public static Matrix3 Euler(float rot, float tilt, float psi)
{
float ca, sa, cb, sb, cg, sg;
float cc, cs, sc, ss;
ca = (float)Math.Cos(rot);
cb = (float)Math.Cos(tilt);
cg = (float)Math.Cos(psi);
sa = (float)Math.Sin(rot);
sb = (float)Math.Sin(tilt);
sg = (float)Math.Sin(psi);
cc = cb * ca;
cs = cb * sa;
sc = sb * ca;
ss = sb * sa;
Matrix3 A = new Matrix3();
A.M11 = cg * cc - sg * sa;
A.M12 = cg * cs + sg * ca;
A.M13 = -cg * sb;
A.M21 = -sg * cc - cg * sa;
A.M22 = -sg * cs + cg * ca;
A.M23 = sg * sb;
A.M31 = sc;
A.M32 = ss;
A.M33 = cb;
return A;
}
public MainWindow()
{
try
{
Options.DeviceCount = GPU.GetDeviceCount();
if (Options.DeviceCount <= 0)
throw new Exception();
}
catch (Exception)
{
MessageBox.Show("No CUDA devices found, shutting down.");
Close();
}
GPU.MemoryChanged += () => Options.UpdateGPUStats();
DataContext = Options;
Options.PropertyChanged += Options_PropertyChanged;
Closing += MainWindow_Closing;
InitializeComponent();
DisableWhenRunning = new List<UIElement>
{
GridOptionsIO,
GridOptionsPreprocessing,
GridOptionsParticles,
GridOptionsCTF,
GridOptionsMovement,
GridOptionsGrids,
GridOptionsPostprocessing
};
if (File.Exists("Previous.settings"))
Options.Load("Previous.settings");
for (int i = 0; i < GPU.GetDeviceCount(); i++)
{
GPU.SetDevice(i);
Console.WriteLine($"Device {i}:");
Console.WriteLine($"Free memory: {GPU.GetFreeMemory(i)} MB");
Console.WriteLine($"Total memory: {GPU.GetTotalMemory(i)} MB");
}
GPU.SetDevice(0);
Options.UpdateGPUStats();
// Create mockup
{
float2[] SplinePoints = { new float2(0f, 0f), new float2(1f / 3f, 1f)};//, new float2(2f / 3f, 0f)};//, new float2(1f, 1f) };
Cubic1D ReferenceSpline = new Cubic1D(SplinePoints);
Cubic1DShort ShortSpline = Cubic1DShort.GetInterpolator(SplinePoints);
for (float i = -1f; i < 2f; i += 0.01f)
{
float Reference = ReferenceSpline.Interp(i);
float Test = ShortSpline.Interp(i);
if (Math.Abs(Reference - Test) > 1e-6f)
throw new Exception();
}
Random Rnd = new Random(123);
int3 GridDim = new int3(1, 1, 1);
float[] GridValues = new float[GridDim.Elements()];
for (int i = 0; i < GridValues.Length; i++)
GridValues[i] = (float)Rnd.NextDouble();
CubicGrid CGrid = new CubicGrid(GridDim, GridValues);
float[] Managed = CGrid.GetInterpolated(new int3(16, 16, 16), new float3(0, 0, 0));
float[] Native = CGrid.GetInterpolatedNative(new int3(16, 16, 16), new float3(0, 0, 0));
for (int i = 0; i < Managed.Length; i++)
if (Math.Abs(Managed[i] - Native[i]) > 1e-6f)
throw new Exception();
Matrix3 A = new Matrix3(1, 2, 3, 4, 5, 6, 7, 8, 9);
Matrix3 B = new Matrix3(11, 12, 13, 14, 15, 16, 17, 18, 19);
Matrix3 C = A * B;
// Euler matrix
{
Matrix3 E = Matrix3.Euler(0 * Helper.ToRad, 20 * Helper.ToRad, 0 * Helper.ToRad);
float3 EE = Matrix3.EulerFromMatrix(E.Transposed()) * Helper.ToDeg;
float3 Transformed = E * new float3(1, 0, 0);
Transformed.Y = 0;
}
//float3[] HealpixAngles = Helper.GetHealpixAngles(3, "D4");
// Deconvolve reconstructions using a separate CTF
//{
// for (int i = 1; i <= 24; i++)
// {
// Image Map = StageDataLoad.LoadMap($"F:\\stefanribo\\vlion\\warped_{i}.mrc", new int2(1, 1), 0, typeof(float));
// Image MapFT = Map.AsFFT(true);
// Map.Dispose();
// Image CTF = StageDataLoad.LoadMap($"F:\\stefanribo\\vlion\\warped_ctf_{i}.mrc", new int2(1, 1), 0, typeof(float));
// foreach (var slice in CTF.GetHost(Intent.ReadWrite))
// for (int s = 0; s < slice.Length; s++)
// slice[s] = Math.Max(1e-3f, slice[s]);
// MapFT.Divide(CTF);
// Map = MapFT.AsIFFT(true);
// MapFT.Dispose();
// Map.WriteMRC($"F:\\stefanribo\\vlion\\warped_deconv_{i}.mrc");
// Map.Dispose();
// }
//}
//{
// Image SumFT = new Image(new int3(220, 220, 220), true, true);
// Image SumWeights = new Image(new int3(220, 220, 220), true);
// int read = 0;
// foreach (var tomoPath in Directory.EnumerateFiles("F:\\stefanribo\\oridata\\particles", "tomo*.mrc"))
// {
// FileInfo Info = new FileInfo(tomoPath);
// Image Tomo = StageDataLoad.LoadMap(tomoPath, new int2(1, 1), 0, typeof(float));
// Image TomoFT = Tomo.AsFFT(true);
// Tomo.Dispose();
// Image TomoWeights = StageDataLoad.LoadMap("F:\\stefanribo\\oridata\\particlectf\\" + Info.Name, new int2(1, 1), 0, typeof(float));
// TomoFT.Multiply(TomoWeights);
// TomoWeights.Multiply(TomoWeights);
// SumFT.Add(TomoFT);
// SumWeights.Add(TomoWeights);
// TomoFT.Dispose();
// TomoWeights.Dispose();
// Debug.WriteLine(read++);
// }
// foreach (var slice in SumWeights.GetHost(Intent.ReadWrite))
// {
// for (int i = 0; i < slice.Length; i++)
// {
// slice[i] = Math.Max(1e-3f, slice[i]);
// }
// }
// SumFT.Divide(SumWeights);
// Image Sum = SumFT.AsIFFT(true);
// Sum.WriteMRC("F:\\stefanribo\\oridata\\particles\\weightedaverage.mrc");
// SumFT.Dispose();
// SumWeights.Dispose();
// Sum.Dispose();
//}
//{
// Image Subtrahend = StageDataLoad.LoadMap("E:\\martinsried\\stefan\\membranebound\\vlion\\relion_subtrahend.mrc", new int2(1, 1), 0, typeof(float));
// Image SubtrahendFT = Subtrahend.AsFFT(true);
// int read = 0;
// foreach (var tomoPath in Directory.EnumerateFiles("E:\\martinsried\\stefan\\membranebound\\oridata\\particles", "tomo*.mrc"))
// {
// FileInfo Info = new FileInfo(tomoPath);
// Image Tomo = StageDataLoad.LoadMap(tomoPath, new int2(1, 1), 0, typeof(float));
// Image TomoFT = Tomo.AsFFT(true);
// Tomo.Dispose();
// Image TomoWeights = StageDataLoad.LoadMap("E:\\martinsried\\stefan\\membranebound\\oridata\\particlectf\\" + Info.Name, new int2(1, 1), 0, typeof(float));
// Image SubtrahendFTMult = new Image(SubtrahendFT.GetDevice(Intent.Read), SubtrahendFT.Dims, true, true);
// SubtrahendFTMult.Multiply(TomoWeights);
// TomoFT.Subtract(SubtrahendFTMult);
// Tomo = TomoFT.AsIFFT(true);
// Tomo.WriteMRC("D:\\stefanribo\\particles\\" + Info.Name);
// Tomo.Dispose();
// TomoFT.Dispose();
// SubtrahendFTMult.Dispose();
// TomoWeights.Dispose();
// Debug.WriteLine(read++);
// }
//}
//{
// Image SubtRef1 = StageDataLoad.LoadMap("E:\\martinsried\\stefan\\membranebound\\vlion\\warp_subtrahend.mrc", new int2(1, 1), 0, typeof(float));
// Projector Subt = new Projector(SubtRef1, 2);
// SubtRef1.Dispose();
// Image ProjFT = Subt.Project(new int2(220, 220), new[] { new float3(0, 0, 0) }, 110);
// Image Proj = ProjFT.AsIFFT();
// Proj.RemapFromFT();
// Proj.WriteMRC("d_testproj.mrc");
//}
// Projector
/*{
Image MapForProjector = StageDataLoad.LoadMap("E:\\youwei\\run36_half1_class001_unfil.mrc", new int2(1, 1), 0, typeof (float));
Projector Proj = new Projector(MapForProjector, 2);
Image Projected = Proj.Project(new int2(240, 240), new[] { new float3(0, 0, 0) }, 120);
Projected = Projected.AsIFFT();
Projected.RemapFromFT();
Projected.WriteMRC("d_projected.mrc");
}*/
// Backprojector
/*{
Image Dot = new Image(new int3(32, 32, 360));
for (int a = 0; a < 360; a++)
Dot.GetHost(Intent.Write)[a][0] = 1;
Dot = Dot.AsFFT();
Dot.AsAmplitudes().WriteMRC("d_dot.mrc");
Image DotWeights = new Image(new int3(32, 32, 360), true);
for (int a = 0; a < 360; a++)
for (int i = 0; i < DotWeights.ElementsSliceReal; i++)
DotWeights.GetHost(Intent.Write)[a][i] = 1;
float3[] Angles = new float3[360];
for (int a = 0; a < 360; a++)
Angles[a] = new float3(0, a * Helper.ToRad * 0.05f, 0);
Projector Proj = new Projector(new int3(32, 32, 32), 2);
Proj.BackProject(Dot, DotWeights, Angles);
Proj.Weights.WriteMRC("d_weights.mrc");
//Image Re = Proj.Data.AsImaginary();
//Re.WriteMRC("d_projdata.mrc");
Image Rec = Proj.Reconstruct(true);
Rec.WriteMRC("d_rec.mrc");
}*/
//Star Models = new Star("D:\\rado27\\Refine3D\\run1_ct5_it005_half1_model.star", "data_model_group_2");
//Debug.WriteLine(Models.GetRow(0)[0]);
/*Image Volume = StageDataLoad.LoadMap("F:\\carragher20s\\ref256.mrc", new int2(1, 1), 0, typeof (float));
Image VolumePadded = Volume.AsPadded(new int3(512, 512, 512));
VolumePadded.WriteMRC("d_padded.mrc");
Volume.Dispose();
VolumePadded.RemapToFT(true);
Image VolumeFT = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
Image VolumeProjFT = VolumeFT.AsProjections(new[] { new float3(Helper.ToRad * 0, Helper.ToRad * 0, Helper.ToRad * 0) }, new int2(256, 256), 2f);
Image VolumeProj = VolumeProjFT.AsIFFT();
VolumeProjFT.Dispose();
VolumeProj.RemapFromFT();
VolumeProj.WriteMRC("d_proj.mrc");
VolumeProj.Dispose();*/
/*Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.44.54.mrc"));
Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.49.06.mrc"));
Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.50.48.mrc"));
Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.52.16.mrc"));
Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.53.43.mrc"));
CTFDisplay.PS2D = new BitmapImage();*/
/*float2[] SimCoords = new float2[512 * 512];
for (int y = 0; y < 512; y++)
for (int x = 0; x < 512; x++)
{
int xcoord = x - 512, ycoord = y - 512;
SimCoords[y * 512 + x] = new float2((float) Math.Sqrt(xcoord * xcoord + ycoord * ycoord),
(float) Math.Atan2(ycoord, xcoord));
}
float[] Sim2D = new CTF {Defocus = -2M}.Get2D(SimCoords, 512, true);
byte[] Sim2DBytes = new byte[Sim2D.Length];
for (int i = 0; i < 512 * 512; i++)
Sim2DBytes[i] = (byte) (Sim2D[i] * 255f);
BitmapSource Sim2DSource = BitmapSource.Create(512, 512, 96, 96, PixelFormats.Indexed8, BitmapPalettes.Gray256, Sim2DBytes, 512);
CTFDisplay.Simulated2D = Sim2DSource;*/
/*float2[] PointsPS1D = new float2[512];
for (int i = 0; i < PointsPS1D.Length; i++)
PointsPS1D[i] = new float2(i, (float) Math.Exp(-i / 300f));
CTFDisplay.PS1D = PointsPS1D;
float[] SimCTF = new CTF { Defocus = -2M }.Get1D(512, true);
float2[] PointsSim1D = new float2[SimCTF.Length];
for (int i = 0; i < SimCTF.Length; i++)
PointsSim1D[i] = new float2(i, SimCTF[i] * (float)Math.Exp(-i / 100f) + (float)Math.Exp(-i / 300f));
CTFDisplay.Simulated1D = PointsSim1D;*/
/*CubicGrid Grid = new CubicGrid(new int3(5, 5, 5), 0, 0, Dimension.X);
Grid.Values[2, 2, 2] = 1f;
float[] Data = new float[11 * 11 * 11];
int i = 0;
for (float z = 0f; z < 1.05f; z += 0.1f)
for (float y = 0f; y < 1.05f; y += 0.1f)
for (float x = 0f; x < 1.05f; x += 0.1f)
Data[i++] = Grid.GetInterpolated(new float3(x, y, z));
Image DataImage = new Image(Data, new int3(11, 11, 11));
DataImage.WriteMRC("bla.mrc");
Image GPUImage = new Image(DataImage.GetDevice(Intent.Read), new int3(11, 11, 11));
GPUImage.WriteMRC("gpu.mrc");*/
/*CubicGrid WiggleGrid = new CubicGrid(new int3(2, 2, 1));
float[][] WiggleWeights = WiggleGrid.GetWiggleWeights(new int3(3, 3, 1));*/
}
}
public static float3 EulerFromMatrix(Matrix3 a)
{
float alpha, beta, gamma;
float abs_sb, sign_sb;
abs_sb = (float)Math.Sqrt(a.M13 * a.M13 + a.M23 * a.M23);
if (abs_sb > 16 * 1.192092896e-07f)
{
gamma = (float)Math.Atan2(a.M23, -a.M13);
alpha = (float)Math.Atan2(a.M32, a.M31);
if (Math.Abs((float)Math.Sin(gamma)) < 1.192092896e-07f)
sign_sb = Math.Sign(-a.M13 / Math.Cos(gamma));
else
sign_sb = (Math.Sin(gamma) > 0) ? Math.Sign(a.M23) : -Math.Sign(a.M23);
beta = (float)Math.Atan2(sign_sb * abs_sb, a.M33);
}
else
{
if (Math.Sign(a.M33) > 0)
{
// Let's consider the matrix as a rotation around Z
alpha = 0;
beta = 0;
gamma = (float)Math.Atan2(-a.M21, a.M11);
}
else
{
alpha = 0;
beta = (float)Math.PI;
gamma = (float)Math.Atan2(a.M21, -a.M11);
}
}
return new float3(alpha, beta, gamma);
}