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fix some bugs #4

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fix some bugs #4

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daf1088
fix some bugs
aomiit Jan 1, 2021
d64d9d2
Merge branch 'anmcgrath:master' into master
aomiit Sep 8, 2023
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60 changes: 46 additions & 14 deletions RT.Core/DICOM/PixelDataInfo.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ public class PixelDataInfo
public double[] PixelSpacing { get; set; }
public string ImageType { get; set; }
public double SliceThickness { get; set; }
public double SpacingBetweenSlices { get; set; }
public int Rows { get; set; }
public int Columns { get; set; }
public int BitsAllocated { get; set; }
Expand All @@ -32,37 +33,68 @@ public class PixelDataInfo

public PixelDataInfo(DicomFile file)
{
var imgOrientationPatient = file.Dataset.Get<double[]>(DicomTag.ImageOrientationPatient, new double[] { 0, 0, 0, 0, 0, 0 });
var imgOrientationPatient = new double[] { 0, 0, 0, 0, 0, 0 };
if (file.Dataset.TryGetValues<double>(DicomTag.ImageOrientationPatient, out double[] tmp))
{
imgOrientationPatient = tmp;
}

RowDir = new Point3d(imgOrientationPatient[0], imgOrientationPatient[1], imgOrientationPatient[2]);
ColDir = new Point3d(imgOrientationPatient[3], imgOrientationPatient[4], imgOrientationPatient[5]);

var imgPositionPatient = file.Dataset.Get<double[]>(DicomTag.ImagePositionPatient, new double[] { 0, 0, 0 });
var imgPositionPatient = new double[] { 0, 0, 0 };
if (file.Dataset.TryGetValues<double>(DicomTag.ImagePositionPatient, out tmp))
{
imgPositionPatient = tmp;
}

ImagePositionPatient = new Point3d(imgPositionPatient[0], imgPositionPatient[1], imgPositionPatient[2]);

SliceThickness = file.Dataset.Get<double>(DicomTag.SliceThickness, 0.0);
Rows = file.Dataset.Get<int>(DicomTag.Rows);
Columns = file.Dataset.Get<int>(DicomTag.Columns);
BitsAllocated = file.Dataset.Get<int>(DicomTag.BitsAllocated, 0);
PixelRepresentation = file.Dataset.Get<int>(DicomTag.PixelRepresentation, 0);
RescaleSlope = file.Dataset.Get<float>(DicomTag.RescaleSlope, 1.0f);
RescaleIntercept = file.Dataset.Get<float>(DicomTag.RescaleIntercept, 0.0f);
PixelSpacing = file.Dataset.Get<double[]>(DicomTag.PixelSpacing, new double[] {1,1,1 });
SliceThickness = file.Dataset.GetSingleValueOrDefault<double>(DicomTag.SliceThickness, 0.0);

//winson add 2020.9.2 - Inconsistent 'Slice Thickness' and 'Spacing Between Slices'
SpacingBetweenSlices = file.Dataset.GetSingleValueOrDefault<double>(DicomTag.SpacingBetweenSlices, 0.0);
if (SpacingBetweenSlices > 0.0)
{
SliceThickness = SpacingBetweenSlices;
}

Rows = file.Dataset.GetSingleValue<int>(DicomTag.Rows);
Columns = file.Dataset.GetSingleValue<int>(DicomTag.Columns);
BitsAllocated = file.Dataset.GetSingleValueOrDefault<int>(DicomTag.BitsAllocated, 0);
PixelRepresentation = file.Dataset.GetSingleValueOrDefault<int>(DicomTag.PixelRepresentation, 0);
RescaleSlope = file.Dataset.GetSingleValueOrDefault<float>(DicomTag.RescaleSlope, 1.0f);
RescaleIntercept = file.Dataset.GetSingleValueOrDefault<float>(DicomTag.RescaleIntercept, 0.0f);

if (file.Dataset.TryGetValues<double>(DicomTag.PixelSpacing, out tmp))
{
PixelSpacing = tmp;
}
else
{
PixelSpacing = new double[] { 1, 1, 1 };
}

try
{
SliceLocation = file.Dataset.Get<double>(DicomTag.SliceLocation, 0.0);
SliceLocation = file.Dataset.GetSingleValueOrDefault<double>(DicomTag.SliceLocation, 0.0);
HasSliceLocation = true;
}
#pragma warning disable CS0168 // The variable 'e' is declared but never used
catch (Exception e)
#pragma warning restore CS0168 // The variable 'e' is declared but never used
{
HasSliceLocation = false;
}

try
if (file.Dataset.TryGetValues<double>(DicomTag.GridFrameOffsetVector, out tmp))//All Z-offsets
{
GridFrameOffsetVector = tmp;
}
else
{
GridFrameOffsetVector = file.Dataset.Get<DicomDecimalString>(DicomTag.GridFrameOffsetVector).Get<double[]>(); //All Z-offsets
GridFrameOffsetVector = new double[1];
}
catch (Exception e) { GridFrameOffsetVector = new double[1]; };
}
}
}
8 changes: 8 additions & 0 deletions RT.Core/Dose/DicomDoseObject.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,14 @@ namespace RT.Core.Dose
{
public class DicomDoseObject:DicomObject, IDoseObject
{
public string SerriesNumber { get; set; }
public string SerriesDescription { get; set; }

public string ClassUID { get; set; }
public string InstanceUID { get; set; }
public string ReferencedClassUID { get; set; }
public string ReferencedInstanceUID { get; set; }

public IVoxelDataStructure Grid { get; set; }
public DicomDoseObject() { }
}
Expand Down
1 change: 1 addition & 0 deletions RT.Core/Dose/RelativeNormalisationOption.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ namespace RT.Core.Dose
{
public enum RelativeNormalisationOption
{
Rx,
Max,
POI,
}
Expand Down
128 changes: 71 additions & 57 deletions RT.Core/Geometry/GridBasedVoxelDataStructure.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -81,73 +81,87 @@ public override void Interpolate(Point3d position, Voxel voxel)
}
else
{
//float x0 = 0, x1 = 0, y0 = 0, y1 = 0, z0 = 0, z1 = 0;
//int ix0 = 0, ix1 = 0, iy0 = 0, iy1 = 0, iz0 = 0, iz1 = 0;

if (ConstantGridSpacing)
try
{
ix0 = (int)((position.X - XCoords[0]) / GridSpacing.X);
if (ix0 == XCoords.Length - 1)
ix1 = ix0;
else
ix1 = ix0 + 1;
x0 = XCoords[ix0];
x1 = XCoords[ix1];
iy0 = (int)((position.Y - YCoords[0]) / GridSpacing.Y);
if (iy0 == YCoords.Length - 1)
iy1 = iy0;
else
iy1 = iy0 + 1;
y0 = YCoords[iy0];
y1 = YCoords[iy1];
if (GridSpacing.Z != 0)
//float x0 = 0, x1 = 0, y0 = 0, y1 = 0, z0 = 0, z1 = 0;
//int ix0 = 0, ix1 = 0, iy0 = 0, iy1 = 0, iz0 = 0, iz1 = 0;

if (ConstantGridSpacing)
{
iz0 = (int)((position.Z - ZCoords[0]) / GridSpacing.Z);
if (iz0 == ZCoords.Length - 1)
iz1 = iz0;
ix0 = (int)((position.X - XCoords[0]) / GridSpacing.X);
if (ix0 >= XCoords.Length - 1)
ix1 = ix0 = XCoords.Length - 1;
else
ix1 = ix0 + 1;
x0 = XCoords[ix0];
x1 = XCoords[ix1];

iy0 = (int)((position.Y - YCoords[0]) / GridSpacing.Y);
if (iy0 >= YCoords.Length - 1)
iy1 = iy0 = YCoords.Length - 1;
else
iy1 = iy0 + 1;

y0 = YCoords[iy0];
y1 = YCoords[iy1];
if (GridSpacing.Z != 0)
{
iz0 = (int)((position.Z - ZCoords[0]) / GridSpacing.Z);
iz1 = iz0 + 1;
z0 = ZCoords[iz0];
z1 = ZCoords[iz1];

if (iz0 >= ZCoords.Length - 1)
iz1 = iz0 = ZCoords.Length - 1;
else
iz1 = iz0 + 1;

z0 = ZCoords[iz0];
z1 = ZCoords[iz1];
}
else
{
iz0 = 0; iz1 = 0;
z0 = ZCoords[iz0];
z1 = ZCoords[iz1];
}
}
else
{
iz0 = 0; iz1 = 0;
z0 = ZCoords[iz0];
z1 = ZCoords[iz1];
var xt = binarySearchForSurroundingCoords(position.X, XCoords);
x0 = (float)xt.Item1;
x1 = (float)xt.Item2;
ix0 = xt.Item3;
ix1 = xt.Item4;
var yt = binarySearchForSurroundingCoords(position.Y, YCoords);
y0 = (float)yt.Item1;
y1 = (float)yt.Item2;
iy0 = yt.Item3;
iy1 = yt.Item4;
var zt = binarySearchForSurroundingCoords(position.Z, ZCoords);
z0 = (float)zt.Item1;
z1 = (float)zt.Item2;
iz0 = zt.Item3;
iz1 = zt.Item4;
}

voxel.Value = Interpolation.TrilinearInterpolate(
(float)position.X, (float)position.Y, (float)position.Z,
x0, y0, z0,
x1, y1, z1,
Data[getIndex(ix0, iy0, iz0)],
Data[getIndex(ix1, iy0, iz0)],
Data[getIndex(ix0, iy0, iz1)],
Data[getIndex(ix1, iy0, iz1)],
Data[getIndex(ix0, iy1, iz0)],
Data[getIndex(ix1, iy1, iz0)],
Data[getIndex(ix0, iy1, iz1)],
Data[getIndex(ix1, iy1, iz1)]);
}
else
#pragma warning disable CS0168 // The variable 'e' is declared but never used
catch(Exception e)
#pragma warning restore CS0168 // The variable 'e' is declared but never used
{
var xt = binarySearchForSurroundingCoords(position.X, XCoords);
x0 = (float)xt.Item1;
x1 = (float)xt.Item2;
ix0 = xt.Item3;
ix1 = xt.Item4;
var yt = binarySearchForSurroundingCoords(position.Y, YCoords);
y0 = (float)yt.Item1;
y1 = (float)yt.Item2;
iy0 = yt.Item3;
iy1 = yt.Item4;
var zt = binarySearchForSurroundingCoords(position.Z, ZCoords);
z0 = (float)zt.Item1;
z1 = (float)zt.Item2;
iz0 = zt.Item3;
iz1 = zt.Item4;
}

voxel.Value = Interpolation.TrilinearInterpolate(
(float)position.X, (float)position.Y, (float)position.Z,
x0, y0, z0,
x1, y1, z1,
Data[getIndex(ix0, iy0, iz0)],
Data[getIndex(ix1, iy0, iz0)],
Data[getIndex(ix0, iy0, iz1)],
Data[getIndex(ix1, iy0, iz1)],
Data[getIndex(ix0, iy1, iz0)],
Data[getIndex(ix1, iy1, iz0)],
Data[getIndex(ix0, iy1, iz1)],
Data[getIndex(ix1, iy1, iz1)]);
voxel.Value = DefaultPhysicalValue;
}
}
}

Expand Down
19 changes: 16 additions & 3 deletions RT.Core/Geometry/VoxelDataStructureBase.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ public abstract class VoxelDataStructureBase
private Point3d positionCache;
private Voxel voxelCache;

public double RxDose { get; set; }
public double NormalisationPercent { get; set; } = 100;
public NormalisationType NormalisationType { get; set; } = NormalisationType.Relative;
public RelativeNormalisationOption RelativeNormalisationOption { get; set; }
Expand Down Expand Up @@ -92,12 +93,24 @@ public float GetNormalisationAmount()
{
if (NormalisationType == NormalisationType.Absolute)
return 1;

if (NormalisationType == NormalisationType.Relative)
{
if (RelativeNormalisationOption == RelativeNormalisationOption.Max)
return MaxVoxel.Value * Scaling * ((float)NormalisationPercent / (100*100));
float value = 1.0f;

if (RelativeNormalisationOption == RelativeNormalisationOption.Rx)
{
value = 1.0f;
}
else if (RelativeNormalisationOption == RelativeNormalisationOption.Max)
{
value = MaxVoxel.Value;
}
else if (RelativeNormalisationOption == RelativeNormalisationOption.POI && NormalisationPOI != null)
return this.Interpolate(NormalisationPOI.Position).Value * Scaling * ((float)NormalisationPercent / (100* 100));
{
value = this.Interpolate(NormalisationPOI.Position).Value;
}
return value * Scaling * ((float)NormalisationPercent / (100* 100));
}
return 1;
}
Expand Down
51 changes: 49 additions & 2 deletions RT.Core/IO/DicomLoader.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,40 @@ public static async Task<DicomDoseObject> LoadDicomDoseAsync(string fileName, IP
return await LoadDicomDoseAsync(new string[] { fileName }, progress);
}

public static DicomDoseObject LoadDicomDoseSync(DicomFile dicomFile)
{
var loader = new DicomDoseLoader();
var dose = new DicomDoseObject();
loader.Load(dicomFile, dose, null);
return dose;
}

public static async Task<DicomPlanObject> LoadDicomPlanAsync(string[] fileNames)
{
var files = await getFilesAsync(fileNames);
var loader = new PlanLoader();
var plan = new DicomPlanObject();
loader.Load(files, plan);
return plan;
}

public static DicomPlanObject LoadDicomPlanAsync(DicomFile dicomFile)
{
var loader = new PlanLoader();
var plan = new DicomPlanObject();
loader.Load(dicomFile, plan);
return plan;
}


public static async Task<DicomPlanObject> LoadDicomPlanAsync(string fileName)
{
return await LoadDicomPlanAsync(new string[] { fileName });
}

#pragma warning disable CS1998 // This async method lacks 'await' operators and will run synchronously. Consider using the 'await' operator to await non-blocking API calls, or 'await Task.Run(...)' to do CPU-bound work on a background thread.
public static async Task<EgsDoseObject> LoadEgsObjectAsync(string file, IProgress<double> progress)
#pragma warning restore CS1998 // This async method lacks 'await' operators and will run synchronously. Consider using the 'await' operator to await non-blocking API calls, or 'await Task.Run(...)' to do CPU-bound work on a background thread.
{
var loader = new EgsDoseLoader();
var dose = new EgsDoseObject();
Expand Down Expand Up @@ -61,9 +94,17 @@ public static async Task<StructureSet> LoadStructureSetAsync(string[] fileNames,
return structureSet;
}

public static async Task<DicomDoseObject> LoadStructureSetAsync(string fileName, IProgress<double> progress)
public static StructureSet LoadStructureSetSync(DicomFile dicomFile, IProgress<double> progress)
{
return await LoadDicomDoseAsync(new string[] { fileName }, progress);
var loader = new ROILoader();
var structureSet = new StructureSet();
loader.Load(dicomFile, structureSet, progress);
return structureSet;
}

public static async Task<StructureSet> LoadStructureSetAsync(string fileName, IProgress<double> progress)
{
return await LoadStructureSetAsync(new string[] { fileName }, progress);
}

private static async Task<DicomFile[]> getFilesAsync(string[] fileNames)
Expand All @@ -73,7 +114,13 @@ private static async Task<DicomFile[]> getFilesAsync(string[] fileNames)
foreach(string fileName in fileNames)
{
if (DicomFile.HasValidHeader(fileName))
{
files.Add(await DicomFile.OpenAsync(fileName));
}
else if(DicomFile.IsDICOMFile(fileName))
{
files.Add(await DicomFile.OpenAsync(fileName));
}
}
return files.ToArray();
}
Expand Down