public static void Encode(
this short[] intensities,
out byte[] spectra,
out double tic,
out double bpi,
out int indexOfMaxIntensity, out int nonZeroCount)
{
// 16-bit integers are 2 bytes
const int dataTypeSize = 2;
spectra = null;
tic = 0;
bpi = 0;
indexOfMaxIntensity = 0;
nonZeroCount = RlzEncode.Encode(intensities, out var runLengthZeroEncodedData, out tic, out bpi, out indexOfMaxIntensity);
// Compress intensities
var encodedDataLength = runLengthZeroEncodedData.Length;
if (encodedDataLength > 0)
{
spectra = new byte[encodedDataLength * dataTypeSize];
Buffer.BlockCopy(runLengthZeroEncodedData, 0, spectra, 0, encodedDataLength * dataTypeSize);
spectra = CLZF2.Compress(spectra);
}
}
/// <summary>
/// Convert a LZF compressed and zero run length encoded byte array to a list of bin-intensity pairs
/// </summary>
/// <param name="compressedBinIntensity">LZF compressed and zero run length encoded byte array</param>
/// <param name="basePeakIntensity">Highest intensity, and a data-type specifying parameter</param>
/// <returns>List of tuples, where Item1 is the bin, and Item2 is the intensity</returns>
public static List <Tuple <int, int> > Decompress(byte[] compressedBinIntensity, out int basePeakIntensity)
{
const int dataTypeSize = sizeof(int);
var output = CLZF2.Decompress(compressedBinIntensity);
var numReturnedBins = output.Length / dataTypeSize;
var encodedIntensityValueArray = new int[numReturnedBins];
Buffer.BlockCopy(output, 0, encodedIntensityValueArray, 0, numReturnedBins * dataTypeSize);
var data = RlzEncode.Decode(encodedIntensityValueArray);
basePeakIntensity = data.Max(x => x.Item2);
return(data);
}
/// <summary>
/// Convert an array of intensities to a zero run length encoded and LZF compressed byte array
/// </summary>
/// <param name="intensities">Array of intensities, including all zeros</param>
/// <param name="spectra">Spectra intensity bytes (output)</param>
/// <param name="tic">TIC (output)</param>
/// <param name="bpi">Base peak intensity (output)</param>
/// <param name="indexOfMaxIntensity">Index number of the BPI</param>
/// <returns>
/// Number of non-zero data points
/// </returns>
public static int Compress(
IReadOnlyList <short> intensities,
out byte[] spectra,
out double tic,
out double bpi,
out int indexOfMaxIntensity)
{
// Get the size of the data type. Use of sizeof() for primitives is allowed in safe code blocks
const int dataTypeSize = sizeof(short);
spectra = null;
var nonZeroCount = RlzEncode.Encode(intensities, out var runLengthZeroEncodedData, out tic, out bpi, out indexOfMaxIntensity);
var encodedDataLength = runLengthZeroEncodedData.Length;
if (encodedDataLength > 0)
{
spectra = new byte[encodedDataLength * dataTypeSize];
Buffer.BlockCopy(runLengthZeroEncodedData, 0, spectra, 0, encodedDataLength * dataTypeSize);
spectra = CLZF2.Compress(spectra);
}
return(nonZeroCount);
}
public static int Encode(
float[] intensities,
out byte[] spectra,
out double tic,
out double bpi,
out int indexOfMaxIntensity)
{
// Floats are 4 bytes
const int dataTypeSize = 4;
spectra = null;
var nonZeroCount = RlzEncode.Encode(intensities, out var runLengthZeroEncodedData, out tic, out bpi, out indexOfMaxIntensity);
var encodedDataLength = runLengthZeroEncodedData.Length;
if (encodedDataLength > 0)
{
spectra = new byte[encodedDataLength * dataTypeSize];
Buffer.BlockCopy(runLengthZeroEncodedData, 0, spectra, 0, encodedDataLength * dataTypeSize);
spectra = CLZF2.Compress(spectra);
}
return(nonZeroCount);
}
/// <summary>
/// Convert an array of intensities to a zero length encoded byte array
/// </summary>
/// <param name="intensities">Array of intensities, including all zeros</param>
/// <param name="spectra">Spectra intensity bytes (output)</param>
/// <param name="tic">TIC (output)</param>
/// <param name="bpi">Base peak intensity (output)</param>
/// <param name="indexOfMaxIntensity">Index number of the BPI</param>
/// <returns>
/// Number of non-zero data points
/// </returns>
public static int EncodeSnappy(
IReadOnlyList <int> intensities,
out byte[] spectra,
out double tic,
out double bpi,
out int indexOfMaxIntensity)
{
// 32-bit integers are 4 bytes
const int dataTypeSize = 4;
spectra = null;
var nonZeroCount = RlzEncode.Encode(intensities, out var runLengthZeroEncodedData, out tic, out bpi, out indexOfMaxIntensity);
var encodedDataLength = runLengthZeroEncodedData.Length;
if (encodedDataLength > 0)
{
spectra = new byte[encodedDataLength * dataTypeSize];
Buffer.BlockCopy(runLengthZeroEncodedData, 0, spectra, 0, encodedDataLength * dataTypeSize);
spectra = Snappy.SnappyCodec.Compress(spectra);
}
return(nonZeroCount);
}