// End ReadClusterLabel_File
// Write label-cluster results into a file
public static void WriteColor_Cluster(string fname, string[] labels, int[] ColorValues, int dataPoints,
bool append)
{
try
{
StreamWriter sw = null;
if (!string.IsNullOrEmpty(fname))
{
sw = new StreamWriter(fname, append, Encoding.UTF8);
}
if (sw != null)
{
for (int i = 0; i < dataPoints; i++)
{
string stripped = labels[i].Trim(new[] { ' ', '\t' });
sw.WriteLine(String.Format(stripped + "\t" + ColorValues[i].ToString() + ".0000000000"));
}
}
sw.Flush();
sw.Close();
}
catch (Exception e)
{
SALSAUtility.SALSAError("Failed writing data on " + fname + " " + e);
throw (e);
}
}
// End WriteColor_Cluster
// Write Point-cluster results into a file
public static void WritePointCluster(string fname, int[] ColorValues, int dataPoints)
{
try
{
StreamWriter sw = null;
if (!string.IsNullOrEmpty(fname))
{
sw = new StreamWriter(fname, false, Encoding.UTF8);
}
if (sw != null)
{
for (int i = 0; i < dataPoints; i++)
{
sw.WriteLine(String.Format((i + 1).ToString() + " " + ColorValues[i].ToString()));
}
}
sw.Flush();
sw.Close();
}
catch (Exception e)
{
SALSAUtility.SALSAError("Failed writing data on " + fname + " " + e);
throw (e);
}
}
public static void SetupHotsunforRotateMDS()
{
PointVectorDimension = ManxcatCentral.Configuration.LocalVectorDimension;
if (PointVectorDimension == 3)
{
Hotsun.npar = 7;
}
else if (PointVectorDimension == 2)
{
Hotsun.npar = 4;
}
else
{
Exception e = SALSAUtility.SALSAError("Unsupported Dimension " + PointVectorDimension.ToString());
}
Hotsun.ndata = SALSAUtility.PointCount_Global * PointVectorDimension;
Hotsun.ParameterVectorDimension = 1;
GenericManxcat.SetupGenericManxcat();
return;
}
// End WritePointCluster
public static bool ReadString_File(string StringFileName, String[] LabelArray, ref int NumberofLines)
{
NumberofLines = 0;
try
{
// Check if file exists
if (!File.Exists(StringFileName))
{
Exception e = SALSAUtility.SALSAError("File " + StringFileName + " does not exists.");
throw (e);
}
// Create a new stream to read from a file
using (StreamReader sr = File.OpenText(StringFileName))
{
// Read contents of a file, line by line, into a string
String inputLineStr;
while ((inputLineStr = sr.ReadLine()) != null)
{
if (inputLineStr.Length < 2)
{
continue; //replace empty line
}
LabelArray[NumberofLines] = inputLineStr.Trim();
++NumberofLines;
}
sr.Close();
}
}
catch (Exception e)
{
SALSAUtility.SALSAError("Failed to read data from " + StringFileName + " " + e);
throw (e);
}
return(true);
}
// End Initialize() in MDSLinearAlgebra
// MaxIndicator = 0 Find Maximum Eigenvalue of Matrix
// MaxIndicator = 1 Find Maximum Eigenvalue of (Maximizr - Matrix)
public static int PowerIterate(Desertwind Solution, int MaxIndicator, double Maximizer,
out double PowerEigenvalue)
{
if (DistributedNewIteratedVector == null)
{
Initialize();
}
Hotsun.UseDiagonalScaling = true;
Hotsun.AddMarquardtQDynamically = false;
// Set up Initial Power Vectors
SetInitialPowerVector(DistributedNewIteratedVector);
double AdotA = SALSABLAS.VectorScalarProduct(DistributedNewIteratedVector, DistributedNewIteratedVector);
int somethingtodo = 0;
int PowerIterationCount = 0;
PowerEigenvalue = -1.0;
while (true)
{
// Iterate over Power Multiplications by Chisq Matrix
// Normalize Current A and move from New to Old
double OldNorm = 1.0 / Math.Sqrt(AdotA);
SALSABLAS.LinearCombineVector(DistributedOldIteratedVector, OldNorm,
DistributedNewIteratedVector, 0.0, DistributedNewIteratedVector);
// Make a Global Vector of DistributedOldIteratedVector
ManxcatCentral.MakeVectorGlobal(DistributedOldIteratedVector, GlobalOldIteratedVector);
// Form Chisq Matrix Product with Old Vector
if (Hotsun.FullSecondDerivative)
{
UserRoutines.GlobalMatrixVectorProduct(DistributedNewIteratedVector, Solution, true,
Hotsun.GlobalParameter, GlobalOldIteratedVector);
}
else
{
UserRoutines.GlobalMatrixVectorProduct(DistributedNewIteratedVector, Solution, false,
Hotsun.GlobalParameter, GlobalOldIteratedVector);
}
// Correct case MaxIndicator = 1
if (MaxIndicator > 0)
{
SALSABLAS.LinearCombineVector(DistributedNewIteratedVector, -1.0, DistributedNewIteratedVector,
Maximizer, DistributedOldIteratedVector);
}
SALSABLAS.LinearCombineVector(DistributedNewIteratedVector, 1.0, DistributedNewIteratedVector,
Hotsun.addonforQcomputation, DistributedOldIteratedVector);
// Form Scalar Products
double NewEigenvalue = SALSABLAS.VectorScalarProduct(DistributedNewIteratedVector,
DistributedOldIteratedVector);
AdotA = SALSABLAS.VectorScalarProduct(DistributedNewIteratedVector, DistributedNewIteratedVector);
++PowerIterationCount;
somethingtodo = -1;
if (SALSAUtility.MPI_Rank == 0)
{
if (PowerIterationCount > 10 && (NewEigenvalue > 0.0))
{
// Arbitary criteria for starting +tests
somethingtodo = 0;
double scaleit = 1.0;
if (MaxIndicator > 0)
{
scaleit = Hotsun.extraprecision;
}
if (Math.Abs(NewEigenvalue - PowerEigenvalue) > PowerEigenvalue * scaleit * Hotsun.eigenvaluechange)
{
++somethingtodo;
}
double delta = AdotA - NewEigenvalue * NewEigenvalue; // (Ax- Eigenvalue*Axold)**2
if (Math.Abs(delta) > NewEigenvalue * NewEigenvalue * scaleit * Hotsun.eigenvectorchange)
{
++somethingtodo;
}
}
}
PowerEigenvalue = NewEigenvalue;
if (SALSAUtility.MPI_Size > 1)
{
SALSAUtility.StartSubTimer(SALSAUtility.MPIBROADCASTTiming);
SALSAUtility.MPI_communicator.Broadcast(ref somethingtodo, 0);
SALSAUtility.StopSubTimer(SALSAUtility.MPIBROADCASTTiming);
}
if (PowerIterationCount >= Hotsun.PowerIterationLimit)
{
somethingtodo = -2;
break;
}
if (somethingtodo == 0)
{
somethingtodo = PowerIterationCount;
break;
}
} // End while over PowerIterationCounts
return(somethingtodo);
}
// End PowerIterate()
// Solve for Distributed Answer = (Matrix-1) First
// Note RealMatrixSize takes account of forced zero parameters which does not crop up in explicit
// algorithm as implemented in Matrix Vector Multiplier
public static bool ConjugateGradientSolver(double[][] Answer, Desertwind Solution, bool useexact,
double[][] GlobalxVector, double[][] DistributedRHS,
ref int NumberofIterations, int RealMatrixSize, double LimitonNormofR)
{
bool matrixsuccess = true;
// Initialize
SALSABLAS.zrword(Answer); // Zero Solution x called xshift in Manxcat and stored in Answer
SALSABLAS.CopyVector(DistributedCGVector_R, DistributedRHS, 0, SALSAUtility.PointCount_Process);
// Set R(0) = RHS
double InitialRNorm = SALSABLAS.VectorScalarProduct(DistributedCGVector_R, DistributedCGVector_R);
double RNormTest = InitialRNorm * LimitonNormofR; // Limit for Test on Iteration of Norm of R
var SaveRNorm = new double[RealMatrixSize + 1];
SaveRNorm[0] = InitialRNorm;
int CountSteps = 0;
double lastrho = 1.0;
double currentrho = 1.0;
// Loop over Conjugate Gradient Steps
while (true)
{
// Set value of rho
lastrho = currentrho;
currentrho = SALSABLAS.VectorScalarProduct(DistributedCGVector_R, DistributedCGVector_R);
// Set Vector P
++CountSteps;
if (CountSteps == 1)
{
SALSABLAS.CopyVector(DistributedCGVector_P, DistributedCGVector_R, 0,
SALSAUtility.PointCount_Process);
}
else
{
SALSABLAS.LinearCombineVector(DistributedCGVector_P, currentrho / lastrho, DistributedCGVector_P,
1.0, DistributedCGVector_R);
}
// Make a Global Vector of DistributedCGVector_P
ManxcatCentral.MakeVectorGlobal(DistributedCGVector_P, GlobalCGVector_P);
// Distributed Q = Matrix . Global P
UserRoutines.GlobalMatrixVectorProduct(DistributedCGVector_Q, Solution, useexact,
Hotsun.GlobalParameter, GlobalCGVector_P);
// New Answer is Old answer + (Current Rho / (P dot Q)) Vector P
double PdotQ = SALSABLAS.VectorScalarProduct(DistributedCGVector_P, DistributedCGVector_Q);
double alpha = currentrho / PdotQ;
SALSABLAS.LinearCombineVector(Answer, alpha, DistributedCGVector_P, 1.0, Answer);
// New residual R = Old Residual - (Current Rho / (P dot Q)) Vector Q
SALSABLAS.LinearCombineVector(DistributedCGVector_R, -alpha, DistributedCGVector_Q, 1.0,
DistributedCGVector_R);
// See if we can or should End
double CurrentRNorm = SALSABLAS.VectorScalarProduct(DistributedCGVector_R, DistributedCGVector_R);
SaveRNorm[CountSteps] = CurrentRNorm;
bool TestRNorm = CurrentRNorm <= RNormTest;
SALSAUtility.SynchronizeMPIvariable(ref TestRNorm);
if (TestRNorm)
{
matrixsuccess = true;
break;
}
// Singular Matrix
if (CountSteps >= RealMatrixSize)
{
matrixsuccess = false;
ManxcatCentral.MakeVectorGlobal(DistributedCGVector_R, GlobalCGVector_R);
if (SALSAUtility.MPI_Rank == 0)
{
SALSAUtility.SALSAPrint(0, " CG Failure after " + RealMatrixSize.ToString() + " Steps");
string ListofNorms = "";
int Normindex = CountSteps;
for (int inorm = 0; inorm < 10; inorm++)
{
ListofNorms += " " + SaveRNorm[Normindex].ToString("E4");
--Normindex;
if (Normindex < 0)
{
break;
}
}
SALSAUtility.SALSAPrint(0, "Last 10 Norms " + ListofNorms);
string fname = ManxcatCentral.ResultDirectoryName + "\\BadCGVector" +
Hotsun.TotalCGFailures.ToString();
var sw = new StreamWriter(fname, false, Encoding.UTF8);
double fractionnorm = 1.0 / Math.Sqrt(CurrentRNorm);
try
{
for (int GlobalPointIndex = 0;
GlobalPointIndex < SALSAUtility.PointCount_Global;
GlobalPointIndex++)
{
string Coordinates = "";
int UsedPointIndex = SALSAUtility.NaivetoActualUsedOrder[GlobalPointIndex];
double pointsize = 0.0;
for (int LocalVectorIndex = 0;
LocalVectorIndex < Hotsun.ParameterVectorDimension;
LocalVectorIndex++)
{
Coordinates += GlobalCGVector_R[UsedPointIndex][LocalVectorIndex].ToString("E4") +
"\t";
pointsize += GlobalCGVector_R[UsedPointIndex][LocalVectorIndex] *
GlobalCGVector_R[UsedPointIndex][LocalVectorIndex];
}
pointsize = Math.Sqrt(pointsize) * fractionnorm;
sw.WriteLine(
String.Format((GlobalPointIndex).ToString() + "\t" + Coordinates + " " +
pointsize.ToString("E4")));
}
sw.Flush();
sw.Close();
}
catch (Exception e)
{
Console.WriteLine("Failed writing data in CG Solver " + e);
throw (e);
}
}
break;
}
} // End Loop over Conjugate Gradient Steps
NumberofIterations = CountSteps;
return(matrixsuccess);
}
public static void WriteRotateMDS(string fname, int OutputOption, double[][] param, double[][] perr)
{
int LocalVectorDimension = param[0].GetLength(0);
if (LocalVectorDimension != perr[0].GetLength(0))
{
SALSAUtility.SALSAError("Inconsistent Dimensions Labels " + LocalVectorDimension.ToString() + " Perr " +
perr[0].GetLength(0).ToString());
}
ManxcatSection Configuration = ManxcatCentral.Configuration;
// set current cosmic scaling
for (int LocalVectorIndex1 = 0; LocalVectorIndex1 < PointVectorDimension; LocalVectorIndex1++)
{
for (int LocalVectorIndex2 = 0; LocalVectorIndex2 < PointVectorDimension; LocalVectorIndex2++)
{
CurrentCosmicScaling[LocalVectorIndex1, LocalVectorIndex2] =
SavedCosmicScaling[Hotsun.BestChisqLoop][LocalVectorIndex1, LocalVectorIndex2];
}
}
// Write SALSA Properties File Header
if (OutputOption == 0)
{
int filetype = 2;
if ((SALSAUtility.NumberFixedPoints > 0) ||
(SALSAUtility.NumberVariedPoints < SALSAUtility.NumberOriginalPoints))
{
filetype = 4;
}
RotationFileProperties.GroupName = "MDS Run:" + Configuration.RunNumber.ToString();
RotationFileProperties.FileGenerationType = filetype;
RotationFileProperties.OriginalPointStartIndex = 0;
RotationFileProperties.LocalPointStartIndex = 0;
// Rotation parameters
RotationFileProperties.NumberRotationParameters = Hotsun.npar;
RotationFileProperties.RotationParameters = "";
for (int CountRotPars = 0; CountRotPars < Hotsun.npar; CountRotPars++)
{
RotationFileProperties.RotationParameters += " " + param[CountRotPars][0].ToString("E4") + ",";
}
for (int Cosmicdiagonals = 0; Cosmicdiagonals < PointVectorDimension; Cosmicdiagonals++)
{
RotationFileProperties.RotationParameters += " " +
CurrentCosmicScaling[Cosmicdiagonals, Cosmicdiagonals].
ToString("E4") + ",";
}
// Comment should have key features of Run
string OldComment = RotationFileProperties.Comment;
if (OldComment != "")
{
OldComment += "\n";
}
OldComment += "MDS ROTATION Run " + Configuration.RunNumber.ToString() + " Start Time " +
SALSAUtility.startTime.ToLocalTime() + " *** ";
OldComment += "\n RotationOption " + Configuration.RotationOption + " First Scale " +
FirstScale.ToString("E4") + " Second Scale " + SecondScale.ToString()
+ "\n First Mean";
for (int PointIndex = 0; PointIndex < PointVectorDimension; PointIndex++)
{
OldComment += " " + FirstMean[PointIndex].ToString("E4");
}
OldComment += " Second Mean";
for (int PointIndex = 0; PointIndex < PointVectorDimension; PointIndex++)
{
OldComment += " " + SecondMean[PointIndex].ToString("E4");
}
RotationFileProperties.Comment = OldComment;
SALSA_Properties.WriteDataPointFile(fname, ManxcatCentral.Configuration.Write2Das3D, "all ",
RotationFileProperties,
RotationPointProperties, SALSAUtility.NumberOriginalPoints);
return;
}
// Option OutputOption = 1 -- write ROTATED Second Data
try
{
StreamWriter sw = null;
if (!string.IsNullOrEmpty(fname))
{
sw = new StreamWriter(fname, false, Encoding.UTF8);
}
if (sw != null)
{
double[] FullTranslation;
double[,] FullRotation;
SetupFinalTransforamation(param, out FullTranslation, out FullRotation);
for (int UsedDataPoint = 0; UsedDataPoint < SALSAUtility.PointCount_Global; UsedDataPoint++)
{
var Vector = new double[PointVectorDimension];
MatrixVectorProduct(Vector, FullRotation, SecondData[UsedDataPoint]);
VectorSum(Vector, FullTranslation, +1.0, Vector);
string Coordinates = "";
int SingleCluster = 1;
for (int LocalVectorIndex = 0; LocalVectorIndex < PointVectorDimension; LocalVectorIndex++)
{
Coordinates += Vector[LocalVectorIndex].ToString("E4") + "\t";
}
sw.WriteLine(
String.Format((UsedDataPoint + 1).ToString() + "\t" + Coordinates + SingleCluster.ToString()));
}
}
sw.Flush();
sw.Close();
}
catch (Exception e)
{
Console.WriteLine("Failed writing data" + e);
throw (e);
}
}
// End SetupHotsunforMDS
public static void SetupRotateMDS()
{
if (Hotsun.InitializationLoops < 2)
{
Hotsun.InitializationLoops = 2;
Hotsun.InitLoopChisq = new double[Hotsun.InitializationLoops];
ManxcatCentral.Configuration.InitializationLoops = Hotsun.InitializationLoops;
}
Hotsun.bnderrLimit = 10;
if (SALSAUtility.NumberFixedPoints > 0)
{
Exception e = SALSAUtility.SALSAError(" Fixed Points not Allowed in Rotations");
throw (e);
}
RotationOption = ManxcatCentral.Configuration.RotationOption; // set Rotation Option
RotationOption_GenerateTestInput = RotationOption / 100;
// Control special test inputs = 0 normal -- don't generate points to rotate;
// RotationOption_GenerateTestInput = 1 full inversion;
// RotationOption_GenerateTestInput = 2 invert x and y only;
// RotationOption_GenerateTestInput = 3 invert x only
// RotationOption_GenerateTestInput = 4 set new file = old file
RotationOption = RotationOption - 100 * RotationOption_GenerateTestInput;
RotationOption_invert = RotationOption / 10;
// Control how to control scaling in fit. = 0 force scaling positive so when cosmic scaling improper, one cannot fit proper rotation
// RotationOption_invert = 1 allow scaling to be negative which can allow fit to be trapped in wring proper/improper domain for all starts.
// If RotationOption_invert=0 then every other initialization loop is proper (0 1 ..) or improper (1 3 ...)
// Note initial angle values are 0 for initialization loops 0 1nd 1, they are random for later loops
// Angles are forced to lie between -PI and PI
RotationOption = RotationOption - 10 * RotationOption_invert;
// RotationOption = 0 usual Chisq; = 1 Each term divided by magnitude of original point so one minimizes realative errors squared
PointVectorDimension = SALSAUtility.GlobalFileProperties.LocalVectorDimension;
if (PointVectorDimension != SALSAUtility.GlobalFileProperties.LocalVectorDimension)
{
Exception e =
SALSAUtility.SALSAError(" Inconsistent Small Dimension in Rotations " +
PointVectorDimension.ToString());
throw (e);
}
int InitializationFileType = -1;
int InitializationNumberofPoints = -1;
// Set Reference Points
if (SALSA_ProcessVariedandFixed.AreValuesSet(SALSAUtility.GlobalPointProperties))
{
SALSAUtility.SALSAPrint(2,
" Reference Points Taken from basic Labels File " +
ManxcatCentral.Configuration.DataLabelsFileName);
}
else
{
// Set up Values of Used Points from Initialization File
var InitializationFileProperties = new SALSAFileProperties();
var InitializationPointProperties = new SALSADataPointProperties[SALSAUtility.NumberOriginalPoints];
string OriginalMDSFileName = ManxcatCentral.Configuration.InitializationFileName;
// if (!OriginalMDSFileName.Contains(":") || !OriginalMDSFileName.Contains("$"))
// OriginalMDSFileName = ManxcatCentral.Configuration.ControlDirectoryName + "\\" + OriginalMDSFileName;
SALSAUtility.SALSAPrint(2, " Reference Points Taken from Initialization File " + OriginalMDSFileName);
// Begin Changes saliya 03/25/11
// Note. I think we can agree on the zero based indices. The following should be removed then.
if (OriginalMDSFileName.Contains("SIMPLE"))
{
InitializationFileProperties.LocalPointStartIndex = 1;
}
// End Changes saliya 03/25/11
SALSA_Properties.ReadDataPointFile(OriginalMDSFileName, ref InitializationFileType,
InitializationFileProperties, ref InitializationPointProperties,
ref InitializationNumberofPoints);
if ((SALSAUtility.NumberOriginalPoints < InitializationNumberofPoints) ||
(InitializationFileProperties.NumberOriginalPoints != SALSAUtility.NumberOriginalPoints))
{
Exception e =
SALSAUtility.SALSAError(" Inconsistent Initialization File Point Counts " +
InitializationNumberofPoints.ToString() + " or "
+ InitializationFileProperties.NumberOriginalPoints.ToString() +
" Expected is " + SALSAUtility.NumberOriginalPoints.ToString());
throw (e);
}
for (int InitialIndex = 0; InitialIndex < InitializationNumberofPoints; InitialIndex++)
{
int OriginalIndex = InitializationPointProperties[InitialIndex].OriginalPointNumber;
if (!InitializationPointProperties[InitialIndex].valuesset)
{
continue;
}
SALSAUtility.GlobalPointProperties[OriginalIndex].x = InitializationPointProperties[InitialIndex].x;
SALSAUtility.GlobalPointProperties[OriginalIndex].y = InitializationPointProperties[InitialIndex].y;
SALSAUtility.GlobalPointProperties[OriginalIndex].z = InitializationPointProperties[InitialIndex].z;
SALSAUtility.GlobalPointProperties[OriginalIndex].valuesset =
InitializationPointProperties[InitialIndex].valuesset;
}
if (!SALSA_ProcessVariedandFixed.AreValuesSet(SALSAUtility.GlobalPointProperties))
{
Exception e = SALSAUtility.SALSAError(" Reference Points Not set");
throw (e);
}
}
// Now Read Points to be Rotated
// Set up Values of Used Points from Rotation File
int RotationFileType = -1;
RotationFileProperties = new SALSAFileProperties();
RotationPointProperties = new SALSADataPointProperties[SALSAUtility.NumberOriginalPoints];
if (RotationOption_GenerateTestInput == 0)
{
int RotationNumberofPoints = -1;
string RotationFileName = ManxcatCentral.Configuration.RotationLabelsFileName;
// if (!RotationFileName.Contains(":"))
// RotationFileName = ManxcatCentral.Configuration.ControlDirectoryName + "\\" + RotationFileName;
if (RotationFileName.Contains("SIMPLE"))
{
RotationFileProperties.LocalPointStartIndex = 1;
}
SALSAUtility.SALSAPrint(2, " Points to be rotated Taken from File " + RotationFileName);
SALSA_Properties.ReadDataPointFile(RotationFileName, ref RotationFileType, RotationFileProperties,
ref RotationPointProperties, ref RotationNumberofPoints);
if ((SALSAUtility.NumberOriginalPoints < RotationNumberofPoints) ||
(RotationFileProperties.NumberOriginalPoints != SALSAUtility.NumberOriginalPoints))
{
Exception e =
SALSAUtility.SALSAError(" Inconsistent Rotation File Point Counts " +
RotationNumberofPoints.ToString() + " or "
+ RotationFileProperties.NumberOriginalPoints.ToString() +
" Expected is " + SALSAUtility.NumberOriginalPoints.ToString());
throw (e);
}
if (!SALSA_ProcessVariedandFixed.AreValuesSet(RotationPointProperties))
{
Exception e = SALSAUtility.SALSAError(" Points to rotate Not set");
throw (e);
}
} // End normal case when we read file of points to be rotated
else
{
// Generate file to be Rotated
RotationFileType = InitializationFileType;
for (int PointIndex = 0; PointIndex < SALSAUtility.NumberOriginalPoints; PointIndex++)
{
RotationPointProperties[PointIndex] = new SALSADataPointProperties();
}
double fudgex = 1.0;
double fudgey = 1.0;
double fudgez = 1.0;
if (RotationOption_GenerateTestInput == 1)
{
SALSAUtility.SALSAPrint(2, " Points to be rotated generated as -x -y -z ");
fudgex = -1.0;
fudgey = -1.0;
fudgez = -1.0;
}
if (RotationOption_GenerateTestInput == 2)
{
SALSAUtility.SALSAPrint(2, " Points to be rotated generated as -x -y +z ");
fudgex = -1.0;
fudgey = -1.0;
}
if (RotationOption_GenerateTestInput == 3)
{
SALSAUtility.SALSAPrint(2, " Points to be rotated generated as -x +y +z ");
fudgex = -1.0;
}
if (RotationOption_GenerateTestInput >= 4)
{
SALSAUtility.SALSAPrint(2, " Points to be rotated generated as +x +y +z ");
}
for (int GlobalPointIndex = 0; GlobalPointIndex < SALSAUtility.PointCount_Global; GlobalPointIndex++)
{
int OriginalIndex = SALSAUtility.UsedPointtoOriginalPointMap[GlobalPointIndex];
RotationPointProperties[OriginalIndex].x = fudgex *
SALSAUtility.GlobalPointProperties[OriginalIndex].x;
;
RotationPointProperties[OriginalIndex].y = fudgey *
SALSAUtility.GlobalPointProperties[OriginalIndex].y;
RotationPointProperties[OriginalIndex].z = fudgez *
SALSAUtility.GlobalPointProperties[OriginalIndex].z;
RotationPointProperties[OriginalIndex].valuesset =
SALSAUtility.GlobalPointProperties[OriginalIndex].valuesset;
}
}
// Set up operational data
FirstData = new double[SALSAUtility.PointCount_Global][]; // Initial point data
SecondData = new double[SALSAUtility.PointCount_Global][];
; // Second point data
FirstMean = new double[PointVectorDimension]; // Mean of initial point data
SecondMean = new double[PointVectorDimension];
for (int GlobalPointIndex = 0; GlobalPointIndex < SALSAUtility.PointCount_Global; GlobalPointIndex++)
{
FirstData[GlobalPointIndex] = new double[PointVectorDimension];
SecondData[GlobalPointIndex] = new double[PointVectorDimension];
}
// Process Data
ProcessPointData(SALSAUtility.GlobalPointProperties, FirstData, FirstMean, out FirstScale);
ProcessPointData(RotationPointProperties, SecondData, SecondMean, out SecondScale);
ScalePosition = 6;
if (PointVectorDimension == 2)
{
ScalePosition = 3;
}
NumberSubRotations = 3;
if (PointVectorDimension == 2)
{
NumberSubRotations = 1;
}
// This holds the inversion transformation
CurrentCosmicScaling = new double[PointVectorDimension, PointVectorDimension];
SavedCosmicScaling = new double[Hotsun.InitializationLoops][, ];
for (int scalingindex = 0; scalingindex < Hotsun.InitializationLoops; scalingindex++)
{
SavedCosmicScaling[scalingindex] = new double[PointVectorDimension, PointVectorDimension];
}
// If ManxcatCentral.MetadataforRun.MinimumDistance is positive, it is absolute Minimum Distance
// If ManxcatCentral.MetadataforRun.MinimumDistance is negative, it is - multiplier of System Average
if (ManxcatCentral.Configuration.MinimumDistance < 0)
{
MinimumDistance = -ManxcatCentral.Configuration.MinimumDistance * FirstScale;
}
else
{
MinimumDistance = ManxcatCentral.Configuration.MinimumDistance;
}
string firstM = "";
string secondM = "";
for (int LocalVectorIndex = 0; LocalVectorIndex < PointVectorDimension; LocalVectorIndex++)
{
firstM += FirstMean[LocalVectorIndex].ToString("E4") + " ";
secondM += SecondMean[LocalVectorIndex].ToString("E4") + " ";
}
SALSAUtility.SALSAPrint(0,
" First Scale " + FirstScale.ToString("E4") + " Second Scale " +
SecondScale.ToString("E4") + " First Mean " + firstM + " Second Mean " + secondM);
}
// End VectorSum(double[] VTotal, double[] V2, double sign, double[] V1)
public static void InitializeParameters(Desertwind Solution, int CountStartingPoints)
{
// Inversion
InvertSolution = false;
if ((CountStartingPoints / 2) * 2 != CountStartingPoints)
{
InvertSolution = true;
}
for (int LocalVectorIndex1 = 0; LocalVectorIndex1 < PointVectorDimension; LocalVectorIndex1++)
{
for (int LocalVectorIndex2 = 0; LocalVectorIndex2 < PointVectorDimension; LocalVectorIndex2++)
{
CurrentCosmicScaling[LocalVectorIndex1, LocalVectorIndex2] = 0.0;
}
CurrentCosmicScaling[LocalVectorIndex1, LocalVectorIndex1] = 1.0;
}
if (InvertSolution)
{
for (int LocalVectorIndex1 = 0; LocalVectorIndex1 < PointVectorDimension; LocalVectorIndex1++)
{
CurrentCosmicScaling[LocalVectorIndex1, LocalVectorIndex1] = -1.0;
}
if (PointVectorDimension == 2)
{
CurrentCosmicScaling[0, 0] = 1.0;
}
}
for (int LocalVectorIndex1 = 0; LocalVectorIndex1 < PointVectorDimension; LocalVectorIndex1++)
{
for (int LocalVectorIndex2 = 0; LocalVectorIndex2 < PointVectorDimension; LocalVectorIndex2++)
{
SavedCosmicScaling[CountStartingPoints][LocalVectorIndex1, LocalVectorIndex2] =
CurrentCosmicScaling[LocalVectorIndex1, LocalVectorIndex2];
}
}
// Scaling
double Scale = FirstScale / SecondScale;
if (ScaleOption == 0)
{
Solution.param[ScalePosition][0] = Scale;
}
else
{
ScaleA1 = 0.5 * (ScaleAlpha + 1.0 / ScaleAlpha);
ScaleA2 = 0.5 * Math.Abs(ScaleAlpha - 1.0 / ScaleAlpha);
Solution.param[ScalePosition][0] = Math.Asin((ScaleA1 - 1.0) / ScaleA2);
ScaleA1 *= Scale;
ScaleA2 *= Scale;
}
var Randobject = new Random();
var RandomAngles = new double[3];
if (SALSAUtility.MPI_Rank == 0)
{
for (int irand = 0; irand < 3; irand++)
{
RandomAngles[irand] = Randobject.NextDouble();
}
}
if (SALSAUtility.MPI_Size > 1)
{
SALSAUtility.StartSubTimer(SALSAUtility.MPIBROADCASTTiming);
SALSAUtility.MPI_communicator.Broadcast(ref RandomAngles, 0);
SALSAUtility.StopSubTimer(SALSAUtility.MPIBROADCASTTiming);
}
// Translation and Rotation
for (int LocalVectorIndex = 0; LocalVectorIndex < PointVectorDimension; LocalVectorIndex++)
{
Solution.param[LocalVectorIndex][0] = FirstMean[LocalVectorIndex] - Scale *
CurrentCosmicScaling[LocalVectorIndex, LocalVectorIndex] *
SecondMean[LocalVectorIndex];
if (PointVectorDimension == 3)
{
Solution.param[LocalVectorIndex + PointVectorDimension][0] = 0.0;
if (CountStartingPoints > 1)
{
Solution.param[LocalVectorIndex + PointVectorDimension][0] = Math.PI *
RandomAngles[LocalVectorIndex];
}
}
}
if (PointVectorDimension == 2)
{
Solution.param[2][0] = 0.0;
if (CountStartingPoints > 1)
{
Solution.param[2][0] = Math.PI * RandomAngles[0];
}
}
}
// End UpdateManxcatMDS_Option12_TraditionalDirectory
public static bool ReadMDSCluster_File(string MDSClusterFileName, String[] InitialString, int[] ColorValue,
ref int NumberofPoints)
{
NumberofPoints = 0;
try
{
// Check if file exists
if (!File.Exists(MDSClusterFileName))
{
Exception e = SALSAUtility.SALSAError("File " + MDSClusterFileName + " does not exists");
throw (e);
}
// Create a new stream to read from a file
using (StreamReader sr = File.OpenText(MDSClusterFileName))
{
// Read contents of a file, line by line, into a string
String inputLineStr;
int newlabelnumber = -1;
while ((inputLineStr = sr.ReadLine()) != null)
{
if (inputLineStr.Length < 2)
{
continue; //replace empty line
}
inputLineStr = inputLineStr.Trim(new[] { ' ', '\t' });
try
{
// Parse each record string
inputLineStr = inputLineStr.Replace("\t\t", "\t");
string[] split = inputLineStr.Split(new[] { ' ', '\t' }, StringSplitOptions.RemoveEmptyEntries);
newlabelnumber = Convert.ToInt32(split[0]);
if (split.Length != Hotsun.ParameterVectorDimension + 2)
{
Console.WriteLine(" Bad Line "
+ split.Length + " " + NumberofPoints + " " + inputLineStr);
}
// Begin Changes saliya 3/22/11
// Note. This seems unnecessary. Let's agree on zero based indices
// if ((NumberofPoints + 1) != newlabelnumber)
// {
// Exception e = SALSAUtility.SALSAError("Unexpected Label Number "
// + newlabelnumber + " Expected " + NumberofPoints + "+1");
//
// throw (e);
// }
// End Changes saliya 3/22/11
inputLineStr = split[0];
for (int i = 1; i < (split.Length - 1); i++)
{
inputLineStr += "\t" + split[i];
}
InitialString[NumberofPoints] = inputLineStr;
ColorValue[NumberofPoints] = (int)Convert.ToDouble(split[split.Length - 1]);
++NumberofPoints;
}
catch (Exception e)
{
SALSAUtility.SALSAError("Failed to load data array " + inputLineStr + " "
+ " "
+ NumberofPoints.ToString() + " " + newlabelnumber.ToString() + " " +
e);
throw (e);
}
}
sr.Close();
}
}
catch (Exception e)
{
SALSAUtility.SALSAError("Failed to read data from " + MDSClusterFileName + " " + e);
throw (e);
}
if (NumberofPoints != SALSAUtility.PointCount_Global)
{
Exception e = SALSAUtility.SALSAError("Incorrect #Points in File "
+ NumberofPoints + " Expected " + SALSAUtility.PointCount_Global);
throw (e);
}
return(true);
}
// End ReadMDSClusterFile
public static bool ReadClusterLabel_File(string LabelFileName, String[] LabelArray, ref int NumberofLabels)
{
NumberofLabels = 0;
int startnumber = 1;
try
{
// Check if file exists
if (!File.Exists(LabelFileName))
{
Exception e = SALSAUtility.SALSAError("File " + LabelFileName + " does not exists.");
throw (e);
}
// Create a new stream to read from a file
using (StreamReader sr = File.OpenText(LabelFileName))
{
// Read contents of a file, line by line, into a string
String inputLineStr;
while ((inputLineStr = sr.ReadLine()) != null)
{
if (inputLineStr.Length < 2)
{
continue; //replace empty line
}
inputLineStr = inputLineStr.Trim();
try
{
// Parse each record string
string[] split = inputLineStr.Split(new[] { ' ', '\t' }, 2,
StringSplitOptions.RemoveEmptyEntries);
int newlabelnumber = Convert.ToInt32(split[0]);
if (NumberofLabels == 0)
{
startnumber = newlabelnumber;
if ((startnumber < 0) || (startnumber > 1))
{
Exception e =
SALSAUtility.SALSAError("Unexpected Start Number " + startnumber.ToString());
throw (e);
}
}
if (NumberofLabels != (newlabelnumber + startnumber))
{
Exception e = SALSAUtility.SALSAError("Unexpected Label Number "
+ newlabelnumber.ToString() + " Expected " +
NumberofLabels.ToString() + " + " +
startnumber.ToString());
throw (e);
}
if (split[1].Length <= 0)
{
Exception e =
SALSAUtility.SALSAError("Zero length label for point " + NumberofLabels.ToString());
throw (e);
}
LabelArray[NumberofLabels] = split[1];
++NumberofLabels;
}
catch (Exception e)
{
SALSAUtility.SALSAError("Failed to load data from " + LabelFileName + " " + e);
throw (e);
}
}
sr.Close();
}
}
catch (Exception e)
{
SALSAUtility.SALSAError("Failed to read data from " + LabelFileName + " " + e);
throw (e);
}
return(true);
}
// End UpdateManxcatMDS_Option12_Cluster()
public static void UpdateManxcatMDS_Option12_TraditionalDirectory()
{
string labelFileDirectory = ManxcatCentral.Configuration.ClusterDirectory; // Input Directory
string MDSandClusterDirectory = labelFileDirectory + "\\" + ManxcatCentral.Configuration.RunSetLabel +
"-R" + ManxcatCentral.Configuration.RunNumber.ToString() + "-ManxcatMDS";
// Output Directory
if (Directory.Exists(MDSandClusterDirectory))
{
SALSAUtility.SALSAPrint(0, "The directory " + MDSandClusterDirectory + " exists");
}
else
{
DirectoryInfo di = Directory.CreateDirectory(MDSandClusterDirectory);
SALSAUtility.SALSAPrint(0, "The directory " + MDSandClusterDirectory + " was created successfully at "
+ Directory.GetCreationTime(MDSandClusterDirectory));
}
string[] SMACOFfileEntries = Directory.GetFiles(MDSandClusterDirectory);
string TypicalMDSFileName = ManxcatCentral.Configuration.ReducedVectorOutputFileName;
if (!TypicalMDSFileName.Contains(":"))
{
TypicalMDSFileName = ManxcatCentral.ResultDirectoryName + "\\SIMPLE" + TypicalMDSFileName;
}
if (!File.Exists(TypicalMDSFileName))
{
Exception e = SALSAUtility.SALSAError(" File " + TypicalMDSFileName + " Does Not Exist");
throw (e);
}
int NumberMDSPoints = 0;
var InitialMDSString = new string[SALSAUtility.PointCount_Global];
var ColorValue = new int[SALSAUtility.PointCount_Global];
if (ReadMDSCluster_File(TypicalMDSFileName, InitialMDSString, ColorValue, ref NumberMDSPoints))
{
Console.WriteLine(TypicalMDSFileName + " Read Successfully");
}
string[] fileEntries = Directory.GetFiles(labelFileDirectory);
foreach (string LabelFileName in fileEntries)
{
if (LabelFileName.Contains(".dot"))
{
continue;
}
if (LabelFileName.Contains("Summary"))
{
continue;
}
if (LabelFileName.Contains("Timing"))
{
continue;
}
string LabelFileName1 = LabelFileName.Replace(labelFileDirectory + "\\", "");
string coreFileName = MDSandClusterDirectory + "\\" + "MDSManxcat-" + LabelFileName1;
if (File.Exists(coreFileName))
{
continue;
}
int NumberOfLabels = 0;
var CategoryLabel = new string[SALSAUtility.PointCount_Global];
ReadClusterLabel_File(LabelFileName, CategoryLabel, ref NumberOfLabels);
if (NumberOfLabels != SALSAUtility.PointCount_Global)
{
Exception e = SALSAUtility.SALSAError(" Illegal Count "
+ NumberOfLabels.ToString() + " in File " + LabelFileName);
throw (e);
}
var CategoryIndex = new int[SALSAUtility.PointCount_Global];
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
CategoryIndex[PointIndex] = Convert.ToInt32(CategoryLabel[PointIndex]);
}
WriteColor_Cluster(coreFileName, InitialMDSString, CategoryIndex, SALSAUtility.PointCount_Global, false);
SALSAUtility.SALSAPrint(0, "Traditional Directory MDS Info Added to " + coreFileName);
}
}
// End UpdateManxcatMDS_Option12_FamilybyCuts
public static void UpdateManxcatMDS_Option12_Cluster()
{
// Read Cluster Information with File specified in ConversionInformation
string ClusterFileName = ManxcatCentral.Configuration.ConversionInformation;
int NumberOfClusterLines = 0;
var CategoryLabel = new string[SALSAUtility.PointCount_Global];
ReadClusterLabel_File(ClusterFileName, CategoryLabel, ref NumberOfClusterLines);
if (NumberOfClusterLines != SALSAUtility.PointCount_Global)
{
Exception e = SALSAUtility.SALSAError(" Illegal Count "
+ NumberOfClusterLines.ToString() + " in File " + ClusterFileName);
throw (e);
}
var CategoryIndex = new int[SALSAUtility.PointCount_Global];
int minlabel = SALSAUtility.PointCount_Global;
int maxlabel = 0;
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
CategoryIndex[PointIndex] = Convert.ToInt32(CategoryLabel[PointIndex]);
if (minlabel > CategoryIndex[PointIndex])
{
minlabel = CategoryIndex[PointIndex];
}
if (maxlabel < CategoryIndex[PointIndex])
{
maxlabel = CategoryIndex[PointIndex];
}
}
int TotalNumberClusters = maxlabel - minlabel + 1;
var ClusterCounts = new int[TotalNumberClusters];
for (int Icount = 0; Icount < TotalNumberClusters; Icount++)
{
ClusterCounts[Icount] = 0;
}
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
++ClusterCounts[CategoryIndex[PointIndex] - minlabel];
}
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
int Icount = CategoryIndex[PointIndex];
SALSAUtility.GlobalPointProperties[PointIndex].cluster = Icount;
SALSAUtility.GlobalPointProperties[PointIndex].clusterlabel = "Cluster "
+ Icount.ToString() + " out of "
+ TotalNumberClusters.ToString() +
" Count " +
ClusterCounts[Icount - minlabel].ToString();
}
SALSAUtility.GlobalFileProperties.ClusterName = "Clusters from " + ClusterFileName;
SALSAUtility.GlobalFileProperties.ClusterStartIndex = minlabel;
string cleandate = SALSAUtility.startTime.ToLocalTime().ToString();
cleandate = cleandate.Replace(":", ".");
cleandate = cleandate.Replace(" ", "-");
string OldComment = SALSAUtility.GlobalFileProperties.Comment;
if (OldComment != "")
{
OldComment += "\n";
}
OldComment += "Cluster Information added from " + ClusterFileName + " Time " + cleandate;
SALSAUtility.GlobalFileProperties.Comment = OldComment;
// Write new label file
string labelfilename = ManxcatCentral.Configuration.DataLabelsFileName;
if (!labelfilename.Contains(":") && !labelfilename.Contains("$"))
{
labelfilename = ManxcatCentral.Configuration.ControlDirectoryName + "\\" + labelfilename;
}
SALSA_Properties.WriteDataPointFile(labelfilename, ManxcatCentral.Configuration.Write2Das3D,
"colon,SameFileName ", SALSAUtility.GlobalFileProperties,
SALSAUtility.GlobalPointProperties, SALSAUtility.NumberOriginalPoints);
SALSAUtility.SALSAPrint(0, "Cluster Info Added to " + labelfilename + " from " + ClusterFileName);
ManxcatCentral.Configuration.Comment += "\nCluster Info Added to "
+ labelfilename + " from " + ClusterFileName;
}
// End UpdateManxcatMDS_Option12()
public static void UpdateManxcatMDS_Option12_Functions(bool statistics)
{
// Setup weight: Only used in statistics
var weights = new double[SALSAUtility.PointCount_Global];
ManxcatMDS.WeightingOption = ManxcatCentral.Configuration.WeightingOption;
ManxcatMDS.SetupWeightings(weights);
string TypicalMDSFileName = "";
// Setup MDS: Only used in statistics
var MDSPoints = new double[SALSAUtility.PointCount_Global, Hotsun.ParameterVectorDimension];
if (statistics)
{
// Set up statistics by reading MDS file
TypicalMDSFileName = ManxcatCentral.ResultDirectoryName + "\\SIMPLE" +
ManxcatCentral.Configuration.ReducedVectorOutputFileName;
if (!File.Exists(TypicalMDSFileName))
{
Exception e = SALSAUtility.SALSAError(" File " + TypicalMDSFileName + " Does Not Exist");
throw (e);
}
int NumberMDSPoints = 0;
var InitialMDSString = new string[SALSAUtility.PointCount_Global];
var ColorValue = new int[SALSAUtility.PointCount_Global];
if (ReadMDSCluster_File(TypicalMDSFileName, InitialMDSString, ColorValue, ref NumberMDSPoints))
{
SALSAUtility.SALSAPrint(0, "MDS File " + TypicalMDSFileName + " Read Successfully");
}
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
// Extract MDS POints
string inputLineStr = InitialMDSString[PointIndex].Trim();
string[] split = inputLineStr.Split(new[] { ' ', '\t' }, StringSplitOptions.RemoveEmptyEntries);
if (split.Length < Hotsun.ParameterVectorDimension)
{
Exception e =
SALSAUtility.SALSAError(" Point " + PointIndex.ToString() + " has wrong number of Entries "
+ inputLineStr + " Entries" + split.Length);
throw (e);
}
for (int VectorIndex = 0; VectorIndex < Hotsun.ParameterVectorDimension; VectorIndex++)
{
MDSPoints[PointIndex, VectorIndex] = Convert.ToDouble(split[VectorIndex].Trim());
}
}
} // End set up of Statistics
// Set Mapping
var ClusterLabel = new int[SALSAUtility.PointCount_Global];
int NumDivisions = 10;
int BasicSize = SALSAUtility.PointCount_Global / NumDivisions;
int LeftOver = SALSAUtility.PointCount_Global - BasicSize * NumDivisions;
int DivisionCount = 0;
int Limit = 0;
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
if (PointIndex >= Limit)
{
++DivisionCount;
Limit += BasicSize;
if (LeftOver >= DivisionCount)
{
++Limit;
}
}
ClusterLabel[PointIndex] = DivisionCount;
}
String FunctionFileName = ManxcatCentral.Configuration.ConversionInformation;
if (!FunctionFileName.Contains(":"))
{
FunctionFileName = ManxcatCentral.Configuration.ControlDirectoryName + "\\" + FunctionFileName;
}
var functionkeys = new double[SALSAUtility.PointCount_Global];
var functionlabels = new int[SALSAUtility.PointCount_Global];
int pickout = -1;
while (true)
{
++pickout;
bool endofdata = true;
int NumberofLines = 0;
double sumabs = 0.0;
double totalweight = 0.0;
double meangamma = 0.0;
double vargamma = 0.0;
var meanxyz = new double[Hotsun.ParameterVectorDimension];
var varxyz = new double[Hotsun.ParameterVectorDimension, Hotsun.ParameterVectorDimension];
var correlxyzgamma = new double[Hotsun.ParameterVectorDimension];
if (statistics)
{
for (int VectorIndex1 = 0; VectorIndex1 < Hotsun.ParameterVectorDimension; VectorIndex1++)
{
meanxyz[VectorIndex1] = 0.0;
for (int VectorIndex2 = 0; VectorIndex2 < Hotsun.ParameterVectorDimension; VectorIndex2++)
{
varxyz[VectorIndex1, VectorIndex2] = 0.0;
}
correlxyzgamma[VectorIndex1] = 0.0;
}
}
try
{
// Check if file exists
if (!File.Exists(FunctionFileName))
{
Exception e = SALSAUtility.SALSAError("File " + FunctionFileName + " does not exists.");
throw (e);
}
// Create a new stream to read from a file
using (StreamReader sr = File.OpenText(FunctionFileName))
{
// Read contents of a file, line by line, into a string
String inputLineStr;
while ((inputLineStr = sr.ReadLine()) != null)
{
inputLineStr = inputLineStr.Trim();
string[] split = inputLineStr.Split(new[] { ' ' }, StringSplitOptions.RemoveEmptyEntries);
if (split.Length <= pickout)
{
break;
}
endofdata = false;
string usethis = split[pickout].Trim();
if (usethis.Length < 1)
{
continue; //replace empty line
}
double gamma = Convert.ToDouble(usethis);
functionkeys[NumberofLines] = gamma;
functionlabels[NumberofLines] = NumberofLines;
sumabs += Math.Abs(gamma);
if (statistics)
{
double wgt = weights[NumberofLines];
meangamma += gamma * wgt;
vargamma += wgt * gamma * gamma;
totalweight += wgt;
for (int VectorIndex1 = 0;
VectorIndex1 < Hotsun.ParameterVectorDimension;
VectorIndex1++)
{
meanxyz[VectorIndex1] += MDSPoints[NumberofLines, VectorIndex1] * wgt;
correlxyzgamma[VectorIndex1] += MDSPoints[NumberofLines, VectorIndex1] * gamma * wgt;
for (int VectorIndex2 = 0;
VectorIndex2 < Hotsun.ParameterVectorDimension;
VectorIndex2++)
{
varxyz[VectorIndex1, VectorIndex2] += MDSPoints[NumberofLines, VectorIndex1] *
MDSPoints[NumberofLines, VectorIndex2] * wgt;
}
}
}
++NumberofLines;
}
sr.Close();
}
}
catch (Exception e)
{
SALSAUtility.SALSAError("Failed to read data from " + FunctionFileName + " " + e);
throw (e);
}
if (endofdata)
{
break;
}
if (NumberofLines != SALSAUtility.PointCount_Global)
{
SALSAUtility.SALSAError("Incorrect Function count read "
+ NumberofLines + " Expected " + SALSAUtility.PointCount_Global);
}
// Set Statistics
if (statistics)
{
var alpha = new double[Hotsun.ParameterVectorDimension];
double alphanorm = 0.0;
meangamma = meangamma / totalweight;
vargamma = (vargamma / totalweight) - meangamma * meangamma;
for (int VectorIndex1 = 0; VectorIndex1 < Hotsun.ParameterVectorDimension; VectorIndex1++)
{
meanxyz[VectorIndex1] = meanxyz[VectorIndex1] / totalweight;
}
for (int VectorIndex1 = 0; VectorIndex1 < Hotsun.ParameterVectorDimension; VectorIndex1++)
{
for (int VectorIndex2 = 0; VectorIndex2 < Hotsun.ParameterVectorDimension; VectorIndex2++)
{
varxyz[VectorIndex1, VectorIndex2] = (varxyz[VectorIndex1, VectorIndex2] / totalweight) -
meanxyz[VectorIndex1] * meanxyz[VectorIndex2];
}
correlxyzgamma[VectorIndex1] = correlxyzgamma[VectorIndex1] / totalweight -
meangamma * meanxyz[VectorIndex1];
alpha[VectorIndex1] = correlxyzgamma[VectorIndex1] / varxyz[VectorIndex1, VectorIndex1];
alphanorm += alpha[VectorIndex1] * alpha[VectorIndex1];
}
// invert Matrix to find best alpha
var ConventionalFirst = new double[Hotsun.ParameterVectorDimension, 1];
var ConventionalAnswer = new double[Hotsun.ParameterVectorDimension][];
var ConventionalMatrix = new double[Hotsun.ParameterVectorDimension, Hotsun.ParameterVectorDimension];
for (int VectorIndex1 = 0; VectorIndex1 < Hotsun.ParameterVectorDimension; VectorIndex1++)
{
ConventionalAnswer[VectorIndex1] = new double[1];
ConventionalFirst[VectorIndex1, 0] = correlxyzgamma[VectorIndex1] /
Math.Sqrt(varxyz[VectorIndex1, VectorIndex1]);
for (int VectorIndex2 = 0; VectorIndex2 < Hotsun.ParameterVectorDimension; VectorIndex2++)
{
ConventionalMatrix[VectorIndex1, VectorIndex2] = varxyz[VectorIndex1, VectorIndex2] /
Math.Sqrt(
varxyz[VectorIndex1, VectorIndex1] *
varxyz[VectorIndex2, VectorIndex2]);
}
}
LMatrix cMatrix = LMatrix.Create(ConventionalMatrix);
LMatrix RightHandSide = LMatrix.Create(ConventionalFirst);
LMatrix MatrixAnswer = cMatrix.Solve(RightHandSide);
ConventionalAnswer = MatrixAnswer;
alphanorm = 0.0;
for (int VectorIndex1 = 0; VectorIndex1 < Hotsun.ParameterVectorDimension; VectorIndex1++)
{
alpha[VectorIndex1] = ConventionalAnswer[VectorIndex1][0] /
Math.Sqrt(varxyz[VectorIndex1, VectorIndex1]);
alphanorm += alpha[VectorIndex1] * alpha[VectorIndex1];
}
double Fullcorrelation = 0.0;
double varalphaxyz = 0.0;
for (int VectorIndex1 = 0; VectorIndex1 < Hotsun.ParameterVectorDimension; VectorIndex1++)
{
alpha[VectorIndex1] = alpha[VectorIndex1] / Math.Sqrt(alphanorm);
Fullcorrelation += alpha[VectorIndex1] * correlxyzgamma[VectorIndex1];
}
for (int VectorIndex1 = 0; VectorIndex1 < Hotsun.ParameterVectorDimension; VectorIndex1++)
{
for (int VectorIndex2 = 0; VectorIndex2 < Hotsun.ParameterVectorDimension; VectorIndex2++)
{
varalphaxyz += alpha[VectorIndex1] * alpha[VectorIndex2] * varxyz[VectorIndex1, VectorIndex2];
}
}
Console.WriteLine(varalphaxyz + " " + Fullcorrelation + " " + vargamma);
Fullcorrelation = Fullcorrelation / (Math.Sqrt(vargamma * varalphaxyz));
SALSAUtility.SALSAPrint(0, "Column "
+ pickout.ToString() + " File " + FunctionFileName + " MDS File " +
TypicalMDSFileName +
" Total Weight "
+ totalweight.ToString() + " Correlation " +
Fullcorrelation.ToString("F4") + " Direction "
+ alpha[0].ToString("F4") + " " + alpha[1].ToString("F4") + " " +
alpha[2].ToString("F4"));
}
// Set Divisions
Array.Sort(functionkeys, functionlabels);
var PointColors = new int[SALSAUtility.PointCount_Global];
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
int UnsortedPosition = functionlabels[PointIndex];
PointColors[UnsortedPosition] = ClusterLabel[PointIndex];
}
string OutputFileExtension = ManxcatCentral.Configuration.ConversionInformation;
OutputFileExtension = OutputFileExtension.Replace(".dat", "");
OutputFileExtension = OutputFileExtension.Replace(".txt", "");
OutputFileExtension = OutputFileExtension + "-" + pickout.ToString() + ".txt";
string labelFileDirectory = ManxcatCentral.Configuration.ClusterDirectory;
// Directory for Colors attached to Points
string OutputFileName = labelFileDirectory + "\\" + OutputFileExtension;
WritePointCluster(OutputFileName, PointColors, SALSAUtility.PointCount_Global);
double test = 0.1 * sumabs / NumberofLines;
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
int UnsortedPosition = functionlabels[PointIndex];
if (Math.Abs(functionkeys[UnsortedPosition]) < test)
{
PointColors[UnsortedPosition] = 0;
}
}
OutputFileName = OutputFileName.Replace(".txt", "NZ.txt");
WritePointCluster(OutputFileName, PointColors, SALSAUtility.PointCount_Global);
} // End while over pickout (columns in data)
return;
}
// End UpdateManxcatMDS_Option12_Functions
public static void UpdateManxcatMDS_Option12_FamilybyCuts()
{
String CutFileName = ManxcatCentral.Configuration.ConversionInformation;
if (!CutFileName.Contains(":"))
{
CutFileName = ManxcatCentral.Configuration.ControlDirectoryName + "\\" + CutFileName;
}
var inputdata = new string[SALSAUtility.PointCount_Global];
int NumberofCuts = 0;
string FamilyLabel = "Family";
int FamilyNumber = 1;
if (ManxcatCentral.Configuration.ConversionOption.ToLower().Contains("family2"))
{
FamilyNumber = 2;
}
ReadString_File(CutFileName, inputdata, ref NumberofCuts);
if (NumberofCuts <= 0)
{
Exception e = SALSAUtility.SALSAError("Too few points "
+ NumberofCuts.ToString() + " in Cut File " + CutFileName);
throw (e);
}
var CutStart = new int[NumberofCuts];
var CutLabel = new string[NumberofCuts];
int CountFamilies = 0;
int itmpold = -2;
for (int CutPos = 0; CutPos < NumberofCuts; CutPos++)
{
string[] split = inputdata[CutPos].Split(new[] { ' ', '\t' }, StringSplitOptions.RemoveEmptyEntries);
int itmp = Convert.ToInt32(split[0]);
if (itmp < 0)
{
FamilyLabel = split[1];
continue;
}
if (itmp <= itmpold)
{
continue;
}
CutStart[CountFamilies] = itmp;
CutLabel[CountFamilies] = FamilyLabel + "-" + split[1];
++CountFamilies;
itmpold = itmp;
}
if (FamilyNumber == 1)
{
SALSAUtility.GlobalFileProperties.FamilyName1 = FamilyLabel + " from " + CutFileName;
}
if (FamilyNumber == 2)
{
SALSAUtility.GlobalFileProperties.FamilyName2 = FamilyLabel + " from " + CutFileName;
}
int minlabel = 1;
int CurrentFamily = 0;
var CategoryIndex = new int[SALSAUtility.PointCount_Global];
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
if (CurrentFamily < CountFamilies - 1)
{
if ((PointIndex + 1) >= CutStart[CurrentFamily + 1])
{
++CurrentFamily;
}
}
CategoryIndex[PointIndex] = minlabel + CurrentFamily;
continue;
}
var FamilyCounts = new int[CountFamilies];
for (int Icount = 0; Icount < CountFamilies; Icount++)
{
FamilyCounts[Icount] = 0;
}
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
++FamilyCounts[CategoryIndex[PointIndex] - minlabel];
}
for (int PointIndex = 0; PointIndex < SALSAUtility.PointCount_Global; PointIndex++)
{
int Icount = CategoryIndex[PointIndex];
if (FamilyNumber == 1)
{
SALSAUtility.GlobalPointProperties[PointIndex].family1 = Icount;
SALSAUtility.GlobalPointProperties[PointIndex].familylabel1 = CutLabel[Icount - minlabel] + " "
+ Icount.ToString() + " out of "
+ CountFamilies.ToString() + " Count " +
FamilyCounts[Icount - minlabel].
ToString();
}
if (FamilyNumber == 2)
{
SALSAUtility.GlobalPointProperties[PointIndex].family2 = Icount;
SALSAUtility.GlobalPointProperties[PointIndex].familylabel2 = CutLabel[Icount - minlabel] + " "
+ Icount.ToString() + " out of "
+ CountFamilies.ToString() + " Count " +
FamilyCounts[Icount - minlabel].
ToString();
}
}
string cleandate = SALSAUtility.startTime.ToLocalTime().ToString();
cleandate = cleandate.Replace(":", ".");
cleandate = cleandate.Replace(" ", "-");
string OldComment = SALSAUtility.GlobalFileProperties.Comment;
if (OldComment != "")
{
OldComment += "\n";
}
OldComment += "Family"
+ FamilyNumber.ToString() + " " + FamilyLabel + " Information added from " + CutFileName +
" Time " + cleandate;
SALSAUtility.GlobalFileProperties.Comment = OldComment;
// Write new label file
string labelfilename = ManxcatCentral.Configuration.DataLabelsFileName;
if (!labelfilename.Contains(":"))
{
labelfilename = ManxcatCentral.Configuration.ControlDirectoryName + "\\" + labelfilename;
}
SALSA_Properties.WriteDataPointFile(labelfilename, ManxcatCentral.Configuration.Write2Das3D,
"colon,SameFileName ", SALSAUtility.GlobalFileProperties,
SALSAUtility.GlobalPointProperties, SALSAUtility.NumberOriginalPoints);
SALSAUtility.SALSAPrint(0, "Family"
+ FamilyNumber.ToString() + " " + FamilyLabel + " Info Added to " + labelfilename +
" from " + CutFileName);
ManxcatCentral.Configuration.Comment += "\nFamily"
+ FamilyNumber.ToString() + " " + FamilyLabel + " Info Added to " +
labelfilename + " from " + CutFileName;
}
// Write label-cluster results into a file
public static void WriteMDS(string fname, int OutputOption, double[][] param, double[][] perr)
{
int LocalVectorDimension = param[0].GetLength(0);
if (LocalVectorDimension != perr[0].GetLength(0))
{
SALSAUtility.SALSAError("Inconsistent Dimensions Labels " + LocalVectorDimension.ToString() + " Perr " +
perr[0].GetLength(0).ToString());
}
ManxcatSection Configuration = ManxcatCentral.Configuration;
// Write SALSA Properties File Header
if (OutputOption == 0)
{
int filetype = 2;
if ((SALSAUtility.NumberFixedPoints > 0) ||
(SALSAUtility.NumberVariedPoints < SALSAUtility.NumberOriginalPoints))
{
filetype = 4;
}
string cleandate = SALSAUtility.startTime.ToLocalTime().ToString();
cleandate = cleandate.Replace(":", ".");
cleandate = cleandate.Replace(" ", "-");
SALSAUtility.GlobalFileProperties.GroupName = "MDSasChisq-" + Configuration.RunSetLabel + "-Run" +
Configuration.RunNumber.ToString() + "-Date-" + cleandate;
SALSAUtility.GlobalFileProperties.FileGenerationType = filetype;
SALSAUtility.GlobalFileProperties.OriginalPointStartIndex = 0;
SALSAUtility.GlobalFileProperties.LocalPointStartIndex = 0;
SALSAUtility.GlobalFileProperties.NumberOriginalPoints = SALSAUtility.NumberOriginalPoints;
SALSAUtility.GlobalFileProperties.NumberPointsinFile = SALSAUtility.PointCount_Global;
// Comment should have key features of Run
string OldComment = SALSAUtility.GlobalFileProperties.Comment;
if (OldComment != "")
{
OldComment += "\n";
}
OldComment += "MDSasChisq " + Configuration.RunNumber.ToString() + " StartTime " + cleandate + " ****";
OldComment += "\n Distance Input Option " + Configuration.DistanceProcessingOption.ToString() +
" Distance Formula " + Configuration.DistanceFormula.ToString() + " Weighting Option " +
Configuration.Chisqnorm.ToString() + " Minimum Distance Value " +
Configuration.MinimumDistance.ToString();
OldComment += "\n" + Hotsun.HotsunComment;
SALSAUtility.GlobalFileProperties.Comment = OldComment;
for (int GlobalPointIndex = 0; GlobalPointIndex < SALSAUtility.PointCount_Global; GlobalPointIndex++)
{
int OriginalPointIndex = SALSAUtility.UsedPointtoOriginalPointMap[GlobalPointIndex];
int groupnumber = -1;
string grouplabel = "Ignored";
SALSAUtility.GlobalPointProperties[GlobalPointIndex].FixedorVaried = 0;
if (ManxcatMDS.PointStatus[GlobalPointIndex] == -1)
{
groupnumber = 3;
grouplabel = "Deleted";
}
else
{
if (SALSAUtility.OriginalPointDisposition[GlobalPointIndex] <= -SALSAUtility.SALSASHIFT)
{
groupnumber = 2;
grouplabel = "Fixed";
SALSAUtility.GlobalPointProperties[GlobalPointIndex].FixedorVaried = 2;
}
if (SALSAUtility.OriginalPointDisposition[GlobalPointIndex] >= SALSAUtility.SALSASHIFT)
{
groupnumber = 1;
grouplabel = "Varied";
SALSAUtility.GlobalPointProperties[GlobalPointIndex].source = "MDSasChisq-" +
Configuration.RunSetLabel +
"-Run" +
Configuration.RunNumber.
ToString() + "-Date-" +
cleandate;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].FixedorVaried = 1;
}
}
SALSAUtility.GlobalPointProperties[GlobalPointIndex].group = groupnumber;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].grouplabel = grouplabel;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].OriginalPointNumber = OriginalPointIndex;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].LocalPointNumber = GlobalPointIndex;
}
for (int GlobalPointIndex = 0; GlobalPointIndex < SALSAUtility.PointCount_Global; GlobalPointIndex++)
{
if (ManxcatMDS.PointStatus[GlobalPointIndex] == -1)
{
SALSAUtility.GlobalPointProperties[GlobalPointIndex].valuesset = false;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].errorsset = false;
continue;
}
SALSAUtility.GlobalPointProperties[GlobalPointIndex].x = param[GlobalPointIndex][0];
SALSAUtility.GlobalPointProperties[GlobalPointIndex].y = param[GlobalPointIndex][1];
if (LocalVectorDimension > 2)
{
SALSAUtility.GlobalPointProperties[GlobalPointIndex].z = param[GlobalPointIndex][2];
}
SALSAUtility.GlobalPointProperties[GlobalPointIndex].xerr = perr[GlobalPointIndex][0];
SALSAUtility.GlobalPointProperties[GlobalPointIndex].yerr = perr[GlobalPointIndex][1];
if (LocalVectorDimension > 2)
{
SALSAUtility.GlobalPointProperties[GlobalPointIndex].zerr = perr[GlobalPointIndex][2];
}
SALSAUtility.GlobalPointProperties[GlobalPointIndex].valuesset = true;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].errorsset = true;
}
if (SALSAUtility.Usedreordered)
{
var NaivePointProperties = new SALSADataPointProperties[SALSAUtility.PointCount_Global];
for (int GlobalPointIndex = 0;
GlobalPointIndex < SALSAUtility.PointCount_Global;
GlobalPointIndex++)
{
int NaivePointIndex = SALSAUtility.ActualtoNaiveUsedOrder[GlobalPointIndex];
NaivePointProperties[NaivePointIndex] =
SALSAUtility.GlobalPointProperties[GlobalPointIndex].ShallowCopy();
}
SALSA_Properties.WriteDataPointFile(fname, ManxcatCentral.Configuration.Write2Das3D, "all ",
SALSAUtility.GlobalFileProperties,
NaivePointProperties, SALSAUtility.PointCount_Global);
return;
}
SALSA_Properties.WriteDataPointFile(fname, ManxcatCentral.Configuration.Write2Das3D, "all ",
SALSAUtility.GlobalFileProperties,
SALSAUtility.GlobalPointProperties, SALSAUtility.PointCount_Global);
return;
}
// Option OutputOption = 1
// Simple output of Used in ORIGINAL not Loadbalanced Order
try
{
StreamWriter sw = null;
if (!string.IsNullOrEmpty(fname))
{
sw = new StreamWriter(fname, false, Encoding.UTF8);
}
if (sw != null)
{
for (int GlobalPointIndex = 0;
GlobalPointIndex < SALSAUtility.PointCount_Global;
GlobalPointIndex++)
{
if (ManxcatMDS.PointStatus[GlobalPointIndex] == -1)
{
continue;
}
string Coordinates = "";
int SingleCluster = 1;
int UsedPointIndex = SALSAUtility.NaivetoActualUsedOrder[GlobalPointIndex];
for (int LocalVectorIndex = 0; LocalVectorIndex < LocalVectorDimension; LocalVectorIndex++)
{
Coordinates += param[UsedPointIndex][LocalVectorIndex].ToString("E4") + "\t";
}
sw.WriteLine(
String.Format((GlobalPointIndex).ToString() + "\t" + Coordinates + SingleCluster.ToString()));
}
}
sw.Flush();
sw.Close();
}
catch (Exception e)
{
Console.WriteLine("Failed writing data" + e);
throw (e);
}
}