public static int StartAsBatchInConsole(string batpath, bool pause, params string[] commands)
{
bool delbat = false;
if ((batpath == null) || batpath.Trim().Length == 0)
{
delbat = true;
batpath = HFile.GetTempPath("bat");
}
HFile.WriteAllLines(batpath, commands);
if (pause)
{
HFile.AppendAllLines(batpath, new string[] { "pause" });
}
System.Diagnostics.Process pdb2gmx = System.Diagnostics.Process.Start(batpath);
pdb2gmx.WaitForExit();
int exitcode = pdb2gmx.ExitCode;
Thread.Sleep(100);
if (delbat)
{
HFile.Delete(batpath);
}
return(exitcode);
}
public static void _Serialize(string filename, int?ver, object[] objs)
{
string lockname = "Serializer: " + filename.Replace("\\", "@");
using (new NamedLock(lockname))
{
Stream stream = HFile.Open(filename, FileMode.Create);
BinaryFormatter bFormatter = new BinaryFormatter();
{
if (ver != null)
{
bFormatter.Serialize(stream, new Ver(ver.Value));
}
}
{
System.Int32 count = objs.Length;
bFormatter.Serialize(stream, count);
for (int i = 0; i < count; i++)
{
bFormatter.Serialize(stream, objs[i]);
}
}
stream.Flush();
stream.Close();
}
}
public static TVector <double> GetVectorLarge(string name, bool bUseFile = false)
{
TVector <double> vector;
try
{
Execute("htlib2_matlab_GetVector = " + name + ";");
int size = GetValueInt("length(htlib2_matlab_GetVector)");
if (size < TVector <double> .MaxBlockCapacity)
{
System.Array real = new double[size];
System.Array imag = new double[size];
matlab.GetFullMatrix("htlib2_matlab_GetVector", "base", ref real, ref imag);
Execute("clear htlib2_matlab_GetVector;");
vector = new TVector <double>(size);
for (int i = 0; i < size; i++)
{
vector[i] = (double)real.GetValue(i);
}
}
else
{
HDebug.Assert(bUseFile, _path_temporary != null);
string tmppath = HFile.GetTempPath(_path_temporary, ".dat");
Execute("htlib2_matlab_GetVectorLarge.vec = " + name + ";");
{
Execute("htlib2_matlab_GetVectorLarge.fid=fopen('" + tmppath + "','w');");
Execute("htlib2_matlab_GetVectorLarge.vec=fwrite(htlib2_matlab_GetVectorLarge.fid,htlib2_matlab_GetVectorLarge.vec','double');");
Execute("fclose(htlib2_matlab_GetVectorLarge.fid);");
Execute("clear htlib2_matlab_GetVectorLarge;");
}
{
bool clear_var = false;
if (clear_var)
{
Execute("clear " + name + ";");
}
}
vector = new TVector <double>(size);
{
System.IO.BinaryReader reader = new System.IO.BinaryReader(new System.IO.FileStream(tmppath, System.IO.FileMode.Open));
for (long i = 0; i < size; i++)
{
vector[i] = reader.ReadDouble();
}
reader.Close();
}
HFile.Delete(tmppath);
return(vector);
}
}
catch (System.Runtime.InteropServices.COMException)
{
HDebug.Assert(false);
vector = null;
}
return(vector);
}
public static void SerializeText2D <T>(string filename, Func <T, string> tostring, T[,] values)
{
string text = values.HToStringSeparated(tostring
, "{ ", "\n, ", "\n}"
, "{", ", ", "}"
);
HFile.WriteAllText(filename, text);
}
public static void CopyResourceTo <T>(string resname, string path)
{
HDebug.Assert(GetResourceNames <T>().Contains(resname));
var assm = typeof(T).Assembly;
var stream = assm.GetManifestResourceStream(FindResourceName <T>(resname));
HFile.WriteStream(path, stream);
stream.Close();
}
//public static FileStream Open(string path, FileMode mode)
//{
// return System.IO.File.Open(path, mode);
//}
//public static FileStream Open(string path, FileMode mode, FileAccess access)
//{
// return System.IO.File.Open(path, mode, access);
//}
//public static FileStream Open(string path, FileMode mode, FileAccess access, FileShare share)
//{
// return System.IO.File.Open(path, mode, access, share);
//}
//public static StreamReader OpenText(string path)
//{
// return System.IO.File.OpenText(path);
//}
//public static StreamWriter CreateText(string path)
//{
// return System.IO.File.CreateText(path);
//}
//public static StreamWriter WriteText(string path)
//{
// return new System.IO.StreamWriter(path);
//}
public static IEnumerable <string> HEnumAllLines(string path)
{
System.IO.StreamReader reader = HFile.OpenText(path);
while (reader.EndOfStream == false)
{
string line = reader.ReadLine();
yield return(line);
}
reader.Close();
}
public static void Run(string scriptpath, bool waitForExit)
{
string currpath = HEnvironment.CurrentDirectory;
HEnvironment.CurrentDirectory = HFile.GetFileInfo(scriptpath).Directory.FullName;
{
System.Diagnostics.Process mathm;
string argument = "-script \"" + HFile.GetFileInfo(scriptpath).Name + "\"";
mathm = System.Diagnostics.Process.Start(@"C:\Program Files\Wolfram Research\Mathematica\8.0\math.exe", argument);
if (waitForExit)
{
mathm.WaitForExit();
}
}
HEnvironment.CurrentDirectory = currpath;
}
public static void PutMatrix(string name, ref IMatrix <double> real, bool bUseFile, bool call_GC)
{
if ((bUseFile == false) || (_path_temporary == null))
{
HDebug.Assert(real.RowSize * real.ColSize < 2000 * 2000);
System.Array arr_real = real.ToArray();
System.Array arr_imag = new double[real.ColSize, real.RowSize];
matlab.PutFullMatrix("htlib2_matlab_PutMatrix", "base", arr_real, arr_imag);
Execute(name + " = htlib2_matlab_PutMatrix;");
Execute("clear htlib2_matlab_PutMatrix;");
}
else
{
HDebug.Assert(bUseFile, _path_temporary != null);
string tmppath = HFile.GetTempPath(_path_temporary, ".dat");
int colsize = real.ColSize;
int rowsize = real.RowSize;
{
System.IO.BinaryWriter writer = new System.IO.BinaryWriter(new System.IO.FileStream(tmppath, System.IO.FileMode.CreateNew));
for (int c = 0; c < colsize; c++)
{
for (int r = 0; r < rowsize; r++)
{
writer.Write(real[c, r]);
}
}
writer.Flush();
writer.Close();
}
if (call_GC)
{
real = null;
System.GC.Collect();
}
{
Execute("htlib2_matlab_PutMatrix.fid=fopen('" + tmppath + "','r');");
Execute("htlib2_matlab_PutMatrix.mat=fread(htlib2_matlab_PutMatrix.fid,[" + rowsize + "," + colsize + "],'*double')';");
Execute("fclose(htlib2_matlab_PutMatrix.fid);");
Execute(name + " = htlib2_matlab_PutMatrix.mat;");
Execute("clear htlib2_matlab_PutMatrix;");
}
HFile.Delete(tmppath);
}
}
public static void DeserializeText <T>(string filename, Func <string, T> parse, out T[] values)
{
string text = HFile.ReadAllText(filename).Trim();
HDebug.Assert(text.StartsWith("{")); text = text.Substring(1);
HDebug.Assert(text.EndsWith("}")); text = text.Substring(0, text.Length - 1);
text = text.Trim();
if (text.Length == 0)
{
values = new T[0];
return;
}
string[] token = text.Split(',');
values = new T[token.Length];
for (int i = 0; i < token.Length; i++)
{
T value = parse(token[i]);
values[i] = value;
}
}
public static bool _Deserialize(string filename, int?ver, out object[] objs)
{
string lockname = "Serializer: " + filename.Replace("\\", "@");
using (new NamedLock(lockname))
{
Stream stream = HFile.Open(filename, FileMode.Open, FileAccess.Read, FileShare.Read);
BinaryFormatter bFormatter = new BinaryFormatter();
{
if (ver != null)
{
try
{
Ver sver = (Ver)bFormatter.Deserialize(stream);
if (sver.ver != ver.Value)
{
stream.Close();
objs = null;
return(false);
}
}
catch (Exception)
{
stream.Close();
objs = null;
return(false);
}
}
}
{
System.Int32 count = (System.Int32)bFormatter.Deserialize(stream);
objs = new object[count];
for (int i = 0; i < count; i++)
{
objs[i] = bFormatter.Deserialize(stream);
}
}
stream.Close();
}
return(true);
}
public static IMATRIX GetMatrix <IMATRIX>(string name, Func <int, int, IMATRIX> Zeros, bool bUseFile, bool clear_var)
where IMATRIX : IMatrix <double>
{
if ((bUseFile == false) || (_path_temporary == null))
{
System.Array real;
System.Array imag;
Execute("htlib2_matlab_GetGetMatrix = " + name + ";");
int colsize = GetValueInt("size(htlib2_matlab_GetGetMatrix, 1)");
int rowsize = GetValueInt("size(htlib2_matlab_GetGetMatrix, 2)");
HDebug.Assert(colsize * rowsize < 2000 * 2000);
real = new double[colsize, rowsize];
imag = new double[colsize, rowsize];
matlab.GetFullMatrix("htlib2_matlab_GetGetMatrix", "base", ref real, ref imag);
Execute("clear htlib2_matlab_GetGetMatrix;");
IMATRIX matrix = Zeros(colsize, rowsize);
for (int c = 0; c < colsize; c++)
{
for (int r = 0; r < rowsize; r++)
{
matrix[c, r] = (double)real.GetValue(c, r);
}
}
real = null;
imag = null;
return(matrix);
}
else
{
HDebug.Assert(bUseFile, _path_temporary != null);
string tmppath = HFile.GetTempPath(_path_temporary, ".dat");
Execute("htlib2_matlab_GetGetMatrix.test = 0;");
Execute("htlib2_matlab_GetGetMatrix.mat = " + name + ";");
int colsize = GetValueInt("size(htlib2_matlab_GetGetMatrix.mat, 1)");
int rowsize = GetValueInt("size(htlib2_matlab_GetGetMatrix.mat, 2)");
{
Execute("htlib2_matlab_GetGetMatrix.fid=fopen('" + tmppath + "','w');");
Execute("htlib2_matlab_GetGetMatrix.mat=fwrite(htlib2_matlab_GetGetMatrix.fid,htlib2_matlab_GetGetMatrix.mat','double');");
Execute("fclose(htlib2_matlab_GetGetMatrix.fid);");
Execute("clear htlib2_matlab_GetGetMatrix;");
}
if (clear_var)
{
Execute("clear " + name + ";");
}
IMATRIX matrix = Zeros(colsize, rowsize);
{
System.IO.BinaryReader reader = new System.IO.BinaryReader(new System.IO.FileStream(tmppath, System.IO.FileMode.Open));
for (int c = 0; c < colsize; c++)
{
for (int r = 0; r < rowsize; r++)
{
matrix[c, r] = reader.ReadDouble();
}
}
reader.Close();
}
HFile.Delete(tmppath);
return(matrix);
}
}
/// Matlab.PutSparseMatrix("H", H.GetMatrixSparse(), 3, 3);
//public static void PutSparseMatrix<MATRIX>(string name, MatrixSparse<MATRIX> real, int elemColSize, int elemRowSize)
//public static void PutSparseMatrix<MATRIX>(string name, IMatrixSparse<MATRIX> real, int elemColSize, int elemRowSize)
// where MATRIX : Matrix
public static void PutSparseMatrix(string name, IMatrixSparse <MatrixByArr> real, int elemColSize, int elemRowSize, string opt = null)
{
/// http://www.mathworks.com/help/matlab/ref/sparse.html
/// S = sparse(i,j,s,m,n)
/// * create m-by-n sparse matrix
/// * where S(i(k),j(k)) = s(k)
/// * Vectors i, j, and s are all the same length.
/// * Any elements of s that are zero are ignored.
/// * Any elementsof s that have duplicate values of i and j are added together.
if (opt == null)
{
int m = real.ColSize * elemColSize;
int n = real.RowSize * elemRowSize;
//if(opt == null)
{
List <int> i = new List <int>();
List <int> j = new List <int>();
List <double> s = new List <double>();
foreach (var c_r_val in real.EnumElements())
{
int c = c_r_val.Item1;
int r = c_r_val.Item2;
Matrix hesscr = c_r_val.Item3;
HDebug.Assert(hesscr != null);
HDebug.Assert(hesscr.ColSize == elemColSize, hesscr.RowSize == elemRowSize);
for (int dc = 0; dc < elemColSize; dc++)
{
for (int dr = 0; dr < elemRowSize; dr++)
{
i.Add(c * elemColSize + dc);
j.Add(r * elemRowSize + dr);
s.Add(hesscr[dc, dr]);
}
}
}
//for(int ii=0; ii<i.Count; ii++)
//{
// if(i[ii] == j[ii])
// HDebug.Assert(s[ii] != 0);
//}
PutVector("htlib2_matlab_PutSparseMatrix.i", i.ToArray());
PutVector("htlib2_matlab_PutSparseMatrix.j", j.ToArray());
PutVector("htlib2_matlab_PutSparseMatrix.s", s.ToArray());
}
//else
//{
// Execute("htlib2_matlab_PutSparseMatrix.i = [];");
// Execute("htlib2_matlab_PutSparseMatrix.j = [];");
// Execute("htlib2_matlab_PutSparseMatrix.s = [];");
//
// int maxleng = 10_000_000; // Count = 134217728 (maximum)
// List<int > i = new List<int >(maxleng);
// List<int > j = new List<int >(maxleng);
// List<double> s = new List<double>(maxleng);
// foreach(var c_r_val in real.EnumElements())
// {
// int c = c_r_val.Item1;
// int r = c_r_val.Item2;
// Matrix hesscr = c_r_val.Item3;
// HDebug.Assert(hesscr != null);
// HDebug.Assert(hesscr.ColSize == elemColSize, hesscr.RowSize == elemRowSize);
// for(int dc=0; dc<elemColSize; dc++)
// for(int dr=0; dr<elemRowSize; dr++)
// {
// if(i.Count == maxleng)
// {
// PutVector("htlib2_matlab_PutSparseMatrix.ix", i.ToArray());
// PutVector("htlib2_matlab_PutSparseMatrix.jx", j.ToArray());
// PutVector("htlib2_matlab_PutSparseMatrix.sx", s.ToArray());
// Execute("htlib2_matlab_PutSparseMatrix.i = [htlib2_matlab_PutSparseMatrix.i; htlib2_matlab_PutSparseMatrix.ix];");
// Execute("htlib2_matlab_PutSparseMatrix.j = [htlib2_matlab_PutSparseMatrix.j; htlib2_matlab_PutSparseMatrix.jx];");
// Execute("htlib2_matlab_PutSparseMatrix.s = [htlib2_matlab_PutSparseMatrix.s; htlib2_matlab_PutSparseMatrix.sx];");
// Execute("clear htlib2_matlab_PutSparseMatrix.ix;");
// Execute("clear htlib2_matlab_PutSparseMatrix.jx;");
// Execute("clear htlib2_matlab_PutSparseMatrix.sx;");
// i.Clear();
// j.Clear();
// s.Clear();
// }
// i.Add(c*elemColSize+dc);
// j.Add(r*elemRowSize+dr);
// s.Add(hesscr[dc, dr]);
// }
// }
// if(i.Count != 0)
// {
// PutVector("htlib2_matlab_PutSparseMatrix.ix", i.ToArray());
// PutVector("htlib2_matlab_PutSparseMatrix.jx", j.ToArray());
// PutVector("htlib2_matlab_PutSparseMatrix.sx", s.ToArray());
// Execute("htlib2_matlab_PutSparseMatrix.i = [htlib2_matlab_PutSparseMatrix.i; htlib2_matlab_PutSparseMatrix.ix];");
// Execute("htlib2_matlab_PutSparseMatrix.j = [htlib2_matlab_PutSparseMatrix.j; htlib2_matlab_PutSparseMatrix.jx];");
// Execute("htlib2_matlab_PutSparseMatrix.s = [htlib2_matlab_PutSparseMatrix.s; htlib2_matlab_PutSparseMatrix.sx];");
// Execute("htlib2_matlab_PutSparseMatrix.ix = [];");
// Execute("htlib2_matlab_PutSparseMatrix.jx = [];");
// Execute("htlib2_matlab_PutSparseMatrix.sx = [];");
// i.Clear();
// j.Clear();
// s.Clear();
// }
// HDebug.Assert(i.Count == 0);
// HDebug.Assert(j.Count == 0);
// HDebug.Assert(s.Count == 0);
//}
PutValue("htlib2_matlab_PutSparseMatrix.m", m);
PutValue("htlib2_matlab_PutSparseMatrix.n", n);
Execute("htlib2_matlab_PutSparseMatrix = sparse(htlib2_matlab_PutSparseMatrix.i+1, htlib2_matlab_PutSparseMatrix.j+1, htlib2_matlab_PutSparseMatrix.s, htlib2_matlab_PutSparseMatrix.m, htlib2_matlab_PutSparseMatrix.n);");
Execute(name + " = htlib2_matlab_PutSparseMatrix;");
Execute("clear htlib2_matlab_PutSparseMatrix;");
}
else if (opt == "use file")
{
string i_path = HFile.GetTempPath(_path_temporary, ".dat");
string j_path = HFile.GetTempPath(_path_temporary, ".dat");
string s_path = HFile.GetTempPath(_path_temporary, ".dat");
ulong count = 0;
{
System.IO.BinaryWriter i_writer = new System.IO.BinaryWriter(new System.IO.FileStream(i_path, System.IO.FileMode.CreateNew));
System.IO.BinaryWriter j_writer = new System.IO.BinaryWriter(new System.IO.FileStream(j_path, System.IO.FileMode.CreateNew));
System.IO.BinaryWriter s_writer = new System.IO.BinaryWriter(new System.IO.FileStream(s_path, System.IO.FileMode.CreateNew));
foreach (var c_r_val in real.EnumElements())
{
int c = c_r_val.Item1;
int r = c_r_val.Item2;
Matrix hesscr = c_r_val.Item3;
HDebug.Assert(hesscr != null);
HDebug.Assert(hesscr.ColSize == elemColSize, hesscr.RowSize == elemRowSize);
for (int dc = 0; dc < elemColSize; dc++)
{
for (int dr = 0; dr < elemRowSize; dr++)
{
count++;
double i = (c * elemColSize + dc);
double j = (r * elemRowSize + dr);
double s = (hesscr[dc, dr]);
i_writer.Write(i);
j_writer.Write(j);
s_writer.Write(s);
HDebug.Exception(count > 0);
}
}
}
i_writer.Flush(); i_writer.Close();
j_writer.Flush(); j_writer.Close();
s_writer.Flush(); s_writer.Close();
}
{
int m = real.ColSize * elemColSize;
int n = real.RowSize * elemRowSize;
PutValue("htlib2_matlab_PutSparseMatrix.m", m);
PutValue("htlib2_matlab_PutSparseMatrix.n", n);
Execute("htlib2_matlab_PutSparseMatrix.ifid=fopen('" + i_path + "','r');");
Execute("htlib2_matlab_PutSparseMatrix.jfid=fopen('" + j_path + "','r');");
Execute("htlib2_matlab_PutSparseMatrix.sfid=fopen('" + s_path + "','r');");
// A = fread(fileID) reads all the data in the file into a vector of class double. By default, fread reads a file 1 byte at a time, interprets each byte as an 8-bit unsigned integer (uint8), and returns a double array.
Execute("htlib2_matlab_PutSparseMatrix.imat=fread(htlib2_matlab_PutSparseMatrix.ifid, [" + count + "],'*double')';");
Execute("htlib2_matlab_PutSparseMatrix.jmat=fread(htlib2_matlab_PutSparseMatrix.jfid, [" + count + "],'*double')';");
Execute("htlib2_matlab_PutSparseMatrix.smat=fread(htlib2_matlab_PutSparseMatrix.sfid, [" + count + "],'*double')';");
Execute("fclose(htlib2_matlab_PutSparseMatrix.ifid);");
Execute("fclose(htlib2_matlab_PutSparseMatrix.jfid);");
Execute("fclose(htlib2_matlab_PutSparseMatrix.sfid);");
Execute("htlib2_matlab_PutSparseMatrix = sparse(htlib2_matlab_PutSparseMatrix.imat+1, htlib2_matlab_PutSparseMatrix.jmat+1, htlib2_matlab_PutSparseMatrix.smat, htlib2_matlab_PutSparseMatrix.m, htlib2_matlab_PutSparseMatrix.n);");
Execute(name + " = htlib2_matlab_PutSparseMatrix;");
Execute("clear htlib2_matlab_PutSparseMatrix;");
}
HFile.Delete(i_path);
HFile.Delete(j_path);
HFile.Delete(s_path);
}
}
public void Release()
{
file.Close();
HFile.Delete(path);
file = null;
}
public static int StartAsBatchSilent(Tuple <string, IList <string>, IList <string> > env,
List <string> lineStdout, List <string> lineStderr, params string[] commands)
{
string tempbase = null;
IList <string> filesIn = null;
IList <string> filesOut = null;
if (env != null)
{
tempbase = env.Item1; HDebug.Assert(tempbase != null); HDebug.Assert(HDirectory.Exists(tempbase));
filesIn = env.Item2;
filesOut = env.Item3;
}
string currdir = HEnvironment.CurrentDirectory;
if (tempbase != null)
{
var dirinfo = HDirectory.CreateTempDirectory(tempbase);
HEnvironment.CurrentDirectory = dirinfo.FullName;
}
if (filesIn != null)
{
foreach (string file in filesIn)
{
HFile.Copy(currdir + "\\" + file, file);
}
}
int exitcode;
{
string tmpbatpath = HFile.GetTempPath("bat");
HFile.WriteAllLines(tmpbatpath, commands);
{
if (lineStderr == null)
{
lineStderr = new List <string>(); // collect into garbage storage if they are initially null.
}
if (lineStdout == null)
{
lineStdout = new List <string>(); // collect into garbage storage if they are initially null.
}
// capture error message in console
System.Diagnostics.Process proc = new System.Diagnostics.Process();
proc.StartInfo.FileName = tmpbatpath;
proc.StartInfo.RedirectStandardError = (lineStderr != null);
proc.StartInfo.RedirectStandardOutput = (lineStdout != null);
proc.StartInfo.UseShellExecute = false;
proc.Start();
if (lineStderr != null)
{
lineStderr.Clear(); lineStderr.AddRange(proc.StandardError.ReadToEnd().Replace("\r", "").Split('\n'));
}
if (lineStdout != null)
{
lineStdout.Clear(); lineStdout.AddRange(proc.StandardOutput.ReadToEnd().Replace("\r", "").Split('\n'));
}
proc.WaitForExit();
exitcode = proc.ExitCode;
}
Thread.Sleep(100);
HFile.Delete(tmpbatpath);
}
if (filesOut != null)
{
foreach (string file in filesOut)
{
if (HFile.Exists(file))
{
HFile.Copy(file, currdir + "\\" + file);
}
}
}
if (HEnvironment.CurrentDirectory != currdir)
{
string delpath = HEnvironment.CurrentDirectory;
HEnvironment.CurrentDirectory = currdir;
try{ HDirectory.Delete(delpath, true); } catch (System.IO.IOException) { }
}
return(exitcode);
}
