def readAllSpectra(rawFile, firstScanNumber: int, lastScanNumber: int,
outputData: bool):
for scanNumber in range(firstScanNumber, lastScanNumber + 1):
scanFilter = rawFile.GetFilterForScanNumber(firstScanNumber)
print(scanFilter.ToString())
# Get the scan from the RAW file. This method uses the Scan.FromFile method which returns a
# Scan object that contains both the segmented and centroid (label) data from an FTMS scan
# or just the segmented data in non-FTMS scans. The GetSpectrum method demonstrates an
# alternative method for reading scans.
scan = Scan.FromFile(rawFile, scanNumber)
# If that scan contains FTMS data then Centroid stream will be populated so check to see if it is present.
labelSize = 0
if scan.HasCentroidStream:
labelSize = scan.CentroidScan.Length
# for non-FTMS data, the preferred data will be populated
dataSize = scan.PreferredMasses.Length
if outputData:
print("Spectrum {0} - {1}: normal {2}, label {3} points".format(
scanNumber, scanFilter.ToString(), dataSize, labelSize))
def CalculateMassPrecision(rawFile, scanNumber: int):
# Get the scan from the RAW file
scan = Scan.FromFile(rawFile, scanNumber)
# Get the scan event and from the scan event get the analyzer type for this scan
scanEvent = rawFile.GetScanEventForScanNumber(scanNumber)
scanFilter = rawFile.GetFilterForScanNumber(scanNumber)
print(scanFilter.MassAnalyzer)
print(scanEvent)
# Get the trailer extra data to get the ion time for this file
logEntry = rawFile.GetTrailerExtraInformation(scanNumber)
print(logEntry.Labels)
trailerHeadings = List[String]()
trailerValues = List[String]()
for i in range(logEntry.Length):
trailerHeadings.Add(String(logEntry.Labels[i]))
trailerValues.Add(String(logEntry.Values[i]))
# create the mass precision estimate object
precisionEstimate = PrecisionEstimate()
# Get the ion time from the trailer extra data values
ionTime = precisionEstimate.GetIonTime(scanFilter.MassAnalyzer, scan,
trailerHeadings, trailerValues)
# Calculate the mass precision for the scan
listResults = precisionEstimate.GetMassPrecisionEstimate(
scan, scanFilter.MassAnalyzer, ionTime,
rawFile.RunHeader.MassResolution)
# Output the mass precision results
if len(listResults) > 0:
print("Mass Precision Results:")
for result in listResults:
print("Mass {}, mmu = {}, ppm = {}".format(
result.Mass, result.MassAccuracyInMmu,
result.MassAccuracyInPpm))
def CalculateMassPrecision(self, scanNumber=1):
'''Calculates the mass precision for a spectrum.
Args:
scanNumber (int): the scan to process.
'''
# Get the scan from the RAW file
scan = Scan.FromFile(self.source, scanNumber)
# Get the scan event and from the scan event get the analyzer type for this scan
scanEvent = IScanEventBase(self.source.GetScanEventForScanNumber(scanNumber))
# Get the trailer extra data to get the ion time for this file
logEntry = self.source.GetTrailerExtraInformation(scanNumber)
trailerHeadings = List[str]()
trailerValues = List[str]()
for i in range(logEntry.Length):
trailerHeadings.Add(logEntry.Labels[i])
trailerValues.Add(logEntry.Values[i])
# Create the mass precision estimate object
precisionEstimate = PrecisionEstimate()
# Get the ion time from the trailer extra data values
ionTime = precisionEstimate.GetIonTime(scanEvent.MassAnalyzer, scan, trailerHeadings, trailerValues)
# Calculate the mass precision for the scan
listResults = precisionEstimate.GetMassPrecisionEstimate(
scan, scanEvent.MassAnalyzer, ionTime, self.source.RunHeader.MassResolution)
# Output the mass precision results
''''''
# if listResults.Count:
# print('Mass Precision Results:')
for result in listResults:
print('Mass {:.5f}, mmu = {:.3f}, ppm = {:.2f}'.format(
result.Mass, result.MassAccuracyInMmu, result.MassAccuracyInPpm))
def AnalyzeAllScans(rawFile, firstScanNumber: int, lastScanNumber: int):
# Test the preferred (normal) data and centroid (high resolution/label) data
failedCentroid = 0
failedPreferred = 0
for scanNumber in range(firstScanNumber, lastScanNumber + 1):
# Get each scan from the RAW file
scan = Scan.FromFile(rawFile, scanNumber)
# Check to see if the RAW file contains label (high-res) data and if it is present
# then look for any data that is out of order
if scan.HasCentroidStream:
if scan.CentroidScan.Length > 0:
currentMass = scan.CentroidScan.Masses[0]
for index in range(1, scan.CentroidScan.Length):
if scan.CentroidScan.Masses[index] > currentMass:
currentMass = scan.CentroidScan.Masses[index]
else:
if failedCentroid == 0:
print(
"First failure: Failed in scan data at: Scan: "
+ scanNumber + " Mass: " +
currentMass.ToString("F4"))
failedCentroid += 1
# Check the normal (non-label) data in the RAW file for any out-of-order data
if scan.PreferredMasses.Length > 0:
currentMass = scan.PreferredMasses[0]
# print(scan.PreferredMasses.Length, scan.CentroidScan.Length, scan.SegmentedScan.Positions.Length)
for index in range(1, scan.PreferredMasses.Length):
if scan.PreferredMasses[index] > currentMass:
currentMass = scan.PreferredMasses[index]
else:
if (failedPreferred == 0):
print("First failure: Failed in scan data at: Scan: " +
str(scanNumber) + " Mass: " +
currentMass.ToString("F2"))
failedPreferred += 1
# Display a message indicating if any of the scans had data that was "out of order"
if failedPreferred == 0 and failedCentroid == 0:
print("Analysis completed: No out of order data found")
else:
print("Analysis completed: Preferred data failed: " +
str(failedPreferred) + " Centroid data failed: " +
str(failedCentroid))