/// <summary>
/// Processes a single input file.
/// </summary>
private void ProcessFile(string inFile, string outFile, WaveFunction.ColorDelegate colorFunc)
{
unsafe
{
int sx = -1;
int sy = -1;
int sz = -1;
string inFormat = "";
float latticeSpacing = 0.0f;
long inDataStartPos = 0;
string nl = Environment.NewLine;
float fa = 0.0f, fb = 0.0f;
byte *fa0 = (byte *)(&fa);
byte *fa1 = fa0 + 1;
byte *fa2 = fa0 + 2;
byte *fa3 = fa0 + 3;
byte *fb0 = (byte *)(&fb);
byte *fb1 = fb0 + 1;
byte *fb2 = fb0 + 2;
byte *fb3 = fb0 + 3;
using (BinaryReader br = new BinaryReader(File.Open(inFile, FileMode.Open)))
{
// Parse the header of the input file
while (br.BaseStream.Position < br.BaseStream.Length)
{
string textLine = WaveFunction.ReadTextLine(br);
if (textLine.StartsWith("Wavefunction3D"))
{
string[] comps = textLine.Split(null);
inFormat = comps[1];
latticeSpacing = Single.Parse(comps[3]);
}
else if (textLine.StartsWith("DIMENSIONS"))
{
string[] comps = textLine.Split(null);
sx = Int32.Parse(comps[1]);
sy = Int32.Parse(comps[2]);
sz = Int32.Parse(comps[3]);
}
else if (textLine.StartsWith("LOOKUP_TABLE default"))
{
break;
}
}
// Bail out if the header was not what we expected
if (string.IsNullOrEmpty(inFormat) || (sx < 0) || (sy < 0) || (sz < 0))
{
throw new ArgumentException("Invalid Wavefunction file, in Colorer.ProcessFile.");
}
if (inFormat != "REAL_AND_IMAG")
{
throw new ArgumentException("Unsupported Wavefunction format, in Colorer.ProcessFile. " + "(" + inFormat + ")");
}
inDataStartPos = br.BaseStream.Position;
// Create output file
using (FileStream fileStream = File.Create(outFile))
{
using (BinaryWriter bw = new BinaryWriter(fileStream))
{
// Write the output header
string outFormat = (colorFunc == null) ? "AMPLITUDE_ONLY" : "AMPLITUDE_AND_COLOR";
bw.Write(Encoding.ASCII.GetBytes("# vtk DataFile Version 3.0" + nl));
bw.Write(Encoding.ASCII.GetBytes("Wavefunction3D " + outFormat.ToString() + " " + "spacing: " + latticeSpacing.ToString() + nl));
bw.Write(Encoding.ASCII.GetBytes("BINARY" + nl));
bw.Write(Encoding.ASCII.GetBytes("DATASET STRUCTURED_POINTS" + nl));
bw.Write(Encoding.ASCII.GetBytes("DIMENSIONS " + sx + " " + sy + " " + sz + nl));
bw.Write(Encoding.ASCII.GetBytes("ORIGIN 0 0 0" + nl));
bw.Write(Encoding.ASCII.GetBytes("SPACING 1 1 1" + nl));
bw.Write(Encoding.ASCII.GetBytes("POINT_DATA " + sx * sy * sz + nl));
bw.Write(Encoding.ASCII.GetBytes("SCALARS amplitude float" + nl));
bw.Write(Encoding.ASCII.GetBytes("LOOKUP_TABLE default" + nl));
// Read {re,im} pairs from the input file, and write the corresponding ampl values to the output file
// (Avoid reading-in the whole input file up-front, as it may be extremely large.)
byte[] outPlane = new byte[sx * sy * 4];
float maxAmpl = 0.0f;
for (int z = 0; z < sz; z++)
{
byte[] inPlane = br.ReadBytes(sx * sy * 8);
int ni = 0, no = 0;;
for (int y = 0; y < sy; y++)
{
for (int x = 0; x < sx; x++)
{
*fa3 = inPlane[ni]; // Reverse the byte order
*fa2 = inPlane[ni + 1];
*fa1 = inPlane[ni + 2];
*fa0 = inPlane[ni + 3];
*fb3 = inPlane[ni + 4];
*fb2 = inPlane[ni + 5];
*fb1 = inPlane[ni + 6];
*fb0 = inPlane[ni + 7];
ni += 8;
fa = (float)Math.Sqrt(fa * fa + fb * fb);
if (fa > maxAmpl)
{
maxAmpl = fa;
}
outPlane[no] = *fa3;
outPlane[no + 1] = *fa2;
outPlane[no + 2] = *fa1;
outPlane[no + 3] = *fa0;
no += 4;
}
}
bw.Write(outPlane);
}
// Now write the colors
if (colorFunc != null)
{
bw.Write(Encoding.ASCII.GetBytes("SCALARS colors unsigned_char 3" + nl));
bw.Write(Encoding.ASCII.GetBytes("LOOKUP_TABLE default" + nl));
br.BaseStream.Seek(inDataStartPos, SeekOrigin.Begin);
byte[] colorPlane = new byte[sx * sy * 3];
for (int z = 0; z < sz; z++)
{
byte[] inPlane = br.ReadBytes(sx * sy * 8);
int ni = 0, no = 0;;
for (int y = 0; y < sy; y++)
{
for (int x = 0; x < sx; x++)
{
*fa3 = inPlane[ni]; // Real part
*fa2 = inPlane[ni + 1];
*fa1 = inPlane[ni + 2];
*fa0 = inPlane[ni + 3];
*fb3 = inPlane[ni + 4]; // Imaginary part
*fb2 = inPlane[ni + 5];
*fb1 = inPlane[ni + 6];
*fb0 = inPlane[ni + 7];
ni += 8;
Color color = (colorFunc == null) ? Color.Blue : colorFunc(fb, fa, maxAmpl);
colorPlane[no] = color.R;
colorPlane[no + 1] = color.G;
colorPlane[no + 2] = color.B;
no += 3;
}
}
bw.Write(colorPlane);
}
}
}
}
}
}
}
/// <summary>
/// Processes a single input file.
/// </summary>
private void ProcessFile(string inFile, string outFile)
{
unsafe
{
int sx = -1, sy = -1, sz = -1;
string format = "";
float latticeSpacing = 0.0f;
string nl = Environment.NewLine;
float[] kernel = CreateGaussianKernel(m_smoothingFactor);
int sk = kernel.Length;
int hsk = (sk - 1) / 2;
using (BinaryReader br = new BinaryReader(File.Open(inFile, FileMode.Open)))
{
// Parse the header of the input file
while (br.BaseStream.Position < br.BaseStream.Length)
{
string textLine = WaveFunction.ReadTextLine(br);
if (textLine.StartsWith("Wavefunction3D"))
{
string[] comps = textLine.Split(null);
format = comps[1];
latticeSpacing = Single.Parse(comps[3]);
}
else if (textLine.StartsWith("DIMENSIONS"))
{
string[] comps = textLine.Split(null);
sx = Int32.Parse(comps[1]);
sy = Int32.Parse(comps[2]);
sz = Int32.Parse(comps[3]);
}
else if (textLine.StartsWith("LOOKUP_TABLE default"))
{
break;
}
}
// Bail out if the header was not what we expected
if (string.IsNullOrEmpty(format) || (sx < 0) || (sy < 0) || (sz < 0))
{
throw new ArgumentException("Invalid Wavefunction file, in Colorer.ProcessFile.");
}
if (format != "REAL_AND_IMAG")
{
throw new ArgumentException("Unsupported Wavefunction format, in Smoother.ProcessFile. " + "(" + format + ")");
}
// Allocate some storage
float[][][] slab = TdseUtils.Misc.Allocate3DArray(sk, sy, 2 * sx);
float[][] outPlane = TdseUtils.Misc.Allocate2DArray(sy, 2 * sx);
float[][] workSpace = TdseUtils.Misc.Allocate2DArray(sy, 2 * sx);
// Create and open the output file
using (FileStream fileStream = File.Create(outFile))
{
using (BinaryWriter bw = new BinaryWriter(fileStream))
{
// Write the output header
bw.Write(Encoding.ASCII.GetBytes("# vtk DataFile Version 3.0" + nl));
bw.Write(Encoding.ASCII.GetBytes("Wavefunction3D " + "REAL_AND_IMAG" + " " + "spacing: " + latticeSpacing.ToString() + nl));
bw.Write(Encoding.ASCII.GetBytes("BINARY" + nl));
bw.Write(Encoding.ASCII.GetBytes("DATASET STRUCTURED_POINTS" + nl));
bw.Write(Encoding.ASCII.GetBytes("DIMENSIONS " + sx + " " + sy + " " + sz + nl));
bw.Write(Encoding.ASCII.GetBytes("ORIGIN 0 0 0" + nl));
bw.Write(Encoding.ASCII.GetBytes("SPACING 1 1 1" + nl));
bw.Write(Encoding.ASCII.GetBytes("POINT_DATA " + sx * sy * sz + nl));
bw.Write(Encoding.ASCII.GetBytes("SCALARS wf float 2" + nl));
bw.Write(Encoding.ASCII.GetBytes("LOOKUP_TABLE default" + nl));
// Read the initial few planes
for (int i = hsk; i < sk; i++)
{
GetNextXYPlane(br, kernel, workSpace, slab[i]);
}
for (int i = 0; i < hsk; i++)
{
TdseUtils.Misc.Copy2DArray(slab[sk - 1 - i], slab[i]); // Mirror boundary conditions on z
}
// Smooth along z, and write-out the result
SmoothAlongZ(slab, kernel, outPlane);
WriteXYPlane(bw, outPlane);
// Loop over remaining planes
for (int z = 1; z < sz; z++)
{
// Cycle the z-planes, and read-in a new one
float[][] temp = slab[0];
for (int i = 0; i < sk - 1; i++)
{
slab[i] = slab[i + 1];
}
slab[sk - 1] = temp;
if (z < sz - hsk)
{
GetNextXYPlane(br, kernel, workSpace, slab[sk - 1]);
}
else
{
TdseUtils.Misc.Copy2DArray(slab[2 * (sz - 1 - z)], slab[sk - 1]); // Mirror boundary conditions on z
}
// Smooth along z, and write-out the result
SmoothAlongZ(slab, kernel, outPlane);
WriteXYPlane(bw, outPlane);
}
}
}
}
}
}
/// <summary>
/// Processes a single input file.
/// </summary>
private void ProcessFile(string inFile, string outFile)
{
unsafe
{
int sx = -1, sy = -1, sz = -1;
string format = "";
float latticeSpacing = 0.0f;
string nl = Environment.NewLine;
using (BinaryReader br = new BinaryReader(File.Open(inFile, FileMode.Open)))
{
// Parse the header of the input file
while (br.BaseStream.Position < br.BaseStream.Length)
{
string textLine = WaveFunction.ReadTextLine(br);
if (textLine.StartsWith("Wavefunction3D"))
{
string[] comps = textLine.Split(null);
format = comps[1];
latticeSpacing = (float)(Single.Parse(comps[3]) / m_upsampFactor);
}
else if (textLine.StartsWith("DIMENSIONS"))
{
string[] comps = textLine.Split(null);
sx = Int32.Parse(comps[1]);
sy = Int32.Parse(comps[2]);
sz = Int32.Parse(comps[3]);
}
else if (textLine.StartsWith("LOOKUP_TABLE default"))
{
break;
}
}
// Bail out if the header was not what we expected
if (string.IsNullOrEmpty(format) || (sx < 0) || (sy < 0) || (sz < 0))
{
throw new ArgumentException("Invalid Wavefunction file, in Colorer.ProcessFile.");
}
if (format != "REAL_AND_IMAG")
{
throw new ArgumentException("Unsupported Wavefunction format, in Smoother.ProcessFile. " + "(" + format + ")");
}
// Allocate some storage
int sxu = (int)Math.Max(1, sx * m_upsampFactor);
int syu = (int)Math.Max(1, sy * m_upsampFactor);
int szu = (int)Math.Max(1, sz * m_upsampFactor);
int sxu2 = 2 * sxu;
float[][] workSpace = TdseUtils.Misc.Allocate2DArray(sy, 2 * sx);
float[][] outPlane = TdseUtils.Misc.Allocate2DArray(syu, sxu2);
// Read the initial few xy planes
float[][][] iXYPlanes = new float[sz][][];
for (int zIn = 0; zIn < 4; zIn++)
{
iXYPlanes[zIn] = TdseUtils.Misc.Allocate2DArray(syu, sxu2);
GetNextXYPlane(br, iXYPlanes[zIn], workSpace, m_upsampFactor);
}
// Precalculate the z-weights and indices
int[] zInm2, zInm1, zInp1, zInp2;
float[] wzm2, wzm1, wzp1, wzp2;
GetUpsampleArrays(sz, m_upsampFactor, out zInm2, out zInm1, out zInp1, out zInp2, out wzm2, out wzm1, out wzp1, out wzp2);
// Create and open the output file
using (FileStream fileStream = File.Create(outFile))
{
using (BinaryWriter bw = new BinaryWriter(fileStream))
{
// Write the output header
bw.Write(Encoding.ASCII.GetBytes("# vtk DataFile Version 3.0" + nl));
bw.Write(Encoding.ASCII.GetBytes("Wavefunction3D " + "REAL_AND_IMAG" + " " + "spacing: " + latticeSpacing.ToString() + nl));
bw.Write(Encoding.ASCII.GetBytes("BINARY" + nl));
bw.Write(Encoding.ASCII.GetBytes("DATASET STRUCTURED_POINTS" + nl));
bw.Write(Encoding.ASCII.GetBytes("DIMENSIONS " + sxu + " " + syu + " " + szu + nl));
bw.Write(Encoding.ASCII.GetBytes("ORIGIN 0 0 0" + nl));
bw.Write(Encoding.ASCII.GetBytes("SPACING 1 1 1" + nl));
bw.Write(Encoding.ASCII.GetBytes("POINT_DATA " + sxu * syu * szu + nl));
bw.Write(Encoding.ASCII.GetBytes("SCALARS wf float 2" + nl));
bw.Write(Encoding.ASCII.GetBytes("LOOKUP_TABLE default" + nl));
// Loop over the output z-planes
for (int zOut = 0; zOut < szu; zOut++)
{
// Cache z-weights and offsets
float Wzm2 = wzm2[zOut];
float Wzm1 = wzm1[zOut];
float Wzp1 = wzp1[zOut];
float Wzp2 = wzp2[zOut];
float[][] pixValsZInm2 = iXYPlanes[zInm2[zOut]];
float[][] pixValsZInm1 = iXYPlanes[zInm1[zOut]];
float[][] pixValsZInp1 = iXYPlanes[zInp1[zOut]];
float[][] pixValsZInp2 = iXYPlanes[zInp2[zOut]];
if (pixValsZInp2 == null)
{
// Load (and upsample) the next xy plane
float[][] temp = iXYPlanes[zInp2[zOut] - 4];
iXYPlanes[zInp2[zOut] - 4] = null;
GetNextXYPlane(br, temp, workSpace, m_upsampFactor);
pixValsZInp2 = iXYPlanes[zInp2[zOut]] = temp;
}
for (int yOut = 0; yOut < syu; yOut++)
{
float[] pixValsZInm2Y = pixValsZInm2[yOut];
float[] pixValsZInm1Y = pixValsZInm1[yOut];
float[] pixValsZInp1Y = pixValsZInp1[yOut];
float[] pixValsZInp2Y = pixValsZInp2[yOut];
float[] outPlaneY = outPlane[yOut];
for (int xOut = 0; xOut < sxu2; xOut++)
{
outPlaneY[xOut] = Wzm2 * pixValsZInm2Y[xOut] + Wzm1 * pixValsZInm1Y[xOut] + Wzp1 * pixValsZInp1Y[xOut] + Wzp2 * pixValsZInp2Y[xOut];
}
}
WriteXYPlane(bw, outPlane);
}
}
}
}
}
}
/// <summary>
/// Processes a single input file.
/// </summary>
private void ProcessFile(string inFile, string outFile)
{
unsafe
{
int sxIn = -1, syIn = -1, szIn = -1;
int sxOut = -1, syOut = -1, szOut = -1;
string format = "";
float latticeSpacing = 0.0f;
string nl = Environment.NewLine;
using (BinaryReader br = new BinaryReader(File.Open(inFile, FileMode.Open)))
{
// Parse the header of the input file
while (br.BaseStream.Position < br.BaseStream.Length)
{
string textLine = WaveFunction.ReadTextLine(br);
if (textLine.StartsWith("Wavefunction3D"))
{
string[] comps = textLine.Split(null);
format = comps[1];
latticeSpacing = Single.Parse(comps[3]);
}
else if (textLine.StartsWith("DIMENSIONS"))
{
string[] comps = textLine.Split(null);
sxIn = Int32.Parse(comps[1]);
syIn = Int32.Parse(comps[2]);
szIn = Int32.Parse(comps[3]);
}
else if (textLine.StartsWith("LOOKUP_TABLE default"))
{
break;
}
}
// Bail out if the header was not what we expected
if (string.IsNullOrEmpty(format) || (sxIn < 0) || (syIn < 0) || (szIn < 0))
{
throw new ArgumentException("Invalid Wavefunction file, in Cropper.ProcessFile.");
}
// Create output file
sxOut = sxIn - m_xCrop1 - m_xCrop2;
syOut = syIn - m_yCrop1 - m_yCrop2;
szOut = szIn - m_zCrop1 - m_zCrop2;
using (FileStream fileStream = File.Create(outFile))
{
using (BinaryWriter bw = new BinaryWriter(fileStream))
{
// Write the output header
bw.Write(Encoding.ASCII.GetBytes("# vtk DataFile Version 3.0" + nl));
bw.Write(Encoding.ASCII.GetBytes("Wavefunction3D " + format.ToString() + " " + "spacing: " + latticeSpacing.ToString() + nl));
bw.Write(Encoding.ASCII.GetBytes("BINARY" + nl));
bw.Write(Encoding.ASCII.GetBytes("DATASET STRUCTURED_POINTS" + nl));
bw.Write(Encoding.ASCII.GetBytes("DIMENSIONS " + sxOut + " " + syOut + " " + szOut + nl));
bw.Write(Encoding.ASCII.GetBytes("ORIGIN 0 0 0" + nl));
bw.Write(Encoding.ASCII.GetBytes("SPACING 1 1 1" + nl));
bw.Write(Encoding.ASCII.GetBytes("POINT_DATA " + sxOut * syOut * szOut + nl));
// Read values from the input file, and write (some of) them to the output file.
// (Avoid reading-in the whole input file up-front, as it may be extremely large.)
if (format == "REAL_AND_IMAG")
{
bw.Write(Encoding.ASCII.GetBytes("SCALARS wf float 2" + nl));
bw.Write(Encoding.ASCII.GetBytes("LOOKUP_TABLE default" + nl));
byte[] outPlane = new byte[sxOut * syOut * 8];
for (int z = 0; z < szIn - m_zCrop2; z++)
{
byte[] inPlane = br.ReadBytes(sxIn * syIn * 8);
if (z < m_zCrop1)
{
continue;
}
for (int y = m_yCrop1; y < syIn - m_yCrop2; y++)
{
Buffer.BlockCopy(inPlane, (y * sxIn + m_xCrop1) * 8, outPlane, (y - m_yCrop1) * sxOut * 8, sxOut * 8);
}
bw.Write(outPlane);
}
}
else if ((format == "AMPLITUDE_ONLY") || (format == "AMPLITUDE_AND_COLOR"))
{
bw.Write(Encoding.ASCII.GetBytes("SCALARS amplitude float" + nl));
bw.Write(Encoding.ASCII.GetBytes("LOOKUP_TABLE default" + nl));
byte[] outPlane = new byte[sxOut * syOut * 4];
for (int z = 0; z < szIn; z++)
{
byte[] inPlane = br.ReadBytes(sxIn * syIn * 4);
if ((z < m_zCrop1) || (z > szIn - m_zCrop2 - 1))
{
continue;
}
for (int y = m_yCrop1; y < syIn - m_yCrop2; y++)
{
Buffer.BlockCopy(inPlane, (y * sxIn + m_xCrop1) * 4, outPlane, (y - m_yCrop1) * sxOut * 4, sxOut * 4);
}
bw.Write(outPlane);
}
if (format == "AMPLITUDE_AND_COLOR")
{
bw.Write(Encoding.ASCII.GetBytes("SCALARS colors unsigned_char 3" + nl));
bw.Write(Encoding.ASCII.GetBytes("LOOKUP_TABLE default" + nl));
outPlane = new byte[sxOut * syOut * 3];
for (int z = 0; z < szIn - m_zCrop2; z++)
{
byte[] inPlane = br.ReadBytes(sxIn * syIn * 3);
if (z < m_zCrop1)
{
continue;
}
for (int y = m_yCrop1; y < syIn - m_yCrop2; y++)
{
Buffer.BlockCopy(inPlane, (y * sxIn + m_xCrop1) * 3, outPlane, (y - m_yCrop1) * sxOut * 3, sxOut * 3);
}
bw.Write(outPlane);
}
}
}
else
{
throw new ArgumentException("Unsupported Wavefunction format, in Cropper.ProcessFile. " + "(" + format + ")");
}
}
}
}
}
}