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Program.cs
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Program.cs
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using System;
using System.Collections.Generic;
using System.Diagnostics;
using System.IO;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using Accord.Math.Optimization;
using CommandLine;
using Warp;
using Warp.Tools;
namespace Warp.Craft
{
class Program
{
static void Main(string[] args)
{
int NIterations = 40;
int NSteps = 20;
int BatchSize = 128;
int ThreadsPerGPU = 1;
int MaxGPUs = 4;
float ParticleDiameter = 350;
float PixelSize = 2.5f;
int OutputBFactor = -100;
int FilterWindowSize = 30;
float FSCThreshold = 0.7f;
int DilateMask = 2;
int BodyOverlap = 6;
string InitCoarsePath = "it000_atomscoarse.mrc";// "NMA_15k_100.mrc";
int NCoarseAtoms = 15000;
int OversampleFineAtoms = 4;
bool DoUpdateModes = false;
int NModes = 15;
int NMaxSegments = 15;
int NSegmentsOptimization = 15;
int NSegmentsReconstruction = 15;
int NSamplesMC = 1;
int NSamplesMCSignificant = 1;
float Sigma2NMA = 1f;
float Sigma2Params = 1f;
bool PrereadParticles = true;
string ProjDir = !Debugger.IsAttached ? Environment.CurrentDirectory : "";
if (ProjDir[ProjDir.Length - 1] != '\\' && ProjDir[ProjDir.Length - 1] != '/')
ProjDir = ProjDir + "\\";
string ModelStarPath = ProjDir + "";
string ForcedBodiesPath = "";
if (!Debugger.IsAttached)
{
Options Options = new Options();
if (Parser.Default.ParseArguments(args, Options))
{
ModelStarPath = ProjDir + Options.ModelStarPath;
ParticleDiameter = Options.ParticleDiameter;
PixelSize = Options.PixelSize;
NIterations = Options.NIterations;
NSteps = Options.NSteps;
BatchSize = Options.BatchSize;
ThreadsPerGPU = Options.ThreadsPerGPU;
OutputBFactor = Options.BFactor;
FilterWindowSize = Options.WindowSize;
FSCThreshold = Options.FSCThreshold;
DilateMask = Options.DilateMask;
BodyOverlap = Options.BodyOverlap;
InitCoarsePath = Options.InitCoarsePath;
NCoarseAtoms = Options.NCoarseAtoms;
OversampleFineAtoms = Options.OversampleFine;
DoUpdateModes = Options.UpdateModes;
NModes = Options.NModes;
PrereadParticles = Options.PrereadParticles;
}
else
{
return;
}
}
Console.WriteLine("Executing with the following parameters:");
Console.WriteLine($" Input model: {ModelStarPath}");
Console.WriteLine($" Particle diameter: {ParticleDiameter} A");
Console.WriteLine($" Pixel size: {PixelSize} A");
Console.WriteLine($" Iterations: {NIterations}");
Console.WriteLine($" Steps per iteration: {NSteps}");
Console.WriteLine($" Batch size: {BatchSize}");
Console.WriteLine($" Threads per GPU: {ThreadsPerGPU}\n");
Console.WriteLine($" Pre-read particles: {PrereadParticles}\n");
Console.WriteLine($" Output B-factor: {OutputBFactor} A^2");
Console.WriteLine($" Local resolution window size: {FilterWindowSize} px");
Console.WriteLine($" Local resolution FSC threshold: {FSCThreshold}\n");
Console.WriteLine($" Dilate mask for fine model: {DilateMask} px");
Console.WriteLine($" Body overlap region: {BodyOverlap} px\n");
Console.WriteLine($" Init coarse atom model with: {InitCoarsePath}");
Console.WriteLine($" Number of coarse atoms: {NCoarseAtoms}");
Console.WriteLine($" Oversample fine atoms by: {OversampleFineAtoms}x");
Console.WriteLine($" Update modes after each iteration: {DoUpdateModes}");
Console.WriteLine($" Normal modes: {NModes}\n");
if (!File.Exists(ModelStarPath))
{
Console.WriteLine("Could not find input model STAR file.");
return;
}
Star TableMap = new Star(ModelStarPath, "map");
Star TableBodies = new Star(ModelStarPath, "bodies");
Star TableAtoms = Star.ContainsTable(ModelStarPath, "atoms") ? new Star(ModelStarPath, "atoms") : null; // Atoms are not necessarily defined for first iteration
// If bodies are specified as a wildcard, find them
{
if (TableBodies.RowCount == 1 && TableBodies.GetRowValue(0, "wrpBodyMaskHard").Contains("*"))
{
string Wildcard = TableBodies.GetRowValue(0, "wrpBodyMaskHard");
TableBodies = new Star(new [] {"wrpBodyMaskHard", "wrpBodyResolution"});
string WildcardFolder = Wildcard.Contains("/") ? Wildcard.Substring(0, Wildcard.LastIndexOf("/")) : "";
Wildcard = Wildcard.Substring(Wildcard.LastIndexOf("/") + 1);
foreach (var file in Directory.EnumerateFiles(ProjDir + WildcardFolder, Wildcard))
{
string MaskPath = file.Substring(ProjDir.Length).Replace("\\", "/");
TableBodies.AddRow(new List<string> { MaskPath, "100" });
}
}
}
int NBodies = TableBodies.RowCount;
int Size; // Get box size from one of the reference maps
{
string MapPath = TableMap.GetRowValue(0, "wrpMapHalf1");
Image Map = Image.FromFile(ProjDir + MapPath, new int2(1, 1), 0, typeof(float));
Size = Map.Dims.X;
Map.Dispose();
}
Console.WriteLine("Calculating masks.\n");
#region Create global mask from the sum of all wide local masks
Image MaskGlobal, MaskGlobalDilated;
int MaskGlobalVoxels, MaskGlobalDilatedVoxels;
//Projector ProjectorMask;
{
MaskGlobal = new Image(new int3(Size, Size, Size));
Parallel.For(0, NBodies, new ParallelOptions { MaxDegreeOfParallelism = 2 }, r =>
{
Image MaskLocal = Image.FromFile(ProjDir + TableBodies.GetRowValue(r, "wrpBodyMaskHard"), new int2(1, 1), 0, typeof (float));
lock (MaskGlobal)
MaskGlobal.Add(MaskLocal);
MaskLocal.Dispose();
});
MaskGlobal.Binarize(1e-5f);
MaskGlobalDilated = MaskGlobal.AsDilatedMask(DilateMask);
MaskGlobalVoxels = (int)(MaskGlobal.GetHostContinuousCopy().Sum() + 0.5f);
MaskGlobalDilatedVoxels = (int)(MaskGlobalDilated.GetHostContinuousCopy().Sum() + 0.5f);
MaskGlobal.FreeDevice();
MaskGlobalDilated.FreeDevice();
MaskGlobal.WriteMRC("d_maskglobal.mrc");
MaskGlobalDilated.WriteMRC("d_maskglobaldilated.mrc");
//Image MaskForParticles = MaskGlobal.AsDilatedMask(10);
//ProjectorMask = new Projector(MaskForParticles, 2);
//MaskForParticles.Dispose();
}
#endregion
#region Calculate masks to insert each body into the frankenmap
float[] BodySegmentation = new float[Size * Size * Size];
{
for (int i = 0; i < BodySegmentation.Length; i++)
BodySegmentation[i] = -1f;
Parallel.For(0, NBodies, new ParallelOptions { MaxDegreeOfParallelism = 2 }, b =>
{
Image HardMask = Image.FromFile(ProjDir + TableBodies.GetRowValue(b, "wrpBodyMaskHard"));
HardMask.Binarize(1e-6f);
float[] HardMaskData = HardMask.GetHostContinuousCopy();
lock (BodySegmentation)
{
Parallel.For(0, HardMaskData.Length, i =>
{
if (HardMaskData[i] > 0)
BodySegmentation[i] = b;
});
}
HardMask.Dispose();
});
}
// If forced body masks are provided:
float[] ForcedSegmentation = null;
if (ForcedBodiesPath != "")
{
ForcedSegmentation = new float[Size * Size * Size];
string Wildcard = ForcedBodiesPath;
string WildcardFolder = Wildcard.Contains("/") ? Wildcard.Substring(0, Wildcard.LastIndexOf("/")) : "";
Wildcard = Wildcard.Substring(Wildcard.LastIndexOf("/") + 1);
int b = 0;
foreach (var file in Directory.EnumerateFiles(ProjDir + WildcardFolder, Wildcard))
{
Image HardMask = Image.FromFile(file);
HardMask.Binarize(1e-6f);
float[] HardMaskData = HardMask.GetHostContinuousCopy();
Parallel.For(0, HardMaskData.Length, i =>
{
if (HardMaskData[i] > 0)
ForcedSegmentation[i] = b;
});
HardMask.Dispose();
b++;
}
NSegmentsOptimization = b;
NSegmentsReconstruction = b;
NMaxSegments = b;
}
#endregion
NMAMap AtomsCoarse;
NMAMap[][] AtomsFineHalves = new NMAMap[GPU.GetDeviceCount()][];
for (int i = 0; i < AtomsFineHalves.Length; i++)
AtomsFineHalves[i] = new NMAMap[2];
#region Pre-read particles into memory if needed
Dictionary<string, float[]> ParticleStorage = new Dictionary<string, float[]>();
if (PrereadParticles)
{
Console.WriteLine("Pre-reading particles:");
#region Load particle parameters
Star TableData = new Star(ProjDir + TableMap.GetRowValue(0, "wrpParticles"));
List<int>[] SubsetRows = { new List<int>(), new List<int>() };
for (int r = 0; r < TableData.RowCount; r++)
SubsetRows[(int)float.Parse(TableData.GetRowValue(r, "rlnRandomSubset")) - 1].Add(r);
#endregion
for (int h = 0, completed = 0; h < 2; h++)
{
Parallel.For(0, SubsetRows[h].Count, r =>
{
int R = SubsetRows[h][r];
string ImageName = TableData.GetRowValue(R, "rlnImageName");
string[] AddressParts = ImageName.Split(new[] { "@" }, StringSplitOptions.RemoveEmptyEntries);
int Layer = int.Parse(AddressParts[0]) - 1;
string FileName = ProjDir + AddressParts[1];
// Get particle
Image Particle = Image.FromFile(FileName, new int2(Size, Size), 0, typeof (float), Layer);
lock (TableMap)
{
ParticleStorage.Add(ImageName, Particle.GetHostContinuousCopy());
completed++;
if (completed % 100 == 0 || completed == SubsetRows.Select(v => v.Count).Sum())
{
ClearCurrentConsoleLine();
Console.Write($" {completed}/{SubsetRows.Select(v => v.Count).Sum()}");
}
}
});
}
Console.Write("\n\n");
}
#endregion
for (int iter = 0; iter < NIterations; iter++)
{
Console.WriteLine($"Started iteration {iter + 1}:\n");
if (iter > 0) // In first iteration, tables are already loaded and possibly modified
{
TableMap = new Star(ModelStarPath, "map");
TableBodies = new Star(ModelStarPath, "bodies");
TableAtoms = Star.ContainsTable(ModelStarPath, "atoms") ? new Star(ModelStarPath, "atoms") : null; // Atoms are not necessarily defined for first iteration
}
#region Load or make atom model
{
if (InitCoarsePath == "" && (iter == 0 || DoUpdateModes)) // Initialize from scratch in first iteration, or update every iteration
{
Console.WriteLine(" Calculating normal modes – this can take a while.");
Image Frankenmap = Image.FromFile(ProjDir + TableMap.GetRowValue(0, "wrpFrankenmap"));
AtomsCoarse = NMAMap.FromScratch(Frankenmap, MaskGlobal, NCoarseAtoms, 100, 2.5f);
Frankenmap.Dispose();
AtomsCoarse.WriteToMRC(ProjDir + $"it000_atomscoarse.mrc");
if (NModes < AtomsCoarse.NModes)
AtomsCoarse.LimitModesTo(NModes);
AtomsCoarse.SmoothModes(128);
}
else if (InitCoarsePath != "" && iter == 0) // Initialize with precalculated model
{
Console.WriteLine($" Initializing normal modes with {InitCoarsePath}.");
AtomsCoarse = new NMAMap(ProjDir + InitCoarsePath);
if (NModes < AtomsCoarse.NModes)
AtomsCoarse.LimitModesTo(NModes);
NModes = AtomsCoarse.NModes;
NCoarseAtoms = AtomsCoarse.NAtoms;
AtomsCoarse.SmoothModes(128);
}
else if (TableAtoms != null) // Take model from previous iteration
{
Console.WriteLine(" Using normal modes from previous iteration.");
AtomsCoarse = new NMAMap(ProjDir + TableAtoms.GetRowValue(0, "wrpAtomsCoarse"));
}
else
{
Console.WriteLine(" Atom model initialization went wrong: after first iteration, model.star should contain a path to the coarse model.");
return;
}
AtomsCoarse.AddSegmentation(new Image(BodySegmentation, new int3(Size, Size, Size)));
// Store coarse atoms for this iteration in a new file, regardless of whether the model is new or old
AtomsCoarse.WriteToMRC(ProjDir + $"it{iter + 1:D3}_atomscoarse.mrc");
if (TableAtoms == null)
{
TableAtoms = new Star(new[] { "wrpAtomsCoarse" });
TableAtoms.AddRow(new List<string> { $"it{(iter + 1):D3}_atomscoarse.mrc" });
}
else
{
if (!TableAtoms.HasColumn("wrpAtomsCoarse"))
TableAtoms.AddColumn("wrpAtomsCoarse");
TableAtoms.SetRowValue(0, "wrpAtomsCoarse", $"it{(iter + 1):D3}_atomscoarse.mrc");
}
AtomsCoarse.RasterizeInVolume(new int3(Size, Size, Size)).WriteMRC("d_atomscoarse_groundmode.mrc");
for (int m = 0; m < AtomsCoarse.NModes; m++)
{
float[] Weights = new float[AtomsCoarse.NModes];
Weights[m] = 2;
AtomsCoarse.RasterizeDeformedInVolume(new int3(Size, Size, Size), Weights).WriteMRC($"d_atomscoarse_mode{m:D2}.mrc");
}
AtomsCoarse.AddSegmentation(new Image(BodySegmentation, new int3(Size, Size, Size)));
Console.WriteLine("");
}
#endregion
//AtomsCoarse.ReduceToNSegments(20);
//Image[] TestMasks = AtomsCoarse.GetSoftSegmentMasks(BodyOverlap, BodyOverlap * 1.5f);
//for (int i = 0; i < TestMasks.Length; i++)
//{
// TestMasks[i].WriteMRC($"d_testmask{i:D2}.mrc");
//}
//float[][] TestMasksData = TestMasks.Select(v => v.GetHostContinuousCopy()).ToArray();
//float[] TestMaskSum = new float[TestMasksData[0].Length];
//for (int i = 0; i < TestMaskSum.Length; i++)
// for (int j = 0; j < AtomsCoarse.NSegments; j++)
// TestMaskSum[i] += TestMasksData[j][i];
//new Image(TestMaskSum, AtomsCoarse.DimsVolume).WriteMRC("d_testmasksum.mrc");
int SizeCoarse;
float ScaleFactor;
#region Estimate current per-body resolution, construct fine atom models from locally filtered maps
int BestResolutionShell = 0;
float[] InitialResolution = new float[NBodies];
int[] BodyMaxShell = new int[NBodies];
float3[] BodyCenter = new float3[NBodies];
Projector[] DebugProjectors = new Projector[2];
{
Console.WriteLine(" Estimating per-body resolution:");
Image Map1 = Image.FromFile(ProjDir + TableMap.GetRowValue(0, "wrpMapHalf1"), new int2(1, 1), 0, typeof (float));
Image Map2 = Image.FromFile(ProjDir + TableMap.GetRowValue(0, "wrpMapHalf2"), new int2(1, 1), 0, typeof (float));
#region Estimate local resolution
{
Image LocalRes = new Image(IntPtr.Zero, new int3(Size, Size, Size));
Image Map1Pristine = Map1;
Image Map2Pristine = Map2;
if (iter > 0)
{
Map1Pristine = Image.FromFile(ProjDir + TableMap.GetRowValue(0, "wrpMapHalfPristine1"), new int2(1, 1), 0, typeof(float));
Map2Pristine = Image.FromFile(ProjDir + TableMap.GetRowValue(0, "wrpMapHalfPristine2"), new int2(1, 1), 0, typeof(float));
}
GPU.LocalRes(Map1Pristine.GetDevice(Intent.Read),
Map2Pristine.GetDevice(Intent.Read),
new int3(Size, Size, Size),
PixelSize,
IntPtr.Zero,
IntPtr.Zero,
LocalRes.GetDevice(Intent.Write),
IntPtr.Zero,
FilterWindowSize,
FSCThreshold,
false,
10,
0,
0,
false,
false);
if (iter > 0)
{
Map1Pristine.Dispose();
Map2Pristine.Dispose();
}
float[] LocalResData = LocalRes.GetHostContinuousCopy().Select(v => Size * PixelSize / Math.Max(1, v)).ToArray(); // LocalResData now as frequencies
float GlobalAverageShell = MathHelper.MeanWeighted(LocalResData, MaskGlobal.GetHostContinuousCopy());
BestResolutionShell = (int)GlobalAverageShell;
LocalRes.WriteMRC("d_localres.mrc");
//Image LocalRes = Image.FromFile("d_localres.mrc");
Image[] MasksHard = AtomsCoarse.GetSegmentMasks();
int Done = 0;
Parallel.For(0, NBodies, b =>
{
Image MaskHard = MasksHard[b];
BodyCenter[b] = MaskHard.AsCenterOfMass();
float[] MaskHardData = MaskHard.GetHostContinuousCopy();
float AverageShell = MathHelper.MeanWeighted(LocalResData, MaskHardData);
BodyMaxShell[b] = (int)AverageShell;
InitialResolution[b] = AverageShell; // Frequency in global volume frame
MaskHard.Dispose();
lock (TableAtoms)
{
//BestResolutionShell = Math.Max((int)AverageShell, BestResolutionShell);
ClearCurrentConsoleLine();
Console.Write($" {++Done}/{NBodies}");
}
});
LocalRes.Dispose();
}
#endregion
Console.Write("\n");
#region Use the Frankenmaps to calculate per-voxel resolution based on the estimated per-body resolutions
Image[] MasksSmooth = AtomsCoarse.GetSoftSegmentMasks(BodyOverlap, BodyOverlap * 1.5f);
Image BodyResolution, BodyBFactor;
{
float[] BodyResolutionData = new float[Size * Size * Size];
for (int b = 0; b < MasksSmooth.Length; b++)
{
float ResVal = InitialResolution[b];
float[] FrankenMaskData = MasksSmooth[b].GetHostContinuousCopy();
for (int i = 0; i < BodyResolutionData.Length; i++)
BodyResolutionData[i] += ResVal * FrankenMaskData[i];
}
for (int i = 0; i < BodyResolutionData.Length; i++)
BodyResolutionData[i] = Math.Min(Size * PixelSize / Math.Max(Math.Min(BestResolutionShell, BodyResolutionData[i]), 1f), FilterWindowSize / 2 * PixelSize);
BodyResolution = new Image(BodyResolutionData, new int3(Size, Size, Size));
BodyBFactor = new Image(new int3(Size, Size, Size));
BodyResolution.WriteMRC("d_bodyresolution.mrc");
}
foreach (var mask in MasksSmooth)
mask.Dispose();
#endregion
#region Filter both half-maps to per-voxel resolution derived from bodies
GPU.LocalFilter(Map1.GetDevice(Intent.Read),
Map1.GetDevice(Intent.Write),
new int3(Size, Size, Size),
PixelSize,
BodyResolution.GetDevice(Intent.Read),
BodyBFactor.GetDevice(Intent.Read),
FilterWindowSize,
0f);
GPU.LocalFilter(Map2.GetDevice(Intent.Read),
Map2.GetDevice(Intent.Write),
new int3(Size, Size, Size),
PixelSize,
BodyResolution.GetDevice(Intent.Read),
BodyBFactor.GetDevice(Intent.Read),
FilterWindowSize,
0f);
//Map1 = Image.FromFile("d_map1.mrc");
//Map2 = Image.FromFile("d_map2.mrc");
Map1.WriteMRC("d_map1.mrc");
Map2.WriteMRC("d_map2.mrc");
BodyResolution.Dispose();
BodyBFactor.Dispose();
#endregion
//Image SoftMask = Image.FromFile(ProjDir + TableMap.GetRowValue(0, "wrpSoftMask"));
//Map1.Multiply(SoftMask);
//Map2.Multiply(SoftMask);
//SoftMask.Dispose();
Map1.FreeDevice();
Map2.FreeDevice();
//DebugProjectors[0] = new Projector(Map1, 2);
//DebugProjectors[1] = new Projector(Map2, 2);
// Set maximum image size and scale factor to match current average resolution
SizeCoarse = BestResolutionShell * 2;
ScaleFactor = (float)SizeCoarse / Size;
Console.WriteLine($" Considering data until {Size * PixelSize / BestResolutionShell:F2} A.");
if (BestResolutionShell < 3)
{
Console.WriteLine(" ERROR: At least one of the bodies cannot be resolved at all. Aborting.");
return;
}
if (iter == 0)
{
Console.WriteLine($" Initial resolution for individual bodies at {FSCThreshold:F3} cutoff is:");
for (int b = 0; b < NBodies; b++)
Console.WriteLine($" {b + 1}: {Size * PixelSize / InitialResolution[b]:F2} A");
Console.Write("\n");
}
#region Construct fine atom models
Console.WriteLine(" Calculating fine NMA models.");
NMAMap AtomsForFine = AtomsCoarse.GetCopy();
if (ForcedSegmentation == null)
AtomsForFine.ReduceToNSegments(NSegmentsOptimization);
else
AtomsForFine.AddSegmentation(new Image(ForcedSegmentation, new int3(Size, Size, Size)));
//int gpuID = 0;
Helper.ForEachGPUOnce(gpuID =>
{
float SigmaFine, CorrFine;
Image Map1Copy = new Image(Map1.GetHost(Intent.Read), Map1.Dims);
Image Map2Copy = new Image(Map2.GetHost(Intent.Read), Map2.Dims);
AtomsFineHalves[gpuID][0] = AtomsForFine.GetCopy();
AtomsFineHalves[gpuID][0].InitializeBodyProjectors(BodyOverlap, BodyOverlap * 1.5f, Map1Copy, SizeCoarse, 2);
AtomsFineHalves[gpuID][0].FreeOnDevice();
AtomsFineHalves[gpuID][1] = AtomsForFine.GetCopy();
AtomsFineHalves[gpuID][1].InitializeBodyProjectors(BodyOverlap, BodyOverlap * 1.5f, Map2Copy, SizeCoarse, 2);
AtomsFineHalves[gpuID][1].FreeOnDevice();
if (gpuID == 0)
{
AtomsFineHalves[0][0].WriteToMRC("d_atomsfine1.mrc");
AtomsFineHalves[0][1].WriteToMRC("d_atomsfine2.mrc");
AtomsFineHalves[0][0].RasterizeInVolume(new int3(Size, Size, Size)).WriteMRC("d_atomsfine.mrc");
for (int m = 0; m < AtomsFineHalves[0][0].NModes; m++)
{
float[] Weights = new float[AtomsFineHalves[0][0].NModes];
Weights[m] = 2;
AtomsFineHalves[0][0].RasterizeDeformedInVolume(new int3(Size, Size, Size), Weights).WriteMRC($"d_atomsfine_mode{m:D2}.mrc");
}
}
}, MaxGPUs);
Map1.Dispose();
Map2.Dispose();
#endregion
}
#endregion
#region Load particle parameters
Star TableData = new Star(ProjDir + TableMap.GetRowValue(0, "wrpParticles"));
int NParticles = TableData.RowCount;
List<int>[] SubsetRows = { new List<int>(), new List<int>() };
for (int r = 0; r < TableData.RowCount; r++)
SubsetRows[(int)float.Parse(TableData.GetRowValue(r, "rlnRandomSubset")) - 1].Add(r);
Dictionary<string, int> GroupMapping = new Dictionary<string, int>();
float3[][] ParticleAngles = { new float3[SubsetRows[0].Count], new float3[SubsetRows[1].Count] };
float2[][] ParticleShifts = { new float2[SubsetRows[0].Count], new float2[SubsetRows[1].Count] };
float[][] ParticleNMAWeights = { new float[SubsetRows[0].Count * NModes], new float[SubsetRows[1].Count * NModes] };
CTFStruct[][] ParticleCTFParams = { new CTFStruct[SubsetRows[0].Count], new CTFStruct[SubsetRows[1].Count] };
int[][] ParticleGroups = { new int[SubsetRows[0].Count], new int[SubsetRows[1].Count] };
float3[][][] MCAngles = { new float3[SubsetRows[0].Count][], new float3[SubsetRows[1].Count][] };
float2[][][] MCShifts = { new float2[SubsetRows[0].Count][], new float2[SubsetRows[1].Count][] };
float[][][] MCNMAWeights = { new float[SubsetRows[0].Count][], new float[SubsetRows[1].Count][] };
float[][][] MCScores = { new float[SubsetRows[0].Count][], new float[SubsetRows[1].Count][] };
for (int h = 0; h < 2; h++)
{
// Get CTF parameters
for (int r = 0; r < SubsetRows[h].Count; r++)
{
int R = SubsetRows[h][r];
float Voltage = TableData.GetRowValueFloat(R, "rlnVoltage");
float DefocusU = TableData.GetRowValueFloat(R, "rlnDefocusU") / 1e4f;
float DefocusV = TableData.GetRowValueFloat(R, "rlnDefocusV") / 1e4f;
float DefocusAngle = TableData.GetRowValueFloat(R, "rlnDefocusAngle");
float Cs = TableData.GetRowValueFloat(R, "rlnSphericalAberration");
//float Phase = TableData[0].GetRowValueFloat(R, "rlnPhaseShift");
float Contrast = TableData.GetRowValueFloat(R, "rlnAmplitudeContrast");
CTF ParticleCTF = new CTF
{
PixelSize = (decimal)PixelSize,
Voltage = (decimal)Voltage,
Defocus = (decimal)(DefocusU + DefocusV) * 0.5M,
DefocusDelta = (decimal)(DefocusU - DefocusV),
DefocusAngle = (decimal)DefocusAngle,
Cs = (decimal)Cs,
//PhaseShift = (decimal)Phase / 180M,
Amplitude = (decimal)Contrast
};
ParticleCTFParams[h][r] = ParticleCTF.ToStruct();
}
// Get rotations and shifts
for (int r = 0; r < SubsetRows[h].Count; r++)
{
int R = SubsetRows[h][r];
ParticleAngles[h][r] = new float3(TableData.GetRowValueFloat(R, "rlnAngleRot"),
TableData.GetRowValueFloat(R, "rlnAngleTilt"),
TableData.GetRowValueFloat(R, "rlnAnglePsi"));
ParticleShifts[h][r] = new float2(TableData.GetRowValueFloat(R, "rlnOriginX"),
TableData.GetRowValueFloat(R, "rlnOriginY"));
}
// Get NMA weights if there are any
{
string[] NMAColumns = TableData.GetColumnNames().Where(v => v.Contains("wrpNMAWeight")).ToArray();
bool AllColumnsPresent = true;
for (int i = 1; i <= NModes; i++)
if (!NMAColumns.Contains($"wrpNMAWeight{i}"))
AllColumnsPresent = false;
if (AllColumnsPresent)
{
for (int m = 0; m < NModes; m++)
for (int r = 0; r < SubsetRows[h].Count; r++)
{
int R = SubsetRows[h][r];
ParticleNMAWeights[h][r * NModes + m] = TableData.GetRowValueFloat(SubsetRows[h][r], $"wrpNMAWeight{m + 1}");
}
}
}
// Figure out groups
for (int r = 0; r < SubsetRows[h].Count; r++)
{
int R = SubsetRows[h][r];
string MicName = TableData.HasColumn("rlnGroupName") ? TableData.GetRowValue(R, "rlnGroupName") :
TableData.GetRowValue(R, "rlnMicrographName");
MicName = MicName.Substring(MicName.LastIndexOf("/") + 1);
if (!GroupMapping.ContainsKey(MicName))
GroupMapping.Add(MicName, GroupMapping.Count);
ParticleGroups[h][r] = GroupMapping[MicName];
}
}
// Map particles to groups
int NGroups = GroupMapping.Count;
List<int>[][] GroupParticles = { new List<int>[NGroups], new List<int>[NGroups] };
for (int h = 0; h < 2; h++)
for (int g = 0; g < NGroups; g++)
GroupParticles[h][g] = new List<int>();
for (int h = 0; h < 2; h++)
for (int p = 0; p < SubsetRows[h].Count; p++)
GroupParticles[h][ParticleGroups[h][p]].Add(p);
#endregion
#region Noise and scale estimation
Console.WriteLine(" Estimating noise spectra for each micrograph:");
//Image Dummy = Image.FromFile("E:\\multibody2\\tf2h\\it040_frankenmap_half1.mrc");
//Projector DummyProj = new Projector(Dummy, 2);
float[][] GroupInvNoise = new float[NGroups][];
float[] GroupScale = new float[NGroups].Select(v => 1f).ToArray();
float[] ParticleNormalization = new float[NParticles].Select(v => 1f).ToArray();
{
int[] PixelShell = new int[(SizeCoarse / 2 + 1) * SizeCoarse];
for (int y = 0; y < SizeCoarse; y++)
for (int x = 0; x < SizeCoarse / 2 + 1; x++)
{
int xx = x;
int yy = y < SizeCoarse / 2 + 1 ? y : y - SizeCoarse;
int R = (int)Math.Round(Math.Sqrt(xx * xx + yy * yy));
PixelShell[y * (SizeCoarse / 2 + 1) + x] = R < SizeCoarse / 2 ? R : -1;
}
#region Iterate over groups
if (true)
{
int GroupsDone = 0;
Helper.ForGPU(0, NGroups, (g, gpuID) =>
{
float[] Noise1D = new float[SizeCoarse / 2];
int[] Samples1D = new int[SizeCoarse / 2];
float SumPart = 0, SumProj = 0;
Image CTFCoordsCoarse = CTF.GetCTFCoords(SizeCoarse, Size);
#region Create mask
Image ParticleMask = new Image(new int3(SizeCoarse, SizeCoarse, 1));
{
float[] ParticleMaskData = ParticleMask.GetHost(Intent.Write)[0];
float Radius2 = ParticleDiameter / 2 / PixelSize * ScaleFactor;
for (int y = 0; y < SizeCoarse; y++)
{
int yy = y - SizeCoarse / 2;
yy *= yy;
for (int x = 0; x < SizeCoarse; x++)
{
int xx = x - SizeCoarse / 2;
xx *= xx;
float R = (float)Math.Sqrt(xx + yy);
float V = R <= Radius2 ? 1f : (float)(Math.Cos(Math.Min(1, (R - Radius2) / 10) * Math.PI) * 0.5 + 0.5);
ParticleMaskData[y * SizeCoarse + x] = V;
}
}
}
#endregion
float2[][][] ParticleData = new float2[2][][];
float2[][][] ProjData = new float2[2][][];
for (int h = 0; h < 2; h++)
{
int NParts = GroupParticles[h][g].Count;
if (NParts == 0)
continue;
#region Get particle parameters
float3[] GroupAngles = new float3[NParts];
float2[] GroupShifts = new float2[NParts];
CTFStruct[] GroupCTFParams = new CTFStruct[NParts];
float[][] GroupNMAWeights = Helper.ArrayOfFunction(() => new float[NModes], NParts);
for (int p = 0; p < NParts; p++)
{
int pi = GroupParticles[h][g][p];
GroupAngles[p] = ParticleAngles[h][pi];
GroupShifts[p] = ParticleShifts[h][pi];
GroupCTFParams[p] = ParticleCTFParams[h][pi];
for (int m = 0; m < NModes; m++)
GroupNMAWeights[p][m] = ParticleNMAWeights[h][pi * NModes + m];
}
#endregion
#region Create CTF
Image GroupCTF;
{
GroupCTF = new Image(new int3(SizeCoarse, SizeCoarse, NParts), true);
GPU.CreateCTF(GroupCTF.GetDevice(Intent.Write),
CTFCoordsCoarse.GetDevice(Intent.Read),
(uint)CTFCoordsCoarse.ElementsComplex,
GroupCTFParams,
false,
(uint)NParts);
//GroupCTF.WriteMRC("d_groupctf.mrc");
}
#endregion
#region Project reference
Image ProjectionsFT = AtomsFineHalves[gpuID][h].ProjectBodies(new int2(SizeCoarse, SizeCoarse),
GroupNMAWeights,
GroupAngles.Select(a => a * Helper.ToRad).ToArray(),
new float2[NParts],
Helper.ArrayOfFunction(() => Helper.ArrayOfConstant(1f, AtomsFineHalves[gpuID][h].NSegments), NParts),
NParts);
//Image ProjectionsFT = DebugProjectors[h].Project(new int2(SizeCoarse, SizeCoarse), GroupAngles.Select(a => a * Helper.ToRad).ToArray(), (int)(192 * 2.74f / 15f));
//Image ProjectionsFT = new Image(new int3(SizeCoarse, SizeCoarse, NParts), true, true);
AtomsFineHalves[gpuID][h].FreeOnDevice();
#endregion
ProjectionsFT.Multiply(GroupCTF);
//ProjectionsFT.Multiply(1f / Size);
#region Load particles
Image ParticlesCoarseFT;
{
Image ParticlesRaw = new Image(new int3(Size, Size, NParts));
float[][] ParticlesRawData = ParticlesRaw.GetHost(Intent.Write);
for (int p = 0; p < NParts; p++)
{
int pi = GroupParticles[h][g][p];
string ImageName = TableData.GetRowValue(SubsetRows[h][pi], "rlnImageName");
if (!PrereadParticles)
{
string[] AddressParts = ImageName.Split(new[] { "@" }, StringSplitOptions.RemoveEmptyEntries);
int Layer = int.Parse(AddressParts[0]) - 1;
string FileName = ProjDir + AddressParts[1];
Image Particle = Image.FromFile(FileName, new int2(Size, Size), 0, typeof (float), Layer);
ParticlesRawData[p] = Particle.GetHostContinuousCopy();
Particle.Dispose();
}
else
{
ParticlesRawData[p] = ParticleStorage[ImageName].ToArray();
}
}
ParticlesRaw.ShiftSlices(GroupShifts.Select(v => new float3(v.X, v.Y, 0)).ToArray());
Image ParticlesCoarse = ParticlesRaw.AsScaled(new int2(SizeCoarse, SizeCoarse));
ParticlesCoarse.Multiply(1f / (SizeCoarse * SizeCoarse));
ParticlesRaw.Dispose();
//ParticlesCoarse.WriteMRC("d_particlescoarse.mrc");
ParticlesCoarse.MultiplySlices(ParticleMask);
ParticlesCoarse.RemapToFT();
ParticlesCoarseFT = ParticlesCoarse.AsFFT();
ParticlesCoarse.Dispose();
}
#endregion
//ParticlesCoarseFT.Subtract(ProjectionsFT);
#region Calculate squared differences for variance estimation
ParticleData[h] = ParticlesCoarseFT.GetHostComplexCopy();
ProjData[h] = ProjectionsFT.GetHostComplexCopy();
for (int p = 0; p < NParts; p++)
{
float2[] PartSlice = ParticleData[h][p];
float2[] ProjSlice = ProjData[h][p];
for (int i = 0; i < PixelShell.Length; i++)
if (PixelShell[i] >= 0)
{
SumPart += PartSlice[i].X * ProjSlice[i].X + PartSlice[i].Y * ProjSlice[i].Y;
SumProj += ProjSlice[i].X * ProjSlice[i].X + ProjSlice[i].Y * ProjSlice[i].Y;
}
}
#endregion
ParticlesCoarseFT.Dispose();
ProjectionsFT.Dispose();
GroupCTF.Dispose();
}
ParticleMask.Dispose();
CTFCoordsCoarse.Dispose();
GroupScale[g] = SumPart / Math.Max(1e-20f, SumProj);
for (int h = 0; h < 2; h++)
{
int NParts = GroupParticles[h][g].Count;
if (NParts == 0)
continue;
for (int p = 0; p < NParts; p++)
{
int pi = SubsetRows[h][GroupParticles[h][g][p]];
float2[] PartSlice = ParticleData[h][p];
float2[] ProjSlice = ProjData[h][p];
for (int i = 0; i < PixelShell.Length; i++)
if (PixelShell[i] >= 0)
{
float2 Diff = PartSlice[i] - ProjSlice[i] * GroupScale[g];
Noise1D[PixelShell[i]] += Diff.X * Diff.X + Diff.Y * Diff.Y;
Samples1D[PixelShell[i]]++;
ParticleNormalization[pi] += Diff.X * Diff.X + Diff.Y * Diff.Y;
}
ParticleNormalization[pi] = (float)Math.Sqrt(ParticleNormalization[pi] * 2);
}
}
for (int r = 0; r < SizeCoarse / 2; r++)
Noise1D[r] /= Samples1D[r] * 2;
float[] InvNoise = new float[PixelShell.Length];
for (int i = 0; i < InvNoise.Length; i++)
if (PixelShell[i] >= 0)
InvNoise[i] = 1f / Noise1D[PixelShell[i]];
GroupInvNoise[g] = InvNoise;
lock (TableData)
{
ClearCurrentConsoleLine();
Console.Write($" {++GroupsDone}/{NGroups}");
}
}, 1, MaxGPUs);
}
#endregion
Console.Write("\n");
}
// Normalize particle norm factors to average to 1.0
{
float AverageNorm = MathHelper.Mean(ParticleNormalization);
ParticleNormalization = ParticleNormalization.Select(v => v / AverageNorm).ToArray();
}
// Normalize group scales to have average of 1.0
{
float AverageScale = MathHelper.Mean(GroupScale);
GroupScale = GroupScale.Select(v => v / AverageScale).ToArray();
}
new Image(GroupInvNoise, new int3(SizeCoarse, SizeCoarse, NGroups), true).WriteMRC("d_invsigma2.mrc");
//GroupInvNoise = Image.FromFile("d_invsigma2.mrc").GetHost(Intent.Read);