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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