mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
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Merge branch 'master' of https://bitbucket.org/cosmicvoids/void_identification
This commit is contained in:
Guilhem Lavaux
commit
ecb4479178
98 changed files with 20520 additions and 493 deletions
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@ -276,7 +276,8 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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periodicLine += "' "
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periodicLine = ""
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if not (continueRun and jobSuccessful(logFile, "NetCDF: Not a valid ID\n")):
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if not (continueRun and (jobSuccessful(logFile, "NetCDF: Not a valid ID\n") \
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or jobSuccessful(logFile, "Done!\n"))):
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cmd = binPath
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cmd += " --partFile=" + zobovDir+"/zobov_slice_"+str(sampleName)
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cmd += " --voidDesc=" + zobovDir+"/voidDesc_"+str(sampleName)+".out"
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@ -310,6 +311,9 @@ def launchPrune(sample, binPath, thisDataPortion=None,
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cmd += " --outSkyPositions=" + zobovDir+"/sky_positions_"+\
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str(thisDataPortion)+"_"+\
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str(sampleName)+".out"
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cmd += " --outShapes=" + zobovDir+"/shapes_"+\
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str(thisDataPortion)+"_"+\
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str(sampleName)+".out"
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cmd += " --outDistances=" + zobovDir+"/boundaryDistances_"+\
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str(thisDataPortion)+"_"+\
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str(sampleName)+".out"
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@ -682,10 +686,15 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
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shutil.copy(sourceStackDir+"/posx.nc", voidDir)
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shutil.copy(sourceStackDir+"/posy.nc", voidDir)
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shutil.copy(sourceStackDir+"/posz.nc", voidDir)
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shutil.copy(sourceStackDir+"/z_posx.nc", voidDir)
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shutil.copy(sourceStackDir+"/z_posy.nc", voidDir)
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shutil.copy(sourceStackDir+"/z_posz.nc", voidDir)
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shutil.copy(sourceStackDir+"/indexes.nc", voidDir)
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shutil.copy(sourceStackDir+"/redshifts.nc", voidDir)
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shutil.copy(sourceStackDir+"/centers.txt", voidDir)
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shutil.copy(sourceStackDir+"/void_indexes.txt", voidDir)
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shutil.copy(sourceStackDir+"/z_centers.txt", voidDir)
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shutil.copy(sourceStackDir+"/z_void_indexes.txt", voidDir)
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shutil.copy(sourceStackDir+"/sky_positions.txt", voidDir)
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shutil.copy(sourceStackDir+"/normalizations.txt", voidDir)
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shutil.copy(sourceStackDir+"/boundaryDistances.txt", voidDir)
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@ -710,20 +719,73 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
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dataTemp = str(dataTemp[0])
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file(voidDir+"/num_particles.txt", "w").write(str(dataTemp))
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dataTemp = file(sourceStackDir+"/z_centers.txt", "r").read()
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file(voidDir+"/z_centers.txt", "a").write(dataTemp)
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dataTemp = file(sourceStackDir+"/centers.txt", "r").read()
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file(voidDir+"/centers.txt", "a").write(dataTemp)
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dataTemp = file(sourceStackDir+"/normalizations.txt", "r").\
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read()
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dataTemp = file(sourceStackDir+"/normalizations.txt", "r").read()
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file(voidDir+"/normalizations.txt", "a").write(dataTemp)
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dataTemp = file(sourceStackDir+"/boundaryDistances.txt","r").\
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read()
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dataTemp = file(sourceStackDir+"/boundaryDistances.txt","r").read()
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file(voidDir+"/boundaryDistances.txt", "a").write(dataTemp)
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dataTemp = file(sourceStackDir+"/sky_positions.txt", "r").\
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read()
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file(voidDir+"/sky_positions.txt", "a").write(dataTemp)
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idxTemp = file(sourceStackDir+"/z_void_indexes.txt", "r").\
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readlines()
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idxTemp = np.array(idxTemp, dtype='i')
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dataTemp = (NetCDFFile(voidDir+"/z_posx.nc").\
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variables['array'])[0:]
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idxTemp[:] += len(dataTemp)
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fp = open(voidDir+"/z_void_indexes.txt", "a")
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for idx in idxTemp:
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fp.write(str(idx)+"\n")
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fp.close()
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dataTemp = ()
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fp = NetCDFFile(voidDir+"/z_posx.nc")
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dataTemp = fp.variables['array'][0:]
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fp.close()
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fp = NetCDFFile(sourceStackDir+"/z_posx.nc")
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dataTemp2 = fp.variables['array'][0:]
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fp.close()
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dataTemp = np.append(dataTemp, dataTemp2)
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outFile = NetCDFFile(voidDir+"/z_posx.nc", mode='w')
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outFile.createDimension("dim", len(dataTemp))
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v = outFile.createVariable("array", ncFloat, ("dim",))
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v[:] = dataTemp
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outFile.close()
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fp = NetCDFFile(voidDir+"/z_posy.nc")
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dataTemp = fp.variables['array'][0:]
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fp.close()
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fp = NetCDFFile(sourceStackDir+"/z_posy.nc")
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dataTemp2 = fp.variables['array'][0:]
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fp.close()
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dataTemp = np.append(dataTemp, dataTemp2)
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outFile = NetCDFFile(voidDir+"/z_posy.nc", mode='w')
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outFile.createDimension("dim", len(dataTemp))
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v = outFile.createVariable("array", ncFloat, ("dim",))
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v[:] = dataTemp
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outFile.close()
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fp = NetCDFFile(voidDir+"/z_posz.nc")
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dataTemp = fp.variables['array'][0:]
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fp.close()
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fp = NetCDFFile(sourceStackDir+"/z_posz.nc")
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dataTemp2 = fp.variables['array'][0:]
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fp.close()
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dataTemp = np.append(dataTemp, dataTemp2)
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outFile = NetCDFFile(voidDir+"/z_posz.nc", mode='w')
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outFile.createDimension("dim", len(dataTemp))
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v = outFile.createVariable("array", ncFloat, ("dim",))
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v[:] = dataTemp
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outFile.close()
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idxTemp = file(sourceStackDir+"/void_indexes.txt", "r").\
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readlines()
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idxTemp = np.array(idxTemp, dtype='i')
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@ -775,6 +837,7 @@ def launchCombine(sample, stack, voidDir=None, logFile=None,
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v[:] = dataTemp
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outFile.close()
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fp = NetCDFFile(voidDir+"/redshifts.nc")
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dataTemp = fp.variables['array'][0:]
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fp.close()
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@ -892,6 +955,14 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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print "no voids here; skipping!"
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return
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numVoids = int(open(voidDir+"/num_voids.txt", "r").readline())
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if numVoids < 15:
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print "not enough voids to fit; skipping!"
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fp = open(voidDir+"/NOFIT", "w")
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fp.write("not enough voids: %d \n" % numVoids)
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fp.close()
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return
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if stack.zMin < sample.zRange[0] or stack.zMax > sample.zRange[1]:
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print "outside sample redshift range; skipping!"
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return
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@ -938,7 +1009,7 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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#badChain = (args[0][0] > 0.5 or args[0][1] > stack.rMax or \
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# args[0][2] > stack.rMax) and \
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# (ntries < maxtries)
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ret,fits,args = vp.compute_inertia(voidDir, stack.rMax)
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ret,fits,args = vp.compute_inertia(voidDir, stack.rMax, mode="symmetric")
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badChain = False
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ntries += 1
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@ -1003,7 +1074,7 @@ def launchFit(sample, stack, logFile=None, voidDir=None, figDir=None,
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def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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INCOHERENT=None, workDir=None, figDir=None, errorBars=None,
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ZOBOV_PATH=None, continueRun=None, voidDir=None,
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doPlot = True):
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doPlot = True, setName=None):
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for thisDataPortion in dataPortions:
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print " For data portion", thisDataPortion
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@ -1239,13 +1310,15 @@ def launchHubble(dataPortions=None, dataSampleList=None, logDir=None,
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sys.stdout = open(logFile, 'w')
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sys.stderr = open(logFile, 'a')
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if doPlot:
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print "DOING PLOT"
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if INCOHERENT:
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#plotTitle = "all samples, incoherent "+\
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# thisDataPortion+" voids"
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plotTitle = ''
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else:
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#plotTitle = "all samples, "+thisDataPortion+" voids"
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plotTitle = ''
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plotTitle = setName
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#plotTitle = ''
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vp.do_all_obs(zbase, allExpList, aveDistList,
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rlist, plotTitle=plotTitle, sampleNames=shortSampleNames,
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plotAve=True, mulfac = 1.0, biasLine = 1.16,
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