/// <summary>
/// Writes the Chromophore dictionary to separate text files
/// </summary>
/// <param name="chromophoreDictionary">The dictionary to write</param>
public static void WriteDatabaseToFiles(ChromophoreSpectrumDictionary chromophoreDictionary)
{
//loop through each of the ChromophoreSpectrum objects
foreach (var item in chromophoreDictionary)
{
var cs = item.Value;
var cd = new StringBuilder();
//Get the spectral units
var units = SpectralConverter.getSpectralUnit(cs.MolarUnit, cs.AbsorptionCoefficientUnit);
var wavelengthUnits = SpectralConverter.getWavelengthUnit(cs.WavelengthUnit);
//write the first line with the header - LAMBDA<space>units<tab>Name<space>units
cd.AppendLine("%LAMBDA " + wavelengthUnits + "\t" + cs.Name + " " + units);
var counter = 0;
foreach (var wavelength in cs.Wavelengths)
{
//need to divide MolarAbsorptionCoefficients by ln(10)
var k = 1.0;
if (cs.ChromophoreCoefficientType == ChromophoreCoefficientType.MolarAbsorptionCoefficient)
{
k = Math.Log(10);
}
var spectrum = cs.Spectrum[counter] / k;
cd.AppendLine(wavelength + "\t" + spectrum);
counter++;
}
//write to text file
FileIO.WriteToTextFile(cd.ToString(), "absorber-" + cs.Name + ".txt");
}
}
public static ChromophoreSpectrumDictionary ToDictionary(this IEnumerable <ChromophoreSpectrum> spectra)
{
var dictionary = new ChromophoreSpectrumDictionary();
foreach (var chromophoreSpectrum in spectra)
{
dictionary.Add(chromophoreSpectrum.Name, chromophoreSpectrum);
}
return(dictionary);
}
/// <summary>
/// Appends a new chromophore spectral dictionary created from a tab-delimited stream onto an existing dictionary of chromophore spectra
/// </summary>
/// <param name="existingDictionary">The existing dictionary to which to append</param>
/// <param name="fileStream">The file stream</param>
/// <returns>The new dictionary of chromophore spectra</returns>
public static ChromophoreSpectrumDictionary AppendDatabaseFromFile(ChromophoreSpectrumDictionary existingDictionary, Stream fileStream)
{
//create a new dictionary
var chromophoreSpectra = GetSpectraFromFile(fileStream, true);
foreach (var item in chromophoreSpectra)
{
ChromophoreSpectrum spectrum;
if (existingDictionary.TryGetValue(item.Name, out spectrum))
{
existingDictionary.Remove(item.Name);
}
existingDictionary.Add(item.Name, item);
}
return(existingDictionary);
}
/// <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);
}
private ChromophoreSpectrumDictionary CreateDictionary()
{
string name = "Melanin";
AbsorptionCoefficientUnit muaUnit = AbsorptionCoefficientUnit.InverseMillimeters;
MolarUnit molarUnit = MolarUnit.MicroMolar;
ChromophoreCoefficientType coeffType = ChromophoreCoefficientType.FractionalAbsorptionCoefficient;
// populate list of wavelengths
List <double> wavelengths = new List <double>();
wavelengths.Add(0.0);
wavelengths.Add(1.0);
wavelengths.Add(2.0);
// populate list of values
List <double> values = new List <double>();
values.Add(0.1);
values.Add(1.1);
values.Add(2.1);
ChromophoreSpectrum chromophoreSpectrum = new ChromophoreSpectrum(wavelengths, values, name, coeffType, muaUnit, molarUnit, WavelengthUnit.Nanometers);
var testDictionary = new ChromophoreSpectrumDictionary();
testDictionary.Add(chromophoreSpectrum.Name, chromophoreSpectrum);
name = "HbO2";
muaUnit = AbsorptionCoefficientUnit.InverseMillimeters;
molarUnit = MolarUnit.MicroMolar;
coeffType = ChromophoreCoefficientType.MolarAbsorptionCoefficient;
chromophoreSpectrum = new ChromophoreSpectrum(wavelengths, values, name, coeffType, muaUnit, molarUnit, WavelengthUnit.Nanometers);
testDictionary.Add(chromophoreSpectrum.Name, chromophoreSpectrum);
return(testDictionary);
}
/// <summary>
/// Saves a given dictionary of Chromophore spectra to the specified file
/// </summary>
/// <param name="dictionary">Name of the chromophore spectrum dictionary</param>
/// <param name="filename">Name of the file</param>
public static void SaveDatabaseToFile(ChromophoreSpectrumDictionary dictionary, string filename)
{
dictionary.WriteToJson(filename);
}
