static DefectModel LoadAndPrepareDefectMap(string path, bool flipX, bool flipY, bool transpose)
{
Image Defects = Image.FromFilePatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType));
if (flipX)
{
Defects = Defects.AsFlippedX();
}
if (flipY)
{
Defects = Defects.AsFlippedY();
}
if (transpose)
{
Defects = Defects.AsTransposed();
}
DefectModel Model = new DefectModel(Defects, 4);
Defects.Dispose();
return(Model);
}
static Image LoadAndPrepareGainReference(string path, bool flipX, bool flipY, bool transpose)
{
Image Gain = Image.FromFilePatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType));
float Mean = MathHelper.Mean(Gain.GetHost(Intent.Read)[0]);
Gain.TransformValues(v => v == 0 ? 1 : v / Mean);
if (flipX)
{
Gain = Gain.AsFlippedX();
}
if (flipY)
{
Gain = Gain.AsFlippedY();
}
if (transpose)
{
Gain = Gain.AsTransposed();
}
return(Gain);
}
static Image LoadAndPrepareGainReference(string path, bool flipX, bool flipY, bool transpose)
{
Image Gain = Image.FromFilePatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType));
if (flipX)
{
Gain = Gain.AsFlippedX();
}
if (flipY)
{
Gain = Gain.AsFlippedY();
}
if (transpose)
{
Gain = Gain.AsTransposed();
}
return(Gain);
}
static Image LoadAndPrepareStack(string path, decimal scaleFactor, int maxThreads = 8)
{
Image stack = null;
MapHeader header = MapHeader.ReadFromFilePatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType));
string Extension = Helper.PathToExtension(path).ToLower();
bool IsTiff = header.GetType() == typeof(HeaderTiff);
bool IsEER = header.GetType() == typeof(HeaderEER);
if (GainRef != null)
{
if (!IsEER)
{
if (header.Dimensions.X != GainRef.Dims.X || header.Dimensions.Y != GainRef.Dims.Y)
{
throw new Exception("Gain reference dimensions do not match image.");
}
}
}
int EERSupersample = 1;
if (GainRef != null && IsEER)
{
if (header.Dimensions.X == GainRef.Dims.X)
{
EERSupersample = 1;
}
else if (header.Dimensions.X * 2 == GainRef.Dims.X)
{
EERSupersample = 2;
}
else if (header.Dimensions.X * 4 == GainRef.Dims.X)
{
EERSupersample = 3;
}
else
{
throw new Exception("Invalid supersampling factor requested for EER based on gain reference dimensions");
}
}
HeaderEER.SuperResolution = EERSupersample;
if (IsEER && GainRef != null)
{
header.Dimensions.X = GainRef.Dims.X;
header.Dimensions.Y = GainRef.Dims.Y;
}
int NThreads = (IsTiff || IsEER) ? 6 : 2;
int GPUThreads = 2;
int CurrentDevice = GPU.GetDevice();
if (RawLayers == null || RawLayers.Length != NThreads || RawLayers[0].Length != header.Dimensions.ElementsSlice())
{
RawLayers = Helper.ArrayOfFunction(i => new float[header.Dimensions.ElementsSlice()], NThreads);
}
Image[] GPULayers = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, header.Dimensions.Slice()), GPUThreads);
Image[] GPULayers2 = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, header.Dimensions.Slice()), GPUThreads);
if (scaleFactor == 1M)
{
stack = new Image(header.Dimensions);
float[][] OriginalStackData = stack.GetHost(Intent.Write);
object[] Locks = Helper.ArrayOfFunction(i => new object(), GPUThreads);
Helper.ForCPU(0, header.Dimensions.Z, NThreads, threadID => GPU.SetDevice(DeviceID), (z, threadID) =>
{
if (IsTiff)
{
TiffNative.ReadTIFFPatient(50, 500, path, z, true, RawLayers[threadID]);
}
else if (IsEER)
{
EERNative.ReadEERPatient(50, 500, path, z * 10, (z + 1) * 10, EERSupersample, RawLayers[threadID]);
}
else
{
IOHelper.ReadMapFloatPatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType),
new[] { z },
null,
new[] { RawLayers[threadID] });
}
int GPUThreadID = threadID % GPUThreads;
lock (Locks[GPUThreadID])
{
GPU.CopyHostToDevice(RawLayers[threadID], GPULayers[GPUThreadID].GetDevice(Intent.Write), RawLayers[threadID].Length);
if (GainRef != null)
{
if (IsEER)
{
GPULayers[GPUThreadID].DivideSlices(GainRef);
}
else
{
GPULayers[GPUThreadID].MultiplySlices(GainRef);
}
}
if (DefectMap != null)
{
GPU.CopyDeviceToDevice(GPULayers[GPUThreadID].GetDevice(Intent.Read),
GPULayers2[GPUThreadID].GetDevice(Intent.Write),
header.Dimensions.Elements());
DefectMap.Correct(GPULayers2[GPUThreadID], GPULayers[GPUThreadID]);
}
GPU.Xray(GPULayers[GPUThreadID].GetDevice(Intent.Read),
GPULayers2[GPUThreadID].GetDevice(Intent.Write),
20f,
new int2(header.Dimensions),
1);
GPU.CopyDeviceToHost(GPULayers2[GPUThreadID].GetDevice(Intent.Read),
OriginalStackData[z],
header.Dimensions.ElementsSlice());
}
}, null);
}
else
{
int3 ScaledDims = new int3((int)Math.Round(header.Dimensions.X * scaleFactor) / 2 * 2,
(int)Math.Round(header.Dimensions.Y * scaleFactor) / 2 * 2,
header.Dimensions.Z);
stack = new Image(ScaledDims);
float[][] OriginalStackData = stack.GetHost(Intent.Write);
int[] PlanForw = Helper.ArrayOfFunction(i => GPU.CreateFFTPlan(header.Dimensions.Slice(), 1), GPUThreads);
int[] PlanBack = Helper.ArrayOfFunction(i => GPU.CreateIFFTPlan(ScaledDims.Slice(), 1), GPUThreads);
Image[] GPULayersInputFT = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, header.Dimensions.Slice(), true, true), GPUThreads);
Image[] GPULayersOutputFT = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, ScaledDims.Slice(), true, true), GPUThreads);
Image[] GPULayersScaled = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, ScaledDims.Slice()), GPUThreads);
object[] Locks = Helper.ArrayOfFunction(i => new object(), GPUThreads);
Helper.ForCPU(0, ScaledDims.Z, NThreads, threadID => GPU.SetDevice(DeviceID), (z, threadID) =>
{
if (IsTiff)
{
TiffNative.ReadTIFFPatient(50, 500, path, z, true, RawLayers[threadID]);
}
else if (IsEER)
{
EERNative.ReadEERPatient(50, 500, path, z * 10, (z + 1) * 10, EERSupersample, RawLayers[threadID]);
}
else
{
IOHelper.ReadMapFloatPatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType),
new[] { z },
null,
new[] { RawLayers[threadID] });
}
int GPUThreadID = threadID % GPUThreads;
lock (Locks[GPUThreadID])
{
GPU.CopyHostToDevice(RawLayers[threadID], GPULayers[GPUThreadID].GetDevice(Intent.Write), RawLayers[threadID].Length);
if (GainRef != null)
{
if (IsEER)
{
GPULayers[GPUThreadID].DivideSlices(GainRef);
}
else
{
GPULayers[GPUThreadID].MultiplySlices(GainRef);
}
}
if (DefectMap != null)
{
GPU.CopyDeviceToDevice(GPULayers[GPUThreadID].GetDevice(Intent.Read),
GPULayers2[GPUThreadID].GetDevice(Intent.Write),
header.Dimensions.Elements());
DefectMap.Correct(GPULayers2[GPUThreadID], GPULayers[GPUThreadID]);
}
GPU.Xray(GPULayers[GPUThreadID].GetDevice(Intent.Read),
GPULayers2[GPUThreadID].GetDevice(Intent.Write),
20f,
new int2(header.Dimensions),
1);
GPU.Scale(GPULayers2[GPUThreadID].GetDevice(Intent.Read),
GPULayersScaled[GPUThreadID].GetDevice(Intent.Write),
header.Dimensions.Slice(),
ScaledDims.Slice(),
1,
PlanForw[GPUThreadID],
PlanBack[GPUThreadID],
GPULayersInputFT[GPUThreadID].GetDevice(Intent.Write),
GPULayersOutputFT[GPUThreadID].GetDevice(Intent.Write));
GPU.CopyDeviceToHost(GPULayersScaled[GPUThreadID].GetDevice(Intent.Read),
OriginalStackData[z],
ScaledDims.ElementsSlice());
}
}, null);
for (int i = 0; i < GPUThreads; i++)
{
GPU.DestroyFFTPlan(PlanForw[i]);
GPU.DestroyFFTPlan(PlanBack[i]);
GPULayersInputFT[i].Dispose();
GPULayersOutputFT[i].Dispose();
GPULayersScaled[i].Dispose();
}
}
foreach (var layer in GPULayers)
{
layer.Dispose();
}
foreach (var layer in GPULayers2)
{
layer.Dispose();
}
return(stack);
}
public static float[][] ReadMapFloat(string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, int layer = -1)
{
MapHeader Header = null;
Type ValueType = null;
FileInfo Info = new FileInfo(path);
float[][] Data;
using (BinaryReader Reader = new BinaryReader(OpenWithBigBuffer(path)))
{
Header = MapHeader.ReadFromFile(Reader, Info, headerlessSliceDims, headerlessOffset, headerlessType);
ValueType = Header.GetValueType();
Data = new float[layer < 0 ? Header.Dimensions.Z : 1][];
if (Header.GetType() != typeof(HeaderTiff))
{
for (int z = 0; z < Data.Length; z++)
{
if (layer >= 0)
{
Reader.BaseStream.Seek((int)Header.Dimensions.ElementsSlice() * (int)ImageFormatsHelper.SizeOf(ValueType) * layer, SeekOrigin.Current);
}
byte[] Bytes = Reader.ReadBytes((int)Header.Dimensions.ElementsSlice() * (int)ImageFormatsHelper.SizeOf(ValueType));
Data[z] = new float[(int)Header.Dimensions.ElementsSlice()];
unsafe
{
int Elements = (int)Header.Dimensions.ElementsSlice();
fixed(byte *BytesPtr = Bytes)
fixed(float *DataPtr = Data[z])
{
float *DataP = DataPtr;
if (ValueType == typeof(byte))
{
byte *BytesP = BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(short))
{
short *BytesP = (short *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(ushort))
{
ushort *BytesP = (ushort *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(int))
{
int *BytesP = (int *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(float))
{
float *BytesP = (float *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = *BytesP++;
}
}
else if (ValueType == typeof(double))
{
double *BytesP = (double *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
}
}
}
}
else
{
Data = ((HeaderTiff)Header).ReadData(layer);
}
}
return(Data);
}
public static void WriteMapFloat(string path, MapHeader header, float[][] data)
{
Type ValueType = header.GetValueType();
using (BinaryWriter Writer = new BinaryWriter(CreateWithBigBuffer(path)))
{
header.Write(Writer);
long Elements = header.Dimensions.ElementsSlice();
for (int z = 0; z < data.Length; z++)
{
byte[] Bytes = new byte[Elements * ImageFormatsHelper.SizeOf(ValueType)];
unsafe
{
fixed(float *DataPtr = data[z])
fixed(byte *BytesPtr = Bytes)
{
float *DataP = DataPtr;
if (ValueType == typeof(byte))
{
byte *BytesP = BytesPtr;
for (long i = 0; i < Elements; i++)
{
*BytesP++ = (byte)*DataP++;
}
}
else if (ValueType == typeof(short))
{
short *BytesP = (short *)BytesPtr;
for (long i = 0; i < Elements; i++)
{
*BytesP++ = (short)*DataP++;
}
}
else if (ValueType == typeof(ushort))
{
ushort *BytesP = (ushort *)BytesPtr;
for (long i = 0; i < Elements; i++)
{
*BytesP++ = (ushort)Math.Min(Math.Max(0f, *DataP++ *16f), 65536f);
}
}
else if (ValueType == typeof(int))
{
int *BytesP = (int *)BytesPtr;
for (long i = 0; i < Elements; i++)
{
*BytesP++ = (int)*DataP++;
}
}
else if (ValueType == typeof(float))
{
float *BytesP = (float *)BytesPtr;
for (long i = 0; i < Elements; i++)
{
*BytesP++ = *DataP++;
}
}
else if (ValueType == typeof(double))
{
double *BytesP = (double *)BytesPtr;
for (long i = 0; i < Elements; i++)
{
*BytesP++ = (double)*DataP++;
}
}
}
}
Writer.Write(Bytes);
}
}
}
public static float[] ReadSmallMapFloat(string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType)
{
FileInfo Info = new FileInfo(path);
float[] Data;
using (BinaryReader Reader = new BinaryReader(OpenWithBigBuffer(path)))
{
MapHeader Header = MapHeader.ReadFromFile(Reader, Info, headerlessSliceDims, headerlessOffset, headerlessType);
Type ValueType = Header.GetValueType();
Data = new float[Header.Dimensions.Elements()];
byte[] Bytes = Reader.ReadBytes((int)Header.Dimensions.Elements() * (int)ImageFormatsHelper.SizeOf(ValueType));
unsafe
{
int Elements = (int)Header.Dimensions.Elements();
fixed(byte *BytesPtr = Bytes)
fixed(float *DataPtr = Data)
{
float *DataP = DataPtr;
if (ValueType == typeof(byte))
{
byte *BytesP = BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(short))
{
short *BytesP = (short *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(ushort))
{
ushort *BytesP = (ushort *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(int))
{
int *BytesP = (int *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(float))
{
float *BytesP = (float *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = *BytesP++;
}
}
else if (ValueType == typeof(double))
{
double *BytesP = (double *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
}
}
}
return(Data);
}
public static float[][] ReadMapFloat(string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, bool isBigEndian, int layer = -1, Stream stream = null, float[][] reuseBuffer = null)
{
MapHeader Header = null;
Type ValueType = null;
float[][] Data;
if (MapHeader.GetHeaderType(path) != typeof(HeaderTiff))
{
using (BinaryReader Reader = isBigEndian ? new BinaryReaderBE(OpenWithBigBuffer(path)) : new BinaryReader(OpenWithBigBuffer(path)))
{
Header = MapHeader.ReadFromFile(Reader, path, headerlessSliceDims, headerlessOffset, headerlessType);
ValueType = Header.GetValueType();
Data = reuseBuffer == null ? new float[layer < 0 ? Header.Dimensions.Z : 1][] : reuseBuffer;
int ReadBatchSize = Math.Min((int)Header.Dimensions.ElementsSlice(), 1 << 20);
int ValueSize = (int)ImageFormatsHelper.SizeOf(ValueType);
byte[] Bytes = new byte[ReadBatchSize * ValueSize];
for (int z = 0; z < Data.Length; z++)
{
if (layer >= 0)
{
Reader.BaseStream.Seek(Header.Dimensions.ElementsSlice() * ImageFormatsHelper.SizeOf(ValueType) * layer, SeekOrigin.Current);
}
if (reuseBuffer == null)
{
Data[z] = new float[(int)Header.Dimensions.ElementsSlice()];
}
unsafe
{
fixed(byte *BytesPtr = Bytes)
fixed(float *DataPtr = Data[z])
{
for (int b = 0; b < (int)Header.Dimensions.ElementsSlice(); b += ReadBatchSize)
{
int CurBatch = Math.Min(ReadBatchSize, (int)Header.Dimensions.ElementsSlice() - b);
Reader.Read(Bytes, 0, CurBatch * ValueSize);
if (isBigEndian)
{
if (ValueType == typeof(short) || ValueType == typeof(ushort))
{
for (int i = 0; i < CurBatch * ValueSize / 2; i++)
{
Array.Reverse(Bytes, i * 2, 2);
}
}
else if (ValueType == typeof(int) || ValueType == typeof(float))
{
for (int i = 0; i < CurBatch * ValueSize / 4; i++)
{
Array.Reverse(Bytes, i * 4, 4);
}
}
else if (ValueType == typeof(double))
{
for (int i = 0; i < CurBatch * ValueSize / 8; i++)
{
Array.Reverse(Bytes, i * 8, 8);
}
}
}
float *DataP = DataPtr + b;
if (ValueType == typeof(byte))
{
byte *BytesP = BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(short))
{
short *BytesP = (short *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(ushort))
{
ushort *BytesP = (ushort *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(int))
{
int *BytesP = (int *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(float))
{
float *BytesP = (float *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = *BytesP++;
}
}
else if (ValueType == typeof(double))
{
double *BytesP = (double *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
}
}
}
}
}
}
else
{
Header = MapHeader.ReadFromFile(null, path, headerlessSliceDims, headerlessOffset, headerlessType, stream);
Data = ((HeaderTiff)Header).ReadData(stream, layer);
}
return(Data);
}
public static float[][] ReadMapFloat(BinaryReader reader, string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, bool isBigEndian, int[] layers = null, Stream stream = null, float[][] reuseBuffer = null)
{
MapHeader Header = null;
Type ValueType = null;
float[][] Data;
BinaryReader Reader = reader;
{
Header = MapHeader.ReadFromFile(Reader, path, headerlessSliceDims, headerlessOffset, headerlessType);
ValueType = Header.GetValueType();
Data = reuseBuffer == null ? new float[layers == null ? Header.Dimensions.Z : layers.Length][] : reuseBuffer;
int ReadBatchSize = Math.Min((int)Header.Dimensions.ElementsSlice(), 1 << 20);
int ValueSize = (int)ImageFormatsHelper.SizeOf(ValueType);
byte[] Bytes = new byte[ReadBatchSize * ValueSize];
long ReaderDataStart = Reader.BaseStream.Position;
for (int z = 0; z < Data.Length; z++)
{
if (layers != null)
{
Reader.BaseStream.Seek(Header.Dimensions.ElementsSlice() * ImageFormatsHelper.SizeOf(ValueType) * layers[z] + ReaderDataStart, SeekOrigin.Begin);
}
if (reuseBuffer == null)
{
Data[z] = new float[(int)Header.Dimensions.ElementsSlice()];
}
unsafe
{
fixed(byte *BytesPtr = Bytes)
fixed(float *DataPtr = Data[z])
{
for (int b = 0; b < (int)Header.Dimensions.ElementsSlice(); b += ReadBatchSize)
{
int CurBatch = Math.Min(ReadBatchSize, (int)Header.Dimensions.ElementsSlice() - b);
Reader.Read(Bytes, 0, CurBatch * ValueSize);
if (isBigEndian)
{
if (ValueType == typeof(short) || ValueType == typeof(ushort))
{
for (int i = 0; i < CurBatch * ValueSize / 2; i++)
{
Array.Reverse(Bytes, i * 2, 2);
}
}
else if (ValueType == typeof(int) || ValueType == typeof(float))
{
for (int i = 0; i < CurBatch * ValueSize / 4; i++)
{
Array.Reverse(Bytes, i * 4, 4);
}
}
else if (ValueType == typeof(double))
{
for (int i = 0; i < CurBatch * ValueSize / 8; i++)
{
Array.Reverse(Bytes, i * 8, 8);
}
}
}
float *DataP = DataPtr + b;
if (ValueType == typeof(byte))
{
byte *BytesP = BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(short))
{
short *BytesP = (short *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(ushort))
{
ushort *BytesP = (ushort *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(int))
{
int *BytesP = (int *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(float))
{
float *BytesP = (float *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = *BytesP++;
}
}
else if (ValueType == typeof(double))
{
double *BytesP = (double *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
}
}
}
}
}
return(Data);
}
private async void ButtonWrite_OnClick(object sender, RoutedEventArgs e)
{
string Suffix = TextSuffix.Text;
float ScaleFactorCoords = (float)(Options.Tasks.InputPixelSize / Options.BinnedPixelSizeMean);
float ScaleFactorShifts = (float)(Options.Tasks.InputShiftPixelSize / Options.BinnedPixelSizeMean);
ProgressWrite.Visibility = Visibility.Visible;
PanelButtons.Visibility = Visibility.Hidden;
await Task.Run(async() =>
{
Star TableIn = new Star(ImportPath);
#region Make sure everything is there
if (TableIn.RowCount == 0 || !TableIn.HasColumn("rlnCoordinateX") || !TableIn.HasColumn("rlnCoordinateY") || !TableIn.HasColumn("rlnMicrographName"))
{
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
"Please make sure the table contains data with rlnCoordinateX, rlnCoordinateY and rlnMicrographName columns.");
Close?.Invoke();
return;
}
if (Movies.Length == 0)
{
Close?.Invoke();
return;
}
#endregion
Directory.CreateDirectory(Movies[0].MatchingDir);
Dispatcher.Invoke(() => ProgressWrite.Maximum = Movies.Length);
int IndexMicName = TableIn.GetColumnID("rlnMicrographName");
TableIn.ModifyAllValuesInColumn("rlnMicrographName", v => Helper.PathToName(v));
int IndexCoordX = TableIn.GetColumnID("rlnCoordinateX");
int IndexCoordY = TableIn.GetColumnID("rlnCoordinateY");
#region Subtract origin from coordinates
int IndexOriginX = TableIn.GetColumnID("rlnOriginX");
if (IndexOriginX >= 0)
{
TableIn.ModifyAllValuesInColumn("rlnCoordinateX", (v, r) => (float.Parse(v) * ScaleFactorCoords - float.Parse(TableIn.GetRowValue(r, IndexOriginX)) * ScaleFactorShifts).ToString("F4"));
TableIn.SetColumn("rlnOriginX", Helper.ArrayOfConstant("0.0", TableIn.RowCount));
}
else
{
TableIn.ModifyAllValuesInColumn("rlnCoordinateX", v => (float.Parse(v) * ScaleFactorCoords).ToString("F4"));
}
int IndexOriginY = TableIn.GetColumnID("rlnOriginY");
if (IndexOriginY >= 0)
{
TableIn.ModifyAllValuesInColumn("rlnCoordinateY", (v, r) => (float.Parse(v) * ScaleFactorCoords - float.Parse(TableIn.GetRowValue(r, IndexOriginY)) * ScaleFactorShifts).ToString("F4"));
TableIn.SetColumn("rlnOriginY", Helper.ArrayOfConstant("0.0", TableIn.RowCount));
}
else
{
TableIn.ModifyAllValuesInColumn("rlnCoordinateY", v => (float.Parse(v) * ScaleFactorCoords).ToString("F4"));
}
#endregion
var GroupedRows = TableIn.GetAllRows().GroupBy(row => row[IndexMicName]).ToDictionary(g => g.Key, g => g.ToList());
foreach (var movie in Movies)
{
if (GroupedRows.ContainsKey(movie.RootName))
{
int3 Dims = MapHeader.ReadFromFile(movie.Path,
new int2(Options.Import.HeaderlessWidth, Options.Import.HeaderlessHeight),
Options.Import.HeaderlessOffset,
ImageFormatsHelper.StringToType(Options.Import.HeaderlessType)).Dimensions;
float3 BinnedDims = new float3(Dims) * (float)Options.PixelSizeMean / (float)Options.BinnedPixelSizeMean;
List <List <string> > Rows = GroupedRows[movie.RootName];
foreach (var row in Rows)
{
row[IndexMicName] = movie.Name;
float CoordX = float.Parse(row[IndexCoordX]);
if (Options.Tasks.InputFlipX)
{
CoordX = BinnedDims.X - CoordX;
}
float CoordY = float.Parse(row[IndexCoordY]);
if (Options.Tasks.InputFlipY)
{
CoordY = BinnedDims.Y - CoordY;
}
row[IndexCoordX] = CoordX.ToString("F4");
row[IndexCoordY] = CoordY.ToString("F4");
}
Star TableOut = new Star(TableIn.GetColumnNames());
foreach (var row in Rows)
{
TableOut.AddRow(row);
}
TableOut.Save(movie.MatchingDir + movie.RootName + "_" + Suffix + ".star");
movie.UpdateParticleCount("_" + Suffix);
}
Dispatcher.Invoke(() => ProgressWrite.Value++);
}
});
Close?.Invoke();
}
public static float[][] ReadMapFloat(string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, bool isBigEndian, int layer = -1, Stream stream = null)
{
MapHeader Header = null;
Type ValueType = null;
float[][] Data;
if (MapHeader.GetHeaderType(path) != typeof(HeaderTiff))
{
using (BinaryReader Reader = isBigEndian ? new BinaryReaderBE(OpenWithBigBuffer(path)) : new BinaryReader(OpenWithBigBuffer(path)))
{
Header = MapHeader.ReadFromFile(Reader, path, headerlessSliceDims, headerlessOffset, headerlessType);
ValueType = Header.GetValueType();
Data = new float[layer < 0 ? Header.Dimensions.Z : 1][];
for (int z = 0; z < Data.Length; z++)
{
if (layer >= 0)
{
Reader.BaseStream.Seek((long)Header.Dimensions.ElementsSlice() * (long)ImageFormatsHelper.SizeOf(ValueType) * layer, SeekOrigin.Current);
}
byte[] Bytes = Reader.ReadBytes((int)Header.Dimensions.ElementsSlice() * (int)ImageFormatsHelper.SizeOf(ValueType));
Data[z] = new float[(int)Header.Dimensions.ElementsSlice()];
if (isBigEndian)
{
if (ValueType == typeof(short) || ValueType == typeof(ushort))
{
for (int i = 0; i < Bytes.Length / 2; i++)
{
Array.Reverse(Bytes, i * 2, 2);
}
}
else if (ValueType == typeof(int) || ValueType == typeof(float))
{
for (int i = 0; i < Bytes.Length / 4; i++)
{
Array.Reverse(Bytes, i * 4, 4);
}
}
else if (ValueType == typeof(double))
{
for (int i = 0; i < Bytes.Length / 8; i++)
{
Array.Reverse(Bytes, i * 8, 8);
}
}
}
unsafe
{
int Elements = (int)Header.Dimensions.ElementsSlice();
fixed(byte *BytesPtr = Bytes)
fixed(float *DataPtr = Data[z])
{
float *DataP = DataPtr;
if (ValueType == typeof(byte))
{
byte *BytesP = BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(short))
{
short *BytesP = (short *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(ushort))
{
ushort *BytesP = (ushort *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(int))
{
int *BytesP = (int *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(float))
{
float *BytesP = (float *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = *BytesP++;
}
}
else if (ValueType == typeof(double))
{
double *BytesP = (double *)BytesPtr;
for (int i = 0; i < Elements; i++)
{
*DataP++ = (float)*BytesP++;
}
}
}
}
}
}
}
else
{
Header = MapHeader.ReadFromFile(null, path, headerlessSliceDims, headerlessOffset, headerlessType, stream);
Data = ((HeaderTiff)Header).ReadData(stream, layer);
}
return(Data);
}
public static float[][] ReadMapFloat(string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, bool isBigEndian, int[] layers = null, Stream stream = null, float[][] reuseBuffer = null)
{
MapHeader Header = null;
Type ValueType = null;
float[][] Data;
if (MapHeader.GetHeaderType(path) != typeof(HeaderTiff))
{
using (BinaryReader Reader = isBigEndian ? new BinaryReaderBE(OpenWithBigBuffer(path)) : new BinaryReader(OpenWithBigBuffer(path)))
{
Header = MapHeader.ReadFromFile(Reader, path, headerlessSliceDims, headerlessOffset, headerlessType);
ValueType = Header.GetValueType();
Data = reuseBuffer == null ? new float[layers == null ? Header.Dimensions.Z : layers.Length][] : reuseBuffer;
int ReadBatchSize = Math.Min((int)Header.Dimensions.ElementsSlice(), 1 << 20);
int ValueSize = (int)ImageFormatsHelper.SizeOf(ValueType);
byte[] Bytes = new byte[ReadBatchSize * ValueSize];
long ReaderDataStart = Reader.BaseStream.Position;
for (int z = 0; z < Data.Length; z++)
{
if (layers != null)
{
Reader.BaseStream.Seek(Header.Dimensions.ElementsSlice() * ImageFormatsHelper.SizeOf(ValueType) * layers[z] + ReaderDataStart, SeekOrigin.Begin);
}
if (reuseBuffer == null)
{
Data[z] = new float[(int)Header.Dimensions.ElementsSlice()];
}
unsafe
{
fixed(byte *BytesPtr = Bytes)
fixed(float *DataPtr = Data[z])
{
for (int b = 0; b < (int)Header.Dimensions.ElementsSlice(); b += ReadBatchSize)
{
int CurBatch = Math.Min(ReadBatchSize, (int)Header.Dimensions.ElementsSlice() - b);
Reader.Read(Bytes, 0, CurBatch * ValueSize);
if (isBigEndian)
{
if (ValueType == typeof(short) || ValueType == typeof(ushort))
{
for (int i = 0; i < CurBatch * ValueSize / 2; i++)
{
Array.Reverse(Bytes, i * 2, 2);
}
}
else if (ValueType == typeof(int) || ValueType == typeof(float))
{
for (int i = 0; i < CurBatch * ValueSize / 4; i++)
{
Array.Reverse(Bytes, i * 4, 4);
}
}
else if (ValueType == typeof(double))
{
for (int i = 0; i < CurBatch * ValueSize / 8; i++)
{
Array.Reverse(Bytes, i * 8, 8);
}
}
}
float *DataP = DataPtr + b;
if (ValueType == typeof(byte))
{
byte *BytesP = BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(short))
{
short *BytesP = (short *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(ushort))
{
ushort *BytesP = (ushort *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(int))
{
int *BytesP = (int *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
else if (ValueType == typeof(float))
{
float *BytesP = (float *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = *BytesP++;
}
}
else if (ValueType == typeof(double))
{
double *BytesP = (double *)BytesPtr;
for (int i = 0; i < CurBatch; i++)
{
*DataP++ = (float)*BytesP++;
}
}
}
}
}
}
}
}
else
{
Header = MapHeader.ReadFromFile(null, path, headerlessSliceDims, headerlessOffset, headerlessType, stream);
if (Helper.PathToExtension(path).ToLower() == ".eer")
{
Data = Helper.ArrayOfFunction(i => new float[Header.Dimensions.ElementsSlice()], layers == null ? Header.Dimensions.Z : layers.Length);
for (int i = 0; i < Data.Length; i++)
{
int z = layers == null ? i : layers[i];
EERNative.ReadEER(path, z * HeaderEER.GroupNFrames, (z + 1) * HeaderEER.GroupNFrames, HeaderEER.SuperResolution, Data[i]);
}
}
else
{
Data = ((HeaderTiff)Header).ReadData(stream, layers);
}
}
return(Data);
}
static Image LoadAndPrepareStack(string path, Image imageGain, decimal scaleFactor, int maxThreads = 8)
{
Image stack = null;
MapHeader header = MapHeader.ReadFromFilePatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType));
if (imageGain != null)
{
if (header.Dimensions.X != imageGain.Dims.X || header.Dimensions.Y != imageGain.Dims.Y)
{
throw new Exception("Gain reference dimensions do not match image.");
}
}
bool IsTiff = header.GetType() == typeof(HeaderTiff);
int NThreads = IsTiff ? 6 : 2;
int GPUThreads = 2;
int CurrentDevice = GPU.GetDevice();
if (RawLayers == null || RawLayers.Length != NThreads || RawLayers[0].Length != header.Dimensions.ElementsSlice())
{
RawLayers = Helper.ArrayOfFunction(i => new float[header.Dimensions.ElementsSlice()], NThreads);
}
Image[] GPULayers = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, header.Dimensions.Slice()), GPUThreads);
Image[] GPULayers2 = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, header.Dimensions.Slice()), GPUThreads);
if (scaleFactor == 1M)
{
stack = new Image(header.Dimensions);
float[][] OriginalStackData = stack.GetHost(Intent.Write);
object[] Locks = Helper.ArrayOfFunction(i => new object(), GPUThreads);
Helper.ForCPU(0, header.Dimensions.Z, NThreads, threadID => GPU.SetDevice(DeviceID), (z, threadID) =>
{
if (IsTiff)
{
TiffNative.ReadTIFFPatient(50, 500, path, z, true, RawLayers[threadID]);
}
else
{
IOHelper.ReadMapFloatPatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType),
z,
null,
new[] { RawLayers[threadID] });
}
int GPUThreadID = threadID % GPUThreads;
lock (Locks[GPUThreadID])
{
GPU.CopyHostToDevice(RawLayers[threadID], GPULayers[GPUThreadID].GetDevice(Intent.Write), RawLayers[threadID].Length);
if (imageGain != null)
{
GPULayers[GPUThreadID].MultiplySlices(imageGain);
}
GPU.Xray(GPULayers[GPUThreadID].GetDevice(Intent.Read),
GPULayers2[GPUThreadID].GetDevice(Intent.Write),
20f,
new int2(header.Dimensions),
1);
GPU.CopyDeviceToHost(GPULayers2[GPUThreadID].GetDevice(Intent.Read),
OriginalStackData[z],
header.Dimensions.ElementsSlice());
}
}, null);
}
else
{
int3 ScaledDims = new int3((int)Math.Round(header.Dimensions.X * scaleFactor) / 2 * 2,
(int)Math.Round(header.Dimensions.Y * scaleFactor) / 2 * 2,
header.Dimensions.Z);
stack = new Image(ScaledDims);
float[][] OriginalStackData = stack.GetHost(Intent.Write);
int[] PlanForw = Helper.ArrayOfFunction(i => GPU.CreateFFTPlan(header.Dimensions.Slice(), 1), GPUThreads);
int[] PlanBack = Helper.ArrayOfFunction(i => GPU.CreateIFFTPlan(ScaledDims.Slice(), 1), GPUThreads);
Image[] GPULayersInputFT = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, header.Dimensions.Slice(), true, true), GPUThreads);
Image[] GPULayersOutputFT = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, ScaledDims.Slice(), true, true), GPUThreads);
Image[] GPULayersScaled = Helper.ArrayOfFunction(i => new Image(IntPtr.Zero, ScaledDims.Slice()), GPUThreads);
object[] Locks = Helper.ArrayOfFunction(i => new object(), GPUThreads);
Helper.ForCPU(0, ScaledDims.Z, NThreads, threadID => GPU.SetDevice(DeviceID), (z, threadID) =>
{
if (IsTiff)
{
TiffNative.ReadTIFFPatient(50, 500, path, z, true, RawLayers[threadID]);
}
else
{
IOHelper.ReadMapFloatPatient(50, 500,
path,
HeaderlessDims,
(int)HeaderlessOffset,
ImageFormatsHelper.StringToType(HeaderlessType),
z,
null,
new[] { RawLayers[threadID] });
}
int GPUThreadID = threadID % GPUThreads;
lock (Locks[GPUThreadID])
{
GPU.CopyHostToDevice(RawLayers[threadID], GPULayers[GPUThreadID].GetDevice(Intent.Write), RawLayers[threadID].Length);
if (imageGain != null)
{
GPULayers[GPUThreadID].MultiplySlices(imageGain);
}
GPU.Xray(GPULayers[GPUThreadID].GetDevice(Intent.Read),
GPULayers2[GPUThreadID].GetDevice(Intent.Write),
20f,
new int2(header.Dimensions),
1);
GPU.Scale(GPULayers2[GPUThreadID].GetDevice(Intent.Read),
GPULayersScaled[GPUThreadID].GetDevice(Intent.Write),
header.Dimensions.Slice(),
ScaledDims.Slice(),
1,
PlanForw[GPUThreadID],
PlanBack[GPUThreadID],
GPULayersInputFT[GPUThreadID].GetDevice(Intent.Write),
GPULayersOutputFT[GPUThreadID].GetDevice(Intent.Write));
GPU.CopyDeviceToHost(GPULayersScaled[GPUThreadID].GetDevice(Intent.Read),
OriginalStackData[z],
ScaledDims.ElementsSlice());
}
}, null);
for (int i = 0; i < GPUThreads; i++)
{
GPU.DestroyFFTPlan(PlanForw[i]);
GPU.DestroyFFTPlan(PlanBack[i]);
GPULayersInputFT[i].Dispose();
GPULayersOutputFT[i].Dispose();
GPULayersScaled[i].Dispose();
}
}
foreach (var layer in GPULayers)
{
layer.Dispose();
}
foreach (var layer in GPULayers2)
{
layer.Dispose();
}
return(stack);
}