriesUID = seriesUID;
// Load the first slice in volume to get meta information:
firstSlice = SimpleITK.ReadImage(filenames[0]);
lastSlice = SimpleITK.ReadImage(filenames[Math.Max(filenames.Count - 1, 0)]);
numberOfSlices = filenames.Count;
// Load the direction cosines:
// ITK stores the direction cosines in a matrix with row-major-ordering. The weird indexing is because
// we need the first and second column (0,3,6 for X and 1,4,7 for Y)
VectorDouble direction = firstSlice.GetDirection();
if (direction.Count < 6)
{
throw(new System.Exception("Invalid direction cosines found in images."));
}
directionCosineX = new Vector3((float)direction [0], (float)direction [3], (float)direction [6]);
directionCosineY = new Vector3((float)direction [1], (float)direction [4], (float)direction [7]);
sliceNormal = Vector3.Cross(directionCosineX, directionCosineY);
if (lastSlice != null)
{
// Get the origins of the two images:
VectorDouble o1 = firstSlice.GetOrigin();
if (o1.Count < 3)
{
throw(new System.Exception("Invalid origins found in first image."));
}
Vector3 origin = new Vector3((float)o1 [0], (float)o1 [1], (float)o1 [2]);
VectorDouble o2 = lastSlice.GetOrigin();
if (o2.Count < 3)
{
throw(new System.Exception("Invalid origins found in last image."));
}
Vector3 lastOrigin = new Vector3((float)o2 [0], (float)o2 [1], (float)o2 [2]);
// Calculate offset between two adjacent slices (assuming all neighbours are the same distance apart):
// Note: I expect sliceOffset.x and sliceOffset.y to be zero most of the time.
// Using a Vector just for completeness.
sliceOffset = (lastOrigin - origin) / (numberOfSlices - 1);
}
if (lastSlice != null && numberOfSlices > 1)
{
// Load the direction cosines:
// ITK stores the direction cosines in a matrix with row-major-ordering. The weird indexing is because
// we need the first and second column (0,3,6 for X and 1,4,7 for Y)
VectorDouble directionLast = lastSlice.GetDirection();
if (directionLast.Count < 6)
{
throw(new System.Exception("Invalid direction cosines found in images."));
}
Vector3 directionCosineXLast = new Vector3((float)directionLast [0], (float)directionLast [3], (float)directionLast [6]);
Vector3 directionCosineYLast = new Vector3((float)directionLast [1], (float)directionLast [4], (float)directionLast [7]);
Vector3 sliceNormalLast = Vector3.Cross(directionCosineXLast, directionCosineYLast);
// If the first and last slice have the same orientation, then consider this series to be a volume.
// TODO: Better check?
if ((sliceNormal == sliceNormalLast))
{
isConsecutiveVolume = true;
}
else
{
Debug.LogWarning("First and last slice of the series do not have the same orientation. This will not be considered a volume.\n" +
"\tNormal first slice, Normal last slice: " + sliceNormal + " " + sliceNormalLast);
}
}
else
{
isConsecutiveVolume = false;
}
if (isConsecutiveVolume)
{
// Calculate which direction the normal is facing to determine the orienation (Transverse,
// Coronal or Saggital).
float absX = Mathf.Abs(sliceNormal.x);
float absY = Mathf.Abs(sliceNormal.y);
float absZ = Mathf.Abs(sliceNormal.z);
if (absX > absY && absX > absZ)
{
sliceOrientation = SliceOrientation.Saggital;
}
else if (absY > absX && absY > absZ)
{
sliceOrientation = SliceOrientation.Coronal;
}
else if (absZ > absX && absZ > absY)
{
sliceOrientation = SliceOrientation.Transverse;
}
else
{
sliceOrientation = SliceOrientation.Unknown;
}
}
else
{
sliceOrientation = SliceOrientation.Unknown; // Can't know what the orientation is if the first and last slice have different normals
}
// Read the minimum and maximum values which are stored in this image:
minPixelValue = UInt16.MinValue;
maxPixelValue = UInt16.MaxValue;
foundMinMaxPixelValues = false;
try {
minPixelValue = UInt32.Parse(firstSlice.GetMetaData("0028|0106"));
maxPixelValue = UInt32.Parse(firstSlice.GetMetaData("0028|0107"));
foundMinMaxPixelValues = true;
} catch {
}
}
