public static float[] FitAndGeneratePlane(float[] intensities, int2 dims)
{
float3[] Points = new float3[dims.Elements()];
for (int y = 0; y < dims.Y; y++)
{
for (int x = 0; x < dims.X; x++)
{
Points[y * dims.X + x] = new float3(x, y, intensities[y * dims.X + x]);
}
}
float3 Plane = FitPlane(Points);
float[] Result = new float[dims.Elements()];
for (int y = 0; y < dims.Y; y++)
{
for (int x = 0; x < dims.X; x++)
{
Result[y * dims.X + x] = x * Plane.X + y * Plane.Y + Plane.Z;
}
}
return Result;
}
public static int3[] GetEqualGridSpacing(int2 dimsImage, int2 dimsRegion, float overlapFraction, out int2 dimsGrid)
{
int2 dimsoverlap = new int2((int)(dimsRegion.X * (1.0f - overlapFraction)), (int)(dimsRegion.Y * (1.0f - overlapFraction)));
dimsGrid = new int2(MathHelper.NextMultipleOf(dimsImage.X - (dimsRegion.X - dimsoverlap.X), dimsoverlap.X) / dimsoverlap.X,
MathHelper.NextMultipleOf(dimsImage.Y - (dimsRegion.Y - dimsoverlap.Y), dimsoverlap.Y) / dimsoverlap.Y);
int2 shift;
shift.X = dimsGrid.X > 1 ? (int)((dimsImage.X - dimsRegion.X) / (float)(dimsGrid.X - 1)) : (dimsImage.X - dimsRegion.X) / 2;
shift.Y = dimsGrid.Y > 1 ? (int)((dimsImage.Y - dimsRegion.Y) / (float)(dimsGrid.Y - 1)) : (dimsImage.Y - dimsRegion.Y) / 2;
int2 offset = new int2((dimsImage.X - shift.X * (dimsGrid.X - 1) - dimsRegion.X) / 2,
(dimsImage.Y - shift.Y * (dimsGrid.Y - 1) - dimsRegion.Y) / 2);
int3[] h_origins = new int3[dimsGrid.Elements()];
for (int y = 0; y < dimsGrid.Y; y++)
{
for (int x = 0; x < dimsGrid.X; x++)
{
h_origins[y * dimsGrid.X + x] = new int3(x * shift.X + offset.X, y * shift.Y + offset.Y, 0);
}
}
return(h_origins);
}
public static void FitAndSubtractGrid(float[] intensities, int2 dims, int2 gridDims)
{
float2 GridSpacing = new float2(dims) / new float2(gridDims + 1);
float2[] GridCentroids = Helper.Combine(Helper.ArrayOfFunction(y =>
Helper.ArrayOfFunction(x => new float2((x + 1) * GridSpacing.X,
(y + 1) * GridSpacing.Y),
gridDims.X), gridDims.Y));
float3[] Planes = new float3[gridDims.Elements()];
Parallel.For(0, gridDims.Elements(), ci =>
{
float2 Centroid = GridCentroids[ci];
int2 PositionStart = int2.Max(new int2(Centroid - GridSpacing), 0);
int2 PositionEnd = int2.Min(new int2(Centroid + GridSpacing + 1), dims);
int2 PatchDims = PositionEnd - PositionStart;
float3[] Points = new float3[PatchDims.Elements()];
for (int y = 0; y < PatchDims.Y; y++)
{
for (int x = 0; x < PatchDims.X; x++)
{
Points[y * PatchDims.X + x] = new float3(x - GridSpacing.X,
y - GridSpacing.Y,
intensities[(y + PositionStart.Y) * dims.X + x + PositionStart.X]);
}
}
Planes[ci] = FitPlane(Points);
});
float[] FittedGrid = new float[dims.Elements()];
Parallel.For(0, dims.Y, y =>
{
for (int x = 0; x < dims.X; x++)
{
int2 Centroid0 = int2.Min(int2.Max(new int2((new float2(x, y) - GridSpacing) / GridSpacing), 0), gridDims - 1);
int CentroidID00 = gridDims.ElementFromPosition(Centroid0);
int CentroidID01 = gridDims.ElementFromPosition(int2.Min(Centroid0 + new int2(1, 0), gridDims - 1));
int CentroidID10 = gridDims.ElementFromPosition(int2.Min(Centroid0 + new int2(0, 1), gridDims - 1));
int CentroidID11 = gridDims.ElementFromPosition(int2.Min(Centroid0 + new int2(1, 1), gridDims - 1));
float2 Centroid00 = GridCentroids[CentroidID00];
float2 Centroid01 = GridCentroids[CentroidID01];
float2 Centroid10 = GridCentroids[CentroidID10];
float2 Centroid11 = GridCentroids[CentroidID11];
float Interp00 = (x - Centroid00.X) * Planes[CentroidID00].X + (y - Centroid00.Y) * Planes[CentroidID00].Y + Planes[CentroidID00].Z;
float Interp01 = (x - Centroid01.X) * Planes[CentroidID01].X + (y - Centroid01.Y) * Planes[CentroidID01].Y + Planes[CentroidID01].Z;
float Interp10 = (x - Centroid10.X) * Planes[CentroidID10].X + (y - Centroid10.Y) * Planes[CentroidID10].Y + Planes[CentroidID10].Z;
float Interp11 = (x - Centroid11.X) * Planes[CentroidID11].X + (y - Centroid11.Y) * Planes[CentroidID11].Y + Planes[CentroidID11].Z;
float fX = Math.Max(0, Math.Min(1, (x - Centroid00.X) / GridSpacing.X));
float fY = Math.Max(0, Math.Min(1, (y - Centroid00.Y) / GridSpacing.Y));
float Interp0 = Interp00 * (1 - fX) + Interp01 * fX;
float Interp1 = Interp10 * (1 - fX) + Interp11 * fX;
float Interp = Interp0 * (1 - fY) + Interp1 * fY;
FittedGrid[y * dims.X + x] = Interp;
}
});
for (int i = 0; i < intensities.Length; i++)
{
intensities[i] -= FittedGrid[i];
}
}
public static MapHeader ReadFromFile(BinaryReader reader, FileInfo info, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType)
{
MapHeader Header = null;
if (info.Extension.ToLower() == ".mrc" || info.Extension.ToLower() == ".mrcs" || info.Extension.ToLower() == ".ali" || info.Extension.ToLower() == ".rec" || info.Extension.ToLower() == ".st")
Header = new HeaderMRC(reader);
else if (info.Extension.ToLower() == ".em")
Header = new HeaderEM(reader);
else if (info.Extension.ToLower() == ".tif" || info.Extension.ToLower() == ".tiff")
Header = new HeaderTiff(info.FullName);
else if (info.Extension.ToLower() == ".dat")
{
long SliceElements = headerlessSliceDims.Elements() * ImageFormatsHelper.SizeOf(headerlessType);
long Slices = (info.Length - headerlessOffset) / SliceElements;
int3 Dims3 = new int3(headerlessSliceDims.X, headerlessSliceDims.Y, (int)Slices);
Header = new HeaderRaw(Dims3, headerlessOffset, headerlessType);
}
else
throw new Exception("File type not supported.");
return Header;
}
