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checkpoint for cleaning up output files and consolidating
This commit is contained in:
Paul M. Sutter
parent
acdb19e6df
commit
d6a939d2cf
3 changed files with 214 additions and 249 deletions
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@ -299,35 +299,35 @@ def findEdgeGalaxies(galFile, maskFile, edgeGalFile, contourFile,
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log.write(" Saving galaxy flags to file...\n")
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np.savetxt(edgeGalFile, flagList, fmt="%d")
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# paint galaxy flags onto healpix map for diagnostics
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# TODO - drop this when done testing
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log.write(" Saving diagnostic maps to file...\n")
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flagMap = np.zeros(len(contourMap))
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justEdgeRA = RA[flagList == 1]
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justEdgeDec = Dec[flagList == 1]
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## paint galaxy flags onto healpix map for diagnostics
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## TODO - drop this when done testing
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#log.write(" Saving diagnostic maps to file...\n")
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#flagMap = np.zeros(len(contourMap))
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#justEdgeRA = RA[flagList == 1]
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#justEdgeDec = Dec[flagList == 1]
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phi, theta = convertAngle(justEdgeRA, justEdgeDec)
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#phi, theta = convertAngle(justEdgeRA, justEdgeDec)
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ipix = healpy.ang2pix(nside, theta, phi)
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for i in ipix:
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flagMap[i] += 1
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#np.put(flagMap, ipix, 1)
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#ipix = healpy.ang2pix(nside, theta, phi)
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#for i in ipix:
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# flagMap[i] += 1
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##np.put(flagMap, ipix, 1)
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healpy.write_map(outputDir+"/flagged_galaxies.fits", flagMap,
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overwrite=True,
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dtype=np.dtype('float64'))
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#healpy.write_map(outputDir+"/flagged_galaxies.fits", flagMap,
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# overwrite=True,
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# dtype=np.dtype('float64'))
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allGalMap = np.zeros(len(contourMap))
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phi, theta = convertAngle(RA, Dec)
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#allGalMap = np.zeros(len(contourMap))
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#phi, theta = convertAngle(RA, Dec)
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ipix = healpy.ang2pix(nside, theta, phi)
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for i in ipix:
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allGalMap[i] += 1
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#np.put(allGalMap, ipix, 1)
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#ipix = healpy.ang2pix(nside, theta, phi)
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#for i in ipix:
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# allGalMap[i] += 1
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##np.put(allGalMap, ipix, 1)
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healpy.write_map(outputDir+"/all_galaxies.fits", allGalMap,
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overwrite=True,
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dtype=np.dtype('float64'))
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#healpy.write_map(outputDir+"/all_galaxies.fits", allGalMap,
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# overwrite=True,
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# dtype=np.dtype('float64'))
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return
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@ -31,7 +31,10 @@ import os
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NetCDFFile = Dataset
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ncFloat = 'f8'
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# -----------------------------------------------------------------------------
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CATALOG_V1 = 1
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CATALOG_V2 = 2
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# -----------------------------------------------------------------------
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def loadPart(sampleDir):
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print(" Loading particle data...")
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sys.stdout.flush()
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@ -270,11 +273,14 @@ def loadVoidCatalog(sampleDir,
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print("Loading catalog from ", sampleDir)
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isOldCatalog = os.path.exists(sampleDir+"/mask_index.txt")
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if os.path.exists(sampleDir+"/mask_index.txt"):
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version = CATALOG_V1
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else:
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version = CATALOG_V2
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if isOldCatalog and clearNearBoundaries:
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if version == CATALOG_V1 and clearNearBoundaries:
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print("WARNING: Old catalog. Unable to clear near boundaries.")
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if isOldCatalog and maxCentralDen != -1:
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if version == CATALOG_V1 and maxCentralDen != -1:
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print("WARNING: Old catalog. Central density cuts already applied.")
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if replicateOldCentralVoids:
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@ -310,19 +316,24 @@ def loadVoidCatalog(sampleDir,
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# for new catalogs, we will load by default the whole shebang, then
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# apply filters later. for old catalogs, we need to pick the right file
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prefix = "untrimmed_"
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if isOldCatalog and clearTree: prefix = ""
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if version == CATALOG_V1:
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if clearTree:
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prefix = ""
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else:
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prefix = "untrimmed_"
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dataPortion = "all"
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if isOldCatalog and clearEdges: dataPortion = "central"
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if clearEdges:
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dataPortion = "central"
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else:
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dataPortion = "all"
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print("Loading voids...")
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fileName = sampleDir+"/"+prefix+"voidDesc_"+dataPortion+"_"+sample.fullName+".out"
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print("Loading version-1 voids...")
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fileName = sampleDir+"/"+prefix+"voidDesc_"+dataPortion+"_"+sample.fullName+".out"
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catData = np.loadtxt(fileName, comments="#", skiprows=2)
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catalog.voids = []
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for line in catData:
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catalog.voids.append(Bunch(iVoid = int(line[0]),
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catData = np.loadtxt(fileName, comments="#", skiprows=2)
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catalog.voids = []
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for line in catData:
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catalog.voids.append(Bunch(iVoid = int(line[0]),
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voidID = int(line[1]),
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coreParticle = line[2],
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coreDens = line[3],
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@ -335,7 +346,6 @@ def loadVoidCatalog(sampleDir,
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voidProb = line[10],
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# below values to be read in or computed later
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radius = 0.,
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macrocenter = np.zeros((3)),
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redshift = 0,
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RA = 0,
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Dec = 0,
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@ -351,78 +361,130 @@ def loadVoidCatalog(sampleDir,
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nearestEdge = 0.
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))
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catalog.numVoids = len(catalog.voids)
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print(" Read %d voids" % catalog.numVoids)
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catalog.numVoids = len(catalog.voids)
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print(" Read %d voids" % catalog.numVoids)
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print("Loading macrocenters...")
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iLine = 0
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for line in open(sampleDir+"/"+prefix+"macrocenters_"+dataPortion+"_"+sample.fullName+".out"):
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line = line.split()
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catalog.voids[iLine].macrocenter[0] = float(line[1])
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catalog.voids[iLine].macrocenter[1] = float(line[2])
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catalog.voids[iLine].macrocenter[2] = float(line[3])
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iLine += 1
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print("Loading macrocenters...")
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iLine = 0
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for line in open(sampleDir+"/"+prefix+"macrocenters_"+dataPortion+"_"+sample.fullName+".out"):
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line = line.split()
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catalog.voids[iLine].macrocenter[0] = float(line[1])
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catalog.voids[iLine].macrocenter[1] = float(line[2])
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catalog.voids[iLine].macrocenter[2] = float(line[3])
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iLine += 1
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iLine = 0
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fileName = sampleDir+"/"+prefix+"sky_positions_"+dataPortion+"_"+sample.fullName+".out"
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catData = np.loadtxt(fileName, comments="#")
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for line in catData:
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catalog.voids[iLine].RA = float(line[0])
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catalog.voids[iLine].Dec = float(line[1])
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iLine += 1
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iLine = 0
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fileName = sampleDir+"/"+prefix+"sky_positions_"+dataPortion+"_"+sample.fullName+".out"
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catData = np.loadtxt(fileName, comments="#")
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for line in catData:
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catalog.voids[iLine].RA = float(line[0])
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catalog.voids[iLine].Dec = float(line[1])
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iLine += 1
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print("Loading derived void information...")
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fileName = sampleDir+"/"+prefix+"centers_"+dataPortion+"_"+sample.fullName+".out"
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catData = np.loadtxt(fileName, comments="#")
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for (iLine,line) in enumerate(catData):
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catalog.voids[iLine].volume = float(line[6])
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catalog.voids[iLine].radius = float(line[4])
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catalog.voids[iLine].redshift = float(line[5])
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catalog.voids[iLine].parentID = float(line[10])
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catalog.voids[iLine].treeLevel = float(line[11])
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catalog.voids[iLine].numChildren = float(line[12])
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catalog.voids[iLine].centralDen = float(line[13])
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iLine += 1
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fileName = sampleDir+"/"+prefix+"shapes_"+dataPortion+"_"+sample.fullName+".out"
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catData = np.loadtxt(fileName, comments="#")
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for (iLine,line) in enumerate(catData):
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catalog.voids[iLine].ellipticity = float(line[1])
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catalog.voids[iLine].eigenVals[0] = float(line[2])
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catalog.voids[iLine].eigenVals[1] = float(line[3])
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catalog.voids[iLine].eigenVals[2] = float(line[4])
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catalog.voids[iLine].eigenVecs[0][0] = float(line[5])
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catalog.voids[iLine].eigenVecs[0][1] = float(line[6])
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catalog.voids[iLine].eigenVecs[0][2] = float(line[7])
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catalog.voids[iLine].eigenVecs[1][0] = float(line[8])
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catalog.voids[iLine].eigenVecs[1][1] = float(line[9])
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catalog.voids[iLine].eigenVecs[1][2] = float(line[10])
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catalog.voids[iLine].eigenVecs[2][0] = float(line[11])
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catalog.voids[iLine].eigenVecs[2][1] = float(line[12])
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catalog.voids[iLine].eigenVecs[2][2] = float(line[13])
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iLine += 1
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fileName = sampleDir+"/"+prefix+"extraInfo_"+dataPortion+"_"+sample.fullName+".out"
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if os.path.exists(fileName):
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print("Loading derived void information...")
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fileName = sampleDir+"/"+prefix+"centers_"+dataPortion+"_"+sample.fullName+".out"
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catData = np.loadtxt(fileName, comments="#")
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for (iLine,line) in enumerate(catData):
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catalog.voids[iLine].voidType = int(line[0])
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catalog.voids[iLine].maxRadius = float(line[1])
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catalog.voids[iLine].nearestEdge = float(line[2])
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catalog.voids[iLine].volume = float(line[6])
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catalog.voids[iLine].radius = float(line[4])
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catalog.voids[iLine].redshift = float(line[5])
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catalog.voids[iLine].parentID = float(line[10])
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catalog.voids[iLine].treeLevel = float(line[11])
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catalog.voids[iLine].numChildren = float(line[12])
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catalog.voids[iLine].centralDen = float(line[13])
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iLine += 1
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fileName = sampleDir+"/"+prefix+"shapes_"+dataPortion+"_"+sample.fullName+".out"
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catData = np.loadtxt(fileName, comments="#")
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for (iLine,line) in enumerate(catData):
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catalog.voids[iLine].ellipticity = float(line[1])
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catalog.voids[iLine].eigenVals[0] = float(line[2])
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catalog.voids[iLine].eigenVals[1] = float(line[3])
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catalog.voids[iLine].eigenVals[2] = float(line[4])
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catalog.voids[iLine].eigenVecs[0][0] = float(line[5])
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catalog.voids[iLine].eigenVecs[0][1] = float(line[6])
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catalog.voids[iLine].eigenVecs[0][2] = float(line[7])
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catalog.voids[iLine].eigenVecs[1][0] = float(line[8])
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catalog.voids[iLine].eigenVecs[1][1] = float(line[9])
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catalog.voids[iLine].eigenVecs[1][2] = float(line[10])
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catalog.voids[iLine].eigenVecs[2][0] = float(line[11])
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catalog.voids[iLine].eigenVecs[2][1] = float(line[12])
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catalog.voids[iLine].eigenVecs[2][2] = float(line[13])
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iLine += 1
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iLine += 1
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else:
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print(" Old catalog: extra info file not found")
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print("Loading version-2 voids...")
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fileName = sampleDir+"/"+prefix+"voidDatabase_"+sample.fullName+".out"
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catalog.voids = []
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for line in catData:
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macrocenter = np.zeros((3))
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macrocenter[0] = float(line[2])
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macrocenter[1] = float(line[3])
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macrocenter[2] = float(line[4])
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eigenVals = np.zeros((3))
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eigenVecs = np.zeros((3,3))
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eigenVals[0] = float(line[26])
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eigenVals[1] = float(line[27])
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eigenVals[2] = float(line[28])
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eigenVecs[0][0] = float(line[29])
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eigenVecs[0][1] = float(line[30])
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eigenVecs[0][2] = float(line[31])
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eigenVecs[1][0] = float(line[32])
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eigenVecs[1][1] = float(line[33])
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eigenVecs[1][2] = float(line[34])
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eigenVecs[2][0] = float(line[35])
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eigenVecs[2][1] = float(line[36])
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eigenVecs[2][2] = float(line[37])
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catalog.voids.append(Bunch(
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voidID = int(line[0]),
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voidType = int(line[1]),
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macrocenter = macrocenter,
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voidVol = float(line[5]),
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volume = float(line[6]),
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radius = float(line[7]),
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redshift = float(line[8]),
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RA = float(line[9]),
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Dec = float(line[10]),
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densCon = float(line[11]),
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maxRadius = float(line[12]),
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nearestEdge = float(line[13]),
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numPart = int(line[14]),
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parentID = int(line[15]),
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treeLevel = int(line[16]),
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numChildren = int(line[17]),
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centralDen = float(line[18]),
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coreParticle = int(line[19]),
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coreDens = float(line[20]),
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zoneVol = float(line[21]),
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zoneNumPart = int(line[22]),
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numZones = int(line[23]),
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voidProb = float(line[24]),
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ellipticity = float(line[25]),
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eigenVals = eigenVals,
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eigenVecs = eigenVecs
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))
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catalog.numVoids = len(catalog.voids)
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print(" Read %d voids" % catalog.numVoids)
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# apply filters to new catalogs
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if not isOldCatalog:
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if version != CATALOG_V1:
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print("Filtering catalog...")
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if clearEdges: catalog = filterOnType(catalog, CENTRAL_VOID)
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if clearTree: catalog = filterOnTreeLevel(catalog, level=-1)
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