private Int32 ExtractFromBitsInt32(int packedValue, byte startBit, byte endBit)
{
int unpackedValue;
if (endBit < 31)
{
if (startBit == 0)
{
unpackedValue = (int)(packedValue & CreateMask(0, endBit));
}
else
{
unpackedValue = (int)((long)(packedValue / Math.Pow(2, startBit)) & CreateMask(0, (byte)(endBit - startBit)));
}
}
else
{
unpackedValue = (int)(NumberConversion.Int32ToUnsigned(packedValue) / Math.Pow(2, startBit));
}
return(unpackedValue);
}
/// <summary>
/// Extracts packed mass data
/// </summary>
/// <param name="packedBasePeakInfo"></param>
/// <param name="acquisitionDataType"></param>
/// <param name="processingFunctionIndexFile"></param>
/// <returns></returns>
public double UnpackMass(int packedBasePeakInfo, short acquisitionDataType, bool processingFunctionIndexFile)
{
// See note for Acquisition Data Types 9 to 12 below
double unpackedMass;
switch (acquisitionDataType)
{
case 9:
case 10:
case 11:
case 12:
// Includes type 9, 11, and 12; type 10 is officially unused
// (9=High accuracy calibrated data, 11=Enhanced uncalibrated data, and 12=Enhanced calibrated data)
// Note: Only use this function to unpack masses for data in the .IDX file, not for data in the .DAT file
// See the NativeIOGetSpectrum function for the method of unpacking masses in .DAT files
// Compute the MassMantissa value by converting the Packed value to an Unsigned Int32 (and storing in a long),
// then right shifting 9 bits by dividing by 2^9
// It would be more straightforward to use packedBasePeakInfo And CreateMask(9, 31) but VB won't let us
// And a Currency value with a Long; this gives an OverFlow error
var massMantissa = (int)(NumberConversion.Int32ToUnsigned(packedBasePeakInfo) / 512f); // 512 = 2^9
// Compute the MassExponent value by multiplying the Packed value by the appropriate BitMask, then right shifting 4 bits by dividing by 2^4
var massExponent = (short)(packedBasePeakInfo & maskBPMassExponent) / 16f; // 16 = 2^4
if (processingFunctionIndexFile)
{
// When computing the BasePeakMass based on data in the _func001.idx
// file, must bump up the Mass Exponent by 8 in order to multiply the
// Mass Mantissa by an additional value of 256 to get the correct value
if (massExponent < 6)
{
if (acquisitionDataType == 9)
{
// This only seems to be necessary for files with Acquisition data type 9
// The following Assertion is here to test for that
massExponent += 8;
}
}
}
// Note that we divide by 2^23 to convert the mass mantissa to fractional form
unpackedMass = massMantissa / 8388608f * Math.Pow(2, massExponent); // 8388608 = 2^23
break;
case 0:
// Compressed data
// Compute the MassMantissa value by converting the Packed value to an Unsigned Int32 (and storing in a long),
// then right shifting 11 bits by dividing by 2^11
// It would be more straightforward to use packedBasePeakInfo And CreateMask(11, 31) but VB won't let us
// And a Currency value with a Long; this gives an OverFlow error
// We must divide the MassMantissa by 128 to get the mass
unpackedMass = (int)(NumberConversion.Int32ToUnsigned(packedBasePeakInfo) / 2048f) / 128f; // 2048 = 2^11
// Debug.Assert(unpackedMass == ExtractFromBitsInt32(packedBasePeakInfo, 11, 31) / 128f);
break;
case 1:
// Standard data
// We must divide the MassMantissa by 1024 to get the mass
unpackedMass = (short)(packedBasePeakInfo & maskBPStandardDataMass) / 1024f;
break;
case 2:
case 3:
case 4:
case 5:
case 6:
case 7:
// Uncalibrated data
// This type of data doesn't have a base peak mass
unpackedMass = 0;
break;
case 8:
// High intensity calibrated data
// Compute the MassMantissa value by converting the Packed value to an Unsigned Int32 (and storing in a long),
// then right shifting 4 bits by dividing by 2^4
// We must divide the MassMantissa by 128 to get the mass
unpackedMass = (int)(NumberConversion.Int32ToUnsigned(packedBasePeakInfo) / 16f) / 128f; // 16 = 2^4
//Debug.Assert(unpackedMass == ExtractFromBitsInt32(packedBasePeakInfo, 4, 31) / 128f);
break;
default:
unpackedMass = 0;
break;
}
return(unpackedMass);
}
public bool GetContainsCalibratedMasses(int packedScanInfo)
{
return(NumberConversion.ValueToBool(packedScanInfo & maskScanContainsCalibratedMasses));
}
public bool GetContinuumDataOverride(int packedScanInfo)
{
return(NumberConversion.ValueToBool(packedScanInfo & maskContinuumDataOverride));
}
public bool GetUseFollowingContinuum(int packedScanInfo)
{
return(NumberConversion.ValueToBool(packedScanInfo & maskUseFollowingContinuum));
}
public short GetMSMSSegmentOrChannelCount(short packedMsMsInfo)
{
return((short)(NumberConversion.Int32ToUnsigned(packedMsMsInfo) / 256f)); // 256 = 2^8
}
