public void validate_data_from_tsv()
{
int linenumber = 5;
string line;
string[] row;
Stream stream = StreamFinder.GetFileStreamFromResources("Modeling/Spectroscopy/Resources/Spectra.txt", "Vts");
var testSpectra = SpectralDatabase.GetSpectraFromFile(stream, true);
var testDictionary = testSpectra.ToDictionary();
stream = StreamFinder.GetFileStreamFromResources("Modeling/Spectroscopy/Resources/Spectra.txt", "Vts");
using (StreamReader readFile = new StreamReader(stream))
{
// read n lines (there is one line of header so
for (int i = 0; i <= linenumber; i++)
{
readFile.ReadLine();
}
// get a line from the stream and split the data
line = readFile.ReadLine();
row = line.Split('\t');
}
Assert.AreEqual(testDictionary["Hb"].Wavelengths[linenumber], Convert.ToDouble(row[0]));
// dc: this would be only for MolarExtinctionCoefficient or FractionalExtinctionCoefficient, not MolarAbsorptionCoefficient or FractionalAbsorptionCoefficient
// multiply the value by ln(10)
// double k = Math.Log(10);
double k = 1D;
double spectra = Convert.ToDouble(row[1]) * k;
// test that the values in the text stream match the ones in the object
Assert.AreEqual(testDictionary["HbO2"].Spectrum[linenumber], spectra);
spectra = Convert.ToDouble(row[2]) * k;
Assert.AreEqual(testDictionary["Hb"].Spectrum[linenumber], spectra);
}
public void validate_loading_spectral_database_from_tsv_in_resources()
{
Stream stream = StreamFinder.GetFileStreamFromResources("Modeling/Spectroscopy/Resources/Spectra.txt", "Vts");
List <ChromophoreSpectrum> myChromophoreList = new List <ChromophoreSpectrum>();
//create 2 sets of values for the tab delimeted file
ChromophoreSpectrum c = new ChromophoreSpectrum();
c.Name = "HbO2";
c.AbsorptionCoefficientUnit = AbsorptionCoefficientUnit.InverseMillimeters;
c.MolarUnit = MolarUnit.None;
c.ChromophoreCoefficientType = ChromophoreCoefficientType.MolarAbsorptionCoefficient;
myChromophoreList.Add(c);
ChromophoreSpectrum c2 = new ChromophoreSpectrum();
c2.Name = "Hb";
c2.AbsorptionCoefficientUnit = AbsorptionCoefficientUnit.InverseMillimeters;
c2.MolarUnit = MolarUnit.None;
c2.ChromophoreCoefficientType = ChromophoreCoefficientType.MolarAbsorptionCoefficient;
myChromophoreList.Add(c2);
var testDictionary = myChromophoreList.ToDictionary();
SpectralDatabase.AppendDatabaseFromFile(testDictionary, stream);
testDictionary.WriteToJson("dictionary3.txt");
Assert.IsTrue(FileIO.FileExists("dictionary3.txt"));
}
public void validate_loading_spectral_database_and_header_from_tsv_no_conversion()
{
Stream stream = StreamFinder.GetFileStreamFromResources("Modeling/Spectroscopy/Resources/Spectra.txt", "Vts");
var testSpectra = SpectralDatabase.GetSpectraFromFile(stream, false);
var testDictionary = testSpectra.ToDictionary();
testDictionary.WriteToJson("dictionary5.txt");
Assert.IsTrue(FileIO.FileExists("dictionary5.txt"));
}
public void validate_Loading_Spectral_Database_and_header_from_tsv_in_resources()
{
Stream stream = StreamFinder.GetFileStreamFromResources("Modeling/Spectroscopy/Resources/Spectra.txt", _assemblyName);
var testSpectra = SpectralDatabase.GetSpectraFromFile(stream, true);
var testDictionary = testSpectra.ToDictionary();
testDictionary.WriteToJson("dictionary4.txt");
Assert.IsTrue(FileIO.FileExists("dictionary4.txt"));
}
public void validate_write_text_files_from_file_in_resources()
{
var testDictionary = SpectralDatabase.GetDefaultDatabaseFromFileInResources();
SpectralDatabase.WriteDatabaseToFiles(testDictionary);
Assert.IsTrue(FileIO.FileExists("absorber-Fat.txt"));
Assert.IsTrue(FileIO.FileExists("absorber-H2O.txt"));
Assert.IsTrue(FileIO.FileExists("absorber-Hb.txt"));
Assert.IsTrue(FileIO.FileExists("absorber-HbO2.txt"));
Assert.IsTrue(FileIO.FileExists("absorber-Melanin.txt"));
Assert.IsTrue(FileIO.FileExists("absorber-Nigrosin.txt"));
}
/// <summary>
///
/// </summary>
/// <param name="importFiles">the name(s) of the file(s) to import</param>
/// <param name="importPath">the path of the files to import (relative or absolute)</param>
/// <param name="outname">the name of the resulting output xml spectral dictionary</param>
/// <param name="outpath">the output directory of the generated xml dictionary (relative or absolute)</param>
public static ChromophoreSpectrumDictionary ImportSpectraFromFile(
string[] importFiles = null,
string importPath = "",
string outname = "SpectralDictionary",
string outpath = "")
{
if (importFiles == null || importFiles.Length == 0 || string.IsNullOrEmpty(importFiles[0]))
{
importFiles = new string[] { "absorber-*.txt" };
}
var allFiles = importFiles.SelectMany(file => Directory.GetFiles(
importPath ?? Directory.GetCurrentDirectory(), file));
var chromophoreDictionary = new ChromophoreSpectrumDictionary();
logger.Info(() => "Importing spectral data files");
foreach (var file in allFiles)
{
if (File.Exists(file))
{
try
{
logger.Info("Importing file: " + file);
var stream = StreamFinder.GetFileStream(file, FileMode.Open);
SpectralDatabase.AppendDatabaseFromFile(chromophoreDictionary, stream);
}
catch (Exception e)
{
logger.Info("**** An error occurred while importing file: " + file);
logger.Info("Detailed error: " + e.Message);
}
}
}
return(chromophoreDictionary);
}
public void validate_loading_spectral_database_from_file_in_resources()
{
var _testDictionary = SpectralDatabase.GetDefaultDatabaseFromFileInResources();
Assert.IsNotNull(_testDictionary);
}
static void Main(string[] args)
{
var skipImport = false;
string[] filenames = null;
string path = null;
string outname = null;
string outpath = null;
args.Process(() =>
{
logger.Info("\nSpectral Data Import\n");
logger.Info("For more information type import.exe help");
logger.Info("For help on a specific topic type import.exe help=<topicname>\n");
},
new CommandLine.Switch("help", val =>
{
var helpTopic = val.FirstOrDefault();
ShowHelp(helpTopic);
skipImport = true;
}),
new CommandLine.Switch("@/help", val =>
{
var helpTopic = val.FirstOrDefault();
ShowHelp(helpTopic);
skipImport = true;
}),
new CommandLine.Switch("generatefiles", val =>
{
logger.Info(() => "Generating spectral data files...");
try
{
var testDictionary = Vts.SpectralMapping.SpectralDatabase.GetDefaultDatabaseFromFileInResources();
SpectralDatabase.WriteDatabaseToFiles(testDictionary);
}
catch (Exception e)
{
logger.Info("**** An error occurred while generating the import files ****");
logger.Info("Detailed error: " + e.Message);
}
skipImport = true;
}),
new CommandLine.Switch("filename", val =>
{
filenames = new[] { val.FirstOrDefault() };
logger.Info(() => "import files specified as: " + filenames[0]);
}),
new CommandLine.Switch("filenames", val =>
{
filenames = val.ToArray();
var message = "import files specified as: ";
if (filenames.Length > 0)
{
message = message + filenames.First();
for (int i = 1; i < filenames.Count(); i++)
{
message = message + ", " + filenames[i];
}
}
logger.Info(() => message);
}),
new CommandLine.Switch("path", val =>
{
path = val.FirstOrDefault();
logger.Info(() => "import path specified as " + path);
}),
new CommandLine.Switch("outname", val =>
{
outname = val.FirstOrDefault();
logger.Info(() => "outname specified as " + outname);
}),
new CommandLine.Switch("outpath", val =>
{
outpath = val.FirstOrDefault();
logger.Info(() => "outpath specified as " + outpath);
}));
if (skipImport)
{
return;
}
var chromophoreDictionary = SpectralImporter.ImportSpectraFromFile(filenames, path);
chromophoreDictionary.WriteToJson(Path.Combine(outpath ?? "", outname ?? "SpectralDictionary.txt"));
}
