def updateErrorCanvas(self):
"""Update error canvas."""
# make container
container = mspy.plot.container([])
# make points object
self.currentErrors.sort()
points = mspy.plot.points(self.currentErrors,
pointColour=(0, 255, 0),
showPoints=True,
showLines=False)
container.append(points)
# make peaklist object
if self.currentPeaklist:
peaks = self.makeCurrentPeaklist()
peaklist = mspy.plot.spectrum(mspy.scan(peaklist=peaks),
tickColour=(170, 170, 170),
showLabels=False)
container.append(peaklist)
# set units
self.errorCanvas.setProperties(yLabel='error (%s)' %
(config.match['units']))
# draw container
self.errorCanvas.draw(container)
def updateSpectrumCanvas(self, rescale=True):
"""Show current profile and peaks in canvas."""
# clear container
self.spectrumContainer.empty()
# check document
if not self.currentDocument:
self.spectrumCanvas.draw(self.spectrumContainer)
return
# get current peaklist
peaklist = self.currentDocument.spectrum.peaklist
# get current profile data
profile = []
if self.currentProfile != None:
profile = self.currentProfile
# add main profile spectrum to container
labelFont = wx.Font(config.spectrum['labelFontSize'], wx.SWISS, wx.FONTSTYLE_NORMAL, wx.FONTWEIGHT_NORMAL, 0)
spectrum = mspy.plot.spectrum(
scan = mspy.scan(profile=profile, peaklist=peaklist),
spectrumColour = (16,71,185),
tickColour = (255,0,0),
showPoints = config.spectrum['showDataPoints'],
showLabels = config.spectrum['showLabels'],
showTicks = True,
labelDigits = config.main['mzDigits'],
labelBgr = config.spectrum['labelBgr'],
labelAngle = config.spectrum['labelAngle'],
labelFont = labelFont
)
self.spectrumContainer.append(spectrum)
# add individual peaks to container
if config.spectrumGenerator['showPeaks']:
if self.currentPeaks != None:
for peak in self.currentPeaks:
spectrum = mspy.plot.points(
points = peak,
lineColour = (50,140,0),
showLines = True,
showPoints = False,
exactFit = True
)
self.spectrumContainer.append(spectrum)
# get current axis
if not rescale:
xAxis = self.spectrumCanvas.getCurrentXRange()
yAxis = self.spectrumCanvas.getCurrentYRange()
else:
xAxis = None
yAxis = None
# draw spectra
self.spectrumCanvas.draw(self.spectrumContainer, xAxis=xAxis, yAxis=yAxis)
def updateErrorCanvas(self):
"""Update error canvas."""
# make container
container = mspy.plot.container([])
# make points object
self.currentErrors.sort()
points = mspy.plot.points(self.currentErrors, pointColour=(0,255,0), showPoints=True, showLines=False)
container.append(points)
# make peaklist object
if self.currentPeaklist:
peaks = self.makeCurrentPeaklist()
peaklist = mspy.plot.spectrum(mspy.scan(peaklist=peaks), tickColour=(170,170,170), showLabels=False)
container.append(peaklist)
# set units
self.errorCanvas.setProperties(yLabel='error (%s)' % (config.match['units']))
# draw container
self.errorCanvas.draw(container)
def updateErrorPlot(self):
"""Update error plot."""
# make container
container = mspy.plot.container([])
minY = 0
maxY = 1
# make points
if self.currentReferences:
intensities = []
# get after points
pointsAfter = []
for item in self.currentReferences:
if item[6] and item[5] != None:
pointsAfter.append([item[2], item[5]])
intensities.append(item[5])
if pointsAfter:
pointsAfter.sort()
obj = mspy.plot.points(pointsAfter,
pointColour=(0, 255, 0),
legend='after',
showLines=False,
showPoints=True)
container.append(obj)
# get before points
pointsBefore = []
for item in self.currentReferences:
if item[6] and item[4] != None:
pointsBefore.append([item[2], item[4]])
intensities.append(item[4])
if pointsBefore:
pointsBefore.sort()
obj = mspy.plot.points(pointsBefore,
pointColour=(255, 100, 100),
legend='before',
showLines=False,
showPoints=True)
container.append(obj)
# set range
if intensities:
minY = min(intensities)
maxY = max(intensities)
if minY == maxY:
minY -= minY * 0.1
maxY += maxY * 0.1
# make calibration curve
if self.currentCalibration and self.currentDocument and self.currentDocument.spectrum.peaklist:
curvePoints = self.makeCalibrationCurve()
curvePoints = numpy.array(curvePoints)
if config.calibration['units'] == 'ppm':
obj = mspy.plot.points(curvePoints,
lineColour=(255, 100, 100),
showLines=True,
showPoints=False,
lineStyle=mwx.DASHED_LINE)
else:
obj = mspy.plot.points(curvePoints,
lineColour=(255, 100, 100),
showLines=True,
showPoints=False)
container.append(obj)
# set range
if intensities:
minY = min(minY,
float(numpy.minimum.reduce(curvePoints)[1]))
maxY = max(maxY,
float(numpy.maximum.reduce(curvePoints)[1]))
else:
minY = float(numpy.minimum.reduce(curvePoints)[1])
maxY = float(numpy.maximum.reduce(curvePoints)[1])
# make peaklist
if self.currentDocument and self.currentDocument.spectrum.peaklist:
peaks = self.makeCurrentPeaklist(minY, maxY)
obj = mspy.plot.spectrum(mspy.scan(peaklist=peaks),
tickColour=(170, 170, 170),
showLabels=False)
container.append(obj)
# set units
self.errorCanvas.setProperties(yLabel='error (%s)' %
(config.calibration['units']))
# draw container
self.errorCanvas.draw(container)
def makeProfile(self):
"""Generate pattern profile."""
self.currentPatternProfile = None
self.currentPatternPeaks = None
self.currentPatternScan = None
# check pattern
if self.currentPattern == None:
return
# get selected charge
charge = 0
if self.currentIon != None:
charge = self.currentIon[3]
# make profile
self.currentPatternProfile = mspy.profile(
peaklist=self.currentPattern,
fwhm=config.massCalculator['patternFwhm'],
points=20,
model=config.massCalculator['patternPeakShape'],
)
# get scale and shift for specified intensity and baseline
basepeak = mspy.basepeak(self.currentPatternProfile)
scale = (config.massCalculator['patternIntensity'] -
config.massCalculator['patternBaseline']
) / self.currentPatternProfile[basepeak][1]
shift = config.massCalculator['patternBaseline']
# rescale profile
self.currentPatternProfile = mspy.multiply(self.currentPatternProfile,
y=scale)
self.currentPatternProfile = mspy.offset(self.currentPatternProfile,
y=shift)
# make real peaklist from profile
peaklist = []
for isotope in mspy.maxima(self.currentPatternProfile):
mz = isotope[0]
centroid = mspy.centroid(self.currentPatternProfile, isotope[0],
isotope[1] * 0.99)
if abs(mz - centroid) < config.massCalculator['patternFwhm'] / 20:
mz = centroid
peak = mspy.peak(mz=mz, ai=isotope[1], base=shift, charge=charge)
peaklist.append(peak)
peaklist = mspy.peaklist(peaklist)
# make individual peak shapes
self.currentPatternPeaks = []
if config.massCalculator['patternShowPeaks']:
# gaussian shape
if config.massCalculator['patternPeakShape'] == 'gaussian':
for isotope in self.currentPattern:
peak = mspy.gaussian(
x=isotope[0],
minY=shift,
maxY=isotope[1] * scale + shift,
fwhm=config.massCalculator['patternFwhm'])
self.currentPatternPeaks.append(peak)
# lorentzian shape
elif config.massCalculator['patternPeakShape'] == 'lorentzian':
for isotope in self.currentPattern:
peak = mspy.lorentzian(
x=isotope[0],
minY=shift,
maxY=isotope[1] * scale + shift,
fwhm=config.massCalculator['patternFwhm'])
self.currentPatternPeaks.append(peak)
# gauss-lorentzian shape
elif config.massCalculator[
'patternPeakShape'] == 'gausslorentzian':
for isotope in self.currentPattern:
peak = mspy.gausslorentzian(
x=isotope[0],
minY=shift,
maxY=isotope[1] * scale + shift,
fwhm=config.massCalculator['patternFwhm'])
self.currentPatternPeaks.append(peak)
# make scan object
self.currentPatternScan = mspy.scan(profile=self.currentPatternProfile,
peaklist=peaklist)
def updateErrorPlot(self):
"""Update error plot."""
# make container
container = mspy.plot.container([])
minY = 0
maxY = 1
# make points
if self.currentReferences:
intensities = []
# get after points
pointsAfter = []
for item in self.currentReferences:
if item[6] and item[5] != None:
pointsAfter.append([item[2], item[5]])
intensities.append(item[5])
if pointsAfter:
pointsAfter.sort()
obj = mspy.plot.points(
pointsAfter, pointColour=(0, 255, 0), legend="after", showLines=False, showPoints=True
)
container.append(obj)
# get before points
pointsBefore = []
for item in self.currentReferences:
if item[6] and item[4] != None:
pointsBefore.append([item[2], item[4]])
intensities.append(item[4])
if pointsBefore:
pointsBefore.sort()
obj = mspy.plot.points(
pointsBefore, pointColour=(255, 100, 100), legend="before", showLines=False, showPoints=True
)
container.append(obj)
# set range
if intensities:
minY = min(intensities)
maxY = max(intensities)
if minY == maxY:
minY -= minY * 0.1
maxY += maxY * 0.1
# make calibration curve
if self.currentCalibration and self.currentDocument and self.currentDocument.spectrum.peaklist:
curvePoints = self.makeCalibrationCurve()
curvePoints = numpy.array(curvePoints)
if config.calibration["units"] == "ppm":
obj = mspy.plot.points(
curvePoints,
lineColour=(255, 100, 100),
showLines=True,
showPoints=False,
lineStyle=mwx.DASHED_LINE,
)
else:
obj = mspy.plot.points(curvePoints, lineColour=(255, 100, 100), showLines=True, showPoints=False)
container.append(obj)
# set range
if intensities:
minY = min(minY, float(numpy.minimum.reduce(curvePoints)[1]))
maxY = max(maxY, float(numpy.maximum.reduce(curvePoints)[1]))
else:
minY = float(numpy.minimum.reduce(curvePoints)[1])
maxY = float(numpy.maximum.reduce(curvePoints)[1])
# make peaklist
if self.currentDocument and self.currentDocument.spectrum.peaklist:
peaks = self.makeCurrentPeaklist(minY, maxY)
obj = mspy.plot.spectrum(mspy.scan(peaklist=peaks), tickColour=(170, 170, 170), showLabels=False)
container.append(obj)
# set units
self.errorCanvas.setProperties(yLabel="error (%s)" % (config.calibration["units"]))
# draw container
self.errorCanvas.draw(container)
def makeProfile(self):
"""Generate pattern profile."""
self.currentPatternProfile = None
self.currentPatternPeaks = None
self.currentPatternScan = None
# check pattern
if self.currentPattern == None:
return
# get selected charge
charge = 0
if self.currentIon != None:
charge = self.currentIon[3]
# make profile
self.currentPatternProfile = mspy.profile(
peaklist = self.currentPattern,
fwhm = config.massCalculator['patternFwhm'],
points = 20,
model = config.massCalculator['patternPeakShape'],
)
# get scale and shift for specified intensity and baseline
basepeak = mspy.basepeak(self.currentPatternProfile)
scale = (config.massCalculator['patternIntensity'] - config.massCalculator['patternBaseline']) / self.currentPatternProfile[basepeak][1]
shift = config.massCalculator['patternBaseline']
# rescale profile
self.currentPatternProfile = mspy.multiply(self.currentPatternProfile, y=scale)
self.currentPatternProfile = mspy.offset(self.currentPatternProfile, y=shift)
# make real peaklist from profile
peaklist = []
for isotope in mspy.maxima(self.currentPatternProfile):
mz = isotope[0]
centroid = mspy.centroid(self.currentPatternProfile, isotope[0], isotope[1]*0.99)
if abs(mz-centroid) < config.massCalculator['patternFwhm']/20:
mz = centroid
peak = mspy.peak(
mz = mz,
ai = isotope[1],
base = shift,
charge = charge
)
peaklist.append(peak)
peaklist = mspy.peaklist(peaklist)
# make individual peak shapes
self.currentPatternPeaks = []
if config.massCalculator['patternShowPeaks']:
# gaussian shape
if config.massCalculator['patternPeakShape'] == 'gaussian':
for isotope in self.currentPattern:
peak = mspy.gaussian(
x = isotope[0],
minY = shift,
maxY = isotope[1]*scale+shift,
fwhm = config.massCalculator['patternFwhm']
)
self.currentPatternPeaks.append(peak)
# lorentzian shape
elif config.massCalculator['patternPeakShape'] == 'lorentzian':
for isotope in self.currentPattern:
peak = mspy.lorentzian(
x = isotope[0],
minY = shift,
maxY = isotope[1]*scale+shift,
fwhm = config.massCalculator['patternFwhm']
)
self.currentPatternPeaks.append(peak)
# gauss-lorentzian shape
elif config.massCalculator['patternPeakShape'] == 'gausslorentzian':
for isotope in self.currentPattern:
peak = mspy.gausslorentzian(
x = isotope[0],
minY = shift,
maxY = isotope[1]*scale+shift,
fwhm = config.massCalculator['patternFwhm']
)
self.currentPatternPeaks.append(peak)
# make scan object
self.currentPatternScan = mspy.scan(profile=self.currentPatternProfile, peaklist=peaklist)
