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fixed bug where netcdf files weren't properly closed

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This commit is contained in:
P.M. Sutter 2013-03-02 21:51:05 -06:00
parent 12ca3bf2e3
commit af4f6cf41e
1 changed files with 12 additions and 7 deletions
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19
python_tools/void_python_tools/backend/launchers.py
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@ -113,12 +113,14 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + thisSubSample outputFile = zobovDir+"/zobov_slice_" + sampleName + "_ss" + thisSubSample
keepFraction = float(thisSubSample) keepFraction = float(thisSubSample)
subSampleLine = "subsample %g" % keepFraction subSampleLine = "subsample %g" % keepFraction
resubSampleLine = ""
else: else:
inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\ inputParameterFlag = "inputParameter " + zobovDir+"/zobov_slice_"+\
sampleName+"_ss"+prevSubSample+".par" sampleName+"_ss"+prevSubSample+".par"
outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + thisSubSample outputFile = zobovDir+"/_zobov_slice_" + sampleName + "_ss" + thisSubSample
keepFraction = float(thisSubSample)/float(prevSubSample) keepFraction = float(thisSubSample)/float(prevSubSample)
subSampleLine = "resubsample %g" % keepFraction subSampleLine += "subsample %g" % keepFraction
resubSampleLine = "resubsample %g" % keepFraction
includePecVelString = "" includePecVelString = ""
if sample.usePecVel: includePecVelString = "peculiarVelocities" if sample.usePecVel: includePecVelString = "peculiarVelocities"
@ -156,6 +158,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
rangeZ_max %g rangeZ_max %g
%s %s
%s %s
%s
""" % (dataFileLine, outputFile, """ % (dataFileLine, outputFile,
outputFile+".par", outputFile+".par",
includePecVelString, includePecVelString,
@ -163,7 +166,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
sample.dataUnit, sample.dataUnit,
xMin, xMax, yMin, yMax, xMin, xMax, yMin, yMax,
sample.zBoundaryMpc[0], sample.zBoundaryMpc[1], sample.zBoundaryMpc[0], sample.zBoundaryMpc[1],
subSampleLine,inputParameterFlag) subSampleLine,resubSampleLine,inputParameterFlag)
parmFile = os.getcwd()+"/generate_"+sample.fullName+".par" parmFile = os.getcwd()+"/generate_"+sample.fullName+".par"
@ -671,7 +674,7 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
shutil.copy(workDir+"/sample_"+comboName+"/galaxies.txt", zobovDir) shutil.copy(workDir+"/sample_"+comboName+"/galaxies.txt", zobovDir)
elif not doneGalUpdate: elif not doneGalUpdate:
dataTemp = file(workDir+"/sample_"+comboName+"/galaxies.txt", dataTemp = file(workDir+"/sample_"+comboName+"/galaxies.txt",
"r").read() "r").read()
file(zobovDir+"/galaxies.txt", "a").write(dataTemp) file(zobovDir+"/galaxies.txt", "a").write(dataTemp)
sourceStackDir = workDir+"/sample_"+comboName+"/stacks_"+\ sourceStackDir = workDir+"/sample_"+comboName+"/stacks_"+\
@ -739,8 +742,9 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
idxTemp = file(sourceStackDir+"/z_void_indexes.txt", "r").\ idxTemp = file(sourceStackDir+"/z_void_indexes.txt", "r").\
readlines() readlines()
idxTemp = np.array(idxTemp, dtype='i') idxTemp = np.array(idxTemp, dtype='i')
dataTemp = (NetCDFFile(voidDir+"/z_posx.nc").\ fp = NetCDFFile(voidDir+"/z_posx.nc")
variables['array'])[0:] dataTemp = fp.variables['array'][0:]
fp.close()
idxTemp[:] += len(dataTemp) idxTemp[:] += len(dataTemp)
fp = open(voidDir+"/z_void_indexes.txt", "a") fp = open(voidDir+"/z_void_indexes.txt", "a")
for idx in idxTemp: for idx in idxTemp:
@ -790,8 +794,9 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
idxTemp = file(sourceStackDir+"/void_indexes.txt", "r").\ idxTemp = file(sourceStackDir+"/void_indexes.txt", "r").\
readlines() readlines()
idxTemp = np.array(idxTemp, dtype='i') idxTemp = np.array(idxTemp, dtype='i')
dataTemp = (NetCDFFile(voidDir+"/posx.nc").\ fp = NetCDFFile(voidDir+"/posx.nc")
variables['array'])[0:] dataTemp = fp.variables['array'][0:]
fp.close()
idxTemp[:] += len(dataTemp) idxTemp[:] += len(dataTemp)
fp = open(voidDir+"/void_indexes.txt", "a") fp = open(voidDir+"/void_indexes.txt", "a")
for idx in idxTemp: for idx in idxTemp: