/// <summary>
/// Constructs a new State associating all computed variables.
/// </summary>
/// <param name="states">Number of observations.</param>
public TemporalState(int states)
{
Alpha = new double[states];
Beta = new double[states];
Gamma = new double[states];
Delta = new double[states];
State = new int[states];
Xi = new MySparse2DMatrix();
}
/// <summary>
/// Returns a random index of the matrix state column using the given distribution.
/// </summary>
/// <param name="state">Current state.</param>
/// <param name="matrix">Probability distribution matrix.</param>
/// <returns>Random index of the matrix state column.</returns>
private int randomExtraction(int state, MySparse2DMatrix matrix)
{
var rand = SystemRandomSource.Default;
var extraction = rand.NextDouble();
for (int i = 0; i < Symbols; i++)
{
if (extraction < matrix.getValue(state, i))
return i;
extraction -= matrix.getValue(state, i);
}
return -1;
}
/// <summary>
/// Determining the frequency of the transition-emission pair values
/// and dividing it by the probability of the entire string.
///
/// Using the scaled values, I don't need to divide it for the
/// probability of the entire string anymore
/// </summary>
/// <param name="t">Current time.</param>
/// <param name="nextObservation">Observation at time t + 1.</param>
/// <returns>Probability of transition from each state to any other at time t</returns>
private MySparse2DMatrix calcXi(int t, int nextObservation)
{
if (tempInstancts == null)
throw new ArgumentNullException("tempInstancts");
if (tempInstancts[t].Alpha == null || tempInstancts[t].Beta == null)
throw new ArgumentNullException("Alpha and Beta aren't set");
MySparse2DMatrix currentXi = new MySparse2DMatrix();
double s = 0;
for (int i = 0; i < States; i++)
{
for (int j = 0; j < States; j++)
{
double temp = tempInstancts[t].Alpha[i] * Transitions.getValue(i, j) * Emissions.getValue(j, nextObservation) * tempInstancts[t + 1].Beta[j];
s += temp;
if (temp != 0)
currentXi.setValue(i, j, temp);
}
}
if (s != 0) // Scaling
{
for (int i = 0; i < States; i++)
{
for (int j = 0; j < States; j++)
{
if (currentXi.getValue(i, j) != 0)
currentXi.setValue(i, j, currentXi.getValue(i, j) / s);
}
}
}
return currentXi;
}
/// <summary>
/// Constructs a new Hidden Markov Model.
/// </summary>
/// <param name="transitions">The transitions matrix A for this model.</param>
/// <param name="emissions">The emissions matrix B for this model.</param>
/// <param name="probabilities">The initial state probabilities for this model.</param>
public HiddenMarkovModel(MySparse2DMatrix transitions, MySparse2DMatrix emissions, double[] probabilities, int emissionSymbols)
{
A = transitions;
B = emissions;
Pi = probabilities;
states = Pi.Length;
symbols = emissionSymbols;
tempInstancts = null;
}
private void openTransition_Click(object sender, EventArgs e)
{
// Set filter options and filter index.
openFileDialog.FileName = "";
openFileDialog.Filter = "Transition Files (.trans)|*.trans|All Files (*.*)|*.*";
openFileDialog.FilterIndex = 1;
openFileDialog.Multiselect = false;
// Call the ShowDialog method to show the dialog box.
if (openFileDialog.ShowDialog() == DialogResult.OK)
{
var firstLine = true;
string line, firstState = "INIT";
A = new MySparse2DMatrix();
Pi = new List<double>();
piSymbols = new List<string>();
stateSymbols = new Id2Str();
System.IO.StreamReader sr = new System.IO.StreamReader(openFileDialog.FileName);
transitionsRichTextBox.Text = "";
while ((line = sr.ReadLine()) != null)
{
transitionsRichTextBox.Text += line + "\n";
if (firstLine)
{
firstState = line;
firstLine = false;
}
else
{
string[] stateValue = line.Split('\t');
if (stateValue.Length == 3)
{
if (stateValue[0] == firstState)
{
stateSymbols.setId(stateValue[1]);
piSymbols.Add(stateValue[1]);
Pi.Add(Double.Parse(stateValue[2], CultureInfo.InvariantCulture));
}
else
{
int row = stateSymbols.setId(stateValue[0]);
int col = stateSymbols.setId(stateValue[1]);
A.setValue(row, col, Double.Parse(stateValue[2], CultureInfo.InvariantCulture));
// Still need to add states to pi with probability 0
if (!piSymbols.Contains(stateValue[0]))
{
piSymbols.Add(stateValue[0]);
Pi.Add(0.0);
}
if (!piSymbols.Contains(stateValue[1]))
{
piSymbols.Add(stateValue[1]);
Pi.Add(0.0);
}
}
}
}
}
sr.Close();
if (A.Count > 0)
{
buttonOpenEmissions.Enabled = true;
openEmissionsToolStripMenuItem.Enabled = true;
}
else
{
buttonOpenEmissions.Enabled = false;
openEmissionsToolStripMenuItem.Enabled = false;
MessageBox.Show("Error! Parsed transitions matrix resulted empty. Check your input file please.", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
}
private void openEmissions_Click(object sender, EventArgs e)
{
// Set filter options and filter index.
openFileDialog.FileName = "";
openFileDialog.Filter = "Emission Files (.emit)|*.emit|All Files (*.*)|*.*";
openFileDialog.FilterIndex = 1;
openFileDialog.Multiselect = false;
// Call the ShowDialog method to show the dialog box.
if (openFileDialog.ShowDialog() == DialogResult.OK)
{
string line;
B = new MySparse2DMatrix();
emissionsSymbols = new Id2Str();
var separator = '\t';
System.IO.StreamReader sr = new System.IO.StreamReader(openFileDialog.FileName);
emissionsRichTextBox.Text = "";
if ((line = sr.ReadLine()) != null)
{
if (line.Split(separator).Length == 1)
separator = ' ';
sr.DiscardBufferedData();
sr.BaseStream.Seek(0, System.IO.SeekOrigin.Begin);
sr.BaseStream.Position = 0;
}
while ((line = sr.ReadLine()) != null)
{
emissionsRichTextBox.Text += line + "\n";
string[] stateValue = line.Split(separator);
if (stateValue.Length == 3)
{
int row = stateSymbols.setId(stateValue[0]);
int col = emissionsSymbols.setId(stateValue[1]);
B.setValue(row, col, Double.Parse(stateValue[2], CultureInfo.InvariantCulture));
}
}
sr.Close();
if (B.Count > 0)
{
buttonCreateHMM.Enabled = true;
openObservationsToolStripMenuItem.Enabled = true;
}
else
{
buttonCreateHMM.Enabled = false;
openObservationsToolStripMenuItem.Enabled = false;
MessageBox.Show("Error! Parsed emissions matrix resulted empty. Check your input file please.", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
}