/// <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");
}
}
/// <summary>
/// Creates a dictionary of chromophore spectra from a file stream of tab-delimited data, converts the data to work in the VTS
/// The header data is written as a comment line starting with %
/// Tab delimited data is in the format: Wavelength 1st Column 2nd Column 3rd Column ...
/// </summary>
/// <param name="fileStream">The file stream of spectral data</param>
/// <param name="convert">Boolean which is true if the data should be converted</param>
/// <returns>The dictionary of chromophore spectrum</returns>
public static IList <ChromophoreSpectrum> GetSpectraFromFile(Stream fileStream, bool convert)
{
//if the file stream is null return a null dictionary
if (fileStream == null)
{
return(null);
}
//create a list of ChromophoreSpectrum
var chromophoreList = new List <ChromophoreSpectrum>();
// create a list of wavelengths
var wavelengths = new List <double>();
// create a list of list of values
var valuesList = new List <List <double> >();
try
{
using (var readFile = new StreamReader(fileStream))
{
var line = readFile.ReadLine();
//check for the comment line where the header data is located
if (line.StartsWith("%"))
{
line = line.Substring(1);
}
var headerrow = line.Split('\t');
//if the number of columns is not greater that 2
if (headerrow.Length < 2)
{
//error, there must be at least 2 columns (4 values in the header)
throw new Exception("There are not enough columns in the header, header is wavelength wavelength_units chromophore_absorber_name units");
}
//get the number of columns in the first line of data
int hcolumns = headerrow.Length;
//read the second line of data, check that the number of columns match
line = readFile.ReadLine();
//keep reading the file until the data row
while (line == "")
{
line = readFile.ReadLine();
}
var row = line.Split('\t');
var columns = row.Length;
//the number of columns of data is equal to the number of header columns
if (hcolumns == columns)
{
//the first column must have a header value of LAMBDA
if (!headerrow[0].StartsWith("LAMBDA", StringComparison.CurrentCultureIgnoreCase))
{
//error, the first column is lambda
throw new Exception("First column must be lambda");
}
//split the units from the name
var header = headerrow[0].Split(' ');
var wavelengthUnit = SpectralConverter.getWavelengthUnit(header[1]);
//loop through the remaining columns and write the header data
for (var i = 1; i < hcolumns; i++)
{
//split the units from the name
header = headerrow[i].Split(' ');
if (header.Length != 2)
{
//error, there must be a name and unit value in the header
throw new Exception("The header columns must be name<space>units");
}
var name = header[0]; //get the name of the chromophore absorber
var chromophoreType = (ChromophoreType)Enum.Parse(typeof(ChromophoreType), name, true);
//get the chromophore coefficient type
var chromophoreCoefficientType = chromophoreType.GetCoefficientType();
//get the absorption coefficient units and the molar units
//parse the value of header[1] - the units
var absorptionCoefficientUnit = SpectralConverter.getAbsorptionCoefficientUnit(header[1]);
var molarUnit = SpectralConverter.getMolarUnit(header[1]);
//write the values to the dictionary
var cs = new ChromophoreSpectrum(name, chromophoreCoefficientType, absorptionCoefficientUnit, molarUnit, wavelengthUnit);
chromophoreList.Add(cs);
}
//loop through the columns and create the lists (ignore the wavelength column)
for (var i = 1; i < columns; i++)
{
//create a list of doubles in the value list
var values = new List <double>();
valuesList.Add(values);
}
do
{
if ((line != "") && (!line.StartsWith("%"))) //check that the line has data and is not a comment
{
row = line.Split('\t');
if (row.Length != columns)
{
throw new Exception("Invalid data at line: " + (wavelengths.Count + 2));
}
//write the wavelength value once
var wlEntry = convert ? Convert.ToDouble(row[0]).ConvertWavelength(wavelengthUnit) : Convert.ToDouble(row[0]);
wavelengths.Add(wlEntry);
//loop through the spectra and get the data
for (var i = 0; i < columns - 1; i++)
{
var k = 1.0;
// dc: this would be only for MolarExtinctionCoefficient or FractionalExtinctionCoefficient, not MolarAbsorptionCoefficient or FractionalAbsorptionCoefficient
//// need to multiply MolarAbsorptionCoefficients by ln(10)
//if (ChromophoreList[i].ChromophoreCoefficientType == ChromophoreCoefficientType.MolarAbsorptionCoefficient)
//{
// k = Math.Log(10);
//}
var valEntry = convert ? Convert.ToDouble(row[i + 1]).ConvertCoefficient(chromophoreList[i].AbsorptionCoefficientUnit, chromophoreList[i].MolarUnit) : Convert.ToDouble(row[i + 1]);
valuesList[i].Add(valEntry * k);
}
}
} while ((line = readFile.ReadLine()) != null);
//loop through the spectra and create the dictionary
for (var i = 0; i < columns - 1; i++)
{
chromophoreList[i].Wavelengths = wavelengths;
chromophoreList[i].Spectrum = valuesList[i];
//if the data was converted, rewrite the absorption coefficient units and the molar units
if (convert)
{
chromophoreList[i].AbsorptionCoefficientUnit = AbsorptionCoefficientUnit.InverseMillimeters;
//only rewrite the molar units if it is not none
if (chromophoreList[i].MolarUnit != MolarUnit.None)
{
chromophoreList[i].MolarUnit = MolarUnit.MicroMolar;
}
chromophoreList[i].WavelengthUnit = WavelengthUnit.Nanometers;
}
}
}
else
{
//error, the data and values do not match
throw new Exception("The chromophore data header columns and data columns do not match");
}
}
}
catch (Exception e)
{
//catch the error
throw new Exception(e.Message);
}
return(chromophoreList);
}
