def _parseSpectrum(self):
"""Parse spectrum data."""
# get acquisition parames
params = self._parseParams()
if not params:
return False
# open spectrum
try:
document = file(self.path, 'rb')
rawData = document.read()
document.close()
except IOError:
return False
# convert to list
try:
count = len(rawData) / struct.calcsize('i')
start, end = 0, len(rawData)
points = struct.unpack('i' * count, rawData[start:end])
except:
return False
# check data length
if len(points) != int(params['TD']):
return False
# shift X-axis
if params['SPTYPE'] == 'psd':
shift = float(params['ML1'])
interval = float(params['DW'])
else:
shift = float(params['DELAY'])
interval = float(params['DW'])
buff = []
for x in points:
buff.append([shift, x])
shift += interval
points = buff
# convert X-axis to m/z
if params['SPTYPE'] == 'tof':
points = self._convertTimeToMZ(points, float(params['ML1']),
float(params['ML2']),
float(params['ML3']))
# convert to scan object
spectrum = objects.scan(points)
# set additional parameters
spectrum.msLevel = 1
if params['SPTYPE'] == 'psd':
spectrum.msLevel = 2
if 'Parent' in params:
spectrum.precursorMZ = params['Parent']
return spectrum
def _parseSpectrum(self):
"""Parse spectrum data."""
# get acquisition parames
params = self._parseParams()
if not params:
return False
# open spectrum
try:
document = file(self.path, 'rb')
rawData = document.read()
document.close()
except IOError:
return False
# convert to list
try:
count = len(rawData)/struct.calcsize('i')
start, end = 0, len(rawData)
points = struct.unpack('i' * count, rawData[start:end])
except:
return False
# check data length
if len(points) != int(params['TD']):
return False
# shift X-axis
if params['SPTYPE'] == 'psd':
shift = float(params['ML1'])
interval = float(params['DW'])
else:
shift = float(params['DELAY'])
interval = float(params['DW'])
buff = []
for x in points:
buff.append([shift, x])
shift += interval
points = buff
# convert X-axis to m/z
if params['SPTYPE'] == 'tof':
points = self._convertTimeToMZ(points, float(params['ML1']), float(params['ML2']), float(params['ML3']))
# convert to scan object
spectrum = objects.scan(points)
# set additional parameters
spectrum.msLevel = 1
if params['SPTYPE'] == 'psd':
spectrum.msLevel = 2
if 'Parent' in params:
spectrum.precursorMZ = params['Parent']
return spectrum
def getSpectrum(self, discrete=False):
"""Get spectrum from document."""
# parse data
data = self._parseData()
if not data:
return False
# parse data as peaklist (discrete points)
if discrete:
for x, p in enumerate(data):
data[x] = objects.peak(p[0], p[1])
spectrum = objects.scan(peaks=data)
# parse data as spectrum (continuous line)
else:
spectrum = objects.scan(points=data)
return spectrum
def getSpectrum(self, discrete=False):
"""Get spectrum from document."""
# parse data
data = self._parseData()
if not data:
return False
# parse data as peaklist (discrete points)
if discrete:
for x, p in enumerate(data):
data[x] = objects.peak(p[0], p[1])
spectrum = objects.scan(peaks=data)
# parse data as spectrum (continuous line)
else:
spectrum = objects.scan(points=data)
return spectrum
def getSpectrum(self, scanNumber=None):
"""Get spectrum from document."""
# init parser
handler = scanHandler(scanNumber)
parser = xml.sax.make_parser()
parser.setContentHandler(handler)
# parse document
try:
document = file(self.path)
parser.parse(document)
document.close()
scan = handler.scan
except stopParsing:
scan = handler.scan
except xml.sax.SAXException:
return False
# check data
if not scan:
return False
# parse peaks
try:
points = self._parsePoints(scan)
except:
return False
# parse data as peaklist (discrete points)
if scan['spectrumType'] == 'discrete':
for x, p in enumerate(points):
points[x] = objects.peak(p[0], p[1])
spectrum = objects.scan(peaks=points)
# parse data as spectrum (continuous line)
else:
spectrum = objects.scan(points=points)
# set metadata
if scan['scanNumber']:
spectrum.scanNumber = int(scan['scanNumber'])
if scan['parentScanNumber']:
spectrum.parentScanNumber = int(scan['parentScanNumber'])
if scan['msLevel']:
spectrum.msLevel = int(scan['msLevel'])
if scan['polarity']:
spectrum.polarity = scan['polarity']
if scan['retentionTime']:
spectrum.retentionTime = scan['retentionTime']
if scan['totIonCurrent']:
spectrum.totIonCurrent = float(scan['totIonCurrent'])
if scan['basePeakMz']:
spectrum.basePeakMZ = float(scan['basePeakMz'])
if scan['basePeakIntensity']:
spectrum.basePeakIntensity = float(scan['basePeakIntensity'])
if scan['precursorMz']:
spectrum.precursorMZ = float(scan['precursorMz'])
if scan['precursorIntensity']:
spectrum.precursorIntensity = float(scan['precursorIntensity'])
return spectrum
def getSpectrum(self, scanNumber=None):
"""Get spectrum from document."""
# init parser
handler = scanHandler(scanNumber)
parser = xml.sax.make_parser()
parser.setContentHandler(handler)
# parse document
try:
document = file(self.path)
parser.parse(document)
document.close()
scan = handler.scan
except stopParsing:
scan = handler.scan
except xml.sax.SAXException:
return False
# check data
if not scan:
return False
# parse peaks
try:
points = self._parsePoints(scan)
except:
return False
# parse data as peaklist (discrete points)
if scan['spectrumType'] == 'discrete':
for x, p in enumerate(points):
points[x] = objects.peak(p[0], p[1])
spectrum = objects.scan(peaks=points)
# parse data as spectrum (continuous line)
else:
spectrum = objects.scan(points=points)
# set metadata
if scan['scanNumber']:
spectrum.scanNumber = int(scan['scanNumber'])
if scan['parentScanNumber']:
spectrum.parentScanNumber = int(scan['parentScanNumber'])
if scan['msLevel']:
spectrum.msLevel = int(scan['msLevel'])
if scan['polarity']:
spectrum.polarity = scan['polarity']
if scan['retentionTime']:
spectrum.retentionTime = scan['retentionTime']
if scan['totIonCurrent']:
spectrum.totIonCurrent = float(scan['totIonCurrent'])
if scan['basePeakMz']:
spectrum.basePeakMZ = float(scan['basePeakMz'])
if scan['basePeakIntensity']:
spectrum.basePeakIntensity = float(scan['basePeakIntensity'])
if scan['precursorMz']:
spectrum.precursorMZ = float(scan['precursorMz'])
if scan['precursorIntensity']:
spectrum.precursorIntensity = float(scan['precursorIntensity'])
return spectrum