public void Will_Dispose_Of_Db_Context()
{
//Arrange
var context = new Mock <IDbContext>();
var projector = new Projector <TestModel>(context.Object);
//Act
projector.Dispose();
//Assert
context.Verify(x => x.Dispose(), Times.Once);
}
public void GatherRefinementProgress(string[] folders)
{
foreach (var species in Species)
{
string SpeciesID = species.GUID.ToString().Substring(0, 8);
Projector Rec1 = species.HalfMap1Reconstruction[0];
Projector Rec2 = species.HalfMap2Reconstruction[0];
Particle[] OriginalParticles = species.Particles.ToList().ToArray();
Particle[] FinalParticles = species.Particles;
foreach (var folder in folders)
{
foreach (var path in Directory.EnumerateFiles(folder, $"{SpeciesID}_half1_*.mrc"))
{
Projector Saved = Projector.FromFile(path);
Rec1.Data.Add(Saved.Data);
Rec1.Weights.Add(Saved.Weights);
Saved.Dispose();
}
foreach (var path in Directory.EnumerateFiles(folder, $"{SpeciesID}_half2_*.mrc"))
{
Projector Saved = Projector.FromFile(path);
Rec2.Data.Add(Saved.Data);
Rec2.Weights.Add(Saved.Weights);
Saved.Dispose();
}
Particle[] UpdatedParticles = species.ParticlesFromStar(new Star(System.IO.Path.Combine(folder, $"{SpeciesID}_particles.star")));
for (int p = 0; p < OriginalParticles.Length; p++)
{
if (OriginalParticles[p].Coordinates.Where((v, i) => v != UpdatedParticles[p].Coordinates[i]).Count() > 0 ||
OriginalParticles[p].Angles.Where((v, i) => v != UpdatedParticles[p].Angles[i]).Count() > 0)
{
FinalParticles[p] = UpdatedParticles[p];
}
}
}
Rec1.FreeDevice();
Rec2.FreeDevice();
}
}
public static Image AlignLocallyToTarget(Image map, Image target, int alignmentSize, int oversampling, out float3 shift, out float3 rotation)
{
float ScaleFactor = (float)alignmentSize / map.Dims.X;
int3 DimsScaled = new int3(alignmentSize, alignmentSize, alignmentSize);
#region Prepare Scaled & FFTed maps
Image MapScaled = map.AsScaled(DimsScaled);
map.FreeDevice();
Image TargetScaled = target.AsScaled(DimsScaled);
target.FreeDevice();
TargetScaled.RemapToFT(true);
TargetScaled.WriteMRC("d_targetscaled.mrc", true);
Image TargetScaledFT = TargetScaled.AsFFT(true);
TargetScaled.Dispose();
Projector ProjMapScaled = new Projector(MapScaled, oversampling);
Image TestFT = ProjMapScaled.Project(DimsScaled, new float3[1]);
Image Test = TestFT.AsIFFT(true);
Test.RemapFromFT(true);
Test.WriteMRC("d_projected.mrc", true);
#endregion
float3 CurShift = new float3(), CurRotation = new float3();
Func <double[], double> GetDiff = input =>
{
CurShift = new float3((float)input[0], (float)input[1], (float)input[2]);
CurRotation = new float3((float)input[3], (float)input[4], (float)input[5]) * Helper.ToRad;
CurRotation = Matrix3.EulerFromMatrix(Matrix3.RotateX(CurRotation.X) * Matrix3.RotateY(CurRotation.Y) * Matrix3.RotateZ(CurRotation.Z)) * Helper.ToDeg;
Image TargetFTShifted = TargetScaledFT.AsShiftedVolume(-CurShift * ScaleFactor);
Image MapRotatedFT = ProjMapScaled.Project(DimsScaled, new[] { CurRotation *Helper.ToRad });
GPU.MultiplySlices(TargetFTShifted.GetDevice(Intent.Read),
MapRotatedFT.GetDevice(Intent.Read),
TargetFTShifted.GetDevice(Intent.Write),
TargetFTShifted.ElementsReal,
1);
MapRotatedFT.Dispose();
IntPtr d_Sum = GPU.MallocDevice(1);
GPU.Sum(TargetFTShifted.GetDevice(Intent.Read), d_Sum, (uint)TargetFTShifted.ElementsReal, 1);
TargetFTShifted.Dispose();
float[] h_Sum = new float[1];
GPU.CopyDeviceToHost(d_Sum, h_Sum, 1);
GPU.FreeDevice(d_Sum);
return(h_Sum[0]);
};
Func <double[], double[]> GetGradient = input =>
{
float Delta = 0.05f;
double[] Result = new double[input.Length];
Console.WriteLine(GetDiff(input));
for (int i = 0; i < input.Length; i++)
{
double[] InputPlus = input.ToList().ToArray();
InputPlus[i] += Delta;
double ScorePlus = GetDiff(InputPlus);
double[] InputMinus = input.ToList().ToArray();
InputMinus[i] -= Delta;
double ScoreMinus = GetDiff(InputMinus);
Result[i] = (ScorePlus - ScoreMinus) / (Delta * 2);
}
return(Result);
};
double[] StartParams = new double[6];
BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, GetDiff, GetGradient);
Optimizer.MaxIterations = 20;
Optimizer.Maximize(StartParams);
GetDiff(StartParams);
shift = CurShift;
rotation = CurRotation;
#region Shift and rotate input map by determined values for final output
ProjMapScaled.Dispose();
Image MapResult = map.AsShiftedVolume(shift);
map.FreeDevice();
Projector ProjMapResult = new Projector(MapResult, oversampling);
MapResult.Dispose();
Image MapResultFT = ProjMapResult.Project(map.Dims, new[] { rotation *Helper.ToRad });
ProjMapResult.Dispose();
MapResult = MapResultFT.AsIFFT(true);
MapResultFT.Dispose();
MapResult.RemapFromFT(true);
#endregion
return(MapResult);
}
