def loadHDF52EICs(self):
#need qualifier to wipe out old one....
msgTitle = 'Overwrite existing EIC set'
overWriteStr = 'Clear current EIC and load a new set?'
if self.__askConfirm__(msgTitle, overWriteStr):
fileName = str(self.LFDialog())
if fileName != None:
self.eicClass = EIC()
t1 = time.clock()
self.eicClass.loadHDF5(fileName)
t2 = time.clock() - t1
self.RoutputTE.append('HDF5 Read Time: %.4f seconds' % t2)
self.updateGUI()
def run(self):
if self.ready:
try:
t1 = time.clock()
# self.Rliblist = ['xcms']
# self.Rlibs = self.initRlibs(self.Rliblist)
#sys.stdout = StdOutFaker(self)
r = ro.r
#a = r('cdfpath = system.file("cdf", package = "faahKO")')
#cdfpath = ri.globalEnv.get("cdfpath")
#r('cdffiles = list.files(cdfpath, recursive = TRUE, full.names = TRUE)')
#r('cdffiles = cdffiles[1:3]')
#cdffiles = ri.globalEnv.get("cdffiles")
self.add2ROutput(self.fileList)
time.sleep(0.5)
rfileList = ri.StrSexpVector(self.fileList)
xset = r.xcmsSet(rfileList,
step=self.matchedFilterParams['step'],
mzdiff=self.matchedFilterParams['mzdiff'],
snthresh=self.matchedFilterParams['snthresh'])
ri.globalEnv["xset"] = xset
# if self.maxMZ != None:
# print type(self.maxMZ)
# r('xset@peaks <- xset@peaks[xset@peaks[,"mz"] < %.2f, ]'%self.maxMZ)
# self.emitUpdate('max m/z truncated at %.2f\n'%self.maxMZ)
xset = r.group(xset,
bw=self.groupParams['bw'],
mzwid=self.groupParams['mzwid'],
minfrac=self.groupParams['minfrac'],
max=self.groupParams['max'])
self.emitUpdate('\n\nXSET')
self.emitUpdate(str(xset) + '\n')
#ri.setWriteConsole(self.setRString)
time.sleep(0.5)
# if self.retcorParams['plottype'] != None:
## print self.retcorParams['plottype']self.retcorParams['plottype']
# r.png(file=self.imageName)
# r('dev.off')
if self.useRetCor:
xset2 = r.retcor(xset,
family=self.retcorParams['f'],
plottype=self.retcorParams['plottype'],
missing=self.retcorParams['missing'],
extra=self.retcorParams['extra'],
span=self.retcorParams['span'])
if self.retcorParams['plottype'] == 'mdevden':
r.savePlot(file=self.imageName, type='png')
r('dev.off()')
elif self.retcorParams['plottype'] == 'deviation':
r.savePlot(file=self.imageName, type='png')
r('dev.off()')
else:
xset2 = xset
retCorStr = "Retention Time Alignment Not Used in Processing!\n"
self.emitUpdate(retCorStr)
ri.globalEnv["xset2"] = xset2
self.emitUpdate('\n\nXSET2')
self.emitUpdate(str(xset2) + '\n')
time.sleep(0.5)
xset2 = r.group(xset2,
bw=self.groupParams['bw'],
mzwid=self.groupParams['mzwid'],
minfrac=self.groupParams['minfrac'],
max=self.groupParams['max'])
xset3 = r.fillPeaks(xset2)
self.emitUpdate('\n\nXSET3')
self.emitUpdate(str(xset3) + '\n')
time.sleep(0.5)
ri.globalEnv["xset3"] = xset3
# gt = r.group(xset3, bw=self.groupParams['bw'],
# mzwid=self.groupParams['mzwid'],
# minfrac=self.groupParams['minfrac'],
# max=self.groupParams['max'])
tsidx = r.groupnames(xset3)
ri.globalEnv["tsidx"] = tsidx
eicmax = r.length(tsidx)
eic = r.getEIC(xset3,
rtrange=self.rtWidth,
groupidx=tsidx,
rt=self.corType)
# print self.buf
eicClass = EIC(eic)
self.emit(QtCore.SIGNAL("xcmsGetEIC(PyQt_PyObject)"), eicClass)
# self.emit(QtCore.SIGNAL("xcmsSet(PyQt_PyObject)"),xset2)
#if this is False then the peak table without the filled peaks will be returned and written to csv
if self.fillPeaksOK:
self.emit(QtCore.SIGNAL("xcmsSet(PyQt_PyObject)"), xset3)
else:
self.emit(QtCore.SIGNAL("xcmsSet(PyQt_PyObject)"), xset2)
t2 = time.clock()
self.emitUpdate('\nProcessing Time: %s seconds' % t2)
# self.updateGUI()
sys.stdout = sys.__stdout__
# ri.endr()
except:
self.stop()
sys.stdout = sys.__stdout__
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info(
)
traceback.print_exception(exceptionType,
exceptionValue,
exceptionTraceback,
file=sys.stdout)
# print 'Error saving figure data'
errorMsg = "Sorry: %s\n\n:%s\n%s\n" % (
exceptionType, exceptionValue, exceptionTraceback)
# if self.parent != None:
# return QtGui.QMessageBox.warning(self.parent, "R Source Error", errorMsg)
print errorMsg
self.emitUpdate(errorMsg)
else:
print "Parameters not set or there is an error"
