/// <summary>
/// Calls RScript executable and runs the given script as a hidden process
/// </summary>
/// <param name="RScriptPath">Path to RScript executable</param>
/// <param name="script">Script location</param>
/// <param name="args">Script arguments</param>
/// <returns>Script output</returns>
internal static RScriptResult RunScript(string RScriptPath, string script, params object[] args)
{
RequireSetupRun();
ProcessStartInfo info = new ProcessStartInfo
{
FileName = RScriptPath,
Arguments = "--verbose \"" + Path.Combine(Scripts, script) + "\" " + String.Join(" ", args),
UseShellExecute = false,
WindowStyle = ProcessWindowStyle.Hidden,
CreateNoWindow = true,
RedirectStandardError = true,
RedirectStandardOutput = true,
};
RScriptResult result = new RScriptResult();
Process R = new Process();
R.StartInfo = info;
R.OutputDataReceived += result.ScriptOutputHandler;
R.ErrorDataReceived += result.ScriptErrorHandler;
R.Start();
R.BeginOutputReadLine();
R.BeginErrorReadLine();
R.WaitForExit();
result.ExitCode = R.ExitCode;
return(result);
}
/// <summary>
/// Executes an R script
/// </summary>
/// <param name="script">R script</param>
/// <returns>Script results</returns>
public object Execute(IRScript script)
{
RController.RequirePackages(_path, script.RequiredPackages);
script.PreCompute();
RScriptResult result = RController.RunScript(_path, script.BaseScript, script.Arguments);
if (result.ExitCode != 0)
{
throw new RExecutionException(script.BaseScript, script.Arguments, result.Output, result.Error);
}
return(script.ImportResults(result));
}
internal static void RequirePackages(string RScriptPath, params string[] args)
{
RequireSetupRun();
// check packages
RScriptResult RCheck = RunScript(RScriptPath, Path.Combine(Scripts, Settings.Default.Resources + "PackageInstaller.R"), "0 " + String.Join(" ", args));
if (RCheck.ExitCode != 0)
{
HasSetupRun = false;
throw new Exception("There was an error in the application:\n" + RCheck.Error);
}
// install missing packages
if (!String.IsNullOrWhiteSpace(RCheck.Output.Trim()))
{
RScriptResult RInstall = RunScriptAdmin(RScriptPath, Path.Combine(Scripts, Settings.Default.Resources + "PackageInstaller.R"), "1 " + RCheck.Output.Trim());
if (RInstall.ExitCode != 0)
{
HasSetupRun = false;
throw new Exception("There was an error installing packages.");
}
}
}
/// <summary>
/// Import script results
/// </summary>
/// <param name="result">RScriptResults object</param>
/// <returns>Script results</returns>
public override object ImportResults(RScriptResult result)
{
return Similarities.Import(_outputFile);
}
/// <summary> /// Imports script results /// </summary> /// <param name="result">RScriptResult object</param> /// <returns>Script results</returns> public abstract object ImportResults(RScriptResult result);
/// <summary>
/// Import script results
/// </summary>
/// <param name="result">RScriptResults object</param>
/// <returns>Script results</returns>
public override object ImportResults(RScriptResult result)
{
TextReader rfile = new StreamReader(_outputFile);
string rawdata = rfile.ReadToEnd();
rfile.Close();
TLSimilarityMatrix matrix = new TLSimilarityMatrix();
string[] sims = rawdata.Remove(0, 2).Replace(")", String.Empty).Split(new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries);
string[] edges = Generics.ImportStrings(_info.Edges);
if (sims.Length != edges.Length)
throw new RDataException("Results are incorrect size: " + sims.Length + " vs " + edges.Length);
for (int i = 0; i < sims.Length; i++)
{
string[] split = edges[i].Split();
matrix.AddLink(_corpus.Map[Convert.ToInt32(split[0])], _corpus.Map[Convert.ToInt32(split[1])], Convert.ToDouble(sims[i]));
}
//int src = 0;
//int tgt = _source.DocMap.Count;
//if (sims.Length != _source.DocMap.Count * _target.DocMap.Count)
//{
// throw new RDataException("Results are incorrect size: " + sims.Length + " vs " + (_source.DocMap.Count * _target.DocMap.Count));
//}
//foreach (string sim in sims)
//{
// matrix.AddLink(_source.DocMap[src], _target.DocMap[tgt - _source.DocMap.Count], Convert.ToDouble(sim.Trim()));
// tgt++;
// if (tgt == _source.DocMap.Count + _target.DocMap.Count)
// {
// tgt = _source.DocMap.Count;
// src++;
// }
//}
return matrix;
}
/// <summary>
/// Returns an ideal GibbsLDA configuration object
/// </summary>
/// <param name="result">REngine results object</param>
/// <returns>GibbsLDAConfig object</returns>
public override object ImportResults(RScriptResult result)
{
TextReader resultFile = new StreamReader(_outputFile);
string[] results = resultFile.ReadToEnd().Split(new char[] { '\t' }, StringSplitOptions.RemoveEmptyEntries);
if (results.Length != 4)
{
throw new RDataException("Results file in incorrect format (" + _outputFile + ")");
}
return new GibbsLDAConfig
{
NumTopics = Convert.ToInt32(Math.Round(Convert.ToDouble(results[0]))),
GibbsIterations = Convert.ToInt32(Math.Round(Convert.ToDouble(results[1]))),
Alpha = Convert.ToDouble(results[2]),
Beta = Convert.ToDouble(results[3]),
Seed = _config.Seed,
};
}
/// <summary>
/// Imports script results
/// </summary>
/// <param name="result">RScriptResults object</param>
/// <returns>Script results</returns>
public override object ImportResults(RScriptResult result)
{
TextReader rfile = new StreamReader(_outputFile);
string rawdata = rfile.ReadToEnd();
rfile.Close();
TLSimilarityMatrix matrix = new TLSimilarityMatrix();
string[] sims = rawdata.Remove(0,2).Replace(")", String.Empty).Split(new char[] {','}, StringSplitOptions.RemoveEmptyEntries);
int src = 0;
int tgt = _source.DocMap.Count;
if (sims.Length != _source.DocMap.Count * _target.DocMap.Count)
{
throw new RDataException("Results are incorrect size: " + sims.Length + " vs " + (_source.DocMap.Count * _target.DocMap.Count));
}
foreach (string sim in sims)
{
matrix.AddLink(_source.DocMap[src], _target.DocMap[tgt - _source.DocMap.Count], Convert.ToDouble(sim.Trim()));
tgt++;
if (tgt == _source.DocMap.Count + _target.DocMap.Count)
{
tgt = _source.DocMap.Count;
src++;
}
}
return matrix;
}
/// <summary> /// Imports script results /// </summary> /// <param name="result">RScriptResult object</param> /// <returns>Script results</returns> public abstract object ImportResults(RScriptResult result);
/// <summary>
/// Calls RScript executable and runs the given script as a hidden process
/// </summary>
/// <param name="RScriptPath">Path to RScript executable</param>
/// <param name="script">Script location</param>
/// <param name="args">Script arguments</param>
/// <returns>Script output</returns>
internal static RScriptResult RunScript(string RScriptPath, string script, params object[] args)
{
RequireSetupRun();
ProcessStartInfo info = new ProcessStartInfo
{
FileName = RScriptPath,
Arguments = "--verbose \"" + Path.Combine(Scripts, script) + "\" " + String.Join(" ", args),
UseShellExecute = false,
WindowStyle = ProcessWindowStyle.Hidden,
CreateNoWindow = true,
RedirectStandardError = true,
RedirectStandardOutput = true,
};
RScriptResult result = new RScriptResult();
Process R = new Process();
R.StartInfo = info;
R.OutputDataReceived += result.ScriptOutputHandler;
R.ErrorDataReceived += result.ScriptErrorHandler;
R.Start();
R.BeginOutputReadLine();
R.BeginErrorReadLine();
R.WaitForExit();
result.ExitCode = R.ExitCode;
return result;
}
/// <summary>
/// Import script results
/// </summary>
/// <param name="result">RScriptResults object</param>
/// <returns>Script results</returns>
public override object ImportResults(RScriptResult result)
{
// index = id - 1
string[] ids = Generics.ImportStrings(_mapFile);
TextReader resultsMatrix = new StreamReader(_outputFile);
TLSimilarityMatrix matrix = new TLSimilarityMatrix();
string[] sources = resultsMatrix.ReadLine().Split();
string line;
while ((line = resultsMatrix.ReadLine()) != null)
{
if (String.IsNullOrWhiteSpace(line))
continue;
// [0] target id, [x+] source sims index = x - 1
string[] entries = line.Split();
string entry = ids[Convert.ToInt32(entries[0]) - 1];
for (int i = 0; i < sources.Length; i++)
{
matrix.AddLink(ids[Convert.ToInt32(sources[i]) - 1], entry, Convert.ToDouble(entries[i + 1]));
}
}
resultsMatrix.Close();
return matrix;
}
/// <summary>
/// Returns an array containing the contributions of each matrix in the order they were added
/// </summary>
/// <param name="result">REngine result object</param>
/// <returns>double[]</returns>
public override object ImportResults(RScriptResult result)
{
List<double> pca = new List<double>();
TextReader file = new StreamReader(_outputFile);
file.ReadLine();
string line = String.Empty;
while ((line = file.ReadLine()) != null)
{
string[] entries = line.Split(',');
if (entries.Length != 3)
{
throw new RDataException("Error in PCA output.");
}
pca.Add(Convert.ToDouble(entries[2]));
}
if (pca.Count != _matrices.Length)
{
throw new RDataException("PCA returned the incorrect number of entries.");
}
return pca.ToArray();
}
/// <summary>
/// Import script results
/// </summary>
/// <param name="result">RScriptResults object</param>
/// <returns>Script results</returns>
public override object ImportResults(RScriptResult result)
{
IEnumerable<double> ranks = Generics.ImportDoubles(_outputFile, false);
IEnumerable<string> map = Generics.ImportStrings(_mappingFile);
if (ranks.Count() != map.Count())
{
throw new RDataException("Results file in incorrect format: incorrect number of entries");
}
TLSimilarityMatrix rankList = new TLSimilarityMatrix();
for (int i = 0; i < map.Count(); i++)
{
rankList.AddLink(_traceID, map.ElementAt(i), ranks.ElementAt(i));
}
return rankList;
}
/// <summary>
/// Imports script results
/// </summary>
/// <param name="result">RScriptResults object</param>
/// <returns>Script results</returns>
public override object ImportResults(RScriptResult result)
{
IEnumerable<double> authorities = Generics.ImportDoubles(_authorityFile, false);
IEnumerable<double> hubs = Generics.ImportDoubles(_hubFile, false);
IEnumerable<string> map = Generics.ImportStrings(_mappingFile);
HITSResult results = new HITSResult();
for (int i = 0; i < map.Count(); i++)
{
results.Hubs.AddLink(_traceID, map.ElementAt(i), hubs.ElementAt(i));
results.Authorities.AddLink(_traceID, map.ElementAt(i), authorities.ElementAt(i));
}
return results;
}
