Currently, the evaluation of R functions do not release Python's GIL
(which is obviously a show-stopper when it comes to multithreading).
I had a quick try at releasing the GIL, but this is appeared to cause
significant(*) trouble when exceptions had to be raised. Having that
working is on the to-do list, but someone looking at it would also be
appreciated.
(*: segfault)
An other suggestion would be to try out if the package mutiprocessing
shipped with Python 2.6 can serve your purpose.
L.
PS: Having R-GUIs from rpy2 is much on the radar (all the callback
functions are much aimed at letting one get overall control of R's
built-in user interaction features).
PPS: I see that there is a bioconductor-using audience. Stay tuned for
more about that.
B Clowers wrote:
> I've managed to get a few functions from R working as I'd expect with
> rpy2, however, I'm trying to move toward embedding some of these
> functions in a gui using PyQt4. There is no specific reason for PyQt4
> other than I'm somewhat familiar with it. Anyway, I tried placing the
> rpy2 functions into a gui thread (QThread) and while I can pass the
> output from the thread to the main application, during the running of
> the R functions is takes over my entire MainWindow. I've done threading
> many times in the past with numpy functions, however, this is my first
> venture with R.
> Can rpy2 be embedded into a thread and does anyone have a working
> example?
>
> Are there any issues as to where the rinterface is initated and which
> thread it will takeover?
>
> I'm pretty stumped, while the program works, the freezing user interface
> while R is chugging seems to defeat the purpose of a GUI.
>
> Cheers,
>
> Brian
>
> ---I've attached a snippet of the thread that uses the xcms and faahko
> libraries from bioconductor in R. Does anyone see any glaring issues
> that would cause the behavior I'm seeing? (I've also tried running the
> thread without the PyQt4 signal emits--same behavior)
> ###########################
>
> import sys
> import rpy2.robjects as ro
> import rpy2.rinterface as ri
> from eicClass import EIC
>
> from PyQt4 import QtCore, QtGui
>
>
> class StdOutFaker:
> def __init__(self, parent):
> self.P = parent
> def write(self, string):
> # print string
> if string != '\n' and string != ' ' and string != '':
> self.P.emitUpdate(string)
>
> class XCMSThread(QtCore.QThread):
>
> def __init__(self, parent = None):
> QtCore.QThread.__init__(self, parent)
>
> self.finished = False
> self.stopped = False
> self.mutex = QtCore.QMutex()
> self.ready = True
> self.numSteps = 25
> self.Rliblist = ['xcms']
> self.Rlibs = self.initRlibs(self.Rliblist)
>
> self.matchedFilterParams = {'fwhm':30.,
> 'sigma':30/2.3548,
> 'max': 5.,
> 'snthresh':10.,
> 'step':0.1,
> 'steps':2.,
> 'mzdiff':0.1,
> }
>
> self.matchedFilterTypes = {'fwhm':float,
> 'sigma':float,
> 'max':float,
> 'snthresh':float,
> 'step':float,
> 'steps':float,
> 'mzdiff':float
> }
>
>
> self.centWaveParams = {'ppm': 10.,
> 'peakwidth': str([20,50]),#this needs to
> be fixed, the new version of PyQt4 handles this better
> 'snthresh':10.,
> 'prefilter':str([3,100]),
> 'mzdiff':-0.001,
> }
> self.centWaveTypes = {'ppm': float,
> 'peakwidth': str,
> 'snthresh':float,
> 'prefilter':str,
> 'mzdiff':float,
> }
> ################################
>
> self.groupParams = {'bw':30.,
> 'minfrac':0.1,
> 'mzwid':0.1,
> 'max':3
> }
>
> self.groupTypes = {}
> ##############################
>
> self.retcorParams = {'extra':2,
> 'span':.5,
> 'f':'symmetric',
> 'plottype':"mdevden",
> 'missing':2,
> }
> self.retcorTypes = {}
>
> #########################
> self.xcmsParamDict = {'Matched Filter':self.matchedFilterParams,
> 'CentWave':self.centWaveParams}
> self.xcmsTypeDict = {'Matched Filter':self.matchedFilterTypes,
> 'CentWave':self.centWaveTypes}
>
>
> def add2ROutput(self, rVector):
> for item in rVector:
> self.emitUpdate(item)
> self.emitUpdate('_\n')
>
> def emitUpdate(self, updateStr):
> self.emit(QtCore.SIGNAL("xcmsOutUpdate(PyQt_PyObject)"),updateStr)
>
> def run(self):
> try:
> 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[1:2]')
> cdffiles = ri.globalEnv.get("cdffiles")
>
> self.add2ROutput(cdffiles)
> xset = r.xcmsSet(cdffiles)
> ri.globalEnv["xset"] = xset
> xset = r.group(xset)
> self.emitUpdate('\n\nXSET')
> self.emitUpdate(str(xset)+'\n')
>
> xset2 = r.retcor(xset, family = "symmetric", plottype =
> "mdevden")
> ri.globalEnv["xset2"] = xset2
> self.emitUpdate('\n\nXSET2')
> self.emitUpdate(str(xset2)+'\n')
> xset2 = r.group(xset2, bw = 10)
> xset3 = r.fillPeaks(xset2)
> self.emitUpdate('\n\nXSET3')
> self.emitUpdate(str(xset3)+'\n')
> ri.globalEnv["xset3"] = xset3
> gt = r.groups(xset3)
> tsidx = r.groupnames(xset3)
> ri.globalEnv["tsidx"] = tsidx
> eicmax = r.length(tsidx)
> eic = r.getEIC(xset3, rtrange = 150, groupidx = tsidx, rt =
> "corrected")
> eicClass = EIC(eic)
> self.emit(QtCore.SIGNAL("xcmsGetEIC(PyQt_PyObject)"),eicClass)
> sys.stdout=sys.__stdout__
> except:
> sys.stdout=sys.__stdout__
>
>
> def stop(self):
> print "stop try"
> try:
> self.mutex.lock()
> self.stopped = True
> finally:
> self.mutex.unlock()
>
> def isStopped(self):
> print "stop try"
> try:
> self.mutex.lock()
> return self.stopped
> finally:
> self.mutex.unlock()
>
> def __del__(self):
> self.exiting = True
> self.wait()
>
> def initRlibs(self,libList):
> libDict = {}
>
> for lib in libList:
> try:
> libDict[lib] = ro.r('library(%s)'%lib)
> except:
> errorMsg ='Error loading R library %s\nCheck Library
> Installation\n'%lib
> errorMsg += "Sorry: %s\n\n:%s\n"%(sys.exc_type,
> sys.exc_value)
> print errorMsg
>
> return libDict
>
> def list2rpyFuntions(self,strList):
> funcDict = {}
> for entry in strList:
> try:
> funcDict[entry] = ro.r['%s'%entry]
> except:
> errorMsg ='Error creating function %s'%entry
> errorMsg += "Sorry: %s\n\n:%s\n"%(sys.exc_type,
> sys.exc_value)
> print errorMsg
>
> return funcDict
>
>
>
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