Merge pull request #78 from migueln/master

Small set of workarounds and bugfixes

enrico/RunGTlike.py

@@ -1,13 +1,11 @@
 #!/usr/bin/env python
-import os
-from enrico import utils
-from enrico import energybin
-from enrico.config import get_config
-from enrico.gtfunction import Observation
-from enrico.fitmaker import FitMaker
 
 
-def Analysis(folder, config, tag="" ,verbose = 1):
+def Analysis(folder, config, tag="", convtyp='-1', verbose = 1):
+    from enrico import utils
+    from enrico.gtfunction import Observation
+    from enrico.fitmaker import FitMaker
+
     """ run an analysis"""
     Obs = Observation(folder, config, tag=tag)
     if verbose:
@@ -47,10 +45,14 @@ def GenAnalysisObjects(config, verbose = 1, xmlfile =""):
     return FitRunner,Fit
 
 def run(infile):
+    from enrico import utils
+    from enrico import energybin
+    from enrico.config import get_config
+
     """Run an entire Fermi analysis (spectrum) by reading a config file"""
     config = get_config(infile)
     folder = config['out']
-    os.system('mkdir -p ' + folder)
+    utils.create_dir(folder)
 
     FitRunner,Fit = GenAnalysisObjects(config)
     # create all the fit files and run gtlike
@@ -62,7 +64,7 @@ def run(infile):
     #plot the SED and model map if possible and asked
     if config['Spectrum']['ResultPlots'] == 'yes' :
         from enrico.constants import SpectrumPath
-    	os.system("mkdir -p "+config['out'] + '/'+SpectrumPath+'/')
+        utils.create_dir("%s/%s/" %(config['out'],SpectrumPath))
         if float(config['UpperLimit']['TSlimit']) < Fit.Ts(config['target']['name']):
             FitRunner.ComputeSED(Fit)
         outXml = utils._dump_xml(config)
@@ -72,7 +74,9 @@ def run(infile):
     #  Make energy bins by running a *new* analysis
     Nbin = config['Ebin']['NumEnergyBins']
     energybin.RunEbin(folder,Nbin,Fit,FitRunner)
-    del FitRunner
+
+    del(Result)
+    del(FitRunner)
 
 # @todo: Should this be a command line utility in bin?
 if __name__ == '__main__':

enrico/energybin.py

@@ -95,8 +95,7 @@ def PrepareEbin(Fit, FitRunner):
         mes.info("Submition # "+str(ibin)+" at energy "+str(E))
         #Update the model for the bin
         NewFitObject = ChangeModel(Fit, ener[ibin], ener[ibin + 1], srcname, Pref[ibin] ,Gamma[ibin])
-        Xmlname = (config['out'] + "/" + srcname +
-                    "_" + str(ibin) + ".xml")
+        Xmlname = (config['out'] + "/" + srcname + "_" + str(ibin) + ".xml")
         NewFitObject.writeXml(Xmlname)# dump the corresponding xml file
         config['file']['xml'] = Xmlname
         #update the energy bounds

enrico/lightcurve.py

@@ -114,13 +114,17 @@ def PrepareLC(self,write = 'no'):
 
 
     def _MakeLC(self,Path=LightcurvePath) :
+        import gc
+        import os
+        gc.enable()
         '''Main function of the Lightcurve script. Read the config file and run the gtlike analysis'''
         enricodir = environ.DIRS.get('ENRICO_DIR')
         fermidir = environ.DIRS.get('FERMI_DIR')
 
         self.PrepareLC(self.config['LightCurve']['MakeConfFile'])#Get the config file
 
         for i in xrange(self.Nbin):
+            gc.collect()
             if self.submit == 'yes':
                 cmd = "enrico_sed "+self.configfile[i]
                 scriptname = self.LCfolder+"LC_Script_"+str(i)+".sh"
@@ -131,7 +135,12 @@ def _MakeLC(self,Path=LightcurvePath) :
 
                 call(cmd,enricodir,fermidir,scriptname,JobLog,JobName)#Submit the job
             else :
-                run(self.configfile[i])#run in command line
+                cmd = "enrico_sed "+self.configfile[i]
+                os.system(cmd)
+
+                #run(self.configfile[i])#run in command line
+
+
 
 
     def _MakePhasebin(self):

enrico/plotting.py

@@ -255,7 +255,8 @@ def PlotNpred(Npred, Flux, FluxErr):
 def PlotLC(Time, TimeErr, x, xErr, tag="Flux (photon cm^{-2} s^{-1})"):
     """Scatter plot X(Time)"""
     ArrowSize = (max(x) + max(xErr) * 1.3 -
-                 (min(x) - max(xErr) * 1.3)) * 0.1
+        (min(x) - max(xErr) * 1.3)) * 0.1
+
     arrows = []
     for i in xrange(len(Time)):
         if xErr[i] == 0:

enrico/utils.py

@@ -276,6 +276,12 @@ def MJD_to_met(mjd):
 def JD_to_met(jd):
   return MJD_to_met(mjd)+2400000.5
 
+def create_dir(path):
+    import os
+    import os.path
+
+    if (not os.path.exists(path)):
+        os.makedirs(path)
 
 def Checkevtclass(evclass):
     classirfs = {1:"P8R2_TRANSIENT100A",2:"P8R2_TRANSIENT100E",4:"P8R2_TRANSIENT100",8:"P8R2_TRANSIENT020E",