public IPcaView Show()
{
INumberTable nt = DataGenerator.App.ScriptApp.New.NumberTable(bodies.Count, 3);
for (int row = 0; row < nt.Rows; row++)
{
nt.Matrix[row][0] = bodies[row].X;
nt.Matrix[row][1] = bodies[row].Y;
nt.Matrix[row][2] = bodies[row].Z;
nt.RowSpecList[row].Type = (short)bodies[row].Type;
}
return(nt.ShowPcaView());
}
public static IPcaView Show(IList <Vector4D> points, int dimension)
{
INumberTable nt = DataGenerator.App.ScriptApp.New.NumberTable(points.Count, dimension);
for (int row = 0; row < nt.Rows; row++)
{
nt.Matrix[row][0] = points[row].x;
nt.Matrix[row][1] = points[row].y;
if (dimension == 4)
{
nt.Matrix[row][2] = points[row].z;
nt.Matrix[row][3] = points[row].w;
}
nt.RowSpecList[row].Type = (short)points[row].type;
}
return(nt.ShowPcaView());
}
public bool ImportFile0(string fileName)
{
IVisuMap app = CustomImporter.App.ScriptApp;
if (!fileName.ToLower().EndsWith(".fcs"))
{
return(false); // Let other import handle it.
}
INumberTable dataTable = null;
IFreeTable textTable = null;
bool compensated = false;
bool logScaled = false;
using (StreamReader sr = new StreamReader(fileName)) {
//
// Read the text segment.
//
char[] header = new char[42];
sr.ReadBlock(header, 0, header.Length);
int textBegin = int.Parse(new string(header, 10, 8));
int textEnd = int.Parse(new string(header, 18, 8));
int beginData = int.Parse(new string(header, 26, 8));
int endData = int.Parse(new string(header, 34, 8));
char[] line = new char[textEnd + 4];
sr.ReadBlock(line, header.Length, line.Length - header.Length);
string textSeg = new string(line, textBegin + 1, textEnd - textBegin);
char delimiter = line[textBegin];
textTable = app.New.FreeTable();
textTable.AddColumn("Value", false);
string[] textFields = textSeg.Split(delimiter);
textTable.AddRows("P", textFields.Length / 2);
IList <IRowSpec> rowSpecList = textTable.RowSpecList;
for (int row = 0; row < textTable.Rows; row++)
{
rowSpecList[row].Id = textFields[2 * row];
textTable.Matrix[row][0] = textFields[2 * row + 1];
}
//
// Read in the data segement
//
fcsInfo = new FcsInfo(textTable, header);
if ((beginData == 0) && (textTable.IndexOfRow("$BEGINDATA") > 0))
{
beginData = int.Parse(textTable.Matrix[textTable.IndexOfRow("$BEGINDATA")][0]);
}
if ((endData == 0) && (textTable.IndexOfRow("$ENDDATA") > 0))
{
endData = int.Parse(textTable.Matrix[textTable.IndexOfRow("$ENDDATA")][0]);
}
dataTable = app.New.NumberTable(fcsInfo.Rows, fcsInfo.Columns);
using (BinaryReader br = new BinaryReader(sr.BaseStream)) {
br.BaseStream.Seek(beginData, SeekOrigin.Begin);
Byte[] buf4 = new byte[4];
Byte[] buf8 = new byte[8];
int bitOffset = 0;
for (int row = 0; row < fcsInfo.Rows; row++)
{
for (int col = 0; col < fcsInfo.Columns; col++)
{
ColumnInfo ci = fcsInfo.ColumnInfo[col];
Byte[] data = ReadBits(br, ci.Bits, ref bitOffset);
if (data.Length < ci.Bytes)
{
row = fcsInfo.Rows; // enforce premature loop-end.
break;
}
Byte[] buf = (fcsInfo.DataType == FcsInfo.DataTypes.Double) ? buf8 : buf4;
Array.Clear(buf, 0, buf.Length);
Array.Copy(data, 0, buf, 0, ci.Bytes);
if (!fcsInfo.BigEndian)
{
// Intel CPU expects BigEndian format.
Array.Reverse(buf, 0, ci.Bytes);
}
switch (fcsInfo.DataType)
{
case FcsInfo.DataTypes.Integer:
dataTable.Matrix[row][col] = (BitConverter.ToUInt32(buf, 0) & ci.RangeMask);
break;
case FcsInfo.DataTypes.Float:
dataTable.Matrix[row][col] = BitConverter.ToSingle(buf, 0);
break;
case FcsInfo.DataTypes.Double:
dataTable.Matrix[row][col] = BitConverter.ToDouble(buf, 0);
break;
}
}
}
}
}
// Post processing
for (int col = 0; col < fcsInfo.Columns; col++)
{
IColumnSpec cs = dataTable.ColumnSpecList[col];
ColumnInfo cInfo = fcsInfo.ColumnInfo[col];
cs.Id = cInfo.ShortName;
//cs.Name = cInfo.Name + ( cInfo.IsLinear ? ".Lin" : ".Log");
cs.Name = cInfo.Name;
if ((cs.Id == "TIME") || (cs.Id == "TIME1"))
{
int timeStepIdx = textTable.IndexOfRow("$TIMESTEP");
if (timeStepIdx >= 0)
{
double timeStep = double.Parse(textTable.Matrix[timeStepIdx][0]);
for (int row = 0; row < fcsInfo.Rows; row++)
{
dataTable.Matrix[row][col] *= timeStep;
}
}
}
}
IList <IRowSpec> rSpecList = dataTable.RowSpecList;
for (int row = 0; row < fcsInfo.Rows; row++)
{
rSpecList[row].Id = row.ToString();
}
FileInfo fInfo = new FileInfo(fileName);
string shortName = fInfo.Name.Substring(0, fInfo.Name.LastIndexOf('.'));
if (saveMetaInfo >= 1)
{
SaveParameterTable(textTable, shortName);
if (saveMetaInfo >= 2)
{
textTable.SaveAsDataset(shortName + " (Text Seg)", "Text segement of data table " + shortName);
}
}
if (autoCompensation)
{
try {
string sMatrix = null;
for (int i = 0; i < textTable.Rows; i++)
{
string id = textTable.RowSpecList[i].Id.ToLower();
if (id.StartsWith("$"))
{
id = id.Substring(1);
}
if ((id == "spill") || (id == "spillover"))
{
sMatrix = textTable.Matrix[i][0];
break;
}
}
if (sMatrix == null)
{
throw new Exception(""); // silently ignore compensation as no compensation matrix available.
}
string[] fs = sMatrix.Split(',');
int dimension = int.Parse(fs[0]);
if (fs.Length != (dimension * dimension + dimension + 1))
{
throw new Exception("Invalid spill over matrix.");
}
INumberTable cMatrix = app.New.NumberTable(dimension, dimension);
List <string> parList = fs.Skip(1).Take(dimension).ToList();
int idx;
if (parList.Count(id => int.TryParse(id, out idx)) == parList.Count)
{
// The columns are specified by a list of indexes. We convert them here to ids
for (int i = 0; i < parList.Count; i++)
{
parList[i] = dataTable.ColumnSpecList[int.Parse(parList[i]) - 1].Id; // index starts with 1 !
}
}
for (int col = 0; col < cMatrix.Columns; col++)
{
cMatrix.ColumnSpecList[col].Id = parList[col];
}
int fsIdx = dimension + 1;
for (int row = 0; row < cMatrix.Rows; row++)
{
for (int col = 0; col < cMatrix.Columns; col++)
{
cMatrix.Matrix[row][col] = double.Parse(fs[fsIdx++]);
}
}
var cData = dataTable.SelectColumnsById(parList);
if (cData.Columns != parList.Count)
{
if (dataTable.ColumnSpecList.Count(cl => cl.Id.Equals("<" + parList[0] + ">")) == 1)
{
// siliently ignore aready compensated data.
throw new Exception("");
}
else
{
throw new Exception("Invalid spill over matrix: unknown names.");
}
}
var math = CustomImporter.App.GetMathAdaptor();
var m = math.InvertMatrix((double[][])cMatrix.Matrix);
for (int row = 0; row < cMatrix.Rows; row++)
{
cMatrix.Matrix[row] = m[row];
}
cData = cData.Multiply(cMatrix); // perform the comensation with the inverse matrix of the spill over matrix.
cData.CopyValuesTo(dataTable);
compensated = true;
} catch (Exception ex) {
if (ex.Message != "")
{
MessageBox.Show("Cannot perform compensation: " + ex.Message);
}
}
}
if (logTransform)
{
double[][] m = (double[][])dataTable.Matrix;
double T = 262144;
double W = 1.0;
double M = 4.5;
string[] settings = app.GetProperty(
"CustomImporter.Logicle.Settings", "262144; 1.0; 4.5").Split(';');
if (settings.Length == 3)
{
double.TryParse(settings[0], out T);
double.TryParse(settings[1], out W);
double.TryParse(settings[2], out M);
}
var fastLogicle = new VisuMap.DataCleansing.FastLogicle(T, W, M);
double maxVal = fastLogicle.MaxValue;
double minVal = fastLogicle.MinValue;
for (int col = 0; col < fcsInfo.Columns; col++)
{
if (fcsInfo.ColumnInfo[col].LogTrans)
{
for (int row = 0; row < fcsInfo.Rows; row++)
{
m[row][col] = M * fastLogicle.scale(Math.Min(maxVal, Math.Max(minVal, m[row][col])));
}
logScaled = true;
}
}
}
string msg = "Dataset imported from " + fileName + ". Version: " + fcsInfo.version;
if (compensated)
{
msg += ", compensated";
}
if (logScaled)
{
msg += ", log-scaled";
}
string dsName = dataTable.SaveAsDataset(shortName, msg);
app.Folder.OpenDataset(dsName);
INumberTable nTable = app.GetNumberTable();
List <IColumnSpec> csList = nTable.ColumnSpecList as List <IColumnSpec>;
int fsc = csList.FindIndex(cs => cs.Id == "FSC-A");
int ssc = csList.FindIndex(cs => cs.Id == "SSC-A");
if ((fsc >= 0) && (ssc >= 0))
{
var xy = app.New.XyPlot(nTable);
xy.Show();
xy.XAxisIndex = fsc;
xy.YAxisIndex = ssc;
xy.AutoScaling = true;
xy.Redraw();
xy.CaptureMap();
xy.Close();
app.Map.Name = "FSC/SSC";
}
else
{
// We just do create a simple PCA view.
IPcaView pca = nTable.ShowPcaView();
pca.ResetView();
pca.CaptureMap();
app.Map.Redraw();
pca.Close();
app.Map.Name = "PCA-All";
}
app.Map.GlyphType = glyphName;
app.Map.Redraw();
if (showResult)
{
app.New.SpectrumBand(nTable).Show();
}
fcsInfo = null;
return(true);
}